Submitted / Under Revision

Joshi, C; Ray, S; Lemma, L; Varghese, M.; Sharp, G; Dogic, Z; Baskaran, A*; Hagan, MF*, “Data- driven discovery of active nematic hydrodynamics”,

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”,
Mohajerani F, Tyukodi B, Schlicksup CJ, Hadden-Perilla JA, Zlotnick A, Hagan MF, “Multiscale Modeling of Hepatitis B Virus Capsid Assembly and its Dimorphism”,
Tsidilkovski L, Hagan MF. “Microcompartment assembly around multicomponent fluid cargoes”,
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)”,
Tyudoki, B; Mohajerani, F; Hall, DM; Grason, GM*, Hagan, MF*, “Thermodynamic size control in curvature-frustrated tubules: Self-limitation with open boundaries”, arxiv:2109.01174
Fily, Y; Baskaran, A; Hagan, MF, “Active Particles on Curved Surfaces”, in revision, arXiv:1601.00324

Accepted or Published

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),
Wagner, C; Hagan, MF; Baskaran, A, “Steady states of active Brownian particles interacting with boundaries”, J. Stat. Mech. 013208 (2022),
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),, 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),
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),, 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)
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)
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)., arXiv:2007.14837
Fang, H; Hagan, MF; Rogers, WB, “Two-step crystallization and solid-solid transitions in binary colloidal mixtures”, Proc. Natl. Acad. Sci. (USA), 117, 27927-27933 (2020),
Varghese, M; Hagan, MF; Basakaran, A, “Confinement-Induced Self-Pumping in 3D Active Fluids”, Phys. Rev. Lett., 125, 268003 (2020),, arXiv:2007.09277.pdf
Norton, MM; Grover, P; Hagan, MF; Fraden, S, “Optimal Control of Active Nematics”, Phys. Rev. Lett. 125, 178005 (2020),, arXiv:2007.14837
Miller, JM; Hall, D; Robaszewski, J; Sharma, P; Hagan, MF; Grason, GM; Dogic Z, “All twist and no bend makes raft edges splay: Spontaneous curvature of domain edges in colloidal membranes”, Sci. Adv., 6, eaba2331(2020),, arXiv:1908.09966
Duclos, G; Adkins, A; Banerjee, D; Peterson, MSE; Varghese, M; Kolvin, I; Baskaran, Ar; Pelcovits, RA; Powers, TR; Baskaran, Ap; Toschi, F; Hagan, MF; Streichan, SJ; Vitelli, V; Beller, DA; Dogic, Z, “Topological structure and dynamics of three dimensional active nematics”, Science, 367, 1120–1124 (2020),,
Peterson, MSE; Hagan, MF; Baskaran, A, “Statistical properties of a tangentially driven active filament”, J. Stat. Mech. (2020) 013216,, arXiv:1908.11286
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),, 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, 18464 (2019), https://doi- org/10.1039/C9NR06570A, arXiv:1805.04214PMCID PMC7155749
Hagan, MF, “Driving assembly far from equilibrium” commentary for the Journal Club for Condensed Matter Physics, 8/2019,
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),
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),
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), link: see News&Views commentary:
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,
Wagner, CG; Hagan, MF; Baskaran, A, “Steady-state distributions of ideal active Brownian particles under confinement and forcing” J. Stat. Mech., 043203 (2017), 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
Perlmutter JD; Mohajerani, F; Hagan, MF, Many-molecule encapsulation by an icosahedral shell, eLife 5, e14078 (2016);
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, [link], 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) (
Perlmutter, J.D.; Qiao, C.; Hagan, M.F. “Viral genome structures are optimal for capsid assembly”, eLife, 2:e00632 (2013); 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).