Teaching the Principles of Statistical Dynamics

Department of Biophysics, University of California, San Francisco, California 94143.
American Journal of Physics (Impact Factor: 0.96). 02/2006; 74(2):123-133. DOI: 10.1119/1.2142789
Source: arXiv


We describe a simple framework for teaching the principles that underlie the dynamical laws of transport: Fick's law of diffusion, Fourier's law of heat flow, the Newtonian viscosity law, and the mass-action laws of chemical kinetics. In analogy with the way that the maximization of entropy over microstates leads to the Boltzmann distribution and predictions about equilibria, maximizing a quantity that E. T. Jaynes called "caliber" over all the possible microtrajectories leads to these dynamical laws. The principle of maximum caliber also leads to dynamical distribution functions that characterize the relative probabilities of different microtrajectories. A great source of recent interest in statistical dynamics has resulted from a new generation of single-particle and single-molecule experiments that make it possible to observe dynamics one trajectory at a time.

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    • "One includes inertia (in Section 4) and the other fluctuations (in Section 5). The former is motivated by [8] [9] [10] and the latter by [11] [12] [13] [14] [15] [16]. In the inertia type lifts the extra state variables are velocities of the original state variables. "
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    • "Despite its apparent simplicity, the marble game can be used as a foundation for a conceptual framework that can be applied across the STEM disciplines as outlined below (Ghosh et al., 2006). 2 "
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    ABSTRACT: Recently there have been multiple calls for curricular reforms to develop new pathways to the science, technology, engineering and math (STEM) disciplines. The Marble Game answers these calls by providing a conceptual framework for quantitative scientific modeling skills useful across all the STEM disciplines. The approach actively engages students in a process of directed scientific discovery. In a "Student Assessment of their Learning Gains" (SALG) survey, students identified this approach as producing "great gains" in their understanding of real world problems and scientific research. Using the marble game, students build a conceptual framework that applies directly to random molecular-level processes in biology such as diffusion and interfacial transport. It is also isomorphic with a reversible first-order chemical reaction providing conceptual preparation for chemical kinetics. The computational and mathematical framework can also be applied to investigate the predictions of quantitative physics models ranging from Newtonian mechanics through RLC circuits. To test this approach, students were asked to derive a novel theory of osmosis. The test results confirm that they were able to successfully apply the conceptual framework to a new situation under final exam conditions. The marble game thus provides a pathway to the STEM disciplines that includes quantitative biology concepts in the undergraduate curriculum - from the very first class.
    Biophysical Journal 10/2012; 104(2). DOI:10.1016/j.bpj.2012.11.2943 · 3.97 Impact Factor
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    • "One includes inertia (in Section 4) and the other fluctuations (in Section 5). The former is motivated by [8] [9] [10] and the latter by [11] [12] [13] [14] [15] [16]. In the inertia type lifts the extra state variables are velocities of the original state variables. "
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    ABSTRACT: Dynamics of chemical reactions, called mass-action-law dynamics, serves in this paper as a motivating example for investigating geometry of nonlinear non-equilibrium thermodynamics and for studying the ways to extend a mesoscopic dynamics to more microscopic levels. The geometry in which the physics involved is naturally expressed appears to be the contact geometry. Two extensions are discussed in detail. In one, the reaction fluxes or forces are adopted as independent state variables, the other takes into account fluctuations. All the time evolution equations arising in the paper are proven to be compatible among themselves and with equilibrium thermodynamics. A quantity closely related to the entropy production plays in the extended dynamics with fluxes and forces as well as in the corresponding fluctuating dynamics the same role that entropy plays in the original mass-action-law dynamics.
    Physica D Nonlinear Phenomena 05/2012; 241(10):976–986. DOI:10.1016/j.physd.2012.02.008 · 1.64 Impact Factor
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