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Chromatin loop extrusion is a popular model for the formation of CTCF loops and topological domains. Recent HiC data have revealed a strong bias in favour of a particular arrangement of the CTCF binding motifs that stabilize loops, and extrusion is the only model to date which can explain this. However, the model requires a motor to generate the loops, and although cohesin is a strong candidate for the extruding factor, a suitable motor protein (or a motor activity in cohesin itself) has yet to be found. Here we explore a new hypothesis: that there is no motor, and thermal motion within the nucleus drives extrusion. Using theoretical modelling and computer simulations we ask whether such diffusive extrusion could feasibly generate loops. Our simulations uncover an interesting ratchet effect (where an osmotic pressure promotes loop growth), and suggest, by comparison to recent in vitro and in vivo measurements, that diffusive extrusion can in principle generate loops of the size observed in the data. Extra View on : C. A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi, P. R. Cook, and D. Marenduzzo "Non-equilibrium chromosome looping via molecular slip-links", Physical Review Letters 119, 138101 (2017), Comment: 7 pages, 3 figures

We propose a model for the formation of chromatin loops based on the diffusive sliding of a DNA-bound factor which can dimerise to form a molecular slip-link. Our slip-links mimic the behaviour of cohesin-like molecules, which, along with the CTCF protein, stabilize loops which organize the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable non-equilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favour of convergent CTCF-mediated chromosome loops observed experimentally. Importantly, our model does not require any underlying, and energetically costly, motor activity of cohesin. We also find that the diffusive motion of multiple slip-links along chromatin may be rectified by an intriguing ratchet effect that arises if slip-links bind to the chromatin at a preferred "loading site". This emergent collective behaviour is driven by a 1D osmotic pressure which is set up near the loading point, and favours the extrusion of loops which are much larger than the ones formed by single slip-links., Comment: 37 pages, 12 figures, Supplementary Movies can be downloaded at http://www2.ph.ed.ac.uk/~dmarendu/Cohesin/SMX.mp4; with X=1, 2 or 3

In multicellular organisms, epithelial cells form layers separating compartments responsible for different physiological functions. At the early stage of epithelial layer formation, each cell of an aggregate defines an inner and an outer side by breaking the symmetry of its initial state, in a process known as epithelial polarization. By integrating recent biochemical and biophysical data with stochastic simulations of the relevant reaction-diffusion system we provide evidence that epithelial cell polarization is a chemical phase separation process induced by a local bistability in the signaling network at the level of the cell membrane. The early symmetry breaking event triggering phase separation is induced by adhesion-dependent mechanical forces localized in the point of convergence of cell surfaces when a threshold number of confluent cells is reached. The generality of the emerging phase separation scenario is likely common to many processes of cell polarity formation., Comment: 7 pages, 6 figures

The non-equilibrium transition from a fluid-like state to a disordered solid-like state, known as the jamming transition, occurs in a wide variety of physical systems, such as colloidal suspensions and molecular fluids, when the temperature is lowered or the density increased. Shear stress, as temperature, favors the fluid-like state, and must be also considered to define the system 'jamming phase diagram' [1-4]. Frictionless athermal systems [1], for instance, can be described by the zero temperature plane of the jamming diagram in the temperature, density, stress space. Here we consider the jamming of athermal frictional systems [8-13] such as granular materials, which are important to a number of applications from geophysics to industry. At constant volume and applied shear stress[1, 2], we show that while in absence of friction a system is either fluid-like or jammed, in the presence of friction a new region in the density shear-stress plane appears, where new dynamical regimes are found. In this region a system may slip, or even flow with a steady velocity for a long time in response to an applied stress, but then eventually jams. Jamming in non-thermal frictional systems is described here by a phase diagram in the density, shear-stress and friction space.

At the onset of X Chromosomes Inactivation, the vital process whereby female mammal cells equalize X products with respect to males, the X chromosomes are colocalized along their Xic (X-Inactivation Center) regions. The mechanism inducing recognition and pairing of the X's remains, though, elusive. Starting from recent discoveries on the molecular factors and on the DNA sequences (the so-called ``pairing sites'') involved, we dissect the mechanical basis of Xic colocalization by using a Statistical Physics model. We show that soluble DNA specific binding molecules, as those experimentally identified, can be indeed sufficient to induce the spontaneous colocalization of the homologous chromosomes, but only when their concentration, or chemical affinity, rises above a threshold value, as a consequence of a thermodynamic phase transition. We derive the likelihood of pairing and its probability distribution. Chromosome dynamics has two stages: an initial independent Brownian diffusion followed, after a characteristic time scale, by recognition and pairing. Finally, we investigate the effects of DNA deletion/insertions in the region of pairing sites and compare model predictions to available experimental data.

A general model for the early recognition and colocalization of homologous DNA sequences is proposed. We show, on a thermodynamic ground, how the distance between two homologous DNA sequences is spontaneously regulated by the concentration and affinity of diffusible mediators binding them, which act as a switch between two phases corresponding to independence or colocalization of pairing regions.

In mammals, dosage compensation of X linked genes in female cells is achieved by inactivation of one of their two X chromosomes which is randomly chosen. The earliest steps in X-inactivation (XCI), namely the mechanism whereby cells count their X chromosomes and choose between two equivalent X, remain mysterious. Starting from the recent discovery of X chromosome colocalization at the onset of X-inactivation, we propose a Statistical Mechanics model of XCI, which is investigated by computer simulations and checked against experimental data. Our model describes how a `blocking factor' complex is self-assembled and why only one is formed out of many diffusible molecules, resulting in a spontaneous symmetry breaking (SB) in the binding to two identical chromosomes. These results are used to derive a scenario of biological implications describing all current experimental evidences, e.g., the importance of colocalization., Comment: See also Nature Physics N&V April 2007

In order to characterize landslide frequency-size distributions and individuate hazard scenarios and their possible precursors, we investigate a cellular automaton where the effects of a finite driving rate and the anisotropy are taken into account. The model is able to reproduce observed features of landslide events, such as power-law distributions, as experimentally reported. We analyze the key role of the driving rate and show that, as it is increased, a crossover from power-law to non power-law behaviors occurs. Finally, a systematic investigation of the model on varying its anisotropy factors is performed and the full diagram of its dynamical behaviors is presented., Comment: 8 pages, 9 figures

Landslide inventories show that the statistical distribution of the area of recorded events is well described by a power law over a range of decades. To understand these distributions, we consider a cellular automaton to model a time and position dependent factor of safety. The model is able to reproduce the complex structure of landslide distribution, as experimentally reported. In particular, we investigate the role of the rate of change of the system dynamical variables, induced by an external drive, on landslide modeling and its implications on hazard assessment. As the rate is increased, the model has a crossover from a critical regime with power-laws to non power-law behaviors. We suggest that the detection of patterns of correlated domains in monitored regions can be crucial to identify the response of the system to perturbations, i.e., for hazard assessment., Comment: 4 pages, 3 figures

Earthquakes and solar flares are phenomena involving huge and rapid releases of energy characterized by complex temporal occurrence. By analysing available experimental catalogs, we show that the stochastic processes underlying these apparently different phenomena have universal properties. Namely both problems exhibit the same distributions of sizes, inter-occurrence times and the same temporal clustering: we find afterflare sequences with power law temporal correlations as the Omori law for seismic sequences. The observed universality suggests a common approach to the interpretation of both phenomena in terms of the same driving physical mechanism.

We present extensive Molecular Dynamics simulations on species segregation in a granular mixture subject to vertical taps. We discuss how grain properties, e.g., size, density, friction, as well as, shaking properties, e.g., amplitude and frequency, affect such a phenomenon. Both Brazil Nut Effect (larger particles on the top, BN) and the Reverse Brazil Nut Effect (larger particles on the bottom, RBN) are found and we derive the system comprehensive ``segregation diagram'' and the BN to RBN crossover line. We also discuss the role of friction and show that particles which differ only for their frictional properties segregate in states depending on the tapping acceleration and frequency., Comment: Physical Review Letters, in press

In order to study analytically the nature of the size segregation in granular mixtures, we introduce a mean field theory in the framework of a statistical mechanics approach, based on Edwards' original ideas. For simplicity we apply the theory to a lattice model for hard sphere binary mixture under gravity, and we find a new purely thermodynamic mechanism which gives rise to the size segregation phenomenon. By varying the number of small grains and the mass ratio, we find a crossover from Brasil nut to reverse Brasil nut effect, which becomes a true phase transition when the number of small grains is larger then a critical value. We suggest that this transition is induced by the effective attraction between large grains due to the presence of small ones (depletion force). Finally the theoretical results are confirmed by numerical simulations of the 3d system under taps., Comment: Submitted to Phys. Rev. Lett

In order to study analytically the nature of the jamming transition in granular material, we have considered a cavity method mean field theory, in the framework of a statistical mechanics approach, based on Edwards' original idea. For simplicity we have applied the theory to a lattice model and a transition with exactly the same nature of the glass transition in mean field models for usual glass formers is found. The model is also simulated in three dimensions under tap dynamics and a jamming transition with glassy features is observed. In particular two step decays appear in the relaxation functions and dynamic heterogeneities resembling ones usually observed in glassy systems. These results confirm early speculations about the connection between the jamming transition in granular media and the glass transition in usual glass formers, giving moreover a precise interpretation of its nature., Comment: 11 pages, 12 figures

We discuss mixing/segregation phenomena in a schematic hard spheres lattice model for binary mixtures of granular media, by analytical evaluation, within Bethe-Peierls approximation, of Edwards' partition function. The presence of fluid-crystal phase transitions in the system drives segregation as a form of phase separation. Within a pure phase, gravity can also induce a kind of vertical segregation not associated to phase transitions.

In the framework of schematic hard spheres lattice models we discuss Edwards' Statistical Mechanics approach to granular media. As this approach appears to hold here to a very good approximation, by analytical calculations of Edwards' partition function at a mean field level we derive the system phase diagram and show that ``jamming'' corresponds to a phase transition from a ``fluid'' to a ``glassy'' phase, observed when crystallization is avoided. The nature of such a ``glassy'' phase turns out to be the same found in mean field models for glass formers. In the same context, we also briefly discuss mixing/segregation phenomena of binary mixtures: the presence of fluid-crystal phase transitions drives segregation as a form of phase separation and, within a given phase, gravity can also induce a kind of ``vertical'' segregation, usually not associated to phase transitions., Comment: Contribution to the volume "Unifying Concepts in Granular Media and Glasses", edt.s A. Coniglio, A. Fierro, H. J. Herrmann and M. Nicodemi

We study the equilibrium and dynamical properties of a spherical version of the frustrated Blume-Emery-Griffiths model at mean field level for attractive particle-particle coupling (K>0). Beyond a second order transition line from a paramagnetic to a (replica symmetric) spin glass phase, the density-temperature phase diagram is characterized by a tricritical point from which, interestingly, a first order transition line starts with coexistence of the two phases. In the Langevin dynamics the paramagnetic/spin glass discontinuous transition line is found to be dependent on the initial density; close to this line, on the paramagnetic side, the correlation-response plot displays interrupted aging., Comment: to be published on Europhysics Letters

In the framework of schematic hard spheres lattice models for granular media we investigate the phenomenon of the ``jamming transition''. In particular, using Edwards' approach, by analytical calculations at a mean field level, we derive the system phase diagram and show that ``jamming'' corresponds to a phase transition from a ``fluid'' to a ``glassy'' phase, observed when crystallization is avoided. Interestingly, the nature of such a ``glassy'' phase turns out to be the same found in mean field models for glass formers., Comment: 7 pages, 4 figures

We introduce a spherical version of the frustrated Blume-Emery-Griffiths model and solve exactly the statics and the Langevin dynamics for zero particle-particle coupling (K=0). In this case the model exhibits an equilibrium transition from a disordered to a spin glass phase which is always continuous for nonzero temperature. The same phase diagram results from the study of the dynamics. Furthermore, we notice the existence of a nonequilibrium time regime in a region of the disordered phase, characterized by aging as occurs in the spin glass phase. Due to a finite equilibration time, the system displays in this region the pattern of interrupted aging., Comment: 19 pages, 8 figures

Reply to the comment, cond-mat/0209398 by by N.W. Watkins, S.C. Chapman, and G. Rowlands, Comment: To appear In Physical Review Letters

We reply to the comment on our published paper `` Universal Fluctuations in Correlated Systems'',Phys. Rev. Lett. Vol; 84, p3744 (2000), by B. Zheng and S. Trimper, cond-mat/0109003. We argue that their results confirm our conjecture, that the probability distribution for order parameter fluctuations in the 2D and 3D Ising models at a temperature $T^{\ast}(L)$ slightly below $T_C$ for the infinite, system approximates the universal functional form of the 2D-XY model in its low temperature phase. We discuss the relevance of the temperature interval $T_C-T^{\ast}$, considered to be large by Zheng and Trimper and explain why the observed phenomena is a critical phenomena., Comment: 1 page, no figures. To appear in Phys. Rev. Lett

The probability density function (PDF) of a global measure in a large class of highly correlated systems has been suggested to be of the same functional form. Here, we identify the analytical form of the PDF of one such measure, the order parameter in the low temperature phase of the 2D-XY model. We demonstrate that this function describes the fluctuations of global quantities in other correlated, equilibrium and non-equilibrium systems. These include a coupled rotor model, Ising and percolation models, models of forest fires, sand-piles, avalanches and granular media in a self organized critical state. We discuss the relationship with both Gaussian and extremal statistics., Comment: 4 pages, 2 figures

We study vortex clustering in type II Superconductors. We demonstrate that the ``second peak'' observed in magnetisation loops may be a dynamical effect associated with a density driven instability of the vortex system. At the microscopic level the instability shows up as the clustering of individual vortices at (rare) preferential regions of the pinning potential. In the limit of quasi-static ramping the instability is related to a phase transition in the equilibrium vortex system., Comment: 11 pages + 3 figures

In the present paper, we analyze the consequences of scaling hypotheses on dynamic functions, as two times correlations $C(t,t')$. We show, under general conditions, that $C(t,t')$ must obey the following scaling behavior $C(t,t') = \phi_1(t)^{f(\beta)}{\cal{S}}(\beta)$, where the scaling variable is $\beta=\beta(\phi_1(t')/\phi_1(t))$ and $\phi_1(t')$, $\phi_1(t)$ two undetermined functions. The presence of a non constant exponent $f(\beta)$ signals the appearance of multiscaling properties in the dynamics., Comment: 6 pages, no figures

We study the phenomenon of internal avalanching within the context of recently introduced lattice models of granular media. The avalanche is produced by pulling out a grain at the base of the packing and studying how many grains have to rearrange before the packing is once more stable. We find that the avalanches are long-ranged, decaying as a power-law. We study the distriution of avalanches as a function of the density of the packing and find that the avalanche distribution is a very sensitive structural probe of the system., Comment: 12 pages including 9 eps figures, LaTeX. To appear in Fractals

We propose a two-dimensional geometrical model, based on the concept of geometrical frustration, conceived for the study of compaction in granular media. The dynamics exhibits an interesting inverse logarithmic law that is well known from real experiments. Moreover we present a simple dynamical model of $N$ planes exchanging particles with excluded volume problems, which allows to clarify the origin of the logarithmic relaxations and the stationary density distribution. A simple mapping allows us to cast this Tetris-like model in the form of an Ising-like spin systems with vacancies., Comment: 4 pages, Latex including 2 PS figures (reference corrected). Subm. to Phys. Rev. Lett. (1997)

A general scheme for devising efficient cluster dynamics proposed in a previous letter [Phys.Rev.Lett. 72, 1541 (1994)] is extensively discussed. In particular the strong connection among equilibrium properties of clusters and dynamic properties as the correlation time for magnetization is emphasized. The general scheme is applied to a number of frustrated spin model and the results discussed., Comment: 17 pages LaTeX + 16 figures; will appear in Phys. Rev. E