相关论文: Thermodynamic Sampling of Molecular Conformations
The swept-field experiments on magnetic molecular solids such as \Fe8 are studied using Monte Carlo simulations. A kinetic equation is developed to understand the phenomenon. It is found that the simulations provide a quantitatively…
We propose a novel computational strategy to study the glass transition of molecular fluids. Our approach combines the construction of simple yet realistic models with the development of Monte Carlo algorithms to accelerate equilibration…
We present an algorithm for rigid body diffusion Monte Carlo with importance sampling, which is based on a rigorous short-time expansion of the Green's function for rotational motion in three dimensions. We show that this short-time…
Aims. Numerical test-particle simulations are a reliable and frequently used tool to test analytical transport theories and to predict mean-free paths. The comparison between solutions of the diffusion equation and the particle flux is used…
Monte Carlo simulation based on Metropolis algorithm has been used with a great success to analyze the dynamic phase transition properties of a single spherical core-shell nanoparticle system with a spin-3/2 core surrounded by a spin-1…
We put forward a simple procedure for extracting dynamical information from Monte Carlo simulations, by appropriate matching of the short-time diffusion tensor with its infinite-dilution limit counterpart, which is supposed to be known.…
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered…
We simulate structural phase behavior of polymer-grafted colloidal particles by molecular Monte Carlo technique. Interparticle potential, which has a finite repulsive square-step outside a rigid core of the colloid, was previously confirmed…
We investigate - with Monte Carlo computer simulations - the phase behaviour of dimeric colloidal molecules on periodic substrates with square symmetry. The molecules are formed in a two-dimensional suspension of like charged colloids…
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible…
The Metropolis Monte Carlo (MC) method is used to extract reaction kinetics from a given equilibrium distribution of states of a complex system. The approach is illustrated by the folding/unfolding reaction for two proteins - a model…
We discuss general thermodynamic properties of molecular structure formation processes like protein folding by means of simplified, coarse-grained models. The conformational transitions accompanying these processes exhibit similarities to…
Monte Carlo simulations are presented for a coarse-grained model of real quadrupolar fluids. Molecules are represented by particles interacting with Lennard-Jones forces plus the thermally averaged quadrupole-quadrupole interaction. The…
Recent years have seen a growing interest in the thermodynamic cost of dissipative structures formed by active particles. Given the strong finite-size effects of such systems, it is essential to develop efficient numerical approaches that…
Metropolis simulations of all-atom models of peptides (i.e. small proteins) are considered. Inspired by the funnel picture of Bryngelson and Wolyness, a transformation of the updating probabilities of the dihedral angles is defined, which…
When a Monte Carlo algorithm is used to evaluate a physical observable A, it is possible to slightly modify the algorithm so that it evaluates simultaneously A and the derivatives $\partial$ $\varsigma$ A of A with respect to each…
We study analytically and by means of an off-lattice bead-spring dynamic Monte Carlo simulation model the adsorption kinetics of a single macromolecule on a structureless flat substrate in the regime of strong physisorption. The underlying…
This chapter is devoted to the computation of equilibrium (thermodynamic) properties of quantum systems. In particular, we will be interested in the situation where the interaction between particles is so strong that it cannot be treated as…
With the guidance offered by nonequilibrium statistical thermodynamics, simulation techniques are elevated from brute-force computer experiments to systematic tools for extracting complete, redundancy-free and consistent coarse grained…
Many problems in materials science and biology involve particles interacting with strong, short-ranged bonds, that can break and form on experimental timescales. Treating such bonds as constraints can significantly speed up sampling their…