Related papers: The need to implement FAIR principles in biomolecu…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…
In the context of collaborative AI research and development projects, it would be ideal to have self-contained encapsulated algorithms that can be easily shared between different parties, executed and validated on data at different sites,…
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…
Although event-driven algorithms have been shown to be far more efficient than time-driven methods such as conventional molecular dynamics, they have not become as popular. The main obstacle seems to be the difficulty of parallelizing…
Computer simulations have become a very powerful tool for scientific research. Given the vast complexity that comes with many open scientific questions, a purely analytical or experimental approach is often not viable. For example,…
In the past few decades, the life sciences have experienced an unprecedented accumulation of data, ranging from genomic sequences and proteomic profiles to heavy-content imaging, clinical assays, and commercial biological products for…
The evolution of molecular dynamics (MD) simulations has been intimately linked to that of computing hardware. For decades following the creation of MD, simulations have improved with computing power along the three principal dimensions of…
Mathematical research data plays a crucial role across scientific disciplines, yet its documentation and dissemination remain challenging due to the lack of standardized research data management practices. The MaRDMO Plugin addresses these…
Data - arguably the most important product of worldwide materials research investment - are rarely shared. The small and biased proportion of results published are buried in plots and text licensed by journals. This situation wastes…
Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
A large number of services for research data management strive to adhere to the FAIR guiding principles for scientific data management and stewardship. To evaluate these services and to indicate possible improvements, use-case-centric…
It has recently been shown that if feedback effects of decisions are ignored, then imposing fairness constraints such as demographic parity or equality of opportunity can actually exacerbate unfairness. We propose to address this challenge…
Interest in the study of in-host microbial communities has increased in recent years due to our improved understanding of the communities' significant role in host health. As a result, the ability to model these communities using…
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…
Bioinformatics has witnessed a paradigm shift with the increasing integration of artificial intelligence (AI), particularly through the adoption of foundation models (FMs). These AI techniques have rapidly advanced, addressing historical…
The FAIR principles are globally accepted guidelines for improved data management practices with the potential to align data spaces on a global scale. In practice, this is only marginally achieved through the different ways in which…
This document focuses on databases disseminating data on (hazardous) substances found on the North American and the European (EU) market. The goal is to analyse the FAIRness (Findability, Accessibility, Interoperability and Reusability) of…
Modular verification is a technique used to face the state explosion problem often encountered in the verification of properties of complex systems such as concurrent interactive systems. The modular approach is based on the observation…
Pedestrian dynamics is an interdisciplinary field of research. Psychologists, sociologists, traffic engineers, physicists, mathematicians and computer scientists all strive to understand the dynamics of a moving crowd. In principle,…