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Margaret S. Cheung
Computational Scientist

Margaret Cheung is a biological physicist and computational scientist with the Systems Modeling and Computational Science team. She holds a dual appointment with the Department of Physics at the University of Washington. She is interested in employing an integrative approach of quantum mechanical calculations, molecular simulations, out-of-equilibrium statistical physics, and network theory to investigate the role of emergent, higher-order protein assemblies in regulating living matter. 

Research Interests

  • Emergent protein assemblies in a cell modeled with statistical physics, machine learning, and big data 

  • Principles for tuning target selectivity in signaling proteins  

  • Molecular physics of learning and memory formation 

  • Organization of protein-mediated actomyosin networks and cellular transport 

  • Molecular design of artificial photosynthetic materials under extreme conditions 


  • Sloan Postdoctoral Fellow, University of Maryland, 2003 – 2006
  • PhD in Physics, University of California at San Diego, 2003
  • BS in Chemistry, National Taiwan University, 1994

Awards and Recognition

  • UW Louise Stokes Alliance for Minority Participation (LSAMP) Faculty of the Year Award (2022)
  • Robert S. Hyer Research Award (2019)         
  • University of Houston Moores Professorship (2018)
  • University of Houston Excellence in Research and Scholarship (Associate Professor) (2016)
  • Fellow of the American Physical Society (2013)
  • University of Houston Excellence in Research and Scholarship (Assistant Professor) (2012)
  • Robert S. Hyer Research Award (2010)
  • University of Houston New Faculty Award (2006)
  • Alfred P. Sloan Foundation Postdoctoral Fellowship (2003 – 2006)
  • National Taiwan University Book Coupon Award (1990 – 1991)

Affiliations and Professional Service

American Physical Society:

  • Organizer: Focus session on “Hydrophobic Interactions in Multiple Scales for Biology” at the Annual March Meeting of the American Physical Society (2008)
  • Organizer: Focus session on “Simulations and Theories for Biomolecules under Cell-like Conditions” at the Annual March Meeting of the American Physical Society (2009)
  • Member at large: Division of Biological Physics, American Physical Society (2010-2013)
  • Chair/Chair line: Division of Biological Physics, American Physical Society (2020-2024)

Biophysical Society:

  • Organizer: Member-organized session on “Biopolymer Dynamics in Cell-like Environment” at the Annual Meeting of the Biophysical Society (2010)
  • Founding Chair and Chair: Biopolymers In Vivo Subgroup, Biophysical Society (2011-2012)
  • Member: Education Committee, Biophysical Society (2012-2015)
  • Program Chair: Biopolymers in vivo Subgroup of the Biophysical Society Meeting (2016-2017)
  • Member at large: Biopolymers in vivo Subgroup of the Biophysical Society Meeting (2018-2021)
  • Member: Biophysical Society Council (2023-2026)

The Protein Society

  • Member: Executive Council, the Protein Society (2021-2024)

Greater Science Community:

  • Co-Director and faculty advisor: Science Teacher Equity Program (UH) for science teachers in elementary schools and for physics teachers in high schools (2012-2017)
  • Faculty member of the steering committee: Houston Area Molecular Biophysics Training Program (2013-2020)
  • Outreach Director: Center for Theoretical Biological Physics at Rice University (2013-2021)
  • Chair: Protein Folding Dynamics -- from protein folding in vitro to hierarchical assembly in vivo, Gordon Research Conference (2020)
  • Co-Organizer, National Science Foundation Virtual Workshop: Growing Equity, Inclusion, and Diversity for the Physics of Living Systems Student Research Network (2020).
  • Faculty mentor of the Physics of Living Systems Student Research Network (2014-present).
  • Faculty mentor of the Physics of Living Systems Physics Teacher Network (2020-2021).



A. George, D. N. Kim, T. Moser, I. T. Gildea, J. Evans, M. S. Cheung, “Graph identification of proteins in tomographs (GripTOMO)”, accepted by Protein Science (2022).

A. Sarkar, A. G. Gasic, M. S. Cheung, G. C. Morrison, “Effects of protein crowders and charge on the folding of superoxide dismutase 1 variants: a computational study”, J. Phys. Chem. B. 126, 4458-4471(2022).

C. Bueno, J. Liman, N. P. Schafer, M. S. Cheung, P. G. Wolynes, “A generalized Flory-Stockmayer kinetic theory of connectivity percolation and rigidity percolation of cytoskeletal network”, PoLS Comp. Biol. 18, e1010105 (2022).

J. Tinnin, S. Bhandari, P. Zhang, E. Geva, B. D. Dunietz, X. Sun, M. S. Cheung, “Correlating interfacial charge transfer rates with interfacial molecular structure in the tetraphenyldibenzoperiflanthene/C70 organic photovoltaic system”, J. Phys. Chem. Lett., 13, 763-769 (2022).


C. Li, J. Liman, Y. Eliaz, M. S. Cheung,“Forecasting avalanches in branched actomyosin networks with network science and machine learning”, J. Phys. Chem. B, 125, 11591-11605 (2021).

J. Nde, P. Zhang, J. C. Ezerski, P. G. Wolynes, M. S. Cheung, “Coarse-grained modeling and molecular dynamics simulations of Ca2+-calmodulin”, Frontiers in Molecular Sciences, 8, 661322 (2021).

.A. G. Gasic, A. Sharkar, M. S. Cheung, “Understanding protein complex assembly through grand canonical maximum entropy modeling”, Physical Rev. Research, 3, 033220 (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).


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). 

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). 

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. Liman, C. Bueno, Y. Eliaz, M. N. Waxham, H. Levine, P. G. Wolynes, M. S. Cheung, “The contractility of actomyosin network in the presence of arp2/3,” Proc. Natl. Acad. Sci. 117, 10825–10831 (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). 

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). 


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). 

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). 

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). 

M. Ghane, M. S. Cheung, S. Chandrasekaran, “Pointerchain: Tracing pointers to their root,” Parallel Computing, 85, 190–203 (2019). 

F. C. Zegarra, D. Homouz, M. Kovermann, A. G. Gasic, L. Babel, 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). 


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). 

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. U.S.A., 115, 10052–10057 (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. 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). 

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). 


Q. Wang, M. R. Diehl, B. Jana, M. S. Cheung, A. B. Kolomeisky, J. N. Onuchic, “Molecular origin of the weak susceptibility of kinesin velocity to loads and its relation to the collective behavior of kinesins,” Proc. Natl. Acad. Sci. U. S. A., 114, E8611–E8617 (2017). 

O.N. Starovoytov, P. Zhang, P. Cieplak, M. S. Cheung, “Induced polarization restricts conformational distribution of a light-harvesting molecular triad in the ground state,” Phys. Chem. Chem. Phys., 19, 22969–22980 (2017). 

P. Zhang, L. S. Tripathi, H. Trinh, M. S. Cheung, "Opposing intermolecular tuning of Ca2+ affinity for calmoduin by target peptide," Biophys. J., 112, 1105–1119 (2017).  

M.Y. Tsai, W. Zheng, D. Balamurugan, N.P. Schafer, B.L. Kim, M.S. Cheung, P.G. Wolynes, "Electrostatics, structure prediction and the energy landscapes for protein folding and binding," Protein Science, 25, 255–269 (2016). 


S. Tripathi, L. Belkacemi, M. S. Cheung, R. N. Bose, "Correlation between gene variants, signaling pathways and efficacy of chemotherapy drugs against colon cancers," Cancer Informatics, 15, 1–13 (2016).   


L. Hoffman, X. Wang, H. Sanabria, M. S. Cheung, J. Putkey, M. N. Waxham, "Tuning of protein function by macromolecular crowding," Biophys. J., 109, 510–520 (2015).  

S. Tripathi, M. N. Waxham, M. S. Cheung, Y. Liu, “Lessons in Protein Design from Combined Evolution and Conformational Dynamics,” Scientific Reports, 5, 14259 (2015). 

A. K. Manna, D. Balamurugan, M. S. Cheung, B. D. Dunietz, “Unraveling the mechanism of photo-induced charge-transfer in carotenoid-porphyrin-C60 molecular triad,” J. Phys. Chem. Lett., 6, 1231–1237 (2015). 

S. Tripathi, P. Zhang, Q. Wang, L. Hoffman, M. N. Waxham, M. S. Cheung, "Conformational Frustration in Calmodulin-Target Recognition," Journal of Molecular Recognition, 28, 74–86 (2015) 


Q. Wang, P. Zhang, S. Tripathi, L. Hoffman, L. Yin, M. N. Waxham, M. S. Cheung, "Protein recognition and selection through conformational and mutually induced fit," Proc. Natl. Acad. Sci. U. S. A., 110, 20545–20550 (2013). 

D. Balamurugan, A. J. A. Aquino, F. De Dios, L. Flores Jr., H. Lischka, M. S. Cheung, "Multiscale simulation of the ground and photo-induced charge-separated states of molecular triad in polar organic solvent: exploring the conformations, fluctuations and the free energy landscapes," J. Phys. Chem. B., 117, 12065–12075 (2013). 


E. Chen, A. Christiansen, Q. Wang, M. S. Cheung, D.S. Kliger, P. Wittung-Stafshede, "Crowd control and the effects of macromolecular crowding on burst phase kinetics of cytochrome c folding," Biochemistry, 51, 9836–9845 (2012).  

A. Kudlay, M. S. Cheung, D. Thirumalai, "Influence of the Shape of Crowding Particles on the Structural Transitions in a Polymer," J. Phys. Chem. B, 116, 8513–8522 (2012).  

Q. Wang, M. S. Cheung, “A Physics-based approach of coarse-graining the cytoplasm of E. coli (CGCYTO),” Biophys. J., 102, 2353–2361 (2012). 

G. Su, A. Czader, D. Homouz, G. Bernardes, S. Mateen, M. S. Cheung, “Multiscale simulation on a light-harvesting molecular triad,” J. Phys. Chem. B, 116, 8460–8473 (2012). 


Q. Wang, A. Christiansen, A. Samiotakis, P. Wittung-Stafshede, M. S. Cheung, “Part II. Comparison of chemical and thermal protein denaturation by combination of computational and experimental approaches," J. Chem. Phys., 135, 175102 (2011). 

A. Samiotakis, M. S. Cheung, "Part I. Folding dynamics of Trp-cage in the presence of chemical interference and macromolecular crowding," J. Chem. Phys., 135, 175101 (2011). 

Q. Wang, K.-C. Liang, A. Czader, M. N. Waxham, M. S. Cheung, "The effect of macromolecular crowding, ionic strength and calcium binding on calmodulin dynamics," PLoS Comp. Biol., 7, e1002114 (2011). 


Q. Wang, G. Hong, J. Glenn, R. Pachter, M. S. Cheung, "Biophysical properties of membrane-active peptides based on micelle modeling: A case study of cell-penetrating and antimicrobial peptides," J. Phys. Chem. B, 114, 13726–13735 (2010). 

A. Dhar, A. Samiotakis, S. Ebbinghaus, L. Nienhaus, D. Homouz, M. Gruebele, M. S. Cheung, "Structure, function and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding," Proc. Natl. Acad. Sci. U. S. A., 107, 17586–17591 (2010). 

•  Commentary "Crowding and Function Reunite" by G. J. Pielak and A. C. Miklos, PNAS, 107, 17457–17458 (2010).  

A. Christiansen, Q. Wang, A. Samiotakis, M. S. Cheung, P. Wittung-Stafshede, "Factors defining effects of macromolecular crowding on protein stability: an in vitro/in silico case study using cytochrome c," Biochemistry, 49, 6519–6530 (2010). 

A. Samiotakis, D. Homouz, M. S. Cheung, "Multiscale investigation of chemical interference in proteins," J. Chem. Phys., 132, 175101 (2010). 

L. Stagg, A. Samiotakis, M. S. Cheung, P. Wittung-Stafshede, “Residue specific analysis of frustration in folding landscape of repeat β/α protein apoflavodoxin,” J. Mol. Biol., 396, 75–89 (2010). 


D. Homouz, H. Sanabria, M. N. Waxham, M. S. Cheung, “Modulation of calmodulin plasticity by the effect of macromolecular crowding,” J. Mol. Biol., 391, 933–943 (2009). 

D. Homouz, B. Hoffman, M. S. Cheung, “Hydrophobic interactions of hexane in nanosized water droplets,” J. Phys. Chem. B, 113, 12337–12342 (2009). 

A. Kudlay, M. S. Cheung, D. Thirumalai, “Crowding effects on the structural transitions in a flexible helical homopolymer,” Phys. Rev. Letts., 102, 118101 (2009). D. Homouz, L. Stagg, P. Wittung-Stafshede, M. S. Cheung, “Macromolecular crowding modulates folding mechanism of α/β protein apoflavodoxin,” Biophys. J., 96, 671–680 (2009). 


D. Homouz, M. Perham, A. Samiotakis, M. S. Cheung, P. Wittung-Stafshede. “Crowded, cell-like environment induces shape changes in aspherical protein,” Proc. Natl. Acad. Sci. U. S. A., 105, 11754–11759 (2008).  

• Featured as best biophysics paper in Research Highlights of 2008 in Nature. 


L. Stagg, S.-Q. Zhang, M. S. Cheung, P. Wittung-Stafshede, “Molecular crowding enhances native structure and stability of α/β protein flavodoxin,” Proc. Natl. Acad. Sci. U. S. A., 104, 18976–18981 (2007). 

S.-Q. Zhang, M. S. Cheung, “Manipulating Biopolymer Dynamics by Anisotropic Nanoconfinement,” Nano Letters, 7, 3438–3442 (2007).  

M. S. Cheung, D. Thirumalai, “Crowding and confinement effects on structures of the transition state ensemble in proteins,” J. Phys. Chem. B, 111, 8250–8257 (2007). 

M. E. Sardiu, M. S. Cheung, Y.-K. Yu, “Cysteine-Cysteine contact preference leads to target-focusing in protein folding,” Biophys., J., 93, 1–14 (2007). 


M. S. Cheung, D. Thirumalai, “Nanopore-protein interactions dramatically alter stability and yield of the native state in restricted spaces,” J. Mol. Biol., 357, 632–643 (2006). 


J. Chahine, M. S. Cheung, “Computational studies of the reversible domain swapping of p13suc1,” Biophys. J., 89, 1–9 (2005). 

M. S. Cheung, D. Klimov, D. Thirumalai, “Molecular crowding enhances native state stability and refolding rates,” Proc. Natl. Acad. Sci. U. S. A., 102, 4753–4758 (2005). 


S. Yang, S. S. Cho, Y. Levy, M. S. Cheung, H. Levine, P. G. Wolynes, J. N. Onuchic, “Domain swapping is a consequence of minimal frustration,” Proc. Natl. Acad. Sci. U. S. A., 101, 13786–13791 (2004). 

J. M. Finke, M. S. Cheung, J. N. Onuchic, “A structural model of polyglutamine determined from a host-guest method combining experiments and landscape theory,” Biophys. J., 87, 1900–1918 (2004). 

A. Fernandez-Escamilla, M. S. Cheung, M. C. Vega, M. Wilmanns, J. N. Onuchic, L. Serrano,  “Solvation in protein folding analysis, combination of theoretical and experimental approaches,” Proc. Natl. Acad. Sci. U. S. A., 101, 2834–2839 (2004). 

M. S. Cheung, L. L. Chavez, J. N. Onuchic, “The Energy Landscape for Protein Folding and Possible Connections to Function,” Polymer, 45, 547–555 (2004). 


M. S. Cheung, J. M. Finke, B. Callahan, J. N. Onuchic, “Exploring the interplay of topology and secondary structural formation in the protein folding problem,” J. Phys. Chem. B, 107, 11193–11200 (2003). 


C. Guo, M. S. Cheung, H. Levine, D. A. Kessler, “Mechanisms underlying sequence-independent beta-sheet formation,” J. Chem. Phys., 116, 4353–4365 (2002). 

M. S. Cheung, A. E. García, J. N. Onuchic, “Protein folding mediated by solvation: water expelling and formation of the hydrophobic core occurs after the structure collapse,” Proc. Natl. Acad. Sci. U. S. A., 99, 685–690 (2002). 


M. S. Cheung, I. Daizadeh, A. A. Stuchebrukhov, P. F. Heelis, “Pathways of Electron Transfer in E. coli DNA Photolyase,” Biophys. J., 76, 1241–1249 (1999).