RECENT PUBLICATIONS
4D Whole-cell Modeling of a Minimal Autotroph Reveals Carbon Metabolism Under Light Disturbance
C. Johnson*, A. Chan*, J. Rozum*, A. George, A. Pavate, P. Bohutskyi, D. N. Kim, S. Feng, Z. Johnson, N. Sadler, M. Garcia, X. Li, J. Trejo, R. Wu, W. Sineath, L. Anderson, J. Evans, W.-J. Qian, A. P. Mehta, Z. Luthey-Schulten+, M. S. Cheung+, accepted by Biophysical Journal (2026)
Physical principles of building protein megacomplexes in a crowded milieu
J. Wang, J. Nde, A. G. Gasice34, J. Haseley, M. S. Cheung, accepted by Physical Review Research (2026)
Graph identification of proteins in tomograms (GRIP-Tomo) 2.0: Topologically aware classification for proteins
C. Li, A. George, R. Neff, D. N. Kim, T. Moser, K. Baldwin, A. Firoozfar, J. E Evans*, and M. S. Cheung*, accepted by Protein Science (2026).
Charge Transport in Solvated Donor-Acceptor Functionalized Peptoids: Molecular Dynamics and Rate Theory
. W. Huang, B. Harris, S. Bakenhaster, R. Khatri, M. S. Cheung, B. Dunietz; M, Baer, E. Geva, accepted by JCTC (2026)
Thiol post-translational modifications modulate allosteric regulation of the OpcA–G6PDH complex through conformational gate control
H. Kim*+, S. Feng,* P. Bohutskyi, X. Li, D. Mejia-Rodriguez, T. Zhang, W.-J. Qian, M. S. Cheung+, acceptd by Protein Science (2026)
Rapid adaptation of cyanobacteria to environmental perturbations is achieved through structural remodeling of the proteome
S. Sarkar, E. M. Van Fossen, X. Li, T. Zhang, S. Feng, V. Prozapas, I. D. Ludovico, A. D Shouaib, C. M. Hutchinson-Bunch, N. Sadler, I. K. Attah, W.-J. Qian, M. S. Cheung, P. Bohutskyi, J. T. Melchior, accepted by Mol. Cell. Proteom. (2026).
Sampling microbial dynamics in the Salish Sea estuary: Evaluating methods to capture cyanobacteria and cyanophage
N. R. Boise, O. P. Leiser, K. Jones, M. Peter-Frank, D. Leach, S. Crafton-Tempel, P. Regier, R. , C. Phillips, M. S. Cheung, C. G. Johnson, S. J. Edmundson, D. Pollock, Frontiers in Marine Science, 13, 1769457 (2026).
Synergy and antagonism in a genome-scale model of metabolic hijacking by bacteriophage
J. C. Rozum*, W. Sineath*, D. N. Kim, P. Bohutskyi, C. Johnson, J. Evans, D. Pollock, W.-J. Qian, M. S. Cheung, R. Wu+, Song Feng+, Science Advances, 12, eaeb7646 (2026).
PTM-Psi on the Cloud: A Cloud-Compatible Workflow for Scalable, High-Throughput Simulation of Post-Translational Modifications in Protein Complexes
S. Samantray#, M. Lockwood#, A. Andersen, H. Kim, P. Rigor, M. S. Cheung*, D. Mejia-Rodriguez*, J. Chem. Inf. Model. 65, 11473-11485 (2025)
Cyanobacterial circadian regulation enhances bioproduction under subjective nighttime through rewiring of carbon partitioning dynamics, redox balance orchestration, and cell cycle modulation
Gene network centrality analysis identifies key regulators coordinating day-night metabolic transitions in Synechococcus elongatus PCC 7942 despite limited accuracy in predicting direct regulator-gene interactions
Multi-Omics Reveals Temporal Scales of Carbon Metabolism in Synechococcus Elongatus PCC 7942 Under Light Disturbance
C. G. M. Johnson*, Zachary Johnson*, L. S. Mackey*, X. Li, N. C. Sadler, T. Zhang, W.-J. Qian, P. Bohutskyi, S. Feng, M. S. Cheung, PRX Life 3, 033017 (2025)
CaX-ML: Chemistry-informed machine learning explains mutual changes between protein conformations and calcium ions in calcium-binding proteins using structural and topological features
P. Zhang*, J. Nde*, Y. Eliaz, N. Jennings, P. Cieplak, M.. S. Cheung, Protein Science, 34, e70023 (2025)
Potential quantum advantage for simulation of fluid dynamics
X. Li, X. Yin, N. Wiebe, J. Chun, G. K. Schenter, M. S. Cheung, J. Muelmenstaedt, Physical Review Research 7, 013036 (2025).
Improved enzyme functional annotation prediction using contrastive learning with structural inference
Y. Yang, A. Jerger, S. Feng, Z. Wang, C. Brasfield, M. S. Cheung, J. Zucker, Q. Guan , Communications Biology, 7, 1690 (2024)
Deciphering the cofilin oligomers via intermolecular disulfide bond formation: A coarse-grained molecular dynamics approach to understanding cofilin’s regulation on actin filament
C. Li, T. Wei, M.S. Cheung, M.Y. Tsai, J. Phys. Chem. B, 128, 4590-4601 (2024).