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The determination of the solvation free energy of ions and molecules holds profound importance across a spectrum of applications spanning chemistry, biology, energy storage, and the environment. Molecular dynamics simulations are a powerful…
The accurate estimation of free energy differences between two states is a long-standing challenge in molecular simulations. Traditional approaches generally rely on sampling multiple intermediate states to ensure sufficient overlap in…
Biased sampling in molecular dynamics simulations overcomes timescale limitations and delivers free-energy landscapes, essential to understand complex atomistic phenomena. However, when applied across diverse systems and processes, biasing…
The structure and function of biological molecules are strongly influenced by the water and dissolved ions that surround them. This aqueous solution (solvent) exerts significant electrostatic forces in response to the biomolecule's…
A crucial aspect in the simulation of electrochemical interfaces consists in treating the distribution of electronic charge of electrode materials that are put in contact with an electrolyte solution. Recently, it has been shown how a…
Free energy calculations based on atomistic Hamiltonians and sampling are key to a first principles understanding of biomolecular processes, material properties, and macromolecular chemistry. Here, we generalize the Free Energy Perturbation…
The electronic charge density plays a central role in determining the behavior of matter at the atomic scale, but its computational evaluation requires demanding electronic-structure calculations. We introduce an atom-centered,…
Molecular dynamics simulations of biomolecules have been widely adopted in biomedical studies. As classical point-charge models continue to be used in routine biomolecular applications, there have been growing demands on developing…
Large thermal fluctuations of the liquid phase obscure the weak macroscopic electric field that drives electrochemical reactions, rendering the extraction of reliable interfacial charge distributions from ab initio molecular dynamics…
Extracting consistent statistics between relevant free-energy minima of a molecular system is essential for physics, chemistry and biology. Molecular dynamics (MD) simulations can aid in this task but are computationally expensive,…
We introduce a machine learning model to predict atomization energies of a diverse set of organic molecules, based on nuclear charges and atomic positions only. The problem of solving the molecular Schr\"odinger equation is mapped onto a…
Accurate absolute binding free energy (ABFE) calculations can reduce the time and cost of identifying drug candidates from a diverse pool of molecules that may have been overlooked experimentally. These calculations typically employ…
Solvation free energy is an important design parameter in reaction kinetics and separation processes, making it a critical property to predict during process development. In previous research, directed message passing neural networks…
Thermodynamics of the XXX Heisenberg model is studied. The trace of the Boltzmann weight with respect to the Hilbert space is taken in the thermodynamic limit with the number of up-spins being fixed. The expression of the trace gives an…
Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another. The hallmark of these methods is the use of "bridging" potential energy…
Estimating the free energy in molecular simulation requires, implicitly or explicitly, counting how many times the system is observed in a finite region. If the simulation is biased by an external potential, the weight of the configurations…
(CoxMn1-x)3O4 is a promising candidate material for solar thermochemical energy storage. A high-temperature model for this system would provide a valuable tool for evaluating its potential. However, predicting phase diagrams of complex…
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…
We examine the influence of the main approximations employed in density-functional theory descriptions of the solid phase of molecular hydrogen near dissociation. We consider the importance of nuclear quantum effects on equilibrium…
The absolute free energy -- or partition function, equivalently -- of a molecule can be estimated computationally using a suitable reference system. Here, we demonstrate a practical method for staging such calculations by growing a molecule…