Related papers: Computing chemical potentials of solutions from st…
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…
The effective potential formalism is applied to glass forming liquids, choosing a coupling potential such that the "order parameter", conjugated to the coupling strength, is the mean square displacement of the particles from their position…
Estimating the free energy in molecular simulation requires, implicitly or explicitly, counting how many times the system is observed in a finite region. If the simulation is biased by an external potential, the weight of the configurations…
Based on an analysis of the short range chemical environment of each atom in a system, standard machine learning based approaches to the construction of interatomic potentials aim at determining directly the central quantity which is the…
The authors present a new molecular dynamics algorithm for sampling the isothermal-isobaric ensemble. In this approach the velocities of all particles and volume degrees of freedom are rescaled by a properly chosen random factor. The…
The pressure-temperature phase diagram of a one-component system, with particles interacting through a spherically symmetric pair potential is studied. It is shown that if the pair potential allows for a discontinuous reduction of the…
The formal structure of geometrical thermodynamics is reviewed with particular emphasis on the geometry of equilibria submanifolds. On these submanifolds thermodynamic metrics are defined as the Hessian of thermodynamic potentials. Links…
Understanding thermodynamics in liquids at the atomic level is challenging because of strong atomic interactions and lack of symmetry. Recent prior theoretical works have focused on describing heat capacity of liquids in terms of…
In the statistical mechanics of quantum harmonic oscillators, the zero-point energy can either be included (Schr\"odinger oscillators) or omitted (Planck oscillators). For the usual results, the type of oscillator makes no difference but,…
Open-system density functional theory may be formulated in terms of ensemble averages arising from interaction with a bath. The system is allowed to exchange particles with the bath and the states in the ensemble average are those…
Chemical potential is an effective way to drive phase transition or express wettability. In this letter, we present a chemical-potential-based lattice Boltzmann model to simulate multiphase flows. The nonideal force is directly evaluated by…
We present a family of alchemical perturbation potentials that enable the calculation of hydration free energies of small to medium-sized molecules in a concerted single alchemical coupling step instead of the commonly used sequence of two…
Aqueous lithium chloride solutions up to very high concentrations were investigated in classical molecular dynamics simulations. Various force fields based on the 12-6 Lennard-Jones model, parametrized for non-polarizable water solvent…
Molecular dynamics simulations are used to generate an ensemble of saddles of the potential energy of a Lennard-Jones liquid. Classifying all extrema by their potential energy u and number of unstable directions k, a well defined relation…
The hybrid form is a combination of the Rydberg potential and the London inverse-sixth-power energy. It is accurate at all relevant distance scales and simple enough for use in all-atom simulations of biomolecules. One may compute the…
We use the two-flavor linear sigma model with quarks to study the phase structure of isospin asymmetric matter at zero temperature. The meson degrees of freedom provide the mean field chiral- and isospin-condensates on top of which we…
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…
The Gibbs free energy is the fundamental thermodynamic potential underlying the relative stability of different states of matter under constant-pressure conditions. However, computing this quantity from atomic-scale simulations is far from…
Extending to continuous potentials a cleaving wall molecular-dynamics simulation method recently developed for the hard-sphere system [Phys.Rev.Lett 85, 4751 (2000)], we calculate the crystal-melt interfacial free energies, $\gamma$, for a…
Classical density-functional theory is the most direct approach to equilibrium structures and free energies of inhomogeneous liquids, but requires the construction of an approximate free-energy functional for each liquid of interest. We…