1
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Domingues TS, Hussain S, Haji-Akbari A. Divergence among Local Structure, Dynamics, and Nucleation Outcome in Heterogeneous Nucleation of Close-Packed Crystals. J Phys Chem Lett 2024; 15:1279-1287. [PMID: 38284350 DOI: 10.1021/acs.jpclett.3c03561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Heterogeneous crystal nucleation is the dominant mechanism of crystallization in most systems, yet its underlying physics remains an enigma. While emergent interfacial crystalline order precedes heterogeneous nucleation, its importance in the nucleation mechanism is unclear. Here, we use path sampling simulations of two model systems to demonstrate that crystalline order in its traditional sense is not predictive of the outcome of the heterogeneous nucleation of close-packed crystals. Consequently, structure-based collective variables (CVs) that reliably describe homogeneous nucleation can be poor descriptors of heterogeneous nucleation. This divergence between structure and nucleation outcome is accompanied by an intriguing dynamical anomaly, wherein low-coordinated crystalline particles outpace their liquid-like counterparts. We use committor analysis, high-throughput screening, and machine learning to devise CV optimization strategies and present suitable structural heuristics within the metastable fluid for CV prescreening. Employing such optimized CVs is pivotal for properly characterizing the mechanism of heterogeneous nucleation in metallic and colloidal systems.
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Affiliation(s)
- Tiago S Domingues
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06511, United States
| | - Sarwar Hussain
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06511, United States
| | - Amir Haji-Akbari
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06511, United States
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2
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Appeldorn JH, Lemcke S, Speck T, Nikoubashman A. Employing Artificial Neural Networks to Identify Reaction Coordinates and Pathways for Self-Assembly. J Phys Chem B 2022; 126:5007-5016. [DOI: 10.1021/acs.jpcb.2c02232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jörn H. Appeldorn
- Institute of Physics, Johannes Gutenberg-University Mainz, Staudingerweg 7-9, 55128 Mainz, Germany
| | - Simon Lemcke
- Institute of Physics, Johannes Gutenberg-University Mainz, Staudingerweg 7-9, 55128 Mainz, Germany
| | - Thomas Speck
- Institute of Physics, Johannes Gutenberg-University Mainz, Staudingerweg 7-9, 55128 Mainz, Germany
| | - Arash Nikoubashman
- Institute of Physics, Johannes Gutenberg-University Mainz, Staudingerweg 7-9, 55128 Mainz, Germany
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3
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Kikutsuji T, Mori Y, Okazaki KI, Mori T, Kim K, Matubayasi N. Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI). J Chem Phys 2022; 156:154108. [DOI: 10.1063/5.0087310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A method for obtaining appropriate reaction coordinates is required to identify transition states distinguishing product and reactant in complex molecular systems. Recently, abundant research has been devoted to obtaining reaction coordinates using artificial neural networks from deep learning literature, where many collective variables are typically utilized in the input layer. However, it is difficult to explain the details of which collective variables contribute to the predicted reaction coordinates owing to the complexity of the nonlinear functions in deep neural networks. To overcome this limitation, we used Explainable Artificial Intelligence (XAI) methods of the Local Interpretable Model-agnostic Explanation (LIME) and the game theory-based framework known as Shapley Additive exPlanations (SHAP). We demonstrated that XAI enables us to obtain the degree of contribution of each collective variable to reaction coordinates that is determined by nonlinear regressions with deep learning for the committor of the alanine dipeptide isomerization in vacuum. In particular, both LIME and SHAP provide important features to the predicted reaction coordinates, which are characterized by appropriate dihedral angles consistent with those previously reported from the committor test analysis. The present study offers an AI-aided framework to explain the appropriate reaction coordinates, which acquires considerable significance when the number of degrees of freedom increases.
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Affiliation(s)
| | | | - Kei-ichi Okazaki
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Japan
| | - Toshifumi Mori
- Kyushu University Institute for Materials Chemistry and Engineering, Japan
| | - Kang Kim
- Graduate School of Engineering Science, Osaka University - Toyonaka Campus, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Japan
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4
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Mori Y, Okazaki KI, Mori T, Kim K, Matubayasi N. Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide. J Chem Phys 2020; 153:054115. [DOI: 10.1063/5.0009066] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Yusuke Mori
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | | | - Toshifumi Mori
- Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
- The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
| | - Kang Kim
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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5
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Hussain S, Haji-Akbari A. Studying rare events using forward-flux sampling: Recent breakthroughs and future outlook. J Chem Phys 2020; 152:060901. [DOI: 10.1063/1.5127780] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] 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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6
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Yappert R, Kamat K, Peters B. The overdamped transmission coefficient: Recovering the true mean first passage time from an inaccurate reaction coordinate. J Chem Phys 2019; 151:184108. [DOI: 10.1063/1.5117237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Ryan Yappert
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Kartik Kamat
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Baron Peters
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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7
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Zimmermann NER, Vorselaars B, Espinosa JR, Quigley D, Smith WR, Sanz E, Vega C, Peters B. NaCl nucleation from brine in seeded simulations: Sources of uncertainty in rate estimates. J Chem Phys 2018; 148:222838. [DOI: 10.1063/1.5024009] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Nils. E. R. Zimmermann
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Bart Vorselaars
- School of Mathematics and Physics, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, United Kingdom
| | - Jorge R. Espinosa
- Departmento de Quimica-Fisica I, Facultad de Ciencias Quimicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - David Quigley
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - William R. Smith
- Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario N1G2W1, Canada
- Department of Chemistry, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Eduardo Sanz
- Departmento de Quimica-Fisica I, Facultad de Ciencias Quimicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Carlos Vega
- Departmento de Quimica-Fisica I, Facultad de Ciencias Quimicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Baron Peters
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
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8
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Richard D, Speck T. Crystallization of hard spheres revisited. I. Extracting kinetics and free energy landscape from forward flux sampling. J Chem Phys 2018; 148:124110. [PMID: 29604868 DOI: 10.1063/1.5016277] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We investigate the kinetics and the free energy landscape of the crystallization of hard spheres from a supersaturated metastable liquid though direct simulations and forward flux sampling. In this first paper, we describe and test two different ways to reconstruct the free energy barriers from the sampled steady state probability distribution of cluster sizes without sampling the equilibrium distribution. The first method is based on mean first passage times, and the second method is based on splitting probabilities. We verify both methods for a single particle moving in a double-well potential. For the nucleation of hard spheres, these methods allow us to probe a wide range of supersaturations and to reconstruct the kinetics and the free energy landscape from the same simulation. Results are consistent with the scaling predicted by classical nucleation theory although a quantitative fit requires a rather large effective interfacial tension.
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Affiliation(s)
- David Richard
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 7-9, 55128 Mainz, Germany
| | - Thomas Speck
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 7-9, 55128 Mainz, Germany
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9
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Abstract
Desolvation barriers are present for solute-solvent exchange events, such as ligand binding to an enzyme active site, during protein folding, and at battery electrodes. For solution-grown crystals, desolvation at kink sites can be the rate-limiting step for growth. However, desolvation and the associated kinetic barriers are poorly understood. In this work, we use rare-event simulation techniques to investigate attachment/detachment events at kink sites of a NaCl crystal in water. We elucidate the desolvation mechanism and present an optimized reaction coordinate, which involves one solute collective variable and one solvent collective variable. The attachment/detachment pathways for Na+ and Cl- are qualitatively similar, with quantitative differences that we attribute to different ion sizes and solvent coordination. The attachment barriers primarily result from kink site desolvation, while detachment barriers largely result from breaking ion-crystal bonds. We compute ion detachment rates from kink sites and compare with results from an independent study. We anticipate that the reaction coordinate and desolvation mechanism identified in this work may be applicable to other alkali halides.
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10
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Dittmar HR, Kusalik PG. Ordering effects of conjugate thermal fields in simulations of molecular liquids: Carbon dioxide and water. J Chem Phys 2016; 145:134504. [DOI: 10.1063/1.4963767] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Harro R. Dittmar
- Department of Chemistry, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Peter G. Kusalik
- Department of Chemistry, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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11
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Jungblut S, Dellago C. Heterogeneous Crystallization on Pairs of Pre-Structured Seeds. J Phys Chem B 2016; 120:9230-9. [PMID: 27479875 PMCID: PMC5011298 DOI: 10.1021/acs.jpcb.6b06510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 07/28/2016] [Indexed: 11/29/2022]
Abstract
Studying the effects of small pre-structured seeds on the crystallization transition in an undercooled monodisperse Lennard-Jones fluid with transition interface path sampling combined with molecular dynamics simulations, we analyze the impact of the simultaneous presence of two seeds with various structures. In the presence of seeds with face- and body-centered cubic structures, we find that decreasing the seed-to-seed distance enhances the probability of the crystalline clusters formed on one of the seeds to grow beyond the critical size, thus, increasing the crystal nucleation rates. In contrast, when seeds have an icosahedral structure, the crystalline clusters form mostly in the bulk. The crystal nucleation rate, however, is also determined by the distance between the seeds with regular structure in which the lattice spacing is equal to the bulk lattice constant, pointing to a heterogeneous crystal nucleation that occurs away from the icosahedrally structured seeds. For slightly squeezed seeds, the effects of the presence of seeds with face- and body-centered cubic structures are reduced in comparison to the regular seeds, and we do not see any effect of the presence of the second seed for seeds with squeezed icosahedral structure.
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Affiliation(s)
- Swetlana Jungblut
- Faculty of Physics, University
of Vienna, Boltzmanngasse
5, 1090 Wien, Austria
| | - Christoph Dellago
- Faculty of Physics, University
of Vienna, Boltzmanngasse
5, 1090 Wien, Austria
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12
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Jungblut S, Dellago C. Pathways to self-organization: Crystallization via nucleation and growth. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2016; 39:77. [PMID: 27498980 DOI: 10.1140/epje/i2016-16077-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 07/13/2016] [Indexed: 06/06/2023]
Abstract
Crystallization, a prototypical self-organization process during which a disordered state spontaneously transforms into a crystal characterized by a regular arrangement of its building blocks, usually proceeds by nucleation and growth. In the initial stages of the transformation, a localized nucleus of the new phase forms in the old one due to a random fluctuation. Most of these nuclei disappear after a short time, but rarely a crystalline embryo may reach a critical size after which further growth becomes thermodynamically favorable and the entire system is converted into the new phase. In this article, we will discuss several theoretical concepts and computational methods to study crystallization. More specifically, we will address the rare event problem arising in the simulation of nucleation processes and explain how to calculate nucleation rates accurately. Particular attention is directed towards discussing statistical tools to analyze crystallization trajectories and identify the transition mechanism.
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Affiliation(s)
- S Jungblut
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Wien, Austria
| | - C Dellago
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Wien, Austria.
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13
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Richard D, Löwen H, Speck T. Nucleation pathway and kinetics of phase-separating active Brownian particles. SOFT MATTER 2016; 12:5257-5264. [PMID: 27126952 DOI: 10.1039/c6sm00485g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Suspensions of purely repulsive but self-propelled Brownian particles might undergo phase separation, a phenomenon that strongly resembles the phase separation of passive particles with attractions. Here we employ computer simulations to study the nucleation kinetics and the microscopic pathway active Brownian disks take in two dimensions when quenched from the homogeneous suspension to propulsion speeds beyond the binodal. We find the same qualitative behavior for the nucleation rate as a function of density as for a passive suspension undergoing liquid-vapor separation, suggesting that the scenario of an effective free energy also extends to the kinetics of phase separation. We study the transition in more detail through a committor analysis and find that transition states are best described by a combination of cluster size and the radial polarization of particles in the cluster.
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Affiliation(s)
- David Richard
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 7-9, 55128 Mainz, Germany.
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14
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Affiliation(s)
- Baron Peters
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106;
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15
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Menzl G, Singraber A, Dellago C. S-shooting: a Bennett–Chandler-like method for the computation of rate constants from committor trajectories. Faraday Discuss 2016; 195:345-364. [DOI: 10.1039/c6fd00124f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mechanisms of rare transitions between long-lived stable states are often analyzed in terms of commitment probabilities, determined from swarms of short molecular dynamics trajectories. Here, we present a computer simulation method to determine rate constants from such short trajectories combined with free energy calculations. The method, akin to the Bennett–Chandler approach for the calculation of reaction rate constants, requires the definition of a valid reaction coordinate and can be applied to both under- and overdamped dynamics. We verify the correctness of the algorithm using a one-dimensional random walker in a double-well potential and demonstrate its applicability to complex transitions in condensed systems by calculating cavitation rates for water at negative pressures.
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Affiliation(s)
- Georg Menzl
- Faculty of Physics and Center for Computational Materials Science
- University of Vienna
- 1090 Vienna
- Austria
| | - Andreas Singraber
- Faculty of Physics and Center for Computational Materials Science
- University of Vienna
- 1090 Vienna
- Austria
| | - Christoph Dellago
- Faculty of Physics and Center for Computational Materials Science
- University of Vienna
- 1090 Vienna
- Austria
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16
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Banushkina PV, Krivov SV. Nonparametric variational optimization of reaction coordinates. J Chem Phys 2015; 143:184108. [DOI: 10.1063/1.4935180] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Polina V. Banushkina
- Astbury Center for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Sergei V. Krivov
- Astbury Center for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
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17
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Magnin Y, Zappelli A, Amara H, Ducastelle F, Bichara C. Size Dependent Phase Diagrams of Nickel-Carbon Nanoparticles. PHYSICAL REVIEW LETTERS 2015; 115:205502. [PMID: 26613451 DOI: 10.1103/physrevlett.115.205502] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Indexed: 06/05/2023]
Abstract
The carbon rich phase diagrams of nickel-carbon nanoparticles, relevant to catalysis and catalytic chemical vapor deposition synthesis of carbon nanotubes, are calculated for system sizes up to about 3 nm (807 Ni atoms). A tight binding model for interatomic interactions drives the grand canonical Monte Carlo simulations used to locate solid, core shell and liquid stability domains, as a function of size, temperature, and carbon chemical potential or concentration. Melting is favored by carbon incorporation from the nanoparticle surface, resulting in a strong relative lowering of the eutectic temperature and a phase diagram topology different from the bulk one. This should lead to a better understanding of the nanotube growth mechanisms.
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Affiliation(s)
- Y Magnin
- Centre Interdisciplinaire de Nanoscience de Marseille, Aix-Marseille University and CNRS, Campus de Luminy, Case 913, F-13288 Marseille, France
| | - A Zappelli
- Centre Interdisciplinaire de Nanoscience de Marseille, Aix-Marseille University and CNRS, Campus de Luminy, Case 913, F-13288 Marseille, France
| | - H Amara
- Laboratoire d'Etude des Microstructures, ONERA-CNRS, BP 72, F-92322 Châtillon, France
| | - F Ducastelle
- Laboratoire d'Etude des Microstructures, ONERA-CNRS, BP 72, F-92322 Châtillon, France
| | - C Bichara
- Centre Interdisciplinaire de Nanoscience de Marseille, Aix-Marseille University and CNRS, Campus de Luminy, Case 913, F-13288 Marseille, France
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18
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Zimmermann NER, Vorselaars B, Quigley D, Peters B. Nucleation of NaCl from Aqueous Solution: Critical Sizes, Ion-Attachment Kinetics, and Rates. J Am Chem Soc 2015; 137:13352-61. [DOI: 10.1021/jacs.5b08098] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Bart Vorselaars
- Department
of Physics and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, U.K
| | - David Quigley
- Department
of Physics and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, U.K
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19
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Affiliation(s)
- Baron Peters
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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21
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Banushkina PV, Krivov SV. Fep1d: A script for the analysis of reaction coordinates. J Comput Chem 2015; 36:878-82. [DOI: 10.1002/jcc.23868] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 01/29/2015] [Accepted: 01/30/2015] [Indexed: 01/23/2023]
Affiliation(s)
- Polina V. Banushkina
- Astbury Center for Structural Molecular Biology, Faculty of Biological Sciences; University of Leeds; Leeds LS2 9JT United Kingdom
| | - Sergei V. Krivov
- Astbury Center for Structural Molecular Biology, Faculty of Biological Sciences; University of Leeds; Leeds LS2 9JT United Kingdom
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22
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Jungblut S, Dellago C. Caveats of mean first-passage time methods applied to the crystallization transition: Effects of non-Markovianity. J Chem Phys 2015; 142:064103. [DOI: 10.1063/1.4907364] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Swetlana Jungblut
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Wien, Austria
| | - Christoph Dellago
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Wien, Austria
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23
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Dittmar H, Kusalik PG. Driving ordering processes in molecular-dynamics simulations. PHYSICAL REVIEW LETTERS 2014; 112:195701. [PMID: 24877946 DOI: 10.1103/physrevlett.112.195701] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Indexed: 05/28/2023]
Abstract
Self-organized criticality describes the emergence of complexity in dynamical nonequilibrium systems. In this paper we introduce a unique approach whereby a driven energy conversion is utilized as a sampling bias for ordered arrangements in molecular dynamics simulations of atomic and molecular fluids. This approach gives rise to dramatically accelerated nucleation rates, by as much as 30 orders of magnitude, without the need of predefined order parameters, which commonly employed rare-event sampling methods rely on. The measured heat fluxes suggest how the approach can be generalized.
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Affiliation(s)
- Harro Dittmar
- Department of Chemistry, University of Calgary, 2500 University drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Peter G Kusalik
- Department of Chemistry, University of Calgary, 2500 University drive NW, Calgary, Alberta T2N 1N4, Canada
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24
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Agarwal V, Peters B. Nucleation near the eutectic point in a Potts-lattice gas model. J Chem Phys 2014; 140:084111. [DOI: 10.1063/1.4865338] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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