Textbook in PDF format

The first comprehensive graduate-level introduction to stochastic thermodynamics
Stochastic thermodynamics is a well-defined subfield of statistical physics that aims to interpret thermodynamic concepts for systems ranging in size from a few to hundreds of nanometers, the behavior of which is inherently random due to thermal fluctuations. This growing field therefore describes the nonequilibrium dynamics of small systems, such as artificial nanodevices and biological molecular machines, which are of increasing scientific and technological relevance.
This textbook provides an up-to-date pedagogical introduction to stochastic thermodynamics, guiding readers from basic concepts in statistical physics, probability theory, and thermodynamics to the most recent developments in the field. Gradually building up to more advanced material, the authors consistently prioritize simplicity and clarity over exhaustiveness and focus on the development of readers’ physical insight over mathematical formalism. This approach allows the reader to grow as the book proceeds, helping interested young scientists to enter the field with less effort and to contribute to its ongoing vibrant development. Chapters provide exercises to complement and reinforce learning.
Appropriate for graduate students in physics and biophysics, as well as researchers, Stochastic Thermodynamics serves as an excellent initiation to this rapidly evolving field.
Emphasizes a pedagogical approach to the subjectHighlights connections with the thermodynamics of informationPays special attention to molecular biophysics applicationsPrivileges physical intuition over mathematical formalismSolutions manual available on request for instructors adopting the book in a course
Foreword
Preface
Acknowledgments
Notation
Motivation
What is stochastic thermodynamics?
Why does it work and why is it useful?
Plan of the work
Basics
Thermodynamics
Thermodynamic efficiency
Free energy and nonequilibrium free energy
Statistical mechanics
Stochastic dynamics
Master equations
Trajectories of master equations
Fokker-Planck equation (*)
Langevin equation (*)
Information
Further reading
Exercises
Stochastic Thermodynamics
The system
Work and heat in stochastic thermodynamics
Mesoscopic and calorimetric heat (*)
ATP hydrolysis by myosin
General reservoirs
Stochastic entropy
Stochastic entropy and entropy production in a manipulated two-level system
Average entropy production rate
Network theory of nonequilibrium steady states (*)
Stochastic chemical reactions
Linear response theory (*)
More on coarse graining (*)
Continuous systems (*)
Further reading
Exercises
Fluctuation Relations
Irreversibility and entropy production
Integral fluctuation relation
Dragged particle on a ring
Back to linear response theory (*)
Detailed fluctuation relation
The Jarzynski and Crooks relations
Instantaneous quench
Fluctuation relations in practice
Adiabatic and nonadiabatic entropy production and the Hatano-Sasa relation
Systems with odd-parity variables
Trajectory probability for Langevin equations (*)
Fluctuation relation for the Langevin equation (*)
Brownian particle in a time-dependent harmonic potential (*)
Brownian motion with inertia (*)
Hamiltonian systems (*)
Further reading
Exercises
Thermodynamics of Information
A brief history
Back to nonequilibrium free energy
Information in stochastic thermodynamics
The Sagawa-Ueda relation
The Mandal-Jarzynski machine
Copying information
Information cost in sensing
Information reservoirs
Fluctuation relations with information reservoirs (*)
Further reading
Exercises
Large Deviations: Theory and Practice
Large deviations in a nutshell
Currents, traffic, and other observables
Large deviations and fluctuation relations
Fluctuation theorem for currents (*)
Tilting
Michaelis-Menten reaction scheme
Fluctuation relations in a model of kinesin (*)
Cloning (*)
Levels of large deviations (*)
Further reading
Exercises
Experimental Applications
The hairpin as a paradigm
A simpler model
Equilibrium free energies from nonequilibrium manipulations
Maxwell demons
Landauer principle
Further reading
Developments
Stochastic efficiency
Uncertainty relations
Applications of uncertainty relations
First-passage times
Fully irreversible processes
Optimal protocols
Martingales
Random time
Population genetics
Further reading
Exercises
Perspectives
Appendixes
Convex functions and the Jensen inequality
Legendre transformation
Probabilities and probability distributions
Generating functions and cumulant generating functions
Ergodic properties of Markov processes
Gillespie algorithm
Derivation of the Fokker-Planck equation
Ito formula and Stratonovich-Ito mapping
Basis of the cycle space
Actions and trajectory probabilities for Langevin equations
The Bennett-Crooks estimator for the free-energy difference
Cauchy-Schwarz inequality
Bound for the current rate function
Bibliography
Author Index
Index