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Results were presented from Brownian dynamics simulations for cyt c molecules approximated as spherical particles with diameter 2R ' 3.3 nm interacting with a charged planar membrane surface. Using the well-known Ermak-McCammon algorithm of ref. [36, 37] for solving the Langevin equations (see Chapter 2), a new computer program in C++ was developed. An overview of the way it is implemented is given in Chapter 3. The program in its current state is able to compute the trajectories (translation and rotation) of hundreds of spherical particles in systems with typical dimensions of 103 − 1003 nm3 . As explained in the introductory Chapter 1 the motivation for studying the dynamics of cyt c molecules in such systems came from the progress in the research of photosynthetic bacteria, e.g. While the internal processes of energy transduction (light harvesting, channelling to RC, charge separation) are quite well understood, the dynamics of soluble cyt c as an electron transporter in this context is not yet clear. In many textbooks one can find illustrations where a single cyt c is responsible for the electron transport between two integral membrane proteins (the reaction centre RC and the bc1 complex). But as pointed out in publications like refs. [49], [59], [60], [61] or [62] biological cells are crowded with different molecules. Consequently, one can assume that the electron transport between two integral membrane proteins is not simply taken on by one single cyt c molecule. Instead it is likely that many of these particles are located in a cyt c pool above the membrane and that they perform the electron transport in turns. Thus, it is desirable to have a simulation package that is able to compute the trajectories of many proteins. Note that the detailed processes of electron transfer and binding to membrane proteins are not modelled here. The details of these processes are quite complicated so that we refrained from including them in the coarse-grained simulations. Here, the actual binding is simply defined by a particle distance zb from the membrane which marks the beginning of the attractive potential. ...