Tony Pan, Patrick Flick, Chirag Jain, Yongchao Liu and Srinivas Aluru;"Kmerind: A flexible parallel library for k-mer indexing of biological sequences on distributed memory systems".;7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB 2016),;2016.

D Stoecklein, CY Wu, D Kim, D Di Carlo, and B Ganapathysubramanian, “Optimization of micropillar sequences for fluid flow sculpting,” arXiv preprint arXiv:1506.01111, 2016.

Srilok Srinivasan, Upamanyu Ray, and Ganesh Balasubramanian;"Thermal conductivity reduction in analogous 2D nanomaterials with isotope substitution: Graphene and silicene".;Chemical Physics Letters,;vol. 650;pp. 88 - 93.;vol. issn 0009-2614 http://dx.doi.org/10.1016/j.cplett.2016.02.073.;2016.

Sharma, A., Singh, P., Johnson, D. D., Liaw, P. K. & Balasubramanian, G.;"Atomistic clustering-ordering and high strain deformation of Al0.1CrCoFeNi high-entropy alloy".;Scientific Reports, Accepted July 2016,;2016.

Liu, Z., A. Passalacqua, M. G. Olsen, R. O. Fox, and J. C. Hill, “Dynamic delayed detached eddy simulation of a multi-inlet vortex reactor,” AIChE Journal (2016).

Kong, B., and R. O. Fox, Simulating gas-particle flows across all flow regimes in an Euler-Euler framework. 2016 NETL Workshop on Multiphase Flow Science, Morgantown, WV, 2016.

Parijat Shukla, Arun Somani, "Parallelization of Data De-duplication for Document Databases using GPGPU", submitted to 35th International Performance Computing and Communications Conference (IPCCC 2016), Dec 9-11 2016, at Las Vegas, Nevada, USA, 2016.

Kramer, L. M.; Abdel Ghaffar, M.A.; Koltes, J. E.; Fritz-Waters E.R.; Mayes M.; Sewell A.D.; Weeks, N.T.; Garrick, D.; Fernando R.; Reecy, J.M.;"Epistatic Interactions associated with Fatty Acid concentrations of beef from Angus Sired Beef Cattle".;BMC Genomics, In Review,;2016.

Malekpour, Hoda and Ramnani, Pankaj and Srinivasan, Srilok and Balasubramanian, Ganesh and Nika, Denis L. and Mulchandani, Ashok and Lake, Roger K. and Balandin, Alexander A.;"Thermal conductivity of graphene with defects induced by electron beam irradiation".;Nanoscale,;vol. The Royal Society of Chemistry, doi 10.1039/C6NR03470E.;2016.

Capecelatro, J., O. Desjardins, and R. O. Fox, “Strongly coupled fluid-particle flows in vertical channels. Part I: Reynolds-averaged two-phase turbulence statistics,” Physics of Fluids 28, 033306 (2016).

Weeks, Nathan T.; Luecke, Glenn R.; Groth, Brandon M.; Kraeva, Marina; Ma, Li; Kramer, Luke M., Koltes, James E.; Reecy, James M. "High Performance Epistasis Detection in Quantitative Trait GWAS." International Journal of High Performance Computing, vol. doi: 10.1177/1094342016658110. July 2016.

Yongchao Liu and Srinivas Aluru;"LightScan: faster scan primitive on CUDA compatible manycore processors".;Journal of Parallel and Distributed Computing, under review,;2016.

Capecelatro, J., O. Desjardins, and R. O. Fox, Recent insight on disperse multiphase turbulence modeling. 2016 NETL Workshop on Multiphase Flow Science, Morgantown, WV, 2016.

Malekpour, Hoda, et al. "Thermal conductivity of graphene with defects induced by electron beam irradiation.";Nanoscale;8.30 (2016): 14608-14616.

Capecelatro, J., O. Desjardins, and R. O. Fox, “Strongly coupled fluid-particle flows in vertical channels. Part II: Turbulence modeling,” Physics of Fluids 28, 033307 (2016).

R. Dyja, B. Ganapathysubramanian, K. G. van der Zee, “Massively parallel-in-space-time, adaptive finite element framework for non-linear parabolic equations.” arXiv preprint, 2016;;;;;;;;;;;;;;;

S. Chockalingam, S.V. Thankachan and S. Aluru, ``A parallel algorithm for k-mismatch all-pair maximal common substrings,'' Proc. ACM/IEEE Supercomputing Conference (SC), 2016, to appear.

B. R. Agrawal and A Sharma, “Numerical Investigations of Bio-Inspired Blade Designs to Reduce Broadband Noise in Aircraft Engines and Wind Turbines,” in AIAA SciTech Meeting ;(AIAA, San Diego, California, USA, 2016), abstract submitted.

Kong, B., and R. O. Fox, Kinetic theory modeling of turbulent multiphase flow, 2016 Crosscutting Research and Rare Earth Elements Portfolios Review, Pittsburgh, PA, 2016.

Jahn, D. E., E. S. Takle, W. A. Gallus, 2016: Improving wind ramp forecasts in the stable boundary layer. Boundary-Layer Meteorology. Provisionally accepted.

Yongchao Liu, Tony Pan, and Srinivas Aluru;"Parallel pairwise correlation computation On Intel Xeon Phi clusters".;28th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD 2016), under review,;2016.

S.R. Pruitt, H. Nakata, T. Nagata, M. Mayes, Y. Alexeev, G.D. Fletcher, D.G. Fedorov, K. Kitaura, and M.S. Gordon, “The Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water”, J. Chem. Theory Comp.,;12, 1423 (2016).

Y. Xie, O. Wodo, B. Ganapathysubramanian, “Incompressible two-phase flow: Diffuse interface approach for large density ratios, grid resolution study, and 3D patterned substrate wetting problem,” Computers & Fluids, 2016. http://www.sciencedirect.com/science/article/pii/S0045793016301141

Q. Guo, D. Rajewski, E. Takle, B. Ganapathysubramanian, “Constructing low-dimensional stochastic wind models through hierarchical spatial temporal decomposition.” arXiv preprint, 2016. http://arxiv.org/abs/1603.08135.;;

Sines, Taleena, Raymond W. Arritt, and Brian Gelder: Increases in extreme precipitation due to agricultural landuse change.;; Science.; In preparation, 2016.

T. Pan, P. Flick, C. Jain, Y. Liu and S. Aluru, ``A flexible parallel library for k-mer indexing of biological sequences on distributed memory systems,''Proc. 7th; ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), 2016, to appear.

A. Sharma, P. Singh, D.D. Johnson, P.K. Liaw and G. Balasubramanian, “Atomistic clustering-ordering and high strain deformation of Al0.1CrCoFeNi high-entropy alloy”, Scientific Reports, 6, 31028, 2016.

Fox, R. O., J. Capecelatro, and O. Desjardins, Strongly coupled particle-laden flows in vertical channels. 9th International Conference on Multiphase Flow, Florence, Italy, 2016.

Weeks, Nathan T.; Luecke, Glenn R.; Groth, Brandon M.; Kraeva, Marina; Ma, Li; Kramer, Luke M., Koltes, James E.; Reecy, James M.;"High Performance Epistasis Detection in Quantitative Trait GWAS".;International Journal of High Performance Computing,;vol. doi: 10.1177/1094342016658110.;July 2016.

Jahn, D. E., E. S. Takle, W. A. Gallus, 2016:; Improving Numerical Wind Forecasts of Wind Ramps at 100m Height in the Stable Boundary Layer.; Oral pres.; 2016 Wind Energy Research Workshop, 15-16 Mar., Lowell, MA.

K. G. Lore, D. Stoecklein, M. Davies, B. Ganapathysubramanian, S. Sarkar, “Deep Action Sequence Learning for Causal Shape Transformation.” arXiv preprint, 2016. http://arxiv.org/abs/1605.05368

Sines, Taleena, and Raymond W. Arritt, 2016: Variations in Mesoscale Convective Complex production among CORDEX models. Journal of Hydrometeorology.; In preparation.

Sines, Taleena, and Raymond W. Arritt, 2016: Analyzing the sensitivity of WRF-ARW to cumulus parameterizations and simple moisture-retaining alterations in simulating MCCs.; Weather and Forecasting.; In preparation.

Pratik Mishra, Mayank Mishra, Arun K. Somani.;Bulk I/O Storage Management for Big Data Applications, to be published in IEEE Modelling Analysis and Simulation of Computer and Telecommunication Systems (MASCOTS), September 2016, London, UK.

P. Flick and S. Aluru, ``Parallel distributed memory construction of suffix and longest common prefix arrays,'' Proc. ACM/IEEE Supercomputing Conference (SC)}, 10 pages, 2015. (Best student paper)

C. J. Kleinheksel and A. K. Somani, "Resource Efficient Redundancy Using Quorum-based Cycle Routing in Optical Networks," in;The 17th International Conference on Transparent Optical Networks (ICTON) 2015, July 2015, held at Budapest, Hungary.

Hill, J. C., Z. Liu, R. O. Fox, A. Passalacqua, and M. G. Olsen, Numerical modeling of turbulent swirling flow in a multi-inlet vortex nanoprecipitation reactor using dynamic DDES. APS-DFD Annual Meeting, Boston, MA, 2015.

Ireland, P., R. G. Patel, J. Capecelatro, R. O. Fox, M. H. Kasbaoui, and O. Desjardins, Numerical simulation of sheared, gas-particle, cluster-induced turbulence. AIChE Annual Meeting, Salt Lake City, UT, 2015.

Luecke, G.R., N.T. Weeks, B.M. Groth, M. Kraeva, L. Ma, L.M. Kramer,;J.E. Koltes;and J.M. Reecy, “Fast epistasis detection in large-scale GWAS for Intel Xeon Phi Clusters,” accepted to The Third International Workshop on Parallelism in Bioinformatics Proceedings (published by the;Institute of Electrical and Electronic Engineers, IEEE), 2015.

Kong, B., H. Feng, J. Capecelatro, O. Desjardins, and R. O. Fox, Euler-Euler anisotropic Gaussian mesoscale direct numerical simulation of cluster-induced turbulent flow. AIChE Annual Meeting, Salt Lake City, UT, 2015.

Parijat Shukla and Arun K. Somani, “Tree Matching Using Data Shaping,” in Proceedings of 4th International Congress on Big Data June 27 - July 2, 2015, New York, USA.

Alex Travesset;"Binary nanoparticle superlattices of soft-particle systems".;Proceedings of the National Academy of Sciences of the United States of America,;vol. doi: 10.1073/pnas.1504677112.;June 2015.

S. K. Samudrala*, J. Zola, S. Aluru, B. Ganapathysubramanian, “Parallel Framework for Dimensionality Reduction of Large-scale Datasets”, Scientific Programming, accepted for publication (2015).;;;;;;;;;;;;;;;;;

Kong, B., and R. O. Fox, Numerical simulation of polydisperse gas-particle flow in a vertical riser with a size-velocity quadrature-based moment method. AIChE Annual Meeting, Salt Lake City, UT, 2015.

O Wodo, J Zola, and B Ganapathysubramanian, “Morphology optimization for enhanced performance in organic photovoltaics,” APS March Meeting Abstracts 1, 1230P, 2015.

Michael Svendsen, Arko Provo Mukherjee, Srikanta Tirthapura, “Mining maximal cliques from a large graph using MapReduce: Tackling highly uneven subproblem sizes,” Journal of Parallel and Distributed Computing, Volumes 79–80, May 2015, Pages 104-114.

Sun, B., Tenneti, S. and Subramaniam, S., Mass transfer in a flow past a non-porous sphere. APS-DFD Annual Meeting, Boston, MA, 2015.

Jansen, K. M., B. Kong, R. O. Fox, J. C. Hill, and M. G. Olsen, “Large eddy simulation of passive scalar transport in a high Schmidt number incompressible wake with experimental validation,” Chemical Engineering Science 137, 862-874 (2015).

HPC-STORY2: http://www.scientificcomputing.com/articles/2015/08/when-it-rains-it-pours-hpcisu-powers-advanced-agronomy-research

D. Kipp, O. Wodo, B. Ganapathysubramanian, V. Ganesan, “Achieving Bicontinuous Microemulsion Like Morphologies in Organic Photovoltaics”, ACS Macro Letters, accepted for publication (2015)

Kong, B., H. Feng, J. Capecelatro, O. Desjardins, and R. O. Fox, Euler-Euler anisotropic Gaussian mesoscale direct numerical simulation of homogeneous and wall-bounded cluster-induced gas-particle turbulence. APS-DFD Annual Meeting, Boston, MA, 2015.

N. Jammula, S. Chockalingam, and S. Aluru;"Parallel Read Error Correction for Big Genomic Datasets".2015 IEEE 22nd International Conference on High Performance Computing (HiPC),;pp. 446-455.;vol. 10.1109/HiPC.2015.47.;December 2015.

Sines, T.R., C.J. Anderson and R.W. Arritt, 2015: Improving prediction of mesoscale convective systems with convective parameterization. Presented at 16th Conference on Mesoscale Processes, American Meteorological Society, 3-6 August 2015, Boston, Massachusetts.

Fox, R. O., J. Capecelatro, and O. Desjardins, Strongly coupled turbulent gas-particle flows in vertical channels. APS-DFD Annual Meeting, Boston, MA, 2015.

P. Flick, C. Jain, T. Pan and S. Aluru, ``A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications,'' Proc. ACM/IEEE Supercomputing Conference (SC)}, 11 pages, 2015.

Patrick Flick, Chirag Jain, Tony Pan, and Srinivas Aluru, “A distributed connected component labeling algorithm for de Bruijn graphs in metagenomics,” In Proc. ACM/IEEE Supercomputing Conference (SC), Nov. 2015, Austin, Texas, in press.

Olsen, M. G., Z. Liu, E. Hitimana, J. C. Hill, and R. O. Fox, Turbulent velocity and concentration measurements in a multi-inlet vortex nanoprecipitation reactor. APS-DFD Annual Meeting, Boston, MA, 2015.

D. Stoecklein, C.Y. Wu, D. Kim, D. Di Carlo, B. Ganapathysubramanian, “Optimization of micropillar sequences for fluid flow sculpting”, Physics of Fluids, in press, 2015;;;;;;;;;

S Pfeifer and B Ganapathysubramanian, “Quantifying the Effects of Noise on Diffuse Interface Models: Cahn-Hilliard-Cook equations,” APS March Meeting Abstracts 1, L3006, 2015.

HPC-STORY1: http://www.scientificcomputing.com/articles/2015/09/so-many-people-so-little-food-helping-feed-world-through-genomics

Capecelatro, J., O. Desjardins, and R. O. Fox, “Effect of domain size on fluid-particle statistics in homogeneous, gravity-driven, cluster-induced turbulence,” Journal of Fluids Engineering 138 (4), 041301 (2015).

Kolakaluri, R., E. Murphy, S. Subramaniam, R. C. Brown, and R. O. Fox, “Filtration model for polydisperse aerosols in gas-solid flow using granule-resolved direct numerical simulation,” AIChE Journal 61 (11), 3594-3606 (2015).

A.D. Fontanini, U. Vaidya, B. Ganapathysubramanian, “Constructing Markov matrices for real-time transient contaminant transport analysis for indoor environments”, Building and Environment 94, 68-81, 2015. http://www.sciencedirect.com/science/article/pii/S0360132315300688

A. Aboulhassan, D. Baum, O. Wodo, B. Ganapathysubramanian, A. Amassian, M.; Hadwiger, “A Novel Framework for Visual Detection and Exploration of Performance Bottlenecks in Organic Photovoltaic Solar Cell Materials”, Computer Graphics Forum 34 (3), 401-410, 2015.

Sines, T.R., C.J. Anderson and R.W. Arritt, 2015: A simple modification to improve interaction between convective parameterization and grid scale microphysics. Presented at 16th WRF Users Workshop, 15-18 June 2015, Boulder, Colorado.

Hu, X., A. Passalacqua, R. O. Fox, “Application of quadrature-based uncertainty quantification to the NETL small-scale challenge problem SSCP-I,” Powder Technology 272, 100-112 (2015).

D Ackerman and B Ganapathysubramanian, “Parallel framework for wormlike chains using self-consistent field theory,” APS Meeting Abstracts 1, 42011, 2015

Capecelatro, J., O. Desjardins, and R. O. Fox, “On fluid-particle dynamics in fully developed cluster-induced turbulence,” Journal of Fluid Mechanics 780, 578-635 (2015).

C. J. Kleinheksel and A. K. Somani, "Optical Quorum Cycles for Efficient Communication," in Photonic Network Communications, Photonic Network Communications, 2015

Koltes JE,;Fritz-Waters;E, Eisley CJ, Choi I, Bao H, Kommadath A, Serão NV, Boddicker NJ, Abrams SM, Schroyen M, Loyd H, Tuggle CK, Plastow GS, Guan L, Stothard P, Lunney JK, Liu P, Carpenter S, Rowland RR, Dekkers JC, Reecy JM., “Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection,” BMC Genomics. 2015 May 28;16:412. doi: 10.1186/s12864-015-1635-9, 2015.

B.S. Pokuri and B Ganapathysubramanian, “Tailoring the morphology of polymer blend particles: 3D simulations and linear stability analysis,” Bulletin of the American Physical Society 60, 2015.

Ghandi, Khashayar, et al. "Ultra-fast electron capture by electrosterically-stabilized gold nanoparticles.";Nanoscale;7.27 (2015): 11545-11551.

Jammula, Nagakishore, Sriram Chockalingam, and Srinivas Aluru. "Parallel Read Error Correction for Big Genomic Datasets.";2015 IEEE 22nd International Conference on High Performance Computing (HiPC). IEEE, 2015.

O. Wodo, J. Zola, B. S.S. Pokuri, P. Du, B. Ganapathysubramanian, “Automated, high throughput exploration of process–structure–property relationships using the MapReduce paradigm”, Materials Discovery, in press, 2015. http://www.sciencedirect.com/science/article/pii/S2352924515000058

D Stoecklein, B Ganapathysubramanian, CY Wu, and D Di Carlo, “Micropillar sequence design for inertial fluid flow sculpting,” Bulletin of the American Physical Society 60, 2015.

S. K. Khaitan and J. McCalley “A High-Performance Parallelization and Load-Balancing Approach for Modern Power-Systems,” International Journal of Business Analytics (IJBAN), Vol. 2, No. 2, 2015. Khaitan, S. and McCalley, J. “A High-Performance Parallelization and Load-Balancing Approach for Modern Power-Systems” International Journal of Business Analytics (IJBAN), Vol. 2, No. 2, 2015.

http://pubs.acs.org/doi/abs/10.1021/acs.jpcc.5b08581

 

Fritz-Waters E, Koltes JE, Markey A, Mayes MS, Reecy JM, “Beef Cattle Metagenomics: Predicting Growth from the Inside Out,” Plant and Animal Genome Conference XXIII. Jan 2015. P0269, 2015.

Luecke, Glenn R.; Weeks, Nathan T.; Groth, Brandon M.; Kraeva, Marina; Ma, Li; Kramer, Luke M.; Koltes, James E.; Reecy, James M. "Fast Epistasis Detection in Large-Scale GWAS for Intel Xeon Phi Clusters". Trustcom/BigDataSE/ISPA, vol. 3 pp. 228-235. vol. doi:10.1109/Trustcom.2015.637. August 2015.

Findlater, Alexander D., Federico Zahariev, and Mark S. Gordon. "Combined fragment molecular orbital cluster in molecule approach to massively parallel electron correlation calculations for large systems.";The Journal of Physical Chemistry A;119.15 (2015): 3587-3593.

P. Flick, S. Aluru;"Parallel distributed memory construction of suffix and longest common prefix arrays".Proc. ACM/IEEE Supercomputing Conference (SC),;2015.

P. Flick, C. Jain, T. Pan, S. Aluru;"A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications".;Proc. ACM/IEEE Supercomputing Conference (SC),;2015.

http://pubs.acs.org/doi/abs/10.1021/acsmacrolett.5b00007

 

C. J. Kleinheksel and A. K. Somani, "Enhancing Fault Tolerance Capabilities in Quorum-based Cycle Routing," in The 7th International Workshop on;Reliable Networks Design and Modeling (RNDM) 2015, to be held at Munich, Germany, September 2015.

Sines, T.R., C.J. Anderson and R.W. Arritt;"A simple modification to improve interaction between convective parameterization and grid scale microphysics".;16th WRF Users Workshop, 15-18 June 2015, Boulder, Colorado,;2015.

Fox, R. O., J. Capecelatro, and O. Desjardins, Turbulent gas-particle flow in wall-bounded vertical risers. AIChE Annual Meeting, Salt Lake City, UT, 2015.

N. Jammula, S. Chockalingam and S. Aluru, ``A parallel algorithm for read error correction of big genomic datasets,''Proc. 22nd International Conference on High Performance Computing (HiPC)”, pp. 446-455, 2015.

Xue, Q., and R. O. Fox, “Computational modeling of biomass thermochemical conversion in fluidized beds: particle density variation and size distribution,” Industrial & Engineering Chemistry Research 54 (16), 4084-4094 (2015).

Luecke, Glenn R.; Weeks, Nathan T.; Groth, Brandon M.; Kraeva, Marina; Ma, Li; Kramer, Luke M.; Koltes, James E.; Reecy, James M.;"Fast Epistasis Detection in Large-Scale GWAS for Intel Xeon Phi Clusters".;Trustcom/BigDataSE/ISPA,;vol. 3;pp. 228-235.;vol. doi: 10.1109/Trustcom.2015.637.August 2015.

Kong, B., H. Feng, J. Capecelatro, O. Desjardins, and R. O. Fox, Euler-Euler anisotropic Gaussian mesoscale direct numerical simulation of homogeneous cluster-induced gas-particle turbulence. 2015 NETL Workshop on Multiphase Flow Science, Morgantown, WV, 2015.

K.G. Lore, D. Stoecklein, M. Davies, B. Ganapathysubramanian, S Sarkar, “Hierarchical Feature Extraction for Efficient Design of Microfluidic Flow Patterns”, Journal of Machine Learning Research, 44 (2015).

Sines, T.R., C.J. Anderson and R.W. Arritt;"Improving prediction of mesoscale convective systems with convective parameterization".;16th Conference on Mesoscale Processes, American Meteorological Society, 3-6 August 2015, Boston, Massachusetts,;2015.

R.S. Gebhardt, P. Du, A. Peer, M. Rock, M.R. Kessler, R. Biswas, B. Ganapathysubramanian, S. Chaudhary, “Utilizing Wide Band Gap, High Dielectric Constant Nanoparticles as Additives in Organic Solar Cells”, The Journal of Physical Chemistry C 119 (42), 23883-23889, 2015.

Fox, R. O., J. Capecelatro and O. Desjardins;"The role of granular temperature in turbulent gas-particle flows".;AIChE Annual Meeting, Atlanta, GA,;2014.

Jahn, D. E., W. A. Gallus, E. S. Takle;"Evaluation of the MYNN PBL scheme closure constants for Low-Level Jet events in a stable boundary layer".;21st Symposium on Boundary Layers and Turbulence, 9-13 June, Amer. Meteor. Soc., Leeds, UK,;2014.

Capecelatro, J., O. Desjardins and R. O. Fox;"Fluid-particle characteristics in fully-developed cluster-induced turbulence".;APS-DFD Annual Meeting, San Francisco, CA,;2014.

Scott Broderick, Upamanyu Ray, Srikant Srinivasan, Krishna Rajan, and Ganesh Balasubramanian;"An informatics based analysis of the impact of isotope substitution on phonon modes in graphene".APPLIED PHYSICS LETTERS 104, 243110 (2014),;July 2014.

Yuan, C., B. Kong, A. Passalacqua, A. Tomiyama and R. O. Fox, An extended quadrature-based mass-velocity moment model for 3-D polydisperse bubbly flows. AIChE Annual Meeting, Atlanta, GA, 2014.

Khaitan, S. and McCalley, J. D., "Parallelization and Load Balancing Techniques for HPC", Encyclopedia of Business Analytics and Optimization (EBAO), IGI Global 2014.

Subramaniam, S., B. Sun, S. Tenneti and R. O. Fox, Heat transfer in gas-solid flow: Model development using particle-resolved direct numerical simulation. AIChE Annual Meeting, Atlanta, GA, 2014.

Desjardins, O., J. Capecelatro and R. O. Fox;"An adaptive filter strategy for extracting multiphase flow statistics from Euler-Lagrange simulations".;NETL Workshop on Multiphase Flow Science, Morgantown, WV,;2014.

Koesterke, L., Koltes, J. E., Weeks, N. T., Milfeld, K., Vaughn, M. W., Reecy, J. M. and Stanzione, D."Discovery of biological networks using an optimized partial correlation coefficient with information theory algorithm on Stampede's Xeon and Xeon Phi processors.;".;Concurrency Computat.: Pract. Exper.,;vol. doi: 10.1002/cpe.3252.;March 2014.

Fox, R. O., J. Capecelatro and O. Desjardins;"Multiphase turbulence in vertical wall-bounded collisional gas-particle flows".;APS-DFD Annual Meeting, San Francisco, CA,;2014.

Sines, T.R. and R.W. Arritt;"WRF-ARW physics parameterizations influence on mesoscale convective system (MCS) forecasts and development of process-oriented verification for WRF-ARW output".American Geophysical Union 2014 Fall Meeting, 15-19 December 2014, San Francisco, California,;2014.

Xue, Q., and R. O. Fox, “Reprint of: Multi-fluid CFD modeling of biomass gasification in polydisperse fluidized-bed gasifiers,” Powder Technology 265, 23-34 (2014).

O Wodo and B Ganapathysubramanian “How do evaporating thin films evolve? Unravelling phase-separation mechanisms during solvent-based fabrication of polymer blends,” Applied Physics Letters 105 (15), 153104, 2014. http://scitation.aip.org/content/aip/journal/apl/105/15/10.1063/1.4898136

Panicker, N. S., A. Passalacqua and R. O. Fox, Analysis and closure verification of multiphase turbulence models for gas-liquid flows. AIChE Annual Meeting, Atlanta, GA, 2014.

SK Samudrala, PV Balachandran, J Zola, and K Rajan, “A software framework for data dimensionality reduction: application to chemical crystallography,” Integrating Materials and Manufacturing Innovation 3 (1), 1-20, 2014.

Pruitt, Spencer; Bertoni, Colleen; Brorsen, Kurt; Gordon, Mark., “Efficient and Accurate Fragmentation Methods,” Accounts of Chemical Research, May 2014.

A Fontanini, M Olsen, A Passalacqua, B. Ganapathysubramanian;"High-Resolution Performance Analysis of a Large Building with Linear Dispersion Ductwork System".;ASHRAE Transactions,;2014.

Hu, X., A. Passalacqua and R. O. Fox;"Multiphase flow research-Uncertainty quantification tools for multiphase gas-solid flow simulations using MFIX".;Crosscutting Research Review Meeting, Pittsburgh, PA,;2014.

Sarom S. Leang, Alistair P. Rendell, Mark S. Gordon;"Quantum Chemical Calculations Using Accelerators: Migrating Matrix Operations to the NVIDIA Kepler GPU and the Intel Xeon Phi".Journal of Chemical Theory and Computation,;vol. ACS Publications.;February 2014.

Siddhartha Kumar Khaitan∗, James D. McCalley;"SCALE: A hybrid MPI and multithreading based work stealing approach for massive contingency analysis in power systems".;Elsevier,;April 2014.

Baes C, von Rohr P, Dolezal MA, Fritz-Waters E, Koltes JE, Bapst B, Flury C, Signer-Hasler H, Stricker C, Fernando R, Reecy J, Garrick D, Schmitz-Hsu F, Gredler B.;"Assessing genomic variation in Swiss dairy cattle breeds using annotated whole genome sequence information".;Proc. of the EAAP. Copehhagen, Denmark,;2014.

Koesterke, L., Koltes, J. E., Weeks, N. T., Milfeld, K., Vaughn, M. W., Reecy, J. M. and Stanzione, D., “Discovery of biological networks using an optimized partial correlation coefficient with information theory algorithm on Stampede's Xeon and Xeon Phi processors,“ Concurrency Computat.: Pract. Exper.. doi: 10.1002/cpe.3252, March 2014.

Nielsen, K., B. Kong, R. O. Fox, J. C. Hill, and M. G. Olsen, “Effect of inlet conditions on the accuracy of large eddy simulations of a turbulent rectangular wake,” Chemical Engineering Journal 250, 175-189 (2014).

Yuan, C., B. Kong, A. Passalacqua, and R. O. Fox, (Invited paper) “An extended quadrature-based mass-velocity moment model for polydisperse bubbly flows,” The Canadian Journal of Chemical Engineering 92, 2053-2066 (2014).

Sai Kiranmayee Samudrala, Jaroslaw Zola, Srinivas Aluru, Baskar Ganapathysubramanian, “Parallel Framework for Dimensionality Reduction of Large-scale Datasets, Scientific Programming,” to be published in journal of Scientific Programming, In Press, 2014.

Baes C, von Rohr P, Dolezal MA, Fritz-Waters E, Koltes JE, Bapst B, Flury C, Signer-Hasler H, Stricker C, Fernando R, Reecy J, Garrick D, Schmitz-Hsu F, Gredler B;"The effect of genome coverage in whole genome sequencing data".;Proc. of the EAAP. Copehhagen, Denmark,;2014.

Shukla, Parijat and Somani, Arun K., “Context-Aware Duplicate Detection in Semi-structured Data Streams,” in proceedings of the IEEE 2014 World Congress on Services, SERVICES 2014, pages 431-442, June 2014.

Hu, X., A. Passalacqua and R. O. Fox;"Validation of a quadrature-based uncertainty quantification approach using NETL small scale challenge problem SSCP-1".;ASME 2014 Verification & Validation Symposium, Las Vegas, NV,;2014.

Pruitt, Spencer; Bertoni, Colleen; Brorsen, Kurt; Gordon, Mark;"Efficient and Accurate Fragmentation Methods".;Accounts of Chemical Research,;May 2014.

Cheng Y, Rachagani S, Canovas A, Mayes MS, Tait Jr. RG, Dekkers JCM, and Reecy JM;"Body composition and geneexpression QTL mapping in mice reveals imprinting and interaction effects.".BMC Genetics,;vol. 14;no. 103;vol. doi: 10.1186/1471-2156-14-103..;January 2014.

Capecelatro, Jesse; Desjardins, Olivier; Fox, Rodney O;"Numerical study of collisional particle dynamics in cluster-induced turbulence".;Journal of Fluid Mechanics vol 747,;pp. R2.;vol. Cambridge University Press.;April 2014.

Nathan T. Weeks, Marina Kraeva, Glenn R. Luecke., “ipcmd: A command-line interface to System V semaphores and message queues." Concurrency and Computation: Practice and Experience,” vol. 26, no. 2, pp. 396-411. John Wiley & Sons Ltd. February 2014.

Fox, R. O., J. Capecelatro and O. Desjardins;"Numerical investigation of particle dynamics in cluster-induced turbulence".;17th U.S. National Congress on Theoretical and Applied Mechanics, East Lansing, MI,;2014.

CK Lee, O Wodo, B Ganapathysubramanian, and CW Pao, “Electrode Materials, Thermal Annealing Sequences, and Lateral/Vertical Phase Separation of Polymer Solar Cells from Multiscale Molecular Simulations,” ACS applied materials & interfaces 6 (23), 20612-20624, 2014. http://pubs.acs.org/doi/abs/10.1021/acsami.6b05027

Nathan T. Weeks, Marina Kraeva, Glenn R. Luecke;"ipcmd: A command-line interface to System V semaphores and message queues".;Concurrency and Computation: Practice and Experience,;vol. 26no. 2;pp. 396-411.;vol. John Wiley & Sons Ltd..;February 2014.

Takle,; E S., D. A. Rajewski, J. K. Lundquist, W. A. Gallus, Jr., and A. Sharma, 2014:; Measurements in support of wind farm simulations and power forecasts:; The Crop/Wind-energy Experiments (CWEX).; The Science of Making Torque From Wind, 2014. Journal of Physics: Conference Series, 524 (2014) 012174; doi:10.1088/1742-6596/524/1/012174 [Available online at http://iopscience.iop.org/1742-6596/524/1/012174]

Subramaniam, S. and Mehrabadi, M. and Horwitz, J. And Mani, A., “Developing improved Lagrangian point particle models of gas-solid flow from particle-resolved direct numerical simulation”, Studying Turbulence Using Numerical Simulation Databases-XV, Proceedings of the CTR 2014 Summer Program, 5-14, Center for Turbulence Research, Stanford University, CA, December, 2014.

Baes C, Dolezal M, Fritz-Waters E, Koltes JE, Bapst B, Flury C, Signer-Hasler H, Stricker C, Fernando R, Reecy J, Garrick D, Schmitz-Hsu F, Fries R, Gredler B;"Comparison of variant calling methods for whole genome sequencing data in dairy cattle".;Proc. of Plant and Animal Genome XXII. San Diego, CA, USA,;2014.

Kong, B., and R. O. Fox, Numerical simulation of polydisperse gas-particle flow in a vertical riser with a size-velocity quadrature-based moment method. 2014 NETL Workshop on Multiphase Flow Science, Morgantown, WV, 2014.

Capecelatro, J., O. Desjardins and R. O. Fox;"Turbulence modeling of collisional gas-particle flows in wall-bounded risers".;AIChE Annual Meeting, Atlanta, GA,;2014.

Sarom S. Leang, Alistair P. Rendell, Mark S. Gordon, “Quantum Chemical Calculations Using Accelerators: Migrating Matrix Operations to the NVIDIA Kepler GPU and the Intel Xeon Phi,” Journal of Chemical Theory and Computation, ACS Publications, February 2014.

Hu, X., Passalacqua, A., Fox, R.O;"Quadrature-Based Uncertainty Quantification Approach in a Multiphase Gas-Particle Flow Simulation in a Riser".;AIChE Annual Meeting, Atlanta, 2014,;June 2014.

R. Liu, A. E. Loraine, and J. A. Dickerson, “Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems,” BMC Bioinformatics, 15(1):364, Dec 2014.

Sines, T.R. and R.W. Arritt, 2014: WRF-ARW physics parameterizations influence on mesoscale convective system (MCS) forecasts and development of process-oriented verification for WRF-ARW output. Abstract A51H-3138. Presented at American Geophysical Union 2014 Fall Meeting, 15-19 December 2014, San Francisco, California, 2014.

S. K. Khaitan and J. McCalley;"PARAGON: an approach for parallelization of power system contingency analysis using go programming language".;International Transactions on Electrical Energy Systems,vol. doi: 10.1002/etep.1999.;2014.

Khaitan, S. and McCalley, J.;"SCALE: A hybrid MPI and Multithreading Based Work Stealing Approach for Massive Contingency Analysis in Power Systems".;Electric Power Systems Research,;vol. 114;pp. 118-125.;June 2014.

Panicker, N.S., Passalacqua, A., Fox, R. O;"Analysis and Closure Verification of Multiphase Turbulence Models for Gas -Liquid Flows".;AIChE Annual Meeting, Atlanta, 2014,;July 2014.

Arko Provo Mukherjee and Srikanta Tirthapura, “Enumerating Maximal Bicliques from a Large Graph using MapReduce,” IEEE Bigdata conference (Alaska), June 2014.

J. Pace, N. Lee*, H. S. Naik*, B. Ganapathysubramanian, T Lübberstedt, “Analysis of maize (Zea mays L.) seedling roots with the high-throughput image analysis tool ARIA (Automatic Root Image Analysis)”.; PLoS ONE, in press (2014).

Capecelatro, J., O. Desjardins, and R. O. Fox;"Investigating multiphase turbulence statistics of large-scale two-way coupled gravity-driven flows".;Proceedings of the ASME 2014 4th Joint US-European Fluids Engineering Division Summer Meeting, Chicago, IL,;2014.

J. M. Carraher, D. Galvin, S. G. Hartke, A. J. Radcliffe, D. Stolee;"On the independence ratio of distance graphs".;February 2014.

D Stoecklein, CY Wu, K Owsley, Y Xie, D Di Carlo and B. Ganapathysubramanian, “Micropillar sequence designs for fundamental inertial flow transformations,” Lab on a Chip 14 (21), 4197-4204, 2014, http://pubs.rsc.org/is/content/articlehtml/2014/lc/c4lc00653d

Baes C.F., Dolezal M.A., Bapst B., Fritz-Waters E., Koltes J.E., Jansen S., Flury C., Signer-Hasler H., Stricker C., Fernando R., Fries R., Moll J., Garrick D.J., Reecy J.M., and Gredler B.;"Evaluation of variant identification methods for whole genome sequencing data in dairy cattle".;BMC Genomics. Nov 1; 15:948,;2014.

Hu, X., Passalacqua, A., Fox, R.O;"Application of quadrature-based uncertainty quantification to the NETL small-scale challenge problem SSCP-I".;Powder Technology,;July 2014.

Xue, Q., and R. O. Fox, “Multi-fluid CFD modeling of biomass gasification in polydisperse fluidized-bed gasifiers,” Powder Technology 254, 187-198 (2014).

Xue, Q., and R. O. Fox, CFD modeling of biomass thermochemical conversion in polydisperse fluidized beds. AIChE Annual Meeting, Atlanta, GA, 2014.

Week, N; Kraeva, M; Luecke, G.R.;"Parallelization of software pipelines using the mpififo Tool".;Cluster Computing (CLUSTER), 2013 IEEE International Conference on,;pp. 1-3.;September 2013.

Olsen, M., Y. Shi, G. Iaccarino and R. O. Fox;"CFD predictions of confined turbulent swirling flows in a microscale multi-inlet vortex reactor".;APS-DFD Annual Meeting, Pittsburgh, PA,;2013.

Selvaraj, S., A. Chaves, E. Takle and A. Sharma;"Numerical Prediction of Surface Flow Convergence Phenomenon in Windfarms".;Proc. of the Conference on Wind Energy Science and Technology, RUZGEM, Ankara, Turkey,;October 2013.

Panicker, N., A. Passalacqua and R. O. Fox;"Mesoscale direct numerical simulations of monodisperse bubbly flow".;AIChE Annual Meeting, San Francisco, CA,;2013.

Bai, W., N. K. G. Keller, T. J. Heindel, and R. O. Fox;"Numerical study of mixing and segregation in a biomass fluidized bed".;Powder Technology,;vol. 237;pp. 355-366.;2013.

Khaitan, S. and McCalley, J;"Achieving Load-Balancing in Power System Parallel Contingency Analysis Using X10 Programming Language".;Proceedings of the third ACM SIGPLAN X10 Workshop, Seattle,;pp. 20-28.;June 2013.

Hu, X., Passalacqua, A., Fox, R.O.;"A Quadrature-Based Uncertainty Quantification Approach with Reconstruction of the Probability Distribution Function of the System Response in Bubbling Fluidized Beds".;AIChE Annual Meeting, San Francisco, 2013,;May 2013.

Kong, B., and R. O. Fox;"Extended conditional quadrature-based moment methods for polydisperse gas-particle flows with size-conditioned velocity".;NETL Workshop on Multiphase Flow Science, Morgantown, WV,;2013.

Saatchi, M, Garrick DJ, Tait Jr. RG, Mayes MS, Drewnoski M, Schoonmaker J, Diaz C, Beitz DC and Reecy JM;"Genome-wide association and prediction of direct genomic breeding values for composition of fatty acids in Angus beef cattle. BMC Genomics.".;BMC Genomics. 2013 Oct 25;,;vol. 14;no. 730;vol. doi: 10.1186/1471-2164-14-730..;October 2013.

Kong, B., A. Passalacqua and R. O. Fox;"Extended conditional quadrature-based moment methods for polydisperse gas-particle flows with size-conditioned velocity".;AIChE Annual Meeting, San Francisco, CA,;2013.

Khaitan, S. and McCalley, J.;"Optimizing cache energy efficiency in multicore power system simulations".;Energy Systems,;vol. doi 10.1007/s12667-013-0090-4.;2013.

Khaitan, S. and McCalley, J;"Parallelizing Power System Contingency Analysis Using D Programming Language".;IEEE PES GM 2013, Vancouver, BC,;pp. 1-5, 21-25.;June 2013.

Yuan, C., V. Vikas, R. O. Fox, and Z. J. Wang;"An extended quadrature-based velocity-mass Euler-Euler model for 2-D bubbly flows".;Proceedings of 8th International Conference on Multiphase Flow (ICMF 2013), Jeju, Korea,;pp. 1-7.;2013.

Rokkam, R. G., A. Sowinski, R. O. Fox, P. Mehrani, and M. E. Muhle;"Computational and experimental study of electrostatics in gas-solid polymerization fluidized beds".;Chemical Engineering Science,vol. 92;pp. 146-156.;2013.

Capecelatro, J., O. Desjardins and R. O. Fox;"Evaluating multiphase turbulence statistics using mesoscale DNS of gravity-driven particle-laden flows".;AIChE Annual Meeting, San Francisco, CA,2013.

Khaitan, S., McCalley, J. D., and Somani, A;"Proactive Task Scheduling and Stealing in Master-Slave Based Load Balancing for Parallel Contingency Analysis".;Electric Power Systems Research,;vol. 103pp. 9-15.;October 2013.

Koesterke L, Milfeld M, Vaughn MW, Stanzione D, Koltes JE, Weeks NT, Reecy JM.;"Optimizing the PCIT algorithm on Stampede's Xeon and Xeon Phi processors for faster discovery of biological networks.".;Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery (XSEDE '13).,;January 2013.

S. G. Hartke, D. Stolee;"A linear programming approach to the Manickam-Miklós-Singhi Conjecture,;".European Journal of Combinatorics 36,;pp. 53-70.;February 2013.

Nathan T. Weeks, Marina Kraeva, Glenn R. Luecke;"Parallelization of software pipelines using the mpififo tool".;Cluster Computing (CLUSTER) 2013 IEEE International Conference on, 23-27 Sept. 2013.,September 2013.

Fox, R. O., J. Capecelatro and O. Desjardins;"Evaluating multiphase turbulence statistics using mesoscale DNS of gravity-driven particle-laden flows".;APS-DFD Annual Meeting, Pittsburgh, PA,2013.

Fox, R. O., J. Capecelatro and O. Desjardins;"Validation of a multiphase turbulence model using mesoscale DNS of gravity-driven gas-particle flows".;NETL Workshop on Multiphase Flow Science, Morgantown, WV,;2013.

Passalacqua, A., X. Hu and R. O. Fox;"Uncertainty quantification tools for multiphase flow simulations using MFIX".;NETL 2013 NETL Workshop on Multiphase Flow Science, Morgantown, WV,;2013.

Marina Kraeva, James Coyle, Glenn R. Luecke, Indranil Roy, Elizabeth Kleiman, James Hoekstra"CompilerCheck: A tool for Evaluating Error Detection Capabilities of UPC Compilers".;Conference Proceedings, Computational Tools 2012,;July 2012.

S. G. Hartke, D. Stolee;"Uniquely Kr-saturated graph;".;Electronic Journal of Combinatorics 19(4),September 2012.

Khaitan, S. and McCalley, J;"EmPower: An Efficient Load Balancing Approach For Massive Dynamic Contingency Analysis in Power Systems".;2nd International Workshop on High Performance Computing, Networking and Analytics for the Power Grid, SC12, Salt Lake City, UT, USA,;November 2012.

James Coyle, Indranil Roy, Marina Kraeva, Glenn R. Luecke;"UPC-CHECK: A scalable tool for detecting run-time errors in Unified Parallel C".;Conference Proceedings, ISC 2012, Hamburg, Germany, June 17-21, 2012,;June 2012.

S. G. Hartke, D. Stolee, D. B. West, M. Yancey;"On extremal graphs with a given number of perfect matchings".;Journal of Graph Theory, 73(4),;pp. 449-468.;April 2012.

D. Stolee;"Generating p-extremal graphs".;August 2011.

Glenn R. Luecke, Olga Weiss, Marina Kraeva, James Coyle, James Hoekstra;"Performance Analysis of Pure MPI Versus MPI+OpenMP for Jacobi Iteration and a 3D FFT on the Cray XT5".;Cray Users Group 2010, Edinburgh, Scotland, May 2010,;May 2010.

Glenn R. Luecke, James Coyle, James Hoekstra, Marina Kraeva, Ying Xu, Elizabeth Kleiman, Olga Weiss"Evaluating Error Detection Capabilities of UPC Run-time Systems".;Third Conference on Partitioned Global Address Space (PGAS) Programming Models, October 2009,;October 2009.

Glenn R. Luecke, James Coyle, James Hoekstra, Marina Kraeva, Ying Xu, Mi-Young Park, Elizabeth Kleiman, Olga Weiss, Andre Wehe, Melissa Yahya;"Evaluating the Capability of Compilers and Tools to Detect Serial and Parallel Run-time Errors".;Supercomputing 2009,;July 2009.

Glenn R. Luecke, James Coyle, James Hoekstra, Marina Kraeva, Ying Xu, Mi-Young Park, Elizabeth Kleiman, Olga Weiss, Andre Wehe, Melissa Yahya;"The Importance of Run-time Error Detection".Tools for High Performance Computing 2009, Proceedings of the 3rd International Workshop on Parallel Tools for High Performance Computing, September 2009, ZIH, Dresden, Springer 2009,;September 2009.

Glenn R. Luecke, James Coyle, Jim Hoekstra, Marina Kraeva, Ying Li, Olga Taborskaia, and Yanmei Wang;"A Survey of Systems for Detecting Serial Run-Time Errors".;Concurrency and Computation: Practice and Experience,;vol. 18;pp. 1885-1907.;March 2006.

Glenn R. Luecke, Silvia Spanoyannis and Marina Kraeva;"The Performance and Scalability of SHMEM and MPI-2 One-Sided Routines on a SGI Origin 2000 and a Cray T3E-600".;Concurrency and Computation: Practice and Experience. 2004,;vol. 16;pp. 1037-1060.;June 2004.

Glenn R. Luecke, Marina Kraeva, Jing Yuan and Silvia Spanoyannis;"Performance and Scalability of MPI on PC Clusters".;Concurrency and Computation: Practice and Experience,;vol. 16;pp. 79-107.;January 2004.

Glenn R. Luecke, Hua Chen, James Coyle, Jim Hoekstra, Marina Kraeva and Yan Zou;"MPI-CHECK: a Tool for Checking Fortran 90 MPI Programs".;Concurrency and Computation: Practice and Experience.,vol. 15;pp. 93-100.;January 2003.

Glenn R. Luecke, Marina Kraeva and Lili Ju;"Comparing the Performance of MPICH with Cray's MPI and with SGI's MPI".;Concurrency and Computation: Practice and Experience,;vol. 15;pp. 779-802.;January 2003.

Glenn R. Luecke, Yan Zou, James Coyle, Jim Hoekstra and Marina Kraeva;"Deadlock Detection In MPI Programs".;Concurrency and Computation: Practice and Experience,;vol. 14;pp. 911-932.;January 2002.