Los Alamos National Laboratory

Los Alamos National Laboratory

Delivering science and technology to protect our nation and promote world stability

2016-2017 Los Alamos National Laboratory Biological and Environmental Research Publications

Peer-reviewed publications sponsored by the DOE Office of Science, Office of Biological and Environmental Research.

2017

  • Chacon, L., et al., (LANL authors:  G. Chen, D. A. Knoll, C. Newman, H. Park, W. Taitano, G. Womeldorff) 2017:  Multiscale high-order/low-order (HOLO) algorithms and applications.  J. Comput. Phys., 330, 21-45.  https://doi.org/10.1016/j.jcp.2016.10.069
  • Chung, Y. A., R. L. Sinsabaugh, C. R. Kuske, S. C. Reed, and J. A. Rudgers, 2017: Spatial variation in edaphic characteristics is a stronger control than nitrogen inputs in regulating soil microbial effects on a desert grass. J. Arid Environ., 142, 59-65.  https://doi.org/10.1016/j.jaridenv.2017.03.005
  • Duarte, P., et al., (LANL authors: N. Jeffery, S. M. Elliott, E. C. Hunke, A. K. Turner) 2017: Sea ice thermohaline dynamics and biogeochemistry in the Arctic Ocean: Empirical and model results.  J. Geophys. Res. Biogeosci., 122, http://dx.doi.org/10.1002/2016JG003660 
  • Elliott, S., et al., (LANL authors: N. Jeffery, E. C. Hunke, S. Wang) 2017:  Strategies for the simulation of sea ice organic chemistry: Arctic tests and development. Geosciences, 7, 52. http://dx.doi.org/10.3390/geosciences7030052
  • Gessler, , M. Schaub, and N. G. McDowell, 2017: Tansley insight:  The role of nutrients in drought-induced mortality and recovery. New Phytol., 214, 513-520.  https://doi.org/10.1111/nph.14340
  • Grossiord, C., et al., (LANL authors: S. Sevanto, I. Borrego, A. M. Chan, A. D. Collins, L. T. Dickman, N. McBranch, S. Michaletz, M. Ryan) 2017: Tree water dynamics in a drying and warming world  Plant Cell Environ., 40, 1861-1873. https://doi.org/1111/pce.12991
  • Grossiord, C., et al., (LANL authors: Sevanto, A. D. Collins, L. T. Dickman, N. McBranch, S. T. Michaletz, E. A. Stockton, M. Vigil, N. G. McDowell) 2017:  Precipitation, not air temperature, drives functional responses of trees in semi-arid ecosystem.  J. Ecology, 105, 163-175. https://doi.org/10.1111/1365-2745.12662
  • Grossiord, C., et al., (LANL authors: S. Sevanto, A. D. Collins, L. T. Dickman, B. D. Newman, E. A. Stockton, N. G. McDowell) 2017:  Warming combined with more extreme precipitation regimes modifies the water sources used by trees. New Phytol., 213, 584-596.  https://doi.org/10.1111/nph.14192
  • Hedelius, J. K., et al., (LANL authors: H. Parker, M. K. Dubey) 2017: Intercomparability of XCO2 and XCH4 from the United States TCCON sites.  Atmos. Meas. Tech., 10, 1481-1493.  https://doi.org/10.5194/amt-10-1481-2017
  • Hu, Z, et al., (LANL authors: C. Xu, N. G. McDowell, D. J. Johnson) 2017: Linking microbial community composition to C loss rates during wood decomposition. Soil Biol. Biochem., 104, 108-116.  https://doi.org/10.1016/j.soilbio.2016.10.017
  • Kennedy, J. H., et al., (LANL authors: J. Evans, S. Price, M. Hoffman, W. H. Lipscomb, J. Fyke, L. Vargo) 2017: LIVVkit: An extensible, python-based, land ice verification and validation toolkit for ice sheet models. J. Adv. Model. Earth Syst., 9, 854-869. https://doi.org/10.1002/2017MS000916
  • McHugh, A., et al., (LANL authors: R. C. Mueller, L. V. Gallegos-Graves, C. R. Kuske) 2017:  Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland. Environ. Microbiol., 19, 1600-1611. https://doi.org/10.111/1462-2920.13678
  • Porras-Alfaro, A., C. N. Muniania, P. S. Hamm, T. J. Torres-Cruz, and C. R. Kuske 2017. Simulated rNA:DNA ratios reveals potential to misclassify active populations as dormant. In B. Steven (ed.), The Biology of Arid Soils, 97-115. DeGruyter Publisher.
  • Price, F., et al., (LANL authors: M. J. Hoffman, W. H. Lipscomb) 2017:  An ice sheet model validation framework for the Greenland ice sheet.  Geosci. Model Dev., 10, 255-270.  https://doi.org/10.5194/gmd-10-255-2017
  • Ringler, T., J. A. Saenz, P. J. Wolfram, and L. Van Roekel, 2017: A thickness-weighted average perspective of force balance in an idealized circumpolar current.  J. Phys. Oceanogr., 47, 285-302.  https://doi.org/10.1175/JPO-D-16-0096.1
  • Santschi, P. H., et al., (LANL author: M Yeager) 2017: Recent advances in the detection of specific natural organic compounds as carriers for radionuclides in soil and water environments, with examples of radioiodine and plutonium. J. Environ. Radioact., 171, 226-233.  https://doi.org/10.1016/j.jenvrad.2017.02.023
  • Shelef, E., C. Rowland, C. J. Wilson, G. E. Hilley, U. Mishra, G. L. Altmann, and C-L. Ping, 2017: Large uncertainty in permafrost carbon stocks due to hillslope soil deposits. Geophy. Res. Lett., 44, 6134-6144. http://dx.doi.org/10.1002/2017GL073823
  • Steven, B., C. Hesse, J. Soghigian, L. V. Gallegos-Graves, and J. Dunbar, 2017: Simulated rRNA/DNA Ratios show potential to misclassify active populations as dormant.  Appl. Environ. Microbiol., 83, e00969-17. https://doi.org/10.1128/AEM.00696-17
  • Tamsitt, V., et al., (LANL author: W. Weijer) 2017: Spiraling pathways of global deep waters to the surface of the Southern Ocean. Nat. Comm., 8. https://doi.org/10.1038/s41467-017-00197-0
  • Torres-Cruz, T. J., et al., (LANL authors: N. Hesse, C. R. Kuske) 2017:  Bifiguratus adelaidae gen. et sp. nov., a new member of Mucoromycotina in endophytic and soil-dwelling habitats.  Mycologia, 109, 361-362 http://dx.doi.org/10.1080/00275514.2017.1364958
  • Urrego-Blanco, J. R., et al. (LANL authors: E. C. Hunke, N. M. Urban, N. Jeffrey, A. K. Turner, J. R. Langenbrunner) 2017: Validation of sea ice models using an uncertainty-based distance metric for multiple model variables. J. Geophys. Res., 122, 2923-2944. http://dx.doi.org/10.1002/2016JC012602
  • Urrego-Blanco, J. R., M. Urban, E. C. Hunke, A. K. Turner, and N. Jeffrey, 2017: Uncertainty quantification and global sensitivity analysis of the Los Alamos sea ice model.  J. Geophys. Res. Ocean, 121, 2709-2732.  http://dx.doi.org/10.1002/2015JC011558
  • Weijer, W., et al., (LANL authors: M. Veneziani, M. W. Hecht, N. Jeffery, A. Jonko) 2017: Local atmospheric response to an open-ocean polynya in a high-resolution climate model.  J. Clim., 30, 1629-1641.  https://doi.org/10.1175/JCLI-D-16-0120.1
  • Wolfram, P. J., and T. Ringler, 2017; Computing Eddy-Driven Effective Diffusivity Using Lagrangian Particles. Ocean Modelling, in press.  https://doi.org/10.1016/j.ocemod.2017.08.008
  • Woo, H. L., et al., (LANL authors: Teshima, K.Davenport, H. Daligault, T. Erkkila, L. Goodwin, W. Gu, C-C. Lo, C. Munk, M. Scholz, Y. Xu, P. Chain, D. Bruce, C. Detter, R. Tapia, C. Han) 2017: High-quality draft genome sequences of four lignocellulose-degrading bacteria isolated from Puerto Rican forest soil: Gordonia sp., Paenibacillus sp., Variovora sp., and Vogesella sp.. Genome Announc., 5, e00300-17.  https://doi.org/10.1128/genomeA.00300-18
  • Yeager M., L. V. Gallegos-Graves, J. Dunbar, C. N. Hesse, and C. R. Kuske, 2017. Polysaccharide degradation capability of Actinomycetales soil isolates from a semi-arid grassland of the Colorado Plateau. Appl. Environ. Microbiol., 83, e03020-16. https://doi.org/10.1128/AEM.03020-16
  • Zhang, , et al., (LANL author: S. F. Price) 2017:  A comparison of two Stokes ice sheet models applied to the Marine Ice Sheet Model Intercomparison Project for plan view models (MISMIP3d). Cryosphere, 11, 179-190.  https://doi.org/10.5194/tc-11-179-2017

 

2016

  • Aiken, A. C., G. R. McMeeking, E. J. T. Levin, K. Dubey, P. J. Demott, and S. M. Kreidenweis, 2016: Quantification of online removal refractory black carbon using laser-induced incandescence in the single particle soot photometer.  Aerosol Sci. Techn., 50, 679-692. http://dx.doi.org/10.1080/02786826.2016.1173647   
  • Ali, A. A., et al., (LANL authors: C. Xu, J. D. Muss, N. G. McDowell, C. J. Wilson) 2016: A global scale mechanistic model of photosynthetic capacity (LUNA V1.0). Geosci. Model Dev., 9, 587-606.  https://doi.org/10.5194/gmd-9-587-2016
  • Anderson, I. J., et al., (LANL authors: C. Bruce, D. Sims, T. S. Brettin, J. C. Detter, C. S. Han) 2016: Complete genome sequence of the Antarctic Halorubrum Iacusprofundi type strain ACAM 34. Stand. Genomic Sci., 11, https://doi.org/10.1186/s40793-016-0194-2
  • Atchley, A. L., T. Coon, S. L. Painter, D. R. Harp, and C. J. Wilson, 2016: Influences and interactions of inundation, peat, and snow on active layer thickness.   Geophy. Res. Lett., 43, 5116-5123.  http://dx.doi.org/10.1002/2016GL068550
  • Burrows, M., et al., (LANL author: S. M. Elliott) 2016: OCEANFILMS-2: Representing coadsorption of saccharides in marine films and potential impacts on modeled marine aerosol chemistry. Geophys. Res. Lett., 43, 8306-8313. http://dx.doi.org/10.1002/2016GL069070
  • Christoffersen, O., et al., (LANL authors: S. Sevanto, C. Xu, N. G. McDowell) 2016: Linking hydraulic traits to tropical forest function in a size-structured and trait-based model. Geosci. Model Dev., 9, 4227-4255.  https://doi.org/10.5194/gmd-9-4227-2016
  • Chylek, P., et al., (LANL authors: N. Hengartner, M. K. Dubey) 2016: Indirect aerosol effect increases CMIP5 Models’ projected Arctic warming.  J. Clim., 29, 1417-1428.  https://doi.org/10.1175/JCLI-D-15-0362.1
  • Coon, T., J. D. Moulton, and S.L. Painter, 2016: Managing complexity in simulations of land surface and near-surface processes. Env. Modell. Softw., 78, 134-149.  https://doi.org/10.1016/j.envsoft.2015.12.017
  • Deshpande, V., et al., (LANL author: C. R. Kuske) 2016:  Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences. Mycologia, 108, 1-5. https://doi.org/10.3852/14-293
  • Fernández-de-Uña, L., N. G. McDowell, I. Cañellas, and G. Gea-Izquierdo, 2016: Disentangling the effects of competition, CO2 and climate on intrinsic water-use efficiency and tree growth. J. Ecol., 104, 678-690. https://doi.org/10.1111/1365-2745.12544
  • Garcia-Forner, N., et al., (LANL authors: D. Adams, S. Servano, A. D. Collins, L. T. Dickman N. G. McDowell) 2016: Responses of two semiarid conifer tree species to reduced precipitation and warming reveal new perspectives for stomatal regulation.  Plant Cell Environ., 39, 38-49.  https://doi.org/10.1111/pce.12588
  • Gentine, P., M. Guerin, M. Uriarte, N. G. McDowell, and W. T. Pockman, 2016: An allometry-based model of the survival strategies of hydraulic failure and carbon starvation. Ecohydrol., 9, 529-546.  https://doi.org/10.1002/eco.1654
  • Harp, R., et al., (LANL authors: A. L. Atchley, E. T. Coon, C. J. Wilson, J. C. Rowland) 2016: Effect of soil property uncertainties on permafrost thaw projections: a calibration-constrained analysis. Cryosphere 10, 341-358. https://doi.org/10.5194/tc-10-341-2016
  • Hesse N., et al., (LANL author: C. R. Kuske) 2016:  Ribosomal RNA gene detection and targeted culture of novel nitrogen-responsive fungal taxa from temperate pine forest soil. Mycologia, 108, 1082-1090. 
  • Hoffman, J., A. G. Fountain, and G. E. Liston, 2016: Distributed modeling of ablation (1996-2011) and climate sensitivity on the glaciers of Taylor Valley, Antarctica.  J. Glaciol., 62, 215–229.  https://doi.org/10.1017/jog.2015.2
  • Hoffman, J., (LANL author: S. F. Price) 2016:  Greenland subglacial drainage evolution regulated by weakly-connected regions of the bed. Nature Comm., 7, 13903.  https://doi.org/10.1038/ncomms13903
  • Lee, D., R. Lowrie, M. Petersen, T. Ringler, and M. Hecht, 2016: A high order characteristic discontinuous Galerkin scheme for advection on unstructured meshes.  J. Comp. Phys., 324, 289-302.  https://doi.org/10.1016/j.jcp.2016.08.010
  • Lenaerts, T. M., M. Vizcaino, J. Fyke, L. van Kampenhout, and M. R. van den Broeke, 2016: Present-day and future Antarctic ice sheet climate and surface mass balance in the Community Earth System Model.  Clim. Dyn., 47, 1367-1381.  https://doi.org/10.1007/s00382-015-2907-4
  • Little, M., and N. M. Urban, 2016: CMIP5 temperature biases and 21st century warming around the Antarctic coast. Ann. Glaciol., 57, 69-78.  https://doi.org/10.1017/aog.2016.25
  • Liljedahl, K., et al., (LANL author: C. J. Wilson) 2016:  Pan-arctic ice-wedge degradation in warming permafrost and its influence on tundra hydrology. Nat. Geosci., 9, 312-318.  https://doi.org/10.1038/NGEO2674
  • Maier, S., L. Muggia, C. R. Kuske, and M Grube, 2016. Bacteria and non-lichenized fungi within biological soil crusts. In B. Weber et al., (eds.), Biological Soil Crusts: An Organizing Principle in Drylands, 91-100. Springer International Publisher.
  • Martin, S., et al., (LANL authors: A. C. Aiken, M. Dubey) 2016:  The Green Ocean Amazon Experiment (GoAmazon2014/5) Observes Pollution Affecting Gases, Aerosols, Clouds, and Rainfall over the Rain Forest.  Bull. Amer. Meteor. Soc., 98, 981-997. https://doi.org/10.1175/BAMS-D-15-00221.1
  • McDowell, N. G., et al., (LANL authors: P. Williams, C. Xu, L. T. Dickman, S. Sevanto, J. Muss) 2016: Multi-scale predictions of massive conifer mortality due to chronic temperature rise.  Nat. Clim. Change, 6, 295-300.  https://doi.org/10.1038/nclimate2873
  • Michaletz, T., et al., (LANL author: N. G. McDowell), 2016: The energetic and carbon economic origins of leaf thermoregulation. Nat. Plants, 2, 16129.  https://doi.org/10.1038/nplants.2016.129
  • Mueller C., L. V. Gallegos-Graves, and C. R. Kuske, 2016: A new fungal large subunit ribosomal RNA primer for high throughput sequencing surveys. FEMS Microbiol. Ecol., 92, https://doi.org/10.1093/femsec/fiv153
  • Mueller, R., D. R. Zac, and C. R. Kuske, 2016: Assembly of active bacterial and fungal communities along a natural environmental gradient. Microbial Ecology, 71, 57-67.  https://doi.org/10.1007/s00248-015-0655-y
  • Nardini, , et al., (LANL author: N. G. McDowell) 2016: Rooting depth, water relations and non-structural carbohydrate dynamics in three woody angiosperms differentially affected by an extreme summer drought. Plant Cell Environ., 39, 618-627.  https://doi.org/10.1111/pce.12646
  • Newman, C., G. Womeldorff, D. A. Knoll, and L. Chacon, 2016: A communication-avoiding implicit-explicit method for a free-surface ocean model.   J. Computational Phys., 305, 877-894. https://doi.org/10.1016/j.jcp.2015.11.008
  • Notz, D., et al., (LANL author: E. C. Hunke) 2016: The CMIP 6 Sea-Ice Model Intercomparison Project (SIMIP): understanding sea ice through climate model simulations.  Geosci. Model Dev., 9, 3427-3446.  https://doi.org/10.5194/gmd-9-3427-2016
  • Nowicki, M., et al., (LANL author: W. Lipscomb) 2016:  Ice Sheet Model Intercomparison Project (ISMIP6) contribution to CMIP6. Geosci. Model Dev., 9, 4521-4545.  https://doi.org/10.5194/gmd-9-4521-2016
  • Painter, L., et al., (LANL authors: E. T. Coon, A. L. Atchley, M. Berndt, R. Garimella, J. D. Moulton, D. Svyatskiy, C. J. Wilson) 2016:  Integrated surface/subsurface permafrost thermal hydrology: Model formulation and proof-of-concept simulations, Water Resour. Res., 52, 6062-6077. https://doi.org/10.1002/2015WR018427
  • Phillips, P., et al., (LANL author: N. G. McDowell) 2016:  A belowground perspective on the drought sensitivity of forests: Towards improved understanding and simulation. Forest Ecol. Manag., 380, 309-320. https://doi.org/10.1016/j.foreco.2016.08.043
  • Reed, S. C., et al., (LANL author: C. R. Kuske) 2016. Biocrusts in the context of global change. In B. Weber et al., (eds.), Biological Soil Crusts: An Organizing Principle in Drylands, 451-476. Springer International Publisher.
  • Rowland, J. C., and T. Coon, 2016: From documentation to prediction: Raising the bar for thermokarst research. Hydrogeology Journal, 24, 645-648.  https://doi.org/10.1007/s10040-015-1331-5
  • Rowland, C., E. Shelef, P. A. Pope, J. Muss, C. Gangodagamage, S. Brumby, and C. J. Wilson) 2016: A morphology independent methodology for quantifying planview river change and characteristics from remotely sensed imagery, Remote Sens. Environ., 184, 212-228.  https://doi.org/10.1016/j.rse.2016.07.005
  • Ryan J., et al., (LANL author: N. G. McDowell) 2016:  Too dry for lizards: short-term rainfall influence on lizard microhabitat use in an experimental rainfall manipulation within a piñon-juniper. Funct. Ecol., 30, 964-973. https://doi.org/10.1111/1365-2435.12595
  • Sinsabaugh, L., et al., (LANL author: C. R. Kuske) 2016:  Stoichiometry of microbial carbon use efficiency in soils. Ecol. Monogr., 86, 172-189.  https://doi.org/10.1890/15-2110.1 (cover article)
  • Sjöberg, Y., (LANL authors: E. Coon, D. Harp) 2016:  Thermal effects of groundwater flow through subarctic fens: A case study based on field observations and numerical modeling, Water Resour. Res., 52, 15911606, https://doi.org/10.1002/2015WR017571
  • Sperry, S., et al., (LANL author: N. G. McDowell) 2016:  Pragmatic hydraulic theory predicts stomatal response to climate water deficits. New Phytol., 212, 577-589.  https://doi.org/10.1111/nph.14059
  • Throckmorton, M., et al., (LANL authors: B. D. Newman, J. M. Heikoop, G. B. Perkins, D. O'Malley, V. V. Vesselinov, C. J. Wilson) 2016:  Active layer hydrology in an arctic tundra ecosystem: quantifying water sources and cycling using water stable isotopes. Hydrol. Process., 30, 4972-4986. https://doi.org/10.1002/hyp.10883
  • Tuminaro, R., M. Perego, I. Tezaur, A. Salinger, and S. Price, 2016: A matrix dependent/algebraic multigrid approach for extruded meshes with applications to ice sheet modeling. SIAM J. Sci. Comput., 38, C504-C532. https://doi.org/10.1137/15M1040839
  • Urrego-Blanco, R., N. M. Urban, E. C. Hunke, A. K. Turner, and N. Jeffery, 2016: Uncertainty quantification and global sensitivity analysis of the Los Alamos sea ice model. J. Geophys. Res. - Oceans, 121, 2709-2732.  https://doi.org/10.1002/2015JC011558
  • Woodring, J., et al., (LANL authors: M. Petersen, A. Patchett, J. Ahrens) 2016:  In situ eddy analysis in a high-resolution ocean climate model, IEEE Trans. Vis. Comput. Graph., 22, 857-866.  https://doi.org/10.1109/TVCG.2015.2467411
  • Xu, L., et al., (LANL author: S. Elliott) 2016: DMS role in ENSO cycle in the tropics. J. Geophys. Res. Atmos., 121, 13,537-13,558. https://doi.org/10.1002/2016JD025333
  • Xu, L., et al., (LANL authors: A. C. Aiken, S. Liu, K. Gorkowski, M. K. Dubey) 2016: Wintertime aerosol chemical composition, volatility, and spatial variability in the greater London area, Atmos. Chem. Phys., 16, 1139-1160.  https://doi.org/10.5194/acp-16-1139-2016

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