Enzo Marinari

Sapienza University of Rome, Roma, Latium, Italy

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Publications (262)692.13 Total impact

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    ABSTRACT: We present our analysis of a system of interacting islands of XY spins on a triangular lattice that has been introduced a few years ago by Eley et al. to account for the phenomenology in experiments on tunable arrays of proximity coupled long superconductor-normal metal-superconductor junctions. The main features of the model are the separation of a local and a global interaction energy scale and the mesoscopic character of the spin islands. Upon lowering the temperature the model undergoes two crossovers corresponding to an increasing phase coherence on a single island and to the onset of global coherence across the array; the latter is a thermodynamical phase transition in the Ising universality class. The dependence of the second transition on the island edge-to-edge spacing is related to the proximity-effect of the coupling constant.
    No preview · Article · Sep 2015
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    ABSTRACT: Cancer cells utilize large amounts of ATP to sustain growth, relying primarily on non-oxidative, fermentative pathways for its production. In many types of cancers this leads, even in the presence of oxygen, to the secretion of carbon equivalents (usually in the form of lactate) in the cell's surroundings, a feature known as the Warburg effect. While the molecular basis of this phenomenon are still to be elucidated, it is clear that the spilling of energy resources contributes to creating a peculiar microenvironment for tumors, possibly characterized by a degree of toxicity. This suggests that mechanisms for recycling the fermentation products (e.g. a lactate shuttle) may be active, effectively inducing a mutually beneficial metabolic coupling between aberrant and non-aberrant cells. Here we analyze this scenario through a large-scale in silico metabolic model of interacting human cells. By going beyond the cell-autonomous description, we show that elementary physico-chemical constraints indeed favor the establishment of such a coupling under very broad conditions. The characterization we obtained by tuning the aberrant cell's demand for ATP, amino-acids and fatty acids and/or the imbalance in nutrient partitioning provides quantitative support to the idea that synergistic multi-cell effects play a central role in cancer sustainment.
    Full-text · Article · Jul 2015 · Scientific Reports
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    ABSTRACT: The quantitative description of cultural evolution is a challenging task. The most difficult part of the problem is probably to find the appropriate measurable quantities that can make more quantitative such evasive concepts as, for example, dynamics of cultural movements, behavior patterns and traditions of the people. A strategy to tackle this issue is to observe particular features of human activities, i.e. cultural traits, such as names given to newborns. We study the names of babies born in the United States of America from 1910 to 2012. Our analysis shows that groups of different correlated states naturally emerge in different epochs, and we are able to follow and decrypt their evolution. While these groups of states are stable across many decades, a sudden reorganization occurs in the last part of the twentieth century. We think that this kind of quantitative analysis can be possibly extended to other cultural traits: although databases covering more than one century (as the one we used) are rare, the cultural evolution on shorter time scales can be studied thanks to the fact that many human activities are usually recorded in the present digital era.
    Full-text · Article · Oct 2014 · Proceedings of the National Academy of Sciences
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    Chiara Cammarota · Enzo Marinari
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    ABSTRACT: The description of activated relaxation of glassy systems in the multidimensional configurational space is a long-standing open problem. We develop a phenomenological description of the out-of-equilibrium dynamics of a model with a rough potential energy landscape and we analyse it both numerically and analytically. The model provides an example of dynamics where typical relaxation channels go over finite potential energy barriers despite the presence of less-energy-demanding escaping paths in configurational space; we expect this phenomenon to be also relevant in the thermally activated regime of realistic models of glass-formers. In this case, we found that typical dynamical paths episodically reach an high fixed threshold energy unexpectedly giving rise to a simple thermally activated aging phenomenology. In order to unveil this peculiar aging behavior we introduce a novel description of the dynamics in terms of spontaneously emerging dynamical basins.
    Preview · Article · Oct 2014 · Physical Review E
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    ABSTRACT: We use a sample-dependent analysis, based on medians and quantiles, to analyze the behavior of the overlap probability distribution of the Sherrington-Kirkpatrick and $3D$ Edwards-Anderson models of Ising spin glasses. We find that this approach is an effective tool to distinguish between replica symmetry breaking\char21{}like and droplet-like behavior of the spin-glass phase. Our results are in agreement with a replica symmetry breaking\char21{}like behavior for the $3D$ Edwards-Anderson model.
    Full-text · Article · Jun 2014 · Physical Review B
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    ABSTRACT: We perform equilibrium parallel-tempering simulations of the 3D Ising Edwards-Anderson spin glass in a field. A traditional analysis shows no signs of a phase transition. Yet, we encounter dramatic fluctuations in the behaviour of the model: Averages over all the data only describe the behaviour of a small fraction of it. Therefore we develop a new approach to study the equilibrium behaviour of the system, by classifying the measurements as a function of a conditioning variate. We propose a finite-size scaling analysis based on the probability distribution function of the conditioning variate, which may accelerate the convergence to the thermodynamic limit. In this way, we find a non-trivial spectrum of behaviours, where a part of the measurements behaves as the average, while the majority of them shows signs of scale invariance. As a result, we can estimate the temperature interval where the phase transition in a field ought to lie, if it exists. Although this would-be critical regime is unreachable with present resources, the numerical challenge is finally well posed.
    Full-text · Article · Mar 2014 · Journal of Statistical Mechanics Theory and Experiment
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    ABSTRACT: We study the off-equilibrium dynamics of the three-dimensional Ising spin glass in the presence of an external magnetic field. We have performed simulations both at fixed temperature and with an annealing protocol. Thanks to the Janus special-purpose computer, based on field-programmable gate array (FPGAs), we have been able to reach times equivalent to 0.01 s in experiments. We have studied the system relaxation both for high and for low temperatures, clearly identifying a dynamical transition point. This dynamical temperature is strictly positive and depends on the external applied magnetic field. We discuss different possibilities for the underlying physics, which include a thermodynamical spin-glass transition, a mode-coupling crossover, or an interpretation reminiscent of the random first-order picture of structural glasses.
    Full-text · Article · Mar 2014 · Physical Review E
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    Matteo Figliuzzi · Andrea De Martino · Enzo Marinari
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    ABSTRACT: The observation that, through a titration mechanism, microRNAs (miRNAs) can act as mediators of effective interactions among their common targets (competing endogenous RNAs or ceRNAs) has brought forward the idea ('ceRNA hypothesis') that RNAs can regulate each other in extended 'cross-talk' networks. Such an ability might play a major role in post-transcriptional regulation (PTR) in shaping a cell's protein repertoire. Recent work focusing on the emergent properties of the cross-talk networks has emphasized the high flexibility and selectivity that may be achieved at stationarity. On the other hand, dynamical aspects, possibly crucial on the relevant time scales, are far less clear. We have carried out a dynamical study of the ceRNA hypothesis on a model of PTR. Sensitivity analysis shows that ceRNA cross-talk is dynamically extended, i.e. it may take place on time scales shorter than those required to achieve stationairity even in cases where no cross-talk occurs in the steady state, and is possibly amplified. Besides, in case of large, transfection-like perturbations the system may develop strongly non-linear, threshold response. Finally, we show that the ceRNA effect provides a very efficient way for a cell to achieve fast positive shifts in the level of a ceRNA when necessary. These results indicate that competition for miRNAs may indeed provide an elementary mechanism to achieve system-level regulatory effects on the transcriptome over physiologically relevant time scales.
    Full-text · Article · Dec 2013 · Biophysical Journal
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    Full-text · Dataset · Oct 2013
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    ABSTRACT: Thermodynamics constrains the flow of matter in a reaction network to occur through routes along which the Gibbs energy decreases, implying that viable steady-state flux patterns should be void of closed reaction cycles. Identifying and removing cycles in large reaction networks can unfortunately be a highly challenging task from a computational viewpoint. We propose here a method that accomplishes it by combining a relaxation algorithm and a Monte Carlo procedure to detect loops, with ad hoc rules (discussed in detail) to eliminate them. As test cases, we tackle (a) the problem of identifying infeasible cycles in the E. coli metabolic network and (b) the problem of correcting thermodynamic infeasibilities in the Flux-Balance-Analysis solutions for 15 human cell-type specific metabolic networks. Results for (a) are compared with previous analyses of the same issue, while results for (b) are weighed against alternative methods to retrieve thermodynamically viable flux patterns based on minimizing specific global quantities. Our method on one hand outperforms previous techniques and, on the other, corrects loopy solutions to Flux Balance Analysis. As a byproduct, it also turns out to be able to reveal possible inconsistencies in model reconstructions.
    Full-text · Article · Oct 2013
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    ABSTRACT: The energetics of cerebral activity critically relies on the functional and metabolic interactions between neurons and astrocytes. Important open questions include the relation between neuronal versus astrocytic energy demand, glucose uptake and intercellular lactate transfer, as well as their dependence on the level of activity. We have developed a large-scale, constraint-based network model of the metabolic partnership between astrocytes and glutamatergic neurons that allows for a quantitative appraisal of the extent to which stoichiometry alone drives the energetics of the system. We find that the velocity of the glutamate-glutamine cycle (Vcyc) explains part of the uncoupling between glucose and oxygen utilization at increasing Vcyc levels. Thus, we are able to characterize different activation states in terms of the tissue oxygen-glucose index (OGI). Calculations show that glucose is taken up and metabolized according to cellular energy requirements, and that partitioning of the sugar between different cell types is not significantly affected by Vcyc. Furthermore, both the direction and magnitude of the lactate shuttle between neurons and astrocytes turn out to depend on the relative cell glucose uptake while being roughly independent of Vcyc. These findings suggest that, in absence of ad hoc activity-related constraints on neuronal and astrocytic metabolism, the glutamate-glutamine cycle does not control the relative energy demand of neurons and astrocytes, and hence their glucose uptake and lactate exchange.
    Full-text · Article · Oct 2013 · BMC Systems Biology
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    ABSTRACT: We report a high-precision finite-size scaling study of the critical behavior of the three-dimensional Ising Edwards-Anderson model (the Ising spin glass). We have thermalized lattices up to L=40 using the Janus dedicated computer. Our analysis takes into account leading-order corrections to scaling. We obtain Tc = 1.1019(29) for the critical temperature, \nu = 2.562(42) for the thermal exponent, \eta = -0.3900(36) for the anomalous dimension and \omega = 1.12(10) for the exponent of the leading corrections to scaling. Standard (hyper)scaling relations yield \alpha = -5.69(13), \beta = 0.782(10) and \gamma = 6.13(11). We also compute several universal quantities at Tc.
    Full-text · Article · Oct 2013 · Physical Review B
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    ABSTRACT: This paper describes the architecture, the development and the implementation of Janus II, a new generation application-driven number cruncher optimized for Monte Carlo simulations of spin systems (mainly spin glasses). This domain of computational physics is a recognized grand challenge of high-performance computing: the resources necessary to study in detail theoretical models that can make contact with experimental data are by far beyond those available using commodity computer systems. On the other hand, several specific features of the associated algorithms suggest that unconventional computer architectures, which can be implemented with available electronics technologies, may lead to order of magnitude increases in performance, reducing to acceptable values on human scales the time needed to carry out simulation campaigns that would take centuries on commercially available machines. Janus II is one such machine, recently developed and commissioned, that builds upon and improves on the successful JANUS machine, which has been used for physics since 2008 and is still in operation today. This paper describes in detail the motivations behind the project, the computational requirements, the architecture and the implementation of this new machine and compares its expected performances with those of currently available commercial systems.
    Full-text · Article · Oct 2013 · Computer Physics Communications
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    ABSTRACT: A Comment on the Letter by B. Yucesoy, H. G. Katzgraber, and J. Machta, Phys. Rev. Lett. 109, 177204 (2012). The authors of the Letter offer a Reply.
    Full-text · Article · May 2013 · Physical Review Letters
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    Matteo Figliuzzi · Enzo Marinari · Andrea De Martino
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    ABSTRACT: It has recently been suggested that the competition for a finite pool of microRNAs (miRNA) gives rise to effective interactions among their common targets (competing endogenous RNAs or ceRNAs) that could prove to be crucial for posttranscriptional regulation. We have studied a minimal model of posttranscriptional regulation where the emergence and the nature of such interactions can be characterized in detail at steady state. Sensitivity analysis shows that binding free energies and repression mechanisms are the key ingredients for the cross-talk between ceRNAs to arise. Interactions emerge in specific ranges of repression values, can be symmetrical (one ceRNA influences another and vice versa) or asymmetrical (one ceRNA influences another but not the reverse), and may be highly selective, while possibly limited by noise. In addition, we show that nontrivial correlations among ceRNAs can emerge in experimental readouts due to transcriptional fluctuations even in the absence of miRNA-mediated cross-talk.
    Full-text · Article · Mar 2013 · Biophysical Journal
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    ABSTRACT: In this chapter we describe the Janus supercomputer, a massively parallel FPGA-based system optimized for the simulation of spin-glasses, theoretical models that describe the behavior of glassy materials. The custom architecture of Janus has been developed to meet the computational requirements of these models. Spin-glass simulations are performed using Monte Carlo methods that lead to algorithms characterized by (1) intrinsic parallelism allowing us to implement many Monte Carlo update engines within a single FPGA; (2) rather small data base (2 MByte) that can be stored on-chip, significantly boosting bandwidth and reducing latency. (3) need to generate a large number of good-quality long (≥ 32 bit) random numbers; (4) mostly integer arithmetic and bitwise logic operations. Careful tailoring of the architecture to the specific features of these algorithms has allowed us to embed up to 1024 special purpose cores within just one FPGA, so that simulations of systems that would take centuries on conventional architectures can be performed in just a few months.
    No preview · Chapter · Feb 2013
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    ABSTRACT: We describe Janus, an application-driven architecture for Monte Carlo simulations of spin glasses. Janus is a massively parallel architecture, based on reconfigurable FPGA nodes; it offers two orders of magnitude better performance than commodity systems for spin glass applications. The first generation Janus machine has been operational since early 2008; we are currently developing a new generation, that will be on line in early 2013. In this paper we present the Janus architecture, describe both implementations and compare their performances with those of commodity systems.
    No preview · Conference Paper · Aug 2012
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    ABSTRACT: We describe the past and future of the Janus project. The collaboration started in 2006 and deployed in early 2008 the Janus supercomputer, a facility that allowed to speed-up Monte Carlo Simulations of a class of model glassy systems and provided unprecedented results for some paradigms in Statistical Mechanics. The Janus Supercomputer was based on state-of-the-art FPGA technology, and provided almost two order of magnitude improvement in terms of cost/performance and power/performance ratios. More than four years later, commercial facilities are closing-up in terms of performance, but FPGA technology has largely improved. A new generation supercomputer, Janus2, will be able to improve by more than one orders of magnitude with respect to the previous one, and will accordingly be again the best choice in Monte Carlo simulations of Spin Glasses for several years to come with respect to commercial solutions.
    No preview · Conference Paper · Jun 2012
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    ABSTRACT: The integration of various types of genomic data into predictive models of biological networks is one of the main challenges currently faced by computational biology. Constraint-based models in particular play a key role in the attempt to obtain a quantitative understanding of cellular metabolism at genome scale. In essence, their goal is to frame the metabolic capabilities of an organism based on minimal assumptions that describe the steady states of the underlying reaction network via suitable stoichiometric constraints, specifically mass balance and energy balance (i.e. thermodynamic feasibility). The implementation of these requirements to generate viable configurations of reaction fluxes and/or to test given flux profiles for thermodynamic feasibility can however prove to be computationally intensive. We propose here a fast and scalable stoichiometry-based method to explore the Gibbs energy landscape of a biochemical network at steady state. The method is applied to the problem of reconstructing the Gibbs energy landscape underlying metabolic activity in the human red blood cell, and to that of identifying and removing thermodynamically infeasible reaction cycles in the Escherichia coli metabolic network (iAF1260). In the former case, we produce consistent predictions for chemical potentials (or log-concentrations) of intracellular metabolites; in the latter, we identify a restricted set of loops (23 in total) in the periplasmic and cytoplasmic core as the origin of thermodynamic infeasibility in a large sample (10(6)) of flux configurations generated randomly and compatibly with the prior information available on reaction reversibility.
    Full-text · Article · Jun 2012 · PLoS Computational Biology
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    Andrea De Martino · Enzo Marinari · Andrea Romualdi
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    ABSTRACT: We review recent work on the statistical mechanics of Von Neumann's growth model and discuss its application to cellular metabolic networks. In this context, we present a detailed analysis of the physiological scenario underlying optimality a la Von Neumann in the metabolism of the bacterium Escherichia coli, showing that optimal solutions are characterized by a considerable microscopic flexibility accompanied by a robust emergent picture for the key physiological functions. This suggests that the ideas behind optimal economic growth in Von Neumann's model can be helpful in uncovering functional organization principles of cell energetics.
    Preview · Article · May 2012 · The European Physical Journal Special Topics

Publication Stats

8k Citations
692.13 Total Impact Points

Institutions

  • 1984-2015
    • Sapienza University of Rome
      • Department of Physics
      Roma, Latium, Italy
  • 1994-2012
    • Università degli studi di Cagliari
      • Department of Physics
      Cagliari, Sardinia, Italy
  • 2010
    • Universidad de Extremadura
      • Department of Electric Engineering, Electronics and Automatics
      Ara Pacis Augustalis, Extremadura, Spain
    • University of Zaragoza
      • Department of Theoretical Physics
      Caesaraugusta, Aragon, Spain
  • 1992-2007
    • Syracuse University
      • Department of Physics
      Syracuse, NY, United States
  • 1987-2007
    • Università degli Studi di Roma "Tor Vergata"
      • Dipartimento di Fisica
      Roma, Latium, Italy
  • 1998-2006
    • Università Degli Studi Roma Tre
      • Department of Mathematics and Physics
      Roma, Latium, Italy
  • 1981-2005
    • INFN - Istituto Nazionale di Fisica Nucleare
      Frascati, Latium, Italy
    • Università degli Studi del Sannio
      Benevento, Campania, Italy
    • The American University of Rome
      Roma, Latium, Italy
  • 1986
    • Università degli Studi Europea di Roma
      Roma, Latium, Italy
  • 1982
    • Brookhaven National Laboratory
      • Physics Department
      New York, New York, United States