He graduated with a BS in Telecom Engineering from Tecnun, Universidad de Navarra in 2009. In 2012, he received his M.Sc. in Electrical and Computer Engineering from Colorado State University’s National Science Foundation Engineering Research Center. Later he continued his joint doctoral program simultaneously at the Research Laboratory of Electronics, Massachusetts Institute of Technology and the Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, and obtained his Ph.D. in Physics in 2015. He has received several awards recognizing his contributions to ultrafast photon sciences and their application in lif and anergy sciences, including the 2021 Horizon Prize from the Royal Society of Chemistry, the 2021 SPIE Early Career Award, the Japan Society for the Promotion of Science Fellowship in 2019, SRI 2018 Young Scientist Award, and the PIER Helmholtz Foundation Dissertation Award in 2015, among others. Sergio teaches photonics, ultrafast and quantum optics, accelerator physics at UCLA and at the U.S. Particle Accelerator School. He currently holds various patents, is the author of over 100 peer-reviewed publications – including two book chapters – and has presented his work in over 60 international conferences.

Current Role at Stanford

Dr. Sergio Carbajo is an assistant professor at the UCLA Electrical & Computer Engineering (ECE) and the UCLA Physics & Astronomy departments and visiting professor at Stanford University’s Photon Science Division at SLAC National Accelerator Laboratory. He is the founder and director of the Quantum Light-Matter Cooperative, a scientific consortium whose mission is to understand, design, and ultimately control light-driven physical processes to help solve interconnected socio-technological challenges.

Photon sciences and technologies establish the building blocks for myriad scientific and engineering frontiers in life and energy sciences. Because of this overarching functionality, the Quantum Light-Matter Cooperative’s areas of study include life sciences, biochemistry, quantum optics, and information sciences, and environmental and chemical engineering. The cooperative seeks to help solve major life and energy challenges by examining the cooperative interaction between photons and matter, and its methodologies are informed by a critically interdisciplinary approach to the science and applications of light by design. He is an active faculty member of the California NanoSystems Institute and the Center for Quantum Science and Engineering. Photon and particle sources are powerful tools with extremely high societal impact because they underpin myriad groundbreaking scientific, technological, and medical advancements. X-ray free electron lasers (XFEL) are the flagship of these instruments, which in the relatively short time since their advent have demonstrated the capacity to reveal conformational dynamics in biomolecules and ultrafast chemistry at atomic-level spatial and femtosecond temporal resolutions. Motivated by this overarching relevance, Sergio has nurtured a research career that is founded on the unification of quantum and nonlinear optics and laser-matter interactions to develop instruments capable of tackling grand fundamental questions in physics, chemistry, and biology. At SLAC, Prof. Carbajo bridges expertise across disciplines in photon sciences and accelerator physics for the advancement of next-generation XFEL technology and science, namely LCLS and LCLS-II science and instrumentation, collaboratively with faculty, post-doctoral fellows, graduate students, technicians, and engineers from various directorates at SLAC and departments at Stanford.

Prof. Carbajo is also the Director of Diversity at the UCLA ECE department and the founder and director of the Queered Science and Technology Center (QSTC) at UCLA. He is laying a ground-breaking framework to address overarching issues of diversity and critical representation in STEM through queer, radical feminist, and black analyses of the impact of science & technology in society. The QSTC employs this critical framework to destabilize sexual, gendered, racialized, anthropocentric, and able-bodies logics and hierarchies in challenging and rethinking knowledge production, as a scientific exercise and introduces new methodological resources for critical interdisciplinarity in traditional STEM studies. In this capacity, he has the opportunity to recruit outstanding faculty, staff, and students, create an exciting and diverse intellectual and educational community; strategically seek out new opportunities in research and education; foster new interdisciplinary connections across campus; and actively empower involvement of (future) STEM workforce, particularly those from underrepresented backgrounds, to affect social change that is representative of the public’s interests. Partnered with non-profit institutions, he participates in several University, county and state, and federal-level sponsored programs tailored to promote equity in STEM fields through action in distinct areas of sciences and engineering.

All Publications

  • Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography. Nature chemistry Wolff, A. M., Nango, E., Young, I. D., Brewster, A. S., Kubo, M., Nomura, T., Sugahara, M., Owada, S., Barad, B. A., Ito, K., Bhowmick, A., Carbajo, S., Hino, T., Holton, J. M., Im, D., O'Riordan, L. J., Tanaka, T., Tanaka, R., Sierra, R. G., Yumoto, F., Tono, K., Iwata, S., Sauter, N. K., Fraser, J. S., Thompson, M. C. 2023


    Understanding and controlling protein motion at atomic resolution is a hallmark challenge for structural biologists and protein engineers because conformational dynamics are essential for complex functions such as enzyme catalysis and allosteric regulation. Time-resolved crystallography offers a window into protein motions, yet without a universal perturbation to initiate conformational changes the method has been limited in scope. Here we couple a solvent-based temperature jump with time-resolved crystallography to visualize structural motions in lysozyme, a dynamic enzyme. We observed widespread atomic vibrations on the nanosecond timescale, which evolve on the submillisecond timescale into localized structural fluctuations that are coupled to the active site. An orthogonal perturbation to the enzyme, inhibitor binding, altered these dynamics by blocking key motions that allow energy to dissipate from vibrations into functional movements linked to the catalytic cycle. Because temperature jump is a universal method for perturbing molecular motion, the method demonstrated here is broadly applicable for studying protein dynamics.

    View details for DOI 10.1038/s41557-023-01329-4

    View details for PubMedID 37723259

  • Detection of a Geminate Photoproduct of Bovine Cytochrome c Oxidase by Time-Resolved Serial Femtosecond Crystallography. Journal of the American Chemical Society Ishigami, I., Carbajo, S., Zatsepin, N., Hikita, M., Conrad, C. E., Nelson, G., Coe, J., Basu, S., Grant, T., Seaberg, M. H., Sierra, R. G., Hunter, M. S., Fromme, P., Fromme, R., Rousseau, D. L., Yeh, S. R. 2023


    Cytochrome c oxidase (CcO) is a large membrane-bound hemeprotein that catalyzes the reduction of dioxygen to water. Unlike classical dioxygen binding hemeproteins with a heme b group in their active sites, CcO has a unique binuclear center (BNC) composed of a copper atom (CuB) and a heme a3 iron, where O2 binds and is reduced to water. CO is a versatile O2 surrogate in ligand binding and escape reactions. Previous time-resolved spectroscopic studies of the CO complexes of bovine CcO (bCcO) revealed that photolyzing CO from the heme a3 iron leads to a metastable intermediate (CuB-CO), where CO is bound to CuB, before it escapes out of the BNC. Here, with a pump-probe based time-resolved serial femtosecond X-ray crystallography, we detected a geminate photoproduct of the bCcO-CO complex, where CO is dissociated from the heme a3 iron and moved to a temporary binding site midway between the CuB and the heme a3 iron, while the locations of the two metal centers and the conformation of Helix-X, housing the proximal histidine ligand of the heme a3 iron, remain in the CO complex state. This new structure, combined with other reported structures of bCcO, allows for a clearer definition of the ligand dissociation trajectory as well as the associated protein dynamics.

    View details for DOI 10.1021/jacs.3c07803

    View details for PubMedID 37695261

  • Optical control of ultrafast structural dynamics in a fluorescent protein. Nature chemistry Hutchison, C. D., Baxter, J. M., Fitzpatrick, A., Dorlhiac, G., Fadini, A., Perrett, S., Maghlaoui, K., Lefevre, S. B., Cordon-Preciado, V., Ferreira, J. L., Chukhutsina, V. U., Garratt, D., Barnard, J., Galinis, G., Glencross, F., Morgan, R. M., Stockton, S., Taylor, B., Yuan, L., Romei, M. G., Lin, C., Marangos, J. P., Schmidt, M., Chatrchyan, V., Buckup, T., Morozov, D., Park, J., Park, S., Eom, I., Kim, M., Jang, D., Choi, H., Hyun, H., Park, G., Nango, E., Tanaka, R., Owada, S., Tono, K., DePonte, D. P., Carbajo, S., Seaberg, M., Aquila, A., Boutet, S., Barty, A., Iwata, S., Boxer, S. G., Groenhof, G., van Thor, J. J. 2023


    The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump-probe X-ray crystallography reveals complex sub-angstrom, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.

    View details for DOI 10.1038/s41557-023-01275-1

    View details for PubMedID 37563326

  • Rational Control of Off-State Heterogeneity in a Photoswitchable Fluorescent Protein Provides Switching Contrast Enhancement. Chemphyschem : a European journal of chemical physics and physical chemistry Adam, V., Hadjidemetriou, K., Jensen, N., Shoeman, R. L., Woodhouse, J., Aquila, A., Banneville, A., Barends, T. R., Bezchastnov, V., Boutet, S., Byrdin, M., Cammarata, M., Carbajo, S., Eleni Christou, N., Coquelle, N., De la Mora, E., El Khatib, M., Moreno Chicano, T., Bruce Doak, R., Fieschi, F., Foucar, L., Glushonkov, O., Gorel, A., Grunbein, M. L., Hilpert, M., Hunter, M., Kloos, M., Koglin, J. E., Lane, T. J., Liang, M., Mantovanelli, A., Nass, K., Nass Kovacs, G., Owada, S., Roome, C. M., Schiro, G., Seaberg, M., Stricker, M., Thepaut, M., Tono, K., Ueda, K., Uriarte, L. M., You, D., Zala, N., Domratcheva, T., Jakobs, S., Sliwa, M., Schlichting, I., Colletier, J., Bourgeois, D., Weik, M. 2022: e202200192


    Reversibly photoswitchable fluorescent proteins are essential markers for advanced biological imaging, and optimization of their photophysical properties underlies improved performance and novel applications. Here we establish a link between photoswitching contrast, one of the key parameters that dictate the achievable resolution in nanoscopy applications, and chromophore conformation in the non-fluorescent state of rsEGFP2, a widely employed label in REversible Saturable OpticaL Fluorescence Transitions (RESOLFT) microscopy. Upon illumination, the cis chromophore of rsEGFP2 isomerizes to two distinct off-state conformations, trans1 and trans2, located on either side of the V151 side chain. Reducing or enlarging the side chain at this position (V151A and V151L variants) leads to single off-state conformations that exhibit higher and lower switching contrast, respectively, compared to the rsEGFP2 parent. The combination of structural information obtained by serial femtosecond crystallography with high-level quantum chemical calculations and with spectroscopic and photophysical data determined in vitro suggests that the changes in switching contrast arise from blue- and red-shifts of the absorption bands associated to trans1 and trans2, respectively. Thus, due to elimination of trans2, the V151A variants of rsEGFP2 and its superfolding variant rsFolder2 display a more than two-fold higher switching contrast than their respective parent proteins, both in vitro and in E. coli cells. The application of the rsFolder2-V151A variant is demonstrated in RESOLFT nanoscopy. Our study rationalizes the connection between structural and photophysical chromophore properties and suggests a means to rationally improve fluorescent proteins for nanoscopy applications.

    View details for DOI 10.1002/cphc.202200192

    View details for PubMedID 35959919

  • Phase retrieval and reconstruction of coherent synthesis by genetic algorithm JOURNAL OF PHYSICS-PHOTONICS Lemons, R., Carbajo, S. 2022; 4 (2)
  • Temporal shaping of narrow-band picosecond pulses via noncolinear sum-frequency mixing of dispersion-controlled pulses PHYSICAL REVIEW ACCELERATORS AND BEAMS Lemons, R., Neveu, N., Duris, J., Marinelli, A., Durfee, C., Carbajo, S. 2022; 25 (1)
  • Structural dynamics in the water and proton channels of photosystem II during the S2 to S3 transition. Nature communications Hussein, R., Ibrahim, M., Bhowmick, A., Simon, P. S., Chatterjee, R., Lassalle, L., Doyle, M., Bogacz, I., Kim, I., Cheah, M. H., Gul, S., de Lichtenberg, C., Chernev, P., Pham, C. C., Young, I. D., Carbajo, S., Fuller, F. D., Alonso-Mori, R., Batyuk, A., Sutherlin, K. D., Brewster, A. S., Bolotovsky, R., Mendez, D., Holton, J. M., Moriarty, N. W., Adams, P. D., Bergmann, U., Sauter, N. K., Dobbek, H., Messinger, J., Zouni, A., Kern, J., Yachandra, V. K., Yano, J. 2021; 12 (1): 6531


    Light-driven oxidation of water to molecular oxygen is catalyzed by the oxygen-evolving complex (OEC) in Photosystem II (PS II). This multi-electron, multi-proton catalysis requires the transport of two water molecules to and four protons from the OEC. A high-resolution 1.89A structure obtained by averaging all the S states and refining the data of various time points during the S2 to S3 transition has provided better visualization of the potential pathways for substrate water insertion and proton release. Our results indicate that the O1 channel is the likely water intake pathway, and the Cl1 channel is the likely proton release pathway based on the structural rearrangements of water molecules and amino acid side chains along these channels. In particular in the Cl1 channel, we suggest that residue D1-E65 serves as a gate for proton transport by minimizing the back reaction. The results show that the water oxidation reaction at the OEC is well coordinated with the amino acid side chains and the H-bonding network over the entire length of the channels, whichis essential in shuttling substrate waters and protons.

    View details for DOI 10.1038/s41467-021-26781-z

    View details for PubMedID 34764256

  • Light by design: emerging frontiers in ultrafast photon sciences and light-matter interactions JOURNAL OF PHYSICS-PHOTONICS Carbajo, S. 2021; 3 (3)
  • Early-stage dynamics of chloride ion-pumping rhodopsin revealed by a femtosecond X-ray laser PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Yun, J., Li, X., Yue, J., Park, J., Jin, Z., Li, C., Hu, H., Shi, Y., Pandey, S., Carbajo, S., Boutet, S., Hunter, M. S., Liang, M., Sierra, R. G., Lane, T. J., Zhou, L., Weierstall, U., Zatsepin, N. A., Ohki, M., Tame, J. H., Park, S., Spence, J. H., Zhang, W., Schmidt, M., Lee, W., Liu, H. 2021; 118 (13)
  • Early-stage dynamics of chloride ion-pumping rhodopsin revealed by a femtosecond X-ray laser. Proceedings of the National Academy of Sciences of the United States of America Yun, J., Li, X., Yue, J., Park, J., Jin, Z., Li, C., Hu, H., Shi, Y., Pandey, S., Carbajo, S., Boutet, S., Hunter, M. S., Liang, M., Sierra, R. G., Lane, T. J., Zhou, L., Weierstall, U., Zatsepin, N. A., Ohki, M., Tame, J. R., Park, S., Spence, J. C., Zhang, W., Schmidt, M., Lee, W., Liu, H. 2021; 118 (13)


    Chloride ion-pumping rhodopsin (ClR) in some marine bacteria utilizes light energy to actively transport Cl- into cells. How the ClR initiates the transport is elusive. Here, we show the dynamics of ion transport observed with time-resolved serial femtosecond (fs) crystallography using the Linac Coherent Light Source. X-ray pulses captured structural changes in ClR upon flash illumination with a 550 nm fs-pumping laser. High-resolution structures for five time points (dark to 100 ps after flashing) reveal complex and coordinated dynamics comprising retinal isomerization, water molecule rearrangement, and conformational changes of various residues. Combining data from time-resolved spectroscopy experiments and molecular dynamics simulations, this study reveals that the chloride ion close to the Schiff base undergoes a dissociation-diffusion process upon light-triggered retinal isomerization.

    View details for DOI 10.1073/pnas.2020486118

    View details for PubMedID 33753488

  • Observation of shock-induced protein crystal damage during megahertz serial femtosecond crystallography PHYSICAL REVIEW RESEARCH Gruenbein, M. L., Foucar, L., Gorel, A., Hilpert, M., Kloos, M., Nass, K., Kovacs, G., Roome, C. M., Shoeman, R. L., Stricker, M., Carbajo, S., Colocho, W., Gilevich, S., Hunter, M., Lewandowski, J., Lutman, A., Koglin, J. E., Lane, T. J., van Driel, T., Sheppard, J., Vetter, S. L., Turner, J. L., Doak, R., Barends, T. M., Boutet, S., Aquila, A. L., Decker, F., Schlichting, I., Stan, C. A. 2021; 3 (1)
  • Integrated structured light architectures. Scientific reports Lemons, R., Liu, W., Frisch, J. C., Fry, A., Robinson, J., Smith, S. R., Carbajo, S. 2021; 11 (1): 796


    The structural versatility of light underpins an outstanding collection of optical phenomena where both geometrical and topological states of light can dictate how matter will respond or display. Light possesses multiple degrees of freedom such as amplitude, and linear, spin angular, and orbital angular momenta, but the ability to adaptively engineer the spatio-temporal distribution of all these characteristics is primarily curtailed by technologies used to impose any desired structure to light. We demonstrate a laser architecture based on coherent beam combination offering integrated spatio-temporal field control and programmability, thereby presenting unique opportunities for generating light by design to exploit its topology.

    View details for DOI 10.1038/s41598-020-80502-y

    View details for PubMedID 33436972

  • Effect of X-ray free-electron laser-induced shockwaves on haemoglobin microcrystals delivered in a liquid jet. Nature communications Grünbein, M. L., Gorel, A. n., Foucar, L. n., Carbajo, S. n., Colocho, W. n., Gilevich, S. n., Hartmann, E. n., Hilpert, M. n., Hunter, M. n., Kloos, M. n., Koglin, J. E., Lane, T. J., Lewandowski, J. n., Lutman, A. n., Nass, K. n., Nass Kovacs, G. n., Roome, C. M., Sheppard, J. n., Shoeman, R. L., Stricker, M. n., van Driel, T. n., Vetter, S. n., Doak, R. B., Boutet, S. n., Aquila, A. n., Decker, F. J., Barends, T. R., Stan, C. A., Schlichting, I. n. 2021; 12 (1): 1672


    X-ray free-electron lasers (XFELs) enable obtaining novel insights in structural biology. The recently available MHz repetition rate XFELs allow full data sets to be collected in shorter time and can also decrease sample consumption. However, the microsecond spacing of MHz XFEL pulses raises new challenges, including possible sample damage induced by shock waves that are launched by preceding pulses in the sample-carrying jet. We explored this matter with an X-ray-pump/X-ray-probe experiment employing haemoglobin microcrystals transported via a liquid jet into the XFEL beam. Diffraction data were collected using a shock-wave-free single-pulse scheme as well as the dual-pulse pump-probe scheme. The latter, relative to the former, reveals significant degradation of crystal hit rate, diffraction resolution and data quality. Crystal structures extracted from the two data sets also differ. Since our pump-probe attributes were chosen to emulate EuXFEL operation at its 4.5 MHz maximum pulse rate, this prompts concern about such data collection.

    View details for DOI 10.1038/s41467-021-21819-8

    View details for PubMedID 33723266

  • Structured Photonics in Light-Matter Interactions, Accelerators, and X-ray Lasers Carbajo, S., IEEE IEEE. 2021
  • Nonlinearly Shaped Pulses in the LCLS-II Photoinjector Neveu, N., Lemons, R., Duris, J., Ding, Y., Marinelli, A., Mayes, C., Durfee, C., Carbajo, S., IEEE IEEE. 2021
  • Femtosecond Slicing for the MHz Repetition Rate LCLS-II X-ray Free Electron Laser Duris, J., Lemons, R., Zhang, Z., Ding, Y., Marinelli, A., Carbajo, S., IEEE IEEE. 2021
  • Towards Real-time Adaptable Machine Learning-based Photoinjector Shaping Hirschman, J., Lemons, R., Coffee, R., Belli, F., Carbajo, S., IEEE IEEE. 2021
  • Ultrafast X-ray scattering offers a structural view of excited-state charge transfer. Proceedings of the National Academy of Sciences of the United States of America Yong, H. n., Xu, X. n., Ruddock, J. M., Stankus, B. n., Carrascosa, A. M., Zotev, N. n., Bellshaw, D. n., Du, W. n., Goff, N. n., Chang, Y. n., Boutet, S. n., Carbajo, S. n., Koglin, J. E., Liang, M. n., Robinson, J. S., Kirrander, A. n., Minitti, M. P., Weber, P. M. 2021; 118 (19)


    Intramolecular charge transfer and the associated changes in molecular structure in N,N'-dimethylpiperazine are tracked using femtosecond gas-phase X-ray scattering. The molecules are optically excited to the 3p state at 200 nm. Following rapid relaxation to the 3s state, distinct charge-localized and charge-delocalized species related by charge transfer are observed. The experiment determines the molecular structure of the two species, with the redistribution of electron density accounted for by a scattering correction factor. The initially dominant charge-localized state has a weakened carbon-carbon bond and reorients one methyl group compared with the ground state. Subsequent charge transfer to the charge-delocalized state elongates the carbon-carbon bond further, creating an extended 1.634 Å bond, and also reorients the second methyl group. At the same time, the bond lengths between the nitrogen and the ring-carbon atoms contract from an average of 1.505 to 1.465 Å. The experiment determines the overall charge transfer time constant for approaching the equilibrium between charge-localized and charge-delocalized species to 3.0 ps.

    View details for DOI 10.1073/pnas.2021714118

    View details for PubMedID 33947814

  • Ultrafast structural changes within a photosynthetic reaction centre. Nature Dods, R., Bath, P., Morozov, D., Gagner, V. A., Arnlund, D., Luk, H. L., Kubel, J., Maj, M., Vallejos, A., Wickstrand, C., Bosman, R., Beyerlein, K. R., Nelson, G., Liang, M., Milathianaki, D., Robinson, J., Harimoorthy, R., Berntsen, P., Malmerberg, E., Johansson, L., Andersson, R., Carbajo, S., Claesson, E., Conrad, C. E., Dahl, P., Hammarin, G., Hunter, M. S., Li, C., Lisova, S., Royant, A., Safari, C., Sharma, A., Williams, G. J., Yefanov, O., Westenhoff, S., Davidsson, J., DePonte, D. P., Boutet, S., Barty, A., Katona, G., Groenhof, G., Branden, G., Neutze, R. 2020


    Photosynthetic reaction centres harvest the energy content of sunlight by transporting electrons across an energy-transducing biological membrane. Here we use time-resolved serial femtosecond crystallography1 using an X-ray free-electron laser2 to observe light-induced structural changes in the photosynthetic reaction centre of Blastochloris viridis on a timescale of picoseconds. Structural perturbations first occur at the special pair of chlorophyll molecules of the photosynthetic reaction centre that are photo-oxidized by light. Electron transfer to the menaquinone acceptor on the opposite side of the membrane induces a movement of this cofactor together with lower amplitude protein rearrangements. These observations reveal how proteins use conformational dynamics to stabilize the charge-separation steps of electron-transfer reactions.

    View details for DOI 10.1038/s41586-020-3000-7

    View details for PubMedID 33268896

  • Long-term hybrid stabilization of the carrier-envelope phase OPTICS EXPRESS Hirschman, J., Lemons, R., Chansky, E., Steinmeyer, G., Carbajo, S. 2020; 28 (23): 34093–103


    Controlling the carrier envelope phase (CEP) in mode-locked lasers over practically long timescales is crucial for real-world applications in ultrafast optics and precision metrology. We present a hybrid solution that combines a feed-forward technique to stabilize the phase offset in fast timescales and a feedback technique that addresses slowly varying sources of interference and locking bandwidth limitations associated with gain media with long upper-state lifetimes. We experimentally realize the hybrid stabilization system in an Er:Yb:glass mode-locked laser and demonstrate 75 hours of stabilization with integrated phase noise of 14 mrad (1 Hz to 3 MHz), corresponding to around 11 as of carrier to envelope jitter. Additionally, we examine the impact of environmental factors, such as humidity and pressure, on the long-term stability and performance of the system.

    View details for DOI 10.1364/OE.400321

    View details for Web of Science ID 000589869600027

    View details for PubMedID 33182886

  • Untangling the sequence of events during the S2 S3 transition in photosystem II and implications for the water oxidation mechanism. Proceedings of the National Academy of Sciences of the United States of America Ibrahim, M., Fransson, T., Chatterjee, R., Cheah, M. H., Hussein, R., Lassalle, L., Sutherlin, K. D., Young, I. D., Fuller, F. D., Gul, S., Kim, I., Simon, P. S., de Lichtenberg, C., Chernev, P., Bogacz, I., Pham, C. C., Orville, A. M., Saichek, N., Northen, T., Batyuk, A., Carbajo, S., Alonso-Mori, R., Tono, K., Owada, S., Bhowmick, A., Bolotovsky, R., Mendez, D., Moriarty, N. W., Holton, J. M., Dobbek, H., Brewster, A. S., Adams, P. D., Sauter, N. K., Bergmann, U., Zouni, A., Messinger, J., Kern, J., Yachandra, V. K., Yano, J. 2020


    In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S1, S2, S3, and S0, showing that a water molecule is inserted during the S2 S3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S2 S3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, QA and QB, are observed. At the donor site, tyrosine YZ and His190 H-bonded to it move by 50 s after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of OX(H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a "water wheel"-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (tau of 350 s) during the S2 S3 transition mirrors the appearance of OX electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.

    View details for DOI 10.1073/pnas.2000529117

    View details for PubMedID 32434915

  • Observation of the molecular response to light upon photoexcitation. Nature communications Yong, H., Zotev, N., Ruddock, J. M., Stankus, B., Simmermacher, M., Carrascosa, A. M., Du, W., Goff, N., Chang, Y., Bellshaw, D., Liang, M., Carbajo, S., Koglin, J. E., Robinson, J. S., Boutet, S., Minitti, M. P., Kirrander, A., Weber, P. M. 2020; 11 (1): 2157


    When a molecule interacts with light, its electrons can absorb energy from the electromagnetic field by rapidly rearranging their positions. This constitutes the first step of photochemical and photophysical processes that include primary events in human vision and photosynthesis. Here, we report the direct measurement of the initial redistribution of electron density when the molecule 1,3-cyclohexadiene (CHD) is optically excited. Our experiments exploit the intense, ultrashort hard x-ray pulses of the Linac Coherent Light Source (LCLS) to map the change in electron density using ultrafast x-ray scattering. The nature of the excited electronic state is identified with excellent spatial resolution and in good agreement with theoretical predictions. The excited state electron density distributions are thus amenable to direct experimental observation.

    View details for DOI 10.1038/s41467-020-15680-4

    View details for PubMedID 32358535

  • Laguerre-Gaussian Mode Laser Heater for Microbunching Instability Suppression in Free-Electron Lasers. Physical review letters Tang, J., Lemons, R., Liu, W., Vetter, S., Maxwell, T., Decker, F. J., Lutman, A., Krzywinski, J., Marcus, G., Moeller, S., Huang, Z., Ratner, D., Carbajo, S. 2020; 124 (13): 134801


    Microbunching instability (MBI) driven by beam collective effects is known to be detrimental to high-brightness storage rings, linacs, and free-electron lasers (FELs). One known way to suppress this instability is to induce a small amount of energy spread to an electron beam by a laser heater. The distribution of the induced energy spread greatly affects MBI suppression and can be controlled by shaping the transverse profile of the heater laser. Here, we present the first experimental demonstration of effective MBI suppression using a LG_{01} transverse laser mode and compare the improved results with respect to traditional Gaussian transverse laser mode at the Linac Coherent Light Source. The effects on MBI suppression are characterized by multiple downstream measurements, including longitudinal phase space analysis and coherent radiation spectroscopy. We also discuss the role of LG_{01} shaping in soft x-ray self-seeded FEL emission, one of the most advanced operation modes of a FEL for which controlled suppression of MBI is critical.

    View details for DOI 10.1103/PhysRevLett.124.134801

    View details for PubMedID 32302180

  • Laguerre-Gaussian Mode Laser Heater for Microbunching Instability Suppression in Free-Electron Lasers PHYSICAL REVIEW LETTERS Tang, J., Liu, W., Lemons, R., Vetter, S., Maxwell, T., Decker, F., Lutman, A., Krzywinski, J., Marcus, G., Moeller, S., Ratner, D., Huang, Z., Carbajo, S. 2020; 124 (13)
  • Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals. IUCrJ Wolff, A. M., Young, I. D., Sierra, R. G., Brewster, A. S., Martynowycz, M. W., Nango, E., Sugahara, M., Nakane, T., Ito, K., Aquila, A., Bhowmick, A., Biel, J. T., Carbajo, S., Cohen, A. E., Cortez, S., Gonzalez, A., Hino, T., Im, D., Koralek, J. D., Kubo, M., Lazarou, T. S., Nomura, T., Owada, S., Samelson, A. J., Tanaka, T., Tanaka, R., Thompson, E. M., van den Bedem, H., Woldeyes, R. A., Yumoto, F., Zhao, W., Tono, K., Boutet, S., Iwata, S., Gonen, T., Sauter, N. K., Fraser, J. S., Thompson, M. C. 2020; 7 (Pt 2): 306–23


    Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme.

    View details for DOI 10.1107/S205225252000072X

    View details for PubMedID 32148858

  • Single-Digit Attosecond Carrier-Envelope Phase Stabilization of an Er:Yb:Glass Laser with Feed-Forward Technique Lemons, R., Liu, W., De Fuentes, I., Droste, S., Steinmeyer, G., Durfee, C. G., Carbajo, S., IEEE IEEE. 2020
  • The LCLS-II Photo-Injector Drive Laser System Gilevich, S., Alverson, S., Carbajo, S., Droste, S., Edstrom, S., Fry, A., Greenberg, M., Lemons, R., Miahnahri, A., Polzin, W., Vetter, S., Zhou, F., IEEE IEEE. 2020
  • Optimization of Simulated Coherent Combination System Using Fourier Optics Based Genetic Algorithm Lemons, R., Carbajo, S., IEEE IEEE. 2020
  • Carrier-envelope phase stabilization of an Er:Yb:glass laser via a feed-forward technique OPTICS LETTERS Lemons, R., Liu, W., de Fuentes, I., Droste, S., Steinmeyer, G., Durfee, C. G., Carbajo, S. 2019; 44 (22): 5610–13


    Few-cycle pulsed laser technology highlights the need for control and stabilization of the carrier-envelope phase (CEP) for applications requiring shot-to-shot timing and phase consistency. This general requirement has been achieved successfully in a number of free-space and fiber lasers via feedback and feed-forward (FF) methods. Expanding on existing results, we demonstrate CEP stabilization through the FF method applied to a SESAM mode-locked Er:Yb:glass laser at 1.55 μm with a measured ultralow timing jitter of 2.9 as (1-3 MHz) and long-term stabilization over a duration of 8 h. Single-digit attosecond stabilization at telecom wavelengths opens a new direction in applications requiring ultra-stable frequency and time precision such as high-resolution spectroscopy and fiber timing networks.

    View details for DOI 10.1364/OL.44.005610

    View details for Web of Science ID 000496981500057

    View details for PubMedID 31730119

  • Editorial: Lasers in Accelerator Science and Secondary Emission Light Source Technology FRONTIERS IN PHYSICS Carbajo, S., Fallahi, A., Faure, J., Wong, L. 2019; 7
  • Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin NATURE COMMUNICATIONS Kovacs, G., Colletier, J., Gruenbein, M., Yang, Y., Stensitzki, T., Batyuk, A., Carbajo, S., Doak, R., Ehrenberg, D., Foucar, L., Gasper, R., Gorel, A., Hilpert, M., Kloos, M., Koglin, J. E., Reinstein, J., Roome, C. M., Schlesinger, R., Seaberg, M., Shoeman, O. L., Stricker, M., Boutet, S., Haacke, S., Heberle, J., Heyne, K., Domratcheva, T., Barends, T. M., Schlichting, I. 2019; 10: 3177


    Bacteriorhodopsin (bR) is a light-driven proton pump. The primary photochemical event upon light absorption is isomerization of the retinal chromophore. Here we used time-resolved crystallography at an X-ray free-electron laser to follow the structural changes in multiphoton-excited bR from 250 femtoseconds to 10 picoseconds. Quantum chemistry and ultrafast spectroscopy were used to identify a sequential two-photon absorption process, leading to excitation of a tryptophan residue flanking the retinal chromophore, as a first manifestation of multiphoton effects. We resolve distinct stages in the structural dynamics of the all-trans retinal in photoexcited bR to a highly twisted 13-cis conformation. Other active site sub-picosecond rearrangements include correlated vibrational motions of the electronically excited retinal chromophore, the surrounding amino acids and water molecules as well as their hydrogen bonding network. These results show that this extended photo-active network forms an electronically and vibrationally coupled system in bR, and most likely in all retinal proteins.

    View details for DOI 10.1038/s41467-019-10758-0

    View details for Web of Science ID 000475852900020

    View details for PubMedID 31320619

    View details for PubMedCentralID PMC6639342

  • Ultrafast X-ray scattering reveals vibrational coherence following Rydberg excitation. Nature chemistry Stankus, B., Yong, H., Zotev, N., Ruddock, J. M., Bellshaw, D., Lane, T. J., Liang, M., Boutet, S., Carbajo, S., Robinson, J. S., Du, W., Goff, N., Chang, Y., Koglin, J. E., Minitti, M. P., Kirrander, A., Weber, P. M. 2019


    The coherence and dephasing of vibrational motions of molecules constitute an integral part of chemical dynamics, influence material properties and underpin schemes to control chemical reactions. Considerable progress has been made in understanding vibrational coherence through spectroscopic measurements, but precise, direct measurement of the structure of a vibrating excited-state polyatomic organic molecule has remained unworkable. Here, we measure the time-evolving molecular structure of optically excited N-methylmorpholine through scattering with ultrashort X-ray pulses. The scattering signals are corrected for the differences in electron density in the excited electronic state of the molecule in comparison to the ground state. The experiment maps the evolution of the molecular geometry with femtosecond resolution, showing coherent motion that survives electronic relaxation and seems to persist for longer than previously seen using other methods.

    View details for DOI 10.1038/s41557-019-0291-0

    View details for PubMedID 31285542

  • Simplicity Beneath Complexity: Counting Molecular Electrons Reveals Transients and Kinetics of Photodissociation Reactions ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Ruddock, J. M., Zotev, N., Stankus, B., Yong, H., Bellshaw, D., Boutet, S., Lane, T. J., Liang, M., Carbajo, S., Du, W., Kirrander, A., Minitti, M., Weber, P. M. 2019; 58 (19): 6371–75
  • Simplicity beneath Complexity: Counting Molecular Electrons Reveals Transients and Kinetics of Photodissociation Reactions. Angewandte Chemie (International ed. in English) Ruddock, J. M., Zotev, N., Stankus, B., Yong, H., Bellshaw, D., Boutet, S., Lane, T. J., Liang, M., Carbajo, S., Du, W., Kirrander, A., Minitti, M. P., Weber, P. M. 2019


    Time-resolved pump-probe gas phase X-ray scattering signals, extrapolated to zero momentum transfer, provide a measure of the number of electrons in a system, an effect that arises from the coherent addition of elastic scattering from the electrons. This allows for the identification of reactive transients and the determination of the chemical reaction kinetics without the need for extensive scattering simulations or complicated inversion of scattering data. We examine the photodissociation reaction of trimethyl amine, and identify two reaction paths upon excitation to the 3p state at 200 nm: a fast dissociation path out of the 3p state to the dimethyl amine radical (16.6±1.2%), and a slower dissociation via internal conversion to the 3s state (83.4±1.2%). The time constants for the two reactions are 640±130 fs and 74±6 ps, respectively. In addition, it is found that the transient dimethyl amine radical has a N-C bond length of 1.45±0.02 A and a CNC bond angle of 118°±4°.

    View details for PubMedID 30866169

  • The Macromolecular Femtosecond Crystallography Instrument at the Linac Coherent Light Source JOURNAL OF SYNCHROTRON RADIATION Sierra, R. G., Batyuk, A., Sun, Z., Aquila, A., Hunter, M. S., Lane, T. J., Liang, M., Yoon, C., Alonso-Mori, R., Armenta, R., Castagna, J., Hollenbeck, M., Osier, T. O., Hayes, M., Aldrich, J., Curtis, R., Koglin, J. E., Rendahl, T., Rodriguez, E., Carbajo, S., Guillet, S., Paul, R., Hart, P., Nakahara, K., Carini, G., DeMirci, H., Dao, E., Hayes, B. M., Rao, Y. P., Chollet, M., Feng, Y., Fuller, F. D., Kupitz, C., Sato, T., Seaberg, M. H., Song, S., van Driel, T. B., Yavas, H., Zhu, D., Cohen, A. E., Wakatsuki, S., Boutet, S. 2019; 26: 346–57
  • A Simple Model for the Fields of a Chirped Laser Pulse With Application to Electron Laser Acceleration FRONTIERS IN PHYSICS Salamin, Y. I., Carbajo, S. 2019; 7
  • Simulated XUV photoelectron spectra of THz-pumped liquid water. The Journal of chemical physics Arnold, C., Inhester, L., Carbajo, S., Welsch, R., Santra, R. 2019; 150 (4): 044505


    Highly intense, sub-picosecond terahertz (THz) pulses can be used to induce ultrafast temperature jumps (T-jumps) in liquid water. A supercritical state of gas-like water with liquid density is established, and the accompanying structural changes are expected to give rise to time-dependent chemical shifts. We investigate the possibility of using extreme ultraviolet photoelectron spectroscopy as a probe for ultrafast dynamics induced by sub-picosecond THz pulses of varying intensities and frequencies. To this end, we use ab initio methods to calculate photoionization cross sections and photoelectron energies of (H2O)20 clusters embedded in an aqueous environment represented by point charges. The cluster geometries are sampled from ab initio molecular dynamics simulations modeling the THz-water interactions. We find that the peaks in the valence photoelectron spectrum are shifted by up to 0.4 eV after the pump pulse and that they are broadened with respect to unheated water. The shifts can be connected to structural changes caused by the heating, but due to saturation effects they are not sensitive enough to serve as a thermometer for T-jumped water.

    View details for PubMedID 30709301

  • Simulated XUV photoelectron spectra of THz-pumped liquid water JOURNAL OF CHEMICAL PHYSICS Arnold, C., Inhester, L., Carbajo, S., Welsch, R., Santra, R. 2019; 150 (4)

    View details for DOI 10.1063/1.5054272

    View details for Web of Science ID 000457414600063

  • Nanofocus characterization at the Coherent X-ray Imaging instrument using 2D single grating interferometry Seaberg, M. H., Aquila, A., Liang, M., Lee, H., Nagler, B., Liu, Y., Sakdinawat, A., Seiboth, F., Makita, M., Sun, Y., Signorato, R., Carbajo, S., Feng, Y., Krzywinski, J., Zhu, D., Boutet, S., Tschentscher, T., Patthey, L., Tiedtke, K., Zangrando, M. SPIE-INT SOC OPTICAL ENGINEERING. 2019

    View details for DOI 10.1117/12.2526647

    View details for Web of Science ID 000502119600002

  • Laguerre-Gaussian Mode Laser Heater for Microbunching Instability Suppression in Free Electron Lasers Tang, J., Liu, W., Lemons, R., Vetter, S., Maxwell, T., Decker, F., Lutman, A., Krzywinski, J., Marcus, G., Moeller, S., Ratner, D., Huang, Z., Carbajo, S., IEEE IEEE. 2019
  • Programmable Control of Femtosecond Structured Light Lemons, R., Liu, W., Durfee, C. G., Frisch, J. C., Smith, S., Robinson, J., Fry, A., Carbajo, S., IEEE IEEE. 2019
  • Scattering off molecules far from equilibrium. The Journal of chemical physics Yong, H. n., Ruddock, J. M., Stankus, B. n., Ma, L. n., Du, W. n., Goff, N. n., Chang, Y. n., Zotev, N. n., Bellshaw, D. n., Boutet, S. n., Carbajo, S. n., Koglin, J. E., Liang, M. n., Robinson, J. S., Kirrander, A. n., Minitti, M. P., Weber, P. M. 2019; 151 (8): 084301


    Pump-probe gas phase X-ray scattering experiments, enabled by the development of X-ray free electron lasers, have advanced to reveal scattering patterns of molecules far from their equilibrium geometry. While dynamic displacements reflecting the motion of wavepackets can probe deeply into the reaction dynamics, in many systems, the thermal excitation embedded in the molecules upon optical excitation and energy randomization can create systems that encompass structures far from the ground state geometry. For polyatomic molecular systems, large amplitude vibrational motions are associated with anharmonicity and shifts of interatomic distances, making analytical solutions using traditional harmonic approximations inapplicable. More generally, the interatomic distances in a polyatomic molecule are not independent and the traditional equations commonly used to interpret the data may give unphysical results. Here, we introduce a novel method based on molecular dynamic trajectories and illustrate it on two examples of hot, vibrating molecules at thermal equilibrium. When excited at 200 nm, 1,3-cyclohexadiene (CHD) relaxes on a subpicosecond time scale back to the reactant molecule, the dominant pathway, and to various forms of 1,3,5-hexatriene (HT). With internal energies of about 6 eV, the energy thermalizes quickly, leading to structure distributions that deviate significantly from their vibrationless equilibrium. The experimental and theoretical results are in excellent agreement and reveal that a significant contribution to the scattering signal arises from transition state structures near the inversion barrier of CHD. In HT, our analysis clarifies that previous inconsistent structural parameters determined by electron diffraction were artifacts that might have resulted from the use of inapplicable analytical equations.

    View details for DOI 10.1063/1.5111979

    View details for PubMedID 31470697

  • A deep UV trigger for ground-state ring-opening dynamics of 1,3-cyclohexadiene. Science advances Ruddock, J. M., Yong, H. n., Stankus, B. n., Du, W. n., Goff, N. n., Chang, Y. n., Odate, A. n., Carrascosa, A. M., Bellshaw, D. n., Zotev, N. n., Liang, M. n., Carbajo, S. n., Koglin, J. n., Robinson, J. S., Boutet, S. n., Kirrander, A. n., Minitti, M. P., Weber, P. M. 2019; 5 (9): eaax6625


    We explore the photo-induced kinetics of 1,3-cyclohexadiene upon excitation at 200 nm to the 3p state by ultrafast time-resolved, gas-phase x-ray scattering using the Linac Coherent Light Source. Analysis of the scattering anisotropy reveals that the excitation leads to the 3px and 3py Rydberg electronic states, which relax to the ground state with a time constant of 208 ± 11 fs. In contrast to the well-studied 266 nm excitation, at 200 nm the majority of the molecules (76 ± 3%) relax to vibrationally hot cyclohexadiene in the ground electronic state. A subsequent reaction on the ground electronic state surface leads from the hot cyclohexadiene to 1,3,5-hexatriene, with rates for the forward and backward reactions of 174 ± 13 and 355 ± 45 ps, respectively. The scattering pattern of the final hexatriene product reveals a thermal distribution of rotamers about the carbon-carbon single bonds.

    View details for DOI 10.1126/sciadv.aax6625

    View details for PubMedID 31523713

    View details for PubMedCentralID PMC6731073

  • Structure and dynamics of chloride ion pumping rhodopsin revealed by time resolved SFX and atomic molecular dynamics simulations Liu, H., Yun, J., Li, X., Park, J., Jin, Z., Shi, Y., Li, C., Hu, H., Wang, Y., Pandey, S., Carbajo, S., Zatsepin, N., Weiersta, U., Hunter, M., Liang, M., Lane, T. J., Yoon, C., Sierra, R., Marius, S., Lee, W. INT UNION CRYSTALLOGRAPHY. 2019: A375
  • The Macromolecular Femtosecond Crystallography Instrument at the Linac Coherent Light Source. Journal of synchrotron radiation Sierra, R. G., Batyuk, A. n., Sun, Z. n., Aquila, A. n., Hunter, M. S., Lane, T. J., Liang, M. n., Yoon, C. H., Alonso-Mori, R. n., Armenta, R. n., Castagna, J. C., Hollenbeck, M. n., Osier, T. O., Hayes, M. n., Aldrich, J. n., Curtis, R. n., Koglin, J. E., Rendahl, T. n., Rodriguez, E. n., Carbajo, S. n., Guillet, S. n., Paul, R. n., Hart, P. n., Nakahara, K. n., Carini, G. n., DeMirci, H. n., Dao, E. H., Hayes, B. M., Rao, Y. P., Chollet, M. n., Feng, Y. n., Fuller, F. D., Kupitz, C. n., Sato, T. n., Seaberg, M. H., Song, S. n., van Driel, T. B., Yavas, H. n., Zhu, D. n., Cohen, A. E., Wakatsuki, S. n., Boutet, S. n. 2019; 26 (Pt 2): 346–57


    The Macromolecular Femtosecond Crystallography (MFX) instrument at the Linac Coherent Light Source (LCLS) is the seventh and newest instrument at the world's first hard X-ray free-electron laser. It was designed with a primary focus on structural biology, employing the ultrafast pulses of X-rays from LCLS at atmospheric conditions to overcome radiation damage limitations in biological measurements. It is also capable of performing various time-resolved measurements. The MFX design consists of a versatile base system capable of supporting multiple methods, techniques and experimental endstations. The primary techniques supported are forward scattering and crystallography, with capabilities for various spectroscopic methods and time-resolved measurements. The location of the MFX instrument allows for utilization of multiplexing methods, increasing user access to LCLS by running multiple experiments simultaneously.

    View details for PubMedID 30855242

  • Determining Orientations of Optical Transition Dipole Moments Using Ultrafast X-ray Scattering JOURNAL OF PHYSICAL CHEMISTRY LETTERS Yong, H., Zotev, N., Stankus, B., Ruddock, J. M., Bellshaw, D., Boutet, S., Lane, T. J., Liang, M., Carbajo, S., Robinson, J. S., Du, W., Goff, N., Chang, Y., Koglin, J. E., Waters, M. J., Solling, T. I., Minitti, M. P., Kirrander, A., Weber, P. M. 2018; 9 (22): 6556–62
  • Structures of the intermediates of Kok's photosynthetic water oxidation clock. Nature Kern, J., Chatterjee, R., Young, I. D., Fuller, F. D., Lassalle, L., Ibrahim, M., Gul, S., Fransson, T., Brewster, A. S., Alonso-Mori, R., Hussein, R., Zhang, M., Douthit, L., de Lichtenberg, C., Cheah, M. H., Shevela, D., Wersig, J., Seuffert, I., Sokaras, D., Pastor, E., Weninger, C., Kroll, T., Sierra, R. G., Aller, P., Butryn, A., Orville, A. M., Liang, M., Batyuk, A., Koglin, J. E., Carbajo, S., Boutet, S., Moriarty, N. W., Holton, J. M., Dobbek, H., Adams, P. D., Bergmann, U., Sauter, N. K., Zouni, A., Messinger, J., Yano, J., Yachandra, V. K. 2018


    Inspired by the period-four oscillation in flash-induced oxygen evolution of photosystem II discovered by Joliot in 1969, Kok performed additional experiments and proposed a five-state kinetic model for photosynthetic oxygen evolution, known as Kok's S-state clock or cycle1,2. The model comprises four (meta)stable intermediates (S0, S1, S2 and S3) and one transient S4 state, which precedes dioxygen formation occurring in a concerted reaction from two water-derived oxygens bound at an oxo-bridged tetra manganese calcium (Mn4CaO5) cluster in the oxygen-evolving complex3-7. This reaction is coupled to the two-step reduction and protonation of the mobile plastoquinone QB at the acceptor side of PSII. Here, using serial femtosecond X-ray crystallography and simultaneous X-ray emission spectroscopy with multi-flash visible laser excitation at room temperature, we visualize all (meta)stable states of Kok's cycle as high-resolution structures (2.04-2.08A). In addition, we report structures of two transient states at 150 and 400s, revealing notable structural changes including the binding of one additional 'water', Ox, during the S2S3 state transition. Our results suggest that one water ligand to calcium (W3) is directly involved in substrate delivery. The binding of the additional oxygen Ox in the S3 state between Ca and Mn1 supports O-O bond formation mechanisms involving O5 as one substrate, where Ox is either the other substrate oxygen or is perfectly positioned to refill the O5 position during O2 release. Thus, our results exclude peroxo-bond formation in the S3 state, and the nucleophilic attack of W3 onto W2 is unlikely.

    View details for DOI 10.1038/s41586-018-0681-2

    View details for PubMedID 30405241

  • Laguerre-Gaussian and beamlet array as second generation laser heater profiles PHYSICAL REVIEW ACCELERATORS AND BEAMS Liebster, N., Tang, J., Ratner, D., Liu, W., Vetter, S., Huang, Z., Carbajo, S. 2018; 21 (9)
  • Self-consistent internal calibration of x-ray scattering patterns from polarized radiation sources Goff, N., Stankus, B., Ruddock, J., Zhang, Y., Lane, T., Liang, M., Boutet, S., Carbajo, S., Robinson, J., Koglin, J., Aquila, A., Minitti, M., Weber, P. AMER CHEMICAL SOC. 2018
  • Deconvoluting the isotropic and anisotropic ultrafast x-ray scattering of gas-phase N-methylmorpholine following Rydberg excitation Stankus, B., Ruddock, J., Yong, H., Zotev, N., Bellshaw, D., Lane, T., Boutet, S., Liang, M., Carbajo, S., Robinson, J., Koglin, J., Aquila, A., Zhang, Y., Du, W., Goff, N., Chang, Y., Minitti, M., Kirrander, A., Weber, P. AMER CHEMICAL SOC. 2018
  • Laser power meters as an X-ray power diagnostic for LCLS-II Heimann, P., Moeller, S., Carbajo, S., Song, S., Dakovski, G., Nordlund, D., Fritz, D. INT UNION CRYSTALLOGRAPHY. 2018: 72–76


    For the LCLS-II X-ray instruments, laser power meters are being developed as compact X-ray power diagnostics to operate at soft and tender X-ray photon energies. These diagnostics can be installed at various locations along an X-ray free-electron laser (FEL) beamline in order to monitor the transmission of X-ray optics along the beam path. In addition, the power meters will be used to determine the absolute X-ray power at the endstations. Here, thermopile power meters, which measure average power, and have been chosen primarily for their compatibility with the high repetition rates at LCLS-II, are evaluated. A number of characteristics in the soft X-ray range are presented including linearity, calibrations conducted with a photodiode and a gas monitor detector as well as ultra-high-vacuum compatibility tests using residual gas analysis. The application of these power meters for LCLS-II and other X-ray FEL sources is discussed.

    View details for DOI 10.1107/S1600577517014096

    View details for Web of Science ID 000418593300012

    View details for PubMedID 29271754

    View details for PubMedCentralID PMC5741121

  • Power handling for LCoS spatial light modulators Carbajo, S., Bauchert, K., Kudryashov, A. V., Paxton, A. H., Ilchenko, V. S. SPIE-INT SOC OPTICAL ENGINEERING. 2018

    View details for DOI 10.1117/12.2288516

    View details for Web of Science ID 000453289100039

  • Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography NATURE CHEMISTRY Coquelle, N., Sliwa, M., Woodhouse, J., Schiro, G., Adam, V., Aquila, A., Barends, T. M., Boutet, S., Byrdin, M., Carbajo, S., De la Mora, E., Doak, R., Feliks, M., Fieschi, F., Foucar, L., Guillon, V., Hilpert, M., Hunter, M. S., Jakobs, S., Koglin, J. E., Kovacsova, G., Lane, T. J., Levy, B., Liang, M., Nass, K., Ridard, J., Robinson, J. S., Roome, C. M., Ruckebusch, C., Seaberg, M., Thepaut, M., Cammarata, M., Demachy, I., Field, M., Shoeman, R. L., Bourgeois, D., Colletier, J., Schlichting, I., Weik, M. 2018; 10 (1): 31–37


    Chromophores absorb light in photosensitive proteins and thereby initiate fundamental biological processes such as photosynthesis, vision and biofluorescence. An important goal in their understanding is the provision of detailed structural descriptions of the ultrafast photochemical events that they undergo, in particular of the excited states that connect chemistry to biological function. Here we report on the structures of two excited states in the reversibly photoswitchable fluorescent protein rsEGFP2. We populated the states through femtosecond illumination of rsEGFP2 in its non-fluorescent off state and observed their build-up (within less than one picosecond) and decay (on the several picosecond timescale). Using an X-ray free-electron laser, we performed picosecond time-resolved crystallography and show that the hydroxybenzylidene imidazolinone chromophore in one of the excited states assumes a near-canonical twisted configuration halfway between the trans and cis isomers. This is in line with excited-state quantum mechanics/molecular mechanics and classical molecular dynamics simulations. Our new understanding of the structure around the twisted chromophore enabled the design of a mutant that displays a twofold increase in its off-to-on photoswitching quantum yield.

    View details for DOI 10.1038/NCHEM.2853

    View details for Web of Science ID 000423143500009

    View details for PubMedID 29256511

  • Determining Orientations of Optical Transition Dipole Moments using Ultrafast X-Ray Scattering. The journal of physical chemistry letters Yong, H. n., Zotev, N. n., Stankus, B. n., Ruddock, J. M., Bellshaw, D. n., Boutet, S. n., Lane, T. J., Liang, M. n., Carbajo, S. n., Robinson, J. S., Du, W. n., Goff, N. n., Chang, Y. n., Koglin, J. E., Waters, M. D., Sølling, T. I., Minitti, M. P., Kirrander, A. n., Weber, P. M. 2018


    The identification of the initially prepared, optically active state remains a challenging problem in many studies of ultrafast photoinduced processes. We show that the initially excited electronic state can be determined using the anisotropic component of ultrafast time-resolved X-ray scattering signals. The concept is demonstrated using the time-dependent X-ray scattering of N-methyl morpholine in the gas-phase upon excitation by a 200 nm linearly polarized optical pulse. Analysis of the angular dependence of the scattering signal near time zero renders the orientation of the transition dipole moment in the molecular frame and identifies the initially excited state as the 3pz Rydberg state, thus bypassing the need for further experimental studies to determine the starting point of the photoinduced dynamics and clarifying inconsistent computational results.

    View details for PubMedID 30380873

  • Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser. Science (New York, N.Y.) Nogly, P. n., Weinert, T. n., James, D. n., Carbajo, S. n., Ozerov, D. n., Furrer, A. n., Gashi, D. n., Borin, V. n., Skopintsev, P. n., Jaeger, K. n., Nass, K. n., Båth, P. n., Bosman, R. n., Koglin, J. n., Seaberg, M. n., Lane, T. n., Kekilli, D. n., Brünle, S. n., Tanaka, T. n., Wu, W. n., Milne, C. n., White, T. n., Barty, A. n., Weierstall, U. n., Panneels, V. n., Nango, E. n., Iwata, S. n., Hunter, M. n., Schapiro, I. n., Schertler, G. n., Neutze, R. n., Standfuss, J. n. 2018; 361 (6398)


    Ultrafast isomerization of retinal is the primary step in photoresponsive biological functions including vision in humans and ion transport across bacterial membranes. We used an x-ray laser to study the subpicosecond structural dynamics of retinal isomerization in the light-driven proton pump bacteriorhodopsin. A series of structural snapshots with near-atomic spatial resolution and temporal resolution in the femtosecond regime show how the excited all-trans retinal samples conformational states within the protein binding pocket before passing through a twisted geometry and emerging in the 13-cis conformation. Our findings suggest ultrafast collective motions of aspartic acid residues and functional water molecules in the proximity of the retinal Schiff base as a key facet of this stereoselective and efficient photochemical reaction.

    View details for PubMedID 29903883

  • Laser-Induced Linear-Field Particle Acceleration in Free Space SCIENTIFIC REPORTS Wong, L., Hong, K., Carbajo, S., Fallahi, A., Piot, P., Soljacic, M., Joannopoulos, J. D., Kaertner, F. X., Kaminer, I. 2017; 7: 11159


    Linear-field particle acceleration in free space (which is distinct from geometries like the linac that requires components in the vicinity of the particle) has been studied for over 20 years, and its ability to eventually produce high-quality, high energy multi-particle bunches has remained a subject of great interest. Arguments can certainly be made that linear-field particle acceleration in free space is very doubtful given that first-order electron-photon interactions are forbidden in free space. Nevertheless, we chose to develop an accurate and truly predictive theoretical formalism to explore this remote possibility when intense, few-cycle electromagnetic pulses are used in a computational experiment. The formalism includes exact treatment of Maxwell's equations and exact treatment of the interaction among the multiple individual particles at near and far field. Several surprising results emerge. We find that electrons interacting with intense laser pulses in free space are capable of gaining substantial amounts of energy that scale linearly with the field amplitude. For example, 30 keV electrons (2.5% energy spread) are accelerated to 61 MeV (0.5% spread) and to 205 MeV (0.25% spread) using 250 mJ and 2.5 J lasers respectively. These findings carry important implications for our understanding of ultrafast electron-photon interactions in strong fields.

    View details for PubMedID 28894271

  • From Macrocrystals to Microcrystals: A Strategy for Membrane Protein Serial Crystallography STRUCTURE Dods, R., Bath, P., Arnlund, D., Beyerlein, K. R., Nelson, G., Liang, M., Harimoorthy, R., Berntsen, P., Malmerberg, E., Johansson, L., Andersson, R., Bosman, R., Carbajo, S., Claesson, E., Conrad, C. E., Dahl, P., Hammarin, G., Hunter, M. S., Li, C., Lisova, S., Milathianaki, D., Robinson, J., Safari, C., Sharma, A., Williams, G., Wickstrand, C., Yefanov, O., Davidsson, J., DePonte, D. P., Barty, A., Branden, G., Neutze, R. 2017; 25 (9): 1461-+


    Serial protein crystallography was developed at X-ray free-electron lasers (XFELs) and is now also being applied at storage ring facilities. Robust strategies for the growth and optimization of microcrystals are needed to advance the field. Here we illustrate a generic strategy for recovering high-density homogeneous samples of microcrystals starting from conditions known to yield large (macro) crystals of the photosynthetic reaction center of Blastochloris viridis (RCvir). We first crushed these crystals prior to multiple rounds of microseeding. Each cycle of microseeding facilitated improvements in the RCvir serial femtosecond crystallography (SFX) structure from 3.3-Å to 2.4-Å resolution. This approach may allow known crystallization conditions for other proteins to be adapted to exploit novel scientific opportunities created by serial crystallography.

    View details for PubMedID 28781082

  • Narrowband terahertz generation with chirped-and-delayed laser pulses in periodically poled lithium niobate OPTICS LETTERS Ahr, F., Jolly, S. W., Matlis, N. H., Carbajo, S., Kroh, T., Ravi, K., Schimpf, D. N., Schulte, J., Ishizuki, H., Taira, T., Maier, A. R., Kaertner, F. X. 2017; 42 (11): 2118–21


    We generate narrowband terahertz (THz) radiation in periodically poled lithium niobate (PPLN) crystals using two chirped-and-delayed driver pulses from a high-energy Ti:sapphire laser. The generated frequency is determined by the phase-matching condition in the PPLN and influences the temporal delay of the two pulses for efficient terahertz generation. We achieve internal conversion efficiencies up to 0.13% as well as a record multicycle THz energy of 40 μJ at 0.544 THz in a cryogenically cooled PPLN.

    View details for DOI 10.1364/OL.42.002118

    View details for Web of Science ID 000403534700018

    View details for PubMedID 28569860

  • Narrowband Terahertz Generation with Broadband Chirped Pulse Trains in Periodically Poled Lithium Niobate Jolly, S. W., Ahr, F., Matlis, N. H., Carbajo, S., Ravi, K., Kroh, T., Schulte, J., Schimpf, D. N., Maier, A. R., Kaertner, F. X., IEEE IEEE. 2017
  • Narrowband THz generation via chirp-and-delay in PPLN Ahr, F., Jolly, S. W., Matlis, N. H., Carbajo, S., Ravi, K., Kroh, T., Schulte, J., Schimpf, D. N., Maier, A. R., Kaertner, F. X., IEEE IEEE. 2017
  • Direct longitudinal laser acceleration of electrons in free space PHYSICAL REVIEW ACCELERATORS AND BEAMS Carbajo, S., Nanni, E. A., Wong, L., Moriena, G., Keathley, P. D., Laurent, G., Miller, R., Kaertner, F. X. 2016; 19 (2)
  • Pulse-train pumping for efficient narrowband terahertz generation in periodically poled lithium niobate Ahr, F., Ravi, K., Carbajo, S., Jolly, S., Kroh, T., Schimpf, D., Matlis, N., Maier, A. R., Kaertner, F. X., IEEE IEEE. 2016
  • Efficient narrowband terahertz generation in cryogenically cooled periodically poled lithium niobate OPTICS LETTERS Carbajo, S., Schulte, J., Wu, X., Ravi, K., Schimpf, D. N., Kaertner, F. X. 2015; 40 (24): 5762–65


    We present an efficiency scaling study of optical rectification in cryogenically cooled periodically poled lithium niobate for the generation of narrowband terahertz radiation using ultrashort pulses. The results show an efficiency and brilliance increase compared to previous schemes of up to 2 orders of magnitude by exploring the optimal pump pulse format at around 800 nm, and reveal saturation mechanisms limiting the conversion efficiency. We achieve >10⁻³ energy conversion efficiencies, μJ-level energies, and bandwidths <20  GHz at ∼0.5  THz, thereby showing unprecedented spectral brightness in the 0.1-1 THz range relevant to terahertz science and technology.

    View details for DOI 10.1364/OL.40.005762

    View details for Web of Science ID 000366681600017

    View details for PubMedID 26670506

  • Theory of terahertz generation by optical rectification using tilted-pulse-fronts OPTICS EXPRESS Ravi, K., Huang, W., Carbajo, S., Nanni, E. A., Schimpf, D. N., Ippen, E. P., Kaertner, F. X. 2015; 23 (4): 5253–76


    A model for terahertz (THz) generation by optical rectification using tilted-pulse-fronts is developed. It simultaneously accounts for in two spatial dimensions (2-D) (i) the spatio-temporal variations of the optical pump pulse imparted by the tilted-pulse-front setup, (ii) the nonlinear coupled interaction of THz and optical radiation, (iii) self-phase modulation and (iv) stimulated Raman scattering. The model is validated by quantitative agreement with experiments and analytic calculations. We show that the optical pump beam is significantly broadened in the transverse-momentum (kx) domain as a consequence of its spectral broadening due to THz generation. In the presence of this large frequency and transverse-momentum (or angular) spread, group velocity dispersion causes a spatio-temporal break-up of the optical pump pulse which inhibits further THz generation. The implications of these effects on energy scaling and optimization of optical-to-THz conversion efficiency are discussed. This suggests the use of optical pump pulses with elliptical beam profiles for large optical pump energies. Furthermore, it is seen that optimization of the setup is highly dependent on optical pump conditions. Trade-offs in optimizing the optical-to-THz conversion efficiency on the spatial and spectral properties of THz radiation are discussed to guide the development of such sources.

    View details for DOI 10.1364/OE.23.005253

    View details for Web of Science ID 000350872700135

    View details for PubMedID 25836558

  • Efficient Generation of Terahertz Radiation at 800 nm Wavelength Wu, X., Carbajo, S., Ravi, K., Huang, W., Fang, S., Ahr, F., Cirmi, G., Rossi, G. M., Muecke, O. D., Kaertner, F. X., IEEE IEEE. 2015
  • On Extracting the Maximum Terahertz Conversion Efficiency from Optical Rectification in Lithium Niobate Carbajo, S., Alcorta, P., Calendron, A., Cankaya, H., Wu, X., Ravi, K., Ahr, F., Huang, W., Kaertner, F. X., IEEE IEEE. 2015
  • Efficiency Scaling of Narrowband Terahertz Wave Generation in PPLN by Optimizing the Pump-Pulse Format Schulte, J., Carbajo, S., Ravi, K., Schimpf, D. N., Kaertner, F. X., IEEE IEEE. 2015
  • Terahertz generation in lithium niobate driven by Ti:sapphire laser pulses and its limitations OPTICS LETTERS Wu, X., Carbajo, S., Ravi, K., Ahr, F., Cirmi, G., Zhou, Y., Muecke, O. D., Kaertner, F. X. 2014; 39 (18): 5403–6


    We experimentally investigate the limits of 800-nm-to-terahertz (THz) energy conversion in lithium niobate at room temperature driven by amplified Ti:sapphire laser pulses with tilted pulse front. The influence of the pump central wavelength, pulse duration, and fluence on THz generation is studied. We achieved a high peak efficiency of 0.12% using transform limited 150 fs pulses and observed saturation of the optical-to-THz conversion efficiency at a fluence of 15 mJ/cm(2) for this pulse duration. We experimentally identify two main limitations for the scaling of optical-to-THz conversion efficiencies: (i) the large spectral broadening of the optical pump spectrum in combination with large angular dispersion of the tilted pulse front and (ii) free-carrier absorption of THz radiation due to multi-photon absorption of the 800 nm radiation.

    View details for DOI 10.1364/OL.39.005403

    View details for Web of Science ID 000341926500043

    View details for PubMedID 26466283

  • Limitations to THz generation by optical rectification using tilted pulse fronts OPTICS EXPRESS Ravi, K., Huang, W., Carbajo, S., Wu, X., Kaertner, F. 2014; 22 (17): 20239–51


    Terahertz (THz) generation by optical rectification (OR) using tilted-pulse-fronts is studied. A one-dimensional (1-D) model which simultaneously accounts for (i) the nonlinear coupled interaction of the THz and optical radiation, (ii) angular and material dispersion, (iii) absorption, iv) self-phase modulation and (v) stimulated Raman scattering is presented. We numerically show that the large experimentally observed cascaded frequency down-shift and spectral broadening (cascading effects) of the optical pump pulse is a direct consequence of THz generation. In the presence of this large spectral broadening, the large angular dispersion associated with tilted-pulse-fronts which is ~15-times larger than material dispersion, accentuates phase mismatch and degrades THz generation. Consequently, this cascading effect in conjunction with angular dispersion is shown to be the strongest limitation to THz generation in lithium niobate for pumping at 1 µm. It is seen that the exclusion of these cascading effects in modeling OR, leads to a significant overestimation of the optical-to-THz conversion efficiency. The results are verified with calculations based on a 2-D spatial model. The simulation results are supported by experiments.

    View details for DOI 10.1364/OE.22.020239

    View details for Web of Science ID 000340717300058

    View details for PubMedID 25321233

  • Efficient generation of ultra-intense few-cycle radially polarized laser pulses OPTICS LETTERS Carbajo, S., Granados, E., Schimpf, D., Sell, A., Hong, K., Moses, J., Kaertner, F. X. 2014; 39 (8): 2487–90


    We report on efficient generation of millijoule-level, kilohertz-repetition-rate few-cycle laser pulses with radial polarization by combining a gas-filled hollow-waveguide compression technique with a suitable polarization mode converter. Peak power levels >85  GW are routinely achieved, capable of reaching relativistic intensities >10(19)  W/cm2 with carrier-envelope-phase control, by employing readily accessible ultrafast high-energy laser technology.

    View details for DOI 10.1364/OL.39.002487

    View details for Web of Science ID 000334163800070

    View details for PubMedID 24979025

  • Imaging at the Nanoscale With Practical Table-Top EUV Laser-Based Full-Field Microscopes IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS Brizuela, F., Howlett, I. D., Carbajo, S., Peterson, D., Sakdinawat, A., Liu, Y., Attwood, D. T., Marconi, M. C., Rocca, J. J., Menoni, C. S. 2012; 18 (1): 434–42
  • Assessment of illumination characteristics of soft x-ray laser-based full-field microscopes Howlett, I. D., Brizuela, F., Carbajo, S., Peterson, D., Sakdinawat, A., Liu, Y., Attwood, D. T., Marconi, M. C., Rocca, J. J., Menoni, C. S., Dunn, J., Klisnick, A. SPIE-INT SOC OPTICAL ENGINEERING. 2011

    View details for DOI 10.1117/12.892927

    View details for Web of Science ID 000297632800023

  • Extreme ultraviolet laser-based table-top aerial image metrology of lithographic masks OPTICS EXPRESS Brizuela, F., Carbajo, S., Sakdinawat, A., Alessi, D., Martz, D. H., Wang, Y., Luther, B., Goldberg, K. A., Mochi, I., Attwood, D. T., La Fontaine, B., Rocca, J. J., Menoni, C. S. 2010; 18 (14): 14467–73


    We have realized the first demonstration of a table-top aerial imaging microscope capable of characterizing pattern and defect printability in extreme ultraviolet lithography masks. The microscope combines the output of a 13.2 nm wavelength, table-top, plasma-based, EUV laser with zone plate optics to mimic the imaging conditions of an EUV lithographic stepper. We have characterized the illumination of the system and performed line-edge roughness measurements on an EUVL mask. The results open a path for the development of a compact aerial imaging microscope for high-volume manufacturing.

    View details for DOI 10.1364/OE.18.014467

    View details for Web of Science ID 000279639900017

    View details for PubMedID 20639931

  • Table-top Extreme Ultraviolet Laser Aerial Imaging of Lithographic Masks Brizuela, F., Carbajo, S., Sakdinawat, A., Wang, Y., Alessi, D., Martz, D., Luther, B., Goldberg, K., Attwood, D., La Fontaine, B., Rocca, J., Menoni, C., IEEE IEEE. 2010