Thermostatting by deterministic scattering

We present a mechanism for thermalizing a moving particle by microscopic deterministic scattering. As an example, we consider the periodic Lorentz gas. We modify the collision rules by including energy transfer between particle and scatterer such that the scatterer mimics a thermal reservoir with arbitrarily many degrees of freedom. The complete system is deterministic, time-reversible, and provides a microcanonical density in equilibrium. In the limit of the disk representing infinitely many degrees of freedom and by applying an electric field the system goes into a nonequilibrium steady state.Comment: 4 pages (revtex) with 4 figures (postscript

Thermostating by deterministic scattering: the periodic Lorentz gas

We present a novel mechanism for thermalizing a system of particles in equilibrium and nonequilibrium situations, based on specifically modeling energy transfer at the boundaries via a microscopic collision process. We apply our method to the periodic Lorentz gas, where a point particle moves diffusively through an ensemble of hard disks arranged on a triangular lattice. First, collision rules are defined for this system in thermal equilibrium. They determine the velocity of the moving particle such that the system is deterministic, time reversible, and microcanonical. These collision rules can systematically be adapted to the case where one associates arbitrarily many degrees of freedom to the disk, which here acts as a boundary. Subsequently, the system is investigated in nonequilibrium situations by applying an external field. We show that in the limit where the disk is endowed by infinitely many degrees of freedom it acts as a thermal reservoir yielding a well-defined nonequilibrium steady state. The characteristic properties of this state, as obtained from computer simulations, are finally compared to the ones of the so-called Gaussian thermostated driven Lorentz gas.Comment: 13 pages (revtex) with 10 figures (encapsulated postscript

The Nose-hoover thermostated Lorentz gas

We apply the Nose-Hoover thermostat and three variations of it, which control different combinations of velocity moments, to the periodic Lorentz gas. Switching on an external electric field leads to nonequilibrium steady states for the four models with a constant average kinetic energy of the moving particle. We study the probability density, the conductivity and the attractor in nonequilibrium and compare the results to the Gaussian thermostated Lorentz gas and to the Lorentz gas as thermostated by deterministic scattering.Comment: 7 pages (revtex) with 10 figures (postscript), most of the figures are bitmapped with low-resolution. The originals are many MB, they can be obtained upon reques

Fluctuation formula for nonreversible dynamics in the thermostated Lorentz gas

We investigate numerically the validity of the Gallavotti-Cohen fluctuation formula in the two and three dimensional periodic Lorentz gas subjected to constant electric and magnetic fields and thermostated by the Gaussian isokinetic thermostat. The magnetic field breaks the time reversal symmetry, and by choosing its orientation with respect to the lattice one can have either a generalized reversing symmetry or no reversibility at all. Our results indicate that the scaling property described by the fluctuation formula may be approximately valid for large fluctuations even in the absence of reversibility.Comment: 6 pages, 6 figure

CORG: a database for COmparative Regulatory Genomics

Sequence conservation in non-coding, upstream regions of orthologous genes from man and mouse is likely to reflect common regulatory DNA sites. Motivated by this assumption we have delineated a catalogue of conserved non-coding sequence blocks and provide the CORG-'COmparative Regulatory Genomics'-database. The data were computed based on statistically significant local suboptimal alignments of 15 kb regions upstream of the translation start sites of, currently, 10 793 pairs of orthologous genes. The resulting conserved non-coding blocks were annotated with EST matches for easier detection of non-coding mRNA and with hits to known transcription factor binding sites. CORG data are accessible from the ENSEMBL web site via a DAS service as well as a specially developed web service (http://corg.molgen.mpg.de) for query and interactive visualization of the conserved blocks and their annotation

Lyapunov instability for a periodic Lorentz gas thermostated by deterministic scattering

In recent work a deterministic and time-reversible boundary thermostat called thermostating by deterministic scattering has been introduced for the periodic Lorentz gas [Phys. Rev. Lett. {\bf 84}, 4268 (2000)]. Here we assess the nonlinear properties of this new dynamical system by numerically calculating its Lyapunov exponents. Based on a revised method for computing Lyapunov exponents, which employs periodic orthonormalization with a constraint, we present results for the Lyapunov exponents and related quantities in equilibrium and nonequilibrium. Finally, we check whether we obtain the same relations between quantities characterizing the microscopic chaotic dynamics and quantities characterizing macroscopic transport as obtained for conventional deterministic and time-reversible bulk thermostats.Comment: 18 pages (revtex), 7 figures (postscript

Rotor interaction in the annulus billiard

Introducing the rotor interaction in the integrable system of the annulus billiard produces a variety of dynamical phenomena, from integrability to ergodicity

Systems biologists seek fuller integration of systems biology approaches in new cancer research programs

Systems biology takes an interdisciplinary approach to the systematic study of complex interactions in biological systems. This approach seeks to decipher the emergent behaviors of complex systems rather than focusing only on their constituent properties. As an increasing number of examples illustrate the value of systems biology approaches to understand the initiation, progression, and treatment of cancer, systems biologists from across Europe and the United States hope for changes in the way their field is currently perceived among cancer researchers. In a recent EU-US workshop, supported by the European Commission, the German Federal Ministry for Education and Research, and the National Cancer Institute of the NIH, the participants discussed the strengths, weaknesses, hurdles, and opportunities in cancer systems biology

On the Fluctuation Relation for Nose-Hoover Boundary Thermostated Systems

We discuss the transient and steady state fluctuation relation for a mechanical system in contact with two deterministic thermostats at different temperatures. The system is a modified Lorentz gas in which the fixed scatterers exchange energy with the gas of particles, and the thermostats are modelled by two Nos\'e-Hoover thermostats applied at the boundaries of the system. The transient fluctuation relation, which holds only for a precise choice of the initial ensemble, is verified at all times, as expected. Times longer than the mesoscopic scale, needed for local equilibrium to be settled, are required if a different initial ensemble is considered. This shows how the transient fluctuation relation asymptotically leads to the steady state relation when, as explicitly checked in our systems, the condition found in [D.J. Searles, {\em et al.}, J. Stat. Phys. 128, 1337 (2007)], for the validity of the steady state fluctuation relation, is verified. For the steady state fluctuations of the phase space contraction rate \zL and of the dissipation function \zW, a similar relaxation regime at shorter averaging times is found. The quantity \zW satisfies with good accuracy the fluctuation relation for times larger than the mesoscopic time scale; the quantity \zL appears to begin a monotonic convergence after such times. This is consistent with the fact that \zW and \zL differ by a total time derivative, and that the tails of the probability distribution function of \zL are Gaussian.Comment: Major revision. Fig.10 was added. Version to appear in Journal of Statistical Physic

Coherent States Measurement Entropy

Coherent states (CS) quantum entropy can be split into two components. The dynamical entropy is linked with the dynamical properties of a quantum system. The measurement entropy, which tends to zero in the semiclassical limit, describes the unpredictability induced by the process of a quantum approximate measurement. We study the CS--measurement entropy for spin coherent states defined on the sphere discussing different methods dealing with the time limit $n \to \infty$. In particular we propose an effective technique of computing the entropy by iterated function systems. The dependence of CS--measurement entropy on the character of the partition of the phase space is analysed.Comment: revtex, 22 pages, 14 figures available upon request (e-mail: [email protected]). Submitted to J.Phys.