Related papers: Molecular Dynamics with Conformationally Dependent…
The development of reliable and extensible molecular mechanics (MM) force fields -- fast, empirical models characterizing the potential energy surface of molecular systems -- is indispensable for biomolecular simulation and computer-aided…
We introduce a system-independent method to derive effective atomic C$_6$ coefficients and polarizabilities in molecules and materials purely from charge population analysis. This enables the use of dispersion-correction schemes in…
Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular…
In CFD simulations of two-phase flows, accurate drag force modeling is essential for predicting particle dynamics. However, a generally valid formulation is lacking, as all available drag force correlations have been established for…
Long ranged electrostatic interactions are time consuming to calculate in molecular dynamics and Monte-Carlo simulations. We introduce an algorithmic framework for simulating charged particles which modifies the dynamics so as to allow…
We present a new scalable algorithm for short-range molecular dynamics simulations on distributed memory MIMD multicomputer based on a message-passing multi-cell approach. We have implemented the algorithm on the Connection Machine 5 (CM-5)…
A current challenge in atomistic machine learning is that of efficiently predicting the response of the electron density under electric fields. We address this challenge with symmetry-adapted kernel functions that are specifically derived…
We propose a new molecular simulation framework that combines the transferability, robustness and chemical flexibility of an ab initio method with the accuracy and efficiency of a machine learned force field. The key to achieve this mix is…
The implementation of Molecular Dynamics (MD) on FPGAs has received substantial attention. Previous work, however, has consisted of either proof-of-concept implementations of components, usually the range-limited force; full systems, but…
The strengths and short-comings of the point-dipole model for polar fluids of spherical molecules are illustrated by considering the physically more relevant case of extended dipoles formed by two opposite charges $\pm q$ separated by a…
Polymorphs in molecular crystals are often very close in energy, yet they may possess markedly different physical and chemical properties. The understanding and prediction of polymorphism is of paramount importance for a variety of…
The fluctuations of the charge on an electrode contain information on the microscopic correlations within the adjacent fluid and their effect on the electronic properties of the interface. We investigate these fluctuations using molecular…
This paper deals with the formulation, calibration, and validation of a Lattice Discrete Particle Model (LDPM) for the simulation of the pressure-dependent inelastic response of granular rocks. LDPM is formulated in the framework of…
Analytic first and second derivatives of the energy are developed for the fragment molecular orbital method interfaced with molecular mechanics in the electrostatic embedding scheme at the level of Hartree-Fock and density functional…
We review our recently developed electronic structure calculation methods used for the dynamics of large-scale solids or liquids with an efficient algorithm for large scale simultaneous linear equations. The electronic structure calculation…
The distribution of the electric microfield at a charged particle moving in a two-component plasma is calculated. The theoretical approximations are obtained via the parameter integration technique and using the screened pair approximation…
Molecular Dynamics (MD) simulations play a central role in physics-driven drug discovery. MD applications often use the Particle Mesh Ewald (PME) algorithm to accelerate electrostatic force computations, but efficient parallelization has…
Mn enrichment at dislocations in Fe-Mn alloys due to segregation and spinodal decomposition along the dislocation line is studied via modeling and experimental characterization. To model these phenomena, both finite-deformation microscopic…
Proteins have been empirically linked to memory. If memory relates to protein structure, then each conformation would_functionally_ code only one bit, making it difficult to explain large memories. Nor is there a simple way to relate memory…
Three dimensional implementations of liquid state theories offer an efficient alternative to computer simulations for the atomic-level description of aqueous solutions in complex environments. In this context, we present a (classical)…