arXiv
(422,153 recursos)
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Mostrando recursos 41 - 60 de 4,680
41.
A new model for the immune clonal networks - Gafiychuk, V. V.; Prykarpatsky, A. K.
This paper deals with a new model for clonal network dynamics. We describe in
detail this model and derive special equations governing immune system dynamics
based on the general gradient type principles that can be inherent to a wide
class of real living objects. A special clonal network is modeled by two
symmetric projector matrix variables simultaneously taking into account both
asymmetry of the interaction to each other and adaptation states that can be
realized owing to possible idiotypic clonal suppresions. We perform computer
simulations of the model dynamics for some simple cases of relatively low
dimension, paying special attention to the dynamics of amounts of activated
receptor strings...
42.
The reaction-diffusion approach to morphogenesis - Dilao, Rui
Morphogenesis is the ensemble of processes that determines form, shape and
patterns in organisms. Based on a reaction-diffusion theoretical setting and
some prototype reaction schemes, we make a review of the models and experiments
that support possible mechanisms of morphogenesis. We present specific case
studies from chemistry (Belousov-Zhabotinsky reaction) and biology (formation
of wing eyespots patterns in butterflies). We show the importance of
conservation laws in the establishment of patterning in biological systems, and
their relevance to explain phenotypic plasticity in living organisms. Mass
conservation introduces a memory effect in biological development and
phenotypic plasticity in patterns of living organisms can be explained by
differences on the initial conditions occurring...
43.
Complete structure of topographic maps in ephrin-A deficient mice - Tsigankov, D. N.; Koulakov, A. A.
Axons of retinal ganglion cells establish orderly projections to the superior
colliculus of the midbrain. Axons of neighboring cells terminate proximally in
the superior colliculus thus forming a topographically precise representation
of the visual world. Coordinate axes are encoded in retina and in the target
through graded expression of chemical labels. Mapping based on chemical labels
alone does not yield required specificity of connections. Additional sharpening
is provided by electrical activity, which is correlated between neighboring
axons. Here we propose a quantitative model which allows combining the effects
of chemical labels and correlated activity in a single approach. Using this
model we study a complete structure of two-dimensional topographic...
44.
Controlled DNA compaction within chromatin: the tail-bridging effect - Muehlbacher, Frank; Holm, Christian; Schiessel, Helmut
We study the mechanism underlying the attraction between nucleosomes, the
fundamental packaging units of DNA inside the chromatin complex. We introduce a
simple model of the nucleosome, the eight-tail colloid, consisting of a charged
sphere with eight oppositely charged, flexible, grafted chains that represent
the terminal histone tails. We demonstrate that our complexes are attracted via
the formation of chain bridges and that this attraction can be tuned by
changing the fraction of charged monomers on the tails. This suggests a
physical mechanism of chromatin compaction where the degree of DNA condensation
can be controlled via biochemical means, namely the acetylation and
deacetylation of lysines in the histone tails.
45.
New symmetry in nucleotide sequences - Makarova, M. A.; Sadovsky, M. G.
Information valuable words are the strings with the significant deviation of
real frequency from the expected one. The expected frequency is determined
through the maximum entropy principle of the reconstructed (extended) frequency
dictionary of strings composed from the shorter words. The information valuable
words are found to be the complementary palindromes: they are read equally in
opposite directions, if nucleotides are changed for the complementary ones (A
<--> T; C <--> G) in one of them. Some properties of such symmetric words are
discussed.
46.
On the Statistical Law of Life - Pugno, N. M.
In this paper we derive a statistical law of Life. It governs the probability
of death, or complementary of survival, of the living organisms. We have
deduced such a law coupling the widely used Weibull statistics, developed for
describing the distribution of the strength of solids, with the universal model
for ontogenetic growth only recently proposed by West and co-authors. The main
idea presented in this paper is that cracks can propagate in solids and cause
their failure as sick cells in living organisms can cause their death. Making a
rough analogy, living organisms are found to behave as growing mechanical
components under cyclic, i.e., fatigue, loadings and...
47.
Sociophysics Simulations III: Retirement Demography - Zekri, Lotfi; Stauffer, Dietrich
This third part of the lecture series deals with the question: Who will pay
for your retirement? For Western Europe the answer may be ``nobody'', but for
Algeria the demography looks more promising.
48.
Simulation of stem cell survival in small crypts - Stauffer, Dietrich; Domany, Eytan
Monte Carlo simulations of the number of stem cells in human colon crypts
allow for fluctuations which kill the population after sufficiently long times.
49.
Species Abundances Distribution in Neutral Community Models - Neda, Z.; Ravasz, M.
An analytical approximation is derived for the Zero Sum Multinomial
distribution which gives the Species Abundance Distribution in Neutral
Community Models. The obtained distribution function describes well computer
simulation results on the model, and leads to an interesting relation between
the total number of individuals, total number of species and the size of the
most abundant species of the considered metacommunity. Computer simulations on
neutral community models, proves also the validity of this scaling relation.
50.
Nucleation and the transition state of the SH3 domain - Hubner, Isaac A.; Edmonds, Katherine A.; Shakhnovich, Eugene I.
We present a verified computational model of the SH3 domain transition state
(TS) ensemble. This model was built for three separate SH3 domains using
experimental s in all-atom protein folding simulations. While averaging over
all conformations incorrectly considers non-TS conformations as transition
states, quantifying structures as pre-TS, TS, and post-TS by measurement of
their transmission coefficient (pfold, or probability to fold) allows for
rigorous conclusions regarding the structure of the folding nucleus and a full
mechanistic analysis of the folding process. Through analysis of the TS, we
observe a highly polarized nucleus in which many residues are solvent-exposed.
Mechanistic analysis suggests the hydrophobic core forms largely after an early
nucleation...
51.
Computational Theory of Biological Function I - Maimon, Ron
This series presents an approach to mathematical biology which makes precise
the function of biological molecules. Because biological systems compute, the
theory is a general purpose computer language. I build a language for
efficiently representing the function of protein-like molecules in a cell. The
first paper only presents the kinematic part of the formalism, but this is
already useful for representing large-scale protein networks. The full
formalism allows us to investigate the properties of protein interaction
models, ultimately yielding an estimate of the random-access memory of the
proteins, a measure of their capacity for computation.
52.
Quantifying Influenza Vaccine Efficacy and Antigenic Distance - Gupta, Vishal; Earl, David J.; Deem, Michael W.
We introduce a new measure of antigenic distance between influenza A vaccine
and circulating strains. The measure correlates well with efficacies of the
H3N2 influenza A component of the annual vaccine between 1971 and 2004, as do
results of a theory of the immune response to influenza following vaccination.
This new measure of antigenic distance is correlated with vaccine efficacy to a
greater degree than are current state-of-the-art phylogenetic sequence analyzes
or ferret antisera inhibition assays. We suggest that this new measure of
antigenic distance be used in the design of the annual influenza vaccine and in
the interpretation of vaccine efficacy monitoring.
53.
Extracellular-to-intracellular signal transfer via G-proteins - Scheler, Gabriele
We look at the problem of signal transduction by extracellular agonist
binding to a receptor protein at the membrane (sensor) via binding of
G-proteins (effectors) to a highly integrative target molecule, such as the
second messenger cAMP (target). We explore the effects of binding times,
effector assignment and effector pool size on the shape of the output signal
under different input scenarios. We conclude that low rates of information
transfer may sometimes coincide with a high probability or efficiency of
plasticity induction.
54.
Free energy adopted stochastic optimization protein folding - Fukumi, Toshio
Optimal structure of proteins is described by linear stochastic differential
equation with mean decrease of free energy and volatility. Structure
determining strategy is given by a twin of stochastic variables for which
empirical conditions are not postulated. Optimal structure determination will
be deformed to be adoptive to trading strategy employing martingale property
where stochastic integral w.r.t. analytical solution of stochastic differential
equation will be employed.
55.
Metabolic Network Modelling: Including Stochastic Effects - Ao, P.
We propose to model the dynamics of metabolic networks from a systems biology
point of view by four dynamical structure elements: potential function,
transverse matrix, degradation matrix, and stochastic force. These four
elements are balanced to determine the network dynamics, which gives arise to a
special stochastic differential equation supplemented by a relationship between
the stochastic force and the degradation matrix. Important network behaviors
can be obtained from the potential function without explicitly solving for the
time-dependent solution. The existence of such a potential function suggests a
global optimization principle, and the existence stochastic force corresponds
natural to the hierarchical structure in metabolic networks. We provide
theoretical evidences to justify...
56.
Geometrical constraints in a gene network model and pattern formation - Diambra, L.; Costa, Luciano da Fontoura
A fundamental task in developmental biology is to identify the mechanisms
which drive morphogenesis. In many cases, pattern formation is driven by the
positional information determined by both the gradient of maternal factors and
hard-wired mechanisms embedded in the genome. Alternative mechanisms of
positional information that contribute to patterning are the influence of
signals derived from surrounding tissues. In this paper, we show that the
interplay of geometrical constraints imposed by tissue shapes and hard-wired
mechanisms, computationally implemented by a gene network model, can able to
induce stable complex patterns. The rise of these patterns depends strongly on
the geometrical constraints such as the shape of the surrounding tissues.
57.
PCA deciphers genome - Gorban, A. N.; Zinovyev, A. Yu.
In this paper, we give a tutorial for undergraduate students studying
statistical methods and/or bioinformatics. The students learn how data
visualization can help in genomic sequences analysis. Students start with a
fragment of genetic text of a bacterial genome and analyze its structure. By
means of principal component analysis they ``discover'' that the information in
genome is encoded by non-overlapping triplets. Next, they learn to find gene
positions. This exercise on principal component analysis and K-Means clustering
gives a possibility for active study of the basic bioinformatics notions. In
Appendix the program listings for MatLab are published.
58.
Mimivirus Relatives in the Sargasso Sea - Ghedin, Elodie; Claverie, Jean-Michel
The discovery and genome analysis of Acanthamoeba polyphaga Mimivirus, the
largest known DNA virus, challenged much of the accepted dogma regarding
viruses. Its particle size (>400 nm), genome length (1.2 million bp) and huge
gene repertoire (911 protein coding genes) all contribute to blur the
established boundaries between viruses and the smallest parasitic cellular
organisms. Phylogenetic analyses also suggested that the Mimivirus lineage
could have emerged prior to the individualization of cellular organisms from
the three established domains, triggering a debate that can only be resolved by
generating and analyzing more data. The next step is then to seek some evidence
that Mimivirus is not the only representative of...
59.
Neutral Theory and Relative Species Abundance in Ecology - Volkov, Igor; Banavar, Jayanth R.; Hubbell, Stephen P.; Maritan, Amos
The theory of island biogeography[1] asserts that an island or a local
community approaches an equilibrium species richness as a result of the
interplay between the immigration of species from the much larger metacommunity
source area and local extinction of species on the island (local community).
Hubbell[2] generalized this neutral theory to explore the expected steady-state
distribution of relative species abundance (RSA) in the local community under
restricted immigration. Here we present a theoretical framework for the unified
neutral theory of biodiversity[2] and an analytical solution for the
distribution of the RSA both in the metacommunity (Fisher's logseries) and in
the local community, where there are fewer rare species....
60.
Scaling properties of the Penna model - Brigatti, E.; Martins, J. S. Sa'; Roditi, I.
We investigate the scaling properties of the Penna model, which has become a
popular tool for the study of population dynamics and evolutionary problems in
recent years. We find that the model generates a normalised age distribution
for which a simple scaling rule is proposed, that is able to reproduce
qualitative features for all genome sizes.
41.
