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We introduce a modified molecular dynamics algorithm that allows one to freeze the dynamics of parts of a physical system, and thus concentrate the simulation effort on selected, central degrees of freedom. This freezing, in contrast to…
Computational systems biology has provided plenty of insights into cell biology. Early on, the focus was on reaction networks between molecular species. Spatial distribution only began to be considered mostly within the last decade.…
We test the performances of two different approaches to the computation of forces for molecular dynamics simulations on Graphics Processing Units. A "vertex-based" approach, where a computing thread is started per particle, is compared to a…
This paper presents a hierarchical planning algorithm for racing with multiple opponents. The two-stage approach consists of a high-level behavioral planning step and a low-level optimization step. By combining discrete and continuous…
Different parallel frameworks for implementing data analysis applications have been proposed by the HPC and Big Data communities. In this paper, we investigate three task-parallel frameworks: Spark, Dask and RADICAL-Pilot with respect to…
Many-body simulations of quantum systems is an active field of research that involves many different methods targeting various computing platforms. Many methods commonly employed, particularly coupled cluster methods, have been adapted to…
Replica exchange molecular dynamics (REMD) becomes more efficient as the frequency of swap between the temperatures is increased. Recently in [Plattner et al, J. Chem. Phys. 135, 134111 (2011)] a method was proposed to implement infinite…
Numerical solution of partial differential equations on parallel computers using domain decomposition usually requires synchronization and communication among the processors. These operations often have a significant overhead in terms of…
A new method for the simulation of evolving multi-domains problems has been introduced in a previous work (RealIMotion), Florez et al. (2020). In this article further developments of the model will be presented. The main focus here is a…
This work aims to automate the design of Multiple Gravity-Assist (MGA) transfers between planets using low-thrust propulsion. In particular, during the preliminary design phase of space missions, the combinatorial complexity of MGA…
Sensor-based human activity recognition is a key technology for many human-centered intelligent applications. However, this research is still in its infancy and faces many unresolved challenges. To address these, we propose a comprehensive…
While load balancing in distributed-memory computing has been well-studied, we present an innovative approach to this problem: a unified, reduced-order model that combines three key components to describe "work" in a distributed system:…
Many-body dissipative particle dynamics (MDPD) offers a significant speed-up in the simulation of various systems, including soft matter, in comparison with molecular dynamics (MD) simulations based on Lennard-Jones nteractions, which is…
Recent advances in both theoretical and computational methods have enabled large-scale, precision calculations of the properties of atomic nuclei. With the growing complexity of modern nuclear theory, however, also comes the need for novel…
The problem of identifying intersections between two sets of d-dimensional axis-parallel rectangles appears frequently in the context of agent-based simulation studies. For this reason, the High Level Architecture (HLA) specification -- a…
We review and compare numerical methods that simultaneously control temperature while preserving the momentum, a family of particle simulation methods commonly used for the modelling of complex fluids and polymers. The class of methods…
In contact-rich tasks, the hybrid, multi-modal nature of contact dynamics poses great challenges in model representation, planning, and control. Recent efforts have attempted to address these challenges via data-driven methods, learning…
High-performance computing (HPC) has revolutionized our ability to perform detailed simulations of complex real-world processes. A prominent contemporary example is from aerospace propulsion, where HPC is used for rotating detonation rocket…
We introduce a new class of machine learning interatomic potentials - fast General Two- and Three-body Potential (GTTP), which is as fast as conventional empirical potentials and require computational time that remains constant with…
Complex systems often show macroscopic coherent behavior due to the interactions of microscopic agents like molecules, cells, or individuals in a population with their environment. However, simulating such systems poses several…