Simulating Crystallization in a Colloidal System Using State Predictive Information Bottleneck Based Enhanced Sampling

Meraz, Vanessa J.; Zou, Ziyue; Tiwary, Pratyush

doi:10.1021/acs.jpcb.4c02740

Simulating Crystallization in a Colloidal System Using State Predictive Information Bottleneck Based Enhanced Sampling

Journal Article · Tue Aug 20 00:00:00 EDT 2024 · Journal of Physical Chemistry. B

DOI:https://doi.org/10.1021/acs.jpcb.4c02740· OSTI ID:3003392

^[1]; Zou, Ziyue ^[1]; ^[2]

Univ. of Maryland, College Park, MD (United States)
Univ. of Maryland, College Park, MD (United States); Univ. of Maryland, Bethesda, MD (United States). Institute for Health Computing

Here, we investigate crystal nucleation in supersaturated colloid suspensions using enhanced molecular dynamics simulations augmented with machine learning techniques. The simulations reveal that crystallization in the model colloidal system studied here, with particles interacting through a repulsive screened Coulomb Yukawa potential, proceeds from vapor to dense liquid droplet to crystalline phases across multiple high barriers. Employing a one-dimensional reaction coordinate derived from the State Predictive Information Bottleneck framework, our simulations capture back-and-forth phase transitions across multiple barriers effectively in biased metadynamics simulations. We obtain relative free energy differences between different phases and also quantify the roles of different molecular level features in driving the phase changes.

View Accepted Manuscript (DOE)

Research Organization:: Univ. of Maryland, College Park, MD (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: SC0021009

OSTI ID:: 3003392

Alternate ID(s):: OSTI ID: 2577478

Journal Information:: Journal of Physical Chemistry. B, Journal Name: Journal of Physical Chemistry. B Journal Issue: 34 Vol. 128; ISSN 1520-6106; ISSN 1520-5207

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

References (37)

Crystallization in Patterns: A Bio-Inspired Approach Aizenberg, J. Advanced Materials, Vol. 16, Issue 15 https://doi.org/10.1002/adma.200400759	journal	August 2004
Nucleation mechanisms in protein folding Fersht, Alan R. Current Opinion in Structural Biology, Vol. 7, Issue 1 https://doi.org/10.1016/S0959-440X(97)80002-4	journal	February 1997
PLUMED 2: New feathers for an old bird Tribello, Gareth A.; Bonomi, Massimiliano; Branduardi, Davide Computer Physics Communications, Vol. 185, Issue 2 https://doi.org/10.1016/j.cpc.2013.09.018	journal	February 2014
LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales Thompson, Aidan P.; Aktulga, H. Metin; Berger, Richard Computer Physics Communications, Vol. 271 https://doi.org/10.1016/j.cpc.2021.108171	journal	February 2022
A Review of Classical and Nonclassical Nucleation Theories Karthika, S.; Radhakrishnan, T. K.; Kalaichelvi, P. Crystal Growth & Design, Vol. 16, Issue 11 https://doi.org/10.1021/acs.cgd.6b00794	journal	October 2016
Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations Sosso, Gabriele C.; Chen, Ji; Cox, Stephen J. Chemical Reviews, Vol. 116, Issue 12 https://doi.org/10.1021/acs.chemrev.5b00744	journal	May 2016
Toward Automated Sampling of Polymorph Nucleation and Free Energies with the SGOOP and Metadynamics Zou, Ziyue; Tsai, Sun-Ting; Tiwary, Pratyush The Journal of Physical Chemistry B, Vol. 125, Issue 47 https://doi.org/10.1021/acs.jpcb.1c07595	journal	November 2021
Influence of Long-Range Forces on the Transition States and Dynamics of NaCl Ion-Pair Dissociation in Water Wang, Dedi; Zhao, Renjie; Weeks, John D. The Journal of Physical Chemistry B, Vol. 126, Issue 2 https://doi.org/10.1021/acs.jpcb.1c09454	journal	January 2022
Microscopic Mechanism and Kinetics of Ice Formation at Complex Interfaces: Zooming in on Kaolinite Sosso, Gabriele C.; Li, Tianshu; Donadio, Davide The Journal of Physical Chemistry Letters, Vol. 7, Issue 13 https://doi.org/10.1021/acs.jpclett.6b01013	journal	June 2016
Collective Variables for Crystallization Simulations─from Early Developments to Recent Advances No authors listed ACS Omega, Vol. 8, Issue 1 https://doi.org/10.1021/acsomega.2c06310	journal	December 2022
Automatic Method for Identifying Reaction Coordinates in Complex Systems ^† Ma, Ao; Dinner, Aaron R. The Journal of Physical Chemistry B, Vol. 109, Issue 14 https://doi.org/10.1021/jp045546c	journal	April 2005
A Time-Independent Free Energy Estimator for Metadynamics Tiwary, Pratyush; Parrinello, Michele The Journal of Physical Chemistry B, Vol. 119, Issue 3 https://doi.org/10.1021/jp504920s	journal	July 2014
Onset of heterogeneous crystal nucleation in colloidal suspensions Cacciuto, A.; Auer, S.; Frenkel, D. Nature, Vol. 428, Issue 6981 https://doi.org/10.1038/nature02397	journal	March 2004
Nucleation and growth of magnetite from solution Baumgartner, Jens; Dey, Archan; Bomans, Paul H. H. Nature Materials, Vol. 12, Issue 4 https://doi.org/10.1038/nmat3558	journal	February 2013
Promoting transparency and reproducibility in enhanced molecular simulations No authors listed Nature Methods, Vol. 16, Issue 8, p. 670-673 https://doi.org/10.1038/s41592-019-0506-8	journal	July 2019
Using metadynamics to explore complex free-energy landscapes Bussi, Giovanni; Laio, Alessandro Nature Reviews Physics, Vol. 2, Issue 4 https://doi.org/10.1038/s42254-020-0153-0	journal	March 2020
Multiple pathways in NaCl homogeneous crystal nucleation Finney, Aaron R.; Salvalaglio, Matteo Faraday Discussions, Vol. 235 https://doi.org/10.1039/D1FD00089F	journal	January 2022
Obtaining reaction coordinates by likelihood maximization Peters, Baron; Trout, Bernhardt L. The Journal of Chemical Physics, Vol. 125, Issue 5 https://doi.org/10.1063/1.2234477	journal	August 2006
Accurate determination of crystal structures based on averaged local bond order parameters Lechner, Wolfgang; Dellago, Christoph The Journal of Chemical Physics, Vol. 129, Issue 11 https://doi.org/10.1063/1.2977970	journal	September 2008
A general set of order parameters for molecular crystals Santiso, Erik E.; Trout, Bernhardt L. The Journal of Chemical Physics, Vol. 134, Issue 6 https://doi.org/10.1063/1.3548889	journal	February 2011
Identification of slow molecular order parameters for Markov model construction Pérez-Hernández, Guillermo; Paul, Fabian; Giorgino, Toni The Journal of Chemical Physics, Vol. 139, Issue 1 https://doi.org/10.1063/1.4811489	journal	July 2013
Overcoming time scale and finite size limitations to compute nucleation rates from small scale well tempered metadynamics simulations Salvalaglio, Matteo; Tiwary, Pratyush; Maggioni, Giovanni Maria The Journal of Chemical Physics, Vol. 145, Issue 21 https://doi.org/10.1063/1.4966265	journal	December 2016
State predictive information bottleneck Wang, Dedi; Tiwary, Pratyush The Journal of Chemical Physics, Vol. 154, Issue 13 https://doi.org/10.1063/5.0038198	journal	April 2021
A variational approach to assess reaction coordinates for two-step crystallization Finney, A. R.; Salvalaglio, M. The Journal of Chemical Physics, Vol. 158, Issue 9 https://doi.org/10.1063/5.0139842	journal	March 2023
Reaction coordinates and rates from transition paths Best, R. B.; Hummer, G. Proceedings of the National Academy of Sciences, Vol. 102, Issue 19 https://doi.org/10.1073/pnas.0408098102	journal	April 2005
Spectral gap optimization of order parameters for sampling complex molecular systems Tiwary, Pratyush; Berne, B. J. Proceedings of the National Academy of Sciences, Vol. 113, Issue 11 https://doi.org/10.1073/pnas.1600917113	journal	February 2016
Escaping free-energy minima Laio, A.; Parrinello, M. Proceedings of the National Academy of Sciences, Vol. 99, Issue 20 https://doi.org/10.1073/pnas.202427399	journal	September 2002
Driving and characterizing nucleation of urea and glycine polymorphs in water Zou, Ziyue; Beyerle, Eric R.; Tsai, Sun-Ting Proceedings of the National Academy of Sciences, Vol. 120, Issue 7 https://doi.org/10.1073/pnas.2216099120	journal	February 2023
Collective variables for the study of crystallisation Karmakar, Tarak; Invernizzi, Michele; Rizzi, Valerio Molecular Physics, Vol. 119, Issue 19-20 https://doi.org/10.1080/00268976.2021.1893848	journal	March 2021
Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science Laio, Alessandro; Gervasio, Francesco L. Reports on Progress in Physics, Vol. 71, Issue 12 https://doi.org/10.1088/0034-4885/71/12/126601	journal	November 2008
Robust structural identification via polyhedral template matching Larsen, Peter Mahler; Schmidt, Søren; Schiøtz, Jakob Modelling and Simulation in Materials Science and Engineering, Vol. 24, Issue 5 https://doi.org/10.1088/0965-0393/24/5/055007	journal	May 2016
Bond-orientational order in liquids and glasses Steinhardt, Paul J.; Nelson, David R.; Ronchetti, Marco Physical Review B, Vol. 28, Issue 2 https://doi.org/10.1103/PhysRevB.28.784	journal	July 1983
Interaction potentials for soft and hard ellipsoids Everaers, R.; Ejtehadi, M. R. Physical Review E, Vol. 67, Issue 4 https://doi.org/10.1103/PhysRevE.67.041710	journal	April 2003
Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method Barducci, Alessandro; Bussi, Giovanni; Parrinello, Michele Physical Review Letters, Vol. 100, Issue 2 https://doi.org/10.1103/PhysRevLett.100.020603	journal	January 2008
Well-Tempered Metadynamics Converges Asymptotically Dama, James F.; Parrinello, Michele; Voth, Gregory A. Physical Review Letters, Vol. 112, Issue 24 https://doi.org/10.1103/PhysRevLett.112.240602	journal	June 2014
Phase Diagram of Yukawa Systems: Model for Charge-Stabilized Colloids Kremer, Kurt; Robbins, Mark O.; Grest, Gary S. Physical Review Letters, Vol. 57, Issue 21 https://doi.org/10.1103/PhysRevLett.57.2694	journal	November 1986
Enhanced Sampling with Machine Learning Mehdi, Shams; Smith, Zachary; Herron, Lukas Annual Review of Physical Chemistry, Vol. 75, Issue 1 https://doi.org/10.1146/annurev-physchem-083122-125941	journal	February 2024

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