PULSE Stanford
SLAC National Accelerator Laboratory

Publications

Department of Energy funded work is marked by *

2009

2008

2007

    2009

  • *Near Edge X-ray Absorption Fine Structure Spectroscopy with X-Ray Free Electron Lasers
    D.P. Bernstein, Y. Acremann, A. Scherz, M. Burkhardt, J. Stöhr, M. Beye, W.F. Schlotter, T. Beeck, F. Sorgenfrei, A. Pietzsch, W. Wurth, and A. Föhlisch
    Appl. Phys. Lett. 95,134102 (2009)
  • *Aerosol imaging with a Soft X-ray Free Electron Laser
    M. J. Bogan, S. Boutet, H. N. Chapman, S. Marchesini, A. Barty, W. H. Benner et al.
    Aerosol Science and Technology, in review (2009)
  • *Charge Conservation and Translational Invariance in Electronegativity Equalization Methods
    Jiahao Chen and Todd J. Martínez
    J. Chem. Phys., 131, 044114 (2009) link to article
  • *Field-Free Alignment in Repetitively Kicked Nitrogen
    J. P. Cryan, P.H. Bucksbaum, and R.N. Coffee
    Phys. Rev. A, submitted, (2009)
  • Force-induced Activation of Covalent Bonds in Mechanoresponsive Polymeric Materials
    D. A. Davis, A. Hamilton, J. Yang, L. D. Cremar, D. Van Gough, S. L. Potisek, M. T. Ong, P. V. Braun, T. J. Martínez, J. S. Moore, S. R. White, and N. R. Sottos
    Nature, 459, 68-72 (2009) link to article
  • *Calibration of a High Harmonic Spectrometer by Laser Induced Plasma Emission
    J. P. Farrell, B. K. McFarland, P. H. Bucksbaum and M. Gühr
    Optics Express, 17, 15134-15144 (2009) link to article
  • *Relation of high harmonic spectra to electronic structure in N2
    J. P. Farrell, B. K. McFarland, M. Gühr and P. H. Bucksbaum
    Chem. Phys., submitted, (2009)
  • *Arresting Sample Explosion for Single Particle Diffraction Imaging
    S. P. Hau-Riege, S. Boutet, A. Barty, S. Bajt, M. J. Bogan, B. Iwan et al.
    Nature Physics, in review (2009)
  • Atomic Resolution Mapping of the Excited State Electronic Structure of Cu2O with Time-Resolved X-Ray Absorption Spectroscopy
    P.B. Hillyard, S.V.N.T. Kuchibhatla, T.E. Glover, M.P. Hertlein, N. Huse, P. Nachimuthu, L.V. Saraf, S. Thevuthasan, K.J. Gaffney
    Physical Review B accepted.
  • * Probing the hydrogen-bond network of water via time-resolved soft x-ray spectroscopy
    N. Huse, H. Wen, D. Nordlund, E. Szilgayi, D. Daranciang, T.A. Miller, A. Nilsson, R.W. Schoenlein and A.M. Lindenberg
    Phys. Chem. Chem. Phys. 11, 3951 (2009) (cover article) link to article
  • Efficient Multiple Exciton Generation Observed in Colloidal PbSe Quantum Dots with Temporally and Spectrally Resolved Intraband Excitation
    M. Ji, S. Park, S. T. Connor, T. Mokari, Y. Cui, and K. J. Gaffney
    Nano Letters, 9, 1217-1222 (2009). link to article
  • Pulsed-laser creation and characterization of giant plasma membrane vesicles from cells
    C. V. Kelly, M. T. Kober, P. Kinnunen, D. A. Reis, B. G. Orr, and M. M. Banaszak Holl
    J. Biol. Phys., 35,279-295 (2009) » link to article
  • *High Harmonic Phase in Molecular Nitrogen
    B. K. McFarland, J. P. Farrell, P. H. Bucksbaum and M. Gühr
    Phys. Rev. A, 80 033412, (2009) link to article
  • First Principles Dynamics and Minimum Energy Pathways for Mechanochemical Ring-Opening of Cyclobutene
    M. T. Ong, J. Leiding, H. Tao, A. M. Virshup and T. J. Martínez
    J. Amer. Chem. Soc., 131, 6377-6379 (2009) link to article
  • Ultrafast Dynamics of Hydrogen Bond Exchange in Aqueous Ionic Solutions
    S. Park, M. Odelius, and K. J. Gaffney
    Journal of Physical Chemistry B, 113, 7825-7835 (2009). link to article
  • *Squeezing more out of ultrafast x-ray measurements
    D. A. Reis
    Physics, 2,33 (2009) » link to article
  • Observation of a Zundel-like Transition State During Proton Transfer in Aqueous Hydroxide Solutions
    S. T. Roberts, P. B. Petersen, K. Ramasesha, A. Tokmakoff, I. S. Ufimtsev, and T. J. Martínez
    Proc. Natl. Acad. Sci., in press link to article
  • Implementation of Scientific Computing Applications on the Cell Broadband Engine
    G. Shi, V. Kindratenko, I. S. Ufimtsev, T. J. Martinez, J. Phillips, and S. Gottlieb
    Sci. Prog., 17, 135-151 (2009) link to article
  • *Magnetization switching without charge or spin currents
    J. Stohr, H.C. Siegmann, A. Kashuba, S.J. Gamble
    Applied Physics Letters 94,072504 (2009)
  • Revisiting Molecular Dissociation in Density Functional Theory: A Simple Model
    D. G. Tempel, T. J. Martínez and N. T. Maitra
    J. Chem. Theo. Comp., 5, 770-780 (2009) link to article
  • Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent Field Implementation
    I. S. Ufimtsev and T. J. Martínez
    J. Chem. Theo. Comp., 5, 1004-1015 (2009) link to article
  • Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients and First Principles Molecular Dynamics
    I. S. Ufimtsev and T. J. Martínez
    J. Chem. Theo. Comp., in press link to article
  • Photodynamics in Complex Environments: Ab Initio Multiple Spawning Quantum Mechanical/Molecular Mechanical Dynamics
    A. M. Virshup, C. Punwong, T. V. Pogorelov, B. Lindquist, C. Ko and T. J. Martínez
    J. Phys. Chem., 113B, 3280-3291 (2009) link to article
  • * Coherent THz polarization control through manipulation of electron trajectories
    H. Wen and A.M. Lindenberg
    Phys. Rev. Lett., 103, 023902 (2009) link to article
  • * Ultrafast conversions between hydrogen-bonded structures in liquid water observed by femtosecond x-ray spectroscopy
    H. Wen, N. Huse, R.W. Schoenlein and A.M. Lindenberg
    (submitted) (2009)
  • An "Optimal" Spawning Algorithm for Adaptive Basis Set Expansion in Nonadiabatic Dynamics
    S. Yang, J. D. Coe, B. Kaduk, and T. J. Martínez
    J. Chem. Phys., 130, 134113 (2009) link to article

    2008

  • *An amplifier concept for spintronics
    Y. Acremann, X. W. Yu, A. A. Tulapurkar, A. Scherz, V. Chembrolu, J. A. Katine, M. J. Carey, H. C. Siegmann, and J. Stöhr
    Appl. Phys. Lett. 93,102513 (2008)
  • *Magnetization dynamics: ultra-fast and ultra-small
    Y. Acremann
    Comptes Rendus Physique 9,585 (2008)
  • *Reagentless Detection of Mycobacteria tuberculosis H37Ra in Respiratory Effluents in Minutes
    K. L. Adams, P. T. Steele, M. J. Bogan, N. M. Sadler, S. I. Martin, A. N. Martin et al.
    Analytical Chemistry, 80, 5350-5357 (2008) » link to article
  • *A Camera for Coherent Diffractive Imaging and Holography with a Soft-X-ray Free Electron Laser
    S. Bajt, H. N. Chapman, E. Spiller, J. Alameda, B. W. Woods, M. Frank et al.
    Applied Optics, 47, 1673-1683 (2008) » link to article
  • *Ultrafast Single-Shot Diffraction Imaging of Nanoscale Dynamics
    A. Barty, S. Boutet, M. J. Bogan, S. Hau-Riege, S. Marchesini, K. Sokolowski-Tinten et al.
    Nature Photonics, 2, 415-419 (2008) » link to article
  • *Non-Destructive Characterization and Alignment of Aerodynamically Focused Particle Beams using Single Particle Charge Detection
    W. H. Benner*, M. J. Bogan*, U. Rohner, S. Boutet, B. Woods and M. Frank.
    Journal of Aerosol Science, 39, 917-928 (2008) » link to article
  • *Strong-field impulsive alignment in the presence of high temperatures and large centrifugal distortion
    D. W. Broege, R. N. Coffee, and P. H. Bucksbaum
    Phys. Rev. A, 78,035401 (2008) » link to article
  • *Single Particle X-ray Diffractive Imaging
    M. J. Bogan, W. H. Benner, S. Boutet, U. Rohner, M. Frank, A. Barty et al.
    Nano Letters, 8, 310-316 (2008) » link to article
  • *Ultrafast Soft X-ray Scattering and Reference-Enhanced Imaging of Weakly Scattering Nanoparticles
    S. Boutet, M. J. Bogan, A. Barty, M. Frank, W. H. Benner, S. Marchesini et al
    . Journal of Electron Spectroscopy and Related Phenomena, 166-167, 65-73 (2008) » link to article
  • *A Unified Framework for Fluctuating-Charge Models in Atom-Space and in Bond-Space
    J. Chen, D. Hundertmark, and T. J. Martínez
    J. Chem. Phys., 129, 214113 (2008) link to article
  • Ab Initio Multiple Spawning Dynamics of Excited State Intramolecular Proton Transfer: The Role of Spectroscopically Dark States
    J. D. Coe and T. J. Martínez, Mol. Phys., 106, 537-545 (2008) link to article
  • On the Extent and Connectivity of Conical Intersection Seams and the Effects of Three-State Intersections
    J. D. Coe, M. T. Ong, B. G. Levine, and T. J. Martínez
    J. Phys. Chem., 112A, 12559-12567 (2008) link to article
  • Control of Chromophore to Bath Coupling by Interferometry
    M. Fushitani, M. Bargheer, M. Gühr, H. Ibrahim and N. Schwentner
    J. Phys. B: At. Mol. Opt. Phys., 41, 074913 (2008) » link to article
  • * Formation of secondary electron cascades in single-crystalline plasma-deposited diamond upon exposure to femtosecond x-ray pulses
    M. Gabrysch, E. Marklund, J. Hajdu et al.
    J. Appl. Phys. 103, 064909 (2008). link to article
  • *Electric field induced magnetic anisotropy in a ferromagnet
    S.J. Gamble, M.H. Burkhardt, A. Kashuba, R. Allenspach, S.S.P. Parkin, H.C. Siegmann, J. Stöhr
    Phys. Rev. Lett. 102,217201 (2009)
  • Carrier-induced disordering dynamics in InSb studied with density functional perturbation theory
    P. B. Hillyard, D. A. Reis, and K. J. Gaffney
    Physical Review B, 77, 195213 (2008). link to article
  • Excited-State Dynamics of Cytosine Reveal Multiple Subpicosecond Pathways
    H. R. Hudock and T. J. Martínez
    ChemPhysChem, 9, 2486-2490 (2008) link to article
  • Valence transitions of Br2 in Ar matrices: Interaction with the lattice and predissociation
    H. Ibrahim, M. Gühr and N. Schwentner
    J. Chem. Phys., 128, 064504 (2008) » link to article
  • Electrostatic Control of Photoisomerization in the Photoactive Yellow Protein Chromophore: Ab Initio Multiple Spawning Dynamics
    C. Ko, A. Virshup, and T. J. Martínez
    Chem. Phys. Lett., 460, 272-277 (2008) link to article
  • *Pseudospectral Time Dependent Density Functional Theory
    C. Ko, D. K. Malick, D. A. Braden, R. A. Friesner, and T. J. Martínez
    J. Chem. Phys., 128, 104103 (2008) link to article
  • Implementation of Ab Initio Multiple Spawning in the MolPro Quantum Chemistry Package
    B. G. Levine, J. D. Coe, A. M. Virshup, and T. J. Martínez
    Chem. Phys., 347, 3-16 (2008) link to article
  • *Optimizing Conical Intersections Without Derivative Coupling Vectors: Application to Multi-State Multireference Second Order Perturbation Theory (MS-CASPT2)
    B. G. Levine, J. D. Coe, and T. J. Martínez, J. Phys. Chem., 112B, 405-413 (2008) link to article
  • X-ray Diffuse Scattering Measurements of Nucleation Dynamics at Femtosecond Resolution
    A. M. Lindenberg, S. Engemann, K. J. Gaffney, K. Sokolowski-Tinten, J. Larsson, P. B. Hillyard, D. A. Reis, D. M. Fritz, J. Arthur, R. A. Akre, M. J. George, A. Deb, P. H. Bucksbaum, J. Hajdu, D. A. Meyer, M. Nicoul, C. Blome, Th. Tschentscher, A. L. Cavalieri, R.W. Falcone, S. H. Lee, R. Pahl, J. Rudati, P. H. Fuoss, A. J. Nelson, P. Krejcik, D. P. Siddons, P. Lorazo, and J. B. Hastings
    Physical Review Letters, 100, 135502 (2008). link to article
  • *Massively Parallel X-ray Holography
    S. Marchesini, S. Boutet, A. E. Sakdinawat, M. J. Bogan, S. Bajt, A. Barty et al.
    Nature Photonics, 2, 560-563 (2008) » link to article
  • *High Harmonic Generation from Multiple Orbitals in N2
    B. K. McFarland, J. P. Farrell, P. H. Bucksbaum and M. Gühr
    Science, 322, 1232 (2008) » link to article
  • *Parameters Contributing to Efficient Ion Generation in Aerosol MALDI Mass Spectrometry
    E. McJimpsey, W. Jackson, C. Lebrilla, H. Tobias, M. J. Bogan, E. Gard et al.
    Journal of the American Society for Mass Spectrometry, 19, 315-324 (2008) » link to article
  • *Probing unfolded acoustic phonons with x rays
    M. Trigo, Y. M. Sheu, D. A. Arms, J. Chen, S. Ghimire, R. S. Goldman, E. Landahl, R. Merlin, E. Peterson, M. Reason, and D. A. Reis.
    Phys. Rev. Lett. 101 , 025505 (2008) » link to article
  • Wideband detection of transient solid-state dynamics using ultrafast fiber lasers and asynchronous optical sampling
    M. Trigo, Y. M. Sheu, D. A. Arms, J. Chen, S. Ghimire, R. S. Goldman, E. Landahl, R. Merlin, E. Peterson, M. Reason, and D. A. Reis.
    Opt. Express 16 , 2322-2335(2008) » link to article
  • *Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation
    I. S. Ufimtsev and T. J. Martínez
    J. Chem. Theo. Comp., 4, 222-231 (2008) link to article
  • *Graphical Processing Units for Quantum Chemistry
    I. S. Ufimtsev and T. J. Martínez
    Comp. in Sci. Eng., Invited article for "Novel Architectures" special issue, 10, 26-34 (2008) link to article
  • * Ultrafast electron cascades in semiconductors driven by intense femtosecond THz pulses
    H. Wen, M. Wiczer and A.M. Lindenberg
    Phys. Rev. B 78, 125203 (2008). link to article
  • * Measurement of high-field THz-induced photocurrents in semiconductors
    M. Wiczer and A.M. Lindenberg
    J. of Undergraduate Research, 8 (2008).

    2007

  • Coherence and control of molecular dynamics in rare gas matrices
    M. Bargheer, A. Borowski, A. Cohen, M. Fushitani, R. B. Gerber, M. Gühr, P. Hamm, H. Ibrahim, T. Kiljunen, M. V. Korolkov, O. Kühn, J. Manz, B. Schmidt, M. Schröder and N. Schwentner
    in: Analysis and Control of Ultrafast Photoinduced Reactions, edited by O. Kühn and L. Wöste (Springer, Heidelberg, 2007)
  • Dynamics of Electronic States and Spin-Flip for Photodissociation of Dihalogens in Matrices: Experiment, Semiclassical Surface-Hopping and Quantum Model Simulations for F2 and ClF in Solid Ar
    M. Bargheer, A. Cohen, R. B. Gerber, M. Gühr, M. V. Korolkov, J. Manz, M. Y. Niv, M. Schröder and N. Schwentner
    J. Phys. Chem. A., 111, 3745-3755 (2007) » link to article
  • A Continuous Spawning Method for Nonadiabatic Dynamics and Validation for the Zero-Temperature Spin-Boson Problem
    M. Ben-Nun and T. J. Martínez
    Isr. J. Chem., 47, 75-88 (2007) link to article
  • *Aerosol Sample Preparation Methods for X-ray Diffractive Imaging: Size-selected Sph erical Nanoparticles on Silicon Nitride Foils
    M. J. Bogan, W. H. Benner, S. P. Hau-Riege, H. N. Chapman and M. Frank.
    Journal of Aerosol Science, 38, 1119-1128 (2007) » link to article
  • *Online Aerosol Mass Spectrometry of Single Micrometer-Sized Particles Containing Poly(ethylene glycol)
    M. J. Bogan, E. Patton, A. Srivastava, S. Martin, D. P. Fergenson, P. T. Steele et al.
    Rapid Communications in Mass Spectrometry, 21, 1214-1220 (2007) » link to article
  • *The Future of Attosecond Spectroscopy
    P. H. Bucksbaum
    Science, 317, 766 (2007) » link to article
  • *Femtosecond Time-Delay X-ray Holography
    H. N. Chapman, S. P. Hau-Riege, M. J. Bogan, S. Bajt, A. Barty, S. Boutet et al.
    Nature, 448, 676-679 (2007) » link to article
  • *QTPIE: Charge Transfer with Polarization Current Equalization. A fluctuating charge model with correct asymptotics
    J. Chen and T. J. Martínez
    Chem. Phys. Lett., 438, 315-320 (2007) link to article
  • The Vibrationally Adiabatic Torsional Potential Energy Surface of trans-Stilbene
    P. D. Chowdary, T. J. Martínez, and M. Gruebele
    Chem. Phys. Lett., 440, 7-11 (2007) link to article
  • Ab Initio Molecular Dynamics of Excited State Proton Transfer Using Multireference Perturbation Theory
    J. D. Coe, B. G. Levine, and T. J. Martínez
    J. Phys. Chem., 111A, 11302-11310 (2007) link to article
  • * Large acoustic transients induced by non-thermal melting of InSb
    H. Enquist, H. Navarian, T.N. Hansen et al.
    Phys. Rev. Lett., 98, 225502 (2007). link to article
  • *Modular Sampling and Analysis Techniques for the Real-Time Analysis of Human Breath
    M. Frank, G. Farquar, K. Adams, M. J. Bogan, A. Martin, W. H. Benner et al.
    in Sensors, (IEEE, 2007) » link to article
  • Ultrafast Bond Softening in Bismuth: Mapping a Solid's Interatomic Potential with X-rays
    D.M. Fritz, D.A. Reis, B. Adams, R.A. Akre, J. Arthur, C. Blome, P.H. Bucksbaum, A.L. Cavalieri, S. Engemann, S. Fahy, R.W. Falcone, P.H. Fuoss, K.J. Gaffney, M.J. George, J. Hajdu, M.P. Hertlein, P.B. Hillyard, M.H.V. Hoegen, M. Kammler, J. Kaspar, R. Kienberger, P. Krejcik, S.H. Lee, A.M. Lindenberg, B. McFarland, D. Meyer, T. Montagne, E.D. Murray, A.J. Nelson, M. Nicoul, R. Pahl, J. Rudati, H. Schlarb, D.P. Siddons, K. Sokolowski-Tinten, Th. Tschentscher, D. von der Linde, J.B. Hastings
    Science 315, 633 (2007). link to article
  • * Ultrafast bond softening in Bismuth: Mapping a solid's interatomic potential with x-rays
    D.M. Fritz, D.A. Reis, B. Adams et al.
    Science, 315, 633 (2007). link to article
  • Imaging Atomic Structure and Dynamics with Ultrafast X-ray Scattering
    K.J. Gaffney and H.N. Chapman
    Science 316, 1444 (2007). link to article
  • Coherent dynamics of halogen molecules in rare gas solids
    M. Gühr
    in: Coherent vibrational dynamics, edited by S. DeSilvestri, G. Cerullo and G. Lanzani (Taylor and Francis, 2007)
  • *High harmonic generation for N2 and CO2 beyond the two point model
    M. Gühr, B. K. McFarland, J. P. Farrell and P. H. Bucksbaum
    J. Phys. B: At. Mol. Opt. Phys., 40, 3745-3755 (2007) » link to article
  • Ultrafast Dynamics of Halogens in Rare Gas Solids
    M. Gühr, M. Bargheer, M. Fushitani, T. Kiljunen and N. Schwentner
    Phys. Chem. Chem. Phys., 9, 779 - 801 (2007) » link to article
  • *Damage-Resistant Single-Pulse Optics for X-ray Free Electron Lasers
    S. P. Hau-Riege, R. A. London, M. J. Bogan, H. N. Chapman and M. Bergh.
    in Damage to VUV, EUV, and X-ray Optics.1 edn 65860T-65867 (SPIE, 2007) » link to article
  • Comparative Genomics and Site-Directed Mutagenesis Support the Existence of Only One Input Channel for Protons in the C-Family (cbb3 Oxidase) of Heme-Copper Oxygen Reductases
    J. Hemp, H. Han, J. H. Roh, S. Kaplan, T. J. Martínez, and R. B. Gennis
    Biochemistry, 46, 9963-9972 (2007) link to article
  • Carrier Density Dependent Lattice Stability in InSb
    P.B. Hillyard, K.J. Gaffney, A.M. Lindenberg, S. Engmann, R.A. Akre, J. Arthur, C. Blome, P.H. Bucksbaum, A.L. Cavalieri, A. Deb, R.W. Falcone, D.M. Fritz, P.H. Fuoss, J. Hajdu, P. Krejcik, J. Larsson, S.H. Lee, D.A. Meyer, A.J. Nelson, R. Pahl, D.A. Reis, J. Rudati, D.P. Siddons, K. Sokolowski-Tinten, D. von der Linde, J.B. Hastings
    Physical Review Letters 98, 125501 (2007). link to article
  • Ab Initio Molecular Dynamics and Time-Resolved Photoelectron Spectroscopy of Electronically Excited Uracil and Thymine
    H. R. Hudock, B. G. Levine, A. L. Thompson, H. Satzger, D. Townsend, N. Gador, S. Ullrich, A. Stolow, and T. J. Martínez,
    J. Phys. Chem., 111A, 8500-8508 (2007). link to article
  • Conformationally controlled chemistry: Excited state dynamics dictate ground state dissociation
    M. H. Kim, L. Shen, H. Tao, T. J. Martínez, and A. G. Suits
    Science, 315, 1561-1565 (2007) link to article
  • Substituent Effects on Dynamics at Conical Intersections: a,b-enones
    A. M. D. Lee, J. D. Coe, S. Ullrich, M.-L. Ho, S.-J. Lee, B.-M. Cheng, M. Z. Zgierski, I.-C. Chen, T. J. Martinez, and A. Stolow
    J. Phys. Chem., 111A, 11948-11960 (2007) link to article
  • *Isomerization Through Conical Intersections
    B. G. Levine and T. J. Martínez
    , Ann. Rev. Phys. Chem., 58, 613-634 (2007) link to article
  • * Ultrafast x-ray scattering in solids
    D. Reis and A.M. Lindenberg
    In: Light Scattering in Solids IX, edited by M. Cardona and R. Merlin, (Springer, 2007)
  • * Phonon dispersion relations and softening in photoexcited bismuth from first principles.
    E. D. Murray, S. Fahy, D. Prendergast, T. Ogitsu, D. M. Fritz, and D. A. Reis.
    Phys. Rev. B. 75 , 184301 (2007) » link to article
  • Optimization of Semiempirical Quantum Chemistry Methods via Multiobjective Genetic Algorithms: Accurate Photodynamics for Larger Molecules and Longer Time Scales
    K. Sastry, D. D. Johnson, A. L. Thompson, D. E. Goldberg, T. J. Martinez, J. Leiding, and J. Owens
    Mat. Manuf. Proc., 22, 553-561 (2007) link to article
  • *A Charged Ring Model for Classical OH-(aq) Simulations
    I. S. Ufimtsev, A. G. Kalinchev, T. J. Martínez, and R. J. Kirkpatrick
    Chem. Phys. Lett., 442, 128-133 (2007) link to article
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