Search results for "Monte Carlo method."
showing 10 items of 1217 documents
Atomistic theory of mesoscopic pattern formation induced by bimolecular surface reactions between oppositely charged molecules
2011
The kinetics of mesoscopic pattern formation is studied for a reversible A+B⇌0 reaction between mobile oppositely charged molecules at the interface. Using formalism of the joint correlation functions, non-equilibrium charge screening and reverse Monte Carlo methods, it is shown that labyrinth-like percolation structure induced by (even moderate-rate) reaction is principally non-steady-state one and is associated with permanently growing segregation of dissimilar reactants and aggregation of similar reactants into mesoscopic size domains. A role of short-range and long-range reactant interactions in pattern formation is discussed.
Simulation of Order-Disorder Phenomena and Diffusion in Metallic Alloys
1991
The application of the Monte Carlo method to lattice-statistics problems in metallurgy is reviewed. Examples are given for the prediction of phase diagrams from simple model assumptions for effective interatomic potentials and for the calculation of parameters describing long- and short-range order, ordering energy, etc., both for face-centered cubic (fcc) and body-centered cubic (bcc) lattices. Applications to real systems such as Cu—Au and Fe—Al alloys are discussed.
Monte Carlo calculation of free energy for a fcc lattice-gas model
1990
A face-centered-cubic Ising lattice-gas model with nearest- and next-nearest-neighbor interactions is studied, and an accurate determination of the transition temperature for the discontinuous order-disorder transition is obtained. This model is of interest in the studies of phase diagrams for metallic alloys. The location of the transition was previously not known accurately, and its estimation has a number of applications. Very accurate absolute free-energy densities for the two coexisting phases have been obtained from a combination of the standard thermodynamic integration method and the method of sampling finite-size dependence. The latent-heat also is calculated with good precision.
Influence of a continuous quenching procedure on the initial stages of spinodal decomposition
1986
Instead of the standard assumption in the theory of phase separation where an instantaneous quench from an initial equilibrium state to the final state in the two-phase region is assumed, we consider the more realistic situation that the change of the external control parameter (e.g. temperature) can only be performed with finite rates. During the initial stages of spinodal decomposition the system then has some “memory” of the states intermediate between the initial and the final one. This influence of the finite quench rate in continuous quenching procedures is studied within the linearized theory of spinodal decomposition, with the Langer-Baron-Miller decoupling, and with Monte Carlo sim…
Monte Carlo Tests of Nucleation Concepts in the Lattice Gas Model
2013
The conventional theory of homogeneous and heterogeneous nucleation in a supersaturated vapor is tested by Monte Carlo simulations of the lattice gas (Ising) model with nearest-neighbor attractive interactions on the simple cubic lattice. The theory considers the nucleation process as a slow (quasi-static) cluster (droplet) growth over a free energy barrier $\Delta F^*$, constructed in terms of a balance of surface and bulk term of a "critical droplet" of radius $R^*$, implying that the rates of droplet growth and shrinking essentially balance each other for droplet radius $R=R^*$. For heterogeneous nucleation at surfaces, the barrier is reduced by a factor depending on the contact angle. U…
Characterizing cavities in model inclusion molecules: a comparative study
1998
We have selected fullerene-60 and -70 cavities as model systems in order to test several methods for characterizing inclusion molecules. The methods are based on different technical foundations such as a square and triangular tessellation of the molecule taken as a unitary sphere, spherical tessellation of the molecular surface, numerical integration of the atomic volumes and surfaces, triangular tessellation of the molecular surface, and a cubic lattice approach to a molecular space. Accurate measures of the molecular volume and surface area have been performed with the pseudo-random Monte Carlo (MCVS) and uniform Monte Carlo (UMCVS) methods. These calculations serve as a reference for the…
Molecular Rearrangement of an Aza-Scorpiand Macrocycle Induced by pH: A Computational Study †
2016
Rearrangements and their control are a hot topic in supramolecular chemistry due to the possibilities that these phenomena open in the design of synthetic receptors and molecular machines. Macrocycle aza-scorpiands constitute an interesting system that can reorganize their spatial structure depending on pH variations or the presence of metal cations. In this study, the relative stabilities of these conformations were predicted computationally by semi-empirical and density functional theory approximations, and the reorganization from closed to open conformations was simulated by using the Monte Carlo multiple minimum method Financial support by the Spanish Ministerio de Economía y Competitiv…
Dynamics of surface of lipid membranes: theoretical considerations and the ESR experiment.
2016
The effect of the surface layer of model membranes on their physical properties was discussed in this paper. The research involved a physical ESR experiment with the use of spin probes and computer simulation based on the Monte Carlo technique. Liposomes formed during the process of sonication of lecithin were scanned in an ESR spectrometer. The membrane surface layer model, represented by the system of electric dipoles arranged in rectangular or hexagonal matrices, was studied. The final states of computer simulations were presented as textures. It was found that in the gel phase some ordered domain structures are formed, while in the liquid–crystal phase we got complex textures comprising…
Effects of confinement and external fields on structure and transport in colloidal dispersions in reduced dimensionality
2012
In this work, we focus on low-dimensional colloidal model systems, via simulation studies and also some complementary experiments, in order to elucidate the interplay between phase behavior, geometric structures and transport properties. In particular, we try to investigate the (nonlinear!) response of these very soft colloidal systems to various perturbations: uniform and uniaxial pressure, laser fields, shear due to moving boundaries and randomly quenched disorder.We study ordering phenomena on surfaces or in monolayers by Monte Carlo computer simulations of binary hard-disk mixtures, the influence of a substrate being modeled by an external potential. Weak external fields allow a control…
Protein search for multiple targets on DNA
2016
Protein-DNA interactions are crucial for all biological processes. One of the most important fundamental aspects of these interactions is the process of protein searching and recognizing specific binding sites on DNA. A large number of experimental and theoretical investigations have been devoted to uncovering the molecular description of these phenomena, but many aspects of the mechanisms of protein search for the targets on DNA remain not well understood. One of the most intriguing problems is the role of multiple targets in protein search dynamics. Using a recently developed theoretical framework we analyze this question in detail. Our method is based on a discrete-state stochastic appro…