Publications of the HPC²

Publications by HPC centers and institutes include items from past years such as an early publication written by one of the HPC founding investigators, Dr. Joe Thompson. Numerical Grid Generation was originally published by Elsevier Science Publishing Co., Inc. in 1985, and the copyright was transferred to Joe F. Thompson in 1997.

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Publications for: Ma
Book or Book Chapter
Takac, T., Pechan, T., Samajova, O., & Samaj, J. (2014). Integrative Chemical Proteomics and Cell Biology Methods to Study Endocytosis and Vesicular Trafficking in Arabidopsis. Plant Endosomes. Springer New York. DOI:10.1007/978-1-4939-1420-3_20.

Rehman, H. U., & Gwaltney, S. R. (2014). Structure and Energetics of Polyhedral Oligomeric Silsesquioxane (T8 ,T10, T12-POSS) Cages with Atomic and Ionic Lithium Species. Practical Aspects of Computational Chemistry III. Springer. 151-165. DOI:10.1007/978-1-4899-7445-7_5.

Peer-Reviewed Journals
Edelmann, M. J., Shack, L., Naske, C., Walters, K. B., & Nanduri, B. (2014). SILAC-based Quantitative Proteomic Analysis of Human Lung Cell Response to Copper Oxide Nanoparticles. PLoS One. e114390, 1. [Document Site]

Takac, T., Samajova, O., Vadovic, P., Pechan, T., Kosutova, P., Ovecka, M., Husickova, A., Komis, G., & Samaj, J. (2014). Proteomic and Biochemical Analyses Show a Functional Network of Proteins Involved in Antioxidant Defense of the Arabidopsis Anp2anp3 Double Mutant. J Proteome Res.. Epub ahead of print], Epub ahead of p. [Document Site]

Narayanan, L., & Edelmann, M. J. (2014). Ubiquitination as an Efficient Molecular Strategy Employed in Salmonella Infection. Frontiers in Immunology. 5(558), 12. DOI:10.3389. [Document Site]

Sukhija, N., Malone, B., Srivastava, S., Banicescu, I., & Ciorba, F. M. (2014). A Learning-based Selection for Portfolio Scheduling of Scientific Applications on Heterogeneous Computing Systems. Journal of Parallel and Cloud Computing. 3(4), 66-81. DOI:10.14511/pcc.2014.030401#sthash.kolV4Znf.dpuf.

Maguire, F., Henriquez, F. L., Leonard, G., Dacks, J. B., Brown, M. W., & Richards, T. A. (2014). Complex Patterns of Gene Fission in the Eukaryotic Folate Biosynthesis Pathway. Genome Biol Evol.. 6(10), 2709-2720.

Magbanua, Z. V., Arick, M., II, Buza, T., Hsu, C. Y., Showmaker, K. C., Chouvarine, P., Deng, P., Peterson, D. G., & Lu, S. (2014). Transcriptomic Dissection of the Rice - Burkholderia glumae Interaction. BMC Genomics. 15, 755. DOI:10.1186/1471-2164-15-755. [Abstract]

Li, S., Tighe, S. W., Nicolet, C., Grove, D., Levy, S., Farmerie, W., Viale, A., Wright, C., Schweitzer, P., Gao, Y., Kim, D., Boland, J., Hicks, B., Kim, R., Changawala, S., Jafari, N., Raghavachari, N., Garcia-Reyero, N., Hendrickson, C., Roberson, D., Rosenfeld, J., Smith, T., Underwood, J., Wang, M., Zumbo, P., Baldwin, D., Grills, G., & Mason, C. (2014). Multi-platform and Cross-methodological Reproducibility of Transcriptome Profiling by RNA-seq in the ABRF Next-Generation Sequencing Study (ABRF-NGS). Nature Biotechnol. 32, 915-925. [Abstract]

Camacho, R. A., Martin, James L., Diaz-Ramirez, J., McAnally, W. H., Rodriguez, H., Suscy, P., & Zhang, S. (2014). Uncertainty Analysis of Estuarine Hydrodynamic Models: an Evaluation of Input Data Uncertainty in the Weeks Bay Estuary, Alabama. Applied Ocean Research. 47, 138-153.

Garcia-Reyero, N., Ekman, D., Habib, T., Villeneuve, D., Collette, T., Bencic, D., Ankley, G., & Perkins, E. (2014). Integrated Approach to Explore the Mechanisms of Aromatase Inhibition and Recovery in Fathead Minnows (Pimephales Promelas). Gen Comp Endocrinol. 203, 193-202. [Abstract]

Islam, M. R., Bujik, A., Rais-Rohani, M., & Motoyama, K. (2014). Simulation-Based Numerical Optimization of Arc Welding Process for Reduced Distortion in Welded Structures. Finite Elements in Analysis and Design. Elsevier. 84, 54-64. DOI:10.1016/j.finel.2014.02.003.

Smékalová, V., Luptoviak, I., Komis, G., Samajova, O., Ovecka, M., Doskocilova, A., Takac, T., Vadovic, P., Novak, O., Pechan, T., Ziemann, A., Kosutova, P., & Samaj, J. (2014). Involvement of YODA and Mitogen Activated Protein Kinase 6 in Arabidopsis Post-embryogenic Root Development through Auxin Up-regulation and Cell Division Plane Orientation. New Phytologist. 203(4), 1175-93. DOI:10.1111/nph.12880.. [Document Site]

Newman, J., Jr., & Daniewicz, S. (2014). Predicting Crack Growth in Specimens with Overloads and Cold-worked Holes with Residual Stresses. Engineering Fracture Mechanics. Elsevier. 127, 252-266. [Abstract]

Guo, H., Wang, X., Gundlach, H., Mayer, K. F., Peterson, D. G., Scheffler, B. E., Chee, P. W., & Paterson, A. H. (2014). Extensive and Biased Intergenomic Non-reciprocal DNA Exchanges Shaped a Nascent Polyploid Genome, Gossypium (Cotton). Genetics. 197(4), 1153-1163. DOI:10.1534/genetics.114.166124. [Abstract] [Document Site]

Burch, R. F., & Strawderman, L. (2014). Leveraging Generational Differences to Reduce Knowledge Transfer and Retention Issues in Public Administration. Public Administration Research. 3(2), 61-75.

Kargarian, A., Fu, Y., DorMohammadi, S., & Rais-Rohani, M. (2014). Optimal Operation of Active Distribution Grids: A System of Systems Framework. IEEE Transactions on Smart Grid. IEEE. 5(3), 1228-1237.

Liu, X., Usher, J., & Strawderman, L. (2014). An Analysis of Activity Scheduling Behavior for Airport Travelers. Computers and Industrial Engineering. 74, 208-218.

McAnally, W. H., Wallen, C. M., Sanborn, S. C., & Maak, E. C. (2014). Composite Risk Assessment for Sacramento-San Joaquin Delta Levee System. Journal of Water Resources Planning and Management. American Society of Civil Engineers. 140(5), 734-743. DOI:10.1061/(ASCE)WR.1943-5452.0000362). [Abstract]

Kiani M., Motoyama, K., Rais-Rohani, M., & Shiozaki, H. (2014). Joint Stiffness Analysis and Optimization as a Mechanism for Improving Vehicle Structural Design and Performance. Proceedings of IMechE, Part D: Journal of Automobile Engineering. Sage Publishing Co. 228(6), 689-700. [Abstract]

Xu, J., Deng, P., Showmaker, K. C., Wang, H, Baird, S. M., & Lu, S. (2014). The PqqC Gene Is Essential for Antifungal Activity of Pseudomonas Kilonensis JX22 against Fusarium Oxysporum F. Sp. Lycopersici. FEMS Microbiology Letters. 353(2), 98-105. DOI:10.1111/1574-6968.12411. [Abstract] [Document Site]

Doyle, J. D., Howard, I. L., Gartrell, C. A., Anderton, G. L., Newman, J. K., & Berney, E. S. (2014). Full-Scale Instremented Testing and Three-Dimensional Modeling of Airfield Matting Systems. International Journal of Geomechanics. American Society of Civil Engineers. 14(2), 161-170. DOI:10.1061/(ASCE)GM.1943-5622.0000272.

Garcia-Reyero, N., Kennedy, A., Escalon, L., Habib, T., Laird, J., Rawat, A., Wiseman, S., Hecker, M., Denslow, N., Steevens, J., & Perkins, E. (2014). Differential Effects and Potential Adverse Outcomes of Ionic Silver and Silver Nanoparticles in Vivo and in Vitro. Environ Sci Technol. 48, 4546-4555. [Abstract]

Hernandez, I., Ramirez-Marquez, J. E., Rainwater, C., Pohl, E., & Medal, H. (2014). Robust Facility Location: Hedging Against Failures. Reliability Engineering & System Safety. 123, 73-80. [Abstract] [Document Site]

Monroe, A. P., Martin, J. A., Riffell, S. K., & Burger, L. W. (2014). Effects of Measuring Nestling Condition on Nest Success in the Dickcissel (Spiza Americana). Wildlife Society Bulletin. 38, 401-406. DOI:10.1002/wsb.412. [Document]

Edelmann, M. J., Nallamilli, B. R., Zhong, X., Tan, F., Mujahid, H., Zhang, J., Nanduri, B., & Peng, Z. (2014). Global Analysis of Lysine Acetylation Suggests the Involvement of Protein Acetylation in Diverse Biological Processes in Rice (Oryza Sativa). PlosOne. 9(2), e89283.

Oedekoven, C. S., Buckland, S. T., MacKenzie, M. L., King, R., Evans, K. O., & Burger, L. W. (2014). Bayesian Methods for Hierarchical Distance Sampling Models. Journal of Agricultural, Biological, and Environmental Statistics. International Biometric Society. 19(2), 219-239. DOI:10.1007/s13253-014-0167-0. [Abstract] [Document]

Berninger, J., Martinovic-Weigelt, D., Garcia-Reyero, N., Escalon, L., Perkins, E. J., Ankley, G., & Villeneuve, D. (2014). Using Transcriptomic Tools to Evaluate Biological Effects across Effluent Gradients at a Diverse Set of Study Sites in Minnesota USA. Environ Sci Technol. 48, 2404-2412. [Abstract]

Ekman, D. R., Ankley, G. T., Blazer, V., Collette, T., Garcia-Reyero, N., Iwanowicz, L., Jorgenson, Z., Lee, K., Miller, D., Perkins, E. J., Smith, E., Tiegte, J., Trowbridge, A., & Villeneuve, D. (2014). Biological Effects-based Tools for Monitoring Impacted Surface Waters in the Great Lakes: a Multi-agency Research Program in Support of the GLRI. Environmental Practice. 15, 409-426. [Abstract]

Glinka, T., Alter, J., Braunstein, I., Tzach, L., Sheng, C. W., Geifman, S., Edelmann, M. J., Kessler, B., & Stanhill, A. (2014). Signal-peptide Mediated Translocation Is Regulated by a P97-AIRAPL Complex. Biochemical Journal. 1, 1-1. DOI:10.1042/BJ20130710. [Abstract] [Document Site]

Mamivand, M., Asle Zaeem, M., & El Kadiri, H. (2014). Phase Field Modeling of Stress-induced Tetragonal-to-monoclinic Transformation in Zirconia and Its Effect on Transformation Toughening. Acta Materialia. 64, 208219. DOI:10.1016/j.actamat.2013.10.031.

Zhang, L., Deng, Q., Machiraju, R., Rangarajan, A., Thompson, D., Walters, K., & Shen, H. (2014). Boosting Techniques for Physics-Based Vortex Detection. Computer Graphics Forum. 33(1), 282-293. DOI:10.1111/cgf.12275. [Abstract]

Hossain, D., , C. U. P. J., & Gwaltney, S. R. (2014). Structures and Stabilities of the Metal Doped Gold Nano-Clusters: M@Au10 (M = W, Mo, Ru, Co). Journal of Inorganic and Organometallic Polymers and Materials. 24(1), 241-249. DOI:10.1007/s10904-013-9995-6.

Peer-Reviewed Conference Abstracts
Bethel, C. L., May, D., Carruth, D., Strawderman, L., Holler, K., Louine, J., & Rogers, S. (2014). Using Robots in Criminal Justice Applications: Experiments in Policing, Gathering Sensitive Data from Bullying Victims, and Military Policing. Annual Meetings of the Southern Criminal Justice Association. Clearwater, FL.

King, K., Carruth, D., Strawderman, L., Garrison, T. M. (2014). Improving Safety of Vulnerable Road Users. 2014 Industrial and Systems Engineering Research Conference. Montreal.

Farek, J., Castillo, J., Musselman-Brown, A., Shah, S., McCarthy, F.M., Xue, J., & Jankun-Kelly, T. J. (2014). Web-Based Visualization for Computational Biology Expression Atlases. Proceedings of the Eleventh Annual Conference of the MidSouth Computational Biology and Bioinformatics Society, Posters. Stillwater, OK.

Peer-Reviewed Conference Papers
Nannapaneni, S., Dubey, A., Abdelwahed, S., Mahadevan, S., & Neema, S. (2014). A Model-Based Approach for Reliability Assessment in Component-Based Systems. The 2014 Annual Conference of the Prognostics and Health Management Society. Fort Worth, TX.

Strawderman, L., & Heiselt, A. (2014). Connecting Students to the Community through Ergonomics Projects. Proceedings of the HFES 2014 International Annual Meeting. Chicago, IL.

Balasubramaniam, M., Banicescu, I., & Ciorba, F. M. (2014). Scalability Analysis and Evaluation of Divisible Load Scheduling. In Proceddings of The International Conference on Parallel Processing (ICPP-2014). Minneapolis, MN: IEEE Computer Society Press. 37-44.

Hansen, T., Ciorba, F. M., Maciejewski, A. A., Siegel, H. J., Srivastava, S., & Banicescu, I. (2014). Heuristics for Robust Al- Location of Resources to Parallel Applications with Uncertain Execution Times in Heterogeneous Systems with Uncertain Availability. In Proceedings of the World Conference on Engineering 2014. London, United Kingdom. 536-541.

Balasubramaniam, M., Banicescu, I., & Ciorba, F. M. (2014). Robustness Prediction and Evaluation of Divisible Load Scheduling on Computing Systems with Unpredictable Variations. In Proceedings of the IEEE 13th International Symposium on Parallel and Distributed Computing. Porquerolles, France: IEEE Engineering Society. 170-177.

AbuOmar, O., Nouranian, S., King, R., Ricks, T., & Lacy, T. (2014). Mechanical Property Classification of Vapor-Grown Carbon Nanofiber/Vinyl Ester Nanocomposites Using Support Vector Machines. The 10th International Conference on Data Mining, July 21-24, 2014. Las Vegas, NV, USA. [Document] [Document Site]

Burch, R. F., & Strawderman, L. (2014). Touchscreen Versus Keypad: Ruggedized Handheld Device Input Effectiveness by Generation. Proceedings of the 2014 Industrial and Systems Engineering Research Conference. Montreal.

Strawderman, L. (2014). Service-Learning in the Industrial Engineering Classroom. Proceedings of the 2014 Industrial and Systems Engineering Research Conference. Montreal.

AbuOmar, O., Nouranian, S., King, R., & Lacy, T. (2014). On Materials Informatics and Knowledge Discovery: Mechanical Characterization of Vapor-Grown Carbon Nanofiber/ Vinyl Ester Nanocomposites. Shechtman International Symposium, June 29- July 04, 2014. Cancun, Mexico. [Document] [Document Site]

Sukhija, N., Malone, B., Srivastava, S., Banicescu, I., & Ciorba, F. M. (2014). Portfolio-based Selection of Robust Dynamic Loop Scheduling Algorithms Using Machine Learning. In Proceedings of the IEEE International Parallel and Distributed Processing Symposium - IPDPS 2014 -(ParLearning). Phoenix, AZ.

M. Al Boni, AbuOmar, O., & King, R. (2014). ReShare: An Operational Ontology Framework for Research Modeling, Combining and Sharing. Computational Science and Computational Intelligence (CSCI), 2014 International Conference on, Vol 1. Las Vegas, NV, USA: IEEE. 1, 327 - 333. DOI:10.1109/CSCI.2014.63. [Abstract] [Document] [Document Site]

Peer-Reviewed Conference Posters
Sukhija, N., Srivastava, S., Ciorba, F. M., Banicescu, I., & Malone, B. (2014). Employing Machine Learning for the Selection of Robust Algorithms for the Dynamic Scheduling of Scientific Applications. ACM Research Poster Session of the Supercomputing conference (SC14) - the International Conference for High Performance Computing, Networking, Storage and Analysis. New Orleans, LA. [Document Site]

Non-Refereed Conference Abstracts
Doude, H., Rhee, H., Wang, P., Horstemeyer, S., Malley, R., Ritter, T., Baker, D., & Radzilowski, R. (2014). Microalloying to Develop Third Generation Advanced High Strength Steels (3GAHSS). AIST Birmingham Region Chapter Meeting. New Orleans, LA. [Document]

Ramirez-Avila, J. J., Oldham, J. L., Ortega-Achury, S. L., Osmond, D., Martin, J. L., & Locke, M. (2014). Refinement and Regionalization of Phosphorus Assessment Tools in Mississippi. 2014 Mississippi Water Resources Conference. Jackson, MS: Mississippi Water Resources Research Institute. [Abstract] [Document Site]

Ward, A. B., Clay, R. T., & Mazumdar, S. (2014). Theory of the Magnetic Ground States of TMTTF_2X. Bulletin of the American Physical Society. Denver, CO: American Physical Society. 59(1). [Abstract] [Document] [Document Site]

Clay, R. T., & Mazumdar, S. (2014). A 1/4-filled Band Model for the Organic Superconductor &#954;-(ET)2X. Bulletin of the American Physical Society. Denver, CO: American Physical Society. 59(1). [Abstract] [Document] [Document Site]

Madsen, J. D. (2014). Flowering Rush in Detroit Lakes: From Research to an Operational Management Program. Midwest Aquatic Plant Management Society Annual Meeting. Lombard, IL. [Abstract]

Madsen, J. D., Sartain, B. T., & Turnage, G. (2014). Herbicide Trials for Management of Flowering Rush in Minnesota. Weed Science Society of America 54th Annual Meeting. Vancouver, BC, Canada. [Abstract]

Wersal, R. M., Madsen, J. D., & Turnage, G. (2014). Evaluating the Sensitivity of Hydrilla and American Lotus to Different Copper Formulations Applied Alone and in Combination with Diquat. 2014 Northeast Aquatic Plant Management Society annual conference. Westbrook, CT.

Non-Refereed Conference Papers
Cost, V. T., Matschei, T., Shannon, J., & Howard, I. L. (2014). Extending the Use of Fly Ash and Slag Cement in Concrete Through the Use of Portland-Limestone Cement. Proceedings of the 2014 International Concrete Sustainability Conference. Boston, MA. pp. 15.

Madsen, J. D. (2014). Ecology and Management of Flowering Rush in Minnesota. Northern Rockies Invasive Plant Coucil Conference. Spokane, WA: Northern Rockies Invasisve Plant Council. [Abstract]

Offenberger, S., Lacy, T., Al-Ostaz, A., Toghiani, H., Kundu, S., Pittman, C., Li, X., & Mansrah, A. H. (2014). Novel Composite Shielding Concepts for Hypervelocity Orbital Debris Impact Mitigation. Proceedings of the AIAA Science and Technology Forum and Exposition 2014, National Harbor, Maryland, January 13-17, 2014. National Harbor, Maryland.

Non-Refereed Conference Posters
Sanders, W. S., Ganji, S., Arnold, J. P., Arick, M., II, Showmaker, K. C., Bartlett, B. D., Cooksey, A., Watts, J., Knudstrup, S., Magbanua, Z. V., Peterson, D. G., & Wubben, M. J. (2014). Assembly, Annotation, and Proteogenomic Mapping of Rotylenchulus reniformis. Plant and Animal Genome XXII. San Diego, CA. [Abstract] [Document] [Document Site]

Madsen, J. D., Turnage, G., & Sartain, B. T. (2014). Management of Flowering Rush Using the Contact Herbicide Diquat in Detroit Lakes, Minnesota 2013. Mississippi State University: Geosystems Research Institute. [Document]

Sartain, B. T., Turnage, G., & Madsen, J. D. (2014). Aquatic Plant Community and Invasive Plant Management Assessment of the Ross Barnett Reservoir, MS in 2013. GRI Report #5062. Mississippi State University, Mississippi State, MS: Geosystems Research Institute. 34. [Document]

Turnage, G., & Madsen, J. D. (2014). Littoral Survey of Noxon and Cabinet Gorge Reservoirs, Montana, 2013. GRI Report #5061. Mississippi State University: Geosystems Research institute. 82. [Document]

Technical Report
Uriarte, F., Hebner, R., Mazzola, M., Henley, G., Card, A., & Abdelwahed, S. (2014). Parallelizing the Simulation of Shipboard Power Systems. The Electric Ship Research and Development Consortium Reports. The office of Naval Research: The office of Naval Research.

Getsinger, K. D., Skogerboe, J. G., Wersal, R. M., Madsen, J. D., Nawrocki, J. J., Richardson, R. J., & Sternberg, M. R. (2014). Selective Control of Eurasian Watermilfoil and Curlyleaf Pondweed in Noxon Rapids Reservoir, Montana: Herbicide Small-Plot Evaluations, 2010-2011. ERDC/EL TR-14-4. Vicksburg, MS: US Army Engineer Research and Development Center. 50. [Document]

Professional Presentations
Shoemaker, C. M., Kroger, R., & Ervin, G. N. (2014). Assessing the Relative Importance of Environmental Factors at Multiple Scales on Wetland Structure and Function in the Mississippi Delta. Southeastern Natural Resources Graduate Student Symposium. Mississippi State University.

Awards and Recognitions
AbuOmar, O. (2014). Graduate Poster Distinguished Competition Award. Bagley College of Engineering, March 2014. [Document Site]

AbuOmar, O. (2014). Graduate Student Publication Award. Bagley College of Engineering, January 2014. [Document Site]

Thesis and Dissertation
AbuOmar, O. (2014). A Data Analytic Methodology for Materials Informatics. Ph.D Dissertation, Mississippi State University Libraries. Mississippi State University: ProQuest/UMI. [Abstract] [Document] [Document Site]