Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach.

Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, in which a ligand in a wrong pose achieves a better docking score than that of native pose, arise as additional protein conformations are added. In the current study, we developed a new ligand-biased ensemble receptor docking method and composite scoring function which combine the use of ligand-based atomic property field (APF) method with receptor structure-based docking. This method helps us to correctly dock 30 out of 36 ligands presented by the D3R docking challenge. For the six mis-docked ligands, the cognate receptor structures prove to be too different from the 40 available experimental Pocketome conformations used for docking and could be identified only by receptor sampling beyond experimentally explored conformational subspace

Understanding the role of chromatin remodeling in the regulation of circadian transcription in Drosophila.

Circadian clocks enable organisms to anticipate daily changes in the environment and coordinate temporal rhythms in physiology and behavior with the 24-h day-night cycle. The robust cycling of circadian gene expression is critical for proper timekeeping, and is regulated by transcription factor binding, RNA polymerase II (RNAPII) recruitment and elongation, and post-transcriptional mechanisms. Recently, it has become clear that dynamic alterations in chromatin landscape at the level of histone posttranslational modification and nucleosome density facilitate rhythms in transcription factor recruitment and RNAPII activity, and are essential for progression through activating and repressive phases of circadian transcription. Here, we discuss the characterization of the BRAHMA (BRM) chromatin-remodeling protein in Drosophila in the context of circadian clock regulation. By dissecting its catalytic vs. non-catalytic activities, we propose a model in which the non-catalytic activity of BRM functions to recruit repressive factors to limit the transcriptional output of CLOCK (CLK) during the active phase of circadian transcription, while the primary function of the ATP-dependent catalytic activity is to tune and prevent over-recruitment of negative regulators by increasing nucleosome density. Finally, we divulge ongoing efforts and investigative directions toward a deeper mechanistic understanding of transcriptional regulation of circadian gene expression at the chromatin level

Direct measurement of penetration length in ultra-thin and/or mesoscopic superconducting structures

We describe a method for direct measurement of the magnetic penetration length in thin (10 - 100 nm) superconducting structures having overall dimensions in the range 1 to 100 micrometers. The method is applicable for broadband magnetic fields from dc to MHz frequencies.Comment: Accepted by Journal of Applied P:hysics (Jun 2006).5 pages, 5 figure

Analysis and control of bifurcation and chaos in averaged queue length in TCP/RED model

This paper studies the bifurcation and chaos phenomena in averaged queue length in a developed Transmission Control Protocol (TCP) model with Random Early Detection (RED) mechanism. Bifurcation and chaos phenomena are nonlinear behaviour in network systems that lead to degradation of the network performance. The TCP/RED model used is a model validated previously. In our study, only the average queue size k q − is considered, and the results are based on analytical model rather than actual measurements. The instabilities in the model are studied numerically using the conventional nonlinear bifurcation analysis. Extending from this bifurcation analysis, a modified RED algorithm is derived to prevent the observed bifurcation and chaos regardless of the selected parameters. Our modification is for the simple scenario of a single RED router carrying only TCP traffic. The algorithm neither compromises the throughput nor the average queuing delay of the system

Finite Symmetry of Leptonic Mass Matrices

We search for possible symmetries present in the leptonic mixing data from SU(3) subgroups of order up to 511. Theoretical results based on symmetry are compared with global fits of experimental data in a chi-squared analysis, yielding the following results. There is no longer a group that can produce all the mixing data without a free parameter, but a number of them can accommodate the first or the second column of the mixing matrix. The only group that fits the third column is $\Delta(150)$. It predicts $\sin^22\theta_{13}=0.11$ and $\sin^22\theta_{23}=0.94$, in good agreement with experimental results.Comment: Version to appear in Physical Review

Implementing Unitarity in Perturbation Theory

Unitarity cannot be perserved order by order in ordinary perturbation theory because the constraint UU^\dagger=\1 is nonlinear. However, the corresponding constraint for $K=\ln U$, being $K=-K^\dagger$, is linear so it can be maintained in every order in a perturbative expansion of $K$. The perturbative expansion of $K$ may be considered as a non-abelian generalization of the linked-cluster expansion in probability theory and in statistical mechanics, and possesses similar advantages resulting from separating the short-range correlations from long-range effects. This point is illustrated in two QCD examples, in which delicate cancellations encountered in summing Feynman diagrams of are avoided when they are calculated via the perturbative expansion of $K$. Applications to other problems are briefly discussed.Comment: to appear in Phys. Rev.