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Modeling biological systems using atomistic and model-based approaches

Ulrich Kleinekathöfer

This course will focus on dynamical aspects in biological systems using both atomistic as well as model-based formalisms. On an atomistic level, systems important in biology often can be described by classical force field approaches. This formalism, which will be introduced by one of the other lecturers, is the basis of the description of transport processes in this lecture series. In the first part we will present several models which are able to catch different aspects of the transport of ions and translocation of substrate molecules through protein channels. These theories range from the all-atom force field description over the coarse-grained Brownian dynamics to continuum models. Advantages and disadvantages of the different levels of description are described as well as their possible comparison to experimental data of transport processes.

The second and larger part of the lectures will deal with the description of optical processes in large bio-molecular aggregates. As an example the light-harvesting systems of purple bacteria will be described. For the functioning of these systems which harvest the light from the sun, the understanding of light absorption is of course essential. These absorption processes involve electronic ground as well as excited states and therefore classical force field methods are not directly applicable. Nevertheless these classical descriptions of the systems are the only possible ways to get atomic details up to now since full quantum chemical calculations are not feasible. So either one uses combined quantum and classical approaches such as QM-MM methods or employs a hierarchy of different formalisms. In the present lecture we will concentrate on the later version in which molecular dynamics, quantum chemistry and quantum mechanical modelling are coupled. Having derived a simplified quantum model makes it possible to study optical and dynamical aspects in a detailed manner. For this one needs techniques of wave packet and density matrix propagation which will be introduced in a detailed manner.

No. of local minima as function of cluster size for a Lennard-Jones pair potential