title: Molecular dynamics simulations through GPU video games technologies.
abstract: Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the mostde novotechniques used to understand the physical movements of atoms and molecules is molecular dynamics (MD). MD is anin silicomethod to simulate the physical motions of atoms and molecules under certain conditions. This has become a state strategic technique and now plays a key role in many areas of exact sciences, such as chemistry, biology, physics and medicine. Due to their complexity, MD calculations could require enormous amounts of computer memory and time and therefore their execution has been a big problem. Despite the huge computational cost, molecular dynamics have been implemented using traditional computers with a central memory unit (CPU). A graphics processing unit (GPU) computing technology was first designed with the goal to improve video games, by rapidly creating and displaying images in a frame buffer such as screens. The hybrid GPU-CPU implementation, combined with parallel computing is a novel technology to perform a wide range of calculations. GPUs have been proposed and used to accelerate many scientific computations including MD simulations. Herein, we describe the new methodologies developed initially as video games and how they are now applied in MD simulations.
authors.affiliation: Computational Biology & Medicine Group, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527, Greece.
authors.forename: Styliani
authors.initials: S
authors.lastname: Loukatou
authors.affiliation: Computational Biology & Medicine Group, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527, Greece; Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, University Campus, Athens 15784, Greece.
authors.forename: Louis
authors.initials: L
authors.lastname: Papageorgiou
authors.affiliation: Computational Biology & Medicine Group, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527, Greece; Department of Computer Engineering and Informatics Faculty, University of Patras, Patras 26500, Greece.
authors.forename: Paraskevas
authors.initials: P
authors.lastname: Fakourelis
authors.affiliation: Computational Biology & Medicine Group, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527, Greece; School of Electrical and Computer Engineering, National Technical University of Athens, Athens, Greece.
authors.forename: Arianna
authors.initials: A
authors.lastname: Filntisi
authors.affiliation: Computational Biology & Medicine Group, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527, Greece; Department of Informatics, Ionian University, Tsirigoti Square 7, Corfu 49100, Greece.
authors.forename: Eleftheria
authors.initials: E
authors.lastname: Polychronidou
authors.affiliation: Computational Biology & Medicine Group, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527, Greece.
authors.forename: Ioannis
authors.initials: I
authors.lastname: Bassis
authors.affiliation: Department of Computer Engineering and Informatics Faculty, University of Patras, Patras 26500, Greece.
authors.forename: Vasileios
authors.initials: V
authors.lastname: Megalooikonomou
authors.affiliation: Institute of Bioinformatics, University of Münster, Niels-Stensen-Straße 14, Münster 48149, Germany.
authors.forename: Wojciech
authors.initials: W
authors.lastname: Makałowski
authors.affiliation: Computational Biology & Medicine Group, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527, Greece; Department of Computer Engineering and Informatics Faculty, University of Patras, Patras 26500, Greece; Bionetwork ltd. 15234, Chalandri, Athens, Greece.
authors.forename: Dimitrios
authors.initials: D
authors.lastname: Vlachakis
authors.affiliation: Computational Biology & Medicine Group, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527, Greece.
authors.forename: Sophia
authors.initials: S
authors.lastname: Kossida