All, Please send the following reminder to your faculty. Thanks Mechanical Engineering Graduate Seminar Thursday, October 12, 2006 4:30 p.m. Mechanical Engineering Building, Room 161 LONG-LENGTH SCALE MECHANICS OF DNA USING COMPUTATIONAL ROD THEORY Dr. Noel Perkins University of Michigan Abstract DNA is a long-chain biopolymer whose structure greatly influences its function. Here, structure may refer to the geometry and stress of the molecule and function may refer to many biological processes including replication, gene transcription and gene repair. For example, the protein-induced ³looping² of certain DNA strands is a well-known mechanism for gene regulation. In cases such as illustrated below, the structural loop serves as a biological ³switch² that prevents transcription. This talk will consider DNA structures that form on scales ranging from tens of nanometers through several microns or longer (hundreds to many thousands of base pairs). Such ³long-length scale² structures include DNA loops and supercoils which are simply too large to resolve using the all-atom descriptions of molecular dynamics. Instead, we¹ll describe these structures using a continuum model for DNA in the form of a nonlinear computational rod theory. The formulation accounts for the elasticity of the DNA strand and its intrinsic curvature and chiral construction (which are also sequence-dependent). Example results will illustrate the formation of supercoils (plectonemes) and the expected DNA loops for wild-type and mutated forms of the Lac-repressor DNA/protein complex. Brief Biosketch Noel Perkins received his education at U. C. Berkeley where he was awarded his B.S. (1982), M.S. (1984), and Ph.D. (1986) degrees in Mechanical Engineering. Following a postdoctoral appointment at the Institute for Sound and Vibration Research (Southampton, England), he joined The University of Michigan in 1987 where he is presently an Arthur F. Thurnau Professor in Mechanical Engineering. Professor Perkins' research interests include vibration analysis, nonlinear dynamics, fluid/structure interaction, and electronic instrumentation, topics on which he has published more than 100 technical papers. His current research projects include the dynamics of flexible cables, the modeling of DNA and DNA-protein complexes, the physics of fly casting and golf, and instrumentation for sports training. Past projects include the dynamics of engine power train systems, belt drive systems, paper forming machinery, and tracked vehicles. He has served as an Associate Editor for the ASME Journal of Applied Mechanics and is a Member of the Editorial Boards for the Journal of Vibration and Control and for Vibroengineering. He is a Fellow of the American Society of Mechanical Engineers. His contributions as a researcher, inventor and educator have been recognized through the Academic Challenge Award from the Technical University of Munich and ISPO, The Arthur F. Thurnau Professorship from the University of Michigan, The Office of Naval Research Young Investigator Award, The SAE Ralph R. Teetor Award, The University of Michigan Faculty Recognition Award, The General Motors Outstanding Distance Learning Faculty Award, and the University of Michigan Amoco Undergraduate Teaching Award. He is also the co-founder and co-owner of CastAnalysis, LLC which produces novel products for the sport of fly fishing. Refreshments will be served at 4:00 p.m. in room ME 254 Donna Cackley Area Secretary School of Mechanical Engineering Purdue University Ph: (765) 494-5737 <mailto:cackley@purdue.edu> ------ End of Forwarded Message