Perspective: Maximum caliber is a general variational principle for dynamical systems.

We review here Maximum Caliber (Max Cal), a general variational principle for inferring distributions of paths in dynamical processes and networks. Max Cal is to dynamical trajectories what the principle of maximum entropy is to equilibrium states or stationary populations. In Max Cal, you maximize a path entropy over all possible pathways, subject to dynamical constraints, in order to predict relative path weights. Many well-known relationships of non-equilibrium statistical physics-such as the Green-Kubo fluctuation-dissipation relations, Onsager's reciprocal relations, and Prigogine's minimum entropy production-are limited to near-equilibrium processes. Max Cal is more general. While it can readily derive these results under those limits, Max Cal is also applicable far from equilibrium. We give examples of Max Cal as a method of inference about trajectory distributions from limited data, finding reaction coordinates in bio-molecular simulations, and modeling the complex dynamics of non-thermal systems such as gene regulatory networks or the collective firing of neurons. We also survey its basis in principle and some limitations.

[1]  A. Szabó,et al.  Electron transfer reaction dynamics in non-Debye solvents , 1998 .

[2]  K. Dill,et al.  Modeling stochastic dynamics in biochemical systems with feedback using maximum caliber. , 2011, The journal of physical chemistry. B.

[3]  E. Jaynes Information Theory and Statistical Mechanics , 1957 .

[4]  R. Kubo Statistical-Mechanical Theory of Irreversible Processes : I. General Theory and Simple Applications to Magnetic and Conduction Problems , 1957 .

[5]  Rodney W. Johnson,et al.  Axiomatic derivation of the principle of maximum entropy and the principle of minimum cross-entropy , 1980, IEEE Trans. Inf. Theory.

[6]  K. Dill,et al.  Principles of maximum entropy and maximum caliber in statistical physics , 2013 .

[7]  K. Dill,et al.  Markov processes follow from the principle of maximum caliber. , 2011, The Journal of chemical physics.

[8]  J. Paulsson Summing up the noise in gene networks , 2004, Nature.

[9]  P. Dixit Detecting temperature fluctuations at equilibrium. , 2015, Physical chemistry chemical physics : PCCP.

[10]  Cohen,et al.  Dynamical Ensembles in Nonequilibrium Statistical Mechanics. , 1994, Physical review letters.

[11]  Evans,et al.  Equilibrium microstates which generate second law violating steady states. , 1994, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[12]  Purushottam D Dixit,et al.  Stationary properties of maximum-entropy random walks. , 2015, Physical review. E, Statistical, nonlinear, and soft matter physics.

[13]  Beyond the Boltzmann factor for corrections to scaling in ferromagnetic materials and critical fluids , 2009, 0905.0011.

[14]  K. Dill,et al.  A maximum entropy framework for nonexponential distributions , 2013, Proceedings of the National Academy of Sciences.

[15]  U. Seifert Stochastic thermodynamics, fluctuation theorems and molecular machines , 2012, Reports on progress in physics. Physical Society.

[16]  Kingshuk Ghosh,et al.  Maximum Caliber: a variational approach applied to two-state dynamics. , 2008, The Journal of chemical physics.

[17]  L. Onsager Reciprocal Relations in Irreversible Processes. II. , 1931 .

[18]  B. Berne,et al.  How wet should be the reaction coordinate for ligand unbinding? , 2016, The Journal of chemical physics.

[19]  W. Bialek,et al.  Maximum entropy models for antibody diversity , 2009, Proceedings of the National Academy of Sciences.

[20]  Ken A Dill,et al.  Communication: Maximum caliber is a general variational principle for nonequilibrium statistical mechanics. , 2015, The Journal of chemical physics.

[21]  Udo Seifert,et al.  Stochastic thermodynamics: principles and perspectives , 2007, 0710.1187.

[22]  G. Wadhams,et al.  Making sense of it all: bacterial chemotaxis , 2004, Nature Reviews Molecular Cell Biology.

[23]  Masahito Ueda,et al.  Fluctuation theorem with information exchange: role of correlations in stochastic thermodynamics. , 2012, Physical review letters.

[24]  Cecile Monthus,et al.  Non-equilibrium steady states: maximization of the Shannon entropy associated with the distribution of dynamical trajectories in the presence of constraints , 2010, 1011.1342.

[25]  E. Cohen,et al.  Dynamical ensembles in stationary states , 1995, chao-dyn/9501015.

[26]  Melville S. Green,et al.  Markoff Random Processes and the Statistical Mechanics of Time‐Dependent Phenomena. II. Irreversible Processes in Fluids , 1954 .

[27]  Vincent A. Voelz,et al.  Bridging Microscopic and Macroscopic Mechanisms of p53-MDM2 Binding with Kinetic Network Models. , 2017, Biophysical journal.

[28]  Purushottam D Dixit,et al.  A maximum entropy thermodynamics of small systems. , 2012, The Journal of chemical physics.

[29]  A new access to path integrals and Fokker Planck equations via the maximum calibre principle , 1986 .

[30]  R. Jack,et al.  Absence of dissipation in trajectory ensembles biased by currents , 2016, 1602.03815.

[31]  Kingshuk Ghosh,et al.  Teaching the principles of statistical dynamics. , 2006, American journal of physics.

[32]  T. Sagawa,et al.  Thermodynamics of information , 2015, Nature Physics.

[33]  Kingshuk Ghosh,et al.  Measuring flux distributions for diffusion in the small-numbers limit. , 2007, The journal of physical chemistry. B.

[34]  Dynamics and Thermodynamics of Systems with Long-Range Interactions: An Introduction , 2002, cond-mat/0208455.

[35]  David Chandler,et al.  Transition path sampling: throwing ropes over rough mountain passes, in the dark. , 2002, Annual review of physical chemistry.

[36]  K. Ghosh,et al.  Building Predictive Models of Genetic Circuits Using the Principle of Maximum Caliber. , 2017, Biophysical journal.

[37]  Gerhard Stock,et al.  Maximum caliber inference of nonequilibrium processes. , 2010, The Journal of chemical physics.

[38]  R. Preuss,et al.  Maximum entropy and Bayesian data analysis: Entropic prior distributions. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[39]  Eric Smith Large-deviation principles, stochastic effective actions, path entropies, and the structure and meaning of thermodynamic descriptions , 2011, 1102.3938.

[40]  F. Ritort,et al.  The nonequilibrium thermodynamics of small systems , 2005 .

[41]  Roy S Herbst,et al.  Review of epidermal growth factor receptor biology. , 2004, International journal of radiation oncology, biology, physics.

[42]  Michael J. Berry,et al.  Weak pairwise correlations imply strongly correlated network states in a neural population , 2005, Nature.

[43]  J. Lebowitz,et al.  A Gallavotti–Cohen-Type Symmetry in the Large Deviation Functional for Stochastic Dynamics , 1998, cond-mat/9811220.

[44]  Pratyush Tiwary,et al.  Molecular Determinants and Bottlenecks in the Dissociation Dynamics of Biotin-Streptavidin. , 2017, The journal of physical chemistry. B.

[45]  Evans,et al.  Probability of second law violations in shearing steady states. , 1993, Physical review letters.

[46]  Roderick C. Dewar,et al.  Maximum Entropy Production as an Inference Algorithm that Translates Physical Assumptions into Macroscopic Predictions: Don't Shoot the Messenger , 2009, Entropy.

[47]  K. Ghosh Stochastic dynamics of complexation reaction in the limit of small numbers. , 2011, The Journal of chemical physics.

[48]  T. L. Hill,et al.  Fluctuations in Energy in Completely Open Small Systems , 2002 .

[49]  Robert P. Anderson,et al.  Maximum entropy modeling of species geographic distributions , 2006 .

[50]  Julian Lee,et al.  A derivation of the master equation from path entropy maximization. , 2012, The Journal of chemical physics.

[51]  The Fluctuation Theorem as a Gibbs Property , 1998, math-ph/9812015.

[52]  Melville S. Green,et al.  Markoff Random Processes and the Statistical Mechanics of Time-Dependent Phenomena , 1952 .

[53]  K. Dill,et al.  Inferring Transition Rates of Networks from Populations in Continuous-Time Markov Processes. , 2015, Journal of chemical theory and computation.

[54]  Pratyush Tiwary,et al.  Predicting reaction coordinates in energy landscapes with diffusion anisotropy. , 2017, The Journal of chemical physics.

[55]  E. Jaynes The Minimum Entropy Production Principle , 1980 .

[56]  Udo Seifert Entropy production along a stochastic trajectory and an integral fluctuation theorem. , 2005, Physical review letters.

[57]  Steve Pressé,et al.  Nonuniversal power law scaling in the probability distribution of scientific citations , 2010, Proceedings of the National Academy of Sciences.

[58]  Hongbin Wan,et al.  A Maximum-Caliber Approach to Predicting Perturbed Folding Kinetics Due to Mutations. , 2016, Journal of chemical theory and computation.

[59]  Maximum Entropy Change and Least Action Principle for Nonequilibrium Systems , 2003, cond-mat/0312329.

[60]  G. Crooks Nonequilibrium Measurements of Free Energy Differences for Microscopically Reversible Markovian Systems , 1998 .

[61]  Ken A. Dill,et al.  Inferring Microscopic Kinetic Rates from Stationary State Distributions , 2014, Journal of chemical theory and computation.

[62]  C. Jarzynski Nonequilibrium Equality for Free Energy Differences , 1996, cond-mat/9610209.

[63]  Lars Onsager,et al.  Fluctuations and Irreversible Processes , 1953 .

[64]  Fluctuation-theory constraint for extensive entropy in Monte-Carlo simulations , 2009, 0904.3942.

[65]  Martin J. Klein,et al.  Principle of Minimum Entropy Production , 1954 .

[66]  Christopher Jarzynski,et al.  Work and information processing in a solvable model of Maxwell’s demon , 2012, Proceedings of the National Academy of Sciences.

[67]  G. Hummer,et al.  Free energy reconstruction from nonequilibrium single-molecule pulling experiments , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[68]  B. Berne,et al.  Spectral gap optimization of order parameters for sampling complex molecular systems , 2015, Proceedings of the National Academy of Sciences.

[69]  Lucas Sawle,et al.  Convergence of Molecular Dynamics Simulation of Protein Native States: Feasibility vs Self-Consistency Dilemma. , 2016, Journal of chemical theory and computation.

[70]  Tânia Tomé,et al.  Entropy production in nonequilibrium systems at stationary states. , 2012, Physical review letters.

[71]  C. E. SHANNON,et al.  A mathematical theory of communication , 1948, MOCO.

[72]  Purushottam D Dixit,et al.  Quantifying extrinsic noise in gene expression using the maximum entropy framework. , 2013, Biophysical journal.

[73]  C. Jarzynski Equalities and Inequalities: Irreversibility and the Second Law of Thermodynamics at the Nanoscale , 2011 .