Publications

Last Updated: July 9, 2010

Undergraduate students are underlined. Graduate students in italics.

Journals Articles

15) Ryan, J., P. Urayama. (in preparation, summer 2010).

14) E. Alquist, L. Regueyra, J. Jasensky, M.J. Farooqi, and P. Urayama. (in preparation, summer 2010).

13) P. Urayama, E.W. Frey, and S.R. Savage. Fluorescent probe dyes for metabolic-ion sensing under high hydrostatic pressures, Annals of the New York Academy of Sciences: High-Pressure Bioscience and Biotechnology, 1189: 104-112 (2010). doi:10.1111/j.1749-6632.2009.05184.x

12) H.M. DePedro, P. Urayama. Using LysoSensor Yellow/Blue DND-160 to sense acidic pH under high hydrostatic pressures, Analytical Biochemistry, 384: 359-361 (2009). doi:10.1016/j.ab.2008.10.007

11) S.B. Keller, J.A. Dudley, K. Binzel, J. Jasensky, H.M. DePedro, E.W. Frey, P. Urayama. A calibration approach for rapid fluorescence lifetime determination for applications using time-gated detection and finite pulse width excitation, Analytical Chemistry, 80: 7876-7881 (2008). doi:10.1021/ac801252q

10) P. Urayama, E.W. Frey, M.J. Eldridge. A fluid handling system with finger-tightened connectors for biological studies at kilo-atmosphere pressures, Review of Scientific Instruments, 79: 046103 (2008). doi:10.1063/1.2907245  Listed in the April 15, 2008 edition of the Virtual Journal of Biological Physics Research.

9) T. Haver, E.C. Raber, P. Urayama. An application of spatial deconvolution to a capillary-based high-pressure chamber for fluorescence microscopy imaging, Journal of Microscopy, 230: 363-371 (2008). doi:10.1111/j.1365-2818.2008.01994.x

8) M. Salerno, J. J. Ajimo, J. A. Dudley, K. Binzel, P. Urayama. Characterization of dual-wavelength SNAFL and SNARF dyes for pH sensing under high hydrostatic pressures, Analytical Biochemistry, 362: 258-267 (2007). doi:10.1016/j.ab.2006.12.042

7) E.C. Raber, J. A. Dudley, M. Salerno, P. Urayama. A capillary-based, high-pressure chamber for fluorescence microscopy imaging, Review of Scientific Instruments, 77: 096106 (2006). doi:10.1063/1.2349303  Listed in the October 1, 2006 edition of the Virtual Journal of Biological Physics Research.

6) P. Urayama, W. Zhong, J.A. Beamish, F.K. Minn, R.D. Sloboda, K.H. Dragnev, E. Dmitrovsky, and M.-A. Mycek: A UV-visible-NIR fluorescence lifetime imaging microscope for laser-based biological sensing with picosecond resolution, Applied Physics B, 76: 483-496 (2003).

5) W. Zhong, P. Urayama, M.-A. Mycek: Imaging fluorescence lifetime modulation of a ruthenium-based dye in living cells: the potential for oxygen sensing, Journal of Physics D: Applied Physics, 36: 1689-1695 (2003).

4) P. Urayama, S.M. Gruner, and G.N. Phillips Jr. Probing substates in sperm whale myoglobin using high pressure crystallography, Structure, 10: 51-60 (2002).

3) D.A. Hajduk, P. Urayama, S.M. Gruner, S. Erramilli, R. Register, K. Brister, and L. J. Fetters: High pressure effects on the disordered phase of block copolymer melts, Macromolecules, 28: 7148-7156 (1995).

2) P. Urayama and G. Benford: Modeling energy flow in turbulent beam-plasma experiments, Physics of Plasmas, 2: 2117-2121 (1995).

1) W.W. Heidbrink, D. Adams, S. Drum, K. Evans, J. Manson, T. Price, P. Urayama, F. J. Wessel.Propagation of a narrow plasma beam in an oblique magnetic field, Physics of Fluids B, 4: 3454-3456 (1992).

Refereed Conference Abstracts

9) P. Urayama, E.W. Frey, S.R. Savage. “High-pressure, fluorescence-based sensing of calcium ions.” Fifth International Conference on High-Pressure Bioscience and Biotechnology (2008).

8) E.W. Frey, P. Urayama. "Fluorescence-based calcium-ion sensing at high hydrostatic pressures.” 2008 Biophysical Society Meeting Abstracts. Biophysical Journal, Supplement: 326a (2008).

7) P. Urayama, M. Salerno, J. Dudley, K. Binzel, J. Jasensky, E. Frey, S. Keller, A. Zorn. "Characterization of dual-wavelength pH-sensing fluorophores under high hydrostatic pressures.” 2007 Biophysical Society Meeting Abstracts. Biophysical Journal, Supplement: 369a (2007).

6) P. Urayama, E. Raber, M. Salerno, J. Ajimo, J. Dudley, K. Binzel. "A capillary-based system for fluorescence microscopy imaging at high pressures.” 2006 Biophysical Society Meeting Abstracts. Biophysical Journal, Supplement: 136a-137a (2006).

5)  M.-A. Mycek, W. Zhong, P. Urayama. Investigating cellular metabolic function using fluorescence lifetime imaging microscopy. in Optical Society of America Topical Conference: Advances in Biomedical Optical Spectroscopy and Diagnostics (BOSD), 2004.

4)  M.-A. Mycek, P. Urayama, K. Heyman, and M. Bussey. Using POPOP's Viscosity Dependent Lifetime as a Picosecond Resolution Standard in Near-UV Fluorescence Lifetime Imaging Microscopy, in SPIE International Symposium on Biomedical Optics (BiOS 2003).

3)   P. Urayama, J.A. Beamish, F.K. Minn, E.A. Hamon, M.-A. Mycek. A UV fluorescence lifetime imaging microscope to probe endogenous cellular fluorescence, in OSA Trends in optics and photonics (TOPS) Vol. 73, Conference on Lasers and Electro-Optics, OSA Technical Digest, Postconference Edition (Optical Society of America, Washington, DC, 2002), pp. 550-551.

2)   P. Urayama, W. Zhong, R.D. Sloboda, K.H. Dragnev, E. Dmitrovsky, and M.-A. Mycek. Probing endogenous fluorophores in cellular cancer models using temporally and spectrally resolved laser induced fluorescence, in OSA Trends in optics and photonics (TOPS) Vol. 73, Conference on Lasers and Electro-Optics, OSA Technical Digest, Postconference Edition (Optical Society of America, Washington, DC, 2002), pp.587-588.

1)   M.-A. Mycek, J. Pitts, R. Sloboda, P. Urayama, W. Zhong, K. Dragnev , and E. Dmitrovsky. Using endogenous fluorescence to probe mitochondrial function in human bronchial epithelial cells, Biophysical Journal 82 Part2: 2113 (2002).

Book Chapters

1)   P. Urayama and M.-A. Mycek: Fluorescence lifetime imaging microscopy of endogenous biological fluorescence, in Handbook of Biomedical Fluorescence, M.-A. Mycek and B. W. Pogue, eds. Marcel Dekker: New York, 2003, pp.211-236.

Fiction

1)   "Living in a Stranger," Analog Science Fiction and Fact, October 1998.

Masters Theses

Use the standard laboratory password to view the file.

M. Junaid Farooqi, M.S., 2009. "Methods for in situ piezophysiological studies: Optical sectioning via structured illumination and fluorescence-based characterization of NADH conformation." thesis (images have been compressed to reduce file size. see me for high quality version.)

Hector Michael DePedro, M.S., 2008. "Characterization of the low pH sensing dye, LysoSensor Yellow/Blue DND-160, under high hydrostatic pressures." thesis

Thomas Haver, M.S., 2007. "The assessment and application of point spread function deconvolution to high pressure fluorescence microscopy imaging." thesis

Erica Raber, M.S., 2006. "Spatial resolution characterization of images taken from a capillary-based high pressure chamber for biological imaging studies." thesis

Jacob J. Ajimo, M.S. 2005. "A UV-Visible-NIR, Time-Resolved Fluorescence Spectrometer for High-Pressure Biological Studies." thesis

Honors Theses

Lauren A. Regueyra, B.S., 2010. "High Pressure Effects on the Solvent Denaturation of NADH probed via Fluorescence Spectroscopy" Department Honors.

Eric W. Frey, B.S., 2008. "Fluorescence-based calcium ion sensing at high hydrostatic pressures." University Honors with Distinction; Department Honors.

Michael J. Maffett, B.S., 2008. "Computations on the role of electrostatics in understanding the effects of pressure on myoglobin structure." University Honors with Distinction; Department Honors.