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Unformatted text preview: A First Exposure to Statistical Mechanics for Life Scientists: Applications to Binding Hernan G. Garcia 1 , Jan´ e Kondev 2 , Nigel Orme 3 , Julie A. Theriot 4 , Rob Phillips 5 1 Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA 2 Department of Physics, Brandeis University Waltham, MA 02454, USA 3 Garland Science Publishing, 270 Madison Avenue, New York, NY 10016, USA 4 Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA 5 Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA September 17, 2007 Abstract Statistical mechanics is one of the most powerful and elegant tools in the quantita- tive sciences. One key virtue of statistical mechanics is that it is designed to examine large systems with many interacting degrees of freedom, providing a clue that it might have some bearing on the analysis of the molecules of living matter. As a result of data on biological systems becoming increasingly quantitative, there is a concomitant demand that the models set forth to describe biological systems be themselves quan- titative. We describe how statistical mechanics is part of the quantitative toolkit that is needed to respond to such data. The power of statistical mechanics is not limited to traditional physical and chemical problems and there are a host of interesting ways in which these ideas can be applied in biology. This article reports on our efforts to teach statistical mechanics to life science students with special reference to binding problems in biology and provides a framework for others interested in bringing these tools to a nontraditional audience in the life sciences. 1 1 Does Statistical Mechanics Matter in Biology? The use of the ideas of equilibrium thermodynamics and statistical mechanics to study biological systems are nearly as old as these disciplines themselves. Whether thinking about the binding constants of transcription factors for their target DNA or proteins on HIV virions for their target cell receptors, often the first discussion of a given problem involves a hidden assumption of equilibrium. There are two key imperatives for students of the life sciences who wish to explore the quantitative underpinnings of their discipline: i) to have a sense of when the equilibrium perspective is a reasonable approximation and ii) given those cases when it is reasonable, to know how to use the key tools of the calculus of equilibrium. Our experiences in teaching both undergraduate and graduate students in the life sciences as well as in participating both as students and instructors in the Physiology Course at the Marine Biological Laboratory in Woods Hole drive home the need for a useful introduction to statistical mechanics for life scientists....
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