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. J. Hou, V. Venkatachalam, A.E. Cohen, Temporal dynamics of microbial rhodopsin fluorescence reports absolute membrane voltage, Biophysical Journal, 106.3, 639-648, 2014.
  2. 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., DOI: 10.1021/ja411338t 2013.
  3. 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 DOI:10.1371/journal.pone.0085221 2013.
  4. A. Fields, E. Meyer, A.E. Cohen, Euler buckling and nonlinear kinking of double-stranded DNA, Nucl. Acids Res. DOI:10.1093/nar/gkt739 2013.
  5. D. Maclaurin*, V. Venkatachalam*, H. Lee, A.E. Cohen,Mechanism of voltage-sensitive fluorescence in a microbial rhodopsin, PNAS DOI: 10.1073/pnas.1215595110 2013.
  6. 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.
  7. Y. Tang, L. Sun, A. E. Cohen, Chiroptical hot spots in twisted nanowire plasmonic oscillators, Applied Physics Letters, 102, 043103, 2013. Supporting Information.
  8. A. P. Fields, A. E. Cohen, Optimal tracking of a Brownian particle, Optics Express, 20, 22585-22601, 2012.
  9. M. J. Shon, A. E. Cohen, Mass action at the single-molecule level, J. Am. Chem. Soc., DOI:10.1021/ja3062425, 2012. Supporting information.
  10. J. Hou, A. E. Cohen, Motion induced by asymmetric degradation of hydrogels, Soft Matter, 8, 4616-4624, 2012. Supplementary video, supplementary text.
  11. 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.
  12. H. Lee, N. Yang, A. E. Cohen, Mapping nanomagnetic fields using a radical pair reaction, Nano Letters, 11, 5367-5372, 2011.
  13. 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.
  14. 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.
  15. 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.
  16. A. P. Fields, A. E. Cohen, Electrokinetic trapping at the one nanometer limit, PNAS, 108, 8937-8942, 2011.
  17. A. E. Cohen and W. E. Moerner, “Anti-Brownian Traps,” in Encyclopedia of Biophysics, G. C. K. Roberts (Ed.) (Springer, Berlin, Heidelberg, appearing 2012).
  18. Y. Tang, A. E. Cohen, Enhanced enantioselectivity in excitation of chiral molecules by superchiral light, Science, 332, 333-336, 2011. Supporting Online Material
  19. 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.
  20. N. Yang, A. E. Cohen, Optical imaging through scattering media via magnetically modulated fluorescence, Optics Express, 18, 25461-25467, 2010.
  21. S. R. Leslie, A. P. Fields, A. E. Cohen, Convex Lens-Induced Confinement for Imaging Single Molecules, Anal. Chem., 82, 6224–6229, 2010.
  22. Y. Tang, A. E. Cohen, Optical chirality and its interaction with matter, Phys. Rev. Lett (cover story), 104,163901, 2010.
  23. A. P. Fields and A. E. Cohen, Anti-Brownian traps for studies on single molecules, Methods in Enzymology, 475, 149-174, 2010.
  24. 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.
  25. A. E. Cohen, Nanomagnetic control of intersystem crossing, J. Phys. Chem. A, 113, 11084–11092, 2009.
  26. N. Yang, Y. Tang, and A. E. Cohen, Spectroscopy in sculpted fields, Nano Today, 4, 269-279, 2009.
  27. 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.
  28. 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.
  29. 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.
  30. 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)
  31. 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.
  32. 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.
  33. A. E. Cohen, W. E. Moerner: Internal mechanical response of a polymer in solution, Phys. Rev. Lett., 98, 116001, 14 Mar. 2007. Supplementary material.
  34. 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.
  35. A. E. Cohen and W. E. Moerner: An all-glass microfluidic cell for the ABEL trap: fabrication and modeling, Proc. SPIE 5930, 2005.
  36. A. E. Cohen: Control of nanoparticles with arbitrary two-dimensional force fields, Phys. Rev. Lett., 94, 118102, 25 Mar. 2005.
  37. A. E. Cohen and W. E. Moerner: The Anti-Brownian Electrophoretic trap (ABEL Trap): tabrication and software, Proc. SPIE 5699, 2005.
  38. 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).
  39. A. E. Cohen and W. E. Moerner: Method for trapping and manipulating nanoscale objects in solution , Appl. Phys. Lett. 86, 093109, 28 Feb. 2005.
  40. A. E. Cohen and S. Mukamel: Resonant enhancement and dissipation in nonequilibrium van der Waals forces, Phys. Rev. Lett. 91, 233202, 5 Dec. 2003.
  41. A. E. Cohen: Force-extension curve of a polymer in a high-frequency electric field, Phys. Rev. Lett. 91, 235506, 5 Dec. 2003.
  42. A. E. Cohen and L. Mahadevan: Kinks, rings, and rackets in filamentous structures, PNAS, 100,12141-12146, 14 Oct. 2003.
  43. A. E. Cohen: Carbon nanotubes provide a charge, Science (letter to the editor) 300, 1235-1235, 23 May 2003.
  44. 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.
  45. 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.
  46. A. E. Cohen and R. Kunz: Large-area interdigitated array microelectrodes for electrochemical sensing, Sensors and Actuators B 62, 23-29, 25 Jan 2000.
  47. 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.
  48. 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 edition)


©2012 Adam E. Cohen