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Publications and acknowledgement

CARC acknowledgement

Please use the following statement when acknowledging use of Center for Advanced Research Computing resources. Select one or more of the items within the braces { }:

We would like to thank the UNM Center for Advanced Research Computing, supported in part by the National Science Foundation, for providing the {high performance computing, large-scale storage, visualization} resources used in this work.


The following list reflects the broad spectrum of computational research at the University of New Mexico. All publications have made use of CARC resources including computation, storage, machine hosting, or resident research space at the Center. To submit a paper or manuscript for inclusion here, email the citation and link to publication to


Foteinopoulou, S., Devarapu, G. C. R., Subramania, G. S., Krishna, S., & Wasserman, D. (2019). Phonon-polaritonics: enabling powerful capabilities for infrared photonics. Nanophotonics.

Fazel, M., Wester, M. J., Mazloom-Farsibaf, H., Meddens, M. B. M., Eklund, A. S., Schlichthaerle, T., & Lidke, K. A. (2019). Bayesian Multiple Emitter Fitting using Reversible Jump Markov Chain Monte Carlo. Scientific Reports, 9(1), 13791.

Morris, J., Cowen, B. J., Teysseyre, S., & Hecht, A. A. (2020). Molecular dynamics investigation of threshold displacement energies in CaF2. Computational Materials Science, 172, 109293.

Cowen, B. J., El-Genk, M. S., Hattar, K., & Briggs, S. A. (2019). Investigations of irradiation effects in crystalline and amorphous SiC. Journal of Applied Physics, 126(13), 135902.

Ajith, M., & Martínez-Ramón, M. (2019). Unsupervised Segmentation of Fire and Smoke from Infra-Red Videos. arXiv.

McCullough, J. M., Moyle, R. G., Smith, B. T., & Andersen, M. J. (2019). A Laurasian origin for a pantropical bird radiation is supported by genomic and fossil data (Aves: Coraciiformes). Proceedings of the Royal Society B: Biological Sciences, 286(1910).

Mineva, T., Matanovic, I., Atanassov, P., Sougrati, M.T., Stievano, L., Clémancey, M., & Jaouen, F. (2019). Understanding Active Sites in Pyrolyzed Fe–N–C Catalysts for Fuel Cell Cathodes by Bridging Density Functional Theory Calculations and 57Fe Mössbauer Spectroscopy. ACS Catalysis, 9(10), 9359-9371.

Manjavacas, A., Zundel, L., & Sanders, S. (2019). Analysis of the Limits of the Near-Field Produced by Nanoparticle Arrays. ASC Nano, 13(9), 10682-10693.

Loring, T. (2019). Bulk spectrum and K-theory for infinite-area topological quasicrystals. Journal of Mathematical Physics, 60(8), 081903.

Loring, T. (2019). A Guide to the Bott Index and Localizer Index. ArXiv.

Palomino, L. M., & El-Genk, M. (2019). Friction factor correlation for hexagonal bundles of bare tubes/rods and with flat and scalloped walls. Nuclear Engineering and Design, 353, 110230.

Zhou, X., Jiang, B., & Guo, H. (2019). Dissociative Chemisorption of Methane on Stepped Ir(332) Surface: Density Functional Theory and Ab Initio Molecular Dynamics Studies. The Journal of Physical Chemistry C, 123(34), 20893-20902.

Rajendra Kurup, A., Ajith, M., & Martínez-Ramón, M. (2019). Semi-supervised facial expression recognition using reduced spatial features and Deep Belief Networks. Neurocomputing, 367, 188-197.

Hutchinson, M. I., Powell, A. J., Herrera, J., & Natvig, D. O. (2019). New Perspectives on the Distribution and Roles of Thermophilic Fungi. In S. M. Tiquia-Arashiro & M. Grube (Eds.), Fungi in Extreme Environments: Ecological Role and Biotechnological Significance, (pp. 59-80). Cham, Switzerland: Springer, Cham.

Liphardt, S. W., Kang, H. J., Dizney, L. J., Ruedas, L. A., Cook, J. A., & Yanagihara, R. (2019). Complex History of Codiversification and Host Switching of a Newfound Soricid-Borne Orthohantavirus in North America. Viruses, 11(7), 637.

Branham, M. S., Hsu, W. C., Yerci, S., Loomis, J., Boriskina, S. V., Hoard, B. R., & Chen, G. (2015). 15.7% Efficient 10‐μm‐Thick Crystalline Silicon Solar Cells Using Periodic Nanostructures. Advanced Materials, 27(13), 2182-2188.

Branham, M. S., Hsu, W. C., Yerci, S., Loomis, J., Boriskina, S. V., Hoard, B. R., & Chen, G. (2016). Empirical Comparison of Random and Periodic Surface Light‐Trapping Structures for Ultrathin Silicon Photovoltaics. Advanced Optical Materials, 4(6), 858-863.

Han, S. J., Ghosh, S., Abudayyeh, O. K., Hoard, B. R., Culler, E. C., Bonilla, J. E., & Han, S. E. (2016). Symmetry-breaking nanostructures on crystalline silicon for enhanced light trapping in thin film solar cells. Optics Express, 24(26), A1586-A1596.

Hoard, B., Jacobson, B., Manavi, K., and Tapia, L. (2015). Extending rule-based methods to model molecular geometry. 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Han, S. J., Ghosh, S., Hoard, B. R., Culler, E. C., Bonilla, J. E., Martin, E. J., & Han, S. E. (2016). Light trapping enhancement in thin film solar cells by breaking symmetry in nanostructures. 2016 IEEE 43rd Photovoltaic Specialists Conference (PVSC).

Ghosh, S., Han, S. J., Hoard, B. R., Culler, E. C., Bonilla, J. E., Martin, E. J., & Han, S. E. (2015). Symmetry-breaking nanostructures for enhanced light-trapping in thin film solar cells. 2015 IEEE 42nd Photovoltaic Specialists Conference (PVSC).

Sanders, S., Kort-Kamp, W. J. M., Dalvit, D. A. R., & Manjavacas, A. (2019). Nanoscale transfer of angular momentum mediated by the Casimir torque. Communications Physics, 2(1), 1-7.

Peysokhan, M., Keeney, J., & Mafi, A. (2019). Impact of spatial correlation in fluctuations of the refractive index on rogue wave generation probability. Optics Letters, 44(9), 2244-2247.

Murray, V. J., Zhou, L., Xu, C., Wang, Y., Guo, H., & Minton, T. K. (2019). Scattering Dynamics of Glycine, H2O, and CO2 on Highly Oriented Pyrolytic Graphite. The Journal of Physical Chemistry C, 123(6), 3605-3621.

Moeinian, A., Gür, F. N., Gonzalez-Torres, J., Zhou, L., Murugesan, V. D., Dashtestani, A. D., & Strehle, S. (2019). Highly Localized SERS Measurements Using Single Silicon Nanowires Decorated with DNA Origami-Based SERS Probe. Nano Letters, 19(2), 1061-1066.

Riley, C., De La Riva, A., Zhou, S., Wan, Q., Peterson, E., Artyushkova, K., & Datye, A. (2019). Synthesis of Nickel-Doped Ceria Catalysts for Selective Acetylene Hydrogenation. ChemCatChem, 11(5), 1526-1533.

Lu, D., Xie, C., Li, J., & Guo, H. (2019). Rate coefficients and branching ratio for multi-channel hydrogen abstractions from CH3OH by F. Chinese Journal of Chemical Physics, 32(1), 84-88.

Xie, C., Malbon, C. L., Xie, D., Yarkony, D. R., & Guo, H. (2019). Nonadiabatic Dynamics in Photodissociation of Hydroxymethyl in the 32A(3px) Rydberg State: A Nine-Dimensional Quantum Study. The Journal of Physical Chemistry A, 123(10), 1937-1944.

Al Taleb, A., Anemone, G., Zhou, L., Guo, H., & Farias, D. (2019). Diffraction of CH4 from a Metal Surface. The Journal of Physical Chemistry Letters, 10(7), 1574-1580.

Kunwar, D., Zhou, S., DeLaRiva, A., Peterson, E. J., Xiong, H., Pereira-Hernández, X. I., & Datye, A. K. (2019). Stabilizing High Metal Loadings of Thermally Stable Platinum Single Atoms on an Industrial Catalyst Support. ACS Catalysis, 9(5), 3978-3990.

Wu, Q., Zhou, L., & Guo, H. (2019). Steric Effects in CO Oxidation on Pt(111) by Impinging Oxygen Atoms Lead to an Exclusive Hot Atom Mechanism. The Journal of Physical Chemistry C, 123(16), 10509-10516.

Owen, C. J., Keyes, N. R., Xie, C., Guo, H., & Armentrout, P. B. (2019). Bond dissociation energy of Au2+: A guided ion beam and theoretical investigation. The Journal of Chemical Physics, 150(17), 174305.

Zhou, L., Kandratsenka, A., Campbell, C. T., Wodtke, A. M., & Guo, H. (2019). Origin of Thermal and Hyperthermal CO2 from CO Oxidation on Pt Surfaces: The Role of Post‐Transition‐State Dynamics, Active Sites, and Chemisorbed CO2. Angewandte Chemie International Edition, 58(21), 6916-6920.

Amarasinghe, C., Li, H., Perera, C. A., Besemer, M., van der Avoird, A., Groenenboom, G. C., & Suits, A. G. (2019). Differential Cross Sections for State-to-State Collisions of NO(v = 10) in Near-Copropagating Beams. The Journal of Physical Chemistry Letters, 10(10), 2422-2427.

Shuman, N. S., Ard, S. G., Sweeny, B. C., Pan, H., Viggiano, A. A., Keyes, N. R., & Armentrout, P. B. (2019). Au2+ cannot catalyze conversion of methane to ethene at low temperature. Catalysis Science & Technology, 9(11), 2767-2780.!divAbstract.

He, C., Sankarasubramanian, S., Matanovic, I., Atanassov, P., & Ramani, V. (2019). Understanding the Oxygen Reduction Reaction Activity and Oxidative Stability of Pt Supported on Nb‐Doped TiO2. ChemSusChem, 12(15), 3468-3480.

Malins, J. B., Obenberger, K. S., Taylor, G. B., & Dowell, J. (2019). Three Dimensional Mapping of Lightning Produced Ionospheric Reflections. Radio Science.

Kent, J., Dowell, J., Beardsley, A., Thyagarajan, N., Taylor, G.B., & Bowman, J. 2019. A Real-Time, All-Sky, High Time Resolution, Direct Imager for the Long Wavelength Array.  Monthly Notices of the Royal Astronomical Society, 486, 5052

I. Matanovic, S. Maurya, E. J. Park, J. Y. Jeon, C. Bae, and Y. S. Kim, Adsorption of Polyaromatic Backbone Impacts the Performance of the Anion Exchange Membrane Fuel cellsChem. Mater., 31, 4195-4204(2019).

D. Li, I. Matanovic, A. S. Lee, C. Fujimoto, H. T. Chung, and Y. S. Kim, Phenyl Oxidation Limits the Durability of Alkaline Membrane Water ElectrolyzerACS Appl. Mater. Interfaces11, 9696−9701 (2019). 

A. S. Lee, Y.-K. Choe, I. Matanovic, Y. S. Kim, The energetics of phosphoric acid interactions reveals a new acid loss mechanismJ. Mater. Chem. A,7, 9867 (2019).

Andersen, Michael J., Jenna M. McCullough, Nicholas R. Friedman, A. Townsend Peterson, Robert G. Moyle, Leo Joseph, and Árpád S. Nyári. "Ultraconserved elements resolve genus-level relationships in a major Australasian bird radiation (Aves: Meliphagidae)." Emu-Austral Ornithology (2019): 1-15.

Vangara, Raviteja, Kahlil Stoltzfus, Mary R. York, Frank B. van Swol, and Dimiter N. Petsev. "Coulombic and non-coulombic effects in charge-regulating electric double layers." Materials Research Express (2019).

McCullough, J.M., Joseph, L., Moyle, R.G. and Andersen, M.J., 2019. Ultraconserved elements put the final nail in the coffin of traditional use of the genus Meliphaga (Aves: Meliphagidae). Zoologica Scripta.

Nayak, S.K., Benavidez, A.D., Matanovic, I. and Garzon, F.H., 2019. Thermochemical Analysis of Mo-CH System for Synthesis of Molybdenum Carbides. Thermochimica Acta.

Yang, Y., Lu, J., Manjavacas, A., Luk, T.S., Liu, H., Kelley, K., Maria, J.P., Sinclair, M.B., Ghimire, S. and Brener, I., 2019. High-harmonic generation from an epsilon-near-zero material. arXiv preprint arXiv:1902.03539.

Fazel, M., Wester, M.J., Mazloom-Farsibaf, H., Meddens, M.B., Eklund, A., Schlichthaerle, T., Schueder, F., Jungmann, R. and Lidke, K.A., 2019. Bayesian Multiple Emitter Fitting using Reversible Jump Markov Chain Monte Carlo. bioRxiv, p.530261.

Han Zhang, Brandon Schmandt, Application of Ps Scattering Kernels to Imaging the Mantle Transition Zone With Receiver Functions, AGU100.

El-Genk, M.S., Schriener, T.M. and Breedlove, J.J., 2019. Thermal Analyses of Heat Source Assembly for a Dual Loop, Turbo-Brayton Radioisotope Power System. Thermal Science and Engineering Progress.

Poe, S. and Anderson, C.G., 2019. The existence and evolution of morphotypes in Anolis lizards: coexistence patterns, not adaptive radiations, distinguish mainland and island faunas. PeerJ, 6, p.e6040.

Pérez, A.M., Lopez, O. and Poroseva, S.V., 2019. Free-Vortex Wake and CFD Simulation of a Small Rotor for a Quadcopter at Hover. In AIAA Scitech 2019 Forum (p. 0597).


S. Mayura, S. Noh, I. Matanovic, E J. Park, C. Narvaez Villarrubia, J. Han, C. Bae, and Y. S. Kim, Rational design of polyaromatic ionomers for alkaline membrane fuel cells with >1 Wcm-2power densityEnergy Environ. Sci., 11, 3283-3291 (2018).

S. Maurya, J. H Dumont, C. N. Villarrubia, I. Matanovic, D. Li, Y. S. Kim, S. Noh, J. Han, C. Bae, H. A. Miller, C. H. Fujimoto, D. R. Dekel, Surface Adsorption Affects the Performance of Alkaline Anion- Exchange Membrane Fuel CellsACS Catalysis, 8, 9429-9439 (2018).

D. Li, T. Chung, S. Maurya, I. Matanovic and Y. S. Kim, Impact of ionomer adsorption on alkaline hydrogen oxidation activity and fuel cell performanceCurr. Opin. in Electrochem., 12, 189-195 (2018).

Y. Chen, I. Matanovic, E. Weiler, P. Atanassov, K. Artyushkova, Mechanism of Oxygen Reduction Reaction on Transition Metal-Nitrogen Carbon Catalysts: Establishing the Role of Nitrogen- containing Active SitesACS Appl. Energy Mater, 1, 5948-5953 (2018).

Y. C. Liu, I. Matanovic, D. P. Hickey, S. D. Minteer, P. Atanassov, S. C. Baron, Cascade Kinetics of an Artificial Metabolon by Molecular Dynamics and Kinetic Monte CarloACS Catalysis, 8,7719-7726 (2018).

T. Asset, M. Padilla, A. J. Roy, I. Matanovic, M. Chatenet, F. Millard, P. Atanassov, Design of Pd-Pb Catalysts for Glycerol and Ethylene Glycol Electrooxidation in Alkaline MediumElectrocatalysis, 9, 480-485 (2018).

I. Matanovic and F. Garzon, Nitrogen electroreduction and hydrogen evolution on cubic molybdenum carbide, a density functional theory studyPhys. Chem. Chem. Phys., 20, 14679-14687 (2018).

S. Rojas-Carbonell, K. Artyushkova, A. Serov, C. Santoro, I. Matanovic, P. Atanassov, Effect of pH on the Activity of Platinum Metal-Free Catalysts in the Oxygen Reduction ReactionACS Catalysis, 8, 3041-3053 (2018) .

I. Matanovic, K. Artyushkova, and P. Atanassov, Understanding PGM-free catalysts by linking density functional theory calculations and structural analysis: Perspectives and challengesCurr. Opin. In Electrochem.,9, 137-144 (2018).

Y. Chen, K. Artyushkova, S. Rojas-Carbonell, A. Serov, I. Matanovic, C. Santoro, T. Asset, P. Atanassov, Inhibition of Surface Chemical Moieties by Tris (hydroxymethyl) aminomethane: A Key to Understanding Oxygen Reduction on Iron–Nitrogen–Carbon CatalystsACS Applied Energy Materials1 (50), 1942-1949 (2018).

Buddenborg, Sarah K., Bishoy Kamel, Ben Hanelt, Lijing Bu, Si-Ming Zhang, Gerald M. Mkoji, and Eric S. Loker. "The in vivo transcriptome of Schistosoma mansoni in two prominent vector species, Biomphalaria pfeifferi and B. glabrata." bioRxiv(2018): 476325.

Yin, Guohua, Sui Sheng T. Hua, Kayla K. Pennerman, Jiujiang Yu, Lijing Bu, Richard T. Sayre, and Joan W. Bennett. "Genome sequence and comparative analyses of atoxigenic Aspergillus flavus WRRL 1519." Mycologia 110, no. 3 (2018): 482-493.

Zhang, Si-Ming, Lijing Bu, Martina R. Laidemitt, Lijun Lu, Martin W. Mutuku, Gerald M. Mkoji, and Eric S. Loker. "Complete mitochondrial and rDNA complex sequences of important vector species of Biomphalaria, obligatory hosts of the human-infecting blood fluke, Schistosoma mansoni." Scientific reports 8, no. 1 (2018): 7341.

Sanders, S., May, A., Alabastri, A. and Manjavacas, A., 2018. Extraordinary Enhancement of Quadrupolar Transitions Using Nanostructured Graphene. ACS Photonics, 5(8), pp.3282-3290.

Gisewhite, D.R., Yang, J., Williams, B.R., Esmail, A., Stein, B., Kirk, M.L. and Burgmayer, S.J., 2018. Implications of Pyran Cyclization and Pterin Conformation on Oxidized Forms of the Molybdenum Cofactor. Journal of the American Chemical Society, 140(40), pp.12808-12818.

Chen, T., Lehr, J.M., Lavrova, O. and Martínez-Ramón, M., 2018. Distribution feeder-level day-ahead peak load forecasting methods and comparative study. IET Generation, Transmission & Distribution, 12(13), pp.3270-3278.

Van Swol, F.B. and Petsev, D.N., 2018. Solution Structure Effects on the Properties of Electric Double Layers with Surface Charge Regulation Assessed by Density Functional Theory. Langmuir, 34(46), pp.13808-13820.

Mclean, B.S., Bell, K.C., Allen, J.M., Helgen, K.M. and Cook, J.A., 2018. Impacts of Inference Method and Data set Filtering on Phylogenomic Resolution in a Rapid Radiation of Ground Squirrels (Xerinae: Marmotini). Systematic biology, 68(2), pp.298-316.

Kafle, B., Gieri, P., Kookhaee, H., Tesema, T.E., Haq, S., Manjavacas, A. and Habteyes, T.G., 2018. Robust Charge Transfer Plasmons in Metallic Particle–Film Systems. ACS Photonics, 5(10), pp.4022-4029.

Cowen, B.J., El-Genk, M.S., Hattar, K. and Briggs, S.A., 2018. A study of irradiation effects in TiO2 using molecular dynamics simulation and complementary in situ transmission electron microscopy. Journal of Applied Physics, 124(9), p.095901.

Zundel, L. and Manjavacas, A., 2018. Finite-size effects on periodic arrays of nanostructures. Journal of Physics: Photonics, 1(1), p.015004.

Cowen, B.J. and El-Genk, M.S., 2018. Characterization of radiation damage in TiO2 using molecular dynamics simulations. Modelling and Simulation in Materials Science and Engineering, 26(8), p.085005.

Shi, Y. and Lee, J.H., 2018. Sample size calculations for group randomized trials with unequal group sizes through Monte Carlo simulations. Statistical methods in medical research, 27(9), pp.2569-2580.

Barrow, L.N., Allen, J.M., Huang, X., Bensch, S. and Witt, C.C., 2018. Genomic sequence capture of haemosporidian parasites: Methods and prospects for enhanced study of host‐parasite evolution. Molecular ecology resources.

Robinson, A.J. and Natvig, D.O., 2018. Diverse members of the Xylariales lack canonical mating-type regions. Fungal Genetics and Biology.

Colella, J.P., Wilson, R.E., Talbot, S.L. and Cook, J.A., 2018. Implications of introgression for wildlife translocations: the case of North American martens. Conservation Genetics, pp.1-14.

van Swol, Frank B., and Dimiter N. Petsev. "Solution Structure Effects on the Properties of Electric Double Layers with Surface Charge Regulation Assessed by Density Functional Theory" Langmuir 34, no. 46 (2018): 13808-13820.

Manjavacas, A., 2018. Controlling light with metallic nanostructures.Bulletin of the American Physical Society.

Heydarian, H., Schueder, F., Strauss, M.T., van Werkhoven, B., Fazel, M., Lidke, K.A., Jungmann, R., Stallinga, S. and Rieger, B., 2018. Template-free 2D particle fusion in localization microscopy.Nature Methods, p.1.

Dunning, D.J. and Marts, W.P., 2018. Adaptive Mesh Refinement in the Fastlane (No. LA-UR-18-28159). Los Alamos National Lab.(LANL), Los Alamos, NM (United States).

Estrada, T., Benson, J., Carrillo-Cabada, H., Razavi, A.M., Cuendet, M.A., Weinstein, H., Deelman, E. and Taufer, M., 2018, August. Graphic Encoding of Macromolecules for Efficient High-Throughput Analysis. In Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (pp. 315-324). ACM.

Maurya, S., Dumont, J., Narvaez Villarrubia, C., Matanovic, I., Li, D., Kim, Y.S., Noh, S., Han, J., Bae, C., Miller, H.A. and Fujimoto, C.H., 2018. Surface Adsorption Affects the Performance of Alkaline Anion-Exchange Membrane Fuel Cells. ACS Catalysis.

Abaie, B., Peysokhan, M., Zhao, J., Antonio-Lopez, J.E., Amezcua-Correa, R., Schülzgen, A. and Mafi, A., 2018. Disorder-induced high-quality wavefront in an Anderson localizing optical fiber. Optica, 5(8), pp.984-987.

Abaie, B. and Mafi, A., 2018. Modal area statistics for transverse Anderson localization in disordered optical fibers. Optics Letters, 43(16), pp.3834-3837.

Zhou, L., Jiang, B., Alducin, M. and Guo, H., 2018. Communication: Fingerprints of reaction mechanisms in product distributions: Eley-Rideal-type reactions between D and CD3/Cu (111). The Journal of Chemical Physics, 149(3), p.031101.

Chen, X., Peterson, M., Benson, J., Taufer, M. and Estrada, T., 2018. KeyBin2: Distributed Clustering for Scalable and In-Situ Analysis.

Benson, B.W., Iyer, S.R., Kemper, K.J. and Zhao, J., 2018. Director Networks and Credit Ratings. Financial Review, 53(2), pp.301-336.

El-Genk, M.S., Talaat, K. and Cowen, B.J., 2018. Thermal conductivity of silicon using reverse non-equilibrium molecular dynamics. Journal of Applied Physics, 123(20), p.205104.

Cowen, B.J. and El-Genk, M.S., 2018. Point defects production and energy thresholds for displacements in crystalline and amorphous SiC. Computational Materials Science, 151, pp.73-83.

Xie, C., Liu, X. and Guo, H., 2018. State-to-State Quantum Dynamics of the H+ LiF→ Li+ HF Reaction on An Accurate Ab Initio Potential Energy Surface. Chemical Physics.

Hoover, J.H., Coker, E., Barney, Y., Shuey, C. and Lewis, J., 2018. Spatial clustering of metal and metalloid mixtures in unregulated water sources on the Navajo Nation–Arizona, New Mexico, and Utah, USA. Science of The Total Environment.

Zhou, S., Lin, S. and Guo, H., 2018. First Principles Insights into Ammonia Decomposition Catalyzed by Ru Clusters Anchored on Carbon Nanotubes: Size Dependence and Interfacial Effects. The Journal of Physical Chemistry C.

Sanders, Stephen, and Alejandro Manjavacas. "Analysis of the Limits of the Local Density of Photonic States Near Nanostructures." ACS Photonics (2018).

Baur, S., Sanders, S. and Manjavacas, A., 2018. Hybridization of Lattice Resonances. ACS nano.

Vangara, R., F. van Swol, and D. N. Petsev. "Solvophilic and solvophobic surfaces and non-Coulombic surface interactions in charge regulating electric double layers." The Journal of Chemical Physics 148, no. 4 (2018): 044702.

Lu, Q., Hecker, J.P. and Moses, M.E., 2018. Multiple-place swarm foraging with dynamic depots. Autonomous Robots, pp.1-18.


I. Matanovic, H. Taek Chungand Y.-S. Kim, Benzene Adsorption: A Significant Inhibitor for the Hydrogen Oxidation Reaction in Alkaline Conditions, 8(19), 4918–4924 (2017).

D. Sebastián, A. Serov, I. Matanovic, K. Artyushkova, P. Atanassov, A.S. Aricò, V. Baglio, Insights on the extraordinary tolerance to alcohols of Fe-N-C cathode catalysts in highly performing direct alcohol fuel cellsNano Energy, 34, 195-204 (2017).

M. Kodali, C. Santoro, A. Serov, S. Kabir, K. Artyushkova, I. Matanovic, P. Atanassov, Air Breathing Cathodes for Microbial Fuel Cell using Mn-, Fe-, Co- and Ni-containing Platinum Group Metal-free CatalystsElectrochimica Acta231, 115-124 (2017).

K. Artyushkova, I. Matanovic, B. Halevi, P. Atanassov, Oxygen Binding to Active Sites of Fe-N-C ORR Electrocatalysts Observed by Ambient-Pressure XPSJ. Phys. Chem. C, 121 (5), 2836-2843 (2017).

Perry III, S. Kabir, I. Matanovic, M. S. Chavez, K. Artyushkova, A. Serov and P. Atanassov, Novel Hybrid Catalyst for the Oxidation of Organic Acids: Pd Nanoparticles Supported on Mn-N-3D-graphene NanosheetsChemElectroChem, 4, 1-10 (2017).

S. Babanova, I. Matanovic, J. Cornejo, O. Bretschger, K. Nealson, and P. Atanassov, Outer membrane cytochromes/flavin interactions in Shewanella spp.—A molecular perspective, Biointerphases12, 021004 (2017).

Manjavacas, A., Fenollosa, R., Rodriguez, I., Jiménez, M.C., Miranda, M.A. and Meseguer, F., 2017. Magnetic light and forbidden photochemistry: the case of singlet oxygen. Journal of Materials Chemistry C, 5(45), pp.11824-11831.

Abdellaoui, S., Chavez, M.S., Matanovic, I., Stephens, A.R., Atanassov, P. and Minteer, S.D., 2017. Hybrid molecular/enzymatic catalytic cascade for complete electro-oxidation of glycerol using a promiscuous NAD-dependent formate dehydrogenase from Candida boidinii. Chemical Communications, 53(39), pp.5368-5371.

Byrne, C.F., 2017. Supporting Data for a Numerical Investigation of the Implications of Altered Channel-Floodplain Connectivity on Hydrodynamic Flood Wave Processes.

Wester, M.J., Lin, J. and Neumann, A.K., 2017. A computational model for regulation of nanoscale glucan exposure in Candida albicans. PloS one, 12(12), p.e0188599.

Qi, X., Jau, Y.Y. and Deutsch, I.H., 2017. Enhanced cooperativity for quantum nondemolition measurement induced spin squeezing of atoms coupled to a nanophotonic waveguide. arXiv preprint arXiv:1712.02916.

Manavi, K., Tashakkori, S. and Tapia, L., 2017, August. Gaussian Mixture Models with Constrained Flexibility for Fitting Tomographic Tilt Series. In Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (pp. 710-715). ACM.

Jacobson, B., David, J.C.L., Malone, M.C., Manavi, K., Atlas, S.R. and Tapia, L., 2017, August. Geometric Sampling Framework for Exploring Molecular Walker Energetics and Dynamics. In Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (pp. 704-709). ACM.

Colmenares, J.D., Poroseva, S., Peet, Y.T. and Murman, S.M., 2017. DNS of a Spatially Developing Turbulent Mixing Layer from Co-flowing Laminar Boundary Layers. In 47th AIAA Fluid Dynamics Conference (p. 3641)

Xie, C., Malbon, C.L., Yarkony, D.R. and Guo, H., 2017. Dynamic mapping of conical intersection seams: A general method for incorporating the geometric phase in adiabatic dynamics in polyatomic systems. The Journal of chemical physics, 147(4), p.044109.

Vangara, R., van Swol, F. and Petsev, D.N., 2017. Ionic solvation and solvent-solvent interaction effects on the charge and potential distributions in electric double layers. The Journal of Chemical Physics, 147(21), p.214704.

Boyd, S.P., Hummatov, R., Kim, G.B., Hall, J.A., Cantor, R. and Friedrich, S., 2017. Integrated SQUID/Sensor Metallic Magnetic Microcalorimeter for Gamma-Ray Spectroscopy (No. LLNL-CONF-741434). Lawrence Livermore National Lab.(LLNL), Livermore, CA (United States).

Andersen, M.J., McCullough, J.M., Mauck, W.M., Smith, B.T. and Moyle, R.G., 2017. A phylogeny of kingfishers reveals an Indomalayan origin and elevated rates of diversification on oceanic islands. Journal of Biogeography.

Zundel, L., Martinez-Herrero, R. and Manjavacas, A., 2017. Flat top surface plasmon polariton beams. Optics Letters, 42(20), pp.4143-4146.

Cowen, B.J. and El-Genk, M., 2017. Directional dependence of the threshold displacement energies in metal oxides. Modelling and Simulation in Materials Science and Engineering.

Peysokhan, M., Mobini, E., Keeney, J. and Mafi, A., 2017, September. Optical rogue wave generation in dielectrics with correlated fluctuations of refractive index. In Frontiers in Optics (pp. JW4A-111). Optical Society of America.

Chen, X., Benson, J. and Estrada, T., 2017, September. keybin: Key-Based Binning for Distributed Clustering. In Cluster Computing (CLUSTER), 2017 IEEE International Conference on (pp. 572-581). IEEE.

Foteinopoulou, S. and Devarapu, G.C.R., 2017, July. Perfectly asymmetric reflection enables unidirectional emission in a phonon-polariton (reststrahlen-band) material platform. In Transparent Optical Networks (ICTON), 2017 19th International Conference on (pp. 1-4). IEEE.

Abaie, B., Mobini, E., Karbasi, S., Hawkins, T., Ballato, J., Mafi, A., Mafi, A., Abaie, B., Mobini, E., Karbasi, S. and Hawkins, T., Random lasing in an Anderson localizing optical fiber Running title: Random lasing in an Anderson localizing fiber

Alanzi, A.R. and Degnan, J.H., 2017. Inferring rooted species trees from unrooted gene trees using approximate Bayesian computation. Molecular Phylogenetics and Evolution.

Alabastri, A., Malerba, M., Calandrini, E., Manjavacas, A., De Angelis, F., Toma, A. and Proietti Zaccaria, R., 2017. Controlling the heat dissipation in temperature-matched plasmonic nanostructures. Nano Letters.

Gustafson, G.T. and Miller, K.B., 2017. Systematics and evolution of the whirligig beetle tribe Dineutini (Coleoptera: Gyrinidae: Gyrininae). Zoological Journal of the Linnean Society, p.zlw014.

Zhou, L., Johnson, R., Habteyes, T. and Guo, H., 2017. Adsorption of methylene blue and its N-demethylated derivatives on the (111) face of coinage metals: The importance of dispersion interactions. The Journal of Chemical Physics, 146(16), p.164701.

Zundel, L. and Manjavacas, A., 2017. Spatially resolved optical sensing using graphene nanodisk arrays. ACS Photonics.

Ard, S.G., Shuman, N.S., Martinez, O., Keyes, N.R., Viggiano, A.A., Guo, H. and Troe, J., 2017. Temperature and Pressure Dependences of the Reactions of Fe+ with Methyl Halides CH3X (X= Cl, Br, I): Experiments and Kinetic Modeling Results. The Journal of Physical Chemistry A.

Cowen, B.J. and El-Genk, M.S., 2017. Estimates of point defect production in α-quartz using molecular dynamics simulations. Modelling and Simulation in Materials Science and Engineering, 25(5), p.055001.

Silantyev, D.A., Lushnikov, P.M. and Rose, H.A., 2017. Langmuir wave filamentation in the kinetic regime. I. Filamentation instability of Bernstein-Greene-Kruskal modes in multidimensional Vlasov simulations. Physics of Plasmas, 24(4), p.042104.

Mahajan, A., Youssef, L.A., Cleyrat, C., Grattan, R., Lucero, S.R., Mattison, C.P., Erasmus, M.F., Jacobson, B., Tapia, L., Hlavacek, W.S. and Schuyler, M., 2017. Allergen Valency, Dose, and FcεRI Occupancy Set Thresholds for Secretory Responses to Pen a 1 and Motivate Design of Hypoallergens. The Journal of Immunology, 198(3), pp.1034-1046.

Abaie, B., Mobini, E., Karbasi, S., Hawkins, T., Ballato, J., Mafi, A., Mafi, A., Abaie, B., Mobini, E., Karbasi, S. and Hawkins, T., Random lasing in an Anderson localizing optical fiber Running title: Random lasing in an Anderson localizing fiber.

Reid, K.M., Patel, S., Robinson, A.J., Bu, L., Jarungsriapisit, J., Moore, L.J. and Salinas, I., 2017. Salmonid alphavirus infection causes skin dysbiosis in Atlantic salmon (Salmo salar L.) post-smolts. PloS one, 12(3), p.e0172856.

Abaie, B. and Mafi, A., 2017, February. Scaling analysis of Anderson localizing optical fibers. In Proc. of SPIE Vol (Vol. 10112, pp. 101121R-1).

Dixon, D.S., Mozumder, P., Vásquez, W.F. and Gladwin, H., 2017. Heterogeneity Within and Across Households in Hurricane Evacuation Response. Networks and Spatial Economics, pp.1-36.

Stone, M.C., Byrne, C.F. and Morrison, R.R., 2017. Evaluating the Impacts of Hydrologic and Geomorphic Alterations on Floodplain Connectivity. Ecohydrology.

Kolb, B., Luo, X., Zhou, X., Jiang, B. and Guo, H., 2017. High-dimensional Atomistic Neural Network Potentials for Molecule-Surface Interactions: HCl Scattering from Au (111). The Journal of Physical Chemistry Letters.

Vangara, R., D. C. R. Brown, F. van Swol, and D. N. Petsev. "Electrolyte solution structure and its effect on the properties of electric double layers with surface charge regulation." Journal of colloid and interface science 488 (2017): 180-189.


I. Matanovic, K. Artyushkova, M. B. Strand, M. J. Dzara, S. Pylypenko, and P. Atanassov, Core Level Shifts of Hydrogenated Pyridinic and Pyrrolic Nitrogen in the Nitrogen-Containing Graphene-Based Electrocatalysts: In-Plane vs Edge DefectsJ. Phys. Chem. C120(51), 29225-29232 (2016).

T. Asset, A. Ray, T. Sakamoto, M. Padilla, I. Matanovic, K. Artyushkova, A. Serov, F. Mailllard, M. Chatenet, K. Asazawa, and P. Atanassov, Highly active and selective nickel molybdenum catalysts for direct hydrazine fuel cellsElectrochim Acta, 2015, 420-426 (2016).

H. Taek Chung, Y.-K. Choe, U. Martinez, J. H. Dumont, A. Mohanty, C. Bae, I. Matanovic, Y.S. Kim, Effect of Organic Cations on Hydrogen Oxidation Reaction of Carbon Supported PlatinumJ. Electrochem. Soc., 163,14, F1503-F1509 (2016).

H. Taek Chung, U. Martinez, I. Matanovic, and Y-S. Kim, Cation–Hydroxide–Water Coadsorption Inhibits the Alkaline Hydrogen Oxidation ReactionJ. Phys. Chem. Lett., 7(22), 4464–4469 (2016).

T. Reshetenko, A. Serov, K. Artyushkova, I. Matanovic, S. Stariha and P. Atanassov, Tolerance of non-platinum group metals cathodes proton exchange membrane fuel cells to air contaminantsJ. Power Sources, 324, 556 (2016).

A. Perry III, S. Babanova, I. Matanovic, A. Neumman, A. Serov, K. Artyushkova, and P. Atanassov, Evaluation of Pt Alloys as Electrocatalysts for Oxalic Acid Oxidation: A Combined Experimental and Computational Study, J.Electrochem. Soc., 163, H787-H795 (2016).

I. Matanovic, S. Babanova, M. S. Chavez, and P. Atanassov, Protein-Support Interactions for Rationally Designed Bilirubin Oxidase Based Cathode: a Computational StudyJ. Phys. Chem. B, 120, 3634–3641 (2016).

R. M. E. Hjelm, K. E. Garcia, S. Babanova, K. Artyushkova, I. Matanovic, S. Banta, and P. Atanassov, Functional Interfaces for Biomimetic Energy Harvesting: CNTs-DNA Matrix for Enzyme AssemblyBiochim. Biophys. Acta,1857, 612-620 (2016).

Serov, T. Asset, M. Padilla, I. Matanovic, U. Martinez, A. Roy, K. Artyushkova, M. Chatenet, F. Maillard, D. Bayer, C. Cremers and P. Atanassov, Highly-active Pd–Cu electrocatalysts for oxidation of ubiquitous oxygenated fuels, Appl. Catal. B, 191, 76-85 (2016).

Coutsias, E.A., Lexa, K.W., Wester, M.J., Pollock, S.N. and Jacobson, M.P., 2016. Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics. Journal of Chemical Theory and Computation, 12(9), pp.4674-4687.

Xie, C., Jiang, B., Yang, M. and Guo, H., 2016. State-to-State Mode Specificity in F+ CHD3→ HF/DF+ CD3/CHD2 Reaction. The Journal of Physical Chemistry A, 120(33), pp.6521-6528.

Manjavacas, A., 2016. Anisotropic optical response of nanostructures with balanced gain and loss. ACS Photonics, 3(7), pp.1301-1307.

Benson, B.W., Iyer, S.R., Kemper, K. and Zhao, J., 2016. Director Networks and Credit Ratings.

Qi, X., Baragiola, B.Q., Jessen, P.S. and Deutsch, I.H., 2016. Dispersive response of atoms trapped near the surface of an optical nanofiber with applications to quantum nondemolition measurement and spin squeezing. Physical Review A, 93(2), p.023817.

Shahbazikhah, P., Kalivas, J.H., Andries, E. and O'Loughlin, T., 2016. Using the L1 norm to select basis set vectors for multivariate calibration and calibration updating. Journal of Chemometrics.

Martin, T.D., Hill, E.H., Whitten, D.G., Chi, E.Y. and Evans, D.G., 2016. Oligomeric Conjugated Polyelectrolytes Display Site-Preferential Binding to an MS2 Viral Capsid. Langmuir, 32(47), pp.12542-12551.

Song, H., Li, A. and Guo, H., 2016. Rotational and Isotopic Effects in the H2+ OH+→ H+ H2O+ Reaction. The Journal of Physical Chemistry A.

Ard, S.G., Johnson, R.S., Martinez, O., Shuman, N.S., Guo, H., Troe, J. and Viggiano, A.A., 2016. Analysis of the Pressure and Temperature Dependence of the Complex-Forming Bimolecular Reaction CH3OCH3+ Fe+. The Journal of Physical Chemistry A.

Ox, J., 2016. Color Systems are Categories that Carry Meaning in Visualizations: A Conceptual Metaphor Theory Approach. Electronic Imaging, 2016(16), pp.1-9.

Manavi, K., Jacobson, B., Hoard, B. and Tapia, L., 2016. Influence of model resolution on geometric simulations of antibody aggregation. Robotica, 34(08), pp.1754-1776.

Hoard, B., Jacobson, B., Manavi, K. and Tapia, L., 2016. Extending rule-based methods to model molecular geometry and 3D model resolution. BMC Systems Biology, 10(2), p.48.

Vangara, R., Brown, D.C.R., van Swol, F. and Petsev, D.N., 2017. Electrolyte solution structure and its effect on the properties of electric double layers with surface charge regulation. Journal of Colloid and Interface Science, 488, pp.180-189.

Tencate, A., Kalivas, J.H. and Andries, E., 2016. Penalty processes for combining roughness and smoothness in spectral multivariate calibration. Journal of Chemometrics, 30(4), pp.144-152.

Zhao, B., Sun, Z. and Guo, H., 2016. A reactant-coordinate-based approach to state-to-state differential cross sections for tetratomic reactions. The Journal of Chemical Physics, 145(18), p.184106.

Cavanagh, J.F. and Castellanos, J., 2016. Identification of canonical neural events during continuous gameplay of an 8-bit style video game. NeuroImage, 133, pp.1-13.

Han, H., Alday, B., Shuman, N.S., Wiens, J.P., Troe, J., Viggiano, A.A. and Guo, H., 2016. Calculations of the active mode and energetic barrier to electron attachment to CF 3 and comparison with kinetic modeling of experimental results. Physical Chemistry Chemical Physics, 18(45), pp.31064-31071.

Cowen, B.J. and El-Genk, M.S., 2016. Probability-based threshold displacement energies for oxygen and silicon atoms in α-quartz silica. Computational Materials Science, 117, pp.164-171.

Kerketta, R., Halász, Á.M., Steinkamp, M.P., Wilson, B.S. and Edwards, J.S., 2016. Effect of spatial inhomogeneities on the membrane surface on receptor dimerization and signal initiation. Frontiers in Cell and Developmental Biology, 4.

Chen, T., Lehr, J., Lavrova, O. and Martinez-Ramonz, M., 2016, July. Distribution-level peak load prediction based on Bayesian Additive Regression Trees. In Power and Energy Society General Meeting (PESGM), 2016 (pp. 1-5). IEEE.

Song, H., Lu, Y., Li, J., Yang, M. and Guo, H., 2016. Mode specificity in the OH+ CHD3 reaction: Reduced-dimensional quantum and quasi-classical studies on an ab initio based full-dimensional potential energy surface. The Journal of chemical physics, 144(16), p.164303.

Manjavacas, A., Rodríguez-Fortuño, F.J., de Abajo, F. and Zayats, A.V., 2016. Lateral Casimir force on a rotating particle near a planar surface. arXiv preprint arXiv:1612.03733.

Cowen, B.J. and El-Genk, M.S., 2016. Bond-order reactive force fields for molecular dynamics simulations of crystalline silica. Computational Materials Science, 111, pp.269-276.

Lin, J., Wester, M.J., Graus, M.S., Lidke, K.A. and Neumann, A.K., 2016. Nanoscopic cell-wall architecture of an immunogenic ligand in Candida albicans during antifungal drug treatment. Molecular biology of the cell, 27(6), pp.1002-1014.

Martinez-Herrero, R. and Manjavacas, A., 2016. Basis for paraxial surface-plasmon-polariton packets. Physical Review A, 94(6), p.063829.

Moradi, C.P., Xie, C., Kaufmann, M., Guo, H. and Douberly, G.E., 2016. Two-center three-electron bonding in ClNH3 revealed via helium droplet infrared laser Stark spectroscopy: Entrance channel complex along the Cl+ NH3→ ClNH2+ H reaction. The Journal of chemical physics, 144(16), p.164301.

Abaie, B., Mobini, E., Karbasi, S., Hawkins, T., Ballato, J. and Mafi, A., 2016. Random lasing in an Anderson localizing optical fiber. arXiv preprint arXiv:1612.03835.

Kolb, B. and Guo, H., 2016. Communication: Energy transfer and reaction dynamics for DCl scattering on Au (111): An ab initio molecular dynamics study.

Lin, S., Gao, H.W. and Peng, Z., 2016, May. High-fidelity, high-performance full-wave computational algorithms for intra-system EMI analysis of IC and electronics. In Signal and Power Integrity (SPI), 2016 IEEE 20th Workshop on (pp. 1-4). IEEE.

Lushnikov, P.M., 2016, September. Nonlinear combining of multiple laser beams in multimode optical fiber. In Australian Conference on Optical Fibre Technology (pp. JM6A-15). Optical Society of America.

Shao, Y., Wang, S. and Peng, Z., 2016, March. Hierarchical modeling and scalable algorithms for in-situ characterization of 3D IC packages. In 2016 IEEE/ACES International Conference on Wireless Information Technology and Systems (ICWITS) and Applied Computational Electromagnetics (ACES) (pp. 1-2). IEEE.

Shi, Y. and Lee, J.H., 2016. Sample size calculations for group randomized trials with unequal group sizes through Monte Carlo simulations. Statistical Methods in Medical Research, p.0962280216682775.

Wheeler, L.B., Galewsky, J., Herold, N. and Huber, M., 2016. Late Cenozoic surface uplift of the southern Sierra Nevada (California, USA): A paleoclimate perspective on lee-side stable isotope paleoaltimetry. Geology, 44(6), pp.451-454.

Winner, K.R.K., Steinkamp, M.P., Lee, R.J., Swat, M., Muller, C.Y., Moses, M.E., Jiang, Y. and Wilson, B.S., 2016. Spatial modeling of drug delivery routes for treatment of disseminated ovarian cancer. Cancer research, 76(6), pp.1320-1334.

Fleharty, M. E., van Swol, F., & Petsev, D. N. (2016). Solvent Role in the Formation of Electric Double Layers with Surface Charge Regulation: A Bystander or a Key Participant?Physical Review Letters116(4), 048301.

Lin, J., Wester, M. J., Graus, M. S., Lidke, K. A., & Neumann, A. K. (2016). Nanoscopic cell wall architecture of an immunogenic ligand in Candida albicans during antifungal drug treatmentMolecular Biology of the Cell, mbc-E15.

Publications archive, 2008-2015