Abelson-Bass-Yalem Building, 347
DegreesUniversity of California, Berkeley, Ph.D.
University of Connecticut, B.S.
ExpertiseStatistical mechanics, biophysics, soft condensed matter physics, computer simulations, theoretical modeling
ProfileMichael 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
|BCBP||297b||Master's Lab Research II|
|PHYS||11a||Introductory Physics I|
|QBIO||110a||Numerical Modeling of Biological Systems|
Awards and Honors
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)
Xie, S; Hagan, MF*; Pelcovits, RA. "Interaction of chiral rafts in self-assembled colloidal membranes." Phys. Rev. E in press. (2016). (forthcoming)
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.
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.