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Schwerdtfeger P, Wales DJ. 100 Years of the Lennard-Jones Potential. J Chem Theory Comput 2024; 20:3379-3405. [PMID: 38669689 DOI: 10.1021/acs.jctc.4c00135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
It is now 100 years since Lennard-Jones published his first paper introducing the now famous potential that bears his name. It is therefore timely to reflect on the many achievements, as well as the limitations, of this potential in the theory of atomic and molecular interactions, where applications range from descriptions of intermolecular forces to molecules, clusters, and condensed matter.
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Affiliation(s)
- Peter Schwerdtfeger
- Centre for Theoretical Chemistry and Physics, The New Zealand Institute for Advanced Study, Massey University Auckland, Private Bag 102904, Auckland 0745, New Zealand
| | - David J Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
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2
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Xi B, Chan MK, Bao K, Zhao W, Chan HM, Chen H, Zhu J. Parameter-Free and Electron Counting Satisfied Material Representation for Machine Learning Potential Energy and Force Fields. J Phys Chem Lett 2024; 15:1636-1643. [PMID: 38306617 PMCID: PMC10875669 DOI: 10.1021/acs.jpclett.3c03250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 02/04/2024]
Abstract
We proposed a parameter-free volume element representation that satisfies the electron counting model and obtains accurate machine learning potential energy and direct force fitting of randomly perturbed hexagonal BN. Our method preserves permutational, translational, and rotational invariance and can be extended to three-dimensional systems, verified by a system of bulk Si. As a result, we obtained 0.57 meV/atom potential energy root mean squared error (RMSE) and 59 meV/Å force RMSE for perturbed bulk BN systems and 0.43 meV/atom potential energy RMSE and 36 meV/Å force RMSE for perturbed Si systems. In addition, an unbiased perturbation-based data set construction scheme is introduced and a continuous population distribution is obtained with a training data set of 4500, which is about 1 order of magnitude smaller than standard methods based on first-principles molecular dynamics simulations and saves a large amount of computing resources. General validity of our model is verified by structure optimization, molecular dynamics simulations, and extrapolations.
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Affiliation(s)
- Bin Xi
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territory, Hong Kong SAR 999077, P.R. China
| | - Man Kit Chan
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territory, Hong Kong SAR 999077, P.R. China
| | - Kejie Bao
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territory, Hong Kong SAR 999077, P.R. China
| | - Wenjing Zhao
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territory, Hong Kong SAR 999077, P.R. China
| | - Ho Ming Chan
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territory, Hong Kong SAR 999077, P.R. China
| | - Hang Chen
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territory, Hong Kong SAR 999077, P.R. China
| | - Junyi Zhu
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territory, Hong Kong SAR 999077, P.R. China
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3
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Fronzi M, Amos RD, Kobayashi R, Matsumura N, Watanabe K, Morizawa RK. Evaluation of Machine Learning Interatomic Potentials for the Properties of Gold Nanoparticles. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:3891. [PMID: 36364667 PMCID: PMC9655512 DOI: 10.3390/nano12213891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/23/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
We have investigated Machine Learning Interatomic Potentials in application to the properties of gold nanoparticles through the DeePMD package, using data generated with the ab-initio VASP program. Benchmarking was carried out on Au20 nanoclusters against ab-initio molecular dynamics simulations and show we can achieve similar accuracy with the machine learned potential at far reduced cost using LAMMPS. We have been able to reproduce structures and heat capacities of several isomeric forms. Comparison of our workflow with similar ML-IP studies is discussed and has identified areas for future improvement.
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Affiliation(s)
- Marco Fronzi
- University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Roger D. Amos
- University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Rika Kobayashi
- Australian National University, Canberra, ACT 2601, Australia
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4
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Fan QY, Liu JL, Gong FQ, Wang Y, Cheng J. Structural dynamics of Ru clusters during nitrogen dissociation in ammonia synthesis. Phys Chem Chem Phys 2022; 24:10820-10825. [PMID: 35482304 DOI: 10.1039/d2cp00678b] [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
The dynamic evolution of catalyst structures greatly influences the reactivity, especially sub-nanometer clusters, exhibiting complex configurational fluctuation. In the present work, we study the structural dynamics of a Ru19 cluster during the dissociation of N2 and calculate the reaction free energies using ab initio molecular dynamics (AIMD). Our AIMD calculation predicts a peak-shaped reaction entropy curve due to the adsorption-induced phase transition of the Ru19 cluster. The low melting points of sub-nanometer clusters make it possible to activate N2 at low temperatures. This work demonstrates that the dynamic changes of cluster structures have a non-negligible effect on reaction free energy and offer an opportunity for achieving ammonia synthesis under mild conditions.
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Affiliation(s)
- Qi-Yuan Fan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Jing-Li Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Fu-Qiang Gong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Ye Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Jun Cheng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
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5
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Louisnard F, Geudtner G, Köster AM, Cuny J. Implementation of the parallel-tempering molecular dynamics method in deMon2k and application to the water hexamer. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02765-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Ray S, Anglin JR, Vardi A. Prethermalization with negative specific heat. Phys Rev E 2020; 102:052107. [PMID: 33327107 DOI: 10.1103/physreve.102.052107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/19/2020] [Indexed: 11/07/2022]
Abstract
We study noncanonical relaxation in an aggregate of subsystems with negative specific heat. The Thirring instability drives the constituent subsystems towards the edges of their energy spectrum, so that the existence of a single adiabatic invariant results in structured noncanonical steady states that are spectacularly different from the grand-canonical prediction. For parameter regimes where this adiabatic invariance breaks down, the system exhibits prethermalization far away from integrability, with an unprecedented contrast between the prethermal- and thermal states.
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Affiliation(s)
- Sayak Ray
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - James R Anglin
- State Research Center OPTIMAS and Fachbereich Physik, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Amichay Vardi
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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7
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Mukuta N, Miura S. Potential energy landscape and thermodynamic transitions of coarse-grained protein models revealed by the multicanonical generalized hybrid Monte Carlo method. Biophys Physicobiol 2020; 17:14-24. [PMID: 32509490 PMCID: PMC7246090 DOI: 10.2142/biophysico.bsj-2019051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/23/2020] [Indexed: 12/01/2022] Open
Abstract
In the present study, thermodynamic properties of coarse-grained protein models have been studied by an extended ensemble method. Two types of protein model were analyzed; one is categorized into a fast folder and the other into a slow folder. Both models exhibit the following thermodynamic transitions: the collapse transition between random coil states and spatially compact, but non-native states and the folding transition between the collapsed states and the folded native states. Caloric curve for the fast folder shows strong statistical ensemble dependence, while almost no ensemble dependence is found for the slow folder. Microcanonical caloric curve for the fast folder exhibits S-shaped temperature dependence on the internal energy around the collapse transition which is reminiscent of the van der Waals loop observed for the first order transition; at the transition temperature, the collapsed and random coil states coexist dynamically. The corresponding microcanonical heat capacity is found to have negative region around the transition. This kind of exotic behaviors could be utilized to distinguish fast folding proteins.
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Affiliation(s)
- Natsuki Mukuta
- Division of Mathematical and Physical Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan
| | - Shinichi Miura
- Faculty of Mathematics and Physics, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan
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Spiegelman F, Tarrat N, Cuny J, Dontot L, Posenitskiy E, Martí C, Simon A, Rapacioli M. Density-functional tight-binding: basic concepts and applications to molecules and clusters. ADVANCES IN PHYSICS: X 2020; 5:1710252. [PMID: 33154977 PMCID: PMC7116320 DOI: 10.1080/23746149.2019.1710252] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023] Open
Abstract
The scope of this article is to present an overview of the Density Functional based Tight Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and its standard formulation up to second order. It also addresses methodological developments such as third order expansion, inclusion of non-covalent interactions, schemes to solve the self-interaction error, implementation of long-range short-range separation, treatment of excited states via the time-dependent DFTB scheme, inclusion of DFTB in hybrid high-level/low level schemes (DFT/DFTB or DFTB/MM), fragment decomposition of large systems, large scale potential energy landscape exploration with molecular dynamics in ground or excited states, non-adiabatic dynamics. A number of applications are reviewed, focusing on -(i)- the variety of systems that have been studied such as small molecules, large molecules and biomolecules, bare orfunctionalized clusters, supported or embedded systems, and -(ii)- properties and processes, such as vibrational spectroscopy, collisions, fragmentation, thermodynamics or non-adiabatic dynamics. Finally outlines and perspectives are given.
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Affiliation(s)
- Fernand Spiegelman
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Nathalie Tarrat
- CEMES, Université de Toulouse (UPS), CNRS, UPR8011, Toulouse, Toulouse, France
| | - Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Leo Dontot
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Evgeny Posenitskiy
- Laboratoire Collisions Agrégats et Réactivité LCAR/IRSAMC, UMR5589, Université de Toulouse (UPS) and CNRS, Toulouse, France
| | - Carles Martí
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
- Laboratoire de Chimie, UMR5182, Ecole Normale Supérieure de Lyon, Université de Lyon and CNRS, Lyon, France
| | - Aude Simon
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
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9
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Yang H, Drossinos Y, Hogan CJ. Excess thermal energy and latent heat in nanocluster collisional growth. J Chem Phys 2019; 151:224304. [PMID: 31837664 DOI: 10.1063/1.5129918] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nanoclusters can form and grow by nanocluster-monomer collisions (condensation) and nanocluster-nanocluster collisions (coagulation). During growth, product nanoclusters have elevated thermal energies due to potential and thermal energy exchange following a collision. Even though nanocluster collisional heating may be significant and strongly size dependent, no prior theory describes this phenomenon for collisions of finite-size clusters. We derive a model to describe the excess thermal energy of collisional growth, defined as the kinetic energy increase in the product cluster, and latent heat of collisional growth, defined as the heat released to the background upon thermalization of the nonequilibrium cluster. Both quantities are composed of a temperature-independent term related to potential energy minimum differences and a size- and temperature-dependent term, which hinges upon heat capacity and energy partitioning. Example calculations using gold nanoclusters demonstrate that collisional heating can be important and strongly size dependent, particularly for reactive collisions involving nanoclusters composed of 14-20 atoms. Excessive latent heat release may have considerable implications in cluster formation and growth.
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Affiliation(s)
- Huan Yang
- Department of Mechanical Engineering, University of Minnesota, 111 Church St. SE, Minneapolis, Minnesota 55455, USA
| | - Yannis Drossinos
- European Commission, Joint Research Centre, 21027 Ispra (VA), Italy
| | - Christopher J Hogan
- Department of Mechanical Engineering, University of Minnesota, 111 Church St. SE, Minneapolis, Minnesota 55455, USA
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10
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Rapacioli M, Spiegelman F, Tarrat N. Evidencing the relationship between isomer spectra and melting: the 20- and 55-atom silver and gold cluster cases. Phys Chem Chem Phys 2019; 21:24857-24866. [PMID: 31539012 DOI: 10.1039/c9cp03897c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The present work highlights the links between melting properties and structural excitation spectra of small gold and silver clusters. The heat capacity curves are computed for Ag20, Au20, Ag55, Au55 and their ions, using a parallel-tempering molecular dynamics scheme to explore the density functional based tight binding (DFTB) potential energy surfaces and the multiple histogram method. It is found that clusters having very symmetric lowest energy structures (Au20, Ag55 and their ions) present sharp or relatively sharp solid-to-liquid transitions and large melting temperatures, important structural excitation energies and a discrete isomer spectrum. Opposite trends are observed for less ordered clusters (Ag20, Au55 and their ions). Regarding the structural evolution with temperature, very symmetric clusters exhibit minor evolution up to the starting melting temperature. The present study also highlights that, in contrast with the case of Au20, a single electron excess or deficiency is not determinant regarding the melting characteristics, even quantitatively, for clusters containing 55 atoms, for gold as for silver.
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Affiliation(s)
- Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
| | - Fernand Spiegelman
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
| | - Nathalie Tarrat
- CEMES, Université de Toulouse, CNRS, 29, rue Jeanne Marvig, 31055 Toulouse, France.
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11
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Abstract
We report an embarrassingly parallel method for the evaluation of thermodynamic properties over an energy landscape exhibiting broken ergodicity, nested is the likelihood of the observed data D givenbasin-sampling (NBS). We also introduce the No Galilean U-Turn Sampler (NoGUTS), a new sampling scheme based on the No U-Turn Sampler (NUTS) introduced by Hoffman and Gelman (2014) that works with the Galilean Monte Carlo scheme introduced by Betancourt (2012) to aid the efficient generation of new live points. NoGUTS can be thought of as a form of reflective slice sampling with an automatic stopping criterion. We apply this approach to a benchmark atomic cluster of 31 Lennard-Jones atoms, which exhibits a low temperature solid-solid heat capacity peak. The calculated heat capacity is compared with results generated by parallel tempering (PT), basin-sampling parallel tempering (BSPT), and standard nested sampling (NS) simulations. NBS reproduces the full heat capacity curve predicted by PT and BSPT, while the NS calculation with similar computational cost fails to resolve the low-temperature solid-solid phase transition.
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Affiliation(s)
- Matthew Griffiths
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - David J Wales
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
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12
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Diagrams of States of Single Flexible-Semiflexible Multi-Block Copolymer Chains: A Flat-Histogram Monte Carlo Study. Polymers (Basel) 2019; 11:polym11050757. [PMID: 31052227 PMCID: PMC6571722 DOI: 10.3390/polym11050757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 01/16/2023] Open
Abstract
The combination of flexibility and semiflexibility in a single molecule is a powerful design principle both in nature and in materials science. We present results on the conformational behavior of a single multiblock-copolymer chain, consisting of equal amounts of Flexible (F) and Semiflexible (S) blocks with different affinity to an implicit solvent. We consider a manifold of macrostates defined by two terms in the total energy: intermonomer interaction energy and stiffness energy. To obtain diagrams of states (pseudo-phase diagrams), we performed flat-histogram Monte Carlo simulations using the Stochastic Approximation Monte Carlo algorithm (SAMC). We have accumulated two-Dimensional Density of States (2D DoS) functions (defined on the 2D manifold of macrostates) for a SF-multiblock-copolymer chain of length N=64 with block lengths b = 4, 8, 16, and 32 in two different selective solvents. In an analysis of the canonical ensemble, we calculated the heat capacity and determined its maxima and the most probable morphologies in different regions of the state diagrams. These are rich in various, non-trivial morphologies, which are formed without any specific interactions, and depend on the block length and the type of solvent selectivity (preferring S or F blocks, respectively). We compared the diagrams with those for the non-selective solvent and reveal essential changes in some cases. Additionally, we implemented microcanonical analysis in the “conformational” microcanonical (NVU, where U is the potential energy) and the true microcanonical (NVE, where E is the total energy) ensembles with the aim to reveal and classify pseudo-phase transitions, occurring under the change of temperature.
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13
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Bililign ES, Kollmer JE, Daniels KE. Protocol Dependence and State Variables in the Force-Moment Ensemble. PHYSICAL REVIEW LETTERS 2019; 122:038001. [PMID: 30735414 DOI: 10.1103/physrevlett.122.038001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 10/11/2018] [Indexed: 06/09/2023]
Abstract
Stress-based ensembles incorporating temperaturelike variables have been proposed as a route to an equation of state for granular materials. To test the efficacy of this approach, we perform experiments on a two-dimensional photoelastic granular system under three loading conditions: uniaxial compression, biaxial compression, and simple shear. From the interparticle forces, we find that the distributions of the normal component of the coarse-grained force-moment tensor are exponential tailed, while the deviatoric component is Gaussian distributed. This implies that the correct stress-based statistical mechanics conserves both the force-moment tensor and the Maxwell-Cremona force-tiling area. As such, two variables of state arise: the tensorial angoricity (α[over ^]) and a new temperaturelike quantity associated with the force-tile area which we name keramicity (κ). Each quantity is observed to be inversely proportional to the global confining pressure; however, only κ exhibits the protocol independence expected of a state variable, while α[over ^] behaves as a variable of process.
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Affiliation(s)
- Ephraim S Bililign
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Jonathan E Kollmer
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Karen E Daniels
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
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14
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Simon A, Rapacioli M, Michoulier E, Zheng L, Korchagina K, Cuny J. Contribution of the density-functional-based tight-binding scheme to the description of water clusters: methods, applications and extension to bulk systems. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1554903] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- A. Simon
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - M. Rapacioli
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - E. Michoulier
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
- Laboratoire Collisions Agrégats et Réactivité LCAR/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - L. Zheng
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - K. Korchagina
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - J. Cuny
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
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15
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Souda R. Probing the solid-liquid transition of thin propanol and butanol films through interactions with LiI. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.06.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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16
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Cuny J, Tarrat N, Spiegelman F, Huguenot A, Rapacioli M. Density-functional tight-binding approach for metal clusters, nanoparticles, surfaces and bulk: application to silver and gold. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:303001. [PMID: 29916820 DOI: 10.1088/1361-648x/aacd6c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Density-functional based tight-binding (DFTB) is an efficient quantum mechanical method that can describe a variety of systems, going from organic and inorganic compounds to metallic and hybrid materials. The present topical review addresses the ability and performance of DFTB to investigate energetic, structural, spectroscopic and dynamical properties of gold and silver materials. After a brief overview of the theoretical basis of DFTB, its parametrization and its transferability, we report its past and recent applications to gold and silver systems, including small clusters, nanoparticles, bulk and surfaces, bare and interacting with various organic and inorganic compounds. The range of applications covered by those studies goes from plasmonics and molecular electronics, to energy conversion and surface chemistry. Finally, perspectives of DFTB in the field of gold and silver surfaces and NPs are outlined.
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Affiliation(s)
- Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
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17
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Abstract
Recent advances in the potential energy landscapes approach are highlighted, including both theoretical and computational contributions. Treating the high dimensionality of molecular and condensed matter systems of contemporary interest is important for understanding how emergent properties are encoded in the landscape and for calculating these properties while faithfully representing barriers between different morphologies. The pathways characterized in full dimensionality, which are used to construct kinetic transition networks, may prove useful in guiding such calculations. The energy landscape perspective has also produced new procedures for structure prediction and analysis of thermodynamic properties. Basin-hopping global optimization, with alternative acceptance criteria and generalizations to multiple metric spaces, has been used to treat systems ranging from biomolecules to nanoalloy clusters and condensed matter. This review also illustrates how all this methodology, developed in the context of chemical physics, can be transferred to landscapes defined by cost functions associated with machine learning.
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Affiliation(s)
- David J Wales
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
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18
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Chiriki S, Jindal S, Bulusu SS. Neural network potentials for dynamics and thermodynamics of gold nanoparticles. J Chem Phys 2018; 146:084314. [PMID: 28249420 DOI: 10.1063/1.4977050] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
For understanding the dynamical and thermodynamical properties of metal nanoparticles, one has to go beyond static and structural predictions of a nanoparticle. Accurate description of dynamical properties may be computationally intensive depending on the size of nanoparticle. Herein, we demonstrate the use of atomistic neural network potentials, obtained by fitting quantum mechanical data, for extensive molecular dynamics simulations of gold nanoparticles. The fitted potential was tested by performing global optimizations of size selected gold nanoparticles (Aun, 17 ≤ n ≤ 58). We performed molecular dynamics simulations in canonical (NVT) and microcanonical (NVE) ensembles on Au17, Au34, Au58 for a total simulation time of around 3 ns for each nanoparticle. Our study based on both NVT and NVE ensembles indicate that there is a dynamical coexistence of solid-like and liquid-like phases near melting transition. We estimate the probability at finite temperatures for set of isomers lying below 0.5 eV from the global minimum structure. In the case of Au17 and Au58, the properties can be estimated using global minimum structure at room temperature, while for Au34, global minimum structure is not a dominant structure even at low temperatures.
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Affiliation(s)
- Siva Chiriki
- Discipline of Chemistry, Indian Institute of Technology (IIT) Indore, Madhya Pradesh 453552, India
| | - Shweta Jindal
- Discipline of Chemistry, Indian Institute of Technology (IIT) Indore, Madhya Pradesh 453552, India
| | - Satya S Bulusu
- Discipline of Chemistry, Indian Institute of Technology (IIT) Indore, Madhya Pradesh 453552, India
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Rapacioli M, Tarrat N, Spiegelman F. Melting of the Au20 Gold Cluster: Does Charge Matter? J Phys Chem A 2018; 122:4092-4098. [DOI: 10.1021/acs.jpca.7b12522] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Nathalie Tarrat
- CEMES, Université de Toulouse, CNRS, 29 rue Jeanne Marvig, 31055 Toulouse, France
| | - Fernand Spiegelman
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
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20
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21
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Melting and structural transitions. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/b978-0-08-102232-0.00009-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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22
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Rostami V, Porta Mana P, Grün S, Helias M. Bistability, non-ergodicity, and inhibition in pairwise maximum-entropy models. PLoS Comput Biol 2017; 13:e1005762. [PMID: 28968396 PMCID: PMC5645158 DOI: 10.1371/journal.pcbi.1005762] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 10/17/2017] [Accepted: 09/05/2017] [Indexed: 11/30/2022] Open
Abstract
Pairwise maximum-entropy models have been used in neuroscience to predict the activity of neuronal populations, given only the time-averaged correlations of the neuron activities. This paper provides evidence that the pairwise model, applied to experimental recordings, would produce a bimodal distribution for the population-averaged activity, and for some population sizes the second mode would peak at high activities, that experimentally would be equivalent to 90% of the neuron population active within time-windows of few milliseconds. Several problems are connected with this bimodality: 1. The presence of the high-activity mode is unrealistic in view of observed neuronal activity and on neurobiological grounds. 2. Boltzmann learning becomes non-ergodic, hence the pairwise maximum-entropy distribution cannot be found: in fact, Boltzmann learning would produce an incorrect distribution; similarly, common variants of mean-field approximations also produce an incorrect distribution. 3. The Glauber dynamics associated with the model is unrealistically bistable and cannot be used to generate realistic surrogate data. This bimodality problem is first demonstrated for an experimental dataset from 159 neurons in the motor cortex of macaque monkey. Evidence is then provided that this problem affects typical neural recordings of population sizes of a couple of hundreds or more neurons. The cause of the bimodality problem is identified as the inability of standard maximum-entropy distributions with a uniform reference measure to model neuronal inhibition. To eliminate this problem a modified maximum-entropy model is presented, which reflects a basic effect of inhibition in the form of a simple but non-uniform reference measure. This model does not lead to unrealistic bimodalities, can be found with Boltzmann learning, and has an associated Glauber dynamics which incorporates a minimal asymmetric inhibition. Networks of interacting units are ubiquitous in various fields of biology; e.g. gene regulatory networks, neuronal networks, social structures. If a limited set of observables is accessible, maximum-entropy models provide a way to construct a statistical model for such networks, under particular assumptions. The pairwise maximum-entropy model only uses the first two moments among those observables, and can be interpreted as a network with only pairwise interactions. If correlations are on average positive, we here show that the maximum entropy distribution tends to become bimodal. In the application to neuronal activity this is a problem, because the bimodality is an artefact of the statistical model and not observed in real data. This problem could also affect other fields in biology. We here explain under which conditions bimodality arises and present a solution to the problem by introducing a collective negative feedback, corresponding to a modified maximum-entropy model. This result may point to the existence of a homeostatic mechanism active in the system that is not part of our set of observable units.
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Affiliation(s)
- Vahid Rostami
- Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA BRAIN Institute I, Jülich Research Centre, Jülich, Germany
- * E-mail:
| | - PierGianLuca Porta Mana
- Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA BRAIN Institute I, Jülich Research Centre, Jülich, Germany
| | - Sonja Grün
- Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA BRAIN Institute I, Jülich Research Centre, Jülich, Germany
- Theoretical Systems Neurobiology, RWTH Aachen University, Aachen, Germany
| | - Moritz Helias
- Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA BRAIN Institute I, Jülich Research Centre, Jülich, Germany
- Department of Physics, Faculty 1, RWTH Aachen University, Aachen, Germany
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23
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Romero-Bastida M, Miranda-Peña JO, López JM. Thermal rectification in mass-graded next-nearest-neighbor Fermi-Pasta-Ulam lattices. Phys Rev E 2017; 95:032146. [PMID: 28415322 DOI: 10.1103/physreve.95.032146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Indexed: 06/07/2023]
Abstract
We study the thermal rectification efficiency, i.e., quantification of asymmetric heat flow, of a one-dimensional mass-graded anharmonic oscillator Fermi-Pasta-Ulam lattice both with nearest-neighbor (NN) and next-nearest-neighbor (NNN) interactions. The system presents a maximum rectification efficiency for a very precise value of the parameter that controls the coupling strength of the NNN interactions, which also optimizes the rectification figure when its dependence on mass asymmetry and temperature differences is considered. The origin of the enhanced rectification is the asymmetric local heat flow response as the heat reservoirs are swapped when a finely tuned NNN contribution is taken into account. A simple theoretical analysis gives an estimate of the optimal NNN coupling in excellent agreement with our simulation results.
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Affiliation(s)
- M Romero-Bastida
- SEPI ESIME-Culhuacán, Instituto Politécnico Nacional, Av. Santa Ana No. 1000, Col. San Francisco Culhuacán, Delegación Coyoacan, Distrito Federal 04430, Mexico
| | - Jorge-Orlando Miranda-Peña
- SEPI ESIME-Culhuacán, Instituto Politécnico Nacional, Av. Santa Ana No. 1000, Col. San Francisco Culhuacán, Delegación Coyoacan, Distrito Federal 04430, Mexico
| | - Juan M López
- Instituto de Física de Cantabria (IFCA), CSIC-Universidad de Cantabria, E-39005 Santander, Spain
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24
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Zierenberg J, Schierz P, Janke W. Canonical free-energy barrier of particle and polymer cluster formation. Nat Commun 2017; 8:14546. [PMID: 28240262 PMCID: PMC5333364 DOI: 10.1038/ncomms14546] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 01/10/2017] [Indexed: 12/16/2022] Open
Abstract
A common approach to study nucleation rates is the estimation of free-energy barriers. This usually requires knowledge about the shape of the forming droplet, a task that becomes notoriously difficult in macromolecular setups starting with a proper definition of the cluster boundary. Here we demonstrate a shape-free determination of the free energy for temperature-driven cluster formation in particle as well as polymer systems. Combined with rigorous results on equilibrium droplet formation, this allows for a well-defined finite-size scaling analysis of the effective interfacial free energy at a fixed density. We first verify the theoretical predictions for the formation of a liquid droplet in a supersaturated particle gas by generalized-ensemble Monte Carlo simulations of a Lennard-Jones system. Going one step further, we then generalize this approach to cluster formation in a dilute polymer solution. Our results suggest an analogy with particle condensation, when the macromolecules are interpreted as extended particles.
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Affiliation(s)
- Johannes Zierenberg
- Institut für Theoretische Physik, Universität Leipzig, Postfach 100 920, D-04009 Leipzig, Germany
| | - Philipp Schierz
- Institut für Theoretische Physik, Universität Leipzig, Postfach 100 920, D-04009 Leipzig, Germany
| | - Wolfhard Janke
- Institut für Theoretische Physik, Universität Leipzig, Postfach 100 920, D-04009 Leipzig, Germany
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25
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Xiong LH, Wang XD, Cao QP, Zhang DX, Xie HL, Xiao TQ, Jiang JZ. Composition- and temperature-dependent liquid structures in Al-Cu alloys: an ab initio molecular dynamics and x-ray diffraction study. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:035101. [PMID: 27849627 DOI: 10.1088/1361-648x/29/3/035101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The composition- and temperature-dependent liquid structures in eight Alrich-Cu binary alloys (from hypoeutectic Al93Cu7 to hypereutectic Al70Cu30) have been experimentally and computationally studied by x-ray diffraction (XRD) experiments and ab initio molecular dynamics (AIMD) simulations. The remarkable agreements of structure factors for all liquid Alrich-Cu alloys obtained from high-temperature high-energy XRD measurements and AIMD simulations have been achieved, which consolidates the analyses of structural evolutions in Alrich-Cu liquids during the cooling processing by AIMD simulations. The heat capacity of liquid Alrich-Cu alloys continuously increases and presents no abnormal peak when reducing the temperature, which differs from the reported prediction for 55-atom Alrich-Cu nanoliquids. The diffusivities of Al and Cu undergo an increasing deviation from Arrhenius behavior by tuning Cu concentration from 7 to 30 atomic percentages, correlated to the local ordering in these liquids by means of coordination number, bond-angle distribution, Honeycutt-Andersen index, bond-orientational order and Voronoi tessellation analyses. Upon cooling, the microstructure of the liquid Alrich-Cu alloys inclines to form Al2Cu crystal-like local atomic ordering, especially in the hypereutectic liquids. The favorable short-range ordering between Cu and Al atoms could cause the non-Arrhenius diffusion behavior.
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Affiliation(s)
- L H Xiong
- International Center for New-Structured Materials (ICNSM), Laboratory of New-Structured Materials, State Key Laboratory of Silicon Materials, and School of Materials Science and Engineering, Zhejiang University, Hangzhou 310027, People's Republic of China
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26
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Korchagina K, Simon A, Rapacioli M, Spiegelman F, L’Hermite JM, Braud I, Zamith S, Cuny J. Theoretical investigation of the solid–liquid phase transition in protonated water clusters. Phys Chem Chem Phys 2017; 19:27288-27298. [DOI: 10.1039/c7cp04863g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular dynamics simulations provide an atomistic scale description of the phase transition in protonated water clusters (H2O)nH+(n= 20–23) and an interpretation to recent nano-calorimetric experiments.
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Affiliation(s)
- Kseniia Korchagina
- Laboratoire de Chimie et Physique Quantiques (LCPQ/IRSAMC)
- Université de Toulouse and CNRS
- F-31062 Toulouse
- France
| | - Aude Simon
- Laboratoire de Chimie et Physique Quantiques (LCPQ/IRSAMC)
- Université de Toulouse and CNRS
- F-31062 Toulouse
- France
| | - Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantiques (LCPQ/IRSAMC)
- Université de Toulouse and CNRS
- F-31062 Toulouse
- France
| | - Fernand Spiegelman
- Laboratoire de Chimie et Physique Quantiques (LCPQ/IRSAMC)
- Université de Toulouse and CNRS
- F-31062 Toulouse
- France
| | - Jean-Marc L’Hermite
- Laboratoire Collisions Agrégats Réactivité (LCAR/IRSAMC)
- Université de Toulouse and CNRS
- F-31062 Toulouse
- France
| | - Isabelle Braud
- Laboratoire Collisions Agrégats Réactivité (LCAR/IRSAMC)
- Université de Toulouse and CNRS
- F-31062 Toulouse
- France
| | - Sébastien Zamith
- Laboratoire Collisions Agrégats Réactivité (LCAR/IRSAMC)
- Université de Toulouse and CNRS
- F-31062 Toulouse
- France
| | - Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques (LCPQ/IRSAMC)
- Université de Toulouse and CNRS
- F-31062 Toulouse
- France
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27
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Hernández-Rojas J, Calvo F, Niblett S, Wales DJ. Dynamics and thermodynamics of the coronene octamer described by coarse-grained potentials. Phys Chem Chem Phys 2017; 19:1884-1895. [DOI: 10.1039/c6cp07671h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coarse-grained models developed for polycyclic aromatic hydrocarbons based on the Paramonov–Yaliraki potential have been employed to investigate the finite temperature thermodynamics, out-of-equilibrium dynamics, energy landscapes, and rearrangement pathways of the coronene octamer.
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Affiliation(s)
| | - F. Calvo
- Laboratoire Interdisciplinaire de Physique
- Université Grenoble Alpes and CNRS
- 38402 St Martin d’Hères
- France
| | - S. Niblett
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
| | - D. J. Wales
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
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28
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Jellinek J, Aleinikava D. Anharmonic densities of states: A general dynamics-based solution. J Chem Phys 2016; 144:214103. [PMID: 27276941 DOI: 10.1063/1.4951695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Density of states is a fundamental physical characteristic that lies at the foundation of statistical mechanics and theoretical constructs that derive from them (e.g., kinetic rate theories, phase diagrams, and others). Even though most real physical systems are anharmonic, the vibrational density of states is customarily treated within the harmonic approximation, or with some partial, often limited, account for anharmonicity. The reason for this is that the problem of anharmonic densities of states stubbornly resisted a general and exact, yet convenient and straightforward in applications, solution. Here we formulate such a solution within both classical and quantum mechanics. It is based on actual dynamical behavior of systems as a function of energy and as observed, or monitored, on a chosen time scale, short or long. As a consequence, the resulting anharmonic densities of states are fully dynamically informed and, in general, time-dependent. As such, they lay the ground for formulation of new statistical mechanical frameworks that incorporate time and are ergodic, by construction, with respect to actual dynamical behavior of systems.
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Affiliation(s)
- Julius Jellinek
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Darya Aleinikava
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
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29
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de Sousa N, Sáenz JJ, Scheffold F, García-Martín A, Froufe-Pérez LS. Self-diffusion and structural properties of confined fluids in dynamic coexistence. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:135101. [PMID: 26940756 DOI: 10.1088/0953-8984/28/13/135101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Self-diffusion and radial distribution functions are studied in a strongly confined Lennard-Jones fluid. Surprisingly, in the solid-liquid phase transition region, where the system exhibits dynamic coexistence, the self-diffusion constants are shown to present up to three-fold variations from solid to liquid phases at fixed temperature, while the radial distribution function corresponding to both the liquid and the solid phases are essentially indistinguishable.
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Affiliation(s)
- N de Sousa
- Departamento de Física de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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30
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Steenbergen KG, Gaston N. A Two-Dimensional Liquid Structure Explains the Elevated Melting Temperatures of Gallium Nanoclusters. NANO LETTERS 2016; 16:21-6. [PMID: 26624938 DOI: 10.1021/acs.nanolett.5b02158] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Melting in finite-sized materials differs in two ways from the solid-liquid phase transition in bulk systems. First, there is an inherent scaling of the melting temperature below that of the bulk, known as melting point depression. Second, at small sizes changes in melting temperature become nonmonotonic and show a size-dependence that is sensitive to the structure of the particle. Melting temperatures that exceed those of the bulk material have been shown to occur for a very limited range of nanoclusters, including gallium, but have still never been ascribed a convincing physical explanation. Here, we analyze the structure of the liquid phase in gallium clusters based on molecular dynamics simulations that reproduce the greater-than-bulk melting behavior observed in experiments. We observe persistent nonspherical shape distortion indicating a stabilization of the surface, which invalidates the paradigm of melting point depression. This shape distortion suggests that the surface acts as a constraint on the liquid state that lowers its entropy relative to that of the bulk liquid and thus raises the melting temperature.
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Affiliation(s)
- Krista G Steenbergen
- Centre for Theoretical Chemistry and Physics, New Zealand Institute for Advanced Study, Massey University , Auckland Campus, Private Bag 102904, North Shore City, 0745 Auckland New Zealand
- Department of Chemistry, University of Kansas , Lawrence, Kansas 66045, United States
| | - Nicola Gaston
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington , P.O. Box 600, 6140 Wellington, New Zealand
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31
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Oliveira LFL, Cuny J, Morinière M, Dontot L, Simon A, Spiegelman F, Rapacioli M. Phase changes of the water hexamer and octamer in the gas phase and adsorbed on polycyclic aromatic hydrocarbons. Phys Chem Chem Phys 2015; 17:17079-89. [PMID: 26067775 DOI: 10.1039/c5cp02099a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate thermodynamic properties of small water clusters adsorbed on polycyclic aromatic hydrocarbons (PAHs), which are relevant systems in the context of astrophysical and atmospheric chemistry. We present heat capacity curves computed from parallel-tempering molecular dynamics and Monte Carlo simulations that were performed using the self-consistent-charge density-functional based tight-binding method. These curves are characteristic of the phase changes occurring in the aggregates and provide useful information on the evolution of the interaction between the water molecules and the PAHs as a function of temperature. After benchmarking our approach on the water hexamer and octamer in the gas phase, we present some results for these same clusters adsorbed on coronene and circumcoronene. When compared to the curves obtained for the isolated water clusters, the phase change temperature significantly decreases for the (H2O)8-PAH clusters whereas it depends on the nature of the PAH in the case of the hexamer. We analyse these differences as connected to the relative energies of the optimized characteristic isomers and to their dynamical behavior. We also evidence the population changes of the various cluster isomers as a function of temperature.
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Affiliation(s)
- Luiz Fernando L Oliveira
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
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32
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Somani S, Okamoto Y, Ballard AJ, Wales DJ. Equilibrium molecular thermodynamics from Kirkwood sampling. J Phys Chem B 2015; 119:6155-69. [PMID: 25915525 PMCID: PMC4500650 DOI: 10.1021/acs.jpcb.5b01800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
We
present two methods for barrierless equilibrium sampling of
molecular systems based on the recently proposed Kirkwood method (J. Chem. Phys.2009, 130,
134102). Kirkwood sampling employs low-order correlations among internal
coordinates of a molecule for random (or non-Markovian) sampling of
the high dimensional conformational space. This is a geometrical sampling
method independent of the potential energy surface. The first method
is a variant of biased Monte Carlo, where Kirkwood sampling is used
for generating trial Monte Carlo moves. Using this method, equilibrium
distributions corresponding to different temperatures and potential
energy functions can be generated from a given set of low-order correlations.
Since Kirkwood samples are generated independently, this method is
ideally suited for massively parallel distributed computing. The second
approach is a variant of reservoir replica exchange, where Kirkwood
sampling is used to construct a reservoir of conformations, which
exchanges conformations with the replicas performing equilibrium sampling
corresponding to different thermodynamic states. Coupling with the
Kirkwood reservoir enhances sampling by facilitating global jumps
in the conformational space. The efficiency of both methods depends
on the overlap of the Kirkwood distribution with the target equilibrium
distribution. We present proof-of-concept results for a model nine-atom
linear molecule and alanine dipeptide.
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Affiliation(s)
- Sandeep Somani
- †University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Yuko Okamoto
- ‡Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.,§Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.,∥Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya, Aichi 464-8603, Japan.,⊥Information Technology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Andrew J Ballard
- †University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - David J Wales
- †University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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33
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Hewage JW. The study of dynamics and phase transitions of small Ag/Pd motifs using molecular dynamics and histogram methods. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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34
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Oka Y, Yanao T, Koon WS. Roles of dynamical symmetry breaking in driving oblate-prolate transitions of atomic clusters. J Chem Phys 2015; 142:134105. [PMID: 25854226 DOI: 10.1063/1.4915928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This paper explores the driving mechanisms for structural transitions of atomic clusters between oblate and prolate isomers. We employ the hyperspherical coordinates to investigate structural dynamics of a seven-atom cluster at a coarse-grained level in terms of the dynamics of three gyration radii and three principal axes, which characterize overall mass distributions of the cluster. Dynamics of gyration radii is governed by two kinds of forces. One is the potential force originating from the interactions between atoms. The other is the dynamical forces called the internal centrifugal forces, which originate from twisting and shearing motions of the system. The internal centrifugal force arising from twisting motions has an effect of breaking the symmetry between two gyration radii. As a result, in an oblate isomer, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two largest gyration radii is crucial in triggering structural transitions into prolate isomers. In a prolate isomer, on the other hand, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two smallest gyration radii is crucial in triggering structural transitions into oblate isomers. Activation of a twisting motion that switches the movement patterns of three principal axes is also important for the onset of structural transitions between oblate and prolate isomers. Based on these trigger mechanisms, we finally show that selective activations of specific gyration radii and twisting motions, depending on the isomer of the cluster, can effectively induce structural transitions of the cluster. The results presented here could provide further insights into the control of molecular reactions.
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Affiliation(s)
- Yurie Oka
- Department of Applied Mechanics and Aerospace Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Tomohiro Yanao
- Department of Applied Mechanics and Aerospace Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Wang Sang Koon
- Control and Dynamical Systems, California Institute of Technology, Pasadena, California 91125, USA
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35
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Wales DJ. Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape. J Chem Phys 2015; 142:130901. [DOI: 10.1063/1.4916307] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- D. J. Wales
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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36
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Abstract
This article reviews recent advances in our understanding of how temperature affects the structure and the phase of multimetallic nanoparticles. Focusing on bimetallic systems, we discuss the interplay of size, shape and chemical order on the stable configurations at thermal equilibrium. Besides some considerations about experimental evidence for thermally-induced transformations, most insight is generally gained from theory and computation. The perspectives offered by mesoscopic approaches (i.e. corrected from the bulk) and atomistic simulations complement each other and often provide detailed information about the respective roles of coordination, composition and more generally surface effects to be evaluated. Order-disorder transitions and the melting phase change are strongly altered in nanoscale systems, and we describe how they possibly impact entire phase diagrams.
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Affiliation(s)
- Florent Calvo
- Laboratoire Interdisciplinaire de Physique, Rue de La Piscine, Campus Saint Martin d'Hres, 38000 Grenoble, France. florent.calvo@ujfgrenoble
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37
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Xiong LH, Yoo H, Lou HB, Wang XD, Cao QP, Zhang DX, Jiang JZ, Xie HL, Xiao TQ, Jeon S, Lee GW. Evolution of atomic structure in Al75Cu25 liquid from experimental and ab initio molecular dynamics simulation studies. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:035102. [PMID: 25524926 DOI: 10.1088/0953-8984/27/3/035102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
X-ray diffraction and electrostatic levitation measurements, together with the ab initio molecular dynamics simulation of liquid Al(75)Cu(25) alloy have been performed from 800 to 1600 K. Experimental and ab initio molecular dynamics simulation results match well with each other. No abnormal changes were experimentally detected in the specific heat capacity over total hemispheric emissivity and density curves in the studied temperature range for a bulk liquid Al(75)Cu(25) alloy measured by the electrostatic levitation technique. The structure factors gained by the ab initio molecular dynamics simulation precisely coincide with the experimental data. The atomic structure analyzed by the Honeycutt-Andersen index and Voronoi tessellation methods shows that icosahedral-like atomic clusters prevail in the liquid Al(75)Cu(25) alloy and the atomic clusters evolve continuously. All results obtained here suggest that no liquid-liquid transition appears in the bulk liquid Al(75)Cu(25) alloy in the studied temperature range.
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Affiliation(s)
- L H Xiong
- International Center for New-Structured Materials (ICNSM), Laboratory of New-Structured Materials, State Key Laboratory of Silicon Materials, Zhejiang University, Hangzhou 310027, People's Republic of China. Department of Materials Science and Engineering, Zhejiang University, Hangzhou 310027, People's Republic of China
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Berthier F, Maras E, Legrand B. Phase diagrams of nanoalloys: influence of size and morphology. Phys Chem Chem Phys 2015; 17:28347-53. [DOI: 10.1039/c5cp01593f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A non-monotonous variation of the critical temperature as a function of the length of the nanotubes.
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Affiliation(s)
- F. Berthier
- CNRS
- F91405 Orsay Cedex
- France
- SP2M/ICMMO
- Univ. Paris Sud
| | - E. Maras
- SP2M/ICMMO
- Univ. Paris Sud
- F91405 Orsay Cedex
- France
- Department of Applied Physics and COMP CoE
| | - B. Legrand
- CEA
- DEN
- Service de Recherches de Métallurgie Physique
- F91191 Gif-sur-Yvette Cedex
- France
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39
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Ojha U, Steenbergen KG, Gaston N. Al20+ does melt, albeit above the bulk melting temperature of aluminium. Phys Chem Chem Phys 2015; 17:3741-8. [DOI: 10.1039/c4cp05143b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Employing first principles parallel tempering molecular dynamics in the microcanonical ensemble, we report the presence of a clear solid–liquid-like melting transition in Al20+ clusters, not found in experiments.
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Affiliation(s)
- Udbhav Ojha
- The MacDiarmid Institute for Advanced Materials and Nanotechnology
- Victoria University of Wellington
- Wellington 6012
- New Zealand
| | | | - Nicola Gaston
- The MacDiarmid Institute for Advanced Materials and Nanotechnology
- Victoria University of Wellington
- Wellington 6012
- New Zealand
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40
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Steenbergen KG, Gaston N. Quantum Size Effects in the Size-Temperature Phase Diagram of Gallium: Structural Characterization of Shape-Shifting Clusters. Chemistry 2014; 21:2862-9. [DOI: 10.1002/chem.201405718] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Indexed: 11/12/2022]
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41
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Asgari M, Behnejad H, Fortunelli A. Composition-dependent melting behaviour of Na xK 55–xcore–shell nanoalloys. Mol Phys 2014. [DOI: 10.1080/00268976.2014.919039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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42
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Calvo F, Yurtsever E. Evidence for broken ergodicity due to chemical alloying from the dissociation kinetics of binary clusters. J Chem Phys 2014; 140:214301. [DOI: 10.1063/1.4880277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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43
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Abstract
Reconciling or somehow linking the macroscopic and microscopic approaches to chemical and physical processes has been a challenge unaddressed for many years. One approach, presented here, treats the issue by examining individual phenomena well described by a macro approach that fails when applied to small systems. The key to the approach is determining the approximate system size below which the breakdown of the macro description is observable. The most developed example is the failure of the Gibbs phase rule for sufficiently small atomic clusters. Other examples, such as the onset, at sufficient size, of the insulator-to-metal transition, are discussed, as are some still more challenging phenomena.
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Affiliation(s)
- R Stephen Berry
- The University of Chicago, 929 East 57th Street, Chicago, Illinois, USA.
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45
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Santamaría-Holek I, Pérez-Madrid A. Thermostatistical description of small systems in nonequilibrium conditions: energy conversion and harvesting. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:012144. [PMID: 24580209 DOI: 10.1103/physreve.89.012144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Indexed: 06/03/2023]
Abstract
Hysteresis cycles are very important features of energy conversion and harvesting devices, such as batteries. The efficiency of these may be strongly affected by the physical size of the system. Here, we show that in systems which are small enough, the existence of physical boundaries which produce nonhomogeneities of the interaction potential gives rise to inflections and barriers in the associated free energy. This in turn brings on irreversible processes which can be triggered under suitable external conditions imposed by a heat bath. As an example, by controlling the temperature, the state of a small system may be impelled to oscillate between two different structural configurations or aggregation states avoiding equilibrium coexistence and therefore dissipating energy. This cyclical behavior associated with a hysteresis cycle may be prototypical of energy conversion, storage, or generating nanodevices, as exemplified by Li-ion insertion batteries.
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Affiliation(s)
- I Santamaría-Holek
- UMDIJ-Facultad de Ciencias, Universidad Nacional Autónoma de México Campus Juriquilla, Querétaro 76230, México
| | - A Pérez-Madrid
- Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, Marti i Franques 1, 08028 Barcelona, Spain
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46
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Abstract
This article presents a perspective on thermodynamic characterization of metal nanoparticles by computational chemistry. Topics emphasized include structural stability, phases, phase changes, and free energy functions of aluminum nanoparticles.
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Affiliation(s)
- Zhen Hua Li
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials
- Fudan University
- Shanghai 200433, China
| | - Donald G. Truhlar
- Department of Chemistry
- Chemical Theory Center, and Supercomputing Institute
- University of Minnesota
- Minneapolis, USA
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47
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Dubbeldam D, Torres-Knoop A, Walton KS. On the inner workings of Monte Carlo codes. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.819102] [Citation(s) in RCA: 202] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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48
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Jenkins R, Curotto E, Mella M. Replica exchange with Smart Monte Carlo and Hybrid Monte Carlo in manifolds. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.10.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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49
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Wales DJ. Surveying a complex potential energy landscape: Overcoming broken ergodicity using basin-sampling. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.07.066] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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50
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Somani S, Wales DJ. Energy landscapes and global thermodynamics for alanine peptides. J Chem Phys 2013; 139:121909. [DOI: 10.1063/1.4813627] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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