@article{barua_faeder_haugh_2008, title={Computational models of tandem Src homology 2 domain interactions and application to phosphoinositide 3-kinase}, volume={283}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.M708359200}, abstractNote={Intracellular signal transduction proteins typically utilize multiple interaction domains for proper targeting, and thus a broad diversity of distinct signaling complexes may be assembled. Considering the coordination of only two such domains, as in tandem Src homology 2 (SH2) domain constructs, gives rise to a kinetic scheme that is not adequately described by simple models used routinely to interpret in vitro binding measurements. To analyze the interactions between tandem SH2 domains and bisphosphorylated peptides, we formulated detailed kinetic models and applied them to the phosphoinositide 3-kinase p85 regulatory subunit/platelet-derived growth factor β-receptor system. Data for this system from different in vitro assay platforms, including surface plasmon resonance, competition binding, and isothermal titration calorimetry, were reconciled to estimate the magnitude of the cooperativity characterizing the sequential binding of the high and low affinity SH2 domains (C-SH2 and N-SH2, respectively). Compared with values based on an effective volume approximation, the estimated cooperativity is 3 orders of magnitude lower, indicative of significant structural constraints. Homodimerization of full-length p85 was found to be an alternative mechanism for high avidity binding to phosphorylated platelet-derived growth factor receptors, which would render the N-SH2 domain dispensable for receptor binding.}, number={12}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, publisher={American Society for Biochemistry & Molecular Biology (ASBMB)}, author={Barua, Dipak and Faeder, James R. and Haugh, Jason M.}, year={2008}, month={Mar}, pages={7338–7345} }
 @article{barua_faeder_haugh_2007, title={Structure-based kinetic models of modular signaling protein function: Focus on Shp2}, volume={92}, ISSN={["0006-3495"]}, DOI={10.1529/biophysj.106.093484}, abstractNote={We present here a computational, rule-based model to study the function of the SH2 domain-containing protein tyrosine phosphatase, Shp2, in intracellular signal transduction. The two SH2 domains of Shp2 differentially regulate the enzymatic activity by a well-characterized mechanism, but they also affect the targeting of Shp2 to signaling receptors in cells. Our kinetic model integrates these potentially competing effects by considering the intra- and intermolecular interactions of the Shp2 SH2 domains and catalytic site as well as the effect of Shp2 phosphorylation. Even for the isolated Shp2/receptor system, which may seem simple by certain standards, we find that the network of possible binding and phosphorylation states is composed of over 1000 members. To our knowledge, this is the first kinetic model to fully consider the modular, multifunctional structure of a signaling protein, and the computational approach should be generally applicable to other complex intermolecular interactions.}, number={7}, journal={BIOPHYSICAL JOURNAL}, publisher={Elsevier BV}, author={Barua, Dipak and Faeder, James R. and Haugh, Jason M.}, year={2007}, month={Apr}, pages={2290–2300} }
 @article{barua_gougousi_young_parsons_2006, title={Supercritical-carbon dioxide-assisted cyclic deposition of metal oxide and metal thin films}, volume={88}, ISSN={["1077-3118"]}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000235736300065&KeyUID=WOS:000235736300065}, DOI={10.1063/1.2181651}, abstractNote={Thin films of aluminum oxide and palladium were deposited on silicon at low temperatures (70–120°C) by a cyclic adsorption/reaction processes using supercritical CO2 solvent. Precursors included Al(hfac)3, Al(acac)3, and Pd(hfac)2, and aqueous H2O2, tert-butyl peracetate, and H2 were used as the oxidants or reductants. For the precursors studied, growth proceeds through a multilayer precursor adsorption in each deposition cycle, and film thickness increased linearly with the number of growth cycles.}, number={9}, journal={APPLIED PHYSICS LETTERS}, author={Barua, D and Gougousi, T and Young, ED and Parsons, GN}, year={2006}, month={Feb} }
 @article{gougousi_barua_young_parsons_2005, title={Metal oxide thin films deposited from metal organic precursors in supercritical CO2 solutions}, volume={17}, ISSN={["0897-4756"]}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000232326700027&KeyUID=WOS:000232326700027}, DOI={10.1021/cm0510965}, abstractNote={This work demonstrates a novel method for deposition of metal oxide thin films, including Al2O3, ZrO2, MnOx, and RuOx where the metal−organic precursors and oxidizing agents are delivered in liquid and supercritical CO2. A cyclic deposition process is presented where reactants are introduced sequentially to control surface adsorption and byproduct removal steps. Reactions are studied in a hot wall reactor at pressures ranging from 1600 to 3600 psi at 80−200 °C, and X-ray photoelectron spectroscopy and infrared transmission confirmed metal oxide formation. We show that hydrogen peroxide is a viable O source for oxide deposition, whereas tert-butyl peracetate, which is a good electron acceptor, is less suited for oxygen donation. Capacitance versus voltage analysis of resulting Al2O3 films show good dielectric properties after post-deposition anneal. We believe that the good solvation properties of supercritical CO2 can aid in the delivery of precursors and in the removal of byproducts for advanced low-temp...}, number={20}, journal={CHEMISTRY OF MATERIALS}, author={Gougousi, T and Barua, D and Young, ED and Parsons, GN}, year={2005}, month={Oct}, pages={5093–5100} }