DNA loci cross-talk through thermodynamics

The recognition and pairing of specific DNA loci, though crucial for a plenty of important cellular processes, are produced by still mysterious physical mechanisms. We propose the first quantitative model from Statistical Mechanics, able to clarify the interaction allowing such “DNA cross-talk” events. Soluble molecules, which bind some DNA recognition sequences, produce an effective attraction between distant DNA loci; if their affinity, their concentration, and the relative DNA binding sites number exceed given thresholds, DNA colocalization occurs as a result of a thermodynamic phase transition. In this paper, after a concise report on some of the most recent experimental results, we introduce our model and carry out a detailed “in silico” analysis of it, by means of Monte Carlo simulations. Our studies, while rationalize several experimental observations, result in very interesting and testable predictions

Creep of superconducting vortices in the limit of vanishing temperature: A fingerprint of off-equilibrium dynamics

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 versio

Off equilibrium properties of vortex creep in superconductors

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 versio

Segregation in hard spheres mixtures under gravity. An extension of Edwards approach with two thermodynamical parameters

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 figure

Self-assembly and DNA binding of the blocking factor in X chromosome inactivation

X chromosome inactivation (XCI) is the phenomenon occurring in female mammals whereby dosage compensation of X-linked genes is obtained by transcriptional silencing of one of their two X chromosomes, randomly chosen during early embryo development. The earliest steps of random X-inactivation, involving counting of the X chromosomes and choice of the active and inactive X, are still not understood. To explain "counting and choice," the longstanding hypothesis is that a molecular complex, a "blocking factor" (BF), exists. The BF is present in a single copy and can randomly bind to just one X per cell which is protected from inactivation, as the second X is inactivated by default. In such a picture, the missing crucial step is to explain how the molecular complex is self-assembled, why only one is formed, and how it binds only one X. We answer these questions within the framework of a schematic Statistical Physics model, investigated by Monte Carlo computer simulations. We show that a single complex is assembled as a result of a thermodynamic process relying on a phase transition occurring in the system which spontaneously breaks the symmetry between the X’s. We discuss, then, the BF interaction with X chromosomes. The thermodynamics of the mechanism that directs the two chromosomes to opposite fates could be, thus, clarified. The insights on the selfassembling and X binding properties of the BF are used to derive a quantitative scenario of biological implications describing current experimental evidences on "counting and choice.

Thermodynamics and Statistical Mechanics of dense granular media

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 adde

Equilibrium properties of the Ising frustrated lattice gas

We study the equilibrium properties of an Ising frustrated lattice gas with a mean field replica approach. This model bridges usual {\em Spin Glasses} and a version of {\em Frustrated Percolation} model, and has proven relevant to describe the glass transition. It shows a rich phase diagram which in a definite limit reduces to the known Sherrington-Kirkpatrick spin glass model.Comment: To appear in J.Physique I (september 96). All figures included in an one-page postscript fil

The Blume-Emery-Griffiths Spin Glass Model

We study the equilibrium properties of the Blume-Emery-Griffiths model with bilinear quenched disorder in the case of attractive as well as repulsive biquadratic interactions. The global phase diagram of the system is calculated in the context of the replica symmetric mean field approximation.Comment: 22 pages and 9 figures. REVTeX. To appear on Journal de Physiqu