Louisiana EPSCoR RII Publications

Work Package 1: Scheduling and Data Services

Chakraborty, Promita, Shantenu Jha, and Daniel S. Katz. "Exploring Submission of Tightly-coupled Jobs Across Distributed Resources for Performance Enhancement." UK e-Science All Hands Meeting (2008).

Katz, D., G. Allen, R. Cortez, C. Cruz-Neira, R. Gottumukkala, Z. D. Greenwood, L. Guice, S. Jha, R. Kolluru, T. Kosar, L. Leger, C. McMahon, J. Nabrzyski, B. Rodriguez-Milla, E. Seidel, G. Speyrer, M. Stubblefield, B. Voss, and S. Whittenburg. "Louisiana: A Model for Advancing Regional e-Science through Cyberinfrastructure." UK e-Science All Hands Meeting (2008).

Katz, Daniel S., Promita Chakraborty, and Shantenu Jha. Exploring Submission of Tightly-coupled Jobs Across Distributed Resources for Performance Enhancement (2008).

Kosar, Tevfik, Gabrielle D. Allen, Mehmet Balman, Emrah Ceyhan, Archit Kulshrestha, Sirish Tummala, and C. White. "Data-Aware Workflow Management for Large Scale Scientific Applications." IEEE Transactions on Automation Science and Engineering (2008).

Kosar, Tevfik, and Mehmet Balman. "A New Paradigm: Data-Aware Scheduling in Grid Computing." Future generation Computer Systems 25.4 (2008): 406-413.

Kulshrestha, Archit, Daniel S. Katz, and K. Muller. "The Highly-Available Resource Co-allocator." Future Generation Computer Systems (2008).

MacLaren, Jon. "HARC: The Highly-Available Resource Co-allocator." Proceedings of GADA'07 (OTM Conferences 2007, Part II) (2007): 1385-1402.

Stamou, Katerina, Prathyusha V. Akunuri, Gabrielle D. Allen, Archit Kulshrestha, Daniel S. Katz. "Feature rich, enhanced grid portal for LONI." 15th ACM Mardi Gras Conference: From Lightweight Mash-Ups To Lambda Grids 320 (2008).

Suslu, Ibrahim, F. Turkmen, Mehmet Balman, and Tevfik Kosar. "Choosing Between Remote I/O versus Staging in Large Scale Distributed Applications." Proceedings of ISCA 21st International Conference on Parallel and Distributed Computing and Applications (PDCCS 2008) (2008).

Wu, Yixin, Maria C. Tugurlan, and Gabrielle Allen. "Advance reservations: a theoretical and practical comparison of GUR & HARC." Proceedings of the 15th ACM Mardi Gras Conference: From Lightweight Mash-Ups To Lambda Grids 320 (2008).

Yildirim, Esma, Mehmet Balman, and Tevfik Kosar. "Dynamically Tuning Level of Parallelism in Wide Area Data Transfers." Proceedings of the International Workshop on Data-Aware Distributed Computing (2008): 39-48.

Yildirim, Esma, Ibrahim H. Suslu, and Tevfik Kosar. "Which Network Measurement Tool is Right for You? A Multidimensional Comparison Study." Proceedings of IEE/ACM Conference on Grid Computing (2008): 266-275.

Work Package 2: Information Services and Portals

Dua, Sumeet, V. Jain, and Hilary W. Thompson. "Patient Classification using Association Mining of Clinical Images." Proceedings of 5th IEEE International Symposium on Biomedical Imaging: from Nano to Macro (2008): 253-256.

Dua, Sumeet, H. Singh, and Hilary W. Thompson. "Associative Classification of Mammograms using Weighted Rules based Classification." Elsevier Expert Systems with Applications (2008).

Dua, Sumeet, and Priti Srinivasan. "A non-voxel based feature extraction to detect cognitive states in fMRI." Proceedings of the 30th Annual International Conference of the IEE (2008): 4431-4434.

Work Package 3: Visualization Services

Benger, Werner, Georg Ritter, and Rene Heinz. "The Concepts of VISH." Proceedings of the High-End Visualization Workshop (2007).

Toole, Cornelius, and Andrei Hutanu. "Network Flow Based Resource Brokering and Optimization Techniques for Distributed Data Streaming over Optical Networks." Proceedings of the Mardi Gras Conference on Distributed Applications 320 (2008).

Ullmer, Brygg. "Network Flow Based Resource Brokering and Optimization Techniques for Distributed Data Streaming over Optical Networks." Proceedings of the Mardi Gras Conference on Distributed Applications 1 (2008).

Ullmer, Brygg, Rajesh Sankaran, Srikanth Jandhyala, Blake Tregre, Cornelius Toole, Karun Kallakuri, Christopher Laan, Matthew Hess, Farid Harhad, Urban Wiggins, and Shining Sun. "Tangible Menus and Interaction Trays: Core tangibles for common physical/digital activities." Proceedings of the 2nd International Conference on Tangible and Embedded Interaction (TEI) (2008): 209-212.

Work Package 4: Application Services and Toolkits

Science Driver: Biosensor Development

Balamurugan, Subramanian, Anne Obubuafo, Steven A. Soper, and David A. Spivak. "Surface immobilization methods for aptamer diagnostic applications." Analytical and Bioanalytical Chemistry 390.4 (2008): 1009-1021.

Batzer, Mark A., K. E. Cherry, S. Galea, J. L. Silva, and Louisiana Healthy Aging Study. Natural disasters and successful aging: Role of adaptation and resiliency in late life. Ed. M. Hersen and A. M. Gross. Vol. 1. Handbook of Clinical Psychology. 2008.

Batzer, Mark A., R. Cordaux, and H. Kehrer-Sawatzki. Evolutionary emergence of genes through retroposition. Ed. D. N. Cooper. Handbook of Human Molecular Evolution. 2008.

Batzer, Mark A., Prescott L. Deininger, and A. M. Roy-Engel. Evolution of human retrosequences: Alu. Ed. D. N. Cooper and H. Kehrer-Sawatzki. Handbook of Human Molecular Evolution. 2008.

Batzer, Mark A., L. Poon, S. M. Jazwinski, and R. C. Green. Contributors of longevity and adaptation: findings and new directions from the Georgia centenarian studies. Ed. T. T. Perls. Exceptional Longevity. 2008.

Belancio, Victoria P., Dale J. Hedges, and Prescott Deininger. "Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health." Genome Research 18 (2008): 343-358. 10.1101/gr.5558208

Belancio, V. P., A. M. Roy-Engel, and P. Deininger. "The impact of multiple splice sites in human L1 elements." Gene 411.1-2 (2008): 38-45. 10.1016/j.gene.2007.12.02

Blidner, Richard A., Kurt R. Svoboda, Robert P. Hammer, Todd W. Monroe. "Photoinduced RNA Interference using DMNPE Caged 2'-Deoxy-2'-Fluoro Substituted Nucleic Acids in vitro and in vivo." Molecular BioSystems 4.5 (2007): 431-440.

Bour, P., J. Kim, J. Kapitan, R. P. Hammer, R. Huang, L. Wu, T. A. Keiderling. "Vibrational circular dichroism and IR spectral analysis as a test of theoretical conformational modeling for a cyclic hexapeptide." Chirality 20 (2008): 1104-1119.

Carroll, Marion L., T. Metoyer, and A. Kelly. "Analysis of a Promiscuous Alu Subfamily." PLoS Computational Biology 1 (2008).

Chen, Guofang, Gregory T. McCandless, Robin L. McCarley, and Steven A. Soper. "Integration of large-area polymer nanopillar arrays into microfluidic devices using in situ polymerization cast molding." Lab on a Chip 7 (2007): 1424-1427.

Chen, Guofang, Steven A. Soper, and Robin L. McCarley. "Free-standing, erect ultrahigh-aspect-ratio polymer nanopillar and nanotube ensembles." Langmuir 23 (2007): 11777-11781.

Chen, P. C., D. E. Nikitopoulos, S. A. Soper, and M. C. Murphy. "Temperature Distribution Effects on Micro-CFPCR Performance." Biomedical Microdevices 10 (2008): 141-152.

Chen, P.-C., B. H. You, D.-S. Park, S.-G. Park, J. Guy, D. E. Nikitopoulos, S. A. Soper, and M. C. Murphy. "Replication of reliable assembly features for polymer modular microfluidic systems." Proceedings of the ASME IMECE 1 (2007): 42206.

Emory, Jason M., and Steven A. Soper. "Charge-coupled device operated in a time-delayed integration mode as an approach to high-throughput flow-based single molecule analysis." Analytical Chemistry 80 (2008): 3897-3903. 10.1021/ac800447

Erdem, S. Sibel, Irina V. Nesterova, Steven A. Soper, and Robert P. Hammer. "Solid-Phase Synthesis of Asymmetrically Substituted 'AB3-type' Phthalocyanines." J. Org. Chem. 73 (2008): 5003-5007.

Gu, Wanjun, Todd A. Castoe, Dale J. Hedges, Mark A. Batzer, David D. Pollock. "Identification of repeat structure in large genomes using repeat probability clouds." Analytical Biochemistry 380 (2008): 77-83.

Huang, Rong, Vladimir Setnicka, Marcus A. Etienne, Joohyun Kim, Jan Kubelka, Robert P. Hammer, Timothy A. Keiderling. "Cross-strand coupling of a beta-hairpin peptide stabilized with an Aib-Gly turn studied using isotope-edited IR Spectroscopy." Journal of the American Chemical Society 129 (2007): 13592-603.

Jang, Wonbong, Minbum Seo, Jongchul Seo, Sunggook Park, Haksoo Han. "Correlation of Residual Stress and Adhesion on Cu by the Effect of Chemical Structure of Polyimide for Copper-Clad Laminates." Polymer International 57.2 (2008): 350-359.

Jiang, J., F. H. Mei, W. J. Meng, G. B. Sinclair, and S. Park. "Direct microscale imprinting of Al at room temperature with Si inserts." Microsystem Technologies 14 (2008): 815-819. 10.1007/s00542-008-0567-6

Li, Qingyou, Marcia Gordon, Marcus A. Etienne, Robert P. Hammer, Dave Morgan"Contrasting in vivo effects of two peptide-based amyloid α-protein aggregation inhibitors in a transgenic mouse model of amyloid deposition." Cell Transplantation 17.4 (2008): 397-408.

Moldovan, Dorel, Dinesh Pinisetty, Ram V. Devireddy. "Molecular dynamics simulation of pore growth in lipid bilayer membranes in the presence of edge-active agents." Applied Physics Letters 91 (2007): 204104.

Murphy, Michael C. "Design and fabrication of fast micro heaters for temperature programming micro gas chromatographs." Proceedings of the ASME IMECE 1 (2007).

Murphy, Michael C., and Steven A. Soper. "Capture of very rare circulating tumor cells for human breast cancer cell diagnosis." Proceedings of the ASME IMECE 1 (2007).

Nesterova, Irina V., Vera T. Verdree, Serhii Pakhomov, Karen L. Strickler, Michael W. Allen, Robert P. Hammer, and Steven A. Soper. "Metallo-Phthalocyanine Near-IR Fluorophores: Oligonucleotide Conjugates and Their Applications in PCR Assays." Bioconjugate Chem 18 (2007): 2159-2168

Nikitopoulos, Dimitris E., Michael C. Murphy, and Steven A. Soper. "Design and fabrication of a ligase detection reaction (LDR) with an integrated passive micromixer." Proceedings of the ASME IMECE 1 (2007).

Nikitopoulos, Dimitris E., Michael C. Murphy, and Steven A. Soper. "Gas-liquid two-phase flow in hot embossed square microchannels." Proceedings of the ASME IMECE 1 (2007): 42158.

Park, D. S.-W., M. L. Hupert, M. A. Witek, B. H. You, P. Datta, J. Guy, J.-B. Lee, S. A. Soper, D. E. Nikitopoulos, and M. C. Murphy. "A titer plate-based polymer microfluidic platform for high throughput nucleic acid purification." Biomedical Microdevices 10.1 (2007): 21-33.

Park, Sunggook. "Fabrication of Free-Standing Membranes via Imprint Lithography and Selective Immobilization of Lipid Vesicles at Micropores in the Membrane." Proceedings for ASME International Mechanical Engineering Congress & Exposition 1 (2007).

Park, Sunggook. "Finite Element Analysis for Demolding Process in Thermal Imprint Lithography." Proceedings for ASME International Mechanical Engineering Congress & Exposition 1 (2007).

Park, Sunggook, Z. Song, L. Brumfield, J. Choi, and J. Lee. "Optimal demolding temperature for nanoimprint lithograph." Nanotechnology (2008).

Pinisetty, Dinesh, R. Alapati, D. Moldovan, R. V. Devireddy. "Molecular Dynamics Simulation Studies of Pore Formation in Lipid Bilayers in the Presence of Dimethylsulfoxide." ASME International Mechanical Engineering Congress and Exposition (2007): 41305.

Song, Zhichao, Junseo Choi, Byoung H. You, Jaejong Lee, Sunggook Park. "Simulation study on stress and deformation of polymeric patterns during the demolding process in thermal imprint lithography." Journal of Vacuum Science & Technology B 26.2 (2007): 598-605.

Song, Zhichao, Byoung H. You, Jaejong Lee, Sunggook Park. "Study on demolding temperature in thermal imprint lithography via finite element analysis." Microsystem Technologies 14.9-11 (2008):1593-1597.

Wang, Y. R., H. W. Chen, Q. H. He, and S. A. Soper, "A high-performance polycarbonate electrophoresis microchip with integrated three-electrode system for end-channel amperometric detection." Electrophoresis 29 (2008): 1881-1888. 10.1002/elps.20070037

Witek, Malgorzata A., Mateusz L. Hupert, Daniel S.-W. Park, Kirby Fears, Michael C. Murphy, and Steven A. Soper. "96-well polycarbonate-based microfluidic titer plate for high-throughput purification of DNA and RNA." Analytical Chemistry 80 (2008): 3483-3491. 10.1021/ac800235

Xu, Feng, Proyag Datta, Hong Wang, Sitanshu Gurung, Masahiko Hashimoto, Suying Wei, Jost Goettert, Robin L. McCarley, and Steven A. Soper. "Polymer microfluidic chips with integrated waveguides for reading microarrays." Analytical Chemistry 79 (2007): 9007-9013.

Young, D. P., A. B. Karki, P. W. Adams, J. N. Ngunjiri, J. C. Garno, H. W. Zhu, B. Q. Wei, and D. Moldovan. "Self-assembly of multiwalled carbon nanotubes from quench-condensed CNi3 films." Journal of Applied Physics 103.5 (2008). 10.1063/1.288857

Science Driver: Transport Processes

Allen, Gabrielle D., Philip Bogden, Tevfik Kosar, Archit Kulshrestha, Gayathri Namala, Sirish Tummala, and Edward Seidel. "Cyberinfrastructure for Coastal Hazard Prediction." CTWatch Quarterly 4.1 (2008).

Cao, Hua, Nathan Brener, and S.S. Iyengar. "High Performance Adaptive Fidelity Algorithms for Multi-Modality Image Fusion". IEEE Transactions on Computers

Manikandan, Karuppasamy, Debnath Pal, Suryanarayanarao Ramakumar, Nathan E. Brener, Sitharama S. Iyengar, and Guna Seetharaman. "Functionally Important Segments in Proteins Dissected Using Gene Ontology and Geometric Clustering of Peptide Fragments." Genome Biology 9.3 (2008).

Thompson, Hilary W., Nathan E. Brener, Sundaraja S. Iyengar, Hua Cao, and Bahram Khoobehi. High Performance Adaptive Fidelity Algorithms for Multi-Modality Image Registration and Fusion. 2008.

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