http://biblioteca.universia.net/verColeccion.do?id=8466 Mostrando recursos 1 - 20 de 4,680 es http://biblioteca.universia.net/img/logotipo.jpg http://biblioteca.universia.net/ http://biblioteca.universia.net/ficha.do?id=20880358 Exact numerical methods and stochastic simulation methods are developed to study the force stretching single RNA issue on the secondary structure level in equilibrium. By computing the force-extension curves on the constant force and the constant extension ensembles, we find the two independent methods agree with each other quite well. To show the precision of our methods in predicting unfolding experiments, the unfolding forces of different RNA molecules under different experimental conditio... Liu, Fei; Zhu, Bi-hui; Ou-Yang, Zhong-can http://biblioteca.universia.net/ficha.do?id=20880362 A model for the processive movement of dynein is presented based on experimental observations available. In the model, the change from strong microtubule-binding to weak binding of dynein is determined naturally by the variation of the relative orientation between the two interacting surfaces of the stalk tip and the microtubule as the stalk rotates from the ADP.Vi-state orientation to the apo-state orientation. This means that the puzzling communication from the ATP binding site in the globu... Xie, Ping; Dou, Shuo-Xing; Wang, Peng-Ye http://biblioteca.universia.net/ficha.do?id=20880363 Gene sequences in the vicinity of splice sites are found to possess dinucleotide periodicities, especially RR and YY, with the period close to the pitch of nucleosome DNA. This confirms previously reported finding about preferential positioning of splice junctions within the nucleosomes. The RR and YY dinucleotides oscillate counterphase, i.e., their respective preferred positions are shifted about half-period one from another, as it was observed earlier for AA and TT dinucleotides. Species s... Kogan, Simon; Trifonov, Edward N. http://biblioteca.universia.net/ficha.do?id=20880364 The evolutionary reason for the increase in gene length from archaea to prokaryotes to eukaryotes observed in large scale genome sequencing efforts has been unclear. We propose here that the increasing complexity of protein-protein interactions has driven the selection of longer proteins, as longer proteins are more able to distinguish among a larger number of distinct interactions due to their greater average surface area. Annotated protein sequences available from the SWISS-PROT database we... Tan, Taison; Frenkel, Daan; Gupta, Vishal; Deem, Michael W. http://biblioteca.universia.net/ficha.do?id=20880365 Most brain models focus on associative memory or calculation capability, experimentally inaccessible using physiological methods. Here we present a model explaining a basic feature of electroencephalograms (EEG). Our model is based on an electrical network with threshold firing and plasticity of synapses that reproduces very robustly the measured exponent 0.8 of the medical EEG spectra, a solid evidence for self-organized criticality. Our result are also valid on small-world lattices. We prop... de Arcangelis, Lucilla; Herrmann, Hans J.; Perrone-Capano, Carla http://biblioteca.universia.net/ficha.do?id=20880366 Finite size effects on the cooperative thermal denaturation of proteins are considered. A dimensionless measure of cooperativity, Omega, scales as N^zeta, where N is the number of amino acids. Surprisingly, we find that zeta is universal with zeta = 1 + gamma, where the exponent gamma characterizes the divergence of the susceptibility for a self-avoiding walk. Our lattice model simulations and experimental data are consistent with the theory. Our finding rationalizes the marginal stability of... Li, Mai Suan; Klimov, D. K.; Thirumalai, D. http://biblioteca.universia.net/ficha.do?id=20880367 We have analysed the possibility of scaling the sexual Penna ageing model. Assuming that the number of genes expressed before the reproduction age grows linearly with the genome size and that the mutation rate per genome and generation is constant, we have found that the fraction of defective genes expressed before the minimum reproduction age drops with the genome size, while the number of defective genes eliminated by the genetic death grows with genome size. Thus, the evolutionary costs de... Laszkiewicz, A.; Cebrat, S.; Stauffer, D. http://biblioteca.universia.net/ficha.do?id=20880369 A simplified interaction potential for protein folding studies at the atomic level is discussed and tested on a set of peptides with about 20 residues each. The test set contains both alpha-helical (Trp cage, Fs) and beta-sheet (GB1p, GB1m2, GB1m3, Betanova, LLM) peptides. The model, which is entirely sequence-based, is able to fold these different peptides for one and the same choice of model parameters. Furthermore, the melting behavior of the peptides is in good quantitative agreement with... Irbäck, Anders; Mohanty, Sandipan http://biblioteca.universia.net/ficha.do?id=20880370 Finite size effects on the calorimetric cooperatity of the folding-unfolding transition in two-state proteins are considered using the Go lattice models with and without side chains. We show that for models without side chains a dimensionless measure of calorimetric cooperativity kappa2 defined as the ratio of the van't Hoff to calorimetric enthalpy does not depend on the number of amino acids N. The average value of kappa2 is about 3/4 which is lower than the experimental value kappa2=1. For... Li, Mai Suan; Klimov, D. K.; Thirumalai, D. http://biblioteca.universia.net/ficha.do?id=20880371 Recent simulations of the solid phase DNA amplification (SPA) by J.-F. Mercier et al (Biophys. J. 85 (2003) 2075) are generalized to include two kinds of primers and the off-lattice character of the primer distribution on the surface. The sigmoidal character of the primer occupation by DNA, observed experimentally, is reproduced in the simulation. We discuss an influence of two parameters on the efficience of the amplification process: the initial density p_0 of the occupied primers from the ... Krawczyk, M. J.; Kulakowski, K. http://biblioteca.universia.net/ficha.do?id=20880372 Sequence comparison across multiple organisms aids in the detection of regions under selection. However, resource limitations require a prioritization of genomes to be sequenced. This prioritization should be grounded in two considerations: the lineal scope encompassing the biological phenomena of interest, and the optimal species within that scope for detecting functional elements. We introduce a statistical framework for optimal species subset selection, based on maximizing power to detect ... McAuliffe, Jon D.; Jordan, Michael I.; Pachter, Lior http://biblioteca.universia.net/ficha.do?id=20880373 Single molecule FRET (fluorescence resonance energy transfer) is a powerful technique for detecting real-time conformational changes and molecular interactions during biological reactions. In this review, we examine different techniques of extending observation times via immobilization and illustrate how useful biological information can be obtained from single molecule FRET time trajectories with or without absolute distance information. Rasnik, Ivan; McKinney, Sean A.; Ha, Taekjip http://biblioteca.universia.net/ficha.do?id=20880374 An ensemble of directed macromolecules on a lattice is considered, where the constituting molecules are chosen as a random sequence of N different types. The same type of molecules experiences a hard-core (exclusion) interaction. We study the robustness of the macromolecules with respect to breaking and substituting individual molecules, using a 1/N expansion. The properties depend strongly on the density of macromolecules. In particular, the macromolecules are robust against breaking and sub... Moseley, Christopher; Ziegler, Klaus http://biblioteca.universia.net/ficha.do?id=20880375 The vibrational dynamics of a DNA molecule with counterions neutralizing the charged phosphate groups have been studied. With the help of elaborated model the conformational vibrations of the DNA double helix with alkaline metal ions have been described both qualitatively and quantitatively. For the complexes of DNA with counterions Li+, Na+, K+, Rb+ and Cs+ the normal modes have been found, and a mode characterized by the most notable ion displacements with respect to the DNA backbone has be... Perepelytsya, S. M.; Volkov, S. N. http://biblioteca.universia.net/ficha.do?id=20880376 Emerging evidence suggests that the introns and intergenic sequences of the genomes of higher eukaryotes (the ``junk'' DNA) codes for a vast, RNA-based, genetic regulatory network. It is believed that this network is responsible for the variety and complexity of terrestrial life. We conjecture that this regulatory network is more properly viewed as an RNA ``community'', composed of a rich and largely unexplored biochemical web of RNA interactions. Viewed as an RNA-community, we hypothesize th... Tannenbaum, Emmanuel http://biblioteca.universia.net/ficha.do?id=20880378 The algebraic structures of the genetic code are most important to obtain additional information about the semantic code and its applications. In this paper we define two dual Boolean codon lattices of the genetic code using hydrogen bond numbers and the chemical types of bases: purines and pyrimidines. The Boolean lattices reflect the role of hydrophobicity in the distribution of codon assignments to each amino acid. Particularly, the symmetric images of codons with adenine as second base co... Sanchez, Robersy; Morgado, Eberto; Grau, Ricardo http://biblioteca.universia.net/ficha.do?id=20880380 Experimental results in recent years have shown that adult neurogenesis is a significant phenomenon in the mammalian brain. Little is known, however, about the functional role played by the generation and destruction of neurons in the context of and adult brain. Here we propose two models where new projection neurons are incorporated. We show that in both models, using incorporation and removal of neurons as a computational tool, it is possible to achieve a higher computational efficiency tha... Cecchi, Guillermo A.; Magnasco, Marcelo O. http://biblioteca.universia.net/ficha.do?id=20880381 Shannon information (SI) and its special case, divergence, are defined for a DNA sequence in terms of probabilities of chemical words in the sequence and are computed for a set of complete genomes highly diverse in length and composition. We find the following: SI (but not divergence) is inversely proportional to sequence length for a random sequence but is length-independent for genomes; the genomic SI is always greater and, for shorter words and longer sequences, hundreds to thousands times... Chen, Hong-Da; Chang, Chang-Heng; Hsieh, Li-Ching; Lee, Hoong-Chien http://biblioteca.universia.net/ficha.do?id=20880382 We discuss stochastic dynamics of finite populations of individuals playing games. We review recent results concerning the dependence of the long-run behavior of such systems on the number of players and the noise level. In the case of two-player games with two symmetric Nash equilibria, when the number of players increases, the population undergoes multiple transitions between its equilibria. Miekisz, Jacek http://biblioteca.universia.net/ficha.do?id=20880383 Animal behavior and evolution can often be described by game-theoretic models. Although in many situations, the number of players is very large, their strategic interactions are usually decomposed into a sum of two-player games. Only recently evolutionarily stable strategies were defined for multi-player games and their properties analyzed (Broom et al., 1997). Here we study the long-run behavior of stochastic dynamics of populations of randomly matched individuals playing symmetric three-pla... Kaminski, Dominik; Miekisz, Jacek; Zaborowski, Marcin