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Abdeljawad F, Völker B, Davis R, McMeeking RM, Haataja M.  2014.  Connecting microstructural coarsening processes to electrochemical performance in solid oxide fuel cells: An integrated modeling approach. Journal of Power Sources. 250:319–331.
Abdul-Wajid S, Veeman MT, Chiba S, Turner TL, Smith WC.  2014.  Exploiting the Extraordinary Genetic Polymorphism of Ciona for Developmental Genetics with Whole Genome Sequencing. Genetics. 197:49–59.
Agarwal V, Metiu H.  2016.  Oxygen Vacancy Formation on $\alpha$-MoO3 Slabs and Ribbons. Journal of Physical Chemistry C. 120(34):19252-19264.
Agarwal V, Peters B.  2014.  Nucleation near the eutectic point in a Potts-lattice gas model. The Journal of Chemical Physics. 140:084111.
Agarwal V, Metiu H.  2016.  Energy of Oxygen-Vacancy Formation on Oxide Surfaces: Role of the Spatial Distribution. Journal of Physical Chemistry C. 120(4):2320-2323.
Agarwal V, Metiu H.  2015.  Hydrogen Abstraction Energies and Ammonia Binding to BEA, ZSM-5, and $\alpha$-Quartz Doped with Al, Sc, B, or Ga. The Journal of Physical Chemistry C. 119:16106–16114.
Alabduljalil M., Tang X., Yang T..  2013.  Cache-Conscious Performance Optimization for Similarity Search. SIGIR’2013 (Proc. of 36th ACM SIGIR conference on Research and Development in Information Retrieval). (in press)
Alabduljalil M, Tang X, Yang T.  2013.  Optimizing Parallel Algorithms for All Pairs Similarity Search. Proceedings of the sixth ACM International Conference on Web Search and data mining. WSDM13:203.
Alexandrou MA, Swartz BA, Matzke NJ, Oakley TH.  2013.  Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae. Molecular phylogenetics and evolution. 69:514–523.
Alexandrou MA, Cardinale BJ, Hall JD, Delwiche CF, Fritschie K, Narwani A, Venail PA, Bentlage B, M. Pankey S, Oakley TH.  2015.  Evolutionary relatedness does not predict competition and co-occurrence in natural or experimental communities of green algae. Proceedings of the Royal Society B: Biological Sciences. 282
Artyukhin S, Delaney KT, Spaldin NA, Mostovoy M.  2013.  Landau theory of topological defects in multiferroic hexagonal manganites. Nature Materials.
Audus DJ, Delaney KT, Ceniceros HD, Fredrickson GH.  2013.  Comparison of Pseudospectral Algorithms for Field-Theoretic Simulations of Polymers. Macromolecules. 46:8383–8391.
Audus DJ, Gopez JD, Krogstad DV, Lynd NA, Kramer EJ, Hawker CJ, Fredrickson GH.  2015.  Phase behavior of electrostatically complexed polyelectrolyte gels using an embedded fluctuation model. Soft Matter. 11:1214-1225.
Aue DBetowski D.  2017.  The Application of Computational Chemistry to Problems in Mass Spectrometry.
Baird B, Cieslak M, Smallwood J, Grafton ST, Schooler JW.  2014.  Regional White Matter Variation Associated with Domain-specific Metacognitive Accuracy.
Barel I, Reich NO, Brown FLH.  2015.  Extracting enzyme processivity from kinetic assays. Journal of Chemical Physics. 143(22):224115.
Barkeshli M, Jiang H-C, Thomale R, Qi X-L.  2014.  Generalized Kitaev Models and Slave Genons. arXiv preprint arXiv:1405.1780.
Barkeshli M, Jiang H-C, Thomale R, Qi X-L.  2015.  Generalized Kitaev Models and Extrinsic Non-Abelian Twist Defects. Physical Review Letters. 114:026401.
Battelle B-A, Kempler KE, Saraf SR, Marten CE, Dugger DR, Speiser DI, Oakley TH.  2015.  Opsins in Limulus eyes: characterization of three visible light-sensitive opsins unique to and co-expressed in median eye photoreceptors and a peropsin/RGR that is expressed in all eyes. Journal of Experimental Biology. 218(3):466–479.
Baumketner A., Shea J.-E..  2005.  Free Energy Landscapes for Amyloidogenic Tetrapeptides Dimerization. Biophysical Journal. 89:1493-1503.
Baumketner A., Bernstein S.L, Wyttenbach T., Lazo N.D, Teplow D.B, Bowers M.T, Shea J.-E..  2006.  Structure of the 21-30 fragment of amyloid Beta protein. Protein Science. 15:1239.
Baumketner A., Shea J.-E..  2006.  Folding landscapes of the Alzheimer A\beta12-28 peptide from all-atom replica exchange molecular dynamics simulations in explicit solvent. J. Mol. Biol.. 362:567-579.
Baumketner A., Shea J.-E..  2005.  The influence of different treatments of electrostatic interactions on the thermodynamics of folding of peptides. J. Phys. Chem. B. 109:21322.
Baumketner A., Shea J.-E..  2006.  The thermodynamics of folding of a beta hairpin peptide probed through replica exchange molecular dynamics simulations. Theor. Chem. Acc.. 116:262.
Bechtel JS, Seshadri R, Van der Ven A.  2016.  Energy Landscape of Molecular Motion in Cubic Methylammonium Lead Iodide from First Principles. Journal of Physical Chemistry C. 120(23):12403-12410.