1
|
Al-Awad AS, Batet L, Rives R, Sedano L. Stochastic computer experiments of the thermodynamic irreversibility of bulk nanobubbles in supersaturated and weak gas-liquid solutions. J Chem Phys 2024; 161:024503. [PMID: 38984961 DOI: 10.1063/5.0204665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/24/2024] [Indexed: 07/11/2024] Open
Abstract
Spontaneous gas-bubble nucleation in weak gas-liquid solutions has been a challenging topic in theory, experimentation, and computer simulations. In analogy with recent advances in crystallization and droplet formation studies, the diffusive-shielding stabilization and thermodynamic irreversibility of bulk nanobubble (bNB) mechanisms are revisited and deployed to characterize nucleation processes in a stochastic framework of computer experiments using the large-scale atomic/molecular massively parallel simulator code. Theoretical bases, assumptions, and limitations underlying the irreversibility hypothesis of bNBs, and their computational counterparts, are extensively described and illustrated. In essence, it is established that the irreversibility hypothesis can be numerically investigated by converging the system volume (due to the finiteness of interatomic forces) and the initial dissolved-gas concentration in the solution (due to the single-bNB limitation). Helium nucleation in liquid Pb17Li alloy is selected as a representative case study, where it exhibits typical characteristics of noble-gas/liquid-metal systems. The proposed framework lays down the bases on which the stability of gas-bNBs in weak and supersaturated gas-liquid solutions can be inferred and explained from a novel perspective. In essence, it stochastically marches toward a unique irreversible state along out-of-equilibrium nucleation/growth trajectories. Moreover, it does not attempt to characterize the interface or any interface-related properties, neither theoretically nor computationally. It was concluded that bNBs of a few tens of He-atoms are irreversible when dissolved-He concentrations in the weak gas-liquid solution are at least ∼50 and ∼105 mol m-3 at 600 and 1000 K (and ∼80 MPa), respectively, whereas classical molecular dynamics -estimated solubilities are at least two orders of magnitude smaller.
Collapse
Affiliation(s)
- Abdulrahman S Al-Awad
- Department of Physics, Universitat Politècnica de Catalunya-BarcelonaTech (UPC), Barcelona 08028, Spain
| | - Lluis Batet
- Department of Physics, Universitat Politècnica de Catalunya-BarcelonaTech (UPC), Barcelona 08028, Spain
| | - Ronny Rives
- Department of Physics, Universitat Politècnica de Catalunya-BarcelonaTech (UPC), Barcelona 08028, Spain
| | - Luis Sedano
- Department of Physics, Universitat Politècnica de Catalunya-BarcelonaTech (UPC), Barcelona 08028, Spain
- Instituto de Ciencia de Materiales de Barcelona (ICMAB/CSIC), Bellaterra 08193, Spain
| |
Collapse
|
2
|
Lam J, Pietrucci F. Critical comparison of general-purpose collective variables for crystal nucleation. Phys Rev E 2023; 107:L012601. [PMID: 36797915 DOI: 10.1103/physreve.107.l012601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 01/06/2023] [Indexed: 06/18/2023]
Abstract
The nucleation of crystals is a prominent phenomenon in science and technology that still lacks a full atomic-scale understanding. Much work has been devoted to identifying order parameters able to track the process, from the inception of early nuclei to their maturing to critical size until growth of an extended crystal. We critically assess and compare two powerful distance-based collective variables, an effective entropy derived from liquid state theory and the path variable based on permutation invariant vectors using the Kob-Andersen binary mixture and a combination of enhanced-sampling techniques. Our findings reveal a comparable ability to drive nucleation when a bias potential is applied, and comparable free-energy barriers and structural features. Yet, we also found an imperfect correlation with the committor probability on the barrier top which was bypassed by changing the order parameter definition.
Collapse
Affiliation(s)
- Julien Lam
- CEMES, Centre National de la Recherche Scientifique and Université de Toulouse, 29 rue Jeanne Marvig, 31055 Toulouse Cedex, France
- Université Lille, Centre National de la Recherche Scientifique, INRA, ENSCL, UMR 8207, UMET, Unité Matériaux et Transformations, F 59000 Lille, France
| | - Fabio Pietrucci
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR 7590, IMPMC, 75005 Paris, France
| |
Collapse
|
3
|
Hall SW, Díaz Leines G, Sarupria S, Rogal J. Practical guide to replica exchange transition interface sampling and forward flux sampling. J Chem Phys 2022; 156:200901. [DOI: 10.1063/5.0080053] [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
Path sampling approaches have become invaluable tools to explore the mechanisms and dynamics of the so-called rare events that are characterized by transitions between metastable states separated by sizable free energy barriers. Their practical application, in particular to ever more complex molecular systems, is, however, not entirely trivial. Focusing on replica exchange transition interface sampling (RETIS) and forward flux sampling (FFS), we discuss a range of analysis tools that can be used to assess the quality and convergence of such simulations, which is crucial to obtain reliable results. The basic ideas of a step-wise evaluation are exemplified for the study of nucleation in several systems with different complexities, providing a general guide for the critical assessment of RETIS and FFS simulations.
Collapse
Affiliation(s)
- Steven W. Hall
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Grisell Díaz Leines
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridgeshire CB2 1EW, United Kingdom
| | - Sapna Sarupria
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, USA
| | - Jutta Rogal
- Department of Chemistry, New York University, New York, New York 10003, USA
- Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Blow KE, Quigley D, Sosso GC. The seven deadly sins: When computing crystal nucleation rates, the devil is in the details. J Chem Phys 2021; 155:040901. [PMID: 34340373 DOI: 10.1063/5.0055248] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The formation of crystals has proven to be one of the most challenging phase transformations to quantitatively model-let alone to actually understand-be it by means of the latest experimental technique or the full arsenal of enhanced sampling approaches at our disposal. One of the most crucial quantities involved with the crystallization process is the nucleation rate, a single elusive number that is supposed to quantify the average probability for a nucleus of critical size to occur within a certain volume and time span. A substantial amount of effort has been devoted to attempt a connection between the crystal nucleation rates computed by means of atomistic simulations and their experimentally measured counterparts. Sadly, this endeavor almost invariably fails to some extent, with the venerable classical nucleation theory typically blamed as the main culprit. Here, we review some of the recent advances in the field, focusing on a number of perhaps more subtle details that are sometimes overlooked when computing nucleation rates. We believe it is important for the community to be aware of the full impact of aspects, such as finite size effects and slow dynamics, that often introduce inconspicuous and yet non-negligible sources of uncertainty into our simulations. In fact, it is key to obtain robust and reproducible trends to be leveraged so as to shed new light on the kinetics of a process, that of crystal nucleation, which is involved into countless practical applications, from the formulation of pharmaceutical drugs to the manufacturing of nano-electronic devices.
Collapse
Affiliation(s)
- Katarina E Blow
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - David Quigley
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Gabriele C Sosso
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| |
Collapse
|
6
|
Arjun A, Bolhuis PG. Homogenous nucleation rate of CO 2 hydrates using transition interface sampling. J Chem Phys 2021; 154:164507. [PMID: 33940852 DOI: 10.1063/5.0044883] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Carbon dioxide and water can form solid clathrate structures in which water cages encapsulate the gas molecules. Such hydrates have sparked much interest due to their possible application in CO2 sequestration. How the solid structure forms exactly from the liquid phase via a homogenous nucleation process is still poorly understood. This nucleation event is rare on the molecular timescale even under moderate undercooling or supersaturation conditions because of the large free energy barrier toward crystallization, rendering a brute force simulation of hydrate nucleation unfeasible for moderate undercooling or supersaturation. Here, we perform transition interface sampling simulations to quantify the homogenous nucleation rate for CO2 hydrate formation using accurate atomistic force fields at 500 bars for three different temperatures between 260 and 273 K. Collecting more than 100 000 pathways comprising roughly two milliseconds of simulation time, we computed a nucleation rate in the amorphous phase of ∼1021 nuclei s-1 cm-3 for a temperature of 260 K and a rate of ∼1012 nuclei s-1 cm-3 for a temperature of 265 K. For a temperature of 273 K, we find that the hydrate forms an sI crystalline phase with a rate of order of ∼101 nuclei s-1 cm-3. We compare these rates to classical nucleation theory estimates as well as experiments, and to nucleation rate estimates for methane hydrates and discuss possible causes of the observed differences. Our findings shed light on the kinetics of this important clathrate and should assist in future hydrate formation investigation.
Collapse
Affiliation(s)
- A Arjun
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Peter G Bolhuis
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| |
Collapse
|
7
|
Bolhuis PG, Swenson DWH. Transition Path Sampling as Markov Chain Monte Carlo of Trajectories: Recent Algorithms, Software, Applications, and Future Outlook. ADVANCED THEORY AND SIMULATIONS 2021. [DOI: 10.1002/adts.202000237] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Peter G. Bolhuis
- Amsterdam Center for Multiscale Modeling van 't Hoff Institute for Molecular Sciences University of Amsterdam PO Box 94157 1090 GD Amsterdam The Netherlands
| | - David W. H. Swenson
- Centre Blaise Pascal Ecole Normale Superieure 46, allée d'Italie 69364 Lyon Cedex 07 France
| |
Collapse
|
8
|
Lata NN, Zhou J, Hamilton P, Larsen M, Sarupria S, Cantrell W. Multivalent Surface Cations Enhance Heterogeneous Freezing of Water on Muscovite Mica. J Phys Chem Lett 2020; 11:8682-8689. [PMID: 32955892 DOI: 10.1021/acs.jpclett.0c02121] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Heterogeneous ice nucleation is a crucial phenomenon in various fields of fundamental and applied science. We investigate the effect of surface cations on freezing of water on muscovite mica. Mica is unique in that the exposed ion on its surface can be readily and easily exchanged without affecting other properties such as surface roughness. We investigate freezing on natural (K+) mica and mica in which we have exchanged K+ for Al3+, Mg2+, Ca2+, and Sr2+. We find that liquid water freezes at higher temperatures when ions of higher valency are present on the surface, thus exposing more of the underlying silica layer. Our data also show that the size of the ion affects the characteristic freezing temperature. Using molecular dynamics simulations, we investigate the effects that the ion valency and exposed silica layer have on the behavior of water on the surface. The results indicate that multivalent cations enhance the probability of forming large clusters of hydrogen bonded water molecules that are anchored by the hydration shells of the cations. These clusters also have a large fraction of free water that can reorient to take ice-like configurations, which are promoted by the regions on mica devoid of the ions. Thus, these clusters could serve as seedbeds for ice nuclei. The combined experimental and simulation studies shed new light on the influence of surface ions on heterogeneous ice nucleation.
Collapse
Affiliation(s)
- Nurun Nahar Lata
- Atmospheric Sciences Program, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Jiarun Zhou
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Pearce Hamilton
- Department of Physics and Astronomy, College of Charleston, Charleston, South Carolina 29424, United States
| | - Michael Larsen
- Department of Physics and Astronomy, College of Charleston, Charleston, South Carolina 29424, United States
- Atmospheric Sciences Program and Department of Physics, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Sapna Sarupria
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Will Cantrell
- Atmospheric Sciences Program and Department of Physics, Michigan Technological University, Houghton, Michigan 49931, United States
| |
Collapse
|