Related papers: Fast Surface Based Electrostatics for biomolecules…
Currently existing energy-stable parametric finite element methods for surface diffusion flow and other flows are usually limited to first-order accuracy in time. Designing a high-order algorithm for geometric flows that can also be…
Sampling diverse, thermodynamically feasible molecular conformations plays a crucial role in predicting properties of a molecule. In this paper we propose to use GFlowNet for sampling conformations of small molecules from the Boltzmann…
We present an implementation of the fast multipole method for computing coulombic electrostatic and polarization forces from polarizable force-fields based on induced point dipole moments. We demonstrate the expected $O(N)$ scaling of that…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
The Bethe-Salpeter equation (BSE) formalism is a computationally affordable method for the calculation of accurate optical excitation energies in molecular systems. Similar to the ubiquitous adiabatic approximation of time-dependent…
We present a clear and rigorous derivation of the Ewald-like method for calculation of the electrostatic energy of the systems infinitely periodic in two-dimensions and of finite size in the third dimension (slabs) which is significantly…
Several implicit (continuum) solvent models are considered: the Polarized Continuum Model (PCM), the Surface Generalized Born model (SGB), and the COnductor-like Screening model (COSMO) as well as their implementation in the form of the…
Electrostatics is of paramount importance to chemistry, physics, biology, and medicine. The Poisson-Boltzmann (PB) theory is a primary model for electrostatic analysis. However, it is highly challenging to compute accurate PB electrostatic…
This document attempts to clarify potential confusion regarding electrostatics calculations, specifically in the context of biomolecular structure and specifically as regards the units typically used to contour/visualize isopotential…
The evaluation of long-range Coulomb interactions is a significant cost in molecular dynamics (MD), even when using Particle Mesh Ewald (PME) or Particle-Particle-Particle-Mesh (PPPM) methods, which rely on Ewald splitting and the fast…
In this paper we have derived explicitly computable bounds on the error in energy norms for the fully nonlinear Poisson-Boltzmann equation. Together with the computable bounds, we have also obtained efficient error indicators which can…
At low reduced electric fields the electron energy distribution function in heavy noble gases can take two distinct shapes. This "bistability effect" - in which electron-electron (Coulomb) collisions play an essential role - is analyzed…
Accurate calculations of solvation free energies remain a central challenge in molecular simulations, often requiring extensive sampling and numerous alchemical intermediates to ensure sufficient overlap between phase-space distributions of…
The formation energy of a solid surface can be extracted from slab calculations if the bulk energy per atom is known. It has been pointed out previously that the resulting surface energy will diverge with slab thickness if the bulk energy…
The lowest electronic excitations of benzene and a set of donor-acceptor molecular complexes are calculated for the gas phase and on the Al(111) surface using the many-body Bethe-Salpeter equation (BSE). The energy of the charge-transfer…
We present a massively parallel, GPU-accelerated implementation of the Bethe-Salpeter equation (BSE) for the calculation of the vertical excitation energies (VEEs) and optical absorption spectra of condensed and molecular systems, starting…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
We propose an efficient and accurate parametric finite element method (PFEM) for solving sharp-interface continuum models for solid-state dewetting of thin films with anisotropic surface energies. The governing equations of the…
We propose a new method to describe three-body breakups of nuclei, in which the Lippmann-Schwinger equation is solved combining with the complex scaling method. The complex-scaled solutions of the Lippmann-Schwinger equation (CSLS) enables…
We present efficient and reliable molecular dynamics simulations of the photodissociation of dichloromethane followed by Coulomb explosion. These simulations are performed by calculating trajectories on accurate potential energy surfaces of…