The dark side of centromeres: types, causes and consequences of structural abnormalities implicating centromeric DNA

Centromeres are the chromosomal domains required to ensure faithful transmission of the genome during cell division. They have a central role in preventing aneuploidy, by orchestrating the assembly of several components required for chromosome separation. However, centromeres also adopt a complex structure that makes them susceptible to being sites of chromosome rearrangements. Therefore, preservation of centromere integrity is a difficult, but important task for the cell. In this review, we discuss how centromeres could potentially be a source of genome instability and how centromere aberrations and rearrangements are linked with human diseases such as cancer

A Hebbian approach to complex network generation

Through a redefinition of patterns in an Hopfield-like model, we introduce and develop an approach to model discrete systems made up of many, interacting components with inner degrees of freedom. Our approach clarifies the intrinsic connection between the kind of interactions among components and the emergent topology describing the system itself; also, it allows to effectively address the statistical mechanics on the resulting networks. Indeed, a wide class of analytically treatable, weighted random graphs with a tunable level of correlation can be recovered and controlled. We especially focus on the case of imitative couplings among components endowed with similar patterns (i.e. attributes), which, as we show, naturally and without any a-priori assumption, gives rise to small-world effects. We also solve the thermodynamics (at a replica symmetric level) by extending the double stochastic stability technique: free energy, self consistency relations and fluctuation analysis for a picture of criticality are obtained

Irreducible free energy expansion and overlaps locking in mean field spin glasses

We introduce a diagrammatic formulation for a cavity field expansion around the critical temperature. This approach allows us to obtain a theory for the overlap's fluctuations and, in particular, the linear part of the Ghirlanda-Guerra relationships (GG) (often called Aizenman-Contucci polynomials (AC)) in a very simple way. We show moreover how these constraints are "superimposed" by the symmetry of the model with respect to the restriction required by thermodynamic stability. Within this framework it is possible to expand the free energy in terms of these irreducible overlaps fluctuations and in a form that simply put in evidence how the complexity of the solution is related to the complexity of the entropy.Comment: 19 page

Non-equilibrium Lorentz gas on a curved space

The periodic Lorentz gas with external field and iso-kinetic thermostat is equivalent, by conformal transformation, to a billiard with expanding phase-space and slightly distorted scatterers, for which the trajectories are straight lines. A further time rescaling allows to keep the speed constant in that new geometry. In the hyperbolic regime, the stationary state of this billiard is characterized by a phase-space contraction rate, equal to that of the iso-kinetic Lorentz gas. In contrast to the iso-kinetic Lorentz gas where phase-space contraction occurs in the bulk, the phase-space contraction rate here takes place at the periodic boundaries

Log-periodic drift oscillations in self-similar billiards

We study a particle moving at unit speed in a self-similar Lorentz billiard channel; the latter consists of an infinite sequence of cells which are identical in shape but growing exponentially in size, from left to right. We present numerical computation of the drift term in this system and establish the logarithmic periodicity of the corrections to the average drift

Analogue neural networks on correlated random graphs

We consider a generalization of the Hopfield model, where the entries of patterns are Gaussian and diluted. We focus on the high-storage regime and we investigate analytically the topological properties of the emergent network, as well as the thermodynamic properties of the model. We find that, by properly tuning the dilution in the pattern entries, the network can recover different topological regimes characterized by peculiar scalings of the average coordination number with respect to the system size. The structure is also shown to exhibit a large degree of cliquishness, even when very sparse. Moreover, we obtain explicitly the replica symmetric free energy and the self-consistency equations for the overlaps (order parameters of the theory), which turn out to be classical weighted sums of 'sub-overlaps' defined on all possible sub-graphs. Finally, a study of criticality is performed through a small-overlap expansion of the self-consistencies and through a whole fluctuation theory developed for their rescaled correlations: Both approaches show that the net effect of dilution in pattern entries is to rescale the critical noise level at which ergodicity breaks down.Comment: 34 pages, 3 figure

How glassy are neural networks?

In this paper we continue our investigation on the high storage regime of a neural network with Gaussian patterns. Through an exact mapping between its partition function and one of a bipartite spin glass (whose parties consist of Ising and Gaussian spins respectively), we give a complete control of the whole annealed region. The strategy explored is based on an interpolation between the bipartite system and two independent spin glasses built respectively by dichotomic and Gaussian spins: Critical line, behavior of the principal thermodynamic observables and their fluctuations as well as overlap fluctuations are obtained and discussed. Then, we move further, extending such an equivalence beyond the critical line, to explore the broken ergodicity phase under the assumption of replica symmetry and we show that the quenched free energy of this (analogical) Hopfield model can be described as a linear combination of the two quenched spin-glass free energies even in the replica symmetric framework

Equilibrium statistical mechanics on correlated random graphs

Biological and social networks have recently attracted enormous attention between physicists. Among several, two main aspects may be stressed: A non trivial topology of the graph describing the mutual interactions between agents exists and/or, typically, such interactions are essentially (weighted) imitative. Despite such aspects are widely accepted and empirically confirmed, the schemes currently exploited in order to generate the expected topology are based on a-priori assumptions and in most cases still implement constant intensities for links. Here we propose a simple shift in the definition of patterns in an Hopfield model to convert frustration into dilution: By varying the bias of the pattern distribution, the network topology -which is generated by the reciprocal affinities among agents - crosses various well known regimes (fully connected, linearly diverging connectivity, extreme dilution scenario, no network), coupled with small world properties, which, in this context, are emergent and no longer imposed a-priori. The model is investigated at first focusing on these topological properties of the emergent network, then its thermodynamics is analytically solved (at a replica symmetric level) by extending the double stochastic stability technique, and presented together with its fluctuation theory for a picture of criticality. At least at equilibrium, dilution simply decreases the strength of the coupling felt by the spins, but leaves the paramagnetic/ferromagnetic flavors unchanged. The main difference with respect to previous investigations and a naive picture is that within our approach replicas do not appear: instead of (multi)-overlaps as order parameters, we introduce a class of magnetizations on all the possible sub-graphs belonging to the main one investigated: As a consequence, for these objects a closure for a self-consistent relation is achieved.Comment: 30 pages, 4 figure

Quantum Phase Interference in Magnetic Molecular Clusters

The Landau Zener model has recently been used to measure very small tunnel splittings in molecular clusters of Fe8, which at low temperature behaves like a nanomagnet with a spin ground state of S = 10. The observed oscillations of the tunnel splittings as a function of the magnetic field applied along the hard anisotropy axis are due to topological quantum interference of two tunnel paths of opposite windings. Transitions between quantum numbers M = -S and (S - n), with n even or odd, revealed a parity effect which is analogous to the suppression of tunnelling predicted for half integer spins. This observation is the first direct evidence of the topological part of the quantum spin phase (Berry or Haldane phase) in a magnetic system. We show here that the quantum interference can also be measured by ac susceptibility measurements in the thermal activated regime.Comment: 3 pages, 2 figures, conference proceedings of LT22 (Helsinki, Finland, August 4-11, 199

Criticality in diluted ferromagnet

We perform a detailed study of the critical behavior of the mean field diluted Ising ferromagnet by analytical and numerical tools. We obtain self-averaging for the magnetization and write down an expansion for the free energy close to the critical line. The scaling of the magnetization is also rigorously obtained and compared with extensive Monte Carlo simulations. We explain the transition from an ergodic region to a non trivial phase by commutativity breaking of the infinite volume limit and a suitable vanishing field. We find full agreement among theory, simulations and previous results.Comment: 23 pages, 3 figure