Related papers: Path-accelerated molecular dynamics: Parallel-in-t…
A novel parallel efficiency analysis on a framework for simulating the growth of Malignant Pleural Mesothelioma (MPM) tumours is presented. Proliferation of MPM tumours in the pleural space is simulated using a Cellular Potts Model (CPM)…
Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in…
Since numerical computing with MATLAB offers a wide variety of advantages, such as easier developing and debugging of computational codes rather than lower-level languages, the popularity of this tool is significantly increased in the past…
We propose a parallel adaptive constraint-tightening approach to solve a linear model predictive control problem for discrete-time systems, based on inexact numerical optimization algorithms and operator splitting methods. The underlying…
Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of simulated models and morphologies have exceeded the capacity of any…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
The implicit 2D3V particle-in-cell (PIC) code developed to study the interaction of ultrashort pulse lasers with matter [G. M. Petrov and J. Davis, Computer Phys. Comm. 179, 868 (2008); Phys. Plasmas 18, 073102 (2011)] has been parallelized…
In view of the existing limitations of sequential computing, parallelization has emerged as an alternative in order to improve the speedup of numerical simulations. In the framework of evolutionary problems, space-time parallel methods…
Path-integral-based molecular dynamics (MD) simulations are widely used for the calculation of numerically exact quantum Boltzmann properties and approximate dynamical quantities. A nearly universal feature of MD numerical integration…
We report an improved method for the calculation of tunneling splittings between degenerate configurations in molecules and clusters using path-integral molecular dynamics (PIMD). Starting from an expression involving a ratio of…
Molecular dynamics (MD) simulations are widely used to study large-scale molecular systems. HPC systems are ideal platforms to run these studies, however, reaching the necessary simulation timescale to detect rare processes is challenging,…
The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious…
The growing demand for multi-DNN workloads with unpredictable task arrival times has highlighted the need for interruptible scheduling on edge accelerators. However, existing preemptive frameworks typically assume known task arrival times…
The purpose of this paper is to propose a time-step-robust cell-to-cell integration of particle trajectories in 3-D unstructured meshes in particle/mesh Lagrangian stochastic methods. The main idea is to dynamically update the mean fields…
From natural language processing to genome sequencing, large-scale machine learning models are bringing advances to a broad range of fields. Many of these models are too large to be trained on a single machine, and instead must be…
The interest in combining model-based control approaches with diffusion models has been growing. Although we have seen many impressive robotic control results in difficult tasks, the performance of diffusion models is highly sensitive to…
Dynamic mode decomposition (DMD) provides a principled approach to extract physically interpretable spatial modes from time-resolved flow field data, along with a linear model for how the amplitudes of these modes evolve in time. Recently,…
Molecular dynamics simulations have emerged as a potent tool for investigating the physical properties and kinetic behaviors of materials at the atomic scale, particularly in extreme conditions. Ab initio accuracy is now achievable with…
We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method.…
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…