247 research outputs found
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 âDNA cross-talkâ 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 âin silicoâ 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 Xâs. 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
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