Recent Publications


Sakhardande, R., Stanojeviea, S., Baskaran, A., Baskaran, A., Hagan, M. F.,  Chakraborty, B., "Theory of microphase separation in bidisperse chiral membranes" Phys. Rev. E (accepted), arXiv:1604.03012 (2017)

Lazaro, GR; Mukhopadhyay, S; Hagan, MF, “The contribution of a nucleocapsid core to viral budding”, under review, arXiv:1706.04867

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/i2017-11551-3, arXiv:1612.08719

Wagner, CG; Hagan, MF; Baskaran, A, “Steady-state distributions of ideal active Brownian particles under confinement and forcing” J. Stat. Mech., in press (2017), arXiv:1611.01834


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

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); the movies.

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)

Fily, Y; Baskaran, A; Hagan, MF, “Active Particles on Curved Surfaces”, submitted, arXiv:1601.00324 [link]

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

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

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

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

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

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


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]

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)  [link]

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., (accepted),arXiv:1408.5068

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

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, [link], arXiv:1410.5151

Perlmutter, J.D.; Hagan, M.F., “Mechanisms of Virus Assembly”, Annu. Rev. Phys. Chem., 66, 217–39, [link], arXiv:1407.385611

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

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]

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]


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),

Fily, Y., Baskaran, A., Hagan, M.F. “Dynamics of Self-Propelled Particles Under Strong Confinement”, Soft Matter, 10, 5609-5617 (2014), 

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) [link]. YouTube Videos: Periodic beating, Non periodic buckling, Rotational motion, Beating of long filament

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

Perkett, M.R., Hagan, M.F., "Using Markov State Models to Study Self-Assembly", J. Chem. Phys., 140, 214101 (2014),


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

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

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

Hagan, M.F. “Modeling Viral Capsid Assembly”, Adv. Chem. Phys., 155, Ch 1 (2014),


[Featured article] Yu, N. and 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)

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)  

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)  

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

T. 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 (2012) 

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

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 

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), arXiv:1103.2760

Gopinath, A., Hagan, M.F., Marchetti, M.C., 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., and Hagan, M.F. “Banding, excitability and chaos in active nematic suspensions”, Nonlinearity, 25, 2245-2269 (2012), arXiv:1110.4338 (2012)


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 106,21801 (2011)

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


[invited] 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 the physical virology.

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

Hagan, M.F.; 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., 2010, 98, 1065 - 1074


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

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., 2009, 102, 108302 

Whitelam, S.; Feng, E.H.; Hagan, M.F.; Geissler, P.G. “The role of collective motion in examples of coarsening and self-assembly”,  Soft Matter, 2009, 6, 1251-1262 


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

Hagan, M. F. “Controlling viral capsid assembly with templating”, Phys. Rev. E, 2008, 77, 051904

Through 2007

Perlmutter, J.D.; Hagan, M.F., “The role of packaging sites in efficient and specific virus assembly”, submitted, arXiv:1502.05029|

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

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

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

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, 2003, 100, 13922  

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

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, 2001, 98, 1560