Development and applications of multiscale methods in molecular modeling and bioinformatics
Group members
prof. dr hab. Bogdan Lesyng
dr Krystiana Krzyśko
dr Joanna Panecka-Hofman
National collaboration
prof. dr hab. Krzysztof Staroń, Faculty of Biology UW
prof. dr hab. Jacek Waluk, IChF PAN
dr Franciszek Rakowski, ICM UW
dr Łukasz Walewski, ICM UW
International collaboration
prof. dr hab. Waldemar Priebe, MD Anderson Cancer Center, Houston, USA
prof. Peter Deuflhard, Centrum Konrada Zuze, FU Berlin
Keywords
multiscale modeling
bioinformatics
molecular dynamics
quantum dynamics
structure
function
causality analysis
Research topic
The description of mechanisms governing complex (bio)molecular systems, as well as methods of molecular design of systems with desired structural and functional properties, require the use of advanced multiscale methods of mathematical and computational modeling. We conduct, among others, research related to:
- proton and electron dynamics in real molecular environments,
- simulations of catalytic processes,
- transformations of (bio)chemical energy into mechanical energy,
- next-generation drug design,
- studies of biological nanomachines,
- as well as fundamental research on the detection and analysis of causal relationships of events in structural transformations.
For example, microscopic quantum and quantum–classical molecular dynamics methods are used to simulate proton transfer (hopping) in (bio)molecular systems and to generate microscopic electrostatic fields. On the other hand, classical mesoscopic molecular dynamics methods are applied in simulations of spontaneous structure self-organization processes. Multistep symplectic algorithms of the above-mentioned dynamics enable simulations over long time scales. Poisson–Boltzmann equation methods are also applied and further developed, enabling the determination of mesoscopic electrostatic fields, which, among others, determine the mutual recognition of (bio)molecular systems (molecular recognition processes).