Computer Modeling Laboratory

Head: Wiesław Nowak

The laboratory is equipped in state-of-the-art linux claster (500 cores, 4QDR Infiniband, 30TB disk space) some smaller clusters and servers, 4 efficient graphical workstations with stereo graphics and NVIDIA-CUDA computational capabilities. The laboratory possesses licenses of numerous molecular modeling tools: Accelrys Discovery Studio software, Schroedinger suite, Gaussian03, GaussView, NAMD, VMD, Gromacs, AMBER, Yassara, BALL-view, MOIL and others. Molecular dynamics simulations are performed here using mainly non-standard computational methods such as Locally Enhanced Sampling and Steered Molecular Dynamics simulations. Investigations conducted in this laboratory includes studies of nanomechanics of single modular proteins from extracellular matrix, mainly related to nervous system and autism: contactins, neurexins, neurologins, neuroglobin and cytoglobin. Single molecule AFM spectra are interpreted. Extensive docking of prospective drugs and neurotoxins to hypothetical binding sites is made (e.g. related to the fight with malaria). Some studies are devoted to quantum dots and charge transfer phenomena in model DNA systems and fluorescent probes. Mechanisms of catalytic activities of biotechnological photoactive proteins and enzymes such as nitrile hydratase are also studied. Our recent programming efforts are related to migration modeling software to GPU cards.

The group is interested in collaboration in the field of theoretical molecular biophysics, heme proteins, photoactive proteins and bioinformatics.