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In eukaryotic cell nuclei, a variety of DNA interactions with nuclear elements occur, which, in combination with intra- and inter- chromosomal cross-talks, shape a functional 3D architecture. In some cases they are organized by active, i.e. actin/myosin, motors. More often, however, they have been related to passive diffusion mechanisms. Yet, the crucial questions on how DNA loci recognize their target and are reliably shuttled to their destination by Brownian diffusion are still open. Here, we complement the current experimental scenario by considering a physics model, in which the interaction between distant loci is mediated by diffusing bridging molecules. We show that, in such a system, the mechanism underlying target recognition and colocalization is a thermodynamic switch-like process (a phase transition) that only occurs if the concentration and affinity of binding molecules is above a threshold, or else stable contacts are not possible. We also briefly discuss the kinetics of this "passive-shuttling" process, as produced by random diffusion of DNA loci and their binders, and derive predictions based on the effects of genomic modifications and deletions.

The architecture of the eukaryotic genome is characterized by a high degree of spatial organization. Chromosomes occupy preferred territories correlated to their state of activity and, yet, displace their genes to interact with remote sites in complex patterns requiring the orchestration of a huge number of DNA loci and molecular regulators. Far from random, this organization serves crucial functional purposes, but its governing principles remain elusive. By computer simulations of a Statistical Mechanics model, we show how architectural patterns spontaneously arise from the physical interaction between soluble binding molecules and chromosomes via collective thermodynamics mechanisms. Chromosomes colocalize, loops and territories form and find their relative positions as stable thermodynamic states. These are selected by "thermodynamic switches" which are regulated by concentrations/affinity of soluble mediators and by number/location of their attachment sites along chromosomes. Our "thermodynamic switch model" of nuclear architecture, thus, explains on quantitative grounds how well known cell strategies of upregulation of DNA binding proteins or modification of chromatin structure can dynamically shape the organization of the nucleus.

Complex diseases are multifactorial traits caused by both genetic and environmental factors. They represent the most part of human diseases and include those with largest prevalence and mortality (cancer, heart disease, obesity, etc.). Despite of a large amount of information that have been collected about both genetic and environmental risk factors, there are relatively few examples of studies on their interactions in epidemiological literature. One reason can be the incomplete knowledge of the power of statistical methods designed to search for risk factors and their interactions in this data sets. An improving in this direction would lead to a better understanding and description of gene-environment interaction. To this aim, a possible strategy is to challenge the different statistical methods against data sets where the underlying phenomenon is completely known and fully controllable, like for example simulated ones. We present a mathematical approach that models gene-environment interactions. By this method it is possible to generate simulated populations having gene-environment interactions of any form. We implemented a simple version of this model in a Gene-Environment iNteraction Simulator (GENS), a tool designed to simulate case-control data sets where a one gene-one environment interaction influences the disease risk. The main effort has been to allow user to describe characteristics of population by using standard epidemiological measures and to implement constraints to make the simulator behavior biologically meaningful.

We study the rheological properties of a granular suspension subject to constant shear stress by constant volume molecular dynamics simulations. We derive the system `flow diagram' in the volume fraction/stress plane $(\phi,F)$: at low $\phi$ the flow is disordered, with the viscosity obeying a Bagnold-like scaling only at small $F$ and diverging as the jamming point is approached; if the shear stress is strong enough, at higher $\phi$ an ordered flow regime is found, the order/disorder transition being marked by a sharp drop of the viscosity. A broad jamming region is also observed where, in analogy with the glassy region of thermal systems, slow dynamics followed by kinetic arrest occurs when the ordering transition is prevented., Comment: 4 pages

The important task of determining the connectivity of gene networks, and at a more detailed level even the kind of interaction existing between genes, can nowadays be tackled by microarraylike technologies. Yet, there is still a large amount of unknowns with respect to the amount of data provided by a single microarray experiment, and therefore reliable gene network retrieval procedures must integrate all of the available biological knowledge, even if coming from different sources and of different nature. In this paper we present a reverse engineering algorithm able to reveal the underlying gene network by using time-series dataset on gene expressions considering the system response to different perturbations. The approach is able to determine the sparsity of the gene network, and to take into account possible {\it a priori} biological knowledge on it. The validity of the reverse engineering approach is highlighted through the deduction of the topology of several {\it simulated} gene networks, where we also discuss how the performance of the algorithm improves enlarging the amount of data or if any a priori knowledge is considered. We also apply the algorithm to experimental data on a nine gene network in {\it Escherichia coli

The compaction dynamics of a granular media subject to a sequence of vertical taps made of fluid pulses is investigated via Molecular Dynamics simulations. Our study focuses on three different levels: macroscopic (volume fraction), mesoscopic (Vorono\"{\i} volumes, force distributions) and microscopic (grain displacements). We show that the compaction process has many characteristics which are reminiscent of the slow dynamics of glass forming systems, as previously suggested. For instance the mean volume fraction slowly increases in time and approaches a stationary value following a stretched exponential law, and the associated compaction time diverges as the tapping intensity decreases. The study of microscopic quantities also put in evidence the existence of analogies with the dynamics of glass formers, as the existence of dynamical heterogeneities and spatially correlated motion of grains; however it also shows that there are important qualitative differences, as for instance in the role of the cage effect. Correlations between geometry and dynamics of the system at the grain level are put in evidence by comparing a particle Vorono\"{\i} volume and its displacement in a single tap.

We discuss the microscopic origin of dynamical instabilities and segregation patterns discovered in granular mixtures under oscillating horizontal shear, by investigating, via molecular dynamics simulations, the effective interaction between like-particles. This turns out to be attractive at short distances and strongly anisotropic, with a longer range repulsive shoulder along the direction of oscillation. This features explain the system rich phenomenology, including segregation and stripe pattern formation. Finally, we show that a modified Cahn-Hilliard equation, taking into account the characteristics of the effective interaction, is capable of describing the dynamics of the mixture.

By detailed Molecular Dynamics and Monte Carlo simulations %of a realistic model we show that granular materials at rest can be described as thermodynamics systems. First we show that granular packs can be characterized by few parameters, as much as fluids or solids. Then, in a second independent step, we demonstrate that these states can be described in terms of equilibrium distributions which coincide with the Statistical Mechanics of powders first proposed by Edwards. We also derive the system equation of state as a function of the ``configurational temperature'', its new intensive thermodynamic parameter., Comment: Supplementary Informations added

We introduce and analytically study a generalized p-spin glass like model that captures some of the main features of attractive glasses, recently found by Mode Coupling investigations, such as a glass/glass transition line and dynamical singularity points characterized by a logarithmic time dependence of the relaxation. The model also displays features not predicted by the Mode Coupling scenario that could further describe the attractive glasses behavior, such as aging effects with new dynamical singularity points ruled by logarithmic laws or the presence of a glass spinodal line.

Dynamical instabilities in fluid mechanics are responsible of a variety of important common phenomena, such as waves on the sea surface or Taylor vorteces in Couette flow. In granular media dynamical instabilities has just begun to be discovered. Here we show by means of molecular dynamics simulation the existence of a new dynamical instability of a granular mixture under oscillating horizontal shear, which leads to the formation of a striped pattern where the components are segregated. We investigate the properties of such a Kelvin-Helmholtz like instability and show how it is connected to pattern formation in granular flow and segregation., Comment: Phys. Rev. Lett. 94, 188001

We use Monte Carlo simulations of a coarse grained three dimensional model to demonstrate that the experimentally observed approximate temperature independence of the magnetic creep rate for a broad range of temperatures may be explained in terms of record dynamics, {\it viz.} the dynamical properties of the times at which a stochastic fluctuating signal establishes records., Comment: 7 pages, 5 figures. Replaced in order to correct the order of the Bessel function in Eq. 4

We compare the predictions of two different statistical mechanics approaches, corresponding to different physical measurements, proposed to describe binary granular mixtures subjected to some external driving (continuous shaking or tap dynamics). In particular we analytically solve at a mean field level the partition function of a simple hard sphere lattice model under gravity and we focus on the phenomenon of size segregation. We find that the two approaches lead to similar results and seem to coincide in the limit of very low shaking amplitude. However they give different predictions of the crossovers from Brazil nut effect to reverse Brazil nut effect with respect to the shaking amplitude, which could be detected experimentally., Comment: to appear on Physical Review Letters

We discuss recent developments in the formulation of a Statistical Mechanics approach to non thermal systems, such as granular media. We review a few important numerical results on the assessment of Edwards' theory and, in particular, we apply these ideas to study a mean field model of a hard sphere binary mixture under gravity, which can be fully analytically investigated. As a consequence, we derive the rich phase diagram and predict the features of segregation patterns of the mixture., Comment: Contribution to November 2002 Santa Fe workshop "Anomalous Distributions, Nonlinear Dynamics and Nonextensivity", to appear in Physica D

We discuss a Statistical Mechanics approach in the manner of Edwards to the ``inherent states'' (defined as the stable configurations in the potential energy landscape) of glassy systems and granular materials. We show that at stationarity the inherent states are distributed according a generalized Gibbs measure obtained assuming the validity of the principle of maximum entropy, under suitable constraints. In particular we consider three lattice models (a diluted Spin Glass, a monodisperse hard-sphere system under gravity and a hard-sphere binary mixture under gravity) undergoing a schematic ``tap dynamics'', showing via Monte Carlo calculations that the time average of macroscopic quantities over the tap dynamics and over such a generalized distribution coincide. We also discuss about the general validity of this approach to non thermal systems., Comment: 10 pages, 16 figures

We study segregation patterns in a hard sphere binary model under gravity subject to sequences of taps. We discuss the appearance of the ``Brazil nut'' effect (where large particles move up) and the ``reverse Brazil nut'' effects in the stationary states reached by ``tap'' dynamics. In particular, we show that the stationary state depends only on two thermodynamical quantities: the gravitational energy of the first and of the second species and not on the sample history. To describe the properties of the system, we generalize Edwards' approach by introducing a canonical distribution characterized by two configurational temperatures, conjugate to the energies of the two species. This is supported by Monte Carlo calculations showing that the average of several quantities over the tap dynamics and over such distribution coincide. The segregation problem can then be understood as an equilibrium statistical mechanics problem with two control parameters., Comment: 7 pages, 4 figures

The present paper proposes a Statistical Mechanics approach to the inherent states of glassy systems and granular materials, following the original ideas developed by Edwards for granular materials. Two lattice models, a diluted Spin Glass and a system of hard-spheres under gravity, introduced in the context of glassy systems and granular materials, are evolved using a ``tap dynamics'' analogous to that of experiments on granular materials. The asymptotic macrostates, reached by the system, are shown to be described by a single thermodynamical parameter, and this parameter to coincide with the temperature, called the ``configurational temperature'', predicted assuming that the distribution among the inherent states satisfies the principle of maximum entropy., Comment: revised and improved version including new results on a 3D hard-spheres model; 4 pages, 4 figures

There is mounting experimental evidence that strong off-equilibrium phenomena, such as ``memory'' or ``aging'' effects, play a crucial role in the physics of vortices in type II superconductors. We give a short review, based on a recently introduced schematic vortex model, of current progresses in understanding out of equilibrium vortex behaviours. We develop a unified description of ``memory'' phenomena in magnetic and transport properties, such as magnetisation loops and their ``anomalous'' 2nd peak, logarithmic creep, ``anomalous'' finite creep rate in the limit of vanishing temperature, ``memory'' and ``irreversibility'' in I-V characteristics, time dependent critical currents, ``rejuvenation'' and ``aging'' of the system response., Comment: updated version

Vortex flow in driven type II superconductors shows strong memory and history dependent effects. Here, we study a schematic microscopic model of driven vortices to propose a scenario for a broad set of these kind of phenomena ranging from ``rejuvenation'' and ``stiffening'' of the system response, to ``memory'' and ``irreversibility'' in I-V characteristics.

We consider a Statistical Mechanics approach to granular systems by following the original ideas developed by Edwards. We use the concept of ``inherent states'', defined as the stable configurations in the potential energy landscape, introduced in the context of glasses. Under simplifying assumptions, the equilibrium inherent states can be characterised by a configurational temperature, $1/\beta$. We link $\beta$ to Edwards' compactivity and address the problem of its experimental measure. We also discuss the possibility to describe the time dependent distribution probability in the inherent states with an appropriate master equation., Comment: revised version in press

We study the properties of a simple lattice model of repulsive particles diffusing in a pinning landscape. The behaviour of the model is very similar to the observed physics of vortices in superconductors. We compare and discuss the equilibrium phase diagram, creep dynamics, the Bean state profiles, hysteresis of magnetisation loops (including the second peak feature), and, in particular, ``off equilibrium'' relaxations. The model is analytically tractable in replica mean field theory and numerically via Monte Carlo simulations. It offers a comprehensive schematic framework of the observed phenomenology.

We study a model for the dynamics of vortices in type II superconductors. In particular, we discuss glassy ``off equilibrium'' properties and ``aging'' in magnetic creep. At low temperatures a crossover point is found, Tg, where relaxation times seem to diverge a' la Vogel-Tamman-Fulcher. Magnetic creep changes by crossing Tg: above Tg power law creep is found asymptotically followed by stretched exponential saturation; below Tg the creep is logarithmic and vortex motion strongly subdiffusive. In this region violation of time translation invariance is found along with important dynamical scaling properties. A thermodynamic glassy transition point can be found at a lower temperature Tc., Comment: published version

We theoretically study the creep of vortex matter in superconductors. The low temperatures experimental phenomenology, previously interpreted in terms of ``quantum tunnelling'' of vortices, is reproduced by Monte Carlo simulations of a purely ``classical'' vortex model. We demonstrate that a non-zero creep rate in the limit of vanishing temperature is to be expected in systems with slow relaxations as a consequence of their off-equilibrium evolution in a complex free energy landscape., Comment: extended references, published version

We briefly review the basics ideas and results of a recently proposed statistical mechanical approach to granular materials. Using lattice models from standard Statistical Mechanics and results from a mean field replica approach and Monte Carlo simulations we find a jamming transition in granular media closely related to the glass transition in super-cooled liquids. These models reproduce the logarithmic relaxation in granular compaction and reversible-irreversible lines, in agreement with experimental data. The models also exhibit aging effects and breakdown of the usual fluctuation dissipation relation. It is shown that the glass transition may be responsible for the logarithmic relaxation and may be related to the cooperative effects underlying many phenomena of granular materials such as the Reynolds transition., Comment: 18 pages with 6 postscript figures. to appear in J.Phys: Cond. Mat

We study the dynamical properties of recently introduced frustrated lattice gas models (IFLG and Tetris) for granular media under gentle shaking. We consider both the case where grains have inter-grain surface interactions and the case where they have not, corresponding, for instance, to the presence or absence of moisture in the packs. To characterise the grains packing structure, we discuss the properties of density distribution. In particular, we consider the phenomenon of grains domains formation under compaction. New results amenable of experimental check are discussed along with some important differences between the dynamics of the present models., Comment: 7 pages, 6 postscript files for figures

We introduce a schematic non-linear diffusion model where density fluctuations induce a rich out of equilibrium dynamics. The properties of the model are studied by numerical simulations and analytically in a mean field approximation. At low temperatures and high densities we find a long off-equilibrium glassy region, where the system evolves out of an initially pinned state showing aging and a slow decay of the autocorrelation as an enhanced power law, along with strong spatial heterogeneities and violation of the fluctuation dissipation theorem., Comment: 4 pages, 2 figures

A simple lattice gas model with random fields and gravity is introduced to describe a system of grains moving in a disordered environment. Off equilibrium relaxations of bulk density and its two time correlation functions are numerically found to show logarithmic time dependences and "aging" effects. Similitudes with dry granular media are stressed. The connections with off equilibrium dynamics in others kinds of "frustrated" lattice models in presence of a directional driving force (gravity) are discussed to single out the appearance of universal features in the relaxation process., Comment: 15 pages, latex, 7 figures included

In recently introduced schematic lattice gas models for vibrated dry granular media, we study the dynamical response of the system to small perturbations of shaking amplitudes and its relations with the characteristic fluctuations. Strong off equilibrium features appear and a generalized version of the fluctuation dissipation theorem is introduced. The relations with thermal glassy systems and the role of Edwards' compactivity are discussed., Comment: 12 pages, 2 postscript figures

In the framework of recently introduced frustrated lattice gas models, we study the out of equilibrium dynamical processes during the compaction process in granular media. We find irreversible-reversible cycles in agreement with recent experimental observations. Moreover in analogy with the phenomenology of the glass transition we find aging effects during the compaction process In particular we find that the two time density correlation function $C(t,t')$ asymptotically scales as a function of the single variable $\ln(t')/\ln(t)$. This result is interpreted in terms of multiscaling properties of the system., Comment: 4 pages