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arXiv (422,153 recursos)
This is one of the most extensive subject based repositories in the world in the field of physics, mathematics, astronomy, computer sciences and quantitative biology. This is the principal site with almost 20 mirror versions around the globe. The site is supported by an extensive collection of information and background documentation. An RSS feed is available for anyone interested in keeping up-to-date with newly added materials.

Mostrando recursos 61 - 80 de 4,680

61. Extraclassical receptive field phenomena & short-range connectivity in V1 - Wielaard, Jim; Sajda, Paul
Neural mechanisms of extraclassical receptive field phenomena in V1 are commonly assumed to result from long-range lateral connections and/or extrastriate feedback. We address two such phenomena: surround suppression and contrast dependent receptive field size. We present rigorous computational support for the hypothesis that the phenomena largely result from local short-range (< 0.5 mm) cortical connections and LGN input. Surround suppression in our simulations results from (A) direct cortical inhibition or (B) suppression of recurrent cortical excitation, or (C) action of both these mechanisms simultaneously. Mechanisms B and C are substantially more prevalent than A. We observe an average growth in the range of spatial summation of excitatory and inhibitory synaptic...

62. Modeling multi-cellular systems using sub-cellular elements - Newman, T. J.
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and inter-cellular potentials. Advantages of the model include i) adaptive cell-shape dynamics, ii) flexible accommodation of additional intra-cellular biology, and iii) the absence of an underlying grid. We present here a detailed description of the model, and use successive mean-field approximations to connect it to more coarse-grained approaches, such as discrete cell-based algorithms and coupled partial differential equations. We also discuss efficient algorithms for encoding the model, and give an example of a simulation of an epithelial sheet....

63. Geometric and physical considerations for realistic protein models - Hubner, Isaac A.; Shakhnovich, Eugene I.
Protein structure is generally conceptualized as the global arrangement or of smaller, local motifs of helices, sheets, and loops. These regular, recurring secondary structural elements have well-understood and standardized definitions in terms of amino acid backbone geometry and the manner in which hydrogen bonding requirements are satisfied. Recently, "tube" models have been proposed to explain protein secondary structure in terms of the geometrically optimal packing of a featureless cylinder. However, atomically detailed simulations demonstrate that such packing considerations alone are insufficient for defining secondary structure; both excluded volume and hydrogen bonding must be explicitly modeled for helix formation. These results have fundamental implications for the construction and interpretation of realistic...

64. Features and dimensions: Motion estimation in fly vision - Bialek, William; van Steveninck, Rob R. de Ruyter
We characterize the computation of motion in the fly visual system as a mapping from the high dimensional space of signals in the retinal photodetector array to the probability of generating an action potential in a motion sensitive neuron. Our approach to this problem identifies a low dimensional subspace of signals within which the neuron is most sensitive, and then samples this subspace to visualize the nonlinear structure of the mapping. The results illustrate the computational strategies predicted for a system that makes optimal motion estimates given the physical noise sources in the detector array. More generally, the hypothesis that neurons are sensitive to low dimensional subspaces of their...

65. Noise-enhanced computation in a model of a cortical column - Mayor, Julien; Gerstner, Wulfram
Varied sensory systems use noise in order to enhance detection of weak signals. It has been conjectured in the literature that this effect, known as stochastic resonance, may take place in central cognitive processes such as the memory retrieval of arithmetical multiplication. We show in a simplified model of cortical tissue, that complex arithmetical calculations can be carried out and are enhanced in the presence of a stochastic background. The performance is shown to be positively correlated to the susceptibility of the network, defined as its sensitivity to a variation of the mean of its inputs. For nontrivial arithmetic tasks such as multiplication, stochastic resonance is an emergent property...

66. Wiring cost in the organization of a biological network - Ahn, Yong-Yeol; Kim, Beom Jun; Jeong, Hawoong
To find out the role of the wiring cost in the organization of the neural network of the nematode \textit{Caenorhapditis elegans} (\textit{C. elegans}), we build the neuronal map of \textit{C. elegans} based on geometrical positions of neurons and define the cost as inter-neuronal Euclidean distance \textit{d}. We show that the wiring probability decays exponentially as a function of \textit{d}. Using the edge exchanging method and the component placement optimization scheme, we show that positions of neurons are not randomly distributed but organized to reduce the total wiring cost. Furthermore, we numerically study the trade-off between the wiring cost and the performance of the Hopfield model on the neural network.

67. Simulation of geographical trends in Chowdhury ecosystem model - Rohde, Klaus; Stauffer, Dietrich
A computer simulation based on individual births and deaths gives a biodiversity increasing from cold to warm climates, in agreement with reality. Complexity of foodwebs increases with time and at a higher rate at low latitudes, and there is a higher rate of species creation at low latitudes. Keeping many niches empty makes the results correspond more closely to natural gradients.

68. Diversity as a product of interspecial interactions - Lawson, Daniel; Jensen, Henrik Jeldtoft; Kaneko, Kunihiko
We demonstrate diversification rather than optimisation for highly interacting organisms in a well mixed biological system by means of a simple model and reference to experiment, and find the cause to be the complex network of interactions formed, allowing species less well adapted to an environment to flourish by co-interaction over the `best' species. This diversification can be considered as the construction of many co-evolutionary niches by the network of interactions between species. Evidence for this comes from work with the bacteria Escherichia coli, which may coexist with their own mutants under certain conditions. Diversification only occurs above a certain threshold interaction strength, below which competitive exclusion occurs.

69. A Predation Behavior Model Based on Game Theory - Chen, Shi; Bao, Sheng; Yan, Ling; Huang, Cheng
This article adopts game theory to build a model for explaining the predation behavior of animals.We assume that both the prey and the preydator have two stratigies in this game,the active one and the passive one.By calculating the outcome and the income of energy in different stratigies, we find the solution to analyze the different evolution path of both the prey and the predator.A simulation result approximately represents the correctness of our model.

70. Combinatorial rules of icosahedral capsid growth - Kerner, Richard
A model of growth of icosahedral viral capsids is proposed. It takes into account the diversity of hexamers' compositions, leading to definite capsid size. We show that the observed yield of capsid production implies a very high level of self-organization of elementary building blocks. The exact number of different protein dimers composing hexamers is related to the size of a given capsid, labeled by its T-number. Simple rules determining these numbers for each value of T are deduced and certain consequences are discussed.

71. Traveling wave solutions of Fitzhugh model with cross-diffusion - Berezovskaya, F.; Camacho, E.; Wirkus, S.; Karev, G.
The Fitzhugh-Nagumo equations have been used as a caricature of the Hodgkin-Huxley equations of neuron firing to better understand the essential dynamics of the interaction of the membrane potential and the restoring force and to capture, qualitatively, the general properties of an excitable membrane. Even though its simplicity allows very valuable insight to be gained, the accuracy of reproducing real experimental results is limited. In this paper, we utilize a modified version of the Fitzhugh-Nagumo equations to model the spatial propagation of neuron firing; we assume that this propagation is (at least, partially) caused by the cross-diffusion connection between the potential and recovery variables. We show that the cross-diffusion...

72. Dynamics of inhomogeneous populations and global demography models - Karev, Georgy P.
The dynamic theory of inhomogeneous populations developed during the last decade predicts several essential new dynamic regimes applicable even to the well-known, simple population models. We show that, in an inhomogeneous population with a distributed reproduction coefficient, the entire initial distribution of the coefficient should be used to investigate real population dynamics. In the general case, neither the average rate of growth nor the variance or any finite number of moments of the initial distribution is sufficient to predict the overall population growth. We developed methods for solving the heterogeneous models and explored the dynamics of the total population size together with the reproduction coefficient distribution. We show that, typically,...

73. Spatial dynamics of homochiralization - Multamaki, Tuomas; Brandenburg, Axel
The emergence and spreading of chirality on the early Earth is considered by studying a set of reaction-diffusion equations based on a polymerization model. It is found that effective mixing of the early oceans is necessary to reach the present homochiral state. The possibility of introducing mass extinctions and modifying the emergence rate of life is discussed.

74. Gene & Genome Duplication in Acanthamoeba Polyphaga Mimivirus - Suhre, Karsten
Gene duplication is key to molecular evolution in all three domains of life and may be the first step in the emergence of new gene function. It is a well recognized feature in large DNA viruses, but has not been studied extensively in the largest known virus to date, the recently discovered Acanthamoeba Polyphaga Mimivirus. Here we present a systematic analysis of gene and genome duplication events in the Mimivirus genome. We find that one third of the Mimivirus genes are related to at least one other gene in the Mimivirus genome, either through a large segmental genome duplication event that occurred in the more remote past, either...

75. Maximum Likelihood Jukes-Cantor Triplets: Analytic Solutions - Chor, Benny; Hendy, Michael D.; Snir, Sagi
Complex systems of polynomial equations have to be set up and solved algebraically in order to obtain analytic solutions for maximum likelihood on phylogenetic trees. This has restricted the types of systems previously resolved to the simplest models - three and four taxa under a molecular clock, with just two state characters. In this work we give, for the first time, analytic solutions for a family of trees with four state characters, like normal DNA or RNA. The model of substitution we use is the Jukes-Cantor model, and the trees are on three taxa under molecular clock, namely rooted triplets. We employ a number of approaches and...

76. Error thresholds in a mutation-selection model with Hopfield-type fitness - Garske, Tini
A deterministic mutation-selection model in the sequence space approach is investigated. Genotypes are identified with two-letter sequences. Mutation is modelled as a Markov process, fitness functions are of Hopfield type, where the fitness of a sequence is determined by the Hamming distances to a number of predefined patterns. Using a maximum principle for the population mean fitness in equilibrium, the error threshold phenomenon is studied for quadratic Hopfield-type fitness functions with small numbers of patterns. Different from previous investigations of the Hopfield model, the system shows error threshold behaviour not for all fitness functions, but only for certain parameter values.

77. Mesoscopic modeling for nucleic acid chain dynamics - Sales-Pardo, M.; Guimera, R.; Moreira, A. A.; Widom, J.; Amaral, L. A. N.
To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a novel mesoscopic-level computational model that provides a new window into nucleic acid dynamics. We model a single-stranded nucleic as a polymer chain whose monomers are the nucleosides. Each monomer comprises a bead representing the sugar molecule and a pin representing the base. The bead-pin complex can rotate about the backbone of the chain. We consider pairwise stacking and hydrogen-bonding interactions. We use a modified Monte Carlo dynamics that splits the dynamics into translational...

78. Robustness and Evolvability of the B Cell Mutator Mechanism - Theodosopoulos, Patricia; Theodosopoulos, Ted
We present a model that considers the maturation of the antibody population following primary antigen presentation as a global optimization problem. The trade-off that emerges from our model describes the balance between the safety of mutations that lead to local improvements in affinity and the necessity of the system to undergo global reconfigurations in the antibody's shape in order to achieve its goals, in this example of fast-paced evolution. The parameter p which quantifies this trade-off appears to be itself both robust and evolvable. This parallels the rapidity and consistency of the optimization operating during the biologic response. In this paper, we explore the robust qualities and evolvability of...

79. Giant viruses in the oceans : the 4th Algal Virus Workshop - Claverie, Jean-Michel
Giant double-stranded DNA viruses (such as record breaking Acanthamoeba polyphaga Mimivirus), with particle sizes of 0.2 to 0.6 micron, genomes of 300 kbp to 1.200 kbp, and commensurate complex gene contents, constitute an evolutionary mystery. They challenge the common vision of viruses, traditionally seen as highly streamlined genomes optimally fitted to the smallest possible -filterable- package. Such giant viruses are now discovered in increasing numbers through the systematic sampling of ocean waters as well as freshwater aquatic environments, where they play a significant role in controlling phyto- and bacterio- plankton populations. The 4th algal virus workshop showed that the study of these ecologically important viruses is now massively entering the...

80. Mutation model for nucleotide sequences based on crystal basis - Minichini, C.; Sciarrino, A.
A nucleotides sequence is identified, in the two (four) letters alphabet, by the the labels of a vector state of an irreducible representation of U_q(sl(2)) (U_q(sl(2) + sl(2))), in the limit q -> 0. A master equation for the distribution function is written, where the intensity of the one-spin flip is assumed to depend from the variation of the labels of the state. In the two letters approximation, the numerically computed equilibrium distribution for short sequences is nicely fitted by a Yule distribution, which is the observed distribution of the ranked short oligonucleotides frequency in DNA. The four letter alphabet description, applied to the codons, is able to...

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