Recent Publications


Mohajerani, F; Sayer, E; Neil, C; Inlow, K; Hagan, MF, “Mechanisms of scaffold-mediated microcompartment assembly and size-control”, under review

Hagan, MF; Grason, GM, “Equilibrium mechanisms of self-limiting assembly”, under review at Rev. Mod. Phys., arXiv:2007.01927

Chelakkot, R; Hagan, MF; Mahadevan, L; Gopinath, A, “Synchronized oscillations, metachronal waves, and jammed clusters in sterically interacting active filament arrays”, under review,

Norton, MM; Grover, P; Hagan, MF; Fraden, S, “Optimal Control of Active Nematics”, under review, arXiv:2007.14837

Zhou, Z; Joshi, C.; Liu, R; Norton, MM; Lemma, LM; Dogic, Z; Hagan, MF; Fraden S; Hong, P, “Machine Learning Forecasting of Active Nematics”, under review, arXiv:2007.14837

Varghese, M; Hagan, MF; Basakaran, A, “Re-entrant Self-pumping of Confined 3D Active Fluids”, under review, arXiv:2007.09277.pdf

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),

Lemma, LM; Norton, MM; DeCamp, SJ; Aghvami, SA; Fraden, S; Hagan, MF; Dogic, Z, "Multiscale dynamics in active nematics", under review, arXiv:2006.15184


Peterson, MSE; Hagan, MF; Baskaran, A, “Statistical properties of a tangentially driven active filament”, J. Stat. Mech. (2020) 013216,

Hagan, MF, “Driving assembly far from equilibrium” commentary for the Journal Club for Condensed Matter Physics.

Dharmavarm, S; She, B.; Lazaro, GR; Hagan, MF; Bruinsma, R, "Gaussian curvature and the budding kinetics of enveloped viruses," Plos. Comp. Biol, 15, e1006602 (2019),

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).

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:

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),

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.

Wagner, C; Hagan, MF*; Baskaran, A*, “Response of active Brownian particles to boundary driving”,PRE, 100, 042610 (2019),, arXiv:1905.12706

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

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:1805.04214, PMCID PMC7155749

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

Zeng, C; Lázaro, 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).

Lázaro, GR; Mukhopadhyay, S; Hagan, MF, “The contribution of a nucleocapsid core to viral budding”, Biophys. J. 114, 619-630.

Norton, MM; Baskaran, A; Opathalage, A; Langeslay, B; Fraden, S; Baskaran, A; Hagan, MF "Dynamics of an active nematic under topologically incommensurate confinement", Phys. Rev. E, 97, 012702 (2018).

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

Sakhardande, R; Stanojeviea, S; Baskaran, A; Hagan, MF; Chakraborty, B. Phys. Rev. E 96, 012704, “Theory of microphase separation in bidisperse chiral membranes”, arXiv:1604.03012 (2017).

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

Wagner, CG; Hagan, MF; Baskaran, A. J. Stat. Mech., “Steady-state distributions of ideal active Brownian particles under confinement and forcing”, (2017).

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


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].

Perlmutter JD; Mohajerani, F; Hagan, MF. “Many-molecule encapsulation by an icosahedral shell”, eLife 5, e14078 (2016); Watch the movies.

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

Fily, Y; Baskaran, A; Hagan, MF. “Active Particles on Curved Surfaces”, arXiv:1601.00324 (2016).

Hagan MF; Zandi, R. “Recent advances in coarse-grained modeling of virus assembly”, Curr Opin Virol, 18, 36-43 (2016).

Hagan MF; Baskaran A. “Emergent self-organization in active materials”, Curr Opin Cell Biol, 38, 74-20 (2016).

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

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

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

Perkett, MR; Mirijanian, DT; Hagan, M.F. “The Allosteric Switching Mechanism in Bacteriophage MS2”, J. Chem. Phys. 145, 035101 [cover article], arXiv:1503.01204, PMC4947040, (2016).


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).

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).

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

Perlmutter, JD; Hagan, MF. “The role of packaging sites in efficient and specific virus assembly”, J. Mol. Biol., 427, 2451–2467 (2015).

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, arXiv:1410.5151.

Perlmutter, JD; Hagan, MF. “Mechanisms of Virus Assembly”, Annu. Rev. Phys. Chem., 66, 217–39, arXiv:1407.3856.

Ruiz-Herrero, T; Hagan, MF. “Simulations show that Virus Assembly on a Membrane is Facilitated by Membrane Microdomains”, Biophys. J., 108, 585-595, arXiv:1403.2269 (2015).

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

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 doi:10.1038/nsmb.2941 (2015).


Sharma, P; Ward, AR; Gibaud, T; Hagan, MF; Dogic, Z. “Hierarchical organization of chiral rafts in colloidal membranes”, Nature, 513, 77-80 (2014).

Perlmutter, JD, Perkett, MR; Hagan, MF. “Pathways for virus assembly around nucleic acids”, J. Mol. Biol., 426, 3148–3165; arXiv:1405.3310 (2014).

Fily, Y; Baskaran, A; Hagan, MF. “Dynamics of Self-Propelled Particles Under Strong Confinement”, Soft Matter, 10, 5609-5617; arXiv:1402.5583 (2014).

Chelakkot, R; Gopinath, A; Mahadevan, L; Hagan, MF. “Flagellar dynamics of a connected chain of active, Brownian particles”, J. R. Soc. Interface, 11, 20130884 (2014). YouTube Videos: Periodic beating, Non periodic buckling, Rotational motion, Beating of long filament.

Villali, J; Pontiggia, F; Clarkson, MW; Hagan, MF; Kern, DJ. “Evidence against the ‘Y-T coupling’ mechanism of activation in the response regulator NtrC”, Mol. Biol, 426, 1554-1567, (2014).doi: 10.1016/j.jmb.2013.12.027.

Perkett, MR; Hagan, MF. “Using Markov State Models to Study Self-Assembly”, J. Chem. Phys., 140, 214101 (2014).

Redner, G; Baskaran, A; Hagan, MF. “Reentrant Phase Behavior in Active Colloids with Attraction”, Phys. Rev. E, 88, 012305 arXiv:1303.3195 (2013).

Perlmutter, JD; Qiao, C; Hagan, MF. “Viral genome structures are optimal for capsid assembly”, eLife (eLife 2013; 2:e00632).

Redner, G; Hagan, MF; Baskaran, A. “Structure and Dynamics of a Phase-Separating Active Colloidal Fluid”, Phys. Rev. Lett. 110, 055701, arXiv:1207.1737 (2013).

Hagan, MF. “Modeling Viral Capsid Assembly”, Adv. Chem. Phys., 155, Ch 1; (2014) arXiv:1301.1657 .


Yu, N and Hagan, MF. “Simulations of HIV capsid protein dimerization reveal the effect of chemistry and topography on the mechanism of hydrophobic protein association”, [Featured article], Biophys J. 103, 1363-1369 (2012) arXiv:1206.1828.

Dhason, MS; Wang, JC; Hagan, MF; 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).

Ni, P; Wang, Z; Ma, X; Das, NC; Sokol, P; Chiu, W; Dragnea, B; Hagan, MF; Kao, CC. “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).

Ruiz-Herrero, T; Velasco, E; Hagan, MF. “Mechanisms of budding of nanoscale particles through lipid bilayers”, J. Phys. Chem B, 116, 9595-603. arXiv:1202.4691.

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

McCandlish, SR; Baskaran, A; Hagan, MF. “Spontaneous Segregation of Self-Propelled Particles with Different Motilities”, Soft Matter, 8, 2527 (2012). arXiv:1110.2479.

Patel, AJ; Varilly, P; Jamadagni, SN; Hagan, MF; 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.

Yang Y; Barry E; Dogic Z; Hagan, MF. “Self-assembly of 2D membranes from mixtures of hard rods and depleting polymers”, Soft Matter, 8, 707 (2012) arXiv:1103.2760

Gopinath, A; Hagan, MF; Marchetti, MC; Baskaran, A. “Dynamical Self-regulation in Self-propelled Particle Flows” Phys. Rev. E, 85, 061903 (2012). arXiv:1112.6011

Giomi L; Mahadevan L; Chakraborty, B; Hagan, MF. “Banding, excitability and chaos in active nematic suspensions”, Nonlinearity, 25, 2245-2269 (2012). arXiv:1110.4338


Yang, Y; Hagan, MF. “Theoretical calculation of the phase behavior of colloidal membranes”, Phys. Rev. E, 84, 051402 (2011). arXiv:1107.2038.

Hagan, MF; Elrad OM; Jack RL.“Mechanisms of kinetic trapping in self-assembly and phase transformation”, J.Chem. Phys, 135, 104115 (2011).

Giomi L; Mahadevan L; Chakraborty, B; Hagan, MF. “Excitable Patterns in Active Nematics”, Phys. Rev. Lett 106, 21801 (2011). arXiv:1011.3841.

Sumedha; Hagan, MF; Chakraborty, B. “Prolonging assembly through dissociation: A self-assembly paradigm in microtubules”, Phys. Rev. E, 83, 051904 (2011). arXiv:0908.1199.


Elrad, OM; Hagan, MF. “Encapsulation of a Polymer by an Icosahedral Virus”, [invited], Phys. Biol., 7, 045003, Part of a special focus issue on the physical virology (2010). arXiv:1006.0459.

Yang, Y; Meyer, RB; Hagan, MF. “Self-limited self-assembly of chiral filaments”, Phys. Rev. Lett., 104, 258102 (2010). arXiv:1001.4780.

Hagan, MF; Elrad, OM. “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, MF. “A theory for viral capsid assembly around electrostatic cores”, J. Chem. Phys., 130, 114902 (2009).

Huang, F; Addas, K; Ward, A; Flynn, NT; Hagan, MF; Dogic, Z; Fraden, S. “The pair potential of colloidal stars”, Phys. Rev. Lett., 102, 108302 (2009).

Whitelam, S; Feng, EH; Hagan, MF; Geissler, PG. “The role of collective motion in examples of coarsening and self-assembly”, Soft Matter, 6, 1251-1262 (2009).


Elrad, OM; Hagan, MF. “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).

Through 2007

Perlmutter, JD; Hagan, MF. “The role of packaging sites in efficient and specific virus assembly”, (2015), arXiv:1502.05029.

Jack, RL; Hagan, MF; Chandler, D. “Fluctuation-dissipation ratios in the dynamics of self-assembly”, Phys. Rev. E, 76, 021119 (2007).

Hagan, MF; Chandler, D. “Dynamic Pathways for Viral Capsid Assembly”, Biophys. J., 91,42 (2006).

Hagan, MF; Chakraborty, AK. “Hybridization Dynamics of Surface Immobilized DNA”, J. Chem. Phys., 120, 4958 (2004).

Hagan, MF; Dinner, AR; Chandler, D; Chakraborty, AK. “Atomistic Understanding of Kinetic Pathways for Single Base-Pair Binding and Unbinding in DNA”, Proc. Natl. Acad. Sci. USA, 100, 13922 (2003).

Hagan, MF; Majumdar, A; Chakraborty, AK. “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, AK; Majumdar, A. “Origin of Nanomechanical Cantilever Motion Generated from Biomolecular Interactions”, Proc. Natl. Acad. Sci. USA, 98, 1560 (2001).