Evolutionary Design in Materials Science and Biological Physics

Professor Michael Deem
Rice University

Date: Thursday, Janaury 12, 2006
Time: 4:00 p.m.
Place: Engineering II, Room 3361

ABSTRACT

I will discuss creation of a hypothetical zeolite database. Each of the 230 space groups is examined for hypothetical structures consistent with potentials of mean force. Unit cell parameters are varied within typical values (a, b, c, alpha, beta, gamma) as are unit cell densities. To date, more than 1 million hypothetical structures have been produced. Properties of the hypothetical structures, and how they relate to known zeolites, will be discussed. An obstacle to synthesizing new zeolites structures is control of the nucleation event. Using an atomic-scale model for silicate solutions, the nucleation process during zeolite synthesis in the absence of a structure directing agent is investigated. The barriers to nucleation is estimated to be on the order of 100 kT, and the critical cluster size is estimated to be between 25 and 50 silicons. Structural analysis shows the results reproduce physical properties of condensed phases of silica, such as the distance distribution and topological features. The smooth distribution of ring sizes suggests the cluster is amorphous up to 200 silicons. That is, the lowest free energy structure is a function of the particle size.

Concomitant with the evolution of biological diversity must have been the evolution of mechanisms that facilitate evolution, due to the essentially infinite complexity of protein sequence space. I will describe how evolvability can be an object of Darwinian selection, emphasizing the collective nature of the process. I will discuss computer simulations of protein evolution that quantify this theory. These simulations demonstrate that rapid or dramatic environmental change leads to selection for greater evolvability. The selective pressure for large scale genetic moves, such as DNA exchange, becomes increasingly strong as the environmental conditions become more uncertain. These results demonstrate that evolvability is a selectable trait and allow for the explanation of a large body of experimental results. Many observations within evolutionary biology, heretofore considered evolutionary happenstance or accidents, are explained by selection for evolvability. As specific examples, I discuss evolution within the immune system and evolution of drug resistant microorganisms. How therapeutics confer selective pressure on the evolvability of pathogens, and how this driving force to antigenic drift should be considered in drug and vaccine design efforts will be discussed. I will also discuss experiments that could complement the theory.