U-M researchers have published hundreds of papers and conference presentations in recent years that have used the Flux HPC cluster to help achieve their results.

A selection of these publications appears below, sorted by year.

2015 | 2014 | 2013 | 2012


M. Henry de Frahan, S. Varadan and E. Johnsen, A new limiting procedure for discontinuous Galerkin methods applied to compressible multiphase flows with shocks and interfaces, J. Comput. Phys. 280 (2015) 489-509, DOI:10.1016/j.jcp.2014.09.030

Esther Wertz, Benjamin P. Isaacoff, Jessica D. Flynn, and Julie S. Biteen. Single-Molecule Super-Resolution Microscopy Reveals How Light Couples to a Plasmonic Nanoantenna on the Nanometer Scale. Nano Letters 2015 15 (4), 2662-2670. DOI: 10.1021/acs.nanolett.5b00319


Tao Hu, Benjamin P. Isaacoff, Joong Hwan Bahng, Changlong Hao, Yunlong Zhou, Jian Zhu, Xinyu Li, Zhenlong Wang, Shaoqin Liu, Chuanlai Xu, Julie S. Biteen, and Nicholas A. Kotov. Self-Organization of Plasmonic and Excitonic Nanoparticles into Resonant Chiral Supraparticle Assemblies. Nano Letters 2014 14 (12), 6799-6810. DOI: 10.1021/nl502237f

Dinov ID, Petrosyan P, Liu Z, Eggert P, Hobel S, Vespa P, Woo Moon S, Van Horn JD, Franco J and Toga AW. (2014) High-throughput neuroimaging-genetics computational infrastructure. Front. Neuroinform., 8:41. DOI:10.3389/fninf.2014.00041

Hitinder S. Gurm, Judith Kooiman, Thomas LaLonde, Cindy Grines, David Share, Milan Seth. (2014). A Random Forest Based Risk Model for Reliable and Accurate Prediction of Receipt of Transfusion in Patients Undergoing Percutaneous Coronary Intervention, 09 May 2014, PLOS ONE, DOI:10.1371/journal.pone.0096385

Reed, M.P., Raschke, U., Tirumali, R., and Parkinson, M.B. (2014). Developing and implementing parametric human body shape models in ergonomics software. Proc. 3rd International Digital Human Modeling Conference. Tokyo, Japan.

Kellogg, Ryan, The Effect of Uncertainty on Investment: Evidence from Texas Oil Drilling, American Economic Review 2014, 104(6): 1698–1734 DOI:10.1257/aer.104.6.1698

Mourão, D. Kreitman and S. Schnell (2014). Unravelling the impact of obstacles in diffusion and kinetics of an enzyme catalysed reaction. Physical Chemistry Chemical Physics 16, 4492-4503. DOI:10.1039/C3CP52417E

Mourão, L. Satin and S. Schnell (2014). Optimal experimental design to estimate statistically significant periods of oscillations in time course data. PLoS ONE 9, e93826. DOI:10.1371/journal.pone.0093826

Lyon SM, Wunsch H, Asch DA, Carr BC, Kahn JM, Cooke CR. Use of intensive care services and associated hospital mortality after Massachusetts healthcare reform. Crit Care Med 2014 Apr;42(4):763-70

Guo, Q., and Jeffers, A.E. (2014). Finite Element Reliability Analysis of Structures Subjected to Fire, J. Struct. Eng. DOI:10.1061/(ASCE)ST.1943-541X.0001082 , 04014129.

Guo, Q., Martinez, J., and Jeffers, A.E. (2014). Framework for Structural Reliability Evaluation in Fire, Society of Fire Protection Engineers (SFPE) Engineering Technology Conference, Long Beach, CA, Oct. 12-17.

Guo, Q., Mozo, E., Martinez, J., and Jeffers, A.E. (2014). Reliability Evaluation of Residential Buildings in Fire, Proceedings of the 8th International Conference on Structures in Fire (SiF), Shanghai, China, June 11-13.

Yang J-R, Ruan S, Zhang J (2014) Determinative Developmental Cell Lineages Are Robust to Cell Deaths. PLoS Genet 10(7): e1004501. DOI:10.1371/journal.pgen.1004501

Wiedenbeck, B.-A. Cassell, and M. P. Wellman, Bootstrap statistics for empirical games, 13th International Conference on Autonomous Agents and Multiagent Systems, pages 597–604, May 2014.

Yan Liu and Matthew Collette, Improving surrogate-assisted Variable Fidelity Multi-Objective Optimization using a Clustering Algorithm, Applied Soft Computing, Volume 24, November 2014, Pages 482–493 doi:10.1016/j.asoc.2014.07.022

Peter Bosler, Lei Wang, Christiane Jablonowski and Robert Krasny, A Lagrangian particle/panel method for the barotropic vorticity equations on a rotating sphere, Fluid Dyn. Res. 46 (2014) 031406 (13pp) DOI:10.1088/0169-5983/46/3/031406

Funk, Russell J. Making the Most of Where You Are: Geography, Networks, and Innovation in Organizations. Academy of Management Journal 57, no. 1 (2014): 193-222.

Christopher A. Onken, Monica Valluri, Jonathan S. Brown, Peter J. McGregor, Bradley M. Peterson, Misty C. Bent, Laura Ferrarese, Richard W. Pogge, Marianne Vestergaard, Thaisa Storchi-Bergman, Rogemar A. Riffell. The Black Hole Mass of NGC 4151 II. Stellar Dynamical Measurement from Near-Infrared Integral Field Spectroscopy. Astrophysical Journal, July 2014 http://arxiv.org/pdf/1406.6735v1.pdf

Ryan P. Welch, Chee Lee, Paul M. Imbriano, Snehal Patil, Terry E. Weymouth, R., Alex Smith, Laura J. Scott and Maureen A. Sartor, ChIP-Enrich: gene set enrichment testing for ChIP-seq data, Nucleic Acids Research, 2014 1 DOI:10.1093/nar/gku463

Perket, J., M. G. Flanner, and J. E. Kay (2014), Diagnosing shortwave cryosphere radiative effect and its 21st century evolution in CESM, J. Geophys. Res. Atmos., 119, 1356–1362, DOI:10.1002/2013JD021139.

Jiao, C., Flanner, M. G., Balkanski, Y., Bauer, S. E., Bellouin, N., Berntsen, T. K., Bian, H., Carslaw, K. S., Chin, M., De Luca, N., Diehl, T., Ghan, S. J., Iversen, T., Kirkevåg, A., Koch, D., Liu, X., Mann, G. W., Penner, J. E., Pitari, G., Schulz, M., Seland, Ø., Skeie, R. B., Steenrod, S. D., Stier, P., Takemura, T., Tsigaridis, K., van Noije, T., Yun, Y., and Zhang, K. (2014), An AeroCom assessment of black carbon in Arctic snow and sea ice, Atmos. Chem. Phys., 14, 2399-2417, DOI:10.5194/acp-14-2399-2014.

Rayborn, L. L. (2014), The Effect of Absorptive Aerosol Layers on Atmospheric Dynamics, Abstract S138, poster presentation at the American Meteorological Society 13th Annual Student Congress, Atlanta GA, Feb. 2–6

Henry A. Boateng, Tim P. Schulze, and Peter Smereka, SIAM Multiscale Modeling and Simulation, Vol 12., No 1, paa 181-199, 2014

Freedman, Z., D. R. Zak. (2014) Atmospheric N Deposition Increases Bacterial Laccase-Like Multicopper Oxidases: Implications for Organic Matter Decay. Applied and Environmental Microbiology. 80(14): 4460-4468.

Lee M. and Geva E. and Dunietz B. (2014) Donor-to-donor vs. donor-to-acceptor interfacial charge transfer states in the phthalocyanine-fullerene organic photovoltaic system Phys. Rev Lett. J. Phys. Chem. Lett., 2014, 5 (21), pp 3810–3816, DOI:10.1021/jz5017203

Talapatra S. and Geva E. (2014) Vibrational Lifetimes of Cyanide Ion in Aqueous Solution From Molecular Dynamics Simulations: Intermolecular vs. Intramolecular Accepting Modes, J. Phys. Chem. B, 2014, 118 (26), pp 7395–7404, DOI:10.1021/jp504460q

Zheng, A. Manna, H. Phillips, M. Hammer, C. Song, E. Geva and B. Dunietz (2014) Molecular structure, spectroscopy and photo induced kinetics in tri-nuclear cyanide bridged complex in solution: A first principle perspective J. Am. Chem. Soc., 2014, 136 (49), pp 16954–16957, DOI:10.1021/ja507131q

Lee M., Geva E. and Dunietz B. (2014) Calculation from First Principles of Golden-Rule Rate Constants for Photo-Induced Subphthalocyanine/Fullerene Interfacial Charge Transfer and Recombination in Organic Photovoltaic Cells J. Phys. Chem. C, 2014, 118 (18), pp 9780–9789 DOI:10.1021/jp501199u

Vazquez F. X., Talapatra S., Sension R. J. and Geva E. (2014) The Entropic Origin of Solvent Effects on The Single Bond cZt-tZt Isomerization Rate Constant of 1,3,5-cis-Hexatriene in Alkane and Alcohol Solvents: A Molecular Dynamics Study, J. Phys. Chem. C, 2014, 118 (18), pp 7869-7877. DOI:10.1021/jp5002644

Phillips H. D., Zheng Z, Geva E. and Dunietz, B. D. (2014) Orbital Gap Predictions for Rational Design of Organic Photovoltaic Materials Organic Electronics, 15 1509-1520

Iyer, M., Pollock, T.M., Gavini, V., Energetics and nucleation of point defects in aluminum under extreme tensile hydrostatic stresses, Phys. Rev. B 89, 014108 (2014).

Anantharaman, K.A., M.B. Duhaime, J.A. Breier, K. Wendt, B.M. Toner, and G.J. Dick (2014).  Sulfur oxidation genes in diverse deep-sea viruses.  Science 344: 757-760. DOI:10.1126/science.1252229

Li, M., B.M. Toner, B.J. Baker, J.A. Breier, C.S. Sheik, and G.J. Dick (2014).  Microbial iron uptake as a mechanism for dispersing iron from deep-sea hydrothermal vents.  Nature Communications 5: 3192.  DOI:10.1038/ncomms4192

Li, M., S. Jain, B.J. Baker1, C. Taylor, and G.J. Dick (2014).  Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep-sea hydrocarbon plume. Environmental Microbiology 16: 60-71.  DOI:10.1111/1462-2920.12182

Sheik, C.S. 2, S. Jain, and G.J. Dick (2014).  Metabolic flexibility of enigmatic SAR324 revealed through metagenomics and metatranscriptomics. Environmental Microbiology 16: 304-317.  DOI:10.1111/1462-2920.12165

Orvananos, R. Malik, H.-C. Yu, A. Abdellahi, C. Grey, G. Ceder, and K. Thornton, Architecture Dependence on the Dynamics of Nano-LiFePO4 Electrodes, Electrochimica Acta, 137, 245–257 (2014).

B. Orvananos, T. Ferguson, H.-C. Yu, M. Bazant, and K. Thornton, Particle-Level Modeling of the Charge-Discharge Behavior of Nanoparticulate Phase-Separating Li-Ion Battery Electrodes. Journal of the Electrochemical Society, 161 (4), A535-A546 (2014).

L.K. Lee, L.K. Aagesen, K. Thornton, P.-C. Ku, Origin of broad luminescence from site-controlled InGaN nanodots fabricated by selective-area epitaxy. Physica Status Solidi A, 211 (3), 531-535 (2014). DOI:10.1002/pssa.201330362

Stephani, K. A., and I. D. Boyd (2014), Detailed modeling and analysis of spacecraft plume/ionosphere interactions in low Earth orbit, J. Geophys. Res. Space Physics, 119, 2101–2116, DOI:10.1002/2013JA019222.

Farbar, E., Alkandry, H., Wiebenga, J., and Boyd, I. D., Simulation of Ablating Hypersonic Vehicles with Finite-Rate Surface Chemistry, AIAA Paper 2014-2124, June 2014.

Gallen, S.F., Clark, M.K., Godt, J.W., Earthquake-triggered landslides reveal that rocks are weak; does lithology matter? 2014 Geological Society of America Penrose Conference, Asheville, NC.

Gallen, S.F., Clark, M.K., Godt, J.W., Inverting earthquake-triggered landslide inventories for rock strength. 2014 Amtrak Club meeting, Bethlehem, PA.

Tang, X., Koenig, P. H., & Larson, R. G. (2014). Molecular dynamics simulations of sodium dodecyl sulfate micelles in water-the effect of the force field. The Journal of Physical Chemistry. B, 118(14), 3864–80. DOI:10.1021/jp410689m

Wang, S., & Larson, R. G. (2014). Water channel formation and ion transport in linear and branched lipid bilayers. Physical Chemistry Chemical Physics : PCCP, 16(16), 7251–62. DOI:10.1039/c3cp55116d

Li, Zifeng; Fichthorn, Kristen; Milner, Scott; Fang, Yuan; Larson, Ronald, A molecular view of polymer/water interfaces in latex , Macromolecules, 2014, 47 (18), pp 6441–6452 DOI:10.1021/ma500866f

Shi X, Cao L, Reed MP, Rupp JD, and Hu J (2014) Effects of Obesity on Occupant Responses in Frontal Crashes: A Simulation Analysis using Human Body Models Computer Methods in Biomechanics and Biomedical Engineering. Published online. DOI:10.1080/10255842.2014.900544

Curtis Jin, Raj Rao Nadakuditi, Eric Michielssen, and Stephen C. Rand, Backscatter analysis based algorithms for increasing transmission through highly scattering random media using phase-only-modulated wavefronts, 1788 J. Opt. Soc. Am. A, Vol. 31, No. 8, 2014 DOI: 10.1364/JOSAA.31.001788

Greg Van Anders; N. Khalid Ahmed; Ross Smith; Michael Engel; Sharon C. Glotzer. Entropically patchy particles: Engineering valence through shape entropy. ACS Nano. 2014;8(1):931-940, DOI: 10.1021/nn4057353

Nguyen H. P. Nguyen; Daphne Klotsa; Michael Engel; Sharon C. Glotzer. Emergent collective phenomena in a mixture of hard shapes through active rotation. Physical Review Letters. 2014;112(7). DOI:10.1103/PhysRevLett.112.075701

Jaime A. Millan; Daniel Ortiz; Greg Van Anders; Sharon C. Glotzer. Self-assembly of archimedean tilings with enthalpically and entropically patchy polygons. ACS Nano. 2014;8(3):2918-2928, DOI: 10.1021/nn500147u

Ryan L. Marson; Carolyn L. Phillips; Joshua A. Anderson; Sharon C. Glotzer. Phase behavior and complex crystal structures of self-assembled tethered nanoparticle telechelics. Nano Letters. 2014;14(4):2071-2078, DOI: 10.1021/nl500236b

Daniel Ortiz; Kevin L. Kohlstedt; Trung Dac Nguyen; Sharon C. Glotzer. Self-assembly of reconfigurable colloidal molecules. Soft Matter. 2014;10(20):3541-3552, DOI:10.1039/C4SM00026A

Jai Il Park; Trung Dac Nguyen; Gleiciani De Queirós Silveira; Joong Hwan Bahng; Sudhanshu Srivastava; Gongpu Zhao; Kai Sun; Peijun Zhang; Sharon C. Glotzer; Nicholas A. Kotov. Terminal supraparticle assemblies from similarly charged protein molecules and nanoparticles. Nature Communications. 2014;5, DOI:10.1038/ncomms4593

Daniel J. Beltran-Villegas; Benjamin A. Schultz; Nguyen H. P. Nguyen; Sharon C. Glotzer; Ronald G. Larson. Phase behavior of Janus colloids determined by sedimentation equilibrium. Soft Matter. 2014;10(26):4593-4602, DOI:10.1039/c3sm53136h.

Sadiq and D. Viswanath, Finite difference weights, spectral differentiation, and superconvergence, Mathematics of Computation, vol. 83 (2014), p. 2403–2427. DOI:10.1090/S0025-5718-2014-02798-1

Daniel Zinder, Trevor Bedford, Edward B Baskerville, Robert J Woods, Manojit Roy, and Mercedes Pascual, Seasonality in the migration and establishment of H3N2 Influenza lineages with epidemic growth and decline, BMC Evolutionary Biology 2014, 14:272 DOI:10.1186/s12862-014-0272-2

Henry de Frahan, S. Varadan and E. Johnsen, A new limiting procedure for discontinuous Galerkin methods applied to compressible multiphase flows with shocks and interfaces, J. Comput. Phys. 280 (2015) 489-509, DOI:10.1016/j.jcp.2014.09.030

T. Henry de Frahan, P. Movahed and E. Johnsen, Numerical simulations of a shock interacting with successive interfaces using the Discontinuous Galerkin method: the multilayered Richtmyer-Meshkov and Rayleigh-Taylor instabilities, Shock Waves (2014), DOI:10.1007/s00193-014-0539-y

A. Di Stefano, G. Malamud, M. T. Henry de Frahan, C. C. Kuranz, A. Shimony, S. R. Klein, R. P. Drake, E. Johnsen, D. Shvarts, V. A. Smalyuk and D. Martinez, Observation and modeling of mixing-layer development in high-energy-density, blast-wave-driven shear flow, Phys. Plasmas 21 (2014) 056306, DOI:10.1063/1.4872223

C.L. Phillips, J.A. Anderson, and S.C. Glotzer, “Molecular Dynamics Models of Shaped Particles Using Filling Solutions,” Physics Procedia 53, 75-81 (2014). DOI:10.1016/j.phpro.2014.06.030

C.L. Phillips, E. Jankowski, B. Krishnatreya, K. Edmond, S. Sacanna, D.G. Grier, D.J. Pine, and S.C. Glotzer, “Digital Colloids: Reconfigurable Clusters as High Information Density Elements,” Soft Matter, (2014).  DOI:10.1039/C4SM00796D


Bauer ME, Bateman BT, Bauer ST, Shanks AM, Mhyre JM. Maternal sepsis mortality and morbidity during hospitalization for delivery: temporal trends and independent associations for severe sepsis. Anesth Analg. 2013 Oct;117(4):944-50. DOI:10.1213/ANE.0b013e3182a009c3.

Dinov, ID, Petrosyan, P, Liu, Z, Eggert, P, Zamanyan, A, Torri, F, Macciardi, F, Hobel, S, Moon, SW, Sung, YH, Jiang, Z, Labus, J, Kurth, F, Ashe-McNalley, C, Mayer, E, Vespa, PM, Van Horn, JD, Toga, AW. (2013) The Perfect Neuroimaging-Genetics-Computation Storm: Collision of Petabytes of Data, Millions of Hardware Devices and Thousands of Software Tools, Brain Imaging and Behavior , DOI:10.1007/s11682-013-9248-x.

Timothy Y. James, Steven Ahrendt, Divya Sain, Nicolas Corradi, Jason E. Stajich, Adrian Pelin, Linda Bonen, Shared Signatures of Parasitism and Phylogenomics Unite Cryptomycota and Microsporidia, Current Biology 23, 1548–1553, August 19, 2013 DOI:10.1016/j.cub.2013.06.057

R. Shellman, C.F. Burant and S. Schnell (2013). Network motifs provide signatures that characterize metabolism. Molecular BioSystems 9, 352-360. DOI:10.1039/C2MB25346A

L. Wynn, P. Rupp, P. A. Trainor, S. Schnell, and P M. Kulesa (2013). Follow-the-leader cell migration requires biased cell–cell contact and local microenvironmental signals. Physical Biology 10, 035003. DOI:10.1088/1478-3975/10/3/035003

Guo, Q., Shi, K., Jia, Z., and Jeffers, A.E. (2013). Probabilistic Evaluation of Structural Fire Resistance, Special Issue: World Trade Center, Fire Technology, 49, 793-811.

Guo, Q., and Jeffers, A.E. (2013). Stochastic Finite Element Methods for the Reliability-Based Fire-Resistant Design of Structures, Proceedings of the 3rd International Conference on Applications in Structural Fire Engineering, Prague, Czech Republic, April 19-20.

Bichir, A., and Jeffers, A.E. (2013). Addressing Uncertainty in Modeling the Fire Resistance of Composite Laminates, Proceedings of the Fire and Materials Conference, San Francisco, CA, Jan. 28-30.

Alben, L.A. Miller, and J. Peng, Efficient kinematics for jet-propelled swimming J. Fluid Mech., (733) 100-133, 2013

Alben, Optimizing snake locomotion in the plane, Proc. Roy. Soc. A, 469 (2156), 2013

Yang JR, Zhang J. Developmental cell lineages are robust to cell deaths. 2013 Annual Meeting of Society for Molecular Biology and Evolution (SMBE 2013). Chicago, Illinois, US. 2013. (poster)

A. Mayer, E. Sodomka, A. Greenwald, and M. P. Wellman, Accounting for price dependencies in simultaneous sealed-bid auctions, 14th ACM Conference on Electronic Commerce, pages 679–696, June 2013.

P. Wellman, T. H. Kim, and Q. Duong, Analyzing incentives for protocol compliance in complex domains: A case study of introduction-based routing, 12th Workshop on the Economics of Information Security, June 2013.

Skiba, A.W., L. Zeng, B.K. Arbic, M. Müller, and W.J. Godwin, 2013: On the resonance and shelf/open-ocean coupling of the global diurnal tides. Journal of Physical Oceanography 43, doi:10.1175/JPO-D-12-054.1, 1301-1324.DOI:10.1175/JPO-D-12-054.1

Jeffrey M Rosen, Junjie Wu, Thomas F Wenisch, J A Fessler. Iterative helical CT reconstruction in the cloud for ten dollars in five minutes. Proc. Intl. Mtg. on Fully 3D Image Recon. in Rad. and Nuc. Med, pp. 241-4, 2013.

Erickson, B.M.S.; Singh, R.; Evrard, A.E.; Becker, M.R.; Busha, M.T.; Kravtsov, A.V.; Marru, S.; Pierce, M.; Wechsler, R.H. 2013,Enabling Dark Energy Survey Science Analysis with Simulations on XSEDE Resources, ACM Proc. of XSEDE13, 16:1-16:8.

Wu, H-Y.; Hahn, O.; Evrard, A.E.; Wechsler, R.H.; Dolag, K., 2013, Virial Scaling of Galaxies in Clusters: Bright to Faint is Cool to Hot, Monthly Notices Royal Astronomical Society, 436, 360.

Dattatreya Mellacheruvu, Zachary Wright, Amber L Couzens, Jean-Philippe Lambert, Nicole A St-Denis, Tuo Li, Yana V Miteva, Simon Hauri, Mihaela E Sardiu, Teck Yew Low,     Vincentius A Halim, Richard D Bagshaw, Nina C Hubner, Abdallah al-Hakim, Annie Bouchard, Denis Faubert, Damian Fermin, Wade H Dunham, Marilyn Goudreault, Zhen-Yuan Lin, Beatriz Gonzalez Badillo, Tony Pawson, Daniel Durocher, Benoit Coulombe, Ruedi Aebersold, The CRAPome: a contaminant repository for affinity purification–mass spectrometry data, Nature Methods 10, 730–736 (2013) DOI:10.1038/nmeth.2557

ElMoaqet, H., Tilbury, D. M., & Ramachandran, S. K. (2013, June). Predicting oxygen saturation levels in blood using autoregressive models: a threshold metric for evaluating predictive models. In American Control Conference (ACC), 2013 (pp. 734-739). IEEE

Bai L, Ritsema J, The effect of large-scale shear-velocity heterogeneity on SS precursor amplitudes, Geophys. Res. Lett., 40, DOI:10.1002/2013GL058669, 2013.

Trampert J, Fichtner A, Ritsema J, Resolution tests revisited: the power of random numbers, Geophys. J. Int., 192, 676–680, 2013.

Goes S, Eakin C, Ritsema J, Lithospheric cooling trends and deviations in oceanic PP-P and SS-S differential traveltimes, J. Geophys. Res., 118, DOI:10.1002/jgrb.50092, 2013.

Perket, J., M. G. Flanner, and J. E. Kay (2014), Diagnosing shortwave cryosphere radiative effect and its 21st century evolution in CESM, J. Geophys. Res. Atmos., 119, 1356–1362, DOI:10.1002/2013JD021139.

Flanner, M. G. (2013), Arctic climate sensitivity to local black carbon, J. Geophys. Res., 118, 1840–1851, DOI:10.1002/jgrd.50176.

Shindell, D. T., J.-F. Lamarque, M. Schulz, M. Flanner, C. Jiao, M. Chin, P. J. Young, Y. H. Lee, L. Rotstayn, N. Mahowald, G. Milly, G. Faluvegi, Y. Balkanski, W. J. Collins, A. J. Conley, S. Dalsoren, R. Easter, S. Ghan, L. Horowitz, X. Liu, G. Myhre, T. Nagashima, V. Naik, S. T. Rumbold, R. Skeie, K. Sudo, S. Szopa, T. Takemura, A. Voulgarakis, J.-H. Yoon, and F. Lo (2013), Radiative forcing in the ACCMIP historical and future climate simulations, Atmos. Chem. Phys., 13, 2939-2974, DOI:10.5194/acp-13-2939-2013.

Lee, Y. H., J.-F. Lamarque, M. G. Flanner, C. Jiao, D. T. Shindell, T. Berntsen, M. M. Bisiaux, J. Cao, W. J. Collins, M. Curran, R. Edwards, G. Faluvegi, S. Ghan, L. W. Horowitz, J. R. McConnell, J. Ming, G. Myhre, T. Nagashima, V. Naik, S. T. Rumbold, R. B. Skeie, K. Sudo, T. Takemura, F. Thevenon, B. Xu and J.-H. Yoon (2013), Evaluation of preindustrial to present-day black carbon and its albedo forcing from Atmospheric Chemistry and Climate Model Intercomparison Project (ACCMIP), Atmos. Chem. Phys., 13, 2607-2634, DOI:10.5194/acp-13-2607-2013.

Jiao and M. G. Flanner (2013), An exploration of the key meteorological features which govern the transport and distribution of black carbon in the Arctic, Abstract A52C-02, oral presentation at 2013 Fall Meeting, AGU, San Francisco, CA, Dec. 9–13.

Schneider, A. and M. G. Flanner (2013), Assessing decadal-scale variability in surface albedo feedback across the CMIP5 simulations, Abstract A21B-0028, poster presentation at 2013 Fall Meeting, AGU, San Francisco, CA, Dec. 9–13.

Perket, M. G. Flanner, and D. M. Lawrence (2013), Expanding Snow Treatment in CESM Vegetation, Abstract C41B-0620, poster presentation at 2013 Fall Meeting, AGU, San Francisco, CA, Dec. 9–13.

Flanner, M. G., A. Gardner, A. Stohl, S. Eckhardt, N. Kristiansen, and J. Perket (2013), Aerosol radiative forcing from the Eyjafjallajökull volcanic eruption, Abstract C14B-07, oral presentation at 2013 Fall Meeting, AGU, San Francisco, CA, Dec. 9–13.

Mei, Wave Vibration Control of L-Shaped and Portal Planar Frames, Journal of Vibration and Acoustics Oct. 2013,Vol.135 / 051022-1

Mei, Vibration Control of H-Shaped Planar Frames Based on the Classical Euler-Bernoulli and the Advanced Timoshenko Bending Theories, Proceedings of the ASME 2013 International Mechanical Engineering Congress and Exposition November 15-21, 2013, San Diego, CA, USA

End-Group Influence on Frontier Molecular Orbital Reorganization and Thermoelectric Properties of Molecular Junctions, Janakiraman Balachandran, Pramod Reddy, Barry D. Dunietz, and Vikram Gavini, dx.doi.org/10.1021/jz401678m, J. Phys. Chem. Lett. 2013, 4, 3825−3833

Kwac, K. and Geva, E. (2013) A Mixed Quantum-Classical Molecular Dynamics Study of anti-Tetrol and syn-Tetrol Dissolved in Liquid Chloroform II: Infrared Emission Spectra, Vibrational Excited-State Life-Times and Nonequilibrium Hydrogen-Bond Dynamics J. Phys. Chem. B, 117 14457-14467

Kwac, K. and Geva, E. (2013) A Mixed Quantum-Classical Molecular Dynamics Study of anti-Tetrol and syn-Tetrol Dissolved in Liquid Chloroform: Hydrogen-Bond Structure and Its Signature on the Infrared Absorption Spectrum J. Phys. Chem. B, 117 16493–16505

Lee, M. H., Dunietz, B. D. and Geva, E. (2013) Calculation From First Principles of Intramolecular Golden-Rule Rate Constants for Photo-Induced Electron Transfer in Molecular Donor-Acceptor Systems J. Phys. Chem. C, 117 23391–23401

Kwac, K. and Geva, E. (2013) Solvation dynamics of formylperylene dissolved in methanol-acetonitrile liquid mixtures: A molecular dynamics study J. Phys. Chem. B 117 9996-10006

Kwac, K. and Geva, E. (2013) A mixed quantum-classical molecular dynamics study of the hydroxyl stretch in methanol/carbon-tetrachloride mixtures III: Nonequilibrium Hydrogen-Bond Dynamics and Infrared Pump-Probe Spectra J. Phys. Chem. B 117 7737-7749

Variable Accretion Outbursts in Protostellar Evolution, 2013a, Jaehan Bae, Lee Hartmann, Zhaohuan Zhu, & Charles Gammie, The Astrophysical Journal, 2013, 764, 141 http://iopscience.iop.org/0004-637X/764/2/141/

The Long-term Evolution of Photoevaporating Protoplanetary Disks, 2013b, Jaehan Bae, Lee Hartmann, Zhaohuan Zhu, & Charles Gammie, The Astrophysical Journal, 2013, 774, 57 http://iopscience.iop.org/0004-637X/774/1/57/

Balachandran, J., Reddy, P., Dunietz, B., Gavini, V., End-group influence on frontier molecular reorganization and thermoelectric propeties of molecular junctions, J. Phys. Chem. Lett. 4, 3825-3833 (2013).

Motamarri, P., Nowak, M.R., Leiter, K., Knap, J., Gavini, V., Higher-order adaptive finite-element methods for Kohn-Sham density functional theory, J. Comp. Phys. 253, 308-343 (2013).

Baker, B.J. 1, C.S. Sheik, C.A. Taylor, S. Jain, A. Bhasi, J.D. Cavalcoli, and G.J. Dick (2013).  Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling.  The ISME Journal 7: 1962-1973.  DOI: 10.1038/ismej.2013.85

Anantharaman, K., J.A. Breier, C.S. Sheik, and G.J. Dick (2013).  Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea bacteria.  Proceedings of the National Academy of Sciences 110: 330-335.  DOI:10.1073/pnas.1215340110.

Pisutha-Arnond, V. W. L. Chan, M. Iyer, V. Gavini, and K. Thornton, Classical density functional theory and the phase-field crystal method using a rational function to describe the two-body direct correlation function. Physical Review E, 87, [SG1] 013313 (2013).N. Pisutha-Arnond, V. W. L. Chan, K. Elder, and K. Thornton, Calculations of Isothermal Elastic Constants in the Phase-Field Crystal Model. Physical Review B, 87, 014103 (2013).

Stephani, K. A., and I. D. Boyd (2013), Detailed modeling and analysis of spacecraft plume/ionosphere interactions in low Earth orbit, 5th AIAA Atmospheric and Space Environments Conference, AIAA 2013-2680.

Farbar, E., Boyd, I. D. and Martin, A., Numerical Prediction of Hypersonic Flow Fields Including Effects of Electron Translational Nonequilibrium, Journal of Thermophysics and Heat Transfer, Vol. 27, No. 4 (2013), pp. 593-606. DOI:10.2514/1.T3963

Jiang, L., Watari, N., & Larson, R. G. (2013). How accurate are stochastic rotation dynamics simulations of polymer dynamics? Journal of Rheology, 57(4), 1177. DOI:10.1122/1.4807857

Wang, S., & Larson, R. G. (2013). Coarse-grained molecular dynamics simulation of tethered lipid assemblies. Soft Matter, 9(2), 480. DOI:10.1039/c2sm26850g

Zhao, T., Wang, X., Jiang, L., & Larson, R. G. (2013). Assessment of mesoscopic particle-based methods in microfluidic geometries. The Journal of Chemical Physics, 139(8), 084109. DOI:10.1063/1.4819124

Hu J, Shi X, Rupp JD, Reed MP, Klein KF, and Cao L (2013) Why Older, Obese, and Female Occupants are Vulnerable in Motor-Vehicle Crashes? A Biomechanical Point of View China Conference of Automotive Safety Technology, Hangzhou, Zhejiang, China.

Constraints on Blazar Jet Conditions During Gamma-Ray Flaring from Radiative Transfer Modeling, Aller, Margo F.; Hughes, Philip A.; Aller, Hugh D.; Hovatta, Talvikki DOI:10.1051/epjconf/20136107002

Curtis Jin, Raj Rao Nadakuditi, Eric Michielssen, and Stephen C. Rand, Iterative, backscatter-analysis algorithms for increasing transmission and focusing light through highly scattering random media, 1592 J. Opt. Soc. Am. A , Vol. 30, No. 8, 2013, DOI:10.1364/JOSAA.30.001592

Xingchen Ye; Jaime A. Millan; Michael Engel; Jun Chen; Benjamin T. Diroll; Sharon C. Glotzer; Christopher B. Murray. Shape alloys of nanorods and nanospheres from self-assembly. Nano Letters. 2013;13(10):4980-4988, DOI:10.1021/nl403149u

Kaylie L. Young; Michelle L. Personick; Michael Engel; Pablo F. Damasceno; Stacey N. Barnaby; Reiner Bleher; Tao Li; Sharon C. Glotzer; Byeongdu Lee; Chad A. Mirkin. A directional entropic force approach to assemble anisotropic nanoparticles into superlattices. Angewandte Chemie – International Edition. 2013;52(52):13980-13984. DOI:10.1002/anie.201306009

Kevin L. Kohlstedt; Sharon C. Glotzer. Self-assembly and tunable mechanics of reconfigurable colloidal crystals. Physical Review E – Statistical, Nonlinear, and Soft Matter Physics, 2013;87(3). DOI:10.1103/PhysRevE.87.032305

Aayush A. Shah; Benjamin Schultz; Kevin L. Kohlstedt; Sharon C. Glotzer; Michael J. Solomon. Synthesis, assembly, and image analysis of spheroidal patchy particles, Langmuir.  2013;29(15):4688-4696. DOI:10.1021/la400317t

Michael Engel; Joshua A. Anderson; Sharon C. Glotzer; Masaharu Isobe; Etienne P. Bernard; Werner Krauth. Hard-disk equation of state: First-order liquid-hexatic transition in two dimensions with three simulation methods. Physical Review E – Statistical, Nonlinear, and Soft Matter Physics. 2013;87(4), DOI:10.1103/PhysRevE.87.042134

Xingchen Ye; Jun Chen; Michael Engel; Jaime A. Millan; Wenbin Li; Liang Qi; Guozhong Xing; Joshua E. Collins; Cherie R. Kagan; Ju Li; et al. Competition of shape and interaction patchiness for self-assembling nanoplates. Nature Chemistry. 2013;5(6):466-473, DOI:10.1038/nchem.1651

Amir Haji-Akbari; Elizabeth R. Chen; Michael Engel; Sharon C. Glotzer. Packing and self-assembly of truncated triangular bipyramids. Physical Review E – Statistical, Nonlinear, and Soft Matter Physics. 2013;88(1), DOI:10.1103/PhysRevE.88.012127

Joshua A. Anderson; Eric Jankowski; Thomas L. Grubb; Michael Engel; Sharon C. Glotzer. Massively parallel monte carlo for many-particle simulations on GPUs. Journal of Computational Physics. 2013;254:27-38, DOI:10.1016/j.jcp.2013.07.023

Viswanath and I. Tobasco, Navier–Stokes solver using Green’s functions I: Channel flow and plane Couette flow, Journal of Computational Physics, vol. 251 (2013), p. 414–431. DOI:10.1016/j.jcp.2013.06.004

Sadiq and D. Viswanath, Barycentric Hermite interpolation, SIAM Journal on Scientific Computing, vol. 35 (2013), p. A1254-A1270.  DOI:10.1137/110833221

Viswanath, K. Serkh and X. Liang, Metric entropy and the optimal prediction of chaotic signals, SIAM Journal on Applied Dynamical Systems, vol. 12 (2013), p. 1085-1113. DOI:10.1137/110824772

Daniel Zinder, Trevor Bedford, Sunetra Gupta, Mercedes Pascual, The Roles of Competition and Mutation in Shaping Antigenic and Genetic Diversity in Influenza, 2013, PLOS Pathogens DOI: 10.1371/journal.ppat.1003104

Movahed and E. Johnsen, A solution-adaptive method for efficient compressible multifluid simulations, with application to the Richtmyer-Meshkov instability, J. Comput. Phys. 239 (2013) 166-186.

Movahed, E. Johnsen, Turbulence diffusion effects at material interfaces, with application to the Rayleigh-Taylor instability, AIAA paper 2013-3121, 43rd AIAA Fluid Dynamics Conference and Exhibit, June 2013, San Diego, California. DOI:10.2514/6.2013-3121


L. Wynn, N. Consul, S. D. Merajver and S. Schnell (2012). Logic-based models in systems biology: a predictive and parameter-free network analysis method.Integrative Biology 4, 1323-1337. DOI:10.1039/C2IB20193C

Seymour CW, Iwashyna TJ, Ehlenbach WJ, Wunsch H, Cooke CR. Hospital variation in the use of intensive care. Health Serv Res. 2012;47:2060-2080

Erickson, B.M.S.; Singh, R.; Evrard, A.E.; Becker, M.R.; Busha, M.T.; Kravtsov, A.V.; Marru, S.; Pierce, M.; Wechsler, R.H. 2012, A High Throughput Workflow Environment for Cosmological Simulations, ACM Proc. of XSEDE12, 34.1-34.8.