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Nicy, Morgan JWR, Wales DJ. Energy landscapes for clusters of hexapeptides. J Chem Phys 2024; 161:054112. [PMID: 39092941 DOI: 10.1063/5.0220652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024] Open
Abstract
We present the results for energy landscapes of hexapeptides obtained using interfaces to the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) program. We have used basin-hopping global optimization and discrete path sampling to explore the landscapes of hexapeptide monomers, dimers, and oligomers containing 10, 100, and 200 monomers modeled using a residue-level coarse-grained potential, Mpipi, implemented in LAMMPS. We find that the dimers of peptides containing amino acid residues that are better at promoting phase separation, such as tyrosine and arginine, have melting peaks at higher temperature in their heat capacity compared to phenylalanine and lysine, respectively. This observation correlates with previous work on the same uncapped hexapeptide monomers modeled using atomistic potential. For oligomers, we compare the variation in monomer conformations with radial distance and observe trends for selected angles calculated for each monomer. The LAMMPS interfaces to the GMIN and OPTIM programs for landscape exploration offer new opportunities to investigate larger systems and provide access to the coarse-grained potentials implemented within LAMMPS.
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Affiliation(s)
- Nicy
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - John W R Morgan
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - David J Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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2
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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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Liu L, Wang S. An improved immune algorithm with parallel mutation and its application. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:12211-12239. [PMID: 37501440 DOI: 10.3934/mbe.2023544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The objective of this paper is to design a fast and efficient immune algorithm for solving various optimization problems. The immune algorithm (IA), which simulates the principle of the biological immune system, is one of the nature-inspired algorithms and its many advantages have been revealed. Although IA has shown its superiority over the traditional algorithms in many fields, it still suffers from the drawbacks of slow convergence and local minima trapping problems due to its inherent stochastic search property. Many efforts have been done to improve the search performance of immune algorithms, such as adaptive parameter setting and population diversity maintenance. In this paper, an improved immune algorithm (IIA) which utilizes a parallel mutation mechanism (PM) is proposed to solve the Lennard-Jones potential problem (LJPP). In IIA, three distinct mutation operators involving cauchy mutation (CM), gaussian mutation (GM) and lateral mutation (LM) are conditionally selected to be implemented. It is expected that IIA can effectively balance the exploration and exploitation of the search and thus speed up the convergence. To illustrate its validity, IIA is tested on a two-dimension function and some benchmark functions. Then IIA is applied to solve the LJPP to exhibit its applicability to the real-world problems. Experimental results demonstrate the effectiveness of IIA in terms of the convergence speed and the solution quality.
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Affiliation(s)
- Lulu Liu
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Shuaiqun Wang
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
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de Mendonça JPA, Calderan FV, Lourenço TC, Quiles MG, Da Silva JLF. Theoretical Framework Based on Molecular Dynamics and Data Mining Analyses for the Study of Potential Energy Surfaces of Finite-Size Particles. J Chem Inf Model 2022; 62:5503-5512. [DOI: 10.1021/acs.jcim.2c00957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- João Paulo A. de Mendonça
- São Carlos Institute of Chemistry, University of São Paulo, P.O. Box 780, 13560-970 São Carlos, São Paulo, Brazil
| | - Felipe V. Calderan
- Institute of Science and Technology, Federal University of São Paulo, 01016 020 São José dos Campos, São Paulo, Brazil
| | - Tuanan C. Lourenço
- São Carlos Institute of Chemistry, University of São Paulo, P.O. Box 780, 13560-970 São Carlos, São Paulo, Brazil
| | - Marcos G. Quiles
- Institute of Science and Technology, Federal University of São Paulo, 01016 020 São José dos Campos, São Paulo, Brazil
| | - Juarez L. F. Da Silva
- São Carlos Institute of Chemistry, University of São Paulo, P.O. Box 780, 13560-970 São Carlos, São Paulo, Brazil
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Abdollahzadeh B, Soleimanian Gharehchopogh F, Mirjalili S. Artificial gorilla troops optimizer: A new nature‐inspired metaheuristic algorithm for global optimization problems. INT J INTELL SYST 2021. [DOI: 10.1002/int.22535] [Citation(s) in RCA: 155] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Seyedali Mirjalili
- Centre for Artificial Intelligence Research and Optimisation Torrens University Australia Fortitude Valley Brisbane Queensland Australia
- YFL (Yonsei Frontier Lab) Yonsei University Seoul Korea
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6
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Morgan JWR, Glotzer SC. The alchemical energy landscape for a pentameric cluster. J Chem Phys 2020; 152:014106. [DOI: 10.1063/1.5130030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- John W. R. Morgan
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Sharon C. Glotzer
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
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7
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A comprehensive study of phase based optimization algorithm on global optimization problems and its applications. APPL INTELL 2018. [DOI: 10.1007/s10489-018-1306-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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8
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Soley MB, Markmann A, Batista VS. Classical Optimal Control for Energy Minimization Based On Diffeomorphic Modulation under Observable-Response-Preserving Homotopy. J Chem Theory Comput 2018; 14:3351-3362. [DOI: 10.1021/acs.jctc.8b00124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Micheline B. Soley
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
- Energy Sciences Institute, Yale University, P.O.
Box 27394, West Haven, Connecticut 06516-7394, United States
| | - Andreas Markmann
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
- Energy Sciences Institute, Yale University, P.O.
Box 27394, West Haven, Connecticut 06516-7394, United States
| | - Victor S. Batista
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
- Energy Sciences Institute, Yale University, P.O.
Box 27394, West Haven, Connecticut 06516-7394, United States
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Abstract
The complex conformational change from B-DNA to Z-DNA requires inversion of helix-handedness. Multiple degrees of freedom are intricately coupled during this transition, and formulating an appropriate reaction coordinate that captures the underlying complexity would be problematic. In this contribution, we adopt an alternative approach, based on the potential energy landscape perspective, to construct a kinetic transition network. Microscopic insight into the B → Z transition is provided in terms of geometrically defined discrete paths consisting of local minima and the transition states that connect them. We find that the inversion of handedness can occur via two competing mechanisms, either involving stretched intermediates, or a B-Z junction, in agreement with previous predictions. The organisation of the free energy landscape further suggests that this process is likely to be slow under physiological conditions. Our results represent a key step towards decoding the more intriguing features of the B → Z transition, such as the role of ionic strength and negative supercoiling in reshaping the landscape.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, UK.
| | - David J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, UK.
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Renzler M, Kuhn M, Mauracher A, Lindinger A, Scheier P, Ellis AM. Anionic Hydrogen Cluster Ions as a New Form of Condensed Hydrogen. PHYSICAL REVIEW LETTERS 2016; 117:273001. [PMID: 28084770 DOI: 10.1103/physrevlett.117.273001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Indexed: 06/06/2023]
Abstract
We report the first experimental observation of negatively charged hydrogen and deuterium cluster ions, H_{n}^{-} and D_{n}^{-}, where n≥5. These anions are formed by an electron addition to liquid helium nanodroplets doped with molecular hydrogen or deuterium. The ions are stable for at least the lifetime of the experiment, which is several tens of microseconds. Only anions with odd values of n are detected, and some specific ions show anomalously high abundances. The sizes of these "magic number" ions suggest an icosahedral framework of H_{2} (D_{2}) molecules in solvent shells around a central H^{-} (D^{-}) ion. The first three shells, which contain a total of 44 H_{2} or D_{2} molecules, appear to be solidlike, but thereafter a more liquidlike arrangement of the H_{2} (D_{2}) molecules is adopted.
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Affiliation(s)
- Michael Renzler
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - Martin Kuhn
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - Andreas Mauracher
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - Albrecht Lindinger
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Paul Scheier
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - Andrew M Ellis
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
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11
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Erickson JD, Mednikov EG, Ivanov SA, Dahl LF. Isolation and Structural Characterization of a Mackay 55-Metal-Atom Two-Shell Icosahedron of Pseudo-Ih Symmetry, Pd55L12(μ3-CO)20 (L = PR3, R = Isopropyl): Comparative Analysis with Interior Two-Shell Icosahedral Geometries in Capped Three-Shell Pd145, Pt-Centered Four-Shell Pd–Pt M165, and Four-Shell Au133 Nanoclusters. J Am Chem Soc 2016; 138:1502-5. [DOI: 10.1021/jacs.5b13076] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jeremiah D. Erickson
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Evgueni G. Mednikov
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Sergei A. Ivanov
- Center
for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Lawrence F. Dahl
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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12
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Morgan JWR, Wales DJ. Energy landscapes of planar colloidal clusters. NANOSCALE 2014; 6:10717-10726. [PMID: 25095731 PMCID: PMC4263186 DOI: 10.1039/c4nr02670e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 07/15/2014] [Indexed: 06/03/2023]
Abstract
A short-ranged pairwise Morse potential is used to model colloidal clusters with planar morphologies. Potential and free energy global minima as well as rearrangement paths, obtained by basin-hopping global optimisation and discrete path sampling, are characterised. The potential and free energy landscapes are visualised using disconnectivity graphs. The short-ranged potential is found to favour close-packed structures, with the potential energy primarily controlled by the number of nearest neighbour contacts. In the case of quasi-degeneracy the free energy global minimum may differ from the potential energy global minimum. This difference is due to symmetry effects, which result in a higher entropy for structures with lower symmetry.
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Affiliation(s)
- John W. R. Morgan
- University Chemical Laboratories , Lensfield Road , Cambridge CB2 1EW , UK
| | - David J. Wales
- University Chemical Laboratories , Lensfield Road , Cambridge CB2 1EW , UK .
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13
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Dryzun C. Continuous symmetry measures for complex symmetry group. J Comput Chem 2014; 35:748-55. [PMID: 24590424 DOI: 10.1002/jcc.23548] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 12/29/2013] [Accepted: 01/02/2014] [Indexed: 12/14/2022]
Abstract
Symmetry is a fundamental property of nature, used extensively in physics, chemistry, and biology. The Continuous symmetry measures (CSM) is a method for estimating the deviation of a given system from having a certain perfect symmetry, which enables us to formulate quantitative relation between symmetry and other physical properties. Analytical procedures for calculating the CSM of all simple cyclic point groups are available for several years. Here, we present a methodology for calculating the CSM of any complex point group, including the dihedral, tetrahedral, octahedral, and icosahedral symmetry groups. We present the method and analyze its performances and errors. We also introduce an analytical method for calculating the CSM of the linear symmetry groups. As an example, we apply these methods for examining the symmetry of water, the symmetry maps of AB4 complexes, and the symmetry of several Lennard-Jones clusters.
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Affiliation(s)
- Chaim Dryzun
- Department of Natural Sciences, The Open University of Israel, Raanana, 43107, Israel
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14
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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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15
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16
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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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17
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Rogan J, Varas A, Valdivia JA, Kiwi M. A strategy to find minimal energy nanocluster structures. J Comput Chem 2013; 34:2548-56. [PMID: 24037778 DOI: 10.1002/jcc.23419] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 07/25/2013] [Accepted: 08/04/2013] [Indexed: 12/19/2022]
Abstract
An unbiased strategy to search for the global and local minimal energy structures of free standing nanoclusters is presented. Our objectives are twofold: to find a diverse set of low lying local minima, as well as the global minimum. To do so, we use massively the fast inertial relaxation engine algorithm as an efficient local minimizer. This procedure turns out to be quite efficient to reach the global minimum, and also most of the local minima. We test the method with the Lennard-Jones (LJ) potential, for which an abundant literature does exist, and obtain novel results, which include a new local minimum for LJ13 , 10 new local minima for LJ14 , and thousands of new local minima for 15≤N≤65. Insights on how to choose the initial configurations, analyzing the effectiveness of the method in reaching low-energy structures, including the global minimum, are developed as a function of the number of atoms of the cluster. Also, a novel characterization of the potential energy surface, analyzing properties of the local minima basins, is provided. The procedure constitutes a promising tool to generate a diverse set of cluster conformations, both two- and three-dimensional, that can be used as an input for refinement by means of ab initio methods.
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Affiliation(s)
- José Rogan
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile 7800024, and Centro para el Desarrollo de la Nanociencia y la Nanotecnología (CEDENNA), Avda., Ecuador 3493, Santiago, Chile, 9170124
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18
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Abdechiri M, Meybodi MR, Bahrami H. Gases Brownian Motion Optimization: an Algorithm for Optimization (GBMO). Appl Soft Comput 2013. [DOI: 10.1016/j.asoc.2012.03.068] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Khan SJ, Weaver OL, Sorensen CM, Chakrabarti A. Nucleation in short-range attractive colloids: ordering and symmetry of clusters. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:16015-16021. [PMID: 23072652 DOI: 10.1021/la303894s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Results from extensive Brownian dynamics simulations are presented for nucleation in a system of colloidal particles interacting via a short-range attractive potential. Our analysis shows that, even though the system is not in equilibrium, structures of small size clusters compare well with the theoretically predicted and experimentally observed ground state structures for short-range colloidal systems. In addition, the distribution of the symmetric structures in nucleation is comparable to the distribution seen in equilibrium. We also investigate how the shape and structure of fluctuating clusters in the prenucleation regime affect the formation of a stable nucleating cluster.
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Affiliation(s)
- Siddique J Khan
- Department of Physics, Kansas State University, Manhattan, Kansas 66503, United States
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21
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Müller CL, Sbalzarini IF. Energy landscapes of atomic clusters as black box optimization benchmarks. EVOLUTIONARY COMPUTATION 2012; 20:543-573. [PMID: 22779442 DOI: 10.1162/evco_a_00086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We present the energy minimization of atomic clusters as a promising problem class for continuous black box optimization benchmarks. Finding the arrangement of atoms that minimizes a given potential energy is a specific instance of the more general class of geometry optimization or packing problems, which are generally NP-complete. Atomic clusters are a well-studied subject in physics and chemistry. From the large set of available cluster optimization problems, we propose two specific instances: Cohn-Kumar clusters and Lennard-Jones clusters. The potential energies of these clusters are governed by distance-dependent pairwise interaction potentials. The resulting collection of landscapes is composed of smooth and rugged single-funnel topologies, as well as tunable double-funnel topologies. In addition, all problems possess a feature that is not covered by the synthetic functions in current black box optimization test suites: isospectral symmetry. This property implies that any atomic arrangement is uniquely defined by the pairwise distance spectrum, rather than the absolute atomic positions. We hence suggest that the presented problem instances should be included in black box optimization benchmark suites.
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Affiliation(s)
- C L Müller
- MOSAIC Group, Institute of Theoretical Computer Science and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, 8092, Switzerland.
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Wales DJ. Decoding the energy landscape: extracting structure, dynamics and thermodynamics. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2012; 370:2877-2899. [PMID: 22615466 DOI: 10.1098/rsta.2011.0208] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Describing a potential energy surface in terms of local minima and the transition states that connect them provides a conceptual and computational framework for understanding and predicting observable properties. Visualizing the potential energy landscape using disconnectivity graphs supplies a graphical connection between different structure-seeking systems, which can relax efficiently to a particular morphology. Landscapes involving competing morphologies support multiple potential energy funnels, which may exhibit characteristic heat capacity features and relaxation time scales. These connections between the organization of the potential energy landscape and structure, dynamics and thermodynamics are common to all the examples presented, ranging from atomic and molecular clusters to biomolecules and soft and condensed matter. Further connections between motifs in the energy landscape and the interparticle forces can be developed using symmetry considerations and results from catastrophe theory.
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Affiliation(s)
- David J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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23
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Singer SJ, Knight C. Hydrogen‐Bond Topology and Proton Ordering in Ice and Water Clusters. ADVANCES IN CHEMICAL PHYSICS 2011. [DOI: 10.1002/9781118135242.ch1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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24
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Mackay AL. What has the Penrose tiling to do with the icosahedral phases? Geometrical aspects of the icosahedral quasicrystal problem. J Microsc 2011. [DOI: 10.1111/j.1365-2818.1987.tb01347.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Rademann K. Photoionization Mass Spectrometry and Valence Photoelectron-Photoion Coincidence Spectroscopy of Isolated Clusters in a Molecular Beam. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19890930604] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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26
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Schemmel D, Schütz M. Molecular aniline clusters. I. The electronic ground state. J Chem Phys 2010; 132:174303. [DOI: 10.1063/1.3419505] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Echt O, Reyes Flotte A, Knapp M, Sattler K, Recknagel E. Magic Numbers in Mass Spectra of Xe, C2F4Cl2 and SF6 Clusters. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19820860919] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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30
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Polymeropoulos EE, Brickmann J. The Influence of Three-Body Forces on the Lifetime and Stability of Rare Gas Clusters. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19830871221] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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31
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Ferreira da Silva F, Waldburger P, Jaksch S, Mauracher A, Denifl S, Echt O, Märk TD, Scheier P. On the size of ions solvated in helium clusters. Chemistry 2009; 15:7101-8. [PMID: 19533729 DOI: 10.1002/chem.200802554] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Helium nanodroplets are doped with SF(6), C(4)F(8), CCl(4), C(6)H(5)Br, CH(3)I, and I(2). Upon interaction with free electrons a variety of positively and negatively charged cluster ions X(+/-)He(n) are observed where X(+/-) = F(+/-), Cl(+/-), Br(+/-), I(+), I(2) (+), or CH(3)I(+). The yield of these ions versus cluster size n drops at characteristic sizes n(s) that range from n(s) = 10.2+/-0.6 for F(+) to n(s) = 22.2+/-0.2 for Br(-). n(s) values for halide anions are about 70% larger than for the corresponding cations. The steps in the ion yield suggest closure of the first solvation shell. We propose a simple classical model to estimate ionic radii from n(s). Assuming the helium density in the first solvation shell equals the helium bulk density one finds that radii of halide anions in helium are nearly twice as large as in alkali halide crystals, indicating the formation of an anion bubble due to the repulsive forces that derive from the exchange interaction. In spite of the simplicity of our model, anion radii derived from it agree within approximately 10% with values derived from the mobility of halide anions in superfluid bulk helium, and with values computed by quantum Monte Carlo methods for X(-)He(n) cluster anions.
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Affiliation(s)
- Filipe Ferreira da Silva
- Institut für Ionenphysik und Angewandte Physik, Leopold Franzens Universität, Technikerstrasse 25, 6020 Innsbruck, Austria
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32
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Daldoss G, Pilla O, Viliani G. Search for tunnelling centres in Lennard-Jones clusters. ACTA ACUST UNITED AC 2009. [DOI: 10.1080/13642819808204996] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- G. Daldoss
- a Dipartimento di Fisica and Isituto Nazionale di Fisica della Materia , Università di Trento , 1-38050 , Povo, Trento , Italy
| | - O. Pilla
- a Dipartimento di Fisica and Isituto Nazionale di Fisica della Materia , Università di Trento , 1-38050 , Povo, Trento , Italy
| | - G. Viliani
- a Dipartimento di Fisica and Isituto Nazionale di Fisica della Materia , Università di Trento , 1-38050 , Povo, Trento , Italy
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Jaksch S, Mauracher A, Bacher A, Denifl S, da Silva FF, Schöbel H, Echt O, Märk TD, Probst M, Bohme DK, Scheier P. Formation of even-numbered hydrogen cluster cations in ultracold helium droplets. J Chem Phys 2009; 129:224306. [PMID: 19071915 DOI: 10.1063/1.3035833] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Neutral hydrogen clusters are grown in ultracold helium nanodroplets by successive pickup of hydrogen molecules. Even-numbered hydrogen cluster cations are observed upon electron-impact ionization with and without attached helium atoms and in addition to the familiar odd-numbered H(n)(+). The helium matrix affects the fragmentation dynamics that usually lead to the formation of overwhelmingly odd-numbered H(n)(+). The use of high-resolution mass spectrometry allows the unambiguous identification of even-numbered H(n)(+) up to n approximately = 120 by their mass excess that distinguishes them from He(n)(+), mixed He(m)H(n)(+), and background ions. The large range in size of these hydrogen cluster ions is unprecedented, as is the accuracy of their definition. Apart from the previously observed magic number n=6, pronounced drops in the abundance of even-numbered cluster ions are seen at n=30 and 114, which suggest icosahedral shell closures at H(6)(+)(H(2))(12) and H(6)(+)(H(2))(54). Possible isomers of H(6)(+) are identified at the quadratic configuration interaction with inclusion of single and double excitations (QCISD)/aug-cc-pVTZ level of theory.
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Affiliation(s)
- S Jaksch
- Institut für Ionenphysik und Angewandte Physik, Leopold Franzens Universität, Technikerstr. 25, A-6020 Innsbruck, Austria
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35
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Guardiola R, Navarro J. Excitation levels and magic numbers of small parahydrogen clusters (N<or=40). J Chem Phys 2008; 128:144303. [PMID: 18412441 DOI: 10.1063/1.2903462] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The excitation energies of parahydrogen clusters have been systematically calculated by the diffusion Monte Carlo technique in steps of 1 molecule from 3 to 40 molecules. These clusters possess a very rich spectra, with angular momentum excitations arriving up to L=13 for the heavier ones. No regular pattern can be guessed in terms of the angular momenta and the size of the cluster. Clusters with N=13 and 36 are characterized by a peak in the chemical potential and a large energy gap of the first excited level, which indicate the magical character of these clusters. From the calculated excitation energies, the partition function has been obtained, thus allowing for an estimate of thermal effects. An enhanced production is predicted for cluster sizes of N=13, 31, and 36, which is in agreement with the experiment.
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Affiliation(s)
- Rafael Guardiola
- Departamento de Física Atómica y Nuclear, Facultad de Física, 46100 Burjassot, Spain
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36
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Murakami H, Iwayama H, Nagaya K, Yao M. Fragmentation channels of K-shell excited rare-gas clusters studied by multiple-ion coincidence momentum imaging. J Chem Phys 2008; 128:054303. [PMID: 18266446 DOI: 10.1063/1.2827131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Multiple-ion coincidence momentum imaging experiments were carried out for K-shell (1s) excited Ar clusters containing about 130 atoms and Kr clusters containing about 30, 90, and 160 atoms. The time-of-flight spectra reveal that the major products of the Coulomb explosion are singly charged ions. With increasing the number of charges generated in clusters, the momentum of monomer ions such as Ar(+) and Kr(+) increases, while that of cluster ions such as Ar(3) (+), Kr(2) (+), and Kr(3) (+) decreases. This observation indicates the site-specific decay process that the heavier ions appear in the central part of clusters. We have also investigated the momentum distribution in various fragmentation channels and the branching ratio of each channel at the Coulomb explosion. When the number N(coin) of coincidently detected ions is four, for example, the most frequent channel from Kr clusters containing 30 atoms is to emit simply four Kr(+) ions, but Kr(2) (+) ions participate in the fragmentation from the larger Kr clusters. The fragmentation channel in which two Ar(2) (+) ions are emitted becomes dominant with increasing N(coin), and the average momentum of Ar(2) (+) ion in this channel is larger than that in the channels where only single Ar(2) (+) is emitted.
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Affiliation(s)
- H Murakami
- Department of Physics, Kyoto University, 606-8502 Kyoto, Japan.
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37
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Laarmann T, Wabnitz H, von Haeften K, Möller T. Photochemical processes in doped argon-neon core-shell clusters: The effect of cage size on the dissociation of molecular oxygen. J Chem Phys 2008; 128:014502. [DOI: 10.1063/1.2815798] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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38
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Carr JM, Wales DJ. Global optimization and folding pathways of selected alpha-helical proteins. J Chem Phys 2007; 123:234901. [PMID: 16392943 DOI: 10.1063/1.2135783] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The results of basin-hopping global optimization simulations are presented for four small, alpha-helical proteins described by a coarse-grained potential. A step-taking scheme that incorporates the local conformational preferences extracted from a large number of high-resolution protein structures is compared with an unbiased scheme. In addition, the discrete path sampling method is used to investigate the folding of one of the proteins, namely, the villin headpiece subdomain. Folding times from kinetic Monte Carlo simulations and iterative calculations based on a Markovian first-step analysis for the resulting stationary-point database are in good mutual agreement, but differ significantly from the experimental values, probably because the native state is not the global free energy minimum for the potential employed.
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Affiliation(s)
- Joanne M Carr
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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39
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40
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Stephen Berry R, Beck TL, Davis HL, Jellinek J. Solid-Liquid Phase Behavior in Microclusters. ADVANCES IN CHEMICAL PHYSICS 2007. [DOI: 10.1002/9780470122693.ch3] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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41
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Affiliation(s)
- N. Quirke
- a BP Research Centre , Chertsey Road, Sunbury on Thames , UK
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42
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Raoult B, Farges J, De Feraudy MF, Torchet G. Comparison between icosahedral, decahedral and crystalline Lennard-Jones models containing 500 to 6000 atoms. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/13642818908209749] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- B. Raoult
- a Laboratoire de Physique des Solides-LA2-Bǎtiment 510 , Université de Paris-Sud , 91405 , Orsay , France
| | - J. Farges
- a Laboratoire de Physique des Solides-LA2-Bǎtiment 510 , Université de Paris-Sud , 91405 , Orsay , France
| | - M. F. De Feraudy
- a Laboratoire de Physique des Solides-LA2-Bǎtiment 510 , Université de Paris-Sud , 91405 , Orsay , France
| | - G. Torchet
- a Laboratoire de Physique des Solides-LA2-Bǎtiment 510 , Université de Paris-Sud , 91405 , Orsay , France
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43
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Knight C, Singer SJ. A reexamination of the ice III/IX hydrogen bond ordering phase transition. J Chem Phys 2006; 125:64506. [PMID: 16942297 DOI: 10.1063/1.2209230] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ice III is a hydrogen bond disordered crystal which when cooled 1 K / min or faster transforms to an antiferroelectric hydrogen bond ordered structure, ice IX. Throughout its region of stability, experiments indicate that the H bonds in ice III are, in fact, partially ordered, i.e., some proton arrangements are preferred. In addition, there has been evidence that the structure of ice IX retains some residual disorder after the transition. Diffraction experiments and calorimetry apparently conflict with regard to the degree of ordering at the ice III/IX transition. Mean field statistical mechanical theories have been used to link partial occupations from diffraction data with thermodynamics. In this work, we investigate the ice III/IX proton ordering phase transition using electronic density functional theory calculations for small unit cells, extended to simulate the phase transition in a large unit cell using graph invariants. In agreement with experiment, we observe partial ordering over a wide range of temperatures as ice III transforms to partially disordered ice IX, near 126 K, which becomes fully ordered at lower temperatures. We compare our results from full statistical mechanical simulations with mean field models, finding small errors for the low-temperature ice IX phase and much larger errors for the high-temperature ice III phase. The failure of mean field theories may explain the apparent conflict between diffraction experiments and calorimetry.
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Affiliation(s)
- Chris Knight
- Department of Chemistry, Ohio State University, Columbus, Ohio 43210, USA
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44
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Lee E, Dyke J, Wilders A, Watts P. Ab initio calculation of relative ion concentrations of protonated water clusters at equilibrium. Mol Phys 2006. [DOI: 10.1080/00268979000101751] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- E.P.F. Lee
- a Department of Chemistry , Southampton University , Southampton , SO9 5NH , U.K
| | - J.M. Dyke
- a Department of Chemistry , Southampton University , Southampton , SO9 5NH , U.K
| | - A.E. Wilders
- b Chemical Defence Establishment , Ministry of Defence , Porton Down, Salisbury , Wilts , SP4 0JQ , U.K
| | - P. Watts
- b Chemical Defence Establishment , Ministry of Defence , Porton Down, Salisbury , Wilts , SP4 0JQ , U.K
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45
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Bogdan TV, Wales DJ, Calvo F. Equilibrium thermodynamics from basin-sampling. J Chem Phys 2006; 124:044102. [PMID: 16460144 DOI: 10.1063/1.2148958] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a "basin-sampling" approach for calculation of the potential energy density of states for classical statistical models. It combines a Wang-Landau-type uniform sampling of local minima and a novel approach for approximating the relative contributions from local minima in terms of the volumes of basins of attraction. We have employed basin-sampling to study phase changes in atomic clusters modeled by the Lennard-Jones potential and for ionic clusters. The approach proves to be efficient for systems involving broken ergodicity and has allowed us to calculate converged heat capacity curves for systems that could previously only be treated using the harmonic superposition approximation. Benchmarks are also provided by comparison with parallel tempering and Wang-Landau simulations, where these proved feasible.
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Affiliation(s)
- Tetyana V Bogdan
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, UK
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46
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47
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Ruckenstein E, Djikaev YS. Recent developments in the kinetic theory of nucleation. Adv Colloid Interface Sci 2005; 118:51-72. [PMID: 16137628 DOI: 10.1016/j.cis.2005.06.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2005] [Accepted: 06/22/2005] [Indexed: 11/17/2022]
Abstract
A review of recent progress in the kinetics of nucleation is presented. In the conventional approach to the kinetic theory of nucleation, it is necessary to know the free energy of formation of a new-phase particle as a function of its independent variables at least for near-critical particles. Thus the conventional kinetic theory of nucleation is based on the thermodynamics of the process. The thermodynamics of nucleation can be examined by using various approaches, such as the capillarity approximation, density functional theory, and molecular simulation, each of which has its own advantages and drawbacks. Relatively recently a new approach to the kinetics of nucleation was proposed [Ruckenstein E, Nowakowski B. J Colloid Interface Sci 1990;137:583; Nowakowski B, Ruckenstein E. J Chem Phys 1991;94:8487], which is based on molecular interactions and does not employ the traditional thermodynamics, thus avoiding such a controversial notion as the surface tension of tiny clusters involved in nucleation. In the new kinetic theory the rate of emission of molecules by a new-phase particle is determined with the help of a mean first passage time analysis. This time is calculated by solving the single-molecule master equation for the probability distribution function of a surface layer molecule moving in a potential field created by the rest of the cluster. The new theory was developed for both liquid-to-solid and vapor-to-liquid phase transitions. In the former case the single-molecule master equation is the Fokker-Planck equation in the phase space which can be reduced to the Smoluchowski equation owing to the hierarchy of characteristic time scales. In the latter case, the starting master equation is a Fokker-Planck equation for the probability distribution function of a surface layer molecule with respect to both its energy and phase coordinates. Unlike the case of liquid-to-solid nucleation, this Fokker-Planck equation cannot be reduced to the Smoluchowski equation, but the hierarchy of time scales does allow one to reduce it to the Fokker-Plank equation in the energy space. The new theory provides an equation for the critical radius of a new-phase particle which in the limit of large clusters (low supersaturations) yields the Kelvin equation and hence an expression for the macroscopic surface tension. The theory was illustrated with numerical calculations for a molecular pair interaction potential combining the dispersive attraction with the hard-sphere repulsion. The results for the liquid-to-solid nucleation clearly show that at given supersaturation the nucleation rate depends on the cluster structure (for three cluster structures considered-amorphous, fcc, and icosahedral). For both the liquid-to-solid and vapor-to-liquid nucleation, the predictions of the theory are consistent with the results of classical nucleation theory (CNT) in the limit of large critical clusters (low supersaturations). For small critical clusters the new theory provides higher nucleation rates than CNT. This can be accounted for by the fact that CNT uses the macroscopic interfacial tension which presumably overpredicts the surface tension of small clusters, and hence underpredicts nucleation rates.
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Affiliation(s)
- E Ruckenstein
- Department of Chemical and Biological Engineering, SUNY at Buffalo, Buffalo, NY 14260, USA.
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48
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Hatsui T, Setoyama H, Kosugi N, Wassermann B, Bradeanu IL, Rühl E. Photoionization of small krypton clusters in the Kr 3d regime: Evidence for site-specific photoemission. J Chem Phys 2005; 123:154304. [PMID: 16252945 DOI: 10.1063/1.2060709] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Kr 3d ionization energies of small, variable size krypton clusters are investigated by photoelectron spectroscopy, where the size regime of clusters with an average size N< or =30 is studied. Characteristic shifts in Kr 3d ionization energies to lower binding energies are found compared to the bare atom. These are also different from those of large krypton clusters. Moreover, we find evidence for photoionization of the krypton dimer. Its 3d ionization energy is barely shifted relative to the atomic value. Results from model calculations considering different isomers and cluster sizes as well as defect sites give evidence that the experimental results can be related to photoionization from different surface sites in variable size krypton clusters. This can be related to site-specific photoemission in small Kr clusters. The results are compared to size effects in Kr 3d near-edge features of variable size Kr clusters as well as recent results on Kr 3d photoionization of large Kr clusters.
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Affiliation(s)
- T Hatsui
- Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan
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49
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White RP, Cleary SM, Mayne HR. Phase changes in Lennard-Jones mixed clusters with composition ArnXe6−n (n=0,1,2). J Chem Phys 2005; 123:94505. [PMID: 16164351 DOI: 10.1063/1.2008260] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
We have carried out parallel tempering Monte Carlo calculations on the binary six-atom mixed Lennard-Jones clusters, Ar(n)Xe(6-n) (n=0,1,2). We have looked at the classical configurational heat capacity C(V)(T) as a probe of phase behavior. All three clusters show a feature in the heat capacity in the region of 15-20 K. The Ar(2)Xe(4) cluster exhibits a further peak in the heat capacity near 7 K. We have also investigated dynamical properties of the Ar(2)Xe(4) cluster as a function of temperature using molecular dynamics. We report the interbasin isomerization rate and the bond fluctuation parameter obtained from these calculations. At 7 K, the isomerization rate is on the order of 0.01 ns(-1); at 20 K, the isomerization rate is greater than 10 ns(-1). Furthermore, at 7 K, the bond fluctuation parameter is less than 3%; at 20 K, it is in the range of 10-15% (depending on the sampling time used). Using this information, together with Monte Carlo quenching data, we assign the 15-20 K feature in the heat capacity to a solid-liquid phase change and the 7-K peak to a solid-solid phase change. We believe this is the smallest Lennard-Jones cluster system yet shown to exhibit solid-solid phase change behavior.
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Affiliation(s)
- Ronald P White
- Department of Computational Biology, University of Pittsburgh School of Medicine, W1054 BST, Pittsburgh, Pennsylvania 15261, USA
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50
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Zhou T, Bai WJ, Cheng LJ, Wang BH. Continuous extremal optimization for Lennard-Jones clusters. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2005; 72:016702. [PMID: 16090129 DOI: 10.1103/physreve.72.016702] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2004] [Revised: 04/19/2005] [Indexed: 05/03/2023]
Abstract
We explore a general-purpose heuristic algorithm for finding high-quality solutions to continuous optimization problems. The method, called continuous extremal optimization (CEO), can be considered as an extension of extremal optimization and consists of two components, one which is responsible for global searching and the other which is responsible for local searching. The CEO's performance proves competitive with some more elaborate stochastic optimization procedures such as simulated annealing, genetic algorithms, and so on. We demonstrate it on a well-known continuous optimization problem: the Lennard-Jones cluster optimization problem.
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Affiliation(s)
- Tao Zhou
- Nonlinear Science Center and Department of Modern Physics, University of Science and Technology of China, Hefei Anhui, 230026, China
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