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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 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.

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