Related papers: HSMA: An O(N) electrostatics package implemented i…
We present a generalized, data-driven collisional operator for one-component plasmas, learned from molecular dynamics simulations, to extend the collisional kinetic model beyond the weakly coupled regime. The proposed operator features an…
I present HPRMAT, a high-performance solver library for the linear systems arising in R-matrix coupled-channel scattering calculations in nuclear physics. Designed as a drop-in replacement for the linear algebra routines in existing…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
High-Level Synthesis (HLS) enables rapid prototyping of complex hardware designs by translating C or C++ code to low-level RTL code. However, the testing and evaluation of HLS designs still typically rely on slow RTL-level simulators that…
Electronic stopping (ES) of energetic atoms is not taken care of by the interatomic potentials used in molecular dynamics (MD) simulations when simulating collision cascades. The Lindhard-Scharff (LS) formula for electronic stopping is…
We develop an online optimisation algorithm for in situ calibration of collision models in simulations of rarefied gas flows. The online optimised collision models are able to achieve similar accuracy to Direct Molecular Simulation (DMS) at…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…
We present a new algorithm for isothermal-isobaric molecular-dynamics simulation. The method uses an extended Hamiltonian with an Andersen piston combined with the Nos'e-Poincar'e thermostat, recently developed by Bond, Leimkuhler and Laird…
Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…
A novel quantum algorithm for solving the Boltzmann-Maxwell equations of the 6D collisionless plasma is proposed. The equation describes the kinetic behavior of plasma particles in electromagnetic fields and is known for the classical…
A recently proposed method for computer simulations in the isothermal-isobaric (NPT) ensemble, based on Langevin-type equations of motion for the particle coordinates and the ``piston'' degree of freedom, is re-derived by straightforward…
Accurate modelling of electrostatic interactions and charge transfer is fundamental to computational chemistry, yet most machine learning interatomic potentials (MLIPs) rely on local atomic descriptors that cannot capture long-range…
Trapped-ion quantum simulators, in analog and digital modes, are considered a primary candidate to achieve quantum advantage in quantum simulation and quantum computation. The underlying controlled ion-laser interactions induce all-to-all…
Molecular dynamics simulations are a cornerstone in science, allowing to investigate from the system's thermodynamics to analyse intricate molecular interactions. In general, to create extended molecular trajectories can be a…
We present OMP2HMPP, a tool that, in a first step, automatically translates OpenMP code into various possible transformations of HMPP. In a second step OMP2HMPP executes all variants to obtain the performance and power consumption of each…
Cold-chain storage limits access to insulin for hundreds of millions of people; a thermally protective patch polymer could help, but the design space is too large for exhaustive experiment. Starting from that problem, we narrow to an…
The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these…
A reliable prediction of 3D protein structures from sequence data remains a big challenge due to both theoretical and computational difficulties. We have previously shown that our kinetostatic compliance method (KCM) implemented into the…
Point-based 3D point cloud models employ computation and memory intensive mapping functions alongside NN layers for classification/segmentation, and are executed on server-grade GPUs. The sparse, and unstructured nature of 3D point cloud…