Biomedical subjects

G Caldarelli

Publications and source records attributed to G Caldarelli.

At least 19 recordsLinked to original sources

PubMed2001

Perturbative approach to the Bak-Sneppen model.

We study the Bak-Sneppen model in the probabilistic framework of the run time statistics (RTS). This model has attracted a large interest for its simplicity being a prototype for the whole class of models showing self-organized criticality. The dynamics is characterized by a self-organization of almost all the species fitnesses above a nontrivial threshold value, and by a lack of spatial and temporal characteristic scales. This results in avalanches of activity power law distributed. In this Letter we use the RTS approach to compute the value of x(c), the value of the avalanche exponent tau, and the asymptotic distribution of minimal fitnesses.

Journal Article↗

PubMed2001

Cold and warm swelling of hydrophobic polymers.

We introduce a polymer model where the transition from swollen to compact configurations is due to interactions between the monomers and the solvent. These interactions are the origin of the effective attractive interactions between hydrophobic amino acids in proteins. We find that in the low and high temperature phases polymers are swollen, and there is an intermediate phase where the most favorable configurations are compact. We argue that such a model captures in a single framework both the cold and the warm denaturation experimentally detected for thermosensitive polymers and for proteins.

Journal Article↗

PubMed2001

Cellular models for river networks.

A cellular model introduced for the evolution of the fluvial landscape is revisited using extensive numerical and scaling analyses. The basic network shapes and their recurrence especially in the aggregation structure are then addressed. The roles of boundary and initial conditions are carefully analyzed as well as the key effect of quenched disorder embedded in random pinning of the landscape surface. It is found that the above features strongly affect the scaling behavior of key morphological quantities. In particular, we conclude that randomly pinned regions (whose structural disorder bears much physical meaning mimicking uneven landscape-forming rainfall events, geological diversity or heterogeneity in surficial properties like vegetation, soil cover or type) play a key role for the robust emergence of aggregation patterns bearing much resemblance to real river networks.

Biophysical Phenomena↗

PubMed2000

Angular structure of lacunarity, and the renormalization group

We formulate the angular structure of lacunarity in fractals, in terms of a symmetry reduction of the three point correlation function. This provides a rich probe of universality, and first measurements yield new evidence in support of the equivalence between self-avoiding walks (SAW's) and percolation perimeters in two dimensions. We argue that the lacunarity reveals much of the renormalization group in real space. This is supported by exact calculations for random walks and measured data for percolation clusters and SAW's. Relationships follow between exponents governing inward and outward propagating perturbations, and we also find a very general test for the contribution of long-range interactions.

Journal Article↗

PubMed2000

Discretized diffusion processes

We study the properties of the "rigid Laplacian" operator; that is we consider solutions of the Laplacian equation in the presence of fixed truncation errors. The dynamics of convergence to the correct analytical solution displays the presence of a metastable set of numerical solutions, whose presence can be related to granularity. We provide some scaling analysis in order to determine the value of the exponents characterizing the process. We believe that this prototype model is also suitable to provide an explanation of the widespread presence of power law in a social and economic system where information and decision diffuse, with errors and delay from agent to agent.

Journal Article↗

PubMed2000

Invasion percolation with temperature and the nature of self-organized criticality in real systems

In this paper we present a theoretical approach that allows us to describe the transition between critical and noncritical behavior when stocastic noise is introduced in extremal models with disorder. Namely, we show that the introduction of thermal noise in invasion percolation (IP) brings the system outside the critical point. This result suggests a possible definition of self-organized criticality systems as ordinary critical systems where the critical point corresponds to set to 0 one of the parameters. We recover both the IP and Eden models for T-->0 and T-->infinity, respectively. For small T we find a dynamical second-order transition with correlation length diverging when T-->0.

Journal Article↗

PubMed2000

Putting proteins back into water

We introduce a simplified protein model where the solvent (water) degrees of freedom appear explicitly (although in an extremely simplified fashion). Using this model we are able to recover the thermodynamic phenomenology of proteins over a wide range of temperatures. In particular we describe both the warm and the cold protein denaturation within a single framework, while addressing important issues about the structure of model proteins.

Journal Article↗

PubMed1998

Modelling Coevolution in Multispecies Communities.

We introduce the Webworld model, which links together the ecological modelling of food web structure with the evolutionary modelling of speciation and extinction events. The model describes dynamics of ecological communities on an evolutionary time-scale. Species are defined as sets of characteristic features, and these features are used to determine interaction scores between species. A simple rule is used to transfer resources from the external environment through the food web to each of the species, and to determine mean population sizes. A time step in the model represents a speciation event. A new species is added with features similar to those of one of the existing species and a new food web structure is than calculated. The new species may (i) add stably to the web, (ii) become extinct immediately because it is poorly adapted, or (iii) cause one or more other species to become extinct due to competition for resources. We measure various properties of the model webs and compare these with data on real food webs. These properties include the proportions of basal, intermediate and top species, the number of links per species and the number of trophic levels. We also study the evolutionary dynamics of the model ecosystem by following the fluctuations in the total number of species in the web. Extinction avalanches occur when novel organisms arise which are significantly better adapted than existing ones. We discuss these results in relation to the observed extinction events in the fossil record, and to the theory of self-organized criticality.Copyright 1998 Academic Press

Journal Article↗

PubMed1998