Related papers: Nonequilibrium free-energy calculation of solids u…
The paper contains a development of the previously proposed generalized lattice model (GLM). In contrast to usual lattice models, the difference of the specific atomic volumes of the components is taken in account in GLM. In addition to…
Binding free energies are a key element in understanding and predicting the strength of protein--drug interactions. While classical free energy simulations yield good results for many purely organic ligands, drugs including transition metal…
Phase diagrams serve as a highly informative tool for materials design, encapsulating information about the phases that a material can manifest under specific conditions. In this work, we develop a method in which Bayesian inference is…
MD simulations of the non-equilibrium melting of aluminum are performed both with and without accounting of the electronic subsystem. A continuum model of melting is purposed basing on the obtained MD results, in which the current phase…
We discuss several general aspects of the free energy of the standard model at high temperatures. In particular the Clausius-Clapeyron equation is shown to yield a relation between the latent heat and the jump in the order parameter. The…
In atomistic simulations, pseudo-dynamics relaxation schemes often exhibit better performance and accuracy in finding local minima than line-search-based descent algorithms like steepest descent or conjugate gradient. Here, an improved…
In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such…
We present a detailed comparison of computational efficiency and precision for several free energy difference ($\Delta F$) methods. The analysis includes both equilibrium and non-equilibrium approaches, and distinguishes between…
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 Monte Carlo algorithm for the free energy calculation based on configuration space sampling. We implement this algorithm for Ising model. Comparison with the exact free energy shows an excellent agreement. We analyse the…
The interfacial free energy between a crystal and a fluid, {\gamma} cf, is a highly relevant parameter in phenomena such as wetting or crystal nucleation and growth. Due to the difficulty of measuring {\gamma} cf experimentally, computer…
We extend the nested sampling algorithm to simulate materials under periodic boundary and constant pressure conditions, and show how it can be used to determine the complete equilibrium phase diagram, for a given potential energy function,…
A new molecular simulation method for the calculation of vapour-liquid equilibria of mixtures is presented. In this method, the independent thermodynamic variables are temperature and liquid composition. In the first step, one isobaric…
Small thermodynamic systems exhibit peculiar behavior different from that observed in long-scale systems. Non-equilibrium processes taking place in those systems are strongly influenced by the presence of fluctuations which can be large.…
Jarzynski Equality (JE) and the thermodynamic integration method are conventional methods to calculate free energy difference (FED) between two equilibrium states with constant temperature of a system. However, a number of ensemble samples…
From the onset of fundamental statistical mechanical constructs formulated in the late 19th century, alchemical free-energy methods slowly emerged and transitioned to become operational tools of biomolecular simulation applicable to a wide…
Computational studies of the thermodynamic properties of materials at the mesoscopic and macroscopic scales -- involving lengths and times of at least $\mu$m and $\mu$s, respectively -- rely on a coarse-graining approximation such that only…
We develop a comprehensive Hamiltonian formulation for plasma dynamics that unifies collisionless gyrokinetic and collisional processes. Our framework rigorously describes the evolution of free energy and entropy during the transition from…
Computing phase diagrams of model systems is an essential part of computational condensed matter physics. In this paper we discuss in detail the interface pinning (IP) method for calculation of the Gibbs free energy difference between a…
We present an implementation of alchemical free energy simulations at the quantum mechanical level by directly interpolating the electronic Hamiltonian. The method is compatible with any level of electronic structure theory and requires…