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At least 991 records · Page 55Linked to original sources

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

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↗

arXiv2003

Unzipping Kinetics of Double-Stranded DNA in a Nanopore

We studied the unzipping kinetics of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. PCR analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip each molecule was inferred from the ionic current signature of DNA traversal. The distribution of times to unzip under various experimental conditions fit a simple kinetic model. Using this model, we estimated the enthalpy barriers to unzipping and the effective charge of a nucleotide in the pore, which was considerably smaller than previously assumed.

cond-mat.soft↗

arXiv2003

Origins of Chevron Rollovers in Non-Two-State Protein Folding Kinetics

Chevron rollovers of some proteins imply that their logarithmic folding rates are nonlinear in native stability. This is predicted by lattice and continuum Gō models to arise from diminished accessibilities of the ground state from transiently populated compact conformations under strongly native conditions. Despite these models' native-centric interactions, the slowdown is due partly to kinetic trapping caused by some of the folding intermediates' nonnative topologies. Notably, simple two-state folding kinetics of small single-domain proteins are not reproduced by common Gō-like schemes.

cond-mat.soft↗

arXiv2003

Particle Dispersion on Rapidly Folding Random Hetero-Polymers

We investigate the dynamics of a particle moving randomly along a disordered hetero-polymer subjected to rapid conformational changes which induce superdiffusive motion in chemical coordinates. We study the antagonistic interplay between the enhanced diffusion and the quenched disorder. The dispersion speed exhibits universal behavior independent of the folding statistics. On the other hand it is strongly affected by the structure of the disordered potential. The results may serve as a reference point for a number of translocation phenomena observed in biological cells, such as protein dynamics on DNA strands.

cond-mat.stat-mech↗

arXiv2003

Synchronization of active mechanical oscillators by an inertial load

Motivated by the operation of myogenic (self-oscillatory) insect flight muscle, we study a model consisting of a large number of identical oscillatory contractile elements joined in a chain, whose end is attached to a damped mass-spring oscillator. When the inertial load is small, the serial coupling favors an antisynchronous state in which the extension of one oscillator is compensated by the contraction of another, in order to preserve the total length. However, a sufficiently massive load can sychronize the oscillators and can even induce oscillation in situations where isolated elements would be stable. The system has a complex phase diagram displaying quiescent, synchronous and antisynchrononous phases, as well as an unsual asynchronous phase in which the total length of the chain oscillates at a different frequency from the individual active elements.

physics.bio-ph↗

arXiv2003

A possible mechanism for cold denaturation of proteins at high pressure

We study cold denaturation of proteins at high pressures. Using multicanonical Monte Carlo simulations of a model protein in a water bath, we investigate the effect of water density fluctuations on protein stability. We find that above the pressure where water freezes to the dense ice phase ($\approx2$ kbar), the mechanism for cold denaturation with decreasing temperature is the loss of local low-density water structure. We find our results in agreement with data of bovine pancreatic ribonuclease A.

cond-mat.soft↗

arXiv2003

Equilibrium Distribution of Mutators in the Single Fitness Peak Model

This paper develops an analytically tractable model for determining the equilibrium distribution of mismatch repair deficient strains in unicellular populations. The approach is based on the single fitness peak (SFP) model, which has been used in Eigen's quasispecies equations in order to understand various aspects of evolutionary dynamics. As with the quasispecies model, our model for mutator-nonmutator equilibrium undergoes a phase transition in the limit of infinite sequence length. This "repair catastrophe" occurs at a critical repair error probability of $ ε_r = L_{via}/L $, where $ L_{via} $ denotes the length of the genome controlling viability, while $ L $ denotes the overall length of the genome. The repair catastrophe therefore occurs when the repair error probability exceeds the fraction of deleterious mutations. Our model also gives a quantitative estimate for the equilibrium fraction of mutators in {\it Escherichia coli}.

cond-mat.stat-mech↗

arXiv2003

Chromatin dynamics: Nucleosomes go mobile through twist defects

We study the spontaneous ''sliding'' of histone spools (nucleosomes) along DNA as a result of thermally activated single base pair twist defects. To this end we map the system onto a suitably extended Frenkel-Kontorova model. Combining results from several recent experiments we are able to estimate the nucleosome mobility without adjustable parameters. Our model shows also how the local mobility is intimately linked to the underlying base pair sequence.

cond-mat.soft↗

arXiv2003

Non-local Interaction Effects on Pattern Formation in Population Dynamics

We consider a model for population dynamics such as for the evolution of bacterial colonies which is of the Fisher type but where the competitive interaction among individuals is non-local, and show that spatial structures with interesting features emerge. These features depend on the nature of the competitive interaction as well as on its range, specifically on the presence or absence of tails in, and the central curvature of, the influence function of the interaction.

nlin.PS↗

arXiv2003

RNA denaturation: excluded volume, pseudoknots and transition scenarios

A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous transition. Otherwise a smooth crossover occurs from the swollen linear polymer behavior to highly ramified, almost compact conformations with secondary structures. In the latter scenario, which is appropriate when these structures are much more stable than pseudoknot links, probability distributions for the lengths of both loops and main branches obey scaling with nonclassical exponents.

cond-mat.soft↗

arXiv2003

An Effective Membrane Model of the Immunological Synapse

The immunological synapse is a patterned collection of different types of receptors and ligands that forms in the intercellular junction between T Cells and antigen presenting cells (APCs) during recognition. The synapse is implicated in information transfer between cells, and is characterized by different spatial patterns of receptors at different stages in the life cycle of T cells. We obtain a minimalist model that captures this experimentally observed phenomenology. A functional RG analysis provides further insights.

cond-mat.soft↗

arXiv2003

The internal states of active inclusions and the dynamics of an active membrane

A theoretical model of a two-component fluid membrane containing lipids and two-state active inclusions is presented. Under strong inclusion activities the membrane can be unstable due to pump-driven undulation or aggregation of high curvature excited inclusions. Depending on the structural details of the inclusions, the active conformation change of the inclusions can also induce finite size domains on the membrane. At long wavelengths a stable membrane has a height fluctuation spectrum similar to previous studies which neglected the inclusion internal states. For a tensionless membrane, $ \sim T_{eff} q_{\perp}^{-4}$, where $T_{eff}$ is an effective temperature which depends on the details of inclusion activities.

cond-mat.soft↗