Related papers: Efficient Formulation of Polarizable Gaussian Mult…
Geometric graph neural networks (GNNs) excel at capturing molecular geometry, yet their locality-biased message passing hampers the modeling of long-range interactions. Current solutions have fundamental limitations: extending cutoff radii…
In spite of missing dynamical correlations, the projected generator coordinate method (PGCM) was recently shown to be a suitable method to tackle the low-lying spectroscopy of complex nuclei. Still, describing absolute binding energies and…
While there have been many developments in computational probes of both strongly-correlated molecular systems and machine-learning accelerated molecular dynamics, there remains a significant gap in capabilities in simulating accurate…
We have simulated the performances of a GEM with a large density of multiplication holes. In particular in this note we fully simulate the GEM detector used in the PixiE experiment. The detector will be employed in the measurement of the…
Computer simulations of differential equations require a time discretization, which inhibits to identify the exact solution with certainty. Probabilistic simulations take this into account via uncertainty quantification. The construction of…
An electrostatic, implicit particle-in-cell (PIC) model for collisionless, fully magnetized, paraxial plasma expansions in a magnetic nozzle is introduced with exact charge, energy, and magnetic moment conservation properties. The approach…
Common time-explicit numerical methods for kinetic simulations of plasmas in the low-collisions limit fall into two classes of algorithms: momentum conserving and energy conserving. Each has certain drawbacks. The PIC algorithm does not…
To accurately model the electron density and polarization, a polarizable multipole (PM) model using the AMOEBA force field has been introduced \cite{Ren:2003, Shi:2013} recently. In the AMOEBA force field, the traditional point atomic…
Polyhalogenated compounds are common in industrial, agricultural, and environmental applications. These compounds contain more halogen bonds than monohalogenated compounds. The presence of coupled {\sigma}-holes in the covalent halogen…
Computational determination of the equilibrium state of heterogeneous phospholipid mem-branes is a significant challenge. We wish to explore the rich phase diagram of these multi-component systems. However, the diffusion and mixing times in…
Hybrid quantum mechanics / molecular mechanics (QM/MM) models successfully describe the properties of biological macromolecules. However, most QM/MM methodologies are constrained to unrealistic gas phase models, thus limiting their…
In this paper, we develop an asymptotic-preserving and energy-conserving (APEC) Particle-In-Cell (PIC) algorithm for the Vlasov-Maxwell system. This algorithm not only guarantees that the asymptotic limiting of the discrete scheme is a…
Recent development of structure-preserving geometric particle-in-cell (PIC) algorithms for Vlasov-Maxwell systems is summarized. With the arriving of 100 petaflop and exaflop computing power, it is now possible to carry out direct…
The fracture simulation of random particle reinforced composite structures remains a challenge. Current techniques either assumed a homogeneous model, ignoring the microstructure characteristics of composite structures, or considered a…
We construct a coarse-grained (CG) model for dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayers and apply it to large-scale simulation studies of lipid membranes. Our CG model is a two-dimensional representation of the membrane,…
We present a geometric Particle-in-Cell (PIC) algorithm on two-dimensional (2D) unstructured meshes for studying electrostatic perturbations in magnetized plasmas. In this method, ions are treated as fully kinetic particles, and electrons…
Conjugated organic molecules play a central role in a wide range of optoelectronic devices, including organic light-emitting diodes, organic field-effect transistors, and organic solar cells. A major bottleneck in the computational design…
This study extends the accurate and transferable molecular-orbital-based machine learning (MOB-ML) approach to modeling the contribution of electron correlation to dipole moments at the cost of Hartree-Fock computations. A…
This paper addresses the problem of active learning of a multi-output Gaussian process (MOGP) model representing multiple types of coexisting correlated environmental phenomena. In contrast to existing works, our active learning problem…
This paper presents the state of the art of kinetic modeling techniques for simulating plasma kinetic dynamics in magnetospheres. We describe the critical numerical techniques for enabling large-scale kinetic simulations of magnetospheres:…