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At least 1,261 records · Page 70Linked to original sources

arXiv2001

Adaptive sampling by information maximization

The investigation of input-output systems often requires a sophisticated choice of test inputs to make best use of limited experimental time. Here we present an iterative algorithm that continuously adjusts an ensemble of test inputs online, subject to the data already acquired about the system under study. The algorithm focuses the input ensemble by maximizing the mutual information between input and output. We apply the algorithm to simulated neurophysiological experiments and show that it serves to extract the ensemble of stimuli that a given neural system ``expects'' as a result of its natural history.

physics.bio-ph↗

arXiv2002

Self-Segregation vs. Clustering in the Evolutionary Minority Game

Complex adaptive systems have been the subject of much recent attention. It is by now well-established that members (`agents') tend to self-segregate into opposing groups characterized by extreme behavior. However, while different social and biological systems manifest different payoffs, the study of such adaptive systems has mostly been restricted to simple situations in which the prize-to-fine ratio, $R$, equals unity. In this Letter we explore the dynamics of evolving populations with various different values of the ratio $R$, and demonstrate that extreme behavior is in fact {\it not} a generic feature of adaptive systems. In particular, we show that ``confusion'' and ``indecisiveness'' take over in times of depression, in which case cautious agents perform better than extreme ones.

cond-mat↗

arXiv2002

Exact Solution of the Munoz-Eaton Model for Protein Folding

A transfer-matrix formalism is introduced to evaluate exactly the partition function of the Munoz-Eaton model, relating the folding kinetics of proteins of known structure to their thermodynamics and topology. This technique can be used for a generic protein, for any choice of the energy and entropy parameters, and in principle allows the model to be used as a first tool to characterize the dynamics of a protein of known native state and equilibrium population. Applications to a $β$-hairpin and to protein CI-2, with comparisons to previous results, are also shown.

cond-mat.stat-mech↗

arXiv2001

A model of inversion of DNA charge by a positive polymer: fractionization of the polymer charge

Charge inversion of a DNA double helix by an oppositely charged flexible polyelectrolyte (PE) is considered. We assume that, in the neutral state of the DNA-PE complex, each of the DNA charges is locally compensated by a PE charge. When an additional PE molecule is adsorbed by DNA, its charge gets fractionized into monomer charges of defects (tails and arches) on the background of the perfectly neutralized DNA. These charges spread all over the DNA eliminating the self-energy of PE. This fractionization mechanism leads to a substantial inversion of the DNA charge, a phenomenon which is widely used for gene delivery.

cond-mat.soft↗

arXiv2002

A model for mutation in bacterial populations

We describe the evolution of $E.coli$ populations through a Bak-Sneppen type model which incorporates random mutations. We show that, for a value of the mutation level which coincides with the one estimated from experiments, this model reproduces the measures of mean fitness relative to that of a common ancestor, performed for over 10,000 bacterial generations.

physics.bio-ph↗

arXiv2001

Rippling patterns in aggregates of myxobacteria arise from cell-cell collisions

Experiments with myxobacterial aggregates reveal standing waves called rippling patterns. Here, these structures are modelled with a simple discrete model based on the interplay between migration and collisions of cells. Head-to-head collisions of cells result in cell reversals. To correctly reproduce the rippling patterns, a refractory phase after each cell reversal has to be assumed, during which further reversal is prohibited. The duration of this phase determines the wavelength and period of the ripple patterns as well as the reversal frequency of single cells.

physics.bio-ph↗

arXiv2002

Epidemic threshold in structured scale-free networks

We analyze the spreading of viruses in scale-free networks with high clustering and degree correlations, as found in the Internet graph. For the Suscetible-Infected-Susceptible model of epidemics the prevalence undergoes a phase transition at a finite threshold of the transmission probability. Comparing with the absence of a finite threshold in networks with purely random wiring, our result suggests that high clustering and degree correlations protect scale-free networks against the spreading of viruses. We introduce and verify a quantitative description of the epidemic threshold based on the connectivity of the neighborhoods of the hubs.

cond-mat↗

arXiv2002

Complementarity and diversity in a soluble model ecosystem

Complementarity among species with different traits is one of the basic processes affecting biodiversity, defined as the number of species in the ecosystem. We present here a soluble model ecosystem in which the species are characterized by binary traits and their pairwise interactions follow a complementarity principle. Manipulation of the species composition, and so the study of its effects on the species diversity is achieved through the introduction of a bias parameter favoring one of the traits. Using statistical mechanics tools we find explicit expressions for the allowed values of the equilibrium species concentrations in terms of the control parameters of the model.

cond-mat.dis-nn↗

arXiv2002

Insulating behavior of lambda-DNA on the micron scale

We have investigated the electrical conductivity of lambda-DNA using DNA covalently bonded to Au electrodes. Thiol-modified dTTP was incorporated into the `sticky' ends of bacteriophage lambda-DNA using DNA polymerase. Two-probe measurements on such molecules provide a hard lower bound for the resistivity ρ>10^6 (Ohm cm) at bias potentials up to 20 volts, in conflict with recent claims of moderate to high conductivity. By direct imaging, we show that the molecules are present after the measurements. We stress the importance of eliminating salt residues in these measurements.

physics.bio-ph↗

arXiv2002

Extreme self-organization in networks constructed from gene expression data

We study networks constructed from gene expression data obtained from many types of cancers. The networks are constructed by connecting vertices that belong to each others' list of K-nearest-neighbors, with K being an a priori selected non-negative integer. We introduce an order parameter for characterizing the homogeneity of the networks. On minimizing the order parameter with respect to K, degree distribution of the networks shows power-law behavior in the tails with an exponent of unity. Analysis of the eigenvalue spectrum of the networks confirms the presence of the power-law and small-world behavior. We discuss the significance of these findings in the context of evolutionary biological processes.

cond-mat.soft↗

arXiv2002

Absence of epidemic threshold in scale-free networks with connectivity correlations

Random scale-free networks have the peculiar property of being prone to the spreading of infections. Here we provide an exact result showing that a scale-free connectivity distribution with diverging second moment is a sufficient condition to have null epidemic threshold in unstructured networks with either assortative or dissortative mixing. Connectivity correlations result therefore ininfluential for the epidemic spreading picture in these scale-free networks. The present result is related to the divergence of the average nearest neighbors connectivity, enforced by the connectivity detailed balance condition.

cond-mat.stat-mech↗

arXiv2002

Power of the power-laws: lessons from unification of small and large time scales for evolution

We develop a ``unified'' model that describes both ``micro'' and ``macro'' evolutions within a single theoretical framework. The eco-system is described as a dynamic network; the population dynamics at each node of this network describes the ``micro''-evolution over ecological time scales (i.e., birth, ageing and natural death of individual organisms) while the appearance of new nodes, the slow changes of the links and the disappearance of existing nodes accounts for the ``macro'' evolution over geological time scales (i.e., the origination, evolution and extinction of species). In contrast to several earlier claims in the literature, we observe strong deviations from power law in the regime of long life times where the statistics is, usually, poor.

cond-mat.stat-mech↗

arXiv2002

Colloid-polymer mixtures in the protein limit

We computed the phase-separation behavior and effective interactions of colloid-polymer mixtures in the "protein limit", where the polymer radius of gyration is much larger than the colloid radius. For ideal polymers, the critical colloidal packing fraction tends to zero, whereas for interacting polymers in a good solvent the behavior is governed by a universal binodal, implying a constant critical colloid packing fraction. In both systems the depletion interaction is not well described by effective pair potentials but requires the incorporation of many-body contributions.

cond-mat.soft↗

arXiv2002

Zipf's Law in Gene Expression

Using data from gene expression databases on various organisms and tissues, including yeast, nematodes, human normal and cancer tissues, and embryonic stem cells, we found that the abundances of expressed genes exhibit a power-law distribution with an exponent close to -1, i.e., they obey Zipf's law. Furthermore, by simulations of a simple model with an intra-cellular reaction network, we found that Zipf's law of chemical abundance is a universal feature of cells where such a network optimizes the efficiency and faithfulness of self-reproduction. These findings provide novel insights into the nature of the organization of reaction dynamics in living cells.

physics.bio-ph↗

arXiv2003

The Active Traveling Wave in the Cochlea

A sound stimulus entering the inner ear excites a deformation of the basilar membrane which travels along the cochlea towards the apex. It is well established that this wave-like disturbance is amplified by an active system. Recently, it has been proposed that the active system consists of a set of self-tuned critical oscillators which automatically operate at an oscillatory instability. Here, we show how the concepts of a traveling wave and of self-tuned critical oscillators can be combined to describe the nonlinear wave in the cochlea.

physics.bio-ph↗

arXiv2003

Comment on "Why is the DNA denaturation transition first order?"

In this comment we argue that while the conclusions in the original paper (Y. Kafri, D. Mukamel and L. Peliti, Phys. Rev. Lett. 85, 4988 (2000)) are correct for asymptotically long DNA chains, they do not apply to the chains used in typical experiments. In the added last paragraph, we point out that for real DNA the average distance between denatured loops is not of the order of the persistence length of a single-stranded chain but much larger. This corroborates our reasoning that the double helix between loops is quite rigid, and thereby our conclusion.

cond-mat.stat-mech↗

arXiv2003

Stochastic Modelling Approach to the Incubation Time of Prionic Diseases

Transmissible spongiform encephalopathies like the bovine spongiform encephalopathy (BSE) and the Creutzfeldt-Jakob disease (CJD) in humans are neurodegenerative diseases for which prions are the attributed pathogenic agents. A widely accepted theory assumes that prion replication is due to a direct interaction between the pathologic (PrPsc) form and the host encoded (PrPc) conformation, in a kind of an autocatalytic process. Here we show that the overall features of the incubation time of prion diseases are readily obtained if the prion reaction is described by a simple mean-field model. An analytical expression for the incubation time distribution then follows by associating the rate constant to a stochastic variable log normally distributed. The incubation time distribution is then also shown to be log normal and fits the observed BSE data very well. The basic ideas of the theoretical model are then incorporated in a cellular automata model. The computer simulation results yield the correct BSE incubation time distribution at low densities of the host encoded protein.

cond-mat.stat-mech↗

arXiv2002

Liquid-liquid phase separation of a surfactant-solubilized membrane protein

The phase behavior of membrane proteins stems from a complex synergy with the amphiphilic molecules required for their solubilization. We show that ionization of a pH-sensitive surfactant, LDAO, bound to a bacterial photosynthetic protein, the Reaction Center (RC), leads in a narrow pH range to protein liquid-liquid phase separation in surprisingly stable `droplets', forerunning reversible aggregation at lower pH. Phase segregation is promoted by increasing temperature and hindered by adding salt. RC light-absorption and photoinduced electron cycle are moreover strongly affected by phase segregation.

cond-mat.soft↗