Principles of maximum entropy and maximum caliber in statistical physics

Markov processes follow from the principle of maximum caliber

(2012) Hao Ge et al.   JOURNAL OF CHEMICAL PHYSICS

A derivation of the master equation from path entropy maximization

(2012) Julian Lee et al.   JOURNAL OF CHEMICAL PHYSICS

Microcanonical origin of the maximum entropy principle for open systems

(2012) Julian Lee et al.   PHYSICAL REVIEW E

Revisiting the Central Dogma One Molecule at a Time

(2011) Carlos Bustamante et al.   CELL

Stochastic dynamics of complexation reaction in the limit of small numbers

(2011) Kingshuk Ghosh   JOURNAL OF CHEMICAL PHYSICS

Modeling Stochastic Dynamics in Biochemical Systems with Feedback Using Maximum Caliber

(2011) S. Pressé et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Non-equilibrium steady states: maximization of the Shannon entropy associated with the distribution of dynamical trajectories in the presence of constraints

(2011) Cécile Monthus   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Large-deviation principles, stochastic effective actions, path entropies, and the structure and meaning of thermodynamic descriptions

(2011) Eric Smith   REPORTS ON PROGRESS IN PHYSICS

Physical Biology of the CellPhysical Biology of the CellRobPhillipsJaneKondevJulieTheriotHernanGarcia. 800 pp. Garland Science, Taylor and Francis Group, London, 2008. Price: $130.00(paper) ISBN 978-0-8153-4163-5.

(2010) Bernard Chasan   AMERICAN JOURNAL OF PHYSICS

The Potential Landscape of Genetic Circuits Imposes the Arrow of Time in Stem Cell Differentiation

(2010) Jin Wang et al.   BIOPHYSICAL JOURNAL

Onsager–Machlup action-based path sampling and its combination with replica exchange for diffusive and multiple pathways

(2010) Hiroshi Fujisaki et al.   JOURNAL OF CHEMICAL PHYSICS

Maximum caliber inference of nonequilibrium processes

(2010) Moritz Otten et al.   JOURNAL OF CHEMICAL PHYSICS

Mechanochemistry of a Viral DNA Packaging Motor

(2010) Jin Yu et al.   JOURNAL OF MOLECULAR BIOLOGY

Functional roles for noise in genetic circuits

(2010) Avigdor Eldar et al.   NATURE

Dynamical fluctuations in biochemical reactions and cycles

(2010) S. Pressé et al.   PHYSICAL REVIEW E

Optimizing information flow in small genetic networks. II. Feed-forward interactions

(2010) Aleksandra M. Walczak et al.   PHYSICAL REVIEW E

Potential and flux landscapes quantify the stability and robustness of budding yeast cell cycle network

(2010) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Robustness and Coherence of a Three-Protein Circadian Oscillator: Landscape and Flux Perspectives

(2009) Jin Wang et al.   BIOPHYSICAL JOURNAL

Architecture-Dependent Noise Discriminates Functionally Analogous Differentiation Circuits

(2009) Tolga Çağatay et al.   CELL

Maximum Entropy Production as an Inference Algorithm that Translates Physical Assumptions into Macroscopic Predictions: Don’t Shoot the Messenger

(2009) Roderick Dewar   Entropy

Fluctuation-theory constraint for extensive entropy in Monte-Carlo simulations

(2009) R. V. Chamberlin et al.   EUROPEAN PHYSICAL JOURNAL B

Beyond the Boltzmann factor for corrections to scaling in ferromagnetic materials and critical fluids

(2009) R. V. Chamberlin et al.   EUROPEAN PHYSICAL JOURNAL B

Current fluctuations in stochastic systems with long-range memory

(2009) R J Harris et al.   Journal of Physics A-Mathematical and Theoretical

Current fluctuations and statistics during a large deviation event in an exactly solvable transport model

(2009) Pablo I Hurtado et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Listening to the noise: random fluctuations reveal gene network parameters

(2009) Brian Munsky et al.   Molecular Systems Biology

Intersubunit coordination in a homomeric ring ATPase

(2009) Jeffrey R. Moffitt et al.   NATURE

The large conformational changes of Hsp90 are only weakly coupled to ATP hydrolysis

(2009) Moritz Mickler et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Optimizing information flow in small genetic networks

(2009) Gašper Tkačik et al.   PHYSICAL REVIEW E

Trajectory Approach to Two-State Kinetics of Single Particles on Sculpted Energy Landscapes

(2009) David Wu et al.   PHYSICAL REVIEW LETTERS

The large deviation approach to statistical mechanics

(2009) Hugo Touchette   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Maximum Entropy Reconstructions of Dynamic Signaling Networks from Quantitative Proteomics Data

(2009) Jason W. Locasale et al.   PLoS One

Fluctuation Theorems

(2008) E.M. Sevick et al.   Annual Review of Physical Chemistry

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

The stochastic nature of biochemical networks

(2008) Vahid Shahrezaei et al.   CURRENT OPINION IN BIOTECHNOLOGY

Fluctuation theorem and mesoscopic chemical clocks

(2008) David Andrieux et al.   JOURNAL OF CHEMICAL PHYSICS

Maximum Caliber: A variational approach applied to two-state dynamics

(2008) Gerhard Stock et al.   JOURNAL OF CHEMICAL PHYSICS

Generic Schemes for Single-Molecule Kinetics. 1: Self-Consistent Pathway Solutions for Renewal Processes

(2008) Jianshu Cao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Analysis of the Entire Sequence of a Single Photon Experiment on a Flavin Protein†

(2008) James B. Witkoskie et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Species-Dependent Ensembles of Conserved Conformational States Define the Hsp90 Chaperone ATPase Cycle

(2008) Daniel R. Southworth et al.   MOLECULAR CELL

Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation, and coherence of biochemical oscillations

(2008) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional control of noise in gene expression

(2008) Álvaro Sánchez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA