Related papers: Absolute free energies estimated by combining pre-…
In this review we focus on the determination of phase diagrams by computer simulation with particular attention to the fluid-solid and solid-solid equilibria. The calculation of the free energy of solid phases using the Einstein crystal and…
The calculation time for the energy of atoms and molecules scales exponentially with system size on a classical computer but polynomially using quantum algorithms. We demonstrate that such algorithms can be applied to problems of chemical…
Binding free energies are a key element in understanding and predicting the strength of protein--drug interactions. While classical free energy simulations yield good results for many purely organic ligands, drugs including transition metal…
We propose an adiabatic reweighting algorithm for computing the free energy along an external parameter from adaptive molecular dynamics simulations. The adaptive bias is estimated using Bayes identity and information from all the sampled…
Accurate free-energy calculations are essential for predicting thermodynamic properties and phase stability, but existing methods are limited: phonon-based approaches neglect anharmonicity and liquids, while molecular dynamics (MD) is…
We develop a rigorous error analysis for coarse-graining of defect-formation free energy. For a one-dimensional constrained atomistic system, we establish the thermodynamic limit of the defect-formation free energy and obtain explicitly the…
A recently developed statistical mechanical Quasi-Chemical Theory (QCT) has led to significant insights into solvation phenomena for both hydrophilic and hydrophobic solutes. The QCT exactly partitions solvation free energies into three…
We find the numerically exact partition potential for 1-D systems of interacting electrons designed to model diatomic molecules. At integer fragment occupations, the kinetic contribution to the partition potential develops sharp features in…
We introduce an orbital free electron density functional approximation based on alchemical perturbation theory. Given convergent perturbations of a suitable reference system, the accuracy of popular self-consistent Kohn-Sham density…
Ligand-receptor interactions are ubiquitous in biology and have become popular in materials in view of their applications to programmable self-assembly. Although, complex functionalities often emerge from the simultaneous interaction of…
We discuss the problem of partitioning a macroscopic system into a collection of independent subsystems. The partitioning of a system into replica-like subsystems is nowadays a subject of major interest in several field of theoretical and…
Protein characterization is one of the key components for understanding the human body and advancing drug discovery processes. While the future of quantum hardware holds the potential to accurately characterize these molecules, current…
The recently introduced nested sampling algorithm allows the direct and efficient calculation of the partition function of atomistic systems. We demonstrate its applicability to condensed phase systems with periodic boundary conditions by…
Machine learning interatomic potentials (MLIPs) have become a workhorse of modern atomistic simulations, and recently published universal MLIPs, pre-trained on large datasets, have demonstrated remarkable accuracy and generalizability.…
Molecular fragment or embedding methods are powerful techniques for overcoming scalability limitations in electronic structure theory by dividing large molecular systems into individual units that are small enough to be treated using…
We apply well-established concepts of Langevin sampling to derive a new class of algorithms for the efficient computation of free energy differences of fluctuating particles embedded in a 'fast' membrane, i.e., a membrane that…
We discuss a computationally efficient classical many-body potential designed to model the Al-Al interaction in a wide range of bonding geometries. We show that the potential yields results in properties in excellent agreement with…
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…
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…
The hydration or binding free energy of a drug-like molecule is a key data for early stage drug discovery. Hundreds of thousands of evaluations are needed, which rules out the exhaustive use of atomistic simulations and free energy methods.…