Michael Hagan

Here I summarize a few of the areas I worked on over the last five years, along with links to some related publications. All of my group’s publications since submission of my tenure package in January 2012 can be found at the bottom of the page (articles 20-63 in the complete list of publications).

1. The role of nucleic acids in viral assembly. We developed a coarse grained computational model for virus capsid assembly around RNA. Model predictions for RNA lengths that optimize capsid thermostability nearly quantitatively agreed with viral genome lengths for seven viruses [1a]. This result demonstrates that viral nucleic acid structures are evolutionarily constrained by their influence on capsid thermostability, in addition to the fitness of the genes they encode. Predicted assembly failures around non-optimal RNA lengths were confirmed by experiment. Our simulations demonstrated that capsid assembly around RNA proceeds through two classes of pathways [1b]. Extending our model to incorporate sequence-specific capsid protein-RNA interactions (packaging signals) demonstrated a mechanism of selective assembly around the viral genomic RNA [1c]. In direct collaborations with experimentalists, we investigated the effect of genome stiffness on the stability of an assembled HBV capsid [1d] and compared theoretical predictions to in vivo experiments on the amount of RNA packaged in virions whose charge was altered by mutagenesis [1e]. For a broader context of this work, and an overall review of modeling capsid assembly, please see these review articles [1f,1g].

1a. Perlmutter, J.D.; Qiao, C.; Hagan, M.F. “Viral genome structures are optimal for capsid assembly”, eLife, 2:e00632, http://elife.elifesciences.org/content/2/e00632

1b. Perlmutter, J.D.; Perkett, M.R.; Hagan, M.F., “Pathways for virus assembly around nucleic acids”, J. Mol. Biol., 426, 3148–3165 (2014), [link]

1c. 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

1d. 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)

1e. 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)

1f. Hagan, M.F. “Modeling Viral Capsid Assembly”, Adv. Chem. Phys., 155, Ch 1, 1-68 (2014), arXiv:1301.1657

1g. Perlmutter, J.D.; Hagan, M.F., “Mechanisms of Virus Assembly”, Annu. Rev. Phys. Chem., 66, 217–39 (2015), [link], arXiv:1407.3856

2. Bacterial microcompartment assembly.  Bacterial microcompartments (BMCs) are icosahedral protein-based organelles found in bacteria that assemble around a dense complex of enzymes and reactants involved in certain metabolic pathways. The best-known example of a BMC is the carboxysome, which enables carbon fixation in photosynthetic bacteria. Understanding the mechanisms that control BMC formation is a central unanswered question in cell biology. My group developed a computational model for BMC assembly [2], which demonstrated that BMCs can assemble by two pathways, in which the enzyme cargo undergoes liquid-liquid phase separation either prior to or during shell assembly. The model also identified factors that determine how many enzymes encapsulated.  Thus, in addition to elucidating how native BMCs assemble, the model can help to redesign them as customizable organelles that assemble around a programmable set of enzymes, introducing capabilities such as biofuel production into new organisms.

2. Perlmutter JD; Mohajerani, F; Hagan, MF, Many-molecule encapsulation by an icosahedral shell, eLife 5, e14078 (2016); http://dx.doi.org/10.7554/eLife.14078

3. Non-equilibrium self-organization in active matter. Active matter describes systems whose constituent elements consume energy to drive motion or generate internal stresses. Examples include flocks or herds of animals, components of the cellular cytoskeleton, and collections of synthetic self-propelled colloids. By developing minimal models for these systems, my group is studying the relationship between molecular-scale energy dissipation (e.g. by molecular motors) and macroscale collective behaviors, such as those responsible for the capabilities of living organisms. Some examples of our work follow, categorized by the class of system studied:

a. Active filaments.  We have found that mixtures of active and equilibrium rods spontaneously demix [3a] and filaments constructed from motile particles exhibit flagella-like beating [3b].  L. Giomi with Mahadevan, B. Chakraborty and me analyzed a continuum theoretical of active nematics [3c], which laid the context for thinking theoretically about the widely studied experimental active nematics model system, the suspension of microtubules propelled by molecular motors developed by Dogic.  Through collaborative modeling (my group) and experiments (Dogic) on the microtubule system we discovered a novel phase of matter, in which motile topological defects self-organize into higher-order structures with long-range orientational order [3d]. This discovery generalizes the concept of defect-ordered phases to non-equilibrium systems.

b. Self-propelled spheres. As a minimal model active system, I worked with Aparna Baskaran to model the behavior of self-propelled repulsive, non-aligning spheres.  This model was motivated by experiments on self-propelled Janus particles (which undergo directed motion due to catalytic activity which occurs on one side of the particle). Computer simulations showed that self-propelled repulsive, non-aligning spheres undergo phase separation between a dilute gas and a new form of matter, an active crystal [3e].  This nonequilibrium phase transition demonstrates all the hallmarks of its equilibrium analog, including a critical point. We developed a kinetic model that explains the mechanism driving phase separation [3f], and showed that phase separation dynamics could be analyzed by an analog to classical nucleation theory [3e]. Further work describing self-propelled spheres with attractive interactions showed that their phase separation is reentrant as a function of activity [3f].

c. Boundaries in active materials. Despite the necessity of having boundaries in any real-world device, their effects on an active systems are incompletely understood. Yaouen Fily, Aparna Baskaran and I developed a general theory relating boundary geometry to the density distribution of self-propelled spheres [3h-3k]. The theory and numerical simulations demonstrate that the boundary shape dramatically affects the active fluid's dynamics and thermomechanical properties in certain limits.  In particular, active particles are confined to the boundary, with a density that is inversely proportional to, and a pressure that decays exponentially with, the local Gaussian curvature of the boundary. The theory enables designing a box shape that yields any desired density distribution on the boundary.

3a. McCandlish, S.R, Baskaran, A., and Hagan, M.F. “Spontaneous Segregation of Self-Propelled Particles with Different Motilities”, Soft Matter, 8, 2527-2534 (2012), [link] arXiv:1110.2479

3b. 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) (http://dx.doi.org/10.1098/rsif.2013.0884)

3c. Giomi L., Mahadevan L., Chakraborty, B., and Hagan, M.F. “Banding, excitability and chaos in active nematic suspensions”, Nonlinearity, 25, 2245–2269 (2012)  [link]

3d. 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]

3e. Redner, G., Hagan, M.F.*, Baskaran, A*., “Structure and Dynamics of a Phase-Separating Active Colloidal Fluid” Phys. Rev. Lett., 110, 055701 (2013),  arXiv:1207.1737

3f. 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

3g. Redner, G.; Baskaran, A.; Hagan, M.F., “Reentrant Phase Behavior in Active Colloids with Attraction”, Phys. Rev. E, 88, 012305 (2013), [Subject of a Physical Review Focus, Physics 6, 134 (2013)]

3h. Fily, Y., Baskaran, A., Hagan, M.F. “Dynamics of Self-Propelled Particles Under Strong Confinement”, Soft Matter, 10, 5609-5617 (2014) [link], arXiv:1402.5583

3i. 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 (2015), [link], arXiv:1410.5151

3j. Fily, Y; Baskaran, A; Hagan, MF, “Active Particles on Curved Surfaces”, under review, arXiv:1601.00324

3k. Fily, Y; Baskaran, A; Hagan, MF, “Equilibrium mappings in polar-isotropic confined active particles”, under review, arXiv:1612.08719

4. Biomimetic assembly. My group has studied the assembly of colloids into biomimetic structures such as filamentous bundles or membranes, focusing on mechanisms that force assembly to self-terminate in one or more dimensions. I combined theory and computation with experiments performed by Z. Dogic (Brandeis) to characterize colloidal membranes (macroscopic monolayer membranes comprised of colloidal rods [4a]. We demonstrated a novel mechanism that stabilizes monolayers, in which protrusions of rods within the monolayer entropically limit growth in the direction perpendicular to the membrane. Subsequently, work with Dogic, Baskaran, and Chakraborty demonstrated that phase separation in 2D is qualitatively different from that in 3D. For example, chirality can drive equilibrium micro-phase separation into monodisperse, finite-size, self-healing domains [4b,4c].

We also studied rod-like particles end-attaching onto a curved surface, creating a finite-thickness monolayer aligned with the surface normal [4d]. This geometry leads to two forms of frustration, one associated with the incompatibility of hexagonal order on surfaces with Gaussian (intrinsic) curvature, and the second reflecting the deformation of a layer with finite thickness on a surface with non-zero mean (extrinsic) curvature. We found latter effect drives a novel faceting mechanism, which leads to a rich variety of morphologies.

4a. 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), [link] arXiv:1103.2760

4b. Sharma, P; Ward, AR; Gibaud, T; Hagan, MF; Dogic, Z, “Hierarchical organization of chiral rafts in colloidal membranes”, Nature, 513, 77–80 (2014) [link]

4c. Sakhardande, R., Stanojeviea, S., Baskaran, A., Baskaran, A., Hagan, M. F.,  Chakraborty, B., “Theory of microphase separation in bidisperse chiral membranes.” Phys. Rev. E, in press, arXiv:1604.03012

4d. 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

Complete List of Publications

Articles under review

65. 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

64. Lazaro, GR; Mukhopadhyay, S; Hagan, MF, “The contribution of a nucleocapsid core to viral budding”, under review, arXiv:1706.04867

63. Fily, Y; Baskaran, A; Hagan, MF, “Active Particles on Curved Surfaces”, under review, arXiv:1601.00324

Articles accepted or published since submission of tenure package

62. 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

61. 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

60. Sakhardande, R., Stanojeviea, S., Baskaran, A., Baskaran, A., Hagan, M. F.,  Chakraborty, B., “Theory of microphase separation in bidisperse chiral membranes.” Phys. Rev. E (in press), arXiv:1604.03012

59. 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

58. 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

57. 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, 20160328 (2017)

56. 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] NIHMSID 846122 http://dx.doi.org/10.1039/C6SM01498D

55. Perlmutter JD; Mohajerani, F; Hagan, MF, Many-molecule encapsulation by an icosahedral shell, eLife 5, e14078 (2016); http://dx.doi.org/10.7554/eLife.14078

54. Lazaro, GR; Hagan, MF, “Allosteric control in icosahedral capsid assembly”, J. Phys. Chem B, 120, 6306-6318 [Bill Gelbart Festschrift] [link] (2016) PMCID 5367391

53. 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

52. Xie, S; Pelcovits, RA*; Hagan, MF*, “Probing a self-assembled fd virus membrane with a microtubule”, Phys. Rev. E, 93, 062608, [link] arXiv:1512.02204 (2016)

51. Xie, S; Hagan, MF*; Pelcovits, RA*, “Interaction of chiral rafts in self-assembled colloidal membranes”, Phys. Rev. E, 93, 032706 (2016), [link] arXiv:1601.08232

50. Hagan MF; Zandi, R, “Recent advances in coarse-grained modeling of virus assembly”, Curr Opin Virol, 18, 36-43 (2016) [link] NIHMSID 772743

49. Hagan MF; Baskaran A, “Emergent self-organization in active materials”, Curr Opin Cell Biol, 38, 74-80 (2016) [link] NIHMS 772743

48. 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]

47. Perlmutter, J.D.; Hagan, M.F., “Mechanisms of Virus Assembly”, Annu. Rev. Phys. Chem., 66, 217–39 (2015), [link], arXiv:1407.3856

46. 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],  PMCID 4317536

45. 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  NIHMSID 691930

44. 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]

43. 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 (2015), [link], arXiv:1410.5151

42. 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) doi:10.1038/ncomms8284, [link], PMCID: PMC4470301

41. 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, 138102 (2015), arXiv:1408.5068

40. 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] PMCID: PMC4318763

39. Sharma, P; Ward, AR; Gibaud, T; Hagan, MF; Dogic, Z, “Hierarchical organization of chiral rafts in colloidal membranes”, Nature, 513, 77–80 (2014) [link]

38. Perlmutter, J.D.; Perkett, M.R.; Hagan, M.F., “Pathways for virus assembly around nucleic acids”, J. Mol. Biol., 426, 3148–3165 (2014), [link], PMC4135015

37. Fily, Y., Baskaran, A., Hagan, M.F. “Dynamics of Self-Propelled Particles Under Strong Confinement”, Soft Matter, 10, 5609-5617 (2014) [link], arXiv:1402.5583

36. Perkett, M.R., Hagan, M.F., "Using Markov State Models to Study Self-Assembly", J. Chem. Phys., 140, 214101 (2014), [link] PMCID: PMC4048447 [Cover Article]

35. 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, PMC4384162

34. 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) (http://dx.doi.org/10.1098/rsif.2013.0884)

33. Perlmutter, J.D.; Qiao, C.; Hagan, M.F. “Viral genome structures are optimal for capsid assembly”, eLife, 2:e00632, http://elife.elifesciences.org/content/2/e00632

32. Redner, G.; Baskaran, A.; Hagan, M.F., “Reentrant Phase Behavior in Active Colloids with Attraction”, Phys. Rev. E, 88, 012305 (2013), [Subject of a Physical Review Focus, Physics 6, 134 (2013)]

31. Hagan, M.F. “Modeling Viral Capsid Assembly”, Adv. Chem. Phys., 155, Ch 1, 1-68 (2014), arXiv:1301.1657 [invited review article] PMC4318123

30. Redner, G., Hagan, M.F.*, Baskaran, A*., “Structure and Dynamics of a Phase-Separating Active Colloidal Fluid” Phys. Rev. Lett., 110, 055701 (2013),  arXiv:1207.1737

* co-corresponding author

29. 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, 1363-1369 (2012) [Featured Article]

28. Ruiz-Herrero, T., Velasco, E., Hagan, M.F., “Mechanisms of budding of nanoscale particles through lipid bilayers” J. Phys. Chem B, 116, 9595-603 (2012) arXiv:1202.4691

27. Giomi L., Mahadevan L., Chakraborty, B., and Hagan, M.F. “Banding, excitability and chaos in active nematic suspensions”, Nonlinearity, 25, 2245–2269 (2012)  [link]

26. 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)

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

24. 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)

*co-corresponding author

23. 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

22. 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, 348-351 (2012)

21. McCandlish, S.R, Baskaran, A., and Hagan, M.F. “Spontaneous Segregation of Self-Propelled Particles with Different Motilities”, Soft Matter, 8, 2527-2534 (2012), [link] arXiv:1110.2479

20. 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), [link], arXiv:1103.2760

Articles published before submission of tenure package

19. Yang Y. and Hagan, M.F. “Theoretical calculation of the phase behavior of colloidal membranes” Phys. Rev. E, 84, 051402 (2011)

18. 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)

17. Giomi L., Mahadevan L., Chakraborty, B., and Hagan, M.F. “Excitable Patterns in Active Nematics”,  Phys. Rev. Lett 106, 218101 (2011)

16. Sumedha; Hagan, M.F.; Chakraborty, B. “Prolonging assembly through dissociation: A self-assembly paradigm in microtubules”,  Phys. Rev. E, 83, 051904 (2011)

15. 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 physical virology.

14. Yang, Y.; Meyer, R.B.; Hagan, M.F. “Self-limited self-assembly of chiral filaments”, Phys. Rev. Lett., 104, 258102 (2010)

13. Kivenson, A.; Hagan, M.F. “Mechanisms of Capsid Assembly around a Polymer”,  Biophys. J,  99, 619-628 (2010)

12. Hagan, M.F. and 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, 98, 1065-1074 (2010)

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

10. 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., 102, 108302 (2009)

9. 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, 6, 1251-1262 (2009) (Special issue on Self-Assembly)

8. Elrad, O.M.; Hagan, M.F. “Mechanisms of size control and polymorphism in viral capsid assembly”, Nano Letters, 8, 3850-3857 (2008)

7. Hagan, M. F. “Controlling viral capsid assembly with templating”, Phys. Rev. E, 77, 051904 (2008)

Articles from postdoctoral and graduate work

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

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

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

3. 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, 100, 13922 (2003)

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

1. 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, 98, 1560 (2001).

(vi) Patents

• Barry, E., Dogic, Z., Hagan, M.F., Yang, Y., Perlman, D. “Aligned Arrays of Nanorods, and Methods of Making and Using Them”, patent pending