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Barbara Coluzzi

Publications and source records attributed to Barbara Coluzzi.

15 recordsLinked to original sources
arXiv2016

An alternative approach to Michaelis-Menten kinetics that is based on the Renormalization Group: Comparison with the perturbation expansion beyond the sQSSA

We recall the perturbation expansion for Michaelis-Menten kinetics, beyond the standard quasi-steady-state approximation (sQSSA). Against this background, we are able to appropriately apply the alternative approach to the study of singularly perturbed differential equations that is based on the renormalization group (SPDERG), by clarifying similarities and differences. In the present demanding situation, we directly renormalize the bare initial condition value for the substrate. Our main results are: i) the 2nd order SPDERG uniform approximations to the correct solutions contain, up to 1st order, the same outer components as the known perturbation expansion ones; ii) the differential equation to be solved for the derivation of the 1st order outer substrate component is simpler within the SPDERG approach; iii) the approximations better reproduce the numerical solutions of the original problem in a region encompassing the matching one, because of the 2nd order terms in the inner components, calculated here for the first time to our knowledge: iv) the refined SPDERG uniform approximations, that we propose, give the correct asymptotically vanishing solutions, too, and allow to obtain results nearly indistinguishable from the solutions of the original problem in a large part of the whole relevant time window, even in the studied unfavourable kinetic constant case, for an expansion parameter value as large as {\epsilon} = 0.5.

physics.chem-ph↗
arXiv2015

Numerical study of DNA denaturation with self-avoidance: pseudo-critical temperatures and finite size behaviour

We perform an extensive numerical study of the disordered Poland-Scheraga (PS) model for DNA denaturation in which self-avoidance is completely taken into account. In complement to our previous work, we focus here on the finite size scaling in terms of pseudo-critical temperatures. We find notably that the mean value and the fluctuations of the pseudo-$T_c$ scale with the same exponent, the correlation length exponent $\nu_r$ (for which we provide the refined evaluation $\nu_r=2.9 \pm 0.4$). This result (coherent with the typical picture that describes random ferromagnets, when disorder is relevant) is at variance with numerical results reported in the literature for the PS model with self-avoidance, leading to an alternative scenario with a pseudo first order transition. We moreover introduce a crossover chain length $N^*$, which we evaluate, appropriate for characterizing the approach to the asymptotic regime in this model. Essentially, below $N^*$, the behaviour of the model in our study could also agree with such alternative scenario. Based on an approximate prediction of the dependence of $N^*$ on the parameters of the model, we show that following the choice of such parameters it could be not possible to reach the asymptotic regime in practice. In such context it becomes then possible to reconcile the apparently contradictory numerical studies.

cond-mat.soft↗
arXiv2006

Boolean Delay Equations: A simple way of looking at complex systems

Boolean Delay Equations (BDEs) are semi-discrete dynamical models with Boolean-valued variables that evolve in continuous time. Systems of BDEs can be classified into conservative or dissipative, in a manner that parallels the classification of ordinary or partial differential equations. Solutions to certain conservative BDEs exhibit growth of complexity in time. They represent therewith metaphors for biological evolution or human history. Dissipative BDEs are structurally stable and exhibit multiple equilibria and limit cycles, as well as more complex, fractal solution sets, such as Devil's staircases and ``fractal sunbursts``. All known solutions of dissipative BDEs have stationary variance. BDE systems of this type, both free and forced, have been used as highly idealized models of climate change on interannual, interdecadal and paleoclimatic time scales. BDEs are also being used as flexible, highly efficient models of colliding cascades in earthquake modeling and prediction, as well as in genetics. In this paper we review the theory of systems of BDEs and illustrate their applications to climatic and solid earth problems. The former have used small systems of BDEs, while the latter have used large networks of BDEs. We moreover introduce BDEs with an infinite number of variables distributed in space (``partial BDEs``) and discuss connections with other types of dynamical systems, including cellular automata and Boolean networks. This research-and-review paper concludes with a set of open questions.

nlin.CG↗
arXiv2006

Numerical study on a disordered model for DNA denaturation transition

We study numerically a disordered version of the model for DNA denaturation transition (DSAW-DNA) consisting of two interacting SAWs in 3d, which undergoes a first order transition in the homogeneous case. The two possible values eAT and eGC of the interactions between base pairs are taken as quenched random variables distributed with equal probability along the chain. We measure quantities averaged over disorder such as the energy density, the specific heat and the probability distribution of the loop lengths. When applying the scaling laws used in the homogeneous case we find that the transition seems to be smoother in presence of disorder, in agreement with general theoretical arguments. Nevertheless we can not rule out the possibility of a still first order transition.

cond-mat.soft↗
arXiv2006

Numerical evidence for relevance of disorder in a Poland-Scheraga DNA denaturation model with self-avoidance: Scaling behavior of average quantities

We study numerically the effect of sequence heterogeneity on the thermodynamic properties of a Poland-Scheraga model for DNA denaturation taking into account self-avoidance, i.e. with exponent c_p=2.15 for the loop length probability distribution. In complement to previous on-lattice Monte Carlo like studies, we consider here off-lattice numerical calculations for large sequence lengths, relying on efficient algorithmic methods. We investigate finite size effects with the definition of an appropriate intrinsic length scale x, depending on the parameters of the model. Based on the occurrence of large enough rare regions, for a given sequence length N, this study provides a qualitative picture for the finite size behavior, suggesting that the effect of disorder could be sensed only with sequence lengths diverging exponentially with x. We further look in detail at average quantities for the particular case x=1.3, ensuring through this parameter choice the correspondence between the off-lattice and the on-lattice studies. Taken together, the various results can be cast in a coherent picture with a crossover between a nearly pure system like behavior for small sizes N < 1000, as observed in the on-lattice simulations, and the apparent asymptotic behavior indicative of disorder relevance, with an (average) correlation length exponent \nu_r >= 2/d (=2).

cond-mat.dis-nn↗
arXiv2003

Numerical study of the SK Model in magnetic field

We study numerically the Sherrington--Kirkpatrick model as function of the magnetic field h, with fixed temperature T=0.6 Tc. We investigate the finite size scaling behavior of several quantities, such as the spin glass susceptibility, looking for numerical evidences of the transition on the De Almeida Thouless line. We find strong corrections to scaling which make difficult to locate the transition point. This shows, in a simple case, the extreme difficulties of spin glass simulations in non-zero magnetic field. Next, we study various sum rules (consequences of stochastic stability) involving overlaps between three and four replicas, which appear to be numerically well satisfied, and in a non-trivial way. Finally, we present data on P(q) for a large lattice size (N=3200) at low temperature T=0.4 Tc, where, for the first time, the shape predicted by the RSB solution of the model for non-zero magnetic field is visible.

cond-mat.stat-mech↗
arXiv2002

Magnetic field chaos in the SK Model

We study the Sherrington--Kirkpatrick model, both above and below the De Almeida Thouless line, by using a modified version of the Parallel Tempering algorithm in which the system is allowed to move between different values of the magnetic field h. The behavior of the probability distribution of the overlap between two replicas at different values of the magnetic field h_0 and h_1 gives clear evidence for the presence of magnetic field chaos already for moderate system sizes, in contrast to the case of temperature chaos, which is not visible on system sizes that can currently be thermalized.

cond-mat.stat-mech↗
arXiv2000

Comment on "Liquid Limits: The Glass Transition and Liquid-Gas Spinodal Boundaries of Metastable Liquids"

In ref. cond-mat/0005372, Sastry studies by numerical simulations the phase diagram of a simple fragile glass-forming liquid, presenting very interesting and clear results. We apply to this system, at various density values, the analytic approach to structural glass thermodynamics recently introduced and we compare our theoretical predictions on the liquid-glass transition temperature with Sastry's data.

cond-mat.dis-nn↗
arXiv2000

On the Energy Minima of the SK Model

We study properties of the energy minima obtained by quenching equilibrium configurations of the Sherrington-Kirkpatrick (SK) mean field spin glass. We measure the probability distribution of the overlap among quenched configurations and the quenched energy, looking at the dependence on the starting equilibrium temperature, and performing a systematic analysis of finite size effects.

cond-mat.dis-nn↗
arXiv1999

The thermodynamical liquid-glass transition in a Lennard-Jones binary mixture

We use the results derived in the framework of the replica approach to study the liquid-glass thermodynamic transition. The main results are rederived without using replicas and applied to the study of the Lennard-Jones binary mixture introduced by Kob and Andersen. We find that there is a phase transition due to the entropy crisis. We compute both analytically and numerically the value of the phase transition point $T_{K}$ and the specific heat in the low temperature phase.

cond-mat.soft↗
arXiv1999

A Simple Model for the DNA Denaturation Transition

We study pairs of interacting self-avoiding walks on the 3d simple cubic lattice. They have a common origin and are allowed to overlap only at the same monomer position along the chain. The latter overlaps are indeed favored by an energetic gain. This is inspired by a model introduced long ago by Poland and Sheraga [J. Chem. Phys. {\bf 45}, 1464 (1966)] for the denaturation transition in DNA where, however, self avoidance was not fully taken into account. For both models, there exists a temperature T_m above which the entropic advantage to open up overcomes the energy gained by forming tightly bound two-stranded structures. Numerical simulations of our model indicate that the transition is of first order (the energy density is discontinuous), but the analog of the surface tension vanishes and the scaling laws near the transition point are exactly those of a second order transition with crossover exponent ϕ=1. Numerical and exact analytic results show that the transition is second order in modified models where the self-avoidance is partially or completely neglected.

cond-mat.soft↗
arXiv1999

Thermodynamics of binary mixture glasses

We compute the thermodynamic properties of the glass phase in a binary mixture of soft spheres. Our approach is a generalization to mixtures of the replica strategy, recently proposed by Mezard and Parisi, providing a first principle statistical mechanics computation of the thermodynamics of glasses. The method starts from the inter-atomic potentials, and translates the problem into the study of a molecular liquid. We compare uor analytical predictions to numerical simulations, focusing onto the values of the thermodynamic transition and the configurational entropy.

cond-mat↗
arXiv1998

Numerical study of a short-range p-spin glass model in three dimensions

In this work we study numerically a short range p-spin glass model in three dimensions. The behaviour of the model appears to be remarkably different from mean field predictions. In fact it shares some features typical of models with full replica-symmetry breaking (FRSB). Nevertheless, we believe that the transition that we study is intrinsically different from the FRSB and basically due to non-perturbative contributions. We study both the statics and the dynamics of the system which seem to confirm our conjectures.

cond-mat.dis-nn↗
arXiv1997

New evidence for super-roughening in crystalline surfaces with disordered substrate

We study the behavior of the Binder cumulant related to long distance correlation functions of the discrete Gaussian model of disordered substrate crystalline surfaces. We exhibit numerical evidence that the non-Gaussian behavior in the low-$T$ region persists on large length scales, in agreement with the broken phase being super-rough.

cond-mat↗