Browsing by Author "Barua, Dipak"

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    Deposition of Metal and Metal Oxide Thin Films from Metal Organic Precursors in Supercritical Carbon Dioxide Solution
    (2005-04-22) Barua, Dipak; Ruben G. Carbonell, Committee Member; Gregory N. Parsons, Committee Chair; Carlton Osburn, Committee Member
    Thin films of metals and metal-oxides are deposited in batch (Chemical Fluid Deposition) and cyclic (Atomic Layer Deposition) processes from metal organic precursors in supercritical carbon dioxide solutions. New materials have been introduced in the deposition processes. Deposited films are analyzed in details in order to evaluate their quality and chemical composition. Analyzing techniques, X-ray photoelectron spectroscopy (XPS), ellipsometry, Fourier transform infrared spectroscopy (FTIR), atomic force microscopy (AFM), and auger electron spectroscopy (AES) are adopted to characterize the films. Capacitance-voltage measurements are performed to prove the device quality deposition of metal oxide films. The process establishes a new approach in metal oxide deposition, and controllable growth of metal and metal oxide films in supercritical carbon dioxide.
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    Rule-based Computational Modeling of Modular Signaling Protein Interactions
    (2008-11-16) Barua, Dipak; Orlin D. Velev, Committee Member; Jason M. Haugh, Committee Chair; Alun L. Lloyd, Committee Member; Balaji M. Rao, Committee Member
    Intracellular signal transduction pathways are comprised of complex interactions among cellular proteins and other biomolecules. The structures of signaling proteins/enzymes are often modular, with conserved domains that carry out specific interactions or catalytic functions, and their core activities are dictated through coordinated intra- and inter-molecular interactions. In collaboration with Prof. James Faeder (Computational Biology, University of Pittsburgh), we have applied a computational algorithm for generating large networks of kinetic equations based on a much smaller set of mechanistic rules. Using this rule-based approach, we have formulated kinetic models that account for the modular domain structure of specific signaling proteins, including Shp2 (Src homology-2 domain containing protein tyrosine phosphatase 2), PI3K (phosphatidilinositol-3-kinase) regulatory subunit, and SH2-B (a Jak2 kinase activating adaptor protein). Analysis of these models reveals the combinatorial possibilities of reactions and interactions that might occur in living cells. We propose here to extend this rule-based approach for larger pathway models through systematic reduction and integration of small subsystem models.