PhD Theses

PhD Theses:

  1. Adam E. Cohen, Nanoscale Mechanics, Cambridge University, defended Dec. 2003
  2. Adam E. Cohen, Trapping and Manipulating Single Molecules in Solution (formatted for single-sided printing), (formatted for double-sided printing), Stanford University, defended Aug. 2006. See also errata.


  1. Y. Adam, J.J. Kim, S. Lou, Y. Zhao, M.E. Xie, D. Brinks, H. Wu, M.A. Mostajo-Radji, S. Kheifets, V. Parot, S. Chettih, K.J. Williams, B. Gmeiner, S.L. Farhi, L. Madisen, E.K. Buchanan, I. Kinsella, D. Zhou, L. Paninski, C.D. Harvey, H. Zeng, P. Arlotta, R.E. Campbell, A.E. Cohen, Voltage imaging and optogenetics reveal behaviour-dependent changes in hippocampal dynamics , Nature, 569, 413-417, 2019.
  2. S.L. Farhi, V.J. Parot, A. Grama, M. Yamagata, A.S. Abdelfattah, Y. Adam, S. Lou, J. J. Kim, R.E. Campbell, D.D. Cox, A.E. Cohen, Wide-area all-optical neurophysiology in acute brain slices, The Journal of Neuroscience, 10, 0168-19, 2019.
  3. V. J. Parot, C. Sing-Long, Y. Adam, U. L. Bohm, L. Z. Fan, S. L. Farhi, A.E. Cohen, Compressed Hadamard microscopy for high-speed optically sectioned neuronal activity recordings, J. Phys. D: Appl. Phys., 52, 144001, 2019.
  4. Z. Shi, Z.T. Graber, T. Baumgart, H.A. Stone, A.E. Cohen, Cell membranes resist flow, Cell, 175, 1-11, 2018.
  5. H.M. McNamara, S. Dodson, Y. Huang, E.W. Miller, B. Sandstede, A.E. Cohen, Geometry-dependent arrhythmias in electrically excitable tissues, Cell Systems, 7, 359-370, 2018.
  6. L.Z. Fan, R. Nehme, Y. Adam, E.S. Jung, H. Wu, K. Eggan, D.B. Arnold, A.E. Cohen, All-optical synaptic electrophysiology probes mechanism of ketamine-induced disinhibition, Nature Methods, 15, 823-831, 2018. Supplementary Information.
  7. E. Kiskinis, J.M. Kralj, P. Zou, E.N. Weinstein, H. Zhang, K. Tisoras, O. Wiskow, J.A. Ortega, K. Eggan, A.E. Cohen, All-optical electrophysiology for high-throughput functional characterization of a human iPSC-derived motor neuron model of ALS, Stem Cell Reports, 10, 1-14, 2018.
  8. A.E. Cohen and S.L. Farhi, Sculpting light to reveal brain function, Nature Neuroscience, 21.6, 776, 2018.
  9. A.H. Squires, A.E. Cohen, W.E. Moerner, Anti-Brownian Traps, Encyclopedia of Biophysics, G. C. K. Robers, A. Watts (eds.)
  10. Y.Adam, J.J.Kim, S.Lou, Y.Zhao, D.Brinks, H.Wu, M.A.Mostajo-Radji, S.Kheifets, V.Parot, S.Chettih, K.J.Williams, S.L.Farhi, L.Madisen, C.D.Harvey, H.Zeng, P.Arlotta, R.E.Campbell, A.E.Cohen, All-optical electrophysiology reveals brain-state dependent changes in hippocampal subthreshold dynamics and excitability, bioRxiv, 281618, 2018.
  11. M.P.Chien, D.Brinks, Y.Adam, W.Bloxham, S.Kheifets, A.E.Cohen, Two-photon photoactivated voltage imaging in tissue with an Archaerhodopsin-derived reporter, bioRxiv, 211946, 2017.
  12. C.A.Werley, M.P.Chien, A.E.Cohen, Ultrawidefield microscope for high-speed fluorescence imaging and targeted optogenetic stiumation, Biomedical Optics Express, 8, 5794-5813, 2017.
  13. H.Zhang, A.E. Cohen, Optogenetic approaches to drug discovery in neuroscience and beyond, Trends in Biotechnology, 35, 625-639, 2017.
  14. Y.Xu, P. Zou, A.E. Cohen, Voltage imaging with genetically encoded indicators, Current Opinion in Chemical Biology, 39, 1-10, 2017.
  15. K.A. Werley, M.P. Chien, J. Gaublomme, K. Shekhar, V. Butty, B.A. Yi, J.M. Kralj, W. Bloxham, L.A. Boyer, A. Regev, A.E. Cohen, Geometry-dependent functional changes in iPSC-derived cardiomyocytes probed by functional imaging and RNA sequencing, PloS one, 12.3, e0172671, 2017.
  16. K. Ogden, W. Chen, S.A. Swanger, M.J. McDaniel, L.Z.Fan, C. Hu, A. Tankovic, H. Kusumoto, G.J. Kosobucki, A.J. Schulien, Z. Su, J. Pecha, S. Bhattacharya, S. Petrovski, A.E. Cohen, E. Aizenman, S.F. Traynelis, H. Yuan, Molecular mechanism of disease-associated mutations in the pre-M1 helix of NMDA receptors and potential rescue pharmacology, PLoS Genetics, 13, e1006536, 2017.
  17. D. Brinks, Y. Adam, S. Kheifets, A.E. Cohen, Painting with rainbows: patterning light in space, time, and wavelength for multiphoton optogenetic sensing and control, Accounts of Chemical Research, 49, 2518-2526, 2016.
  18. S. Lou, Y. Adam, E.N. Weinstein, E.Williams, K. Williams, V. Parot, N. Kavokine, S. Liberles, L. Madisen, H. Zeng, A.E. Cohen, Genetically targeted all-optical electrophysiology with a transgenic Cre-dependent Optopatch mouse, The Journal of Neuroscience, 43, 11059-11073, 2016.
    • Supplementary Information here.
    • Animal request form at JAX here.
  19. Y.K. Cho, G. Zheng, G.J. Augustine, D.R. Hochbaum, A.E. Cohen, T. Knöpfel, F. Pisanello, F.S. Pavone, I.M. Vellekoop, M.J. Booth, S. Hu, J. Zhu, Z. Chen, Y. Hoshi, Roadmap on neurophotonics, Journal of Optics, 18, 093007, 2016.
  20. H.McNamara, H. Zhang, C.A. Werley, A.E. Cohen, Optically controlled oscillators in an engineered bioelectric tissue, Phys. Rev., X 6, 031001, 2016. Supplementary material.
  21. H.Zhang, E.Reichert, A.E. Cohen, Optical electrophysiology for probing function and pharmacology of voltage-gated ion channels, eLife, 5, e15202, 2016.
  22. G. T. Dempsey, K.W. Chaudhary, N. Atwater, C. Nguyen, B.S. Brown, J.D. McNeish, A.E. Cohen, J.M. Kralj, Cardiotoxicity screening with simultaneous optogenetic pacing, voltage imaging and calcium imaging, Journal of Pharmacological and Toxicological Methods, 2016.
  23. A.E. Cohen, Optogenetics: turning the microscope on its head, Biophysical Journal, 110.5, 997, 2016.
  24. A. S. Abdelfatta, S. L. Farhi, Y. Zhao, D. Brinks, P. Zou, A. Ruangkittisakul, I. Platisa, V. A. Pieribone, K. Ballanyi, A. E. Cohen, R. E. Campbell, A bright and fast red fluorescent protein voltage indicator that reports neuronal activity in organotypic brain slices, The Journal of Neuroscience, 36.8, 2458-2472, 2016.
  25. M.J. Shon, A.E. Cohen, Nano-mechanical measurements of protein-DNA interactions with a silicon nitride pulley, Nucl. Acids Res., 44, e7, 2016.
  26. M.J. Henderson, H.A. Baldwin, C.A. Werley, S. Boccardo, L.R. Whitaker, X. Yan, G.T. Holt, E.R. Schreiter, L.L. Looger, A.E. Cohen, D.S. Kim, B.K. Harvey, A low affinity GCaMP3 variant (GCaMPer) for imaging the endoplasmic reticulum calcium store, PLoS One, 10.10, e0139273, 2015.
  27. V. Emiliani, A. E. Cohen, K. Deisseroth, M. Hausser, All-optical interrogation of neural circuits, J. Neurosci., 35.41, 13917-13926, 2015.
  28. H. Lee, D. Brinks, A.E. Cohen, Two-photon imaging of a magneto-fluorescent indicator for 3D optical magnetometry, Optics Express, 23.21, 28022-28030, 2015.
  29. D. Brinks, A.J. Klein, A.E. Cohen, Two-photon lifetime imaging of voltage indicating proteins as a probe of absolute membrane voltage, Biophysical Journal, 109, 914-921, 2015.
  30. M.P. Chien, C.A. Werley, S.L. Farhi, A.E. Cohen, Photostick: a method for selective isolation of target cells from culture, Chemical Science, 6, 1701-1705, 2015.
  31. V. Venkatachalam, A.E. Cohen, Imaging GFP-based reporters in neurons with multiwavelength optogenetic control, Biophys. J., 107, 1554-1563, 2014.
  32. D. Yang, A.E. Cohen, Chirality-dependent friction of bulk molecular solids, Langmuir, 30, 9972- 9976, 2014.
  33. J. Hou, J.M. Kralj, A.D. Douglass, F. Engert, A.E. Cohen, Simultaneous mapping of membrane voltage and calcium in zebrafish heart in vivo reveals chamber-specific development transitions in ionic currents, Front. Physiol., 5, 344, 2014. Supporting videos.
  34. P. Zou*, Y. Zhao*, A.D. Doughlass, D.R. Hochbaum, D. Brinks, C.A. Werley, D.J. Harrison, R.E. Campbell, A.E. Cohen (*Co-first authors), Bright and fast multicoloured voltage reporters via electrochromic FRET, Nature Communications, 5, 2014.
  35. D.R. Hochbaum*, Y. Zhao*, S.L. Farhi, N. Klapoetke, C.A. Werley, V. Kapoor, P. Zou, J.M. Kralj, D. Maclaurin, N. Smedemark-Margulies, J.L. Saulnier, G.L. Boulting, C. Straub, Y.K. Cho, M. Melkonian, G.K-S. Wong, D.J. Harrison, V.N. Murthy, B.L. Sebatini, E.S. Boyden, R.E. Campbell, A.E. Cohen (*Co-first authors), All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins, Nature Methods, 11, 825-833, 2014.
  36. A.E. Cohen, V. Venkatachalam, Bringing bioelectricity to light, Annu. Rev.Biophys., 43, 211-232, 2014.
  37. J. Hou, V. Venkatachalam, A.E. Cohen, Temporal dynamics of microbial rhodopsin fluorescence reports absolute membrane voltage, Biophysical Journal, 106.3, 639-648, 2014.
  38. V. Venkatachalam, D. Brinks, D. Maclaurin, D. Hochbaum, J.M. Kralj, A.E. Cohen, Flash memory: photochemical imprinting of neuronal action potentials onto a microbial rhodopsin, J. Am. Chem. Soci., 136, 2529-2537 2013.
  39. J. Park , C.A. Werley, V. Venkatachalam, J.M. Kralj, S.D. Dib-Hajj, S.G. Waxman, A.E. Cohen, Screening fluorescent voltage indicators with spontaneously spiking HEK cells, PLoS ONE, 8, e85221, 2013.
  40. A. Fields, E. Meyer, A.E. Cohen, Euler buckling and nonlinear kinking of double-stranded DNA, Nucl. Acids Res., 41, 9881-9890, 2013.
  41. D. Maclaurin*, V. Venkatachalam*, H. Lee, A.E. Cohen, Mechanism of voltage-sensitive fluorescence in a microbial rhodopsin, PNAS, 110, 5939-5944, 2013.
  42. M. W. Elting, S.R. Leslie, L.S. Churchman, J. Korlach, C.M.J. McFaul, J.S. Leith, M.J. Levene, A.E. Cohen, J.A. Spudich, Single-molecule fluorescence imaging of processive myosin with enhanced background suppression using linear zero-mode waveguides (ZMWs) and convex lens induced confinement (CLIC), Optics Express, 21, 1189-1202, 2013.
  43. Y. Tang, L. Sun, A. E. Cohen, Chiroptical hot spots in twisted nanowire plasmonic oscillators, Applied Physics Letters, 102, 043103, 2013. Supporting Information.
  44. A. P. Fields, A. E. Cohen, Optimal tracking of a Brownian particle, Optics Express, 20, 22585-22601, 2012.
  45. M. J. Shon, A. E. Cohen, Mass action at the single-molecule level, J. Am. Chem. Soc., 134, 14618-14623, 2012. Supporting information.
  46. J. Hou, A. E. Cohen, Motion induced by asymmetric degradation of hydrogels, Soft Matter, 8, 4616-4624, 2012. Supplementary video, supplementary text.
  47. J. M. Kralj*, A. D. Douglass*, D. R. Hochbaum*, D. Maclaurin, A. E. Cohen, (*co-first authors) Optical recording of action potentials in mammalian neurons using a microbial rhodopsin, Nature Methods, 9, 90-95, 2012. Supporting Online Text and Videos.
  48. H. Lee, N. Yang, A. E. Cohen, Mapping nanomagnetic fields using a radical pair reaction, Nano Letters, 11, 5367-5372, 2011.
  49. H. Bayraktar, A. P. Fields, J. M. Kralj, J. L. Spudich, K. J. Rothschild, A. E. Cohen, Ultrasensitive measurements of microbial rhodopsin photocycles using photochromic FRET, Photochem. & Photobiol. 88, 90-97, 2012.
  50. J. M. Kralj, D. R. Hochbaum, A. D. Douglass, A. E. Cohen, Electrical spiking in Escherichia coli probed with a fluorescent voltage-indicating protein, Science, 333, 345-348, 2011. Supporting Online Text and Videos.
  51. A. E. Cohen, A. P. Fields, The cat that caught the canary: what to do with single-molecule trapping, ACS Nano, 5, 5296-5299, 2011.
  52. A. P. Fields, A. E. Cohen, Electrokinetic trapping at the one nanometer limit, PNAS, 108, 8937-8942, 2011.
  53. A. E. Cohen and W. E. Moerner, Anti-Brownian Traps, in Encyclopedia of Biophysics, G. C. K. Roberts (Ed.) (Springer, Berlin, Heidelberg, appearing 2012).
  54. Y. Tang, A. E. Cohen, Enhanced enantioselectivity in excitation of chiral molecules by superchiral light, Science, 332, 333-336, 2011. Supporting Online Material
  55. N. Yang, A. E. Cohen, Local geometry of electromagnetic fields and its role in molecular multipole transitions, J. Phys. Chem. B, 115, 5304-5311, 2011.
  56. N. Yang, A. E. Cohen, Optical imaging through scattering media via magnetically modulated fluorescence, Optics Express, 18, 25461-25467, 2010.
  57. S. R. Leslie, A. P. Fields, A. E. Cohen, Convex lens-induced confinement for imaging single molecules, Anal. Chem., 82, 6224-6229, 2010.
  58. Y. Tang, A. E. Cohen, Optical chirality and its interaction with matter, Phys. Rev. Lett (cover story), 104,163901, 2010.
  59. A. P. Fields and A. E. Cohen, Anti-Brownian traps for studies on single molecules, Methods in Enzymology, 475, 149-174, 2010.
  60. A. E. Cohen, A. P. Fields, J. H. Hou, S. Leslie, M. J. Shon, In honor of W. E. Moerner: Confining molecules for single-molecule spectroscopy, Israeli J. Chem, 49, 275-282, 2009.
  61. A. E. Cohen, Nanomagnetic control of intersystem crossing, J. Phys. Chem. A, 113, 11084-11092, 2009.
  62. N. Yang, Y. Tang, and A. E. Cohen, Spectroscopy in sculpted fields, Nano Today, 4, 269-279, 2009.
  63. Y. Tang, T. A. Cook, A. E. Cohen, Limits on fluorescence detected circular dichroism of single helicene molecules, J. Phys. Chem. A, 113, 6213-6216, 2009.
  64. P. Jain, Y. Xiao, R. Walsworth and A. E. Cohen, Surface plasmon resonance enhanced magneto-optics (SuPREMO): Faraday rotation enhancement in gold-coated iron oxide nanocrystals, NanoLetters, 9, 1644-1650, 2009.
  65. E. Tran, A. E. Cohen, R. W. Murray, M. A. Rampi and G. M. Whitesides, Redox site-mediated charge transport in a Hg−SAM//Ru(NH3)63+/2+//SAM−Hg Junction with a dynamic interelectrode separation: compatibility with redox cycling and electron hopping mechanisms, J. Am. Chem. Soc., 131, 2141-2150, 22 Jan. 2009.
  66. Y. Jiang, Q. Wang, A. E. Cohen, N. Douglas, J. Frydman, W. E. Moerner, Hardware-based anti-Brownian electrokinetic trap (ABEL trap) for single molecules: Control loop simulations and application to ATP binding stoichiometry in multi-subunit enzymes, Proc. SPIE, 7038, 703807, (2008)
  67. A. E. Cohen, W. E. Moerner: Controlling Brownian motion of single protein molecules and single fluorophores in aqueous buffer, Opt. Express, 16, 6941-6956, 12 May 2008.
  68. A. E. Cohen, W. E. Moerner: Principal components analysis of shape fluctuations of single DNA molecules, PNAS, 104, 12622-12627, 31 July 2007. Journal link and Supporting Material and Movies.
  69. A. E. Cohen, W. E. Moerner: Internal mechanical response of a polymer in solution, Phys. Rev. Lett., 98, 116001, 14 Mar. 2007. Supplementary material.
  70. A. E. Cohen and W. E. Moerner: Suppressing Brownian motion of individual biomolecules in solution, PNAS, 103, 4362-4365, 14 Mar. 2006. Journal link and Supporting Material and Movies.
  71. A. E. Cohen and W. E. Moerner: An all-glass microfluidic cell for the ABEL trap: fabrication and modeling, Proc. SPIE 5930, 2005.
  72. A. E. Cohen: Control of nanoparticles with arbitrary two-dimensional force fields, Phys. Rev. Lett., 94, 118102, 25 Mar. 2005.
  73. A. E. Cohen and W. E. Moerner: The Anti-Brownian Electrophoretic trap (ABEL Trap): tabrication and software, Proc. SPIE 5699, 2005.
  74. S. Mukamel, A. E. Cohen, and U. Harbola: Intermolecular forces and generalized TDDFT response functions in Liouville Space, Time-Dependent Density Functional Theory (eds. M. A. L. Marques, C. A. Ullrich, F. Nogueira, A. Rubio, K. Burke and E. K. U. Gross, Springer, 2006).
  75. A. E. Cohen and W. E. Moerner: Method for trapping and manipulating nanoscale objects in solution , Appl. Phys. Lett. 86, 093109, 28 Feb. 2005.
  76. A. E. Cohen and S. Mukamel: Resonant enhancement and dissipation in nonequilibrium van der Waals forces, Phys. Rev. Lett. 91, 233202, 5 Dec. 2003.
  77. A. E. Cohen: Force-extension curve of a polymer in a high-frequency electric field, Phys. Rev. Lett. 91, 235506, 5 Dec. 2003.
  78. A. E. Cohen and L. Mahadevan: Kinks, rings, and rackets in filamentous structures, PNAS, 100,12141-12146, 14 Oct. 2003.
  79. A. E. Cohen: Carbon nanotubes provide a charge, Science (letter to the editor) 300, 1235-1235, 23 May 2003.
  80. A. E. Cohen and S. Mukamel: A mechanical force accompanies fluorescence resonance energy transfer (FRET), J. Phys. Chem. A 107, 3633-3638, 15 May 2003.
  81. Holmlin RE, Haag R, Chabinyc ML, Ismagilov RF, Cohen AE, Terfort A, Rampi MA, Whitesides GM: Electron transport through thin organic films in metal-insulator-metal junctions based on self-assembled monolayers,  J. Am. Chem. Soc., 123, 5075-5085, 30 May 2001, and Supporting Material.
  82. A. E. Cohen and R. Kunz: Large-area interdigitated array microelectrodes for electrochemical sensing, Sensors and Actuators B 62, 23-29, 25 Jan 2000.
  83. J. E. Cohen, C. M. Newman, A. E. Cohen, O. L. Petchey, A. Gonzalez: Spectral mimicry: A method of synthesizing matching time series with different Fourier spectra, Circuits Systems and Signal Processing, 18, 431-442, 1999.
  84. A. E. Cohen, A. Gonzalez, J. H. Lawton, O. L. Petchey, D. Wildman, J. E. Cohen: A novel experimental apparatus to study the impact of white noise and 1/f noise on animal populations, Proc. Roy. Soc. Lond. B 265, 11-15, 7 Jan 1998.



  1. Adam Cohen: Near-field photolithographic masks and photolithography; nanoscale patterning techniques; apparatus and method therefor, US patent 5,865,978 February 2, 1999
  2. Charles T. Black, Adam Cohen, Chris Murray, Robert Sandstrom: Scanning probe microscopy tips composed of nanoparticles and methods to form same, US patent 7,282,710 October 16, 2007
  3. Adam Cohen and W. E. Moerner, Sub-micron object control arrangement and approach therefor, U.S. patent 8,057,655 Nov. 15, 2011
  4. Adam Cohen and Sabrina Leslie: Convex Lens-Induced Confinement (CLIC) for measuring distributions of molecular sizes, US patent pending
  5. Adam Cohen, Joel Kralj, Adam Douglass: Optogenetic probes of membrane potential, US patent pending
  6. Adam Cohen, Dougal Maclaurin, Daniel Hochbaum, Joel Kralj: Systems and methods for imaging at high spatial and/or temporal resolution, US patent pending
  7. Adam Cohen, Jennifer Hou: Improvement to spinning disk microscopy, US patent pending



  1. Let's Go 2000: Peru and Ecuador (Here's a link to the current website)


©2012 Adam E. Cohen