Related papers: Using binding free energy to guide ligand design
We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in…
To address the large gap between time scales that can be easily reached by molecular simulations and those required to understand protein dynamics, we propose a rapid self-consistent approximation of the side chain free energy at every…
We discuss the potential advantages of calculating the effective mass of quasiparticles in the interacting electron liquid from the low-temperature free energy vis-a-vis the conventional approach, in which the effective mass is obtained…
We use thermodynamic perturbation theory to calculate the free energies and resulting phase diagrams of binary systems of spherical colloidal particles and interacting polymer coils in good solvent within an effective one-component…
We review a recently devised Monte Carlo simulation method for the direct study of quasi-stationary properties of stochastic processes with an absorbing state. The method is used to determine the static correlation function and the…
This paper introduces a method for computing the Helmholtz free energy using the flow matching technique. Unlike previous work that utilized flow-based models for variational free energy calculations, this method provides bounds for free…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
We extract values for the free symmetry energy as a function of the fragment size (the proton number Z) from antisymmetrized molecular dynamics (AMD) calculations of calcium collisions. Simple statistical physics describe well the…
The variational and diffusion quantum Monte Carlo methods are used to calculate the correlation energy of the paramagnetic three-dimensional homogeneous electron gas at intermediate to high density. Ground state energies in finite cells are…
Molecular crystals play a central role in a wide range of scientific fields, including pharmaceuticals and organic semiconductor devices. However, they are challenging systems to model accurately with computational approaches because of a…
We apply the recently developed triangular tessellation technique as presented in [J. de Graaf et al., Phys. Rev. E 80, 051405 (2009)] to calculate the free energy associated with the adsorption of anisotropic colloidal particles at a flat…
Zero- and two-dimensional crystal defects form in open statistical ensembles, such as the grand canonical, that are usually inaccessible with conventional simulation techniques. This longstanding challenge is overcome with a new Hamiltonian…
A simple, approximate relation is found between the total energy of a free atom and its atomic number: E ~= -Z^{2.411}. The existence of this index is inherent in the Coulomb and many-body nature of the electron-electron interaction in the…
The phase diagram of numerous materials of technological importance features high-symmetry high-temperature phases that exhibit phonon instabilities. Leading examples include shape-memory alloys, as well as ferroelectric, refractory, and…
The massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed [H. Fujitani, Y. Tanida, M. Ito, G. Jayachandran, C. D. Snow, M. R. Shirts, E. J. Sorin, and V. S. Pande, J.…
Current theories of heteropolymers are inherently macrpscopic, but are applied to folding proteins which are only mesoscopic. In these theories, one computes the averaged free energy over sequences, always assuming that it is self-averaging…
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…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
We explore the recently introduced $\eta$-ensemble approach to compute the free energy directly from \emph{ab initio} path integral Monte Carlo (PIMC) simulations [T.~Dornheim \emph{et al.}, arXiv:2407.01044] and apply it to the archetypal…
Using a thermodynamic integration scheme, we compute the free energy cost per unit area, $\gamma$, of forming an interface between a crystal and a frozen structured wall, formed by particles frozen into the same equilibrium structure as the…