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2015

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.

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.

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.

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.

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.

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.

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.

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.

2014

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.

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.

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.

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.

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.

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.

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

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

2013

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

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.

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.

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.

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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.