https://iridia.ulb.ac.be/w/api.php?action=feedcontributions&user=Dj&feedformat=atomIridiaWiki - User contributions [en]2022-12-04T22:54:01ZUser contributionsMediaWiki 1.35.4https://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7953PhDSupervision:Dhananjay Ipparthi2017-05-18T08:59:35Z<p>Dj: /* Personal Information */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
WhatsApp number: +32 483 382 207<br />
<br />
Telephone number: +32 479 406 747<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
** [http://iridia.ulb.ac.be/wiki/PhDSupervision:Dhananjay_Ipparthi/Table_of_contents Table of contents]<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress == <br />
Updated March 2, 2017<br />
* <b>Yield Predictions for a Model of Homogeneous Parallel Aggregation</b><br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Metin Sitti, Marco Dorigo, Massimo Mastrangeli. <br />
** Target journal: Soft Matter<br />
** Synopsis: Statistics to compare model and physical experiments.<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
** Forecast submission: March 15, 2017<br />
<br />
* <b>Velocities of 2D constrained orbitally shaken particles are Rayleigh distributed</b><br />
** Authors: Dhananjay Ipparthi, Tijmen Hageman, Nicolas Cambier, Metin Sitti, Marco Dorigo, Leon Abelmann and Massimo Mastrangeli<br />
** Target journal: Advanced Physics Letters<br />
** Synopsis: Experimental evidence that velocities of components constrained in 2D that are orbitally shaken are Rayleigh distributed<br />
** Project page: [[Dynamics of self-assembly]]<br />
** Draft to Massimo: March 7th, 2017<br />
** Forecast submission: May 10th, 2017<br />
<br />
* <b>1, 2 and 3 order Chi-distribution </b><br />
** Authors: Tijmen Hageman, Dhananjay Ipparthi, Marc Pichel, Per Arvid Loethman, Marco Dorigo, Massimo Mastrangeli and Leon Abelmann<br />
** Target journal: TBD<br />
** Synopsis: The velocity distribution of 1 particle shaken in 1D, 2D and 3D are respectively Gaussian, Rayleigh and Maxwell-Boltzman distributed. That is, their velocity distributions are nth order of Chi.<br />
** Forecast submission: April 30, 2017<br />
<br />
* <b>Solutions to the incompatible substructures problem in macroscale systems</b><br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
** Missing: Conformational switching design still not working<br />
** Forecast submission: July 31, 2017 (it will include parts of PPSN 2015 paper and parts of Theoretical Computer Science 2015 paper)<br />
<br />
* <b>Review of macroscale parallel self-assembling systems</b> - Not sure it will be done<br />
** Authors: Dhananjay Ipparthi, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 5: Feb 2016 - Feb 2017]] ===<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7944PhDSupervision:Dhananjay Ipparthi2017-04-28T15:02:51Z<p>Dj: /* Papers in progress */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
** [http://iridia.ulb.ac.be/wiki/PhDSupervision:Dhananjay_Ipparthi/Table_of_contents Table of contents]<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress == <br />
Updated March 2, 2017<br />
* <b>Yield Predictions for a Model of Homogeneous Parallel Aggregation</b><br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Metin Sitti, Marco Dorigo, Massimo Mastrangeli. <br />
** Target journal: Soft Matter<br />
** Synopsis: Statistics to compare model and physical experiments.<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
** Forecast submission: March 15, 2017<br />
<br />
* <b>Velocities of 2D constrained orbitally shaken particles are Rayleigh distributed</b><br />
** Authors: Dhananjay Ipparthi, Tijmen Hageman, Nicolas Cambier, Metin Sitti, Marco Dorigo, Leon Abelmann and Massimo Mastrangeli<br />
** Target journal: Advanced Physics Letters<br />
** Synopsis: Experimental evidence that velocities of components constrained in 2D that are orbitally shaken are Rayleigh distributed<br />
** Project page: [[Dynamics of self-assembly]]<br />
** Draft to Massimo: March 7th, 2017<br />
** Forecast submission: May 10th, 2017<br />
<br />
* <b>1, 2 and 3 order Chi-distribution </b><br />
** Authors: Tijmen Hageman, Dhananjay Ipparthi, Marc Pichel, Per Arvid Loethman, Marco Dorigo, Massimo Mastrangeli and Leon Abelmann<br />
** Target journal: TBD<br />
** Synopsis: The velocity distribution of 1 particle shaken in 1D, 2D and 3D are respectively Gaussian, Rayleigh and Maxwell-Boltzman distributed. That is, their velocity distributions are nth order of Chi.<br />
** Forecast submission: April 30, 2017<br />
<br />
* <b>Solutions to the incompatible substructures problem in macroscale systems</b><br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
** Missing: Conformational switching design still not working<br />
** Forecast submission: July 31, 2017 (it will include parts of PPSN 2015 paper and parts of Theoretical Computer Science 2015 paper)<br />
<br />
* <b>Review of macroscale parallel self-assembling systems</b> - Not sure it will be done<br />
** Authors: Dhananjay Ipparthi, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 5: Feb 2016 - Feb 2017]] ===<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7913PhDSupervision:Dhananjay Ipparthi2017-03-02T16:00:19Z<p>Dj: /* Academic Activities */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
** [http://iridia.ulb.ac.be/wiki/PhDSupervision:Dhananjay_Ipparthi/Table_of_contents Table of contents]<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress == <br />
Updated March 2, 2017<br />
* <b>Yield Predictions for a Model of Homogeneous Parallel Aggregation</b><br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Metin Sitti, Marco Dorigo, Massimo Mastrangeli. <br />
** Target journal: Soft Matter<br />
** Synopsis: Statistics to compare model and physical experiments.<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
** Forecast submission: March 15, 2017<br />
<br />
* <b>Velocities of 2D constrained orbitally shaken particles are Rayleigh distributed</b><br />
** Authors: Dhananjay Ipparthi, Tijmen Hageman, Nicolas Cambier, Metin Sitti, Marco Dorigo, Leon Abelmann and Massimo Mastrangeli<br />
** Target journal: Advanced Physics Letters<br />
** Synopsis: Experimental evidence that velocities of components constrained in 2D that are orbitally shaken are Rayleigh distributed<br />
** Project page: [[Dynamics of self-assembly]]<br />
** Draft to Massimo: March 7th, 2017<br />
** Forecast submission: March 31, 2017<br />
<br />
* <b>1, 2 and 3 order Chi-distribution </b><br />
** Authors: Tijmen Hageman, Dhananjay Ipparthi, Marc Pichel, Per Arvid Loethman, Marco Dorigo, Massimo Mastrangeli and Leon Abelmann<br />
** Target journal: TBD<br />
** Synopsis: The velocity distribution of 1 particle shaken in 1D, 2D and 3D are respectively Gaussian, Rayleigh and Maxwell-Boltzman distributed. That is, their velocity distributions are nth order of Chi.<br />
** Forecast submission: April 30, 2017<br />
<br />
* <b>Solutions to the incompatible substructures problem in macroscale systems</b><br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
** Missing: Conformational switching design still not working<br />
** Forecast submission: July 31, 2017 (it will include parts of PPSN 2015 paper and parts of Theoretical Computer Science 2015 paper)<br />
<br />
* <b>Review of macroscale parallel self-assembling systems</b> - Not sure it will be done<br />
** Authors: Dhananjay Ipparthi, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 5: Feb 2016 - Feb 2017]] ===<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=Year_5:_Feb_2016_-_Feb_2017&diff=7912Year 5: Feb 2016 - Feb 20172017-03-02T15:59:58Z<p>Dj: Created page with "=== 17th February - 20th April, 2016 === * Setup experiment workspace ** Installed shaker + universal platform ** Cut out containers ** Installed lighting system ** Installed ..."</p>
<hr />
<div>=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7911PhDSupervision:Dhananjay Ipparthi2017-03-02T15:59:42Z<p>Dj: /* Year 5: Feb 2016 - Feb 2017 */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
** [http://iridia.ulb.ac.be/wiki/PhDSupervision:Dhananjay_Ipparthi/Table_of_contents Table of contents]<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress == <br />
Updated March 2, 2017<br />
* <b>Yield Predictions for a Model of Homogeneous Parallel Aggregation</b><br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Metin Sitti, Marco Dorigo, Massimo Mastrangeli. <br />
** Target journal: Soft Matter<br />
** Synopsis: Statistics to compare model and physical experiments.<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
** Forecast submission: March 15, 2017<br />
<br />
* <b>Velocities of 2D constrained orbitally shaken particles are Rayleigh distributed</b><br />
** Authors: Dhananjay Ipparthi, Tijmen Hageman, Nicolas Cambier, Metin Sitti, Marco Dorigo, Leon Abelmann and Massimo Mastrangeli<br />
** Target journal: Advanced Physics Letters<br />
** Synopsis: Experimental evidence that velocities of components constrained in 2D that are orbitally shaken are Rayleigh distributed<br />
** Project page: [[Dynamics of self-assembly]]<br />
** Draft to Massimo: March 7th, 2017<br />
** Forecast submission: March 31, 2017<br />
<br />
* <b>1, 2 and 3 order Chi-distribution </b><br />
** Authors: Tijmen Hageman, Dhananjay Ipparthi, Marc Pichel, Per Arvid Loethman, Marco Dorigo, Massimo Mastrangeli and Leon Abelmann<br />
** Target journal: TBD<br />
** Synopsis: The velocity distribution of 1 particle shaken in 1D, 2D and 3D are respectively Gaussian, Rayleigh and Maxwell-Boltzman distributed. That is, their velocity distributions are nth order of Chi.<br />
** Forecast submission: April 30, 2017<br />
<br />
* <b>Solutions to the incompatible substructures problem in macroscale systems</b><br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
** Missing: Conformational switching design still not working<br />
** Forecast submission: July 31, 2017 (it will include parts of PPSN 2015 paper and parts of Theoretical Computer Science 2015 paper)<br />
<br />
* <b>Review of macroscale parallel self-assembling systems</b> - Not sure it will be done<br />
** Authors: Dhananjay Ipparthi, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 5: Feb 2016 - Feb 2017]] ===<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7910PhDSupervision:Dhananjay Ipparthi2017-03-02T15:59:36Z<p>Dj: /* Academic Activities */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
** [http://iridia.ulb.ac.be/wiki/PhDSupervision:Dhananjay_Ipparthi/Table_of_contents Table of contents]<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress == <br />
Updated March 2, 2017<br />
* <b>Yield Predictions for a Model of Homogeneous Parallel Aggregation</b><br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Metin Sitti, Marco Dorigo, Massimo Mastrangeli. <br />
** Target journal: Soft Matter<br />
** Synopsis: Statistics to compare model and physical experiments.<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
** Forecast submission: March 15, 2017<br />
<br />
* <b>Velocities of 2D constrained orbitally shaken particles are Rayleigh distributed</b><br />
** Authors: Dhananjay Ipparthi, Tijmen Hageman, Nicolas Cambier, Metin Sitti, Marco Dorigo, Leon Abelmann and Massimo Mastrangeli<br />
** Target journal: Advanced Physics Letters<br />
** Synopsis: Experimental evidence that velocities of components constrained in 2D that are orbitally shaken are Rayleigh distributed<br />
** Project page: [[Dynamics of self-assembly]]<br />
** Draft to Massimo: March 7th, 2017<br />
** Forecast submission: March 31, 2017<br />
<br />
* <b>1, 2 and 3 order Chi-distribution </b><br />
** Authors: Tijmen Hageman, Dhananjay Ipparthi, Marc Pichel, Per Arvid Loethman, Marco Dorigo, Massimo Mastrangeli and Leon Abelmann<br />
** Target journal: TBD<br />
** Synopsis: The velocity distribution of 1 particle shaken in 1D, 2D and 3D are respectively Gaussian, Rayleigh and Maxwell-Boltzman distributed. That is, their velocity distributions are nth order of Chi.<br />
** Forecast submission: April 30, 2017<br />
<br />
* <b>Solutions to the incompatible substructures problem in macroscale systems</b><br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
** Missing: Conformational switching design still not working<br />
** Forecast submission: July 31, 2017 (it will include parts of PPSN 2015 paper and parts of Theoretical Computer Science 2015 paper)<br />
<br />
* <b>Review of macroscale parallel self-assembling systems</b> - Not sure it will be done<br />
** Authors: Dhananjay Ipparthi, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 5: Feb 2016 - Feb 2017]] ===<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7909PhDSupervision:Dhananjay Ipparthi2017-03-02T15:59:20Z<p>Dj: /* Academic Activities */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
** [http://iridia.ulb.ac.be/wiki/PhDSupervision:Dhananjay_Ipparthi/Table_of_contents Table of contents]<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress == <br />
Updated March 2, 2017<br />
* <b>Yield Predictions for a Model of Homogeneous Parallel Aggregation</b><br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Metin Sitti, Marco Dorigo, Massimo Mastrangeli. <br />
** Target journal: Soft Matter<br />
** Synopsis: Statistics to compare model and physical experiments.<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
** Forecast submission: March 15, 2017<br />
<br />
* <b>Velocities of 2D constrained orbitally shaken particles are Rayleigh distributed</b><br />
** Authors: Dhananjay Ipparthi, Tijmen Hageman, Nicolas Cambier, Metin Sitti, Marco Dorigo, Leon Abelmann and Massimo Mastrangeli<br />
** Target journal: Advanced Physics Letters<br />
** Synopsis: Experimental evidence that velocities of components constrained in 2D that are orbitally shaken are Rayleigh distributed<br />
** Project page: [[Dynamics of self-assembly]]<br />
** Draft to Massimo: March 7th, 2017<br />
** Forecast submission: March 31, 2017<br />
<br />
* <b>1, 2 and 3 order Chi-distribution </b><br />
** Authors: Tijmen Hageman, Dhananjay Ipparthi, Marc Pichel, Per Arvid Loethman, Marco Dorigo, Massimo Mastrangeli and Leon Abelmann<br />
** Target journal: TBD<br />
** Synopsis: The velocity distribution of 1 particle shaken in 1D, 2D and 3D are respectively Gaussian, Rayleigh and Maxwell-Boltzman distributed. That is, their velocity distributions are nth order of Chi.<br />
** Forecast submission: April 30, 2017<br />
<br />
* <b>Solutions to the incompatible substructures problem in macroscale systems</b><br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
** Missing: Conformational switching design still not working<br />
** Forecast submission: July 31, 2017 (it will include parts of PPSN 2015 paper and parts of Theoretical Computer Science 2015 paper)<br />
<br />
* <b>Review of macroscale parallel self-assembling systems</b> - Not sure it will be done<br />
** Authors: Dhananjay Ipparthi, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 5: Feb 2016 - Feb 2017]] ===<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7908PhDSupervision:Dhananjay Ipparthi2017-03-02T15:57:47Z<p>Dj: /* Papers in progress */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
** [http://iridia.ulb.ac.be/wiki/PhDSupervision:Dhananjay_Ipparthi/Table_of_contents Table of contents]<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress == <br />
Updated March 2, 2017<br />
* <b>Yield Predictions for a Model of Homogeneous Parallel Aggregation</b><br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Metin Sitti, Marco Dorigo, Massimo Mastrangeli. <br />
** Target journal: Soft Matter<br />
** Synopsis: Statistics to compare model and physical experiments.<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
** Forecast submission: March 15, 2017<br />
<br />
* <b>Velocities of 2D constrained orbitally shaken particles are Rayleigh distributed</b><br />
** Authors: Dhananjay Ipparthi, Tijmen Hageman, Nicolas Cambier, Metin Sitti, Marco Dorigo, Leon Abelmann and Massimo Mastrangeli<br />
** Target journal: Advanced Physics Letters<br />
** Synopsis: Experimental evidence that velocities of components constrained in 2D that are orbitally shaken are Rayleigh distributed<br />
** Project page: [[Dynamics of self-assembly]]<br />
** Draft to Massimo: March 7th, 2017<br />
** Forecast submission: March 31, 2017<br />
<br />
* <b>1, 2 and 3 order Chi-distribution </b><br />
** Authors: Tijmen Hageman, Dhananjay Ipparthi, Marc Pichel, Per Arvid Loethman, Marco Dorigo, Massimo Mastrangeli and Leon Abelmann<br />
** Target journal: TBD<br />
** Synopsis: The velocity distribution of 1 particle shaken in 1D, 2D and 3D are respectively Gaussian, Rayleigh and Maxwell-Boltzman distributed. That is, their velocity distributions are nth order of Chi.<br />
** Forecast submission: April 30, 2017<br />
<br />
* <b>Solutions to the incompatible substructures problem in macroscale systems</b><br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
** Missing: Conformational switching design still not working<br />
** Forecast submission: July 31, 2017 (it will include parts of PPSN 2015 paper and parts of Theoretical Computer Science 2015 paper)<br />
<br />
* <b>Review of macroscale parallel self-assembling systems</b> - Not sure it will be done<br />
** Authors: Dhananjay Ipparthi, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7907PhDSupervision:Dhananjay Ipparthi2017-03-02T15:56:15Z<p>Dj: </p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
** [http://iridia.ulb.ac.be/wiki/PhDSupervision:Dhananjay_Ipparthi/Table_of_contents Table of contents]<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress == <br />
Updated August 17, 2016<br />
* <b>Yield Predictions for a Model of Homogeneous Parallel Aggregation</b><br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Metin Sitti, Marco Dorigo, Massimo Mastrangeli. <br />
** Target journal: Soft Matter<br />
** Synopsis: Statistics to compare model and physical experiments.<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
** Forecast submission: March 15, 2017<br />
<br />
* <b>Velocities of 2D constrained orbitally shaken particles are Rayleigh distributed</b><br />
** Authors: Dhananjay Ipparthi, Tijmen Hageman, Nicolas Cambier, Metin Sitti, Marco Dorigo, Leon Abelmann and Massimo Mastrangeli<br />
** Target journal: Advanced Physics Letters<br />
** Synopsis: Experimental evidence that velocities of components constrained in 2D that are orbitally shaken are Rayleigh distributed<br />
** Project page: [[Dynamics of self-assembly]]<br />
** Forecast submission: March 31, 2017<br />
<br />
* <b>1, 2 and 3 order Chi-distribution </b><br />
** Authors: Tijmen Hageman, Dhananjay Ipparthi, Marc Pichel, Per Arvid Loethman, Marco Dorigo, Massimo Mastrangeli and Leon Abelmann<br />
** Target journal: TBD<br />
** Synopsis: The velocity distribution of 1 particle shaken in 1D, 2D and 3D are respectively Gaussian, Rayleigh and Maxwell-Boltzman distributed. That is, their velocity distributions are nth order of Chi.<br />
** Forecast submission: April 30, 2017<br />
<br />
* <b>Solutions to the incompatible substructures problem in macroscale systems</b><br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
** Missing: Conformational switching design still not working<br />
** Forecast submission: July 31, 2017 (it will include parts of PPSN 2015 paper and parts of Theoretical Computer Science 2015 paper)<br />
<br />
* <b>Review of macroscale parallel self-assembling systems</b> - Not sure it will be done<br />
** Authors: Dhananjay Ipparthi, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=Parallel_self-assembling_systems_review_paper&diff=7342Parallel self-assembling systems review paper2016-10-10T14:32:10Z<p>Dj: </p>
<hr />
<div>[[/Users/boite/Documents/ULB/Teaching/INFOH415/teaching/infoh415/tps/1516/infoh415_tp02+03_slides.pdf|pdfright]]<br />
* Outline<br />
** Introduction.<br />
** Summaries.<br />
** Categorisations.<br />
** Differentiations of the various works till date. <br />
** Open problems. <br />
** Conclusion.</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=Parallel_self-assembling_systems_review_paper&diff=7341Parallel self-assembling systems review paper2016-10-10T14:31:30Z<p>Dj: </p>
<hr />
<div>[[/Users/boite/Documents/ULB/Teaching/INFOH415/teaching/infoh415/tps/1516/infoh415_tp02+03_slides.pdf]]<br />
* Outline<br />
** Introduction.<br />
** Summaries.<br />
** Categorisations.<br />
** Differentiations of the various works till date. <br />
** Open problems. <br />
** Conclusion.</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi/Table_of_contents&diff=7257PhDSupervision:Dhananjay Ipparthi/Table of contents2016-05-30T08:25:39Z<p>Dj: /* Dynamics of aggregating / self-assembling systems */</p>
<hr />
<div>== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
* SWARM2015 conference paper presents initial findings of yield predictions [published]<br />
* Extended yield predictions journal paper [not yet published. submission deadline: 5th June, 2016]<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
* Two geometries<br />
* Two modes of shaking<br />
* Nicolas has developed visual tracking system and used it to find:<br />
** Time evolution of aggregation<br />
** Distance distribution<br />
** Velocity distribution<br />
* Collaboration with Korean Institute of Science and Technology [Leon Abelmann, Tijmen Hageman, etc.]<br />
** Found the different energy regimes for our aggregating system<br />
** Established that outside the ballistic regime, the components perform "random walk"<br />
*** The data neatly fits into a Rayleigh distribution<br />
* TODO: Get new camera, re-analyse data<br />
* TODO: Write a "methodology" style paper [submission deadline:?]<br />
<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Compartmentalisation =====<br />
* To publish in approaches paper<br />
===== Self-assembly =====<br />
* TODO: Tune the magnetism of the components such that the fully formed target structures are stable, but substructures are susceptible to breakage<br />
===== Changing geometry =====<br />
* [Published: PPSN]<br />
===== Conformational switching =====<br />
* TODO: Close to final design of components<br />
===== Use of high inertia components =====<br />
* Successfully conducted preliminary experiments<br />
* TODO: Define experiment and collect data<br />
===== Dipole codes =====<br />
* [Published: Theoretical Computer Science]<br />
<br />
* Massimo suggested, and I agree, that I write an "approaches to the yield predictions" paper. In that paper, I would include the aforementioned approaches. [submission deadline: ??]<br />
===== Comparison of the different approaches. Perhaps time and/or yield comparisons? =====<br />
<br />
=== Conclusions ===<br />
* Contribution 1: Theoretical analysis of parallel assembly vis-a-vis the incompatible substructure problem<br />
* Contribution 2: 5 approaches to avoid the incompatible substructure problem<br />
* Contribution 3: Study of the dynamics of aggregation / parallel assembly</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi/Table_of_contents&diff=7256PhDSupervision:Dhananjay Ipparthi/Table of contents2016-05-30T08:24:33Z<p>Dj: /* Approaches to solve the incompatible substructure problem */</p>
<hr />
<div>== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
* SWARM2015 conference paper presents initial findings of yield predictions [published]<br />
* Extended yield predictions journal paper [not yet published. submission deadline: 5th June, 2016]<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
* Nicolas has developed visual tracking system and used it to find:<br />
** Time evolution of aggregation<br />
** Distance distribution<br />
** Velocity distribution<br />
* Collaboration with Korean Institute of Science and Technology [Leon Abelmann, Tijmen Hageman, etc.]<br />
** Found the different energy regimes for our aggregating system<br />
** Established that outside the ballistic regime, the components perform "random walk"<br />
*** The data neatly fits into a Rayleigh distribution<br />
* TODO: Get new camera, re-analyse data<br />
* TODO: Write a "methodology" style paper [submission deadline:?]<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Compartmentalisation =====<br />
* To publish in approaches paper<br />
===== Self-assembly =====<br />
* TODO: Tune the magnetism of the components such that the fully formed target structures are stable, but substructures are susceptible to breakage<br />
===== Changing geometry =====<br />
* [Published: PPSN]<br />
===== Conformational switching =====<br />
* TODO: Close to final design of components<br />
===== Use of high inertia components =====<br />
* Successfully conducted preliminary experiments<br />
* TODO: Define experiment and collect data<br />
===== Dipole codes =====<br />
* [Published: Theoretical Computer Science]<br />
<br />
* Massimo suggested, and I agree, that I write an "approaches to the yield predictions" paper. In that paper, I would include the aforementioned approaches. [submission deadline: ??]<br />
===== Comparison of the different approaches. Perhaps time and/or yield comparisons? =====<br />
<br />
=== Conclusions ===<br />
* Contribution 1: Theoretical analysis of parallel assembly vis-a-vis the incompatible substructure problem<br />
* Contribution 2: 5 approaches to avoid the incompatible substructure problem<br />
* Contribution 3: Study of the dynamics of aggregation / parallel assembly</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi/Table_of_contents&diff=7255PhDSupervision:Dhananjay Ipparthi/Table of contents2016-05-30T08:23:53Z<p>Dj: </p>
<hr />
<div>== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
* SWARM2015 conference paper presents initial findings of yield predictions [published]<br />
* Extended yield predictions journal paper [not yet published. submission deadline: 5th June, 2016]<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
* Nicolas has developed visual tracking system and used it to find:<br />
** Time evolution of aggregation<br />
** Distance distribution<br />
** Velocity distribution<br />
* Collaboration with Korean Institute of Science and Technology [Leon Abelmann, Tijmen Hageman, etc.]<br />
** Found the different energy regimes for our aggregating system<br />
** Established that outside the ballistic regime, the components perform "random walk"<br />
*** The data neatly fits into a Rayleigh distribution<br />
* TODO: Get new camera, re-analyse data<br />
* TODO: Write a "methodology" style paper [submission deadline:?]<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Compartmentalisation =====<br />
* To publish in approaches paper<br />
===== Self-assembly =====<br />
* TODO: Tune the magnetism of the components such that the fully formed target structures are stable, but substructures are susceptible to breakage<br />
===== Changing geometry =====<br />
* [Published: PPSN]<br />
===== Conformational switching =====<br />
* TODO: Close to final design of components<br />
===== Use of high inertia components =====<br />
* Successfully conducted preliminary experiments<br />
* TODO: Define experiment and collect data<br />
===== Dipole codes =====<br />
* [Published: Theoretical Computer Science]<br />
<br />
* Massimo suggested, and I agree, that I write an "approaches to the yield predictions" paper. In that paper, I would include the aforementioned approaches. [submission deadline: ??]<br />
* Comparison of the different approaches. Perhaps time and/or yield comparisons?<br />
<br />
<br />
=== Conclusions ===<br />
* Contribution 1: Theoretical analysis of parallel assembly vis-a-vis the incompatible substructure problem<br />
* Contribution 2: 5 approaches to avoid the incompatible substructure problem<br />
* Contribution 3: Study of the dynamics of aggregation / parallel assembly</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi/Table_of_contents&diff=7254PhDSupervision:Dhananjay Ipparthi/Table of contents2016-05-30T08:21:49Z<p>Dj: /* Approaches to solve the incompatible substructure problem */</p>
<hr />
<div>== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
* SWARM2015 conference paper presents initial findings of yield predictions [published]<br />
* Extended yield predictions journal paper [not yet published. submission deadline: 5th June, 2016]<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Compartmentalisation =====<br />
* To publish in approaches paper<br />
===== Self-assembly =====<br />
* TODO: Tune the magnetism of the components such that the fully formed target structures are stable, but substructures are susceptible to breakage<br />
===== Changing geometry =====<br />
* [Published: PPSN]<br />
===== Conformational switching =====<br />
* TODO: Close to final design of components<br />
===== Use of high inertia components =====<br />
* Successfully conducted preliminary experiments<br />
* TODO: Define experiment and collect data<br />
===== Dipole codes =====<br />
* [Published: Theoretical Computer Science]<br />
<br />
* Massimo suggested, and I agree, that I write an "approaches to the yield predictions" paper. In that paper, I would include the aforementioned approaches. [submission deadline: ??]<br />
* Comparison of the different approaches. Perhaps time and/or yield comparisons?<br />
<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
* Nicolas has developed visual tracking system and used it to find:<br />
** Time evolution of aggregation<br />
** Distance distribution<br />
** Velocity distribution<br />
* Collaboration with Korean Institute of Science and Technology [Leon Abelmann, Tijmen Hageman, etc.]<br />
** Found the different energy regimes for our aggregating system<br />
** Established that outside the ballistic regime, the components perform "random walk"<br />
*** The data neatly fits into a Rayleigh distribution<br />
* TODO: Get new camera, re-analyse data<br />
* TODO: Write a "methodology" style paper [submission deadline:?]<br />
<br />
=== Conclusions ===<br />
* Contribution 1: Theoretical analysis of parallel assembly vis-a-vis the incompatible substructure problem<br />
* Contribution 2: 5 approaches to avoid the incompatible substructure problem<br />
* Contribution 3: Study of the dynamics of aggregation / parallel assembly</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi/Table_of_contents&diff=7253PhDSupervision:Dhananjay Ipparthi/Table of contents2016-05-17T14:12:13Z<p>Dj: /* Table of content of thesis */</p>
<hr />
<div>== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
* SWARM2015 conference paper presents initial findings of yield predictions [published]<br />
* Extended yield predictions journal paper [not yet published. submission deadline: 5th June, 2016]<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Self-assembly =====<br />
* TODO: Tune the magnetism of the components such that the fully formed target structures are stable, but substructures are susceptible to breakage<br />
===== Changing geometry =====<br />
* [Published: PPSN]<br />
===== Conformational switching =====<br />
* TODO: Close to final design of components<br />
===== Use of high inertia components =====<br />
* Successfully conducted preliminary experiments<br />
* TODO: Define experiment and collect data<br />
===== Dipole codes =====<br />
* [Published: Theoretical Computer Science]<br />
<br />
* Massimo suggested, and I agree, that I write an "approaches to the yield predictions" paper. In that paper, I would include the aforementioned approaches. [submission deadline: ??]<br />
* Comparison of the different approaches. Perhaps time and/or yield comparisons? <br />
<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
* Nicolas has developed visual tracking system and used it to find:<br />
** Time evolution of aggregation<br />
** Distance distribution<br />
** Velocity distribution<br />
* Collaboration with Korean Institute of Science and Technology [Leon Abelmann, Tijmen Hageman, etc.]<br />
** Found the different energy regimes for our aggregating system<br />
** Established that outside the ballistic regime, the components perform "random walk"<br />
*** The data neatly fits into a Rayleigh distribution<br />
* TODO: Get new camera, re-analyse data<br />
* TODO: Write a "methodology" style paper [submission deadline:?]<br />
<br />
=== Conclusions ===<br />
* Contribution 1: Theoretical analysis of parallel assembly vis-a-vis the incompatible substructure problem<br />
* Contribution 2: 5 approaches to avoid the incompatible substructure problem<br />
* Contribution 3: Study of the dynamics of aggregation / parallel assembly</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi/Table_of_contents&diff=7252PhDSupervision:Dhananjay Ipparthi/Table of contents2016-05-17T13:25:43Z<p>Dj: /* Dynamics of aggregating / self-assembling systems */</p>
<hr />
<div>== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
* SWARM2015 conference paper presents initial findings of yield predictions [published]<br />
* Extended yield predictions journal paper [not yet published. submission deadline: 5th June, 2016]<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Self-assembly =====<br />
* TODO: Tune the magnetism of the components such that the fully formed target structures are stable, but substructures are susceptible to breakage<br />
===== Changing geometry =====<br />
* [Published: PPSN]<br />
===== Conformational switching =====<br />
* TODO: Close to final design of components<br />
===== Use of high inertia components =====<br />
* Successfully conducted preliminary experiments<br />
* TODO: Define experiment and collect data<br />
===== Dipole codes =====<br />
* [Published: Theoretical Computer Science]<br />
<br />
* Massimo suggested, and I agree, that I write an "approaches to the yield predictions" paper. In that paper, I would include the aforementioned approaches. [submission deadline: ??]<br />
<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
* Nicolas has developed visual tracking system and used it to find:<br />
** Time evolution of aggregation<br />
** Distance distribution<br />
** Velocity distribution<br />
* Collaboration with Korean Institute of Science and Technology [Leon Abelmann, Tijmen Hageman, etc.]<br />
** Found the different energy regimes for our aggregating system<br />
** Established that outside the ballistic regime, the components perform "random walk"<br />
*** The data neatly fits into a Rayleigh distribution<br />
* TODO: Get new camera, re-analyse data<br />
* TODO: Write a "methodology" style paper [submission deadline:?]<br />
<br />
=== Conclusions ===<br />
* Contribution 1: Theoretical analysis of parallel assembly vis-a-vis the incompatible substructure problem<br />
* Contribution 2: 5 approaches to avoid the incompatible substructure problem<br />
* Contribution 3: Study of the dynamics of aggregation / parallel assembly</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi/Table_of_contents&diff=7251PhDSupervision:Dhananjay Ipparthi/Table of contents2016-05-17T13:25:24Z<p>Dj: /* Dynamics of aggregating / self-assembling systems */</p>
<hr />
<div>== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
* SWARM2015 conference paper presents initial findings of yield predictions [published]<br />
* Extended yield predictions journal paper [not yet published. submission deadline: 5th June, 2016]<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Self-assembly =====<br />
* TODO: Tune the magnetism of the components such that the fully formed target structures are stable, but substructures are susceptible to breakage<br />
===== Changing geometry =====<br />
* [Published: PPSN]<br />
===== Conformational switching =====<br />
* TODO: Close to final design of components<br />
===== Use of high inertia components =====<br />
* Successfully conducted preliminary experiments<br />
* TODO: Define experiment and collect data<br />
===== Dipole codes =====<br />
* [Published: Theoretical Computer Science]<br />
<br />
* Massimo suggested, and I agree, that I write an "approaches to the yield predictions" paper. In that paper, I would include the aforementioned approaches. [submission deadline: ??]<br />
<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
* Nicolas has developed visual tracking system and used it to find:<br />
** Time evolution of aggregation<br />
** Distance distribution<br />
** Velocity distribution<br />
* Collaboration with Korean Institute of Science and Technology [Leon Abelmann, Tijmen Hageman, etc.]<br />
** Found the different energy regimes for our aggregating system<br />
** Established that outside the ballistic regime, the components perform "random walk"<br />
*** The data neatly fits into a Rayleigh distribution<br />
* TODO: Get new camera, re-analyse data<br />
* TODO: Write a "methodology" style paper [submission: deadline]<br />
<br />
=== Conclusions ===<br />
* Contribution 1: Theoretical analysis of parallel assembly vis-a-vis the incompatible substructure problem<br />
* Contribution 2: 5 approaches to avoid the incompatible substructure problem<br />
* Contribution 3: Study of the dynamics of aggregation / parallel assembly</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi/Table_of_contents&diff=7250PhDSupervision:Dhananjay Ipparthi/Table of contents2016-05-17T13:23:58Z<p>Dj: /* Table of content of thesis */</p>
<hr />
<div>== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
* SWARM2015 conference paper presents initial findings of yield predictions [published]<br />
* Extended yield predictions journal paper [not yet published. submission deadline: 5th June, 2016]<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Self-assembly =====<br />
* TODO: Tune the magnetism of the components such that the fully formed target structures are stable, but substructures are susceptible to breakage<br />
===== Changing geometry =====<br />
* [Published: PPSN]<br />
===== Conformational switching =====<br />
* TODO: Close to final design of components<br />
===== Use of high inertia components =====<br />
* Successfully conducted preliminary experiments<br />
* TODO: Define experiment and collect data<br />
===== Dipole codes =====<br />
* [Published: Theoretical Computer Science]<br />
<br />
* Massimo suggested, and I agree, that I write an "approaches to the yield predictions" paper. In that paper, I would include the aforementioned approaches. [submission deadline: ??]<br />
<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
* Nicolas has developed visual tracking system and used it to find:<br />
** Time evolution of aggregation<br />
** Distance distribution<br />
** Velocity distribution<br />
* Collaboration with Korean Institute of Science and Technology [Leon Abelmann, Tijmen Hageman, etc.]<br />
** Found the different energy regimes for our aggregating system<br />
** Established that outside the ballistic regime, the components perform "random walk"<br />
*** The data neatly fits into a Rayleigh distribution<br />
* TODO: Get new camera, re-analyse data<br />
* TODO: Write a "methodology" style paper<br />
=== Conclusions ===<br />
* Contribution 1: Theoretical analysis of parallel assembly vis-a-vis the incompatible substructure problem<br />
* Contribution 2: 5 approaches to avoid the incompatible substructure problem<br />
* Contribution 3: Study of the dynamics of aggregation / parallel assembly</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi/Table_of_contents&diff=7249PhDSupervision:Dhananjay Ipparthi/Table of contents2016-05-17T13:22:19Z<p>Dj: /* Table of content of thesis */</p>
<hr />
<div>== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
* SWARM2015 conference paper presents initial findings of yield predictions [published]<br />
* Extended yield predictions journal paper [not yet published. submission deadline: 5th June, 2016]<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Self-assembly =====<br />
** TODO: Tune the magnetism of the components such that the fully formed target structures are stable, but substructures are susceptible to breakage<br />
===== Changing geometry =====<br />
** [Published: PPSN]<br />
===== Conformational switching =====<br />
** TODO: Close to final design of components<br />
===== Use of high inertia components =====<br />
** Successfully conducted preliminary experiments<br />
** TODO: Define experiment and collect data<br />
===== Dipole codes =====<br />
** [Published: Theoretical Computer Science]<br />
* Massimo suggested, and I agree, that I write an "approaches to the yield predictions" paper. In that paper, I would include the aforementioned approaches. [not yet published]<br />
<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
* Nicolas has developed visual tracking system and used it to find:<br />
** Time evolution of aggregation<br />
** Distance distribution<br />
** Velocity distribution<br />
* Collaboration with Korean Institute of Science and Technology [Leon Abelmann, Tijmen Hageman, etc.]<br />
** Found the different energy regimes for our aggregating system<br />
** Established that outside the ballistic regime, the components perform "random walk"<br />
*** The data neatly fits into a Rayleigh distribution<br />
* TODO: Get new camera, re-analyse data<br />
* TODO: Write a "methodology" style paper<br />
=== Conclusions ===<br />
* Contribution 1: Theoretical analysis of parallel assembly vis-a-vis the incompatible substructure problem<br />
* Contribution 2: 5 approaches to avoid the incompatible substructure problem<br />
* Contribution 3: Study of the dynamics of aggregation / parallel assembly</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi/Table_of_contents&diff=7248PhDSupervision:Dhananjay Ipparthi/Table of contents2016-05-17T13:20:55Z<p>Dj: </p>
<hr />
<div>== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
* SWARM2015 conference paper presents initial findings of yield predictions [published]<br />
* Extended yield predictions journal paper [not yet published. submission deadline: 5th June, 2016]<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Self-assembly =====<br />
* TODO: Tune the magnetism of the components such that the fully formed target structures are stable, but substructures are susceptible to breakage<br />
===== Changing geometry =====<br />
* [Published: PPSN]<br />
===== Conformational switching =====<br />
* TODO: Close to final design of components<br />
===== Use of high inertia components =====<br />
* Successfully conducted preliminary experiments<br />
* TODO: Define experiment and collect data<br />
* Massimo suggested, and I agree, that I write an "approaches to the yield predictions" paper. In that paper, I would include the aforementioned approaches. [not yet published]<br />
===== Dipole codes =====<br />
* [Published: Theoretical Computer Science]<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
* Nicolas has developed visual tracking system and used it to find:<br />
** Time evolution of aggregation<br />
** Distance distribution<br />
** Velocity distribution<br />
* Collaboration with Korean Institute of Science and Technology [Leon Abelmann, Tijmen Hageman, etc.]<br />
** Found the different energy regimes for our aggregating system<br />
** Established that outside the ballistic regime, the components perform "random walk"<br />
*** The data neatly fits into a Rayleigh distribution<br />
* TODO: Get new camera, re-analyse data<br />
* TODO: Write a "methodology" style paper<br />
=== Conclusions ===<br />
* Contribution 1: Theoretical analysis of parallel assembly vis-a-vis the incompatible substructure problem<br />
* Contribution 2: 5 approaches to avoid the incompatible substructure problem<br />
* Contribution 3: Study of the dynamics of aggregation / parallel assembly</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7247PhDSupervision:Dhananjay Ipparthi2016-05-17T11:47:34Z<p>Dj: /* Milestones */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
** [http://iridia.ulb.ac.be/wiki/PhDSupervision:Dhananjay_Ipparthi/Table_of_contents Table of contents]<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress ==<br />
* A Study of Yield Predictions for a Model of Homogeneous Self-Assembling Components: extended version<br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli, and Marco Dorigo. <br />
** Target journal: ''Artificial Life and Robotics Special Issue''<br />
** Synopsis: Statistics to compare model and physical experiments. A closed form model for the formation of incompatible substructures??<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
<br />
* Solutions to the incompatible substructures problem in macroscale systems<br />
** Authors: Dhananjay, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
<br />
* Dynamics of a macro-scale self-assembling system<br />
** Authors: Dhananjay Ipparthi, Nicolas Cambier, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Study of how the incompatible substructures are formed, how the grow and a summary of possible ways to eliminate the problem. Experiments to validate incompatible substructures model and growth of incompatible substructures. Impact of different modes of shaking on a self-assembling system: orbital, linear, orbital + linear with kicks (random)<br />
** Project page: [[Dynamics of self-assembly]]<br />
<br />
* Review of macroscale parallel self-assembling systems<br />
** Authors: Dhananjay Ipparthi, Marco Dorigo and Massimo Mastrangeli.<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7246PhDSupervision:Dhananjay Ipparthi2016-05-17T11:42:38Z<p>Dj: /* Milestones */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
** [Table of contents:http://iridia.ulb.ac.be/wiki/PhDSupervision:Dhananjay_Ipparthi/Table_of_contents]<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress ==<br />
* A Study of Yield Predictions for a Model of Homogeneous Self-Assembling Components: extended version<br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli, and Marco Dorigo. <br />
** Target journal: ''Artificial Life and Robotics Special Issue''<br />
** Synopsis: Statistics to compare model and physical experiments. A closed form model for the formation of incompatible substructures??<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
<br />
* Solutions to the incompatible substructures problem in macroscale systems<br />
** Authors: Dhananjay, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
<br />
* Dynamics of a macro-scale self-assembling system<br />
** Authors: Dhananjay Ipparthi, Nicolas Cambier, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Study of how the incompatible substructures are formed, how the grow and a summary of possible ways to eliminate the problem. Experiments to validate incompatible substructures model and growth of incompatible substructures. Impact of different modes of shaking on a self-assembling system: orbital, linear, orbital + linear with kicks (random)<br />
** Project page: [[Dynamics of self-assembly]]<br />
<br />
* Review of macroscale parallel self-assembling systems<br />
** Authors: Dhananjay Ipparthi, Marco Dorigo and Massimo Mastrangeli.<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7245PhDSupervision:Dhananjay Ipparthi2016-05-17T11:40:55Z<p>Dj: /* Milestones */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
** [Table of contents http://iridia.ulb.ac.be/wiki/PhDSupervision:Dhananjay_Ipparthi/Table_of_contents]<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress ==<br />
* A Study of Yield Predictions for a Model of Homogeneous Self-Assembling Components: extended version<br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli, and Marco Dorigo. <br />
** Target journal: ''Artificial Life and Robotics Special Issue''<br />
** Synopsis: Statistics to compare model and physical experiments. A closed form model for the formation of incompatible substructures??<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
<br />
* Solutions to the incompatible substructures problem in macroscale systems<br />
** Authors: Dhananjay, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
<br />
* Dynamics of a macro-scale self-assembling system<br />
** Authors: Dhananjay Ipparthi, Nicolas Cambier, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Study of how the incompatible substructures are formed, how the grow and a summary of possible ways to eliminate the problem. Experiments to validate incompatible substructures model and growth of incompatible substructures. Impact of different modes of shaking on a self-assembling system: orbital, linear, orbital + linear with kicks (random)<br />
** Project page: [[Dynamics of self-assembly]]<br />
<br />
* Review of macroscale parallel self-assembling systems<br />
** Authors: Dhananjay Ipparthi, Marco Dorigo and Massimo Mastrangeli.<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=Table_of_contents&diff=7244Table of contents2016-05-17T11:40:39Z<p>Dj: Blanked the page</p>
<hr />
<div></div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7243PhDSupervision:Dhananjay Ipparthi2016-05-17T11:40:01Z<p>Dj: /* Milestones */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
** [[Table of contents]]<br />
** [Table of contents http://iridia.ulb.ac.be/wiki/PhDSupervision:Dhananjay_Ipparthi/Table_of_contents]<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress ==<br />
* A Study of Yield Predictions for a Model of Homogeneous Self-Assembling Components: extended version<br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli, and Marco Dorigo. <br />
** Target journal: ''Artificial Life and Robotics Special Issue''<br />
** Synopsis: Statistics to compare model and physical experiments. A closed form model for the formation of incompatible substructures??<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
<br />
* Solutions to the incompatible substructures problem in macroscale systems<br />
** Authors: Dhananjay, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
<br />
* Dynamics of a macro-scale self-assembling system<br />
** Authors: Dhananjay Ipparthi, Nicolas Cambier, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Study of how the incompatible substructures are formed, how the grow and a summary of possible ways to eliminate the problem. Experiments to validate incompatible substructures model and growth of incompatible substructures. Impact of different modes of shaking on a self-assembling system: orbital, linear, orbital + linear with kicks (random)<br />
** Project page: [[Dynamics of self-assembly]]<br />
<br />
* Review of macroscale parallel self-assembling systems<br />
** Authors: Dhananjay Ipparthi, Marco Dorigo and Massimo Mastrangeli.<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi/Table_of_contents&diff=7242PhDSupervision:Dhananjay Ipparthi/Table of contents2016-05-17T11:37:51Z<p>Dj: Created page with "== Table of content of thesis == === Introduction === === Background === * The literature review section of my rapport d'avancement covers about 60% of work that I will cover ..."</p>
<hr />
<div>== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
* SWARM2015 conference paper presents initial findings of yield predictions [published]<br />
* Extended yield predictions journal paper [not yet published]<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Self-assembly =====<br />
* TODO: Tune the magnetism of the components such that the fully formed target structures are stable, but substructures are susceptible to breakage<br />
===== Changing geometry =====<br />
* [Published: PPSN]<br />
===== Conformational switching =====<br />
* TODO: Close to final design of components<br />
===== Use of high inertia components =====<br />
* Successfully conducted preliminary experiments<br />
* TODO: Define experiment and collect data<br />
* Massimo suggested, and I agree, that I write an "approaches to the yield predictions" paper. In that paper, I would include the aforementioned approaches. [not yet published]<br />
===== Dipole codes =====<br />
* [Published: Theoretical Computer Science]<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
* Nicolas has developed visual tracking system and used it to find:<br />
** Time evolution of aggregation<br />
** Distance distribution<br />
** Velocity distribution<br />
* Collaboration with Korean Institute of Science and Technology [Leon Abelmann, Tijmen Hageman, etc.]<br />
** Found the different energy regimes for our aggregating system<br />
** Established that outside the ballistic regime, the components perform "random walk"<br />
*** The data neatly fits into a Rayleigh distribution<br />
* TODO: Get new camera, re-analyse data<br />
* TODO: Write a "methodology" style paper<br />
=== Conclusions ===<br />
* Contribution 1: Theoretical analysis of parallel assembly vis-a-vis the incompatible substructure problem<br />
* Contribution 2: 5 approaches to avoid the incompatible substructure problem<br />
* Contribution 3: Study of the dynamics of aggregation / parallel assembly</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7241PhDSupervision:Dhananjay Ipparthi2016-05-17T11:36:10Z<p>Dj: /* Milestones */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
** [[Table of contents]]<br />
** [http://iridia.ulb.ac.be/wiki/PhDSupervision:Dhananjay_Ipparthi/Table_of_contents]<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress ==<br />
* A Study of Yield Predictions for a Model of Homogeneous Self-Assembling Components: extended version<br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli, and Marco Dorigo. <br />
** Target journal: ''Artificial Life and Robotics Special Issue''<br />
** Synopsis: Statistics to compare model and physical experiments. A closed form model for the formation of incompatible substructures??<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
<br />
* Solutions to the incompatible substructures problem in macroscale systems<br />
** Authors: Dhananjay, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
<br />
* Dynamics of a macro-scale self-assembling system<br />
** Authors: Dhananjay Ipparthi, Nicolas Cambier, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Study of how the incompatible substructures are formed, how the grow and a summary of possible ways to eliminate the problem. Experiments to validate incompatible substructures model and growth of incompatible substructures. Impact of different modes of shaking on a self-assembling system: orbital, linear, orbital + linear with kicks (random)<br />
** Project page: [[Dynamics of self-assembly]]<br />
<br />
* Review of macroscale parallel self-assembling systems<br />
** Authors: Dhananjay Ipparthi, Marco Dorigo and Massimo Mastrangeli.<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7240PhDSupervision:Dhananjay Ipparthi2016-05-17T11:33:12Z<p>Dj: /* Milestones */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
** [[Table of contents]]<br />
**<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress ==<br />
* A Study of Yield Predictions for a Model of Homogeneous Self-Assembling Components: extended version<br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli, and Marco Dorigo. <br />
** Target journal: ''Artificial Life and Robotics Special Issue''<br />
** Synopsis: Statistics to compare model and physical experiments. A closed form model for the formation of incompatible substructures??<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
<br />
* Solutions to the incompatible substructures problem in macroscale systems<br />
** Authors: Dhananjay, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
<br />
* Dynamics of a macro-scale self-assembling system<br />
** Authors: Dhananjay Ipparthi, Nicolas Cambier, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Study of how the incompatible substructures are formed, how the grow and a summary of possible ways to eliminate the problem. Experiments to validate incompatible substructures model and growth of incompatible substructures. Impact of different modes of shaking on a self-assembling system: orbital, linear, orbital + linear with kicks (random)<br />
** Project page: [[Dynamics of self-assembly]]<br />
<br />
* Review of macroscale parallel self-assembling systems<br />
** Authors: Dhananjay Ipparthi, Marco Dorigo and Massimo Mastrangeli.<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=Table_of_contents&diff=7239Table of contents2016-05-17T11:29:50Z<p>Dj: /* Table of content of thesis */</p>
<hr />
<div>== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
* SWARM2015 conference paper presents initial findings of yield predictions [published]<br />
* Extended yield predictions journal paper [not yet published]<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Self-assembly =====<br />
* TODO: Tune the magnetism of the components such that the fully formed target structures are stable, but substructures are susceptible to breakage<br />
===== Changing geometry =====<br />
* [Published: PPSN]<br />
===== Conformational switching =====<br />
* TODO: Close to final design of components<br />
===== Use of high inertia components =====<br />
* Successfully conducted preliminary experiments<br />
* TODO: Define experiment and collect data<br />
* Massimo suggested, and I agree, that I write an "approaches to the yield predictions" paper. In that paper, I would include the aforementioned approaches. [not yet published]<br />
===== Dipole codes =====<br />
* [Published: Theoretical Computer Science]<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
* Nicolas has developed visual tracking system and used it to find:<br />
** Time evolution of aggregation<br />
** Distance distribution<br />
** Velocity distribution<br />
* Collaboration with Korean Institute of Science and Technology [Leon Abelmann, Tijmen Hageman, etc.]<br />
** Found the different energy regimes for our aggregating system<br />
** Established that outside the ballistic regime, the components perform "random walk"<br />
*** The data neatly fits into a Rayleigh distribution<br />
* TODO: Get new camera, re-analyse data<br />
* TODO: Write a "methodology" style paper<br />
=== Conclusions ===<br />
* Contribution 1: Theoretical analysis of parallel assembly vis-a-vis the incompatible substructure problem<br />
* Contribution 2: 5 approaches to avoid the incompatible substructure problem<br />
* Contribution 3: Study of the dynamics of aggregation / parallel assembly</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=Table_of_contents&diff=7238Table of contents2016-05-17T11:27:18Z<p>Dj: /* Table of content of thesis */</p>
<hr />
<div>== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
* SWARM2015 conference paper presents initial findings of yield predictions [published]<br />
* Extended yield predictions journal paper [not yet published]<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Self-assembly =====<br />
* TODO: Tune the magnetism of the components such that the fully formed target structures are stable, but substructures are susceptible to breakage<br />
===== Changing geometry =====<br />
* [Published: PPSN]<br />
===== Conformational switching =====<br />
* TODO: Close to final design of components<br />
===== Use of high inertia components =====<br />
* Successfully conducted preliminary experiments<br />
* TODO: Define experiment and collect data<br />
* Massimo suggested, and I agree, that I write an "approaches to the yield predictions" paper. In that paper, I would include the aforementioned approaches. [not yet published]<br />
===== Dipole codes =====<br />
* [Published: Theoretical Computer Science]<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
* Nicolas has developed visual tracking system and used it to find:<br />
** Time evolution of aggregation<br />
** Distance distribution<br />
** Velocity distribution<br />
* Collaboration with Korean Institute of Science and Technology [Leon Abelmann, Tijmen Hageman, etc.]<br />
** Found the different energy regimes for our aggregating system<br />
** Established that outside the ballistic regime, the components perform "random walk"<br />
*** The data neatly fits into a Rayleigh distribution<br />
* TODO: Get new camera, re-analyse data<br />
* TODO: Write paper<br />
=== Conclusions ===<br />
* Contribution 1:</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=Table_of_contents&diff=7237Table of contents2016-05-17T11:26:45Z<p>Dj: /* Table of content of thesis */</p>
<hr />
<div>== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
* SWARM2015 conference paper presents initial findings of yield predictions [published]<br />
* Extended yield predictions journal paper [not yet published]<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Self-assembly =====<br />
* TODO: Tune the magnetism of the components such that the fully formed target structures are stable, but substructures are susceptible to breakage<br />
===== Changing geometry =====<br />
* [Published: PPSN]<br />
===== Conformational switching =====<br />
* TODO: Close to final design of components<br />
===== Use of high inertia components =====<br />
* Successfully conducted preliminary experiments<br />
* TODO: Define experiment and collect data<br />
* Massimo suggested, and I agree, that I write an "approaches to the yield predictions" paper. In that paper, I would include the aforementioned approaches. [not yet published]<br />
===== Dipole codes =====<br />
* Theoretical work [published]<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
* Nicolas has developed visual tracking system and used it to find:<br />
** Time evolution of aggregation<br />
** Distance distribution<br />
** Velocity distribution<br />
* Collaboration with Korean Institute of Science and Technology [Leon Abelmann, Tijmen Hageman, etc.]<br />
** Found the different energy regimes for our aggregating system<br />
** Established that outside the ballistic regime, the components perform "random walk"<br />
*** The data neatly fits into a Rayleigh distribution<br />
* TODO: Get new camera, re-analyse data<br />
* TODO: Write paper<br />
=== Conclusions ===<br />
* Contribution 1:</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=Table_of_contents&diff=7236Table of contents2016-05-17T11:22:01Z<p>Dj: /* Table of content of thesis */</p>
<hr />
<div>== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
* SWARM2015 conference paper presents initial findings of yield predictions [published]<br />
* Extended yield predictions journal paper [not yet published]<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Self-assembly =====<br />
===== Changing geometry =====<br />
* [Published: PPSN]<br />
===== Conformational switching =====<br />
* Close to final design of components<br />
===== Use of high inertia components =====<br />
* Successfully conducted preliminary experiments<br />
* TODO: Define experiment and collect data<br />
* Massimo suggested, and I agree, that I write an "approaches to the yield predictions" paper. In that paper, I would include the aforementioned approaches. [not yet published]<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
* Nicolas has developed visual tracking system and used it to find:<br />
** Time evolution of aggregation<br />
** Distance distribution<br />
** Velocity distribution<br />
* Collaboration with Korean Institute of Science and Technology [Leon Abelmann, Tijmen Hageman, etc.]<br />
** Found the different energy regimes for our aggregating system<br />
** Established that outside the ballistic regime, the components perform "random walk"<br />
*** The data neatly fits into a Rayleigh distribution<br />
=== Conclusions ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=Table_of_contents&diff=7235Table of contents2016-05-17T11:16:21Z<p>Dj: /* Table of content of thesis */</p>
<hr />
<div>== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
* SWARM2015 conference paper presents initial findings of yield predictions [published]<br />
* Extended yield predictions journal paper [not yet published]<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Self-assembly =====<br />
===== Changing geometry =====<br />
* [Published: PPSN]<br />
===== Conformational switching ===== <br />
===== Use of high inertia components =====<br />
* Massimo suggested, and I agree, that I write an "approaches to the yield predictions" paper. In that paper, I would include the aforementioned approaches. [not yet published]<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
* Nicolas has developed visual tracking system and used it to find:<br />
** Time evolution of aggregation<br />
** Distance distribution<br />
** Velocity distribution<br />
* Collaboration with Korean Institute of Science and Technology [Leon Abelmann, Tijmen Hageman, etc.]<br />
** Found the different energy regimes for our aggregating system<br />
** Established that outside the ballistic regime, the components perform "random walk"<br />
*** The data neatly fits into a Rayleigh distribution<br />
=== Conclusions ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=Table_of_contents&diff=7234Table of contents2016-05-17T11:15:39Z<p>Dj: /* Table of content of thesis */</p>
<hr />
<div>== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
* SWARM2015 conference paper presents initial findings of yield predictions [published]<br />
* Extended yield predictions journal paper [not yet published]<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Self-assembly =====<br />
===== Changing geometry =====<br />
===== Conformational switching ===== <br />
===== Use of high inertia components =====<br />
* Massimo suggested, and I agree, that I write an "approaches to the yield predictions" paper. In that paper, I would include the aforementioned approaches. [not yet published]<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
* Nicolas has developed visual tracking system and used it to find:<br />
** Time evolution of aggregation<br />
** Distance distribution<br />
** Velocity distribution<br />
* Collaboration with Korean Institute of Science and Technology [Leon Abelmann, Tijmen Hageman, etc.]<br />
** Found the different energy regimes for our aggregating system<br />
** Established that outside the ballistic regime, the components perform "random walk"<br />
*** The data neatly fits into a Rayleigh distribution<br />
=== Conclusions ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7233PhDSupervision:Dhananjay Ipparthi2016-05-17T11:08:12Z<p>Dj: </p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
** [[Table of contents]]<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress ==<br />
* A Study of Yield Predictions for a Model of Homogeneous Self-Assembling Components: extended version<br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli, and Marco Dorigo. <br />
** Target journal: ''Artificial Life and Robotics Special Issue''<br />
** Synopsis: Statistics to compare model and physical experiments. A closed form model for the formation of incompatible substructures??<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
<br />
* Solutions to the incompatible substructures problem in macroscale systems<br />
** Authors: Dhananjay, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
<br />
* Dynamics of a macro-scale self-assembling system<br />
** Authors: Dhananjay Ipparthi, Nicolas Cambier, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Study of how the incompatible substructures are formed, how the grow and a summary of possible ways to eliminate the problem. Experiments to validate incompatible substructures model and growth of incompatible substructures. Impact of different modes of shaking on a self-assembling system: orbital, linear, orbital + linear with kicks (random)<br />
** Project page: [[Dynamics of self-assembly]]<br />
<br />
* Review of macroscale parallel self-assembling systems<br />
** Authors: Dhananjay Ipparthi, Marco Dorigo and Massimo Mastrangeli.<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=Table_of_contents&diff=7232Table of contents2016-05-17T11:07:45Z<p>Dj: Created page with "== Table of content of thesis == === Introduction === === Background === * The literature review section of my rapport d'avancement covers about 60% of work that I will cover ..."</p>
<hr />
<div>== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
* SWARM2015 conference paper presents initial findings of yield predictions [published]<br />
* Extended yield predictions journal paper [not yet published]<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Self-assembly =====<br />
===== Changing geometry =====<br />
===== Conformational switching ===== <br />
===== Use of high inertia components =====<br />
* Massimo suggested, and I agree, that I write an "approaches to the yield predictions" paper. In that paper, I would include the aforementioned approaches. [not yet published]<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
* Nicolas has developed visual tracking system and used it to find <br />
* Collaboration with Korean Institute of Science and Technology [Leon Abelmann, Tijmen Hageman, etc.]<br />
** Found the different energy regimes for our aggregating system<br />
** Established that outside the ballistic regime, the components perform "random walk"<br />
*** The data neatly fits into a Rayleigh distribution<br />
=== Conclusions ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7231PhDSupervision:Dhananjay Ipparthi2016-05-17T11:07:39Z<p>Dj: /* Milestones */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
** [[Table of contents]]<br />
<br />
== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
* SWARM2015 conference paper presents initial findings of yield predictions [published]<br />
* Extended yield predictions journal paper [not yet published]<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Self-assembly =====<br />
===== Changing geometry =====<br />
===== Conformational switching ===== <br />
===== Use of high inertia components =====<br />
* Massimo suggested, and I agree, that I write an "approaches to the yield predictions" paper. In that paper, I would include the aforementioned approaches. [not yet published]<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
* Nicolas has developed visual tracking system and used it to find <br />
* Collaboration with Korean Institute of Science and Technology [Leon Abelmann, Tijmen Hageman, etc.]<br />
** Found the different energy regimes for our aggregating system<br />
** Established that outside the ballistic regime, the components perform "random walk"<br />
*** The data neatly fits into a Rayleigh distribution<br />
=== Conclusions ===<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress ==<br />
* A Study of Yield Predictions for a Model of Homogeneous Self-Assembling Components: extended version<br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli, and Marco Dorigo. <br />
** Target journal: ''Artificial Life and Robotics Special Issue''<br />
** Synopsis: Statistics to compare model and physical experiments. A closed form model for the formation of incompatible substructures??<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
<br />
* Solutions to the incompatible substructures problem in macroscale systems<br />
** Authors: Dhananjay, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
<br />
* Dynamics of a macro-scale self-assembling system<br />
** Authors: Dhananjay Ipparthi, Nicolas Cambier, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Study of how the incompatible substructures are formed, how the grow and a summary of possible ways to eliminate the problem. Experiments to validate incompatible substructures model and growth of incompatible substructures. Impact of different modes of shaking on a self-assembling system: orbital, linear, orbital + linear with kicks (random)<br />
** Project page: [[Dynamics of self-assembly]]<br />
<br />
* Review of macroscale parallel self-assembling systems<br />
** Authors: Dhananjay Ipparthi, Marco Dorigo and Massimo Mastrangeli.<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7230PhDSupervision:Dhananjay Ipparthi2016-05-17T11:06:42Z<p>Dj: /* Table of content of thesis */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
<br />
== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
* SWARM2015 conference paper presents initial findings of yield predictions [published]<br />
* Extended yield predictions journal paper [not yet published]<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Self-assembly =====<br />
===== Changing geometry =====<br />
===== Conformational switching ===== <br />
===== Use of high inertia components =====<br />
* Massimo suggested, and I agree, that I write an "approaches to the yield predictions" paper. In that paper, I would include the aforementioned approaches. [not yet published]<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
* Nicolas has developed visual tracking system and used it to find <br />
* Collaboration with Korean Institute of Science and Technology [Leon Abelmann, Tijmen Hageman, etc.]<br />
** Found the different energy regimes for our aggregating system<br />
** Established that outside the ballistic regime, the components perform "random walk"<br />
*** The data neatly fits into a Rayleigh distribution<br />
=== Conclusions ===<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress ==<br />
* A Study of Yield Predictions for a Model of Homogeneous Self-Assembling Components: extended version<br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli, and Marco Dorigo. <br />
** Target journal: ''Artificial Life and Robotics Special Issue''<br />
** Synopsis: Statistics to compare model and physical experiments. A closed form model for the formation of incompatible substructures??<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
<br />
* Solutions to the incompatible substructures problem in macroscale systems<br />
** Authors: Dhananjay, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
<br />
* Dynamics of a macro-scale self-assembling system<br />
** Authors: Dhananjay Ipparthi, Nicolas Cambier, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Study of how the incompatible substructures are formed, how the grow and a summary of possible ways to eliminate the problem. Experiments to validate incompatible substructures model and growth of incompatible substructures. Impact of different modes of shaking on a self-assembling system: orbital, linear, orbital + linear with kicks (random)<br />
** Project page: [[Dynamics of self-assembly]]<br />
<br />
* Review of macroscale parallel self-assembling systems<br />
** Authors: Dhananjay Ipparthi, Marco Dorigo and Massimo Mastrangeli.<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7229PhDSupervision:Dhananjay Ipparthi2016-05-17T10:59:32Z<p>Dj: /* Table of content of thesis */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
<br />
== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
* SWARM2015 conference paper presents initial findings of yield predictions [published]<br />
* Extended yield predictions journal paper [not yet published]<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Self-assembly =====<br />
===== Changing geometry =====<br />
===== Conformational switching ===== <br />
===== Use of high inertia components =====<br />
* Massimo suggested, and I agree, that I write an "approaches to the yield predictions" paper. In that paper, I would include the aforementioned approaches. [not yet published]<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
* Nicolas has developed visual tracking system and used it to find <br />
* Collaborating with <br />
=== Conclusions ===<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress ==<br />
* A Study of Yield Predictions for a Model of Homogeneous Self-Assembling Components: extended version<br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli, and Marco Dorigo. <br />
** Target journal: ''Artificial Life and Robotics Special Issue''<br />
** Synopsis: Statistics to compare model and physical experiments. A closed form model for the formation of incompatible substructures??<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
<br />
* Solutions to the incompatible substructures problem in macroscale systems<br />
** Authors: Dhananjay, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
<br />
* Dynamics of a macro-scale self-assembling system<br />
** Authors: Dhananjay Ipparthi, Nicolas Cambier, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Study of how the incompatible substructures are formed, how the grow and a summary of possible ways to eliminate the problem. Experiments to validate incompatible substructures model and growth of incompatible substructures. Impact of different modes of shaking on a self-assembling system: orbital, linear, orbital + linear with kicks (random)<br />
** Project page: [[Dynamics of self-assembly]]<br />
<br />
* Review of macroscale parallel self-assembling systems<br />
** Authors: Dhananjay Ipparthi, Marco Dorigo and Massimo Mastrangeli.<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7228PhDSupervision:Dhananjay Ipparthi2016-05-17T10:54:28Z<p>Dj: /* Table of content of thesis */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
<br />
== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ===<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Self-assembly =====<br />
===== Changing geometry =====<br />
===== Conformational switching ===== <br />
===== Use of high inertia components =====<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
=== Conclusions ===<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress ==<br />
* A Study of Yield Predictions for a Model of Homogeneous Self-Assembling Components: extended version<br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli, and Marco Dorigo. <br />
** Target journal: ''Artificial Life and Robotics Special Issue''<br />
** Synopsis: Statistics to compare model and physical experiments. A closed form model for the formation of incompatible substructures??<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
<br />
* Solutions to the incompatible substructures problem in macroscale systems<br />
** Authors: Dhananjay, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
<br />
* Dynamics of a macro-scale self-assembling system<br />
** Authors: Dhananjay Ipparthi, Nicolas Cambier, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Study of how the incompatible substructures are formed, how the grow and a summary of possible ways to eliminate the problem. Experiments to validate incompatible substructures model and growth of incompatible substructures. Impact of different modes of shaking on a self-assembling system: orbital, linear, orbital + linear with kicks (random)<br />
** Project page: [[Dynamics of self-assembly]]<br />
<br />
* Review of macroscale parallel self-assembling systems<br />
** Authors: Dhananjay Ipparthi, Marco Dorigo and Massimo Mastrangeli.<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7227PhDSupervision:Dhananjay Ipparthi2016-05-17T10:54:15Z<p>Dj: /* Table of content of thesis */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
<br />
== Table of content of thesis ==<br />
=== Introduction ===<br />
=== Background ====<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
=== Theoretical treatment of incompatible substructure problem ===<br />
=== Approaches to solve the incompatible substructure problem ===<br />
===== Self-assembly =====<br />
===== Changing geometry =====<br />
===== Conformational switching ===== <br />
===== Use of high inertia components =====<br />
=== Dynamics of aggregating / self-assembling systems ===<br />
=== Conclusions ===<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress ==<br />
* A Study of Yield Predictions for a Model of Homogeneous Self-Assembling Components: extended version<br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli, and Marco Dorigo. <br />
** Target journal: ''Artificial Life and Robotics Special Issue''<br />
** Synopsis: Statistics to compare model and physical experiments. A closed form model for the formation of incompatible substructures??<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
<br />
* Solutions to the incompatible substructures problem in macroscale systems<br />
** Authors: Dhananjay, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
<br />
* Dynamics of a macro-scale self-assembling system<br />
** Authors: Dhananjay Ipparthi, Nicolas Cambier, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Study of how the incompatible substructures are formed, how the grow and a summary of possible ways to eliminate the problem. Experiments to validate incompatible substructures model and growth of incompatible substructures. Impact of different modes of shaking on a self-assembling system: orbital, linear, orbital + linear with kicks (random)<br />
** Project page: [[Dynamics of self-assembly]]<br />
<br />
* Review of macroscale parallel self-assembling systems<br />
** Authors: Dhananjay Ipparthi, Marco Dorigo and Massimo Mastrangeli.<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7226PhDSupervision:Dhananjay Ipparthi2016-05-17T10:53:21Z<p>Dj: /* Table of content of thesis */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
<br />
== Table of content of thesis ==<br />
==== Introduction ====<br />
==== Background ====<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
==== Theoretical treatment of incompatible substructure problem ====<br />
==== Approaches to solve the incompatible substructure problem ====<br />
===== Self-assembly =====<br />
===== Changing geometry =====<br />
===== Conformational switching ===== <br />
===== Use of high inertia components =====<br />
==== Dynamics of aggregating / self-assembling systems ====<br />
==== Conclusions ====<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress ==<br />
* A Study of Yield Predictions for a Model of Homogeneous Self-Assembling Components: extended version<br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli, and Marco Dorigo. <br />
** Target journal: ''Artificial Life and Robotics Special Issue''<br />
** Synopsis: Statistics to compare model and physical experiments. A closed form model for the formation of incompatible substructures??<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
<br />
* Solutions to the incompatible substructures problem in macroscale systems<br />
** Authors: Dhananjay, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
<br />
* Dynamics of a macro-scale self-assembling system<br />
** Authors: Dhananjay Ipparthi, Nicolas Cambier, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Study of how the incompatible substructures are formed, how the grow and a summary of possible ways to eliminate the problem. Experiments to validate incompatible substructures model and growth of incompatible substructures. Impact of different modes of shaking on a self-assembling system: orbital, linear, orbital + linear with kicks (random)<br />
** Project page: [[Dynamics of self-assembly]]<br />
<br />
* Review of macroscale parallel self-assembling systems<br />
** Authors: Dhananjay Ipparthi, Marco Dorigo and Massimo Mastrangeli.<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7225PhDSupervision:Dhananjay Ipparthi2016-05-17T10:53:05Z<p>Dj: /* Table of content of thesis */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
<br />
== Table of content of thesis ==<br />
==== Introduction ====<br />
==== Background ====<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis <br />
==== Theoretical treatment of incompatible substructure problem ====<br />
==== Approaches to solve the incompatible substructure problem ====<br />
===== Self-assembly =====<br />
===== Changing geometry =====<br />
===== Conformational switching ===== <br />
===== Use of high inertia components =====<br />
==== Dynamics of aggregating / self-assembling systems =====<br />
==== Conclusions ====<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress ==<br />
* A Study of Yield Predictions for a Model of Homogeneous Self-Assembling Components: extended version<br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli, and Marco Dorigo. <br />
** Target journal: ''Artificial Life and Robotics Special Issue''<br />
** Synopsis: Statistics to compare model and physical experiments. A closed form model for the formation of incompatible substructures??<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
<br />
* Solutions to the incompatible substructures problem in macroscale systems<br />
** Authors: Dhananjay, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
<br />
* Dynamics of a macro-scale self-assembling system<br />
** Authors: Dhananjay Ipparthi, Nicolas Cambier, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Study of how the incompatible substructures are formed, how the grow and a summary of possible ways to eliminate the problem. Experiments to validate incompatible substructures model and growth of incompatible substructures. Impact of different modes of shaking on a self-assembling system: orbital, linear, orbital + linear with kicks (random)<br />
** Project page: [[Dynamics of self-assembly]]<br />
<br />
* Review of macroscale parallel self-assembling systems<br />
** Authors: Dhananjay Ipparthi, Marco Dorigo and Massimo Mastrangeli.<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7224PhDSupervision:Dhananjay Ipparthi2016-05-17T10:50:37Z<p>Dj: /* Table of content of thesis */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
<br />
== Table of content of thesis ==<br />
* Introduction<br />
* Background<br />
*** The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis<br />
* Theoretical treatment of incompatible substructure problem<br />
* Approaches to solve the incompatible substructure problem<br />
** Self-assembly<br />
** Changing geometry<br />
** Conformational switching<br />
** Use of high inertia components<br />
* Dynamics of aggregating / self-assembling systems<br />
* Conclusions<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress ==<br />
* A Study of Yield Predictions for a Model of Homogeneous Self-Assembling Components: extended version<br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli, and Marco Dorigo. <br />
** Target journal: ''Artificial Life and Robotics Special Issue''<br />
** Synopsis: Statistics to compare model and physical experiments. A closed form model for the formation of incompatible substructures??<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
<br />
* Solutions to the incompatible substructures problem in macroscale systems<br />
** Authors: Dhananjay, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
<br />
* Dynamics of a macro-scale self-assembling system<br />
** Authors: Dhananjay Ipparthi, Nicolas Cambier, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Study of how the incompatible substructures are formed, how the grow and a summary of possible ways to eliminate the problem. Experiments to validate incompatible substructures model and growth of incompatible substructures. Impact of different modes of shaking on a self-assembling system: orbital, linear, orbital + linear with kicks (random)<br />
** Project page: [[Dynamics of self-assembly]]<br />
<br />
* Review of macroscale parallel self-assembling systems<br />
** Authors: Dhananjay Ipparthi, Marco Dorigo and Massimo Mastrangeli.<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7223PhDSupervision:Dhananjay Ipparthi2016-05-17T10:49:41Z<p>Dj: /* Table of content of thesis */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
<br />
== Table of content of thesis ==<br />
# Introduction<br />
# Background<br />
The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis<br />
# Theoretical treatment of incompatible substructure problem<br />
# Approaches to solve the incompatible substructure problem<br />
## Self-assembly<br />
## Changing geometry<br />
## Conformational switching<br />
## Use of high inertia components<br />
# Dynamics of aggregating / self-assembling systems<br />
# Conclusions<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress ==<br />
* A Study of Yield Predictions for a Model of Homogeneous Self-Assembling Components: extended version<br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli, and Marco Dorigo. <br />
** Target journal: ''Artificial Life and Robotics Special Issue''<br />
** Synopsis: Statistics to compare model and physical experiments. A closed form model for the formation of incompatible substructures??<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
<br />
* Solutions to the incompatible substructures problem in macroscale systems<br />
** Authors: Dhananjay, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
<br />
* Dynamics of a macro-scale self-assembling system<br />
** Authors: Dhananjay Ipparthi, Nicolas Cambier, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Study of how the incompatible substructures are formed, how the grow and a summary of possible ways to eliminate the problem. Experiments to validate incompatible substructures model and growth of incompatible substructures. Impact of different modes of shaking on a self-assembling system: orbital, linear, orbital + linear with kicks (random)<br />
** Project page: [[Dynamics of self-assembly]]<br />
<br />
* Review of macroscale parallel self-assembling systems<br />
** Authors: Dhananjay Ipparthi, Marco Dorigo and Massimo Mastrangeli.<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7222PhDSupervision:Dhananjay Ipparthi2016-05-17T10:49:32Z<p>Dj: /* Table of content of thesis */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
<br />
== Table of content of thesis ==<br />
# Introduction<br />
# Background<br />
** The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis<br />
# Theoretical treatment of incompatible substructure problem<br />
# Approaches to solve the incompatible substructure problem<br />
## Self-assembly<br />
## Changing geometry<br />
## Conformational switching<br />
## Use of high inertia components<br />
# Dynamics of aggregating / self-assembling systems<br />
# Conclusions<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress ==<br />
* A Study of Yield Predictions for a Model of Homogeneous Self-Assembling Components: extended version<br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli, and Marco Dorigo. <br />
** Target journal: ''Artificial Life and Robotics Special Issue''<br />
** Synopsis: Statistics to compare model and physical experiments. A closed form model for the formation of incompatible substructures??<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
<br />
* Solutions to the incompatible substructures problem in macroscale systems<br />
** Authors: Dhananjay, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
<br />
* Dynamics of a macro-scale self-assembling system<br />
** Authors: Dhananjay Ipparthi, Nicolas Cambier, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Study of how the incompatible substructures are formed, how the grow and a summary of possible ways to eliminate the problem. Experiments to validate incompatible substructures model and growth of incompatible substructures. Impact of different modes of shaking on a self-assembling system: orbital, linear, orbital + linear with kicks (random)<br />
** Project page: [[Dynamics of self-assembly]]<br />
<br />
* Review of macroscale parallel self-assembling systems<br />
** Authors: Dhananjay Ipparthi, Marco Dorigo and Massimo Mastrangeli.<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7221PhDSupervision:Dhananjay Ipparthi2016-05-17T10:49:14Z<p>Dj: /* Table of content of thesis */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
<br />
== Table of content of thesis ==<br />
# Introduction<br />
# Background<br />
* The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis<br />
# Theoretical treatment of incompatible substructure problem<br />
# Approaches to solve the incompatible substructure problem<br />
## Self-assembly<br />
## Changing geometry<br />
## Conformational switching<br />
## Use of high inertia components<br />
# Dynamics of aggregating / self-assembling systems<br />
# Conclusions<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress ==<br />
* A Study of Yield Predictions for a Model of Homogeneous Self-Assembling Components: extended version<br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli, and Marco Dorigo. <br />
** Target journal: ''Artificial Life and Robotics Special Issue''<br />
** Synopsis: Statistics to compare model and physical experiments. A closed form model for the formation of incompatible substructures??<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
<br />
* Solutions to the incompatible substructures problem in macroscale systems<br />
** Authors: Dhananjay, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
<br />
* Dynamics of a macro-scale self-assembling system<br />
** Authors: Dhananjay Ipparthi, Nicolas Cambier, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Study of how the incompatible substructures are formed, how the grow and a summary of possible ways to eliminate the problem. Experiments to validate incompatible substructures model and growth of incompatible substructures. Impact of different modes of shaking on a self-assembling system: orbital, linear, orbital + linear with kicks (random)<br />
** Project page: [[Dynamics of self-assembly]]<br />
<br />
* Review of macroscale parallel self-assembling systems<br />
** Authors: Dhananjay Ipparthi, Marco Dorigo and Massimo Mastrangeli.<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7220PhDSupervision:Dhananjay Ipparthi2016-05-17T10:49:04Z<p>Dj: /* Table of content of thesis */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
<br />
== Table of content of thesis ==<br />
# Introduction<br />
# Background<br />
** The literature review section of my rapport d'avancement covers about 60% of work that I will cover in my doctoral thesis<br />
# Theoretical treatment of incompatible substructure problem<br />
# Approaches to solve the incompatible substructure problem<br />
## Self-assembly<br />
## Changing geometry<br />
## Conformational switching<br />
## Use of high inertia components<br />
# Dynamics of aggregating / self-assembling systems<br />
# Conclusions<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress ==<br />
* A Study of Yield Predictions for a Model of Homogeneous Self-Assembling Components: extended version<br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli, and Marco Dorigo. <br />
** Target journal: ''Artificial Life and Robotics Special Issue''<br />
** Synopsis: Statistics to compare model and physical experiments. A closed form model for the formation of incompatible substructures??<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
<br />
* Solutions to the incompatible substructures problem in macroscale systems<br />
** Authors: Dhananjay, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
<br />
* Dynamics of a macro-scale self-assembling system<br />
** Authors: Dhananjay Ipparthi, Nicolas Cambier, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Study of how the incompatible substructures are formed, how the grow and a summary of possible ways to eliminate the problem. Experiments to validate incompatible substructures model and growth of incompatible substructures. Impact of different modes of shaking on a self-assembling system: orbital, linear, orbital + linear with kicks (random)<br />
** Project page: [[Dynamics of self-assembly]]<br />
<br />
* Review of macroscale parallel self-assembling systems<br />
** Authors: Dhananjay Ipparthi, Marco Dorigo and Massimo Mastrangeli.<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Djhttps://iridia.ulb.ac.be/w/index.php?title=PhDSupervision:Dhananjay_Ipparthi&diff=7219PhDSupervision:Dhananjay Ipparthi2016-05-17T10:46:42Z<p>Dj: /* Table of content of thesis */</p>
<hr />
<div>[[Category:PhDSupervision_Dhananjay_Ipparthi]]<br />
<br />
== Personal Information ==<br />
Name: Dhananjay Ipparthi<br />
<br />
Date of arrival in Brussels: 08th February, 2012<br />
<br />
Home address: Rue des Vierges 58, 1000 Bruxelles<br />
<br />
Telephone number: +32 483 382 207<br />
<br />
== Milestones ==<br />
* Three papers<br />
* Thesis<br />
<br />
== Table of content of thesis ==<br />
# Introduction<br />
# Theoretical treatment of incompatible substructure problem<br />
# Approaches to solve the incompatible substructure problem<br />
## Self-assembly<br />
## Changing geometry<br />
## Conformational switching<br />
## Use of high inertia components<br />
# Dynamics of aggregating / self-assembling systems<br />
# Conclusions<br />
<br />
== Project pages ==<br />
<br />
=== [[Study of yield predictions of a self-assembling system - extended]] ===<br />
=== [[Conformational Switching]] ===<br />
<br />
=== [[Dynamics of self-assembly]] ===<br />
=== [[Dipole words]] ===<br />
=== [[Parallel self-assembling systems review paper]] ===<br />
<br />
== Papers in progress ==<br />
* A Study of Yield Predictions for a Model of Homogeneous Self-Assembling Components: extended version<br />
** Authors: Dhananjay Ipparthi, Andrew Winslow, Massimo Mastrangeli, and Marco Dorigo. <br />
** Target journal: ''Artificial Life and Robotics Special Issue''<br />
** Synopsis: Statistics to compare model and physical experiments. A closed form model for the formation of incompatible substructures??<br />
** Project page: [[Theory of incompatible substructure problem]]<br />
<br />
* Solutions to the incompatible substructures problem in macroscale systems<br />
** Authors: Dhananjay, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Presentation of the different approaches to the incompatible substurcture problem: modifying geometry, modifying bonding rules, conformational switching, high inertia particles, partitioning the container and self-assembly. <br />
** Project pages: [[Conformational Switching]], [[Use of a external agent to break incompatible substructures]]<br />
<br />
* Dynamics of a macro-scale self-assembling system<br />
** Authors: Dhananjay Ipparthi, Nicolas Cambier, Andrew Winslow, Massimo Mastrangeli and Marco Dorigo<br />
** Target journal: <br />
** Synopsis: Study of how the incompatible substructures are formed, how the grow and a summary of possible ways to eliminate the problem. Experiments to validate incompatible substructures model and growth of incompatible substructures. Impact of different modes of shaking on a self-assembling system: orbital, linear, orbital + linear with kicks (random)<br />
** Project page: [[Dynamics of self-assembly]]<br />
<br />
* Review of macroscale parallel self-assembling systems<br />
** Authors: Dhananjay Ipparthi, Marco Dorigo and Massimo Mastrangeli.<br />
** Target journal: ''Micromachines: Special Issue on Building by Self-Assembly''<br />
** Synopsis: An in-depth review of macroscale parallel self-assembling systems. Summaries, categorisations and differentiations of the various works till date. Provide open problems.<br />
** Project page: [[Parallel self-assembling systems review paper]]<br />
<br />
== Academic Activities ==<br />
=== 17th February - 20th April, 2016 ===<br />
* Setup experiment workspace<br />
** Installed shaker + universal platform<br />
** Cut out containers<br />
** Installed lighting system<br />
** Installed and calibrated video tracking system<br />
* Conducted ~ 1100 trials for extended yield predictions paper<br />
* Modified master equation based simulation in order to collect relevant data<br />
* Plotted model vs. physical experiment data<br />
* Plotted possible number of combination vs. observed combinations data<br />
* Complete revision of the conformational switching design --- pendulum based<br />
** 3 iteration of the pendulum design<br />
* Random shaker design and fabrication<br />
* Preliminary experiments with high inertia particles<br />
* Designed and fabricated jib for shaking with periodic kicks<br />
* Preliminary work on theoretical study on homogeneous set of components<br />
* Designed and fabricated container with no walls<br />
** Conducted preliminary tests<br />
** Test results not particularly promising<br />
* Preliminary setup of dynamic self-assembly system<br />
<br />
=== 8th February - 16th February, 2016 ===<br />
* Presented my work to the "Programmable self-assembly subgroup" on the 11th of February. Metin attended that presentation. The group expressed interest in one of the results presented in "A geometrical approach to the incompatible substructure problem in parallel self-assembly". The wanted to know why the 90 deg component experiments resulted in a high yield. I told the group that we suspect that symmetry and the high probability of forming pairs could be the reason for the high yield. I added that we would be studying this phenomenon in detail using video tracking in our upcoming work on the extended yield prediction paper. The group also had some input for the issues I have with regard to the conformational switching work. <br />
* Increased the shielding of conformational switching components. The increased shielding seems to reduce the local effects of magnets in the vicinity. <br />
* Finished designing the jig that we will use to create "random kicks" during orbital shaking. I will be meeting the in-house production engineer this afternoon before getting it fabricated. <br />
* The shaker has not yet arrived. The secretary here (Janina) says we would have to wait for a few more weeks.<br />
<br />
=== [[Things I'm taking to MPI]] ===<br />
<br />
=== [[Year 4: Feb 2015 - Feb 2016]] ===<br />
=== [[Year 3: Feb 2014 - Feb 2015]] ===<br />
=== [[Year 2: Feb 2013 - Feb 2014]] ===<br />
=== [[Year 1: Feb 2012 - Feb 2013]] ===</div>Dj