arXiv subjects

P. De Los Rios

Publications and source records attributed to P. De Los Rios.

9 recordsLinked to original sources

arXiv2010

Diffusion-limited reactions in crowded environments

Diffusion-limited reactions (DLR) are usually described within the Smoluchowski theory, which neglects interactions between the diffusing components. We propose a first extension of such frame- work that incorporates excluded-volume effects, considering hard diffusing agents in the presence of an absorbing sink. For large values of the absorber-to-diffuser size ratio Rs, the encounter rate obtained from the simulations is in very good agreement with a simple generalization of the Smolu- chowski equation at high densities. Reducing Rs, the rate gets substantially depressed at interme- diate packing and become even non-monotonic for Rs << 1. Concurrently with the saturation of the rate, stationary density waves set in close to the absorbing center. A mean-field, effective-potential analysis of the Smoluchowski equation under crowding sheds light on the subtle link between such ordering and the slowing down of the encounter dynamics. Finally, we show how an infinitesimal amount of non-reacting impurities can equally slow down dramatically the reaction.

cond-mat.stat-mech↗

arXiv2005

Gel Electrophoresis of DNA Knots in Weak and Strong Electric Fields

Gel electrophoresis allows to separate knotted DNA (nicked circular) of equal length according to the knot type. At low electric fields, complex knots being more compact, drift faster than simpler knots. Recent experiments have shown that the drift velocity dependence on the knot type is inverted when changing from low to high electric fields. We present a computer simulation on a lattice of a closed, knotted, charged DNA chain drifting in an external electric field in a topologically restricted medium. Using a simple Monte Carlo algorithm, the dependence of the electrophoretic migration of the DNA molecules on the type of knot and on the electric field intensity was investigated. The results are in qualitative agreement with electrophoretic experiments done under conditions of low and high electric fields: especially the inversion of the behavior from low to high electric field could be reproduced. The knot topology imposes on the problem the constrain of self-avoidance, which is the final cause of the observed behavior in strong electric field.

physics.bio-ph↗

arXiv2004

Solvent-induced micelle formation in a hydrophobic interaction model

We investigate the aggregation of amphiphilic molecules by adapting the two-state Muller-Lee-Graziano model for water, in which a solvent-induced hydrophobic interaction is included implicitly. We study the formation of various types of micelle as a function of the distribution of hydrophobic regions at the molecular surface. Successive substitution of non-polar surfaces by polar ones demonstrates the influence of hydrophobicity on the upper and lower critical solution temperatures. Aggregates of lipid molecules, described by a refinement of the model in which a hydrophobic tail of variable length interacts with different numbers of water molecules, are stabilized as the length of the tail increases. We demonstrate that the essential features of micelle formation are primarily solvent-induced, and are explained within a model which focuses only on the alteration of water structure in the vicinity of the hydrophobic surface regions of amphiphiles in solution.

cond-mat.stat-mech↗

arXiv2002

Scale-free Networks without Growth or Preferential Attachment: Good get Richer

A new mechanism leading to scale-free networks is proposed in this letter. It is shown that in many cases of interest, the connectivity power-law behavior is neither related to dynamical properties nor to preferential attachment. Instead, we show that without increasing the number of vertices in time and without applying the so called {\it ``rich-get-richer''} condition we obtain networks whose statistical properties are scale-free. Assigning a quenched fitness value $x_i$ to every vertex, and drawing links among vertices with a probability depending on the fitnesses of the two involved sites, gives rise to what we call a {\it ``good-get-richer''} mechanism, in which sites with larger fitness are more likely to become hubs (i.e., to be highly connected). This procedure generates power-law behaviors for various fitness distributions and attaching rules.

cond-mat.dis-nn↗

arXiv2002

Quantitative description and modeling of real networks

In this letter we present data analysis and modeling of two particular cases of study in the field of growing networks. We analyze WWW data set and authorship collaboration networks in order to check the presence of correlation in the data. The results are reproduced with a pretty good agreement through a suitable modification of the standard AB model of network growth. In particular, intrinsic relevance of sites plays a role in determining the future degree of the vertex.

cond-mat.dis-nn↗

arXiv1999

Levy-Nearest-Neighbors Bak-Sneppen Model

We study a random neighbor version of the Bak-Sneppen model, where "nearest neighbors" are chosen according to a probability distribution decaying as a power-law of the distance from the active site, P(x) \sim |x-x_{ac }|^{-ω}. All the exponents characterizing the self-organized critical state of this model depend on the exponent ω. As ωtends to 1 we recover the usual random nearest neighbor version of the model. The pattern of results obtained for a range of values of ωis also compatible with the results of simulations of the original BS model in high dimensions. Moreover, our results suggest a critical dimension d_c=6 for the Bak-Sneppen model, in contrast with previous claims.

cond-mat.stat-mech↗

arXiv1999

Universal 1/f Noise from Dissipative SOC Models

We introduce a model able to reproduce the main features of 1/f noise: hyper-universality (the power-law exponents are independent on the dimension of the system; we show here results in d=1,2) and apparent lack of a low-frequency cutoff in the power spectrum. Essential ingredients of this model are an activation-deactivation process and dissipation.

cond-mat.stat-mech↗

arXiv1998

On the High-dimensional Bak-Sneppen model

We report on extensive numerical simulations on the Bak-Sneppen model in high dimensions. We uncover a very rich behavior as a function of dimensionality. For d>2 the avalanche cluster becomes fractal and for d \ge 4 the process becomes transient. Finally the exponents reach their mean field values for d=d_c=8, which is then the upper critical dimension of the Bak Sneppen model.

cond-mat.stat-mech↗

arXiv1995

Dynamical Jahn-Teller Effect and Berry Phase in Positively Charged Fullerene I. Basic Considerations

We study the Jahn-Teller effect of positive fullerene ions $^2$C$_{60}^{+}$ and $^1$C$_{60}^{2+}$. The aim is to discover if this case, in analogy with the negative ion, possesses a Berry phase or not, and what are the consequences on dynamical Jahn-Teller quantization. Working in the linear and spherical approximation, we find no Berry phase in $^1$C$_{60}^{2+}$, and presence/absence of Berry phase for coupling of one $L=2$ hole to an $L=4$/$L=2$ vibration. We study in particular the special equal-coupling case ($g_2=g_4$), which is reduced to the motion of a particle on a 5-dimensional sphere. In the icosahedral molecule, the final outcome assesses the presence/absence of a Berry phase of $π$ for the $h_u$ hole coupled to $G_g$/$H_h$ vibrations. Some qualitative consequences on ground-state symmetry, low-lying excitations, and electron emission from C$_{60}$ are spelled out.

cond-mat↗