arXiv subjects

Angelo Rosa

Publications and source records attributed to Angelo Rosa.

42 records · Page 3Linked to original sources

arXiv2013

Colocalization of coregulated genes: a steered molecular dynamics study of human chromosome 19

The connection between chromatin nuclear organization and gene activity is vividly illustrated by the observation that transcriptional coregulation of certain genes appears to be directly influenced by their spatial proximity. This fact poses the more general question of whether it is at all feasible that the numerous genes that are coregulated on a given chromosome, especially those at large genomic distances, might become proximate inside the nucleus. This problem is studied here using steered molecular dynamics simulations in order to enforce the colocalization of thousands of knowledge-based gene sequences on a model for the gene-rich human chromosome 19. Remarkably, it is found that most (~80%) gene pairs can be brought simultaneously into contact. This is made possible by the low degree of intra-chromosome entanglement and the large number of cliques in the gene coregulatory network, that is the many groups of genes that are all mutually coregulated. The constrained conformations for the model chromosome 19 are further shown to be organised in spatial macrodomains that are similar to those inferred from recent HiC measurements. The findings indicate that gene coregulation and colocalization are largely compatible and that this relationship can be exploited to draft the overall spatial organization of the chromosome in vivo. The more general validity and implications of these findings could be investigated by applying to other eukaryotic chromosomes the general and transferable computational strategy introduced here.

q-bio.GN↗

arXiv2011

Structure and dynamics of ring polymers: entanglement effects because of solution density and ring topology

The effects of entanglement in solutions and melts of unknotted ring polymers have been addressed by several theoretical and numerical studies. The system properties have been typically profiled as a function of ring contour length at fixed solution density. Here, we use a different approach to investigate numerically the equilibrium and kinetic properties of solutions of model ring polymers. Specifically, the ring contour length is maintained fixed, while the interplay of inter- and intra-chain entanglement is modulated by varying both solution density (from infinite dilution up to \approx 40 % volume occupancy) and ring topology (by considering unknotted and trefoil-knotted chains). The equilibrium metric properties of rings with either topology are found to be only weakly affected by the increase of solution density. Even at the highest density, the average ring size, shape anisotropy and length of the knotted region differ at most by 40% from those of isolated rings. Conversely, kinetics are strongly affected by the degree of inter-chain entanglement: for both unknots and trefoils the characteristic times of ring size relaxation, reorientation and diffusion change by one order of magnitude across the considered range of concentrations. Yet, significant topology-dependent differences in kinetics are observed only for very dilute solutions (much below the ring overlap threshold). For knotted rings, the slowest kinetic process is found to correspond to the diffusion of the knotted region along the ring backbone.

cond-mat.soft↗

arXiv2005

Scaling exponents and probability distributions of DNA end-to-end distance

Correlation length exponent $ν$ for long linear DNA molecules was determined by direct measurement of the average end-to-end distance as a function of the contour length $s$ by means of atomic force microscopy (AFM). Linear DNA, up to 48'502 base pairs (bp), was irreversibly deposited from a solution onto silanized mica and imaged in air. Under the adsorption conditions used, the DNA is trapped onto the surface without any two-dimensional equilibration. The measured exponent is $ν= 0.589 \pm 0.006$, in agreement with the theoretical 3D value of $ν= 0.5880 \pm 0.0010$. The persistence length $\ell_p$ of DNA was estimated to be 44$\pm$3 nm, in agreement with the literature values. The distribution of the end-to-end distances for a given contour length $s$ and the exponents characterizing the distribution were determined for different $s$. For $s$ smaller or comparable to $\ell_p$, a delta function like distribution was observed, while for larger $s$, a probability distribution of the type $x^{d-1}x^g e^{-bx^δ}$ was observed with $g=0.33\pm0.22$ and $δ=2.58\pm0.76$. These values are compared to the theoretical exponents for Self-Avoiding Walk (SAW): namely $g=\frac{γ-1}ν$ and $δ=(1-ν)^{-1}$. So for $d=2$, $g\approx0.44$ and $δ=4$, while for $d=3$, $g\approx0.33$ and $δ\approx2.5$. The derived entropic exponent $γ$ is $γ=1.194\pm0.129$. The present data indicate that the DNA behaves on large length scales like a 3 dimensional SAW.

cond-mat.soft↗

arXiv2004

Correlation function and generalized master equation of arbitrary age

We study a two-state statistical process with a non-Poisson distribution of sojourn times. In accordance with earlier work, we find that this process is characterized by aging and we study three different ways to define the correlation function of arbitrary age of the corresponding dichotomous fluctuation based respectively on the Generalized Master Equation formalism, on a Liouville-like approach and on a trajectory perspective.

cond-mat.stat-mech↗

arXiv2003

Breakdown of the Onsager principle as a sign of aging

We discuss the problem of the equivalence between Continuous Time Random Walk (CTRW) and Generalized Master Equation (GME). The walker, making instantaneous jumps from one site of the lattice to another, resides in each site for extended times. The sojourn times have a distribution psi(t) that is assumed to be an inverse power law. We assume that the Onsager principle is fulfilled, and we use this assumption to establish a complete equivalence between GME and the Montroll-Weiss CTRW. We prove that this equivalence is confined to the case when psi(t) is an exponential. We argue that is so because the Montroll-Weiss CTRW, as recently proved by Barkai [E. Barkai, Phys. Rev. Lett. 90, 104101 (2003)], is non-stationary, thereby implying aging, while the Onsager principle, is valid only in the case of fully aged systems. We consider the case of a dichotomous fluctuation, and we prove that the Onsager principle is fulfilled for any form of regression to equilibrium provided that the stationary condition holds true. We set the stationary condition on both the CTRW and the GME, thereby creating a condition of total equivalence, regardless the nature of the waiting time distribution. As a consequence of this procedure we create a GME that it is a "bona fide" master equation, in spite of being non-Markovian. We note that the memory kernel of the GME affords information on the interaction between system of interest and its bath. The Poisson case yields a bath with infinitely fast fluctuations. We argue that departing from the Poisson form has the effect of creating a condition of infinite memory and that these results might be useful to shed light into the problem of how to unravel non-Markovian master equations.

cond-mat.stat-mech↗

arXiv2002

Conflict between trajectories and density description: the statistical source of disagreement

We study an idealized version of intermittent process leading the fluctuations of a stochastic dichotomous variable $ξ$. It consists of an overdamped and symmetric potential well with a cusp-like minimum. The right-hand and left-hand portions of the potential corresponds to $ξ= W$ and $ξ= -W$, respectively. When the particle reaches this minimum is injected back to a different and randomly chosen position, still within the potential well. We build up the corresponding Frobenius-Perron equation and we evaluate the correlation function of the stochastic variable $ξ$, called $Φ_ξ(t)$. We assign to the potential well a form yielding $Φ_ξ(t) = (T/(t + T))^β$, with $β> 0$. We limit ourselves to considering correlation functions with an even number of times, indicated for concision, by $<12>$, $<1234>$ and, more, in general, by $<1 ... 2n>$. The adoption of a treatment based on density yields $<1 ... 2n > = < 1 2 > ... < (2n-1) 2n>$. We study the same dynamic problem using trajectories, and we establish that the resulting two-time correlation function coincides with that afforded by the density picture, as it should. We then study the four-times correlation function and we prove that in the non-Poisson case it departs from the density prescription, namely, from $<1234 > = < 12 > < 34>$. We conclude that this is the main reason why the two pictures yield two different diffusion processes, as noticed in an earlier work [M. Bologna, P. Grigolini, B.J. West, Chem. Phys. {\bf 284}, (1-2) 115-128 (2002)].

cond-mat.stat-mech↗