Diffusion and association processes in biological systems: theory, computation and experiment

In biological systems, macromolecules are constantly moving around by diffusion. How do the molecules find their binding partners? How do they fold to form a particular shape? How do they diffuse through the crowded environment of the cell interior? How does the presence of many diffusing macromolecules in a cell affect the function of the individual molecules? These are just some of the questions that are being pursued with the experimental and theoretical approaches that were discussed at the second Biological Diffusion and Brownian Dynamics Brainstorm (BDBDB2, http://mcm.h-its.org/BDBDB2 webcite) workshop. BDBDB2 was held on October 11-13, 2010 at the Heidelberg Institute for Theoretical Studies (HITS), with live evening videoconferencing sessions to the University of California, San Diego. The workshop brought together in Heidelberg about 40 theoreticians and experimentalists from around the world and a further 15 scientists in San Diego.Brownian dynamics (BD) is a computational technique that allows the diffusive motion of molecules in solvent to be simulated, and a particular focus of the meeting was the discussion of current developments in this simulation methodology. Here we describe the main themes of the meeting, which provide a snapshot of the current state-of-the-art of studies of macromolecular diffusion, with a particular focus on BD simulation methods. We first discuss theories and methods for computer simulations for studying diffusional processes. In the next section, we describe theoretical and experimental studies on diffusion-influenced biochemical reactions. In the final section, experimental approaches for investigating diffusional processes in vivo are briefly described.BD and Langevin dynamics (LD) simulation methods may be applied for the purpose of studying the motion and the interactions of biological macromolecules in solvent. The macromolecules are modelled as particles diffusing in a solvent that is modelled as a continuum that exerts