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Research Publications

Research Publications

This is a collection of research conducted with the assistance of the High Performance Computing Cluster. A link to an online version of the articles is provided when available.

Important Notes

  • If you use HPCC resources in your research work, we ask that you acknowledge the use of the HPC cluster in your publications and presentations as "This work made use of the High Performance Computing Resource in the Core Facility for Advanced Research Computing at Case Western Reserve University."
  • Please email references of your published research papers or poster presentations at   to include it here.

Publication Year

2013

  • S. Gajurel and R. Bielefeld, "Fast Vertex Cover Algorithms and Its Implementation using CWRU High Performance Computing Cluster (HPCC)", Poster Presentation at Research ShowCase 2013. Link to poster

  • Huang, W., Greene, G.L., Ravikumar, K., and Yang, S. "Cross-talk between the ligand- and DNA-binding domains of estrogen receptor," Proteins. doi: 10.1002/prot.24331 (2013). [Applied multiscale simulations for the energy landscape of a multidomain protein complex]

  • Ravikumar, K., Huang, W., and Yang, S. "Fast-SAXS-pro: A unified approach to computing SAXS profiles of DNA, RNA, protein, and their complexes," J. Chem. Phys. 138 (2) 024112, (2013) [Developed a new SAXS computing algorithm for protein-DNA/RNA complexes]

  • Yang, S.*, Ravikumar, K., Levine, H.* "Energy evaluation of β-strand packing in a fibril-forming SH3 domain," J. Phys. Chem. B. doi: 10.1021/jp402442p (2013). [*Corr authors]

  • Toth, R., Traghber, B., Ellis, R., Kurhanewicz, J., Madabhushi, A. “Registration of Pre and Post Intensity Modulated Radiation Therapy Prostate MRI for Quantification of MR Imaging Marker Changes and Precise Local Prostate Deformations,” at: Research ShowCASE, Case Western Reserve University, Cleveland, OH, Apr 2013.

  • Toth, R., Ribault, J., Gentile, J.C., Sperling, D., Madabhushi, A. “Simultaneous Segmentation of Prostatic Zones Using Active Appearance Models with Multiple Coupled Levelsets,” CVIU Special Issue on Shape Modeling, April 2013. doi: 10.1016/j.cviu.2012.11.013.

  • Toth, R., Kurhanewicz, J., Madabhushi, A. “Registration of Pre and Post Intensity Modulated Radiation Therapy Prostate MRI for Quantification of MR Imaging Marker Changes and Precise Local Prostate Deformations” ISMRM 2013.

  • Singanamalli A., Sparks R., Rusu M., Shih N., Ziober A., Tomaszewski J., Rosen M., Feldman M, and Madabhushi A. "Radiohistomorphometric Image Analysis and Coregistration Scheme to identify DCE MRI markers for prostate cancer aggressiveness." 2013 ShowCASE.

  • Singanamalli A., Sparks R., Rusu M., Shih N., Ziober A., Tomaszewski J., Rosen M., Feldman M, and Madabhushi A. "Radiohistomorphometric Image Analysis and Coregistration Scheme to identify DCE MRI markers for prostate cancer aggressiveness." 2013 ISMRM.

  • Haibo Wang, Anant Madabhushi, Discriminatively Weighted Multi-Scale Local Binary Patterns: Applications in Prostate Cancer Diagnosis on T2W MRI, ISBI (oral), 2013.

  • Eileen Hwuang, Shabbar Danish, Mirabela Rusu, Robert Sparks, Robert Toth, Anant Madabhushi. Anisotropic Smoothing Regularization (AnSR) in Thirion's Demons Registration Evaluates Brain MRI Tissue Changes Post-Laser Ablation. Conf Proc IEEE Eng Med Biol Soc. 2013.

  • Singanamalli, Asha, et al. "Identifying in vivo DCE MRI parameters correlated with ex vivo quantitative microvessel architecture: A radiohistomorphometric approach." SPIE Medical Imaging. International Society for Optics and Photonics, 2013.

  • Mirabela Rusu, B. Nicolas Bloch, C. Carl Jaffe, Neil M. Rofsky, Elizabeth M. Genega, Robert E. Lenkinski, Anant Madabhushi; Statistical 3D prostate imaging atlas construction via anatomically constrained registration
    SPIE Medical Imaging Feb 2013

  • Mirabela Rusu, Haibo Wang, Thea Golden, Andrew Gow, Anant Madabhushi
    Multiscale, multimodal fusion of histological and MRI lung volumes for characterization of airways SPIE Medical Imaging Feb 2013

  • Mirabela Rusu, B. Nicolas Bloch, Carl Jaffe, Neil Rofsky, Elizabeth Genega, Robert Lenkinski, Anant Madabhushi; Statistical 3D prostate imaging atlas construction via anatomically constrained registration; ShowCase Case Western Research University, April 12, 2013 Cleveland; *Postdoctoral Research Award

  • Viswanath, S, Bloch, BN, Chappelow, J, Genega, E, Lenkinski, R, Rofsky, N, Madabhushi, A, “Comparing Classifier Ensembles for Discriminating Central Gland and Peripheral Zone Tumors on In Vivo 3 Tesla T2-weighted Prostate MRI”, BMC Bioinformatics (under review).

  • Viswanath, S, Toth, R, Rusu, M, Sperling, D, Lepor, H, Futterer, J, Madabhushi, A, “Quantitative evaluation of treatment related changes on multi-parametric MRI after laser interstitial thermal therapy of prostate cancer”, SPIE Medical Imaging, 2013, vol 8671, 86711F.

  • Viswanath, S, Toth, R, Rusu, M, Sperling, D, Lepor, H, Futterer, J, Madabhushi, A, “Quantitative Evaluation of Treatment Related Changes on Multi-Parametric MRI after Laser Interstitial Thermal Therapy of Prostate Cancer”, ISMRM, Apr 2013.

  • Viswanath, S, Toth, R, Rusu, M, Sperling, D, Lepor, H, Futterer, J, Madabhushi, A, “Quantitative Evaluation of Treatment Related Changes on Multi-Parametric MRI after Laser Interstitial Thermal Therapy of Prostate Cancer“, Research ShowCASE, Case Western Reserve University, Cleveland, OH Apr 2013.

  • A. B. Anderson, R. Jinnouchi, and J. Uddin, "Effective Reversible Potentials and Onset Potentials for O2 Electroreduction on Transition Metal Electrodes: Theoretical Analysis", J. Phys. Chem. C 117, 41-48 (2013).

  • L. García Domínguez, J.L. Pérez Domínguez, R. F. Galán (2013). A Model of Functional Brain Connectivity and
    Background Noise as a Biomarker for Cognitive Phenotypes: Application to Autism. PLoS ONE 8(4): e61493.
    Link to article

  • Villarreal SA, Williams DR, Johnson CH, Egli M, Stewart PL. (2013) Examining the S. elongatus KaiBC Complex by CryoEM and MDFF. Microscopy and Microanalysis Annual meeting presentation.

  • Seth A. Villarreal, Rekha Pattanayak, Dewight R. Williams, Carl H. Johnson, Martin Egli, Phoebe L. Stewart. Modeling of the Circadian Clock KaiBC Complex. Poster Presentation at Research ShowCase 2013.

  • Justin W. Flatt, Eric Irons, Konstantin Doronin, Tara L. Fox, Dmitry M. Shayakhmetov, and Phoebe L. Stewart Adenovirus Immunity: Insights from coagulation factor VII on how X marks the spot. Poster Presentation at Research ShowCase 2013.

  • Flatt JW, Kim, R Smith JG, Nemerow GR, Stewart PL (2013). An intrinsically disordered region of the adenovirus capsid is implicated in neutralization by human alpha defensin 5. PLoS One, In press.

  • Guo, H.; Zehavi, I.; Zheng, Z.; Weinberg, D. H.; Berlind, A. A.; Blanton, M.; Chen, Y.; Eisenstein, D. J.; Ho, S.; Kazin, E.; Manera, M.; Maraston, C.; McBride, C. K.; Nuza, S. E.; Padmanabhan, N.; Parejko, J. K.; Percival, W. J.; Ross, A. J.; Ross, N. P.; Samushia, L.; Sánchez, A. G.; Schlegel, D. J.; Schneider, D. P.; Skibba, R. A.; Swanson, M. E. C.; Tinker, J. L.; Tojeiro, R.; Wake, D. A.; White, M.; Bahcall, N. A.; Bizyaev, D.; Brewington, H.; Bundy, K.; da Costa, L. N. A.; Ebelke, G.; Malanushenko, E.; Malanushenko, V.; Oravetz, D.; Rossi, G.; Simmons, A.; Snedden, S.; Streblyanska, A.; Thomas, D., "The Clustering of Galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: Luminosity and Color Dependence and Redshift Evolution", The Astrophysical Journal 2013, 767, 122-140

2012

  • S. Gajurel and R. Bielefeld, "A Fast Near Optimal Vertex Cover Algorithm (NOVCA)", IJEA, vol. 3, issue 1, 2012.
    Link to article

  • Haibo Wang, Mirabela Rusu, Thea Golden, Andrew Gow and Anant Madabhushi, Mouse Lung Volume Reconstruction from Efficient Groupwise Registration of Individual Histological Slices with Natural Gradient, SPIE Medical Imaging (oral), 2012.

  • Haleema Asiri and A. B. Anderson,"Cyclic Voltammograms for Hupd on Pt(111) Calculated from Total Gibbs Energies", 222 ECS Fall Meeting, October 7-12, 2012.  Poster presentation by Haleema Asiri.  A conference proceedings abstract was published by the Electrochemical Society.

  • Heckler, J. E.; Zeller, M.; Hunter, A. D.; Gray, T. G. Angewandte Chemie (International ed. in English) 2012, 51, 5924–8.

  • Flatt JW, Fox TL, Makarova N, Blackwell JL, Dmitriev IP, Kashentseva EA, Curiel DT, Stewart PL.
    (2012) CryoEM visualization of an adenovirus capsid-incorporated HIV antigen. PLoS One, 7(11): e49607. BPoD Biomedical Picture of the Day, bpod.mrc.ac.uk, December 14, 2012.

  • Doronin K*, Flatt JF*, Di Paolo NC*, Khare R, Kalyuzhniy O, Acchione M, Sumida JP, Ohto U, Shimizu T, Akashi-Takamura S, Miyake K, MacDonald JW, Bammler TK, Beyer RP, Farin FM, Stewart PL, Shayakhmetov DM. (2012) Coagulation factor X activates innate immunity to human species C adenovirus. Science, 338:795-798 (*Equal contribution authors)

  • Guo, H.; Zehavi, I.; Zheng, Z., "A New Method to Correct for Fiber Collisions in Galaxy Two-point Statistics", The Astrophysical Journal 2012, 756, 127-139

  • Yang, Y.; Kennedy, V. O.; Updegraph, J. B.; Samas, B.; Macikenas, D.; Chaloux, B.; Miller, J. A.; Van Goethem, E. M.; Kenney, M. E., "Long Directional Interactions (LDIs) in Oligomeric Cofacial Silicon Phthalocyanines and Other Oligomeric and Polymeric Cofacial Phthalocyanines," The Journal of Physical Chemistry A 2012116, 8718-8730. Link to article

  • Yang, Y. "Metal–ligand coordination in subphthalocyanines and phthalocyanines: DFT, AIM and ELF analyses," Polyhedron 201233, 310-318. Link to article

  • Yang, Y. "Pyrrolic macrocycles with stabilized triplet states: Metal-centered and ligand-centered separation of unpaired electrons," Polyhedron 201242, 249-257. Link to Article

  • Yu X, Guda K, Willis J, Veigl M, Wang Z, Markowitz S, Adams MD, Sun S., " How do alignment programs perform on sequencing data with varying qualities and from repetitive regions?," BioData Min. 2012 Jun 18;5(1):6. Link to Article

  • Adams MD, Veigl ML, Wang Z, Molyneux N, Sun S, Guda K, Yu X, Markowitz SD, Willis J., "Global mutational profiling of formalin-fixed human colon cancers from a pathology archive," Mod Pathol. 2012 Aug 10. doi: 10.1038/modpathol.2012.121. Link to Article

  • Sanjaya Gajurel and Roger Bielefeld, A Simple NOVCA: Near Optimal Vertex Cover Algorithm, ICCS 2012, vol 9, 
    pp-747-753. Link to article

  • Krishnakumar M. Ravikumar, Wei Huang, and Sichun Yang*, Coarse-Grained Simulations of Protein-Protein Association: An Energy Landscape PerspectiveBiophysical Journal Volume 103 August 2012 837–845. Link to article

  • Cheiwchanchamnangij, T. & Lambrecht, W. R. L. Quasiparticle band structure calculation of monolayer, bilayer, and bulk MoS_{2}. Phys. Rev. B 85, 205302 (2012). Link to article

  • Zuber, M. T., D. E. Smith, R. J. Phillips, S. C. Solomon, G. A. Neumann, S. A. Hauck, II, S. J. Peale, O. S. Barnouin, J. W. Head, C. L. Johnson, F. G. Lemoine, E. Mazarico, X. Sun, M. H. Torrence, A. M. Freed, C. Klimczak, J.-L. Margot, J. Oberst, M. E. Perry, R. L. McNutt, Jr., J. A. Balcerski, N. Michel, M. J., Talpe, D. Yang, Topography of the northern hemisphere of Mercury from MESSENGER laser altimetry, Science, 336, 217-220, doi: 10.1126/science.1218805, 2012. Link to article.

  • Smith, D. E., M. T. Zuber, R. J. Phillips, S. C. Solomon, S. A. Hauck, II, F. G. Lemoine, E. Mazarico, G. A. Neumann, S. J. Peale, J.-L. Margot, C. L. Johnson, M. H. Torrence, M. E. Perry, D. D. Rowlands, S. Goossens, J. W. Head, A. H. Taylor, Gravity field and internal structure of Mercury from MESSENGER, Science, 336, 214-217, 2012. Link to article.

  • Alfred  B. Anderson, “Insights Into Electrocatalysis,” Phys. Chem. Chem. Phys. 2012, 14, 1330-1338. Link to article

  • Alfred B. Anderson, “Volcano Plots and Effective Reversible Potentials for Oxygen Electroreduction,” Electrocatalysis 9 March 2012. Online First, and open access DOI: 10.1007/s12678-012-0088-z.

2011

  • Peay, M. A.; Heckler, J. E.; Deligonul, N.; Gray, T. G. Organometallics 2011, 30, 5071–5074.

  • Yang, Y.; Samas, B.; Kennedy, V. O.; Macikenas, D.; Chaloux, B. L.; Miller, J. A.; Speer, R. L.; Protasiewicz, J.; Pinkerton, A. A.; Kenney, M. E. Long, Directional Interactions in Cofacial Silicon Phthalocyanine Oligomers. J. Phys. Chem. A 2011115, 12474-12485. Link to article

  • Yang, Y. Effects Induced by Axial Ligands Binding to Tetrapyrrole-Based Aromatic Metallomacrocycles. J. Phys. Chem. A 2011115, 9043-9054. Link to article

  • Yang, Y. Electron localization in nonplanar conjugated macrocycles: Failure of electron buffers to delocalize electrons. Chem. Phys. Lett. 2011516, 268-271. Link to article
     
  • Yang, Y. A theoretical study of experimentally unknown metallosubphthalocyanines. Chem. Phys. Lett. 2011511, 51-56. Link to article
  • Steinke GK, Galán RF, 2011 Brain Rhythms Reveal a Hierarchical Network Organization. PLoS Comput Biol 7(10): e1002207. doi:10.1371/journal.pcbi.1002207. Link to article

  • Yang, S. and Roux, B. "EROS: Better than SAXS!", Structure. 19 (1), 3-4 (2011). Link to article

  • Feng Tian and Alfred B. Anderson, "Effective Reversible Potentials, Energy Loss and Overpotential on Platinum Fuel Cell Cathodes", J. Phys Chem. C, 115, 4076-4088 (2011). Link to article

  • "The Quantity of Intracluster Light: Comparing Theoretical and Observational Measurement Techniques using Simulated Clusters", Rudick, C.S., Mihos, J.C., and McBride, C.K. (2011), The Astrophysical Journal, 732, 48. Link to article


  • E. Allahyarov and P. L. Taylor "Simulation study of the equilibrium morphology in ionomers with different architectures" J. Polym. Sci. B, Pol. Phys. 49 368 (2011) Link to article

  • E. Allahyarov and P. L. Taylor "Simulation study of field-induced proton-conduction pathways in dry ionomers" J. Phys.: Condens. Matter 23 234105 (2011). Link to article

  • Cheiwchanchamnangij, T. & Lambrecht, W. R. L. Calculated x-ray linear dichroism spectra for Gd-doped GaN. Phys. Rev. B 84, 205119 (2011). Link to article

  • Cheiwchanchamnangij, T. & Lambrecht, W. R. L. Band structure parameters of wurtzite and zinc-blende GaAs under strain in the GW approximation. Phys. Rev. B 84, 035203 (2011). Link to article

2010

  • Yang, Y. Hexacoordinate Bonding and Aromaticity in Silicon Phthalocyanine. J. Phys. Chem. A 2010114, 13257-13267. Link to article
  • Tivadar Orban, Grzegorz Bereta, Masaru Miyagi, Benlian Wang, Mark R. Chance, Marcelo Carlos Sousa, and Krzysztof Palczewski, "Conformational Changes in Guanylate Cyclase-Activating Protein 1 Induced by Ca2+ and N-Terminal Fatty Acid Acylation", Structure 18, 116–126 (2010). Link to article

  • Alfred. B. Anderson, ¿Theories for Predicting Reversible Potentials of Reactions on Electrode Surfaces from Internal and Gibbs Energies¿: Applications to ORR, ECS Transactions 28, 1-17 (2010). Link to article
  • K. A. Kurak and A. B. Anderson, “Selenium: a Nonprecious Metal Cathode Catalyst fort Oxygen Electroreduction”, J. Electrochem. Soc. 157, B173-B179 (2010). Link to article

  • Alfred B. Anderson, Jamal Uddin, and Ryosuke Jinnouchi, “Solvent Effects on OH(ads) Reduction on Pt(111) Electrodes”, under revision.

  • Elshad Allahyarov, Philip L. Taylor, and Harmut Löwen, "Simulation study of field-induced morphological changes in a proton-conducting ionomer", Phys. Rev. E 81, 031805 (2010). Link to article

  • "The Formation and Evolution of Intracluster Light", conference talk by Craig Rudick at the 2010 Meeting of the American Astronomical Society, Washington, DC, January 2010. Link to article

  • Chen, Y., Eldho, N. V., Dayie, T. K., Carey, P.R., "Probing adenine rings and backbone linkages using base specific isotope-edited Raman spectroscopy: application to group II intron ribozyme domain V" Biochemistry, 49, 3427-35 (2010). Link to article

  • "Kinetic crystallography using Raman microscopy", Invited talk by Paul Carey to the American Crystallography Association, Chicago. July 2010.

  • "The Raman revolution in structural biology", Invited talk by Paul Carey to the Int Conf Raman Spectrosc. Boston. August 2010. Link to article

  • Y. Chen, P. Carey et al "Following RNA initiation in RNA Polymerase crystals by Raman microscopy", Poster at the meeting of the American Chem Soc, San Francisco, March 2010.

  • Bo Gong, P. Carey, et al., "Measuring individual pKas in crystals of the Glms ribozyme be Raman crystallography", Poster at the meeting of the American Chem Soc, San Francisco, March 2010.

  • S.-Y. Hsu and J.S. T’ien, “Flame spread over solids in buoyant and forced concurrent flows: Model computations and comparison with experiments,” 33rd International Symposium on Combustion, Beijing, China, Aug. 1-6, 2010.
  • S.-Y. Hsu and J.S. T’ien, “Flame spread over solids in buoyant and forced concurrent flows: Model computations and comparison with experiments,” Proc. of Combust. Inst. 33, In Press. Link to article

  • Ya-Ting Tseng, James S. T’ien: Limiting Length, Steady Spread and Non-growing Flames in Concurrent Flow over Solids, Journal of Heat Transfer, September 2010, Vol. 132, Issue 9. Link to article

  • M. Shoham, V. Khodaveridan*, M. Pesho*, B. Truitt*, L. Bollinger and P. Patel, Discovery of Antipathogenic Agents Against MRSA, 50th Interscience Conference on Antimicrobial Agents and Chemotherapy (ICAAC), Boston, 12-15 September 2010, poster presentation

  • Wang, S.; Dormidontova, E. E.; Nanoparticle Design Optimization for Enhanced Targeting: Monte Carlo Simulations; Biomacromolecules, 2010, 11, 1785-1795. Link to article

  • Wang, S.; Dormidontova, E. E.; Monte Carlo Simulation of Metallo-Supramolecular Micelles; Macromolecular Rapid Communications, 2010, 31, 897-903 Link to article

  • Li, Z.; Dormidontova, E. E.  Kinetics of diblock copolymer micellization by dissipative particle dynamics; Macromolecules 2010, 43 3521. Lick to article

  • Li, Z.; Djohari, H.; Dormidontova, E. E. Molecular dynamics simulations of supramolecular polymer rheology; J. Chem. Phys. 2010 accepted. Link to article

  • Wang, S.; Hagy, M. C.; Dormidontova, E. E.; “Comparisons of polymer layer and nanoparticle targeting”, ACS National Meeting, March 2010, San Francisco CA

  • Djohari, H.; Wang, S.; Dormidontova, E. E.; “Role of tether length in nanoparticle”, ACS National Meeting, March 2010, San Francisco CA

  • Li, Z.; Dormidontova, E. E. Dissipative particles dynamics simulations of micellization kinetics, ACS National Meeting & Exposition, March 21, 2010 San Francisco, CA

2009

  • Y. Chen, P. L. Taylor, and D. A. Scherson "Electrochemical and In-Situ Optical Studies of Supported Iridium Oxide Films in Aqueous Solutions" J. Electrochem. Soc. 156 (1) F14-F21 (2009) Link to article

  • E. Allahyarov and P. L. Taylor "Predicted field-induced hexatic structure in an ionomer membrane" Phys. Rev. E. 80 020801 (2009) Link to article

  • E. Allahyarov, P. L. Taylor, and H. Löwen "Simulation study of sulfonate cluster swelling in ionomers" Phys. Rev. E. 80 061802 (2009) Link to article
  • E. Allahyarov and P. L. Taylor, "Simulation Study of the correlation between structure and conductivity in stretched Nafion" J. Phys. Chem. B 113, 610-617 (2009)  Link to article
  • K. Kamal, G. Mittal, and C.J. Sung, "Autoignition of n-Decane under Elevated Pressure and Low-to-Intermediate Temperature Conditions" Combustion and Flame 156, 1278-1288 (2009) Link to article
  • X-L Yin and J Li, "A general graphical framework for detecting copy number variation" Accepted by Comput Syst Bioinformatics Conf (CSB2009) - http://csb2009.org/pdf/060Li.pdf
  • X. Li and J. Li, "An almost linear time algorithm for a general haplotype solution on tree pedigrees with no recombination and its extensions" Journal of Bioinformatics and Computational Biology (JBCB), 7(3), 521-545 (2009) Link to article
  • H. Djohari and E.E. Dormidontova, "Dissipative Particle Dynamics Simulations of Nanoparticle Targeting Dynamics" Poster at CWRU Research ShowCASE 2009
  • H. Djohari and E.E. Dormidontova, "Dissipative Particle Dynamics Simulations of Micelle Targeting Dynamics" Central Regional Meeting of ACS, Cleveland, OH, May 2009
  • Gavin A. Buxton, Sandra L. Siedlak, George Perry and Mark A. Smith. There and Back Again: A Numerical Tale of Microtubule Dynamics. Submitted.
  • Gavin A. Buxton, Alexander Alexeev, O. Berk Usta and Anna C. Balazs. Using Synthetic Cilia to Regulate the Transport of Microscopic Particles. Submitted.
  • Rajat Ghosh, Gavin A. Buxton, O. Berk Usta, Anna C. Balazs, and Alexander Alexeev. Designing oscillating cilia that capture or release microscopic particles. Accepted in Langmuir.
  • Ernest Durbin and Gavin A. Buxton. Controlling Drug Release using Responsive Polymer Core-Shell Nanoparticles. Submitted to Soft Matter: Responsive and Active Soft Materials issue.
  • Gavin A. Buxton, N. Clarke and P. J. Hussey. Actin Dynamics and the Elasticity of Cytoskeletal Networks. Accepted in Express Polymer Letters.
  • Gavin A. Buxton, Ultrathin, dynamic and groovy: the physics of Dutcher films. Annu. Rep. Prog. Chem., Sect. C: Phys. Chem. (2009)
  • Yang J, Ma YQ, Page RC, Misra S, Plow EF, Qin J. Structure of an integrin alphaIIb beta3 transmembrane-cytoplasmic heterocomplex provides insight into integrin activation. Proc Natl Acad Sci U S A. 2009 Oct 20;106(42):17729-34. Epub 2009 Oct 1. PubMed PMID: 19805198; PubMed Central PMCID: PMC2764936.
  • Kalp, M., Bethel. C. R., Bonomo, R. A. and Carey, P. R. "Why extended-spectrum beta-lactamases SHV-2 and SHV-5 are "hypersusceptible" to mechanism-based inhibitors". Biochemistry, 48, 9912-9920 (2009).
  • Kalp, M., Totir, M. A., Buynak, J. D., and Carey, P. R. "Different intermediate populations formed by tazobactam, sulbactam, and clavulanate reacting with SHV-1 beta-lactamases: Raman crystallographic evidence." J. Amer. Chem. Soc, 131, 2338-2347 (2009).
  • Qingfu Feng, Joseph Abraham, Tao Feng, Yeunjoo Song, Robert C Elston, Xiaofeng Zhu, BMC Genetics. In press
  • “Predicting Reversible Potentials of Reactions on Electrode Surfaces from Internal and Gibbs Energies”, Talk given by A. B. Anderson, at the 38th Great Lakes Regional Meeting of the American Chemical Society, Lincolnshire Il May13-16, 2009.
  • “Theories for Predicting Reversible Potentials of Reactions on Electrode Surfaces from Internal and Gibbs Energies: Applications to ORR”, talk given by A. B. Anderson at Brookhaven National Laboratory, August 26, 2009.
  • “Theories for Predicting Reversible Potentials of Reactions on Electrode Surfaces from Internal and Gibbs Energies: Applications to ORR”, talk given by A. B. Anderson at the Pittsburgh-Cleveland Catalysis Society Meeting, October 9, 2009.
  • "Theory for Coverage Dependence of Reversible Potential for H2O Oxidation on Pt(111) in Acid", F. Tian, and A. B. Anderson, poster presentation at the 215th Electrochemical Society Meeting, San Francisco CA May 24-29, 2009.
  • “Electroreduction of O2 on Selenium Nanotubes: Theoretical Prediction”, K. A. Kurak and A. B. Anderson, poster presentation at the 215th Electrochemical Society Meeting, San Francisco CA May 24-29, 2009.
  • F. Tian, R. Jinnouchi, and A. B. Anderson, “How Potentials of Zero Charge and Potentials for Water Oxidation to OH(ads) on Pt(111) Electrodes Vary With Coverage”, J. Phys. Chem. C 113, 17484-17492 (2009).
  • Rudick, C.S., Mihos, J.C., Frey, L.H. , and McBride, C.K., "Tidal Streams of Intracluster Light", The Astrophysical Journal, 699, 1518 (2009)
  • Elshad Allahyarov and Philip L. Taylor, "Predicted electric-field-induced hexatic structure in an ionomer membrane", Phys. Rev. E 80, 020801(R) (2009)
  • Elshad Allahyarov, Philip L. Taylor, and Hartmut Löwen, "Simulation study of sulfonate cluster swelling in ionomers", Phys. Rev. E 80, 061802 (2009)
  • Morris NJ, Elston RC and Stein CM. “Calculating Asymptotic Significance Levels of the Constrained Likelihood Ratio Test with Application to Multivariate Genetic Linkage Analysis.” Statistical Applications in Genetics and Molecular Biology, v. 8 issue 1, 2009, p. 39.
  • Morris NJ, Elston RC and Stein CM (2009) Robust Score Tests for Multivariate Linkage Analysis. Poster presentation at the 2009 Meeting of the American Society of Human Genetics.

  • S.J. Fleming, H.F. McGinnis, S. Sarkar, H. Baskaran, & P.J. Thomas. "Analysis of gradient sensing based on maximum likelihood." Poster presented to conference of the Society for Mathematical Biology.  Vancouver, Canada. July 2009.
  • "Using Intracluster Light to Weigh Galaxy Clusters", conference talk by Chris Mihos at the international conference "Unveiling the Mass: Extracting and Interpreting Galaxy Masses", Kingston, Ontario, June 2009.
  • Kalp, M., Buynak, J. D. and Carey, P. R. "Role of E166 in the Imine to Enamine Tautomerism of the Cllinical beta-Lactamase Inhibitor Sulbactam" Biochemistry, (2009) 48, 10196-98.
  • Guo, M., Spitale, R. C., Volpini, R., Krucinska, J., Cristalli, G., Carey, P. R., and Wedekind, J. E. "Direct Raman Measurement of an Elevated Base pKa in the Active Site of a Small Ribozyme in a Pre-Catalytic Conformation" J. Amer. Chem. Soc., (2009) 131, 12908-9.
  • Chen, J.-H., Gong, B., Bevilacqua, P. C., Carey, P. R., and Golden, B. L. "A Catalytic Metal Interacts with the Cleavage Site G.U Wobble in the HDV Ribozyme" Biochemistry, (2009) 48, 498-507.
  • Gong, B., Chen, J.-H., Yajima, R., Chen, Y., Chase, E., Chadalavada, D. M., Golden, B. L., Carey, P. R., Bevilacqua, P. C. "Raman crystallography of RNA" Methods, (2009)
  • Gong, B., Chen, J. H.,  Golden, B. L., Bevilacqua, P. C., and Carey, P. R. “Competition Between Co(NH3)63+and Inner-sphere Mg2+in the HDV Ribozyme”. Biochemistry., (2009) 48: 11961-70

  • Y.-T. Tseng and J. S. T'ien: The Effect of Different Pyrolysis Descriptions on flame spread over Solids in Concurrent Flows, 6th U.S. National Combustion Meeting, Ann Arbor, Michigan 2009
  • S.-Y. Hsu, Y.-T. Tseng and J.S. T’ien, “Modeling flame spread and extinction of solids in space exploration atmospheres,” International Conference on Environmental Systems, Fire Safety in Spacecraft and Enclosed Habitats, 09ICES-0333/2009-01-2492, 2009

  • Kyle E. Niemeyer, Chih-Jen Sung, Mandhapati P. Raju, "Skeletal mechanism generation for surrogate fuels using directed relation graph with error propagation and sensitivity analysis," Combustion and Flame 57 (2010) 1760-1770. doi:10.1016/j.combustflame.2009.12.0

  • G. Karl Steinke and Roberto F. Galán (2009). Reverse-engineering neural network topology from large-scale recording dynamics. Program No. 895.15. 2009 Neuroscience Meeting Planner. Chicago, IL: Society for Neuroscience, 2009. Online. SfN 39th Annual Meeting, October 17-21, 2009.

  • G. Karl Steinke and Roberto F. Galán (2009). Inferring large-scale brain connectivity from spectral properties of the EEG. Computational Neuroscience Meeting, CNS 2009, Berlin, Germany.

2008

  • J. Li, "Prioritize and Select SNPs for Association Studies with Multi-stage Designs" Journal of Computational Biology. 15, 241–57 (2008)
  • J. Li, and Y. Chen, "Generating samples for association studies based on HapMap data" BMC Bioinformatics 9, 44, 2008
  • X. Zheng, P.L. Wintrode, and M.R. Chance, "Complementary Structural Mass Spectrometry Techniques Reveal Local Dynamics in Functionally Important Regions of a Metastable Serpin" Structure 16, 38-51 (2008)
  • M.B. Hamaneh and P.L. Taylor, "Simulated anchoring of a nematic liquid crystal at a polymer surface" Physical Review E 77, 021707 (2008)
  • Elshad Allahyarov, "Macrophase Ordering in Ionomers Under External Potential" Poster at CWRU Research ShowCASE 2008
  • Zhenlong Li, Matthew C. Hagy, and Elena E. Dormidontova, "Dynamics of Amphiphile Self-assembly by DPD simulation" Poster at CWRU Research ShowCASE 2008
  • Tula Paudel, "Theoretical study of native defects in Cadmium Germanium Arsenide" Poster at CWRU Research ShowCASE 2008
  • P.L. Wintrode, "Exploring the link between folding, dynamics and metastability in human serpins" Gordon Research Conference on Biopolymers, Newport, RI, 2008
  • N. Duff, E.K. Mann, and D.J. Lacks, "Molecular Dynamics Investigation of the Effects of a Water Surface on the Aggregation of Bent-Core Molecules" Langmuir 24, 4456 (2008)
  • K. Forward, D.J. Lacks, and R.M. Sankaran, "Triboelectric Charging of Binary Granular Mixtures due solely to Particle-Particle Interactions" Electrostatics Society of America Annual Conference, Minneapolis, MN, June 2008
  • X. Zheng, P.L. Wintrode, and M.R. Chance, "Complementary structural mass spectrometry techniques reveal local dynamics in functionally important regions of a metastable serpin" Structure 16, 1-14 (2008)
  • Y. Tong, P.K. Hota, M.B. Hamaneh, and M. Buck, "Insights into Oncogenic Mutations of plexin-B1 based on the Solution Structure of the Rho GTPase Binding Domain Structure" Structure 16, 246-258 (2008)
  • M.B. Hamaneh and P.L. Taylor, "Simulated Anchoring of a Nematic Liquid Crystal at a Polymer Surface" Virtual Journal of Biological Physics Research 15 (5) March 1, 2008
  • E. Allahyarov and P. L. Taylor, “Correlation between structure and conductivity of stretched Nafion”, J. Phys. Chem. (submitted)
  • M.B. Hamaneh and P.L. Taylor, "Simulated Anchoring of a Nematic Liquid Crystal at a Polymer Surface" Virtual Journal of Nanoscale Science & Technology 17 (11) March 17, 2008
  • J. Zhu and X. Zhang, "Efficient VLSI architecture for soft-decision decoding of Reed-Solomon codes" to appear IEEE Trans. on Circuits & Systems –I, 2008.
  • J. Zhu and X. Zhang, "Backward interpolation for algebraic soft-decision Reed-Solomon decoding" submitted to IEEE Trans. On VLSI Systems, Mar. 2008.
  • J. Zhu, X. Zhang and Z. Wang, "Combined interpolation architecture for soft-decision decoding of Reed-Solomon codes" IEEE Conference on Computer Design, May 2008.
  • G. Mittal, M.P. Raju, and C.J. Sung, "Computational Fluid Dynamics Modeling of a Rapid Compression Machine with Creviced Piston: Influence of Physical and Operating Parameters on its Performance" submitted.
  • K. Kumar, G. Mittal, C.J. Sung, and C.K. Law, "An Experimental Investigation on Ethylene/O2/Diluent Mixtures: Laminar Flame Speeds with Preheat and Ignition Delays at High Pressures" Combustion and Flame 153, 343-354 (2008).
  • G. Mittal, M.P. Raju, and C.J. Sung, "Computational Fluid Dynamics Modeling of Hydrogen Ignition in a Rapid Compression Machine" Combustion and Flame 155(3), 417-428, (2008)
  • G. Mittal and C.J. Sung, “Homogeneous Charge Compression Ignition of Binary Fuel Blends,” Combustion and Flame 155, 431-439 (2008)
  • M.P. Raju, and J.S. T’ien, "Modeling of candle burning with a self-trimmed wick" Combustion Theory and Modelling 12 (2), 367-388 (2008)
  • M.P. Raju, and J.S. T’ien, "Development of Direct Multifrontal Solvers for Combustion Problems" Numerical Heat Transfer, Part B: Fundamentals 53(3), 189-205 (2008)
  • M.P. Raju, and J.S. T’ien, "Two-Phase Flow inside an Externally Heated Axisymmetric Porous Wick" Journal of Porous Media 11(8), 701-718 (2008)
  • J. Kleinhenz, I.I. Feier, S.Y. Hsu, J.S. T’ien, P.V. Ferkul, and K.R. Sacksteder, "Pressure modeling of upward flame spread and burning rates over solids in partial gravity" Combustion and Flame 154, 637-643 (2008)
  • J. Zhu, X. Zhang and Z. Wang, "Backward interpolation for algebraic soft-decision Reed-Solomon decoding" IEEE Trans. on VLSI Systems, in press.
  • Gavin A. Buxton, The Fate of a Polymer Nanoparticle Subject to Flow-Induced Shear Stresses. Europhys. Lett. 84 26006 (2008).
  • Kalp, M. and Carey, P. R. "Carbapenems and SHV-1 beta-lactamase form different acyl-enzyme populations in crystals and solution", Biochemistry, 47, 11830-11837 (2008).
  • Totir M.A., Cha, J., Wang B., Sheri, A., Anderson, V.E., Buynak J., Mobashery, S., and Carey, P.R. “Why tazobactam and Sublactam Are Poor Inhibitors of OXA-10 β-Lactamase: Raman Crystallographic Evidence” Biochemistry, (2008) 47, 4094-4101.
  • Gong, B., Chen, Y., Christian, E. L., Chen, J.-H., Chase, E., Chadalavada, D. M., Yajima, R., Golden, B. L., Bevilacqua, Carey, P. R., J. Amer. Chem. Soc. 130, 9670-9672 (2008).

2007

  • P. Larson, Walter R.L. Lambrecht, Athanasios Chantis, and Mark van Schilfgaarde, "Electronic structure of rare-earth nitrides using the LSDA+U approach: Importance of allowing 4f orbitals to break the cubic crystal symmetry" Phys. Rev. B 75, 045114 (2007)
  • M.B. Hamaneh and P.L. Taylor, "Range of Interlayer Interactions in Smectic-C Liquid Crystals" Phys. Rev. E 75, 011703 (2007)
  • Mehdi Bagheri Hamaneh and Matthias Buck, "Acceptable Protein and Solvent Behavior in Primary Hydration Shell Simulations of Hen Lysozyme" Biophysical Journal 92, L49-L51 (2007)
  • Chandrima Mitra and Walter R. Lambrecht, "Band-gap bowing in AgGa(Se1-xTex)2 and its effect on the second-order response coefficient and refractive indices" Phys. Rev. B 76, 205206 (2007)
  • Chandrima Mitra and Walter R. Lambrecht, "Large band-gap bowing in Cu1−xAgxGaS2 chalcopyrite semiconductors and its effect on optical parameters" Phys. Rev. B 76, 035207 (2007)
  • Pavel Lukashev, Walter R. Lambrecht, Takao Kotani, and Mark van Schilfgaarde, "Electronic and crystal structure of Cu2-xS : Full-potential electronic structure calculations" Phys. Rev. B 76, 195202 (2007)
  • Tula R. Paudel and Walter R. Lambrecht, "First-principles calculation of the zone center phonons in ZnSiN2: Comparison with infrared data" Phys. Rev. B 76, 115205 (2007)
  • M. S. Miao and Walter R. Lambrecht, "Effects of vacancies and impurities on the relative stability of rocksalt and zincblende structures for MnN" Phys. Rev. B 76, 195209 (2007)
  • J.M. Kimmel, R. M. Salter, and P.J. Thomas, "An Information Theoretic Framework for Eukaryotic Gradient Sensing", Advances in Neural Information Processing Systems 19, MIT Press, pp 705-712, 2007
  • Elshad Allahyarov and Philip L. Taylor. "Role of electrostatic forces in cluster formation in a dry ionomer" The Journal of Chemical Physics 127, 154901 (2007)
  • Elshad Allahyarov, "Conformational Structures in Dry Ionomers" Poster at CWRU Research ShowCASE (2007).
  • K. Kumar, J.E. Freeh, C.J. Sung, and Y. Huang, "Laminar Flame Speeds of Preheated iso-Octane/O2/N2 and n-Heptane/O2/N2 Mixtures" Journal of Propulsion and Power 23 (2), 428-436 (2007).
  • G. Mittal and C.J. Sung, "Autoignition of Toluene and Benzene at Elevated Pressures in a Rapid Compression Machine" Combustion and Flame 150, 355-368 (2007).
  • K. Kumar and C.J. Sung, "Laminar Flame Speeds and Extinction Limits of Preheated n-Decane/O2/N2 and n-Dodecane/O2/N2 Mixtures" Combustion and Flame 151, 209-224 (2007).
  • Y. Huang, C.J. Sung, and K. Kumar, "Ultra-Dilute Combustion of Primary Reference Fuels" Combustion Science and Technology 179 (11), 2361-2379 (2007).
  • S.Y. Hsu, and J.S. T’ien, "Effect of Chemical Kinetics on Concurrent-flow Flame Spread over Solids: A Comparison between Buoyant flow and Forced Flow Cases" IMECE2007-42293, ASME INTERNATIONAL MECHANICAL ENGINEERING CONGRESS AND EXPOSITION, Seattle, WA, November 11-15 2007.
  • Y.T. Tseng, and J.S. T’ien, "Limiting Length and Non-growth of Flames in Concurrent Flow over Thick Solids" Eastern States Meeting/Combustion Institute, Charlottesville, VA. Oct. 21-24, 2007.
  • X. Li and J Li, "Comparisons of haplotype inference from pedigree data and population data" BMC Proceedings 1:S55, 2007.
  • G. Mittal, M.P. Raju, C. J. Sung, and K. P. Kundu, "A Computational Fluid Dynamics Study of a Rapid Compression Machine" Fall Technical Meeting of the Eastern States Section of the Combustion Institute, University of Virginia, VA, 2007.
  • M.P. Raju and C.J. Sung, "Optimization of Combustion Application Codes using Sparse Matrix Techniques" Fall Technical Meeting of the Eastern States Section of the Combustion Institute, University of Virginia, VA, 2007.
  • K. Kumar, G. Mittal, and C.J. Sung, "Autoignition of n-Decane under High Pressure Conditions" Fifth Joint Meeting of the U.S. Sections of the Combustion Institute, San Diego, CA, 2007.
  • X. Zhang, "Further exploring the strength of prediction in the factorization of soft-decision Reed-Solomon decoding" IEEE Trans. on VLSI Systems, vol. 15(7), pp. 811-820, Jul. 2007.
  • J. Zhu and X. Zhang, "Efficient interpolation architecture for soft-decision Reed-Solomon decoding" Proc. of IEEE Workshop on Signal Processing Systems, pp. 663-668, Shanghai, China, Oct. 2007.
  • Kalp, M., Sheri, A., Buynak, J.D., Bethel, C.R., Bonomo R.A., and Carey, P.R. “Efficient inhibition of class A and class D β-Lactamases by Michaelis complexes.” J. Biol. Chem. 282, 21588-91, 2007.
  • M. Stetner, D.M. Taylor “Evaluating Synchrony Between Neurons as a Signal for Brain Computer Interfaces” Intersections SOURCE Symposium, Cleveland, OH, April 2007. (1st Place Winner, poster competition; engineering category)

2006

  • P. Larson and Walter R. L. Lambrecht, "Electronic structure of Gd pnictides calculated within the LSDA+U approach" Phys. Rev. B 74, 085108 (2006)
  • P.L. Wintrode, "The dynamical properties of a metastable protein studied by molecular dynamics simulations and normal mode analysis" 1st Ohio Collaborative Conference on Bioinformatics, Athens, Ohio (2006).
  • Walter R. L. Lambrecht and M. S. Miao. "Electronic driving force for stacking fault expansion in 4H-SiC" Phys. Rev. B 73, 155312 (2006)
  • N. Duff, D. J. Lacks, J. Wang and E. K. Mann, "Molecular simulation of the self-assembly of bent-core molecules at water surfaces", Midwest Thermodynamics and Statistical Mechanics Conference, Akron, OH, May 2006.
  • N. Duff, J. Wang, E.K. Mann, and D.J. Lacks, "Molecular Dynamics Investigation of Bent-Core Molecules on a Water Surface" Langmuir 22, 9082 (2006).
  • M. S. Miao and Walter R. Lambrecht, "Electronic structure and magnetic properties of transition-metal-doped 3C and 4H silicon carbide" Phys. Rev. B 74, 235218 (2006)
  • N. Duff and D. J. Lacks, "Mechanical Properties of Proteins: the Dynamic Energy Landscape" AIChE Annual Meeting, San Francisco, CA, November 2006.
  • N. Duff, D. J. Lacks, J. Wang and E. K. Mann "Molecular simulation of the self-assembly of bent-core molecules at water surfaces" AIChE Annual Meeting, San Francisco, CA, November 2006.
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Sanjaya Gajurel,
Apr 16, 2013, 8:23 AM
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