Related papers: Absolute free energies estimated by combining pre-…
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…
We propose a new Monte Carlo algorithm for the free energy calculation based on configuration space sampling. We implement this algorithm for Ising model. Comparison with the exact free energy shows an excellent agreement. We analyse the…
Metadynamics is a powerful computational tool to obtain the free energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantities associated with simplified models of proteins, and thus…
We present a method for determining the free energy of coexisting states from irreversible work measurements. Our approach is based on a fluctuation relation that is valid for dissipative transformations in partially equilibrated systems.…
We study alchemical atomic energy partitioning as a method to estimate atomisation energies from atomic contributions which are defined in physically rigorous and general ways through use of the uniform electron gas as a joint reference. We…
Using a recently developed technique to estimate the equilibrium free energy of glassy materials, we explore if equilibrium simulation methods can be used to estimate the solubility of amorphous solids. As an illustration, we compute the…
We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary…
We explore further the classical QGP using methods from classical liquids. The partition function of an ensemble of SU(N_c) colored charge spheres is constructed. We analyze it using a cumulant expansion (low density) and a loop expansion…
The molecular distributions obtained from canonical Monte Carlo simulations can be used to find an approximate interaction energy. This serves as the basis of a method for estimating the binding free energy for a ligand to a protein which…
While most work on the quantum simulation of chemistry has focused on computing energy surfaces, a similarly important application requiring subtly different algorithms is the computation of energy derivatives. Almost all molecular…
In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such…
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 calculate the partition function for "composite particles". For any finite number of states d, and in the following two cases: 1)all states have the same energy, 2)the energy is linearly distributed over the states, we transform the…
In this paper, we demonstrate the efficiency of simulations via direct computation of the partition function under various macroscopic conditions, such as different temperatures or volumes. The method can compute partition functions by…
We carry out highly accurate \emph{ab initio} path integral Monte Carlo (PIMC) simulations to directly estimate the free energy of various warm dense matter systems including the uniform electron gas and hydrogen without any nodal…
We present a methodology for accelerating the estimation of the free energy from path integral Monte Carlo simulations by considering an intermediate artificial reference system where interactions are inexpensive to evaluate numerically.…
Free energy perturbation (FEP) is frequently used to evaluate the free energy change of a biological process, e.g. the drug binding free energy or the ligand solvation free energy. Due to the sampling inefficiency, FEP is often employed…
We study fragmentation of small atomistic clusters via molecular dynamics. We calculate the time scales related to fragment formation and emission. We also show that some degree of thermalization is achieved during the expansion process,…
Using molecular simulation, we study the nucleation of liquid droplets from binary mixtures and determine the free energy of nucleation along entropic pathways. To this aim, we develop the $\mu_1 \mu_2 VT-S$ method, based on the…
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…