Mariusz Hoppe (CSSM)
CSSM
Wednesday, October 05
Seminar Room, First Floor, Physics, University of Adelaide
Studies of Complexity and Chaos in Idealized Protein--like System.
The mechanism by which protein molecules fold up into a unique and very intricate three-dimensional structure is an important but as yet unsolved riddle. Especially amazing is how proteins manage to find their final conformation out of so many other possible (mis-folded) configurations, and moreover, that this process is quick, reversible, reproducible, and reliable (most of the time). Understanding of this mechanism poses a major challenge for theoretical physics and the solution does not appear easy to find. What is definitely certain is that mathematically, proteins constitute a highly nonlinear and also a complex system. The primary task at hand for a theoretician physicist is, then, to strive to understand the behaviour of such nonlinear protein--like systems by beginning the investigation with simplified `toy models'. Tools from chaos theory, statistical mechanics, and theory of complexity can then be utilized to gain insight into possibilities that might arise within the model; some of these may carry over to real proteins. Such is the proposed direction of research to be undertaken. The talk will outline the approach, and possibly also provide some preliminary results of computer simulations. In addition, since a crucial part of protein dynamics is temperature at which folding occurs---mis-folded structures are produced outside the range of physiological temperatures---it is therefore necessary to modify Hamilton's equations of motion to include finite temperature dependence. A method will be explained which achieves this goal without addition of any stochastic force terms to the equation of motion, but rather, by a clever switch between canonical and microcanonical ensembles.