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Chekmarev SF. Extraction of kinetics from equilibrium distributions of states using the Metropolis Monte Carlo method. Phys Rev E 2022; 105:034407. [PMID: 35428044 DOI: 10.1103/physreve.105.034407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
The Metropolis Monte Carlo (MMC) method is used to extract reaction kinetics from a given equilibrium distribution of states of a complex system. The approach is illustrated by the folding/unfolding reaction for two proteins: a model β-hairpin and α-helical protein α_{3}D. For the β-hairpin, the free energy surfaces (FESs) and free energy profiles (FEPs) are employed as the equilibrium distributions of states, playing a role of the potentials of mean force to determine the acceptance probabilities of new states in the MMC simulations. Based on the FESs and PESs for a set of temperatures that were simulated with the molecular dynamics (MD) method, the MMC simulations are performed to extract folding/unfolding rates. It has been found that the rate constants and first-passage time (FPT) distributions obtained in the MMC simulations change with temperature in good agreement with those from the MD simulations. For α_{3}D protein, whose equilibrium folding/unfolding was studied with the single-molecule FRET method [Chung et al., J. Phys. Chem. A 115, 3642 (2011)1089-563910.1021/jp1009669], the FRET-efficiency histograms at different denaturant concentrations were used as the equilibrium distributions of protein states. It has been found that the rate constants for folding and unfolding obtained in the MMC simulations change with denaturant concentration in reasonable agreement with the constants that were extracted from the photon trajectories on the basis of theoretical models. The simulated FPT distributions are single-exponential, which is consistent with the assumption of two-state kinetics that was made in the theoretical models. The promising feature of the present approach is that it is based solely on the equilibrium distributions of states, without introducing any additional parameters to perform simulations, which suggests its applicability to other complex systems.
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Affiliation(s)
- Sergei F Chekmarev
- Institute of Thermophysics, SB RAS, 630090 Novosibirsk, Russia and Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
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Chekmarev SF. First-passage times in protein folding: exploring the native-like states vs. overcoming the free energy barrier. Phys Chem Chem Phys 2021; 23:17856-17865. [PMID: 34378547 DOI: 10.1039/d0cp06560a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Using a model β-hairpin protein as a representative example of simple two-state folders whose kinetics are uncomplicated by the presence of on- and off-pathway intermediates, it is studied how the search for the protein's native state among native-like states affects the folding kinetics. It is revealed that the first-passage time (FPT) distributions are essentially single-exponential not only for the times to overcome the free energy barrier between the unfolded and native-like states but also for the times to find the native state among the native-like ones. The FPT distributions of this type are observed through all studied two-state-like regimes of protein folding, varying from a regime close to two-state folding to a regime close to downhill folding. If the protein explores native-like states for a time much longer than the time to overcome the free energy barrier, which is characteristic of high temperatures, the resulting FPT distribution to reach the native state remains close to exponential but the mean FPT (MFPT) is determined not by the height of the free energy barrier but by the time to explore native-like states. In particular, the mean time to overcome the free energy barrier is in reasonable agreement with the Kramers rate formula and generally far shorter than the overall MFPT to reach the native state. The observed increase of the overall MFPT, as a result of longer exploration of native-like states, may lead to an overestimate of the height of the free energy barrier between the unfolded and folded states when it is calculated from the overall MFPT.
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Ying X, Rui G, Zou S, Gu B, Zhan Q, Cui Y. Synthesis of multiple longitudinal polarization vortex structures and its application in sorting chiral nanoparticles. OPTICS EXPRESS 2021; 29:19001-19014. [PMID: 34154143 DOI: 10.1364/oe.427482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/21/2021] [Indexed: 06/13/2023]
Abstract
As the essential properties of organisms, detection and characterization of chirality are of supreme importance in physiology and pharmacology. In this work, we propose an optical technique to sort chiral materials by use of longitudinal polarization vortex (LPV) structures, which is generated with tightly focusing Pancharatnam-Berry tailored Laguerre-Gaussian beam. The nonparaxial propagation of the focusing field leads to the creation of multiple pairs of dual LPV structures with arbitrary topological charge and location, which can be independently controlled by the spatial phase modulation applied on the illumination. More importantly, the opposite spin angular momentums carried by each pair of dual foci lead to different energy flow directions, making it suitable to sort nanoparticles by their handedness. In addition, the LPV structures would also bring different dynamic behaviors to the enantiomers, providing a feasible route toward all-optical enantiopure chemical syntheses and enantiomer separations in pharmaceuticals.
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Luy JN, Molla M, Pecher L, Tonner R. Efficient hierarchical models for reactivity of organic layers on semiconductor surfaces. J Comput Chem 2021; 42:827-839. [PMID: 33617671 DOI: 10.1002/jcc.26503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/20/2021] [Accepted: 02/03/2021] [Indexed: 01/23/2023]
Abstract
Computational modeling of organic interface formation on semiconductors poses a challenge to a density functional theory-based description due to structural and chemical complexity. A hierarchical approach is presented, where parts of the interface are successively removed in order to increase computational efficiency while maintaining the necessary accuracy. First, a benchmark is performed to probe the validity of this approach for three model reactions and five dispersion corrected density functionals. Reaction energies are generally well reproduced by generalized gradient approximation-type functionals but accurate reaction barriers require the use of hybrid functionals. Best performance is found for the model system that does not explicitly consider the substrate but includes its templating effects. Finally, this efficient model is used to provide coverage dependent reaction energies and suggest synthetic principles for the prevention of unwanted growth termination reactions for organic layers on semiconductor surfaces.
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Affiliation(s)
- Jan-Niclas Luy
- Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany.,Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstraße 2, Leipzig, Germany
| | - Mahlet Molla
- Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Lisa Pecher
- Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Ralf Tonner
- Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany.,Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstraße 2, Leipzig, Germany
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Cheng Z, Zhao D, Ma J, Li W, Li S. An On-the-Fly Approach to Construct Generalized Energy-Based Fragmentation Machine Learning Force Fields of Complex Systems. J Phys Chem A 2020; 124:5007-5014. [DOI: 10.1021/acs.jpca.0c04526] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Zheng Cheng
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Dongbo Zhao
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Jing Ma
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Wei Li
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Shuhua Li
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
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Ahuja P, Molayem M, Gadre SR. Electrostatics-Assisted Building-Up Procedure for Capturing Energy Minima of Metal Clusters: Test Case of Ag n Clusters. J Phys Chem A 2019; 123:7872-7880. [PMID: 31433180 DOI: 10.1021/acs.jpca.9b05601] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Global geometry optimization of metal clusters is an important problem in nanophysics. The starting geometries of the clusters generated with empirical or other model potentials are generally optimized further by density functional theory (DFT)-based energy minimization. For this purpose, several algorithms such as simulated annealing, genetic algorithms, basin hopping, etc. are used. Our building-up procedure generates putative lower-energy structures of metal (M) clusters, Mn+1, Mn+2, etc., by anchoring one or more metal atoms in the vicinity of the minima of the molecular electrostatic potential (MESP) of Mn. Here, we report an application of this method to Agn clusters, for 5 ≤ n ≤ 20, followed up by DFT-based geometry optimization, generating several lower-energy structures than those reported in the literature. New low-energy isomers are obtained by applying the same procedure to the test case of mixed-metal clusters, NinAgm, for n + m = 4 and 5. In conclusion, our MESP-based building-up procedure offers a new general methodology for generating lower-energy geometries of metal clusters.
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Affiliation(s)
- Prateek Ahuja
- Department of Chemical Sciences , IISER Mohali , Sector-81, Mohali 140306 , India
| | - Mohammad Molayem
- Physical and Theoretical Chemistry , Saarland University , Saarbrücken 66123 , Germany
| | - Shridhar R Gadre
- Interdisciplinary School of Scientific Computing and Department of Chemistry , Savitribai Phule Pune University , Pune 411007 , India
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Chekmarev SF. How the dyes affect folding of small proteins in single-molecule FRET experiments: A simulation study. Biophys Chem 2019; 254:106243. [PMID: 31442765 DOI: 10.1016/j.bpc.2019.106243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/01/2019] [Accepted: 08/02/2019] [Indexed: 11/18/2022]
Abstract
A key question in the application of the single-molecule Förster resonance energy transfer (smFRET) technique to study protein folding is how the dyes affect the protein behavior. Understanding of these effects is particularly important for small proteins, for which the dyes, along with their linkers, can be comparable in size (mass) with the protein. Using a coarse-grained model, we simulated folding of BBL protein and two of its FRET constructs. The obtained results suggest that even for small proteins, such as the 45-residue BBL, the appearance of the excluded volume in the protein conformation space due to the presence of dyes does not change the overall picture of folding. At the same time, some deviations from folding of the original protein are observed, in particular, the FRET constructs fold considerably slower than the original protein because the protein collapse in the initial state of folding is slowed down due to the protein loading with relatively massive dyes.
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Affiliation(s)
- Sergei F Chekmarev
- Institute of Thermophysics, SB RAS, 630090 Novosibirsk, Russia; Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia.
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Chekmarev SF. Alternation of phases of regular and irregular dynamics in protein folding. Phys Rev E 2019; 99:022412. [PMID: 30934237 DOI: 10.1103/physreve.99.022412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Indexed: 06/09/2023]
Abstract
The regularity of the dynamics in different phases of protein folding is investigated for a set of proteins which undergo a cooperative, two-state folding transition. To determine the degree of regularity of the dynamics, the fractal dimension of probability fluxes is calculated on the basis of simulated folding trajectories. It has been found that the phases of regular and irregular dynamics alternate as follows. In the initial (collapse) phase of folding, the dynamics are essentially regular. Then, as the protein comes to the basin of semicompact states that precedes the transition state, the dynamics become irregular. At the transition state, the dynamics are regularized again but become less regular when the nativelike states are explored. Depending on the specific conditions at which the protein folding was considered, some phases of the dynamics could not be well resolved, but no significant deviation from this general picture has been observed. The regularization of the dynamics at the transition state is discussed in relation to the recent studies of the Hamiltonian dynamics of small clusters, where both regular and chaotic dynamics were observed depending on the flatness of the energy surface at the transition state.
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Affiliation(s)
- Sergei F Chekmarev
- Institute of Thermophysics, SB RAS, 630090 Novosibirsk, Russia and Physics Department, Novosibirsk State University, 630090 Novosibirsk, Russia
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Andryushchenko VA, Chekmarev SF. Modeling of Multicolor Single-Molecule Förster Resonance Energy-Transfer Experiments on Protein Folding. J Phys Chem B 2018; 122:10678-10685. [PMID: 30383961 DOI: 10.1021/acs.jpcb.8b07737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Using a coarse-grained, Cα-model of BBL protein, a multicolor single-molecule Förster resonance energy transfer (FRET) experiment is modeled. Three fluorophores are introduced, which, for simplicity, are associated with Cα beads. Two fluorophores are placed at the ends of protein chain and the third one at the middle of the chain. The free-energy surfaces (FESs) depending on the interfluorophore distances and on the FRET efficiencies corresponding to these distances have been constructed and compared with the FESs depending on the conventional collective variables, such as the fraction of native contacts and radius of gyration. It has been found that multicolor experiments can successfully resolve all essential BBL states that are revealed by the conventional FESs. The resolution of these states with the FRET-efficiency histogram is found to be successful if the energy transfer is measured between the fluorophores at the BBL ends. We also show that, although the present model construct of BBL is very simple, it captures some characteristic features of the single-molecule FRET experiments, such as the pattern of the FRET-efficiency histograms and their evolution with the denaturant concentration.
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Affiliation(s)
- Vladimir A Andryushchenko
- Institute of Thermophysics , SB RAS , 630090 Novosibirsk , Russia.,Department of Physics , Novosibirsk State University , 630090 Novosibirsk , Russia
| | - Sergei F Chekmarev
- Institute of Thermophysics , SB RAS , 630090 Novosibirsk , Russia.,Department of Physics , Novosibirsk State University , 630090 Novosibirsk , Russia
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Wang SW, Hsing CR, Wei CM. Expedite random structure searching using objects from Wyckoff positions. J Chem Phys 2018; 148:054101. [PMID: 29421895 DOI: 10.1063/1.5006104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Random structure searching has been proved to be a powerful approach to search and find the global minimum and the metastable structures. A true random sampling is in principle needed yet it would be highly time-consuming and/or practically impossible to find the global minimum for the complicated systems in their high-dimensional configuration space. Thus the implementations of reasonable constraints, such as adopting system symmetries to reduce the independent dimension in structural space and/or imposing chemical information to reach and relax into low-energy regions, are the most essential issues in the approach. In this paper, we propose the concept of "object" which is either an atom or composed of a set of atoms (such as molecules or carbonates) carrying a symmetry defined by one of the Wyckoff positions of space group and through this process it allows the searching of global minimum for a complicated system to be confined in a greatly reduced structural space and becomes accessible in practice. We examined several representative materials, including Cd3As2 crystal, solid methanol, high-pressure carbonates (FeCO3), and Si(111)-7 × 7 reconstructed surface, to demonstrate the power and the advantages of using "object" concept in random structure searching.
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Affiliation(s)
- Shu-Wei Wang
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Cheng-Rong Hsing
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
| | - Ching-Ming Wei
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan
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Sule N, Rice SA, Gray SK, Scherer NF. An electrodynamics-Langevin dynamics (ED-LD) approach to simulate metal nanoparticle interactions and motion. OPTICS EXPRESS 2015; 23:29978-29992. [PMID: 26698479 DOI: 10.1364/oe.23.029978] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Understanding the formation of electrodynamically interacting assemblies of metal nanoparticles requires accurate computational methods for determining the forces and propagating trajectories. However, since computation of electromagnetic forces occurs on attosecond to femtosecond timescales, simulating the motion of colloidal nanoparticles on milliseconds to seconds timescales is a challenging multi-scale computational problem. Here, we present a computational technique for performing accurate simulations of laser-illuminated metal nanoparticles. In the simulation, we self-consistently combine the finite-difference time-domain method for electrodynamics (ED) with Langevin dynamics (LD) for the particle motions. We demonstrate the ED-LD method by calculating the 3D trajectories of a single 100-nm-diameter Ag nanoparticle and optical trapping and optical binding of two and three 150-nm-diameter Ag nanoparticles in simulated optical tweezers. We show that surface charge on the colloidal metal nanoparticles plays an important role in their optically driven self-organization. In fact, these simulations provide a more complete understanding of the assembly of different structures of two and three Ag nanoparticles that have been observed experimentally, demonstrating that the ED-LD method will be a very useful tool for understanding the self-organization of optical matter.
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Chekmarev SF. Protein folding as a complex reaction: a two-component potential for the driving force of folding and its variation with folding scenario. PLoS One 2015; 10:e0121640. [PMID: 25848943 PMCID: PMC4388825 DOI: 10.1371/journal.pone.0121640] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/11/2015] [Indexed: 11/19/2022] Open
Abstract
The Helmholtz decomposition of the vector field of probability fluxes in a two-dimensional space of collective variables makes it possible to introduce a potential for the driving force of protein folding [Chekmarev, J. Chem. Phys. 139 (2013) 145103]. The potential has two components: one component (Φ) is responsible for the source and sink of the folding flow, which represent, respectively, the unfolded and native state of the protein, and the other (Ψ) accounts for the flow vorticity inherently generated at the periphery of the flow field and provides the canalization of the flow between the source and sink. Both components obey Poisson’s equations with the corresponding source/sink terms. In the present paper, we consider how the shape of the potential changes depending on the scenario of protein folding. To mimic protein folding dynamics projected onto a two-dimensional space of collective variables, the two-dimensional Müller and Brown potential is employed. Three characteristic scenarios are considered: a single pathway from the unfolded to the native state without intermediates, two parallel pathways without intermediates, and a single pathway with an off-pathway intermediate. To determine the probability fluxes, the hydrodynamic description of the folding reaction is used, in which the first-passage folding is viewed as a steady flow of the representative points of the protein from the unfolded to the native state. We show that despite the possible complexity of the folding process, the Φ-component is simple and universal in shape. The Ψ-component is more complex and reveals characteristic features of the process of folding. The present approach is potentially applicable to other complex reactions, for which the transition from the reactant to the product can be described in a space of two (collective) variables.
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Affiliation(s)
- Sergei F. Chekmarev
- Institute of Thermophysics, 630090 Novosibirsk, Russia and Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
- * E-mail:
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Chekmarev SF. Protein folding: complex potential for the driving force in a two-dimensional space of collective variables. J Chem Phys 2014; 139:145103. [PMID: 24116649 DOI: 10.1063/1.4824133] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using the Helmholtz decomposition of the vector field of folding fluxes in a two-dimensional space of collective variables, a potential of the driving force for protein folding is introduced. The potential has two components. One component is responsible for the source and sink of the folding flows, which represent respectively, the unfolded states and the native state of the protein, and the other, which accounts for the flow vorticity inherently generated at the periphery of the flow field, is responsible for the canalization of the flow between the source and sink. The theoretical consideration is illustrated by calculations for a model β-hairpin protein.
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Affiliation(s)
- Sergei F Chekmarev
- Institute of Thermophysics, 630090 Novosibirsk, Russia and Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
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Drocco JA, Olson Reichhardt CJ, Reichhardt C. Characterizing plastic depinning dynamics with the fluctuation theorem. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2011; 34:117. [PMID: 22033615 DOI: 10.1140/epje/i2011-11117-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 06/14/2011] [Accepted: 09/09/2011] [Indexed: 05/31/2023]
Abstract
We demonstrate that the fluctuation theorem can be used to characterize plastic flow phases in collectively interacting particle assemblies driven over quenched disorder when strong fluctuations and crackling noise with 1/f(α) character occur. By measuring the frequency of entropy-destroying trajectories and the diffusivity near the threshold for motion, we map out the different dynamic phases and demonstrate that the fluctuation theorem holds in the strongly fluctuating plastic flow regime which was previously shown to be chaotic. For different driving rates and disorder strength, we find that it is possible to define an effective temperature which decreases with increasing drive, as expected for this type of system. When the size of the pinning sites is large, we identify specific regimes where the fluctuation theorem holds only at long times due to an excess of negative entropy events that occur when particles undergo circular motions within the traps. We discuss how the fluctuation theorem could be applied to plastic flow in other driven nonthermal systems with quenched disorder such as superconducting vortices, magnetic domain walls, Coulomb glasses, and earthquake models.
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Affiliation(s)
- J A Drocco
- Department of Physics, Princeton University, Princeton, NJ 08544, USA
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Chelikowsky JR, ÖĞüt S, Jingc X, Wu K, Stathopoulos A, Saad Y. Atomic and Electronic Structure of Germanium Clusters at Finite Temperature Using Finite Difference Methods. ACTA ACUST UNITED AC 2011. [DOI: 10.1557/proc-408-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractDetermining the electronic and structural properties of semiconductor clusters is one of the outstanding problems in materials science. The existence of numerous structures with nearly identical energies makes it very difficult to determine a realistic ground state structure. Moreover, even if an effective procedure can be devised to predict the ground state structure, questions can arise about the relevancy of the structure at finite temperatures. Kinetic effects and non-equilibrium structures may dominate the structural configurations present in clusters created under laboratory conditions. We illustrate theoretical techniques for predicting the structure and electronic properties of small germanium clusters. Spefically, we illustate that the detailed agreement between theoretical and experimental features can be exploited to identify the relevant isomers present under experimental conditions.
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Ko E, Alemany MMG, Derby JJ, Chelikowsky JR. Ab Initio simulations of nonstoichiometric CdxTe1−x liquids. J Chem Phys 2005; 123:084508. [PMID: 16164313 DOI: 10.1063/1.2008247] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present ab initio molecular-dynamics simulations for Cd(x)Te(1-x) liquids where the composition is nonstoichiometric. The simulations are performed following Born-Oppenheimer molecular dynamics. The required forces are obtained from a solution of the Kohn-Sham equation using ab initio pseudopotentials. We consider stoichiometries of the form: Cd(x)Te(1-x), where x=0.2, 0.4, 0.6, and 0.8. For each composition of the melt, we consider a range of temperatures near the experimentally determined liquid temperatures. We examine the microstructural properties of the melt, the viscosity, and self-diffusion properties of the liquid as a function of the stoichiometry and temperature. We also perform an analysis of the distribution of the electronic density of states in these liquids. We find that structural changes in the local order, experimentally predicted to occur when the concentration of Cd is increased, are closely related to changes in the electronic properties of the melt.
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Affiliation(s)
- Eunjung Ko
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Xia Y, Zhao M, Li F, Huang B, Tan Z, Liu X, Ji Y, Mei L. Recombination and Exchange Reactions of Hydrogen and Dihydrogen Molecular Condensation in Single-Walled Carbon Nanotubes. J Phys Chem B 2004. [DOI: 10.1021/jp049370q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Yueyuan Xia
- Department of Physics, Shandong University, Jinan, Shandong, 250100 P. R. China, Department of Optoelectronics, Shandong University, Jinan,Shandong, 250100 P. R. China, and State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100 P. R. China
| | - Mingwen Zhao
- Department of Physics, Shandong University, Jinan, Shandong, 250100 P. R. China, Department of Optoelectronics, Shandong University, Jinan,Shandong, 250100 P. R. China, and State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100 P. R. China
| | - Feng Li
- Department of Physics, Shandong University, Jinan, Shandong, 250100 P. R. China, Department of Optoelectronics, Shandong University, Jinan,Shandong, 250100 P. R. China, and State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100 P. R. China
| | - Boda Huang
- Department of Physics, Shandong University, Jinan, Shandong, 250100 P. R. China, Department of Optoelectronics, Shandong University, Jinan,Shandong, 250100 P. R. China, and State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100 P. R. China
| | - Zhenyu Tan
- Department of Physics, Shandong University, Jinan, Shandong, 250100 P. R. China, Department of Optoelectronics, Shandong University, Jinan,Shandong, 250100 P. R. China, and State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100 P. R. China
| | - Xiangdong Liu
- Department of Physics, Shandong University, Jinan, Shandong, 250100 P. R. China, Department of Optoelectronics, Shandong University, Jinan,Shandong, 250100 P. R. China, and State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100 P. R. China
| | - Yanju Ji
- Department of Physics, Shandong University, Jinan, Shandong, 250100 P. R. China, Department of Optoelectronics, Shandong University, Jinan,Shandong, 250100 P. R. China, and State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100 P. R. China
| | - Liangmo Mei
- Department of Physics, Shandong University, Jinan, Shandong, 250100 P. R. China, Department of Optoelectronics, Shandong University, Jinan,Shandong, 250100 P. R. China, and State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100 P. R. China
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Simulated Annealing Algorithms for Continuous Global Optimization. NONCONVEX OPTIMIZATION AND ITS APPLICATIONS 2002. [DOI: 10.1007/978-1-4757-5362-2_6] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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21
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Ma Y, Xia Y, Zhao M, Ying M, Liu X, Liu P. Collision of hydrogen atom with single-walled carbon nanotube: Adsorption, insertion, and healing. J Chem Phys 2001. [DOI: 10.1063/1.1409541] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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22
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Chekmarev SF. Taboo search by successive confinement: surveying a potential energy surface. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2001; 64:036703. [PMID: 11580478 DOI: 10.1103/physreve.64.036703] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2000] [Indexed: 05/23/2023]
Abstract
A taboo search for minima on a potential energy surface (PES) is performed by means of confinement molecular dynamics: the molecular dynamics trajectory of the system is successively confined to various basins on the PES that have not been sampled yet. The approach is illustrated for a 13-atom Lennard-Jones cluster. It is shown that the taboo search radically accelerates the process of surveying the PES, with the probability of finding a new minimum defined by a propagating Fermi-like distribution.
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Affiliation(s)
- S F Chekmarev
- Institute of Thermophysics, 630090 Novosibirsk, Russia
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23
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Raty JY, Godlevsky V, Ghosez P, Bichara C, Gaspard JP, Chelikowsky JR. Evidence of a reentrant peierls distortion in liquid GeTe. PHYSICAL REVIEW LETTERS 2000; 85:1950-1953. [PMID: 10970655 DOI: 10.1103/physrevlett.85.1950] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2000] [Indexed: 05/23/2023]
Abstract
The local atomic order of semiconducting liquid GeTe is studied using first-principles molecular-dynamics simulations. Our work points out a high degree of alternating chemical order in the liquid and demonstrates the presence of a Peierls distortion close above the melting temperature. This distortion, absent in the high temperature crystalline structure of NaCl type, is a remnant of the atomic arrangement in the A7 low temperature crystalline phase. It disappears slowly with temperature, as the liquid evolves from a semiconducting to a metallic state.
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Affiliation(s)
- JY Raty
- Institut de Physique, B5, Universite de Liege, B4000 Sart-Tilman, Belgium
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24
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Yoshida S, Fuke K. Photoionization studies of germanium and tin clusters in the energy region of 5.0–8.8 eV: Ionization potentials for Gen (n=2–57) and Snn (n=2–41). J Chem Phys 1999. [DOI: 10.1063/1.479691] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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26
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27
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Soneda N, de la Rubia TD. Defect production, annealing kinetics and damage evolution in α-Fe: An atomic-scale computer simulation. ACTA ACUST UNITED AC 1998. [DOI: 10.1080/01418619808239970] [Citation(s) in RCA: 212] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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28
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Abstract
▪ Abstract The experimental and computational study of clusters has been an active field of research for over a decade. This review provides an overview of some of the methods that have been developed to study clusters and some of the results that have been obtained. Included are computational approaches to explore the potential energy surface for clusters, methods to extract thermodynamic properties from the potential surface information and approaches to insure simulation studies are performed in an ergodic fashion. The methods have proved to be useful in studying the structural transition from clusters to bulk phases, phase changes in small clusters and the importance of quantum effects. The review ends with a discussion of problems in cluster chemistry and physics that are of interest for future investigations.
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Affiliation(s)
- David L. Freeman
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881
| | - J. D. Doll
- Department of Chemistry, Brown University, Providence, Rhode Island 02912
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29
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Zachariah MR, Carrier MJ, Blaisten-Barojas E. Properties of Silicon Nanoparticles: A Molecular Dynamics Study. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp953773w] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Michael J. Carrier
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899
| | - Estela Blaisten-Barojas
- Institute for Computational Sciences and Informatics, George Mason University, Fairfax, Virginia 22030
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30
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Martins JL. Stability of NanPb (n <~ 7) clusters: A first-principles molecular-dynamics study. PHYSICAL REVIEW. B, CONDENSED MATTER 1996; 54:2937-2941. [PMID: 9986152 DOI: 10.1103/physrevb.54.2937] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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31
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Gingerich KA, Ran Q, Schmude RW. Mass spectrometric investigation of the thermodynamic properties of the Si6 molecule. Chem Phys Lett 1996. [DOI: 10.1016/0009-2614(96)00430-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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32
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Binggeli N, Chelikowsky JR. Langevin molecular dynamics with quantum forces: Application to silicon clusters. PHYSICAL REVIEW. B, CONDENSED MATTER 1994; 50:11764-11770. [PMID: 9975314 DOI: 10.1103/physrevb.50.11764] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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33
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Blandin P, Massobrio C, Ballone P. Nucleation and growth of metallic submonolayers on compact metal surfaces. PHYSICAL REVIEW. B, CONDENSED MATTER 1994; 49:16637-16648. [PMID: 10010823 DOI: 10.1103/physrevb.49.16637] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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34
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Poteau R, Spiegelmann F, Labastie P. Isomerisation and phase transitions in small sodium clusters. ACTA ACUST UNITED AC 1994. [DOI: 10.1007/bf01437480] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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35
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Chelikowsky JR, Binggeli N, Glassford KM. Simulation of silicon clusters from ?quantum? Langevin molecular dynamics. ACTA ACUST UNITED AC 1993. [DOI: 10.1007/bf01429105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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36
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Jing X, Chelikowsky JR. Nucleation of carbon clusters. PHYSICAL REVIEW. B, CONDENSED MATTER 1992; 46:15503-15508. [PMID: 10003674 DOI: 10.1103/physrevb.46.15503] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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37
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Jing X, Chelikowsky JR. Nucleation of carbon clusters via an accretion model. PHYSICAL REVIEW. B, CONDENSED MATTER 1992; 46:5028-5031. [PMID: 10004276 DOI: 10.1103/physrevb.46.5028] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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38
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Chelikowsky JR. Formation of C60 clusters via Langevin molecular dynamics. PHYSICAL REVIEW. B, CONDENSED MATTER 1992; 45:12062-12070. [PMID: 10001226 DOI: 10.1103/physrevb.45.12062] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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39
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Binggeli N, Martins JL, Chelikowsky JR. Simulation of Si clusters via Langevin molecular dynamics with quantum forces. PHYSICAL REVIEW LETTERS 1992; 68:2956-2959. [PMID: 10045538 DOI: 10.1103/physrevlett.68.2956] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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40
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Jarrold MF, Constant VA. Silicon cluster ions: Evidence for a structural transition. PHYSICAL REVIEW LETTERS 1991; 67:2994-2997. [PMID: 10044611 DOI: 10.1103/physrevlett.67.2994] [Citation(s) in RCA: 175] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Stave MS, Sanders DE, Raeker TJ, DePristo AE. Corrected effective medium method. V. Simplifications for molecular dynamics and Monte Carlo simulations. J Chem Phys 1990. [DOI: 10.1063/1.458724] [Citation(s) in RCA: 113] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Chelikowsky JR, Phillips JC. Surface and thermodynamic interatomic force fields for silicon clusters and bulk phases. PHYSICAL REVIEW. B, CONDENSED MATTER 1990; 41:5735-5745. [PMID: 9994457 DOI: 10.1103/physrevb.41.5735] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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44
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Hsieh H, Averback RS, Benedek R. Effect of temperature on the dynamics of energetic displacement cascades: A molecular dynamics study. PHYSICAL REVIEW. B, CONDENSED MATTER 1989; 40:9986-9988. [PMID: 9991533 DOI: 10.1103/physrevb.40.9986] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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45
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Zhang C, Freeman DL, Doll JD. Monte Carlo studies of hydrogen fluoride clusters: Cluster size distributions in hydrogen fluoride vapor. J Chem Phys 1989. [DOI: 10.1063/1.457008] [Citation(s) in RCA: 44] [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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46
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Menon M, Allen RE. Simulations of atomic processes at semiconductor surfaces: General method and chemisorption on GaAs(110). PHYSICAL REVIEW. B, CONDENSED MATTER 1988; 38:6196-6205. [PMID: 9947081 DOI: 10.1103/physrevb.38.6196] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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47
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Chelikowsky JR. Transition from metallic to covalent structures in silicon clusters. PHYSICAL REVIEW LETTERS 1988; 60:2669-2672. [PMID: 10038418 DOI: 10.1103/physrevlett.60.2669] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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48
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Sabochick MJ, Richlin DL. New global energy-minimization method. PHYSICAL REVIEW. B, CONDENSED MATTER 1988; 37:10846-10850. [PMID: 9944539 DOI: 10.1103/physrevb.37.10846] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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49
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Feuston BP, Ma M, Mahanti SD, Kalia RK. Molecular-orientational pinning on a surface: A simulated annealing study. PHYSICAL REVIEW. A, GENERAL PHYSICS 1988; 37:902-910. [PMID: 9899733 DOI: 10.1103/physreva.37.902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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50
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Ballone P, Andreoni W, Car R, Parrinello M. Equilibrium structures and finite temperature properties of silicon microclusters from ab initio molecular-dynamics calculations. PHYSICAL REVIEW LETTERS 1988; 60:271-274. [PMID: 10038499 DOI: 10.1103/physrevlett.60.271] [Citation(s) in RCA: 126] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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