arXiv
(422,153 recursos)
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Mostrando recursos 181 - 200 de 4,680
181.
DNA condensation and redissolution: Interaction between overcharged DNA
molecules - Allahyarov, E.; Gompper, G.; Löwen, H.
The effective DNA-DNA interaction force is calculated by computer simulations
with explicit tetravalent counterions and monovalent salt. For overcharged DNA
molecules, the interaction force shows a double-minimum structure. The
positions and depths of these minima are regulated by the counterion density in
the bulk. Using two-dimensional lattice sum and free energy perturbation
theories, the coexisting phases for DNA bundles are calculated. A
DNA-condensation and redissolution transition and a stable mesocrystal with an
intermediate lattice constant for high counterion concentration are obtained.
182.
Energetic model of tumor growth - Castorina, Paolo; Zappalá, Dario
A macroscopic model of the tumor Gompertzian growth is proposed. This
approach is based on the energetic balance among the different cell activities,
described by methods of statistical mechanics and related to the growth
inhibitor factors. The model is successfully applied to the multicellular tumor
spheroid data.
183.
Is abundant A-to-I RNA editing primate-specific? - Eisenberg, Eli; Nemzer, Sergey; Kinar, Yaron; Sorek, Rotem; Rechavi, Gideon; Levanon, Erez Y.
A-To-I RNA editing is common to all eukaryotes, associated with various
neurological functions. Recently, A-to-I editing was found to occur abundantly
in the human transcriptome. Here we show that the frequency of A-to-I editing
in humans is at least an order of magnitude higher as that of mouse, rat,
chicken or fly. The extraordinary frequency of RNA editing in human is
explained by the dominance of the primate-specific Alu element in the human
transcriptome, which increases the number of double-stranded RNA substrates.
184.
The efficiency of multi-target drugs: the network approach might help
drug design - Csermely, Peter; Agoston, Vilmos; Pongor, Sandor
Despite considerable progress in genome- and proteome-based high-throughput
screening methods and rational drug design, the number of successful single
target drugs did not increase appreciably during the past decade. Network
models suggest that partial inhibition of a surprisingly small number of
targets can be more efficient than the complete inhibition of a single target.
This and the success stories of multi-target drugs and combinatorial therapies
led us to suggest that systematic drug design strategies should be directed
against multiple targets. We propose that the final effect of partial, but
multiple drug actions might often surpass that of complete drug action at a
single target. The future success of this...
185.
Elasticities and stabilities: lipid membranes vs cell membranes - Tu, Z. C.; An, R.; Ou-Yang, Z. C.
A cell membrane can be simply regarded as composite material consisting of
lipid bilayer, membrane cytoskeleton beneath lipid bilayer, and proteins
embedded in lipid bilayer and linked with membrane cytoskeleton if one only
concerns its mechanical properties. In this Chapter, above all, the authors
give a brief introduction to some important work on mechanical properties of
lipid bilayers following Helfrich's seminal work on spontaneous curvature
energy of lipid bilayers. Next, the entropy of a polymer confined in a curved
surface and the free energy of membrane cytoskeleton are obtained by scaling
analysis. It is found that the free energy of cell membranes has the form of
the in-plane strain...
186.
An approximate threshold condition for non-autonomous system: an
application to a vector-borne infection - Coutinho, F. A. B.; Burattini, M. N.; Lopez, L. F.; Massad, E.
An non-autonomous system is proposed to model the seasonal pattern of dengue
fever. We found that an approximate threshold condition for infection
persistence describes all possible behavior of the system. As far as we know,
the kind of analysis here proposed is entirely new. No precise mathematical
theorems are demonstrated but we give enough numerical evidence to support the
conclusions.
187.
Base pair interactions and hybridization isotherms of matched and
mismatched oligonucleotide probes on microarrays - Binder, Hans; Preibisch, Stephan; Kirsten, Toralf
The lack of specificity in microarray experiments due to non-specific
hybridization raises a serious problem for the analysis of microarray data
because the residual chemical background intensity is not related to the
expression degree of the gene of interest. We analyzed the concentration
dependence of the signal intensity of perfect match (PM) and mismatch (MM)
probes in terms using a microscopic binding model using a combination of mean
hybridization isotherms and single base related affinity terms. The signal
intensities of the PM and MM probes and their difference are assessed with
regard to their sensitivity, specificity and resolution for gene expression
measures. The presented theory implies the refinement of...
188.
A schematic age-structured compartment model of the impact of
antiretroviral therapy on HIV incidence and prevalence - Lopez, L. F.; Coutinho, F. A. B.; Burattini, M. N.; Massad, E.
A simple deterministic model is proposed to represent the basic aspects
concerning the effects of different antiretroviral treatment schedules on HIV
incidence and prevalence of affected populations. The model mimics current
treatment guidelines applied in Brazil. However, the model does not intend to
fit the data with any acceptable degree of accuracy since uncertainties on the
values of the parameters and on the precise effect of the treatment put some
limits on the practical implications of our model from which only orders of
magnitude and some qualitative effects can be deduced. So, this paper intends
to provide a conceptual and mechanistic understanding of the possible long term
effects of...
189.
A New Simulated Annealing Algorithm for the Multiple Sequence Alignment
Problem: The approach of Polymers in a Random Media - Hernández-Guía, M.; Mulet, R.; Rodríguez-Pérez, S.
We proposed a probabilistic algorithm to solve the Multiple Sequence
Alignment problem. The algorithm is a Simulated Annealing (SA) that exploits
the representation of the Multiple Alignment between $D$ sequences as a
directed polymer in $D$ dimensions. Within this representation we can easily
track the evolution in the configuration space of the alignment through local
moves of low computational cost. At variance with other probabilistic
algorithms proposed to solve this problem, our approach allows for the creation
and deletion of gaps without extra computational cost. The algorithm was tested
aligning proteins from the kinases family. When D=3 the results are consistent
with those obtained using a complete algorithm. For...
190.
Thermosynthesis as energy source for the RNA World: a new model for the
origin of life - Muller, Anthonie W. J.
The thermosynthesis concept, biological free energy gain from thermal
cycling, is combined with the concept of the RNA World. The resulting overall
origin of life model gives new explanations for the emergence of the genetic
code and the ribosome. The first protein named pF1 obtains the energy to
support the RNA world by a thermal variation of F1 ATP synthase's binding
change mechanism. This pF1 is the single translation product during the
emergence of the genetic machinery. During thermal cycling pF1 condenses many
substrates with broad specificity, yielding NTPs and randomly constituted
protein and RNA libraries that contain (self)-replicating RNA. The smallness of
pF1 permits the emergence of the...
191.
Predicting Residue-wise Contact Orders of Native Protein Structure from
Amino Acid Sequence - Kinjo, Akira R.; Nishikawa, Ken
Residue-wise contact order (RWCO) is a new kind of one-dimensional protein
structures which represents the extent of long-range contacts. We have recently
shown that a set of three types of one-dimensional structures (secondary
structure, contact number, and RWCO) contains sufficient information for
reconstructing the three-dimensional structure of proteins. Currently, there
exist prediction methods for secondary structure and contact number from amino
acid sequence, but none exists for RWCO. Also, the properties of amino acids
that affect RWCO is not clearly understood. Here, we present a linear
regression-based method to predict RWCO from amino acid sequence, and analyze
the regression parameters to identify the properties that correlates with the
RWCO. The...
192.
Chemical organization theory: towards a theory of constructive dynamical
systems - Dittrich, Peter; di Fenizio, Pietro Speroni
Complex dynamical networks consisting of many components that interact and
produce each other are difficult to understand, especially, when new components
may appear. In this paper we outline a theory to deal with such systems. The
theory consists of two parts. The first part introduces the concept of a
chemical organization as a closed and mass-maintaining set of components. This
concept allows to map a complex (reaction) network to the set of organizations,
providing a new view on the system's structure. The second part connects
dynamics with the set of organizations, which allows to map a movement of the
system in state space to a movement in the...
193.
Identification and Measurement of Neighbor Dependent Nucleotide
Substitution Processes - Arndt, Peter F.; Hwa, Terence
The presence of neighbor dependencies generated a specific pattern of
dinucleotide frequencies in all organisms. Especially, the
CpG-methylation-deamination process is the predominant substitution process in
vertebrates and needs to be incorporated into a more realistic model for
nucleotide substitutions. Based on a general framework of nucleotide
substitutions we develop a method that is able to identify the most relevant
neighbor dependent substitution processes, measure their strength, and judge
their importance to be included into the modeling. Starting from a model for
neighbor independent nucleotide substitution we successively add neighbor
dependent substitution processes in the order of their ability to increase the
likelihood of the model describing given data. The analysis...
194.
Substantial regional variation in substitution rates in the human
genome: importance of GC content, gene density and telomere-specific effects - Arndt, Peter F; Hwa, Terence; Petrov, Dmitri A
This study presents the first global, 1 Mbp level analysis of patterns of
nucleotide substitutions along the human lineage. The study is based on the
analysis of a large amount of repetitive elements deposited into the human
genome since the mammalian radiation, yielding a number of results that would
have been difficult to obtain using the more conventional comparative method of
analysis. This analysis revealed substantial and consistent variability of
rates of substitution, with the variability ranging up to 2-fold among
different regions. The rates of substitutions of C or G nucleotides with A or T
nucleotides vary much more sharply than the reverse rates suggesting that much
of...
195.
Predator-prey cycles from resonant amplification of demographic
stochasticity - McKane, A. J.; Newman, T. J.
In this paper we present the simplest individual level model of predator-prey
dynamics and show, via direct calculation, that it exhibits cycling behavior.
The deterministic analogue of our model, recovered when the number of
individuals is infinitely large, is the Volterra system (with density-dependent
prey reproduction) which is well-known to fail to predict cycles. This
difference in behavior can be traced to a resonant amplification of demographic
fluctuations which disappears only when the number of individuals is strictly
infinite. Our results indicate that additional biological mechanisms, such as
predator satiation, may not be necessary to explain observed predator-prey
cycles in real (finite) populations.
196.
Competing Polymerization of Actin Skeleton explains Relation between
Network Polarity and Cell Movements - Nandy, B.; Baumgaertner, A.
Based on experimental observations it is known that various biological cells
exhibit a persistent random walk during migration on flat substrates. The
persistent random walk is characterized by `stop-and-go' movements :
unidirectional motions over distances of the order of several cell diameter are
separated by localized short time erratic movements. Using computer simulations
the reasons for this phenomena had been unveiled and shown to be attributed to
two antagonistic nucleation processes during the polymerization of the cell's
actin cytoskeleton : the (ordinary) spontaneous nucleation and the dendritic
nucleation processes. Whereas spontaneous nucleations generate actin filaments
growing in different directions and hence create motions in random directions,
dendritic nucleations provide a...
197.
Dynamics of competing species in a model of adaptive radiations and
macroevolution - De Blasio, Birgitte Freiesleben; De Blasio, Fabio Vittorio
We present a simple model of adaptive radiations in evolution based on
species competition. Competition is found to promote species divergence and
branching, and to dampen the net species production. In the model simulations,
high taxonomic diversification and branching take place during the beginning of
the radiation. The results show striking similarities with empirical data and
highlight the mechanism of competition as an important driving factor for
accelerated evolutionary transformation.
198.
Uncorrelated two-state single molecule trajectories from reducible
kinetic schemes - Flomenbom, Ophir; Klafter, Joseph
Trajectories of on-off events are the output of many single molecule
experiments. Usually, one describes the underlying mechanism that generates the
trajectory using a kinetic scheme, and by analyzing the trajectory aims at
deducing this scheme. In a previous work [O. Flomenbom, J. Klafter, and A.
Szabo, submitted (2004)], we showed that when successive events along a
trajectory are uncorrelated, all the information in the trajectory is contained
in two basic functions, which are the waiting time probability functions (PDFs)
of the on state and of the off state. The kinetic schemes that lead to such
uncorrelated trajectories were termed reducible. Here we discuss the reasons
that lead to...
199.
Molecular Phylogenetic Analyses and Real Life Data - Hoef-Emden, Kerstin
In molecular phylogeny, relationships among organisms are reconstructed using
DNA or protein sequences and are displayed as trees. A linear increase in the
number of sequences results in an exponential increase of possible trees. Thus,
inferring trees from molecular data was shown to be NP-hard. This causes
problems, if large data sets are used. This review gives an introduction to
molecular phylogenetic methods and to the problems biologists are facing in
molecular phylogenetic analyses.
200.
Heisenberg uncertainty principle for thermal response of the
microtubules excited by ultra-short laser pulses - Marciak-Kozlowska, J.; Kozlowski, M.; Pelc, M.
In this paper the heat signaling in microtubules (MT) is investigated. It is
argued that for the description of the heat signaling phenomena in MT, the
hyperbolic heat transport (HHT) equation must be used. It is shown that HHT is
the Klein-Gordon (K-G) equation. The general solution for the K-G equation for
MT is obtained. For the undistorted signal propagation in MT the Heisenberg
uncertainty principle is formulated and discussed.
Key words: Microtubules; Heat signaling; Klein-Gordon equation; Heisenberg
principle.
181.
