Topic
Monte Carlo molecular modeling
About: Monte Carlo molecular modeling is a research topic. Over the lifetime, 11307 publications have been published within this topic receiving 409122 citations.
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31 Mar 2010TL;DR: This work explores the use of tempered Markov Chain Monte-Carlo for sampling in RBMs and finds both through visualization of samples and measures of likelihood that it helps both sampling and learning.
Abstract: Alternating Gibbs sampling is the most common scheme used for sampling from Restricted Boltzmann Machines (RBM), a crucial component in deep architectures such as Deep Belief Networks. However, we find that it often does a very poor job of rendering the diversity of modes captured by the trained model. We suspect that this hinders the advantage that could in principle be brought by training algorithms relying on Gibbs sampling for uncovering spurious modes, such as the Persistent Contrastive Divergence algorithm. To alleviate this problem, we explore the use of tempered Markov Chain Monte-Carlo for sampling in RBMs. We find both through visualization of samples and measures of likelihood that it helps both sampling and learning.
134 citations
TL;DR: In this paper, the authors assess the validity of these approximations with grand canonical Monte Carlo simulations for a well-known Zn-based MOF (IRMOF-1), using potential parameters specifically derived for IRMOF, and compare the results with experimental results for hydrogen and xenon adsorption at room temperature.
Abstract: The gas storage capacity of metal−organic frameworks (MOFs) is well-known and has been investigated using both experimental and computational methods. Previous Monte Carlo computer simulations of gas adsorption by MOFs have made several questionable approximations regarding framework−framework and framework−adsorbate interactions: potential parameters from general force fields have been used, and framework atoms were fixed at their crystallographic coordinates (rigid framework). We assess the validity of these approximations with grand canonical Monte Carlo simulations for a well-known Zn-based MOF (IRMOF-1), using potential parameters specifically derived for IRMOF-1. Our approach is validated by comparison with experimental results for hydrogen and xenon adsorption at room temperature. The effects of framework flexibility on the adsorption of noble gases and hydrogen are described, as well as the selectivity of IRMOF-1 for xenon versus other noble gases. At both low temperature (78 K) and room temperatu...
134 citations
TL;DR: A particle-based Monte Carlo formalism for the study of polymeric melts, where the interaction energy is given by a local density functional, as is done in traditional field-theoretic models, is introduced.
Abstract: We introduce a particle-based Monte Carlo formalism for the study of polymeric melts, where the interaction energy is given by a local density functional, as is done in traditional field-theoretic models. The method enables Monte Carlo simulations in arbitrary ensembles and direct calculation of free energies. We present results for the phase diagram and the critical point of a binary homopolymer blend. For a symmetric diblock copolymer, we compute the distribution of local stress in lamellae and locate the order-disorder transition.
134 citations
TL;DR: The first numerical determination of the thermodynamic isotropic-nematic transition in a simple three-dimensional model fluid, viz., a system of infinitely thin hard platelets, is reported in this article.
Abstract: The first numerical determination of the thermodynamic isotropic-nematic transition in a simple three-dimensional model fluid, viz., a system of infinitely thin hard platelets, is reported. Thermodynamic properties were studied with use of the constant-pressure Monte Carlo method; Widom's particle-insertion method was used to measure the chemical potential. The phase diagram is found to differ considerably from predictions of a second-virial ("Onsager") theory. Virial coefficients up to the fifth were computed; b5 is found to be negative.
133 citations
17 Oct 1999
TL;DR: It is proved that, under certain circumstances, the mixing time in a box of side length L with periodic boundary conditions can be exponential in L/sup d-1/.
Abstract: Studies two widely used algorithms, Glauber dynamics and the Swendsen-Wang (1987) algorithm, on rectangular subsets of the hypercubic lattice Z/sup d/. We prove that, under certain circumstances, the mixing time in a box of side length L with periodic boundary conditions can be exponential in L/sup d-1/. In other words, under these circumstances, the mixing in these widely used algorithms is not rapid; instead it is torpid. The models we study are the independent set model and the q-state Potts model. For both models, we prove that Glauber dynamics is torpid in the region with phase coexistence. For the Potts model, we prove that the Swendsen-Wang mixing is torpid at the phase transition point.
133 citations