1. Hecht, J., City of light: The story of fiber optics, New York: Oxford University Press. 1999
2. Jackson, J.D., Classical Electrodinamics, New York: John Wiley&Sons, Inc., 1998 3. Kozma, P., et al., Integrated planar optical waveguide interferometer biosensors: A
comparative review, Biosensors & Bioelectronics, 58: p. 287-307, 2014
4. Tien, P.K., Integrated optics and new wave phenomena in optical waveguides, Reviews of Modern Physics, 49(2): p. 361-420, 1977
5. Newton, I., Opticks, Book 3, London: William Innys. 1730
6. de Fornel, F., Evanescent Waves: From Newtonian Optics to Atomic Optics.
Springer Series in Optical Sciences. Vol. 73. Springer. 2002
7. Thompson, L.L., Sankar, S., and Tong, Y., Complex wave-number dispersion analysis of stabilized finite element methods for acoustic fluid - structure interaction, Proceedings of SECTAM-XX, 2000
8. Hunsperger, R.G., Integrated Optics: Theory and Technology, 3rd edBerlin:
Springer. 1991
9. Borner, S., et al., Evanescent field sensors and the implementation of waveguiding nanostructures, Applied Optics, 48(4): p. B183-B189, 2009
10. Hecht, B., et al., Scanning near-field optical microscopy with aperture probes:
Fundamentals and applications, Journal of Chemical Physics, 112(18): p. 7761-7774, 2000
11. Barbastathis, G., Optics course notes, MIT, 2002
12. Fan, X., et al., Sensitive optical biosensors for unlabeled targets: A review, Analytica Chimica Acta, 620(1–2): p. 8-26, 2008
13. Janner, D., et al., Micro-structured integrated electro-optic LiNbO3 modulators, Laser & Photonics Reviews, 3(3): p. 301-313, 2009
14. Ormos, P., et al., Protein-based integrated optical switching and modulation, Applied Physics Letters, 80(21): p. 4060-4062, 2002
15. Hampp, N., Bacteriorhodopsin as a photochromic retinal protein for optical memories, Chemical Reviews, 100(5): p. 1755-1776, 2000
16. Luecke, H., et al., Structure of bacteriorhodopsin at 1.55 angstrom resolution, Journal of Molecular Biology, 291(4): p. 899-911, 1999
17. Erokhin, V., et al., On the role of molecular close packing on the protein thermal stability, Thin Solid Films, 284: p. 805-808, 1996
18. Cladera, J., et al., The role of retinal in the thermal-stability of the purple membrane, European Journal of Biochemistry, 207(2): p. 581-585, 1992
19. Lozier, R.H., Bogomolni, R.A., and Stoeckenius, W., Bacteriorhodopsin: a light-driven proton pump in Halobacterium Halobium, Biophysical Journal, 15(9): p.
955-962, 1975
20. Ovchinnikov, Y.A., et al., The structural basis of the functioning of bacteriorhodopsin: An overview, FEBS Letters, 100(2): p. 219-224, 1979
21. Stoeckenius, W., Lozier, R.H., and Bogomolni, R.A., Bacteriorhodopsin and the purple membrane of halobacteria, Biochimica et Biophysica Acta (BBA) - Reviews on Bioenergetics, 505(3–4): p. 215-278, 1979
22. Váró, G. and Bryl, K., Light- and dark-adaptation of bacteriorhodopsin measured by a photoelectric method, Biochimica et Biophysica Acta (BBA) - Bioenergetics, 934(2): p. 247-252, 1988
23. Kouyama, T., Bogomolni, R.A., and Stoeckenius, W., Photoconversion from the light-adapted to the dark-adapted state of bacteriorhodopsin, Biophysical Journal, 48(2): p. 201-208, 1985
24. Stuart, J.A., Marcy, D.L., and Birge, R.R., Photonic And Optoelectronic Applications Of Bacteriorhodopsin, in Bioelectronic Applications of Photochromic Pigments, A. Dér, L.K., Editor, IOS Press: Amsterdam. p. 15-29, 2001
25. Fischer, U. and Oesterhelt, D., Chromophore equilibria in bacteriorhodopsin, Biophysical Journal, 28(2): p. 211-230, 1979
26. Casadio, R., et al., Light-dark adaptation of bacteriorhodopsin in Triton-treated purple membrane, Biochimica et Biophysica Acta (BBA) - Bioenergetics, 590(1):
p. 13-23, 1980 decomposition with self-modeling: A critical evaluation using realistic simulated data, Journal of Physical Chemistry B, 108(13): p. 4199-4209, 2004
30. Oesterhelt, D., The structure and mechanism of the family of retinal proteins from halophilic archaea, Current Opinion in Structural Biology, 8(4): p. 489-500, 1998 31. Haupts, U., Tittor, J., and Oesterhelt, D., Closing in on bacteriorhodopsin:
Progress in understanding the molecule, Annual Review of Biophysics and Biomolecular Structure, 28: p. 367-399, 1999
32. Stoeckenius, W., Bacterial rhodopsins: Evolution of a mechanistic model for the ion pumps, Protein Science, 8(2): p. 447-459, 1999
33. Hessling, B., et al., Fourier transform infrared double-flash experiments resolve bacteriorhodopsin's M-1 to M-2 transition, Biophysical Journal, 73(4): p. 2071-2080, 1997
34. Ormos, P., Dancsházy, Z., and Keszthelyi, L., Electric-response of a back photoreaction in the bacterhiorodopsin photocycle, Biophysical Journal, 31(2): p.
207-213, 1980
35. Ludmann, K., Ganea, C., and Váró, G., Back photoreaction from intermediate M of bacteriorhodopsin photocycle, Journal of Photochemistry and Photobiology B-Biology, 49(1): p. 23-28, 1999
36. Tóth-Boconádi, R., Taneva, S.G., and Keszthelyi, L., Photoexcitation of the O intermediate of bacteriorhodopsin and its mutant E204Q, Journal of Biological Physics and Chemistry, 1: p. 58–63, 2001
37. Tóth-Boconádi, R., et al., Excitation of the L intermediate of bacteriorhodopsin:
Electric responses to test X-ray structures, Biophysical Journal, 90(7): p. 2651-2655, 2006
38. Wooten, F., Optical Properties of Solids, New York: Academic Press. 1972 39. Boyd, R.W., Nonlinear Optics 3rd ed., New York: Academic Press. 2008
40. Oesterhelt, D. and Stoeckenius, W., Rhodopsin-like protein from the purple membrane of Halobacterium halobium, Nature New Biology, 39(233): p. 149-152, 1971
41. Oesterhelt, D. and Stoeckenius, W., Functions of a new photoreceptor membrane, PNAS, 70(10): p. 2853-2857, 1973
42. Dér, A., Hargittai, P., and Simon, J., Time-resolved photoelectric and absorption signals from oriented purple membranes immobilized in gel, Journal of Biochemical and Biophysical Methods, 10(5–6): p. 295-300, 1985
43. Oesterhelt, D., Brauchle, C., and Hampp, N., Bacteriorhodopsin - A biological-material for information-processing, Quarterly Reviews of Biophysics, 24(4): p.
425-478, 1991
44. Stuart, J.A., et al., Volumetric optical memory based on bacteriorhodopsin, Synthetic Metals, 127(1-3): p. 3-15, 2002
45. Crivello, J.V. and Reichmanis, E., Photopolymer Materials and Processes for Advanced Technologies, Chemistry of Materials, 26(1): p. 533-548, 2014
46. Thorlabs. http://www.thorlabs.de/newgrouppage9.cfm?objectgroup_id=196.
47. Tortora, G.J. and Derrickson, B.H., Principles of anatomy and physiology, 13th ed:
John Wiley & Sons. 2011
48. Gravesen, P., Branebjerg, J., and Jensen, O.S., Microfluidics - a review, Journal of Micromechanics and Microengineering, 3(4), 1993
49. Becker, H. and Locascio, L.E., Polymer microfluidic devices, Talanta, 56(2): p.
267-287, 2002
50. Santini, J.T., Cima, M.J., and Langer, R., A controlled-release microchip, Nature, 397(6717): p. 335-338, 1999
51. Ramsey, J.M., Jacobson, S.C., and Knapp, M.R., Microfabricated Chemical Measurement Systems, Nature Medicine, 1(10): p. 1093-1096, 1995
52. Roberts, M.A., et al., UV laser machined polymer substrates for the development of microdiagnostic systems, Analytical Chemistry, 69(11): p. 2035-2042, 1997 53. Ford, S.M., et al., Micromachining in plastics using X-ray lithography for the
fabrication of micro-electrophoresis devices, Journal of Biomechanical Engineering-Transactions of the Asme, 121(1): p. 13-21, 1999
54. Nguyen, N.-T. and Wereley, S.T., Fundamentals and Applications of Microfluidics:
Artech House, 2002
55. McDonald, J.C., et al., Fabrication of microfluidic systems in poly(dimethylsiloxane), Electrophoresis, 21(1): p. 27-40, 2000
56. Friend, J. and Yeo, L., Fabrication of microfluidic devices using polydimethylsiloxane, Biomicrofluidics, 4(2), 2010
57. Oesterhelt, D. and Stoeckenius, W., Isolation of the cell membrane of Halobacterium halobium and its fractionation into red and purple membrane, Methods Enzymol, 31: p. 667-78, 1974
58. Alocilja, E.C. and Radke, S.M., Market analysis of biosensors for food safety, Biosensors and Bioelectronics, 18(5–6): p. 841-846, 2003
59. Klenkar, G. and Liedberg, B., A microarray chip for label-free detection of narcotics, Analytical and Bioanalytical Chemistry, 391(5): p. 1679-1688, 2008 60. Turner, A.P.F., Biosensors: sense and sensibility, Chemical Society Reviews,
42(8): p. 3184-3196, 2013
61. Clark, L.C. and Lyons, C., Electrode systems for continuous monitoring in cardiovascular surgery, Annals of the New York Academy of sciences, 102(1): p.
29-45, 1962
62. Alivisatos, A.P., Less is more in medicine - Sophisticated forms of nanotechnology will find some of their first real-world applications in biomedical research, disease diagnosis and, possibly, therapy, Scientific American, 285(3): p. 66-73, 2001 63. Jain, K.K., Nanotechnology in clinical laboratory diagnostics, Clinica Chimica
Acta, 358(1–2): p. 37-54, 2005
64. Cooper, M.A., Optical biosensors in drug discovery, Nat Rev Drug Discov, 1(7):
p. 515-528, 2002
65. Kozma, P., et al., A novel handheld fluorescent microarray reader for point-of-care diagnostic, Biosensors and Bioelectronics, 47(0): p. 415-420, 2013
66. Heideman, R.G. and Lambeck, P.V., Remote opto-chemical sensing with extreme sensitivity: design, fabrication and performance of a pigtailed integrated optical phase-modulated Mach-Zehnder interferometer system, Sensors and Actuators B-Chemical, 61(1-3): p. 100-127, 1999
67. Ymeti, A., et al., Development of a multichannel integrated interferometer immunosensor, Sensors and Actuators B-Chemical, 83(1-3): p. 1-7, 2002
68. Schmitt, K., et al., Interferometric biosensor based on planar optical waveguide sensor chips for label-free detection of surface bound bioreactions, Biosensors &
Bioelectronics, 22(11): p. 2591-2597, 2007
69. Shew, B.Y., et al., UV-LIGA interferometer biosensor based on the SU-8 optical waveguide, Sensors and Actuators A: Physical, 120(2): p. 383-389, 2005
70. Bissonnette, L. and Bergeron, M.G., Infectious Disease Management through Point-of-Care Personalized Medicine Molecular Diagnostic Technologies, J Pers Med, 2(2): p. 50-70, 2012
71. Ramsden, J.J., et al., Optical Method, for Measurement of Number and Shape of Attached Cells in Real-Time, Cytometry, 19(2): p. 97-102, 1995
72. Principles of Bacterial Detection: Biosensors, Recognition Receptors and Microsystems ed. Zourob, M., Elwary, S., and Turner, A.P.F.: Springer Science &
Business Media. 2008
73. Moore, G.E., Cramming more components onto integrated circuits (Reprinted from Electronics, pg 114-117, April 19, 1965), Proceedings of the Ieee, 86(1): p. 82-85, 1998
74. Excerpts from a conversation with Gordon Moore: Moore’s law, Video Transcript, 2005
75. Brenner, K.-H., Digital Optical Computing, in Organic Materials for Photonics, Zerbi, G., Editor, Elsevier: Oxford. p. 399-417, 1993
76. Schaller, R.R., Moore's Law: Past, present, and future, Ieee Spectrum, 34(6): p.
52-&, 1997
77. Roy, S., Optical Computing Circuits, Devices and Systems, Iet Circuits Devices &
Systems, 5(2): p. 73-75, 2011
78. Keyes, R.W., Optical logic - In the light of computer-technology, Optica Acta, 32(5): p. 525-535, 1985
79. Caulfield, H.J., Vikram, C.S., and Zavalin, A., Optical logic redux, Optik, 117(5):
p. 199-209, 2006
80. Caulfield, H.J., Soref, R.A., and Vikram, C.S., Universal reconfigurable optical logic with silicon-on-insulator resonant structures, Photonics and Nanostructures-Fundamentals and Applications, 5(1): p. 14-20, 2007
81. Sawchuk, A.A. and Strand, T.C., Digital optical computing, Proceedings of the Ieee, 72(7): p. 758-779, 1984
82. Lytel, R., et al., Optical interconnections within modern high-performance computing systems, Proceedings of the Ieee, 88(6): p. 758-763, 2000
83. Intel:
86. Simonite, T. Computing at the Speed of Light, Computing News, 2010.
87. Smit, M., van der Tol, J., and Hill, M., Moore's law in photonics, Laser &
Photonics Reviews, 6(1), 2012
88. Hoq, M.E., Krile, T.F., and Walkup, J.F., Optical logic function implementation using a one-dimensional deformable mirror device, Optical Engineering, 31(11):
p. 2413-2421, 1992
89. Rao, D.V.G.L.N., et al., All-optical logic gates with bacteriorhodopsin films, Optics Communications, 127(4-6): p. 193-199, 1996
90. Chattopadhyay, T., Table-top mirror based parallel programmable optical logic device, Optics and Laser Technology, 64: p. 308-318, 2014
91. Singh, C.P. and Roy, S., All-optical switching in bacteriorhodopsin based on M state dynamics and its application to photonic logic gates, Optics Communications, 218(1-3): p. 55-66, 2003
92. Roy, J.N., Mach-Zehnder interferometer-based tree architecture for all-optical logic and arithmetic operations, Optik, 120(7): p. 318-324, 2009
93. Roy, S. and Prasad, M., Design of All-Optical Reconfigurable Logic Unit With Bacteriorhodopsin Protein Coated Microcavity Switches, Ieee Transactions on Nanobioscience, 10(3): p. 160-171, 2011
94. Nazemosadat, E.S. and Shum, P.P., All-optical XOR logic gate operating on inputs with different modulation formats, Optik, 123(22): p. 2028-2030, 2012
95. Nurmohammadi, T., et al., Design of an ultrafast all-optical NOR logic gate based on Mach-Zehnder interferometer using quantum-dot SOA, Optik, 125(15): p.
4023-4029, 2014
96. Topolancik, J. and Vollmer, F., All-optical switching in the near infrared with bacteriorhodopsin-coated microcavities, Applied Physics Letters, 89(18), 2006 97. Chattopadhyay, T. and Roy, J.N., Design of SOA-MZI based all-optical Bacteriorhodopsin Protein-Coated Microresonators, Advances in Optical Technologies, 2012: p. 12, 2012
100. Li, Z.Y. and Meng, Z.M., Polystyrene Kerr nonlinear photonic crystals for building ultrafast optical switching and logic devices, Journal of Materials Chemistry C, 2(5): p. 783-800, 2014
101. Wolff, E.K. and Dér, A., All-optical logic, Nanotechnology Perceptions, 6: p. 1-6, 2010
102. Dér, A., et al., Integrated optical switching based on the protein bacteriorhodopsin, Photochemistry and Photobiology, 83(2): p. 393-396, 2007
103. Hurst, S.L., Multiple-valued logic - Its status and its future, Ieee Transactions on Computers, 33(12): p. 1160-1179, 1984
104. Connelly, J., Ternary Computing Testbed 3-Trit Computer Architecture, Computer Engineering Department, California Polytechnic State University: San Luis Obispo, California. 2008
105. Porat, D.I. Three-valued digital systems, Proceedings of the Institution of Electrical Engineers, 1969. 116, 947-954
106. Smith, K.C., The Prospects for Multivalued Logic: A Technology and Applications View, Computers, IEEE Transactions on, C-30(9): p. 619-634, 1981
107. Balla, P.C. and Antoniou, A., Low power dissipation MOS ternary logic family, Solid-State Circuits, IEEE Journal of, 19(5): p. 739-749, 1984
108. Wu, C.-Y. and Huang, H.-Y., Design and application of pipelined dynamic CMOS ternary logic and simple ternary differential logic, Solid-State Circuits, IEEE Journal of, 28(8): p. 895-906, 1993
109. Fábián, L., et al., Protein-based ultrafast photonic switching, Optics Express, 19(20): p. 18861-18870, 2011