Related papers: Adaptively Biased Molecular Dynamics for Free Ener…
Using the entropy $S$ as a reaction coordinate, we determine the free energy barrier associated with the formation of a liquid droplet from a supersaturated vapor for atomic and molecular fluids. For this purpose, we develop the $\mu VT-S$…
Mixed-quantum classical (MQC) methods for simulating the dynamics of molecules at metal surfaces have the potential to accurately and efficiently provide mechanistic insight into reactive processes. Here, we introduce simple two-dimensional…
In this paper we present a convex formulation of the Model Predictive Control (MPC) optimisation for energy management in hybrid electric vehicles, and an Alternating Direction Method of Multipliers (ADMM) algorithm for its solution. We…
Absorption heat pumping devices (AHPDs, comprising absorption heat pumps and chillers) are devices that use thermal energy instead of electricity to generate heating and cooling, thereby facilitating the use of waste heat and renewable…
This paper introduces a random-batch molecular dynamics (RBMD) package for fast simulations of particle systems at the nano/micro scale. Different from existing packages, the RBMD uses random batch methods for nonbonded interactions of…
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…
In this contribution I critically revise the alchemical reversible approach in the context of the statistical mechanics theory of non covalent bonding in drug receptor systems. I show that most of the pitfalls and entanglements for the…
We investigate relations between spatial properties of the free energy and the radius of Gaussian curvature of the underlying curved lattice geometries. For this purpose we derive recurrence relations for the analysis of the free energy…
We develop a method to fit high-temperature Gibbs free energy data for the development of interatomic potentials for atomic systems. The approach is based on Hamiltonian thermodynamic integration, enabling the identification of suitable…
The powerful molecular dynamics (MD) simulation is basically based on a picture that the atoms experience classical-like trajectories under the exertion of classical force field determined by the quantum mechanically solved electronic…
Free energy calculations are widely used tools in computational chemistry, but their dependence on the assignment of partial charges during force field parametrization reduces their accuracy and reproducibility. In this work, we highlight…
We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the…
The alternating direction method of multipliers (ADMM) is a versatile tool for solving a wide range of constrained optimization problems, with differentiable or non-differentiable objective functions. Unfortunately, its performance is…
Molecular dynamics (MD) simulations are essential tools in computational chemistry and drug discovery, offering crucial insights into dynamic molecular behavior. However, their utility is significantly limited by substantial computational…
Molecular Dynamics (MD) simulations are essential for accurately predicting the physical and chemical properties of large molecular systems across various pressure and temperature ensembles. However, the high computational costs associated…
We analyze deficiencies of commonly used Coulomb approximations in Generalized Born solvation energy calculation models and report a development of a new fast surface-based method (FSBE) for numerical calculations of the solvation energy of…
We present a fast adaptive method for the evaluation of heat potentials, which plays a key role in the integral equation approach for the solution of the heat equation, especially in a non-stationary domain. The algorithm utilizes a…
We have developed a thorough and accurate method of determining anharmonic free energies, the temperature dependent effective potential technique (TDEP). It is based on \emph{ab initio} molecular dynamics followed by a mapping onto a model…
We present a general extension of the metadynamics allowing for an automatic sampling of quantum property manifolds (ASQPM) giving rise to functional landscapes that are analogous to the potential energy surfaces in the frame of the…
We present a generalized framework, renormalized density matrix downfolding (RDMD), to derive systematically improvable, highly accurate, and nonperturbative effective models from ab initio calculations. This framework moves beyond the…