Literature DB >> 29306272

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

Purushottam D Dixit1, Jason Wagoner2, Corey Weistuch2, Steve Pressé3, Kingshuk Ghosh4, Ken A Dill2.   

Abstract

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.

Year:  2018        PMID: 29306272     DOI: 10.1063/1.5012990

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  14 in total

1.  Maximum Caliber Can Build and Infer Models of Oscillation in a Three-Gene Feedback Network.

Authors:  Taylor Firman; Anar Amgalan; Kingshuk Ghosh
Journal:  J Phys Chem B       Date:  2019-01-09       Impact factor: 2.991

2.  Estimation of binding rates and affinities from multiensemble Markov models and ligand decoupling.

Authors:  Yunhui Ge; Vincent A Voelz
Journal:  J Chem Phys       Date:  2022-04-07       Impact factor: 3.488

Review 3.  Information theory: A foundation for complexity science.

Authors:  Amos Golan; John Harte
Journal:  Proc Natl Acad Sci U S A       Date:  2022-07-27       Impact factor: 12.779

4.  Maximum Entropy Framework for Predictive Inference of Cell Population Heterogeneity and Responses in Signaling Networks.

Authors:  Purushottam D Dixit; Eugenia Lyashenko; Mario Niepel; Dennis Vitkup
Journal:  Cell Syst       Date:  2019-12-18       Impact factor: 10.304

5.  Maximum Entropy (Most Likely) Double Helical and Double Logarithmic Spiral Trajectories in Space-Time.

Authors:  M C Parker; C Jeynes
Journal:  Sci Rep       Date:  2019-07-25       Impact factor: 4.379

6.  Probabilistic Inference for Dynamical Systems.

Authors:  Sergio Davis; Diego González; Gonzalo Gutiérrez
Journal:  Entropy (Basel)       Date:  2018-09-12       Impact factor: 2.524

7.  Calibration Invariance of the MaxEnt Distribution in the Maximum Entropy Principle.

Authors:  Jan Korbel
Journal:  Entropy (Basel)       Date:  2021-01-11       Impact factor: 2.524

8.  Inferring a network from dynamical signals at its nodes.

Authors:  Corey Weistuch; Luca Agozzino; Lilianne R Mujica-Parodi; Ken A Dill
Journal:  PLoS Comput Biol       Date:  2020-11-30       Impact factor: 4.475

9.  Binocular rivalry reveals an out-of-equilibrium neural dynamics suited for decision-making.

Authors:  Maurizio Mattia; Jochen Braun; Robin Cao; Alexander Pastukhov; Stepan Aleshin
Journal:  Elife       Date:  2021-08-09       Impact factor: 8.140

10.  Critical Comparison of MaxCal and Other Stochastic Modeling Approaches in Analysis of Gene Networks.

Authors:  Taylor Firman; Jonathan Huihui; Austin R Clark; Kingshuk Ghosh
Journal:  Entropy (Basel)       Date:  2021-03-17       Impact factor: 2.524

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