Related papers: Peptide Conformational Equilibria Computed via a S…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
Several approximations are tested by calculating the ground-state energy and the energy of the first excited $0^{+}$ state using an exactly solvable model with two symmetric levels interacting via a pairing force. They are the BCS…
Accurate calculations of solvation free energies remain a central challenge in molecular simulations, often requiring extensive sampling and numerous alchemical intermediates to ensure sufficient overlap between phase-space distributions of…
We propose and analyze a two-level method for mimetic finite difference approximations of second order elliptic boundary value problems. We prove that the two-level algorithm is uniformly convergent, i.e., the number of iterations needed to…
Small peptides are model molecules for the amino acid residues that are the constituents of proteins. In any bottom-up approach to understand the properties of these macromolecules essential in the functioning of every living being, to…
In this paper we analyze a PDE system modelling (non-isothermal) phase transitions and damage phenomena in thermoviscoelastic materials. The model is thermodynamically consistent: in particular, no {\em small perturbation assumption} is…
We show in numerical simulations that a system of two coupled replicas of a binary mixture of hard spheres undergoes a phase transition in equilibrium at a density slightly smaller than the glass transition density for an unreplicated…
This paper studies two fundamental problems in power systems: the economic dispatch problem (EDP) and load shedding. For the EDP, an extension of the problem considering the transmission losses is presented. Because the optimization problem…
We present a construction of non-equilibrium steady states within conformal field theory. These states sustain energy flows between two quantum systems, initially prepared at different temperatures, whose dynamical properties are…
Inverse problems involving systems of partial differential equations (PDEs) with many measurements or experiments can be very expensive to solve numerically. In a recent paper we examined dimensionality reduction methods, both stochastic…
We propose a new method to compute the free energy or enthalpy of fluids or disordered solids by computer simulation . The main idea is to construct a reference system by freezing one representative configuration, and then carry out a…
We provide an explicit analytical calculation that shows the asymptotic approach of the one dimensional Caldeira-Leggett model to thermal equilibrium in the high temperature and weak coupling limit. We investigate a free particle and a…
For many chemical processes the accurate description of solvent effects are vitally important. Here, we describe a hybrid ansatz for the explicit quantum mechanical description of solute-solvent and solvent-solvent interactions based on…
This work is an enquiry into the circumstances under which entropy methods can give an answer to the questions of both quantum separability and classical correlations of a composite state. Several entropy functionals are employed to examine…
Harmonic vibrational entropy is a key finite-temperature contribution to defect thermodynamics, but direct evaluation by dense Hessian diagonalization scales cubically with atom count and is too costly for supercell convergence,…
Self-gravitating systems are expected to reach a statistical equilibrium state either through collisional relaxation or violent collisionless relaxation. However, a maximum entropy state does not always exist and the system may undergo a…
Understanding how different classes of molecules move across biological membranes is a prerequisite to predicting a solute's permeation rate, which is a critical factor in the fields of drug design and pharmacology. We use biased Molecular…
A diffusive model of osmosis is presented that explains currently available experimental data. It makes predictions that distinguish it from the traditional convective flow model of osmosis, some of which have already been confirmed…
We propose and analyze a second-order partitioned time-stepping method for a two-phase flow problem in porous media. The algorithm is based on a refactorization of Cauchy's one-leg $\theta$-method. The main part consists of the implicit…
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…