Large-scale bio and materials modelling across spatial and temporal scales
Title: Large-scale bio and materials modelling across spatial and temporal scales
SNIC Project: SNIC 2019/1-32
Project Type: SNIC Large Compute
Principal Investigator: Aatto Laaksonen <aatto@mmk.su.se>
Affiliation: Stockholms universitet
Duration: 2019-07-01 – 2020-07-01
Classification: 10407 10402 10403
Homepage: https://e-science.se/people-and-research/people/aatto-laaksonen/
Keywords:

Abstract

This project consists of several interrelated investigations with the focus on (A) complex soft matter and (B) challenging biomedical problems, all chosen as they require extensive amounts of computing cycles. (A) Ionic liquids (IL) and liquid crystals (LC) are notoriously among the most challenging molecular systems to study due to the strong short (IL, LC) and long-range (IL) interactions. ILs are highly heterogeneous with slowly converging liquid structures showing very intricate structural and dynamical correlations. As designable green solvents with numerous applications it is important to understand them to predict their properties using modelling and simulations. Projects P1-P3 are devoted to demanding multi-scale simulations also including method and model development to be tested. Project P4 is about calculations of transport properties of LCs using mainly non-equilibrium MD. Concerning (B) the project P5 is both about development a new constant pH simulation method and applications to study processes behind protein-protein and protein-virus interactions while project P6 is about developing artificial synthetic ion and water channels. The projects P7 and P8 are about modelling intra-cellular Ca2+ sensors and monoclonal antibody cancer drugs, respectively. P9 is to compute IR spectra for polypeptides. Each of the project descriptions below starts with the scientific challenge and ends with the needed resources, used software and in some cases analysis/benchmark.