The Evolution of High-Throughput Macromolecular Crystallography at Synchrotrons

On May 11 and 12, 2000, the Stanford Synchrotron Radiation Laboratory, as it was then known, hosted a “Workshop on Techniques for Automated Mounting, Viewing and Centering Pre-Cooled Protein Crystals” [1 http://www-ssrl.slac.stanford.edu/conferences/workshops/px-robotics/. [Google Scholar], 2 E. Abola, Nature Structural Biology 7, 973–977 (2000).[Crossref], [PubMed] , [Google Scholar]]. The 12 presentations during the meeting all focused on the impact that automation could have on the performance of synchrotron beamlines and thus on research in structural biology. Two principal themes ran through the workshop: (1) robotics to mount crystals on a diffractometer; and (2) methods to place a crystal in the X-ray beam. Five conceptual and prototype robotic systems for automated mounting were described—the original ACTOR from Abbott Laboratories, later modified and marketed by Rigaku/MSC, and the systems which in final form become the ALS [3 G. Snell, Structure 12, 537–545 (2004).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]], EMBL/ESRF SC3 [4 F. Cipriani, Acta Cryst. D62(10), 1251–1259 (2006). [Google Scholar]], APS/SBC [5 D. Shu, AIP Conference Proceedings 705(1), 1201–1204 (2004).[Crossref] , [Google Scholar]], and SSRL SAM robots [6 A. E. Cohen, J. Appl. Cryst. 5(6), 720–726 (2002).[Crossref], [Web of Science ®] , [Google Scholar]]. By December of that year, the ACTOR had been installed for testing at Sector 32 of the Advanced Photon Source (Figure 1). Within three years, by the end of 2003, several of these robots, plus the commercial MARcsc from MAR Research, had been deployed to handle frozen protein crystals at beamlines for macromolecular crystallography (MX). Currently, at least 13 distinct robot types, not including variants of the ALS automounter, are employed at synchrotron beamlines to transfer crystals from storage to beam position.     

Consortium GARR and the European National Research and Education Networks Optical Infrastructure Developments

Abstract

GARR is engineering its next generation of the Italian Research and Education Network (GARR-X), which will exploit a countrywide optical infrastructure based on DWDM equipment and advanced multi-domain services. The trend is common in all National Research and Education Networks [1 TERENA NREN Compendium. http://www.terena.org/activities/compendium ISSN 1569-4496 [Google Scholar]] in Europe and worldwide. NRENs are relying more and more on direct use of optical equipment to fulfill the researchers' requirements. These hybrid networks are built to provide services on a multi-domain environment both at the circuit and at the IP layer for researchers in, for example, radio astronomy (eVLBI [2 European Very Long Baseline Interferometry http://www.evlbi.org [Google Scholar]]), GRID computing (EGEE [3 Enabling Grids for E-sciencE http://public.eu-egee.org [Google Scholar]], LHC [4 The Large Hadron Collider http://lhc.web.cern.ch/lhc [Google Scholar]]), high-performance computing (DEISA [5 The Distributed European Infrastructure for Supercomputing Applications http://www.deisa.org [Google Scholar]]). This article outlines the status and issues of ongoing research activities in GARR [6 http://www.garr.it/garr-b-home-engl.shtmlConsortium GARR, the Italian NREN [Google Scholar]] and NRENs to provide, manage, and evolve dedicated optical-based networks for providing multi-domain end-to-end services. The research is performed mainly in the framework of the European Commission co-funded project GÉANT2 [7 The pan-European R&E network http://www.geant2.net [Google Scholar]].     

Ultrafast Soft X-ray Probing of Gas Phase Molecular Dynamics

The molecular ability to selectively and efficiently convert sunlight into other forms of energy like heat, bond change, or charge separation is truly remarkable. The decisive steps in these transformations often happen on a femtosecond timescale and require transitions among different electronic states that violate the Born-Oppenheimer approximation (BOA) [1 W. Domcke, D. Yarkony, and H. Köppel, Conical Intersections Electronic Structure, Dynamics &; Spectroscopy, World Scientific, Singapore (2004).[Crossref] , [Google Scholar]]. Non-BOA transitions pose challenges to both theory and experiment. From a theoretical point of view, excited state dynamics and nonadiabatic transitions both are difficult problems [2 F. Plasser, Theor. Chem. Acc. 131, 233902 (2012).[Crossref], [Web of Science ®] , [Google Scholar], 3 J. C. Tully, J. Chem. Phys. 137, 22A301 (2012).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]] (see Figure 1(a)). However, the theory on non-BOA dynamics has advanced significantly over the last two decades. Full dynamical simulations for molecules of the size of nucleobases have been possible for a couple of years [4 H. R. Hudock, J. Phys. Chem. A 111, 8500–8508 (2007).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar], 5 J. J. Szymczak, J. Phys. Chem. A 113, 12686–12693 (2009).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]] and allow predictions of experimental observables like photoelectron energy [6 S. Ullrich, Phys. Chem. Chem. Phys. 6, 2796 (2004).[Crossref], [Web of Science ®] , [Google Scholar]] or ion yield [7 H. Tao, J. Chem. Phys. 134, 244306 (2011).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]–9 M. Assmann, T. Weinacht, and S. Matsika, J. Chem. Phys. 144, 34301 (2016).[Crossref], [Web of Science ®] , [Google Scholar]]. The availability of these calculations for isolated molecules has spurred new experimental efforts to develop methods that are sufficiently different from all optical techniques. For determination of transient molecular structure, femtosecond X-ray diffraction [10 M. P. Minitti, Phys. Rev. Lett. 114, 255501 (2015).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar], 11 J. Küpper, Phys. Rev. Lett. 112, 083002 (2014). [Google Scholar]] and electron diffraction [12 J. Yang, Nat. Commun. 7, 11232 (2016).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]] have been implemented on optically excited molecules.     

Ultrafast Electronic and Molecular Dynamics Induced by Ultrashort FEL Pulses

In recent years, short wavelength free electron lasers (FELs) have opened up access to ultrafast electronic and structural dynamics in matter. Currently, four FEL facilities are in operation in the world. FLASH [1 W. Ackermann, Nat. Photonics 1, 336 (2007).[Crossref], [Web of Science ®] , [Google Scholar]] in Germany and FERMI [2 P. Emma, Nat. Photonics 4, 641 (2010).[Crossref], [Web of Science ®] , [Google Scholar]] in Italy cover the range from extreme ultraviolet (EUV) to soft X-rays, while LCLS [3 T. Ishikawa, Nat. Photonics 6, 540 (2012).[Crossref], [Web of Science ®] , [Google Scholar]] in the U.S. and SACLA [4 E. Allaria, Nat. Photonics 6, 699 (2012).[Crossref], [Web of Science ®] , [Google Scholar]] in Japan provide pulses in the hard X-ray regime. In addition, an upgrade version of SCSS [5 T. Shintake, Nat. Photonics 2, 555 (2008).[Crossref], [Web of Science ®] , [Google Scholar]], nicknamed SCSS+, has also just started user operation as a beamline of SACLA [6 See http://xfel.riken.jp/eng/users/index.html [Google Scholar]]. These FELs deliver coherent pulses combining unprecedented power densities up to ~10²⁰ W/cm² and extremely short pulse durations down to a few femtoseconds. The intense coherent FEL pulse focused down to ~1 μm² makes single-shot diffractive imaging of nano-crystals or even non-crystallized bio-samples as well as other small objects a reality. Time-resolved spectroscopic and structural studies on the timescale of femtoseconds, having FEL pulses as a probe, allow us to probe electrons and atoms in action. Additionally, since FEL pulses are in a new regime of intensity, they are opening up new research fields that exploit the interaction between intense short wavelength pulses and matter, leading to matter at extremely high energy. Relevant theories dealing with such extreme conditions are also rapidly growing.     

Photon-In/Photon-Out Soft X-ray Spectroscopy at the TPS 45A Beamline

Owing to the current energy crisis and extreme changes in the global climate, there is great interest in finding renewable energy resources. Vast progress has been made in the development of new materials related to renewable energy, and their physical/chemical properties can be tailored by nanostructuring and other advanced synthetic approaches. In many important energy systems, such as solar hydrogen systems, the atomic/electronic structures of materials and fundamental interfacial phenomena of systems critically determine the energy conversion efficiency of materials [1 S. Shen et al., Energy Environ. Sci. 9, 2744 (2016).[Crossref], [Web of Science ®] , [Google Scholar], 2 J. Chen et al., J. Mater. Chem. A 2, 4605 (2014).[Crossref], [Web of Science ®] , [Google Scholar]]. Without knowledge of the fundamental electronic structures of the materials during conversion reactions, better engineering of the material for practical use is difficult. Understanding and controlling the interfaces in energy generation/conversion/storage materials requires in-situ/operando approaches [3 V. Iablokov et al., Nano Lett. 12, 2091 (2012).[Crossref], [Web of Science ®] , [Google Scholar], 4 F. Zheng et al., Nano Lett. 11, 847 (2011).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]. The Taiwan Photon Source (TPS) Soft X-ray Spectroscopic beamline provides the capabilities for X-ray absorption (XAS) and X-ray emission (XES) spectroscopies, which can be utilized to investigate unoccupied (conduction-band) and occupied (valence-band) electronic states, respectively. Moreover, resonant inelastic X-ray scattering (RIXS) can be used to study intra-band (including d-d or f-f excitations) and inter-band (charge transfer) transitions [5 S. M. Butorin et al., Phys. Rev. Lett. 77, 574 (1996).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar], 6 P. Kuiper et al., Phys. Rev. Lett. 80, 5204 (1988).[Crossref], [Web of Science ®] , [Google Scholar]]. The former provides details about electronic energy splitting in various crystal fields and the latter involves electron transfer between a metal and a ligand, which determines chemical activity [7 H. Liu, Nano Lett. 7, 1919 (2007).[Crossref], [Web of Science ®] , [Google Scholar], 8 V. Bisogni et al., Phys. Rev. Lett. 114, 096402 (2015).[Crossref], [Web of Science ®] , [Google Scholar]].     

MXCuBE3: A New Era of MX-Beamline Control Begins

The outstanding success of structural biology within the last two decades is closely related to the development and evolution of macromolecular crystallography (MX) beamlines. Indeed, many of today's synchrotron-based MX experimental sessions aim for fast but rigorous evaluations and data collections from very large numbers of samples [1 A. Joachimiak, Current Opinion in Structural Biology 19, 573–584 (2009).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]–7 R. L. Owen, Archives of Biochemistry and Biophysics 602, 21–31 (2016).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]. To facilitate this, sample changing on most MX beamlines is now carried out by robots and the centering of a crystal in the X-ray beam to micrometer precision is now automatically performed using either optical or diffraction-based techniques [8 D. Nurizzo, Acta Cryst. D 72, 966–975 (2016).[Crossref] , [Google Scholar]]. Once a crystal is centered, users have a wide array of options at their disposal to prepare any given experiment. This includes: X-ray fluorescence (XRF) [9 G. A. Leonard, Journal of Applied Crystallography 42, 333–335 (2009).[Crossref], [Web of Science ®] , [Google Scholar]] analysis to confirm the presence of anomalous scatterers in crystals; X-ray absorption near-edge scans (XANES) to determine the best X-ray wavelengths for MAD/SAD data collection [10 W. A. Hendrickson, Methods Enzymol. 276, 494–523 (1997).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]; and the probing of the diffraction properties of crystals to determine the best crystal, or area of a crystal [11 M. W. Bowler, Acta Cryst. D 66, 855–864 (2010).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]], for data collection. All of these operations are now also automated, as is the collection of the final diffraction data set either from single or multiple crystals and the subsequent data analysis and reduction.     

Imaging Non-Local Magnetization Dynamics

Many fundamental processes in magnetism take place on a nanometer length and sub-picosecond time scale. An important example of such phenomena in magnetism is ultrafast, spin-polarized transport of laser-excited hot electrons, which is now being recognized as playing a crucial role for novel spintronic devices and for optically induced magnetic switching. Recent experimental examples include the demonstration of all-optical helicity dependent control of spin-polarized currents at interfaces [1 T.J. Huisman, Nature Nanotechn., doi:10.1038/nnano.2015.331 (2016).[Crossref] , [Google Scholar]], the design of novel and efficient terahertz emitters [2 T. Seifert, arXiv:1510.03729 (2015). [Google Scholar]], and nanoscale spin reversal in chemically heterogeneous GdFeCo driven by non-local transfer of angular momentum [3 C.E. Graves, Nat. Mater. 12, 293–298 (2013).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]. In particular, for advanced information technologies with bit densities already exceeding 1 terabit per square inch with bit cell dimensions of (15 × 38 nm²) [4 R. Wood, IEEE Transaction on Magnetics 38, 1711 (2000).[Crossref], [Web of Science ®] , [Google Scholar]], it is of fundamental importance to understand and eventually control the mechanisms responsible for optically induced spin dynamics on the nanoscale.     

Surface Science Studies with Free Electron Lasers: Real-Time Observations of Electronic Structure Changes during Reactions

New light sources based on linear accelerators such as FLASH at DESY in Hamburg, the first free-electron laser in the extreme ultraviolet (XUV) and soft X-ray regime, which started user operation in 2005 [1 W. Ackermann, Nature Photonics 1, 336–342 (2007).[Crossref], [Web of Science ®] , [Google Scholar]], the Linac Coherent Light Source LCLS in Stanford [2 P. Emma, Nature Photonics 4, 641–647 (2010).[Crossref], [Web of Science ®] , [Google Scholar]], and SACLA at Spring-8 in Japan [3 T. Ishikawa, Nature Photonics 6, 540–544 (2012).[Crossref], [Web of Science ®] , [Google Scholar]], as X-ray lasers dedicated to the hard X-ray regime down to below 1 Å in wavelength, or FERMI at ELETTRA in Trieste [4 E. Allaria, Nature Photonics 6, 699–704 (2012).[Crossref], [Web of Science ®] , [Google Scholar]] as the first fully externally seeded free electron laser also operating in the XUV and soft X-ray regime, provide ultrashort, extremely powerful, short wavelength pulses with unprecedented coherence properties. With the European XFEL in Hamburg, the Swiss FEL at PSI in Villigen, Switzerland, and the PAL-XFEL in Pohang, Korea, three more FELs are expected to produce first light by the end of 2016 and the beginning of 2017, respectively.     

Biomedical Imaging Using Synchrotron Radiation: Experience at the Biomedical Imaging and Therapy (BMIT) Facility at the Canadian Light Source

The Biomedical Imaging and Therapy (BMIT) beamlines at the Canadian Light Source (CLS) comprise a multi-modality synchrotron imaging facility capable of imaging objects with 2–200 μm resolution with beam sizes up to ~200 mm wide and ~10 mm high in the experimental hutches [1 T. W. Wysokinski, Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment 775, 1–4 (2015).[Crossref], [Web of Science ®] , [Google Scholar]–3 T. W. Wysokinski, Nucl Instr Meth Phys Res A 582, 73–76 (2007).[Crossref], [Web of Science ®] , [Google Scholar]]. BMIT hosts two beamlines, a bend magnet 05B1-1 and an insertion device 05ID-2, with capabilities to apply absorption imaging, in-line phase contrast imaging (PCI), analyzer-based imaging (ABI) or diffraction-enhanced imaging (DEI), and K-Edge Subtraction (KES) imaging. Talbot or grating interferometry is under development.     

Undulator Development for SPring-8-II

After the construction of the X-ray free electron laser facility SACLA, which achieved first lasing in 2011 [1 T. Ishikawa, Nature Photon. 6, 540 (2012)[Crossref], [Web of Science ®] , [Google Scholar]] and has been successfully operated for nearly four years, SPring-8 has now turned to upgrading its storage ring to further enhance the light source performance in terms of brilliance. In this “SPring-8-II” project, a new lattice structure composed of five bending magnets has been chosen [2 SPring-8-II Conceptual Design Report (2014), available from http://rsc.riken.jp/pdf/SPring-8-II.pdf [Google Scholar]] in order to reduce the horizontal emittance, which, in turn, requires us to shorten the straight sections available for undulators by roughly 1 m. In addition, the electron energy will be reduced down to 6 GeV from the current 8 GeV for further reduction of the emittance. This upgrade plan is not necessarily compatible with the existing undulators in SPring-8 and thus most of them need to be replaced with new ones optimized for operation in the new ring in order to maximize the brilliance. This raises a number of technical challenges toward realization of SPring-8-II, including considerable reduction of the manufacturing cost and further shortening of the magnetic period of undulators. In this article, we report relevant R&;D activities to overcome these challenges, together with a new concept to enable a flexible polarization control, which is one of the important options in synchrotron radiation (SR) beamlines.     

Recent Developments in Insertion Devices at the ESRF: Working Toward Diffraction-Limited Storage Rings

The development of permanent-magnet insertion devices (IDs) is a feature of third-generation light sources (3GLS). Since the early 1990s, an important research and engineering effort has been carried out on various types of undulators at the ESRF, as in many other 3GLS facilities. We are presently at the forefront of an interesting migration toward new storage ring lattices with ultra-low horizontal emittance [1 M. Erikson, Journal of Synchrotron Radiation, 21(5), 837–842 (2014).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar], 2 M. Borland, Synchrotron Radiation News, 27(6), 2–31 (2014).[Taylor &; Francis Online] , [Google Scholar]]. The upgrade of the ESRF accelerator will take place before 2020. A new magnet lattice comprising seven bending magnets per cell will replace the existing DBA structure, leading to a dramatic reduction of the horizontal emittance from 4 nm to about 130 pm. Because the new ring will be operated at the same energy as the current ring, the majority of existing IDs will be used in the upgraded ring, at least as a starting point. From the present state of the art in ID technology, one can obviously identify the development of very short-period, small-gap undulators as potential major X-ray sources in such new storage rings. Technically, various methods in magnetic field processing and correction need to be revisited and possibly updated.     

Advancement of Hard X-ray Nano-focusing Ellipsoidal Mirror at SPring-8

Ellipsoidal mirror optics can produce a smaller, two-dimensional focus with diffraction-limited properties than is possible when using mirror optics in Kirkpatrick–Baez (K–B) geometry [1 P. Kirkpatrick and A.V. Baez, Journal of the Optical Society of America 38, 766–773 (1948).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]. This is because ellipsoidal focusing mirrors can be designed such that they have a larger numerical aperture in the sagittal focusing direction as compared to that in the meridional focusing direction. Although ellipsoidal focusing mirrors have this crucial advantage over K–B optics, K–B optics are widely utilized as micro-/nano-focusing devices [2 H. Mimura, Nature Physics 6, 122–125 (2010).[Crossref], [Web of Science ®] , [Google Scholar]–8 H. Mimura, Nature Communications 5, 3539 (2014).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]] in synchrotron radiation facilities and X-ray free electron laser facilities [9 P. Emma, Nature Photonics 4, 641–647 (2010).[Crossref], [Web of Science ®] , [Google Scholar], 10 T. Ishikawa, Nature Photonics 6, 540–544 (2012).[Crossref], [Web of Science ®] , [Google Scholar]]. Figure 1 shows a schematic of focusing mirror optics; Figure 1(a) shows the ellipsoidal mirror and Figure 1(b) the K–B mirror arrangement. In K–B geometry, two mirrors with a one-dimensionally curved surface, such as an elliptical cylinder, are orthogonally arranged in tandem to reflect and focus light independently in a direction perpendicular to each other under grazing-incidence conditions. Ellipsoidal focusing mirrors, which can generate a two-dimensional focusing beam by a single reflection, have a highly sloped surface with a two-dimensional aspherical shape, when compared to elliptical-cylinder mirrors that are used for line-focusing in K–B geometry. In addition, surface shapes of nano-focusing mirrors must be fabricated with nanometer-level accuracy. Therefore, fabrication of ellipsoidal nano-focusing mirrors is extremely difficult. There are no reports on ellipsoidal nano-focusing mirrors in the hard X-ray region with superior performances to provide diffraction-limited beams.     

Quantitative measurements of undiilator spatial coherence at the ALS

Modern synchrotron-based X-ray fluorescence microscopy (XFM) has become a critical tool for many a research program, addressing extremely broad and highly relevant scientific questions. Their ability to map trace elemental content and probe local chemical state has been applied to numerous scientific areas in the life sciences [1 Paunesku, T. 2006. J Cell Biochem, 99(6): 1489–502. [Crossref], [PubMed] , [Google Scholar]–3 Bohic, S. 2012. J Struct Biol, 177(2): 248–58. [Crossref], [PubMed] , [Google Scholar]], the environmental and earth sciences [4 Fittschen, U. E. A. and Falkenberg, G. 2011. Spectrochimica Acta Part B-Atomic Spectroscopy, 66(8): 567–580. [Crossref] , [Google Scholar], 5 Lombi, E. 2011. Analytical and Bioanalytical Chemistry, 400(6): 1637–1644. [Crossref], [PubMed] , [Google Scholar]], the materials sciences, as well as in cultural heritage studies. The newest generation of instruments utilizes high-brightness X-ray sources and incorporate state-of-the-art focusing optics and detector systems. Advances in X-ray sources and nanofocusing optics, for example, have allowed these instruments to achieve spatial resolutions of 20–30 nm using diffractive optics such as Fresnel zone plates and 200 nm using reflective optics such as Kirkpatrick-Baez mirrors. New beamlines, now in the design stage, aim to achieve similar (and better) resolutions within the next five years.     

Results and Perspectives for Short-Wavelength,Four-Wave-Mixing Experiments with Fully Coherent Free Electron Lasers

The discovery of the nonlinear optical response [1 P.A. Franken, A.E. Hill, and C.W. Peters, Physical Review Letters 7(4), 118–119 (1961).[Crossref], [Web of Science ®] , [Google Scholar]] has triggered the development of new theoretical and experimental approaches. These are based on the perspective that light-matter interactions are not necessarily cast in the picture of “one photon at a time,” typical of linear processes, but more photons can “work together” in order to coherently stimulate and probe (via nonlinear interactions) different kinds of dynamics in a sample. Nowadays, such a “multi-wave” concept is extensively used in a large array of methods, also termed wave-mixing, that have found numerous applications in almost all fields of physics, chemistry, and biology [2 N. Bloembergen, Review of Modern Physics 54(3), 685–695 (1982).[Crossref], [Web of Science ®] , [Google Scholar], 3 R.W. Boyd, Nonlinear Optics, 3^rd ed., Academic Press, New York (2008). [Google Scholar]]. Such methods are often based on third-order processes, referred to as four-wave-mixing (FWM), in which a threefold light-matter interaction results in the generation of a (fourth) signal photon, whose photon parameters (frequency, wave vector, polarization, etc.) may differ from those of the input fields. The possibility to control the latter parameters turns into the capability to selectively probe different FWM processes, which can contain distinct and complementary information. In addition to this high degree of selectivity, FWM is often featured in ultrafast time resolution and can be used to study dynamics hardly accessible by linear methods [3 R.W. Boyd, Nonlinear Optics, 3^rd ed., Academic Press, New York (2008). [Google Scholar]], such as spin waves and relaxations [4 A.R. Cameron, P. Riblet, and A. Miller, Physical Review Letters 76(25), 7493–7496 (1996).[Crossref], [Web of Science ®] , [Google Scholar], 5 C.P. Weber, Nature 437(7063), 1330–1333 (2005).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]] or Raman transitions between unoccupied electronic states [6 Y. Prior, Phys. Rev. Lett. 46(2), 111–114 (1981).[Crossref], [Web of Science ®] , [Google Scholar], 7 J.R. Andrews and R.M. Hochstrasser, Chemical Physics Letters 82(3), 381–385 (1981).[Crossref], [Web of Science ®] , [Google Scholar]].     

Femtosecond Structural Dynamics of Proteins

Proteins are the workhorses of living cells, providing essential functions such as structural support, signal transduction, enzymatic catalysis, transport and storage of small ligands. Atomic-resolution structures obtained with conventional X-ray crystallography show proteins essentially as static. In reality, however, proteins move and their motion is crucial for functioning. Although the structure and dynamics of proteins are intimately related, they are not equally well understood. A very large number of protein structures have been determined, but only a few studies have been able to monitor experimentally the dynamics of proteins in real time. In the last two decades, the availability of short (~100 ps) and intense (~10⁹–10¹⁰ photons) X-ray pulses produced by third-generation synchrotrons have allowed the implementation of structural methods like time-resolved X-ray crystallography and time-resolved X-ray solution scattering that have allowed us to monitor protein motion in the nanosecond-to-millisecond timescale [1 K. Moffat, Chem. Rev. 101, 1569–1582 (2001).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]–4 J. G. Kim, Acc. Chem. Res. 48, 2200–2208 (2015).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]. Time-resolved X-ray crystallography has been used to monitor processes such as the migration of a ligand from the protein active site to the surrounding solvent [5 V. Srajer, Science 274, 1726–1729 (1996).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]–7 D. Bourgeois, Proc. Natl. Acad. Sci. U. S. A. 100, 8704–8709 (2003).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]] or tertiary structural changes associated with allosteric transitions [8 J. E. Knapp, Proc. Natl. Acad. Sci. 103, 7649–7654 (2006).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar], 9 J. G. Kim, Struct. Dyn. 3, 023610 (2016). [Google Scholar]]. On the other hand, time-resolved X-ray scattering in the so-called wide-angle X-ray scattering (WAXS) region [10 M. Cammarata, Nat. Methods 5, 881–886 (2008).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]] has been used to track conformational changes corresponding to large-amplitude protein motions such as the quaternary R-T transition of human hemoglobin [11 M. Cammarata, J. Mol. Biol. 400, 951–962 (2010).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]–13 A. Spilotros, Soft Matter 8, 6434–6437 (2012).[Crossref], [Web of Science ®] , [Google Scholar]], the relative motion of bacteriorhodopsin α-helices following retinal isomerization [14 M. Andersson, Structure 17, 1265–1275 (2009).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]], or the open-to-close transition in bacterial phytochromes [15 H. Takala, Nature 509, 245–8 (2014).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]].     

Serial Femtosecond Crystallography

X-ray free-electron lasers produce brief flashes of X-rays that are of about a billion times higher peak brightness than achievable from storage ring sources. Such a tremendous jump in X-ray source capabilities, which came in 2009 when the Linac Coherent Light Source began operations, was unprecedented in the history of X-ray science. Protein structure determination through the method of macromolecular crystallography has consistently benefited from the many increases in source performance from rotating anodes to all generations of synchrotron facilities. But when confronted with the prospects of such bright beams for structural biology, enthusiastic proposals were tempered by trepidation of the effects of such beams on samples and challenges to record data [1 M. Wilmanns, J. Synchr. Rad. 7, 41 (2000).[Crossref], [PubMed] , [Google Scholar]]. A decade after these discussions (and others in the USA) on the applications of X-ray FELs for biology, the first experiments took place at LCLS, giving results that fulfilled many of the dreams of the early visionaries. In particular, the concept that diffraction representing the pristine object could be recorded before the X-ray pulse completely vaporizes the object was validated [2 H.N. Chapman, Nature 470, 73 (2011).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]], confirming predictions [3 R. Neutze, Nature 406, 753 (2000).[Crossref], [Web of Science ®] , [Google Scholar]] that established dose limits could be vastly exceeded using femtosecond-duration pulses. The first experiments illuminated a path to achieve room-temperature structures free of radiation damage, from samples too small to provide useful data at synchrotron facilities, as well as providing the means to carry out time-resolved crystallography at femtoseconds to milliseconds. In the five years since, progress has been substantial and rapid, invigorating the field of macromolecular crystallography [4 J.C.H. Spence and H.N. Chapman, Phi. Trans. Roy. Soc. B 369, 20130309 (2014).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar], 5 I. Schlichting, IUCrJ 2, 246 (2015).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]. This phase of development is far from over, but with both the LCLS and the SPring-8 Ångström Compact Free-electron Laser (SACLA) providing facilities for measurements, the benefits of X-ray FELs are already being translated into new biological insights.     

Ambient-Pressure X-ray Photoelectron Spectroscopy to Characterize the Solid/Liquid Interface: Probing the Electrochemical Double Layer

Ambient-pressure X-ray photoelectron spectroscopy (APXPS) has contributed greatly to a wide range of research fields, including environmental science [1 H. Bluhm, Journal of Electron Spectroscopy and Related Phenomena 177, 71–84 (2010).[Crossref], [Web of Science ®] , [Google Scholar]], catalysis [2 D.E. Starr et al., Chemical Society Reviews 42, 5833–5857 (2013).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]], and electrochemistry [3 E.J. Crumlin, H. Bluhm, and Z. Liu, Journal of Electron Spectroscopy and Related Phenomena 190, 84–92 (2013).[Crossref], [Web of Science ®] , [Google Scholar]], to name a few. The use of this technique at synchrotron facilities primarily focused on probing the solid/gas interface; however, it quickly advanced to the probing of liquid/vapor interfaces [4 D.E. Starr et al., Physical Chemistry Chemical Physics 10, 3093–3098 (2008).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar], 5 M.A. Brown et al., Physical Chemistry Chemical Physics 10, 4778–4784 (2008).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]] and solid/liquid interfaces through an X-ray-transparent window [6 J. Kraus et al., Nanoscale 6, 14394–14403 (2014).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]–8 T. Masuda et al., Appl Phys Lett 103 (2013).[Crossref], [Web of Science ®] , [Google Scholar]]. Most recently, combining APXPS with “Tender” X-rays (~2.5 keV to 8 keV) on beamline 9.3.1 at the Advanced Light Source in Lawrence Berkeley National Laboratory (which can generate photoelectrons with much longer inelastic mean free paths) has enabled us to probe the solid/liquid interface without needing a window [9 S. Axnanda et al., Scientific Reports 5 (2015).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]. This innovation allows us to probe interfacial chemistries of electrochemically controlled solid/liquid interfaces undergoing charge transfer reactions [9 S. Axnanda et al., Scientific Reports 5 (2015).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]. These advancements have transitioned APXPS from a traditional surface science tool to an essential interface science technique.     

Seeded Multicolor FEL Pulses: Status and Future Plans

The advent of FEL sources delivering two synchronized pulses of different wavelengths has made available a whole range of novel pump-probe experiments [1 E. Ferrari, Nat. Commun. 7, 10343 (2016).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]], allowing the exploration of the dynamics of matter driven to extreme non-equilibrium states by an intense ultrashort X-ray pulse and then probing the sample response at variable time delay with a second pulse [2 E. Allaria, Nat. Commun. 4, 2476 (2013).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]].     

Thermodynamics of two-dimensional single-component elastic crystalline solids: single-wall carbon nanotubes

The thermodynamic behaviour of two-dimensional single-component elastic crystalline solids is developed: the surface Euler's equation, the surface Gibbs equation, the surface Gibbs–Duhem equation, and the conditions to be expected at equilibrium, including the stress-deformation behaviour of the crystal. The analysis recognizes that the surface Helmholtz free energy is an explicit function of the lattice vectors defining the crystalline structure. As an application, we obtain the stress-deformation behaviour of single-wall carbon nanotubes which are composed of a regular two-dimensional array of hexagonal lattices of carbon atoms. Using two potentials, Tersoff [1] Tersoff J Phys. Rev. B 37 6991 1988 [Crossref], [Web of Science ®] , [Google Scholar]–Brenner [2] Brenner DW Phys. Rev. B 42 9458 1990 [Crossref], [Web of Science ®] , [Google Scholar] and Brenner et al. [3] Brenner, DW, Shenderova, OA, Harrison, JA, Stuart, SJ, Ni, B and Sinnott, SB. 2002. J. Phys. Condens. Matter, 14: 783[Crossref], [Web of Science ®] , [Google Scholar] to describe interatomic potentials and hence the specific surface Helmholtz free energy, we compute the surface elastic properties for the single-wall carbon nanotubes. These are compared with the available experimental values.