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E. Marinari

Publications and source records attributed to E. Marinari.

At least 55 records · Page 3Linked to original sources
arXiv2012

Thermodynamic glass transition in a spin glass without time-reversal symmetry

Spin glasses are a longstanding model for the sluggish dynamics that appears at the glass transition. However, spin glasses differ from structural glasses for a crucial feature: they enjoy a time reversal symmetry. This symmetry can be broken by applying an external magnetic field, but embarrassingly little is known about the critical behaviour of a spin glass in a field. In this context, the space dimension is crucial. Simulations are easier to interpret in a large number of dimensions, but one must work below the upper critical dimension (i.e., in d<6) in order for results to have relevance for experiments. Here we show conclusive evidence for the presence of a phase transition in a four-dimensional spin glass in a field. Two ingredients were crucial for this achievement: massive numerical simulations were carried out on the Janus special-purpose computer, and a new and powerful finite-size scaling method.

cond-mat.dis-nn↗
arXiv2011

Sample-to-sample fluctuations of the overlap distributions in the three-dimensional Edwards-Anderson spin glass

We study the sample-to-sample fluctuations of the overlap probability densities from large-scale equilibrium simulations of the three-dimensional Edwards-Anderson spin glass below the critical temperature. Ultrametricity, Stochastic Stability and Overlap Equivalence impose constraints on the moments of the overlap probability densities that can be tested against numerical data. We found small deviations from the Ghirlanda-Guerra predictions, which get smaller as system size increases. We also focus on the shape of the overlap distribution, comparing the numerical data to a mean-field-like prediction in which finite-size effects are taken into account by substituting delta functions with broad peaks

cond-mat.dis-nn↗
arXiv2010

Static versus dynamic heterogeneities in the D = 3 Edwards-Anderson-Ising spin glass

We numerically study the aging properties of the dynamical heterogeneities in the Ising spin glass. We find that a phase transition takes place during the aging process. Statics-dynamics correspondence implies that systems of finite size in equilibrium have static heterogeneities that obey Finite-Size Scaling, thus signaling an analogous phase transition in the thermodynamical limit. We compute the critical exponents and the transition point in the equilibrium setting, and use them to show that aging in dynamic heterogeneities can be described by a Finite-Time Scaling Ansatz, with potential implications for experimental work.

cond-mat.dis-nn↗
arXiv2010

Nature of the spin-glass phase at experimental length scales

We present a massive equilibrium simulation of the three-dimensional Ising spin glass at low temperatures. The Janus special-purpose computer has allowed us to equilibrate, using parallel tempering, L=32 lattices down to T=0.64 Tc. We demonstrate the relevance of equilibrium finite-size simulations to understand experimental non-equilibrium spin glasses in the thermodynamical limit by establishing a time-length dictionary. We conclude that non-equilibrium experiments performed on a time scale of one hour can be matched with equilibrium results on L=110 lattices. A detailed investigation of the probability distribution functions of the spin and link overlap, as well as of their correlation functions, shows that Replica Symmetry Breaking is the appropriate theoretical framework for the physically relevant length scales. Besides, we improve over existing methodologies to ensure equilibration in parallel tempering simulations.

cond-mat.dis-nn↗
arXiv2010

Critical Behavior of Three-Dimensional Disordered Potts Models with Many States

We study the 3D Disordered Potts Model with p=5 and p=6. Our numerical simulations (that severely slow down for increasing p) detect a very clear spin glass phase transition. We evaluate the critical exponents and the critical value of the temperature, and we use known results at lower $p$ values to discuss how they evolve for increasing p. We do not find any sign of the presence of a transition to a ferromagnetic regime.

cond-mat.dis-nn↗
arXiv2010

The solution space of metabolic networks: producibility, robustness and fluctuations

Flux analysis is a class of constraint-based approaches to the study of biochemical reaction networks: they are based on determining the reaction flux configurations compatible with given stoichiometric and thermodynamic constraints. One of its main areas of application is the study of cellular metabolic networks. We briefly and selectively review the main approaches to this problem and then, building on recent work, we provide a characterization of the productive capabilities of the metabolic network of the bacterium E.coli in a specified growth medium in terms of the producible biochemical species. While a robust and physiologically meaningful production profile clearly emerges (including biomass components, biomass products, waste etc.), the underlying constraints still allow for significant fluctuations even in key metabolites like ATP and, as a consequence, apparently lay the ground for very different growth scenarios.

q-bio.MN↗
arXiv2009

A Non-Disordered Glassy Model with a Tunable Interaction Range

We introduce a non-disordered lattice spin model, based on the principle of minimizing spin-spin correlations up to a (tunable) distance R. The model can be defined in any spatial dimension D, but already for D=1 and small values of R (e.g. R=5) the model shows the properties of a glassy system: deep and well separated energy minima, very slow relaxation dynamics, aging and non-trivial fluctuation-dissipation ratio.

cond-mat.dis-nn↗
arXiv2009

Optimal flux states, reaction replaceability and response to knockouts in the human red blood cell

Characterizing the capabilities, criticalities and response to perturbations of genome-scale metabolic networks is a basic problem with important applications. A key question concerns the identification of the potentially most harmful knockouts. The integration of combinatorial methods with sampling techniques to explore the space of viable flux states may provide crucial insights on this issue. We assess the replaceability of every metabolic conversion in the human red blood cell by enumerating the alternative paths from substrate to product, obtaining a complete map of the potential damage of single enzymopathies. Sampling the space of optimal flux states in the healthy and in the mutated cell reveals both correlations and complementarity between topologic and dynamical aspects.

q-bio.MN↗
arXiv2009

Identifying essential genes in E. coli from a metabolic optimization principle

Understanding the organization of reaction fluxes in cellular metabolism from the stoichiometry and the topology of the underlying biochemical network is a central issue in systems biology. In this task, it is important to devise reasonable approximation schemes that rely on the stoichiometric data only, because full-scale kinetic approaches are computationally affordable only for small networks (e.g. red blood cells, about 50 reactions). Methods commonly employed are based on finding the stationary flux configurations that satisfy mass-balance conditions for metabolites, often coupling them to local optimization rules (e.g. maximization of biomass production) to reduce the size of the solution space to a single point. Such methods have been widely applied and have proven able to reproduce experimental findings for relatively simple organisms in specific conditions. Here we define and study a constraint-based model of cellular metabolism where neither mass balance nor flux stationarity are postulated, and where the relevant flux configurations optimize the global growth of the system. In the case of E. coli, steady flux states are recovered as solutions, though mass-balance conditions are violated for some metabolites, implying a non-zero net production of the latter. Such solutions furthermore turn out to provide the correct statistics of fluxes for the bacterium E. coli in different environments and compare well with the available experimental evidence on individual fluxes. Conserved metabolic pools play a key role in determining growth rate and flux variability. Finally, we are able to connect phenomenological gene essentiality with `frozen' fluxes (i.e. fluxes with smaller allowed variability) in E. coli metabolism.

q-bio.MN↗
arXiv2008

The Spin Glass Phase in the Four-State, Three-Dimensional Potts Model

We perform numerical simulations, including parallel tempering, on the Potts glass model with binary random quenched couplings using the JANUS application-oriented computer. We find and characterize a glassy transition, estimating the location of the transition and the value of the critical exponents. We show that there is no ferromagnetic transition in a large temperature range around the glassy critical temperature. We also compare our results with those obtained recently on the "random permutation" Potts glass.

cond-mat.dis-nn↗
arXiv2008

An in-depth view of the microscopic dynamics of Ising spin glasses at fixed temperature

Using the dedicated computer Janus, we follow the nonequilibrium dynamics of the Ising spin glass in three dimensions for eleven orders of magnitude. The use of integral estimators for the coherence and correlation lengths allows us to study dynamic heterogeneities and the presence of a replicon mode and to obtain safe bounds on the Edwards-Anderson order parameter below the critical temperature. We obtain good agreement with experimental determinations of the temperature-dependent decay exponents for the thermoremanent magnetization. This magnitude is observed to scale with the much harder to measure coherence length, a potentially useful result for experimentalists. The exponents for energy relaxation display a linear dependence on temperature and reasonable extrapolations to the critical point. We conclude examining the time growth of the coherence length, with a comparison of critical and activated dynamics.

cond-mat.dis-nn↗
arXiv2008

Nonequilibrium spin glass dynamics from picoseconds to 0.1 seconds

We study numerically the nonequilibrium dynamics of the Ising Spin Glass, for a time that spans eleven orders of magnitude, thus approaching the experimentally relevant scale (i.e. {\em seconds}). We introduce novel analysis techniques that allow to compute the coherence length in a model-independent way. Besides, we present strong evidence for a replicon correlator and for overlap equivalence. The emerging picture is compatible with non-coarsening behavior.

cond-mat.dis-nn↗
arXiv2008

Critical properties of the four-state Commutative Random Permutation Glassy Potts model in three and four dimensions

We investigate the critical properties of the four-state commutative random permutation glassy Potts model in three and four dimensions by means of Monte Carlo simulation and of a finite size scaling analysis. Thanks to the use of a field programmable gate array we have been able to thermalize a large number of samples of systems with large volume. This has allowed us to observe a spin-glass ordered phase in d=4 and to study the critical properties of the transition. In d=3, our results are consistent with the presence of a Kosterlitz-Thouless transition, but we cannot exclude transient effects due to a value of the lower critical dimension slightly below 3.

cond-mat.dis-nn↗
arXiv2008

JANUS: an FPGA-based System for High Performance Scientific Computing

This paper describes JANUS, a modular massively parallel and reconfigurable FPGA-based computing system. Each JANUS module has a computational core and a host. The computational core is a 4x4 array of FPGA-based processing elements with nearest-neighbor data links. Processors are also directly connected to an I/O node attached to the JANUS host, a conventional PC. JANUS is tailored for, but not limited to, the requirements of a class of hard scientific applications characterized by regular code structure, unconventional data manipulation instructions and not too large data-base size. We discuss the architecture of this configurable machine, and focus on its use on Monte Carlo simulations of statistical mechanics. On this class of application JANUS achieves impressive performances: in some cases one JANUS processing element outperfoms high-end PCs by a factor ~ 1000. We also discuss the role of JANUS on other classes of scientific applications.

cs.AR↗
arXiv2007

Finite size corrections in the Sherrington-Kirkpatrick model

We argue that when the number of spins $N$ in the SK model is finite, the Parisi scheme can be terminated after $K$ replica-symmetry breaking steps, where $K(N) \propto N^{1/6}$. We have checked this idea by Monte Carlo simulations: we expect the typical number of peaks and features $R$ in the (non-bond averaged) Parisi overlap function $P_J(q)$ to be of order $2K(N)$, and our counting (for samples of size $N$ up to 4096 spins) gives results which are consistent with our arguments. We can estimate the leading finite size correction for any thermodynamic quantity by finding its $K$ dependence in the Parisi scheme and then replacing $K$ by K(N). Our predictions of how the Edwards-Anderson order parameter and the internal energy of the system approach their thermodynamic limit compare well with the results of our Monte Carlo simulations. The $N$-dependence of the sample-to-sample fluctuations of thermodynamic quantities can also be obtained; the total internal energy should have sample-to-sample fluctuations of order $N^{1/6}$, which is again consistent with the results of our numerical simulations.

cond-mat.dis-nn↗
arXiv2007

Simulating spin systems on IANUS, an FPGA-based computer

We describe the hardwired implementation of algorithms for Monte Carlo simulations of a large class of spin models. We have implemented these algorithms as VHDL codes and we have mapped them onto a dedicated processor based on a large FPGA device. The measured performance on one such processor is comparable to O(100) carefully programmed high-end PCs: it turns out to be even better for some selected spin models. We describe here codes that we are currently executing on the IANUS massively parallel FPGA-based system.

cond-mat.dis-nn↗
arXiv2006

Strong universality and algebraic scaling in two-dimensional Ising spin glasses

At zero temperature, two-dimensional Ising spin glasses are known to fall into several universality classes. Here we consider the scaling at low but non-zero temperature and provide numerical evidence that $η\approx 0$ and $ν\approx 3.5$ in all cases, suggesting a unique universality class. This algebraic (as opposed to exponential) scaling holds in particular for the $\pm J$ model, with or without dilutions and for the plaquette diluted model. Such a picture, associated with an exceptional behavior at T=0, is consistent with a real space renormalization group approach. We also explain how the scaling of the specific heat is compatible with the hyperscaling prediction.

cond-mat.dis-nn↗