MULTICANONICAL ENSEMBLE - A NEW APPROACH TO SIMULATE 1ST-ORDER PHASE-TRANSITIONS

BERG BA, Neuhaus T (1992)
PHYSICAL REVIEW LETTERS 68(1): 9-12.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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DOI
Autor*in
BERG, BA; Neuhaus, ThomasUniBi
Einrichtung
Fakultät für Physik > AG Elementarteilchen und Quantenfelder
Abstract / Bemerkung
Relying on the recently proposed multicanonical algorithm, we present a numerical simulation of the first-order phase transition in the 2D 10-state Potts model on lattices up to sizes 100 x 100. It is demonstrated that the new algorithm lacks an exponentially fast increase of the tunneling time between metastable states as a function of the linear size L of the system. Instead, the tunneling time diverges approximately proportional to L 2.65. On our largest lattice we gain more than 2 orders of magnitude as compared to a standard heat-bath algorithm. As a first physical application we report a high-precision computation of the interfacial free energy per unit area.
Erscheinungsjahr
1992
Zeitschriftentitel
PHYSICAL REVIEW LETTERS
Band
68
Ausgabe
1
Seite(n)
9-12
ISSN
0031-9007
Page URI
https://pub.uni-bielefeld.de/record/1648814

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BERG BA, Neuhaus T. MULTICANONICAL ENSEMBLE - A NEW APPROACH TO SIMULATE 1ST-ORDER PHASE-TRANSITIONS. PHYSICAL REVIEW LETTERS. 1992;68(1):9-12.
BERG, B. A., & Neuhaus, T. (1992). MULTICANONICAL ENSEMBLE - A NEW APPROACH TO SIMULATE 1ST-ORDER PHASE-TRANSITIONS. PHYSICAL REVIEW LETTERS, 68(1), 9-12. https://doi.org/10.1103/PhysRevLett.68.9
BERG, BA, and Neuhaus, Thomas. 1992. “MULTICANONICAL ENSEMBLE - A NEW APPROACH TO SIMULATE 1ST-ORDER PHASE-TRANSITIONS”. PHYSICAL REVIEW LETTERS 68 (1): 9-12.
BERG, B. A., and Neuhaus, T. (1992). MULTICANONICAL ENSEMBLE - A NEW APPROACH TO SIMULATE 1ST-ORDER PHASE-TRANSITIONS. PHYSICAL REVIEW LETTERS 68, 9-12.
BERG, B.A., & Neuhaus, T., 1992. MULTICANONICAL ENSEMBLE - A NEW APPROACH TO SIMULATE 1ST-ORDER PHASE-TRANSITIONS. PHYSICAL REVIEW LETTERS, 68(1), p 9-12.
B.A. BERG and T. Neuhaus, “MULTICANONICAL ENSEMBLE - A NEW APPROACH TO SIMULATE 1ST-ORDER PHASE-TRANSITIONS”, PHYSICAL REVIEW LETTERS, vol. 68, 1992, pp. 9-12.
BERG, B.A., Neuhaus, T.: MULTICANONICAL ENSEMBLE - A NEW APPROACH TO SIMULATE 1ST-ORDER PHASE-TRANSITIONS. PHYSICAL REVIEW LETTERS. 68, 9-12 (1992).
BERG, BA, and Neuhaus, Thomas. “MULTICANONICAL ENSEMBLE - A NEW APPROACH TO SIMULATE 1ST-ORDER PHASE-TRANSITIONS”. PHYSICAL REVIEW LETTERS 68.1 (1992): 9-12.

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Multidimensional generalized-ensemble algorithms for complex systems.
Mitsutake A, Okamoto Y., J Chem Phys 130(21), 2009
PMID: 19508054
Application of the Wang-Landau algorithm to the dimerization of glycophorin A.
Gervais C, Wüst T, Landau DP, Xu Y., J Chem Phys 130(21), 2009
PMID: 19508105
Phase equilibria of molecular fluids via hybrid Monte Carlo Wang-Landau simulations: applications to benzene and n-alkanes.
Desgranges C, Delhommelle J., J Chem Phys 130(24), 2009
PMID: 19566144
CHARMM: the biomolecular simulation program.
Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M., J Comput Chem 30(10), 2009
PMID: 19444816
VARICELLA: a variable-cell direct space method for structure determination from powder diffraction data.
Rapallo A., J Chem Phys 131(4), 2009
PMID: 19655843
Thermodynamics of tubelike flexible polymers.
Vogel T, Neuhaus T, Bachmann M, Janke W., Phys Rev E Stat Nonlin Soft Matter Phys 80(1 pt 1), 2009
PMID: 19658721
Free-energy-driven folding and thermodynamics of the 67-residue protein GS-alpha3W--a large-scale Monte Carlo study.
Meinke JH, Hansmann UH., J Comput Chem 30(11), 2009
PMID: 19499540
Comparison of three enveloping distribution sampling Hamiltonians for the estimation of multiple free energy differences from a single simulation.
Christ CD, Van Gunsteren WF., J Comput Chem 30(11), 2009
PMID: 19504591
Simulated-tempering replica-exchange method for the multidimensional version.
Mitsutake A., J Chem Phys 131(9), 2009
PMID: 19739847
Elastic Lennard-Jones polymers meet clusters: differences and similarities.
Schnabel S, Bachmann M, Janke W., J Chem Phys 131(12), 2009
PMID: 19791918
Ground-state properties of tubelike flexible polymers.
Vogel T, Neuhaus T, Bachmann M, Janke W., Eur Phys J E Soft Matter 30(1), 2009
PMID: 19777280
Spatial updating in the great grand canonical ensemble.
Orkoulas G, Noon DP., J Chem Phys 131(16), 2009
PMID: 19894918
Isochronal sampling in non-Boltzmann Monte Carlo methods.
Abreu CR., J Chem Phys 131(15), 2009
PMID: 20568853
Six-state clock model on the square lattice: fisher zero approach with Wang-Landau sampling.
Hwang CO., Phys Rev E Stat Nonlin Soft Matter Phys 80(4 pt 1), 2009
PMID: 19905369
Computation of interfacial properties via grand canonical transition matrix Monte Carlo simulation.
Grzelak EM, Errington JR., J Chem Phys 128(1), 2008
PMID: 18190215
The interfacial tension and phase diagram of the Widom-Rowlinson mixture via Monte Carlo simulations.
Djikaev Y., J Chem Phys 128(1), 2008
PMID: 18190217
Exchange frequency in replica exchange molecular dynamics.
Sindhikara D, Meng Y, Roitberg AE., J Chem Phys 128(2), 2008
PMID: 18205439
Thin-thick surface phase coexistence and boundary tension of the square-well fluid on a weak attractive surface.
Singh JK, Sarma G, Kwak SK., J Chem Phys 128(4), 2008
PMID: 18247982
Polydisperse lattice-gas model.
Wilding NB, Sollich P, Buzzacchi M., Phys Rev E Stat Nonlin Soft Matter Phys 77(1 pt 1), 2008
PMID: 18351856
Computational techniques for efficient conformational sampling of proteins.
Liwo A, Czaplewski C, Ołdziej S, Scheraga HA., Curr Opin Struct Biol 18(2), 2008
PMID: 18215513
Thermodynamics of peptide aggregation processes: an analysis from perspectives of three statistical ensembles.
Junghans C, Bachmann M, Janke W., J Chem Phys 128(8), 2008
PMID: 18315086
Quantitative computer simulations of biomolecules: a snapshot.
Yang W, Nymeyer H, Zhou HX, Berg B, Brüschweiler R., J Comput Chem 29(4), 2008
PMID: 17708535
A divide-and-conquer strategy to improve diffusion sampling in generalized ensemble simulations.
Min D, Yang W., J Chem Phys 128(9), 2008
PMID: 18331086
Efficient prediction of thermodynamic properties of quadrupolar fluids from simulation of a coarse-grained model: the case of carbon dioxide.
Mognetti BM, Yelash L, Virnau P, Paul W, Binder K, Müller M, MacDowell LG., J Chem Phys 128(10), 2008
PMID: 18345900
Calculation of free-energy differences and potentials of mean force by a multi-energy gap method.
Zhou HX., J Chem Phys 128(11), 2008
PMID: 18361551
Molecular simulation of protein dynamics in nanopores. I. Stability and folding.
Javidpour L, Tabar MR, Sahimi M., J Chem Phys 128(11), 2008
PMID: 18361620
Comparing the density of states of binary Lennard-Jones glasses in bulk and film.
Ghosh J, Faller R., J Chem Phys 128(12), 2008
PMID: 18376945
Effect of polydispersity on the relative stability of hard-sphere crystals.
Yang M, Ma H., J Chem Phys 128(13), 2008
PMID: 18397080
Adaptive biasing force method for scalar and vector free energy calculations.
Darve E, Rodríguez-Gómez D, Pohorille A., J Chem Phys 128(14), 2008
PMID: 18412436
Relaxation of caloric curves on complex potential energy surfaces.
Calvo F, Wales DJ., J Chem Phys 128(15), 2008
PMID: 18433229
Bridging coarse-grained models by jump-in-sample simulations.
Zhou X, Jiang Y, Rasmussen S, Ziock H., J Chem Phys 128(17), 2008
PMID: 18465910
Multiple free energies from a single simulation: extending enveloping distribution sampling to nonoverlapping phase-space distributions.
Christ CD, van Gunsteren WF., J Chem Phys 128(17), 2008
PMID: 18465915
Monte Carlo simulation in the isobaric-multithermal ensemble of a bulk Lennard-Jones fluid system: thermodynamic quantities for pressure from P{ *}=2.42 to 7.25.
Muguruma C, Okamoto Y., Phys Rev E Stat Nonlin Soft Matter Phys 77(5 pt 1), 2008
PMID: 18643054
Multipolar ordering in electro- and magnetostatic coupled nanosystems.
Vedmedenko EY, Mikuszeit N., Chemphyschem 9(9), 2008
PMID: 18553291
Accurate calculations of free-energy differences by the distribution method.
Wu D., J Chem Phys 128(22), 2008
PMID: 18554004
Improved configuration space sampling: Langevin dynamics with alternative mobility.
Chau CD, Sevink GJ, Fraaije JG., J Chem Phys 128(24), 2008
PMID: 18601320
Optimizing the sampling and staging for simulations of rare events via forward flux sampling schemes.
Borrero EE, Escobedo FA., J Chem Phys 129(2), 2008
PMID: 18624524
Elasticity of a polydisperse hard-sphere crystal.
Yang M, Ma H., Phys Rev E Stat Nonlin Soft Matter Phys 78(1 pt 1), 2008
PMID: 18763953
Ab initio folding simulation of Trpcage by replica exchange with hybrid Hamiltonian.
Xu W, Mu Y., Biophys Chem 137(2-3), 2008
PMID: 18775599
An experimentally guided umbrella sampling protocol for biomolecules.
Mills M, Andricioaei I., J Chem Phys 129(11), 2008
PMID: 19044944
Partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations.
Okumura H., J Chem Phys 129(12), 2008
PMID: 19045015
Flat histogram Monte Carlo sampling for mechanical variables and conjugate thermodynamic fields with example applications to strongly correlated electronic systems.
Ganzenmüller G, Pawłowski G., Phys Rev E Stat Nonlin Soft Matter Phys 78(3 pt 2), 2008
PMID: 18851185
Modeling molecular and ionic absolute solvation free energies with quasichemical theory bounds.
Rogers DM, Beck TL., J Chem Phys 129(13), 2008
PMID: 19045103
Optimization of expanded ensemble methods.
Escobedo FA, Martinez-Veracoechea FJ., J Chem Phys 129(15), 2008
PMID: 19045176
Phase diagram of a model of nanoparticles in electrolyte solutions.
Li X, Lettieri S, Wentzel N, Gunton JD., J Chem Phys 129(16), 2008
PMID: 19045253
Fluid phase behavior of a model colloid-polymer mixture: Influence of polymer size and interaction strength.
Rosch TW, Errington JR., J Chem Phys 129(16), 2008
PMID: 19045314
First-order phase transitions: a study through the parallel tempering method.
Fiore CE., Phys Rev E Stat Nonlin Soft Matter Phys 78(4 pt 1), 2008
PMID: 18999381
Thermodynamics of two lattice ice models in three dimensions.
Muguruma C, Okamoto Y, Berg BA., Phys Rev E Stat Nonlin Soft Matter Phys 78(4 pt 1), 2008
PMID: 18999385
Optimal modification factor and convergence of the Wang-Landau algorithm.
Zhou C, Su J., Phys Rev E Stat Nonlin Soft Matter Phys 78(4 pt 2), 2008
PMID: 18999559
Re-examination of structure optimization of off-lattice protein AB models by conformational space annealing.
Lee J, Joo K, Kim SY, Lee J., J Comput Chem 29(14), 2008
PMID: 18470971
Surface tension and vapor-liquid phase coexistence of confined square-well fluid.
Singh JK, Kwak SK., J Chem Phys 126(2), 2007
PMID: 17228961
Entropic sampling of flexible polyelectrolytes within the Wang-Landau algorithm.
Volkov NA, Vorontsov-Velyaminov PN, Lyubartsev AP., Phys Rev E Stat Nonlin Soft Matter Phys 75(1 pt 2), 2007
PMID: 17358290
Wang-Landau multibondic cluster simulations for second-order phase transitions.
Berg BA, Janke W., Phys Rev Lett 98(4), 2007
PMID: 17358751
Two-state folding, folding through intermediates, and metastability in a minimalistic hydrophobic-polar model for proteins.
Schnabel S, Bachmann M, Janke W., Phys Rev Lett 98(4), 2007
PMID: 17358817
Efficient combination of Wang-Landau and transition matrix Monte Carlo methods for protein simulations.
Ghulghazaryan RG, Hayryan S, Hu CK., J Comput Chem 28(3), 2007
PMID: 17195159
Replica exchange with dynamical scaling.
Rick SW., J Chem Phys 126(5), 2007
PMID: 17302469
Free energy landscapes of electron transfer system in dipolar environment below and above the rotational freezing temperature.
Suzuki Y, Tanimura Y., J Chem Phys 126(5), 2007
PMID: 17302482
Cooperative folding mechanism of a beta-hairpin peptide studied by a multicanonical replica-exchange molecular dynamics simulation.
Yoda T, Sugita Y, Okamoto Y., Proteins 66(4), 2007
PMID: 17173285
Identification of characteristic protein folding channels in a coarse-grained hydrophobic-polar peptide model.
Schnabel S, Bachmann M, Janke W., J Chem Phys 126(10), 2007
PMID: 17362088
Sampling enhancement for the quantum mechanical potential based molecular dynamics simulations: a general algorithm and its extension for free energy calculation on rugged energy surface.
Li H, Yang W., J Chem Phys 126(11), 2007
PMID: 17381193
Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange.
Kubitzki MB, de Groot BL., Biophys J 92(12), 2007
PMID: 17384062
Microcanonical approach to the simulation of first-order phase transitions.
Martin-Mayor V., Phys Rev Lett 98(13), 2007
PMID: 17501239
Fast algorithm to calculate density of states.
Belardinelli RE, Pereyra VD., Phys Rev E Stat Nonlin Soft Matter Phys 75(4 pt 2), 2007
PMID: 17501010
Ring polymer simulations with global radius of curvature.
Neuhaus T, Zimmermann O, Hansmann UH., Phys Rev E Stat Nonlin Soft Matter Phys 75(5 pt 1), 2007
PMID: 17677089
Critical endpoint behavior in an asymmetric Ising model: application of Wang-Landau sampling to calculate the density of states.
Tsai SH, Wang F, Landau DP., Phys Rev E Stat Nonlin Soft Matter Phys 75(6 pt 1), 2007
PMID: 17677221
Wang-Landau molecular dynamics technique to search for low-energy conformational space of proteins.
Nagasima T, Kinjo AR, Mitsui T, Nishikawa K., Phys Rev E Stat Nonlin Soft Matter Phys 75(6 pt 2), 2007
PMID: 17677388
Direct calculation of interfacial tensions from computer simulation: results for freely jointed tangent hard sphere chains.
Macdowell LG, Bryk P., Phys Rev E Stat Nonlin Soft Matter Phys 75(6 pt 1), 2007
PMID: 17677275
Enhanced sampling via strong coupling to a heat bath: relationship between Tsallis and multicanonical algorithms.
Morishita T, Mikami M., J Chem Phys 127(3), 2007
PMID: 17655428
Structure optimization and folding mechanisms of off-lattice protein models using statistical temperature molecular dynamics simulation: Statistical temperature annealing.
Kim J, Straub JE, Keyes T., Phys Rev E Stat Nonlin Soft Matter Phys 76(1 pt 1), 2007
PMID: 17677500
Entropic effects in large-scale Monte Carlo simulations.
Predescu C., Phys Rev E Stat Nonlin Soft Matter Phys 76(1 pt 2), 2007
PMID: 17677591
Projected single-spin-flip dynamics in the Ising model.
Ferreira AL, Toral R., Phys Rev E Stat Nonlin Soft Matter Phys 76(1 pt 1), 2007
PMID: 17677420
Hybrid Hamiltonian replica exchange molecular dynamics simulation method employing the Poisson-Boltzmann model.
Mu Y, Yang Y, Xu W., J Chem Phys 127(8), 2007
PMID: 17764241
Effective sampling in the configurational space of a small peptide by the multicanonical-multioverlap algorithm.
Itoh SG, Okamoto Y., Phys Rev E Stat Nonlin Soft Matter Phys 76(2 pt 2), 2007
PMID: 17930172
Obtaining pressure versus concentration phase diagrams in spin systems from Monte Carlo simulations.
Fiore CE, Carneiro CE., Phys Rev E Stat Nonlin Soft Matter Phys 76(2 pt 1), 2007
PMID: 17930017
Conjugate field and fluctuation-dissipation relation for the dynamic phase transition in the two-dimensional kinetic Ising model.
Robb DT, Rikvold PA, Berger A, Novotny MA., Phys Rev E Stat Nonlin Soft Matter Phys 76(2 pt 1), 2007
PMID: 17930023
Essential energy space random walk via energy space metadynamics method to accelerate molecular dynamics simulations.
Li H, Min D, Liu Y, Yang W., J Chem Phys 127(9), 2007
PMID: 17824726
Phase behavior of a fluid with competing attractive and repulsive interactions.
Archer AJ, Wilding NB., Phys Rev E Stat Nonlin Soft Matter Phys 76(3 pt 1), 2007
PMID: 17930245
Simulation via direct computation of partition functions.
Zhang C, Ma J., Phys Rev E Stat Nonlin Soft Matter Phys 76(3 pt 2), 2007
PMID: 17930362
Applications of Wang-Landau sampling to determine phase equilibria in complex fluids.
Ganzenmüller G, Camp PJ., J Chem Phys 127(15), 2007
PMID: 17949170
Efficient parallel tempering for first-order phase transitions.
Neuhaus T, Magiera MP, Hansmann UH., Phys Rev E Stat Nonlin Soft Matter Phys 76(4 pt 2), 2007
PMID: 17995052
Optimized expanded ensembles for simulations involving molecular insertions and deletions. I. Closed systems.
Escobedo FA, Martínez-Veracoechea FJ., J Chem Phys 127(17), 2007
PMID: 17994803
Calculation of surface tension via area sampling.
Errington JR, Kofke DA., J Chem Phys 127(17), 2007
PMID: 17994844
Wang-Landau algorithm: a theoretical analysis of the saturation of the error.
Belardinelli RE, Pereyra VD., J Chem Phys 127(18), 2007
PMID: 18020628
Global perspectives on the energy landscapes of liquids, supercooled liquids, and glassy systems: the potential energy landscape ensemble.
Wang C, Stratt RM., J Chem Phys 127(22), 2007
PMID: 18081402
Numerical calculation of the combinatorial entropy of partially ordered ice.
Berg BA, Yang W., J Chem Phys 127(22), 2007
PMID: 18081401
Coarse-grained strategy for modeling protein stability in concentrated solutions. II: phase behavior.
Shen VK, Cheung JK, Errington JR, Truskett TM., Biophys J 90(6), 2006
PMID: 16387768
Monte Carlo simulations of biomolecules: The MC module in CHARMM.
Hu J, Ma A, Dinner AR., J Comput Chem 27(2), 2006
PMID: 16323162
Determination of surface tension in binary mixtures using transition-matrix Monte Carlo.
Shen VK, Errington JR., J Chem Phys 124(2), 2006
PMID: 16422640
Equilibrium thermodynamics from basin-sampling.
Bogdan TV, Wales DJ, Calvo F., J Chem Phys 124(4), 2006
PMID: 16460144
Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field.
Nanias M, Czaplewski C, Scheraga HA., J Chem Theory Comput 2(3), 2006
PMID: 18797518
Multibaric-multithermal ensemble molecular dynamics simulations.
Okumura H, Okamoto Y., J Comput Chem 27(3), 2006
PMID: 16381079
An advanced Gibbs-Duhem integration method: theory and applications.
van 't Hof A, Peters CJ, de Leeuw SW., J Chem Phys 124(5), 2006
PMID: 16468917
Acceleration of Markov chain Monte Carlo simulations through sequential updating.
Ren R, Orkoulas G., J Chem Phys 124(6), 2006
PMID: 16483198
Freezing line of the Lennard-Jones fluid: a phase switch Monte Carlo study.
McNeil-Watson GC, Wilding NB., J Chem Phys 124(6), 2006
PMID: 16483217
Theoretical studies of transition states by the multioverlap molecular dynamics methods.
Itoh SG, Okamoto Y., J Chem Phys 124(10), 2006
PMID: 16542064
On the use of transition matrix methods with extended ensembles.
Escobedo FA, Abreu CR., J Chem Phys 124(10), 2006
PMID: 16542071
Free energy landscape analysis of two-dimensional dipolar solvent model at temperatures below and above the rotational freezing point.
Suzuki Y, Tanimura Y., J Chem Phys 124(12), 2006
PMID: 16599698
Wang-Landau Monte Carlo simulation of the Blume-Capel model.
Silva CJ, Caparica AA, Plascak JA., Phys Rev E Stat Nonlin Soft Matter Phys 73(3 pt 2), 2006
PMID: 16605693
Improved Wang-Landau sampling through the use of smoothed potential-energy surfaces.
Nguyen PH, Mittag E, Torda AE, Stock G., J Chem Phys 124(15), 2006
PMID: 16674218
Simulation estimates of cloud points of polydisperse fluids.
Buzzacchi M, Sollich P, Wilding NB, Müller M., Phys Rev E Stat Nonlin Soft Matter Phys 73(4 pt 2), 2006
PMID: 16711881
Bit error rate improvement by nonlinear optical decision element.
Nasieva IO, Boscolo S, Turitsyn SK., Opt Lett 31(9), 2006
PMID: 16642060
Conformational sampling via a self-regulating effective energy surface.
Bitetti-Putzer R, Dinner AR, Yang W, Karplus M., J Chem Phys 124(17), 2006
PMID: 16689598
Simulation of the density of states in isothermal and adiabatic ensembles.
Escobedo FA., Phys Rev E Stat Nonlin Soft Matter Phys 73(5 pt 2), 2006
PMID: 16803068
Universal features and tail analysis of the order-parameter distribution of the two-dimensional Ising model: an entropic sampling Monte Carlo study.
Malakis A, Fytas NG., Phys Rev E Stat Nonlin Soft Matter Phys 73(5 pt 2), 2006
PMID: 16803005
Thermodynamic features characterizing good and bad folding sequences obtained using a simplified off-lattice protein model.
Amatori A, Ferkinghoff-Borg J, Tiana G, Broglia RA., Phys Rev E Stat Nonlin Soft Matter Phys 73(6 pt 1), 2006
PMID: 16906862
Application of the multiensemble sampling to the equilibrium folding of proteins.
Son HS, Kim SY, Lee J, Han KK., Bioinformatics 22(15), 2006
PMID: 16766555
Metastable liquid-liquid coexistence and density anomalies in a core-softened fluid.
Gibson HM, Wilding NB., Phys Rev E Stat Nonlin Soft Matter Phys 73(6 pt 1), 2006
PMID: 16906836
Phase behavior and particle size cutoff effects in polydisperse fluids.
Wilding NB, Sollich P, Fasolo M, Buzzacchi M., J Chem Phys 125(1), 2006
PMID: 16863334
Nucleation and cavitation of spherical, cylindrical, and slablike droplets and bubbles in small systems.
MacDowell LG, Shen VK, Errington JR., J Chem Phys 125(3), 2006
PMID: 16863371
Conformational study of Met-enkephalin based on the ECEPP force fields.
Zhan L, Chen JZ, Liu WK., Biophys J 91(7), 2006
PMID: 16829555
Simulation of symmetric tricritical behavior in electrolytes.
Ren R, O'Keeffe CJ, Orkoulas G., J Chem Phys 125(12), 2006
PMID: 17014188
Free-energy calculations with multiple Gaussian modified ensembles.
Neuhaus T, Hager JS., Phys Rev E Stat Nonlin Soft Matter Phys 74(3 pt 2), 2006
PMID: 17025781
Wetting transitions in polydisperse fluids.
Buzzacchi M, Wilding NB, Sollich P., Phys Rev Lett 97(13), 2006
PMID: 17026051
Accurate estimation of the density of states from Monte Carlo transition probability data.
Fenwick MK., J Chem Phys 125(14), 2006
PMID: 17042648
Canonical and microcanonical Monte Carlo simulations of lattice-gas mixtures.
Fiore CE, Henriques VB, de Oliveira MJ., J Chem Phys 125(16), 2006
PMID: 17092107
Structural properties of small semiconductor-binding synthetic peptides.
Gökoğlu G, Bachmann M, Celik T, Janke W., Phys Rev E Stat Nonlin Soft Matter Phys 74(4 pt 1), 2006
PMID: 17155083
Extended multicanonical method combined with thermodynamically optimized potential: application to the liquid-crystal transition of silicon.
Yoshimoto Y., J Chem Phys 125(18), 2006
PMID: 17115734
Microcanonical analyses of peptide aggregation processes.
Junghans C, Bachmann M, Janke W., Phys Rev Lett 97(21), 2006
PMID: 17155776
Phase behavior of a symmetrical binary fluid mixture.
Köfinger J, Wilding NB, Kahl G., J Chem Phys 125(23), 2006
PMID: 17190563
Excess-entropy-based anomalies for a waterlike fluid.
Errington JR, Truskett TM, Mittal J., J Chem Phys 125(24), 2006
PMID: 17199350
Scanning the critical fluctuations: application to the phenomenology of the two-dimensional XY model.
Paredes RV, Botet R., Phys Rev E Stat Nonlin Soft Matter Phys 74(6 pt 1), 2006
PMID: 17280029
Phase diagram of a binary symmetric hard-core Yukawa mixture.
Schöll-Paschinger E, Levesque D, Weis JJ, Kahl G., J Chem Phys 122(2), 2005
PMID: 15638598
Replica-exchange Monte Carlo scheme for bayesian data analysis.
Habeck M, Nilges M, Rieping W., Phys Rev Lett 94(1), 2005
PMID: 15698139
Determination of fluid-phase behavior using transition-matrix Monte Carlo: binary Lennard-Jones mixtures.
Shen VK, Errington JR., J Chem Phys 122(6), 2005
PMID: 15740389
Conformational transition free energy profiles of an adsorbed, lattice model protein by multicanonical Monte Carlo simulation.
Castells V, Van Tassel PR., J Chem Phys 122(8), 2005
PMID: 15836077
An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem.
Shmygelska A, Hoos HH., BMC Bioinformatics 6(), 2005
PMID: 15710037
Molecular mechanism for stabilizing a short helical peptide studied by generalized-ensemble simulations with explicit solvent.
Sugita Y, Okamoto Y., Biophys J 88(5), 2005
PMID: 15749777
Multicanonical study of coarse-grained off-lattice models for folding heteropolymers.
Bachmann M, Arkin H, Janke W., Phys Rev E Stat Nonlin Soft Matter Phys 71(3 pt 1), 2005
PMID: 15903458
Multicanonical schemes for mapping out free-energy landscapes of single-component and multicomponent systems.
Gospodinov ID, Escobedo FA., J Chem Phys 122(16), 2005
PMID: 15945668
Asynchronous multicanonical basin hopping method and its application to cobalt nanoclusters.
Zhan L, Chen JZ, Liu WK, Lai SK., J Chem Phys 122(24), 2005
PMID: 16035793
Wang-Landau sampling with self-adaptive range.
Tröster A, Dellago C., Phys Rev E Stat Nonlin Soft Matter Phys 71(6 pt 2), 2005
PMID: 16089909
A unified methodological framework for the simulation of nonisothermal ensembles.
Escobedo FA., J Chem Phys 123(4), 2005
PMID: 16095349
Kertész line in the three-dimensional compact U(1) lattice Higgs model.
Wenzel S, Bittner E, Janke W, Schakel AM, Schiller A., Phys Rev Lett 95(5), 2005
PMID: 16090862
Phase-space overlap measures. I. Fail-safe bias detection in free energies calculated by molecular simulation.
Wu D, Kofke DA., J Chem Phys 123(5), 2005
PMID: 16108627
Isotropic-nematic interfacial tension of hard and soft rods: application of advanced grand canonical biased-sampling techniques.
Vink RL, Wolfsheimer S, Schilling T., J Chem Phys 123(7), 2005
PMID: 16229614
Virtual-move parallel tempering.
Coluzza I, Frenkel D., Chemphyschem 6(9), 2005
PMID: 16110517
All-exchanges parallel tempering.
Calvo F., J Chem Phys 123(12), 2005
PMID: 16392474
Equilibrium sampling of self-associating polymer solutions: a parallel selective tempering approach.
Ayyagari C, Bedrov D, Smith GD., J Chem Phys 123(12), 2005
PMID: 16392532
Wang-Landau Monte Carlo simulation of isotropic-nematic transition in liquid crystals.
Jayasri D, Sastry VS, Murthy KP., Phys Rev E Stat Nonlin Soft Matter Phys 72(3 pt 2), 2005
PMID: 16241609
Test-area simulation method for the direct determination of the interfacial tension of systems with continuous or discontinuous potentials.
Gloor GJ, Jackson G, Blas FJ, de Miguel E., J Chem Phys 123(13), 2005
PMID: 16223322
Direct evaluation of multicomponent phase equilibria using flat-histogram methods.
Errington JR, Shen VK., J Chem Phys 123(16), 2005
PMID: 16268677
Overcoming the slowing down of flat-histogram Monte Carlo simulations: cluster updates and optimized broad-histogram ensembles.
Wu Y, Körner M, Colonna-Romano L, Trebst S, Gould H, Machta J, Troyer M., Phys Rev E Stat Nonlin Soft Matter Phys 72(4 pt 2), 2005
PMID: 16383564
Finite-size scaling and particle-size cutoff effects in phase-separating polydisperse fluids.
Wilding NB, Sollich P, Fasolo M., Phys Rev Lett 95(15), 2005
PMID: 16241739
Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC.
Nanias M, Chinchio M, Ołdziej S, Czaplewski C, Scheraga HA., J Comput Chem 26(14), 2005
PMID: 16088925
Histogram analysis as a method for determining the line tension of a three-phase contact region by Monte Carlo simulations.
Djikaev Y., J Chem Phys 123(18), 2005
PMID: 16292918
Optimized ensemble Monte Carlo simulations of dense Lennard-Jones fluids.
Trebst S, Gull E, Troyer M., J Chem Phys 123(20), 2005
PMID: 16351275
A methodology for efficiently sampling the conformation space of molecular structures.
Lee A, Streinu I, Brock O., Phys Biol 2(4), 2005
PMID: 16280616
Prewetting boundary tensions from Monte Carlo simulation.
Errington JR, Wilbert DW., Phys Rev Lett 95(22), 2005
PMID: 16384244
Fast flat-histogram method for generalized spin models.
Reynal S, Diep HT., Phys Rev E Stat Nonlin Soft Matter Phys 72(5 pt 2), 2005
PMID: 16383788
Activated sampling in complex materials at finite temperature: the properly obeying probability activation-relaxation technique.
Vocks H, Chubynsky MV, Barkema GT, Mousseau N., J Chem Phys 123(24), 2005
PMID: 16396563
Entropic sampling via Wang-Landau random walks in dominant energy subspaces.
Malakis A, Martinos SS, Hadjiagapiou IA, Fytas NG, Kalozoumis P., Phys Rev E Stat Nonlin Soft Matter Phys 72(6 pt 2), 2005
PMID: 16486023
Prediction of peptide conformation using a scale-transformed entropy sampling algorithm.
Nakamura H., Comput Biol Chem 28(1), 2004
PMID: 15022644
On the use of Bennett's acceptance ratio method in multi-canonical-type simulations.
Fenwick MK, Escobedo FA., J Chem Phys 120(7), 2004
PMID: 15268459
Determination of solvation free energies by adaptive expanded ensemble molecular dynamics.
Aberg KM, Lyubartsev AP, Jacobsson SP, Laaksonen A., J Chem Phys 120(8), 2004
PMID: 15268541
Reexamination of the long-range Potts model: a multicanonical approach.
Reynal S, Diep HT., Phys Rev E Stat Nonlin Soft Matter Phys 69(2 pt 2), 2004
PMID: 14995522
The evaporation/condensation transition of liquid droplets.
MacDowell LG, Virnau P, Müller M, Binder K., J Chem Phys 120(11), 2004
PMID: 15267401
Multicanonical basin hopping: a new global optimization method for complex systems.
Zhan L, Piwowar B, Liu WK, Hsu PJ, Lai SK, Chen JZ., J Chem Phys 120(12), 2004
PMID: 15267429
Performance limitations of flat-histogram methods.
Dayal P, Trebst S, Wessel S, Würtz D, Troyer M, Sabhapandit S, Coppersmith SN., Phys Rev Lett 92(9), 2004
PMID: 15089505
Large effect of polydispersity on defect concentrations in colloidal crystals.
Pronk S, Frenkel D., J Chem Phys 120(14), 2004
PMID: 15267571
New approach to the first-order phase transition of Lennard-Jones fluids.
Muguruma C, Okamoto Y, Mikami M., J Chem Phys 120(16), 2004
PMID: 15267668
Reconstructing the density of states by history-dependent metadynamics.
Micheletti C, Laio A, Parrinello M., Phys Rev Lett 92(17), 2004
PMID: 15169135
Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations.
Okamoto Y., J Mol Graph Model 22(5), 2004
PMID: 15099838
A finite-size scaling study of a model of globular proteins.
Pagan DL, Gracheva ME, Gunton JD., J Chem Phys 120(17), 2004
PMID: 15267750
Adaptive integration method for Monte Carlo simulations.
Fasnacht M, Swendsen RH, Rosenberg JM., Phys Rev E Stat Nonlin Soft Matter Phys 69(5 pt 2), 2004
PMID: 15244974
Calculation of free energy through successive umbrella sampling.
Virnau P, Muller M., J Chem Phys 120(23), 2004
PMID: 15268122
Freezing and folding behavior in simple off-lattice heteropolymers.
Magee JE, Warwicker J, Lue L., J Chem Phys 120(23), 2004
PMID: 15268156
Generalized 1/k-ensemble algorithm.
Liang F., Phys Rev E Stat Nonlin Soft Matter Phys 69(6 pt 2), 2004
PMID: 15244777
Phase behavior of n-alkanes in supercritical solution: a Monte Carlo study.
Virnau P, Müller M, MacDowell LG, Binder K., J Chem Phys 121(5), 2004
PMID: 15260771
Replica-exchange extensions of simulated tempering method.
Mitsutake A, Okamoto Y., J Chem Phys 121(6), 2004
PMID: 15281846
Monte Carlo simulations in generalized isobaric-isothermal ensembles.
Okumura H, Okamoto Y., Phys Rev E Stat Nonlin Soft Matter Phys 70(2 pt 2), 2004
PMID: 15447615
Modelling of third cytoplasmic loop of bovine rhodopsin by multicanonical molecular dynamics.
Watanabe YS, Fukunishi Y, Nakamura H., J Mol Graph Model 23(1), 2004
PMID: 15331054
Liquid-gas coexistence and critical point shifts in size-disperse fluids.
Wilding NB, Fasolo M, Sollich P., J Chem Phys 121(14), 2004
PMID: 15473748
Optimizing the ensemble for equilibration in broad-histogram Monte Carlo simulations.
Trebst S, Huse DA, Troyer M., Phys Rev E Stat Nonlin Soft Matter Phys 70(4 pt 2), 2004
PMID: 15600559
Long time molecular dynamics for enhanced conformational sampling in biomolecular systems.
Minary P, Tuckerman ME, Martyna GJ., Phys Rev Lett 93(15), 2004
PMID: 15524853
Directional ordering of fluctuations in a two-dimensional compass model.
Mishra A, Ma M, Zhang FC, Guertler S, Tang LH, Wan S., Phys Rev Lett 93(20), 2004
PMID: 15600961
Density of states determined from Monte Carlo simulations.
Hove J., Phys Rev E Stat Nonlin Soft Matter Phys 70(5 pt 2), 2004
PMID: 15600796
Computer simulation of the phase diagram for a fluid confined in a fractal and disordered porous material.
De Grandis V, Gallo P, Rovere M., Phys Rev E Stat Nonlin Soft Matter Phys 70(6 pt 1), 2004
PMID: 15697372
Estimation of critical behavior from the density of states in classical statistical models.
Malakis A, Peratzakis A, Fytas NG., Phys Rev E Stat Nonlin Soft Matter Phys 70(6 pt 2), 2004
PMID: 15697455
Approximate calculation of the ground-state energy for Potts spin-glass models.
Bittner E, Janke W, Saakian DB., Phys Rev E Stat Nonlin Soft Matter Phys 67(1 pt 2), 2003
PMID: 12636562
Evaluating surface tension using grand-canonical transition-matrix Monte Carlo simulation and finite-size scaling.
Errington JR., Phys Rev E Stat Nonlin Soft Matter Phys 67(1 pt 1), 2003
PMID: 12636539
Multiplexed-replica exchange molecular dynamics method for protein folding simulation.
Rhee YM, Pande VS., Biophys J 84(2 pt 1), 2003
PMID: 12547762
Hybrid Monte Carlo with multidimensional replica exchanges: conformational equilibria of the hypervariable regions of a llama VHH antibody domain.
Fenwick MK, Escobedo FA., Biopolymers 68(2), 2003
PMID: 12548621
beta-Hairpins, alpha-helices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal beta-hairpin of SH3 domain.
Ikeda K, Galzitskaya OV, Nakamura H, Higo J., J Comput Chem 24(3), 2003
PMID: 12548722
Flat histogram methods for quantum systems: algorithms to overcome tunneling problems and calculate the free energy.
Troyer M, Wessel S, Alet F., Phys Rev Lett 90(12), 2003
PMID: 12688855
Continuous demixing at liquid-vapor coexistence in a symmetrical binary fluid mixture.
Wilding NB., Phys Rev E Stat Nonlin Soft Matter Phys 67(5 pt 1), 2003
PMID: 12786203
A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition.
Kolinski A, Gront D, Pokarowski P, Skolnick J., Biopolymers 69(3), 2003
PMID: 12833266
Use of multicanonical Monte Carlo simulations to obtain accurate bit error rates in optical communications systems.
Holzlöhner R, Menyuk CR., Opt Lett 28(20), 2003
PMID: 14587767
Designing refoldable model molecules.
Coluzza I, Muller HG, Frenkel D., Phys Rev E Stat Nonlin Soft Matter Phys 68(4 pt 2), 2003
PMID: 14683075
Multicanonical Monte Carlo study and analysis of tails for the order-parameter distribution of the two-dimensional Ising model.
Hilfer R, Biswal B, Mattutis HG, Janke W., Phys Rev E Stat Nonlin Soft Matter Phys 68(4 pt 2), 2003
PMID: 14683018
Free-energy landscape of a chameleon sequence in explicit water and its inherent alpha/beta bifacial property.
Ikeda K, Higo J., Protein Sci 12(11), 2003
PMID: 14573865
Multicanonical chain-growth algorithm.
Bachmann M, Janke W., Phys Rev Lett 91(20), 2003
PMID: 14683403
Transition path sampling: throwing ropes over rough mountain passes, in the dark.
Bolhuis PG, Chandler D, Dellago C, Geissler PL., Annu Rev Phys Chem 53(), 2002
PMID: 11972010
Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse.
Cheung MS, García AE, Onuchic JN., Proc Natl Acad Sci U S A 99(2), 2002
PMID: 11805324
Random-cluster multihistogram sampling for the q-state Potts model.
Weigel M, Janke W, Hu CK., Phys Rev E Stat Nonlin Soft Matter Phys 65(3 pt 2a), 2002
PMID: 11909167
Using novel variable transformations to enhance conformational sampling in molecular dynamics.
Zhu Z, Tuckerman ME, Samuelson SO, Martyna GJ., Phys Rev Lett 88(10), 2002
PMID: 11909330
Monte Carlo sampling algorithm for searching a scale-transformed energy space of polypeptides.
Nakamura H., J Comput Chem 23(4), 2002
PMID: 11908088
Lattice-switch Monte Carlo method: application to soft potentials.
Jackson AN, Bruce AD, Ackland GJ., Phys Rev E Stat Nonlin Soft Matter Phys 65(3 pt 2b), 2002
PMID: 11909310
Functional form of the Parisi overlap distribution for the three-dimensional Edwards-Anderson Ising spin glass.
Berg BA, Billoire A, Janke W., Phys Rev E Stat Nonlin Soft Matter Phys 65(4 pt 2a), 2002
PMID: 12005902
Sampling rare events: statistics of local sequence alignments.
Hartmann AK., Phys Rev E Stat Nonlin Soft Matter Phys 65(5 pt 2), 2002
PMID: 12059642
Combination of improved multibondic method and the Wang-Landau method.
Yamaguchi C, Kawashima N., Phys Rev E Stat Nonlin Soft Matter Phys 65(5 pt 2), 2002
PMID: 12059753
Classification of amino acids based on statistical results of known structures and cooperativity of protein folding.
Chen H, Zhou X, Ou-Yang ZC., Phys Rev E Stat Nonlin Soft Matter Phys 65(6 pt 1), 2002
PMID: 12188759
Broad histogram relation for the bond number and its applications.
Yamaguchi C, Kawashima N, Okabe Y., Phys Rev E Stat Nonlin Soft Matter Phys 66(3 pt 2b), 2002
PMID: 12366295
Phase behavior and thermodynamic anomalies of core-softened fluids.
Wilding NB, Magee JE., Phys Rev E Stat Nonlin Soft Matter Phys 66(3 pt 1), 2002
PMID: 12366122
Generalization of the Wang-Landau method for off-lattice simulations.
Shell MS, Debenedetti PG, Panagiotopoulos AZ., Phys Rev E Stat Nonlin Soft Matter Phys 66(5 pt 2), 2002
PMID: 12513633
Parallel excluded volume tempering for polymer melts.
Bunker A, Dünweg B., Phys Rev E Stat Nonlin Soft Matter Phys 63(1 pt 2), 2001
PMID: 11304387
Generalized-ensemble algorithms for molecular simulations of biopolymers.
Mitsutake A, Sugita Y, Okamoto Y., Biopolymers 60(2), 2001
PMID: 11455545
Interface localization-delocalization transition in a symmetric polymer blend: a finite-size scaling Monte Carlo study.
Müller M, Binder K., Phys Rev E Stat Nonlin Soft Matter Phys 63(2 pt 1), 2001
PMID: 11308503
Efficient, multiple-range random walk algorithm to calculate the density of states.
Wang F, Landau DP., Phys Rev Lett 86(10), 2001
PMID: 11289852
Fast Monte Carlo algorithm for supercooled soft spheres.
Grigera TS, Parisi G., Phys Rev E Stat Nonlin Soft Matter Phys 63(4 pt 2), 2001
PMID: 11308895
Extended state-space Monte Carlo methods.
Opps SB, Schofield J., Phys Rev E Stat Nonlin Soft Matter Phys 63(5 pt 2), 2001
PMID: 11415039
Precise simulation of criticality in asymmetric fluids.
Orkoulas G, Fisher ME, Panagiotopoulos AZ., Phys Rev E Stat Nonlin Soft Matter Phys 63(5 pt 1), 2001
PMID: 11414909
Energy landscape of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin, and other disordered conformations.
Higo J, Ito N, Kuroda M, Ono S, Nakajima N, Nakamura H., Protein Sci 10(6), 2001
PMID: 11369854
Monte Carlo study of the three-dimensional Coulomb frustrated Ising ferromagnet.
Grousson M, Tarjus G, Viot P., Phys Rev E Stat Nonlin Soft Matter Phys 64(3 pt 2), 2001
PMID: 11580396
Taboo search by successive confinement: surveying a potential energy surface.
Chekmarev SF., Phys Rev E Stat Nonlin Soft Matter Phys 64(3 pt 2), 2001
PMID: 11580478
Determining the density of states for classical statistical models: a random walk algorithm to produce a flat histogram.
Wang F, Landau DP., Phys Rev E Stat Nonlin Soft Matter Phys 64(5 pt 2), 2001
PMID: 11736008
Lattice-switch monte carlo method
Bruce AD, Jackson AN, Ackland GJ, Wilding NB., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 61(1), 2000
PMID: 11046340
Free energy landscapes of peptides by enhanced conformational sampling.
Nakajima N, Higo J, Kidera A, Nakamura H., J Mol Biol 296(1), 2000
PMID: 10656827
Temperature and density extrapolations in canonical ensemble monte carlo simulations
Ferreira AL, Barroso MA., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 61(2), 2000
PMID: 11046394
Optimized energy calculation in lattice systems with long-range interactions
Krech M, Luijten E., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 61(2), 2000
PMID: 11046497
Replica-exchange molecular dynamics simulation for supercooled liquids
Yamamoto R, Kob W., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 61(5b), 2000
PMID: 11031600
Approach to Monte Carlo calculation of the buckling of supercoiled DNA loops.
Zhang Y., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 62(5 pt a), 2000
PMID: 11102016
Freezing by monte carlo phase switch
Wilding NB, Bruce AD., Phys Rev Lett 85(24), 2000
PMID: 11102205
Enhanced sampling of rare events
Melchionna S., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 62(6 pt b), 2000
PMID: 11138179
Simulation of phase transitions in fluids.
de Pablo JJ, Yan Q, Escobedo FA., Annu Rev Phys Chem 50(), 1999
PMID: 15012417
Off-lattice model for the phase behavior of lipid-cholesterol bilayers.
Nielsen M, Miao L, Ipsen JH, Zuckermann MJ, Mouritsen OG., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 59(5 pt b), 1999
PMID: 11969560
De novo simulations of the folding thermodynamics of the GCN4 leucine zipper.
Mohanty D, Kolinski A, Skolnick J., Biophys J 77(1), 1999
PMID: 10388740
Understanding beta-hairpin formation.
Dinner AR, Lazaridis T, Karplus M., Proc Natl Acad Sci U S A 96(16), 1999
PMID: 10430896
Metastable states of an Ising-like thermally bistable system.
Shteto I, Boukheddaden K, Varret F., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 60(5 pt a), 1999
PMID: 11970382
Monte Carlo approach to the gas-liquid transition in porous materials.
Alvarez M, Levesque D, Weis JJ., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 60(5 pt a), 1999
PMID: 11970424
Enhanced conformational diversity search of CDR-H3 in antibodies: role of the first CDR-H3 residue.
Kim ST, Shirai H, Nakajima N, Higo J, Nakamura H., Proteins 37(4), 1999
PMID: 10651282
Conformational sampling of CDR-H3 in antibodies by multicanonical molecular dynamics simulation.
Shirai H, Nakajima N, Higo J, Kidera A, Nakamura H., J Mol Biol 278(2), 1998
PMID: 9571065
Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model.
Schaefer M, Bartels C, Karplus M., J Mol Biol 284(3), 1998
PMID: 9826519
Characterization of flexible molecules in solution: the RGDW peptide.
Bartels C, Stote RH, Karplus M., J Mol Biol 284(5), 1998
PMID: 9878376
Cooling-rate dependence of the ground-state energy using microcanonical simulated annealing.
Ocampo-Alfaro P, Guo H., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 53(2), 1996
PMID: 9964462
Reconstruction of a first-order phase transition from computer simulations of individual phases and subphases.
Ebeling M, Nadler W., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 53(4), 1996
PMID: 9964644
Monte Carlo study of a compressible Ising antiferromagnet on a triangular lattice.
Gu L, Chakraborty B, Garrido PL, Phani M, Lebowitz JL., Phys Rev B Condens Matter 53(18), 1996
PMID: 9982824
Multicanonical Monte Carlo study of solid-solid phase coexistence in a model colloid.
Smith GR, Bruce AD., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 53(6), 1996
PMID: 9965016
Eliminating metastability in first-order phase transitions.
Bouabci MB, Carneiro CE., Phys Rev B Condens Matter 54(1), 1996
PMID: 9984266
Invaded cluster algorithm for Potts models.
Machta J, Choi YS, Lucke A, Schweizer T, Chayes LM., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 54(2), 1996
PMID: 9965202
Adaptation and linear-response theory.
Munakata T, Oyama S., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 54(4), 1996
PMID: 9965591
On the origin of the cooperativity of protein folding: implications from model simulations.
Kolinski A, Galazka W, Skolnick J., Proteins 26(3), 1996
PMID: 8953649
Monte Carlo simulations in generalized ensemble: Multicanonical algorithm versus simulated tempering.
Hansmann UH, Okamoto Y., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 54(5), 1996
PMID: 9965783
Four-dimensional pure compact U(1) gauge theory on a spherical lattice.
Jersák J, Lang CB, Neuhaus T., Phys Rev D Part Fields 54(11), 1996
PMID: 10020700
Multibondic cluster algorithm for Monte Carlo simulations of first-order phase transitions.
Janke W, Kappler S., Phys Rev Lett 74(2), 1995
PMID: 10058331
Monte Carlo simulation and global optimization without parameters.
Hesselbo B, Stinchcombe RB., Phys Rev Lett 74(12), 1995
PMID: 10057856
Statistical errors in histogram reweighting.
Ferrenberg AM, Landau DP, Swendsen RH., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 51(5), 1995
PMID: 9963222
Method to study relaxation of metastable phases: Macroscopic mean-field dynamics.
Lee J, Novotny MA, Rikvold PA., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 52(1), 1995
PMID: 9963440
Critical-point and coexistence-curve properties of the Lennard-Jones fluid: A finite-size scaling study.
Wilding NB., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 52(1), 1995
PMID: 9963461
Multicanonical multigrid Monte Carlo method.
Janke W, Sauer T., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 49(4), 1994
PMID: 9961616
Optimization by multicanonical annealing and the traveling salesman problem.
Lee J, Choi MY., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 50(2), 1994
PMID: 9962167
Simulated-tempering procedure for spin-glass simulations.
Kerler W, Rehberg P., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 50(5), 1994
PMID: 9962477
Phase structure and monopoles in U(1) gauge theory.
Kerler W, Rebbi C, Weber A., Phys Rev D Part Fields 50(11), 1994
PMID: 10017679
Ground-state properties of the three-dimensional Ising spin glass.
Berg BA, Hansmann UE, Celik T., Phys Rev B Condens Matter 50(22), 1994
PMID: 9976031
Simulation of an ensemble with varying magnetic field: A numerical determination of the order-order interface tension in the D=2 Ising model.
Berg BA, Hansmann U, Neuhaus T., Phys Rev B Condens Matter 47(1), 1993
PMID: 10004471
Exhaustive conformational search and simulated annealing for models of lattice peptides.
Brower RC, Vasmatzis G, Silverman M, Delisi C., Biopolymers 33(3), 1993
PMID: 8461447
Cluster dynamics for first-order phase transitions in the Potts model.
Kerler W, Weber A., Phys Rev B Condens Matter 47(17), 1993
PMID: 10005311
Accurate first-order transition points from finite-size data without power-law corrections.
Janke W., Phys Rev B Condens Matter 47(22), 1993
PMID: 10005849
New Monte Carlo algorithm: Entropic sampling.
Lee J., Phys Rev Lett 71(2), 1993
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Microcanonical renormalization-group simulation of Ising systems.
de Souza AJ, Brady Moreira FG., Phys Rev B Condens Matter 48(13), 1993
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Numerical transfer-matrix study of surface-tension anisotropy in Ising models on square and cubic lattices.
Richards HL, Novotny MA, Rikvold PA., Phys Rev B Condens Matter 48(19), 1993
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Surface tension in SU(3) at finite temperature.
Alves NA., Phys Rev D Part Fields 46(8), 1992
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Application of cluster algorithms to spin glasses.
Liang S., Phys Rev Lett 69(14), 1992
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New approach to spin-glass simulations.
Berg BA, Celik T., Phys Rev Lett 69(15), 1992
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Interface tension and chiral order parameter profile with dynamical quarks.
Hackel M, Faber M, Markum H, Müller M., Phys Rev D Part Fields 46(12), 1992
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