Related papers: A continuum solvent model: the DISOLV program - al…
We present an algorithm to simulate the many-body depletion interaction between anisotropic colloids in an implicit way, integrating out the degrees of freedom of the depletants, which we treat as an ideal gas. Because the depletant…
A multiscale QM/classical approach is presented, that is able to model the optical properties of complex nanostructures composed of a molecular system adsorbed on metal nanoparticles. The latter are described by a combined…
Molecular conformation generation (MCG) is a fundamental and important problem in drug discovery. Many traditional methods have been developed to solve the MCG problem, such as systematic searching, model-building, random searching,…
In recent years, molecular dynamics (MD) simulations have emerged as a pivotal tool for understanding the structure, dynamics, and phase behavior in charged soft matter systems. To explore phenomena across greater length and time scales in…
Recent results on supercomputers show that beyond 65K cores, the efficiency of molecular dynamics simulations of interfacial systems decreases significantly. In this paper, we introduce a dynamic cutoff method (DCM) for interfacial systems…
The goal of co-salient object detection (CoSOD) is to discover salient objects that commonly appear in a query group containing two or more relevant images. Therefore, how to effectively extract inter-image correspondence is crucial for the…
Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…
Newly developed coupled-cluster (CC) methods enable simulations of ionization potentials and spectral functions of molecular systems in a wide range of energy scales ranging from core-binding to valence. This paper discusses results…
We discuss the scalable parallel solution of the Poisson equation within a Particle-In-Cell (PIC) code for the simulation of electron beams in particle accelerators of irregular shape. The problem is discretized by Finite Differences.…
PCMSolver is an open-source library for continuum electrostatic solvation. It can be combined with any quantum chemistry code and requires a minimal interface with the host program, greatly reducing programming effort. As input, PCMSolver…
We present a Newton-Krylov solver for a viscous-plastic sea-ice model. This constitutive relation is commonly used in climate models to describe the material properties of sea ice. Due to the strong nonlinearity introduced by the material…
Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the…
Differential geometry (DG) based solvation models are a new class of variational implicit solvent approaches that are able to avoid unphysical solvent-solute boundary definitions and associated geometric singularities, and dynamically…
Resolving numerically Vlasov-Poisson equations for initially cold systems can be reduced to following the evolution of a three-dimensional sheet evolving in six-dimensional phase-space. We describe a public parallel numerical algorithm…
The impact of targeted replacement of individual terms in empirical force fields is quantitatively assessed for pure water, dichloromethane (DCM), and solvated K$^+$ and Cl$^-$ ions. For the electrostatics, point charges (PCs) and machine…
Surface-subsurface flow models for hydrological applications solve a coupled multiphysics problem. This usually consists of some form of the Richards and shallow water equations. A typical setup couples these two nonlinear partial…
We establish, through coarse-grained computation, a connection between traditional, continuum numerical algorithms (initial value problems as well as fixed point algorithms) and atomistic simulations of the Larson model of micelle…
The COSMO-RS (Conductor-like Screening Model for Real Solvents) is a predictive thermodynamic model that has found diverse applications in various domains like chemical engineering, environmental chemistry, nanotechnology, material science,…
High-resolution simulations of particle-based kinetic plasma models typically require a high number of particles and thus often become computationally intractable. This is exacerbated in multi-query simulations, where the problem depends on…
We introduce quantum algorithms able to sample equilibrium water solvent molecules configurations within proteins thanks to analog quantum computing. To do so, we combine a quantum placement strategy to the 3D Reference Interaction Site…