arXiv subjects

Michele Caselle

Publications and source records attributed to Michele Caselle.

At least 91 records · Page 5Linked to original sources

arXiv2012

Thermodynamics of SU(N) Yang-Mills theories in 2+1 dimensions II - The deconfined phase

We present a non-perturbative study of the equation of state in the deconfined phase of Yang-Mills theories in D=2+1 dimensions. We introduce a holographic model, based on the improved holographic QCD model, from which we derive a non-trivial relation between the order of the deconfinement phase transition and the behavior of the trace of the energy-momentum tensor as a function of the temperature T. We compare the theoretical predictions of this holographic model with a new set of high-precision numerical results from lattice simulations of SU(N) theories with N=2, 3, 4, 5 and 6 colors. The latter reveal that, similarly to the D=3+1 case, the bulk equilibrium thermodynamic quantities (pressure, trace of the energy-momentum tensor, energy density and entropy density) exhibit nearly perfect proportionality to the number of gluons, and can be successfully compared with the holographic predictions in a broad range of temperatures. Finally, we also show that, again similarly to the D=3+1 case, the trace of the energy-momentum tensor appears to be proportional to T^2 in a wide temperature range, starting from approximately 1.2 T_c, where T_c denotes the critical deconfinement temperature.

hep-th↗

arXiv2011

The role of incoherent microRNA-mediated feedforward loops in noise buffering

MicroRNAs are endogenous non-coding RNAs which negatively regulate the expression of protein-coding genes in plants and animals. They are known to play an important role in several biological processes and, together with transcription factors, form a complex and highly interconnected regulatory network. Looking at the structure of this network it is possible to recognize a few overrepresented motifs which are expected to perform important elementary regulatory functions. Among them a special role is played by the microRNA-mediated feedforward loop in which a master transcription factor regulates a microRNA and, together with it, a set of target genes. In this paper we show analytically and through simulations that the incoherent version of this motif can couple the fine-tuning of a target protein level with an efficient noise control, thus conferring precision and stability to the overall gene expression program, especially in the presence of fluctuations in upstream regulators. Among the other results, a nontrivial prediction of our model is that the optimal attenuation of fluctuations coincides with a modest repression of the target expression. This feature is coherent with the expected fine-tuning function and in agreement with experimental observations of the actual impact of a wide class of microRNAs on the protein output of their targets. Finally we describe the impact on noise-buffering efficiency of the cross-talk between microRNA targets that can naturally arise if the microRNA-mediated circuit is not considered as isolated, but embedded in a larger network of regulations.

q-bio.MN↗

arXiv2011

Thermodynamics of SU(N) Yang-Mills theories in 2+1 dimensions I - The confining phase

We compute the equation of state in the confining phase of SU(N) Yang-Mills theories with N=2, 3, 4, 5 and 6 colors in 2+1 dimensions, via lattice simulations. At low enough temperatures, the results are accurately described by a gas of glueballs, including all known states below the two-particle threshold. Close to the deconfinement temperature, however, this prediction underestimates the numerical results, and the contribution from heavier glueballs has to be included. We show that the spectral density of the latter can be accurately described using a simple bosonic string model.

hep-lat↗

arXiv2011

Universal signatures of the effective string in finite temperature lattice gauge theories

We study the behaviour of the interquark potential in lattice gauge theories at high temperature, but still in the confining phase, and propose a new observable which could play in this regime the same role played by the Luscher term in the low temperature limit. This quantity is related to the exponent of the power prefactor in the effective string partition function or, equivalently, to the coefficient of the logarithmic correction in the interquark potential and, as for the usual Luscher term, its value does not depend on the particular gauge group under consideration or on the form of the effective string action used to model the flux tube. In this respect it can be considered as a universal signature of the effective string behaviour of the flux tube. As a test of our proposal we studied this quantity with a set of high-precision numerical simulations in the (2+1) dimensional SU(2), SU(3) and SU(4) Yang-Mills theories and in the Z_2 gauge model, always finding a perfect agreement with the predicted values.

hep-lat↗

arXiv2010

Thermodynamics of SU(N) gauge theories in 2+1 dimensions in the $T <\ T_c$ regime

We present Monte Carlo results for the thermodynamics of pure SU(N) gauge theories with $N=2,...,6$ in 2+1 dimensions. We focus on the confined phase region $T<T_c$ and study thermodynamics variables such as the trace of the energy-momentum tensor, pressure, energy and entropy density using the integral method. We also investigate scaling properties with $N$ of the different observables. We compare our results with a gas of free glueballs and the bosonic string predictions for the Hagedorn spectrum.

hep-lat↗

arXiv2010

Nucleation dynamics in 2d cylindrical Ising models and chemotaxis

The aim of our work is to study the effect of geometry variation on nucleation times and to address its role in the context of eukaryotic chemotaxis (i.e. the process which allows cells to identify and follow a gradient of chemical attractant). As a first step in this direction we study the nucleation dynamics of the 2d Ising model defined on a cylindrical lattice whose radius changes as a function of time. Geometry variation is obtained by changing the relative value of the couplings between spins in the compactified (vertical) direction with respect to the horizontal one. This allows us to keep the lattice size unchanged and study in a single simulation the values of the compactification radius which change in time. We show, both with theoretical arguments and numerical simulations that squeezing the geometry allows the system to speed up nucleation times even in presence of a very small energy gap between the stable and the metastable states. We then address the implications of our analysis for directional chemotaxis. The initial steps of chemotaxis can be modelled as a nucleation process occurring on the cell membrane as a consequence of the external chemical gradient (which plays the role of energy gap between the stable and metastable phases). In nature most of the cells modify their geometry by extending quasi-onedimensional protrusions (filopodia) so as to enhance their sensitivity to chemoattractant. Our results show that this geometry variation has indeed the effect of greatly decreasing the timescale of the nucleation process even in presence of very small amounts of chemoattractants.

cond-mat.stat-mech↗

arXiv2009

Genome-Wide Survey of MicroRNA - Transcription Factor Feed-Forward Regulatory Circuits in Human

In this work, we describe a computational framework for the genome-wide identification and characterization of mixed transcriptional/post-transcriptional regulatory circuits in humans. We concentrated in particular on feed-forward loops (FFL), in which a master transcription factor regulates a microRNA, and together with it, a set of joint target protein coding genes. The circuits were assembled with a two step procedure. We first constructed separately the transcriptional and post-transcriptional components of the human regulatory network by looking for conserved over-represented motifs in human and mouse promoters, and 3'-UTRs. Then, we combined the two subnetworks looking for mixed feed-forward regulatory interactions, finding a total of 638 putative (merged) FFLs. In order to investigate their biological relevance, we filtered these circuits using three selection criteria: (I) GeneOntology enrichment among the joint targets of the FFL, (II) independent computational evidence for the regulatory interactions of the FFL, extracted from external databases, and (III) relevance of the FFL in cancer. Most of the selected FFLs seem to be involved in various aspects of organism development and differentiation. We finally discuss a few of the most interesting cases in detail.

q-bio.GN↗

arXiv2007

K-string tensions at finite temperature and integrable models

It has recently been pointed out that simple scaling properties of Polyakov correlation functions of gauge systems in the confining phase suggest that the ratios of k-string tensions in the low temperature region is constant up to terms of order T^3. Here we argue that, at least in a three-dimensional Z_4 gauge model, the above ratios are constant in the whole confining phase. This result is obtained by combining numerical experiments with known exact results on the mass spectrum of an integrable two-dimensional spin model describing the infrared behaviour of the gauge system near the deconfining transition.

hep-lat↗

arXiv2007

The interface free energy: Comparison of accurate Monte Carlo results for the 3D Ising model with effective interface models

We provide accurate Monte Carlo results for the free energy of interfaces with periodic boundary conditions in the 3D Ising model. We study a large range of inverse temperatures, allowing to control corrections to scaling. In addition to square interfaces, we study rectangular interfaces for a large range of aspect ratios u=L_1/L_2. Our numerical results are compared with predictions of effective interface models. This comparison verifies clearly the effective Nambu-Goto model up to two-loop order. Our data also allow us to obtain the estimates T_c sigma^-1/2=1.235(2), m_0++ sigma^-1/2=3.037(16) and R_+=f_+^2 sigma_0 =0.387(2), which are more precise than previous ones.

hep-lat↗

arXiv2007

Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions

3' untranslated regions (3' UTRs) contain binding sites for many regulatory elements, and in particular for microRNAs (miRNAs). The importance of miRNA-mediated post-transcriptional regulation has become increasingly clear in the last few years. We propose two complementary approaches to the statistical analysis of oligonucleotide frequencies in mammalian 3' UTRs aimed at the identification of candidate binding sites for regulatory elements. The first method is based on the identification of sets of genes characterized by evolutionarily conserved overrepresentation of an oligonucleotide. The second method is based on the identification of oligonucleotides showing statistically significant strand asymmetry in their distribution in 3' UTRs. Both methods are able to identify many previously known binding sites located in 3'UTRs, and in particular seed regions of known miRNAs. Many new candidates are proposed for experimental verification.

q-bio.GN↗

arXiv2006

High precision Monte Carlo simulations of interfaces in the three-dimensional Ising model: a comparison with the Nambu-Goto effective string model

Motivated by the recent progress in the effective string description of the interquark potential in lattice gauge theory, we study interfaces with periodic boundary conditions in the three-dimensional Ising model. Our Monte Carlo results for the associated free energy are compared with the next-to-leading order (NLO) approximation of the Nambu-Goto string model. We find clear evidence for the validity of the effective string model at the level of the NLO truncation.

hep-lat↗

arXiv2005

On the effective string spectrum of the tridimensional Z(2) gauge model

We study the Z(2) lattice gauge theory in three dimensions, and present high precision estimates for the first few energy levels of the string spectrum. These results are obtained from new numerical data for the two-point Polyakov loop correlation function, which is measured in the 3d Ising spin system using duality. This allows us to perform a stringent comparison with the predictions of effective string models. We find a remarkable agreement between the numerical estimates and the Nambu-Goto predictions for the energy gaps at intermediate and large distances. The precision of our data allows to distinguish clearly between the predictions of the full Nambu-Goto action and the simple free string model up to an interquark distance $r \approx 10/\sqrtσ$. At the same time, our results also confirm the breakdown of the effective picture at short distances, supporting the hypothesis that terms which are not taken into account in the usual Nambu-Goto string formulation yield a non-trivial shift to the energy levels. Furthermore, we discuss the theoretical implications of these results.

hep-lat↗

arXiv2005

Ab initio identification of putative human transcription factor binding sites by comparative genomics

We discuss a simple and powerful approach for the ab initio identification of cis-regulatory motifs involved in transcriptional regulation. The method we present integrates several elements: human-mouse comparison, statistical analysis of genomic sequences and the concept of coregulation. We apply it to a complete scan of the human genome. By using the catalogue of conserved upstream sequences collected in the CORG database we construct sets of genes sharing the same overrepresented motif (short DNA sequence) in their upstream regions both in human and in mouse. We perform this construction for all possible motifs from 5 to 8 nucleotides in length and then filter the resulting sets looking for two types of evidence of coregulation: first, we analyze the Gene Ontology annotation of the genes in the set, searching for statistically significant common annotations; second, we analyze the expression profiles of the genes in the set as measured by microarray experiments, searching for evidence of coexpression. The sets which pass one or both filters are conjectured to contain a significant fraction of coregulated genes, and the upstream motifs characterizing the sets are thus good candidates to be the binding sites of the TF's involved in such regulation. In this way we find various known motifs and also some new candidate binding sites.

q-bio.GN↗

arXiv2005

Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrepresented upstream motifs

BACKGROUND: Transcriptional regulation is a key mechanism in the functioning of the cell, and is mostly effected through transcription factors binding to specific recognition motifs located upstream of the coding region of the regulated gene. The computational identification of such motifs is made easier by the fact that they often appear several times in the upstream region of the regulated genes, so that the number of occurrences of relevant motifs is often significantly larger than expected by pure chance. RESULTS: To exploit this fact, we construct sets of genes characterized by the statistical overrepresentation of a certain motif in their upstream regions. Then we study the functional characterization of these sets by analyzing their annotation to Gene Ontology terms. For the sets showing a statistically significant specific functional characterization, we conjecture that the upstream motif characterizing the set is a binding site for a transcription factor involved in the regulation of the genes in the set. CONCLUSIONS: The method we propose is able to identify many known binding sites in S. cerevisiae and new candidate targets of regulation by known transcription factors. Its application to less well studied organisms is likely to be valuable in the exploration of their regulatory interaction network.

q-bio.GN↗

arXiv2005

Comparing the Nambu-Goto string with LGT results

We discuss a way to evaluate the full prediction for the interquark potential which is expected from the effective Nambu-Goto string model. We check the correctness of the prescription reproducing the results obtained with the zeta function regularization for the first two perturbative orders. We compare the predictions with existing Monte Carlo data for the (2+1) dimensional Z(2), SU(2) and SU(3) gauge theories: in the low temperature regime, we find good agreement for large enough interquark distances, but an increasing mismatch between theoretical predictions and numerical results is observed as shorter and shorter distances are investigated. On the contrary, at high temperatures (approaching the deconfinement transition from below) a remarkable agreement between Monte Carlo data and the expectations from the Nambu-Goto effective string is observed for a wide range of interquark distances.

hep-lat↗

arXiv2003

Effective String Picture for Confining Gauge Theories at Finite Temperature

We study the ``effective string picture'' of confinement, deriving theoretical predictions for the interquark potential at finite temperature. At low temperatures, the leading string correction to the linear confining potential between a heavy quark-antiquark pair is the "Lüscher term''. Assuming a Nambu-Goto effective string action, subleading contributions can be worked out in an analytical way. We also discuss the contribution given by a possible ``boundary term'' in the effective action, and compare these predictions with high precision results from simulations of lattice Z(2) gauge theory in three dimensions, obtained with an algorithm that exploits the duality of the Z(2) gauge model with the Ising spin model.

hep-lat↗

arXiv2003

Effective string picture for confinement at finite temperature: theoretical predictions and high precision numerical results

The effective string picture of confinement is used to derive theoretical predictions for the interquark potential at finite temperature. At short distances, the leading string correction to the linear confining potential between a heavy quark-antiquark pair is the "Lüscher term''. We assume a Nambu--Goto effective string action, and work out subleading contributions in an analytical way. We discuss the contribution given by a possible ``boundary term'' in the effective action, comparing these predictions with results from simulations of lattice $Z_2$ gauge theory in three dimensions, obtained with an algorithm which exploits the duality of the $Z_2$ gauge model with the Ising spin model.

hep-lat↗

arXiv2001

Irrelevant operators in the two-dimensional Ising model

By using conformal-field theory, we classify the possible irrelevant operators for the Ising model on the square and triangular lattices. We analyze the existing results for the free energy and its derivatives and for the correlation length, showing that they are in agreement with the conformal-field theory predictions. Moreover, these results imply that the nonlinear scaling field of the energy-momentum tensor vanishes at the critical point. Several other peculiar cancellations are explained in terms of a number of general conjectures. We show that all existing results on the square and triangular lattice are consistent with the assumption that only nonzero spin operators are present.

cond-mat.stat-mech↗