Consistent description of fluctuations requires negative temperatures

• Angelo Vulpiani (Dipartimento di Fisica, Universita' Sapienza)

Room: 132:028

Dynamics of protein synthesis: transcription, translation, and mRNA degradation

• Namiko Mitarai (Niels Bohr Institute)

Room: 132:028 Protein synthesis in bacteria is a very dynamical process. Typically ribosomes start translation while the mRNA is still being transcribed, resulting in translation-transcription coupling. In addition mRNAs are subject to active degradation. I discuss this complex dynamics using a stochastic model of ribosome initiation and traffic, especially focusing on recent experimental results about interplay between ribosome dynamics and mRNA degradation as well as transcription.

Stochastic Thermodynamics in Biology: a historical (but rather personal) overview

• Alberto Imparato (Aarhus University)

Room: 132:028 I will first review some of the fluctuation relations involving the work done on a microscopic system by an external force, and show how they have been used to evaluate the free energy of bio-polymers such as proteins and nucleic acids. I will then discuss some more recent results concerning the thermodynamic properties of molecular motors.

Thermodynamics with continuous information flow

• Jordan Horowitz (Massachusetts Institute of Technology)

Room: 132:028 When two systems interact they exchange not only energy, but also information. In this talk, I will discuss a consistent way to incorporate this information flow into the second law of thermodynamics, thereby placing information on equal footing with other thermodynamic quantities, like energy and entropy. From this framework, we will see how information continuously generated in an auxiliary system can then be transferred to another system that can utilize it to fuel an otherwise impossible process, of which the Maxwell’s demon is a prime example. I will then compare how these results fit into the growing theoretical framework for the thermodynamics of information.

Stochastic thermodynamics with a viscoelastic heat bath

• Michael Lomholt (University of Southern Denmark)

Room: 132:028 Molecules in a channel or proteins on DNA perform single-file motion, where a single particle is limited in its motion by its neighbors. I will discuss how an effective description, in the form of a generalized Langevin equation, can be derived for such a single particle. In this description the heat bath consisting of the surrounding particles will behave viscoelastically. A curios consequence of this is that the average entropy can transiently decrease.

Thermodynamic Costs in Implementing Optimal Estimators

• Henrik Sandberg (KTH Royal Institute of Technology)

Room: 132:028 In this talk, we discuss fundamental limits for physical implementations of the Kalman-Bucy filter for linear passive systems. (The Kalman-Bucy filter is often used in signal processing and control theory because it optimally estimates the state of an uncertain system, continuously in time.) In particular, we show that the Kalman-Bucy filter itself is a passive system and by invoking the second law of thermodynamics, we can characterize the external power supply needed to operate the filter. We also show how the required external power supply can be decreased by allowing the filter to perturb the measured system to a larger extent. Hence, it is possible to decrease the so-called back action of the filter by spending more energy. By computing the information flow into the filter, we can also relate our result to the so-called Landauer's principle, and interpret it as a Maxwell's demon.

AlbaNova Colloquium Room: Oskar Klein Auditorium

Kinetics and thermodynamics of reversible polymerization

• David Lacoste (ESPCI)

Room: 132:028 Biological systems make extensive use of reversible polymerization: key biological functions are accomplished by biopolymers such as peptides, assembled from amino-acids, or actin and microtubules, assembled respectively from G-actin and tubulin monomers. On the theoretical side, such systems represent an ideal ground to test non-equilibrium statistical physics and thermodynamics, as illustrated by the pioneering work of T. Hill. In this talk, inspired by a recent experimental study on the metabolism of carbohydrates, we model reversible polymerization from the point of view of non-equilibrium thermodynamics. We first consider a closed system and show that the polymers dynamically evolve towards equilibrium where detailed balance is satisfied. We then consider open systems, in which the polymers are in contact with chemostats, characterized by fixed polymer concentrations of a given length.

Stochastic thermodynamics in many-particle systems

• Alberto Imparato (Aarhus University)

Room: 132:028 I will discuss the thermodynamic properties of systems consisting of interacting microscopic particles. In particular I will first characterize the efficiency at maximum power (EMP) in a system of interacting molecular motors. I will then consider the case of a microscopic model of coupled particles that exhibits a dynamical phase transition from a desynchronized to a synchronized phase.

Jam Session Room: 132:028

Fluctuations in stochastic systems with memory

• Rosemary Harris (Queen Mary University of London)

Room: 132:028 I will give a gentle introduction to some recent work on the effects of long-range temporal correlations in stochastic particle systems, focusing particularly on fluctuations about the typical behaviour. Specifically, in the first part of the talk, I will discuss how long-range memory dependence can modify the large deviation principle describing the probability of rare currents and lead, for example, to superdiffusive behaviour. In the second part of the talk, I will describe a more interdisciplinary project incorporating the psychological "peak-end" heuristic for human memory into a simple discrete choice model from economics. Along the way, I will attempt to indicate connections between different approaches, other possible applications (especially to biology), and open questions.

Simple models of evolution with selection and genealogies

• Bernard Derrida (Collège de France, Paris)

Room: 132:028

Adaptation and irreversibility in microevolution

• Antonio Celani (ICTP, Trieste)

Room: 132:028 I will review some classical and recent ideas about the notion of irreversibility in evolution and explore their connections with stochastic thermodynamics and implications for microevolution. As an example, I will discuss the population genetics of asexual haploid individuals under the effect of rapidly varying natural selection. (Joint work with Stefano Bo and Andrea Mazzolini).

Efficiency of thermal machines

• Bart Cleuren (Universiteit Hasselt)

Room: 132:028 Two topics will be covered. The first topic is the development of a general framework to characterise the efficiency of steady state thermal machines operating a maximum power. The second topic concerns the efficiency and efficiency fluctuations of a single particle Szilard and Carnot engine.

Universal constraints for biomolecular systems

• Udo Seifert (II. Institute for Theoretical Physics, University of Stuttgart)

Room: 132:028 After briefly introducing the principles of stochastic thermodynamics [1], I will discuss our recent work concerning three universal results for biomolecular system that go beyond the second law and the fluctuation theorem. First, I will show how the presence of a slow hidden degree of freedom leads to a "fine-structured" fluctuation theorem using our hybrid molecular motor model as illustration [2]. Second, I will discuss a universal thermodynamic inequality quantifying the trade-off between precision of a process and its thermodynamic cost [3]. Third, I will show how in bacterial sensing, thermodynamics puts constraints on the maximal achievable "learning rate" with which a sensory system acquires information about changing external conditions [4]. [1] U.S., Rep Prog Phys 75, 126001, 2012. [2] P. Pietzonka, E. Zimmermann and U.S., EPL 107, 20002, 2014. [3] A.C. Barato and U.S., Phys Rev Lett 114, 158101, 2015. [4] A.C. Barato, D. Hartich, and U.S., New J Phys 16, 103024, 2014.

Jam Session Room: 132:028

Single-molecule measurement of the effective temperature in non-equilibrium steady states

• Felix Ritort (Universitat de Barcelona)

Room: 132:028 Temperature is a well-defined quantity for systems in equilibrium. For glassy systems, it has been extended to the non-equilibrium regime, showing up as an effective quantity in a modified version of the fluctuation–dissipation theorem. However, experimental evidence supporting this definition remains scarce. Here, we present the first direct experimental demonstration of the effective temperature by measuring correlations and responses in single molecules in non-equilibrium steady states generated under external random forces. We combine experiment, analytical theory and simulations for systems with different levels of complexity, ranging from a single bead in an optical trap to two-state and multiple-state DNA hairpins. From these data, we extract a unifying picture for the existence of an effective temperature based on the relative order of various timescales characterizing intrinsic relaxation and external driving. Our study thus introduces driven small systems as a fertile ground to address fundamental concepts in statistical physics, condensed-matter physics and biophysics. Ref: Nature Physics (2015) doi:10.1038/nphys3435

Integral fluctuation theorem for inertial particles in turbulent flow

• Dhrubaditya Mitra

Room: 132:028

Fluctuation Theorems and the Dissipation Function: providing Insight for Thermodynamics

• Debra Bernhardt (The University of Queensland)

Room: 132:028

Jam Session Room: 132:028

Stochastic Thermodynamics of Chemical Networks

• Matteo Polettini (University of Luxembourg)

Room: 132:028 Today, high-throughput technologies in genomics allow to draft complete Chemical Networks (CN) for complex biochemical processes such as gene regulation and cellular metabolism, which are repositories of thousands of pathways, metabolites, and their stoichiometry. Dwelling into these data is an excruciating task in Systems Biology. Because of the very small numbers of enzymes (in a cell some can be expressed in but a few copies), these processes are intrinsically stochastic. Moreover, closed reaction pathways within CNs can be seen as thermodynamic cycles processing nutrients and information into waste and products, in a way reminiscent of thermodynamic machines. In this talk, we argue that ideas and techniques from Stochastic Thermodynamics can be used to decipher the enormous complexity of (bio)Chemical Networks. In particular, we present and address the themes of network reconstruction of the fluxes and of free energy landscapes, and of the effect of noise on dissipation.