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At least 973 records · Page 54Linked to original sources
arXiv2000

Regularization of Synchronized Chaotic Bursts

The onset of regular bursts in a group of irregularly bursting neurons with different individual properties is one of the most interesting dynamical properties found in neurobiological systems. In this paper we show how synchronization among chaotically bursting cells can lead to the onset of regular bursting. In order to clearly present the mechanism behind such regularization we model the individual dynamics of each cell with a simple two-dimensional map that produces chaotic bursting behavior similar to biological neurons.

nlin.CD↗
arXiv2001

Dynamic concentration of motors in microtubule arrays

We present experimental and theoretical studies of the dynamics of molecular motors in microtubule arrays and asters. By solving a convection-diffusion equation we find that the density profile of motors in a two-dimensional aster is characterized by continuously varying exponents. Simulations are used to verify the assumptions of the continuum model. We observe the concentration profiles of kinesin moving in quasi two-dimensional artificial asters by fluorescent microscopy and compare with our theoretical results.

cond-mat.soft↗
arXiv2001

The coherent dynamics of photoexcited green fluorescent proteins

The coherent dynamics of vibronic wave packets in the green fluorescent protein is reported. At room temperature the non-stationary dynamics following impulsive photoexcitation displays an oscillating optical transmissivity pattern with components at 67 fs (497 cm-1) and 59 fs (593 cm-1). Our results are complemented by ab initio calculations of the vibrational spectrum of the chromophore. This analysis shows the interplay between the dynamics of the aminoacidic structure and the electronic excitation in the primary optical events of green fluorescent proteins.

physics.bio-ph↗
arXiv2001

The shape of ecological networks

We study the statistics of ecosystems with a variable number of co-evolving species. The species interact in two ways: by prey-predator relationships and by direct competition with similar kinds. The interaction coefficients change slowly through successful adaptations and speciations. We treat them as quenched random variables. These interactions determine long-term topological features of the species network, which are found to agree with those of biological systems.

nlin.AO↗
arXiv2001

Mutual Information of Population Codes and Distance Measures in Probability Space

We studied the mutual information between a stimulus and a large system consisting of stochastic, statistically independent elements that respond to a stimulus. The Mutual Information (MI) of the system saturates exponentially with system size. A theory of the rate of saturation of the MI is developed. We show that this rate is controlled by a distance function between the response probabilities induced by different stimuli. This function, which we term the {\it Confusion Distance} between two probabilities, is related to the Renyi $α$-Information.

cond-mat.stat-mech↗
arXiv2001

The future is noisy: on the role of spatial fluctuations in genetic switching

A genetic switch may be realised by a certain operator sector on the DNA strand from which either genetic code, to the left or to the right of this operator sector, can be transcribed and the corresponding information processed. This switch is controlled by messenger molecules, i.e., they determine to which side the switch is flipped. Recently, it has been realised that noise plays an elementary role in genetic switching, and the effect of number fluctuations of the messenger molecules have been explored. Here we argue that the assumption of well-stirredness taken in the previous models may not be sufficient to characterise the influence of noise: {\em spatial} fluctuations play a non-negligible part in cellular genetic switching processes.

cond-mat.stat-mech↗
arXiv2001

Noise Effects on the Complex Patterns of Abnormal Heartbeats

Patients at high risk for sudden death often exhibit complex heart rhythms in which abnormal heartbeats are interspersed with normal heartbeats. We analyze such a complex rhythm in a single patient over a 12-hour period and show that the rhythm can be described by a theoretical model consisting of two interacting oscillators with stochastic elements. By varying the magnitude of the noise, we show that for an intermediate level of noise, the model gives best agreement with key statistical features of the dynamics.

cond-mat.stat-mech↗
arXiv2001

Swarming ring patterns in bacterial colonies exposed to ultraviolet radiation

We report a novel morphological transition in a Bacillus subtilis colony initially growing under ambient conditions, after ultraviolet radiation exposure. The bacteria in the central regions of the colonies are observed to migrate towards the colony edge forming a ring during uniform spatial exposure. When the radiation is switched off, the colonies were observed to grow both inward into the evacuated regions as well as outward indicating that the pattern is not formed due to depletion of nutrients at the center of the colony. We also propose a reaction-diffusion model in which waste-limited chemotaxis initiated by the UV radiation leads to the observed phenomenology.

cond-mat↗
arXiv2002

Neural Network Model for Apparent Deterministic Chaos in Spontaneously Bursting Hippocampal Slices

A neural network model that exhibits stochastic population bursting is studied by simulation. First return maps of inter-burst intervals exhibit recurrent unstable periodic orbit (UPO)-like trajectories similar to those found in experiments on hippocampal slices. Applications of various control methods and surrogate analysis for UPO-detection also yield results similar to those of experiments. Our results question the interpretation of the experimental data as evidence for deterministic chaos and suggest caution in the use of UPO-based methods for detecting determinism in time-series data.

cond-mat.dis-nn↗
arXiv2002

Roles of stiffness and excluded volume in DNA denaturation

The nature and the universal properties of DNA thermal denaturation are investigated by Monte Carlo simulations. For suitable lattice models we determine the exponent c describing the decay of the probability distribution of denaturated loops of length l, $P \sim l^{-c}$. If excluded volume effects are fully taken into account, c= 2.10(4) is consistent with a first order transition. The stiffness of the double stranded chain has the effect of sharpening the transition, if it is continuous, but not of changing its order and the value of the exponent c, which is also robust with respect to inclusion of specific base-pair sequence heterogeneities.

cond-mat.stat-mech↗
arXiv2001

Adaptive sampling by information maximization

The investigation of input-output systems often requires a sophisticated choice of test inputs to make best use of limited experimental time. Here we present an iterative algorithm that continuously adjusts an ensemble of test inputs online, subject to the data already acquired about the system under study. The algorithm focuses the input ensemble by maximizing the mutual information between input and output. We apply the algorithm to simulated neurophysiological experiments and show that it serves to extract the ensemble of stimuli that a given neural system ``expects'' as a result of its natural history.

physics.bio-ph↗
arXiv2002

Self-Segregation vs. Clustering in the Evolutionary Minority Game

Complex adaptive systems have been the subject of much recent attention. It is by now well-established that members (`agents') tend to self-segregate into opposing groups characterized by extreme behavior. However, while different social and biological systems manifest different payoffs, the study of such adaptive systems has mostly been restricted to simple situations in which the prize-to-fine ratio, $R$, equals unity. In this Letter we explore the dynamics of evolving populations with various different values of the ratio $R$, and demonstrate that extreme behavior is in fact {\it not} a generic feature of adaptive systems. In particular, we show that ``confusion'' and ``indecisiveness'' take over in times of depression, in which case cautious agents perform better than extreme ones.

cond-mat↗
arXiv2001

A model of inversion of DNA charge by a positive polymer: fractionization of the polymer charge

Charge inversion of a DNA double helix by an oppositely charged flexible polyelectrolyte (PE) is considered. We assume that, in the neutral state of the DNA-PE complex, each of the DNA charges is locally compensated by a PE charge. When an additional PE molecule is adsorbed by DNA, its charge gets fractionized into monomer charges of defects (tails and arches) on the background of the perfectly neutralized DNA. These charges spread all over the DNA eliminating the self-energy of PE. This fractionization mechanism leads to a substantial inversion of the DNA charge, a phenomenon which is widely used for gene delivery.

cond-mat.soft↗
arXiv2002

A model for mutation in bacterial populations

We describe the evolution of $E.coli$ populations through a Bak-Sneppen type model which incorporates random mutations. We show that, for a value of the mutation level which coincides with the one estimated from experiments, this model reproduces the measures of mean fitness relative to that of a common ancestor, performed for over 10,000 bacterial generations.

physics.bio-ph↗
arXiv2001

Rippling patterns in aggregates of myxobacteria arise from cell-cell collisions

Experiments with myxobacterial aggregates reveal standing waves called rippling patterns. Here, these structures are modelled with a simple discrete model based on the interplay between migration and collisions of cells. Head-to-head collisions of cells result in cell reversals. To correctly reproduce the rippling patterns, a refractory phase after each cell reversal has to be assumed, during which further reversal is prohibited. The duration of this phase determines the wavelength and period of the ripple patterns as well as the reversal frequency of single cells.

physics.bio-ph↗
arXiv2002

Complementarity and diversity in a soluble model ecosystem

Complementarity among species with different traits is one of the basic processes affecting biodiversity, defined as the number of species in the ecosystem. We present here a soluble model ecosystem in which the species are characterized by binary traits and their pairwise interactions follow a complementarity principle. Manipulation of the species composition, and so the study of its effects on the species diversity is achieved through the introduction of a bias parameter favoring one of the traits. Using statistical mechanics tools we find explicit expressions for the allowed values of the equilibrium species concentrations in terms of the control parameters of the model.

cond-mat.dis-nn↗
arXiv2002

Extreme self-organization in networks constructed from gene expression data

We study networks constructed from gene expression data obtained from many types of cancers. The networks are constructed by connecting vertices that belong to each others' list of K-nearest-neighbors, with K being an a priori selected non-negative integer. We introduce an order parameter for characterizing the homogeneity of the networks. On minimizing the order parameter with respect to K, degree distribution of the networks shows power-law behavior in the tails with an exponent of unity. Analysis of the eigenvalue spectrum of the networks confirms the presence of the power-law and small-world behavior. We discuss the significance of these findings in the context of evolutionary biological processes.

cond-mat.soft↗