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.

Monte carlo filter using the genetic algorithm operators

Abstract: We consider the generalized state space model (GSSM) which is an extension of the state space model to the non-Gaussian and non-linear model. There are serious problems in the GSSM approach because of the need for numerical integration over a state space. A Monte Carlo method for filtering and smoothing, called the Monte Carlo Filter (MCF), has been proposed to overcome this numerical problem. It has been pointed out that there exists a close relationship between the MCF and the genetic algorithm (GA) and that an essential structure involved in the MCF is quite similar to that in the GA. In this study, we try to replace the step of the prediction by the mutation and crossover operators in the GA, and demonstrate their performance as the system noise. We furthermore propose a smoothing algorithm in which a massively simple parallel procedure plays an important role. The proposed method is first applied to a simple problem and then to a seasonal adjustment for quarterly data sets in order to illustrate its ...

Kinetic and thermodynamic analysis of proteinlike heteropolymers: Monte Carlo histogram technique

Abstract: Using Monte Carlo dynamics and the Monte Carlo histogram method, the simple three‐dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good and poor folding sequences. The good (fast folding) sequences have sharp well‐defined thermodynamic transitions while the slow folding sequences have broad ones. We find two independent transitions: a collapse transition to compact states and a folding transition from compact states to the native state. The collapse transition is second‐order‐like, while folding is first‐order‐like. The system is also studied as a function of the energy parameters. In particular, as the average energetic drive toward compactness is reduced, the two transitions approach each other. At zero average drive, collapse and folding occur almost simultaneously; i.e., the chain collapses directly into the native state. At a specific value of this energy drive the folding temperature falls below ...

Entropic forces in binary hard sphere mixtures: theory and simulation

Abstract: We perform extensive Monte Carlo simulations of binary hard-sphere mixtures (with diameter ratios of 5 and 10), to determine the entropic force between (1) a macrosphere and a hard wall, and (2) a pair of macrospheres. The microsphere background fluid (at volume fractions ranging from 0.1 to 0.34) induces an entropic force on the macrosphere(s); the latter component is at infinite dilution. We find good overall agreement, in both cases, with the predictions of a hypernetted chain-based theory for the entropic force. Our results also argue for the validity of the Derjaguin approximation relating the force between convex bodies to that between planar surfaces. The earlier Asakura-Oosawa theory, based on a simple geometric argument, is only accurate in the low-density limit.

Universality in three-dimensional Ising spin glasses: A Monte Carlo study

Abstract: We study universality in three-dimensional Ising spin glasses by large-scale Monte Carlo simulations of the Edwards-Anderson Ising spin glass for several choices of bond distributions, with particular emphasis on Gaussian and bimodal interactions. A finite-size scaling analysis suggests that three-dimensional Ising spin glasses obey universality.