Topic
Dynamic Monte Carlo method
About: Dynamic Monte Carlo method is a research topic. Over the lifetime, 13294 publications have been published within this topic receiving 371256 citations.
Papers published on a yearly basis
Papers
More filters
IBM1
TL;DR: In this article, a four-body interaction potential for water molecules is derived for the correlation function g(OO), for the X-ray and neutron-beam scattering intensities, and for the enthalpy.
114 citations
TL;DR: In this article, the authors present a self-learning method for performing kinetic Monte Carlo simulations that does not require an a priori list of diffusion processes and their associated energy and reaction rates.
Abstract: We present a method of performing kinetic Monte Carlo simulations that does not require an a priori list of diffusion processes and their associated energetics and reaction rates. Rather, at any time during the simulation, energetics for all possible (single- or multiatom) processes, within a specific interaction range, are either computed accurately using a saddle-point search procedure, or retrieved from a database in which previously encountered processes are stored. This self-learning procedure enhances the speed of the simulations along with a substantial gain in reliability because of the inclusion of many-particle processes. Accompanying results from the application of the method to the case of two-dimensional Cu adatom-cluster diffusion and coalescence on Cu(111) with detailed statistics of involved atomistic processes and contributing diffusion coefficients attest to the suitability of the method for the purpose.
114 citations
TL;DR: In this paper, Monte Carlo principles and Neutron Transport Problems are used to solve transport problems in nuclear power plants, and the Monte Carlo principle is applied to the transport of neutrons.
Abstract: (1971). Monte Carlo Principles and Neutron Transport Problems. Nuclear Science and Engineering: Vol. 46, No. 3, pp. 439-440.
113 citations
TL;DR: In this paper, a random flight procedure is proposed to replace a large number of local scattering events by a single advance of the coordinates and time of a particle, which can substantially improve the computational efficiency of the implicit Monte Carlo method without affecting its accuracy.
113 citations
TL;DR: The reliability and robustness of the new method should enable its routine application in model building protocols based on various (very sparse) experimentally derived structural restraints, and increasing the number of tertiary restraints improves the accuracy of the assembled structures.
Abstract: A new, efficient method for the assembly of protein tertiary structure from known, loosely encoded secondary structure restraints and sparse information about exact side chain contacts is proposed and evaluated. The method is based on a new, very simple method for the reduced modeling of protein structure and dynamics, where the protein is described as a lattice chain connecting side chain centers of mass rather than Calphas. The model has implicit built-in multibody correlations that simulate short- and long-range packing preferences, hydrogen bonding cooperativity and a mean force potential describing hydrophobic interactions. Due to the simplicity of the protein representation and definition of the model force field, the Monte Carlo algorithm is at least an order of magnitude faster than previously published Monte Carlo algorithms for structure assembly. In contrast to existing algorithms, the new method requires a smaller number of tertiary restraints for successful fold assembly; on average, one for every seven residues as compared to one for every four residues. For example, for smaller proteins such as the B domain of protein G, the resulting structures have a coordinate root mean square deviation (cRMSD), which is about 3 A from the experimental structure; for myoglobin, structures whose backbone cRMSD is 4.3 A are produced, and for a 247-residue TIM barrel, the cRMSD of the resulting folds is about 6 A. As would be expected, increasing the number of tertiary restraints improves the accuracy of the assembled structures. The reliability and robustness of the new method should enable its routine application in model building protocols based on various (very sparse) experimentally derived structural restraints.
113 citations