Multiscale molecular modeling methods

Advanced multiscale (bio)molecular modeling technologies are required to describe structure and function of complex (bio)molecular systems. This can be achieved by developing and applying advanced mathematical and computational modeling methods.

At the lowest, microscopic level we have been carrying out studies related to the quantum dynamics of protons and electrons in their real (bio)molecular environment. Going to larger mezoscopic systems, we are involved in simulations of catalytic processes, energy transfer proceses and functioning mechanisms of biological nanomachines, and finaly in studies of causal realations between dynamical structural changes. Regarding applications, we are involved in a numer of drug design projects.

Giving some examples - methods of quantum and quantum-classical molecular dynamics are applied to simulations of proton transfer processes (hopping) in (bio)moleculat systems and to compute microscopic electrostatic fields.

On the other hand, mesoscopic classical molecular dynamics is applied to describe spontaneous structure formation phenomena. Multistep, symplectic MD algoritms are capable to simulate (bio)molecular processes in longer time-scales.

In turn, methods of the Poisson-Boltzmann equation are being applied to compute mesoscopic electrostatic fields, which are amongst others responsible for the mutual recognition of (bio)molecular systems (molecular recognition processes).

 

A porphycene molecule contains two mobile protons inside the molecular cavity.

The protons dynamics is coverned by laws of quantum molecular dynamics.

(see: J.Phys. Chem. A, 114, 2313-2318, 2010)

 

 

Biomolecular machine - Topoisomerase 1 (Topo 1) (yellow), interacting with a DNA molecule (blue) and a hnRNPA1 regulatory protein (rose).

Topo1 is capable to relax DNA structures. It plays also another, a protein kinase role. Misfunctioning of Topo 1 may lead to cancer processes.

(see:  J. Mol. Biol., 369, 1098-1112, 2007)