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At least 883 records · Page 49Linked to original sources

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↗

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↗

arXiv2003

Protein induced morphological transitions in KCl crystal growth

We investigated the formation of KCl crystals on glass surface by phase contrast, fluorescent, and atomic force microscopy on the micrometer scale, and observed interesting morphological transitions as a function of the experimental conditions. The presence of proteins in the solution from which the salt crystals grow during the drying up leads to complex microscopic patterns of crystals some of which are analogous to those commonly observed on the macroscopic scale. We tested the effect of tubulin, FITC-labeled albumin and IgG on the morphology of crystals grown either slowly or fast. A rich variety of protein specific and concentration dependent morphologies was found and described by a morphological diagram. We give a phenomenological interpretation, which can explain the growth of complex patterns. Fluorescent images prove that a protein layer covers the surface of the KCl structures. We propose that this layer reduces the anisotropy of the effective surface tension during growth. The tip splitting fractal regime is attributed to the decrease of anisotropy. Other possible mechanisms, which can cause morphological transition, are also discussed. We found elongated saw-toothed crystals induced by proteins, especially IgG and identified their structure.

physics.bio-ph↗

arXiv2003

Compact phases of polymers with hydrogen bonding

We propose an off-lattice model for a self-avoiding homopolymer chain with two different competing attractive interactions, mimicking the hydrophobic effect and the hydrogen bond formation respectively. By means of Monte Carlo simulations, we are able to trace out the complete phase diagram for different values of the relative strength of the two competing interactions. For strong enough hydrogen bonding, the ground state is a helical conformation, whereas with decreasing hydrogen bonding strength, helices get eventually destabilized at low temperature in favor of more compact conformations resembling $β$-sheets appearing in native structures of proteins. For weaker hydrogen bonding helices are not thermodynamically relevant anymore.

cond-mat.stat-mech↗

arXiv2002

Inter-strand distance distribution of DNA near melting

The distance distribution between complementary base pairs of the two strands of a DNA molecule is studied near the melting transition. Scaling arguments are presented for a generalized Poland-Scheraga type model which includes self-avoiding interactions. At the transition temperature and for a large distance r the distribution decays as 1/r^κwith κ=1+(c-2)/ ν. Here νis the self-avoiding walk correlation length exponent and c is the exponent associated with the entropy of an open loop in the chain. Results for the distribution function just below the melting point are also presented. Numerical simulations which fully take into account the self-avoiding interactions are in good agreement with the scaling approach.

cond-mat.stat-mech↗

arXiv2002

An evolution equation of the population genetics: relation to the density-matrix theory of quasiparticles with general dispersion laws

The Waxman-Peck theory of the population genetics is discussed in regard of soil bacteria. Each bacterium is understood as a carrier of a phenotypic parameter p. The central aim is the calculation of the probability density with respect to p of the carriers living at time t>0. The theory involves two small parameters: the mutation probability $μ$ and a parameter $γ$ involved in a function w(p) defining the fitness of the bacteria to survive the generation time $τ$ and give birth to offspring. The mutation from a state p to a state q is defined by a Gaussian. The author focuses attention on an equation generalizing Waxman's equation. The author solves this equation in the standard style of a perturbation theory and discusses how the solution depends on the choice of the fitness function w(p). In a sense, the function $c(p)=1-w(p)/w(0)$ is analogous to the dispersion function E(p) of fictitious quasiparticles. With a general function c(p), the distribution function ${\mathitΦ}(p,t;0)$ is composed of a delta-function component, $N(t)δ(p)$, and a blurred component. The author shows that asymptotically N(t) may tend to a positive value, in contrast with zero resulting from Waxman's approximation where $c(p)\sim p^2$.

physics.bio-ph↗

arXiv2003

Correlated noise in a logistic growth model

The logistic differential equation is used to analyze cancer cell population, in the presence of a correlated Gaussian white noise. We study the steady state properties of tumor cell growth and discuss the effects of the correlated noise. It is found that the degree of correlation of the noise can cause tumor cell extinction.

physics.bio-ph↗

arXiv2003

Interactions between proteins bound to biomembranes

We study a physical model for the interaction between general inclusions bound to fluid membranes that possess finite tension, as well as the usual bending rigidity. We are motivated by an interest in proteins bound to cell membranes that apply forces to these membranes, due to either entropic or direct chemical interactions. We find an exact analytic solution for the repulsive interaction between two similar circularly symmetric inclusions. This repulsion extends over length scales of order tens of nanometers, and contrasts with the membrane-mediated contact attraction for similar inclusions on tensionless membranes. For non circularly symmetric inclusions we study the small, algebraically long-ranged, attractive contribution to the force that arises. We discuss the relevance of our results to biological phenomena, such as the budding of caveolae from cell membranes and the striations that are observed on their coats.

cond-mat.soft↗

arXiv2003

Universal behavior of localization of residue fluctuations in globular proteins

Localization properties of residue fluctuations in globular proteins are studied theoretically by using the Gaussian network model. Participation ratio for each residue fluctuation mode is calculated. It is found that the relationship between participation ratio and frequency is similar for all globular proteins, indicating a universal behavior in spite of their different size, shape, and architecture.

physics.bio-ph↗

arXiv2002

Non-monotonic variation with salt concentration of the second virial coefficient in protein solutions

The osmotic virial coefficient $B_2$ of globular protein solutions is calculated as a function of added salt concentration at fixed pH by computer simulations of the ``primitive model''. The salt and counter-ions as well as a discrete charge pattern on the protein surface are explicitly incorporated. For parameters roughly corresponding to lysozyme, we find that $B_2$ first decreases with added salt concentration up to a threshold concentration, then increases to a maximum, and then decreases again upon further raising the ionic strength. Our studies demonstrate that the existence of a discrete charge pattern on the protein surface profoundly influences the effective interactions and that non-linear Poisson Boltzmann and Derjaguin-Landau-Verwey-Overbeek (DLVO) theory fail for large ionic strength. The observed non-monotonicity of $B_2$ is compared to experiments. Implications for protein crystallization are discussed.

cond-mat.soft↗

arXiv2002

Role of bulk and of interface contacts in the behaviour of model dimeric proteins

Some dimeric proteins first fold and then dimerize (three--state dimers) while others first dimerize and then fold (two--state dimers). Within the framework of a minimal lattice model, we can distinguish between sequences obeying to one or to the other mechanism on the basis of the partition of the ground state energy between bulk than for interface contacts. The topology of contacts is very different for the bulk than for the interface: while the bulk displays a rich network of interactions, the dimer interface is built up a set of essentially independent contacts. Consequently, the two sets of interactions play very different roles both in the the folding and in the evolutionary history of the protein. Three--state dimers, where a large fraction of the energy is concentrated in few contacts buried in the bulk, and where the relative contact energy of interface contacts is considerably smaller than that associated with bulk contacts, fold according to a hierarchycal pathway controlled by local elementary structures, as also happens in the folding of single--domain monomeric proteins. On the other hand, two--state dimers display a relative contact energy of interface contacts which is larger than the corresponding quantity associated with the bulk. In this case, the assembly of the interface stabilizes the system and lead the two chains to fold. The specific properties of three--state dimers acquired through evolution are expected to be more robust than those of two--state dimers, a fact which has consequences on proteins connected with viral diseases.

cond-mat↗

arXiv2003

Self-organization and Mechanical Properties of Active Filament Bundles

A phenomenological description for active bundles of polar filaments is presented. The activity of the bundle results from crosslinks, that induce relative displacements between the aligned filaments. Our generic description is based on momentum conservation within the bundle. By specifying the internal forces, a simple minimal model for the bundle dynamics is obtained, capturing generic dynamic behaviors. In particular, contracted states as well as solitary and oscillatory waves appear through dynamic instabilities. The introduction of filament adhesion leads to self-organized persistent filament transport. Furthermore, calculating the tension, homogeneous bundles are shown to be able to actively contract and to perform work against external forces. Our description is motivated by dynamic phenomena in the cytoskeleton and could apply to stress-fibers and self-organization phenomena during cell-locomotion.

cond-mat.stat-mech↗

arXiv2002

A nonlinear dynamical model of human gait

We present a nonlinear stochastic model of the human gait control system in a variety of gait regimes. The stride interval time series in normal human gait is characterized by slightly multifractal fluctuations. The fractal nature of the fluctuations become more pronounced under both an increase and decrease in the average gait. Moreover, the long-range memory in these fluctuations is lost when the gait is keyed on a metronome. The human locomotion is controlled by a network of neurons capable of producing a correlated syncopated output. The central nervous system is coupled to the motocontrol system, and together they control the locomotion of the gait cycle itself. The metronomic gait is simulated by a forced nonlinear oscillator with a periodic external force associated with the conscious act of walking in a particular way.

cond-mat.stat-mech↗

arXiv2002

Applicability of the Fisher Equation to Bacterial Population Dynamics

The applicability of the Fisher equation, which combines diffusion with logistic nonlinearity, to population dynamics of bacterial colonies is studied with the help of explicit analytic solutions for the spatial distribution of a stationary bacterial population under a static mask. The mask protects the bacteria from ultraviolet light. The solution, which is in terms of Jacobian elliptic functions, is used to provide a practical prescription to extract Fisher equation parameters from observations and to decide on the validity of the Fisher equation.

nlin.AO↗

arXiv2003

Distances and classification of amino acids for different protein secondary structures

Window profiles of amino acids in protein sequences are taken as a description of the amino acid environment. The relative entropy or Kullback-Leibler distance derived from profiles is used as a measure of dissimilarity for comparison of amino acids and secondary structure conformations. Distance matrices of amino acid pairs at different conformations are obtained, which display a non-negligible dependence of amino acid similarity on conformations. Based on the conformation specific distances clustering analysis for amino acids is conducted.

physics.bio-ph↗