Related papers: Efficient Formulation of Polarizable Gaussian Mult…
The Many-Body Expansion (MBE) is a useful tool to simulate condensed phase chemical systems, often avoiding the steep computational cost of usual electronic structure methods. However, it often requires higher than 2-body terms to achieve…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
Raman spectroscopy is an important tool for studies of molecules, liquids and solids. While Raman spectra can be obtained theoretically from molecular dynamics (MD) simulations, this requires the calculation of the electronic polarizability…
The Poisson-Boltzmann equation offers an efficient way to study electrostatics in molecular settings. Its numerical solution with the boundary element method is widely used, as the complicated molecular surface is accurately represented by…
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…
The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chemical simulations. However, its application in quantum mechanical calculations of large-scale…
Gaussian process (GP) emulator has been used as a surrogate model for predicting force field and molecular potential, to overcome the computational bottleneck of molecular dynamics simulation. Integrating both atomic force and energy in…
In this perspective, we discuss where and how accounting for electronic many-body polarization affects the accuracy of classical molecular dynamics simulations of biomolecules.While the effects of electronic polarization are highly…
It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
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…
Machine learning force fields offer the ability to simulate biomolecules with quantum mechanical accuracy while significantly reducing computational costs, attracting growing attention in biophysics. Meanwhile, leveraging the efficiency of…
Quantum Mechanics/Molecular Mechanics (QM/MM) simulations are a popular approach to study various features of large systems. A common application of QM/MM calculations is in the investigation of reaction mechanisms in condensed-phase and…
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…
Global particle-in-cell (PIC) simulations of pulsar magnetospheres are performed with a volume, surface and pair production-based plasma injection schemes to systematically investigate the transition between electrosphere and force-free…
With the great development of parallel computing techniques, the particle-particle (PP) model has been successfully applied in a number of plasma applications. Comparing to particle-mesh (PM) models, for example the widely used…
The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or their complexes, are strongly influenced by protonation changes of their typically many titratable groups, which explains their pH sensitivity. In turn,…
Three different polarizable ion models for molten AgBr have been studied by molecular dynamics simulations. The three models are based on a rigid ion model (RIM) with a pair potential of the type proposed by Vashishta and Rahman for…
This paper discusses a novel fully implicit formulation for a 1D electrostatic particle-in-cell (PIC) plasma simulation approach. Unlike earlier implicit electrostatic PIC approaches (which are based on a linearized Vlasov-Poisson…
A challenging topic in materials engineering is the development of numerical models that can accurately predict material properties with atomistic accuracy, matching the scale and level of detail achieved by experiments. In this regard,…