Related papers: Relative Binding Free Energy Calculations for Liga…
We devise automated workflows for the calculation of Helmholtz and Gibbs free energies and their temperature and pressure dependence and provide the corresponding computational tools. We employ non-equilibrium thermodynamics for evaluating…
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…
The surface free energies, interfacial tensions and correlation lengths of the Andrews-Baxter-Forrester models in regimes III and IV are calculated with fixed boundary conditions. The interfacial tensions are calculated between arbitrary…
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…
Reduced density-matrix functional theory (RDMFT) is a promising alternative approach to the problem of electron correlation. Like standard density functional theory, it contains an unknown exchange-correlation functional, for which several…
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…
Quantitative evaluations of the free energy of materials must take into account thermal and zero-point energy fluctuations. While these effects can easily be estimated within a harmonic approximation, corrections arising from the anharmonic…
A new simulated tempering method, which is referred to as simulated tempering umbrella sampling, for calculating the free energy of chemical reactions is proposed. First principles molecular dynamics simulations with this simulated…
A new approximate method to calculate exchange-correlation contributions in the framework of first-principles tight-binding molecular dynamics methods has been developed. In the proposed scheme on-site (off-site) exchange-correlation matrix…
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…
Free energy perturbation (FEP) is considered the gold-standard simulation method for estimating small molecule binding affinity, a quantity of vital importance to drug discovery. The accuracy of FEP critically depends on an accurate model…
Vacancy mechanism plays a dominant role in the atomic migration when a close-packed disordered alloy undergoes ordering transition. However, the calculation of thermal vacancy formation energies (VFEs) of random solid solutions is usually…
We present a theoretical first-principles method to calculate the free energy of a magnetic system in its high-temperature paramagnetic phase, including vibrational, electronic, and magnetic contributions. The method for calculating free…
Calculating relative free energies is a topic of substantial interest and has many applications including solvation and binding free energies, which are used in computational drug discovery. However, there remain the challenges of accuracy,…
Free energies play a central role in characterising the behaviour of chemical systems and are among the most important quantities that can be calculated by molecular dynamics simulations. Solvation free energies in various organic solvents,…
Alchemical free energy calculations via molecular dynamics have been widely used to obtain thermodynamic properties related to protein-ligand binding and solute-solvent interactions. Although soft-core modeling is the most common approach,…
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…
Free-energy differences between pairs of end-states can be estimated based on molecular dynamics (MD) simulations using standard pathway-dependent methods such as thermodynamic integration (TI), free-energy perturbation, or Bennett's…
The theory of receptor-ligand binding equilibria has long been well-established in biochemistry, and was primarily constructed to describe dilute aqueous solutions. Accordingly, few computational approaches have been developed for making…
For classical discrete systems under constant composition typically refferred to substitutional alloys, we propose calculation method of Helmholtz free energy based on a set of special microscopic states. The advantage of the method is that…