Yariv Kafri

From quantum chaos and eigenstate thermalization to statistical mechanics and thermodynamics

This review gives a pedagogical introduction to the eigenstate thermalization hypothesis (ETH), its basis, and its implications to statistical mechanics and thermodynamics. In the first part, ETH is introduced as a natural extension of ideas from quantum chaos and random matrix theory (RMT). To this end, we present a brief overview of classical and quantum chaos, as well as RMT and some of its most important predictions. The latter include the statistics of energy levels, eigenstate components, and matrix elements of observables. Building on these, we introduce the ETH and show that it allows one to describe thermalization in isolated chaotic systems without invoking the notion of an external bath. We examine numerical evidence of eigenstate thermalization from studies of many-body lattice systems. We also introduce the concept of a quench as a means of taking isolated systems out of equilibrium, and discuss results of numerical experiments on quantum quenches. The second part of the review explores the implications of quantum chaos and ETH to thermodynamics. Basic thermodynamic relations are derived, including the second law of thermodynamics, the fundamental thermodynamic relation, fluctuation theorems, the fluctuation–dissipation relation, and the Einstein and Onsager relations. In particular, it is shown that quantum chaos allows one to prove these relations for individual Hamiltonian eigenstates and thus extend them to arbitrary stationary statistical ensembles. In some cases, it is possible to extend their regimes of applicability beyond the standard thermal equilibrium domain. We then show how one can use these relations to obtain nontrivial universal energy distributions in continuously driven systems. At the end of the review, we briefly discuss the relaxation dynamics and description after relaxation of integrable quantum systems, for which ETH is violated. We present results from numerical experiments and analytical studies of quantum quenches at integrability. We introduce the concept of the generalized Gibbs ensemble and discuss its connection with ideas of prethermalization in weakly interacting systems.

Why is the DNA denaturation transition first order

We study a model for the denaturation transition of DNA in which the molecules are considered as being composed of a sequence of alternating bound segments and denaturated loops. We take into account the excluded-volume interactions between denaturated loops and the rest of the chain by exploiting recent results on scaling properties of polymer networks of arbitrary topology. The phase transition is found to be first order in d = 2 dimensions and above, in agreement with experiments and at variance with previous theoretical results, in which only excluded-volume interactions within denaturated loops were taken into account. Our results agree with recent numerical simulations.

Criterion for phase separation in one-dimensional driven systems.

A general criterion for the existence of phase separation in driven density-conserving one-dimensional systems is proposed. It is suggested that phase separation is related to the size dependence of the steady-state currents of domains in the system. A quantitative criterion for the existence of phase separation is conjectured using a correspondence made between driven diffusive models and zero-range processes. The criterion is verified in all cases where analytical results are available, and predictions for other models are provided.

Pressure and Phase Equilibria in Interacting Active Brownian Spheres

We derive a microscopic expression for the mechanical pressure P in a system of spherical active Brownian particles at density ρ. Our exact result relates P, defined as the force per unit area on a bounding wall, to bulk correlation functions evaluated far away from the wall. It shows that (i) P(ρ) is a state function, independent of the particle-wall interaction; (ii) interactions contribute two terms to P, one encoding the slow-down that drives motility-induced phase separation, and the other a direct contribution well known for passive systems; and (iii) P is equal in coexisting phases. We discuss the consequences of these results for the motility-induced phase separation of active Brownian particles and show that the densities at coexistence do not satisfy a Maxwell construction on P.

Pressure is not a state function for generic active fluids

The pressure that a fluid of self-propelled particles exerts on its container is shown to depend on microscopic interactions between fluid and container, suggesting that there is no equation of state for mechanical pressure in generic active systems.

Phase Separation in One-Dimensional Driven Diffusive Systems

Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot 76100, Israel(February 7, 2008)A driven diffusive model of three types of particles that exhibits phase separation on a ring isintroduced. The dynamics is local and comprises nearest neighbor exchanges that conserve each ofthe three species. For the case in which the three densities are equal, it is shown that the modelobeys detailed balance. The Hamiltonian governing the steady state distribution in this case is givenand is found to have long range asymmetric interactions. The partition sum and bounds on somecorrelation functions are calculated analytically demonstrating phase separation.PACS numbers: 02.50.Ey; 05.20.-y; 64.75.+g

Dynamics of Molecular Motors and Polymer Translocation with Sequence Heterogeneity

The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease, and RNA polymerase is studied in detail. Pore translocation of RNA or DNA is biased due to the different chemical environments on the two sides of the membrane, whereas the molecular motor motion is biased through a coupling to chemical energy. An externally applied force can oppose these biases. For both systems we solve lattice models exactly both with and without disorder. The models incorporate explicitly the coupling to the different chemical environments for polymer translocation and the coupling to the chemical energy (as well as nucleotide pairing energies) for molecular motors. Using the exact solutions and general arguments, we show that the heterogeneity leads to anomalous dynamics. Most notably, over a range of forces around the stall force (or stall tension for DNA polymerase/exonuclease systems) the displacement grows sublinearly as t(micro), with micro < 1. The range over which this behavior can be observed experimentally is estimated for several systems and argued to be detectable for appropriate forces and buffers. Similar sequence heterogeneity effects may arise in the packing of viral DNA.

Classes of fast and specific search mechanisms for proteins on DNA

Problems of search and recognition appear over different scales in biological systems. In this review we focus on the challenges posed by interactions between proteins, in particular transcription factors, and DNA and possible mechanisms which allow for fast and selective target location. Initially we argue that DNA-binding proteins can be classified, broadly, into three distinct classes which we illustrate using experimental data. Each class calls for a different search process and we discuss the possible application of different search mechanisms proposed over the years to each class. The main thrust of this review is a new mechanism which is based on barrier discrimination. We introduce the model and analyze in detail its consequences. It is shown that this mechanism applies to all classes of transcription factors and can lead to a fast and specific search. Moreover, it is shown that the mechanism has interesting transient features which allow for stability at the target despite rapid binding and unbinding of the transcription factor from the target.

Collective Dynamics of Interacting Molecular Motors

O. Campàs, 2 Y. Kafri, 3 K. B. Zeldovich, J. Casademunt, and J.-F. Joanny Institut Curie, UMR CNRS 168, 26 rue d’Ulm 75248 Paris Cedex 05 France. Departament d’ECM, Universitat de Barcelona, Avinguda Diagonal 647, E-08028 Barcelona, Spain. Physics Department, Technion, Haifa 32000, Israel. Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, MA 02138 USA. (Dated: February 9, 2008)

Phase Separation and Coarsening in One-Dimensional Driven Diffusive Systems: Local Dynamics Leading to Long-Range Hamiltonians

A driven system of three species of particles diffusing on a ring is studied in detail. The dynamics is local and conserves the three densities. A simple argument suggesting that the model should phase separate and break the translational symmetry is given. We show that for the special case where the three densities are equal the model obeys detailed balance, and the steady-state distribution is governed by a Hamiltonian with asymmetric long-range interactions. This provides an explicit demonstration of a simple mechanism for breaking of ergodicity in one dimension. The steady state of finite-size systems is studied using a generalized matrix product ansatz. The coarsening process leading to phase separation is studied numerically and in a mean-field model. The system exhibits slow dynamics due to trapping in metastable states whose number is exponentially large in the system size. The typical domain size is shown to grow logarithmically in time. Generalizations to a larger number of species are discussed.