arXiv subjects

Paolo De Los Rios

Publications and source records attributed to Paolo De Los Rios.

At least 55 records · Page 3Linked to original sources

arXiv2004

Kosmotropes and chaotropes: modelling preferential exclusion, binding and aggregate stability

Kosmotropic cosolvents added to an aqueous solution promote the aggregation of hydrophobic solute particles, while chaotropic cosolvents act to destabilise such aggregates. We discuss the mechanism for these phenomena within an adapted version of the two-state Muller-Lee-Graziano model for water, which provides a complete description of the ternary water/cosolvent/solute system for small solute particles. This model contains the dominant effect of a kosmotropic substance, which is to enhance the formation of water structure. The consequent preferential exclusion both of cosolvent molecules from the solvation shell of hydrophobic particles and of these particles from the solution leads to a stabilisation of aggregates. By contrast, chaotropic substances disrupt the formation of water structure, are themselves preferentially excluded from the solution, and thereby contribute to solvation of hydrophobic particles. We use Monte Carlo simulations to demonstrate at the molecular level the preferential exclusion or binding of cosolvent molecules in the solvation shell of hydrophobic particles, and the consequent enhancement or suppression of aggregate formation. We illustrate the influence of structure-changing cosolvents on effective hydrophobic interactions by modelling qualitatively the kosmotropic effect of sodium chloride and the chaotropic effect of urea.

cond-mat.soft↗

arXiv2004

The role of clustering and gridlike ordering in epidemic spreading

The spreading of an epidemic is determined by the connectiviy patterns which underlie the population. While it has been noted that a virus spreads more easily on a network in which global distances are small, it remains a great challenge to find approaches that unravel the precise role of local interconnectedness. Such topological properties enter very naturally in the framework of our two-timestep description, also providing a novel approach to tract a probabilistic system. The method is elaborated for SIS-type epidemic processes, leading to a quantitative interpretation of the role of loops up to length 4 in the onset of an epidemic.

cond-mat.stat-mech↗

arXiv2004

Cluster approximations for probabilistic systems: a new perspective of epidemiological modelling

Especially in lattice structured populations, homogeneous mixing represents an inadequate assumption. Various improvements upon the ordinary pair approximation based on a number of assumptions concerning the higher-order correlations have been proposed. To find approaches that allow for a derivation of their dynamics remains a great challenge. By representing the population with its connectivity patterns as a homogeneous network, we propose a systematic methodology for the description of the epidemic dynamics that takes into account spatial correlations up to a desired range. The equations which the dynamical correlations are subject to, are derived in a straightforward way, and they are solved very efficiently due to their binary character. The method embeds very naturally spatial patterns such as the presence of loops characterizing the square lattice or the treelike structure ubiquitous in random networks, providing an improved description of the steady state as well as the invasion dynamics.

q-bio.PE↗

arXiv2004

Exploration of scale-free networks

The increased availability of data on real networks has favoured an explosion of activity in the elaboration of models able to reproduce both qualitatively and quantitatively the measured properties. What has been less explored is the reliability of the data, and whether the measurement technique biases them. Here we show that tree-like explorations (similar in principle to traceroute) can indeed change the measured exponents of a scale-free network.

cond-mat.dis-nn↗

arXiv2003

Preferential Exchange: Strengthening Connections in Complex Networks

Many social, technological and biological interactions involve network relationships whose outcome intimately depends on the structure of the network and on the strengths of the connections. Yet, although much information is now available concerning the structure of many networks, the strengths are more difficult to measure. Here we show that, for one particular social network, notably the e-mail network, a suitable measure of the strength of the connections can be available. We also propose a simple mechanism, based on positive feedback and reciprocity, that can explain the observed behavior and that hints toward specific dynamics of formation and reinforcement of network connections. Network data from contexts different from social sciences indicate that power-law, and generally broad, distributions of the connection strength are ubiquitous, and the proposed mechanism has a wide range of applicability.

cond-mat.stat-mech↗

arXiv2003

On the Widespread Occurrence of the Inverse Square Distribution in Social Sciences and Taxonomy

The widespread occurrence of an inverse square relation in the hierarchical distribution of sub-communities within communities (or sub-species within species) has been recently invoked as a signature of hierarchical self-organization within social and ecological systems. Here we show that, whether such systems are self-organized or not, this behavior is the consequence of the tree-like classification method. Different tree-like classifications (both of real and truly random systems) display a similar statistical behaviour when considering the sizes of their sub-branches.

cond-mat.stat-mech↗

arXiv2003

Generalized Network Growth: from Microscopic Strategies to the Real Internet Properties

In this paper we present a generalized model for network growth that links the microscopical agent strategies with the large scale behavior. This model is intended to reproduce the largest number of features of the Internet network at the Autonomous System (AS) level. Our model of network grows by adding both new vertices and new edges between old vertices. In the latter case a ``rewarding attachment'' takes place mimicking the disassortative mixing between small routers to larger ones. We find a good agreement between experimental data and the model for the degree distribution, the betweenness distribution, the clustering coefficient and the correlation functions for the degrees.

cond-mat.stat-mech↗

arXiv2003

Hydrophobic Interaction Model for Upper and Lower Critical Solution Temperatures

Hydration of hydrophobic solutes in water is the cause of different phenomena, including the hydrophobic heat-capacity anomaly, which are not yet fully understood. Because of its topicality, there has recently been growing interest in the mechanism of hydrophobic aggregation, and in the physics on which it is based. In this study we use a simple yet powerful mixture model for water, an adapted two-state Muller-Lee-Graziano model, to describe the energy levels of water molecules as a function of their proximity to non-polar solute molecules. The model is shown to provide an appropriate description of many-body interactions between the hydrophobic solute particles. The solubility and aggregation of hydrophobic substances is studied by evaluating detailed Monte Carlo simulations in the vicinity of the first-order aggregation phase transition. A closed-loop coexistence curve is found, which is consistent with a mean-field calculation carried out for the same system. In addition, the destabilizing effect of a chaotropic substance in the solution is studied by suitable modification of the MLG model. These findings suggest that a simple model for the hydrophobic interaction may contain the primary physical processes involved in hydrophobic aggregation and in the chaotropic effect.

cond-mat.soft↗

arXiv2002

Cold and Warm Denaturation of Proteins

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

cond-mat.stat-mech↗

arXiv2001

Power-law size distribution of supercritical random trees

The probability distribution P(k) of the sizes k of critical trees (branching ratio m=1) is well known to show a power-law behavior k^(-3/2). Such behavior corresponds to the mean-field approximation for many critical and self-organized critical phenomena. Here we show numerically and analytically that also supercritical trees (branching ration m>1) are "critical" in that their size distribution obeys a power-law k^(-2). We mention some possible applications of these results.

cond-mat.stat-mech↗

arXiv2001

The Local Minority Game

Ecologists and economists try to explain collective behavior in terms of competitive systems of selfish individuals with the ability to learn from the past. Statistical physicists have been investigating models which might contribute to the understanding of the underlying mechanisms of these systems. During the last three years one intuitive model, commonly referred to as the Minority Game, has attracted broad attention. Powerful yet simple, the minority game has produced encouraging results which can explain the temporal behaviour of competitive systems. Here we switch the interest to phenomena due to a distribution of the individuals in space. For analyzing these effects we modify the Minority Game and the Local Minority Game is introduced. We study the system both numerically and analytically, using the customary techniques already developped for the ordinary Minority Game.

cond-mat.stat-mech↗

arXiv2001

Statistical Features of Drainage Basins in Mars Channel Networks

Erosion by flowing water is one of the major forces shaping the surface of Earth. Studies in the last decade have shown, in particular, that the drainage region of rivers, where water is collected, exhibits scale invariant features characterized by exponents that are the same for rivers around the world. Here we show that from the data obtained by the MOLA altimeter of the Mars Global Surveyor one can perform the same analysis for mountain sides on Mars. We then show that in some regions fluid erosion might have played a role in the present martian landscape.

cond-mat.stat-mech↗

arXiv2000

Bethe approximation for self-interacting lattice trees

In this paper we develop a Bethe approximation, based on the cluster variation method, which is apt to study lattice models of branched polymers. We show that the method is extremely accurate in cases where exact results are known as, for instance, in the enumeration of spanning trees. Moreover, the expressions we obtain for the asymptotic number of spanning trees and lattice trees on a graph coincide with analogous expressions derived through different approaches. We study the phase diagram of lattice trees with nearest-neighbour attraction and branching energies. We find a collapse transition at a tricritical theta point, which separates an expanded phase from a compact phase. We compare our results for the theta transition in two and three dimensions with available numerical estimates.

cond-mat.stat-mech↗

arXiv2000

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 social and economic system where information and decision diffuse, with errors and delay from agent to agent.

cond-mat.stat-mech↗

arXiv2000

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 {\it cold} protein denaturation within a single framework, while addressing important issues about the structure of model proteins.

cond-mat.stat-mech↗

arXiv2000

Statistical Analysis of Genealogical Trees for Polygamic Species

Repetitions within a given genealogical tree provides some information about the degree of consanguineity of a population. They can be analyzed with techniques usually employed in statistical physics when dealing with fixed point transformations. In particular we show that the tree features strongly depend on the fractions of males and females in the population, and also on the offspring probability distribution. We check different possibilities, some of them relevant to human groups, and compare them with simulations.

cond-mat.stat-mech↗

arXiv1999

Cold and Warm Denaturation 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 amminoacids 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 proteins. Some consequences for protein folding are discussed.

cond-mat.stat-mech↗

arXiv1999

Berry Phase and Ground State Symmetry in H x h Dynamical Jahn-Teller Systems

Due to the ubiquitous presence of a Berry phase, in most cases of dynamical Jahn-Teller systems the symmetry of the vibronic ground state is the same as that of the original degenerate electronic state. As a single exception, the linear H x h icosahedral model, relevant to the physics of C60 cations, is determined by an additional free parameter, which can be continuously tuned to eliminate the Berry phase from the low-energy closed paths: accordingly, the ground state changes to a totally-symmetric nondegenerate state.

cond-mat.mtrl-sci↗