Publications

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2010 – Present

Light Harvesting by Equally Contributing Mechanisms in a Photosynthetic Antenna Protein. M. J. Guberman-Pfeffer, J. A. Greco, R. R. Birge, H. A. Frank, and J. A. Gascon. (2018) J. Phys. Chem. Lett. 9, 563-568pdf

The Forbidden 11Bu– Excited Singlet State of Peridinin and Peridinin Analogues. J. A. Greco, N. L. Wagner, H. A. Frank, and R. R. Birge. (2018) J. Phys. Chem. A 122, 130-139pdf

Purification and Characterization of RhoGC, a Retinylidene/Guanylyl Cyclase Fusion Protein from Blastocladiella emersonii. M. M. Trieu, E. L. Devine, L. B. Lamarche, A. E. Ammerman, J. A. Greco, R. R. Birge, D. L. Theobald, and D. D. Oprian. (2017) J. Biol. Chem. 292, 10379-10389pdf

Pixel Characterization of a Protein-Based Retinal Implant Using a Microfabricated Sensor Array. J. A. Greco, L. A. L. Fernandes, N. L. Wagner, M. Azadmehr, P. Hӓfliger, E. A. Johannessen, and R. R. Birge. (2017) Int. J. High Speed Electron. Syst. 26, 1740012-1-1740012-20pdf

Bacteriochlorins with a Twist: Discovery of a Unique Mechanism to Red-shift the Optical Spectra of Bacteriochlorins. M. J. Guberman-Pfeffer, J. A. Greco, L. P. Samankumara, M. Zeller, R. R. Birge, J. A. Gascon, and C. Bruckner. (2017) J. Am. Chem. Soc. 139, 548-560 pdf

Spectroscopic Investigation of the Carotenoid Deoxyperidinin: Direct Observation of the Forbidden S0 to S1 Transition. J. A. Greco, A. M. LaFountain, S. Katsumura, N. M. Magdaong, D. M. Niedzwiedzki, R. R. Birge, and H. A. Frank. (2016) J. Phys. Chem. B 120, 2731-2744 pdf

Spectroscopic Investigation of a Brightly Colored Psittacofulvin Pigment from Parrot Feathers. A. František, J. A. Greco, A. M. LaFountain, N. M. Magdaong, M. Fuciman, R. R. Birge, T. Polivka, and H. A. Frank. (2016) Chem. Phys. Lett. 648, 195-199 pdf

Effects of Strong Electronic Coupling in Chlorin and Bacteriochlorin Dyads. H. S. Kang, N. N. Esemoto, J. R. Diers, D. M. Niedzwiedzki, J. A. Greco, J. Akhigbe, Z. Yu, C. Pancholi, G. V. Bhagvathy, J. K. Nguyen, C. Kirmaier, R. R. Birge, M. Ptaszek, D. Holten, and D. F. Bocian. (2016) J. Phys. Chem. A 120, 379-395 pdf

Two-Photon Spectroscopy of the Q-Bands of meso-Tetraphenyl-Porphyrin and –Chlorin Framework Derivatives. J. A. Greco, S. Shima, N. L. Wagner, J. R. McCarthy, K. Atticks, C. Bruckner, and R. R. Birge. (2015) J. Phys. Chem. C 119, 3711-3724 pdf

Low-Temperature Trapping of Photointermediates of the Rhodopsin E181Q Mutant. M. N. Sandberg, J. A. Greco, N. L. Wagner, T. L. Amora, L. A. Ramos, M.-H. Chen, B. E. Knox, and R. R. Birge (2014) SOJ Biochem. 1, 1-12 pdf

High Efficiency Light-Harvesting by Carotenoids in the LH2 Complex from Photosynthetic Bacteria: Unique Adaptation to Growth Under Low-Light Conditions. N. M. Magdaong, A. M. LaFountain, J. A. Greco, A. T. Gardiner, A.-M. Carey, R. J. Cogdell, G. N. Gibson, R. R. Birge, and H. A. Frank (2014) J. Phys. Chem. B 118, 11172-11189 pdf

Diels-Alder Polysulfones as Dielectric Materials: Computational Guidance and Synthesis. R. G. Lorenzini, J. A. Greco, R. R. Birge, and G. A. Sotzing (2014) Polymer 55, 3573-3578 pdf

A Spectroscopic and Theoretical Investigation of a Free-Base meso-Trithienylcorrole. J. A. Greco, A. Rossi, R. R. Birge, and C. Bruckner (2014) Photochem. Photobiol. 90, 402-414 pdf

Photochromic Bacteriorhodopsin Mutant with High Holographic Efficiency and Enhanced Stability via a Putative Self-Repair Mechanism. M. J. Ranaghan, J. A. Greco, N. L. Wagner, R. Grewal, R. Rangarajan, J. Koscielecki, K. Wise, and R. R. Birge (2014) ACS Appl. Mater. Interfaces 6, 2799-2808 pdf

Excited States Properties of a Short π-Electron Conjugated Peridinin Analogue. N. M. Magdaong, D. M. Niedzwiedzki, J. A. Greco, H. Liu, K. Yano, T. Kajikawa, K. Sakaguchi, S. Katsumura, R. R. Birge, and H. A. Frank. (2014) Chem. Phys. Lett. 593, 132-139 pdf

Directed Evolution of Bacteriorhodopsin for Applications in Bioelectronics. N. L. Wagner, J. A. Greco, M. J. Ranaghan, and R. R. Birge. (2013) J. R. Soc. Interface 10, 20130197 pdf

Nature of the ICT State in Peridinin. N. L. Wagner, J. A. Greco, M. M. Enriquez, H. A. Frank, and R. R. Birge. (2013) Biophys. J.104, 1314-1325 pdf

Energetics and Dynamics of the Low-Lying Electronic States of Constrained Polyenes: Implications for Infinite Polyenes. R. L. Christensen, M. M. Enriquez, N. L. Wagner, A. Y. Peacock-Villada, C. Scriban, R. R. Schrock, T. Polivka, H. A. Frank, and R. R. Birge (2013) J. Phys. Chem A 117, 1449-1465 pdf

Visual Resotoration Using Microbial Rhodopsins. N. L. Wagner, J. A. Greco, and R. R. Birge, in Bionanotechnology: Biological Self-Assembly and Its Applications, B. H. A. Rehm, ed. Caister Academic Press, Norfolk, United Kingdom (2013), pp. 205-240.

Effect of Molecular Symmetry on the Spectra and Dynamics of the Intramolecular Charge Transfer (ICT) State of Peridinin. M. M. Enriquez, S. Hananoki, S. Hasegawa, T. Kajikawa, S. Katsumura, N. L. Wagner, R. R. Birge, and H. A. Frank (2012) J. Phys. Chem B 116, 10748-10756 pdf

meso-Arylporpholactones and their Reduction Products. C. Bruckner, J. Ogikubo, J. R. McCarthy, J. Akhigbe, M. A. Hyland, P. Daddario, J. L. Worlinsky, M. Zeller, J. T. Engle, C. J. Ziegler, M. J. Ranaghan, M. N. Sandberg, and R. R. Birge (2012) J. Org. Chem. 77, 6480-6494 pdf

Biomolecular Electronics and Protein-Based Optical Computing. J. A. Greco, N. L. Wagner, M. J. Ranaghan, S. Rajasekaran, and R. R. Birge, in Biomolecular Information Processing: From Logic Systems to Smart Sensors and Actuators, E. Katz, ed. Wiley-VCH, Weinheim, Germany (2012), pp. 33-59.

Rapid Release of Retinal from a Cone Pigment following Photoactivation. M-. H. Chen, C. Kuemmel, R. R. Birge, and B. E. Knox (2012) Biochem. 51, 4117-4125 pdf

Optical Applications of Biomolecules. M. J. Ranaghan, N. L. Wagner, M. N. Sandberg, and R. R. Birge, in Optical biomimetics: Materials and applications, M. Large, ed. Woodhead Publishing, Cambridge, United Kingdom (2012)

MNDO-PSDCI Theory and the Excited States of Biological Chromophores. D. J. Sandberg, N. L. Wagner, M. N. Sandberg, J. M. Crowley, and R. R. Birge, in Comprehensive Biophysics, E. Egelman, ed. Academic Press, (2012)

Green Proteorhodopsin Reconstituted into Nanoscale Phospholipid Bilayers (Nanodiscs) as Photoactive Monomers. M. J. Ranaghan, C. T. Schwall, N. N. Alder, and R. R. Birge (2011) J. Am. Chem. Soc. 133, 18318-18327 pdf

Conserved Residues in the Extracellular Loops of Short-Wavelength Cone Visual Pigments. M.-H. Chen, D. J. Sandberg, K. R. Babu, J. Bubis, A. Surya, L. S. Ramos, H. J. Zapata, J. F. Galan, M. N. Sandberg, R. R. Birge, B. E. Knox (2011) Biochemistry 50, 6763-6773 pdf

Glutamic Acid 181 Is Negatively Charged in the Bathorhodopsin Photointermediate of Visual Rhodopsin. M. N. Sandberg, T. L. Amora, L. S. Ramos, M.-H. Chen, B. E. Knox, and R. R. Birge (2011) J. Am. Chem. Soc. 133, 2208-2211 pdf

Femtosecond Transient Absorption Spectroscopic Study of a Carbonyl-Containing Carotenoid Analogue, 2-(all-trans-Retinylidene)-indan-1,3-dione. T. Kusumoto, D. Kosumi, C. Uragami, H. A. Frank, R. R. Birge, R. J. Cogdell, and H. Hashimoto (2011) J. Phys. Chem. A 115, 2110-2119 pdf

Photochemical and Thermal Stability of Green and Blue Proteorhodopsins: Implications for Application in Protein-Based Devices. M. J. Ranaghan, S. Shima, L. Ramos, D. S. Poulin, G. Whited, S. Rajasekaran, J. A. Stuart, A. D. Albert, R. R. Birge (2010) J. Phys. Chem. B 114, 14064-14070 pdf

The intramolecular charge transfer state in carbonyl-containing polyenes and carotenoids. M. M. Enriquez, M. Fuciman, A. M. LaFountain, N. L. Wagner, R. R. Birge, H. A. Frank (2010) J. Phys. Chem. B 114, 12416-12426 pdf

Excited-State Photodynamics of Perylene-Porphyrin Dyads. 5. Tuning Light-Harvesting Characteristics via Perylene Substituents, Connection Motif, and Three-Dimensional Architecture, C. Kirmaier, H. E. Song, E. Yang, J. K. Schwartz, E. Hindin, J. R. Diers, R. S. Loewe, K. Y. Tomizaki, F. Chevalier, L. Ramos, R. R. Birge, J. S. Lindsey, D. F. Bocian, D. Holten (2010) J. Phys. Chem. B 114, 14249-14264 pdf

Stark absorption spectroscopy of peridinin and allene-modified analogues. T. Kusumoto, T. Horibe, T. Kajikawa, S. Hasegawa, T. Iwashita, R. J. Cogdell, R. R. Birge, H. A. Frank, S. Katsumura, H. Hashimoto (2010) Chem. Phys. 373, 71-79 pdf

2000 – 2009

Ultrafast time-resolved absorption spectroscopy of geometric isomers of carotenoids. D. M. Niedzwiedzki, D. J. Sandberg, H. Cong, M. N. Sandberg, G. N. Gibson, R. R. Birge, H. A. Frank (2009) Chem. Phys. 357, 4-16 pdf

Identification of a single peridinin sensing Chl-a excitation in reconstituted PCP by crystallography and spectroscopy. T. Schulte, D. M. Niedzwiedzkib, R. R. Birge, R. G. Hiller, T. Polívka, E. Hofmann, and H. A. Frank (2009) Proc. Natl. Acad. Sci. USA 106, 20764 –20769 pdf

The Charge-Transfer Properties of the S2 State of Fucoxanthin in Solution and in Fucoxanthin Chlorophyll-a/c2 Protein (FCP) Based on Stark Spectroscopy and Molecular-Orbital Theory, L. Premvardhan, D. J. Sandberg, H. Fey, R. R. Birge, C. Bchel and R. van Grondelle (2008) J. Chem. Phys. B 112, 11838–11853pdf

Spectral Tuning of Deep Red Cone Pigments, T. L. Amora, L. S. Ramos, J. F. Galan, and R. R. Birge (2008) Biochem. 47, 4614-4620 pdf

Evaluation of Blue and Green Absorbing Proteorhodopsins as Holographic Materials, B. Xi, W. C. Tetley, D. L. Marcy, C. Zhong, G. Whited, R. R. Birge, and J. A. Stuart (2008) J. Phys. Chem. B 112, 2524-2529 pdf

Mechanism of Spectral Tuning in Green-Absorbing Proteorhodopsin, R. Rangarahan, J. F. Galan, G. Whited and R.R. Birge (2007) Biochem. 46, 12679-12686 pdf

Response to comment on Coherent "Control of Retinal Isomerization in Bacteriorhodopsin", V. I. Prokhorenko, A. M. Nagy, S. A. Waschuk, L. S. Brown, R. R. Birge, and R. J. Miller (2007) Science 317 (5837), 453C pdf

Cation radicals of xanthophylls, M. G. I. Galinato, D. Niedzwiedzki, C. Deal, R. R. Birge, and H. A. Frank (2007) Photosynth. Res. 94, 67-78 pdf

Regulation of Photoactivation in Vertebrate Short Wavelength Visual Pigments: Protonation of the Retinylidene Schiff Base and a Counterion Switch, L. S. Ramos, M. H. Chen, B. E. Knox, and R. R. Birge, (2007) Biochem. 46, 5330-5340 pdf

Coherent Control of Retinal Isomerization in Bacteriorhodopsin, V. I. Prokhorenko, A. M. Nagy, S. A. Waschuk, L. S. Brown, R. R. Birge, and R. J. Miller (2006) Science 313 (5791), 1257-1261 pdf

Femtosecond Time-Resolved Transient Absorption Spectroscopy of Xanthophylls, D. M. Niedzwiedzki, J. O. Sullivan, T. Polívka, R. R. Birge, and H. A. Frank, (2006) J. Phys. Chem. B 110 (45), 22872-22885 pdf

Femtosecond Time-Resolved Absorption Spectroscopy of Main-Form and High-Salt Peridinin-Chlorophyll a-Proteins at Low Temperatures, R. P. Ilagan, J. F. Koscielecki, R. G. Hiller, F. P. Sharples, G. N. Gibson, R. R. Birge, and H. A. Frank (2006) Biochem. 45 (47), 14052-14063 pdf

Photoinduced Surface Potential Change of Bacteriorhodopsin Mutant D96N Measured by Scanning Surface Potential Microscopy I. Lee, E. Greenbaum, S. Budy, J. R. Hillebrecht, R. R. Birge, J. A. Stuart (2006) J. Phys. Chem. B. 110, 10982-10990 pdf

Directed Evolution of Proteins for Device Applications. J. F. Koscielecki, J. R. Hillebrecht, and R. R. Birge, (2006) Bionanotechnology vol. 4, D.E. Reisner, Ed., CRC Press

Structure, function, and wavelength selection in blue-absorbing proteorhodopsin. J. R. Hillebrecht, J. Galan, R. Rangarajan, L. Ramos, K. McCleary, D. E. Ward, J. A. Stuart and R. R. Birge (2006) Biochem. 45, 1579 – 1590 pdf

Rhodopsin and the First Step in Vision, R. R. Birge, in Encyclopedia Of Condensed Matter Physics, vol 5, Eds. G. Bassani, G. Liedl and P. Wyder, (2005) pp. 145-158, Academic Press

Optimization of protein-based volumetric optical memories and associative processors by using directed evolution. J. R. Hillebrecht, J. F. Koscielecki, K. J. Wise, D. L. Marcy, W. Tetley, R. Rangarajan, J. Sullivan, M. Brideau, M P. Krebs, J. A. Stuart, R. R. Birge (2005) Nanobiotech. 1, 141-152 pdf

Stereoisomers of carotenoids: spectroscopic properties of locked and unlocked cis-isomers of spheroidene. Z. D. Pendon, J. O. Sullivan, I. van der Hoef, J. Lugtenburg, A. Cua, D. F. Bocian, R. R. Birge and H. A. Frank (2005) Photosynth. Res. 86, 5-24 pdf

Structural control of the photodynamics of boron-dipyrrin complexes. H. L. Kee, C. Kirmaier, L. Yu, P. Thamyongkit, W. J. Youngblood, M. E. Calder, L. Ramos, B. C. Noll, D. F. Bocian, W. R. Scheidt, R. R. Birge, J. S. Lindsey, and D. Holten (2005) J. Phys. Chem. B 109, 20433-20443 pdf

Characterization and photochemistry of 13-desmethyl bacteriorhodopsin. N. B. Gillespie, L. Ren, L. Ramos, H. Daniell, D. Dews, K. A. Utzat, J. A. Stuart, C. H. Buck, and R. R. Birge (2005) J. Phys. Chem. B 109, 16142 -16152 pdf

Directed evolution of bacteriorhodopsin for device applications. J. R. Hillebrecht, K. J. Wise and R. R. Birge (2004) Meth. Enzym. 388, 333-347 pdf

Photoelectric response of polarization sensitive bacteriorhodopsin films. Q. Li, J. A. Stuart, R.R. Birge, J. Xu, A. Stickrath, P. Bhattacharya (2004) Biosens. Bioelect. 19, 869-874 pdf

Vertebrate ultraviolet visual pigments: protonation of the retinylidene Schiff base and a counterion switch during photoactivation. A. K. Kusnetzow, A. Dukkipati, K. R. Babu, L. Ramos, B. E. Knox, R. R. Birge (2004) Proc. Natl. Acad. Sci. USA 101, 941-946 pdf

Biomolecular photonics based on bacteriorhodopsin. K. J. Wise and R. R. Birge, CRC Handbook Org. (2004) Photochem. Photobiol. (2nd Ed.) 135/1 – 135/20

Terahertz circular dichroism spectroscopy of biomolecules. J. Xu, J. Galan, G. Ramian, P. Savvidis, A. Scopatz, R. R. Birge, S. J. Allen and K. Plaxco (2004) Proc. SPIE-Int. Soc. Opt. Eng. 5268, 19-26

Spectroscopic properties of the main-form and high-salt peridinin-chlorophyll a proteins from Amphidinium carterae. R. P. Ilagan, S. Shima, A. Melkozernov, S. Lin, R. E. Blankenship, F. P. Sharples, R. G. Hiller, R. R. Birge and H. A. Frank (2004) Biochem. 43, 1478-1487 pdf

Humidity-dependent open-circit photovoltage from a bacteriorhodopsin/indium tin oxide bioelectronic heterostructure. S. Crittenden, S. Howell, R. Reifenberger, J. Hillebrecht and R.R. Birge (2003) Nanotech. 14, 562-565 pdf

Terahertz Circular Dichroism Spectroscopy: A Potential Approach to the In Situ Detection of Life's Metabolic and Genetic Machinery. J. Xu, G. J. Ramian, J. F. Galan, P. G. Savvidis, A. M. Scopatz, R. R. Birge, S. J. Allen and K. W. (2003) Plaxco. Astrobiol. 3, 489-504 pdf

A spectroscopic and computational study of the singlet and triplet excited states of synthetic beta-functionalized chlorins. C. Bruckner, J. R. McCarthy, J. W. Caniell, Z. D. Pendon, R. P. Ilagan, T. M. Francis, L. Ren, R. R. Birge and H. A. Frank. (2003) Chem. Phys. 294, 285-303 pdf

Two-photon and fluorescence spectroscopy and the effect of environment on the photochemical properties of peridinin in solution and in the peridinin-chlorophyll-protein from Amphidinium carterae. S. Shima, R. P. Ilagan, N. Gillespie, B. J. Sommer, R. G. Hiller, F. P. Sharples, H. A. Frank and R. R. Birge (2003) J. Phys. Chem. A 107, 8052-8066 pdf

Thermolysis of fluorinated cycloalkylidene fulgides yields a new class of photochromic compounds. M. N. Wolak, N. B. Gillespie, R. R. Birge and W. J. Lees (2003) Chem Commun (Camb). 8, 992-993 pdf

Protein flexibility and conformational state: a comparison of collective vibrational modes of wild-type and D96N bacteriorhodopsin. S. E. Whitmire, D. Wolpert, A. G. Markels, J. R. Hillebrecht, J. Galan and R. R. Birge (2003) Biophys. J. 85, 1269-1277 pdf

Direct measurement of the photoelectric response time of bacteriorhodopsin via electro-optic sampling. J. Xu, A. B. Stickrath, P. Bhattacharya, J. Nees, G. Varo, J. R. Hillebrecht, L. Ren and R. R. Birge (2003) Biophys J. 85, 1128-1134 pdf

Perspectives on the counterion switch-induced photoactivation of the G protein-coupled receptor rhodopsin. R. R. Birge and B. E. Knox (2003) Proc. Natl. Acad. Sci. USA 100, 9105-9107 pdf

Biomolecular electronic device applications of bacteriorhodopsin. J. A. Stuart, D. L. Marcy, K. J. Wise and R. R. Birge, in Molecular Electronics: Biosensors and Biocomputers, L. Barsanti et al., eds. Kluwer Academic (2003) pp. 265-299

Tuning the optical properties of fluorinated indolylfulgimides. M. A. Wolak, C. J. Thomas, N. B. Gillespie, R. R. Birge and W. J. Lees (2003) J. Org. Chem. 68 319-26 pdf

Optical and thermal properties of photochromic fluorinated adamantylidene indolylfulgides. M. A. Wolak, N. B. Gillespie, C. J. Thomas, R. R. Birge and W. J. Lees (2002) J. Photochem. Photobiol. A 147, 39-44 pdf

Characterization of the branched-photocycle intermediates P and Q of bacteriorhodopsin. N. B. Gillespie, K. J. Wise, L. Ren, J. A. Stuart, D. L. Marcy, J. Hillebrecht, Q. Li, L. Ramos, K. Jordan, S. Fyvie and R. R. Birge (2002) J. Phys. Chem. B 106, 13352-13361 pdf

THz time domain spectroscopy of biomolecular conformational modes. A. Markelz, S. Whitmire, J. Hillebrecht and R. R. Birge (2002) Phys. Med. Biol. 47 3797-3805 pdf

Charge transfer in molecular conductors - oxidation or reduction? A. W. Ghosh, F. Zahid, S. Datta and R.R. Birge (2002) Chem. Phys. 281, 225-230 pdf

Phototransduction by vertebrate ultraviolet visual pigments: protonation of the retinylidene Schiff base following photobleaching. A. Dukkipati, A. Kusnetzow, K.R. Babu, L. Ramos, D. Singh, B.E. Knox and R.R. Birge (2002) Biochem. 41, 9842-9851 pdf

Optimization of bacteriorhodopsin for bioelectronic devices. K. J. Wise, N. B. Gillespie, J. A. Stuart, M. P. Krebs and R. R. Birge (2002) Trends Biotech. 20, 387-394 pdf

Structural Properties of a Series of Photochromic Fluorinated Indolylfulgides. M. A. Wolak, R. C. Finn, C. J. Thomas, R. P. Hammond, R. R. Birge, J. Zubieta, W. J. Lees, Acta Cryst. C, 58, o389-o393 (2002).

Structural studies of Metarhodopsin II, the activated form of the G-protein coupled receptor, rhodopsin. G. Choi, J. Landin, J. F. Galan, R. R. Birge, A. D. Albert, and P. L. Yeagle (2002) Biochem. 41, 7318-7324 pdf

Monolithically integrated bacteriorhodopsin GaAs field-effect transistor photoreceiver. P. Bhattacharya, J. Xu, G. Varo, D. L. Marcy and R. R. Birge (2002) Opt. Lett. 27, 839-841 pdf

Volumetic optical memory based on bacteriorhodopsin. J. A. Stuart, D. L. Marcy, K. J. Wise and R. R. Birge (2002) Synth. Met. 127, 3-15 pdf

Bacteriorhodopsin-based three-diemsional optical memory. J. A. Stuart, D. L. Marcy, K. J. Wise and R. R. Birge (2001) NATO Sci. Ser., Ser. I, 335, 30-43

Photonic and optoelectronic applications of bacteriorhodopsin. J. A. Stuart, D. L. Marcy and R. R. Birge (2001) NATO Sci. Ser., Ser. I, 335, 16-29

Serine 85 in transmembrane helix 2 of short-wavelength visual pigments interacts with the retinylidene Schiff base counterion. A. Dukkipati, B. W. Vought, D. Singh, R. R. Birge and B. E. Knox (2001) Biochem. 40, 15098-108 pdf

Regulation of phototransduction in short-wavelength cone visual pigments via the retinylidene Schiff base counterion. K. R. Babu, A. Dukkipati, R. R. Birge and B. E. Knox (2001) Biochem. 40, 13760-13766 pdf

Linear dichroism and the transition dipole moment orientation of the carotenoid in the LH2 antenna complex in membranes of Rhodopseudomonas acidophila strain 10050. P. M. Dolan, D. Miller, R. J. Cogdell, R. R. Birge and H. A. Frank (2001) J. Phys. Chem. B 105, 12134-12142 pdf

Molecular mechanism of spectral tuning in sensory rhodopsin II. L. Ren, C. H. Martin, K. J. Wise, N. B. Gillespie, J. Luecke, J. K. Lanyi, J. L. Spudich and R. R. Birge (2001) Biochem. 40, 13906-13914 pdf

Thermolysis of a Fluorinated Indolylfulgide Features a Novel 1,5-Indolyl Shift, M. A. Wolak, J. M. Sullivan, C. J. Thomas, R. C. Finn, R. R. Birge, W. J. Lees (2001) J. Org. Chem., 66, 4739-4741 pdf

Optical Properties of Photochromic Fluorinated Indolylfulgides, M. A. Wolak, N. R. Gillespie, C. J. Thomas, R. R. Birge, W. J. Lees, J. (2001) Photochem. Photobiol. A, 144, 83-91 pdf

Photoconduction in bacteriorhodopsin/GaAs heterostructures, J. Xu, P. Bhattacharya, D. L. Marcy, J. A. Stuart, and R. R. Birge (2001) Electron. Lett. 37, 648-649 pdf

The Photobleaching Sequence of a Short-Wavelength Visual Pigment, A. A. Kusnetzow, A. Dukkipati, K. R. Babu, D. Singh, B. W. Vought, B. E. Knox, and R. R. Birge (2001) Biochem. 40, 7832-7844 pdf

Improved Synthesis of Indolyl Fulgides, C. J. Thomas, M. A. Wolak, R. R. Birge, and Watson J. Lees (2001) J. Org. Chem. 66, 1914-1918 pdf

Conformation and orientation of the retinyl chromophore in rhodopsin: A critical evaluation of recent NMR data on the basis of theoretical calculations results in a minimum energy structure consistent with all experimental data. D. Singh, B. S. Hudson, C. Middleton, and R. R. Birge (2001) Biochem 40, 4201-4204 pdf

Theoretical studies on excited states of a phenolate anion in the environment of photoactive yellow protein. Z. He, C. H. Martin, R. R. Birge, and K. F. Freed (2000) J. Phys. Chem. A 104, 2939-2952 pdf

Characterization of the primary photointermediates of Drosophila rhodopsin. B. W. Vought, E. Salcedo, L. V. Chadwell, S. G. Britt, R. R. Birge, and B. E. Knox (2000) Biochem. 39, 14128-14137 pdf

Energetics of rhodopsin photobleaching: photocalorimetric studies of energy storage in the early and later intermediates. in Methods in Enzymology (eds. K. Palczewski), R.R. Birge and B.W. Vought (2000) vol. 315, Academic Press, New York, 143-163

1990 – 1999

Ligand Influences on Copper Cyanide Solid-State Architecture: Flattened and Fused “Slinky”, Corrugated Sheet, and Ribbon Motifs in the Coper-Cyanide-Triazolate-Organoamine Family. D. J. Chestnut, A. Kusnetzow, R.R. Birge and J. Zubieta (1999) Inorg. Chem. 38, 5484-5499 pdf

Biomolecular electronics: Protein-based associative processors and volumetric memories. R.R. Birge, N.B. Gillespie, E.W. Izaguirre, A. Kusnetzow, A.F. Lawrence, D. Singh, Q.W. Song, E. Schmidt, J.A. Stuart, S. Seetharaman and K.J. Wise (19990 J. Phys. Chem. B. 103, 10746-10766 pdf

Photochemistry of the primary event in short-wavelength visual opsins at low temperature. B.W. Vought, A. Dukkipatti, M. Max, B.E. Knox and R.R. Birge (1999) Biochem. 38, 11287-11297 pdf

Solid state coordination chemiostry of the copper halide- and pseudo-halide-organoamine system, Cu-X-[(bis-2,3-(2-pyridyl)pyrazine)] (X = Cl, Br, CM): Hydrothermal synthesis and strctural characterization. D. J. Chesnut, A. Kusnetzow, R. R. Birge and J. Zubieta (1999) Inorg. Chem. 38, 2663-2671 pdf

Molecular electronics and hybrid computers. B. W. Vought and R. R. Birge, Wiley Encyclopedia of Electrical & Electronics Engineering (1999) 13, 477-490

The nature of the chromophore binding site of bacteriorhodopsin: The potential role of Arg-82 as a principal counterion, A. Kusnetzow, D.L. Singh, C.H. Martin, I. Barani and R.R. Birge (1999) Biophys. J. 76, 2370-2389 pdf

Bit-error sources in 3D optical memory: experiments and models. A. F. Lawrence, J. A. Stuart, D. L. Singh and R. R. Birge (1999) Proc. SPIE 3468, 258-268

The angular orientation of the retinyl chromophore of bacteriorhodopsin: reconciliation of 2H NMR and optical measurements. B.S. Hudson and R.R. Birge (1999) J. Phys. Chem. A 103, 2251-2256 pdf

The transition dipole orientation of linear polyenes: Semi-empirical models and extrapolation to the infinite chain limit, R.R. Birge, M.Z. Zgierski, L. Serrano-Andres and B.S. Hudson (1999) J. Phys. Chem. A 103, 2251-2256 pdf

Propagation of a Gaussian beam in a bacteriorhodopsin film. Q.W. Song, X.M. Wang, R.R. Birge, J.D. Downie, D. Timucin and C. Gary (1998) J. Opt. Soc. Am. B. 15, 1602-1609 pdf

Photochemistry in dried polymer films incorporating the deionized blue membrane form of bacteriorhodopsin. J.R. Tallent, J.A. Stuart, Q.W. Song, E.J. Schmidt, C.H. Martin and R.R. Birge (1998) Biophys. J. 75, 1619-1634 pdf

Design, synthesis and photodynamics of light-harvesting arrays comprised of a porphyrin and one, two or eight boron-dipyrrin accessory pigments. F. Li, S.I. Yang, Y. Ciringh, J. Seth, C.H. martin, D.L. Singh, D. Kim, R.R. Birge, D.F. Bocian, D. Holten and J.S. Lindsey (1998) J. Am. Chem. Soc. 120, 10001-10017 pdf

Quadratic electrooptic effects in bacteriorhodopsin. Measurement of y(-w;0,0,w) in dried gelatin thin films. M. Yamazaki, J. Goodisman and R. R. Birge (1998) J. Chem. Phys. 108, 5876-5887 pdf

Reparameterizing MNDO for excited state calculations using ab initio effective Hamiltonian theory: Application to the 2,4-pentadien-1-iminium cation. C.H. Martin and R.R. Birge (1998) J. Phys. Chem. A 102, 852-860 pdf

Addressing considerations of 3-D optical memories with photoabsorptive and refractive materials. Q W. Song, X. M. Wang, R. R. Birge, J. D. Downie, D. Timucin and C. Gary (1997) Opt. Mem. Neurarl Netw. 6, 297-303

Protein-based three-dimensional memories and associative processors. R.R. Birge, B. Parsons, Q.W. Song and J.R. Tallent, in Molecular Electronics (eds. M.A. Ratner and J. Jortner), Blackweel Science Ltd., Oxford (1997) pp. 439-471

Towards a Bacteriorhodopsin-Silicon Neuromorphic Photosensor. C. H. Martin, Z. P. Chen, and R. R. Birge, Proceedings of the Pacific Symposium on Biocomputing (eds. R.B. Altman, A.K. Dunker, L. Hunter and T.E. Klein), (1997) 268-279

Bioelectronics. R.R. Birge, 1997 Yearbook of Science & Technology McGraw-Hill, New York (1997) pp. 212-216.

Protein-based volumetric memory. J.A. Stuart, J.R. Tallent, E.H.L. Tan and R.R. Birge (1996) Proc. IEEE Nonvol. Mem. Tech. (INVMTC) 6, 45-51

Effective photochromic nonlinearity of dried blue-membrane bacteriorhodopsin films. J. Tallent, Q.W. Song, Z. Li, J. Stuart and R.R. Birge (1996) Opt. Lett. 17, 1339-1341 pdf

Biological photochrome bactertiorhodopsin film based photon transistor- applications study. G. Liqun, Z. Chunping, Z. Guangyin, L. Jia, C. Xiaobo, W. Yongmei, T. Mingrong, P. Jilun, Q.W. Song, B. Parsons and R.R. Birge (1996) Acta Scient. Naturalium Univ. Nankaiensis 29, 1-4 (in Chinese).

Biological photochrome bactertiorhodopsin film based photon transistor- model establishment. Z. Chunping, G. Liqun, C. Xiaobo, L. Jia, Z. Guangyin, W. Yongmei, T. Mingrong, P. Jilun, Q.W. Song, R.B. Gross and R.R. Birge, Acta. Sci. Naturalium Univ. Nankaiensis, 29, No. 1, 30-34 (1996) (in Chinese).

Bacteriorhodopsin based photonic logic gate and its application to gray level image subtraction. Gu, L. Q., C. P. Zhang, A. F. Niu, J. Li, G. Y. Zhang, Y. M. Wang, M. R. Tong, J. L. Pan, Q. W. Song, B. Parsons, and R. R. Birge (1996) Opt. Commun. 131, 25-30 pdf

Role of calcium in the proton pump of bacteriorhodopsin. Microwave evidence for a cation-gated mechanism. R.R. Birge, D.S.K. Govender, K.C. Izgi and E.H.L. Tan (1996) J. Phys. Chem. A 100, 9990-10004 pdf

Correlation between surfactant/micelle structure and the stability of bacteriorhodopsin in solution. E.H.L. Tan and R.R. Birge (1996) Biophys. J. 70, 2385-2395 pdf

Large Organic Cations can Replace Mg2+ and Ca2+ Ions in Bacteriorhodopsin and Maintain Proton Pumping Ability, E. H. L. Tan and R. R. Birge (1996) J. Am. Chem. Soc. 118, 2752-2753 pdf

Characterization of the primary photochemical events in bacteriorhodopsin and rhodopsin. J. A. Stuart and R.R. Birge (1996) Biomem. 2A, 33-139

Advances in protein-based three-dimensional optical memories. Z. Chen, D. Govender, R. Gross and R. Birge, (1995) BioSys. 35, 145-151 pdf

Real-time holographic imaging with a bacteriorhodopsin film. Y.H. Zhang, Q. W. Song, C. Tseronic and R.R. Birge (1995) Opt. Lett. 20, 2429-2431 pdf

Modified critical angle method for measuring the refractive index of bio-optical materials and its application to bacteriorhodopsin. Q.W. Song, C.Y. Ku, C. Zhang, R.B. Gross, R.R. Birge and R. Michalak (1995) J. Opt. Soc. Amer. B. 12, 797-803 pdf

Biomolecular photonics based on bacteriorhodopsin. R.R. Birge and R.B. Gross, in CRC Handbook of Organic Photochemistry and Photobiology, W.M. Horspool and P-S Song, eds. (CRC Press, New York, 1995), pp. 1568-1586.

On the molecular origins of thermal noise in vertebrate and invertebrate photoreceptors. R.R. Birge and R.B. Barlow (1995) Biophys. Chem. 55, 115-126 pdf

The active site of bacteriorhodopsin. Two-photon spectroscopic evidence for a positively charged chromophore binding site mediated by calcium. J.A. Stuart, B.W. Vought, C.F. Zhang and R.R. Birge (1995) Biospec. 1, 9-28

Determination of the thermal expansion and thermo-optical coefficients of a bacteriorhodospin film. Q.W. Song, C. Zhang, C.Y. Ku, M.C. Huang, R.B. Gross and R.R. Birge (1995) Opt. Commun. 115, 471-474 pdf

Protein-based computers. R.R. Birge (1995) Sci. Amer. 272, 90-95

Biomolecular optoelectronics. R.R. Birge and R.B. Gross, in Introduction to Molecular Electronics, M.C. Petty, M.R. Bryce and D. Bloor, eds, Edward Arnold, Kent, UK (1995) pp. 315-344

Bioelectronics, three-dimensional memories and hybrid computers, R.R. Birge, D.S.K. Govender, R.B. Gross, A.F. Lawrence, J.A. Stuart, J.R. Tallent, E.H.L. Tan and B.W. Vought (1994) Proc. IEEE IEDM 94, 3-6

The intensity-dependent refractive index of chemically enhanced bacteriorhodopsin, Q.W. Song, C. Zhang, R.B. Gross and R.R. Birge (1994) Opt. Commun. 112, 296-301

Bacteriorhodopsin. R.R. Birge in Encyclopedia of Advanced Materials, Pergamon Press, Oxford, UK.(1994) pp. 199-204

Determination of the refractive index of a bacteriorhodopsin film. C. Zhang, Q.W. Song, C.Y. Ku, R.B. Gross and R.R. Birge (1994) Opt. Lett. 19, 1406-1411 pdf

Bacteriorhodopsin, a nonlinear proton pump. R.R. Birge (1994) Nature 371, 659-660

Observation and analysis of self-diffraction in bacteriorhodopsin films. R.B. Gross, Z. Chen and R.R. Birge (1994) Proc. Mat. Res. Soc. 330, 251-256

Fundamentals of reliability calculations for molecular devices and photochromic memories. A.F. Lawrence and R.R. Birge (1994) Adv. Chem. 240, 131-160

Introduction to molecular and biomolecular electronics. R.R. Birge (1994) Adv. Chem. 240, 1-14

Three-Dimensional Optical Memories. R.R. Birge (1994) Amer. Sci. 82, 349-355

Chemically enhanced bacteriorhodopsin thin film spatial light modulator, Q.W. Song, C. Zhang, R. Blumer, R.B. Gross, Z. Chen and R.R. Birge (1993) Proc. SPIE 2051, 77-82

On the molecular origin of photoreceptor noise. R.B. Barlow, R.R. Birge, E. Kaplan and J.R. Tallent (1993) Nature 366, 64-66 pdf

Chemically enhanced bacteriorhodopsin thin-film spatial light modulator. Q.W. Song, C. Zhang, R. Blumer, R.B. Gross, Z.P. Chen and R.R. Birge (1993) Opt. Lett. 18, 1373-1375 pdf

Protein based artificial retinas. Z.P. Chen and R.R. Birge (1993) Trends Biotech. 11, 292-300 pdf

Optical limiting by chemically enhanced bacteriorhodopsin films. Q.W. Song, C. Zhang, R. Gross and R.R. Birge (1993) Opt. Lett. 18, 775-777 pdf

The unusual pKa of the rhodopsin chromophore. Is this how nature minimizes photoreceptor noise? R.R. Birge (1993) Biophys. J. 64, 1371-1372 pdf

The potential application of optical phased arrays in two-photon three-dimensional optical memories. A.F. Lawrence and R.R. Birge (1992) Proc. SPIE 1773, 401-412

Molecular Electronics, in Nanotechnology, Research and Perspectives, R.R. Birge (B.C. Crandall and James Lewis, eds.), MIT Press, Cambridge, Mass. (1992) pp. 149-170

On the Molecular Origins of Thermal Noise in Vertebrate and Invertebrate Photoreceptors. R.R. Birge, R.B. Barlow Jr. and J.R. Tallent, in “Structures and Functions of Retinal Proteins”, Ed. J.L Rigaud, Col. INSERM (1992) 221, 283-286

Conformational energetics and excited state level ordering in 11-cis retinal. J.R. Tallent, J.R. Birge, C.F. Zhang, E. Wenderholm and R.R. Birge (1992) Photochem. Photobiol. 56, 935-952

Protein based optical computing and optical memories, R.R. Birge (1992) IEEE Computer 25, 56-67

Nonlinear optical properties of bacteriorhodopsin and protein based two-photon three-dimensional memories. R.R. Birge, R.B. Gross, M.B. Masthay, J.A. Stuart, J.R. Tallent & C.F. Zhang. Mol. Cryst. Liq. Cryst. Sci. Technol. Sec. B. Nonlin. Opt. 3, 133-147

Theoretical analysis of third-order polarizability enhancement of disubstituted diphenyl polyenes via oxidative doping. J. R. Tallent, R.R. Birge, C.W. Spangler and K.O. Havelka (1992) Am. Inst. Phys. Conf. Proc. 262, 191-203

Molecular dynamics of the primary photochemical event in rhodopsin. J.R. Tallent, E.Q. Hyde, L.A. Findsen, G.C. Fox & R.R. Birge (1992) J. Am. Chem. Soc. 114, 1581-1592 pdf

Holographic thin films, spatial light modulators and optical associative memories based on bacteriorhodopsin, R.B. Gross, K.C. Izgi & R.R. Birge (1992) Proc. SPIE 1662, 186-196

Quantum Effects, Thermal Statistics and Reliability of Nanoscale Molecular and Semiconductor Devices. R.R. Birge, A.F. Lawrence and J.R. Tallent (1991) Nanotech. 2, 73-87 pdf

Revised Assignment of Energy Storage in the Primary Photochemical Event in Bacteriorhodopsin. R.R. Birge, T.M. Cooper, A.F. Lawrence, M.B. Masthay, C.F. Zhang and R. Zidovetzki (1991) J. Am. Chem. Soc. 113, 4327-4328 pdf

Nonlinear Optical Properties of Bacteriorhodopsin: Assignment of the Third-Order Polarizability Based on Two-Photon Absorption Spectroscopy. R.R. Birge, M.B. Masthay, J.A. Stuart, J.R. Tallent and C.F. Zhang, in Biomolecular Spectroscopy, R.R. Birge and L.A. Nafie, eds. (1991) Proc. SPIE 1432, 129-140

Wavelength Dependence of the Photorefractive and Photodiffractive Properties of Holographic Thin Films Based on Bacteriorhodopsin. R. R. Birge, K. C. Izgi, J. A. Stuart and J.A. Tallent (1991) Proc. Mat. Res. Soc. 218, 131-140

Structural and Electrostatic Studies of Benzodiazepine Receptor Ligands, P. W. Codding, A. W. Roszak, M. B. Szkaradzinska, P. A. Fleitz and R. R. Birge (1990) Frontiers Drug Res. 28, 78-90

Photophysics and Molecular Electronic Applications of the Rhodopsins, R.R. Birge (1990) Annu. Rev. Phys. Chem. 41, 683-733 pdf

Two-Photon Spectroscopy of Light-Adapted Bacteriorhodopsin. R.R. Birge and C.F. Zhang J. (1990) Chem. Phys. 92, 7178-7195 pdf

Nonlinear Optical Properties of Bacteriorhodopsin. Assignment of Second Order Hyperpolarizabilities of Randomly Oriented Systems by using Two-Photon Spectroscopy. R.R. Birge, P. A. Fleitz, A. F. Lawrence, M. A. Masthay and C. F. Zhang (1990) Mol. Cryst. Liq. Cryst. 189, 107-122

The Nature of the Primary Photochemical Events in Rhodopsin and Bacteriorhodopsin, R.R. Birge (1990) Biochim. Biophys. Acta, 1016, 293-327 pdf