Variational design principles for nonequilibrium colloidal assembly
Abstract
Using large deviation theory and principles of stochastic optimal control, we show that rare molecular dynamics trajectories conditioned on assembling a specific target structure encode a set of interactions and external forces that lead to enhanced stability of that structure. Such a relationship can be formulated into a variational principle, for which we have developed an associated optimization algorithm and have used it to determine optimal forces for targeted self-assembly within nonequilibrium steady-states. We illustrate this perspective on inverse design in a model of colloidal cluster assembly within linear shear flow. We find that colloidal clusters can be assembled with high yield using specific short-range interactions of tunable complexity. Shear decreases the yields of rigid clusters, while small values of shear increase the yields of nonrigid clusters. The enhancement or suppression of the yield due to shear is rationalized with a generalized linear response theory. Furthermore, by studying 21 unique clusters made of six, seven, or eight particles, we uncover basic design principles for targeted assembly out of equilibrium.
- Authors:
-
[1];
[2]
- Univ. of California, Berkeley, CA (United States)
- Univ. of California, Berkeley, CA (United States); Kavli Energy NanoScience Inst., Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1832544
- Alternate Identifier(s):
- OSTI ID: 1755961
- Grant/Contract Number:
- AC02-05CH11231; SC0019375
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Chemical Physics
- Additional Journal Information:
- Journal Volume: 154; Journal Issue: 1; Journal ID: ISSN 0021-9606
- Publisher:
- American Institute of Physics (AIP)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Molecular dynamics; Calculus of variations; Optimization algorithms; Stochastic processes; Probability theory; Linear response; Control theory; Machine learning; Self assembly; Colloids
Citation Formats
Das, Avishek, and Limmer, David T. Variational design principles for nonequilibrium colloidal assembly. United States: N. p., 2021.
Web. doi:10.1063/5.0038652.
Das, Avishek, & Limmer, David T. Variational design principles for nonequilibrium colloidal assembly. United States. https://doi.org/10.1063/5.0038652
Das, Avishek, and Limmer, David T. Wed .
"Variational design principles for nonequilibrium colloidal assembly". United States. https://doi.org/10.1063/5.0038652. https://www.osti.gov/servlets/purl/1832544.
@article{osti_1832544,
title = {Variational design principles for nonequilibrium colloidal assembly},
author = {Das, Avishek and Limmer, David T.},
abstractNote = {Using large deviation theory and principles of stochastic optimal control, we show that rare molecular dynamics trajectories conditioned on assembling a specific target structure encode a set of interactions and external forces that lead to enhanced stability of that structure. Such a relationship can be formulated into a variational principle, for which we have developed an associated optimization algorithm and have used it to determine optimal forces for targeted self-assembly within nonequilibrium steady-states. We illustrate this perspective on inverse design in a model of colloidal cluster assembly within linear shear flow. We find that colloidal clusters can be assembled with high yield using specific short-range interactions of tunable complexity. Shear decreases the yields of rigid clusters, while small values of shear increase the yields of nonrigid clusters. The enhancement or suppression of the yield due to shear is rationalized with a generalized linear response theory. Furthermore, by studying 21 unique clusters made of six, seven, or eight particles, we uncover basic design principles for targeted assembly out of equilibrium.},
doi = {10.1063/5.0038652},
journal = {Journal of Chemical Physics},
number = 1,
volume = 154,
place = {United States},
year = {Wed Jan 06 00:00:00 EST 2021},
month = {Wed Jan 06 00:00:00 EST 2021}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
The Free-Energy Landscape of Clusters of Attractive Hard Spheres
journal, January 2010
- Meng, G.; Arkus, N.; Brenner, M. P.
- Science, Vol. 327, Issue 5965
Optimising self-assembly through time-dependent interactions
journal, December 2016
- Fullerton, Christopher J.; Jack, Robert L.
- The Journal of Chemical Physics, Vol. 145, Issue 24
Stochastic thermodynamics, fluctuation theorems and molecular machines
journal, November 2012
- Seifert, Udo
- Reports on Progress in Physics, Vol. 75, Issue 12
Nonequilibrium Linear Response for Markov Dynamics, I: Jump Processes and Overdamped Diffusions
journal, November 2009
- Baiesi, Marco; Maes, Christian; Wynants, Bram
- Journal of Statistical Physics, Vol. 137, Issue 5-6
Importance sampling large deviations in nonequilibrium steady states. I
journal, March 2018
- Ray, Ushnish; Chan, Garnet Kin-Lic; Limmer, David T.
- The Journal of Chemical Physics, Vol. 148, Issue 12
Molecular dynamics study of melting and freezing of small Lennard-Jones clusters
journal, September 1987
- Honeycutt, J. Dana.; Andersen, Hans C.
- The Journal of Physical Chemistry, Vol. 91, Issue 19, p. 4950-4963
Colloidal matter: Packing, geometry, and entropy
journal, August 2015
- Manoharan, V. N.
- Science, Vol. 349, Issue 6251
Nonequilibrium Linear Response for Markov Dynamics, I: Jump Processes and Overdamped Diffusions
journal, November 2009
- Baiesi, Marco; Maes, Christian; Wynants, Bram
- Journal of Statistical Physics, Vol. 137, Issue 5-6
Self-assembly of colloidal micelles in microfluidic channels
journal, January 2017
- Nikoubashman, Arash
- Soft Matter, Vol. 13, Issue 1
Minimal Energy Clusters of Hard Spheres with Short Range Attractions
journal, September 2009
- Arkus, Natalie; Manoharan, Vinothan N.; Brenner, Michael P.
- Physical Review Letters, Vol. 103, Issue 11
Minimal Energy Clusters of Hard Spheres with Short Range Attractions
journal, September 2009
- Arkus, Natalie; Manoharan, Vinothan N.; Brenner, Michael P.
- Physical Review Letters, Vol. 103, Issue 11
Size limits of self-assembled colloidal structures made using specific interactions
journal, October 2014
- Zeravcic, Zorana; Manoharan, Vinothan N.; Brenner, Michael P.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 45
Self-assembly of colloidal molecules due to self-generated flow
text, January 2017
- Niu, Ran; Speck, Thomas; Palberg, Thomas
- arXiv
Drying-mediated self-assembly of nanoparticles
journal, November 2003
- Rabani, Eran; Reichman, David R.; Geissler, Phillip L.
- Nature, Vol. 426, Issue 6964
Nonlinear Machine Learning of Patchy Colloid Self-Assembly Pathways and Mechanisms
journal, April 2014
- Long, Andrew W.; Ferguson, Andrew L.
- The Journal of Physical Chemistry B, Vol. 118, Issue 15
Ultra thin films of diblock copolymers under shear
journal, January 2010
- Chremos, Alexandros; Margaritis, Kelly; Panagiotopoulos, Athanassios Z.
- Soft Matter, Vol. 6, Issue 15
Self-Assembly of Colloidal Molecules due to Self-Generated Flow
journal, July 2017
- Niu, Ran; Palberg, Thomas; Speck, Thomas
- Physical Review Letters, Vol. 119, Issue 2
Nonlinear transport coefficients from large deviation functions
journal, July 2019
- Gao, Chloe Ya; Limmer, David T.
- The Journal of Chemical Physics, Vol. 151, Issue 1
Rotational diffusion affects the dynamical self-assembly pathways of patchy particles
journal, November 2015
- Newton, Arthur C.; Groenewold, Jan; Kegel, Willem K.
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 50
Adaptive Sampling of Large Deviations
journal, July 2018
- Ferré, Grégoire; Touchette, Hugo
- Journal of Statistical Physics, Vol. 172, Issue 6
Drying-mediated self-assembly of nanoparticles
journal, November 2003
- Rabani, Eran; Reichman, David R.; Geissler, Phillip L.
- Nature, Vol. 426, Issue 6964
Predictive Self-Assembly of Polyhedra into Complex Structures
journal, July 2012
- Damasceno, P. F.; Engel, M.; Glotzer, S. C.
- Science, Vol. 337, Issue 6093
Energy consumption in chemical fuel-driven self-assembly
journal, September 2018
- Ragazzon, Giulio; Prins, Leonard J.
- Nature Nanotechnology, Vol. 13, Issue 10
Programmable dynamic steady states in ATP-driven nonequilibrium DNA systems
journal, July 2019
- Heinen, Laura; Walther, Andreas
- Science Advances, Vol. 5, Issue 7
Nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging genome or polyelectrolyte
journal, August 2018
- Chevreuil, Maelenn; Law-Hine, Didier; Chen, Jingzhi
- Nature Communications, Vol. 9, Issue 1
Adaptive Sampling of Large Deviations
journal, July 2018
- Ferré, Grégoire; Touchette, Hugo
- Journal of Statistical Physics, Vol. 172, Issue 6
Non-equilibrium phase separation with reactions: a canonical model and its behaviour
journal, May 2020
- Li, Yuting I.; Cates, Michael E.
- Journal of Statistical Mechanics: Theory and Experiment, Vol. 2020, Issue 5
Design principles for self-assembly with short-range interactions
journal, March 2011
- Hormoz, S.; Brenner, M. P.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 13
Effects of layering and magnetic annealing on the texture of CoPt films
journal, November 2010
- Markou, A.; Panagiotopoulos, I.; Bakas, T.
- Journal of Magnetism and Magnetic Materials, Vol. 322, Issue 22
Importance sampling large deviations in nonequilibrium steady states. I
journal, March 2018
- Ray, Ushnish; Chan, Garnet Kin-Lic; Limmer, David T.
- The Journal of Chemical Physics, Vol. 148, Issue 12
Dynamic Pathways for Viral Capsid Assembly
journal, July 2006
- Hagan, Michael F.; Chandler, David
- Biophysical Journal, Vol. 91, Issue 1
A review on self-assembly in microfluidic devices
journal, October 2017
- Dou, Yingying; Wang, Bingsheng; Jin, Mingliang
- Journal of Micromechanics and Microengineering, Vol. 27, Issue 11
Optimal Feedback Controlled Assembly of Perfect Crystals
journal, July 2016
- Tang, Xun; Rupp, Bradley; Yang, Yuguang
- ACS Nano, Vol. 10, Issue 7
A DNA-based method for rationally assembling nanoparticles into macroscopic materials
journal, August 1996
- Mirkin, Chad A.; Letsinger, Robert L.; Mucic, Robert C.
- Nature, Vol. 382, Issue 6592, p. 607-609
Kinetically guided colloidal structure formation
journal, July 2016
- Hecht, Fabian M.; Bausch, Andreas R.
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 31
Neural networks-based variationally enhanced sampling
journal, August 2019
- Bonati, Luigi; Zhang, Yue-Yu; Parrinello, Michele
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 36
Nonequilibrium Markov processes conditioned on large deviations
text, January 2014
- Chetrite, Raphael; Touchette, Hugo
- arXiv
Non-equilibrium steady states: fluctuations and large deviations of the density and of the current
journal, July 2007
- Derrida, Bernard
- Journal of Statistical Mechanics: Theory and Experiment, Vol. 2007, Issue 07
Shear-induced alignment of colloidal particles in the presence of a shear flow
journal, January 1990
- Xue, Weige; Grest, Gary S.
- Physical Review Letters, Vol. 64, Issue 4
Quasicrystalline order in self-assembled binary nanoparticle superlattices
journal, October 2009
- Talapin, Dmitri V.; Shevchenko, Elena V.; Bodnarchuk, Maryna I.
- Nature, Vol. 461, Issue 7266
Two-Dimensional Clusters of Colloidal Particles Induced by Emulsion Droplet Evaporation
journal, January 2020
- Pham-Van, Hai; Tran-Phan-Thuy, Linh; Tran-Manh, Cuong
- Nanomaterials, Vol. 10, Issue 1
Understanding Gelation as a Nonequilibrium Self-Assembly Process
journal, April 2018
- Arango-Restrepo, Andrés; Rubi, J. Miguel; Barragán, Daniel
- The Journal of Physical Chemistry B, Vol. 122, Issue 18
Dynamic Pathways for Viral Capsid Assembly
text, January 2005
- Hagan, Michael F.; Chandler, David
- arXiv
Hydrodynamics and phases of flocks
journal, July 2005
- Toner, John; Tu, Yuhai; Ramaswamy, Sriram
- Annals of Physics, Vol. 318, Issue 1
Programming colloidal phase transitions with DNA strand displacement
journal, February 2015
- Rogers, W. Benjamin; Manoharan, Vinothan N.
- Science, Vol. 347, Issue 6222
Controlling crystal self-assembly using a real-time feedback scheme
journal, March 2013
- Klotsa, Daphne; Jack, Robert L.
- The Journal of Chemical Physics, Vol. 138, Issue 9
A Variational Approach to Enhanced Sampling and Free Energy Calculations
text, January 2014
- Valsson, Omar; Parrinello, Michele
- arXiv
Fabrication of In Situ Nanofiber-Reinforced Molecular Composites by Nonequilibrium Self-Assembly
journal, October 2018
- Guan, Qingbao; Yuan, Li; Gu, Aijuan
- ACS Applied Materials & Interfaces, Vol. 10, Issue 45
Controlling crystal self-assembly using a real-time feedback scheme
journal, March 2013
- Klotsa, Daphne; Jack, Robert L.
- The Journal of Chemical Physics, Vol. 138, Issue 9
Nucleation of colloidal crystals on configurable seed structures
journal, January 2011
- Hermes, M.; Vermolen, E. C. M.; Leunissen, M. E.
- Soft Matter, Vol. 7, Issue 10
Inverse methods for design of soft materials
journal, April 2020
- Sherman, Zachary M.; Howard, Michael P.; Lindquist, Beth A.
- The Journal of Chemical Physics, Vol. 152, Issue 14
Laser-induced wavelength-controlled self-assembly of colloidal quasi-resonant quantum dots
journal, January 2016
- Tsipotan, Aleksey S.; Gerasimova, Marina A.; Slabko, Vitaliy V.
- Optics Express, Vol. 24, Issue 10
Direct measurements of DNA-mediated colloidal interactions and their quantitative modeling
journal, September 2011
- Rogers, W. B.; Crocker, J. C.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 38
Assembly of vorticity-aligned hard-sphere colloidal strings in a simple shear flow
journal, December 2011
- Cheng, X.; Xu, X.; Rice, S. A.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 1
Role of External Flow and Frame Invariance in Stochastic Thermodynamics
journal, April 2008
- Speck, Thomas; Mehl, Jakob; Seifert, Udo
- Physical Review Letters, Vol. 100, Issue 17
Variational control forces for enhanced sampling of nonequilibrium molecular dynamics simulations
journal, December 2019
- Das, Avishek; Limmer, David T.
- The Journal of Chemical Physics, Vol. 151, Issue 24
Response of active Brownian particles to shear flow
journal, April 2019
- Asheichyk, Kiryl; Solon, Alexandre P.; Rohwer, Christian M.
- The Journal of Chemical Physics, Vol. 150, Issue 14
The Statistical Mechanics of Dynamic Pathways to Self-Assembly
journal, April 2015
- Whitelam, Stephen; Jack, Robert L.
- Annual Review of Physical Chemistry, Vol. 66, Issue 1
The computer study of transport processes under extreme conditions
journal, August 1972
- Lees, A. W.; Edwards, S. F.
- Journal of Physics C: Solid State Physics, Vol. 5, Issue 15
Strong bonds and far-from-equilibrium conditions minimize errors in lattice-gas growth
journal, September 2018
- Whitelam, Stephen
- The Journal of Chemical Physics, Vol. 149, Issue 10
Underground Engineering and Trenchless Technologies at the Defense of Environment
journal, January 2016
- Gerasimova, Vera
- Procedia Engineering, Vol. 165
A continuum theory of phase separation kinetics for active Brownian particles
text, January 2013
- Stenhammar, Joakim; Tiribocchi, Adriano; Allen, Rosalind J.
- arXiv
Molecular self-assembly of surfactant-like peptides to form nanotubes and nanovesicles
journal, April 2002
- Vauthey, S.; Santoso, S.; Gong, H.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 8, p. 5355-5360
Design principles for nonequilibrium self-assembly
journal, November 2016
- Nguyen, Michael; Vaikuntanathan, Suriyanarayanan
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 50
Communication: Shifted forces in molecular dynamics
journal, February 2011
- Toxvaerd, Søren; Dyre, Jeppe C.
- The Journal of Chemical Physics, Vol. 134, Issue 8
Energy consumption in chemical fuel-driven self-assembly
journal, September 2018
- Ragazzon, Giulio; Prins, Leonard J.
- Nature Nanotechnology, Vol. 13, Issue 10
Self-Assembly of Colloidal Nanocrystals: From Intricate Structures to Functional Materials
journal, August 2016
- Boles, Michael A.; Engel, Michael; Talapin, Dmitri V.
- Chemical Reviews, Vol. 116, Issue 18
Size limits of self-assembled colloidal structures made using specific interactions
journal, October 2014
- Zeravcic, Zorana; Manoharan, Vinothan N.; Brenner, Michael P.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 45
Current fluctuations of interacting active Brownian particles
journal, December 2018
- GrandPre, Trevor; Limmer, David T.
- Physical Review E, Vol. 98, Issue 6
Turning statistical physics models into materials design engines
journal, December 2015
- Miskin, Marc Z.; Khaira, Gurdaman; de Pablo, Juan J.
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 1
Dissipation bounds the amplification of transition rates far from equilibrium
journal, February 2021
- Kuznets-Speck, Benjamin; Limmer, David T.
- Proceedings of the National Academy of Sciences, Vol. 118, Issue 8
Correspondence between neuroevolution and gradient descent
journal, November 2021
- Whitelam, Stephen; Selin, Viktor; Park, Sang-Won
- Nature Communications, Vol. 12, Issue 1
Variational Design Principles For Nonequilibrium Colloidal Assembly
dataset, January 2020
- Avishek Das, David T. Limmer
- Zenodo
Works referencing / citing this record:
Shortcuts in stochastic systems and control of biophysical processes
preprint, January 2021
- Ilker, Efe; Güngör, Özenç; Kuznets-Speck, Benjamin
- arXiv