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At least 847 records · Page 47Linked to original sources

arXiv2000

Correlation property of length sequences based on global structure of complete genome

This paper considers three kinds of length sequences of the complete genome. Detrended fluctuation analysis, spectral analysis, and the mean distance spanned within time $L$ are used to discuss the correlation property of these sequences. The values of the exponents from these methods of these three kinds of length sequences of bacteria indicate that the long-range correlations exist in most of these sequences. The correlation have a rich variety of behaviours including the presence of anti-correlations. Further more, using the exponent $γ$, it is found that these correlations are all linear ($γ=1.0\pm 0.03$). It is also found that these sequences exhibit $1/f$ noise in some interval of frequency ($f>1$). The length of this interval of frequency depends on the length of the sequence. The shape of the periodogram in $f>1$ exhibits some periodicity. The period seems to depend on the length and the complexity of the length sequence.

physics.bio-ph↗

arXiv2000

Group selection models in prebiotic evolution

The evolution of enzyme production is studied analytically using ideas of the group selection theory for the evolution of altruistic behavior. In particular, we argue that the mathematical formulation of Wilson's structured deme model ({\it The Evolution of Populations and Communities}, Benjamin/Cumings, Menlo Park, 1980) is a mean-field approach in which the actual environment that a particular individual experiences is replaced by an {\it average} environment. That formalism is further developed so as to avoid the mean-field approximation and then applied to the problem of enzyme production in the prebiotic context, where the enzyme producer molecules play the altruists role while the molecules that benefit from the catalyst without paying its production cost play the non-altruists role. The effects of synergism (i.e., division of labor) as well as of mutations are also considered and the results of the equilibrium analysis are summarized in phase diagrams showing the regions of the space of parameters where the altruistic, non-altruistic and the coexistence regimes are stable. In general, those regions are delimitated by discontinuous transition lines which end at critical points.

cond-mat.stat-mech↗

arXiv2000

Coiling Instability of Multilamellar Membrane Tubes with Anchored Polymers

We study experimentally a coiling instability of cylindrical multilamellar stacks of phospholipid membranes, induced by polymers with hydrophobic anchors grafted along their hydrophilic backbone. Our system is unique in that coils form in the absence of both twist and adhesion. We interpret our experimental results in terms of a model in which local membrane curvature and polymer concentration are coupled. The model predicts the occurrence of maximally tight coils above a threshold polymer occupancy. A proper comparison between the model and experiment involved imaging of projections from simulated coiled tubes with maximal curvature and complicated torsions.

cond-mat.soft↗

arXiv2000

Theory of periodic swarming of bacteria: application to Proteus mirabilis

The periodic swarming of bacteria is one of the simplest examples for pattern formation produced by the self-organized collective behavior of a large number of organisms. In the spectacular colonies of Proteus mirabilis (the most common species exhibiting this type of growth) a series of concentric rings are developed as the bacteria multiply and swarm following a scenario periodically repeating itself. We have developed a theoretical description for this process in order to get a deeper insight into some of the typical processes governing the phenomena in systems of many interacting living units. All of our theoretical results are in excellent quantitative agreement with the complete set of available observations.

physics.bio-ph↗

arXiv2000

Thermodynamically Important Contacts in Folding of Model Proteins

We introduce a quantity, the entropic susceptibility, that measures the thermodynamic importance-for the folding transition-of the contacts between amino acids in model proteins. Using this quantity, we find that only one equilibrium run of a computer simulation of a model protein is sufficient to select a subset of contacts that give rise to the peak in the specific heat observed at the folding transition. To illustrate the method, we identify thermodynamically important contacts in a model 46-mer. We show that only about 50% of all contacts present in the protein native state are responsible for the sharp peak in the specific heat at the folding transition temperature, while the remaining 50% of contacts do not affect the specific heat.

cond-mat.stat-mech↗

arXiv2001

Stochastic Resonance in Neuron Models: Endogenous Stimulation Revisited

The paradigm of stochastic resonance (SR)---the idea that signal detection and transmission may benefit from noise---has met with great interest in both physics and the neurosciences. We investigate here the consequences of reducing the dynamics of a periodically driven neuron to a renewal process (stimulation with reset or endogenous stimulation). This greatly simplifies the mathematical analysis, but we show that stochastic resonance as reported earlier occurs in this model only as a consequence of the reduced dynamics.

physics.bio-ph↗

arXiv2001

Codon Distributions in DNA

The codons, sixtyfour in number, are distributed over the coding parts of DNA sequences. The distribution function is the plot of frequency-versus-rank of the codons. These distributions are characterised by parameters that are almost universal, i.e., gene independent. There is but a small part that depends on the gene. We present the theory to calculate the universal (gene-independent) part. The part that is gene-specific, however, has undetermined overlaps and fluctuations.

physics.bio-ph↗

arXiv2001

Diffusing-wave spectroscopy of nonergodic media

We introduce an elegant method which allows the application of diffusing-wave spectroscopy (DWS) to nonergodic, solid-like samples. The method is based on the idea that light transmitted through a sandwich of two turbid cells can be considered ergodic even though only the second cell is ergodic. If absorption and/or leakage of light take place at the interface between the cells, we establish a so-called "multiplication rule", which relates the intensity autocorrelation function of light transmitted through the double-cell sandwich to the autocorrelation functions of individual cells by a simple multiplication. To test the proposed method, we perform a series of DWS experiments using colloidal gels as model nonergodic media. Our experimental data are consistent with the theoretical predictions, allowing quantitative characterization of nonergodic media and demonstrating the validity of the proposed technique.

cond-mat.soft↗

arXiv2001

Epidemic dynamics and endemic states in complex networks

We study by analytical methods and large scale simulations a dynamical model for the spreading of epidemics in complex networks. In networks with exponentially bounded connectivity we recover the usual epidemic behavior with a threshold defining a critical point below which the infection prevalence is null. On the contrary, on a wide range of scale-free networks we observe the absence of an epidemic threshold and its associated critical behavior. This implies that scale-free networks are prone to the spreading and the persistence of infections whatever spreading rate the epidemic agents might possess. These results can help understanding computer virus epidemics and other spreading phenomena on communication and social networks.

cond-mat.stat-mech↗

arXiv2001

Designability of lattice model heteropolymers

Protein folds are highly designable, in the sense that many sequences fold to the same conformation. In the present work we derive an expression for the designability in a 20 letter lattice model of proteins which, relying only on the Central Limit Theorem, has a generality which goes beyond the simple model used in its derivation. This expression displays an exponential dependence on the energy of the optimal sequence folding on the given conformation measured with respect to the lowest energy of the conformational dissimilar structures, energy difference which constitutes the only parameter controlling designability. Accordingly, the designability of a native conformation is intimately connected to the stability of the sequences folding to them.

cond-mat↗

arXiv2001

Simulated ecology-driven sympatric speciation

We introduce a multi-locus genetically acquired phenotype, submitted to mutations and with selective value, in an age-structured model for biological aging. This phenotype describes a single-trait effect of the environment on an individual, and we study the resulting distribution of this trait among the population. In particular, our simulations show that the appearance of a double phenotypic attractor in the ecology induces the emergence of a stable polymorphism, as observed in the Galapagos finches. In the presence of this polymorphism, the simulations generate short-term speciation, when mating preferences are also allowed to suffer mutations and acquire selective value.

cond-mat.stat-mech↗

arXiv2001

Measure representation and multifractal analysis of complete genomes

This paper introduces the notion of measure representation of DNA sequences. Spectral analysis and multifractal analysis are then performed on the measure representations of a large number of complete genomes. The main aim of this paper is to discuss the multifractal property of the measure representation and the classification of bacteria. From the measure representations and the values of the $D_{q}$ spectra and related $C_{q}$ curves, it is concluded that these complete genomes are not random sequences. In fact, spectral analyses performed indicate that these measure representations considered as time series, exhibit strong long-range correlation. For substrings with length K=8, the $D_{q}$ spectra of all organisms studied are multifractal-like and sufficiently smooth for the $C_{q}$ curves to be meaningful. The $C_{q}$ curves of all bacteria resemble a classical phase transition at a critical point. But the 'analogous' phase transitions of chromosomes of non-bacteria organisms are different. Apart from Chromosome 1 of {\it C. elegans}, they exhibit the shape of double-peaked specific heat function.

physics.bio-ph↗

arXiv2001

Topological Properties of Citation and Metabolic Networks

Topological properties of "scale-free" networks are investigated by determining their spectral dimensions $d_S$, which reflect a diffusion process in the corresponding graphs. Data bases for citation networks and metabolic networks together with simulation results from the growing network model \cite{barab} are probed. For completeness and comparisons lattice, random, small-world models are also investigated. We find that $d_S$ is around 3 for citation and metabolic networks, which is significantly different from the growing network model, for which $d_S$ is approximately 7.5. This signals a substantial difference in network topology despite the observed similarities in vertex order distributions. In addition, the diffusion analysis indicates that whereas the citation networks are tree-like in structure, the metabolic networks contain many loops.

cond-mat.dis-nn↗

arXiv2001

Defensive alliances in spatial models of cyclical population interactions

As a generalization of the 3-strategy Rock-Scissors-Paper game dynamics in space, cyclical interaction models of six mutating species are studied on a square lattice, in which each species is supposed to have two dominant, two subordinated and a neutral interacting partner. Depending on their interaction topologies, these systems can be classified into four (isomorphic) groups exhibiting significantly different behaviors as a function of mutation rate. On three out of four cases three (or four) species form defensive alliances which maintain themselves in a self-organizing polydomain structure via cyclic invasions. Varying the mutation rate this mechanism results in an ordering phenomenon analogous to that of magnetic Ising model.

cond-mat.stat-mech↗

arXiv2001

Extinctions in the random replicator model

The statistical properties of an ecosystem composed of species interacting via pairwise, random interactions and deterministic, concentration limiting self-interaction are studied analytically with tools of equilibrium statistical mechanics of disordered systems. Emphasis is given to the effects of externally induced extinction of a fixed fraction of species at the outset of the evolutionary process. The manner the ecosystem copes with the initial extinction event depends on the degree of competition among the species as well as on the strength of that event. For instance, in the regime of high competition the ecosystem diversity, given by the fraction of surviving species, is practically insensitive to the strengt of the initial extinction provided it is not too large, while in the less competitive regime the diversity decreases linearly with the size of the event. In the case of large extinction events we find that no further biotic extinctions take place and, furthermore, that rare species become very unlikely to be found in the ecosystem at equilibrium. In addition, we show that the reciprocal of the Edwards-Anderson order parameter yields a good measure of the diversity of the model ecosystem.

cond-mat.dis-nn↗

arXiv2001

Proteinlike behavior of a spin system near the transition between ferromagnet and spin glass

A simple spin system is studied as an analog for proteins. We investigate how the introduction of randomness and frustration into the system effects the designability and stability of ground state configurations. We observe that the spin system exhibits protein-like behavior in the vicinity of the transition between ferromagnet and spin glass. Our results illuminate some guiding principles in protein evolution.

cond-mat.stat-mech↗

arXiv2001

Macroscopic equations for pattern formation in mixtures of microtubules and motors

Inspired by patterns observed in mixtures of microtubules and molecular motors, we propose continuum equations for the evolution of motor density, and microtubule orientation. The chief ingredients are the transport of motors along tubules, and the alignment of tubules in the process. The macroscopic equations lead to aster and vortex patterns in qualitative agreement with experiments. While the early stages of evolution of tubules are similar to coarsening of spins following a quench, the rearrangement of motors leads to arrested coarsening at low densities. Even in one dimension, the equations exhibit a variety of interesting behaviors, such as symmetry breaking, moving fronts, and motor localization.

cond-mat.stat-mech↗

arXiv2003

Statistical and Dynamical Study of Disease Propagation in a Small World Network

We study numerically statistical properties and dynamical disease propagation using a percolation model on a one dimensional small world network. The parameters chosen correspond to a realistic network of school age children. We found that percolation threshold decreases as a power law as the short cut fluctuations increase. We found also the number of infected sites grows exponentially with time and its rate depends logarithmically on the density of susceptibles. This behavior provides an interesting way to estimate the serology for a given population from the measurement of the disease growing rate during an epidemic phase. We have also examined the case in which the infection probability of nearest neighbors is different from that of short cuts. We found a double diffusion behavior with a slower diffusion between the characteristic times.

cond-mat.dis-nn↗