arXiv
(422,153 recursos)
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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...
61.
