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We study the transition from integrability to chaos for the three-particle Fermi-Pasta-Ulam-Tsingou (FPUT) model. We can show that both the quartic β-FPUT model (α=0) and the cubic one (β=0) are integrable by introducing an appropriate Fourier representation to express the nonlinear terms of the Hamiltonian. For generic values of α and β, the model is non-integrable and displays a mixed phase space with both chaotic and regular trajectories. In the classical case, chaos is diagnosed by the investigation of Poincaré sections. In the quantum case, the level spacing statistics in the energy basis belongs to the Gaussian orthogonal ensemble in the chaotic regime, and crosses over to Poissonian behavior in the quasi-integrable low-energy limit. In the chaotic part of the spectrum, two generic observables obey the eigenstate thermalization hypothesis .

We prove analytically and show numerically that the dynamics of the Fermi-Pasta-Ulam-Tsingou chain is characterized by a transient Burgers turbulence regime on a wide range of time and energy scales. This regime is present at long wavelengths and energy per particle small enough that equipartition is not reached on a fast timescale. In this range, we prove that the driving mechanism to thermalization is the formation of a shock that can be predicted using a pair of generalized Burgers equations. We perform a perturbative calculation at small energy per particle, proving that the energy spectrum of the chain E_{k} decays as a power law, E_{k}∼k^{-ζ(t)}, on an extensive range of wave numbers k. We predict that ζ(t) takes first the value 8/3 at the Burgers shock time, and then reaches a value close to 2 within two shock times. The value of the exponent ζ=2 persists for several shock times before the system eventually relaxes to equipartition. During this wide time window, an exponential cutoff in the spectrum is observed at large k, in agreement with previous results. Such a scenario turns out to be universal, i.e., independent of the parameters characterizing the system and of the initial condition, once time is measured in units of the shock time.

Engineering long-range interactions in experimental platforms has been achieved with great success in a large variety of quantum systems in recent years. Inspired by this progress, we propose a generalization of the classical Hamiltonian mean-field model to fermionic particles. We study the phase diagram and thermodynamic properties of the model in the canonical ensemble for ferromagnetic interactions as a function of temperature and hopping. At zero temperature, small charge fluctuations drive the many-body system through a first-order quantum phase transition from an ordered to a disordered phase. At higher temperatures, the fluctuation-induced phase transition remains first order initially and switches to second-order only at a tricritical point. Our results offer an intriguing example of tricriticality in a quantum system with long-range couplings, which bears direct experimental relevance. The analysis is performed by exact diagonalization and mean-field theory.

The Berezinskii-Kosterlitz-Thouless (BKT) transition is the paradigmatic example of a topological phase transition without symmetry breaking, where a quasiordered phase, characterized by a power-law scaling of the correlation functions at low temperature, is disrupted by the proliferation of topological excitations above the critical temperature T&#95;{BKT}. In this Letter, we consider the effect of long-range decaying couplings ∼r^{-2-σ} on the BKT transition. After pointing out the relevance of this nontrivial problem, we discuss the phase diagram, which is far richer than the corresponding short-range one. It features-for 7/4<σ<2-a quasiordered phase in a finite temperature range T&#95;{c}T&#95;{BKT}. The transition temperature T&#95;{c} displays unique universal features quite different from those of the traditional, short-range XY model. Given the universal nature of our findings, they may be observed in current experimental realizations in 2D atomic, molecular, and optical quantum systems.

The unconstrained ensemble describes completely open systems whose control parameters are the chemical potential, pressure, and temperature. For macroscopic systems with short-range interactions, thermodynamics prevents the simultaneous use of these intensive variables as control parameters, because they are not independent and cannot account for the system size. When the range of the interactions is comparable with the size of the system, however, these variables are not truly intensive and may become independent, so equilibrium states defined by the values of these parameters may exist. Here, we derive a Monte Carlo algorithm for the unconstrained ensemble and show that simulations can be performed using the chemical potential, pressure, and temperature as control parameters. We illustrate the algorithm by applying it to physical systems where either the system has long-range interactions or is confined by external conditions. The method opens up an avenue for the simulation of completely open systems exchanging heat, work, and matter with the environment.

We study dipolarly coupled three-dimensional spin systems in both the microcanonical and the canonical ensembles by introducing appropriate numerical methods to determine the microcanonical temperature and by realizing a canonical model of heat bath. In the microcanonical ensemble, we show the existence of a branch of stable antiferromagnetic states in the low-energy region. Other metastable ferromagnetic states exist in this region: by externally perturbing them, an effective negative specific heat is obtained. In the canonical ensemble, for low temperatures, the same metastable states are unstable and reach a new branch of more robust metastable states which is distinct from the stable one. Our statistical physics approach allows us to put some order in the complex structure of stable and metastable states of dipolar systems.

The canonical phase diagram of the Blume-Emery-Griffiths model with infinite-range interactions is known to exhibit a fourth-order critical point at some negative value of the biquadratic interaction K<0. Here we study the microcanonical phase diagram of this model for K<0, extending previous studies which were restricted to positive K. A fourth-order critical point is found to exist at coupling parameters which are different from those of the canonical ensemble. The microcanonical phase diagram of the model close to the fourth-order critical point is studied in detail revealing some distinct features from the canonical counterpart.

We study synchronization between periodically driven, interacting classical spins undergoing a Hamiltonian dynamics. In the thermodynamic limit there is a transition between a regime where all the spins oscillate synchronously for an infinite time with a period twice the driving period (synchronized regime) and a regime where the oscillations die after a finite transient (chaotic regime). We emphasize the peculiarity of our result, having been synchronization observed so far only in driven-dissipative systems. We discuss how our findings can be interpreted as a period-doubling time crystal and we show that synchronization can appear both for an overall regular and overall chaotic dynamics.

In nonadditive systems, like small systems or like long-range interacting systems even in the thermodynamic limit, ensemble inequivalence can be related to the occurrence of negative response functions, this in turn being connected with anomalous concavity properties of the thermodynamic potentials associated with the various ensembles. We show how the type and number of negative response functions depend on which of the quantities E , V and N (energy, volume and number of particles) are constrained in the ensemble. In particular, we consider the unconstrained ensemble in which E , V and N fluctuate, which is physically meaningful only for nonadditive systems. In fact, its partition function is associated with the replica energy, a thermodynamic function that identically vanishes when additivity holds, but that contains relevant information in nonadditive systems.

Completely open systems can exchange heat, work, and matter with the environment. While energy, volume, and number of particles fluctuate under completely open conditions, the equilibrium states of the system, if they exist, can be specified using the temperature, pressure, and chemical potential as control parameters. The unconstrained ensemble is the statistical ensemble describing completely open systems and the replica energy is the appropriate free energy for these control parameters from which the thermodynamics must be derived. It turns out that macroscopic systems with short-range interactions cannot attain equilibrium configurations in the unconstrained ensemble, since temperature, pressure, and chemical potential cannot be taken as a set of independent variables in this case. In contrast, we show that systems with long-range interactions can reach states of thermodynamic equilibrium in the unconstrained ensemble. To illustrate this fact, we consider a modification of the Thirring model and compare the unconstrained ensemble with the canonical and grand-canonical ones: The more the ensemble is constrained by fixing the volume or number of particles, the larger the space of parameters defining the equilibrium configurations.

The usual formulation of thermodynamics is based on the additivity of macroscopic systems. However, there are numerous examples of macroscopic systems that are not additive, due to the long-range character of the interaction among the constituents. We present here an approach in which nonadditive systems can be described within a purely thermodynamics formalism. The basic concept is to consider a large ensemble of replicas of the system where the standard formulation of thermodynamics can be naturally applied and the properties of a single system can be consequently inferred. After presenting the approach, we show its implementation in systems where the interaction decays as 1/r(α) in the interparticle distance r, with α smaller than the embedding dimension d, and in the Thirring model for gravitational systems.

We study instabilities and relaxation to equilibrium in a long-range extension of the Fermi-Pasta-Ulam-Tsingou (FPU) oscillator chain by exciting initially the lowest Fourier mode. Localization in mode space is stronger for the long-range FPU model. This allows us to uncover the sporadic nature of instabilities, i.e., by varying initially the excitation amplitude of the lowest mode, which is the control parameter, instabilities occur in narrow amplitude intervals. Only for sufficiently large values of the amplitude, the system enters a permanently unstable regime. These findings also clarify the long-standing problem of the relaxation to equilibrium in the short-range FPU model. Because of the weaker localization in mode space of this latter model, the transfer of energy is retarded and relaxation occurs on a much longer timescale.

We explore ensemble inequivalence in long-range interacting systems by studying an XY model of classical spins with ferromagnetic and nematic coupling. We demonstrate the inequivalence by mapping the microcanonical phase diagram onto the canonical one, and also by doing the inverse mapping. We show that the equilibrium phase diagrams within the two ensembles strongly disagree within the regions of first-order transitions, exhibiting interesting features like temperature jumps. In particular, we discuss the coexistence and forbidden regions of different macroscopic states in both the phase diagrams.

The classical wave-particle Hamiltonian is considered in its generalized version, where two modes are assumed to interact with the coevolving charged particles. The equilibrium statistical mechanics solution of the model is worked out analytically, both in the canonical and the microcanonical ensembles. The competition between the two modes is shown to yield ensemble inequivalence, at variance with the standard scenario where just one wave is allowed to develop. As a consequence, both temperature jumps and negative specific heat can show up in the microcanonical ensemble. The relevance of these findings for both plasma physics and free electron laser applications is discussed.

We study the dynamics of a system of coupled oscillators of distributed natural frequencies, by including the features of both thermal noise, parametrized by a temperature, and inertial terms, parametrized by a moment of inertia. For a general unimodal frequency distribution, we report here the complete phase diagram of the model in the space of dimensionless moment of inertia, temperature, and width of the frequency distribution. We demonstrate that the system undergoes a nonequilibrium first-order phase transition from a synchronized phase at low parameter values to an incoherent phase at high values. We provide strong numerical evidence for the existence of both the synchronized and the incoherent phase, treating the latter analytically to obtain the corresponding linear stability threshold that bounds the first-order transition point from below. In the limit of zero noise and inertia, when the dynamics reduces to the one of the Kuramoto model, we recover the associated known continuous transition. At finite noise and inertia but in the absence of natural frequencies, the dynamics becomes that of a well-studied model of long-range interactions, the Hamiltonian mean-field model. Close to the first-order phase transition, we show that the escape time out of metastable states scales exponentially with the number of oscillators, which we explain to be stemming from the long-range nature of the interaction between the oscillators.

We consider the overdamped dynamics of a paradigmatic long-range system of particles residing on the sites of a one-dimensional lattice and in the presence of thermal noise. The internal degree of freedom of each particle is a periodic variable that is coupled to those of other particles with an attractive XY-like interaction. The coupling strength decays with the interparticle separation r in space as 1/r^{α}; 0<α<1. We study the dynamics of the model in the continuum limit by considering the Fokker-Planck equation for the evolution of the spatial density of particles. We show that the equation allows a linearly stable stationary state, which is always uniform in space, being nonuniform in the internal degrees below a critical temperature T=1/2 and uniform above, with a phase transition between the two at T=1/2. The state is the same as the equilibrium state of the mean-field version of the model, obtained by considering α=0. Our analysis also allows us to compute the growth and decay rates of spatial Fourier modes of density fluctuations. The growth rates compare very well with numerical simulations.

We study synchronization in a system of phase-only oscillators residing on the sites of a one-dimensional periodic lattice. The oscillators interact with a strength that decays as a power law of the separation along the lattice length and is normalized by a size-dependent constant. The exponent α of the power law is taken in the range 0≤α<1. The oscillator frequency distribution is symmetric about its mean (taken to be zero) and is nonincreasing on [0,∞). In the continuum limit, the local density of oscillators evolves in time following the continuity equation that expresses the conservation of the number of oscillators of each frequency under the dynamics. This equation admits as a stationary solution the unsynchronized state uniform both in phase and over the space of the lattice. We perform a linear stability analysis of this state to show that when it is unstable, different spatial Fourier modes of fluctuations have different stability thresholds beyond which they grow exponentially in time with rates that depend on the Fourier modes. However, numerical simulations show that at long times all the nonzero Fourier modes decay in time, while only the zero Fourier mode (i.e., the "mean-field" mode) grows in time, thereby dominating the instability process and driving the system to a synchronized state. Our theoretical analysis is supported by extensive numerical simulations.

Long-range interacting systems, while relaxing to equilibrium, often get trapped in long-lived quasistationary states which have lifetimes that diverge with the system size. In this work, we address the question of how a long-range system in a quasistationary state (QSS) responds to an external perturbation. We consider a long-range system that evolves under deterministic Hamilton dynamics. The perturbation is taken to couple to the canonical coordinates of the individual constituents. Our study is based on analyzing the Vlasov equation for the single-particle phase-space distribution. The QSS represents a stable stationary solution of the Vlasov equation in the absence of the external perturbation. In the presence of small perturbation, we linearize the perturbed Vlasov equation about the QSS to obtain a formal expression for the response observed in a single-particle dynamical quantity. For a QSS that is homogeneous in the coordinate, we obtain an explicit formula for the response. We apply our analysis to a paradigmatic model, the Hamiltonian mean-field model, which involves particles moving on a circle under Hamiltonian dynamics. Our prediction for the response of three representative QSSs in this model (the water-bag QSS, the Fermi-Dirac QSS, and the Gaussian QSS) is found to be in good agreement with N-particle simulations for large N. We also show the long-time relaxation of the water-bag QSS to the Boltzmann-Gibbs equilibrium state., (© 2012 American Physical Society)

Predicting the biological function of all the genes of an organism is one of the fundamental goals of computational system biology. In the last decade, high-throughput experimental methods for studying the functional interactions between gene products (GPs) have been combined with computational approaches based on Bayesian networks for data integration. The result of these computational approaches is an interaction network with weighted links representing connectivity likelihood between two functionally related GPs. The weighted network generated by these computational approaches can be used to predict annotations for functionally uncharacterized GPs. Here we introduce Weighted Network Predictor (WNP), a novel algorithm for function prediction of biologically uncharacterized GPs. Tests conducted on simulated data show that WNP outperforms other 5 state-of-the-art methods in terms of both specificity and sensitivity and that it is able to better exploit and propagate the functional and topological information of the network. We apply our method to Saccharomyces cerevisiae yeast and Arabidopsis thaliana networks and we predict Gene Ontology function for about 500 and 10000 uncharacterized GPs respectively.

Long-lived quasistationary states, associated with stationary stable solutions of the Vlasov equation, are found in systems with long-range interactions. Studies of the relaxation time in a model of N globally coupled particles moving on a ring, the Hamiltonian mean-field model (HMF), have shown that it diverges as N(γ) for large N, with γ1.7 for some initial conditions with homogeneously distributed particles. We propose a method for identifying exact inhomogeneous steady states in the thermodynamic limit, based on analyzing models of uncoupled particles moving in an external field. For the HMF model, we show numerically that the relaxation time of these states diverges with N with the exponent γ ~/= 1. The method, applicable to other models with globally coupled particles, also allows an exact evaluation of the stability limit of homogeneous steady states. In some cases, it provides a good approximation for the correspondence between the initial condition and the final steady state.

We introduce a model of uncoupled pendula, which mimics the dynamical behaviour of the Hamiltonian mean-field (HMF) model. This model has become a paradigm for long-range interactions, such as Coulomb or dipolar forces. As in the HMF model, this simplified integrable model is found to obey the Vlasov equation and to exhibit quasi-stationary states (QSSs), which arise after a 'collisionless' relaxation process. Both the magnetization and the single-particle distribution function in these QSSs can be predicted using Lynden-Bell's theory. The existence of an extra conserved quantity for this model, the energy distribution function, allows us to understand the origin of some discrepancies of the theory with numerical experiments. It also suggests an improvement of Lynden-Bell's theory, which we fully implement for the zero-field case.

We consider a damped beta-Fermi-Pasta-Ulam chain, driven at one boundary subjected to stochastic noise. It is shown that, for a fixed driving amplitude and frequency, increasing the noise intensity, the system's energy resonantly responds to the modulating frequency of the forcing signal. Multiple peaks appear in the signal-to-noise ratio, signaling the phenomenon of stochastic resonance. The presence of multiple peaks is explained by the existence of many stable and metastable states that are found when solving this boundary value problem for a semicontinuum approximation of the model. Stochastic resonance is shown to be generated by transitions between these states.

We study a generalized isotropic XY model which includes both two- and four-spin mean-field interactions. This model can be solved in the microcanonical ensemble. It is shown that in certain parameter regions the model exhibits gaps in the magnetization at fixed energy, resulting in ergodicity breaking. This phenomenon has previously been reported in anisotropic and discrete spin models. The entropy of the model is calculated and the microcanonical phase diagram is derived, showing the existence of first-order phase transitions from the ferromagnetic to a paramagnetic disordered phase. It is found that ergodicity breaking takes place in both the ferromagnetic and paramagnetic phases. As a consequence, the system can exhibit a stable ferromagnetic phase within the paramagnetic region, and conversely a disordered phase within the magnetically ordered region.

Systems with long-range interactions display a short-time relaxation towards quasistationary states whose lifetime increases with system size. With reference to the Hamiltonian mean field model, we here show that a maximum entropy principle, based on Lynden-Bell's pioneering idea of "violent relaxation," predicts the presence of out-of-equilibrium phase transitions separating the relaxation towards homogeneous (zero magnetization) or inhomogeneous (nonzero magnetization) quasistationary states. When varying the initial condition within a family of "water bags" with different initial magnetization and energy, first- and second-order phase transition lines are found that merge at an out-of-equilibrium tricritical point. Metastability is theoretically predicted and numerically checked around the first-order phase transition line.

We here discuss the emergence of quasistationary states (QSS), a universal feature of systems with long-range interactions. With reference to the Hamiltonian mean-field model, numerical simulations are performed based on both the original N-body setting and the continuum Vlasov model which is supposed to hold in the thermodynamic limit. A detailed comparison unambiguously demonstrates that the Vlasov-wave system provides the correct framework to address the study of QSS. Further, analytical calculations based on Lynden-Bell's theory of violent relaxation are shown to result in accurate predictions. Finally, in specific regions of parameters space, Vlasov numerical solutions are shown to be affected by small scale fluctuations, a finding that points to the need for novel schemes able to account for particle correlations.

A generic feature of systems with long-range interactions is the presence of quasistationary states with non-Gaussian single particle velocity distributions. For the case of the Hamiltonian mean-field model, we demonstrate that a maximum entropy principle applied to the associated Vlasov equation explains known features of such states for a wide range of initial conditions. We are able to reproduce velocity distribution functions with an analytic expression which is derived from the theory with no adjustable parameters. A normal diffusion of angles is detected, which is consistent with Gaussian tails of velocity distributions. A dynamical effect, two oscillating clusters surrounded by a halo, is also found and theoretically justified.

Considering the coherent nonlinear dynamics between two weakly linked optical waveguide arrays, we find the first example of coexistence of Josephson oscillations with a novel self-trapping regime. This macroscopic bistability is explained by proving analytically the simultaneous existence of symmetric, antisymmetric, and asymmetric stationary solutions of the associated nonlinear Schrödinger equation. The effect is illustrated and confirmed by numerical simulations. This property allows us to conceive an optical switch based on the variation of the refractive index of the linking central waveguide.

Anisotropic classical Heisenberg models with all-to-all spin coupling display a topological nonconnectivity threshold (TNT) for any number N of spins. Below this threshold, the energy surface is disconnected in two components with positive and negative total magnetizations, respectively, so that magnetization cannot reverse its sign and ergodicity is broken, even at finite N. Here, we solve the model in the microcanonical ensemble, using a recently developed method based on large deviation techniques, and show that a phase transition is present at an energy higher than the TNT energy. In the energy range between the TNT energy and the phase transition, magnetization changes sign stochastically and its behavior can be fully characterized by an average magnetization reversal time. The time scale for magnetic reversal can be computed analytically, using statistical mechanics. Numerical simulations confirm this calculation and further show that the magnetic reversal time diverges with a power law at the TNT threshold, with a size-dependent exponent. This exponent can be computed in the thermodynamic limit N-->(infinity), by the knowledge of entropy as a function of magnetization, and turns out to be in reasonable agreement with finite numerical simulations. We finally generalize our results to other models: Heisenberg chains with distance-dependent coupling, small 3D clusters with nearest-neighbor interactions, metastable states. We conjecture that the power-law divergence of the magnetic reversal time scale might be a universal signature of the presence of a TNT.

The thermodynamic and dynamical properties of an Ising model with both short-range and long-range, mean-field-like, interactions are studied within the microcanonical ensemble. It is found that the relaxation time of thermodynamically unstable states diverges logarithmically with system size. This is in contrast with the case of short-range interactions where this time is finite. Moreover, at sufficiently low energies, gaps in the magnetization interval may develop to which no microscopic configuration corresponds. As a result, in local microcanonical dynamics the system cannot move across the gap, leading to breaking of ergodicity even in finite systems. These are general features of systems with long-range interactions and are expected to be valid even when the interaction is slowly decaying with distance.

We present the phase diagram, in both the microcanonical and the canonical ensemble, of the self-gravitating-ring (SGR) model, which describes the motion of equal point masses constrained on a ring and subject to 3D gravitational attraction. If the interaction is regularized at short distances by the introduction of a softening parameter, a global entropy maximum always exists, and thermodynamics is well defined in the mean-field limit. However, ensembles are not equivalent and a phase of negative specific heat in the microcanonical ensemble appears in a wide intermediate energy region, if the softening parameter is small enough. The phase transition changes from second to first order at a tricritical point, whose location is not the same in the two ensembles. All these features make of the SGR model the best prototype of a self-gravitating system in one dimension. In order to obtain the stable stationary mass distribution, we apply an iterative method, inspired by a previous one used in 2D turbulence, which ensures entropy increase and, hence, convergence towards an equilibrium state.

Landau-Zener tunneling is discussed in connection with optical waveguide arrays. Light injected in a specific band of the Bloch spectrum in the propagation constant can be transmitted to another band, changing its physical properties. This can be achieved using two coupled waveguide arrays with different refractive indices. The step in the refractive index causes wave "acceleration" and thus induces strongly nonadiabatic Landau-Zener tunneling. Theoretically, the analysis is performed by considering a Schrödinger equation in a periodic potential with a step. The region of physical parameters where this phenomenon can occur is analytically determined and a realistic experimental setup is suggested. Its application could allow the realization of light filters.

We present a detailed analysis of the modulational instability of the zone-boundary mode for one and higher-dimensional Fermi-Pasta-Ulam (FPU) lattices. Following this instability, a process of relaxation to equipartition takes place, which we have called the Anti-FPU problem because the energy is initially fed into the highest frequency part of the spectrum, at variance with the original FPU problem (low frequency excitations of the lattice). This process leads to the formation of chaotic breathers in both one and two dimensions. Finally, the system relaxes to energy equipartition on time scales which increase as the energy density is decreased. We show that breathers formed when cooling the lattice at the edges, starting from a random initial state, bear strong qualitative similarities with chaotic breathers.

The recently discovered phenomenon of nonlinear supratransmission consists in a sudden increase of the amplitude of a transmitted wave triggered by the excitation of nonlinear localized modes of the medium. We examine this process for the Fermi-Pasta-Ulam chain, sinusoidally driven at one edge and damped at the other. The supratransmission regime occurs for driving frequencies above the upper band edge and originates from direct moving discrete breather creation. We derive approximate analytical estimates of the supratransmission threshold, which are in excellent agreement with numerics. When analyzing the long-time behavior, we discover that, below the supratransmission threshold, a conducting stationary state coexists with the insulating one. We explain the bistable nature of the energy flux in terms of the excitation of quasiharmonic extended waves. This leads to the analytical calculation of a lower-transmission threshold which is also in reasonable agreement with numerical experiments.

We propose an approach, based on statistical mechanics, to predict the saturated state of a single-pass, high-gain free-electron laser. In analogy with the violent relaxation process in self-gravitating systems and in the Euler equation of two-dimensional turbulence, the initial relaxation of the laser can be described by the statistical mechanics of an associated Vlasov equation. The laser field intensity and the electron bunching parameter reach a quasistationary value which is well fitted by a Vlasov stationary state if the number of electrons N is sufficiently large. Finite N effects (granularity) finally drive the system to Boltzmann-Gibbs statistical equilibrium, but this occurs on times that are unphysical (i.e., excessively long undulators). All theoretical predictions are successfully tested by means of finite- N numerical experiments.

We study the formation of coherent structures in a system with long-range interactions where particles moving on a circle interact through a repulsive cosine potential. Nonequilibrium structures are shown to correspond to statistical equilibria of an effective dynamics, which is derived using averaging techniques. This simple behavior might be a prototype of others observed in more complicated systems with long-range interactions, such as two-dimensional incompressible fluids and wave-particle interaction in a plasma.

We consider a Hamiltonian system made of N classical particles moving in two dimensions, coupled via an infinite-range interaction gauged by a parameter A. This system shows a low energy phase with most of the particles trapped in a unique cluster. At higher energy it exhibits a transition towards a homogenous phase. For sufficiently strong coupling A, an intermediate phase characterized by two clusters appears. Depending on the value of A, the observed transitions can be either second or first order in the canonical ensemble. In the latter case, microcanonical results differ dramatically from canonical ones. However, a canonical analysis, extended to metastable and unstable states, is able to describe the microcanonical equilibrium phase. In particular, a microcanonical negative specific heat regime is observed in the proximity of the transition whenever it is canonically discontinuous. In this regime, microcanonically stable states are shown to correspond to saddles of the Helmholtz free energy, located inside the spinodal region.

We study spatial pattern formation and energy localization in the dynamics of an anharmonic chain with quadratic and quartic intersite potential, subject to an optical, sinusoidally oscillating field and a weak damping. The zone-boundary mode is stable and locked to the driving field below a critical forcing that we determine analytically using an approximate model, which describes mode interactions. Above such a forcing, a standing modulated wave forms for driving frequencies below the band edge, while a "multibreather" state develops at higher frequencies. Of the former, we give an explicit approximate analytical expression, which compares well with numerical data. At higher forcing, space-time chaotic patterns are observed.

We study the behavior of a point particle incident on a slab of a randomly diluted triangular array of circular scatterers. Various scattering properties, such as the reflection and transmission probabilities and the scattering time are studied as a function of thickness and dilution. We show that a diffusion model satisfactorily describes the mentioned scattering properties. We also show how some of these quantities can be evaluated exactly and their agreement with numerical experiments. Our results exhibit the dependence of these scattering data on the mean free path. This dependence again shows excellent agreement with the predictions of a Brownian motion model.

We study the global phase diagram of the infinite-range Blume-Emery-Griffiths model both in the canonical and in the microcanonical ensembles. The canonical phase diagram shows first-order and continuous transition lines separated by a tricritical point. We find that below the tricritical point, when the canonical transition is first order, the phase diagrams of the two ensembles disagree. In this region the microcanonical ensemble exhibits energy ranges with negative specific heat and temperature jumps at transition energies. These results can be extended to weakly decaying nonintegrable interactions.

The real mechanisms of several biological processes involving DNA are not yet understood. We discuss here some aspects of the initiation of transcription, in particular the formation of the open complex and the activation mechanism associated to enhancer binding proteins. Transcription activation seems to be governed by underlying dynamical mechanisms related to several distortions of the double chain structure: a dynamical approach on a mesoscopic description level could then allow a deeper understanding of this complex process. Starting from the Peyrard Bishop (PB) model, that considers only the hydrogen bond stretching of each base pair, we describe here an extended DNA model, proposed in [1], that allows a rather good representation of the double helix geometry and of its structural features by the introduction of angular variables related to the twist angle. Using a generalized multiple scale expansion for the case of vectorial lattices derived elsewhere [2], we derive analytically small amplitude approximate solutions of the model which are movable and spatially localized: we present here the results of this calculation and show how the special shape of the solutions is in good agreement with what can be expected for coupled angular radial distortions in the real molecule.

We have analysed some aspects of the primary structure of the chromosome of the prokaryote Haemophilus influenzae and of the eukaryote Saccharomyces cerevisiae that share the same G + C content. In particular, we have investigated genomic patchiness over the gene size level (10 Kb) and that patchiness due to long homogenous tracts. Long polypurine and polypyrmidine tracts that are largely over-represented in S. cerevisiae chromosomes and under-represented in H. influenzae, are responsible for a large fraction of long correlation signals. Generating mechanisms of long homogenous tracts are DNA replication slippage and duplication events that appear to be linked processes driving chromosome primary structure evolution.

We have used an improved block-entropy measure in order to gain some further insights into the short-range correlations present in whole chromosomes of S. cerevisiae, viruses and organelles and very large genomic regions of E. coli. Although DNA sequences are largely inhomogeneous and word frequencies are unevenly distributed, the comparison of entire chromosomes and large genomic regions show a "bulk" composition homogeneity. This property suggests that biases in selection, directional mutational pressure and recombination processes act in homogenizing the base composition of the DNA molecules within a genome but their mode of action, relative impact and direction may vary in different organisms. The most interesting results appear to be the differences between the SW (C,G/A,T) and RY (A,G/C,T) two-letter alphabet entropies. Deviations from randomness in E. coli and S. cerevisiae sequences particularly concern SW dinucleotide frequencies and RY tetranucleotide frequencies.

Quasi-local analysis methods, such as window Fast Fourier Transform and an information theoretical quantity known as mutual information, have allowed us to gain some further insights on the importance and the contextual dependence of a pattern found in DNA sequences showing a periodicity of three with a G or C base in the third position. We have screened for such a periodicity, in terms of the alternative "strong" (S = C or G) versus "weak" (W = A or T) base, a large sample of DNA coding and non-coding sequences from both prokaryotes and eukaryotes, with the aim of testing whether this pattern could be considered as a significant signal for past or present constraints regarding DNA organization and/or function. This periodicity was indeed found in a number of sequences always associated with open reading frames, generally confined in prokaryotes living in extreme environments or in highly conserved eukaryotic genes. Moreover, codon usage was found to be very similar even in genes coding for very different functions. The data are discussed in view of their possible implications for an adaptive value of such a periodicity, in terms of more accurate translation processing and better overall stability.

The first nontrivial example of coupled map lattices that admits a rigorous analysis in the whole range of the strength of space interactions is considered. This class is generated by one-dimensional maps with a globally attracting superstable periodic trajectory that are coupled by a diffusive nearest-neighbor interaction.

A pharmacokinetic program that allows individualization of Factor VIII dosage regiments in hemophilia patients undergoing major surgery is described. The program, which is designed for the IBM PC microcomputer and compatible machines, is based upon the one-compartment open model with instantaneous input. In the framework of such a pharmacokinetic model, it is assumed that the elimination of Factor VIII is faster during the early post-operative period and that it decreases progressively over the following days. Since Factor VIII half-life is dependent on the time elapsed since the operation (short half-life values during the early post-operative period, longer half-life values thereafter), the pharmacokinetic model is a nonlinear one. A first-order 'variation' rate constant is used to describe the prolongation of Factor VIII half-life from the initial value immediately after surgery to the final value achieved several days later. Individualized estimation of the patient's kinetic parameters (initial half-life, 'variation' rate constant and volume of distribution) is performed through the Bayesian method. Therefore, for such estimation the program exploits the Factor VIII plasma levels measured in the individual patient as well as the population pharmacokinetic data of Factor VIII. After estimating the individual's Bayesian parameters, the program predicts the dosage regimen that will elicit the desired time-course of Factor VIII plasma levels. If requested, the program is able to calculate the least-squares estimates for the parameters of the pharmacokinetic model and dosage prediction can also be made on the basis of such estimates. The least-squares estimates are useful for calculating population pharmacokinetic parameters according to the Standard Two-Stage method. Some examples of clinical use of the program are presented.

The usefulness of a calculator programme that enables individualization of the dosage of Factor VIII, based on the concentration-time data measured after a test-dose, was assessed. The programme was tested in 12 haemophiliacs who required multiple-dose treatment with Factor VIII. Individual kinetic parameters were estimated in each patient from the plasma level data following the test-dose. Then, each patient received the multiple dose treatment with Factor VIII according to the dosage regimen suggested by the calculator programme. The time-curve of Factor VIII plasma levels at steady state was predicted by using the kinetic variables previously estimated. The plasma levels of Factor VIII were measured in all patients at steady state. As a result, good agreement between predicted and measured steady state concentrations was observed (r2 = 0.9797; P less than 0.001). The calculator programme tested in the present study appears to be a useful tool for individualizing the dosage regimen of Factor VIII in haemophiliacs.