Related papers: Methods and Conversations in (Post)Modern Thermody…
These are lecture notes of a course that I gave to people doing research for their Ph.D. thesis in theoretical chemistry or spectroscopy. The course was given on December 9-13, 2002, in Han-sur-Lesse, Belgium. The lecture notes start with…
Lecture notes for a master-level applied mathematics course on stochastic processes and applications, held at the University of Orl\'eans, France. Contents: Markov chains, Poisson point processes, Markovian jump processes, queueing theory.…
My ten-week Massive Open Online Course "Statistical Mechanics: Algorithms and Computations", in early 2014, focused on subjects such as Monte Carlo sampling, molecular dynamics, transition phases in hard-sphere liquids, simulated annealing,…
Stochastic thermodynamics is a framework for describing non-equilibrium processes at the level of fluctuating trajectories, where the state of a system evolves as a stochastic time series, allowing thermodynamic quantities such as work,…
Chemical and biological networks can describe a wide variety of processes, from gene regulatory networks to biochemical oscillations. Modeled by chemical master equations, these processes are inherently stochastic, as fluctuations dominate…
We consider stochastic thermodynamics as a theory of statistical inference for experimentally observed fluctuating time-series. To that end, we introduce a general framework for quantifying the knowledge about the dynamical state of the…
These lecture notes are written as reference material for the Advanced Course "Hydrodynamical Methods in Last Passage Percolation Models", given at the 28th Coloquio Brasileiro de Matematica at IMPA, Rio de Janeiro, July 2011.
A brief survey of the major themes and developments of black hole thermodynamics in the 1990's is given, followed by summaries of the talks on this subject at MG8 together with a bit of commentary, and closing with a look towards the…
We use Monte Carlo simulations to investigate the thermodynamical behaviour of aggregates consisting of few superparamagnetic particles in a colloidal suspension. The potential energy surface of this classical two-level system with a stable…
A general formulation of stochastic thermodynamics is presented for open systems exchanging energy and particles with multiple reservoirs. By introducing a partition in terms of "macrostates" (e.g. sets of "microstates"), the consequence on…
Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological,…
We review theoretical results obtained recently in the framework of statistical mechanics to study systems with long range forces. This fundamental and methodological study leads us to consider the different domains of applications in a…
Post-translational modification (PTM) of proteins plays a key role in signal transduction, and hence significant effort has gone toward understanding how PTM networks process information. This involves, on the theory side, analyzing the…
I give a brief introduction to the goals, challenges, and technical difficulties of lattice QCD thermodynamics and present some recent results from the HotQCD collaboration for the crossover temperature, equation of state, and other…
We review the theory of martingales as applied to stochastic thermodynamics and stochastic processes in physics more generally.
Estimating the free energy, as well as other thermodynamic observables, is a key task in lattice field theories. Recently, it has been pointed out that deep generative models can be used in this context [1]. Crucially, these models allow…
Markedly increased computational power and data acquisition have led to growing interest in data-driven inverse dynamics problems. These seek to answer a fundamental question: What can we learn from time series measurements of a complex…
Large fluctuations have received considerable attention as they encode information on the fine-scale dynamics. Large deviation relations known as fluctuation theorems also capture crucial nonequilibrium thermodynamical properties. Here we…
Stochastic thermodynamics as reviewed here systematically provides a framework for extending the notions of classical thermodynamics like work, heat and entropy production to the level of individual trajectories of well-defined…
Stochastic Thermodynamics (ST) extends the notions of classical thermodynamics to trajectories taken from a nonequilibrium ensemble. This extension yields a simple approach to fluctuation relations in small systems. Multiple time- and…