Related papers: Nonequilibrium free-energy calculation of solids u…
Sets of free energy differences are useful for finding the equilibria of chemical reactions, while absolute free energies have little physical meaning. However finding the relative free energy between two macrostates by subtraction of their…
Accurate phase diagram calculation from molecular dynamics requires systematic treatment and convergence of statistical averages. In this work we propose a Gaussian process regression based framework for reconstructing the free energy…
A robust, simple and fast procedure for the calculation of uncertainties in relative static dielectric permittivity ($\varepsilon_s$) computed via molecular dynamics (MD) is proposed. It arises as a direct application of well founded…
We present some applications of an Interacting Particle System (IPS) methodology to the field of Molecular Dynamics. This IPS method allows several simulations of a switched random process to keep closer to equilibrium at each time, thanks…
We propose a numerical technique to compute the equilibrium free energy of glasses that cannot be prepared quasi-reversibly. For such systems, standard techniques for estimating the free energy by extrapolation, cannot be used. Instead, we…
The calculation of the interfacial free energy between two thermodynamic phases is crucial across various fields, including materials science, chemistry, and condensed matter physics. In this study, we apply an existing thermodynamic…
Taking advantage of the advances in generative deep learning, particularly normalizing flow, a framework, called Boltzmann Generator, has recently been proposed for the purpose of generating equilibrium atomic configurations from the…
Comparison of free energies between different phases and different compositions underlies the prediction of alloy phase diagrams. To allow direct comparison, consistent reference points for the energies or enthalpies are required, and the…
When matter is exposed to a high-intensity x-ray free-electron-laser pulse, the x rays excite inner-shell electrons leading to the ionization of the electrons through various atomic processes and creating high-energy-density plasma, i.e.,…
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 present an Adaptively Biased Molecular Dynamics (ABMD) method for the computation of the free energy surface of a reaction coordinate using non-equilibrium dynamics. The ABMD method belongs to the general category of umbrella sampling…
In this thesis we examine methodologies for determining free energy differences (FEDs) of phases via Monte Carlo simulation. We identify and address three generic issues that arise in FED calculations; the choice of representation, the…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…
An expression is derived for the free energy of nonideal atomic plasma, which corresponds to exact asymptotic expansions. The analytical dependence of correction for the interaction of free charges on the partition function of atom is…
Two-dimensional Raman and hybrid terahertz/Raman spectroscopic techniques provide invaluable insight into molecular structure and dynamics of condensed-phase systems. However, corroborating experimental results with theory is difficult due…
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…
Free energy calculations based on atomistic Hamiltonians and sampling are key to a first principles understanding of biomolecular processes, material properties, and macromolecular chemistry. Here, we generalize the Free Energy Perturbation…
Calculations of elastic and mechanical characteristics of non-crystalline solids are challenging due to high computation cost of $ab$ $initio$ methods and low accuracy of empirical potentials. We propose a computational technique towards…
Entropy and free-energy estimation are key in thermodynamic characterization of simulated systems ranging from spin models through polymers, colloids, protein structure, and drug-design. Current techniques suffer from being model specific,…
This report details an approach to improve the accuracy and precision of free energy difference estimates using thermodynamic integration data (slope of the free energy with respect to the switching variable lambda) and its application to…