Michael Francis Hagan

Professor of Physics and of Quantitative Biology

hagan@brandeis.edu
781-736-2845
Abelson-Bass-Yalem Building, 312

Departments/Programs

Physics

Degrees

University of California, Berkeley, Ph.D.
University of Connecticut, B.S.

Expertise

Statistical mechanics, biophysics, soft condensed matter physics, computer simulations, theoretical modeling

Profile

Please visit my new faculty profile page.

Michael Hagan is Associate Professor of Physics and of Quantitative Biology at Brandeis. He received a BSE and PhD in Chemical Engineering respectively from the University of Connecticut and University of California at Berkeley. Michael’s lab uses computational modeling and theory to understand the physical principles that control assembly and dynamical organization in biological, biomimetic, and other soft condensed matter systems. Because assembling structures can be orders of magnitude larger than the individual components that comprise them, the lab develops and apply computational and theoretical methods that bridge disparate length and time scales. Applications include understanding the assembly of viral capsids and other large protein complexes, discovering the mechanisms by which proteins interconvert between different conformations, and understanding emergent behaviors in active matter systems (materials whose constituent elements consume energy to generate motion, such as the internal components of a cell).

For more information, please visit Prof. Hagan's webpage at http://www.brandeis.edu/departments/physics/hagan/index.html

Courses Taught

PHYS	91g	Introduction to Research Practice
PHYS	105a	Biological Physics
PHYS	163a	Statistical Physics and Thermodynamics
QBIO	110a	Numerical Modeling of Biological Systems

Awards and Honors

APS Fellow (Fellow of the American Physical Society) (2020)

Alberta Gotthardt Strage '56 and Henry Strage Award for Aspiring Young Science Faculty (2012)

National Institutes of Health Ruth L. Kirchstein National Research Service Award, Individual Postdoctoral Fellowship (2005)

National Science Foundation Graduate Research Fellow (1999)

Scholarship

Hagan, MF; Grason, GM. "Equilibrium mechanisms of self-limiting assembly." Rev. Mod. Phys. (2021): in press. (forthcoming)

Sigl, C; Willner, EM; Engelen, W; Sachenbacher, K; Liedl, A; Kolbe, F; Wilsch, F; Aghvami, SA; Protzer, U; Hagan, MF; Fraden, S; Dietz, H. "Programmable icosahedral shells for virus neutralization." Nature Materials (2021): in press. (forthcoming)

Chelakkot, R; Hagan, MF; Mahadevan, L; Gopinath, A. "Synchronized oscillations, metachronal waves, and jammed clusters in sterically interacting active filament arrays." Soft Matter 117. (2021): 1091-1104.

Mohajerani, F; Sayer, E; Neil, C; Inlow, K; Hagan, MF. "Mechanisms of scaffold-mediated microcompartment assembly and size-control." ACS Nano 15. (2021): 4197–4212.

Zhou, Z; Joshi, C.; Liu, R; Norton, MM; Lemma, LM; Dogic, Z; Hagan, MF; Fraden S; Hong, P. "Machine Learning Forecasting of Active Nematics." Soft Matter 17. (2021): 738-747.

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. (2020): 1120–1124.

Fang, H; Hagan, MF; Rogers, WB. "Two-step crystallization and solid-solid transitions in binary colloidal mixtures." Proc. Natl. Acad. Sci. (USA) 117. (2020): 27927-27933.

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. (2020): eaba2331.

Norton, MM; Grover, P; Hagan, MF; Fraden, S. "Optimal Control of Active Nematics." Phys. Rev. Lett. 125. (2020): 178005.

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

Varghese, M; Hagan, MF; Basakaran, A. "Confinement-Induced Self-Pumping in 3D Active Fluids." Phys. Rev. Lett. 125. (2020): 268003.

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. (2019): 6791-6802.

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

Hagan, Michael Francis. "Driving assembly far from equilibrium." Journal Club for Condensed Matter Physics (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. (2019): 94.

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." Proc. Natl. Acad. Sci. 116. (2019): 15792–15801.

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. (2019): 7033-7042.

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. (2019): 726–734.

Wagner, C; Hagan, MF*; Baskaran, A*. "Response of active Brownian particles to boundary driving." Phys. Rev. E 100. (2019): 042610.

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. (2019): 18464.

Lazaro, GR; Dragnea, B; Hagan, MF. "Self-assembly of convex particles on spherocylindrical surfaces." Soft Matter 14. (2018): 5728 - 5740.

Lazaro, GR; Mukhopadhyay, S; Hagan, MF. "Why Enveloped Viruses Need Cores—The Contribution of a Nucleocapsid Core to Viral Budding." Biophys. J. 114. (2018): 619.

Mohajerani F; Hagan MF. "The role of the encapsulated cargo in microcompartment assembly." Plos. Comp. Biol. 14. (2018): e1006351.

Norton, MM; Baskaran, A; Opathalage, A; Langeslay, B; Fraden, S; Baskaran, A*; Hagan, MF*. "Insensitivity of active nematic liquid crystal dynamics to topological constraints." Phys. Rev. E 97. (2018): 012702.

Zeng, C; Lazaro, 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. (2018): 5323–5332.

Fily, Y; Baskaran, A; Hagan, MF. "Equilibrium mappings in polar-isotropic confined active particles." Eur. Phys. J. E 40. (2017): 61.

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

Michaels, TCT; Bellaiche, MMJ; Hagan, MF; Knowles, TPJ. "Kinetic constraints on the self-assembly of building blocks into closed supramolecular structures." Sci. Reports 7. (2017): 12295.

Sakhardande, R., Stanojeviea, S., Baskaran, A., Baskaran, A., Hagan, M. F.*, Chakraborty, B.. "Theory of microphase separation in bidisperse chiral membranes." Phys. Rev. E 96. (2017): 012704.

Wagner, CG; Hagan, MF; Baskaran, A. "Steady-state distributions of ideal active Brownian particles under confinement and forcing." J. Stat. Mech. (2017): 043203.

Hagan MF; Baskaran A. "Emergent self-organization in active materials." Curr Opin Cell Biol 38 (2016): 74-80.

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

Lazaro, GR; Hagan, MF. "Allosteric control in icosahedral capsid assembly." J. Phys. Chem. B 120. (2016): 6306-6318.

Perkett, M.R.; Mirijanian, D.T.; Hagan, M.F.. "The Allosteric Switching Mechanism in Bacteriophage MS2." J. Chem. Phys. 145. (2016): 035101.

Perlmutter JD; Mohajerani, F; Hagan, MF. "Many-molecule encapsulation by an icosahedral shell." eLife 5. (2016): e14078.

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

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

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

Yu, N; Ghosh, A; Hagan, MF. "Faceted particles formed by the frustrated packing of anisotropic colloids on curved surfaces." Soft Matter 12. (2016): 8990.

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

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. (2015): 012125.

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. 114. (2015): 138102.

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. (2015): 2597–2609.

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. (2015): 124–131.

Perlmutter, J.D.; Hagan, M.F.. "Mechanisms of Virus Assembly." Annu. Rev. Phys. Chem. 66. (2015): 217–39.

Perlmutter, J.D.; Hagan, M.F.. "The role of packaging sites in efficient and specific virus assembly." J. Mol. Biol. 427. (2015): 2451–2467.

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." Nature Comm. 6. (2015): 7284.

Ruiz-Herrero, T., Hagan, M.F.. "Simulations show that Virus Assembly on a Membrane is Facilitated by Membrane Microdomains." Biophys. J. 108. (2015): 585-595.

Chelakkot, R.; Gopinath, A; Mahadevan, L.; Hagan, M.F.. "Flagellar dynamics of a connected chain of active, Brownian particles." J. R. Soc. Interface 11. (2014): 20130884.

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

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

Perlmutter, J.D.; Perkett, M.R.; Hagan, M.F.. "Pathways for virus assembly around nucleic acids." J. Mol. Biol. 426. (2014): 3148–3165.

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

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. (2014): 1554–1567.

Barry, E., Dogic, Z., Hagan, M.F., Yang, Y., Perlman, D.. Aligned Arrays of Nanorods, and Methods of Making and Using Them. Patent Pending.

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

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

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

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. (2012): 20-29.

Gibaud, T., Barry, E., Zakhary, M. J., Henglin, M., Ward, A., Yang, Y. S., Berciu, C., Oldenbourg, R., Hagan, M. F., Nicastro, D., Meyer, R. B., Dogic, Z.. "Reconfigurable self-assembly through chiral control of interfacial tension." Nature 481. 7381 (2012): 348-U127.

Giomi L., Mahadevan L., Chakraborty, B., and Hagan, M.F.. "Banding, excitability and chaos in active nematic suspensions." Nonlinearity 25. (2012): 2245–2269.

Gopinath, A., Hagan, M.F., Marchetti, M.C., Baskaran, A.. "Dynamical Self-regulation in Self-propelled Particle Flows." Phys. Rev. E 85. (2012): 061903.

McCandlish, S. R., Baskaran, A., Hagan, M. F.. "Spontaneous segregation of self-propelled particles with different motilities." Soft Matter 8. 8 (2012): 2527-2534.

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. (2012): 284-300.

Patel, Amish J., Varilly, Patrick, Jamadagni, Sumanth N., Hagan, Michael F., Chandler, David, Garde, Shekhar. "Sitting at the Edge: How Biomolecules use Hydrophobicity to Tune Their Interactions and Function." The Journal of Physical Chemistry B 116. 8 (2012): 2498-2503.

Ruiz-Herrero, T., Velasco, E., Hagan, M.F. "Mechanisms of budding of nanoscale particles through lipid bilayers." J. Phys. Chem B 116. (2012): 9595-603.

Yang, Y., Barry, E., Dogic, Z., Hagan, M. F.. "Self-assembly of 2D membranes from mixtures of hard rods and depleting polymers." Soft Matter 8. (2012): 707-714.

Yu, N., 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. (2012): 1363-1369.

Giomi, L., Mahadevan, L., Chakraborty, B., Hagan, M. F.. "Excitable Patterns in Active Nematics." Physical Review Letters 106. 21 (2011).

Hagan, M. F., Elrad, O. M., Jack, R. L.. "Mechanisms of kinetic trapping in self-assembly and phase transformation." J. Chem. Phys. 135. (2011): 104115.

Sumedha,, Hagan, M. F., Chakraborty, B.. "Prolonging assembly through dissociation: A self-assembly paradigm in microtubules." Physical Review E 83. 5 (2011).

Yang, Yasheng, Hagan, Michael F.. "Theoretical calculation of the phase behavior of colloidal membranes." Physical Review E 84. 5 (2011): 051402.

Elrad, O.M., Hagan, M. F.. "Encapsulation of a polymer by an icosahedral virus." Physical Biology 7. (2010): 045003.

Giomi, L., Mahadevan, L., Chakraborty, B., Hagan, M. F.. "Excitable Patterns in Active Nematics." arXiv:1011.3841 (2010).

Hagan, M. F.. "Understanding the Concentration Dependence of Viral Capsid Assembly Kinetics - the Origin of the Lag Time and Identifying the Critical Nucleus Size." Biophysical Journal 98. (2010): 1065-74.

Kivenson, A, Hagan, M. F.. "Mechanisms of Capsid around a Polymer." Biophysical Journal 99. (2010): 619-628.

Yang, Y., Meyer, R. B., Hagan, M. F.. "Self-Limited Self-Assembly of Chiral Filaments." Physical Review Letters 104. 25 (2010): 258102.

Hagan, M. F.. "A theory for viral capsid assembly around electrostatic cores." Journal of Chemical Physics 130. (2009): 114902.

Huang, F., Addas, K., Ward, A., Flynn, N. T., Velasco, E., Hagan, M. F., Dogic, Z., Fraden, S.. "Pair Potential of Charged Colloidal Stars." Physical Review Letters 102. 10 (2009).

Sumehda, Hagan, M. F., Chakraborty, B.. "Role of GTP remnants in microtubule dynamics." arXiv:0908.1199v1 (2009).

Whitelam, S., Feng, E. H., Hagan, M. F., Geissler, P. L.. "The role of collective motion in examples of coarsening and self-assembly." Soft Matter 5. 6 (2009): 1251-1262.

Elrad, O. M., Hagan, M. F.. "Mechanisms of Size Control and Polymorphism in Viral Capsid Assembly." Nano Letters 8. 11 (2008): 3850-3857.

Hagan, M. F.. "Controlling viral capsid assembly with templating." Physical Review E 77. 5 (2008).

Jack, R. L., Hagan, M. F., Chandler, D.. "Fluctuation-dissipation ratios in the dynamics of self-assembly." Phys. Rev. E 76. (2007): 021119.

Hagan, M. F., Chandler, D.. "Dynamic pathways for viral capsid assembly." Biophysical Journal 91. 1 (2006): 42-54.

Hagan, M. F., Chakraborty, A. K.. "Hybridization dynamics of surface immobilized DNA." Journal of Chemical Physics 120. 10 (2004): 4958-4968.

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." Proceedings of the National Academy of Sciences of the United States of America 100. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences24 (2003): 13922-13927.

Hagan, M. F., Majumdar, A., Chakraborty, A. K.. "Nanomechanical forces generated by surface grafted DNA." Journal of Physical Chemistry B 106. 39 (2002): 10163-10173.

Wu, G. H., Ji, H. F., 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." Proceedings of the National Academy of Sciences of the United States of America 98. 4 (2001): 1560-1564.