Related papers: On the hierarchical parallelization of ab initio s…
All-atom, force field-based molecular dynamics simulations are essential tools in computational chemistry, enabling the prediction and analysis of biomolecular systems with atomic-level resolution. However, as system sizes and simulation…
This work presents new parallelizable numerical schemes for the integration of Dissipative Particle Dynamics with Energy conservation (DPDE). So far, no numerical scheme introduced in the literature is able to correctly preserve the energy…
This paper addresses the question of what exactly is an analogue of the preconditioned steepest descent (PSD) algorithm in the case of a symmetric indefinite system with an SPD preconditioner. We show that a basic PSD-like scheme for an…
The recently developed Hierarchical Poincar\'e-Steklov (HPS) method is a high-order discretization technique that comes with a direct solver. Results from previous papers demonstrate the method's ability to solve Helmholtz problems to high…
We have applied path integral simulations, in combination with new ab initio based water potentials, to investigate nuclear quantum effects in liquid water. Because direct ab initio path integral simulations are computationally expensive, a…
We developed a portable code for dissipative particle dynamics (DPD) simulations. This Fortran program named CAMUS has a couple of notable features. One is the omission of constructing the so-called neighboring particles list, providing a…
Pipeline parallelism is an essential technique in the training of large-scale Transformer models. However, it suffers from imbalanced memory consumption, leading to insufficient memory utilization. The BPipe technique was proposed to…
This study concerns with singularly perturbed systems of second-order reaction-diffusion equations in ODE's. To handle this type of problems, a numerical-asymptotic hybrid method is employed. In this hybrid method, an efficient asymptotic…
Modeling multi-scale collisionless magnetized processes constitutes an important numerical challenge. By treating electrons as a fluid and ions kinetically, the so-called hybrid Particle-In-Cell (PIC) codes represent a promising…
Parallel simulation and control of large-scale robotic systems often rely on partitioned time stepping, yet finite-iteration coupling can inject spurious energy by violating power consistency--even when each subsystem is passive. This…
This paper presents a large-scale $ab$ $initio$ simulation study of amorphous silicon hydride ($a$-Si$_{\text{1-x}}$H$_{\text{x}}$) with an emphasis on the structure and properties of the material across a range of hydrogen concentration by…
Constructing accurate, high dimensional molecular potential energy surfaces (PESs) for polyatomic molecules is challenging. Reproducing Kernel Hilbert space (RKHS) interpolation is an efficient way to construct such PESs. However, the…
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…
A means to take advantage of molecular similarity to lower the computational cost of electronic structure theory is explored, in which parameters are embedded into a low-cost, low-level (LL) ab initio model and adjusted to obtain agreement…
The strongly coupled electron liquid provides a unique opportunity to study the complex interplay of strong coupling with quantum degeneracy effects and thermal excitations. To this end, we carry out extensive \textit{ab initio} path…
Molecular dynamics (MD) simulations are essential tools in computational chemistry and drug discovery, offering crucial insights into dynamic molecular behavior. However, their utility is significantly limited by substantial computational…
This paper presents an efficient parallel approximation scheme for a new class of min-max problems. The algorithm is derived from the matrix multiplicative weights update method and can be used to find near-optimal strategies for…
The particle-in-cell (PIC) method is successfully used to study magnetized plasmas. However, this requires large computational costs and limits simulations to short physical run-times and often to setups in less than three spatial…
For the parallel-in-time integration method Parareal, pipelining can be used to hide some of the cost of the serial correction step and improve its efficiency. The paper introduces a basic OpenMP implementation of pipelined Parareal and…
Conventional molecular dynamics (MD) simulation approaches, such as $\textit{ab initio}$ MD (AIMD) and empirical force field MD (EFFMD), face significant trade-offs between physical accuracy and computational efficiency. This work presents…