1
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Akgüller Ö, Balcı MA, Cioca G. Network Models of BACE-1 Inhibitors: Exploring Structural and Biochemical Relationships. Int J Mol Sci 2024; 25:6890. [PMID: 38999999 PMCID: PMC11240958 DOI: 10.3390/ijms25136890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/14/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024] Open
Abstract
This study investigates the clustering patterns of human β-secretase 1 (BACE-1) inhibitors using complex network methodologies based on various distance functions, including Euclidean, Tanimoto, Hamming, and Levenshtein distances. Molecular descriptor vectors such as molecular mass, Merck Molecular Force Field (MMFF) energy, Crippen partition coefficient (ClogP), Crippen molar refractivity (MR), eccentricity, Kappa indices, Synthetic Accessibility Score, Topological Polar Surface Area (TPSA), and 2D/3D autocorrelation entropies are employed to capture the diverse properties of these inhibitors. The Euclidean distance network demonstrates the most reliable clustering results, with strong agreement metrics and minimal information loss, indicating its robustness in capturing essential structural and physicochemical properties. Tanimoto and Hamming distance networks yield valuable clustering outcomes, albeit with moderate performance, while the Levenshtein distance network shows significant discrepancies. The analysis of eigenvector centrality across different networks identifies key inhibitors acting as hubs, which are likely critical in biochemical pathways. Community detection results highlight distinct clustering patterns, with well-defined communities providing insights into the functional and structural groupings of BACE-1 inhibitors. The study also conducts non-parametric tests, revealing significant differences in molecular descriptors, validating the clustering methodology. Despite its limitations, including reliance on specific descriptors and computational complexity, this study offers a comprehensive framework for understanding molecular interactions and guiding therapeutic interventions. Future research could integrate additional descriptors, advanced machine learning techniques, and dynamic network analysis to enhance clustering accuracy and applicability.
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Affiliation(s)
- Ömer Akgüller
- Department of Mathematics, Faculty of Science, Mugla Sitki Kocman University, 48000 Mugla, Turkey;
| | - Mehmet Ali Balcı
- Department of Mathematics, Faculty of Science, Mugla Sitki Kocman University, 48000 Mugla, Turkey;
| | - Gabriela Cioca
- Preclinical Department, Faculty of Medicine, Lucian Blaga University of Sibiu, 550024 Sibiu, Romania;
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2
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France-Lanord A, Vroylandt H, Salanne M, Rotenberg B, Saitta AM, Pietrucci F. Data-Driven Path Collective Variables. J Chem Theory Comput 2024; 20:3069-3084. [PMID: 38619076 DOI: 10.1021/acs.jctc.4c00123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Identifying optimal collective variables to model transformations using atomic-scale simulations is a long-standing challenge. We propose a new method for the generation, optimization, and comparison of collective variables that can be thought of as a data-driven generalization of the path collective variable concept. It consists of a kernel ridge regression of the committor probability, which encodes a transformation's progress. The resulting collective variable is one-dimensional, interpretable, and differentiable, making it appropriate for enhanced sampling simulations requiring biasing. We demonstrate the validity of the method on two different applications: a precipitation model and the association of Li+ and F- in water. For the former, we show that global descriptors such as the permutation invariant vector allow reaching an accuracy far from the one achieved via simpler, more intuitive variables. For the latter, we show that information correlated with the transformation mechanism is contained in the first solvation shell only and that inertial effects prevent the derivation of optimal collective variables from the atomic positions only.
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Affiliation(s)
- Arthur France-Lanord
- Institut des Sciences du Calcul et des Données, ISCD, Sorbonne Université, F-75005 Paris, France
- Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Sorbonne Université, F-75005 Paris, France
| | - Hadrien Vroylandt
- Institut des Sciences du Calcul et des Données, ISCD, Sorbonne Université, F-75005 Paris, France
| | - Mathieu Salanne
- Physicochimie des Électrolytes et Nanosystèmes Interfaciaux, Sorbonne Université, CNRS, 4 Place Jussieu, F-75005 Paris, France
- Institut Universitaire de France (IUF), 75231 Paris, France
| | - Benjamin Rotenberg
- Physicochimie des Électrolytes et Nanosystèmes Interfaciaux, Sorbonne Université, CNRS, 4 Place Jussieu, F-75005 Paris, France
| | - A Marco Saitta
- Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Sorbonne Université, F-75005 Paris, France
| | - Fabio Pietrucci
- Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Sorbonne Université, F-75005 Paris, France
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3
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Herringer NSM, Dasetty S, Gandhi D, Lee J, Ferguson AL. Permutationally Invariant Networks for Enhanced Sampling (PINES): Discovery of Multimolecular and Solvent-Inclusive Collective Variables. J Chem Theory Comput 2024; 20:178-198. [PMID: 38150421 DOI: 10.1021/acs.jctc.3c00923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
The typically rugged nature of molecular free-energy landscapes can frustrate efficient sampling of the thermodynamically relevant phase space due to the presence of high free-energy barriers. Enhanced sampling techniques can improve phase space exploration by accelerating sampling along particular collective variables (CVs). A number of techniques exist for the data-driven discovery of CVs parametrizing the important large-scale motions of the system. A challenge to CV discovery is learning CVs invariant to the symmetries of the molecular system, frequently rigid translation, rigid rotation, and permutational relabeling of identical particles. Of these, permutational invariance has proved a persistent challenge in frustrating the data-driven discovery of multimolecular CVs in systems of self-assembling particles and solvent-inclusive CVs for solvated systems. In this work, we integrate permutation invariant vector (PIV) featurizations with autoencoding neural networks to learn nonlinear CVs invariant to translation, rotation, and permutation and perform interleaved rounds of CV discovery and enhanced sampling to iteratively expand the sampling of configurational phase space and obtain converged CVs and free-energy landscapes. We demonstrate the permutationally invariant network for enhanced sampling (PINES) approach in applications to the self-assembly of a 13-atom argon cluster, association/dissociation of a NaCl ion pair in water, and hydrophobic collapse of a C45H92 n-pentatetracontane polymer chain. We make the approach freely available as a new module within the PLUMED2 enhanced sampling libraries.
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Affiliation(s)
| | - Siva Dasetty
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Diya Gandhi
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Junhee Lee
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
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4
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Kulkarni M, Söderhjelm P. Free-Energy Landscape and Rate Estimation of the Aromatic Ring Flips in Basic Pancreatic Trypsin Inhibitors Using Metadynamics. J Chem Theory Comput 2023; 19:6605-6618. [PMID: 37698852 PMCID: PMC10569046 DOI: 10.1021/acs.jctc.3c00460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Indexed: 09/13/2023]
Abstract
Aromatic side chains (phenylalanine and tyrosine) of a protein flip by 180° around the Cβ-Cγ axis (χ2 dihedral of the side chain), producing two symmetry-equivalent states. The study of ring flip dynamics with nuclear magnetic resonance (NMR) experiments helps to understand local conformational fluctuations. Ring flips are categorized as slow (milliseconds and onward) or fast (nanoseconds to near milliseconds) based on timescales accessible to NMR experiments. In this study, we investigated the ability of the infrequent metadynamics approach to estimate the flip rate and discriminate between slow and fast ring flips for eight individual aromatic side chains (F4, Y10, Y21, F22, Y23, F33, Y35, and F45) of the basic pancreatic trypsin inhibitor. Well-tempered metadynamics simulations were performed to estimate the ring-flipping free-energy surfaces for all eight aromatic residues. The results indicate that χ2 as a standalone collective variable (CV) is not sufficient to obtain computationally consistent results. Inclusion of a complementary CV, such as χ1(Cα-Cβ), solved the problem for most residues and enabled us to classify fast and slow ring flips. This indicates the importance of librational motions in ring flips. Multiple pathways and mechanisms were observed for residues F4, Y10, and F22. Recrossing events were observed for residues F22 and F33, indicating a possible role of friction effects in ring flipping. The results demonstrate the successful application of infrequent metadynamics to estimate ring flip rates and identify certain limitations of the approach.
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Affiliation(s)
- Mandar Kulkarni
- Division of Biophysical Chemistry, Lund University, Chemical Center, 22100 Lund, Sweden
| | - Pär Söderhjelm
- Division of Biophysical Chemistry, Lund University, Chemical Center, 22100 Lund, Sweden
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5
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Shmilovich K, Ferguson AL. Girsanov Reweighting Enhanced Sampling Technique (GREST): On-the-Fly Data-Driven Discovery of and Enhanced Sampling in Slow Collective Variables. J Phys Chem A 2023; 127:3497-3517. [PMID: 37036804 DOI: 10.1021/acs.jpca.3c00505] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Molecular dynamics simulations of microscopic phenomena are limited by the short integration time steps which are required for numerical stability but which limit the practically achievable simulation time scales. Collective variable (CV) enhanced sampling techniques apply biases to predefined collective coordinates to promote barrier crossing, phase space exploration, and sampling of rare events. The efficacy of these techniques is contingent on the selection of good CVs correlated with the molecular motions governing the long-time dynamical evolution of the system. In this work, we introduce Girsanov Reweighting Enhanced Sampling Technique (GREST) as an adaptive sampling scheme that interleaves rounds of data-driven slow CV discovery and enhanced sampling along these coordinates. Since slow CVs are inherently dynamical quantities, a key ingredient in our approach is the use of both thermodynamic and dynamical Girsanov reweighting corrections for rigorous estimation of slow CVs from biased simulation data. We demonstrate our approach on a toy 1D 4-well potential, a simple biomolecular system alanine dipeptide, and the Trp-Leu-Ala-Leu-Leu (WLALL) pentapeptide. In each case GREST learns appropriate slow CVs and drives sampling of all thermally accessible metastable states starting from zero prior knowledge of the system. We make GREST accessible to the community via a publicly available open source Python package.
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Affiliation(s)
- Kirill Shmilovich
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
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6
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Jedrecy A, Saitta AM, Pietrucci F. Free energy calculations and unbiased molecular dynamics targeting the liquid-liquid transition in water no man's land. J Chem Phys 2023; 158:014502. [PMID: 36610960 DOI: 10.1063/5.0120789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The existence of a first-order phase transition between a low-density liquid (LDL) and a high-density liquid (HDL) form of supercooled water has been a central and highly debated issue of physics and chemistry for the last three decades. We present a computational study that allows us to determine the free-energy landscapes of supercooled water over a wide range of pressure and temperature conditions using the TIP4P/2005 force field. Our approach combines topology-based structural transformation coordinates, state-of-the-art free-energy calculation methods, and extensive unbiased molecular dynamics. All our diverse simulations cannot detect any barrier within the investigated timescales and system size, for a discontinuous transition between the LDL and HDL forms throughout the so-called "no man's land," until the onset of the solid, non-diffusive amorphous forms.
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Affiliation(s)
- Alexandre Jedrecy
- Insitut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, CNRS, MNHN, UMR 7590, Paris, France
| | - A Marco Saitta
- Insitut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, CNRS, MNHN, UMR 7590, Paris, France
| | - Fabio Pietrucci
- Insitut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, CNRS, MNHN, UMR 7590, Paris, France
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7
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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.
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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
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8
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Agglomerative and divisive hierarchical Bayesian clustering. Comput Stat Data Anal 2022. [DOI: 10.1016/j.csda.2022.107566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Han R, Ketkaew R, Luber S. A Concise Review on Recent Developments of Machine Learning for the Prediction of Vibrational Spectra. J Phys Chem A 2022; 126:801-812. [PMID: 35133168 DOI: 10.1021/acs.jpca.1c10417] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Machine learning has become more and more popular in computational chemistry, as well as in the important field of spectroscopy. In this concise review, we walk the reader through a short summary of machine learning algorithms and a comprehensive discussion on the connection between machine learning methods and vibrational spectroscopy, particularly for the case of infrared and Raman spectroscopy. We also briefly discuss state-of-the-art molecular representations which serve as meaningful inputs for machine learning to predict vibrational spectra. In addition, this review provides an overview of the transferability and best practices of machine learning in the prediction of vibrational spectra as well as possible future research directions.
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Affiliation(s)
- Ruocheng Han
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Rangsiman Ketkaew
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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10
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Nelli D, Pietrucci F, Ferrando R. Impurity diffusion in magic-size icosahedral clusters. J Chem Phys 2021; 155:144304. [PMID: 34654289 DOI: 10.1063/5.0060236] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Atomic diffusion is at the basis of chemical ordering transformations in nanoalloys. Understanding the diffusion mechanisms at the atomic level is therefore a key issue in the study of the thermodynamic behavior of these systems and, in particular, of their evolution from out-of-equilibrium chemical ordering types often obtained in the experiments. Here, the diffusion is studied in the case of a single-atom impurity of Ag or Au moving within otherwise pure magic-size icosahedral clusters of Cu or Co by means of two different computational techniques, i.e., molecular dynamics and metadynamics. Our simulations reveal unexpected diffusion pathways, in which the displacement of the impurity is coupled with the creation of vacancies in the central part of the cluster. We show that the observed mechanism is quite different from the vacancy-mediated diffusion processes identified so far, and we demonstrate that it can be related to the presence of non-homogeneous compressive stress in the inner part of the icosahedral structure.
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Affiliation(s)
- Diana Nelli
- Dipartimento di Fisica dell'Università di Genova, via Dodecaneso 33, Genova 16146, Italy
| | - Fabio Pietrucci
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IMPMC, 75005 Paris, France
| | - Riccardo Ferrando
- Dipartimento di Fisica dell'Università di Genova and CNR-IMEM, via Dodecaneso 33, Genova 16146, Italy
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11
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Musil F, Grisafi A, Bartók AP, Ortner C, Csányi G, Ceriotti M. Physics-Inspired Structural Representations for Molecules and Materials. Chem Rev 2021; 121:9759-9815. [PMID: 34310133 DOI: 10.1021/acs.chemrev.1c00021] [Citation(s) in RCA: 145] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The first step in the construction of a regression model or a data-driven analysis, aiming to predict or elucidate the relationship between the atomic-scale structure of matter and its properties, involves transforming the Cartesian coordinates of the atoms into a suitable representation. The development of atomic-scale representations has played, and continues to play, a central role in the success of machine-learning methods for chemistry and materials science. This review summarizes the current understanding of the nature and characteristics of the most commonly used structural and chemical descriptions of atomistic structures, highlighting the deep underlying connections between different frameworks and the ideas that lead to computationally efficient and universally applicable models. It emphasizes the link between properties, structures, their physical chemistry, and their mathematical description, provides examples of recent applications to a diverse set of chemical and materials science problems, and outlines the open questions and the most promising research directions in the field.
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Affiliation(s)
- Felix Musil
- Laboratory of Computational Science and Modeling, IMX, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Andrea Grisafi
- Laboratory of Computational Science and Modeling, IMX, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Albert P Bartók
- Department of Physics and Warwick Centre for Predictive Modelling, School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Christoph Ortner
- University of British Columbia, Vancouver, British Columbia V6T 1Z2, Canada
| | - Gábor Csányi
- Engineering Laboratory, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, United Kingdom
| | - Michele Ceriotti
- Laboratory of Computational Science and Modeling, IMX, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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12
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Goscinski A, Fraux G, Imbalzano G, Ceriotti M. The role of feature space in atomistic learning. MACHINE LEARNING-SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1088/2632-2153/abdaf7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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13
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Nada H. Melt crystallization mechanism analyzed with dimensional reduction of high-dimensional data representing distribution function geometries. Sci Rep 2020; 10:15465. [PMID: 32963268 PMCID: PMC7508891 DOI: 10.1038/s41598-020-72455-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/02/2020] [Indexed: 11/21/2022] Open
Abstract
Melt crystallization is essential to many industrial processes, including semiconductor, ice, and food manufacturing. Nevertheless, our understanding of the melt crystallization mechanism remains poor. This is because the molecular-scale structures of melts are difficult to clarify experimentally. Computer simulations, such as molecular dynamics (MD), are often used to investigate melt structures. However, the time evolution of the structural order in a melt during crystallization must be analyzed properly. In this study, dimensional reduction (DR), which is an unsupervised machine learning technique, is used to evaluate the time evolution of structural order. The DR is performed for high-dimensional data representing an atom–atom pair distribution function and the distribution function of the angle formed by three nearest neighboring atoms at each period during crystallization, which are obtained by an MD simulation of a supercooled Lennard–Jones melt. The results indicate that crystallization occurs via the following activation processes: nucleation of a crystal with a distorted structure and reconstruction of the crystal to a more stable structure. The time evolution of the local structures during crystallization is also evaluated with this method. The present method can be applied to studies of the mechanism of crystallization from a disordered system for real materials, even for complicated multicomponent materials.
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14
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Schaack S, Depondt P, Moog M, Pietrucci F, Finocchi F. How methane hydrate recovers at very high pressure the hexagonal ice structure. J Chem Phys 2020; 152:024504. [DOI: 10.1063/1.5129617] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- S. Schaack
- Sorbonne Université, Institut des Nanosciences de Paris (INSP), CNRS UMR 7588, Paris, France
| | - Ph. Depondt
- Sorbonne Université, Institut des Nanosciences de Paris (INSP), CNRS UMR 7588, Paris, France
| | - M. Moog
- Sorbonne Université, Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC), CNRS UMR 7590, Paris, France
| | - F. Pietrucci
- Sorbonne Université, Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC), CNRS UMR 7590, Paris, France
| | - F. Finocchi
- Sorbonne Université, Institut des Nanosciences de Paris (INSP), CNRS UMR 7588, Paris, France
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15
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Bove LE, Pietrucci F, Saitta AM, Klotz S, Teixeira J. On the link between polyamorphism and liquid-liquid transition: The case of salty water. J Chem Phys 2019; 151:044503. [DOI: 10.1063/1.5100959] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Livia E. Bove
- Dipartimento di Fisica, Università di Roma ‘La Sapienza’, 00185 Roma, Italy
- Sorbonne Université, CNRS UMR 7590, IMPMC, 75005 Paris, France
| | - Fabio Pietrucci
- Sorbonne Université, CNRS UMR 7590, IMPMC, 75005 Paris, France
| | - A. Marco Saitta
- Sorbonne Université, CNRS UMR 7590, IMPMC, 75005 Paris, France
| | - Stefan Klotz
- Sorbonne Université, CNRS UMR 7590, IMPMC, 75005 Paris, France
| | - José Teixeira
- Laboratoire Léon Brillouin (CEA/CNRS), CEA Saclay, 91191 Gif-sur-Yvette Cedex, France
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16
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Pedevilla P, Fitzner M, Sosso GC, Michaelides A. Heterogeneous seeded molecular dynamics as a tool to probe the ice nucleating ability of crystalline surfaces. J Chem Phys 2018; 149:072327. [PMID: 30134662 DOI: 10.1063/1.5029336] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ice nucleation plays a significant role in a large number of natural and technological processes, but it is challenging to investigate experimentally because of the small time scales (ns) and short length scales (nm) involved. On the other hand, conventional molecular simulations struggle to cope with the relatively long time scale required for critical ice nuclei to form. One way to tackle this issue is to take advantage of free energy or path sampling techniques. Unfortunately, these are computationally costly. Seeded molecular dynamics is a much less demanding alternative that has been successfully applied already to study the homogeneous freezing of water. However, in the case of heterogeneous ice nucleation, nature's favourite route to form ice, an array of suitable interfaces between the ice seeds and the substrate of interest has to be built, and this is no trivial task. In this paper, we present a Heterogeneous SEEDing (HSEED) approach which harnesses a random structure search framework to tackle the ice-substrate challenge, thus enabling seeded molecular dynamics simulations of heterogeneous ice nucleation on crystalline surfaces. We validate the HSEED framework by investigating the nucleation of ice on (i) model crystalline surfaces, using the coarse-grained mW model, and (ii) cholesterol crystals, employing the fully atomistic TIP4P/ice water model. We show that the HSEED technique yields results in excellent agreement with both metadynamics and forward flux sampling simulations. Because of its computational efficiency, the HSEED method allows one to rapidly assess the ice nucleation ability of whole libraries of crystalline substrates-a long-awaited computational development in, e.g., atmospheric science.
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Affiliation(s)
- Philipp Pedevilla
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Martin Fitzner
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Gabriele C Sosso
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Angelos Michaelides
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
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17
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Fitzner M, Sosso GC, Pietrucci F, Pipolo S, Michaelides A. Pre-critical fluctuations and what they disclose about heterogeneous crystal nucleation. Nat Commun 2017; 8:2257. [PMID: 29273707 PMCID: PMC5741629 DOI: 10.1038/s41467-017-02300-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/17/2017] [Indexed: 11/29/2022] Open
Abstract
Heterogeneous crystal nucleation is ubiquitous in nature and at the heart of many industrial applications. At the molecular scale, however, major gaps in understanding this phenomenon persist. Here we investigate through molecular dynamics simulations how the formation of precritical crystalline clusters is connected to the kinetics of nucleation. Considering heterogeneous water freezing as a prototypical scenario of practical relevance, we find that precritical fluctuations connote which crystalline polymorph will form. The emergence of metastable phases can thus be promoted by templating crystal faces characteristic of specific polymorphs. As a consequence, heterogeneous classical nucleation theory cannot describe our simulation results, because the different substrates lead to the formation of different ice polytypes. We discuss how the issue of polymorphism needs to be incorporated into analysis and comparison of heterogeneous and homogeneous nucleation. Our results will help to interpret and analyze the growing number of experiments and simulations dealing with crystal polymorph selection.
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Affiliation(s)
- Martin Fitzner
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street London, London, WC1E 6BT, UK
| | - Gabriele C Sosso
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Fabio Pietrucci
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, CNRS UMR 7590, IRD UMR 206, MNHN, Sorbonne Universités-Université Pierre et Marie Curie Paris 6, F-75005, Paris, France
| | - Silvio Pipolo
- Université de Lille, CNRS, Centrale Lille, ENSCL, Université d' Artois UMR 8181- UCCS Unité de Catalyse et Chimie du Solide, F-59000, Lille, France
| | - Angelos Michaelides
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, Gower Street London, London, WC1E 6BT, UK.
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18
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Pipolo S, Salanne M, Ferlat G, Klotz S, Saitta AM, Pietrucci F. Navigating at Will on the Water Phase Diagram. PHYSICAL REVIEW LETTERS 2017; 119:245701. [PMID: 29286747 DOI: 10.1103/physrevlett.119.245701] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 06/07/2023]
Abstract
Despite the simplicity of its molecular unit, water is a challenging system because of its uniquely rich polymorphism and predicted but yet unconfirmed features. Introducing a novel space of generalized coordinates that capture changes in the topology of the interatomic network, we are able to systematically track transitions among liquid, amorphous, and crystalline forms throughout the whole phase diagram of water, including the nucleation of crystals above and below the melting point. Our approach, based on molecular dynamics and enhanced sampling or free energy calculation techniques, is not specific to water and could be applied to very different structural phase transitions, paving the way towards the prediction of kinetic routes connecting polymorphic structures in a range of materials.
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Affiliation(s)
- S Pipolo
- Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 7590, IRD UMR 206, MNHN, IMPMC, F-75005 Paris, France
| | - M Salanne
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire PHENIX, F-75005 Paris, France
| | - G Ferlat
- Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 7590, IRD UMR 206, MNHN, IMPMC, F-75005 Paris, France
| | - S Klotz
- Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 7590, IRD UMR 206, MNHN, IMPMC, F-75005 Paris, France
| | - A M Saitta
- Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 7590, IRD UMR 206, MNHN, IMPMC, F-75005 Paris, France
| | - F Pietrucci
- Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 7590, IRD UMR 206, MNHN, IMPMC, F-75005 Paris, France
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19
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Yonetani Y. Distinct dissociation kinetics between ion pairs: Solvent-coordinate free-energy landscape analysis. J Chem Phys 2015; 143:044506. [DOI: 10.1063/1.4927093] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yoshiteru Yonetani
- Quantum Beam Science Center, Japan Atomic Energy Agency, 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
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20
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Pietrucci F, Martoňák R. Systematic comparison of crystalline and amorphous phases: Charting the landscape of water structures and transformations. J Chem Phys 2015; 142:104704. [DOI: 10.1063/1.4914138] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Fabio Pietrucci
- Sorbonne Universités, UPMC University Paris 6, UMR 7590, IMPMC, F-75005 Paris, France
| | - Roman Martoňák
- Department of Experimental Physics, Comenius University, Mlynská Dolina F2, 842 48 Bratislava, Slovakia
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21
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Gasparotto P, Ceriotti M. Recognizing molecular patterns by machine learning: An agnostic structural definition of the hydrogen bond. J Chem Phys 2014; 141:174110. [DOI: 10.1063/1.4900655] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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