相关论文: Free energy calculations for atomic solids through…

Recent very large molecular dynamics simulations of homogeneous nucleation with $(1-8) \cdot 10^9$ Lennard-Jones atoms [Diemand et al. J. Chem. Phys. {\bf 139}, 074309 (2013)] allow us to accurately determine the formation free energy of…

We present a method for computing free-energy differences using thermodynamic integration with a neural network potential that interpolates between two target Hamiltonians. The interpolation is defined at the sample distribution level, and…

The thesis consists of two projects. In the first project, we present a software that analyses RNA secondary structures and compares them. The goal of this software is to find the differences between two secondary structures (experimental…

A variational approach, based on a discrete representation of the chain, is used to calculate free energy and conformational properties in polyelectrolytes. The true bond and Coulomb potentials are approximated by a trial isotropic harmonic…

We investigate the dynamics of a gas of non-interacting particle-like soliton waves, demonstrating that phase transitions originate from their collective behavior. This is predicted by solving exactly the nonlinear equations and by…

We report a development of a new fast surface-based method for numerical calculations of solvation energy of biomolecules with a large number of charged groups. The procedure scales linearly with the system size both in time and memory…

Quantum Monte Carlo (QMC) methods such as Variational Monte Carlo, Diffusion Monte Carlo or Path Integral Monte Carlo are the most accurate and general methods for computing total electronic energies. We will review methods we have…

The free energy of the solid and fluid phases of the Girifalco C60 model are determined through extensive Monte Carlo simulations. In this model the molecules interact through a spherical pair potential, characterized by a narrow and…

We construct a tensor model for nematic phases of bent-core molecules from molecular theory. The form of free energy is determined by molecular symmetry, which includes the couplings and derivatives of a vector and two second-order tensors,…

Steered molecular dynamics (SMD) simulations for the calculation of free energies are well suited for high-throughput molecular simulations on a distributed infrastructure due to the simplicity of the setup and parallel granularity of the…

Various methods achieving importance sampling in ensembles of nonequilibrium trajectories enable to estimate free energy differences and, by maximum-likelihood post-processing, to reconstruct free energy landscapes. Here, based on Bayes…

One-dimensional ideal diatomic gas is simulated through possible types of motion of a molecule. Energy of each type of its motion is calculated from theory and numerical method. Calculation of kinetic energy of an atom in…

A novel thermodynamic integration (TI) scheme is presented to compute the crystal-liquid interfacial free energy ($\gamma_{\rm cl}$) from molecular dynamics simulation. The scheme is applied to a Lennard-Jones system. By using extremely…

Thermodynamic phase transitions, a central concept in physics and chemistry, are typically controlled by an interplay of enthalpic and entropic contributions. In most cases, the estimation of the enthalpy in simulations is straightforward…

Density matrix quantum Monte Carlo (DMQMC) is used to sample exact-on-average $N$-body density matrices for uniform electron gas systems of up to 10$^{124}$ matrix elements via a stochastic solution of the Bloch equation. The results of…

Free-energy differences between pairs of end-states can be estimated based on molecular dynamics (MD) simulations using standard pathway-dependent methods such as thermodynamic integration (TI), free-energy perturbation, or Bennett's…

Using molecular simulation, we analyze the capillary condensation and evaporation processes for Argon confined in a cylindrical nanopore. For this purpose, we define the entropy of the adsorbed fluid as a reaction coordinate and determine…

In this paper, we review the physical concepts of the nonequilibrium techniques for the calculation of free energies applied to magnetic systems using Monte Carlo simulations of different nonequilibrium processes. The methodology allows the…

The first part of this paper develops a theory for the free energy of lyotropic polymer nematic liquid crystals. We use a continuum model with macroscopic elastic moduli for a polymer nematic phase. By evaluating the partition function,…

Pre-calculated libraries of molecular fragment configurations have previously been used as a basis for both equilibrium sampling (via "library-based Monte Carlo") and for obtaining absolute free energies using a polymer-growth formalism.…