We propose a new global optimization method (Simulated Tempering) for simulating effectively a system with a rough free energy landscape (i.e. many coexisting states) at finite non-zero temperature. This method is related to simulated annealing, but here the temperature becomes a dynamic variable, and the system is always kept at equilibrium. We analyze the method on the Random Field Ising Model, and we find a dramatic improvement over conventional Metropolis and cluster methods. We analyze and discuss the conditions under which the method has optimal performances. -92-06, SCCS 241, hep-lat/9205018 ROM2F

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We discuss replica symmetry breaking (RSB) in spin glasses. We update work in this area, from both the analytical and numerical points of view. We give particular attention to the difficulties stressed by Newman and Stein concerning the problem of constructing pure states in spin glass systems. We mainly discuss what happens in finite-dimensional, realistic spin glasses. Together with a detailed review of some of the most important features, facts, data, and phenomena, we present some new theoretical ideas and numerical results. We discuss among others the basic idea of the RSB theory, correlation functions, interfaces, overlaps, pure states, random field, and the dynamical approach. We present new numerical results for the behaviors of coupled replicas and about the numerical verification of sum rules, and we review some of the available numerical results that we consider of larger importance (for example, the determination of the phase transition point, the correlation functions, the window overlaps, and the dynamical behavior of the system).

We introduce and study a model which admits a complex landscape without containing quenched disorder. Continuing our previous investigation we introduce a disordered model which allows us to reconstruct all the main features of the original phase diagram, including a low T spin glass phase and a complex dynamical behavior.

Time-dependent processes are often analysed using the power spectral density (PSD), calculated by taking an appropriate Fourier transform of individual trajectories and finding the associated ensemble-average. Frequently, the available experimental data sets are too small for such ensemble averages, and hence it is of a great conceptual and practical importance to understand to which extent relevant information can be gained from S(f, T ), the PSD of a single trajectory. Here we focus on the behavior of this random, realization-dependent variable, parametrized by frequency f and observation-time T , for a broad family of anomalous diffusions-fractional Brownian motion (fBm) with Hurst-index H-and derive exactly its probability density function. We show that S(f, T ) is proportional-up to a random numerical factor whose universal distribution we determine-to the ensemble-averaged PSD. For subdiffusion (H < 1/2) we find that S(f, T ) ∼ A/f 2H+1 with random-amplitude A. In sharp contrast, for superdiffusion (H > 1/2) S(f, T ) ∼ BT 2H−1 /f 2 with random amplitude B. Remarkably, for H > 1/2 the PSD exhibits the same frequency-dependence as Brownian motion, a deceptive property that may lead to false conclusions when interpreting experimental data. Notably, for H > 1/2 the PSD is ageing and is dependent on T . Our predictions for both sub-and superdiffusion are confirmed by experiments in live cells and in agarose hydrogels, and by extensive simulations.

New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement Flux Balance Analysis. We introduce here Constrained Allocation Flux Balance Analysis, CAFBA, in which the biosynthetic costs associated to growth are accounted for in an effective way through a single additional genome-wide constraint. Its roots lie in the experimentally observed pattern of proteome allocation for metabolic functions, allowing to bridge regulation and metabolism in a transparent way under the principle of growth-rate maximization. We provide a simple method to solve CAFBA efficiently and propose an “ensemble averaging” procedure to account for unknown protein costs. Applying this approach to modeling E. coli metabolism, we find that, as the growth rate increases, CAFBA solutions cross over from respiratory, growth-yield maximizing states (preferred at slow growth) to fermentative states with carbon overflow (preferred at fast growth). In addition, CAFBA allows for quantitatively accurate predictions on the rate of acetate excretion and growth yield based on only 3 parameters determined by empirical growth laws.

We study the KPZ equation (in D = 2, 3 and 4 spatial dimensions) by using a RSOS discretization of the surface. We measure the critical exponents very precisely, and we show that the rational guess is not appropriate, and that 4D is not the upper critical dimension. We are also able to determine very precisely the exponent of the sub-leading scaling corrections, that turns out to be close to 1 in all cases. We introduce and use a multi-surface coding technique, that allow a gain of order 30 over usual numerical simulations.

Using the special-purpose 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