Searcharxiv⌕ Search

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 865 records · Page 48Linked to original sources

The spike-timing-dependent learning rule to encode spatiotemporal patterns in a network of spiking neurons

We study associative memory neural networks based on the Hodgkin-Huxley type of spiking neurons. We introduce the spike-timing-dependent learning rule, in which the time window with the negative part as well as the positive part is used to describe the biologically plausible synaptic plasticity. The learning rule is applied to encode a number of periodical spatiotemporal patterns, which are successfully reproduced in the periodical firing pattern of spiking neurons in the process of memory retrieval. The global inhibition is incorporated into the model so as to induce the gamma oscillation. The occurrence of gamma oscillation turns out to give appropriate spike timings for memory retrieval of discrete type of spatiotemporal pattern. The theoretical analysis to elucidate the stationary properties of perfect retrieval state is conducted in the limit of an infinite number of neurons and shows the good agreement with the result of numerical simulations. The result of this analysis indicates that the presence of the negative and positive parts in the form of the time window contributes to reduce the size of crosstalk term, implying that the time window with the negative and positive parts is suitable to encode a number of spatiotemporal patterns. We draw some phase diagrams, in which we find various types of phase transitions with change of the intensity of global inhibition.

cond-mat.dis-nn↗

Nonequilibrium phase transitions in a model for the origin of life

The requisites for the persistence of small colonies of self-replicating molecules living in a two-dimensional lattice are investigated analytically in the infinite diffusion or mean-field limit and through Monte Carlo simulations in the position-fixed or contact process limit. The molecules are modeled by hipercyclic replicators A which are capable of replicating via binary fission A + E --2A with production rates s as well as via catalytically assisted replication 2A + E --3A with rate c. In addition, a molecule can degrade into its source materials E with rate $γ$. In the asymptotic regime the population can be characterized by the presence (active phase) and the absence (empty phase) of replicators in the lattice. In both diffusion regimes, we find that for small values of the ratio c/$γ$ these phases are separated by a second-order phase transition which is in the universality class of the directed percolation, while for small values s/$gamma$ the phase transition is of first order. Furthermore, we illustrate the suitability of the dynamic Monte Carlo method, which is based on the analysis of the spreading behaviour of a few active cells in the center of an otherwise infinite empty lattice, to adress the problem of emergence of replicators. Rather surprisingly, we show that this method allows an unambiguous identification of the order of the nonequilibrium phase transition.

physics.bio-ph↗

Percolation and epidemics in a two-dimensional small world

Percolation on two-dimensional small-world networks has been proposed as a model for the spread of plant diseases. In this paper we give an analytic solution of this model using a combination of generating function methods and high-order series expansion. Our solution gives accurate predictions for quantities such as the position of the percolation threshold and the typical size of disease outbreaks as a function of the density of "shortcuts" in the small-world network. Our results agree with scaling hypotheses and numerical simulations for the same model.

cond-mat.stat-mech↗

Epidemic dynamics in finite size scale-free networks

Many real networks present a bounded scale-free behavior with a connectivity cut-off due to physical constraints or a finite network size. We study epidemic dynamics in bounded scale-free networks with soft and hard connectivity cut-offs. The finite size effects introduced by the cut-off induce an epidemic threshold that approaches zero at increasing sizes. The induced epidemic threshold is very small even at a relatively small cut-off, showing that the neglection of connectivity fluctuations in bounded scale-free networks leads to a strong over-estimation of the epidemic threshold. We provide the expression for the infection prevalence and discuss its finite size corrections. The present work shows that the highly heterogeneous nature of scale-free networks does not allow the use of homogeneous approximations even for systems of a relatively small number of nodes.

cond-mat.stat-mech↗

Numerical comparison of two approaches for the study of phase transitions in small systems

We compare two recently proposed methods for the characterization of phase transitions in small systems. The validity and usefulness of these approaches are studied for the case of the q=4 and q=5 Potts model, i.e. systems where a thermodynamic limit and exact results exist. Guided by this analysis we discuss then the helix-coil transition in polyalanine, an example of structural transitions in biological molecules.

cond-mat.stat-mech↗

DNA hybridization to mismatched templates: a chip study

High-density oligonucleotide arrays are among the most rapidly expanding technologies in biology today. In the {\sl GeneChip} system, the reconstruction of the target concentration depends upon the differential signal generated from hybridizing the target RNA to two nearly identical templates: a perfect match (PM) and a single mismatch (MM) probe. It has been observed that a large fraction of MM probes repeatably bind targets better than the PMs, against the usual expectation from sequence-specific hybridization; this is difficult to interpret in terms of the underlying physics. We examine this problem via a statistical analysis of a large set of microarray experiments. We classify the probes according to their signal to noise ($S/N$) ratio, defined as the eccentricity of a (PM, MM) pair's `trajectory' across many experiments. Of those probes having large $S/N$ ($>3$) only a fraction behave consistently with the commonly assumed hybridization model. Our results imply that the physics of DNA hybridization in microarrays is more complex than expected, and they suggest new ways of constructing estimators for the target RNA concentration.

physics.bio-ph↗

The role of body rotation in bacterial flagellar bundling

In bacterial chemotaxis, E. coli cells drift up chemical gradients by a series of runs and tumbles. Runs are periods of directed swimming, and tumbles are abrupt changes in swimming direction. Near the beginning of each run, the rotating helical flagellar filaments which propel the cell form a bundle. Using resistive-force theory, we show that the counter-rotation of the cell body necessary for torque balance is sufficient to wrap the filaments into a bundle, even in the absence of the swirling flows produced by each individual filament.

cond-mat.soft↗

Atomic Force Microscopy of height fluctuations of fibroblast cells

We investigated the nanometer scale height fluctuations of 3T3 fibroblast cells with the atomic force microscope (AFM) under physiological conditions. Correlation between these fluctuations and lateral cellular motility can be observed. Fluctuations measured on leading edges appear to be predominantly related to actin polymerization-depolymerization processes. We found fast (5 Hz) pulsatory behavior with 1--2 nm amplitude on a cell with low motility showing emphasized structure of stress fibres. Myosin driven contractions of stress fibres are thought to induce this pulsation.

physics.bio-ph↗

Modeling of Spiking-Bursting Neural Behavior Using Two-Dimensional Map

A simple model that replicates the dynamics of spiking and spiking-bursting activity of real biological neurons is proposed. The model is a two-dimensional map which contains one fast and one slow variable. The mechanisms behind generation of spikes, bursts of spikes, and restructuring of the map behavior are explained using phase portrait analysis. The dynamics of two coupled maps which model the behavior of two electrically coupled neurons is discussed. Synchronization regimes for spiking and bursting activity of these maps are studied as a function of coupling strength. It is demonstrated that the results of this model are in agreement with the synchronization of chaotic spiking-bursting behavior experimentally found in real biological neurons.

nlin.CD↗

Monte Carlo simulation of the transmission of measles: Beyond the mass action principle

We present a Monte Carlo simulation of the transmission of measles within a population sample during its growing and equilibrium states by introducing two different vaccination schedules of one and two doses. We study the effects of the contact rate per unit time $ξ$ as well as the initial conditions on the persistence of the disease. We found a weak effect of the initial conditions while the disease persists when $ξ$ lies in the range 1/L-10/L ($L$ being the latent period). Further comparison with existing data, prediction of future epidemics and other estimations of the vaccination efficiency are provided. Finally, we compare our approach to the models using the mass action principle in the first and another epidemic region and found the incidence independent of the number of susceptibles after the epidemic peak while it strongly fluctuates in its growing region. This method can be easily applied to other human, animals and vegetable diseases and includes more complicated parameters.

cond-mat.dis-nn↗

Morphological Instability and Dynamics of Fronts in Bacterial Growth Models with Nonlinear Diffusion

It has been argued that there is biological and modeling evidence that a non-linear diffusion coefficient of the type D(b) = D_0 b^{k} underlies the formation of a number of growth patterns of bacterial colonies. We study a reaction-diffusion system with a non-linear diffusion coefficient introduced by Ben-Jacob et al. Due to the fact that the bacterial diffusion coefficient vanishes when the bacterial density b -> 0, the standard linear stability analysis for fronts cannot be used. We introduce an extension of the stability analysis which can be applied to such singular fronts, map out the region of stability in the D-k-plane and derive an interfacial approximation in some limits. Our linear stability analysis and sharp interface formulation will also be applicable to other examples of interface formation due to nonlinear diffusion, like in porous media or in the problem of vortex motion in superconductors.

cond-mat.stat-mech↗

Class of self-limiting growth models in the presence of nonlinear diffusion

The source term in a reaction-diffusion system, in general, does not involve explicit time dependence. A class of self-limiting growth models dealing with animal and tumor growth and bacterial population in a culture, on the other hand are described by kinetics with explicit functions of time. We analyze a reaction-diffusion system to study the propagation of spatial front for these models.

physics.bio-ph↗

The spread of epidemic disease on networks

The study of social networks, and in particular the spread of disease on networks, has attracted considerable recent attention in the physics community. In this paper, we show that a large class of standard epidemiological models, the so-called susceptible/infective/removed (SIR) models can be solved exactly on a wide variety of networks. In addition to the standard but unrealistic case of fixed infectiveness time and fixed and uncorrelated probability of transmission between all pairs of individuals, we solve cases in which times and probabilities are non-uniform and correlated. We also consider one simple case of an epidemic in a structured population, that of a sexually transmitted disease in a population divided into men and women. We confirm the correctness of our exact solutions with numerical simulations of SIR epidemics on networks.

cond-mat.stat-mech↗

On the nonlinear dynamics of topological solitons in DNA

Dynamics of topological solitons describing open states in the DNA double helix are studied in the frameworks of the model which takes into account asymmetry of the helix. It is shown that three types of topological solitons can occur in the DNA double chain. Interaction between the solitons, their interactions with the chain inhomogeneities and stability of the solitons with respect to thermal oscillations are investigated.

physics.bio-ph↗

Scaling in DNA unzipping models: denaturated loops and end-segments as branches of a block copolymer network

For a model of DNA denaturation, exponents describing the distributions of denaturated loops and unzipped end-segments are determined by exact enumeration and by Monte Carlo simulations in two and three dimensions. The loop distributions are consistent with first order thermal denaturation in both cases. Results for end-segments show a coexistence of two distinct power laws in the relative distributions, which is not foreseen by a recent approach in which DNA is treated as a homogeneous network of linear polymer segments. This unexpected feature, and the discrepancies with such an approach, are explained in terms of a refined scaling picture in which a precise distinction is made between network branches representing single stranded and effective double stranded segments.

cond-mat.stat-mech↗

Fluctuation Analysis of Human Electroencephalogram

The scaling behaviors of the human electroencephalogram (EEG) time series are studied using detrended fluctuation analysis. Two scaling regions are found in nearly every channel for all subjects examined. The scatter plot of the scaling exponents for all channels (up to 129) reveals the complicated structure of a subject's brain activity. Moment analyses are performed to extract the gross features of all the scaling exponents, and another universal scaling behavior is identified. A one-parameter description is found to characterize the fluctuation properties of the nonlinear behaviors of the brain dynamics.

physics.med-ph↗

Simplified amino acid alphabets based on deviation of conditional probability from random background

The primitive data for deducing the Miyazawa-Jernigan contact energy or BLOSUM score matrix consists of pair frequency counts. Each amino acid corresponds to a conditional probability distribution. Based on the deviation of such conditional probability from random background, a scheme for reduction of amino acid alphabet is proposed. It is observed that evident discrepancy exists between reduced alphabets obtained from raw data of the Miyazawa-Jernigan's and BLOSUM's residue pair counts. Taking homologous sequence database SCOP40 as a test set, we detect homology with the obtained coarse-grained substitution matrices. It is verified that the reduced alphabets obtained well preserve information contained in the original 20-letter alphabet.

physics.bio-ph↗