Publications

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A
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
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.
Arsiccio A, McCarty J, Pisano R, Shea J-E.  2018.  Effect of Surfactants on Surface-Induced Denaturation of Proteins: Evidence of an Orientation-Dependent Mechanism. The Journal of Physical Chemistry B. 122:11390–11399.
Arsiccio A, Ganguly P, La Cortiglia L, Shea J-E, Pisano R.  2020.  ADD Force Field for Sugars and Polyols: Predicting the Additivity of Protein–Osmolyte Interaction. The Journal of Physical Chemistry B. 124:7779–7790.
Arsiccio A, Shea J-E.  2021.  Protein Cold Denaturation in Implicit Solvent Simulations: A Transfer Free Energy Approach. The Journal of Physical Chemistry B.
Arsiccio A, McCarty J, Pisano R, Shea J-E.  2020.  Heightened Cold-Denaturation of Proteins at the Ice-Water Interface. Journal of the American Chemical Society.
Artyukhin S, Delaney KT, Spaldin NA, Mostovoy M.  2013.  Landau theory of topological defects in multiferroic hexagonal manganites. Nature Materials.
Arya S, Ganguly P, Arsiccio A, Claud SL, Trapp B, Schonfeld GE, Liu X, Cantrell KLazar, Shea J-E, Bowers MT.  2020.  Terminal capping of an amyloidogenic Tau fragment modulates its fibrillation propensity. The Journal of Physical Chemistry B.
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.
B
Bagnell A, DeVries T.  2021.  20th century cooling of the deep ocean contributed to delayed acceleration of Earth’s energy imbalance. Nature Communications. 12:1–10.
Baird B, Cieslak M, Smallwood J, Grafton ST, Schooler JW.  2014.  Regional White Matter Variation Associated with Domain-specific Metacognitive Accuracy.
Bales B, Petzold L, Goodlet BR, Lenthe WC, Pollock TM.  2018.  Bayesian inference of elastic properties with resonant ultrasound spectroscopy. The Journal of the Acoustical Society of America. 143:71–83.
Barel I, Reich NO, Brown FLH.  2019.  Integrated rate laws for processive and distributive enzymatic turnover. The Journal of chemical physics. 150:244120.
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.
Bates MW, Lequieu J, Barbon SM, Lewis RM, Delaney KT, Anastasaki A, Hawker CJ, Fredrickson GH, Bates CM.  2019.  Stability of the A15 phase in diblock copolymer melts. Proceedings of the National Academy of Sciences. :201900121.
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.  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.
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.

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