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

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

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

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

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

Longitudinal claudin gene expression analyses in canine mammary tissues and thereof derived primary cultures and cell lines

Human and canine mammary tumours show partial claudin expression deregulations. Further, claudins have been used for directed therapeutic approaches. However, the development of claudin targeting approaches requires stable claudin expressing cell lines. This study reports the establishment and characterisation of canine mammary tissue derived cell lines, analysing longitudinally the claudin-1, -3, -4 and -7 expressions in original tissue samples, primary cultures and developed cell lines. Primary cultures were derived from 17 canine mammary tissues: healthy, lobular hyperplasia, simple adenoma, complex adenoma, simple tubular carcinoma, complex carcinoma, carcinoma arising in a benign mixed tumour and benign mixed tissue. Cultivation was performed, if possible, until passage 30. Claudin mRNA and protein expressions were analysed by PCR, QuantiGene Plex Assay, immunocytochemistry and immunofluorescence. Further, cytokeratin expression was analysed immunocytochemically. Cultivation resulted in 11 established cell lines, eight showing epithelial character. In five of the early passages the claudin expressions decreased compared to the original tissues. In general, claudin expressions were diminished during cultivation. Three cell lines kept longitudinally claudin, as well as epithelial marker expressions, representing valuable tools for the development of claudin targeted anti-tumour therapies

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

Enabling multiscale modeling in systems medicine: From reactions in cells to organ physiology

International audienceSystems medicine is an interdisciplinary approach that integrates data from basic research and clinical practice to improve our understanding and treatment of diseases. Systems medicine can be seen as a further development of systems biology and bioinformatics towards applica-tions of clinical relevance. The term 'systems' refers to systems approaches, emphasizing a close integration of data generation with mathematical modeling [1-3]. The (mal)functioning of the human body is a complex process, characterized by multiple interactions between systems that act across multiple levels of structural and functional organization -from molecular reactions to cell-cell interac-tions in tissues to the physiology of organs and organ systems. Over the past decade, we have gained detailed insights into the structure and function of molecular, cellu-lar and organ-level systems, with technologies playing an important role in the generation of data at these different scales