Related papers: The MOLDY short-range molecular dynamics package
The growing complexity of Cyber-Physical Systems (CPS), together with increasingly available parallelism provided by multi-core chips, fosters the parallelization of simulation. Simulation speed-ups are expected from co-simulation and…
OpenMP is the de facto API for parallel programming in HPC applications. These programs are often computed in data centers, where energy consumption is a major issue. Whereas previous work has focused almost entirely on performance, we here…
The Massive Parallel Computing (MPC) model gained popularity during the last decade and it is now seen as the standard model for processing large scale data. One significant shortcoming of the model is that it assumes to work on static…
A software package, called DFTBaby, is published, which provides the electronic structure needed for running non-adiabatic molecular dynamics simulations at the level of charge-consistent tight-binding DFT. A long-range correction is…
Molecular dynamics (MD) simulation has long been the principal computational tool for exploring protein conformational landscapes and dynamics, but its application is limited by high computational cost. We present ProTDyn, a foundation…
Molecular Field-Coupled Nanocomputing (MolFCN) is a promising beyond-CMOS paradigm in which information is propagated electrostatically rather than through charge transport, enabling ultra-low-power logic. Identifying molecules with stable…
We present MELODI, a novel memory architecture designed to efficiently process long documents using short context windows. The key principle behind MELODI is to represent short-term and long-term memory as a hierarchical compression scheme…
The objective of this article is to report the parallel implementation of the 3D molecular dynamic simulation code for laser-cluster interactions. The benchmarking of the code has been done by comparing the simulation results with some of…
This paper introduces a parallel directional fast multipole method (FMM) for solving N-body problems with highly oscillatory kernels, with a focus on the Helmholtz kernel in three dimensions. This class of oscillatory kernels requires a…
Force matching is an established technique to generate effective potentials for molecular dynamics simulations from first-principles data. This method has been implemented in the open source code potfit. Here, we present a review of the…
The electrical and electronic engineering has used parallel programming to solve its large scale complex problems for performance reasons. However, as parallel programming requires a non-trivial distribution of tasks and data, developers…
Large-scale HPC simulations of plasma dynamics in fusion devices require efficient parallel I/O to avoid slowing down the simulation and to enable the post-processing of critical information. Such complex simulations lacking parallel I/O…
The interaction of condensed phase systems with external electric fields is crucial in myriad processes in nature and technology ranging from the field-directed motion of cells (galvanotaxis), to energy storage and conversion systems…
Persistent Memory (PM) makes possible recoverable applications that can preserve application progress across system reboots and power failures. Actual recoverability requires careful ordering of cacheline flushes, currently done in two…
We describe a methodology for designing efficient parallel and distributed scientific software. This methodology utilizes sequences of mechanizable algebra--based optimizing transformations. In this study, we apply our methodology to the…
Heliospheric plasmas require multi-scale and multi-physics considerations. On one hand, MHD codes are widely used for global simulations of the solar-terrestrial environments, but do not provide the most elaborate physical description of…
Power density constraints are limiting the performance improvements of modern CPUs. To address this we have seen the introduction of lower-power, multi-core processors such as GPGPU, ARM and Intel MIC. To stay within the power density…
Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
The hopping model for cargo transport by molecular motors introduced in Refs. goldman1, goldman2, is extended here in order to incorporate the movement of cargo-motor complexes. In this context, hopping process expresses the possibility for…
Constant potential method molecular dynamics simulation (CPM MD) enables the accurate modelling of atomistic electrode charges when studying the electrode-electrolyte interface at the nanoscale. Here we extend the theoretical framework of…