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Webinar: High Performance Computing in Structural Biology

Event Details:

  • Date:          Tuesday, 19 January 2021
  • Time:         Starts: 16:00
  • Venue:        Live streaming of the discussion will be available on Zoom (Password: VsSCz1).
  • Speaker:    Vangelis Daskalakis, Assistant Professor in Computational Physics – Dept. of Chemical Engineering (CM), Cyprus University of Technology (CUT)

 CaSToRC, HPC National Competence Centre
 invites you to the EuroCC and SimEA Online Seminar Series

EuroCC Simea Seminar Series 2

 
The webinar will be in English and the live stream is open to the public.
Live streaming of the discussion will be available on Zoom (Password: VsSCz1)
Images and/or recordings of our open public events may be used by The Cyprus Institute for dissemination purposes including print and digital media such as websites, press-releases, social media, and live streaming.

 


                                                                                                             


Abstract

Structural biology is a branch of molecular biology, biochemistry, and biophysics with the focus on the molecu-lar structure of biological macromolecules (like proteins and membranes). A key question of Structural Biology is how these macromolecules acquire their structures. A combination of methodologies like Molecular Dynam-ics and Markov state moideling that is supported by High Performance Computing (HPC) leads to an ideal de-scription of macromolecule conformations and dynamics at all-atom resolution. The latter is a valuable infor-mation in Structural Biology. In this seminar two key HPC projects will be presented that relate to: (A) the out-break of the novel coronavirus (SARS-CoV-2) that causes the respiratory tract disease COVID-19 and the dynam-ics of two key viral proteins that can potentially be used as drug-targets or source of epitope vaccines, and (B) the delicate balance between light harvesting and photoprotective modes of the Light Harvesting Complexes of Photosystem II, that can potentially be used as models for artificial photosynthesis.


About the Speaker

Vangelis Daskalakis CUTAssistant Professor Vangelis Daskalakis is the Head of the Computational Environmental Modeling (CEM) group in the de-partment of Chemical Engineering of the Cyprus University of Technology (CUT). His research focuses on the bio-physics of large biological and small gaseous molecules involved in processes related to life sciences and/ or the environmental. He uses elaborate computational techniques based on the Molecular Dynam-ics (MD) method (like the metadynamics in the multiwalkers variant, or the parallel tempering metady-namics at the well-tempered ensemble variant), in combination with ab-initio Density Functional Theory (DFT) Methods. The setup of the models and the analysis of the results is based on bioinformatics tools (protein-protein docking algorithms, sequence and structural alignments, Markov State Modeling).

He has 35 publications as articles in peer-reviewed journals (30), book chapters (4) and conference pro-ceedings (1). First author in 18/35 and the corresponding author in 16/35 publications, exerting strong independence (h-index 11, Scopus/ Web of Science). Publications in leading journals of chemistry, bio-physics and physical chemistry (i.e. J. Am. Chem. Soc. Proc. Natl. Acad. Sci USA, Biochim. Biophys. Acta, NPG Sci. Rep., J. Phys. Chem. B-C, Phys. Chem. Chem. Phys., Chem. Commun.). Reviewer duties for Nature Journals, ACS Physical Chemistry Journals, RSC Phys. Chem. Chem. Phys., RSC Advances, Springer J. Molecular Modeling (95 Reviews for Journals, Web of Science – publons). Reviewer for proposals to High Performance Computing (HPC) facilities (LinkSCEEM, CyTera-EM, GRNET HPC, CSCS-Swiss National Supercomputing Centre). 35 participations in International Conferences, including 9 invited lectures. My research is featured in the PRACE DIGEST 2017, 2020 from Insight Publishers.


Download the Spring 2021 Online EuroCC & SimEA Seminar Series Programme here.

 



 

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Additional Info

  • Date: Tuesday, 19 January 2021
  • Time: Starts: 16:00
  • Speaker: Vangelis Daskalakis, Assistant Professor in Computational Physics – Dept. of Chemical Engineering (CM), Cyprus University of Technology (CUT)