The group of Computational biophysics shares interests in the range of physical phenomena produced by the interplay of different scales, for instance between single and collections of molecules (mesoscale). We study protein dynamics, kinetics and energetics using mainly molecular dynamics simulations (ACEMD) on graphics processing units (GPUs) and GPUGRID.net. In our research, we attempt to solve new scientific problems by developing new methodologies, software and ideas for bridging between the atomistic scale (femtoseconds, nanometers) and the biological molecular scale (micro- to milli-seconds and hundreds of nanometers).
Main research lines
1. Energetics of molecular systems and protein interactions. Calculations of energetics for molecular systems is of great importance for understanding and controlling protein functions. We apply several techniques for free energy calculations to the understanding of molecular mechanisms like ion permeation, ion binding, ligand binding and protein aggregation. In particular, we are interested to in-silico high-throughput approaches but maintaining thermodynamic accuracy. For this, we are using our GPUGRID.net infrastructure.
2. Accelerated and distributed molecular simulation methods. In order to support our research we developed innovative software solutions ACEMD, for molecular dynamics on accelerator processors (GPUs), as well as one of the largest distributed computing project worldwide, GPUGRID.net. This gives us the computational power to tackle problems substantially beyond the state of the art. In fact, whilst the fundamental thermodynamic framework behind the simulation of macromolecules is well characterized, exploration of biological time scales remains beyond the computational capacity routinely available to many researchers. With ACEMD and GPUGRID our group can address problems at the fore front of computational biophysics and biochemistry.
3. Hydrodynamics-molecular interaction. Building on our previous research for molecular-hydrodynamics interactions, we are looking at resonance patterns of proteins embedded in a hydrodynamics solvent description and how external sound waves can perturb their equilibrium state.