Nonequilibrium Thermodynamics of Chemical Reaction Networks: Wisdom from Stochastic Thermodynamics

Nonequilibrium thermodynamic formalism of nonlinear chemical reaction systems with Waage–Guldberg’s law of mass action

(2016) Hao Ge et al.   CHEMICAL PHYSICS

Product-Form Poisson-Like Distributions and Complex Balanced Reaction Systems

(2016) Daniele Cappelletti et al.   SIAM JOURNAL ON APPLIED MATHEMATICS

Lyapunov Functions, Stationary Distributions, and Non-equilibrium Potential for Reaction Networks

(2015) David F. Anderson et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Glucans monomer-exchange dynamics as an open chemical network

(2015) Riccardo Rao et al.   JOURNAL OF CHEMICAL PHYSICS

Dissipation in noisy chemical networks: The role of deficiency

(2015) M. Polettini et al.   JOURNAL OF CHEMICAL PHYSICS

Complex and detailed balancing of chemical reaction networks revisited

(2015) Arjan van der Schaft et al.   JOURNAL OF MATHEMATICAL CHEMISTRY

Thermodynamics of accuracy in kinetic proofreading: dissipation and efficiency trade-offs

(2015) Riccardo Rao et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Energy dissipation in an adaptive molecular circuit

(2015) Shou-Wen Wang et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Thermodynamic limits to information harvesting by sensory systems

(2015) Stefano Bo et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Thermodynamics of information

(2015) Juan M. R. Parrondo et al.   Nature Physics

Kinetics and thermodynamics of reversible polymerization in closed systems

(2015) Sourabh Lahiri et al.   NEW JOURNAL OF PHYSICS

Nonequilibrium sensing and its analogy to kinetic proofreading

(2015) David Hartich et al.   NEW JOURNAL OF PHYSICS

Ensemble and trajectory thermodynamics: A brief introduction

(2015) C. Van den Broeck et al.   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

Fluctuating currents in stochastic thermodynamics. II. Energy conversion and nonequilibrium response in kinesin models

(2015) Bernhard Altaner et al.   PHYSICAL REVIEW E

Thermodynamics of Error Correction

(2015) Pablo Sartori et al.   Physical Review X

Irreversible thermodynamics of open chemical networks. I. Emergent cycles and broken conservation laws

(2014) Matteo Polettini et al.   JOURNAL OF CHEMICAL PHYSICS

Unifying Three Perspectives on Information Processing in Stochastic Thermodynamics

(2014) A. C. Barato et al.   PHYSICAL REVIEW LETTERS

Protein accumulation in the endoplasmic reticulum as a non-equilibrium phase transition

(2014) Zoe Budrikis et al.   Nature Communications

Discriminatory Proofreading Regimes in Nonequilibrium Systems

(2014) Arvind Murugan et al.   Physical Review X

Thermodynamics with Continuous Information Flow

(2014) Jordan M. Horowitz et al.   Physical Review X

Thermodynamic Costs of Information Processing in Sensory Adaptation

(2014) Pablo Sartori et al.   PLoS Computational Biology

Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints

(2013) Anirikh Chakrabarti et al.   Biotechnology Journal

Metabolite damage and its repair or pre-emption

(2013) Carole L Linster et al.   Nature Chemical Biology

Finite-time erasing of information stored in fermionic bits

(2013) Giovanni Diana et al.   PHYSICAL REVIEW E

Kinetic versus Energetic Discrimination in Biological Copying

(2013) Pablo Sartori et al.   PHYSICAL REVIEW LETTERS

Thermodynamics of a Physical Model Implementing a Maxwell Demon

(2013) Philipp Strasberg et al.   PHYSICAL REVIEW LETTERS

Proliferation of amyloid- 42 aggregates occurs through a secondary nucleation mechanism

(2013) S. I. A. Cohen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the Mathematical Structure of Balanced Chemical Reaction Networks Governed by Mass Action Kinetics

(2013) Arjan van der Schaft et al.   SIAM JOURNAL ON APPLIED MATHEMATICS

Stochastic thermodynamics for “Maxwell demon” feedbacks

(2012) Massimiliano Esposito et al.   EPL

An Information Theoretical Analysis of Kinase Activated Phosphorylation Dephosphorylation Cycle

(2012) Hong Qian et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

Stochastic thermodynamics under coarse graining

(2012) Massimiliano Esposito   PHYSICAL REVIEW E

Efficiency at Maximum Power of Interacting Molecular Machines

(2012) N. Golubeva et al.   PHYSICAL REVIEW LETTERS

Entropy Involved in Fidelity of DNA Replication

(2012) J. Ricardo Arias-Gonzalez   PLoS One

Energetic costs of cellular computation

(2012) P. Mehta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Speed, dissipation, and error in kinetic proofreading

(2012) Arvind Murugan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stochastic thermodynamics, fluctuation theorems and molecular machines

(2012) Udo Seifert   REPORTS ON PROGRESS IN PHYSICS

How Far is Complex Balancing from Detailed Balancing?

(2011) Alicia Dickenstein et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Second law and Landauer principle far from equilibrium

(2011) M. Esposito et al.   EPL

Stochastic thermodynamics of single enzymes and molecular motors

(2011) U. Seifert   EUROPEAN PHYSICAL JOURNAL E

Carbohydrate-active enzymes exemplify entropic principles in metabolism

(2011) O. Kartal et al.   Molecular Systems Biology

Stochastic theory of nonequilibrium steady states. Part II: Applications in chemical biophysics

(2011) Hao Ge et al.   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Equalities and Inequalities: Irreversibility and the Second Law of Thermodynamics at the Nanoscale

(2011) Christopher Jarzynski   Annual Review of Condensed Matter Physics

Product-Form Stationary Distributions for Deficiency Zero Chemical Reaction Networks

(2010) David F. Anderson et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Physical origins of entropy production, free energy dissipation, and their mathematical representations

(2010) Hao Ge et al.   PHYSICAL REVIEW E

Three faces of the second law. II. Fokker-Planck formulation

(2010) Christian Van den Broeck et al.   PHYSICAL REVIEW E

Three faces of the second law. I. Master equation formulation

(2010) Massimiliano Esposito et al.   PHYSICAL REVIEW E

Generalization of the second law for a transition between nonequilibrium states

(2010) K. Takara et al.   PHYSICS LETTERS A

Dissipation and lag in irreversible processes

(2009) S. Vaikuntanathan et al.   EPL

Molecular information processing in nonequilibrium copolymerizations

(2009) David Andrieux et al.   JOURNAL OF CHEMICAL PHYSICS

Generalization of the second law for a nonequilibrium initial state

(2009) H.-H. Hasegawa et al.   PHYSICS LETTERS A

An Analytical Solution to the Kinetics of Breakable Filament Assembly

(2009) T. P. J. Knowles et al.   SCIENCE

Hypergraphs and Cellular Networks

(2009) Steffen Klamt et al.   PLoS Computational Biology

Computation with finite stochastic chemical reaction networks

(2008) David Soloveichik et al.   Natural Computing

Nonequilibrium generation of information in copolymerization processes

(2008) D. Andrieux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA