Recent Publications

2017

Norton, MM; Baskaran, A; Opathalage, A; Langeslay, B; Fraden, S; Baskaran, A; Hagan, MF "Dynamics of an active nematic under topologically incommensurate confinement", under review, arXiv:1708.05773

Michaels, TCT; Bellaiche, MMJ; Hagan, MF; Knowles, TPJ, "Kinetic constraints on the self-assembly of building blocks into closed supramolecular structures", Sci. Reports, in press

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



2016

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]  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.14078Watch 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


2015

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]


2014

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), arxiv.org/abs/1405.3310

Fily, Y., Baskaran, A., Hagan, M.F. “Dynamics of Self-Propelled Particles Under Strong Confinement”, Soft Matter, 10, 5609-5617 (2014), arxiv.org/abs/1402.5583 

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), www.ncbi.nlm.nih.gov/pubmed/24907984



2013

Redner, G.; Baskaran, A.; Hagan, M.F., “Reentrant Phase Behavior in Active Colloids with Attraction”, Phys. Rev. E, 88, 012305 (2013)  arxiv.org/abs/1303.3195

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)  arxiv.org/abs/1207.1737

Hagan, M.F. “Modeling Viral Capsid Assembly”, Adv. Chem. Phys., 155, Ch 1 (2014), arxiv.org/abs/1301.1657



2012

[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)  arxiv.org/abs/1206.1828

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)



2011

Yang, Y., and Hagan, M.F. "Theoretical calculation of the phase behavior of colloidal membranes" Phys. Rev. E, 84, 051402 (2011) arxiv.org/abs/1107.2038

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)  aip.scitation.org/doi/full/10.1063/1.3635775

Giomi L., Mahadevan L., Chakraborty, B., and Hagan, M.F. “Excitable Patterns in Active Nematics”,  Phys. Rev. Lett 106,21801 (2011)  arxiv.org/abs/1011.3841

Sumedha; Hagan, M.F.; Chakraborty, B. "Prolonging assembly through dissociation: A self-assembly paradigm in microtubules", Phys. Rev. E, 83, 051904 (2011)  arxiv.org/abs/0908.1199



2010

[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.  arxiv.org/abs/1006.0459

Yang, Y.; Meyer, R.B.; Hagan, M.F. "Self-limited self-assembly of chiral filaments", Phys. Rev. Lett., 2010,104, 258102  arxiv.org/abs/1001.4780

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



2009

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 



2008

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