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

Synchnonization, zero-resistance states and rotating Wigner crystal

We show that rotational angles of electrons moving in two dimensions (2D) in a perpendicular magnetic field can be synchronized by an external microwave field which frequency is close to the Larmor frequency. The synchronization eliminates collisions between electrons and thus creates a regime with zero diffusion corresponding to the zero-resistance states observed in experiments with high mobility 2D electron gas (2DEG). For long range Coulomb interactions electrons form a rotating hexagonal Wigner crystal. Possible relevance of this effect for planetary rings is discussed.Comment: 4 pages, 4 fig

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

Studies on mechanisms of interferon-gamma action in pancreatic cancer using a data-driven and model-based approach

<p>Abstract</p> <p>Background</p> <p>Interferon-gamma (IFNγ) is a multifunctional cytokine with antifibrotic and antiproliferative efficiency. We previously found that pancreatic stellate cells (PSC), the main effector cells in cancer-associated fibrosis, are targets of IFNγ action in the pancreas. Applying a combined experimental and computational approach, we have demonstrated a pivotal role of STAT1 in IFNγ signaling in PSC. Using <it>in vivo </it>and <it>in vitro </it>models of pancreatic cancer, we have now studied IFNγ effects on the tumor cells themselves. We hypothesize that IFNγ inhibits tumor progression through two mechanisms, reduction of fibrogenesis and antiproliferative effects on the tumor cells. To elucidate the molecular action of IFNγ, we have established a mathematical model of STAT1 activation and combined experimental studies with computer simulations.</p> <p>Results</p> <p>In BALB/c-<it>nu/nu </it>mice, flank tumors composed of DSL-6A/C1 pancreatic cancer cells and PSC grew faster than pure DSL-6A/C1 cell tumors. IFNγ inhibited the growth of both types of tumors to a similar degree. Since the stroma reaction typically reduces the efficiency of therapeutic agents, these data suggested that IFNγ may retain its antitumor efficiency in PSC-containing tumors by targeting the stellate cells. Studies with cocultures of DSL-6A/C1 cells and PSC revealed a modest antiproliferative effect of IFNγ under serum-free conditions. Immunoblot analysis of STAT1 phosphorylation and confocal microscopy studies on the nuclear translocation of STAT1 in DSL-6A/C1 cells suggested that IFNγ-induced activation of the transcription factor was weaker than in PSC. The mathematical model not only reproduced the experimental data, but also underscored the conclusions drawn from the experiments by indicating that a maximum of 1/500 of total STAT1 is located as phosphorylated STAT1 in the nucleus upon IFNγ treatment of the tumor cells.</p> <p>Conclusions</p> <p>IFNγ is equally effective in DSL-6A/C1 tumors with and without stellate cells. While its action in the presence of PSC may be explained by inhibition of fibrogenesis, its efficiency in PSC-free tumors is unlikely to be caused by direct effects on the tumor cells alone but may involve inhibitory effects on local stroma cells as well. To gain further insights, we also plan to apply computer simulations to the analysis of tumor growth <it>in vivo</it>.</p

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