Regge Trajectories of Tetraquarks and Pentaquarks with Massive Quarks in the Flux Tube Model

In recent years, many tetraquarks and pentaquarks have been discovered by various experimental groups and X(3872), Zc(3900), X(4430), P + c (4312), P + c (4457) are some of the interesting observed tetraquark and pentaquark states. The Regge trajectories of some such states are studied in view of the flux tube model of hadrons with finite quark masses. The effect of flux tube (or string) length variation on the Regge trajectories of these sates is analysed in detail. It is observed that for a fixed angular momentum, the string length has a constant value. Some other states are also proposed and the results obtained are then compared with the studies by others. Our findings correspond rather well with those of other researchers and with those of the experiment.Comment: 10 pages, 4 figures, Published in IJMP

Modifications to the Hadronic Regge Trajectories

The effect of quark mass on the Regge trajectory is analysed. Modifications in the equations of Regge trajectories are shown for mesonic as well as baryonic systems. For mesonic systems, the Regge trajectories get modified, but still remain linear. Contrary to the mesonic case, the Regge trajectories for baryonic systems indicate non-linearity. It is shown that in low mass and angular momentum region two hadrons with different quark compositions can have same mass and angular momentum.Comment: 20 pages, 13 figures, Published in MPLA, corrected versio

BioBuilder as a database development and functional annotation platform for proteins

BACKGROUND: The explosion in biological information creates the need for databases that are easy to develop, easy to maintain and can be easily manipulated by annotators who are most likely to be biologists. However, deployment of scalable and extensible databases is not an easy task and generally requires substantial expertise in database development. RESULTS: BioBuilder is a Zope-based software tool that was developed to facilitate intuitive creation of protein databases. Protein data can be entered and annotated through web forms along with the flexibility to add customized annotation features to protein entries. A built-in review system permits a global team of scientists to coordinate their annotation efforts. We have already used BioBuilder to develop Human Protein Reference Database , a comprehensive annotated repository of the human proteome. The data can be exported in the extensible markup language (XML) format, which is rapidly becoming as the standard format for data exchange. CONCLUSIONS: As the proteomic data for several organisms begins to accumulate, BioBuilder will prove to be an invaluable platform for functional annotation and development of customizable protein centric databases. BioBuilder is open source and is available under the terms of LGPL

Human protein reference database—2006 update

Human Protein Reference Database (HPRD) () was developed to serve as a comprehensive collection of protein features, post-translational modifications (PTMs) and protein–protein interactions. Since the original report, this database has increased to >20 000 proteins entries and has become the largest database for literature-derived protein–protein interactions (>30 000) and PTMs (>8000) for human proteins. We have also introduced several new features in HPRD including: (i) protein isoforms, (ii) enhanced search options, (iii) linking of pathway annotations and (iv) integration of a novel browser, GenProt Viewer (), developed by us that allows integration of genomic and proteomic information. With the continued support and active participation by the biomedical community, we expect HPRD to become a unique source of curated information for the human proteome and spur biomedical discoveries based on integration of genomic, transcriptomic and proteomic data

Non-asymptotic transients away from steady states determine cellular responsiveness to dynamic spatial-temporal signals.

Majority of the theory on cell polarization and the understanding of cellular sensing and responsiveness to localized chemical cues has been based on the idea that non-polarized and polarized cell states can be represented by stable asymptotic switching between them. The existing model classes that describe the dynamics of signaling networks underlying polarization are formulated within the framework of autonomous systems. However these models do not simultaneously capture both, robust maintenance of polarized state longer than the signal duration, and retained responsiveness to signals with complex spatial-temporal distribution. Based on recent experimental evidence for criticality organization of biochemical networks, we challenge the current concepts and demonstrate that non-asymptotic signaling dynamics arising at criticality uniquely ensures optimal responsiveness to changing chemoattractant fields. We provide a framework to characterize non-asymptotic dynamics of system's state trajectories through a non-autonomous treatment of the system, further emphasizing the importance of (long) transient dynamics, as well as the necessity to change the mathematical formalism when describing biological systems that operate in changing environments