Related papers: Absolute free energies estimated by combining pre-…

Exact free energy minimization is a convex optimization problem that is usually approximated with stochastic sampling methods. Deterministic approximations have been less successful because many desirable properties have been difficult to…

Abstract Machine learning models, trained on data from ab initio quantum simulations, are yielding molecular dynamics potentials with unprecedented accuracy. One limiting factor is the quantity of available training data, which can be…

We present a simulation scheme to calculate defect formation free energies at a molecular crystal/water interface based on force-field molecular dynamics (MD) simulations. To this end we adopt and modify existing approaches to calculate…

We address the problem of constructing accurate mathematical models of the dynamics of molecular systems projected on a collective variable. To this aim we introduce an algorithm optimizing the parameters of a standard or generalized…

We report a development of a new fast surface-based method for numerical calculations of solvation energy of biomolecules with a large number of charged groups. The procedure scales linearly with the system size both in time and memory…

It has been shown that minimum free energy structure for RNAs and RNA-RNA interaction is often incorrect due to inaccuracies in the energy parameters and inherent limitations of the energy model. In contrast, ensemble based quantities such…

The package "fhi96md" is an efficient code to perform density-functional theory total-energy calculations for materials ranging from insulators to transition metals. The package employs first-principles pseudopotentials, and a plane-wave…

Free energies play a central role in many descriptions of equilibrium and non-equilibrium properties of solids. Continuum partial differential equations (PDEs) of atomic transport, phase transformations and mechanics often rely on first and…

Predicting the binding affinity between small molecules and target macromolecules while combining both speed and accuracy, is a cornerstone of modern computational drug discovery which is critical for accelerating therapeutic development.…

We study the conformational equilibria of two peptides using a novel statistical mechanics approach designed for calculating free energy differences between highly dis-similar conformational states. Our results elucidate the contrasting…

In this paper we study multi-matrix models whose potentials are perturbations of the quadratic potential associated with independent GUE random matrices. More precisely, we compute the free energy and the expectation of the trace of…

We present a family of alchemical perturbation potentials that enable the calculation of hydration free energies of small to medium-sized molecules in a concerted single alchemical coupling step instead of the commonly used sequence of two…

Understanding and computing the entropic forces exerted by polymer chains under confinement is important for many reasons, from research to applications. However, extracting properties related to the free energy, such as the force (or…

While the treatment of chemically relevant systems containing hundreds or even thousands of electrons remains beyond the reach of quantum devices, the development of quantum-classical hybrid algorithms to resolve electronic correlation…

We discuss a novel approach to quantum information processing with molecules based on molecular degrees of freedom which are isolated from the environment as well as from the rest of the molecule. Such a degree of freedom can provide…

Many methods to accelerate sampling of molecular configurations are based on the idea that temperature can be used to accelerate rare transitions. These methods typically compute equilibrium properties at a target temperature using…

Fragment partitions of fragmenting hot nuclei produced in central and semiperipheral collisions have been compared in the excitation energy region 4-10 MeV per nucleon where radial collective expansion takes place. It is shown that, for a…

Ab initio molecular dynamics (AIMD) simulations employing density functional theory (DFT) and plane waves are routinely carried out using density functionals at the level of Generalized Gradient Approximation (GGA). AIMD simulations…

Using computer simulations, we validate a simple free energy model that can be analytically solved to predict the equilibrium size of self-limiting clusters of particles in the fluid state governed by a combination of short-range attractive…

We show how to localize and quantify the functional evolutionary constraints on natural proteins. The method compares the perturbations caused by local sequence variants to the energetics of the protein folding process and to the…