Search

In the vicinity of the deconfinement transition the behaviour of the interquark potential can be precisely predicted using the Effective String Theory (EST). If the transition is continuous we can combine EST results with a conformal perturbation analysis and reach the degree of precision needed to detect the corrections beyond the Nambu-Goto approximation in the EST. We discuss in detail this issue in the case of the deconfinement transition of the SU(2) gauge theory in $(2+1)$ dimensions (which belongs to the same universality class of the 2d Ising model) by means of an extensive set of high precision simulations. We show that the Polyakov loops correlator of the SU(2) model is precisely described by the spin-spin correlator of the 2d Ising model not only at the critical point, but also down to temperatures of the order of $0.8 T_c$. Thanks to the exact integrability of the Ising model we can extend the comparison in the whole range of Polyakov loop separations, even beyond the conformal perturbation regime. We use these results to quantify the first EST correction beyond Nambu-Goto and show that it is compatible with the bounds imposed by a bootstrap analysis of EST. This correction encodes important physical information and may shed light on the nature of the flux tube and of its EST description., Comment: 9 pages, 1 pdf figure, to appear in the proceedings of the 38th International Symposium on Lattice Field Theory "LATTICE21" (26.-30.07.2021, Zoom/Gather@Massachusetts Institute of Technology)

Electro-optical detection has proven to be a valuable technique to study temporal profiles of THz pulses with pulse durations down to femtoseconds. As the Coulomb field around a relativistic electron bunch resembles the current profile, electro-optical detection can be exploited for non-invasive bunch length measurements at accelerators. We have developed a very compact and robust electro-optical detection system based on spectral decoding for bunch length monitoring at the European XFEL with single-shot resolution better than 200~fs. Apart from the GaP crystal and the corresponding laser optics at the electron beamline, all components are housed in 19\" chassis for rack mount and remote operation inside the accelerator tunnel. An advanced laser synchronization scheme based on radio-frequency down-conversion has been developed for locking a custom-made Yb-fiber laser to the radio-frequency of the European XFEL accelerator. In order to cope with the high bunch repetition rate of the superconducting accelerator, a novel linear array detector (KALYPSO) has been employed for spectral measurements of the Yb-fiber laser pulses at frame rates of up to 2.26~MHz. In this paper, we describe all sub-systems of the electro-optical detection system as well as the measurement procedure in detail, and discuss first measurement results of longitudinal bunch profiles of around 400~fs (rms) with an arrival-time jitter of 35~fs (rms).

Conformal perturbation theory is a powerful tool to describe the behavior of statistical-mechanics models and quantum field theories in the vicinity of a critical point. In the past few years, it has been extensively used to describe two-dimensional models and recently has also been extended to three-dimensional models. We show here that it can also be used to describe the behavior of four-dimensional lattice gauge theories in the vicinity of a critical point. As an example, we discuss the two-point correlator of Polyakov loops close to the thermal deconfinement transition of $SU(2)$ Yang-Mills theory. We show that the short-distance behavior of this correlation function (and, thus, of the interquark potential) is described very well by conformal perturbation theory. This method is expected to work with a similarly high accuracy for all critical points in the same universality class, including, in particular, the critical endpoint in the QCD phase diagram., Comment: 10 pages, 2 figures. Talk presented at the Quark Confinement and the Hadron Spectrum XIII conference (Confinement 2018), Maynooth, Ireland, August 2018, Reference updated

Multi-pixel fast silicon detectors represent the enabling technology for the next generation of space-borne experiments devoted to high-resolution spectral-timing studies of low-flux compact cosmic sources. Several imaging detectors based on frame-integration have been developed as focal plane devices for X-ray space-borne missions but, when coupled to large-area concentrator X-ray optics, these detectors are affected by strong pile-up and dead-time effects, thus limiting the time and energy resolution as well as the overall system sensitivity. The current technological gap in the capability to realize pixelated silicon detectors for soft X-rays with fast, photon-by-photon response and nearly Fano-limited energy resolution therefore translates into the unavailability of sparse read-out sensors suitable for high throughput X-ray astronomy applications. In the framework of the ReDSoX Italian collaboration, we developed a new, sparse read-out, pixelated silicon drift detector which operates in the energy range 0.5-15 keV with nearly Fano-limited energy resolution ($\leq$150 eV FWHM @ 6 keV) at room temperature or with moderate cooling ($\sim$0 {\deg}C to +20 {\deg}C). In this paper, we present the design and the laboratory characterization of the first 16-pixel (4$\times$4) drift detector prototype (PixDD), read-out by individual ultra low-noise charge sensitive preamplifiers (SIRIO) and we discuss the future PixDD prototype developments., Comment: Accepted for publication in Journal of Instrumentation (JINST) on 29th August 2018

We propose a general method for the numerical evaluation of OPE coefficients in three dimensional Conformal Field Theories based on the study of the conformal perturbation of two point functions in the vicinity of the critical point. We test our proposal in the three dimensional Ising Model, looking at the magnetic perturbation of the $<\sigma (\mathbf {r})\sigma(0)>$, $<\sigma (\mathbf {r})\epsilon(0)>$ and $<\epsilon (\mathbf {r})\epsilon(0)>$ correlators from which we extract the values of $C^{\sigma}_{\sigma\epsilon}=1.07(3)$ and $C^{\epsilon}_{\epsilon\epsilon}=1.45(30)$. Our estimate for $C^{\sigma}_{\sigma\epsilon}$ agrees with those recently obtained using conformal bootstrap methods, while $C^{\epsilon}_{\epsilon\epsilon}$, as far as we know, is new and could be used to further constrain conformal bootstrap analyses of the 3d Ising universality class., Comment: 4 pages, typos corrected, a few references added

We model long range correlations of nucleotides in the human DNA sequence using the long range one dimensional Ising model. We show that for distances between $10^3$ and $10^6$ bp the correlations show an universal behaviour and may be described by the non-mean field limit of the long range 1d Ising model. This allows us to make some testable hypothesis on the nature of the interaction between distant portions of the DNA chain which led to the DNA structure that we observe today in higher eukaryotes., Comment: 15 pages, 6 figures. Substantial changes in sect. 4.2. Some clarifications and comments added throughout the paper. Journal version

We investigate the properties of the twist line defect in the critical 3d Ising model using Monte Carlo simulations. In this model the twist line defect is the boundary of a surface of frustrated links or, in a dual description, the Wilson line of the Z2 gauge theory. We test the hypothesis that the twist line defect flows to a conformal line defect at criticality and evaluate numerically the low-lying spectrum of anomalous dimensions of the local operators which live on the defect as well as mixed correlation functions of local operators in the bulk and on the defect., Comment: 20 pages, 9 figures, Latex2e

We study the boundary contribution to the low energy effective action of the open string describing the confining flux tube in gauge theories. The form of the boundary terms is strongly constrained by the requirement of Lorentz symmetry, which is spontaneously broken by the formation of a long confining flux tube in the vacuum. Writing the boundary action as an expansion in the derivatives of the Nambu-Goldstone modes describing the transverse fluctuations of the string, we single out and put in a closed form the first few Lorentz invariant boundary terms. We also evaluate the leading deviation from the Nambu-Goto string produced by the boundary action on the vacuum expectation value of the Wilson loop and we test this prediction in the 3d Ising gauge model. Our simulation attains a level of precision which is sufficient to test the contribution of this term., Comment: 17 pages, 5 figures, LateX 2e. V2: Final version published on JHEP. Fixed typos in eq.s 2.2, 2.3, 3.7, 3.8, A.4. Extended explanation of the procedures used in sec 2 to determine the possible boundary terms up to field redefinitions and of the procedure used in sec 4 to take the continuum limit. V3: typos corrected in eq.s (4.3) (4.5) and (4.6), acknowledgements added

We propose a new approach to the study of the inter-quark potential in Lattice Gauge Theories. Instead of looking at the expectation value of Polyakov loop correlators we study the modifications induced in the chromoelectric flux by the presence of the Polyakov loops. In abelian LGTs, thanks to duality, this study can be performed in a very efficient way, allowing to reach high precision with a reasonable CPU cost. The major advantage of this numerical strategy is that it allows to eliminate the dominant effective string correction to the inter-quark potential (the Luscher term) thus giving an unique opportunity to test higher order corrections. Performing a set of simulations in the 3d gauge Ising model we were thus able to precisely identify and measure both the quartic and the sextic effective string corrections to the inter-quark potential. While the quartic term perfectly agrees with the Nambu-Goto one the sextic term is definitely different. Our result seems to disagree with the recent proof by Aharony and Karzbrun of the universality of the sextic correction. We discuss a few possible explanations of this disagreement. The numerical approach described above can also be applied to the study of Wilson loops. In this case, the numerical results are precise enough to test the two-loop prediction of the Nambu-Goto action. The two-loop NG result computed time ago by by Dietz and Filk is incompatible with the data; however, after correcting some mistakes in their expression, compatibility is restored. The viability of a first-order, operatorial description of the Wilson loop is also pointed out., Comment: 7 pages, 1 figures, proceedings of the XXVIII Int'l Symposium on Lattice Field Theory (Lattice2010), June 14-19 2010, Villasimius (Sardinia), Italy

We propose a new approach to the study of the interquark potential in Lattice Gauge Theories. Instead of looking at the expectation value of Polyakov loop correlators we study the modifications induced in the chromoelectric flux by the presence of the Polyakov loops. In abelian LGTs, thanks to duality, this study can be performed in a very efficient way, allowing to reach high precision at a reasonable CPU cost. The major advantage of this strategy is that it allows to eliminate the dominant effective string correction to the interquark potential (the Luscher term) thus giving an unique opportunity to test higher order corrections. Performing a set of simulations in the 3d gauge Ising model we were thus able to precisely identify and measure both the quartic and the sextic effective string corrections to the interquark potential. While the quartic term perfectly agrees with the Nambu-Goto one the sextic term is definitely different. Our result seems to disagree with the recent proof of the universality of the sextic correction. We discuss a few possible explanations of this disagreement., Comment: 22 pages, 5 figures. Comment added in the last section

We study the behaviour of the flux tube thickness in the vicinity of the deconfinement transition. We show, using effective string methods, that in this regime the square width increases linearly and not logarithmically with the interquark distance. The amplitude of this linear growth is an increasing function of the temperature and diverges as the deconfinement transition is approached from below. These predictions are in good agreement with a set of simulations performed in the 3d gauge Ising model., Comment: 16 pages, 1 figure. Revised version, with an improved discussion of the dimensional reduction approach. Accepted for publication in JHEP

In this contribution we review some recent results about the emergence of 2D integrable systems in 3D Lattice Gauge Theories near the deconfinement transition. We focus on some concrete examples involving the flux tube thickness, the ratio of k-string tensions and Polyakov loops correlators in various models., Comment: 8 pages, Poster contribution to the XXVII International Symposium on Lattice Field Theory, July 26-31, 2009, Peking University, Beijing, China

We study the fractal properties of interfaces in the 2d Ashkin-Teller model. The fractal dimension of the symmetric interfaces is calculated along the critical line of the model in the interval between the Ising and the four-states Potts models. Using Schramm's formula for crossing probabilities we show that such interfaces can not be related to the simple SLE$_\kappa$, except for the Ising point. The same calculation on non-symmetric interfaces is performed at the four-states Potts model: the fractal dimension is compatible with the result coming from Schramm's formula, and we expect a simple SLE$_\kappa$ in this case., Comment: Final version published in JSTAT. 13 pages, 5 figures. Substantial changes in the data production, analysis and in the conclusions. Added a section about the crossing probability. Typeset with 'iopart'

It has been recently argued that the depletion attraction may play an important role in different aspects of the cellular organization, ranging from the organization of transcriptional activity in transcription factories to the formation of the nuclear bodies. In this paper we suggest a new application of these ideas in the context of the splicing process, a crucial step of messanger RNA maturation in Eukaryotes. We shall show that entropy effects and the resulting depletion attraction may explain the relevance of the aspecific intron length variable in the choice of the splice-site recognition modality. On top of that, some qualitative features of the genome architecture of higher Eukaryotes can find an evolutionary realistic motivation in the light of our model., Comment: 15 pages, 6 figures. Extended version, accepted for publication in Physical Biology

We study the flux tube thickness of a generic Lattice Gauge Theory near the deconfining phase transition. It is well known that the effective string model predicts a logarithmic increase of the flux tube thickness as a function of the interquark distance for any confining LGT at zero temperature. It is perhaps less known that this same model predicts a linear increase in the vicinity of the deconfinement transition. We present a precise derivation of this result and compare it with a set of high precision simulations in the case of the 3d gauge Ising model., Comment: 20 pages, 4 figures, minor changes. Accepted for publication in JHEP

Analyzing the properties of duplicate genes during evolution is useful to understand the development of new cell functions. The yeast S. cerevisiae is a useful testing ground for this problem, because its duplicated genes with different evolutionary birth and destiny are well distinguishable. In particular, there is a clear detection for the occurrence of a Whole Genome Duplication (WGD) event in S. cerevisiae, and the genes derived from this event (WGD paralogs) are known. We studied WGD and non-WGD duplicates by two parallel analysis based on structural protein domains and on Gene Ontology annotation scheme respectively. The results show that while a large number of ``duplicable'' structural domains is shared in local and global duplications, WGD and non-WGD paralogs tend to have different functions. The reason for this is the existence of WGD and non-WGD specific domains with largely different functions. In agreement with the recent findings of Wapinski and collaborators (Nature 449, 2007), WGD paralogs often perform ``core'' cell functions, such as translation and DNA replication, while local duplications associate with ``peripheral'' functions such as response to stress. Our results also support the fact that domain architectures are a reliable tool to detect homology, as the domains of duplicates are largely invariant with date and nature of the duplication, while their sequences and also their functions might migrate., Comment: 19 pages, 5 figures, Supporting Information

Specific binding of proteins to DNA is one of the most common ways in which gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a simple recognition code, therefore the prediction of DNA target sequences is not straightforward. DNA-protein interactions can be studied using computational methods which can complement the current experimental methods and offer some advantages. In the present work we use physical effective potentials to evaluate the DNA-protein binding affinities for the lambda repressor-DNA complex for which structural and thermodynamic experimental data are available. The effect of conformational sampling by Molecular Dynamics simulations on the computed binding energy is assessed; results show that this effect is in general negative and the reproducibility of the experimental values decreases with the increase of simulation time considered. The free energy of binding for non-specific complexes agrees with earlier theoretical suggestions. Moreover, as a results of these analyses, we propose a protocol for the prediction of DNA-binding target sequences. The possibility of searching regulatory elements within the bacteriophage-lambda genome using this protocol is explored. Our analysis shows good prediction capabilities, even in the absence of any thermodynamic data and information on the naturally recognized sequence. This study supports the conclusion that physics-based methods can offer a completely complementary methodology to sequence-based methods for the identification of DNA-binding protein target sequences., Comment: 35 pages,8 figures

We compare the predictions of the Nambu-Goto effective string model with a set of high precision Monte Carlo results for interfaces with periodic boundary conditions in the 3D Ising model. We compute the free energy in the covariant gauge exactly, up to the inclusion of the Liouville mode. The perturbative expansion of this result agrees both with the result evaluated several years ago by Dietz and Filk in the physical gauge and with a recent calculation with the Polchinski-Strominger action. We also derive the effective string spectrum which, because of the different boundary conditions, is very different from the well known one of Arvis. Taking into proper account the effective string corrections and exploiting some technical improvements in the simulations we obtain precise estimate of the amplitude ratios T_c/\sqrt{sigma}, m_{0++}/\sqrt{\sigma} and sigma xi_{2nd}^2. We also discuss the behaviour of the effective string free energy in the dimensional reduction limit (i.e., near the deconfinement transition of the dual 3d gauge Ising model) and its relationship with the 2d Ising model interfaces, Comment: 7 pages, 2 figures. Talk given by M. Caselle at The XXV International Symposium on Lattice Field Theory, July 30 - August 4 2007, Regensburg

Comparative genomics methods are widely used to aid the functional annotation of non coding DNA regions. However, aligning non coding sequences requires new algorithms and strategies, in order to take into account extensive rearrangements and turnover during evolution. Here we present a novel large scale alignment strategy which aims at drawing a precise map of conserved non coding regions between genomes, even when these regions have undergone small scale rearrangments events and a certain degree of sequence variability. We applied our alignment approach to obtain a genome-wide catalogue of conserved non coding blocks (CNBs) between Drosophila melanogaster and 11 other Drosophila species. Interestingly, we observe numerous small scale rearrangement events, such as local inversions, duplications and translocations, which are not observable in the whole genome alignments currently available. The high rate of observed low scale reshuffling show that this database of CNBs can constitute the starting point for several investigations, related to the evolution of regulatory DNA in Drosophila and the in silico identification of unannotated functional elements., Comment: 12 pages, 5 figures. Talk given by L.Martignetti at the JOBIM 2007 Conference, Marseille

It was recently 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., Comment: 7 pages, Presented at the XXV International Symposium on Lattice Field Theory, July 30 - August 4 2007, Regensburg, Germany

We propose a simple effective model for the description of interfaces in 2d statistical models, based on the first-order treatment of an action corresponding to the length of the interface. The universal prediction of this model for the interface free energy agrees with the result of an exact calculation in the case of the 2d Ising model. This model appears as a dimensional reduction of the Nambu-Goto stringy description of interfaces in 3d, i.e., of the capillary wave model., Comment: 14 pages, 1 figure

We study the length distribution of a particular class of DNA sequences known as 5'UTR exons. These exons belong to the messanger RNA of protein coding genes, but they are not coding (they are located upstream of the coding portion of the mRNA) and are thus less constrained from an evolutionary point of view. We show that both in mouse and in human these exons show a very clean power law decay in their length distribution and suggest a simple evolutionary model which may explain this finding. We conjecture that this power law behaviour could indeed be a general feature of higher eukaryotes., Comment: 15 pages, 3 figures

Common fragile sites (cfs) are specific regions in the human genome that are particularly prone to genomic instability under conditions of replicative stress. Several investigations support the view that common fragile sites play a role in carcinogenesis. We discuss a genome-wide approach based on graph theory and Gene Ontology vocabulary for the functional characterization of common fragile sites and for the identification of genes that contribute to tumour cell biology. CFS were assembled in a network based on a simple measure of correlation among common fragile site patterns of expression. By applying robust measurements to capture in quantitative terms the non triviality of the network, we identified several topological features clearly indicating departure from the Erdos-Renyi random graph model. The most important outcome was the presence of an unexpected large connected component far below the percolation threshold. Most of the best characterized common fragile sites belonged to this connected component. By filtering this connected component with Gene Ontology, statistically significant shared functional features were detected. Common fragile sites were found to be enriched for genes associated to the immune response and to mechanisms involved in tumour progression such as extracellular space remodeling and angiogenesis. Our results support the hypothesis that fragile sites serve a function; we propose that fragility is linked to a coordinated regulation of fragile genes expression., Comment: 18 pages, accepted for publication in BMC Bioinformatics

We study the flux tube thickness in the confining phase of the (2+1)d SU(2) Lattice Gauge Theory near the deconfining phase transition. Following the Svetitsky-Yaffe conjecture, we map the problem to the study of the correlation function in the two-dimensional spin model with Z_2 global symmetry, (i.e. the 2d Ising model) in the high-temperature phase. Using the form factor approach we obtain an explicit expression for this function and from it we infer the behaviour of the flux density of the original (2+1)d LGT. Remarkably enough the result we obtain for the flux tube thickness agrees (a part from an overall normalization) with the effective string prediction for the same quantity., Comment: 13 pages, 4 eps figures, LaTeX; reference added

We consider the Nambu-Goto bosonic string model as a description of the physics of interfaces. By using the standard covariant quantization of the bosonic string, we derive an exact expression for the partition function in dependence of the geometry of the interface. Our expression, obtained by operatorial methods, resums the loop expansion of the NG model in the "physical gauge" computed perturbatively by functional integral methods in the literature. Recently, very accurate Monte Carlo data for the interface free energy in the 3d Ising model became avaliable. Our proposed expression compares very well to the data for values of the area sufficiently large in terms of the inverse string tension. This pattern is expected on theoretical grounds and agrees with previous analyses of other observables in the Ising model., Comment: 28 pages, 4 figures

We discuss the two- and three-point correlators in the two-dimensional three-state Potts model in the high-temperature phase of the model. By using the form factor approach and perturbed conformal field theory methods we are able to describe both the large distance and the short distance behaviours of the correlators. We compare our predictions with a set of high precision Monte-Carlo simulations (performed on the triangular lattice realization of the model) finding a complete agreement in both regimes. In particular we use the two-point correlators to fix the various non-universal constants involved in the comparison (whose determination is one of the results of our analysis) and then use these constants to compare numerical results and theoretical predictions for the three-point correlator with no free parameter. Our results can be used to shed some light on the behaviour of the three-quark correlator in the confining phase of the (2+1)-dimensional SU(3) lattice gauge theory which is related by dimensional reduction to the three-spin correlator in the high-temperature phase of the three-state Potts model. The picture which emerges is that of a smooth crossover between a \Delta type law at short distances and a Y type law at large distances., Comment: 38 pages, 13 eps figures, LaTeX

We report the results of a set of high precision simulations performed in the 3d gauge Ising model. We evaluated the interquark potential and the first few energy levels and compared them with the predictions obtained with the effective Nambu-Goto string and with the free bosonic string. The data are precise enough to unambiguously distinguish between the free string predictions and those obtained using the N-G effective string. At large distances we find a remarkable agreement between Monte Carlo data and N-G predictions for the first excited energy level, while the free string picture is definitely excluded. As the interquark distance is decreased (and/or the finite temperature becomes higher) the Monte Carlo results show larger and larger deviations both from the N-G and from the free string predictions. In order to better understand this behaviour we re-derived the effective Nambu-Goto theory result for the Polyakov loop correlator using a covariant quantization. We chose as boundary conditions those of an open string attached to two D0-branes at spatial distance $R$, in a target space with compact euclidean time. Obviously our treatment is fully consistent only in $d=26$. The extension to generic $d$ requires taking into account the Liouville mode of Polyakov's formulation. The analogy with the standard light cone calculation suggests that the contribution due to the Liouville field can be neglected for large $R$. At shorter scales, the Liouville mode cannot be neglected and its contribution to the interquark potential might be the source of the discrepancies with respect to the effective N-G results that we observe in our Monte Carlo simulations., Comment: 6 pages, 2 figures, talk presented at Lattice 2005

Using an innovative technique arising from the theory of symmetric spaces, we obtain an approximate analytic solution of the Dorokhov-Mello-Pereyra-Kumar (DMPK) equation in the insulating regime of a metallic carbon nanotube with symplectic symmetry and an odd number of conducting channels. This symmetry class is characterized by the presence of a perfectly conducting channel in the limit of infinite length of the nanotube. The derivation of the DMPK equation for this system has recently been performed by Takane, who also obtained the average conductance both analytically and numerically. Using the Jacobian corresponding to the transformation to radial coordinates and the parameterization of the transfer matrix given by Takane, we identify the ensemble of transfer matrices as the symmetric space of negative curvature SO^*(4m+2)/[SU(2m+1)xU(1)] belonging to the DIII-odd Cartan class. We rederive the leading-order correction to the conductance of the perfectly conducting channel and its variance Var(log(delta g)). Our results are in complete agreement with Takane's. In addition, our approach based on the mapping to a symmetric space enables us to obtain new universal quantities: a universal group theoretical expression for the ratio Var(log(delta g)/ and as a byproduct, a novel expression for the localization length for the most general case of a symmetric space with BC_m root system, in which all three types of roots are present., Comment: 23 pages. Text concerning symmetric space description augmented, table and references added. Version to be published on JSTAT

In this paper we re-derive the effective Nambu-Goto theory result for the Polyakov loop correlator, starting from the free bosonic string and using a covariant quantization. The boundary conditions are those of an open string attached to two D0-branes at spatial distance R, in a target space with compact euclidean time. The one-loop free energy contains topologically distinct sectors corresponding to multiple covers of the cylinder in target space bordered by the Polyakov loops. The sector that winds once reproduces exactly the Nambu-Goto partition function. In our approach, the world-sheet duality between the open and closed channel is most evident and allows for an explicit interpretation of the free energy in terms of tree level exchange of closed strings between boundary states. Our treatment is fully consistent only in d=26; extension to generic d may be justified for large R, and is supported by Montecarlo data. At shorter scales, consistency and Montecarlo data seem to suggest the necessity of taking into account the Liouville mode of Polyakov's formulation., Comment: 17 pages, 4 figures, minor corrections, a few references added, version accepted for publication in JHEP

We study the behaviour of the 2d Ising model in the symmetric high temperature phase in presence of a small magnetic perturbation. We successfully compare the quantum field theory predictions for the shift in the mass spectrum of the theory with a set of high precision transfer matrix results. Our results rule out a prediction for the same quantity obtained some years ago with strong coupling methods., Comment: 16 pages, 1 eps figure

We report on a very accurate measurement of the static quark potential in SU(2) Yang-Mills theory in (2+1) dimensions in order to study the corrections to the linear behaviour. We perform numerical simulations at zero and finite temperature comparing our results with the corrections given by the effective string picture in these two regimes. We also check for universal features discussing our results together with those recently published for the (2+1)-d Z(2) and SU(3) pure gauge theories., Comment: 29 pages, 6 figures

We study the Polyakov loop correlator in the (2+1) dimensional Z_2 gauge model. An algorithm that we have presented recently, allows us to reach high precision results for a large range of distances and temperatures, giving us the opportunity to test predictions of the effective Nambu-Goto string model. Here we focus on the regime of low temperatures and small distances. In contrast to the high temperature, large distance regime, we find that our numerical results are not well described by the two loop-prediction of the Nambu-Goto model. In addition we compare our data with those for the SU(2) and SU(3) gauge models in (2+1) dimensions obtained by other authors. We generalize the result of L\"uscher and Weisz for a boundary term in the interquark potential to the finite temperature case., Comment: 38 pages, 7 figures, version accepted for publication in JHEP

We discuss the effective string picture for the confining regime of lattice gauge theories at zero and finite temperature. We present results of extensive Monte Carlo simulations - performed with the Luscher and Weisz algorithm - for SU(2) Yang-Mills theory in 2+1 dimensions. We also address the issue of "string universality" by comparing our results with those obtained in other lattice gauge theories., Comment: 3 pages, 2 figures, Lattice2003(topology)

We propose a new class of universal amplitude ratios which involve the first terms of the short distance expansion of the correlators of a statistical model in the vicinity of a critical point. We will describe the critical system with a conformal field theory (UV fixed point) perturbed by an appropriate relevant operator. In two dimensions the exact knowledge of the UV fixed point allows for accurate predictions of the ratios and in many nontrivial integrable perturbations they can even be evaluated exactly. In three dimensional O(N) scalar systems feasible extensions of some existing results should allow to obtain perturbative expansions for the ratios. By construction these universal ratios are a perfect tool to explore the short distance properties of the underlying quantum field theory even in regimes where the correlation length and one point functions are not accessible in experiments or simulations., Comment: 8 pages, revised version, references added

Gene regulation in Eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory elements in the upstream region of Eukaryotic genes. The genes are grouped in sets sharing an overrepresented short motif in their upstream sequence. For each set, the average expression level from a microarray experiment is determined: if this level is significantly higher or lower than the average taken over the whole genome, then the overrepresented motif shared by the genes in the set is likely to play a role in their regulation. We illustrate the method by applying it to the genome of {\it S. cerevisiae}, for which many datasets of microarray experiments are publicly available. Several known binding motifs are correctly recognized by our algorithm, and a new candidate is suggested for experimental verification., Comment: 7 pages, 2 figures

In this review we discuss the relationship between random matrix theories and symmetric spaces. We show that the integration manifolds of random matrix theories, the eigenvalue distribution, and the Dyson and boundary indices characterizing the ensembles are in strict correspondence with symmetric spaces and the intrinsic characteristics of their restricted root lattices. Several important results can be obtained from this identification. In particular the Cartan classification of triplets of symmetric spaces with positive, zero and negative curvature gives rise to a new classification of random matrix ensembles. The review is organized into two main parts. In Part I the theory of symmetric spaces is reviewed with particular emphasis on the ideas relevant for appreciating the correspondence with random matrix theories. In Part II we discuss various applications of symmetric spaces to random matrix theories and in particular the new classification of disordered systems derived from the classification of symmetric spaces. We also review how the mapping from integrable Calogero--Sutherland models to symmetric spaces can be used in the theory of random matrices, with particular consequences for quantum transport problems. We conclude indicating some interesting new directions of research based on these identifications., Comment: 161 pages, LaTeX, no figures. Revised version with major additions in the second part of the review. Version accepted for publication on Physics Reports

We introduce and discuss a new class of solutions of the DMPK equation in which some of the eigenvalues are grouped into clusters which are conserved in the asymptotic large distance limit (i.e. as the length of the wire increases). We give an explicit expression for the asymptotic expansion of these solutions and suggest some possible applications. In particular these new solution could be useful to avoid the quasi one dimensional constraint in the DMPK equation and to study the crossover between the metallic and insulating phases., Comment: 13 pages. Enlarged version, with a detailed introduction to the method and new applications. To appear in J.Phys. C

We compare the predictions of the effective string description of confinement with a set of Montecarlo data for the 3d gauge Ising model at finite temperature. Thanks to a new algorithm which makes use of the dual symmetry of the model we can reach very high precisions even for large quark-antiquark distances. We are thus able to explore the large R regime of the effective string. We find that for large enough distances and low enough temperature the data are well described by a pure bosonic string. As the temperature increases higher order corrections become important and cannot be neglected even at large distances. These higher order corrections seem to be well described by the Nambu-Goto action truncated at the first perturbative order., Comment: 49 pages, 8 figures. Added a section on the performances of the algorithm

We compare the predictions of the effective string description of confinement in finite temperature gauge theories to high precision Monte Carlo data for the three-dimensional Z(2) gauge theory. We show that string interaction effects become more relevant as the temperature is increased towards the deconfinement one, and are well modeled by a Nambu-Goto string action., Comment: Lattice2002(nonzerot)

We study the finite size corrections for the magnetization and the internal energy of the 2d Ising model in a magnetic field by using transfer matrix techniques. We compare these corrections with the functional form recently proposed by Delfino and LeClair-Mussardo for the finite temperature behaviour of one-point functions in integrable 2d quantum field theories. We find a perfect agreement between theoretical expectations and numerical results. Assuming the proposed functional form as an input in our analysis we obtain a relevant improvement in the precision of the continuum limit estimates of both quantities., Comment: 16 pages, LaTex, no figures, v2: references added, to appear in Nucl. Phys. B

Gene regulation in eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory elements in the upstream region of eukaryotic genes. The genes are grouped in sets sharing an overrepresented short motif in their upstream sequence. For each set, the average expression level from a microarray experiment is determined: If this level is significantly higher or lower than the average taken over the whole genome, then the overerpresented motif shared by the genes in the set is likely to play a role in their regulation. The method was tested by applying it to the genome of Saccharomyces cerevisiae, using the publicly available results of a DNA microarray experiment, in which expression levels for virtually all the genes were measured during the diauxic shift from fermentation to respiration. Several known motifs were correctly identified, and a new candidate regulatory sequence was determined., Comment: Published version available from http://www.biomedcentral.com/1471-2105/3/7

We discuss two new approaches to extract relevant biological information on the Transcription Factors (and in particular to identify their binding sequences) from the statistical distribution of oligonucleotides in the upstream region of the genes. Both the methods are based on the notion of a ``regulatory network'' responsible for the various expression patterns of the genes. In particular we concentrate on families of coregulated genes and look for the simultaneous presence in the upstream regions of these genes of the same set of transcription factor binding sites. We discuss two instances which well exemplify the features of the two methods: the coregulation of glycolysis in Drosophila melanogaster and the diauxic shift in Saccharomyces cerevisiae., Comment: 12 pages. Contribution to the proceedings of the International Workshop ``Modelling Bio-medical signals'', Bari, September 2001