Seth Fraden
Degrees
Brandeis University, Ph.D.University of California, Berkeley, B.A.
Expertise
We study a broad range of topics in Soft Matter utilizing a variety of methods spanning experiment, theory, and simulation. Current research thrusts are in active matter, non-linear chemical dynamics & chemical networks, chemomechanics & soft robotics, protein crystallization, microfluidics, DNA origami, self-assembly and anti-viral theurapeutics. As our research interests lie at the intersection of physics, chemistry, biology, materials science and engineering, we are interdisciplinary, but as these projects are large and challenging, we collaborate in multi-investigator projects.Profile
The research group of Seth Fraden is focused on four topics; non-linear chemical dynamics, active matter, microfluidics technology and colloidal self-assembly.In living systems, chemistry is commonly used in ways that are extremely rare in inanimate systems. For example, muscles consume chemical energy to perform work and oscillating chemical reactions such as the pace maker in the heart control contractions. Working with colleagues in the chemistry department we are using microfluidic manufacturing technology to construct model synthetic systems that contain artificial neural networks coupled to a synthetic musculature. Working with colleagues in the math department, we are modeling chemical networks of different topologies using dynamical systems theory.
Our goal in active matter research is to develop robust systems that will serve as paradigms for investigations of active matter across different length scales ranging from the micro to macroscopic. Our model system, developed at Brandeis by Zvonimir Dogic, is an in vitro biologic system based upon microtubules and kinesin motors that is intentionally simplified to contain the minimal number of biological components needed to exhibit active matter behavior. We study how turbulent flows in unconfined active nematics become ordered under confinement.
Protein crystallization is of importance in biotechnology as a necessary step to obtain the structure of proteins. We seek to elucidate the physics of protein crystallization and guided by our understanding of nucleogenesis are developing microfluidic based high throughput crystallization devices.
We are developing new methods for the rapid prototyping of thermplastic microfluidics that is suitable for start-ups and academic labs.
Caspar and Klug elucidated the geometric principles that govern the structure of natural viral capsids in 1962 by providing the minimum number of distinct local symmetries that are required to form an icosahedral shell of a given size. However, understanding the symmetry rules is not sufficient to understand assembly in nature nor to determine the engineering principles to build synthetic capsids. Working with the Hagan group at Brandeis and the Dietz group at TUM, we use accurately-designed and rigid building blocks fabricated using DNA origami to provide a general and modular solution to de-novo creation of icosahedral virus-like shells, thereby expanding Caspar and Klug theory with engineering principles for building synthetic capsids, providing strategies for controlling the pathways, kinetics, and the yield by which subunits will arrange themselves into icosahedral symmetry. One application we are exploring is the development of a novel antivirals agent. Webpage
Courses Taught
| PHYS | 10a | Introduction to Physical Laws and Phenomena I |
| PHYS | 18a | Introductory Laboratory I |
| PHYS | 18b | Introductory Laboratory II |
| PHYS | 39a | Advanced Physics Laboratory |
| PHYS | 91g | Introduction to Research Practice |
| PHYS | 169b | Advanced Laboratory |
| QBIO | 120b | Quantitative Biology Instrumentation Laboratory |
Awards and Honors
Fellow of the American Physical Society (2020)
Innovation Prize of the International Organization of Biological Crystallization (2008)
National Science Foundation Fellowship (1987 - 1989)
Scholarship
James Sheehy, Ian Hunter, Maria Eleni Moustaka, S. Ali Aghvami, Youssef Fahmy, and Seth Fraden. "Impact of PDMS-Based Microfluidics on Belousov−Zhabotinsky Chemical Oscillators." Journal of Physical Chemistry B 124. (2021): 11690-11698.
Norton, M. M., Grover, P., Hagan, M. F. and Fraden, S.. "Optimal Control of Active Nematics." Physical Review Letters 125. (2021): 178005.
Theodore Lupinski, Markus Ludwig, Seth Fraden, and Nathan Tompkins. "An Arduino-based constant pressure fluid pump." Eur. Phys. J. E 44:14. (2021).
Wang, Jiaqing; Tan, Weiyi; Li, Guanying; Wu, Difei; He, Hongjian; Xu, Jiashu; Yi, Meihui; Zhang, Ye; Aghvami, S Ali; Fraden, Seth; Xu, Bing. "Enzymatic Insertion of Lipids Increases Membrane Tension for Inhibiting Drug Resistant Cancer Cells." Chemistry: A European Journal 26. (2021): 15116-15120.
Zhengyang Zhou, Chaitanya Joshi, Ruoshi Liu,Michael M. Norton, Linnea Lemma, Zvonimir Dogic, Michael F. Hagan, Seth Fraden and Pengyu Hong. "Machine learning forecasting of active nematics." Soft Matter 17. (2021): 738-747.
A. J. Balchunas, R. A. Cabanas, M. J. Zakhary, T. Gibaud, S. Fraden, P. Sharma, M. F. Hagan and Z. Dogic. "Equation of state of colloidal membranes." Soft Matter 15. (2020): 6791.
Fraden, Seth. "Turbulent beginnings." Nature Physics 15. (2020): 311-312.
Michael M. Norton, Nathan Tompkins, Baptiste Blanc, Matthew Carl Cambria, Jesse Held, and Seth Fraden. "Dynamics of Reaction-Diffusion Oscillators in Star and other Networks with Cyclic Symmetries Exhibiting Multiple Clusters." Phys. Rev. Lett. 123. (2020): 148301.
Wang, H., Feng, Z., Yang, C., Liu, J., Medina, J.E., Aghvami, S.A., Dinulescu, D.M., Liu, J., Fraden, S., Xu, B.. "Unraveling the cellular mechanism of assembling cholesterols for selective cancer cell death." Molecular Cancer Research 17. (2020): 907-917.
Achini Opathalage, Michael M. Norton, Michael P. N. Juniper, Blake Langeslay, S. Ali Aghvami, Seth Fraden, and Zvonimir Dogic. "Self-organized dynamics and the transition to turbulence of confined active nematics." Proceedings of the National Academy of Science 116. (2019): 4788 - 4797.
Michael M. Norton, Arvind Baskaran, Achini Opathalage, Blake Langeslay, Seth Fraden, Aparna Baskaran, and Michael Hagan. "Dynamics of an active nematic under topologically incommensurate confinement." PHYSICAL REVIEW E 97. (2018): 012702.
Thomas Litschel, Michael M. Norton, Vardges Tserunyan and Seth Fraden. "Engineering reaction–diffusion networks with properties of neural tissue." Lab on a Chip 18. (2018): 714-722.
C. Girabawe, S. Fraden. "An image-driven drop-on-demand system." Sensors and Actuators B: Chemical 238. (2017): 532-539.
Kun-Ta Wu, Jean Bernard Hishamunda, Daniel T. N. Chen, Stephen J. DeCamp, Ya-Wen Chang, Alberto Fernández-Nieves, Seth Fraden, Zvonimir Dogic. "Transition from turbulent to coherent flows in confined three-dimensional active fluids." Science (2017): eaal1979.
S. Ali Aghvami, Achini Opathalage, Z.K. Zhang, Markus Ludwig, Michael Heymann, Michael Norton, Niya Wilkins, Seth Fraden. "Rapid prototyping of cyclic olefin copolymer (COC) microfluidic devices." Sensors and Actuators B: Chemical 247. (2017): 940-949.
A.L. Wang, J.M. Gold, N. Tompkins, M. Heymann, K.I. Harrington, S. Fraden. "Configurable NOR gate arrays from Belousov-Zhabotinsky micro-droplets." The European Physical Journal Special Topics 225. (2016): 211-227.
Nathan Tompkins and Seth Fraden. "An inexpensive programmable illumination microscope with active feedback." American Journal of Physics 84. (2016): 150.
Markus Ludwig and Seth Fraden. "A simple and inexpensive device to remove edge beads." Chips and Tips (2015).
Ning Li, Nathan Tompkins, Hector Gonzalez-Ochoa and Seth Fraden. "Tunable diffusive lateral inhibition in chemical cells." Eur. Phys. J. E 38 (2015): 18.
R. R. Unwin, R. A. Cabanas, T. Yanagishima, T. R. Blower, H. Takahashi, G. P. C. Salmond, J. M. Edwardson, S. Fraden and E. Eiser. "DNA driven self-assembly of micron-sized rods using DNA-grafted bacteriophage fd virions." Phys. Chem. Chem. Phys. 17 (2015): 8194-8202.
Micha Kornreich, Michael Heymann, Seth Fraden and Roy Beck. "Cross polarization compatible dialysis chip." Lab on a Chip 14 (2014): 3700-3704.
Michael Heymann, Achini Opthalage, Jennifer L. Wierman, Sathish Akella, Doletha M. E. Szebenyi, Sol M. Gruner and Seth Fraden. "Room-temperature serial crystallography using a kinetically optimized microfluidic device for protein crystallization and on-chip X-ray diffraction." IUCrJ 1. (2014): 349–360.
N. Li, J. Delgado, H. O. González-Ochoa, I. R. Epstein and S. Fraden. "Combined excitatory and inhibitory coupling in a 1D array of Belousov- Zhabotinsky droplets." Phys. Chem. Chem. Phys. 16 (2014): 10965-10978.
Nathan Tompkins, Ning Li, Camille Girabawe, Michael Heymann, G. Bard Ermentrout, Irving R. Epstein, and Seth Fraden. "Testing Turing's Theory of Morphogenesis in Chemical Cells." Proceedings of the National Academy of Sciences 111 (2014): 4397–4402.
Sathish V. Akella, Aaron Mowitz, Michael Heymann, and Seth Fraden. "Emulsion-Based Technique To Measure Protein Crystal Nucleation Rates of Lysozyme." Crystal Growth & Design 14 (2014): 4487-4509.
Sukho Park, Dongshin Kim, Seong Young Ko, Jong-Oh Park, Sathish Akella, Bing Xu, Ye Zhang and Seth Fraden. "Controlling uniformity of photopolymerized microscopic hydrogels." Lab on a Chip 14 9. (2014): 1551 - 1563.
Ye Zhang, Ning Zhou, Ning Li, Megan Sun, Dongshin Kim, Seth Fraden, Irving R. Epstein, and Bing Xu. "Giant Volume Change of Active Gels under Continuous Flow." JACS (2014).
Michael Heymann, Seth Fraden, and Dongshin Kim. "Multi-Height Precision Alignment With Selectively Developed Alignment Marks." Journal of Microelectromechanical Systems (2013).
Ye Zhang, Ning Zhou, Sathish Akella, Yi Kuang, Dongshin Kim, Alyssa Schwartz, Marc Bezpalko, Bruce M. Foxman, Seth Fraden, Irving R. Epstein, Bing Xu. "Active Cross-Linkers that Lead to Active Gels." Angewandte Chemie International Edition (2013).
Ye Zhang, Ning Li, Jorge Delgado, Ning Zhou, Ryo Yoshida, Seth Fraden, Irving R. Epstein and Bing Xu. "Structural modulation of self-oscillating gels: changing the proximity of the catalyst to the polymer backbone to tailor chemomechanical oscillation." Soft Matter (2012).
Ye Zhang, Ning Li, Jorge Delgado, Yuan Gao, Yi Kuang, Seth Fraden, Irving R. Epstein, and Bing Xu. "Post-Self-Assembly Cross-Linking of Molecular Nanofibers for Oscillatory Hydrogels." Langmuir (2012).
Jorge Delgado, Ning Li, Marcin Leda, Hector O. Gonzalez-Ochoa, Seth Fraden and Irving R. Epstein. "Coupled oscillations in a 1D emulsion of Belousov–Zhabotinsky droplets." Soft Matter (2011).
Lorenzo Di Michele, Taiki Yanagishima, Anthony R. Brewer, Jurij Kotar, Erika Eiser and Seth Fraden. "Interactions between Colloids Induced by a Soft Cross-Linked Polymer Substrate." Physical Reveiw Letters (2011): 136101.
Romanowsky, M. B., Heymann, M., Abate, A. R., Krummel, A. T., Fraden, S., Weitz, D. A.. "Functional patterning of PDMS microfluidic devices using integrated chemo-masks." Lab on a Chip 10. 12 (2010): 1521-1524.
Selimovic, S., Gobeaux, F., Fraden, S.. "Mapping and manipulating temperature-concentration phase diagrams using microfluidics." Lab on a Chip 10. (2010): 1696-1699.
Toiya, M., Gonzalez-Ochoa, H. O., Vanag, V. K., Fraden, S., Epstein, I. R.. "Synchronization of Chemical Micro-oscillators." Journal of Physical Chemistry Letters 1. 8 (2010): 1241-1246.
Boukellal, H., Selimovic, S., Jia, Y. W., Cristobal, G., Fraden, S.. "Simple, robust storage of drops and fluids in a microfluidic device." Lab on a Chip 9. 2 (2009): 331-338.
F. Huang, K. Addas, A. Ward, N. T. Flynn, E. Velasco, M. F. Hagan, Z. Dogic, S. Fraden. "Pair Potential of Charged Colloidal Stars." Phys. Rev. Letts. 102. (2009): 108302.
Huang F, Rotstein R, Fraden S, Kasza KE , Flynn NT. "Phase behavior and rheology of attractive rod-like particles." Soft Matter 14. (2009): 2766-2771.
Selimovic, Seila, Jia, Yanwei, Fraden, Seth. "Measuring the Nucleation Rate of Lysozyme using Microfluidics." Crystal Growth & Design 9. (2009): 1806-1810.
Blouwolff, J., Fraden, S.. "Crystallization conditions of membrane protein CLC-ec1: An example outside the crystallization slot." Journal of Crystal Growth 303. 2 (2007): 546-553.
Purdy, K. R., Fraden, S.. "Influence of charge and flexibility on smectic phase formation in filamentous virus suspensions." Physical Review E 76. 1 (2007): Art. No. 011705 .
Shim, J. U., Cristobal, G., Link, D. R., Thorsen, T., Fraden, S.. "Using microfluidics to decouple nucleation and growth of protein crystals." Crystal Growth & Design 7. 11 (2007): 2192-2194.
Shim, J. U., Cristobal, G., Link, D. R., Thorsen, T., Jia, Y. W., Piattelli, K., Fraden, S.. "Control and measurement of the phase behavior of aqueous solutions using microfluidics." Journal of the American Chemical Society 129. 28 (2007): 8825-8835.
Varga, S., Fraden, S.. "Smectic ordering in athermal systems of rodlike triblock copolymers." Journal of Chemical Physics 127. 15 (2007).
Bloustine, J., Virmani, T., Thurston, G. M., Fraden, S.. "Light scattering and phase behavior of lysozyme-poly(ethylene glycol) mixtures." Physical Review Letters 96. 8 (2006).
Blouwolff, J., Fraden, S.. "The coordination number of granular cylinders." Europhysics Letters 76. 6 (2006): 1095-1101.
Dogic, Z., Fraden, S.. "Ordered phases of filamentous viruses." Current Opinion in Colloid & Interface Science 11. 1 (2006): 47-55.
Fraden, S., Dogic, Z.. "Phase Behavior of Rod-Like Viruses and Virus-Sphere Mixtures." Soft Matter, vol. 2: Complex Colloidal Suspensions. vol. 2 Ed. Gompper, G., Schick, M.. Weinheim: Wiley-VCH, 2006
Fraden, Seth Purdy, K.R. Varga, S Galindo, A. & Jackson, G.. "Nematic Phase Transitions in Mixtures of Thin and Thick Colloidal Rods." Phys. Rev. Lett. 94. 057801 (2005).
Purdy, K. R., Varga, S., Galindo, A., Jackson, G., Fraden, S.. "Nematic phase transitions in mixtures of thin and thick colloidal rods." Physical Review Letters 94. 5 (2005): 057801.
Varga, S., Purdy, K., Galindo, A., Fraden, S., Jackson, G.. "Nematic-nematic phase separation in binary mixtures of thick and thin hard rods: Results from Onsager-like theories." Physical Review E 72. 5 (2005).
Dogic, Z., Purdy, K. R., Grelet, E., Adams, M., Fraden, S.. "Isotropic-nematic phase transition in suspensions of filamentous virus and the neutral polymer Dextran." Physical Review E 69. (2004): 051702.
Fraden, Seth & Purdy, K.R.. "Isotropic-Cholesteric Phase Transition of Filamentous Virus Suspensions as a Function of Rod Length and Charge." Phys. Rev. E 70. 061703 (2004).
Fraden,Seth Dogic, Z. Purdy, K. Grelet, E. & Adams, M.. "Isotropic-Nematic Phase Transition in Suspensions of Filamentous Virus and the Neutral Polymer Dextran." Phys. Rev. E 69. 051702 (2004).
Purdy, K. R., Fraden, S.. "Isotropic-cholesteric phase transition of filamentous virus suspensions as a function of rod length and charge." Physical Review E 70. 6 (2004): 061703.
Bloustine, J., Berejnov, V., Fraden, S.. "Measurements of protein-protein interactions by size exclusion chromatography." Biophysical Journal 85. 4 (2003): 2619-2623.
Grelet, E., Fraden, S.. "What is the origin of chirality in the cholesteric phase of virus suspensions?." Physical Review Letters 90. 19 (2003): 198302.
Purdy, K. R., Dogic, Z., Fraden, S., Ruhm, A., Lurio, L., Mochrie, S. G. J.. "Measuring the nematic order of suspensions of colloidal fd virus by x-ray diffraction and optical birefringence." Physical Review E 67. 3 (2003): 031708.
Dogic, Z., Fraden, S.. "Development of model colloidal liquid crystals and the kinetics of the isotropic-smectic transition." Philosophical Transactions of the Royal Society of London Series A-Mathematical Physical and Engineering Sciences 359. 1782 (2001): 997-1014.
Jones, R., Fraden, S., Hamley, I.. "Development of model colloidal liquid crystals and the kinetics of the isotropic-smectic transition - Discussion." Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences 359. 1782 (2001): 1014-1015.
Dassanayake, U., Fraden, S., van Blaaderen, A.. "Structure of electrorheological fluids." Journal of Chemical Physics 112. 8 (2000): 3851-3858.
Dogic, Z., Fraden, S.. "Cholesteric phase in virus suspensions." Langmuir 16. 20 (2000): 7820-7824.
Dogic, Z., Frenkel, D., Fraden, S.. "Enhanced stability of layered phases in parallel hard spherocylinders due to addition of hard spheres." Physical Review E 62. 3 (2000): 3925-3933.
Dogic, Z., Philipse, A. P., Fraden, S., Dhont, J. K. G.. "Concentration-dependent sedimentation of colloidal rods." Journal of Chemical Physics 113. 18 (2000): 8368-8380.
Fraden, S., Kamien, R. D.. "Self-assembly in vivo." Biophysical Journal 78. 5 (2000): 2189-2190.
Adams, M., Dogic, Z., Keller, S. L., Fraden, S.. "Entropically driven microphase transitions in mixtures of colloidal rods and spheres." Nature 393. 6683 (1998): 349-352.
Adams, M., Fraden, S.. "Phase behavior of mixture's of rods (tobacco mosaic virus) and spheres (polyethylene oxide, bovine serum albumin)." Biophysical Journal 74. 1 (1998): 669-677.
Ospeck, M., Fraden, S.. "Solving the Poisson-Boltzmann equation to obtain interaction energies between confined, like-charged cylinders." Journal of Chemical Physics 109. 20 (1998): 9166-9171.
Dogic, Z., Fraden, S.. "Smectic phase in a colloidal suspension of semiflexible virus particles." Physical Review Letters 78. 12 (1997): 2417-2420.
Tang, J. X., Fraden, S.. "Nonmonotonic temperature dependence of the flexibility of bacteriophage fd." Biopolymers 39. 1 (1996): 13-22.
Fraden, S.. "Phase transitions in colloidal suspensions of virus particles." Observation, Prediction, and Simulation of Phase Transitions in Complex Fluids. vol. 460 Ed. Baus, M., Rull, L. F., Ryckaert, J. P.. Kluwer Academic Publishers, 1995. 113 - 164.
Tang, J. X., Fraden, S.. "Isotropic-Cholesteric Phase-Transition in Colloidal Suspensions of Filamentous Bacteriophage-Fd." Liquid Crystals 19. 4 (1995): 459-467.
Hu, Y., Glass, J. L., Griffith, A. E., Fraden, S.. "Observation and Simulation of Electrohydrodynamic Instabilities in Aqueous Colloidal Suspensions." Journal of Chemical Physics 100. 6 (1994): 4674-4682.
Kepler, G. M., Fraden, S.. "Attractive Potential between Confined Colloids at Low Ionic-Strength." Physical Review Letters 73. 2 (1994): 356-359.
Kepler, G. M., Fraden, S.. "Video Microscopy Study of the Potential-Energy of a Colloidal Particle Confined between 2 Plates." Langmuir 10. 8 (1994): 2501-2506.
Ospeck, M., Fraden, S.. "Influence of Reflecting Boundaries and Finite Interfacial Thickness on the Coherent Backscattering Cone." Physical Review E 49. 5 (1994): 4578-4589.
Fraden, S., Maret, G., Caspar, D. L. D.. "Angular-Correlations and the Isotropic-Nematic Phase-Transition in Suspensions of Tobacco Mosaic-Virus." Physical Review E 48. 4 (1993): 2816-2837.
Tang, J. X., Fraden, S.. "Magnetic-Field-Induced Isotropic-Nematic Phase-Transition in a Colloidal Suspension." Physical Review Letters 71. 21 (1993): 3509-3512.
Maier, E. E., Krause, R., Deggelmann, M., Hagenbuchle, M., Weber, R., Fraden, S.. "Liquid-Like Order of Charged Rodlike Particle Solutions." Macromolecules 25. 3 (1992): 1125-1133.
Fraden, S., Maret, G.. "Multiple Light-Scattering from Concentrated, Interacting Suspensions." Physical Review Letters 65. 4 (1990): 512-515.
Fraden, S., Hurd, A. J., Meyer, R. B.. "Electric-Field-Induced Association of Colloidal Particles." Physical Review Letters 63. 21 (1989): 2373-2376.
Fraden, S., Maret, G., Caspar, D. L. D., Meyer, R. B.. "Isotropic-Nematic Phase-Transition and Angular-Correlations in Isotropic Suspensions of Tobacco Mosaic-Virus." Physical Review Letters 63. 19 (1989): 2068-2071.
Srajer, G., Fraden, S., Meyer, R. B.. "Field-Induced Nonequilibrium Periodic Structures in Nematic Liquid-Crystals - Nonlinear Study of the Twist Frederiks Transition." Physical Review A 39. 9 (1989): 4828-4834.
Srajer, G., Fraden, S., Meyer, R. B.. "Measurement of the Viscoelastic Coefficients of Main-Chain Nematic Polymers by an Nmr Technique - Comment." Physical Review Letters 61. 7 (1988): 899-899.
Fraden, S., Meyer, R. B.. "Nonequilibrium Periodic Structures Induced by Rotating and Static Fields in a Lyotropic Nematic Liquid-Crystal - Comment." Physical Review Letters 57. 24 (1986): 3122-3122.
Fraden, S., Hurd, A. J., Meyer, R. B., Cahoon, M., Caspar, D. L. D.. "Magnetic-Field Induced Alignment and Instabilities in Ordered Colloids of Tobacco Mosaic-Virus." Journal De Physique 46. C3 (1985): 85-113.
Hurd, A. J., Fraden, S., Lonberg, F., Meyer, R. B.. "Field-Induced Transient Periodic Structures in Nematic Liquid-Crystals - the Splay Frederiks Transition." Journal De Physique 46. 6 (1985): 905-917.
Meyer, R. B., Lonberg, F., Taratuta, V., Fraden, S., Lee, S. D., Hurd, A. J.. "Measurements of the Anisotropic Viscous and Elastic Properties of Lyotropic Polymer Nematics." Faraday Discussions 79 (1985): 125-132.
Lonberg, F., Fraden, S., Hurd, A. J., Meyer, R. B.. "Periodic Director Patterns in Twist and Splay Frederiks Transitions in Tobacco Mosaic-Virus Liquid-Crystals." Molecular Crystals and Liquid Crystals 106. 3-4 (1984): 419-419.
Lonberg, F., Fraden, S., Hurd, A. J., Meyer, R. E.. "Field-Induced Transient Periodic Structures in Nematic Liquid-Crystals - the Twist-Freedericksz Transition." Physical Review Letters 52. 21 (1984): 1903-1906.
Fraden, S., Caspar, D. L. D., Phillips, W.. "X-Ray-Diffraction Studies of Colloid Crystalline Tmv." Biophysical Journal 37. 2 (1982): A97-A97.