Publications

Before 2006, 2006-2011, 2012-2017

2018

F. C. Zegarra, D. Homouz, Y. Eliaz, A. G. Gasic, M. S. Cheung, “The impact of hydrodynamic interactions on protein folding rates depends on temperature”, Phys. Rev. E, 97, 032402 (2018). *Selected for Editor's suggestion.

M. Misiura, Q. Wang, M. S. Cheung, A. B. Kolomeisky, "Theoretical investigation of the role of mutation in dynamics of kinesin motor protein", J. Phys. Chem. B, 122, 4653-4661 (2018).

X. Sun, P. Zhang, Y. Lai, K. Williams, M. S. Cheung, B. Dunietz, E. Geva, “A computational study of charge transfer dynamics in the carotenoid porphyrin C60 molecular triad solvated in explicit tetrahydrofuran and its spectroscopic signature”, J. Phys. Chem. C, 122, 11288–11299 (2018).

M. S. Cheung, A.G. Gasic "Towards Developing Principles of Protein Folding and Dynamics in the Cell", Phys. Biol. 15, 063001 (2018).

Q. Wang, B. Janab, M. R. Diehl, M. S. Cheung, A. B. Kolomeisky, J. N. Onuchic, “Molecular mechanisms of the interhead coordination by interhead tension in cytoplasmic dyneins”, Proc. Natl. Acad. Sci. 115, 10052-10057 (2018).

J. C. Ezerski, M. S. Cheung, "CATS: a tool for clustering the ensemble of intrinsically disordered peptides on a flat energy landscape", J. Phys. Chem. B, 122, 11807–11816 (2018).

S. Bhandari, M. S. Cheung, E. Geva, L. Kronik, B. D. Dunietz, "Fundamental gaps of condensed-phase organic semiconductors from single-molecule calculations using polarizable consistent optimally tuned screened range-separated hybrid functionals", J. Chem. Theory Comput., 14, 6287-6294 (2018).

M. Ghane, S. Chandrasekaran, R. Searles, M. S. Cheung, O. Hermandez, “Path forward for softwarization to tackle evolving hardware”, Proc. SPIE, 10652, Disruptive Technologies in Information Sciences (2018).

2019

M. Ghane, S. Chandrasekaran, M. S. Cheung, “Gecko: Hierarchical heterogeneous portable shared memory abstraction”, Proceedings of the 10th International Workshop on Programming Models and Applications for Multicores and Manycores (PMAM) (2019).

F. C. Zegarra, D. Homouz, A. G. Gasic, L. Babel, M. Kovermann, P. Wittung-Stafshede, M. S. Cheung, “Crowding-induced elongated conformation of urea-unfolded apoazurin explained by in silico computations: Key role of crowder shape", J. Phys. Chem. B, 123, 3607–3617 (2019).

M. Ghane, M. S. Cheung, S. Chandrasekaran, “Pointerchain: Tracing Pointers to Their Roots”, Parallel Computing, 85, 190-203 (2019).

Q. Wang, M. Chen, C. Bueno, S. S. Song, A. Hudman, M. N. Waxham, P. G. Wolynes, M. S. Cheung, “Calcium/Calmodulin dependent kinase II – actin assemblies and their dynamic regulation by calmodulin in dendritic spines”, Proc. Natl. Acad. Sci., 116, 18937-18942 (2019)

A. G. Gasic, M. M. Boob, M. B. Prigozhin D. Homouz, C. M. Daugherty, M. Gruebele, M. S. Cheung, “Critical phenomena in the temperature-pressure-crowding phase diagram of a protein.” Phys. Rev. X, 9, 041035 (2019).

K. Dave, A. G. Gasic, M. S. Cheung, M. Gruebele, “Competition of folding and inter-domain aggregation in tethered WW domains”, Phys. Chem. Chem. Phys., 21, 24393-24405 (2019).

2020

A. G. Gasic, M. S. Cheung, “A tale of two desolvation potentials: an investigation of protein behavior under high hydrostatic pressure”, J. Phys. Chem. B. 124, 1619−1627 (2020).

J. C. Ezerski, P. Zhang, N. C. Jennings, M. N. Waxham, M. S. Cheung, “Molecular dynamics ensemble refinement of intrinsically disordered peptides from circular dichroism spectra”, Biophys. J, 118, 1665-1678 (2020).

J. Liman, C. Bueno, Y. Eliaz, M. N. Waxham, H. Levine, P. G. Wolynes, M. S. Cheung, “The role of the Arp2/3 complex in shaping the dynamics and structures of branched actomyosin networks”, Proc. Natl. Acad. Sci. 117, 10825-10831 (2020).

J. Tinnin, S. Bhandari, P. Zhang, H. Aksu, B. Maiti, E. Geva, B. D. Dunietz, X. Sun, M. S. Cheung, "Molecular-Level exploration of the structure-function relations underlying interfacial charge transfer in the subphthalocyanine:C₆₀ organic photovoltaic system", Phys. Rev. Applied, 13, 054075 (2020).

J. Han, P. Zhang, H. Aksu, B. Maiti, X. Sun, E. Geva, B. Dunietz, M. S. Cheung, “On the interplay between electronic structure and polarizable force fields when calculating solution-phase charge-transfer rates”, J. Chem. Theory Comput. 16, 6481–6490 (2020).

Z. Hu, Z. Tong, M. S. Cheung, B. Dunietz, E. Geva, X. Sun, “Photoinduced charge transfer dynamics in carotenoid-porphyrin-C₆₀ triad via the linearized semiclassical nonequilibrium Fermi's golden rule”, J. Phys. Chem. B, 124, 9579–9591 (2020).

Z. Tong, X. Gao, M. S. Cheung, B. Dunietz, E. Geva, X. Sun, “Charge transfer rate constants for the carotenoid-porphyrin-C₆₀ molecular triad dissolved in tetrahydrofuran: the spin-boson model vs. the linearized semiclassical approximation”, J. Chem. Phys. 153, 044105 (2020).

Y. Eliaz, F. Nedelec, G. Morrison, H. Levine, M. S. Cheung, “Multivalent actin-binding proteins augment the variety of morphologies in actomyosin networks”, Phys. Rev. E 102, 062420 (2020).

G. Qin, J. M. Choi, H. Lin, A. G. Gasic, M. S. Cheung, S. Y. Jung, and C. Cai, "Evaluation of timsTOF Pro mass spectrometer for deep shotgun proteomics with low sample loading", submitted (2020).

2021

J. Nde, P. Zhang, J. C. Ezerski, P. G. Wolynes, M. S. Cheung, “Coarse-grained modeling and molecular dynamics simulations of Ca²⁺-calmodulin”, in press, Frontiers in Molecular Sciences (2021).

A. G. Gasic, A. Sharkar, M. S. Cheung, “Understanding protein complex assembly through grand canonical maximum entropy modeling”, in press, Physical Rev. Research (2021).

J. Tinnin, S. Bhandari, P. Zhang, H. Aksu, B. Maiti, E. Geva, B. D. Dunietz, X. Sun, M. S. Cheung, “CTRAMER: software for calculating charge-transfer-rate constants with condensed-phase effects”, J. Chem. Phys. 154, 214108 (2021)

F. C. Zegarra, D. Homouz, P. Wittung-Stafshede, M. S. Cheung, “The zero-order loop in apoazurin modulates unfolding in silico", J. Phys. Chem. B, 125, 3501-3509 (2021).

P. Zhang, J. Han, P. Cieplak, M. S. Cheung, “Determining the atomic charge of calcium ion in a calcium-binding protein requires the information of its dynamic coordination geometry in aqueous solution", J. Chem. Phys. 154, 124104 (2021).