Recent Publications


  • Perlmutter JD; Mohajerani, F; Hagan, MF, Many-molecule encapsulation by an icosahedral shell, eLife 2016;10.7554/eLife.14078 (2016) [link]
  • Xie, S; Pelcovits, RA; Hagan, MF, “Probing a self-assembled fd virus membrane with a microtubule”, submitted, arXiv:1512.02204 [link]  
  • 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”, under review, arXiv:1603.05497

  • Redner, GS; Wagner, CG; Baskaran, A; Hagan, MF, “A classical nucleation theory description of active colloid assembly”, under review, arXiv:1603.01362

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

  • Sakhardande, R., Stanojeviea, S., Baskaran, A., Baskaran, A., Hagan, M. F.,  Chakraborty, B., Theory of microphase separation in bidisperse chiral membranes. submitted arXiv:1604.03012 (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) [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]

  • Perkett, M.R.; Hagan, M.F., “The Allosteric Switching Mechanism in Bacteriophage MS2”, submitted, arXiv:1503.01204 (2015)
  • 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). [PDF].
  • Fily, Y., Baskaran, A., Hagan, M.F. “Dynamics of Self-Propelled Particles Under Strong Confinement”, Soft Matter, 10, 5609-5617 (2014). [PDF]
  • 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) [PDF]


  • Redner, G.; Baskaran, A.; Hagan, M.F., “Reentrant Phase Behavior in Active Colloids with Attraction”, Phys. Rev. E, 88, 012305 (2013) [PDF]. Subject of a Physical Review Focus.
  • Perlmutter, J.D., Qiao, C., Hagan, M.F. “Viral genome structures are optimal for capsid assembly”, eLife (eLife 2013;2:e00632) [PDF]
  • Redner, G., Hagan, M.F., Baskaran, A., “Structure and Dynamics of a Phase-Separating Active Colloidal Fluid”, Phys. Rev. Lett. 110, 055701 (2013) [PDF]

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


  • [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)  [PDF]
  • 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) [PDF]

  • 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)  [PDF]
  • 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 [PDF]
  • 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) [PDF] [Supp]
  • 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 [PDF] [Supp]
  • 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 [PDF]
  • 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 [PDF] [Supp]

  • 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) [PDF]


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

  • Giomi L., Mahadevan L., Chakraborty, B., and Hagan, M.F. “Excitable Patterns in Active Nematics”,  Phys. Rev. Lett 106,21801 (2011)  [PDF]

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


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


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

  • 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  PDF


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

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

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

  • 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. PDF