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At least 1,099 records · Page 61Linked to original sources

arXiv2002

Halting viruses in scale-free networks

The vanishing epidemic threshold for viruses spreading on scale-free networks indicate that traditional methods, aiming to decrease a virus' spreading rate cannot succeed in eradicating an epidemic. We demonstrate that policies that discriminate between the nodes, curing mostly the highly connected nodes, can restore a finite epidemic threshold and potentially eradicate a virus. We find that the more biased a policy is towards the hubs, the more chance it has to bring the epidemic threshold above the virus' spreading rate. Furthermore, such biased policies are more cost effective, requiring less cures to eradicate the virus.

cond-mat.stat-mech↗

arXiv2001

Sampling rare events: statistics of local sequence alignments

A new method to simulate probability distributions in regions where the events are VERY unlikely (e.g. p ~ 10^{-40}) is presented. The basic idea is to represent the underlying probability space by the phase space of a physical system. The system is held at a temperature T, which is chosen such that the system preferably generates configurations which originally have low probabilities. Since the distribution of such a physical system is know from statistical physics, the original unbiased distribution can be obtained. As an application, local alignment of protein sequences based on BLOSUM62 substitution scores with (12,1) affine gap costs are considered The distribution of optimum sequence-alignment scores S is studied numerically over a large range of scores. The deviation of p(S) from the extreme-value (or Gumbel) distribution is quantified. This deviation decreases with growing sequence length.

cond-mat.dis-nn↗

arXiv2001

Reversible stretching of homopolymers and random heteropolymers

We have analyzed the equilibrium response of chain molecules to stretching. For a homogeneous sequence of monomers, the induced transition from compact globule to extended coil below the $θ$-temperature is predicted to be sharp. For random sequences, however, the transition may be smoothed by a prevalence of necklace-like structures, in which globular regions and coil regions coexist in a single chain. As we show in the context of a random copolymer, preferential solvation of one monomer type lends stability to such structures. The range of stretching forces over which necklaces are stable is sensitive to chain length as well as sequence statistics.

cond-mat.soft↗

arXiv2002

Morphological Instability and Dynamics of Fronts in Bacterial Growth Models with Nonlinear Diffusion

It has been argued that there is biological and modeling evidence that a non-linear diffusion coefficient of the type D(b) = D_0 b^{k} underlies the formation of a number of growth patterns of bacterial colonies. We study a reaction-diffusion system with a non-linear diffusion coefficient introduced by Ben-Jacob et al. Due to the fact that the bacterial diffusion coefficient vanishes when the bacterial density b -> 0, the standard linear stability analysis for fronts cannot be used. We introduce an extension of the stability analysis which can be applied to such singular fronts, map out the region of stability in the D-k-plane and derive an interfacial approximation in some limits. Our linear stability analysis and sharp interface formulation will also be applicable to other examples of interface formation due to nonlinear diffusion, like in porous media or in the problem of vortex motion in superconductors.

cond-mat.stat-mech↗

arXiv2002

Class of self-limiting growth models in the presence of nonlinear diffusion

The source term in a reaction-diffusion system, in general, does not involve explicit time dependence. A class of self-limiting growth models dealing with animal and tumor growth and bacterial population in a culture, on the other hand are described by kinetics with explicit functions of time. We analyze a reaction-diffusion system to study the propagation of spatial front for these models.

physics.bio-ph↗

arXiv2002

The spread of epidemic disease on networks

The study of social networks, and in particular the spread of disease on networks, has attracted considerable recent attention in the physics community. In this paper, we show that a large class of standard epidemiological models, the so-called susceptible/infective/removed (SIR) models can be solved exactly on a wide variety of networks. In addition to the standard but unrealistic case of fixed infectiveness time and fixed and uncorrelated probability of transmission between all pairs of individuals, we solve cases in which times and probabilities are non-uniform and correlated. We also consider one simple case of an epidemic in a structured population, that of a sexually transmitted disease in a population divided into men and women. We confirm the correctness of our exact solutions with numerical simulations of SIR epidemics on networks.

cond-mat.stat-mech↗

arXiv2002

On the nonlinear dynamics of topological solitons in DNA

Dynamics of topological solitons describing open states in the DNA double helix are studied in the frameworks of the model which takes into account asymmetry of the helix. It is shown that three types of topological solitons can occur in the DNA double chain. Interaction between the solitons, their interactions with the chain inhomogeneities and stability of the solitons with respect to thermal oscillations are investigated.

physics.bio-ph↗

arXiv2002

Scaling in DNA unzipping models: denaturated loops and end-segments as branches of a block copolymer network

For a model of DNA denaturation, exponents describing the distributions of denaturated loops and unzipped end-segments are determined by exact enumeration and by Monte Carlo simulations in two and three dimensions. The loop distributions are consistent with first order thermal denaturation in both cases. Results for end-segments show a coexistence of two distinct power laws in the relative distributions, which is not foreseen by a recent approach in which DNA is treated as a homogeneous network of linear polymer segments. This unexpected feature, and the discrepancies with such an approach, are explained in terms of a refined scaling picture in which a precise distinction is made between network branches representing single stranded and effective double stranded segments.

cond-mat.stat-mech↗

arXiv2001

Fluctuation Analysis of Human Electroencephalogram

The scaling behaviors of the human electroencephalogram (EEG) time series are studied using detrended fluctuation analysis. Two scaling regions are found in nearly every channel for all subjects examined. The scatter plot of the scaling exponents for all channels (up to 129) reveals the complicated structure of a subject's brain activity. Moment analyses are performed to extract the gross features of all the scaling exponents, and another universal scaling behavior is identified. A one-parameter description is found to characterize the fluctuation properties of the nonlinear behaviors of the brain dynamics.

physics.med-ph↗

arXiv2002

Simplified amino acid alphabets based on deviation of conditional probability from random background

The primitive data for deducing the Miyazawa-Jernigan contact energy or BLOSUM score matrix consists of pair frequency counts. Each amino acid corresponds to a conditional probability distribution. Based on the deviation of such conditional probability from random background, a scheme for reduction of amino acid alphabet is proposed. It is observed that evident discrepancy exists between reduced alphabets obtained from raw data of the Miyazawa-Jernigan's and BLOSUM's residue pair counts. Taking homologous sequence database SCOP40 as a test set, we detect homology with the obtained coarse-grained substitution matrices. It is verified that the reduced alphabets obtained well preserve information contained in the original 20-letter alphabet.

physics.bio-ph↗

arXiv2002

Recognition of an organism from fragments of its complete genome

This paper considers the problem of matching fragment to organism using its complete genome. Our method is based on the probability measure representation of a genome. We first demonstrate that these probability measures can be modelled as recurrent iterated function systems (RIFS) consisting of four contractive similarities. Our hypothesis is that the multifractal characteristic of the probability measure of a complete genome, as captured by the RIFS, is preserved in its reasonably long fragments. We compute the RIFS of fragments of various lengths and random starting points, and compare with that of the original sequence for recognition using the Euclidean distance. A demonstration on five randomly selected organisms supports the above hypothesis.

physics.bio-ph↗

arXiv2002

Phase diagram for unzipping DNA with long-range interactions

We present a critique and extension of the mean-field approach to the mechanical pulling transition in bound polymer systems. Our model is motivated by the theoretically and experimentally important examples of adsorbed polymers and double-stranded DNA, and we focus on the case in which quenched disorder in the sequence of monomers is unimportant for the statistical mechanics. We show how including excluded volume interactions in the model affects the phase diagram for the critical pulling force, and we predict a re-entrancy phase at low temperatures which has not been previously discussed. We also consider the case of non-equilibrium pulling, in which the external force probes the local, rather than the global structure of the dsDNA or adsorbed polymer. The dynamics of the pulling transition in such experiments could illuminate the polymer's loop structure, which depends on the nature of excluded volume interactions.

cond-mat.soft↗

arXiv2002

Epidemic spreading in correlated complex networks

We study a dynamical model of epidemic spreading on complex networks in which there are explicit correlations among the node's connectivities. For the case of Markovian complex networks, showing only correlations between pairs of nodes, we find an epidemic threshold inversely proportional to the largest eigenvalue of the connectivity matrix that gives the average number of links that from a node with connectivity $k$ go to nodes with connectivity $k'$. Numerical simulations on a correlated growing network model provide support for our conclusions.

cond-mat.stat-mech↗

arXiv2002

Unzipping Dynamics of Long DNAs

The two strands of the DNA double helix can be `unzipped' by application of 15 pN force. We analyze the dynamics of unzipping and rezipping, for the case where the molecule ends are separated and re-approached at constant velocity. For unzipping of 50 kilobase DNAs at less than about 1000 bases per second, thermal equilibrium-based theory applies. However, for higher unzipping velocities, rotational viscous drag creates a buildup of elastic torque to levels above kBT in the dsDNA region, causing the unzipping force to be well above or well below the equilibrium unzipping force during respectively unzipping and rezipping, in accord with recent experimental results of Thomen et al. [Phys. Rev. Lett. 88, 248102 (2002)]. Our analysis includes the effect of sequence on unzipping and rezipping, and the transient delay in buildup of the unzipping force due to the approach to the steady state.

cond-mat.soft↗

arXiv2002

Multifractal analysis of DNA walks and trails

The characterization of the long-range order and fractal properties of DNA sequences has proved a difficult though highly rewarding task due mainly to the mosaic character of DNA consisting of many interwoven patches of various lengths with different nucleotide constitutions. We apply here a recently proposed generalization of the detrended fluctuation analysis method to show that the DNA walk construction, in which the DNA sequence is viewed as a time series, exhibits a monofractal structure regardless of the existence of local trends in the series. In addition, we point out that the monofractal structure of the DNA walks carries over to an apparently alternative graphical construction given by the projection of the DNA walk into the $d$ spatial coordinates, termed DNA trails. In particular, we calculate the fractal dimension $D_t$ of the DNA trails using a well-known result of fractal theory linking $D_t$ to the Hurst exponent $H$ of the corresponding DNA walk. Comparison with estimates obtained by the standard box-counting method allows the evaluation of both finite-length and local trends effects.

cond-mat.stat-mech↗

arXiv2002

Linear stability analysis of retrieval state in associative memory neural networks of spiking neurons

We study associative memory neural networks of the Hodgkin-Huxley type of spiking neurons in which multiple periodic spatio-temporal patterns of spike timing are memorized as limit-cycle-type attractors. In encoding the spatio-temporal patterns, we assume the spike-timing-dependent synaptic plasticity with the asymmetric time window. Analysis for periodic solution of retrieval state reveals that if the area of the negative part of the time window is equivalent to the positive part, then crosstalk among encoded patterns vanishes. Phase transition due to the loss of the stability of periodic solution is observed when we assume fast alpha-function for direct interaction among neurons. In order to evaluate the critical point of this phase transition, we employ Floquet theory in which the stability problem of the infinite number of spiking neurons interacting with alpha-function is reduced into the eigenvalue problem with the finite size of matrix. Numerical integration of the single-body dynamics yields the explicit value of the matrix, which enables us to determine the critical point of the phase transition with a high degree of precision.

cond-mat.dis-nn↗

arXiv2001

Correlation Differences in Heartbeat Fluctuations During Rest and Exercise

We study the heartbeat activity of healthy individuals at rest and during exercise. We focus on correlation properties of the intervals formed by successive peaks in the pulse wave and find significant scaling differences between rest and exercise. For exercise the interval series is anticorrelated at short time scales and correlated at intermediate time scales, while for rest we observe the opposite crossover pattern -- from strong correlations in the short-time regime to weaker correlations at larger scales. We suggest a physiologically motivated stochastic scenario to explain the scaling differences between rest and exercise and the observed crossover patterns.

cond-mat.stat-mech↗

arXiv2002

Oscillations and dynamics in a two-dimensional prey-predator system

Using Monte Carlo simulations we study two-dimensional prey-predator systems. Measuring the variance of densities of prey and predators on the triangular lattice and on the lattice with eight neighbours, we conclude that temporal oscillations of these densities vanish in the thermodynamic limit. This result suggests that such oscillations do not exist in two-dimensional models, at least when driven by local dynamics. Depending on the control parameter, the model could be either in an active or in an absorbing phase, which are separated by the critical point. The critical behaviour of this model is studied using the dynamical Monte Carlo method. This model has two dynamically nonsymmetric absorbing states. In principle both absorbing states can be used for the analysis of the critical point. However, dynamical simulations which start from the unstable absorbing state suffer from metastable-like effects, which sometimes renders the method inefficient.

cond-mat.stat-mech↗