Literature DB >> 23585693

Teaching the principles of statistical dynamics.

Kingshuk Ghosh1, Ken A Dill, Mandar M Inamdar, Effrosyni Seitaridou, Rob Phillips.   

Abstract

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.

Year:  2006        PMID: 23585693      PMCID: PMC3622476          DOI: 10.1119/1.2142789

Source DB:  PubMed          Journal:  Am J Phys        ISSN: 0002-9505            Impact factor:   1.022


  9 in total

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2.  Reverse engineering of the giant muscle protein titin.

Authors:  Hongbin Li; Wolfgang A Linke; Andres F Oberhauser; Mariano Carrion-Vazquez; Jason G Kerkvliet; Hui Lu; Piotr E Marszalek; Julio M Fernandez
Journal:  Nature       Date:  2002-08-29       Impact factor: 49.962

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Review 4.  Ten years of tension: single-molecule DNA mechanics.

Authors:  Carlos Bustamante; Zev Bryant; Steven B Smith
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5.  Experimental demonstration of violations of the second law of thermodynamics for small systems and short time scales.

Authors:  G M Wang; E M Sevick; Emil Mittag; Debra J Searles; Denis J Evans
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6.  Characterization of individual polynucleotide molecules using a membrane channel.

Authors:  J J Kasianowicz; E Brandin; D Branton; D W Deamer
Journal:  Proc Natl Acad Sci U S A       Date:  1996-11-26       Impact factor: 11.205

7.  Myosin-V stepping kinetics: a molecular model for processivity.

Authors:  M Rief; R S Rock; A D Mehta; M S Mooseker; R E Cheney; J A Spudich
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8.  The bacteriophage straight phi29 portal motor can package DNA against a large internal force.

Authors:  D E Smith; S J Tans; S B Smith; S Grimes; D L Anderson; C Bustamante
Journal:  Nature       Date:  2001-10-18       Impact factor: 49.962

9.  Single-molecule enzymatic dynamics.

Authors:  H P Lu; L Xun; X S Xie
Journal:  Science       Date:  1998-12-04       Impact factor: 47.728

  9 in total
  13 in total

1.  Measuring flux distributions for diffusion in the small-numbers limit.

Authors:  Effrosyni Seitaridou; Mandar M Inamdar; Rob Phillips; Kingshuk Ghosh; Ken Dill
Journal:  J Phys Chem B       Date:  2007-02-13       Impact factor: 2.991

2.  Computer-aided drug design: the next 20 years.

Authors:  John H Van Drie
Journal:  J Comput Aided Mol Des       Date:  2007-11-08       Impact factor: 3.686

3.  Maximum Caliber: a variational approach applied to two-state dynamics.

Authors:  Gerhard Stock; Kingshuk Ghosh; Ken A Dill
Journal:  J Chem Phys       Date:  2008-05-21       Impact factor: 3.488

4.  A derivation of the master equation from path entropy maximization.

Authors:  Julian Lee; Steve Pressé
Journal:  J Chem Phys       Date:  2012-08-21       Impact factor: 3.488

5.  Improved spatial direct method with gradient-based diffusion to retain full diffusive fluctuations.

Authors:  Wonryull Koh; Kim T Blackwell
Journal:  J Chem Phys       Date:  2012-10-21       Impact factor: 3.488

6.  Modeling stochastic dynamics in biochemical systems with feedback using maximum caliber.

Authors:  S Pressé; K Ghosh; K A Dill
Journal:  J Phys Chem B       Date:  2011-04-27       Impact factor: 2.991

7.  A gentle introduction to the non-equilibrium physics of trajectories: Theory, algorithms, and biomolecular applications.

Authors:  Daniel M Zuckerman; John D Russo
Journal:  Am J Phys       Date:  2021-10-22       Impact factor: 0.835

8.  Building Predictive Models of Genetic Circuits Using the Principle of Maximum Caliber.

Authors:  Taylor Firman; Gábor Balázsi; Kingshuk Ghosh
Journal:  Biophys J       Date:  2017-11-07       Impact factor: 4.033

9.  Trajectory approach to two-state kinetics of single particles on sculpted energy landscapes.

Authors:  David Wu; Kingshuk Ghosh; Mandar Inamdar; Heun Jin Lee; Scott Fraser; Ken Dill; Rob Phillips
Journal:  Phys Rev Lett       Date:  2009-07-31       Impact factor: 9.161

10.  Inferring Microscopic Kinetic Rates from Stationary State Distributions.

Authors:  Purushottam D Dixit; Ken A Dill
Journal:  J Chem Theory Comput       Date:  2014-06-02       Impact factor: 6.006

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