MD analysis mainly uses methods from statistical mechanics. Also visualization plays an important role. We are currently able to display our structures in 3D on a screen and interact with them by means of 3D-pointers with the program VMD . Simulations of Actin Actin filaments are dynamic polymers whose assembly and disassembly in the cytoplasm drives shape changes, cell locomotion and chemotactic migration. Filament elongation is thought to be stabilized by the hydrolysis of ATP nucleotide.
Actin filaments are also part of muscle tissue and participate in muscle contraction.
There is substantial experimental evidence for the influence of the nucleotide and ion on the mechanical properties of the monomer and filament. We are also interested in the diffusion of water molecules into the nucleotide binding site and the role of water diffusion in the hydrolysis of ATP and product exchange. MD simulations show that these water molecules diffuse along two distinct pathways. Another goal of our studies is the investigation of monomer interactions in F-actin. A frequently updated account of actin simulation results can be found at our group's actin site .