OPIL Publications page 1

Harris, D.A. and Walter, N.G. (2005) "Terbium(III) footprinting as a probe of RNA structure and metal-binding sites." In Handbook of RNA Biochemistry Vol. 1, pp. 205-213 (R.K. Hartmann, A. Bindereif, A. Schon, and E. Westhof, eds.), Wiley-VCH Verlag, Weinheim.

Krasovska, M.V., Sefcikova, J., Spackova, N., Sponer, J. and Nils G. Walter, "Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations." J. Mol. Biol. 351, 731-748 (2005).

Lambert, M.N., Hoerter, J.A.H., Pereira, M.J.B. and Walter, N.G. "Solution probing of metal ion binding by helix 27 from Escherichia coli 16S rRNA." RNA 11, 1688–1700 (2005).

Rueda, D. and Walter, N.G. "Single molecule fluorescence control for nanotechnology." J. Nanosci. Nanotechnol. 5, 1990–2000 (2005).

*Rueda, D., Hsieh, J., Day-Storms, J.J., Fierke, C.A. and Walter, N.G. "The 5' leader of precursor tRNAAsp bound to the Bacillus subtilis RNase P holoenzyme has an extended conformation." Biochemistry 44, 16130-16139 (2005).

Walter, N.G. "Michaelis-Menten is dead, long live Michaelis-Menten!" Nature Chem. Biol. 2, 66-67 (2006).

Rueda, D. and Walter, N.G. "Fluorescent energy transfer readout of an aptazyme-based biosensor." Methods Mol. Biol. 355, 289-310 (2006).

Tinsley, R.A. and Walter, N.G. "Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation." RNA 12, 522-529 (2006).

*Lambert, M.N., Vocker, E., Blumberg, S., Redemann, S., Gajraj, A., Meiners, J.C. and Walter, N.G. "Mg2+-Induced compaction of single RNA molecules monitored by tethered particle microscopy. Biophys. J., in press (2006)."

Navrotskaya, I. and Geva, E. "The influence of nonbilinear system-bath coupling on quantum-mechanical activated rate processes" Chem. Phys. 322, 223 (2006).

Shang, J. and Geva, E. "A computational study of the correlations between structure and dynamics in free and surface-immobilized polymer chains" J. Phys. Chem. B 109, 16340 (2006)

Ka, B.J., Shi, Q. and Geva, E. "Vibrational energy relaxation rates via the linearized semiclassical approximation: Applications to neat diatomic liquids and atomic-diatomic liquid mixtures" J. Phys. Chem. A 109, 5527 (2006)

Shi, Q. and Geva, E. "A comparison between different semiclassical approximations for optical response functions in nonpolar liquid solutions" J. Chem. Phys. 122, 064506 (7 pages) (2005).

Wang, D. and Geva, E. "Protein structure and dynamics from single-molecule fluorescence-resonance energy transfer" J. Phys. Chem. B 109, 1626-1634 (2005).

Batteh, E. T., Jun Cheng, Gang Chen, D.G. Steel, D. Gammon, D.S. Katzer, D. Park, "Coherent nonlinear optical spectroscopy o fluctuation quantum dots: evidence of coupling between quantum dots," Phys. Rev. B 71 p155327 (2005).

Gurudev Dutt, M. V., Yanwen Wu, Xiaoqin Li, D.G. Steel, D. Gammon, L.J. Sham, "Semiconductor quantum dots for quantum information processing : An optical approach", Physics of Semiconductor, Jose Menendez and Chris G. Van de Walle, eds, Proceedings of the 27th ICPS, Flagstaff, AZ, American Institute of Physics Vol 772, p32-37, (2005).

Sophia E. Economou, Ren-Bao Liu, L.J. Sham, and D.G. Steel, "A Unified Theory of Consequences of Spontaneous Emission in a L System", Phys. Rev. B 71, 195327 (2005)

*M.V. Gurudev Dutt, Jun Cheng, Bo Li, Xiaodong Xu, Xiaoqin Li, P.R. Berman, D.G. Steel, A.S. Bracker, D. Gammon, Sophia E Economou, Renbao Liu and L.J. Sham, "Stimulated and spontaneous optical generation of electron spin coherence in charged GaAs quantum dots," Phys. Rev. Lett. 94, 227403 (2005).

*Jeffrey R. Brender, Joe Dertouzos, David P. Ballou, Vincent Massey, Bruce A. Palfey, Barrie Entsch Ari Gafni, and Duncan Steel, "Conformational Dynamics of the Isoalloxazine Ring in Substrate-free PHBH: Single Molecule Studies", JACS 27, pp18171-18178 (2005).

*Yanwen Wu, Xiaoqin Li,. L. M. Duan, and D. G. Steel, D. Gammon, Lu Sham, "Density Matrix Tomography through Coherent Optical Rotation of an Exciton Qubit in a Single Quantum Dot," Phys. Rev. Lett. 96, 087402 (2006).

*Jue Shi, Ari Gafni, and Duncan Steel, "Simulated Data Sets for Single Molecule Kinetics: Some Limitations and Complications of Data Analysis," European Biophysics Journal, in press (2006).

Xiaoqin Li, Yanwen Wu, Xiaodong Xu, D.G. Steel, and D. Gammon, "Transient nonlinear optical spectroscopy studies involving biexciton coherence in single quantum dots," in press Physical Review B (2006).

*Shi, J., Gafni, A. and Steel, DG: "Application of single molecule spectroscopy in studies of enzyme kinetics and mechanisms." Meth. Enzymol. in press (2005).

*Jue Shi, Joe Dertouzos, Ari Gafni, Duncan Steel, Bruce A. Palfey "Single-Molecule Kinetics Reveals New Signatures of Half-sites Reactivity in Dihydroorotate Dehydrogenase A Catalysis," Proc. National Academy of Sciences, USA in press (2006).

Kubarych, K. J., M. Joffre, A. Moore, N. Belabas, D. M. Jonas, "Mid-infrared electric field characterization using a visible charge-coupled-device-based spectrometer" Opt. Lett. 30, 1228 (2005).

*J. P. Ogilvie, K. J. Kubarych, A. Alexandrou, M. Joffre,"Fourier transform measurement of two-photon excitation spectra: applications to microscopy and optimal control" Opt. Lett. 30, 911 (2005).

Reis, D. A. and A. M. Lindenberg. "Ultrafast x-ray scattering in solids." In M. Cardona and R. Merlin,editors, Light Scattering in Solids IX. Springer-Verlag, in press, (2006).

Reis, D. A., K. J. Gaffney, B. Torralva, and G. H. Gilmer. "Ultrafast lattice dynamics." MRS bulletin, in press, (2006).

*S. H. Lee, A. L. Cavalieri, D. M. Fritz, M. C. Swan, R. S. Hegde, M. Reason, R. S. Goldman, and D. A. Reis. "Generation and propagation of a picosecond acoustic pulse at a buried interface: Time-resolved x-ray diffraction measurements." Phys. Rev. Lett., 95(24):246104, (2005).

David A. Reis. "A film of picosecond vibrations of a film." Solid State Communications, 136(9-10):564 565, (2005).

*K. J. Gaffney, A. M. Lindenberg, J. Larsson, K. Sokolowski-Tinten, C. Blome, O. Synnergren, J. Sheppard, C. Caleman, A. G. MacPhee, D. Weinstein, D. P. Lowney, T. Allison, T. Matthews, R. W. Falcone, A. L. Cavalieri, D. M. Fritz, S. H. Lee, P. H. Bucksbaum, D. A. Reis, J. Rudati, A. T. Macrander, P. H. Fuoss, C. C. Kao, D. P. Siddons, R. Pahl, K. Moffat, J. Als- Nielsen, S. Duesterer, R. Ischebeck, H. Schlarb, H. Schulte-Schrepping, J. Schneider, D. von der Linde, O. Hignette, F. Sette, H. N. Chapman, R. W. Lee, T. N. Hansen, J. S. Wark, M. Bergh, G. Huldt, D. van der Spoel, N. Timneanu, J. Hajdu, R. A. Akre, E. Bong, P. Krejcik, J. Arthur, S. Brennan, K. Luening, and J. B. Hastings. "Observation of structural anisotropy and the onset of liquidlike motion during the nonthermal melting of InSb." Physical Review Letters, 95(12):125701, (2005).

*A. M. Lindenberg, J. Larsson, K. Sokolowski-Tinten, K. J. Gaffney, C. Blome, O. Synnergren, J. Sheppard, C. Caleman, A. G. MacPhee, D. Weinstein, D. P. Lowney, T. K. Allison, T. Matthews, R. W. Falcone, A. L. Cavalieri, D. M. Fritz, S. H. Lee, P. H. Bucksbaum, D. A. Reis, J. Rudati, P. H. Fuoss, C. C. Kao, D. P. Siddons, R. Pahl, J. Als-Nielson, S. Duerster, Ischebeck R., H. Schlarb, H. Schulte Schrepping, Th. Tschentscher, J. Schneider, D. von der Linde, O. Hignette, F. Sette, H. N. Chapman, R. W. Lee, T. N. Hansen, S. Techert, J. S. Wark, M. Bergh, G. Huldt, D. van der Spoel, Timneanu N., J. Hajdu, R. A. Akre, E. Bong, P. Krejcik, J. Arthur, S. Brennan, Luening K., and J. B. Hastings. "Atomic-scale visualization of inertial dynamics." Science, 308:392-395, (2005).

*A. L. Cavalieri, D. M. Fritz, S. H. Lee, P. H. Bucksbaum, D. A. Reis, J. Rudati, D. M. Mills, P. H. Fuoss, G. B. Stephenson, C. C. Kao, D. P. Siddons, D. P. Lowney, A. G. MacPhee, D. Weinstein, R. W. Falcone, R. Pahl, J. Als-Nielsen, C. Blome, S. Dursterer, R. Ischebeck, H. Schlarb, H. Schulte-Schrepping, Th. Tschentscher, J. Schneider, O. Hignette, F. Sette, k. Sokolowski- Tinten, H. N. Chapman, R. W. Lee, T. N. Hansen, O. Synnergren, J. Larsson, S. Techert, J. Sheppard, J. S. Wark, M. Bergh, C. Caleman, G. Huldt, D. van der Spoel, N. Timneanu, J. Hajdu, R. A. Akre, E. Bong, P. Emma, P. Krejcik, J. Arthur, S. Brennan, K. J. Gaffney, A. M. Lindenberg, K. Luening, and J. B. Hastings. "Clocking femtosecond x-rays." Phys. Rev. Lett., 94:114801, (2005).

Murray, E. D., D. M. Fritz, J. K. Wahlstrand, S. Fahy, and D. A. Reis. "Effect of lattice anharmonicity on high-amplitude phonon dynamics in photoexcited bismuth." Phys. Rev. B, 72(6):060301, (2005).

*M. F. DeCamp, D. A. Reis, D. M. Fritz, P. H. Bucksbaum, E. M. Dufresne, and R. Clarke. "X-ray synchrotron studies of ultrafast cyrstalline dynamics." J. Synch. Rad., 12:177-192, (2005).

Acton, M., L. Deslauriers, K.-A. Brickman, P. C. Haljan, P. J. Lee, S. Olmschenk, and C. Monroe, "Near-Perfect Simultaneous Detection of a Qubit Register," Quant. Inf. Comp. in press (2006) quant-ph/0511257.

Moehring, D. L., B. B. Blinov, D. W. Gidley, R. N. Kohn, M. J. Madsen, T. B. Sanderson, R. S. Vallery, and C. Monroe, "Precision Lifetime Measurement of a Single Trapped Ion with Ultrafast Laser Pulses," Phys. Rev. A 73, 023413 (2006).

Hensinger, W. K., S. Olmschenk, D. Stick, D. Hucul, M. Yeo, M. Acton, L. Deslauriers, J. Rabchuk, and C. Monroe, "T-junction ion trap array for two dimensional ion shuttling, storage and manipulation" Appl. Phys. Lett. 88, 034101 (2006).

*Shi-Liang Zhu, C. Monroe, L.-M. Duan, "Arbitrary-speed quantum gates within large ion crystals through minimum control of laser beams," Europhys. Lett. 73 (4), 1-7 (2006); quant-ph/0508037.

Stick, D., W. K. Hensinger, S. Olmschenk, M. J. Madsen, K. Schwab, and C. Monroe, "Ion Trap in a Semiconductor Chip," Nature Physics 2, 36 (2006).

Blinov, B. B., R. N. Kohn, M. J. Madsen, D. L. Moehring, and C. Monroe, "Broadband Laser Cooling of Trapped Atoms with Ultrafast Laser Pulses," J. Opt. Soc. Am. B in press (2006); quant-ph/0505111.

Haljan, P. C., P. J. Lee, K.-A. Brickman, M. Acton, L. Deslauriers, and C. Monroe, "Entanglement of Trapped-Ion Clock States," Phys. Rev. A 72, 062316 (2005).

Brickman, K.-A., P. C. Haljan, P. J. Lee, M. Acton, L. Deslauriers, and C. Monroe, "Implementation of Grover's Quantum Search Algorithm in a Scalable System," Phys. Rev. A 72, 050306 (2005).

Hensinger, W. K., D. W. Utami, H.-S. Goan, K. Schwab, C. Monroe, and G. J. Milburn, "Ion trap transducers for quantum electromechanical oscillators", Phys. Rev. A (2005).

Haljan, P. C., K.-A. Brickman, L. Deslauriers, P. J. Lee, and C. Monroe, "Spin-dependent Forces on Trapped Ions for Phase-Stable Quantum Gates and Motional Schr dinger Cat States," Phys. Rev. Lett. 94, 153602 (2005).

Bragas, A. V. and R. Merlin, "Squeezed Phonons in Solids." in Encyclopedia of Modern Optics, Vol. 4, ed. by B. Guenther, D. G. Steel and L. Bayvel (Academic Press, London, 2005), pp. 280-287.

Bao, J. M., A. V. Bragas, J. K. Furdyna and R. Merlin, "Control of spin dynamics with laser pulses: Generation of entangled states of donor-bound electrons in a Cd1-xMnxTe quantum well." Phys. Rev. B 71, 045314 (2005).

Pascual Winter, M. F. , A. Fainstein, M. Trigo, T. Eckhause, R. Merlin, A. Y. Cho and J. Chen, "InP acoustic cavity phonon spectra probed by Raman scattering." Phys. Rev. B 71, 085305 (2005).

Bragas, A. V., C. Aku-Leh and R. Merlin, "Ultrafast generation of optical and acoustic phonons in nanocrystallites." in Ultrafast Phenomena in Semiconductors and Nanostructure Materials IX, ed. by K. -T. Tsen, J. -J. Song and H. Jiang, SPIE Proceedings 5725, pp. 126-135

Wahlstrand, J. K., R. Merlin, X. Li, S. T. Cundiff and O. E. Martinez, "Impulsive stimulated Raman scattering: Comparison between phase-sensitive and spectrally-filtered techniques." Optics Lett. 30, 926-929 (2005).

Aku-Leh, C., J. Zhao, R. Merlin, J. Menéndez and M. Cardona, "Long-lived optical phonons in ZnO studied with impulsive stimulated Raman scattering." Phys. Rev.B 71, 205211 (2005).

Aku-Leh, C., J. Zhao, R. Merlin, J. Menéndez and M. Cardona, "Anharmonic Interactions in ZnO Probed with Impulsive-Stimulated Raman Scattering." in Physics of Semiconductors, ed. by J. Menendez and C. G. Van de Walle, AIP Conference Proceedings 772, 1128-1129 (2005).

Trigo, M., T. A. Eckhause, J. K. Wahlstrand, R. Merlin, M. Reason and R. S. Goldman, "Generation and Remote Detection of Coherent Folded Acoustic Phonons." in Physics of Semiconductors, ed. by J. Menendez and C. G. Van de Walle, AIP Conference Proceedings 772, 1190-1191 (2005).