Related papers: Free energy calculations for atomic solids through…
The microscopic approach to calculating the free energy of a three-dimensional Ising-like system in a homogeneous external field is developed in the higher non-Gaussian approximation (the $\rho^6$ model) at temperatures above the critical…
Computational modeling is an integral part of catalysis research. With it, new methodologies are being developed and implemented to improve the accuracy of simulations while reducing the computational cost. In particular, specific…
Recently, nanofluidics experiments have been used to characterize the behavior of single DNA molecules confined to narrow slits etched with arrays of nanopits. Analysis of the experimental data relies on analytical estimates of the…
Free energy as a function of polarization is calculated for the square-lattice $J_1$-$J_2$ Ising model for $J_2 < |J_1|/2$ using the random local field approximation (RLFA) and Monte Carlo (MC) simulations. Within RLFA, it reveals a…
We present a simulation technique to evaluate the most important quantity for nucleation processes: the nucleation barrier, i.e. the free energy of formation of the critical cluster. The method is based on stabilizing a small cluster by…
For classical discrete systems under constant composition typically refferred to substitutional alloys, we propose calculation method of Helmholtz free energy based on a set of special microscopic states. The advantage of the method is that…
We propose an approach to calculate the anharmonic part of the volumetric-strain and temperature dependent free energy of a crystal. The method strikes an effective balance between accuracy and computational efficiency, showing a $\times10$…
The computational modelling of reactions is simple in theory but can be quite tricky in practice. This article aims at the purpose of providing an assistance to a proper way of describing reactions theoretically and provides rough…
GROMACS is one of the most widely used HPC software packages using the Molecular Dynamics (MD) simulation technique. In this work, we quantify GROMACS parallel performance using different configurations, HPC systems, and FFT libraries…
We study the electrostatic energy of binary ionic mixtures (BIMs) in the form of Coulomb crystals with the main focus on ordered crystals. We consider 15 different binary bcc-like lattices, accurately calculate their electrostatic energies…
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…
A methodology to sample the isothermal-isobaric ensemble using Langevin dynamics is proposed, which combines novel features of geometric integrators for the equations of motion. By employing the Trotter expansion, the methodology generates…
We obtain an exact formula for the equilibrium free energy of a charged quantum particle moving in a harmonic potential in the presence of a uniform external magnetic field and linearly coupled to a heat bath of independent quantum harmonic…
A numerical framework is proposed and analyzed for computing the ground state of Bose--Einstein condensates. A gradient flow approach is developed, incorporating both a Lagrange multiplier to enforce the $L^2$ conservation and a free energy…
We calculate the entropy and the temperature dependent part of the free energy for a free standing plane plasma sheet and for the a free standing plane slab of finite thickness with dispersion described by the plasma model. In case the…
We perform, with the help of cloud computing resources, extensive Langevin simulations which provide free energy estimates for unbiased three dimensional polymer translocation. We employ the Jarzynski equality in its rigorous setting, to…
We propose an algorithm for molecular dynamics or Monte Carlo simulations that uses an interpolation procedure to estimate potential energy values from energies and gradients evaluated previously at points of a simplicial mesh. We chose an…
Monte Carlo simulations of crystal nuclei coexisting with the fluid phase in thermal equilibrium in finite volumes are presented and analyzed, for fluid densities from dense melts to the vapor. Generalizing the lever-rule for two-phase…
We report the status of a high-statistics Monte Carlo simulation of non-self-avoiding crystalline surfaces with extrinsic curvature on lattices of size up to $128^2$ nodes. We impose free boundary conditions. The free energy is a gaussian…
Within the framework of density functional theory (DFT), the total energy of crystal structures is calculated at zero temperature. Herein, we briefly discuss the DFT-based lattice-dynamics approach for computing crystal free energy, the…