Department of Chemistry and Biochemistry
Institute for Computational Engineering and Sciences
University of Texas at Austin
December 4, 2012
Molecular Machines (MM) are essential components of living cells and are therefore of considerable interest. They transport cargo, transform biological energy to mechanical energy, catalyze biochemical reactions, and more. They are typically proteins, though similar functions are frequently found for RNA molecules.
Atomically Detailed Simulations (ADS) hold the promise of elucidating fundamental principles of these machines. However, a significant limitation of these simulations is that of time scales. The time scales of typical ADS are far too short to address relevant events of molecular machines. In this talk I will describe how the reaction path approach and the method of Milestoning are reasonable approaches to these problems. The physical motivation behind this modeling is the relatively narrow tube in phase space that account for most of the conformational transition executed by the machines. I will discuss the MM Scapharca hemoglobin, myosin II, HIV RT, and the mechanical stability of a leg of a motor (a long helix) under load. General physical principles will be discussed and the algorithms will be described in details.
This is joint work with Serdal Kirmizialtin, Steve Kreuzer, Victoria Nguyen, Kenneth Johnson, and Tess Moon.