Recent Publications

2017

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