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James J. McCarty, Ph.D. - Publications

Affiliations: 
2019- Chemistry Western Washington University, Bellingham, WA, United States 
Area:
Computational Biochemistry
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25 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Najafi S, McCarty J, Delaney KT, Fredrickson GH, Shea JE. Field-Theoretic Simulation Method to Study the Liquid-Liquid Phase Separation of Polymers. Methods in Molecular Biology (Clifton, N.J.). 2563: 37-49. PMID 36227467 DOI: 10.1007/978-1-0716-2663-4_2  0.576
2021 Nguyen PH, Ramamoorthy A, Sahoo BR, Zheng J, Faller P, Straub JE, Dominguez L, Shea JE, Dokholyan NV, De Simone A, Ma B, Nussinov R, Najafi S, Ngo ST, Loquet A, ... ... McCarty J, et al. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chemical Reviews. PMID 33543942 DOI: 10.1021/acs.chemrev.0c01122  0.668
2020 Zhang X, Vigers M, McCarty J, Rauch JN, Fredrickson GH, Wilson MZ, Shea JE, Han S, Kosik KS. The proline-rich domain promotes Tau liquid-liquid phase separation in cells. The Journal of Cell Biology. 219. PMID 32997736 DOI: 10.1083/jcb.202006054  0.473
2020 Arsiccio A, McCarty J, Pisano R, Shea JE. Heightened Cold-Denaturation of Proteins at the Ice-Water Interface. Journal of the American Chemical Society. PMID 32122128 DOI: 10.1021/Jacs.9B13454  0.442
2019 Danielsen SPO, McCarty J, Shea JE, Delaney KT, Fredrickson GH. Small ion effects on self-coacervation phenomena in block polyampholytes. The Journal of Chemical Physics. 151: 034904. PMID 31325933 DOI: 10.1063/1.5109045  0.562
2019 Lin Y, McCarty J, Rauch JN, Delaney KT, Kosik KS, Fredrickson GH, Shea JE, Han S. Narrow equilibrium window for complex coacervation of tau and RNA under cellular conditions. Elife. 8. PMID 30950394 DOI: 10.7554/Elife.42571  0.552
2019 Danielsen SPO, McCarty J, Shea JE, Delaney KT, Fredrickson GH. Molecular design of self-coacervation phenomena in block polyampholytes. Proceedings of the National Academy of Sciences of the United States of America. PMID 30948640 DOI: 10.1073/Pnas.1900435116  0.604
2019 McCarty JJ, Delaney KT, Danielsen SPO, Fredrickson GH, Shea JE. Complete Phase Diagram for Liquid-liquid Phase Separation of Intrinsically Disordered Proteins. The Journal of Physical Chemistry Letters. PMID 30873835 DOI: 10.1021/Acs.Jpclett.9B00099  0.523
2019 Lin Y, McCarty J, Rauch JN, Delaney KT, Kosik KS, Fredrickson GH, Shea J, Han S. Author response: Narrow equilibrium window for complex coacervation of tau and RNA under cellular conditions Elife. DOI: 10.7554/Elife.42571.028  0.446
2018 Guenza MG, Dinpajooh M, McCarty J, Lyubimov IY. Accuracy, Transferability, and Efficiency of Coarse-Grained Models of Molecular Liquids. The Journal of Physical Chemistry. B. 122: 10257-10278. PMID 30153027 DOI: 10.1021/Acs.Jpcb.8B06687  0.733
2018 Arsiccio A, McCarty JJ, Pisano R, Shea JE. The Effect of Surfactants on Surface-Induced Denaturation of Proteins: Evidence of an Orientation-Dependent Mechanism. The Journal of Physical Chemistry. B. PMID 30118226 DOI: 10.1021/Acs.Jpcb.8B07368  0.478
2018 Mendels D, McCarty JJ, Piaggi PM, Parrinello M. Searching for Entropically Stabilized Phases: The Case of Silver Iodide Journal of Physical Chemistry C. 122: 1786-1790. DOI: 10.1021/Acs.Jpcc.7B11002  0.472
2017 McCarty J, Parrinello M. A variational conformational dynamics approach to the selection of collective variables in metadynamics. The Journal of Chemical Physics. 147: 204109. PMID 29195289 DOI: 10.1063/1.4998598  0.49
2017 Piccini G, McCarty J, Valsson O, Parrinello M. Variational Flooding Study of a SN2 Reaction. The Journal of Physical Chemistry Letters. PMID 28071915 DOI: 10.1021/Acs.Jpclett.6B02852  0.677
2016 McCarty J, Valsson O, Parrinello M. Bespoke Bias for Obtaining Free Energy Differences within Variationally Enhanced Sampling. Journal of Chemical Theory and Computation. PMID 27057791 DOI: 10.1021/Acs.Jctc.6B00125  0.502
2015 McCarty J, Valsson O, Tiwary P, Parrinello M. Variationally Optimized Free-Energy Flooding for Rate Calculation. Physical Review Letters. 115: 070601. PMID 26317704 DOI: 10.1103/Physrevlett.115.070601  0.689
2015 Clark AJ, McCarty J, Guenza MG. Comment on "Systematic and simulation-free coarse graining of homopolymer melts: A structure-based study" [J. Chem. Phys. 142, 054905 (2015)]. The Journal of Chemical Physics. 143: 067101. PMID 26277169 DOI: 10.1063/1.4928457  0.701
2015 McCarty J, Valsson O, Tiwary P, Parrinello M. Variationally Optimized Free-Energy Flooding for Rate Calculation Physical Review Letters. 115. DOI: 10.1103/PhysRevLett.115.070601  0.58
2014 McCarty J, Clark AJ, Copperman J, Guenza MG. An analytical coarse-graining method which preserves the free energy, structural correlations, and thermodynamic state of polymer melts from the atomistic to the mesoscale. The Journal of Chemical Physics. 140: 204913. PMID 24880331 DOI: 10.1063/1.4875923  0.752
2013 Clark AJ, McCarty J, Guenza MG. Effective potentials for representing polymers in melts as chains of interacting soft particles. The Journal of Chemical Physics. 139: 124906. PMID 24089803 DOI: 10.1063/1.4821818  0.718
2012 McCarty J, Clark AJ, Lyubimov IY, Guenza MG. Thermodynamic consistency between analytic integral equation theory and coarse-grained molecular dynamics simulations of homopolymer melts Macromolecules. 45: 8482-8493. DOI: 10.1021/Ma301502W  0.771
2010 Lyubimov IY, McCarty J, Clark A, Guenza MG. Analytical rescaling of polymer dynamics from mesoscale simulations. The Journal of Chemical Physics. 132: 224903. PMID 20550415 DOI: 10.1063/1.3450301  0.779
2010 McCarty J, Guenza MG. Multiscale modeling of binary polymer mixtures: Scale bridging in the athermal and thermal regime Journal of Chemical Physics. 133. DOI: 10.1063/1.3483236  0.733
2010 McCarty J, Lyubimov IY, Guenza MG. Effective soft-core potentials and mesoscopic simulations of binary polymer mixtures Macromolecules. 43: 3964-3979. DOI: 10.1021/Ma100052Z  0.781
2009 McCarty J, Lyubimov IY, Guenza MG. Multiscale modeling of coarse-grained macromolecular liquids. The Journal of Physical Chemistry. B. 113: 11876-86. PMID 19678631 DOI: 10.1021/Jp905071W  0.781
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