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Lee J. Microcanonical analysis of a finite-size nonequilibrium system. Phys Rev E 2016; 93:052148. [PMID: 27300870 DOI: 10.1103/physreve.93.052148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Indexed: 11/07/2022]
Abstract
Microcanonical analysis is a powerful method that can be used to generalize the concept of phase transitions to finite-size systems. However, microcanonical analysis has only been applied to equilibrium systems. I show that it is possible to conduct the microcanonical analysis of a finite-size nonequilibrium system by generalizing the concept of microcanonical entropy. A one-dimensional asymmetric diffusion process is studied as an example for which such a generalized entropy can be explicitly found, and the microcanonical method is used to define a generalized phase transition for the finite-size nonequilibrium system.
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Affiliation(s)
- Julian Lee
- Department of Bioinformatics and Life Science, Soongsil University, Seoul, Korea
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2
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Qi K, Bachmann M. Autocorrelation study of the Θ transition for a coarse-grained polymer model. J Chem Phys 2014; 141:074101. [PMID: 25149769 DOI: 10.1063/1.4891800] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kai Qi
- Soft Matter Systems Research Group, Center for Simulational Physics, The University of Georgia, Athens, Georgia 30602, USA
| | - Michael Bachmann
- Soft Matter Systems Research Group, Center for Simulational Physics, The University of Georgia, Athens, Georgia 30602, USA
- Instituto de Física, Universidade Federal de Mato Grosso, 78060-900 Cuiabá (MT), Brazil
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte (MG), Brazil
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Behringer H, Gemünden P. Homopolymer adsorption on periodically structured surfaces in systems with incommensurable lengths. J Chem Phys 2013; 138:174905. [DOI: 10.1063/1.4803021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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4
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Gruyer D, Frankland JD, Botet R, Płoszajczak M, Bonnet E, Chbihi A, Ademard G, Boisjoli M, Borderie B, Bougault R, Guinet D, Lautesse P, Manduci L, Le Neindre N, Marini P, Pawłowski P, Rivet MF, Rosato E, Spadaccini G, Vigilante M, Wieleczko JP. Nuclear multifragmentation time scale and fluctuations of the largest fragment size. PHYSICAL REVIEW LETTERS 2013; 110:172701. [PMID: 23679716 DOI: 10.1103/physrevlett.110.172701] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 02/26/2013] [Indexed: 06/02/2023]
Abstract
Distributions of the largest fragment charge, Zmax, in multifragmentation reactions around the Fermi energy can be decomposed into a sum of a Gaussian and a Gumbel distribution, whereas at much higher or lower energies one or the other distribution is asymptotically dominant. We demonstrate the same generic behavior for the largest cluster size in critical aggregation models for small systems, in or out of equilibrium, around the critical point. By analogy with the time-dependent irreversible aggregation model, we infer that Zmax distributions are characteristic of the multifragmentation time scale, which is largely determined by the onset of radial expansion in this energy range.
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Affiliation(s)
- D Gruyer
- GANIL, CEA-DSM/CNRS-IN2P3, Boulevard Henri Becquerel, F-14076 Caen Cedex, France
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Davis S. Calculation of microcanonical entropy differences from configurational averages. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:050101. [PMID: 22181355 DOI: 10.1103/physreve.84.050101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Indexed: 05/31/2023]
Abstract
A simple expression is derived, enabling the calculation of the entropy difference between two microcanonical equilibrium states at different energies in atomistic computer simulations. This expression only requires potential energy samples from molecular dynamics or Monte Carlo simulations at the relevant energies. This presents an alternative to switching methods such as thermodynamic integration or nonequilibrium work relations, as well as flat-histogram random walks, all of which involve sampling in between the relevant states. The method is especially suited for small (nanoscopic) systems such as clusters and proteins, and is applicable to first-principles data directly.
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Affiliation(s)
- Sergio Davis
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile.
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Schnabel S, Seaton DT, Landau DP, Bachmann M. Microcanonical entropy inflection points: key to systematic understanding of transitions in finite systems. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:011127. [PMID: 21867133 DOI: 10.1103/physreve.84.011127] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Revised: 05/31/2011] [Indexed: 05/31/2023]
Abstract
We introduce a systematic classification method for the analogs of phase transitions in finite systems. This completely general analysis, which is applicable to any physical system and extends toward the thermodynamic limit, is based on the microcanonical entropy and its energetic derivative, the inverse caloric temperature. Inflection points of this quantity signal cooperative activity and thus serve as distinct indicators of transitions. We demonstrate the power of this method through application to the long-standing problem of liquid-solid transitions in elastic, flexible homopolymers.
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Affiliation(s)
- Stefan Schnabel
- Center for Simulational Physics, The University of Georgia, Athens, Georgia 30602, USA.
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8
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Kim J, Keyes T, Straub JE. Generalized replica exchange method. J Chem Phys 2010; 132:224107. [PMID: 20550390 PMCID: PMC2896417 DOI: 10.1063/1.3432176] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Accepted: 04/30/2010] [Indexed: 01/28/2023] Open
Abstract
We present a powerful replica exchange method, particularly suited to first-order phase transitions associated with the backbending in the statistical temperature, by merging an optimally designed generalized ensemble sampling with replica exchanges. The key ingredients of our method are parametrized effective sampling weights, smoothly joining ordered and disordered phases with a succession of unimodal energy distributions by transforming unstable or metastable energy states of canonical ensembles into stable ones. The inverse mapping between the sampling weight and the effective temperature provides a systematic way to design the effective sampling weights and determine a dynamic range of relevant parameters. Illustrative simulations on Potts spins with varying system size and simulation conditions demonstrate a comprehensive sampling for phase-coexistent states with a dramatic acceleration of tunneling transitions. A significant improvement over the power-law slowing down of mean tunneling times with increasing system size is obtained, and the underlying mechanism for accelerated tunneling is discussed.
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Affiliation(s)
- Jaegil Kim
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.
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10
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Möddel M, Janke W, Bachmann M. Systematic microcanonical analyses of polymer adsorption transitions. Phys Chem Chem Phys 2010; 12:11548-54. [DOI: 10.1039/c002862b] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Fernandez LA, Gordillo-Guerrero A, Martin-Mayor V, Ruiz-Lorenzo JJ. Microcanonical finite-size scaling in second-order phase transitions with diverging specific heat. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:051105. [PMID: 20364945 DOI: 10.1103/physreve.80.051105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 09/23/2009] [Indexed: 05/29/2023]
Abstract
A microcanonical finite-size ansatz in terms of quantities measurable in a finite lattice allows extending phenomenological renormalization (the so-called quotients method) to the microcanonical ensemble. The ansatz is tested numerically in two models where the canonical specific heat diverges at criticality, thus implying Fisher renormalization of the critical exponents: the three-dimensional ferromagnetic Ising model and the two-dimensional four-state Potts model (where large logarithmic corrections are known to occur in the canonical ensemble). A recently proposed microcanonical cluster method allows simulating systems as large as L=1024 (Potts) or L=128 (Ising). The quotients method provides accurate determinations of the anomalous dimension, eta, and of the (Fisher-renormalized) thermal nu exponent. While in the Ising model the numerical agreement with our theoretical expectations is very good, in the Potts case, we need to carefully incorporate logarithmic corrections to the microcanonical ansatz in order to rationalize our data.
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Affiliation(s)
- L A Fernandez
- Departamento de Física Teórica I, Universidad Complutense, 28040 Madrid, Spain
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Chen T, Lin X, Liu Y, Lu T, Liang H. Microcanonical analyses of homopolymer aggregation processes. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 78:056101. [PMID: 19113184 DOI: 10.1103/physreve.78.056101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Indexed: 05/27/2023]
Abstract
Using replica-exchange multicanonical Monte Carlo simulation, the aggregates of two homopolymers were numerically investigated through the microcanonical analysis method. The microcanonical entropy showed one convex function in the transition region, leading to a negative microcanonical specific heat. The origin of temperature backbending was the rearrangement of the segments during the process of aggregation; this aggregation process proceeded via a nucleation and growth mechanism. It was observed that the segments with a sequence number from 10 to 13 in the polymer chain have leading effects on the aggregation.
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Affiliation(s)
- Tao Chen
- Hefei National Laboratory for Physical Sciences at Microscale, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China
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Hernández-Rojas J, Gomez Llorente JM. Microcanonical versus canonical analysis of protein folding. PHYSICAL REVIEW LETTERS 2008; 100:258104. [PMID: 18643708 DOI: 10.1103/physrevlett.100.258104] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Indexed: 05/26/2023]
Abstract
The microcanonical analysis is shown to be a powerful tool to characterize the protein folding transition and to neatly distinguish between good and bad folders. An off-lattice model with parameter chosen to represent polymers of these two types is used to illustrate this approach. Both canonical and microcanonical ensembles are employed. The required calculations were performed using parallel tempering Monte Carlo simulations. The most revealing features of the folding transition are related to its first-order-like character, namely, the S-bend pattern in the caloric curve, which gives rise to negative microcanonical specific heats, and the bimodality of the energy distribution function at the transition temperatures. Models for a good folder are shown to be quite robust against perturbations in the interaction potential parameters.
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Affiliation(s)
- J Hernández-Rojas
- Departamento de Física Fundamental II and IUDEA, Universidad de La Laguna, 38205 Tenerife, Spain.
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Junghans C, Bachmann M, Janke W. Thermodynamics of peptide aggregation processes: an analysis from perspectives of three statistical ensembles. J Chem Phys 2008; 128:085103. [PMID: 18315086 DOI: 10.1063/1.2830233] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We employ a mesoscopic model for studying aggregation processes of proteinlike hydrophobic-polar heteropolymers. By means of multicanonical Monte Carlo computer simulations, we find strong indications that peptide aggregation is a phase separation process, in which the microcanonical entropy exhibits a convex intruder due to non-negligible surface effects of the small systems. We analyze thermodynamic properties of the conformational transitions accompanying the aggregation process from the multicanonical, canonical, and microcanonical perspective. It turns out that the microcanonical description is particularly advantageous as it allows for unraveling details of the phase-separation transition in the thermodynamic region, where the temperature is not a suitable external control parameter anymore.
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Affiliation(s)
- Christoph Junghans
- Institut für Theoretische Physik and Centre for Theoretical Sciences NTZ, Universität Leipzig, Postfach 100920, D-04009 Leipzig, Germany.
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Chen T, Lin X, Liu Y, Liang H. Microcanonical analysis of association of hydrophobic segments in a heteropolymer. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 76:046110. [PMID: 17995063 DOI: 10.1103/physreve.76.046110] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Indexed: 05/25/2023]
Abstract
Using the replica-exchange multicanonical Monte Carlo simulation, the intra-association of hydrophobic segments in a heteropolymer was numerically investigated by the microcanonical analysis method. We demonstrated that the microcanonical entropy shows the features of one or multiple convexes in the association transition region depending on the number and distribution of hydrophobic segments in the chain. We found that one or multiple negative specific heats imply a first-order-like transition with the coexistence of multiple phases.
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Affiliation(s)
- Tao Chen
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China
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Junghans C, Bachmann M, Janke W. Microcanonical analyses of peptide aggregation processes. PHYSICAL REVIEW LETTERS 2006; 97:218103. [PMID: 17155776 DOI: 10.1103/physrevlett.97.218103] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Indexed: 05/12/2023]
Abstract
We propose the use of microcanonical analyses for numerical studies of peptide aggregation transitions. Performing multicanonical Monte Carlo simulations of a simple hydrophobic-polar continuum model for interacting heteropolymers of finite length, we find that the microcanonical entropy behaves convex in the transition region, leading to a negative microcanonical specific heat. As this effect is also seen in first-order-like transitions of other finite systems, our results provide clear evidence for recent hints that the characterization of phase separation in first-order-like transitions of finite systems profits from this microcanonical view.
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Affiliation(s)
- Christoph Junghans
- Institut für Theoretische Physik and Centre for Theoretical Sciences (NTZ), Universität Leipzig, Augustusplatz 10/11, D-04109 Leipzig, Germany.
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