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Free energy sampling methods allow studying the full dynamics of activated processes. Unfortunately, the affordable accuracy of the potential describing the energy and forces of the system is usually rather low. Here we introduce a new…
The computation of molecular excitation energies is essential for predicting photo-induced reactions of chemical and technological interest. While the classical computing resources needed for this task scale poorly, quantum algorithms…
In this letter, based on the exponential scalar auxiliary variable technology, we propose and study a new class of explicit energy-preserving splitting methods for solving the charged-particle dynamics. The energy-preserving property of…
We propose a new model for estimating the free energy of forming a molecular cavity in a solvent, by assuming this energy is dominated by the electrostatic energy associated with creating the static (interface) potential inside the cavity.…
An iterative method for calculating the polar component of the solvation Gibbs energy under a smooth change in dielectric permittivity, both between a substrate and a solvent and in a solvent is formulated on the basis of a previously…
A brief review of the SIESTA project is presented in the context of linear-scaling density-functional methods for electronic-structure calculations and molecular-dynamics simulations of systems with a large number of atoms. Applications of…
We describe a new computational method for the numerically stable particle-based simulation of open-boundary flows, including volume conserving chemical reactions. The novel method is validated for the case of heterogeneous catalysis…
Alchemical free energy calculations via molecular dynamics have been widely used to obtain thermodynamic properties related to protein-ligand binding and solute-solvent interactions. Although soft-core modeling is the most common approach,…
A new method is presented for calculation of the shell correction with the inclusion of the continuum part of the spectrum. The smoothing function used has a finite energy range in contrast to the Gaussian shape of the Strutinski method.…
Closed-form, analytical approximations for electrostatic properties of molecules are of unique value, as these can provide computational speed, versatility, and physical insight. Here, we derive a simple, closed-form formula for the…
We devise automated workflows for the calculation of Helmholtz and Gibbs free energies and their temperature and pressure dependence and provide the corresponding computational tools. We employ non-equilibrium thermodynamics for evaluating…
Ab initio modeling of electrochemical systems is becoming a key tool for understanding and predicting electrochemical behavior. Development and careful benchmarking of computational electrochemical methods are essential to ensure their…
For large scale electronic structure calculation, the Krylov subspace method is introduced to calculate the one-body density matrix instead of the eigenstates of given Hamiltonian. This method provides an efficient way to extract the…
We present a pipeline to study the device performance of organic solar cells in silico. We introduce a mathematical model that includes the dynamics of excitons as well as their dissociation at bulk heterojunctions within the nanomorphology…
For problems in astrophysics, planetary science and beyond, numerical simulations are often limited to simulating fewer particles than in the real system. To model collisions, the simulated particles (aka superparticles) need to be inflated…
Molecular dynamics (MD) simulations of the zeta potential are so poor that it has become common to term their predictions 'apparent'. Here we demonstrate how zeta potentials that agree with measured values can be calculated by: (1)…
Quantum--Mechanical methods that are both computationally fast and accurate are not yet available for electronic excitations having charge transfer character. In this work, we present a significant step forward towards this goal for those…
The electronic structure and total energy were calculated for ordered and disordered MgO-CaO solid solutions within the multiple scattering theory in real space and the local density approximation. Based on the dependence of the total…
We present a fast and accurate method to calculate the electrostatic energy and forces of interacting particles with the boundary conditions appropriate to surfaces, i.e periodic in the two directions parallel to the surface and free in the…
The quality of biomolecular simulations critically depends on the accuracy of the force field used to calculate the potential energy of the molecular configurations. Currently, most simulations employ non-polarisable force fields, which…