Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case

M Wieczor, V Genna, J Aranda… - Wiley …, 2023 - Wiley Online Library
Exascale computing has been a dream for ages and is close to becoming a reality that will
impact how molecular simulations are being performed, as well as the quantity and quality of …

Visualizing the knowledge domain of pulsed light technology in the food field: A scientometrics review

M Ren, X Yu, AS Mujumdar, AEGA Yagoub… - Innovative Food Science …, 2021 - Elsevier
Pulsed Light (PL) is now recognized as a promising non-thermal food processing
technology with a wide range of applications in disinfection, extending shelf life, and …

Intelligent building construction management based on BIM digital twin

Y Jiang - Computational Intelligence and Neuroscience, 2021 - Wiley Online Library
In order to improve the construction effect of intelligent buildings, this paper combines the
BIM digital twin technology to construct the overall structure of the building construction …

Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange

ML Evans, J Bergsma, A Merkys, CW Andersen… - Digital …, 2024 - pubs.rsc.org
The Open Databases Integration for Materials Design (OPTIMADE) application
programming interface (API) empowers users with holistic access to a growing federation of …

Comprehensive detection and characterization of human druggable pockets through binding site descriptors

A Comajuncosa-Creus, G Jorba, X Barril… - Nature …, 2024 - nature.com
Druggable pockets are protein regions that have the ability to bind organic small molecules,
and their characterization is essential in target-based drug discovery. However, deriving …

Modern design of rural green buildings based on big data technology

X Gao - Cities, 2023 - Elsevier
In order to explore the intelligent algorithms that can be used in the modern design of rural
green buildings, this paper conducts factor analysis based on the modern design …

pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science

JVS Guerra, HV Ribeiro-Filho, GE Jara, LO Bortot… - BMC …, 2021 - Springer
Background Biomolecular interactions that modulate biological processes occur mainly in
cavities throughout the surface of biomolecular structures. In the data science era, structural …

Conserved water networks identification for drug design using density clustering approaches on positional and orientational data

J Tosovic, D Fijan, M Jukic, U Bren - Journal of chemical …, 2022 - ACS Publications
This work describes the development and testing of a method for the identification and
classification of conserved water molecules and their networks from molecular dynamics …

Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs

B Ashwood, MS Jones, A Radakovic, S Khanna… - Biophysical …, 2023 - cell.com
Hybridization of short nucleic acid segments (< 4 nt) to single-strand templates occurs as a
critical intermediate in processes such as nonenzymatic nucleic acid replication and toehold …

Martignac: Computational workflows for reproducible, traceable, and composable coarse-grained Martini simulations

T Bereau, LJ Walter, JF Rudzinski - Journal of Chemical …, 2024 - ACS Publications
Despite their wide use and far-reaching implications, molecular dynamics (MD) simulations
suffer from a lack of both traceability and reproducibility. We introduce Martignac …