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Biomedical subjects

S Ruffo

Publications and source records attributed to S Ruffo.

At least 19 recordsLinked to original sources
PubMed2006

Time scale for magnetic reversal and the topological nonconnectivity threshold.

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.

Journal Article↗
PubMed2005

Breaking of ergodicity and long relaxation times in systems with long-range interactions.

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.

Journal Article↗
PubMed2002

First- and second-order clustering transitions for a system with infinite-range attractive interaction.

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.

Journal Article↗
PubMed2001

Pattern formation and localization in the forced-damped Fermi-Pasta-Ulam lattice.

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.

Journal Article↗
PubMed2001

Transport properties of the diluted Lorentz slab.

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.

Journal Article↗
PubMed2001

Inequivalence of ensembles in a system with long-range interactions.

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.

Journal Article↗
PubMed2001

One-dimensional toy model of globular clusters.

We introduce a one-dimensional toy model of globular clusters. The model is a version of the well-known gravitational sheets system, where we also take into account mass and energy loss by evaporation of stars at the boundaries. Numerical integration by the "exact" event-driven dynamics is performed, for initial uniform density and Gaussian random velocities. Two distinct quasistationary asymptotic regimes are attained, depending on the initial energy of the system. We guess the forms of the density and velocity profiles that fit numerical data extremely well and allow us to perform an independent calculation of the self-consistent gravitational potential. Some power laws for the asymptotic number of stars and for the collision times are suggested.

Journal Article↗
PubMed1999

Finite times to equipartition in the thermodynamic limit.

We study the time scale T to equipartition in a 1D lattice of N masses coupled by quartic nonlinear (hard) springs (the Fermi-Pasta-Ulam beta model). We take the initial energy to be either in a single mode gamma or in a package of low-frequency modes centered at gamma and of width deltagamma, with both gamma and deltagamma proportional to N. These initial conditions both give, for finite energy densities E/N, a scaling in the thermodynamic limit (large N), of a finite time to equipartition which is inversely proportional to the central mode frequency times a power of the energy density (E/N). A theory of the scaling with (E/N) is presented and compared to the numerical results in the range 0.03<or=E/N<or=0.8.

Journal Article↗
PubMed1996

Analysis of genomic patchiness of Haemophilus influenzae and Saccharomyces cerevisiae chromosomes.

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.

Base Sequence↗
PubMed1996

High statistics block entropy measures of DNA sequences.

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.

Base Sequence↗
PubMed1994

Third codon G + C periodicity as a possible signal for an "internal" selective constraint.

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.

Animals↗
PubMed1986

A microcomputer program for individualizing factor VIII dosage in hemophilia patients undergoing major surgery.

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.

Computers↗