Research Gallery

Below are examples of research that was supported by the Research Computing staff. If you would like your research to be listed in our gallery or featured on our home page, submit your research via Google form, or contact us via email.

 

Publications

2016 

Haulsee*, D.E., Fox, D.A., Breece*, M.W., Brown, L.M., Kneebone, J., Skomal, G.B. and Oliver, M.J., 2016. Social Network Analysis Reveals Potential Fission-Fusion Behavior in a Shark. Scientific Reports, 6. doi: 10.1038/srep34087

Cimino*, M.A., Lynch, H.J., Saba, V.S. and Oliver, M.J., 2016. Projected asymmetric response of Adélie penguins to Antarctic climate change. Scientific Reports, 6. doi: 10.1038/srep28785

Breece*, M. W., Fox, D. A., Dunton, K. J., Frisk, M. G., Jordaan, A., Oliver, M. J. (2016), Dynamic seascapes predict the marine occurrence of an endangered species: Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus. Methods in Ecology and Evolution. doi: 10.1111/2041-210X.12532

Breece, M. W., Fox, D. A., Dunton, K. J., Frisk, M. G., Jordaan, A. and Oliver, M. J. (2016), Dynamic seascapes predict the marine occurrence of an endangered species: Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus. Methods Ecol Evol, 7: 725–733. doi:10.1111/2041-210X.12532

S. K. Brand, T. R. Josephson, J. A. Labinger, S. Caratzoulas, D. G. Vlachos and M. E. Davis, Methyl-ligated tin silsesquioxane catalyzed reactions of glucose, J. Catal. 341, 62-71 (2016). 10.1016/j.jcat.2016.06.013

J. Luo, H. Yun, A. V. Mironenko, K. Goulas, J. D. Lee, M. Monai, C. Wang, V. Vorotnikov, C. B. Murray, D. G. Vlachos, P. Fornasiero and R. J. Gorte, Mechanisms for High Selectivity in the Hydrodeoxygenation of 5-Hydroxymethylfurfural over PtCo Nanocrystals, ACS Catal. 6 (7), 4095-4104 (2016). 10.1021/acscatal.6b00750

A. V. Mironenko and D. G. Vlachos, Conjugation-Driven “Reverse Mars-van Krevelen”-Type Radical Mechanism for Low-Temperature C-O Bond Activation, J. Am. Chem. Soc. 138 (26), 8104-8113 (2016). 10.1021/jacs.6b02871

C. P. O’Brien, G. R. Jenness, H. Dong, D. G. Vlachos and I. C. Lee, Deactivation of Pt/Al2O3 during propane oxidation at low temperatures: Kinetic regimes and platinum oxide formation, J. Catal. 337, 122-132 (2016). 10.1016/j.jcat.2016.02.012

C. L. Williams, K. P. Vinter, R. E. Patet, C. C. Chang, N. Nikbin, S. T. Feng, M. R. Wiatrowski, S. Caratzoulas, W. Fan, D. G. Vlachos and P. J. Dauenhauer, Inhibition of Xylene Isomerization in the Production of Renewable Aromatic Chemicals from Biomass-Derived Furans, ACS Catal. 6 (3), 2076-2088 (2016). 10.1021/acscatal.5b02329

Z. B. Zhuang, S. A. Giles, J. Zheng, G. R. Jenness, S. Caratzoulas, D. G. Vlachos and Y. S. Yan, Nickel supported on nitrogen-doped carbon nanotubes as hydrogen oxidation reaction catalyst in alkaline electrolyte, Nat. Commun. 7, 8 (2016). 10.1038/ncomms10141

W. Guo and D. G. Vlachos, Patched bimetallic surfaces are active catalysts for ammonia decomposition, Nat. Commun. 6, Article number 8619 (2015). 10.1038/ncomms9619

S. K. Green, R. E. Patet, N. Nikbin, C. L. Williams, C. C. Chang, J. Y. Yu, R. J. Gorte, S. Caratzoulas, W. Fan, D. G. Vlachos and P. J. Dauenhauer, Diels-Alder cycloaddition of 2-methylfuran and ethylene for renewable toluene, Appl. Catal. B-Environ. 180, 487-496 (2016). 10.1016/j.apcatb.2015.06.044

S. G. Wang, V. Vorotnikov and D. G. Vlachos, Coverage-Induced Conformational Effects on Activity and Selectivity: Hydrogenation and Decarbonylation of Furfural on Pd(111), ACS Catal. 5 (1), 104-112 (2015). 10.1021/cs5015145

V. Vorotnikov and D. G. Vlachos, Group Additivity and Modified Linear Scaling Relations for Estimating Surface Thermochemistry on Transition Metal Surfaces: Application to Furanics, J. Phys. Chem. C 119 (19), 10417-10426 (2015). 10.1021/acs.jpcc.5b01696

R. E. Patet, N. Nikbin, C. L. Williams, S. K. Green, C.-C. Chang, W. Fan, S. Caratzoulas, P. J. Dauenhauer and D. G. Vlachos, Kinetic Regime Change in the Tandem Dehydrative Aromatization of Furan Diels–Alder Products, ACS Catal. 5 (4), 2367-2375 (2015). 10.1021/cs5020783

A. V. Mironenko, M. J. Gilkey, P. Panagiotopoulou, G. Facas, D. G. Vlachos and B. Xu, Ring Activation of Furanic Compounds on Ruthenium-Based Catalysts, J. Phys. Chem. C 119 (11), 6075-6085 (2015). 10.1021/jp512649b

G. R. Jenness and D. G. Vlachos, DFT Study of the Conversion of Furfuryl Alcohol to 2-Methylfuran on RuO2 (110), J. Phys. Chem. C 119 (11), 5938-5945 (2015). 10.1021/jp5109015

M. J. Gilkey, P. Panagiotopoulou, A. V. Mironenko, G. R. Jenness, D. G. Vlachos and B. Xu, Mechanistic Insights into Metal Lewis Acid-Mediated Catalytic Transfer Hydrogenation of Furfural to 2-Methylfuran, ACS Catal. 5 (7), 3988–3994 (2015). 10.1021/acscatal.5b00586

J. R. Christianson, S. Caratzoulas and D. G. Vlachos, Computational Insight into the Effect of Sn-Beta Na Exchange and Solvent on Glucose Isomerization and Epimerization, ACS Catal. 5 (9), 5256-5263 (2015). 10.1021/acscatal.5b01258

Kirby, J. T., Shi, F., Tehranirad, B., Harris, J. C. and Grilli, S. T., 2013, “Dispersive tsunami waves in the ocean: model equations and sensitivity to dispersion and Coriolis effects”, Ocean Modelling, 62, 39-55.
(pdf).

Geiman, J. D. and Kirby, J. T., 2013, “Unforced oscillation of rip-current vortex cells”, Journal of Physical Oceanography, 43, 477-497.
(pdf).

Shi, F., Cai, F., Kirby, J. T. and Zheng, J., 2013, “Morphological modeling of a nourished bayside beach with a low tide terrace”, Coastal Engineering, 78, 23-34, doi:10.1016/j.coastaleng.2013.03.005.

Grilli, S. T., Harris, J. C., Tajalli Bakhsh, T., Masterlark, T. L., Kyriakopoulus, C., Kirby, J. T. and Shi, F., 2013, “Numerical simulation of the 2011 Tohoku tsunami based on a new transient FEM co-seismic source: Comparison to far- and near-field observation”, Pure and Applied Geophysics, 170, 1333-1359, doi:10.1007/s00024-012-0528-y .

Ma, G., Kirby, J T., Su, S. F., Figlus, J. and Shi, F., 2013, “Numerical study of turbulence and wave damping induced by vegetation canopies”, Coastal Engineering, 80, 68-78, doi:10.1016/j.coastaleng.2013.05.007

Ma, G., Kirby, J. T. and Shi, F., 2013, “Numerical simulation of tsunami waves generated by deformable submarine landslides”, Ocean Modelling, 69, 146-165, doi:10.1016/j.ocemod.2013.07.001.

Chen, J.-L., Shi, F., Hsu, T. J. and Kirby, J. T., 2014, “NearCoM-TVD – a quasi-3D nearshore circulation and sediment transport model”, Coastal Engineering, 91, 200-212, doi:10.1016/j.coastaleng.2014.06.002

Tappin, D. R., Grilli, S. T., Harris, J. C., Geller, R. J., Masterlark, T., Kirby, J. T., Shi, F., Ma, G., Thingbaijam, K. K. S. and Mai, P. M., 2014, “Did a submarine landslide contribute to the 2011 Tohoku tsunami?”, Marine Geology, 357, 344-361, doi:10.1016/j.margeo.2014.09.043

Derakhti, M. and Kirby, J. T., 2014, “Bubble entrainment and liquid-bubble interaction under unsteady breaking waves”, Journal of Fluid Mechanics, 761, 464-506, doi:10.1017/jfm.2014.637

Shi, F., Vittori, G. and Kirby, J. T., 2015, “Concurrent correction method for modeling morphological response to dredging an offshore sandpit”, Coastal Engineering, 97, 1-10, doi:10.1016/j.coastaleng.2014.12.008

Grilli, S. T., O’Reilly, C., Harris, J. C., Tajalli Bakhsh, T., Tehranirad, B., Banihashemi, S., Kirby, J. T., Baxter, C. D. P., Eggeling, T., Ma, G. and Shi, F., 2015, “Modeling of SMF tsunami hazard along the upper U. S. East Coast: Detailed impact around Ocean City, MD”, Nat. Hazards, 76, 705-746, doi:10.1007/s11069-014-1522-8

Ma, G., Kirby, J. T., Hsu, T.-J. and Shi, F., 2015, “A two-layer granular landslide model for tsunami wave generation: Theory and computation”, Ocean Modelling, 93, 40-55, doi:10.1016/j.ocemod.2015.07.012

Tehranirad, B., Harris, J. C., Grilli, A. R., Grilli, S. T., Abadie, S., Kirby, J. T. and Shi, F., 2015, “Far-field tsunami hazard on the western European and US east coast from a large scale flank collapse of the Cumbre Vieja volcano, La Palma”, Pure and Applied Geophysics, 172, 3589-3616, doi:10.1007/s00024-015-1135-5

Shi, J., Shi, F., Kirby, J. T., Ma, G.. Wu, G., Tong, C. and Zheng, J., 2015, “Pressure decimation and interpolation (PDI) method for a baroclinic non-hydrostatic model”, Ocean Modelling, 96, 265-279, doi:10.1016/j.ocemod.2015.09.010

Wu, G., Shi, F., Kirby, J. T., Mieras, R., Liang, B., Li, H. and Shi, J., 2016, “A pre-storage, subgrid model for simulating flooding and draining processes in salt marshes”, Coastal Engineering, 108, 65-78, doi:10.1016/j.coastaleng.2015.11.008.

Derakhti, M. and Kirby, J. T., 2016, “Breaking-onset, energy and momentum flux in unsteady focused wave packets”, Journal of Fluid Mechanics, 790, 553-581, doi:10.1017/jfm.2016.17.

Orzech, M., Shi, F., Veeramony, J., Bateman, S., Calantoni, J. and Kirby, J. T., 2016, “Incorporating floating surface objects into a fully dispersive surface wave model”, Ocean Modelling, 102, 14-26, doi:10.1016/j.ocemod.2016.04.007.

Ma, G., Farahani, A. A., Kirby, J. T. and Shi, F., 2016, “Modeling wave-structure interactions by an immersed boundary method in a sigma-coordinate model”, Ocean Engineering, 125, 238-247, doi:10.1016/j.oceaneng.2016.08.027.

Derakhti, M., Kirby, J. T., Shi, F. and Ma, G., 2016, “NHWAVE: Consistent boundary conditions and turbulence modeling”, Ocean Modelling, 106, 121-130, doi:10.1016/j.ocemod.2016.09.002.

Kirby, J. T., Shi, F., Nicolsky, D. and Misra, S., 2016, “The 27 April 1975 Kitimat, British Columbia submarine landslide tsunami: A comparison of modeling approaches”, Landslides, doi:10.1007/s10346-016-0682-x.

Shi, F., Chickadel, C., Hsu, T.-J., Kirby, J. T., Farquharson, G. and Ma, G., 2016, “High-resolution non-hydrostatic modeling of frontal features in the mouth of the Columbia River”, Estuaries and Coasts, doi:10.1007/s12237-016-0132-y.

Derakhti, M., Kirby, J. T., Shi, F. and Ma, G., 2016, “Wave breaking in the surf zone and deep water in a non-hydrostatic RANS model. Part 1: Organized wave motions”, Ocean Modelling, doi:10.1016/j.ocemod.2016.09.001.

Derakhti, M., Kirby, J. T., Shi, F. and Ma, G., 2016, “Wave breaking in the surf zone and deep water in a non-hydrostatic RANS model. Part 2: Turbulence and mean circulation”, Ocean Modelling, doi:10.1016/j.ocemod.2016.09.011.

2015

Brown, Nerissa C. and Stice, J. Han and White, Roger, Mobile Communication and Local Information Flow: Evidence from Distracted Driving Laws (February 16, 2015). Journal of Accounting Research, Forthcoming. Available at SSRN: http://ssrn.com/abstract=2410372 or http://dx.doi.org/10.2139/ssrn.2410372

Fu, Weixuan, Jack CM Dekkers, William R. Lee, and Behnam Abasht. “Linkage disequilibrium in crossbred and pure line chickens.” Genetics Selection Evolution 47, no. 1 (2015): 11.

Zhou, Nan, William R. Lee, and Behnam Abasht. “Messenger RNA sequencing and pathway analysis provide novel insights into the biological basis of chickens’ feed efficiency.” BMC genomics 16.1 (2015): 195.

Rabe, T., Kukulka, T., I. Ginis, T. Hara, B. Reichl, E. D’Asaro, R. Harcourt, P. P. Sullivan, Langmuir turbulence under Hurricane Gustav (2008), J. Phys. Oceanogr., 45(3), 657–677, 2015. [pdf]

Sha, J., Young-Heon, J., Oliver, M. J., Kohut, J. T., Shatley, M., Liu, W. T., Yan, X. H. 2015. A case study of large phytoplankton blooms off the New Jersey coast with multi-sensor observations. Continental Shelf Research. doi:10.1016/j.csr.2015.07.006.

2014

Morteza Derakhti and James T. Kirby (2014). Bubble entrainment and liquid–bubble interaction under unsteady breaking waves. Journal of Fluid Mechanics, 761, pp 464-506 doi:10.1017/jfm.2014.637

Xie Shengbai, and Archer Cristina (2014), Self-similarity and turbulence characteristics of wind turbine wakes via large-eddy simulation, Wind Energ., doi: 10.1002/we.1792

Zhou, Z., J. Sangermano, T.-J. Hsu, and F. C. K. Ting (2014), A numerical investigation of wave-breaking induced turbulent coherent structure under a solitary wave, J. Geophys. Res. Oceans, 119, doi:10.1002/2014JC009854.

Severin T., Conan P., Durrieu de Madron X., Houpert L, Oliver M. J., Oriol L., Caparros J., Ghiglione J. F., Pujo-Pay M. 2014. Impact of open-ocean convection on nutrients, phytoplankton biomass and activity. Deep-Sea Research I. doi: 10.1016/j.dsr.2014.07.015

2013

Archer, C. L., S. Mirzaeisefat, and S. Lee (2013), Quantifying the sensitivity of wind farm performance to array layout options using large-eddy simulation, Geophys. Res. Lett., 40, 49634970, doi:10.1002/grl.50911.

Kukulka, T., A.J. Plueddemann, P. P. Sullivan, Inhibited upper ocean restratification in nonequilibrium swell conditions, Geophys. Res. Lett., 40, doi:10.1002/grl.50708, 2013. [pdf]

Oliver, M. J., Breece*, M. W., Fox, D. A., Haulsee*, D., Kohut, J. T., Manderson, J., Savoy, T. 2013. Shrinking the Haystack: Using an AUV in an Integrated Ocean Observatory to Map Atlantic Sturgeon in the Coastal Ocean. Fisheries, doi:10.1080/03632415.2013.782861

Voynova*, Y. G., Oliver, M. J., Sharp, J. H. 2013. Wind to Zooplankton: Ecosystem-wide Influence of Seasonal Wind-Driven Upwelling in and around the Delaware Bay. Journal of Geophysical Research. doi: 10.1002/2013JC008793

2012

Kukulka, T., K. Brunner, Passive buoyant tracers in the ocean surface boundary layer: I. Influence of equilibrium wind-waves on vertical distributions (accepted in J. Geophys. Res.) [pdf]

Mutryn F.M., E.M. Brannick, W. Fu, W.R. Lee, B. Abasht. Characterization of a novel chicken muscle disorder through differential gene expression and pathway analysis using RNA-sequencing. BMC Genomics. [In Press]

2011

Manderson, J., Palamara, L., Kohut, J., Oliver, M. J. 2011. Ocean Observatory Data are Useful for Regional Habitat Modeling of Species with Different Vertical Habitat Preferences, Marine Ecology Progress Series, Vol 438, 1-17, doi:10.3354/meps09308. FEATURED ARTICLE

Presentations

Oliver, M. J., Fox, D. A., Kohut, J. Manedrson, J. Irwin, A. (2014) A Satellite Driven Dynamic Biome Product to Assist in Fisheries Management and Marine Spatial Planning. Annual Meeting of the Mid-Atlantic Chapter of the American Fisheries Society. Lewes, Delaware.

 

Breece, M. W., Fox, D. A., Dunton, K., Oliver, M. (2014) Identifying Marine Habitat Preferences for Atlantic Sturgeon Using Auvs, Satellites, and Telemetry. 144th National American Fisheries Society. Quebec City, Canada.

 

Breece, M. W., Fox, D. A., Dunton, K., Oliver, M. Identifying Marine Habitat Preferences for Atlantic Sturgeon Using Auvs, Satellites, and Telemetry. Annual Meeting of the Mid-Atlantic Chapter of the American Fisheries Society. Lewes, Delaware.

 

Breece*, M. W., Haulsee*, D. E., Fox, D, A, Oliver, M. J. (2014) Integration of Satellite, glider and biotelemetry observations to protect endangered. NASA Biodiversity and Ecological Forecasting Team Meeting, Silver Spring, MD.

 

Breece*, M. W., Oliver, M. J., Dunton, K. J., Fox, D. A. (2014) Using Satellites and AUVS in and Integrated Ocean Observatory to Identify Atlantic Sturgeon Habitat.  Ocean Sciences Meeting, Honolulu, HI.

 

Breece*, M. W., M. J. Oliver, K. J. Dunton, and D. A. Fox. (2013) Testing Atlantic sturgeon spring habitat selection with an autonomous underwater vehicle. Annual meeting of the Mid-Atlantic Chapter of the American Fisheries Society, Tuckerton, NJ.

 

Breece*, M. W., M. J. Oliver, K. J. Dunton, and D. A. Fox.  (2013)  Dynamic environments, dynamic sampling: using gliders, satellites and transmitters to determine Atlantic sturgeon habitat selection in the mid-Atlantic Bight. 7th International Symposium on Sturgeon. Naniamo, Canada, BC.

 

Breece*, M. W., Haulsee*, D. E., Fox, D, A, Oliver, M. J. (2013) Testing Habitat Associations of Atlantic Sturgeon Using Remote Sensing and Acoustic Biotelemetry NASA Biodiversity and Ecological Forecasting Team Meeting, April 23-25, 2013, Arlington, VA.

 

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