Related papers: Free energy analysis for a system of interacting p…
The lattice fluid model of the system with short range and long range Coulomb interactions is suggested. In the framework of the collective variables method, the screening of the Coulomb interactions in the bulk is considered. It is shown…
Calculating free energy differences is a topic of substantial interest and has many applications including molecular docking and hydration, solvation, and binding free energies which is used in computational drug discovery. However, in…
We investigate lattice energies for radially symmetric, spatially extended particles interacting via a radial potential and arranged on the sites of a two-dimensional Bravais lattice. We show the global minimality of the triangular lattice…
This article describes nonequilibrium techniques for the calculation of free energies of solids using molecular dynamics (MD) simulations. These methods provide an alternative to standard equilibrium thermodynamic integration methods and…
We present an efficient Monte-Carlo method for long-range interacting systems to calculate free energy as a function of an order parameter. In this method, a variant of the Wang-Landau method regarding the order parameter is combined with…
Free energy calculations in molecular simulations have a variety of applications including determining the strength of molecular processes such as solvation and binding. It has been recently shown that when removing the VDW and Coulomb…
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…
We present a lattice Boltzmann algorithm based on an underlying free energy that allows the simulation of the dynamics of a multicomponent system with an arbitrary number of components. The thermodynamic properties, such as the chemical…
We propose a new approach, "structure integration", enabling direct evaluation of configurational free energy for large systems. The present approach is based on the statistical information of lattice. Through first-principles-based…
This work addresses the question of whether it is possible to define simple pair-wise interaction terms to approximate free energies of proteins or polymers. Rather than ask how reliable a potential of mean force is, one can ask how…
We investigate relations between spatial properties of the free energy and the radius of Gaussian curvature of the underlying curved lattice geometries. For this purpose we derive recurrence relations for the analysis of the free energy…
A variety of methods are developed for characterising the free energy landscapes of continuum, Landau-type free energy models. Using morphologies of lipid vesicles and a multistable liquid crystal device as examples, I show that the methods…
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…
We apply well-established concepts of Langevin sampling to derive a new class of algorithms for the efficient computation of free energy differences of fluctuating particles embedded in a 'fast' membrane, i.e., a membrane that…
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…
We present a method for the direct evaluation of the difference between the free energies of two crystalline structures, of different symmetry. The method rests on a Monte Carlo procedure which allows one to sample along a path, through…
A melting transition for a system of hard spheres interacting by a repulsive Yukawa potential of DLVO form is studied. To find the location of the phase boundary, we propose a simple theory to calculate the free energies for the coexisting…
The equilibrium statistical mechanics of one-dimensional lattice gases with interactions of arbitrary range and shape between first-neighbor atoms is solved exactly on the basis of statistically interacting vacancy particles. Two sets of…
The phase diagram of numerous materials of technological importance features high-symmetry high-temperature phases that exhibit phonon instabilities. Leading examples include shape-memory alloys, as well as ferroelectric, refractory, and…
We describe a self-contained procedure to evaluate the free energy of liquid and solid phases of an alloy system. The free energy of a single-element solid phase is calculated with thermodynamic integration using the Einstein crystal as the…