SEARCH · Searcharxiv

Results for “q-bio”

Search indexed arXiv papers on artificial intelligence, large language models, computer vision and robotics. Read source abstracts and follow links to arXiv.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 829 records · Page 46Linked to original sources

arXiv1999

Multiplicity of species in some replicative systems

In an attempt to explain the uniqueness of the coding mechanism of living cells as contrasted with multi-species structure of ecosystems we examine two models of individuals with some replicative properties. In the first model the system generically remains in a multi-species state. Even though for some of these species the replicative probability is very high, they are unable to invade the system. In the second model, in which the death rate depends on the type of the species, the system relatively quickly reaches a single-species state and fluctuations might at most bring it to yet another single-species state.

cond-mat.stat-mech↗

arXiv2000

Statistical Analysis of Genealogical Trees for Polygamic Species

Repetitions within a given genealogical tree provides some information about the degree of consanguineity of a population. They can be analyzed with techniques usually employed in statistical physics when dealing with fixed point transformations. In particular we show that the tree features strongly depend on the fractions of males and females in the population, and also on the offspring probability distribution. We check different possibilities, some of them relevant to human groups, and compare them with simulations.

cond-mat.stat-mech↗

arXiv1999

Early Stages of Homopolymer Collapse

Interest in the protein folding problem has motivated a wide range of theoretical and experimental studies of the kinetics of the collapse of flexible homopolymers. In this Paper a phenomenological model is proposed for the kinetics of the early stages of homopolymer collapse following a quench from temperatures above to below the theta temperature. In the first stage, nascent droplets of the dense phase are formed, with little effect on the configurations of the bridges that join them. The droplets then grow by accreting monomers from the bridges, thus causing the bridges to stretch. During these two stages the overall dimensions of the chain decrease only weakly. Further growth of the droplets is accomplished by the shortening of the bridges, which causes the shrinking of the overall dimensions of the chain. The characteristic times of the three stages respectively scale as the zeroth, 1/5 and 6/5 power of the the degree of polymerization of the chain.

cond-mat.soft↗

arXiv2000

Modeling study on the validity of a possibly simplified representation of proteins

The folding characteristics of sequences reduced with a possibly simplified representation of five types of residues are shown to be similar to their original ones with the natural set of residues (20 types or 20 letters). The reduced sequences have a good foldability and fold to the same native structure of their optimized original ones. A large ground state gap for the native structure shows the thermodynamic stability of the reduced sequences. The general validity of such a five-letter reduction is further studied via the correlation between the reduced sequences and the original ones. As a comparison, a reduction with two letters is found not to reproduce the native structure of the original sequences due to its homopolymeric features.

physics.bio-ph↗

arXiv2000

Simulated Coevolution in a Mutating Ecology

The bit-string Penna Model is used to simulate the competition between an asexual parthenogenetic and a sexual population sharing the same environment. A new-born of either population can mutate and become a part of the other with some probability. In a stable environment the sexual population soon dies out. When an infestation by fastly mutating genetically coupled parasites is introduced however, sexual reproduction prevails, as predicted by the so-called Red Queen hypothesis for the evolution of sex.

cond-mat.stat-mech↗

arXiv2000

Extinction transition in bacterial colonies under forced convection

We report the spatio-temporal response of {\it Bacillus subtilis} growing on a nutrient-rich layer of agar to ultra-violet (UV) radiation. Below a crossover temperature, the bacteria are confined to regions that are shielded from UV radiation. A forced convection of the population is effected by rotating a UV radiation shield relative to the petri dish. The extinction speed at which the bacterial colony lags behind the shield is found to be qualitatively similar to the front velocity of the colony growing in the absence of the hostile environment as predicted by the model of Dahmen, Nelson and Shnerb. A quantitative comparison is not possible without considering the slow dynamics and the time-dependent interaction of the population with the hostile environment.

cond-mat↗

arXiv2000

Emergent global oscillations in heterogeneous excitable media: The example of pancreatic beta cells

Using the standard van der Pol-FitzHugh-Nagumo excitable medium model I demonstrate a novel generic mechanism, diversity, that provokes the emergence of global oscillations from individually quiescent elements in heterogeneous excitable media. This mechanism may be operating in the mammalian pancreas, where excitable beta cells, quiescent when isolated, are found to oscillate when coupled despite the absence of a pacemaker region.

nlin.CD↗

arXiv2000

Learning and generation of long-range correlated sequences

We study the capability to learn and to generate long-range, power-law correlated sequences by a fully connected asymmetric network. The focus is set on the ability of neural networks to extract statistical features from a sequence. We demonstrate that the average power-law behavior is learnable, namely, the sequence generated by the trained network obeys the same statistical behavior. The interplay between a correlated weight matrix and the sequence generated by such a network is explored. A weight matrix with a power-law correlation function along the vertical direction, gives rise to a sequence with a similar statistical behavior.

cond-mat.dis-nn↗

arXiv2000

Synchronous Behavior of Two Coupled Electronic Neurons

We report on experimental studies of synchronization phenomena in a pair of analog electronic neurons (ENs). The ENs were designed to reproduce the observed membrane voltage oscillations of isolated biological neurons from the stomatogastric ganglion of the California spiny lobster Panulirus interruptus. The ENs are simple analog circuits which integrate four dimensional differential equations representing fast and slow subcellular mechanisms that produce the characteristic regular/chaotic spiking-bursting behavior of these cells. In this paper we study their dynamical behavior as we couple them in the same configurations as we have done for their counterpart biological neurons. The interconnections we use for these neural oscillators are both direct electrical connections and excitatory and inhibitory chemical connections: each realized by analog circuitry and suggested by biological examples. We provide here quantitative evidence that the ENs and the biological neurons behave similarly when coupled in the same manner. They each display well defined bifurcations in their mutual synchronization and regularization. We report briefly on an experiment on coupled biological neurons and four dimensional ENs which provides further ground for testing the validity of our numerical and electronic models of individual neural behavior. Our experiments as a whole present interesting new examples of regularization and synchronization in coupled nonlinear oscillators.

nlin.CD↗

arXiv2000

Dynamical chaos and power spectra in toy models of heteropolymers and proteins

The dynamical chaos in Lennard-Jones toy models of heteropolymers is studied by molecular dynamics simulations. It is shown that two nearby trajectories quickly diverge from each other if the heteropolymer corresponds to a random sequence. For good folders, on the other hand, two nearby trajectories may initially move apart but eventually they come together. Thus good folders are intrinsically non-chaotic. A choice of a distance of the initial conformation from the native state affects the way in which a separation between the twin trajectories behaves in time. This observation allows one to determine the size of a folding funnel in good folders. We study the energy landscapes of the toy models by determining the power spectra and fractal characteristics of the dependence of the potential energy on time. For good folders, folding and unfolding trajectories have distinctly different correlated behaviors at low frequencies.

cond-mat.stat-mech↗

arXiv2000

Temporal correlations versus noise in the correlation matrix formalism: an example of the brain auditory response

We adopt the concept of the correlation matrix to study correlations among sequences of time-extended events occuring repeatedly at consecutive time-intervals. As an application we analyse the magnetoencephalography recordings obtained from human auditory cortex in epoch mode during delivery of sound stimuli to the left or right ear. We look into statistical properties and the eigenvalue spectrum of the correlation matrix C calculated for signals corresponding to different trials and originating from the same or opposite hemispheres. The spectrum of C largely agrees with the universal properties of the Gaussian orthogonal ensemble of random matrices, with deviations characterised by eigenvectors with high eigenvalues. The properties of these eigenvectors and eigenvalues provide an elegant and powerful way of quantifying the degree of the underlying collectivity during well defined latency intervals with respect to stimulus onset. We also extend this analysis to study the time-lagged interhemispheric correlations, as a computationally less demanding alternative to other methods such as mutual information.

cond-mat.stat-mech↗

arXiv2000

New approach to Monte Carlo calculation of buckling of supercoiled DNA loops

The short supercoiled circular DNA molecules are shown to be glassy systems and canonical Metropolis Monte Carlo simulations of the systems tend to get stuck in local metastable energy basins. A novel Monte Carlo algorithm is developed to alleviate the problem of ``ergodicity breaking'' of the glassy systems, in which the Markov process is driven by an explicitly analytic weight factor with enhanced probability in both low- and high-energy regions. To characterize the degree of puckering of the supercoiled DNA loops, a new quantity of aplanarity is introduced as the shortest principal axis of configurational ellipsoid of DNA. With the suggested Monte Carlo method, the quantitative correlation between supercoiling degree and buckling of DNA is attained. With supercoiling stress increasing, the conformational transition from a circle to mono-, diplo- or triple interwound superhelical structure will take place in a successive but decreasingly abrupt mode.

cond-mat.soft↗

arXiv2000

Random networks created by biological evolution

We investigate a model of evolving random network, introduced by us previously {[}{\it Phys. Rev. Lett.} {\bf 83}, 5587 (1999){]} . The model is a generalization of the Bak-Sneppen model of biological evolution, with the modification that the underlying network can evolve by adding and removing sites. The behavior and the averaged properties of the network depend on the parameter $p$, the probability to establish link to the newly introduced site. For $p=1$ the system is self-organized critical, with two distinct power-law regimes with forward-avalanche exponents $τ=1.98\pm 0.04$ and $τ^\prime = 1.65\pm 0.05$. The average size of the network diverge as power-law when $p\to 1$. We study various geometrical properties of the network: probability distribution of sizes and connectivities, size and number of disconnected clusters and the dependence of mean distance between two sites on the cluster size. The connection with models of growing networks with preferential attachment is discussed.

cond-mat.stat-mech↗

arXiv2000

A Cellular Automata Model for Citrus Variagated Chlorosis

A cellular automata model is proposed to analyze the progress of Citrus Variegated Chlorosis epidemics in São Paulo oranges plantation. In this model epidemiological and environmental features, such as motility of sharpshooter vectors which perform Lévy flights, hydric and nutritional level of plant stress and seasonal climatic effects, are included. The observed epidemics data were quantitatively reproduced by the proposed model varying the parameters controlling vectors motility, plant stress and initial population of diseased plants.

cond-mat.stat-mech↗

arXiv2000

Symmetry breaking and coarsening in spatially distributed evolutionary processes including sexual reproduction and disruptive selection

Sexual reproduction presents significant challenges to formal treatment of evolutionary processes. A starting point for systematic treatments of ecological and evolutionary phenomena has been provided by the gene centered view of evolution which assigns effective fitness to each allele instead of each organism. The gene centered view can be formalized as a dynamic mean field approximation applied to genes in reproduction / selection dynamics. We show that the gene centered view breaks down for symmetry breaking and pattern formation within a population; and show that spatial distributions of organisms with local mating neighborhoods in the presence of disruptive selection give rise to such symmetry breaking and pattern formation in the genetic composition of local populations. Global dynamics follows conventional coarsening of systems with nonconserved order parameters. The results have significant implications for the ecology of genetic diversity and species formation.

physics.bio-ph↗

arXiv2000

Fast Quantum Search Algorithms in Protein Sequence Comparison - Quantum Biocomputing

Quantum search algorithms are considered in the context of protein sequence comparison in biocomputing. Given a sample protein sequence of length m (i.e m residues), the problem considered is to find an optimal match in a large database containing N residues. Initially, Grover's quantum search algorithm is applied to a simple illustrative case - namely where the database forms a complete set of states over the 2^m basis states of a m qubit register, and thus is known to contain the exact sequence of interest. This example demonstrates explicitly the typical O(sqrt{N}) speedup on the classical O(N) requirements. An algorithm is then presented for the (more realistic) case where the database may contain repeat sequences, and may not necessarily contain an exact match to the sample sequence. In terms of minimizing the Hamming distance between the sample sequence and the database subsequences the algorithm finds an optimal alignment, in O(sqrt{N}) steps, by employing an extension of Grover's algorithm, due to Boyer, Brassard, Hoyer and Tapp for the case when the number of matches is not a priori known.

quant-ph↗

arXiv1999

Kullback-Leibler and Renormalized Entropy: Applications to EEGs of Epilepsy Patients

Recently, renormalized entropy was proposed as a novel measure of relative entropy (P. Saparin et al., Chaos, Solitons & Fractals 4, 1907 (1994)) and applied to several physiological time sequences, including EEGs of patients with epilepsy. We show here that this measure is just a modified Kullback-Leibler (K-L) relative entropy, and it gives similar numerical results to the standard K-L entropy. The latter better distinguishes frequency contents of e.g. seizure and background EEGs than renormalized entropy. We thus propose that renormalized entropy might not be as useful as claimed by its proponents. In passing we also make some critical remarks about the implementation of these methods.

physics.bio-ph↗

arXiv2000

Putting Proteins back into Water

We introduce a simplified protein model where the solvent (water) degrees of freedom appear explicitly (although in an extremely simplified fashion). Using this model we are able to recover the thermodynamic phenomenology of proteins over a wide range of temperatures. In particular we describe both the warm and the {\it cold} protein denaturation within a single framework, while addressing important issues about the structure of model proteins.

cond-mat.stat-mech↗