Publications
For a full list see Google Scholar or ResearchID
Published while at Western
D. Cummins, C. Longstreth, and J. McCarty, “Analysis of transition rates from variational flooding using analytical theory" J. Chem. Phys, 161, 194104 (2024)
K. A. Croney and J. McCarty, “Exploring Product Release from Yeast Cytosine Deaminase with Metadynamics" J. Phys. Chem. B, 128, 13, 3102-3112 (2024)
D. A. Johnson, I. M. Piper, B. A. Vogel, Sophie N. Jackson, J. E. Svendsen, H. M. Kodama, D. E. Lee, K. M. Linblom, J. McCarty, J. M. Antos, and J. F. Amacher, “Structures of Streptococcus pyogenes class A sortase in complex with substrate and product mimics provide key details of target recognition” J. Biol. Chem. 298(10), 102446 (2022)
C. Leonard, C. Phillips, and J. McCarty, “Insight Into Seeded Tau Fibril Growth From Molecular Dynamics Simulation of the Alzheimer’s Disease Protofibril Core” Front. Mol. Biosci. 8: 624302 (2021)
P. H. Nguyen, A. Ramamoorthy, B. R. Sahoo, [and 31 others, including J. McCarty], “Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer’s Disease, Parkinson’s Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis” Chem. Rev. 121, 4, 2545-2647 (2021)
X. Zhang, M. Vigers, J. McCarty, J. N. Rauch, G. H. Fredrickson, M. Z. Wilson, J.-E. Shea, S. Han, and K. S. Kosik, “The proline-rich domain promotes Tau liquid-liquid phase separation in cells” J. Cell Biol. 219, 11, e202006054 (2020)
A. Arsiccio, J. McCarty, R. Pisano, and J.-E. Shea, “Heightened Cold-Denaturation of Proteins at the Ice–Water Interface,” J. Am. Chem. Soc. 142, 12, 5722-5730 (2020)
Published prior to appointment at Western
S.P.O. Danielsen, J. McCarty, J.-E. Shea, K. T. Delaney, and G. H. Fredrickson, “Small ion effects on self-coacervation phenomena in block polyampholytes,” J. Chem. Phys. 151, 034904 (2019)
S.P.O. Danielsen, J. McCarty, J.-E. Shea, K. T. Delaney, and G. H. Fredrickson, “Molecular design of self-coacervation phenomena in block polyampholytes,” Proc. Natl. Acad. Sci. USA, 116 (17), 8224-8232 (2019)
Y. Lin, J. McCarty, J. N. Rauch, K. T. Delaney, K. S. Kosik, G. H. Fredrickson, J.-E. Shea, and S. Han, “Narrow equilibrium window for complex coacervation of tau and RNA under cellular conditions,” eLIFE, 8:e42571 (2019) [co-first author]
J. McCarty, K. T. Delaney, S. P. O. Danielsen, G. H. Fredrickson, and J.-E. Shea, “Complete phase diagram for liquid-liquid phase separation of intrinsically disordered proteins,” J. Phys. Chem. Lett., 10, 1644-1652 (2019)
M. G. Guenza, M. Dinpajooh, J. McCarty, and I. Y. Lyubimov, “On the accuracy, transferability, and efficiency of coarse-grained models of molecular liquids,” J. Phys. Chem. B, 122, 10257 (2018) [selected for ACS Editors’ Choice]
A. Arsiccio, J. McCarty, R. Pisano, and J.-E. Shea, “The effect of surfactants on surface-induced denaturation of proteins: evidence of an orientation-dependent mechanism,” J. Phys. Chem. B, 122, 11390 (2018)
D. Mendels, J. McCarty, P. Piaggi, and M. Parrinello, “Searching for entropically stabilized phases: the case of silver iodide,” J. Phys. Chem. C, 122, 1786 (2018)
J. McCarty and M. Parrinello, “A variational conformational dynamics approach to the selection of collective variables in metadynamics,” J. Chem. Phys., 147, 204109 (2017). [Editor’s picks]
G. Piccini, J. McCarty, O. Valsson, and M. Parrinello, “Variational Flooding Study of a SN2 Reaction,” J. Phys. Chem. Lett., 8, 580 (2017)
J. McCarty, O. Valsson, and M. Parrinello, “Bespoke bias for obtaining free energy differences within variationally enhanced sampling,” J. Chem. Theory Comput., 12, 2162 (2016).
J. McCarty, O. Valsson, P. Tiwary, and M. Parrinello, “Variationally optimized free energy flooding for rate calculation,” Phys. Rev. Lett., 115, 070601 (2015).
D. Ozog, J. McCarty, G. Gossett, A. Malony, and M. Guenza, “Fast equilibration of coarse-grained polymer liquids,” J. Comput. Sci., 9, 33 (2015). [SPECIAL ISSUE: Computational Science at the Gates of Nature]
J. McCarty, A. J. Clark, J. Copperman, and M. G. Guenza, “An analytical coarse-graining method which preserves the free energy, structural correlations, and thermodynamic state of polymer melts from the atomistic to the mesoscale,” J. Chem. Phys., 140, 204913 (2014).
A. J. Clark, J. McCarty, and M. G. Guenza, “Effective potentials for representing polymers in melts as chains of interacting soft particles,” J. Chem. Phys., 139, 124906 (2013). [co-first author]
A. J. Clark, J. McCarty, I. Y. Lyubimov, and M. G. Guenza, “Thermodynamic consistency in variable-level coarse- graining of polymeric liquids,” Phys. Rev. Lett., 109, 168301 (2012).
J. McCarty, A. J. Clark, I. Y. Lyubimov, and M. G. Guenza, “Thermodynamic consistency between analytic integral equation theory and coarse-grained molecular dynamics simulations of homopolymer melts,” Macromol., 45, 8482 (2012).
J. McCarty and M. G. Guenza, “Multiscale modeling of binary polymer mixtures: scale bridging in the athermal and thermal regime,” J. Chem. Phys., 133, 094904 (2010).
I. Y. Lyubimov, J. McCarty, A. Clark, and M. G. Guenza, “Analytical rescaling of polymer dynamics from mesoscale simulations,” J. Chem. Phys., 132, 224903 (2010).
J. McCarty, I. Y. Lyubimov, and M. G. Guenza. “Effective soft-core potentials and mesoscopic simulations of binary polymer mixtures,” Macromol., 43, 3964-3979 (2010).
J. McCarty, I. Y. Lyubimov, and M. G. Guenza. “Multiscale modeling of coarse-grained macromolecular liquids,” J. Phys. Chem. B., 113, 11876-11886 (2009).