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Simulating Normalized Constants: From Importance Sampling to Bridge Sampling to Path Sampling
 Statistical Science, 13, 163–185. COMPARISON OF METHODS FOR COMPUTING BAYES FACTORS 435
, 1998
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Cited by 146 (4 self)
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Extended ensemble Monte Carlo
 Int. J. Mod. Phys
, 2001
"... “Extended Ensemble Monte Carlo ” is a generic term that indicates a set of algorithms which are now popular in a variety of fields in physics and statistical information processing. Exchange Monte Carlo (MetropolisCoupled Chain, Parallel Tempering), Simulated Tempering (Expanded Ensemble Monte Carl ..."
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Cited by 29 (1 self)
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“Extended Ensemble Monte Carlo ” is a generic term that indicates a set of algorithms which are now popular in a variety of fields in physics and statistical information processing. Exchange Monte Carlo (MetropolisCoupled Chain, Parallel Tempering), Simulated Tempering (Expanded Ensemble Monte Carlo), and Multicanonical Monte Carlo (Adaptive Umbrella Sampling) are typical members of this family. Here we give a crossdisciplinary survey of these algorithms with special emphasis on the great flexibility of the underlying idea. In Sec. 2, we discuss the background of Extended Ensemble Monte Carlo. In Sec. 3, 4 and 5, three types of the algorithms, i.e., Exchange Monte Carlo, Simulated Tempering, Multicanonical Monte Carlo, are introduced. In Sec. 6, we give an introduction to Replica Monte Carlo algorithm by Swendsen and Wang. Strategies for the construction of specialpurpose extended ensembles are discussed in Sec. 7. We stress
EQUIENERGY SAMPLER WITH APPLICATIONS IN STATISTICAL INFERENCE AND STATISTICAL MECHANICS
, 2006
"... We introduce a new sampling algorithm, the equienergy sampler, for efficient statistical sampling and estimation. Complementary to the widely used temperaturedomain methods, the equienergy sampler, utilizing the temperature–energy duality, targets the energy directly. The focus on the energy func ..."
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Cited by 26 (4 self)
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We introduce a new sampling algorithm, the equienergy sampler, for efficient statistical sampling and estimation. Complementary to the widely used temperaturedomain methods, the equienergy sampler, utilizing the temperature–energy duality, targets the energy directly. The focus on the energy function not only facilitates efficient sampling, but also provides a powerful means for statistical estimation, for example, the calculation of the density of states and microcanonical averages in statistical mechanics. The equienergy sampler is applied to a variety of problems, including exponential regression in statistics, motif sampling in computational biology and protein folding in biophysics.
Multiplexedreplica exchange molecular dynamics method for protein folding simulation
 Biophys. J
, 2003
"... ABSTRACT Simulating protein folding thermodynamics starting purely from a protein sequence is a grand challenge of computational biology. Here, we present an algorithm to calculate a canonical distribution from molecular dynamics simulation of protein folding. This algorithm is based on the replica ..."
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Cited by 18 (0 self)
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ABSTRACT Simulating protein folding thermodynamics starting purely from a protein sequence is a grand challenge of computational biology. Here, we present an algorithm to calculate a canonical distribution from molecular dynamics simulation of protein folding. This algorithm is based on the replica exchange method where the kinetic trapping problem is overcome by exchanging noninteracting replicas simulated at different temperatures. Our algorithm uses multiplexedreplicas with a number of independent molecular dynamics runs at each temperature. Exchanges of configurations between these multiplexedreplicas are also tried, rendering the algorithm applicable to largescale distributed computing (i.e., highly heterogeneous parallel computers with processors having different computational power). We demonstrate the enhanced sampling of this algorithm by simulating the folding thermodynamics of a 23 amino acid miniprotein. We show that better convergence is achieved compared to constant temperature molecular dynamics simulation, with an efficient scaling to large number of computer processors. Indeed, this enhanced sampling results in (to our knowledge) the first example of a replica exchange algorithm that samples a folded structure starting from a completely unfolded state.
Hybrid Monte Carlo with Adaptive Temperature in a MixedCanonical Ensemble: Efficient Conformational Analysis of RNA
 J. COMPUT. CHEM
, 1997
"... A hybrid Monte Carlo method with adaptive temperature choice is presented, which exactly generates the distribution of a mixedcanonical ensemble composed of two canonical ensembles at low and high temperature. The analysis of resulting Markov chains with the reweighting technique shows an effici ..."
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Cited by 9 (4 self)
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A hybrid Monte Carlo method with adaptive temperature choice is presented, which exactly generates the distribution of a mixedcanonical ensemble composed of two canonical ensembles at low and high temperature. The analysis of resulting Markov chains with the reweighting technique shows an efficient sampling of the canonical distribution at low temperature, whereas the high temperature component facilitates conformational transitions, which allows shorter simulation times. The algorithm was tested by comparing analytical and numerical results for the small nbutane molecule before simulations were performed for a triribonucleotide. Sampling the complex multiminima energy landscape of this small RNA segment, we observe enforced crossing of energy barriers.
Importance sampling for families of distributions
 Annals of Applied Probability
, 1999
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Cited by 9 (1 self)
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Equilibrium sampling from nonequilibrium dynamics
 Jardin Botanique  BP 101  54602 VillerslèsNancy Cedex Centre de recherche INRIA Paris – Rocquencourt : Domaine de Voluceau  Rocquencourt  BP 105  78153 Le Chesnay Cedex Centre de recherche INRIA Rennes – Bretagne Atlantique : IRISA, Campus universi
, 2006
"... We present some applications of an Interacting Particle System (IPS) methodology to the field of Molecular Dynamics. This IPS method allows several simulations of a switched random process to keep closer to equilibrium at each time, thanks to a selection mechanism based on the relative virtual work ..."
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Cited by 6 (1 self)
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We present some applications of an Interacting Particle System (IPS) methodology to the field of Molecular Dynamics. This IPS method allows several simulations of a switched random process to keep closer to equilibrium at each time, thanks to a selection mechanism based on the relative virtual work induced on the system. It is therefore an efficient improvement of usual nonequilibrium simulations, which can be used to compute canonical averages, free energy differences, and typical transitions paths. Keywords: Nonequilibrium molecular dynamics, Interacting Particle System, Genetic Algorithms, Free energy Estimation. AMS: 65C05, 65C35, 80A10. Phasespace integrals are widely used in Statistical Physics to relate the macroscopic properties of a system to the elementary phenomenon at the microscopic scale [14]. In constant temperature (NVT) molecular simulations, 1 these integrals often take the form µ(A) = 〈A 〉 =
Progress in lattice field theory algorithms," in Smit and van Baal [23
 96107. Proceedings of the International Symposium on Lattice Field Theory
, 1992
"... heplat/9212017 I present a summary of recent algorithmic developments for lattice field theories. In particular I give a pedagogical introduction to the new Multicanonical algorithm, and discuss the relation between the Hybrid Overrelaxation and Hybrid Monte Carlo algorithms. I also attempt to clar ..."
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Cited by 4 (2 self)
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heplat/9212017 I present a summary of recent algorithmic developments for lattice field theories. In particular I give a pedagogical introduction to the new Multicanonical algorithm, and discuss the relation between the Hybrid Overrelaxation and Hybrid Monte Carlo algorithms. I also attempt to clarify the rôle of the dynamical critical exponent z and its connection with “computational cost.” This research was supported by the Florida State University Supercomputer Computations
Progress in fourdimensional lattice supersymmetryarXiv: 0903.2443
"... We are entering an era where a number of largescale lattice simulations of fourdimensional supersymmetric theories are under way. Moreover, proposals for how to approach such studies continue to progress. One particular line of research in this direction is described here. General actions for supe ..."
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Cited by 2 (0 self)
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We are entering an era where a number of largescale lattice simulations of fourdimensional supersymmetric theories are under way. Moreover, proposals for how to approach such studies continue to progress. One particular line of research in this direction is described here. General actions for superQCD, including counterterms required on the lattice, are given. We obtain the number of finetunings that is required, once gauge and flavor symmetries are accounted for, provided GinspargWilson fermions are used for the gauginos. We also review and extend our recent work on lattice formulations of N = 4 superYangMills and N = 1 superYangMills that exploit GinspargWilson fermions.