Microscopic formula for transport coefficients of causal hydrodynamics

The Green-Kubo-Nakano formula should be modified in relativistic hydrodynamics because of the problem of acausality and the breaking of sum rules. In this work, we propose a formula to calculate the transport coefficients of causal hydrodynamics based on the projection operator method. As concrete examples, we derive the expressions for the diffusion coefficient, the shear viscosity coefficient, and corresponding relaxation times.Comment: 4 pages, title was modified, final version published in Phys. Rev.

Thermal Conductivity and Chiral Critical Point in Heavy Ion Collisions

Background: Quantum Chromodynamics is expected to have a phase transition in the same static universality class as the 3D Ising model and the liquid-gas phase transition. The properties of the equation of state, the transport coefficients, and especially the location of the critical point are under intense theoretical investigation. Some experiments are underway, and many more are planned, at high energy heavy ion accelerators. Purpose: Develop a model of the thermal conductivity, which diverges at the critical point, and use it to study the impact of hydrodynamic fluctuations on observables in high energy heavy ion collisions. Methods: We apply mode coupling theory, together with a previously developed model of the free energy that incorporates the critical exponents and amplitudes, to construct a model of the thermal conductivity in the vicinity of the critical point. The effect of the thermal conductivity on correlation functions in heavy ion collisions is studied in a boost invariant hydrodynamic model via fluctuations, or noise. Results: We find that the closer a thermodynamic trajectory comes to the critical point the greater is the magnitude of the fluctuations in thermodynamic variables and in the 2-particle correlation functions in momentum space. Conclusions: It may be possible to discern the existence of a critical point, its location, and thermodynamic and transport properties near to it in heavy ion collisions using the methods developed here.Comment: 36 pages, 8 figures. Version published in Phys.Rev.C86, 054911 (2012). It contains some minor improvements with respect to v1: further clarifications, small changes on figures and two extra reference

Interference effects in the counting statistics of electron transfers through a double quantum dot

We investigate the effect of quantum interferences and Coulomb interaction on the counting statistics of electrons crossing a double quantum dot in a parallel geometry using a generating function technique based on a quantum master equation approach. The skewness and the average residence time of electrons in the dots are shown to be the quantities most sensitive to interferences and Coulomb coupling. The joint probabilities of consecutive electron transfer processes show characteristic temporal oscillations due to interference. The steady-state fluctuation theorem which predicts a universal connection between the number of forward and backward transfer events is shown to hold even in the presence of Coulomb coupling and interference.Comment: 11 pages, 12 figure

A homogenization theorem for Langevin systems with an application to Hamiltonian dynamics

This paper studies homogenization of stochastic differential systems. The standard example of this phenomenon is the small mass limit of Hamiltonian systems. We consider this case first from the heuristic point of view, stressing the role of detailed balance and presenting the heuristics based on a multiscale expansion. This is used to propose a physical interpretation of recent results by the authors, as well as to motivate a new theorem proven here. Its main content is a sufficient condition, expressed in terms of solvability of an associated partial differential equation ("the cell problem"), under which the homogenization limit of an SDE is calculated explicitly. The general theorem is applied to a class of systems, satisfying a generalized detailed balance condition with a position-dependent temperature.Comment: 32 page

Survival probability (heat content) and the lowest eigenvalue of Dirichlet Laplacian

We study the survival probability of a particle diffusing in a two-dimensional domain, bounded by a smooth absorbing boundary. The short-time expansion of this quantity depends on the geometric characteristics of the boundary, whilst its long-time asymptotics is governed by the lowest eigenvalue of the Dirichlet Laplacian defined on the domain. We present a simple algorithm for calculation of the short-time expansion for an arbitrary "star-shaped" domain. The coefficients are expressed in terms of powers of boundary curvature, integrated around the circumference of the domain. Based on this expansion, we look for a Pad\'e interpolation between the short-time and the long-time behavior of the survival probability, i.e. between geometric characteristics of the boundary and the lowest eigenvalue of the Dirichlet Laplacian.Comment: Accepted in IJMP

Dynamics of Atom-Field Entanglement from Exact Solutions: Towards Strong Coupling and Non-Markovian Regimes

We examine the dynamics of bipartite entanglement between a two-level atom and the electromagnetic field. We treat the Jaynes-Cummings model with a single field mode and examine in detail the exact time evolution of entanglement, including cases where the atomic state is initially mixed and the atomic transition is detuned from resonance. We then explore the effects of other nearby modes by calculating the exact time evolution of entanglement in more complex systems with two, three, and five field modes. For these cases we can obtain exact solutions which include the strong coupling regimes. Finally, we consider the entanglement of a two-level atom with the infinite collection of modes present in the intracavity field of a Fabre-Perot cavity. In contrast to the usual treatment of atom-field interactions with a continuum of modes using the Born-Markov approximation, our treatment in all cases describes the full non-Markovian dynamics of the atomic subsystem. Only when an analytic expression for the infinite mode case is desired do we need to make a weak coupling assumption which at long times approximates Markovian dynamics.Comment: 12 pages, 5 figures; minor changes in grammar, wording, and formatting. One unnecessary figure removed. Figure number revised (no longer counts subfigures separately

Confinement and Viscoelastic effects on Chain Closure Dynamics

Chemical reactions inside cells are typically subject to the effects both of the cell's confining surfaces and of the viscoelastic behavior of its contents. In this paper, we show how the outcome of one particular reaction of relevance to cellular biochemistry - the diffusion-limited cyclization of long chain polymers - is influenced by such confinement and crowding effects. More specifically, starting from the Rouse model of polymer dynamics, and invoking the Wilemski-Fixman approximation, we determine the scaling relationship between the mean closure time t_{c} of a flexible chain (no excluded volume or hydrodynamic interactions) and the length N of its contour under the following separate conditions: (a) confinement of the chain to a sphere of radius D, and (b) modulation of its dynamics by colored Gaussian noise. Among other results, we find that in case (a) when D is much smaller than the size of the chain, t_{c}\simND^{2}, and that in case (b), t_{c}\simN^{2/(2-2H)}, H being a number between 1/2 and 1 that characterizes the decay of the noise correlations. H is not known \`a priori, but values of about 0.7 have been used in the successful characterization of protein conformational dynamics. At this value of H (selected for purposes of illustration), t_{c}\simN^3.4, the high scaling exponent reflecting the slow relaxation of the chain in a viscoelastic medium

Measuring the energy landscape roughness and the transition state location of biomolecules using single molecule mechanical unfolding experiments

Single molecule mechanical unfolding experiments are beginning to provide profiles of the complex energy landscape of biomolecules. In order to obtain reliable estimates of the energy landscape characteristics it is necessary to combine the experimental measurements with sound theoretical models and simulations. Here, we show how by using temperature as a variable in mechanical unfolding of biomolecules in laser optical tweezer or AFM experiments the roughness of the energy landscape can be measured without making any assumptions about the underlying reaction oordinate. The efficacy of the formalism is illustrated by reviewing experimental results that have directly measured roughness in a protein-protein complex. The roughness model can also be used to interpret experiments on forced-unfolding of proteins in which temperature is varied. Estimates of other aspects of the energy landscape such as free energy barriers or the transition state (TS) locations could depend on the precise model used to analyze the experimental data. We illustrate the inherent difficulties in obtaining the transition state location from loading rate or force-dependent unfolding rates. Because the transition state moves as the force or the loading rate is varied it is in general difficult to invert the experimental data unless the curvature at the top of the one dimensional free energy profile is large, i.e the barrier is sharp. The independence of the TS location on force holds good only for brittle or hard biomolecules whereas the TS location changes considerably if the molecule is soft or plastic. We also comment on the usefulness of extension of the molecule as a surrogate reaction coordinate especially in the context of force-quench refolding of proteins and RNA.Comment: 44 pages, 7 figure

Bubbling the False Vacuum Away

We investigate the role of nonperturbative, bubble-like inhomogeneities on the decay rate of false-vacuum states in two and three-dimensional scalar field theories. The inhomogeneities are induced by setting up large-amplitude oscillations of the field about the false vacuum as, for example, after a rapid quench or in certain models of cosmological inflation. We show that, for a wide range of parameters, the presence of large-amplitude bubble-like inhomogeneities greatly accelerates the decay rate, changing it from the well-known exponential suppression of homogeneous nucleation to a power-law suppression. It is argued that this fast, power-law vacuum decay -- known as resonant nucleation -- is promoted by the presence of long-lived oscillons among the nonperturbative fluctuations about the false vacuum. A phase diagram is obtained distinguishing three possible mechanisms for vacuum decay: homogeneous nucleation, resonant nucleation, and cross-over. Possible applications are briefly discussed.Comment: 13 Pages, 16 figures, revtex4, submitted to pr

On solutions of a class of non-Markovian Fokker-Planck equations

We show that a formal solution of a rather general non-Markovian Fokker-Planck equation can be represented in a form of an integral decomposition and thus can be expressed through the solution of the Markovian equation with the same Fokker-Planck operator. This allows us to classify memory kernels into safe ones, for which the solution is always a probability density, and dangerous ones, when this is not guaranteed. The first situation describes random processes subordinated to a Wiener process, while the second one typically corresponds to random processes showing a strong ballistic component. In this case the non-Markovian Fokker-Planck equation is only valid in a restricted range of parameters, initial and boundary conditions.Comment: A new ref.12 is added and discusse