Interactions and dynamics in biophysical model systems

Sammanfattning: Computer simulations of simplified model systems provide understanding of how complex biological systems behave. The simulations give detailed information about the systems, with atomistic resolution, that can be used in combination with experimental knowledge to shed light on underlying physical principles. The thesis presents background information about the studies of two important model systems in biological physics.First, metal ion-binding to proteins is investigated in a computational study on a zinc-binding synthetic peptide, to elucidate the binding details. The major scientific contributions from the study are the identification and mapping of the detailed contributions to the binding. A novel correction scheme is worked out, where classic free energy calculations are combined with density functional theory to adjust for quantum mechanical effects.  The sensitivity of the zinc-binding to a specific amino acid segment can be explained in terms of the zinc coordination.Second, equilibrium density fluctuations in biological membranes are studied using computer simulations of the lipid bilayer. The fluctuations are linked to several processes; pore formation, membrane permeability and transport of small molecules across themembrane. Because the lipid bilayer behaves similar to a 2D fluid the density fluctuations can be described in the framework of generalized hydrodynamics. The major scientific contributions from the study are the direct calculation of the density-density autocorrelation function from raw data and the observation that the diffusive contribution to the power spectrum (the Rayleigh line) is not single-exponential. In addition, the accuracy of the approximate hydrodynamic solutions is questionable for the propagation of sound waves in the membrane.