Hagan Group


Submitted / Under Revision

  • Fang, H; Tyukodi, B; Rogers, WB; Hagan, MF, “Polymorphic self-assembly of helical tubules is kinetically controlled," submitted, arxiv.2205.11598

  • Joshi, C; Ray, S; Lemma, L; Varghese, M.; Sharp, G; Dogic, Z; Baskaran, A*; Hagan, MF*, “Data- driven discovery of active nematic hydrodynamics," doi.org/10.48550/arXiv.2202.12854

  • Hayakawa, D; Videbæk, TE; Hall, DM; Fang, H; Sigl, C; Feigl, E; Dietz, H; Fraden, S; Hagan, MF; Grason, GM; Rogers, WB, “Geometrically programmed self-limited assembly of tubules using DNA origami colloids," doi.org/10.48550/arXiv.2203.01421

  • Mohajerani F, Tyukodi B, Schlicksup CJ, Hadden-Perilla JA, Zlotnick A, Hagan MF, “Multiscale Modeling of Hepatitis B Virus Capsid Assembly and its Dimorphism," doi.org/10.1101/2022.02.23.481637

  • Asor R, Singaram SW, Levi-Kalisman Y, Hagan MF*, Raviv U*. “Effect of Ionic Strength on the Assembly of Simian Vacuolating Virus Capsid Protein Around Poly(Styrene Sulfonate),"  doi.org/10.1101/2022.02.25.481942

  • Fily, Y; Baskaran, A; Hagan, MF, “Active Particles on Curved Surfaces," in revision, arXiv:1601.00324

Accepted or Published


  • Tyudoki, B; Mohajerani, F; Hall, DM; Grason, GM*, Hagan, MF*, “Thermodynamic size control in curvature-frustrated tubules: Self-limitation with open boundaries,"  ACS Nano (accepted), arxiv:2109.01174

  • Tsidilkovski L; Mohajerani, F; Hagan MF. “Microcompartment assembly around multicomponent fluid cargoes," J. Chem. Phys (accepted), doi.org/10.1101/2022.02.23.481520

  • Videbaek, TE; Fang, H; Hayakawa, D; Tyukodi, B; Hagan, MF; Rogers, WB, “Tiling a tubule: How increasing complexity improves the yield of self-limited assembly,"  J. Phys. Condens. Matter, 34, 134003 (2022), https://dx.doi.org/10.1007/s11071-022-07202-2

  • Wagner, C; Hagan, MF; Baskaran, A, “Steady states of active Brownian particles interacting with boundaries,"  J. Stat. Mech. 013208 (2022), https://doi.org/10.1088/1742-5468/ac42cfarxiv:2109.06353


  • Peterson, MSE; Baskaran, A; Hagan, MF, “Vesicle shape transformations driven by confined active filaments,"  Nat. Comm., 12, 7247 (2021), link, arXiv:2102.02733

  • Lemma, LM; Norton, MM; DeCamp, SJ; Aghvami, SA; Fraden, S; Hagan, MF; Dogic, Z, "Multiscale dynamics in active nematics,"  Phys. Rev. Lett. 127, 148001 (2021), https://doi.org/10.1103/PhysRevLett.127.148001, arXiv:2006.15184

  • Tayar, AM; Hagan, MF; Dogic, Z, "Active liquid crystals powered by force-sensing DNA-motor clusters,"  Proc. Natl. Acad. Sci. (USA), 118, e2102873118 (2021), https://doi.org/10.1073/pnas.2102873118

  • Merminod, S; Edison, JR; Fang, H; Hagan, MF; Rogers, WB, “Avidity and surface mobility in multivalent ligand-receptor binding," Nanoscale, 13, 12602-12612 (2021), DOI: 10.1039/D1NR02083H

  • Hagan, MF; Grason, GM, “Equilibrium mechanisms of self-limiting assembly,"  Rev. Mod. Phys., 93, 025008 (2021), https://doi.org/10.1103/RevModPhys.93.025008, arXiv:2007.01927

  • Mohajerani, F; Sayer, E; Neil, C; Inlow, K; Hagan, MF, “Mechanisms of scaffold-mediated microcompartment assembly and size-control,"  ACS Nano, 15, 4197–4212 (2021) https://doi.org/10.1021/acsnano.0c05715

  • Sigl, C; Willner, EM; Engelen, W; Sachenbacher, K; Liedl, A; Kolbe, F; Wilsch, F; Aghvami, SA; Protzer, U; Hagan, MF; Fraden, S; Dietz, H, “Programmable icosahedral shells for virus neutralization,"  Nat. Mater., 20, 1281–1289 (2021), DOI:10.1038/s41563-021-01020-4, [link]

  • Chelakkot, R; Hagan, MF; Mahadevan, L; Gopinath, A, “Synchronized oscillations, metachronal waves, and jammed clusters in sterically interacting active filament arrays,"  Soft Matter, 17, 1091-1104, (2021) https://doi.org/10.1039/D0SM01162B

  • Zhou, Z; Joshi, C.; Liu, R; Norton, MM; Lemma, LM; Dogic, Z; Hagan, MF; Fraden S; Hong, P, “Machine Learning Forecasting of Active Nematics," Soft Matter, 17, 738-747 (2021). https://doi.org/10.1039/D0SM01316A, arXiv:2007.14837



  • Joshi, A; Putzig, E; Baskaran, A*; Hagan, MF*, “The interplay between activity and filament flexibility determines the emergent properties of active nematics,"  Soft Matter, 15, 94 (2019), doi:10.1039/C8SM02202J, link

  • Wagner, C; Hagan, MF*; Baskaran, A*, “Response of active Brownian particles to boundary driving,"  PRE, 100, 042610 (2019), https://doi.org/10.1103/PhysRevE.100.042610, arXiv:1905.12706

  • Zuraw-Weston, S; Wood, DA; Torres, IK; Lee, YW; Wang, LS; Jiang, Z; Lázaro, GR; Wang, SY; Rodal, AA; Hagan, MF; Rotello, VR; Dinsmore; AD, “Nanoparticles Binding to Lipid Membranes: from Vesicle-Based Gels to Vesicle Inversion and Destruction," Nanoscale, 11, 1846 (2019), https://doi- org/10.1039/C9NR06570A, arXiv:1805.04214, PMCID PMC7155749

  • Hagan, MF, “Driving assembly far from equilibrium” commentary for the Journal Club for Condensed Matter Physics, 8/2019, https://www.condmatjclub.org

  • Siavashpouri, M; Sharma, P; Fung, J; Hagan, MF; Dogic, Z, “Structure, dynamics and phase behavior of short rod inclusions dissolved in a colloidal membrane," Soft Matter, 15, 7033-7042 (2019), https://doi-org/10.1039/C9SM01064E, arXiv:1906.06551

  • Balchunas, AJ; Cabanas, RA; Zakhary MJ; Gibaud, T; Sharma, P; Hagan MF; Fraden, S; Dogic, Z, “Equation of State of Colloidal Membranes," Soft Matter, 15, p.6791-6802 (2019), DOI:10.1039/C9SM01054H, arXiv:1905.13227

  • Miller, J; Joshi, C; Sharma, P; Baskaran, A; Grason, GM; Hagan, MF; Dogic, Z, “Conformational switching of chiral colloidal rafts regulates raft-raft attractions and repulsions," PNAS, 116, 15792– 15801 (2019), https://doi.org/10.1073/pnas.1900615116

  • Dharmavaram, S; She, B.; Lazaro, GR; Hagan, MF; Bruinsma, R, “Gaussian curvature and the budding kinetics of enveloped viruses," Plos. Comp. Biol, 15, e1006602 (2019), https://doi.org/10.1371/journal.pcbi.1006602

  • Stiller, JB; Kerns, J; Pachov, D; Cho, YJ; Otten, R; Hagan, MF; Kern D “Probing the transition state in enzyme catalysis by high-pressure NMR dynamics," Nat. Catal., 2, 726–734 (2019), https://doi.org/10.1038/s41929-019-0307-6 ; News & Views commentary: https://doi.org/10.1038/s41929-019-0326-3


  • Mohajerani F; Hagan MF “The role of the encapsulated cargo in microcompartment assembly," Plos. Comp. Biol., 14, e1006351 (2018), link, PMC6086489

  • Lazaro, GR; Dragnea, B; Hagan, MF, “Self-assembly of convex particles on spherocylindrical surfaces," Soft Matter, 14, 5728-5740 (2018) DOI: 10.1039/C8SM00129D, link, NIHMS970685

  • Zeng, C; Lazaro, GR; Tsvetkova, I; Hagan, MF*; Dragnea, B*, “Defects and Chirality in the Nanoparticle-Directed Assembly of Spherocylindrical Shells of Virus Coat Proteins," ACS Nano, 12, 5323–5332 (2018), [DOI:10.1021/acsnano.8b00069], NIHMSID 986481

  • Lazaro, GR; Mukhopadhyay, S; Hagan, MF, “Why Enveloped Viruses Need Cores — The Contribution of a Nucleocapsid Core to Viral Budding," Biophys. J., 114, 619-630 (2018), link

  • Norton, MM; Baskaran, A; Opathalage, A; Langeslay, B; Fraden, S; Baskaran, A*; Hagan, MF* Insensitivity of active nematic liquid crystal dynamics to topological constraints," Phys. Rev. E, 97, 012702 (2018), link

  • Michaels, TCT; Bellaiche, MMJ; Hagan, MF; Knowles, TPJ, “Kinetic constraints on the self- assembly of building blocks into closed supramolecular structures," Sci. Reports, 7, 12295 (2017), [link]

  • Fily, Y; Baskaran, A; Hagan, MF, “Equilibrium mappings in polar-isotropic confined active particles," Eur. Phys. J. E 40, 61 (2017). doi:10.1140/epje/i2017-11551-3arXiv:1612.08719

  • Sakhardande, R., Stanojeviea, S., Baskaran, A., Baskaran, A., Hagan, M.F.*, Chakraborty, B., “Theory of microphase separation in bidisperse chiral membranes.” Phys. Rev. E, 96, 012704 (2017), arXiv:1604.03012, https://doi.org/10.1103/PhysRevE.96.012704

  • Wagner, CG; Hagan, MF; Baskaran, A, “Steady-state distributions of ideal active Brownian particles under confinement and forcing," J. Stat. Mech., 043203 (2017), http://iopscience.iop.org/article/10.1088/1742- 5468/aa60a8/meta

  • Liu, K; Hagan, MF; Lisman, JE, “Gradation (~10 size states) of synaptic strength by quantal addition of structural modules” Phil. Trans. R. Soc. B, 372, 20160328 (2017) [link]


  • Redner, GS; Wagner, CG; Baskaran, A; Hagan, MF, “A classical nucleation theory description of active colloid assembly," Phys. Rev. Lett., 117, 148002, [link] (2016), arXiv:1603.01362

  • Yu, N; Ghosh, A; Hagan, MF, “Faceted particles formed by the frustrated packing of anisotropic colloids on curved surfaces," Soft Matter, 12, 8990 (2016), [cover article] NIHMSID 846122 http://dx.doi.org/10.1039/C6SM01498D

  • Perlmutter JD; Mohajerani, F; Hagan, MF, Many-molecule encapsulation by an icosahedral shell, eLife 5, e14078 (2016); http://dx.doi.org/10.7554/eLife.14078

  • Lazaro, GR; Hagan, MF, “Allosteric control in icosahedral capsid assembly," J. Phys. Chem B, 120, 6306-6318 [Bill Gelbart Festschrift] [link] (2016) PMCID 5367391

  • Perkett, M.R.; Mirijanian, D.T.; Hagan, M.F., “The Allosteric Switching Mechanism in Bacteriophage MS2," J. Chem. Phys. 145, 035101 [cover article],[link], arXiv:1503.01204 (2016). PMC4947040

  • Xie, S; Pelcovits, RA*; Hagan, MF*, “Probing a self-assembled fd virus membrane with a microtubule,"  Phys. Rev. E, 93, 062608, [linkarXiv:1512.02204 (2016)

  • Xie, S; Hagan, MF*; Pelcovits, RA*, “Interaction of chiral rafts in self-assembled colloidal membranes,"  Phys. Rev. E, 93, 032706 (2016), [linkarXiv:1601.08232

  • Hagan MF; Zandi, R, “Recent advances in coarse-grained modeling of virus assembly," Curr Opin Virol, 18, 36-43 (2016) [link] NIHMSID 772743

  • Hagan MF; Baskaran A, “Emergent self-organization in active materials," Curr Opin Cell Biol, 38, 74-80 (2016) [link] NIHMS 772743


  • Kelley, CF; Messelaar, EM; Eskin, T; Wang, S; Song, K; Vishnia, K; Becalska, AN; Shupliakov, O; Hagan, MF; Danino, D; Sokolova, O; Nicastro, D; Rodal, AA, “Membrane charge directs the outcome of F-BAR domain lipid binding and autoregulation," Cell Reports, 13, 2597–2609 (2015) [link]

  • Perlmutter, J.D.; Hagan, M.F., “Mechanisms of Virus Assembly," Annu. Rev. Phys. Chem., 66, 217-39 (2015), [link], arXiv:1407.3856

  • Ruiz-Herrero, T., Hagan, M.F., “Simulations show that Virus Assembly on a Membrane is Facilitated by Membrane Microdomains," Biophys. J., 108, 585-595 (2015), arXiv:1403.2269,  PMCID 4317536

  • Perlmutter, J.D.; Hagan, M.F., “The role of packaging sites in efficient and specific virus assembly," J. Mol. Biol., 427, 2451–2467 (2015), doi:10.1016/j.jmb.2015.05.008  NIHMSID 691930

  • DeCamp, SJ; Redner, G; Baskaran, A; Hagan, MF*; Dogic, Z*, “Orientational order of motile defects in active nematics," Nature Mater., 14, 1110–1115 (2015) [link]

  • Fily, Y; Baskaran, A; Hagan, MF, “Dynamics and density distribution of strongly confined noninteracting nonaligning self-propelled particles in a nonconvex boundary," Phys. Rev. E, 91, 012125 (2015), [link], arXiv:1410.5151

  • Pontiggia, F; Pachov, D; Clarkson, M; Villali, J; Hagan, MF; Pande, V; Kern, D, “Free energy landscape of activation in a signaling protein at atomic resolution," Nat. Comm., 6, 7284 (2015) doi:10.1038/ncomms8284, [link], PMCID: PMC4470301

  • Hilitski, F.; Ward, AR; Cajamarca, L; Hagan, MF; Grason, GM; Dogic, Z, Measuring cohesion between macromolecular filaments, one pair at a time: Depletion-induced microtubule bundling," Phys. Rev. Lett., 114, 138102 (2015), arXiv:1408.5068

  • Kerns, SJ; Agafonov, RV; Cho, YJ; Pontiggia, F; Otten, R; Pachov, DV; Kutter, S; Phung, LA; Murphy, PN; Thai, V; Alber T; Hagan, MF; Kern, D, “The energy landscape of adenylate kinase during catalysis," Nat. Struct. Mol. Biol. 22, 124–131 (2015) doi:10.1038/nsmb.2941, [link] PMCID: PMC4318763


  • Sharma, P; Ward, AR; Gibaud, T; Hagan, MF; Dogic, Z, “Hierarchical organization of chiral rafts in colloidal membranes," Nature, 513, 77–80 (2014) [link]

  • Perlmutter, J.D.; Perkett, M.R.; Hagan, M.F., “Pathways for virus assembly around nucleic acids," J. Mol. Biol., 426, 3148–3165 (2014), [link], PMC4135015

  • Fily, Y., Baskaran, A., Hagan, M.F. “Dynamics of Self-Propelled Particles Under Strong Confinement," Soft Matter, 10, 5609-5617 (2014) [link], arXiv:1402.5583

  • Perkett, M.R., Hagan, M.F., "Using Markov State Models to Study Self-Assembly," J. Chem. Phys., 214101 (2014), [link] PMCID: PMC4048447 [Cover Article]

  • Villali, J., Pontiggia, F., Clarkson, M.W., Hagan, M.F., Kern, D. “Evidence against the ‘Y-T coupling’ mechanism of activation in the response regulator NtrC," J. Mol. Biol, 426, 1554–1567, (2014), doi: 10.1016/j.jmb.2013.12.027, PMC4384162

  • Chelakkot, R.; Gopinath, A; Mahadevan, L.*; Hagan, M.F.*, “Flagellar dynamics of a connected chain of active, Brownian particles," J.R. Soc. Interface, 11, 20130884 (2014) (http://dx.doi.org/10.1098/rsif.2013.0884)


  • Perlmutter, J.D.; Qiao, C.; Hagan, M.F. “Viral genome structures are optimal for capsid assembly," eLife, 2:e00632 (2013) http://elife.elifesciences.org/content/2/e00632; PMC3683802

  • Redner, G.; Baskaran, A.; Hagan, M.F., “Reentrant Phase Behavior in Active Colloids with Attraction,"  Phys. Rev. E, 88, 012305 (2013), [Subject of a Physical Review Focus, Physics 6, 134 (2013)]

  • Hagan, M.F. “Modeling Viral Capsid Assembly," Adv. Chem. Phys., 155, Ch 1, 1-68 (2014), arXiv:1301.1657  [invited review article] PMC4318123

  • Redner, G., Hagan, M.F.*, Baskaran, A*., “Structure and Dynamics of a Phase-Separating Active Colloidal Fluid," Phys. Rev. Lett., 110, 055701 (2013), arXiv:1207.1737 * co-corresponding author

  • Yu, N., Hagan, M.F., “Simulations of HIV capsid protein dimerization reveal the effect of chemistry and topography on the mechanism of hydrophobic protein association” Biophys. J. 103, 1363-1369 (2012) [Featured Article]

  • Ruiz-Herrero, T., Velasco, E., Hagan, M.F., “Mechanisms of budding of nanoscale particles through lipid bilayers” J. Phys. Chem B, 116, 9595-603 (2012) arXiv:1202.4691

  • Giomi L., Mahadevan L., Chakraborty, B., and Hagan, M.F. “Banding, excitability and chaos in active nematic suspensions," Nonlinearity, 25, 2245–2269 (2012) [link]

  • Dhason, M.S, Wang, J.C., Hagan, M.F., Zlotnick, A. “Differential assembly of Hepatitis B Virus core protein on single- and double-stranded nucleic acid suggests the dsDNA-filled core is springloaded," Virology, 430, 20-29 (2012)

  • Gopinath, A., Hagan, M.F., Marchetti, M.C., Baskaran, A. “Dynamical Self-regulation in Self- propelled Particle Flows," Phys. Rev. E, 85, 061903 (2012)

  • Ni, P., Wang, Z., Ma, X., Das, N.C., Sokol, P., Chiu, W., Dragnea, B., Hagan, M.F.*, Kao, C.C*., “An Examination of the Electrostatic Interactions between the N-Terminal Tail of the Coat Protein and RNA in Brome Mosaic Virus," J. Mol. Biol., 419, 284-300 (2012) *co-corresponding author

  • Patel, A.J; Varilly, P.; Jamadagni, S.N.; Hagan, M.F.; Chandler, D.; and Garde, S. “Sitting at the edge: How biomolecules use hydrophobicity to tune their interactions and function," J. Phys. Chem. B, 116, 2498-2503 (2012), arXiv:1109.4431

  • Gibaud, E. Barry, M. Zakhary, A. Ward, C. Berciu, Y. Yang, M.F. Hagan, R. Oldenbourg, D. Nicastro, R. Meyer, Z. Dogic. “Reconfigurable self-assembly through chiral control of interfacial tension," Nature, 481, 348-351 (2012)

  • McCandlish, S.R, Baskaran, A., and Hagan, M.F. “Spontaneous Segregation of Self-Propelled Particles with Different Motilities," Soft Matter, 8, 2527-2534 (2012), [link] arXiv:1110.2479

  • Yang Y., Barry E., Dogic Z. and Hagan, M.F. “Self-assembly of 2D membranes from mixtures of hard rods and depleting polymers," Soft Matter, 8, 707 (2012), [link], arXiv:1103.2760


  • Yang Y. and Hagan, M.F. “Theoretical calculation of the phase behavior of colloidal membranes," Phys. Rev. E, 84, 051402 (2011)

  • Hagan, M.F., Elrad O.M., and Jack R.L. “Mechanisms of kinetic trapping in self-assembly and phase transformation," J. Chem. Phys, 135, 104115 (2011)

  • Giomi L., Mahadevan L., Chakraborty, B., and Hagan, M.F. “Excitable Patterns in Active Nematics," Phys. Rev. Lett 106, 218101 (2011)

  • Sumedha; Hagan, M.F.; Chakraborty, B. “Prolonging assembly through dissociation: A self-assembly paradigm in microtubules," Phys. Rev. E, 83, 051904 (2011)

  • Elrad O.M.; Hagan, M.F. “Encapsulation of a Polymer by an Icosahedral Virus," Phys. Biol., 7, 045003 (2010), Part of a special focus issue on physical virology.

  • Yang, Y.; Meyer, R.B.; Hagan, M.F. “Self-limited self-assembly of chiral filaments," Phys. Rev. Lett., 104, 258102 (2010)

  •  Kivenson, A.; Hagan, M.F. “Mechanisms of Capsid Assembly around a Polymer," Biophys. J, 99, 619-628 (2010)

  • Hagan, M.F. and Elrad O.M. “Understanding the Concentration Dependence of Viral Capsid Assembly Kinetics — the Origin of the Lag Time and Identifying the Critical Nucleus Size," Biophys. J, 98, 1065-1074 (2010)

  • Hagan, M.F. “A theory for viral capsid assembly around electrostatic cores,"  J. Chem. Phys., 130, 114902 (2009)

  • Huang, F.; Addas, K.; Ward, A ; Flynn, N.T.; Hagan, M.F.; Dogic, Z.; Fraden, S. “The pair potential of colloidal stars,"  Phys. Rev. Lett., 102, 108302 (2009)

  • Whitelam, S.; Feng, E.H.; Hagan, M.F.; Geissler, P.L. “The role of collective motion in examples of coarsening and self-assembly," Soft Matter, 6, 1251-1262 (2009) (Special issue on Self-Assembly)

  • Elrad, O.M.; Hagan, M.F. “Mechanisms of size control and polymorphism in viral capsid assembly," Nano Letters, 8, 3850-3857 (2008)

  • Hagan, M.F. “Controlling viral capsid assembly with templating," Phys. Rev. E, 77, 051904 (2008)

Publications from postdoctoral and graduate work

  • Jack, R.L.; Hagan, M.F.; Chandler, D. “Fluctuation-dissipation ratios in the dynamics of self- assembly," Phys. Rev. E, 76, 021119 (2007)

  • Hagan, M.F.; Chandler, D. “Dynamic Pathways for Viral Capsid Assembly," Biophys. J., 91,42 (2006)

  • Hagan, M.F.; Chakraborty, A.K. “Hybridization Dynamics of Surface Immobilized DNA,"  J. Chem. Phys., 120, 4958 (2004)

  • Hagan, M.F.; Dinner, A.R.; Chandler, D.; Chakraborty, A.K. “Atomistic Understanding of Kinetic Pathways for Single Base-Pair Binding and Unbinding in DNA,"  Proc. Natl. Acad. Sci. USA, 100, 13922 (2003)

  • Hagan, M.F.; Majumdar, A.; Chakraborty, A.K. “Nanomechanical Forces Generated by Surface Grafted DNA,"  J. Phys. Chem. B, 106, 10163 (2002)

  • Wu, G.; Haifeng, J.; Hansen, K.; Thundat, T.; Datar, R.; Cote, R.; Hagan, M.F.; Chakraborty, A.K.; Majumdar, A. “Origin of Nanomechanical Cantilever Motion Generated from Biomolecular Interactions," Proc. Natl. Acad. Sci. USA, 98, 1560 (2001).