1
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Möller J, Schottelius A, Caresana M, Boesenberg U, Kim C, Dallari F, Ezquerra TA, Fernández JM, Gelisio L, Glaesener A, Goy C, Hallmann J, Kalinin A, Kurta RP, Lapkin D, Lehmkühler F, Mambretti F, Scholz M, Shayduk R, Trinter F, Vartaniants IA, Zozulya A, Galli DE, Grübel G, Madsen A, Caupin F, Grisenti RE. Crystal Nucleation in Supercooled Atomic Liquids. PHYSICAL REVIEW LETTERS 2024; 132:206102. [PMID: 38829060 DOI: 10.1103/physrevlett.132.206102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/22/2024] [Accepted: 03/28/2024] [Indexed: 06/05/2024]
Abstract
The liquid-to-solid phase transition is a complex process that is difficult to investigate experimentally with sufficient spatial and temporal resolution. A key aspect of the transition is the formation of a critical seed of the crystalline phase in a supercooled liquid, that is, a liquid in a metastable state below the melting temperature. This stochastic process is commonly described within the framework of classical nucleation theory, but accurate tests of the theory in atomic and molecular liquids are challenging. Here, we employ femtosecond x-ray diffraction from microscopic liquid jets to study crystal nucleation in supercooled liquids of the rare gases argon and krypton. Our results provide stringent limits to the validity of classical nucleation theory in atomic liquids, and offer the long-sought possibility of testing nonclassical extensions of the theory.
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Affiliation(s)
- Johannes Möller
- European X-ray Free-Electron Laser Facility, 22869 Schenefeld, Germany
| | - Alexander Schottelius
- Institut für Kernphysik, Goethe-Universität Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Michele Caresana
- Institut für Kernphysik, Goethe-Universität Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Ulrike Boesenberg
- European X-ray Free-Electron Laser Facility, 22869 Schenefeld, Germany
| | - Chan Kim
- European X-ray Free-Electron Laser Facility, 22869 Schenefeld, Germany
| | | | - Tiberio A Ezquerra
- Macromolecular Physics Department, Instituto de Estructura de la Materia, IEM-CSIC, 28006 Madrid, Spain
| | - José M Fernández
- Laboratory of Molecular Fluid Dynamics, Instituto de Estructura de la Materia, IEM-CSIC, 28006 Madrid, Spain
| | - Luca Gelisio
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Andrea Glaesener
- Dipartimento di Fisica "Aldo Pontremoli," Università degli Studi di Milano, 20133 Milano, Italy
| | - Claudia Goy
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Jörg Hallmann
- European X-ray Free-Electron Laser Facility, 22869 Schenefeld, Germany
| | - Anton Kalinin
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
| | - Ruslan P Kurta
- European X-ray Free-Electron Laser Facility, 22869 Schenefeld, Germany
| | - Dmitry Lapkin
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | | | - Francesco Mambretti
- Dipartimento di Fisica "Aldo Pontremoli," Università degli Studi di Milano, 20133 Milano, Italy
| | - Markus Scholz
- European X-ray Free-Electron Laser Facility, 22869 Schenefeld, Germany
| | - Roman Shayduk
- European X-ray Free-Electron Laser Facility, 22869 Schenefeld, Germany
| | - Florian Trinter
- Institut für Kernphysik, Goethe-Universität Frankfurt am Main, 60438 Frankfurt am Main, Germany
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
- Molecular Physics, Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
| | | | - Alexey Zozulya
- European X-ray Free-Electron Laser Facility, 22869 Schenefeld, Germany
| | - Davide E Galli
- Dipartimento di Fisica "Aldo Pontremoli," Università degli Studi di Milano, 20133 Milano, Italy
| | - Gerhard Grübel
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, 22761 Hamburg, Germany
| | - Anders Madsen
- European X-ray Free-Electron Laser Facility, 22869 Schenefeld, Germany
| | - Frédéric Caupin
- Institut Lumière Matière, Université Claude Bernard Lyon 1, CNRS, Institut Universitaire de France, 69622 Villeurbanne, France
| | - Robert E Grisenti
- Institut für Kernphysik, Goethe-Universität Frankfurt am Main, 60438 Frankfurt am Main, Germany
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
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2
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Hoy RS. Homogeneous crystallization in four-dimensional Lennard-Jones liquids. Phys Rev E 2024; 109:044604. [PMID: 38755930 DOI: 10.1103/physreve.109.044604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/25/2024] [Indexed: 05/18/2024]
Abstract
We observe homogeneous crystallization in simulated high-dimensional (d>3) liquids that follow physically realistic dynamics and have system sizes that are large enough to eliminate the possibility that crystallization was induced by the periodic boundary conditions. Supercooled four-dimensional (4D) Lennard-Jones (LJ) liquids maintained at zero pressure and constant temperatures 0.59
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Affiliation(s)
- Robert S Hoy
- Department of Physics, University of South Florida, Tampa, Florida 33620, USA
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3
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Zou Z, Tiwary P. Enhanced Sampling of Crystal Nucleation with Graph Representation Learnt Variables. J Phys Chem B 2024. [PMID: 38502931 DOI: 10.1021/acs.jpcb.4c00080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
In this study, we present a graph neural network (GNN)-based learning approach using an autoencoder setup to derive low-dimensional variables from features observed in experimental crystal structures. These variables are then biased in enhanced sampling to observe state-to-state transitions and reliable thermodynamic weights. In our approach, we used simple convolution and pooling methods. To verify the effectiveness of our protocol, we examined the nucleation of various allotropes and polymorphs of iron and glycine in their molten states. Our graph latent variables, when biased in well-tempered metadynamics, consistently show transitions between states and achieve accurate thermodynamic rankings in agreement with experiments, both of which are indicators of dependable sampling. This underscores the strength and promise of our GNN variables for improved sampling. The protocol shown here should be applicable for other systems and other sampling methods.
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Affiliation(s)
- Ziyue Zou
- Department of Chemistry and Biochemistry, University of Maryland, College Park 20742, Maryland, United States
| | - Pratyush Tiwary
- Department of Chemistry and Biochemistry, University of Maryland, College Park 20742, Maryland, United States
- Institute for Physical Science and Technology, University of Maryland, College Park 20742, Maryland, United States
- University of Maryland Institute for Health Computing, Rockville, Maryland 20852, United States
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4
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Zhao R, Zou Z, Weeks JD, Tiwary P. Quantifying the Relevance of Long-Range Forces for Crystal Nucleation in Water. J Chem Theory Comput 2023; 19:9093-9101. [PMID: 38084039 DOI: 10.1021/acs.jctc.3c01120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Understanding nucleation from aqueous solutions is of fundamental importance in a multitude of fields, ranging from materials science to biophysics. The complex solvent-mediated interactions in aqueous solutions hamper the development of a simple physical picture, elucidating the roles of different interactions in nucleation processes. In this work, we make use of three complementary techniques to disentangle the role played by short- and long-range interactions in solvent-mediated nucleation. Specifically, the first approach we utilize is the local molecular field (LMF) theory to renormalize long-range Coulomb electrostatics. Second, we use well-tempered metadynamics to speed up rare events governed by short-range interactions. Third, the deep learning-based State Predictive Information Bottleneck approach is employed in analyzing the reaction coordinate of the nucleation processes obtained from the LMF treatment coupled with well-tempered metadynamics. We find that the two-step nucleation mechanism can largely be captured by the short-range interactions, while the long-range interactions further contribute to the stability of the primary crystal state under ambient conditions. Furthermore, by analyzing the reaction coordinate obtained from the combined LMF-metadynamics treatment, we discern the fluctuations on different time scales, highlighting the need for long-range interactions when accounting for metastability.
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Affiliation(s)
- Renjie Zhao
- Chemical Physics Program and Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
| | - Ziyue Zou
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - John D Weeks
- Institute for Physical Science and Technology and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Pratyush Tiwary
- Institute for Physical Science and Technology and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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5
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Gispen W, Dijkstra M. Brute-force nucleation rates of hard spheres compared with rare-event methods and classical nucleation theory. J Chem Phys 2023; 159:086101. [PMID: 37638626 DOI: 10.1063/5.0165159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/09/2023] [Indexed: 08/29/2023] Open
Abstract
We determine nucleation rates of hard spheres using brute-force molecular dynamics simulations. We overcome nucleation barriers of up to 28 kBT, leading to a rigorous test of nucleation rates obtained from rare-event methods and classical nucleation theory. Our brute-force nucleation rates show excellent agreement with umbrella sampling simulations by Filion et al. [J. Chem. Phys. 133, 244115 (2010)] and seeding simulations by Espinosa et al. [J. Chem. Phys. 144, 034501 (2016)].
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Affiliation(s)
- Willem Gispen
- Soft Condensed Matter and Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, Netherlands
| | - Marjolein Dijkstra
- Soft Condensed Matter and Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, Netherlands
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6
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Rogal J, Díaz Leines G. Controlling crystallization: what liquid structure and dynamics reveal about crystal nucleation mechanisms. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2023; 381:20220249. [PMID: 37211029 DOI: 10.1098/rsta.2022.0249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/06/2022] [Indexed: 05/23/2023]
Abstract
Over recent years, molecular simulations have provided invaluable insights into the microscopic processes governing the initial stages of crystal nucleation and growth. A key aspect that has been observed in many different systems is the formation of precursors in the supercooled liquid that precedes the emergence of crystalline nuclei. The structural and dynamical properties of these precursors determine to a large extent the nucleation probability as well as the formation of specific polymorphs. This novel microscopic view on nucleation mechanisms has further implications for our understanding of the nucleating ability and polymorph selectivity of nucleating agents, as these appear to be strongly linked to their ability in modifying structural and dynamical characteristics of the supercooled liquid, namely liquid heterogeneity. In this perspective, we highlight recent progress in exploring the connection between liquid heterogeneity and crystallization, including the effects of templates, and the potential impact for controlling crystallization processes. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.
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Affiliation(s)
- Jutta Rogal
- Department of Chemistry, New York University, New York, NY 10003, USA
- Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Grisell Díaz Leines
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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7
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Cedeno R, Grossier R, Candoni N, Levernier N, Flood AE, Veesler S. CNT effective interfacial energy and pre-exponential kinetic factor from measured NaCl crystal nucleation time distributions in contracting microdroplets. J Chem Phys 2023; 158:2891367. [PMID: 37191406 DOI: 10.1063/5.0143704] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/29/2023] [Indexed: 05/17/2023] Open
Abstract
Nucleation, the birth of a stable cluster from a disorder, is inherently stochastic. Yet up to date, there are no quantitative studies on NaCl nucleation that accounts for its stochastic nature. Here, we report the first stochastic treatment of NaCl-water nucleation kinetics. Using a recently developed microfluidic system and evaporation model, our measured interfacial energies extracted from a modified Poisson distribution of nucleation time show an excellent agreement with theoretical predictions. Furthermore, analysis of nucleation parameters in 0.5, 1.5, and 5.5 pl microdroplets reveals an interesting interplay between confinement effects and shifting of nucleation mechanisms. Overall, our findings highlight the need to treat nucleation stochastically rather than deterministically to bridge the gap between theory and experiment.
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Affiliation(s)
- Ruel Cedeno
- CNRS, Aix-Marseille University, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, F-13288 Marseille Cedex 09, France
- Department of Chemical and Biomolecular Engineering, School of Energy Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Rayong 21210, Thailand
| | - Romain Grossier
- CNRS, Aix-Marseille University, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, F-13288 Marseille Cedex 09, France
| | - Nadine Candoni
- CNRS, Aix-Marseille University, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, F-13288 Marseille Cedex 09, France
| | - Nicolas Levernier
- INMED, INSERM, Aix Marseille University, Turing Centre for Living Systems, Marseille, France
- Aix-Marseille University, Université de Toulon, CNRS, CPT (UMR 7332), Turing Centre for Living Systems, Marseille, France
| | - Adrian E Flood
- Department of Chemical and Biomolecular Engineering, School of Energy Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Rayong 21210, Thailand
| | - Stéphane Veesler
- CNRS, Aix-Marseille University, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, F-13288 Marseille Cedex 09, France
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8
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Guidarelli Mattioli F, Sciortino F, Russo J. Are Neural Network Potentials Trained on Liquid States Transferable to Crystal Nucleation? A Test on Ice Nucleation in the mW Water Model. J Phys Chem B 2023; 127:3894-3901. [PMID: 37075256 PMCID: PMC10165654 DOI: 10.1021/acs.jpcb.3c00693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/06/2023] [Indexed: 04/21/2023]
Abstract
Neural network potentials (NNPs) are increasingly being used to study processes that happen on long time scales. A typical example is crystal nucleation, which rate is controlled by the occurrence of a rare fluctuation, i.e., the appearance of the critical nucleus. Because the properties of this nucleus are far from those of the bulk crystal, it is yet unclear whether NN potentials trained on equilibrium liquid states can accurately describe nucleation processes. So far, nucleation studies on NNPs have been limited to ab initio models whose nucleation properties are unknown, preventing an accurate comparison. Here we train a NN potential on the mW model of water─a classical three-body potential whose nucleation time scale is accessible in standard simulations. We show that a NNP trained only on a small number of liquid state points can reproduce with great accuracy the nucleation rates and free energy barriers of the original model, computed from both spontaneous and biased trajectories, strongly supporting the use of NNPs to study nucleation events.
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Affiliation(s)
| | | | - John Russo
- Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Rome, Italy
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9
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Aasen A, Wilhelmsen Ø, Hammer M, Reguera D. Free energy of critical droplets-from the binodal to the spinodal. J Chem Phys 2023; 158:114108. [PMID: 36948791 DOI: 10.1063/5.0142533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Arguably, the main challenge of nucleation theory is to accurately evaluate the work of formation of a critical embryo in the new phase, which governs the nucleation rate. In Classical Nucleation Theory (CNT), this work of formation is estimated using the capillarity approximation, which relies on the value of the planar surface tension. This approximation has been blamed for the large discrepancies between predictions from CNT and experiments. In this work, we present a study of the free energy of formation of critical clusters of the Lennard-Jones fluid truncated and shifted at 2.5σ using Monte Carlo simulations, density gradient theory, and density functional theory. We find that density gradient theory and density functional theory accurately reproduce molecular simulation results for critical droplet sizes and their free energies. The capillarity approximation grossly overestimates the free energy of small droplets. The incorporation of curvature corrections up to the second order with the Helfrich expansion greatly remedies this and performs very well for most of the experimentally accessible regions. However, it is imprecise for the smallest droplets and largest metastabilities since it does not account for a vanishing nucleation barrier at the spinodal. To remedy this, we propose a scaling function that uses all relevant ingredients without adding fitting parameters. The scaling function reproduces accurately the free energy of the formation of critical droplets for the entire metastability range and all temperatures examined and deviates from density gradient theory by less than one kBT.
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Affiliation(s)
- Ailo Aasen
- SINTEF Energy Research, NO-7465 Trondheim, Norway
| | | | | | - David Reguera
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
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10
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Finney AR, Salvalaglio M. A variational approach to assess reaction coordinates for two-step crystallization. J Chem Phys 2023; 158:094503. [PMID: 36889939 DOI: 10.1063/5.0139842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
Molecule- and particle-based simulations provide the tools to test, in microscopic detail, the validity of classical nucleation theory. In this endeavor, determining nucleation mechanisms and rates for phase separation requires an appropriately defined reaction coordinate to describe the transformation of an out-of-equilibrium parent phase for which myriad options are available to the simulator. In this article, we describe the application of the variational approach to Markov processes to quantify the suitability of reaction coordinates to study crystallization from supersaturated colloid suspensions. Our analysis indicates that collective variables (CVs) that correlate with the number of particles in the condensed phase, the system potential energy, and approximate configurational entropy often feature as the most appropriate order parameters to quantitatively describe the crystallization process. We apply time-lagged independent component analysis to reduce high-dimensional reaction coordinates constructed from these CVs to build Markov State Models (MSMs), which indicate that two barriers separate a supersaturated fluid phase from crystals in the simulated environment. The MSMs provide consistent estimates for crystal nucleation rates, regardless of the dimensionality of the order parameter space adopted; however, the two-step mechanism is only consistently evident from spectral clustering of the MSMs in higher dimensions. As the method is general and easily transferable, the variational approach we adopt could provide a useful framework to study controls for crystal nucleation.
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Affiliation(s)
- A R Finney
- Thomas Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, United Kingdom
| | - M Salvalaglio
- Thomas Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, United Kingdom
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11
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Chew PY, Reinhardt A. Phase diagrams-Why they matter and how to predict them. J Chem Phys 2023; 158:030902. [PMID: 36681642 DOI: 10.1063/5.0131028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Understanding the thermodynamic stability and metastability of materials can help us to, for example, gauge whether crystalline polymorphs in pharmaceutical formulations are likely to be durable. It can also help us to design experimental routes to novel phases with potentially interesting properties. In this Perspective, we provide an overview of how thermodynamic phase behavior can be quantified both in computer simulations and machine-learning approaches to determine phase diagrams, as well as combinations of the two. We review the basic workflow of free-energy computations for condensed phases, including some practical implementation advice, ranging from the Frenkel-Ladd approach to thermodynamic integration and to direct-coexistence simulations. We illustrate the applications of such methods on a range of systems from materials chemistry to biological phase separation. Finally, we outline some challenges, questions, and practical applications of phase-diagram determination which we believe are likely to be possible to address in the near future using such state-of-the-art free-energy calculations, which may provide fundamental insight into separation processes using multicomponent solvents.
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Affiliation(s)
- Pin Yu Chew
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Aleks Reinhardt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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12
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Takahashi KZ. Molecular cluster analysis using local order parameters selected by machine learning. Phys Chem Chem Phys 2022; 25:658-672. [PMID: 36484716 DOI: 10.1039/d2cp03696g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Accurately extracting local molecular structures is essential for understanding the mechanisms of phase and structural transitions. A promising method to characterize the local molecular structure is defining the value of the local order parameter (LOP) for each particle. This work develops the Molecular Assembly structure Learning package for Identifying Order parameters (MALIO), a machine learning package that can propose an optimal (set of) LOP(s) quickly and automatically for a huge number of LOP species and various methods of selecting neighboring particles for the calculation. We applied this package to distinguish between the nematic and smectic phases of uniaxial liquid crystal molecules, and selected candidate LOPs that could be used to precisely observe the nematic-smectic phase transition. The LOP candidates were used to observe the nucleation and subsequent percolation transition, and the effect of the choice of LOP species and neighboring particles on the statistics of local molecular structures (clusters) was examined. The procedure revealed the time evolution of the number of clusters and the dependence of the percolation curve on the number of neighboring particles for each LOP species. The LOP species with the lowest dependence on the number of neighboring particles was the best-performing LOP species in the MALIO screening strategy. These results not only show that machine learning can powerfully screen a huge number of LOP species and suggest only a few promising candidates, but also indicate that MALIO can select the best LOP species.
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Affiliation(s)
- Kazuaki Z Takahashi
- Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1 Umezono, Tsukuba, 305-8568, Ibaraki, Japan.
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13
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Blumer O, Reuveni S, Hirshberg B. Stochastic Resetting for Enhanced Sampling. J Phys Chem Lett 2022; 13:11230-11236. [PMID: 36446130 PMCID: PMC9743203 DOI: 10.1021/acs.jpclett.2c03055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/23/2022] [Indexed: 06/16/2023]
Abstract
We present a method for enhanced sampling of molecular dynamics simulations using stochastic resetting. Various phenomena, ranging from crystal nucleation to protein folding, occur on time scales that are unreachable in standard simulations. They are often characterized by broad transition time distributions, in which extremely slow events have a non-negligible probability. Stochastic resetting, i.e., restarting simulations at random times, was recently shown to significantly expedite processes that follow such distributions. Here, we employ resetting for enhanced sampling of molecular simulations for the first time. We show that it accelerates long time scale processes by up to an order of magnitude in examples ranging from simple models to a molecular system. Most importantly, we recover the mean transition time without resetting, which is typically too long to be sampled directly, from accelerated simulations at a single restart rate. Stochastic resetting can be used as a standalone method or combined with other sampling algorithms to further accelerate simulations.
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Affiliation(s)
- Ofir Blumer
- School
of Chemistry, Tel Aviv University, Tel Aviv6997801, Israel
| | - Shlomi Reuveni
- School
of Chemistry, Tel Aviv University, Tel Aviv6997801, Israel
- The
Center for Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv6997801, Israel
- The
Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv6997801, Israel
| | - Barak Hirshberg
- School
of Chemistry, Tel Aviv University, Tel Aviv6997801, Israel
- The
Center for Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv6997801, Israel
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14
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Guo D, Zhang P, Cao X, Liu Y, Cao H, Bian J. Effect of temperature on heavy hydrocarbon crystallization in natural gas. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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15
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Bal KM, Neyts EC. Extending and validating bubble nucleation rate predictions in a Lennard-Jones fluid with enhanced sampling methods and transition state theory. J Chem Phys 2022; 157:184113. [DOI: 10.1063/5.0120136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We calculate bubble nucleation rates in a Lennard-Jones fluid through explicit molecular dynamics simulations. Our approach—based on a recent free energy method (dubbed reweighted Jarzynski sampling), transition state theory, and a simple recrossing correction—allows us to probe a fairly wide range of rates in several superheated and cavitation regimes in a consistent manner. Rate predictions from this approach bridge disparate independent literature studies on the same model system. As such, we find that rate predictions based on classical nucleation theory, direct brute force molecular dynamics simulations, and seeding are consistent with our approach and one another. Published rates derived from forward flux sampling simulations are, however, found to be outliers. This study serves two purposes: First, we validate the reliability of common modeling techniques and extrapolation approaches on a paradigmatic problem in materials science and chemical physics. Second, we further test our highly generic recipe for rate calculations, and establish its applicability to nucleation processes.
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Affiliation(s)
- Kristof M. Bal
- Department of Chemistry and NANOlab Center of Excellence, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Erik C. Neyts
- Department of Chemistry and NANOlab Center of Excellence, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
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16
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Abstract
Crystal nucleation is one of the most fundamental processes in the physical sciences and almost always occurs heterogeneously with the aid of a nucleating substrate. No example of nucleation is more ubiquitous and impactful than the formation of ice, vital to fields as diverse as geology, biology, aeronautics, and climate science. However, despite considerable effort, we still cannot predict a priori the efficacy of a nucleating agent. Here we utilize deep learning methods to accurately predict nucleation ability from images of room temperature liquid water-generated from molecular dynamics simulations-on a broad range of substrates. The resulting model, named IcePic, can rapidly and accurately infer nucleation ability, eliminating the requirement for either notoriously expensive simulations or direct experimental measurement. In an online poll, IcePic was found to significantly outperform humans in predicting the ice nucleating efficacy of materials. By analyzing the typical errors made by humans, as well as the application of reverse interpretation methods, physical insights into the role the water contact layer plays in ice nucleation have been obtained. Moving forward, we suggest that IcePic can be used as an easy, cheap, and rapid way to discern the nucleation ability of substrates, also with potential for learning other properties related to interfacial water.
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17
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Díaz Leines G, Rogal J. Template-Induced Precursor Formation in Heterogeneous Nucleation: Controlling Polymorph Selection and Nucleation Efficiency. PHYSICAL REVIEW LETTERS 2022; 128:166001. [PMID: 35522521 DOI: 10.1103/physrevlett.128.166001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
We present an atomistic study of heterogeneous nucleation in Ni employing transition path sampling, which reveals a template precursor-mediated mechanism of crystallization. Most notably, we find that the ability of tiny templates to modify the structural features of the liquid and promote the formation of precursor regions with enhanced bond-orientational order is key to determining their nucleation efficiency and the polymorphs that crystallize. Our results reveal an intrinsic link between structural liquid heterogeneity and the nucleating ability of templates, which significantly advances our understanding toward the control of nucleation efficiency and polymorph selection.
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Affiliation(s)
- Grisell Díaz Leines
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridgeshire CB2 1EW, United Kingdom
| | - Jutta Rogal
- Department of Chemistry, New York University, New York, New York 10003, USA and Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
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18
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Hussain S, Haji-Akbari A. How to quantify and avoid finite size effects in computational studies of crystal nucleation: The case of homogeneous crystal nucleation. J Chem Phys 2022; 156:054503. [DOI: 10.1063/5.0079702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Sarwar Hussain
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, USA
| | - Amir Haji-Akbari
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, USA
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19
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Zou Z, Tsai ST, Tiwary P. Toward Automated Sampling of Polymorph Nucleation and Free Energies with the SGOOP and Metadynamics. J Phys Chem B 2021; 125:13049-13056. [PMID: 34788047 DOI: 10.1021/acs.jpcb.1c07595] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding the driving forces behind the nucleation of different polymorphs is of great importance for material sciences and the pharmaceutical industry. This includes understanding the reaction coordinate that governs the nucleation process and correctly calculating the relative free energies of different polymorphs. Here, we demonstrate, for the prototypical case of urea nucleation from the melt, how one can learn such a one-dimensional reaction coordinate as a function of prespecified order parameters and use it to perform efficient biased all-atom molecular dynamics simulations. The reaction coordinate is learnt as a function of the generic thermodynamic and structural order parameters using the "spectral gap optimization of order parameters (SGOOP)" approach [Tiwary, P. and Berne, B. J. Proc. Natl. Acad. Sci. U.S.A. (2016)] and is biased using well-tempered metadynamics simulations. The reaction coordinate gives insights into the role played by different structural and thermodynamics order parameters, and the biased simulations obtain accurate relative free energies for different polymorphs. This includes an accurate prediction of the approximate pressure at which urea undergoes a phase transition and one of the metastable polymorphs becomes the most stable conformation. We believe the ideas demonstrated in this work will facilitate efficient sampling of nucleation in complex, generic systems.
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Affiliation(s)
- Ziyue Zou
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Sun-Ting Tsai
- Department of Physics, University of Maryland, College Park, Maryland 20742, United States.,Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
| | - Pratyush Tiwary
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States.,Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
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20
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Bal KM. Nucleation rates from small scale atomistic simulations and transition state theory. J Chem Phys 2021; 155:144111. [PMID: 34654300 DOI: 10.1063/5.0063398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The evaluation of nucleation rates from molecular dynamics trajectories is hampered by the slow nucleation time scale and impact of finite size effects. Here, we show that accurate nucleation rates can be obtained in a very general fashion relying only on the free energy barrier, transition state theory, and a simple dynamical correction for diffusive recrossing. In this setup, the time scale problem is overcome by using enhanced sampling methods, in casu metadynamics, whereas the impact of finite size effects can be naturally circumvented by reconstructing the free energy surface from an appropriate ensemble. Approximations from classical nucleation theory are avoided. We demonstrate the accuracy of the approach by calculating macroscopic rates of droplet nucleation from argon vapor, spanning 16 orders of magnitude and in excellent agreement with literature results, all from simulations of very small (512 atom) systems.
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Affiliation(s)
- Kristof M Bal
- Department of Chemistry and NANOlab Center of Excellence, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
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21
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Takahashi KZ, Aoyagi T, Fukuda JI. Multistep nucleation of anisotropic molecules. Nat Commun 2021; 12:5278. [PMID: 34489445 PMCID: PMC8421422 DOI: 10.1038/s41467-021-25586-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 08/18/2021] [Indexed: 12/31/2022] Open
Abstract
Phase transition of anisotropic materials is ubiquitously observed in physics, biology, materials science, and engineering. Nevertheless, how anisotropy of constituent molecules affects the phase transition dynamics is still poorly understood. Here we investigate numerically the phase transition of a simple model system composed of anisotropic molecules, and report on our discovery of multistep nucleation of nuclei with layered positional ordering (smectic ordering), from a fluid-like nematic phase with orientational order only (no positional order). A trinity of molecular dynamics simulation, machine learning, and molecular cluster analysis yielding free energy landscapes unambiguously demonstrates the dynamics of multistep nucleation process involving characteristic metastable clusters that precede supercritical smectic nuclei and cannot be accounted for by the classical nucleation theory. Our work suggests that molecules of simple shape can exhibit rich and complex nucleation processes, and our numerical approach will provide deeper understanding of phase transitions and resulting structures in anisotropic materials such as biological systems and functional materials.
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Affiliation(s)
- Kazuaki Z Takahashi
- Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
| | - Takeshi Aoyagi
- Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Jun-Ichi Fukuda
- Department of Physics, Faculty of Science, Kyushu University, Fukuoka, Fukuoka, Japan
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22
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Díaz Leines G, Michaelides A, Rogal J. Interplay of structural and dynamical heterogeneity in the nucleation mechanism in Ni. Faraday Discuss 2021; 235:406-415. [DOI: 10.1039/d1fd00099c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gaining fundamental understanding of crystal nucleation processes in metal alloys is crucial for the development and design of high-performance materials with targeted properties. Yet, crystallizationis a complex non-equilibrium process and,...
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