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2. Model for processive movement of dynein - Xie, Ping; Dou, Shuo-Xing; Wang, Peng-Ye In the model, the change from strongmicrotubule-binding to weak binding of dynein is determined naturally by thevariation of the relative orientation between the two interacting surfaces ofthe stalk tip and the microtubule as the stalk rotates from the ADP.Vi-stateorientation to the apo-state orientation.
3. Gene splice sites correlate with nucleosome positions - Kogan, Simon; Trifonov, Edward N. The RR andYY dinucleotides oscillate counterphase, i.e., their respective preferredpositions are shifted about half-period one from another, as it was observedearlier for AA and TT dinucleotides.
4. Length, Protein-Protein Interactions, and Complexity - Tan, Taison; Frenkel, Daan; Gupta, Vishal; Deem, Michael W. We propose here that the increasing complexity of protein-proteininteractions has driven the selection of longer proteins, as longer proteinsare more able to distinguish among a larger number of distinct interactions dueto their greater average surface area.
5. Activity-dependent brain model explaining EEG spectra - de Arcangelis, Lucilla; Herrmann, Hans J.; Perrone-Capano, Carla Our model isbased on an electrical network with threshold firing and plasticity of synapsesthat reproduces very robustly the measured exponent 0.8 of the medical EEGspectra, a solid evidence for self-organized criticality.
7. Scaling effects in the Penna ageing model - Laszkiewicz, A.; Cebrat, S.; Stauffer, D. Assuming that the number of genes expressed before the reproduction age growslinearly with the genome size and that the mutation rate per genome andgeneration is constant, we have found that the fraction of defective genesexpressed before the minimum reproduction age drops with the genome size, whilethe number of defective genes eliminated by the genetic death grows with genomesize.
8. Folding thermodynamics of peptides - Irbäck, Anders; Mohanty, Sandipan A simplified interaction potential for protein folding studies at the atomiclevel is discussed and tested on a set of peptides with about 20 residues each.
9. Finite size effects on calorimetric cooperativity of two-state proteins - Li, Mai Suan; Klimov, D. K.; Thirumalai, D. We show that for models without side chains adimensionless measure of calorimetric cooperativity kappa2 defined as the ratioof the van't Hoff to calorimetric enthalpy does not depend on the number ofamino acids N.
11. Subtree power analysis finds optimal species for comparative genomics - McAuliffe, Jon D.; Jordan, Michael I.; Pachter, Lior This prioritization should be grounded in twoconsiderations: the lineal scope encompassing the biological phenomena ofinterest, and the optimal species within that scope for detecting functionalelements.
12. Surfaces and orientations: much to fret about? - Rasnik, Ivan; McKinney, Sean A.; Ha, Taekjip Single molecule FRET (fluorescence resonance energy transfer) is a powerfultechnique for detecting real-time conformational changes and molecularinteractions during biological reactions.
13. Correlations in Systems of Complex Directed Macromolecules - Moseley, Christopher; Ziegler, Klaus An ensemble of directed macromolecules on a lattice is considered, where theconstituting molecules are chosen as a random sequence of N different types.
14. Ion-Phosphate Mode in the DNA Low-Frequency Spectra - Perepelytsya, S. M.; Volkov, S. N. The vibrational dynamics of a DNA molecule with counterions neutralizing thecharged phosphate groups have been studied.
15. An RNA-centered view of eukaryotic cells - Tannenbaum, Emmanuel Emerging evidence suggests that the introns and intergenic sequences of thegenomes of higher eukaryotes (the ``junk'' DNA) codes for a vast, RNA-based,genetic regulatory network.
16. The Genetic Code Boolean Lattice - Sanchez, Robersy; Morgado, Eberto; Grau, Ricardo The Boolean lattices reflect the role of hydrophobicity in the distribution ofcodon assignments to each amino acid.
17. Computational Models of Adult Neurogenesis - Cecchi, Guillermo A.; Magnasco, Marcelo O. Little is known, however, aboutthe functional role played by the generation and destruction of neurons in thecontext of and adult brain.
18. Divergence and Shannon information in genomes - Chen, Hong-Da; Chang, Chang-Heng; Hsieh, Li-Ching; Lee, Hoong-Chien Shannon information (SI) and its special case, divergence, are defined for aDNA sequence in terms of probabilities of chemical words in the sequence andare computed for a set of complete genomes highly diverse in length andcomposition.
20. Stochastic stability in three-player games - Kaminski, Dominik; Miekisz, Jacek; Zaborowski, Marcin Although in many situations, the number of players is very large, theirstrategic interactions are usually decomposed into a sum of two-player games.
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