Search results for " molecular modeling"

Isotropic–isotropic phase separation in mixtures of rods and spheres: Some aspects of Monte Carlo simulation in the grand canonical ensemble

2008

Abstract In this article we consider mixtures of non-adsorbing polymers and rod-like colloids in the isotropic phase, which upon the addition of polymers show an effective attraction via depletion forces. Above a certain concentration, the depletant causes phase separation of the mixture. We performed Monte Carlo simulations to estimate the phase boundaries of isotropic–isotropic coexistence. To determine the phase boundaries we simulated in the grand canonical ensemble using successive umbrella sampling [J. Chem. Phys. 120 (2004) 10925]. The location of the critical point was estimated by a finite size scaling analysis. In order to equilibrate the system efficiently, we used a cluster move…

Never Cared for What They Do: High Structural Stability of Guanine-Quadruplexes in the Presence of Strand-Break Damage

2022

DNA integrity is an important factor that assures genome stability and, more generally, the viability of cells and organisms. In the presence of DNA damage, the normal cell cycle is perturbed when cells activate their repair processes. Although efficient, the repair system is not always able to ensure complete restoration of gene integrity. In these cases, mutations not only may occur, but the accumulation of lesions can either lead to carcinogenesis or reach a threshold that induces apoptosis and programmed cell death. Among the different types of DNA lesions, strand breaks produced by ionizing radiation are the most toxic due to the inherent difficultly of repair, which may lead to genomi…

Monte Carlo simulation of DNA electrophoresis

1989

This paper describes an attempt to study the electrophoresis mobility of a DNA molecule in a gel by means of a Monte Carlo simulation. We find that the electrophoresis mobility mu can be well described by the empirical equation mu v kappa 1/N + kappa 2E2 with N being the number of monomers of the model chain and E being the applied field. For small E the data can merge into the linear response result mu = kappa 1/N. The paper also discusses necessary extensions of the present approach.

Monte carlo methods in quantum many-body theories

2008

This is an introduction of Monte Carlo methods for beginners and their application to some quantum many-body problems. Special emphasis is done on the methodology and the general characteristics of Monte Carlo calculations. An introduction to the applications to many-body physics, specifically the Variational Monte Carlo and the Green Function Monte Carlo, is also included.

Off-lattice models

2005

A Monte Carlo Simulation of the Stillinger-Weber Model for Si-Ge Alloys

1994

ABSTRACTThe bulk phase behavior of silicon-germanium alloys is investigated by means of a constant pressure Monte Carlo simulation of the Stillinger-Weber potential in the semi-grand-canonical ensemble. At low temperatures, Si and Ge phase separate into a Si-rich phase and a Ge-rich phase. The two-phase region is terminated by a critical point whose nature is investigated thoroughly by the multihistogram method combined with finite size scaling analysis. These results showed that the critical behavior of the alloy belongs to the mean field universality class, presumably due to the elastic degrees of freedom. We have also studied the structural properties of the mixture and found that the li…

Analysis of multilayer adsorption models without screening

1991

A class of recently introduced irreversible multilayer adsorption models without screening is analysed. The basic kinetic process of these models leads to power law behaviour for the decay of the jamming coverage as a function of height. The authors find the exact value for the power law exponent. An approximate analytical treatment of these models and previous Monte Carlo simulations are found to be in good agreement.

Crossover scaling in semidilute polymer solutions: a Monte Carlo test

1991

Monte Carlo test of the self-consistent field theory of a polymer brush

1992

Medium-range interactions and crossover to classical critical behavior

1996

We study the crossover from Ising-like to classical critical behavior as a function of the range R of interactions. The power-law dependence on R of several critical amplitudes is calculated from renormalization theory. The results confirm the predictions of Mon and Binder, which were obtained from phenomenological scaling arguments. In addition, we calculate the range dependence of several corrections to scaling. We have tested the results in Monte Carlo simulations of two-dimensional systems with an extended range of interaction. An efficient Monte Carlo algorithm enabled us to carry out simulations for sufficiently large values of R, so that the theoretical predictions could actually be …