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Journal Article

de Almeida NEC, Do TD, LaPointe NE, Tro M, Feinstein SC, Shea J-E, Bowers MT. 2017. 1,2,3,4,6-penta-O-galloyl-β-d-glucopyranose binds to the N-terminal metal binding region to inhibit amyloid β-protein oligomer and fibril formation. International Journal of Mass Spectrometry. 420

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.

Kim B, Do TD, Hayden EY, Teplow DB, Bowers MT, Shea J-E. 2016. Aggregation of Chameleon Peptides: Implications of $\alpha$-Helicity in Fibril Formation. Journal of Physical Chemistry B. 120(26):5874-5883.

Wong AG, Wu C, Hannaberry E, Watson MD, Shea J-E, Raleigh DP. 2016. Analysis of the Amyloidogenic Potential of Pufferfish (Takifugu rubripes) Islet Amyloid Polypeptide Highlights the Limitations of Thioflavin-T Assays and the Difficulties in Defining Amyloidogenicity. Biochemistry. 55:510–518.

Kristoffersen HH, Shea J-E, Metiu H. 2015. Catechol and HCl Adsorption on TiO2 (110) in Vacuum and at the Water–TiO2 Interface. The journal of physical chemistry letters. 6:2277–2281.

Morriss-Andrews A, Brown FLeon Halet, Shea J-E. 2014. A Coarse-Grained Model for Peptide Aggregation on a Membrane Surface. The Journal of Physical Chemistry B.

Mullen RGotchy, Shea J-E, Peters B. 2014. Communication: An existence test for dividing surfaces without recrossing. The Journal of Chemical Physics. 140:041104.

Morriss-Andrews A, Shea J-E. 2015. Computational Studies of Protein Aggregation: Methods and Applications. Annual review of physical chemistry. 66:643–666.

Susa AC, Wu C, Bernstein SL, Dupuis NF, Wang H, Raleigh DP, Shea J-E, Bowers MT. 2014. Defining the Molecular Basis of Amyloid Inhibitors: Human Islet Amyloid Polypeptide-Insulin Interactions. Journal of the American Chemical Society.

Park S, Barnes R, Lin Y, Jeon B-jin, Najafi S, Delaney KT, Fredrickson GH, Shea J-E, Hwang DSoo, Han S. 2020. Dehydration entropy drives liquid-liquid phase separation by molecular crowding. Communications Chemistry. 3:1–12.

Levine ZA, Venable RM, Watson MC, Lerner MG, Shea J-E, Pastor RW, Brown FLH. 2014. Determination of Biomembrane Bending Moduli in Fully Atomistic Simulations. Journal of the American Chemical Society. 136:13582–13585.

Ganguly P, Shea J-E. 2019. Distinct and Nonadditive Effects of Urea and Guanidinium Chloride on Peptide Solvation. The journal of physical chemistry letters. 10:7406–7413.

Larini L, Shea J-E. 2013. Double Resolution Model for Studying TMAO/Water Effective Interactions. The Journal of Physical Chemistry B. 117:13268–13277.

Wonderly WR, Cristiani TR, Cunha KC, Degen GD, Shea J-E, J Waite H. 2020. Dueling Backbones: Comparing Peptoid and Peptide Analogues of a Mussel Adhesive Protein. Macromolecules. 53:6767–6779.

Mullen RGotchy, Shea J-E, Peters B. 2015. Easy Transition Path Sampling Methods: Flexible Length Aimless Shooting and Permutation Shooting. Journal of Chemical Theory and Computation.

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.

Do TD, LaPointe NE, Economou NJ, Buratto SK, Feinstein SC, Shea J-E, Bowers MT. 2013. Effects of pH and Charge State on Peptide Assembly: the YVIFL Model System. Journal of Physical Chemistry B. 117(13):10768.

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.

Peter EK, Agarwal M, Kim B, Pivkin IV, Shea J-E. 2014. How water layers on graphene affect folding and adsorption of TrpZip2. The Journal of Chemical Physics. 141:22D511.

Shea J-E, Peter EKarl. 2014. A hybrid MD-kMC algorithm for folding proteins in explicit solvent. Physical Chemistry Chemical Physics.

Ganguly P, van der Vegt NFA, Shea J-E. 2016. Hydrophobic Association in Mixed Urea–TMAO Solutions. Journal of Physical Chemistry Letters. 7(15):3052-3059.

Do TD, Economou NJ, Chamas A, Buratto SK, Shea J-E, Bowers MT. 2014. Interactions between Amyloid-$\beta$ and Tau Fragments Promote Aberrant Aggregates: Implications for Amyloid Toxicity. The Journal of Physical Chemistry B. 118:11220–11230.

Bleiholder C, Do TD, Wu C, Economou NJ, Bernstein SS, Buratto SK, Shea J-E, Bowers MT. 2013. Ion Mobility Spectrometry Reveals the Mechanism of Amyloid Formation of A beta (25–35) and Its Modulation by Inhibitors at the Molecular Level: Epigallocatechin Gallate and Scyllo-inositol. Journal of the American Chemical Society. 135:16926–16937.

Peter EK, Pivkin IV, Shea J-E. 2015. A kMC-MD method with generalized move-sets for the simulation of folding of $\alpha$-helical and $\beta$-stranded peptides. The Journal of chemical physics. 142:144903.

Charest N, Tro M, Bowers MT, Shea J-E. 2020. Latent Models of Molecular Dynamics Data: Automatic Order Parameter Generation for Peptide Fibrillization. The Journal of Physical Chemistry B. 124:8012–8022.

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Acknowledgements

Please acknowledge the CSC in publications and presentations if you are using our facilities computing resources in your research.

Use was made of computational facilities purchased with funds from the National Science Foundation (CNS-1725797) and administered by the Center for Scientific Computing (CSC). The CSC is supported by the California NanoSystems Institute and the Materials Research Science and Engineering Center (MRSEC; NSF DMR 1720256) at UC Santa Barbara.