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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.

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.

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.

Danielsen SPO, McCarty J, Shea J-E, Delaney KT, Fredrickson GH. 2019. Small ion effects on self-coacervation phenomena in block polyampholytes. The Journal of chemical physics. 151:034904.

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.

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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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Ganguly P, Polak J, van der Vegt NFA, Heyda J, Shea J-E. 2020. Protein Stability in TMAO and Mixed Urea-TMAO Solutions. The Journal of Physical Chemistry B.

Arsiccio A, Shea J-E. 2021. Protein Cold Denaturation in Implicit Solvent Simulations: A Transfer Free Energy Approach. The Journal of Physical Chemistry B.

Zhang X, Vigers M, McCarty J, Rauch JN, Fredrickson GH, Wilson MZ, Shea J-E, Han S, Kosik K. 2020. The Proline-rich Domain Promotes Tau Liquid Liquid Phase Separation in Cells. bioRxiv.

Shea J-E, Best RB, Mittal J. 2021. Physics-based computational and theoretical approaches to intrinsically disordered proteins. Current Opinion in Structural Biology. 67:219–225.

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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.

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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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Najafi S, Lin Y, Longhini AP, Zhang X, Delaney KT, Kosik KS, Fredrickson GH, Shea J-E, Han S. 2021. Liquid-liquid phase separation of Tau by self and complex coacervation. Protein Science.

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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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.