Related papers: Free Energy Computation by Monte Carlo Integration
We extend our previously developed method, "structure integration", to evaluate free energy directly for magnetic large systems on given lattice. The present method express the density of states(DOS) as the parameters independent of system…
According to implicit ligand theory, the standard binding free energy is an exponential average of the binding potential of mean force (BPMF), an exponential average of the interaction energy between the ligand apo ensemble and a rigid…
Monte Carlo (MC) simulations of lattice models are a widely used way to compute thermodynamic properties of substitutional alloys. A limitation to their more widespread use is the difficulty of driving a MC simulation in order to obtain the…
We provide accurate Monte Carlo results for the free energy of interfaces with periodic boundary conditions in the 3D Ising model. We study a large range of inverse temperatures, allowing to control corrections to scaling. In addition to…
Ligand-receptor interactions are ubiquitous in biology and have become popular in materials in view of their applications to programmable self-assembly. Although, complex functionalities often emerge from the simultaneous interaction of…
The theory behind computation of absolute binding free energies using explicit-solvent molecular simulations is well-established, yet somewhat complex, with counter-intuitive aspects. This leads to frequent frustration, common…
We propose a new method to compute the free energy or enthalpy of fluids or disordered solids by computer simulation . The main idea is to construct a reference system by freezing one representative configuration, and then carry out a…
In this review we focus on the determination of phase diagrams by computer simulation with particular attention to the fluid-solid and solid-solid equilibria. The calculation of the free energy of solid phases using the Einstein crystal and…
We propose an efficient method for Monte Carlo simulation of quantum lattice models. Unlike most other quantum Monte Carlo methods, a single run of the proposed method yields the free energy and the entropy with high precision for the whole…
Monte Carlo techniques play a central role in statistical mechanics approaches for connecting macroscopic thermodynamic and kinetic properties to the electronic structure of a material. This paper describes the implementation of Monte Carlo…
The ability of widely used sampling methods, such as molecular dynamics or Monte Carlo, to explore complex free energy landscapes is severely hampered by the presence of kinetic bottlenecks. A large number of solutions have been proposed to…
We review a recently developed micellization theory, which is based on a free-energy approach and offers several advantages over the conventional one, based on mass action and rate equations. As all the results are derived from a single…
One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is…
The massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed [H. Fujitani, Y. Tanida, M. Ito, G. Jayachandran, C. D. Snow, M. R. Shirts, E. J. Sorin, and V. S. Pande, J.…
The proposed method of the free energy calculation is based on the approximation of the energy distribution in the microcanonical ensemble by the Gaussian distribution. We hope that our approach will be effective for the systems with…
Lattice-switch Monte Carlo (LSMC) is a method for evaluating the free energy between two given solid phases. LSMC is a general method, being applicable to a wide range of problems and interatomic potentials. Furthermore it is extremely…
In this work the free energy of solid phases is computed for the Lennard-Jones potential and for a model of NaCl. The free energy is evaluated through the Einstein crystal/molecule methodologies using the Molecular Dynamics programs:…
The determination of the solvation free energy of ions and molecules holds profound importance across a spectrum of applications spanning chemistry, biology, energy storage, and the environment. Molecular dynamics simulations are a powerful…
According to the shock jump conditions, the total fluid's mass, momentum, and energy should be conserved in the entire simulation box. We perform the dynamical Monte Carlo simulations with the multiple scattering law for energy analysis.…
We introduce and implement a Monte Carlo scheme to study the equilibrium statistics of polymers in the globular phase. It is based on a model of "interacting elastic lattice polymers" and allows a sufficiently good sampling of long and…