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We examine the performance of various commonly used integration schemes in dissipative particle dynamics simulations. We consider this issue using three different model systems, which characterize a variety of different conditions often…
Evaluating multi-center molecular integrals with Cartesian Gaussian-type basis sets has been a long-standing bottleneck in electronic structure theory calculation for solids and molecules. We have developed a vector-coupling and…
Numerous real-world applications of uncertain multiobjective optimization problems (UMOPs) can be found in science, engineering, business, and management. To handle the solution of uncertain optimization problems, robust optimization is a…
Solid-On-Solid (SOS) computer simulations are employed to investigate the sublimation of surfaces. We distinguish three sublimation regimes: layer-by-layer sublimation, free step flow and hindered step flow. The sublimation regime is…
Continuum solvation methods can provide an accurate and inexpensive embedding of quantum simulations in liquid or complex dielectric environments. Notwithstanding a long history and manifold applications to isolated systems in open boundary…
Molecular dynamics (MD) simulations provide atomistic insight into biomolecular systems but are often limited by high computational costs required to access long timescales. Coarse-grained machine learning models offer a promising avenue…
Rapid and accurate assessment of protein structural models is essential for protein structure prediction and design. Great progress has been made in this regard, especially by recent development of ``knowledge-based'' potentials. Various…
We develop a computational method based on Dissipative Particle Dynamics (DPD) that introduces solvent hydrodynamic interactions to coarse-grained models of solutes, such as ions, molecules, or polymers. DPD-solvent (DPDS) is a fully…
In this paper, the Immersed Boundary Method (IBM) proposed by Pinelli is implemented for finite volume approximations of incompressible Navier-Stokes equations solutions in the open source toolbox OpenFOAM version 2.2. Solid obstacles are…
We present a generalized version of the ITIM algorithm for the identification of interfacial molecules, which is able to treat arbitrarily shaped interfaces. The algorithm exploits the similarities between the concept of probe sphere used…
We present an optimized implementation of the recently proposed symmetric gradient domain machine learning (sGDML) model. The sGDML model is able to faithfully reproduce global potential energy surfaces (PES) for molecules with a few dozen…
In this paper, we consider a nonlinear and nonlocal parabolic model for multi-species ionic fluids and introduce a semi-implicit finite volume scheme, which is second order accurate in space, first order in time and satisfies the following…
In this paper, we focus on solving a sequence of linear systems with an identical (or similar) coefficient matrix. For this type of problems, we investigate the subspace correction and deflation methods, which use an auxiliary matrix…
Differentiable simulation is a promising toolkit for fast gradient-based policy optimization and system identification. However, existing approaches to differentiable simulation have largely tackled scenarios where obtaining smooth…
We present a novel hybrid algorithm for training Deep Neural Networks that combines the state-of-the-art Gradient Descent (GD) method with a Mixed Integer Linear Programming (MILP) solver, outperforming GD and variants in terms of accuracy,…
We present in this work the implementation of the Energy Conserving Semi-Implicit Method in a parallel code called ECsim. This new code is a three-dimensional, fully electromagnetic particle in cell (PIC) code. It is written in C/C++ and…
Linear scaling quantum chemical methods for Density Functional Theory are extended to the condensed phase at the $\Gamma$-point. For the two-electron Coulomb matrix, this is achieved with a tree-code algorithm for fast Coulomb summation [J.…
A polymer network can imbibe water, forming an aggregate called hydrogel, and undergo large and inhomogeneous deformation with external mechanical constraint. Due to the large deformation, nonlinearity plays a crucial role, which also…
Deformable elastic bodies in viscous and viscoelastic media constitute a large portion of synthetic and biological complex fluids. We present a parallelized 3D-simulation methodology which fully resolves the momentum balance in the solid…
We present a highly efficient molecular dynamics scheme for calculating the concentration profile of dopants implanted in group-IV alloy, and III-V zinc blende structure materials. Our program incorporates methods for reducing computational…