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T

Levine ZA, Fischer SA, Shea J-E, Pfaendtner J. 2015. Trp-Cage Folding on Organic Surfaces. The Journal of Physical Chemistry B. 119:10417–10425.

Mullen RGotchy, Shea J-E, Peters B. 2014. Transmission coefficients, committors, and solvent coordinates in ion-pair dissociation. Journal of Chemical Theory and Computation.

Zerze GH, Mullen RGotchy, Levine ZA, Shea J-E, Mittal J. 2015. To what extent does surface hydrophobicity dictate peptide folding and stability near surfaces? Langmuir. 31(44):12223–12230.

Ganguly P, Do TD, Larini L, LaPointe NE, Sercel AJ, Shade MF, Feinstein SC, Bowers MT, Shea J-E. 2015. Tau Assembly: The Dominant Role of PHF6 (VQIVYK) in Microtubule Binding Region Repeat R3. The Journal of Physical Chemistry B. 119:4582–4593.

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Levine ZA, Rapp MV, Wei W, Mullen RGotchy, Wu C, Zerze GH, Mittal J, J Waite H, Israelachvili JN, Shea J-E. 2016. Surface force measurements and simulations of mussel-derived peptide adhesives on wet organic surfaces. Proceedings of the National Academy of Sciences. :201603065.

Wu C, Shea J-E. 2013. Structural Similarities and Differences between Amyloidogenic and Non-Amyloidogenic Islet Amyloid Polypeptide (IAPP) Sequences and Implications for the Dual Physiological and Pathological Activities of These Peptides. PLoS computational biology. 9:e1003211.

Morriss-Andrews A, Shea J-E. 2014. Simulations of Protein Aggregation: Insights from Atomistic and Coarse-Grained Models. The Journal of Physical Chemistry Letters.

Levine ZA, Shea J-E. 2017. Simulations of disordered proteins and systems with conformational heterogeneity. Current Opinion in Structural Biology. 43:95–103.

Eschmann NA, Georgieva ER, Ganguly P, Borbat PP, Rappaport MD, Akdogan Y, Freed JH, Shea J-E, Han S. 2017. Signature of an aggregation-prone conformation of tau. Scientific Reports. 7:44739.

R

Levine ZA, Larini L, LaPointe NE, Feinstein SC, Shea J-E. 2015. Regulation and aggregation of intrinsically disordered peptides. Proceedings of the National Academy of Sciences. 112:2758–2763.

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de Almeida NEC, Do TD, Tro M, LaPointe NE, Feinstein SC, Shea J-E, Bowers MT. 2015. Opposing Effects of Cucurbit [7] uril and 1, 2, 3, 4, 6-Penta-O-galloyl-$\beta$-d-glucopyranose on Amyloid $\beta$25–35 Assembly. ACS chemical neuroscience.

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Lin Y, McCarty J, Rauch JN, Delaney KT, Kosik KS, Fredrickson GH, Shea J-E, Han S. 2019. Narrow equilibrium window for complex coacervation of tau and RNA under cellular conditions. Elife. 8:e42571.

M

Ganguly P, Hajari T, Shea J-E, van der Vegt NFA. 2015. Mutual Exclusion of Urea and Trimethylamine N-oxide from Amino Acids in Mixed Solvent Environment. The Journal of Physical Chemistry Letters. 6:581–585.

Das S, Lee BHoon, Linstadt R, Cunha K, Li Y, Kaufman Y, Levine ZA, Lipshutz BH, Lins RD, Shea J-E et al.. 2016. Molecularly Smooth Self-Assembled Monolayer for High-Mobility Organic Field-Effect Transistors. Nano Letters. 16(10):6709-6715.

Danielsen SPO, McCarty J, Shea J-E, Delaney KT, Fredrickson GH. 2019. Molecular design of self-coacervation phenomena in block polyampholytes. Proceedings of the National Academy of Sciences. 116:8224–8232.

Levine ZA, Teranishi K, Okada AK, Langen R, Shea J-E. 2019. The Mitochondrial Peptide Humanin Targets, but does not Denature Amyloid Oligomers in Type II Diabetes. Journal of the American Chemical Society.

Zheng X, Wu C, Liu D, Li H, Bitan G, Shea J-E, Bowers MThomas. 2016. Mechanism of C-Terminal Fragments of Amyloid $\beta$-Protein as A$\beta$ Inhibitors: Do C-Terminal Interactions Play a Key Role in Their Inhibitory Activity? Journal of Physical Chemistry B. 120(8):1615-1623.

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Wang X, Vallurupalli P, Vu A, Lee K, Sun S, Bai W-J, Wu C, Zhou H, Shea J-E, Kay LE et al.. 2014. The linker between the dimerization and catalytic domains of the CheA histidine kinase propagates changes in structure and dynamics that are important for enzymatic activity. Biochemistry. 53:855–861.

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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.

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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.

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.

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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.

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

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.

E

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.

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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.