Related papers: Flexible framework of computing binding free energ…
Interactions of polyelectrolytes (PEs) with proteins play a crucial role in numerous biological processes, such as the internalization of virus particles into host cells. Although docking, machine learning methods, and molecular dynamics…
The multistate Bennett acceptance ratio (MBAR) method is a prevalent approach for computing free energies of thermodynamic states. In this work, we introduce BayesMBAR, a Bayesian generalization of the MBAR method. By integrating…
The efficiency of soft particles to stabilize emulsions is examined by measuring their desorption free energy, i.e., the mechanical work required to detach the particle from a fluid interface. Here, we consider rubber-like elastic as well…
The behaviour of molecules in space is to a large extent governed by where they freeze out or sublimate. The molecular binding energy is thus an important parameter for many astrochemical studies. This parameter is usually determined with…
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…
Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into…
The semi-classical Wigner-Kirkwood $\hbar$ expansion method is used to calculate shell corrections for spherical and deformed nuclei. The expansion is carried out up to fourth order in $\hbar$. A systematic study of Wigner-Kirkwood averaged…
We present an extension of Alchemical Transfer Method (ATM) for the estimation of relative binding free energies of molecular complexes applicable to conventional as well as scaffold-hopping alchemical transformations. The method, named…
A rigorous formalism for estimating noncovalent binding free energies and thermodynamic expectations from calculations in which receptor configurations are sampled independently from the ligand is derived. Due to this separation, receptor…
The Free Energy Principle (FEP) states that under suitable conditions of weak coupling, random dynamical systems with sufficient degrees of freedom will behave so as to minimize an upper bound, formalized as a variational free energy, on…
A methodology for calculating the contribution of charged defects to the configurational free energy of an ionic crystal is introduced. The temperature-independent Wang-Landau Monte Carlo technique is applied to a simple model of a solid…
We compute the temperature-dependent barrier for alpha-relaxations in several liquids, without adjustable parameters, using experimentally determined elastic, structural, and calorimetric data. We employ the random first order…
We describe a two-step approach for combining interactive molecular dynamics in virtual reality (iMD-VR) with free energy (FE) calculation to explore the dynamics of biological processes at the molecular level. We refer to this combined…
Given a chemical reaction going from reactant (R) to the product (P) on a potential energy surface (PES) and a collective variable (CV) that discriminates between R and P, one can define a free-energy profile (FEP) as the logarithm of the…
We present a parameterized analytical model of alchemical molecular binding. The model describes accurately the free energy profiles of linear single-decoupling alchemical binding free energy calculations. The parameters of the model, which…
The conformational free energy landscape of a system is a fundamental thermodynamic quantity of importance particularly in the study of soft matter and biological systems, in which the entropic contributions play a dominant role. While…
Atomistic simulations are employed to demonstrate the existence of a well-defined thermodynamic phase transformation between grain boundary (GB) phases with different atomic structures. The free energy of different interface structures for…
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…
In this work a method is proposed for computing step free energies for faceted solid-liquid interfaces based on atomistic simulations. The method is demonstrated in an application to (111) interfaces in elemental Si, modeled with the…
The quality of astrochemical models is highly dependent on reliable binding energy (BE) values that consider the morphological and energetic variety of binding sites on the surface of ice-grain mantles. Here, we present the Binding Energy…