Jason Koglin

Los Alamos National Laboratory | LANL

With the development of X-ray free-electron lasers (XFELs), producing pulses of femtosecond durations comparable with the coherence times of X-ray fluorescence, it has become possible to observe intensity–intensity correlations due to the interference of emission from independent atoms. This has been used to compare durations of X-ray pulses and to...

The Cover Feature displays a comparison of chromophore conformations in the X‐ray crystal structures of the reversibly photoswitchable fluorescent protein rsEGFP2 in its on state (green) and its V151L (purple) and V151A (yellow) variants in their off states. The latter displays an increased photoswitching contrast, as indicated by the displayed swi...

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 appli...

A spatially resolved air-wedge shearing interferometer and shadowgraph diagnostic provides measurements of electron density with a resolution of 40 μm. A 100-ns-long, monoenergetic electron bunch at 19.8 MeV and a current of 1.4 kA (8.5 x 10^14 e-) heats 100-μm-thick aluminum (Al) foils in a 1-mm-spot to T ~ 1 eV. A 5-ns-long, 60 mJ, frequency doub...

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, a key parameter that largely dictates the achievable resolution in nanoscopy applic...

X-ray free-electron lasers can generate radiation pulses with extreme peak intensities at short wavelengths. This enables the investigation of laser–matter interactions in a regime of high fields, yet at a non-relativistic ponderomotive potential, where ordinary rules of light–matter interaction may no longer apply and nonlinear processes are start...

The interaction of intense femtosecond x-ray pulses with molecules sensitively depends on the interplay between multiple photoabsorptions, Auger decay, charge rearrangement, and nuclear motion. Here, we report on a combined experimental and theoretical study of the ionization and fragmentation of iodomethane (CH3I) by ultraintense (∼1019 W/cm2) x-r...

Significance Charge transfer plays a fundamental role in many areas of chemistry, physics, biology, and materials science. The spatial redistribution of electrons is typically associated with changes in the molecular geometry. A comprehensive understanding of this process requires atomic spatial resolution and femtosecond temporal resolution. Here,...

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...

Shock waves launched by x-ray pulses in sample-carrying liquid jets may affect protein crystallography data collected at MHz repetition rate x-ray free-electron laser (XFEL) facilities, by damaging the crystals before they are probed. We investigated the shock damage in lysozyme microcrystals using a double-pulse operation mode at a low repetition...

Understanding high-velocity impact, and the subsequent high strain rate material deformation and potential catastrophic failure, is of critical importance across a range of scientific and engineering disciplines that include astrophysics, materials science, and aerospace engineering. The deformation and failure mechanisms are not thoroughly underst...

Kβ x-ray emission spectroscopy is a powerful probe for electronic structure analysis of 3d transition metal systems and their ultrafast dynamics. Selectively enhancing specific spectral regions would increase this sensitivity and provide fundamentally new insights. Recently we reported the observation and analysis of Kα amplified spontaneous x-ray...

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...

X-ray free-electron lasers (XFELs) enable crystallographic structure determination beyond the limitations imposed upon synchrotron measurements by radiation damage. The need for very short XFEL pulses is relieved through gating of Bragg diffraction by loss of crystalline order as damage progresses, but not if ionization events are spatially non-uni...

DOI:https://doi.org/10.1103/PhysRevLett.124.129903

We report experimental results on the diffractive imaging of three-dimensionally aligned 2,5-diiodothiophene molecules. The molecules were aligned by chirped near-infrared laser pulses, and their structure was probed at a photon energy of 9.5 keV (λ ≈ 130 pm) provided by the Linac Coherent Light Source. Diffracted photons were recorded on the Corne...

A major barrier to defining the structural intermediates that arise during the reversible photointerconversion of phytochromes between their biologically inactive and active states has been the lack of crystals that faithfully undergo this transition within the crystal lattice. Here, we describe a crystalline form of the cyclic GMP phosphodiesteras...

We report experimental results on the diffractive imaging of three-dimensionally aligned 2,5-diiodothiophene molecules. The molecules were aligned by chirped near-infrared laser pulses, and their structure was probed at a photon energy of 9.5 keV ($\lambda\approx130 \text{pm}$) provided by the Linac Coherent Light Source. Diffracted photons were re...

The role of surface wetting properties and their impact on the performance of 3D printed microfluidic droplet generation devices for serial femtosecond crystallography (SFX) are reported. SFX is a novel crystallography method enabling structure determination of proteins at room temperature with atomic resolution using X-ray free-electron lasers (XF...

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...

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 excitati...

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 stru...

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...

Bacteriorhodopsin (bR) is a light-driven proton pump. We use 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 allow identifying a sequential two-photon absorption process, leading to excitatio...

We investigated the generation and propagation of ultrasonic pressure waves produced by focused x-ray free-electron laser pulses in 14 to 30μm diameter liquid water microjets. The pressure waves formed through reflections, at the surface of the microjets, of the initial shock launched in the liquid by the x-ray pulse. These waves developed a charac...

Corrections to the article by Daurer et al.[IUCrJ (2017). 4, 251–262] are given.

ePix10K is a hybrid pixel detector developed at SLAC for demanding free-electron laser (FEL) applications, providing an ultrahigh dynamic range (245 eV to 88 MeV) through gain auto-ranging. It has three gain modes (high, medium and low) and two auto-ranging modes (high-to-low and medium-to-low). The first ePix10K cameras are built around modules co...

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 radia...

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)...

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-...

An accurate description of the interaction of intense hard X-ray pulses with heavy atoms, which is crucial for many applications of free-electron lasers, represents a hitherto unresolved challenge for theory because of the enormous number of electronic configurations and relativistic effects, which need to be taken into account. Here we report resu...

The ribosome translates nucleotide sequences of messenger RNA to proteins through selection of cognate transfer RNA according to the genetic code. To date, structural studies of ribosomal decoding complexes yielding high-resolution data have predominantly relied on experiments performed at cryogenic temperatures. New lightsources like the X-ray fre...

In this work, we monitor the onset of nonthermal melting in single-crystal silicon by implementing an x-ray pump–x-ray probe scheme. Using the ultrashort pulses provided by the Linac Coherent Light Source (SLAC) and a custom-built split-and-delay line for hard x rays, we achieve the temporal resolution needed to detect the onset of the transition....

ePix10K is a hybrid pixel detector developed at SLAC for demanding free-electron laser (FEL) applications, providing an ultrahigh dynamic range (245 eV to 88 MeV) through gain auto-ranging. It has three gain modes (high, medium and low) and two auto-ranging modes (high-to-low and medium-to-low). The first ePix10K cameras are built around modules co...

Look fast Organisms from bacteria to humans sense and react to light. Proteins that contain the light-sensitive molecule retinal couple absorption of light to conformational changes that produce a signal or move ions across a membrane. Nogly et al. used an x-ray laser to probe the earliest structural changes to the retinal chromophore within microc...

Background: Ever since the first atomic structure of an enzyme was solved, the discovery of the mechanism and dynamics of reactions catalyzed by biomolecules has been the key goal for the understanding of the molecular processes that drive life on earth. Despite a large number of successful methods for trapping reaction intermediates, the direct o...

Significance X-ray Free-Electron Lasers have opened the door to a new era in structural biology, enabling imaging of biomolecules and dynamics that were impossible to access with conventional methods. A vast majority of imaging experiments, including Serial Femtosecond Crystallography, use a liquid jet to deliver the sample into the interaction reg...

Here we present a new approach to diffraction imaging of amyloid fibrils, combining a free-standing graphene support and single nanofocused X-ray pulses of femtosecond duration from an X-ray free-electron laser. Due to the very low background scattering from the graphene support and mutual alignment of filaments, diffraction from tobacco mosaic vir...

We report the observation and analysis of the gain curve of amplified Kα x-ray emission from solutions of Mn(II) and Mn(VII) complexes using an x-ray free electron laser to create the 1s core-hole population inversion. We find spectra at amplification levels extending over 4 orders of magnitude until saturation. We observe bandwidths below the Mn 1...

The ribosome translates nucleotide sequences of messenger RNA to proteins through selection of cognate transfer RNA according to the genetic code. To date, structural studies of ribosomal decoding complexes yielding high-resolution data have predominantly relied on experiments performed at cryogenic temperatures. New lightsources like the X-ray fre...

Ever since the first atomic structure of an enzyme was solved, the discovery of the mechanism and dynamics of reactions catalyzed by biomolecules has been the key goal for the understanding of the molecular processes that drive life on earth. Despite a large number of successful methods for trapping reaction intermediates, the direct observation of...

Silicon drift detectors (SDDs) revolutionized spectroscopy in fields as diverse as geology and dentistry. For a subset of experiments at ultra-fast, x-ray free-electron lasers (FELs), SDDs can make substantial contributions. Often the unknown spectrum is interesting, carrying science data, or the background measurement is useful to identify unexpec...

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...

Silicon drift detectors (SDDs) revolutionized spectroscopy in fields as diverse as geology and dentistry. For a subset of experiments at ultra-fast, x-ray free-electron lasers (FELs), SDDs can make substantial contributions. Often the unknown spectrum is interesting, carrying science data, or the background measurement is useful to identify unexpec...

A major goal for X-ray free-electron laser (XFEL) based science is to elucidate structures of biological molecules without the need for crystals. Filament systems may provide some of the first single macromolecular structures elucidated by XFEL radiation, since they contain one-dimensional translational symmetry and thereby occupy the diffraction i...

X-ray free-electron lasers enable the investigation of the structure and dynamics of diverse systems, including atoms, molecules, nanocrystals and single bioparticles, under extreme conditions. Many imaging applications that target biological systems and complex materials use hard X-ray pulses with extremely high peak intensities (exceeding 10 20 w...

We provide a detailed description of selenobiotinyl-streptavidin (Se-B SA) co-crystal datasets recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS) for selenium single-wavelength anomalous diffraction (Se-SAD) structure determination. Se-B SA was chosen as the model system for its high affinity betwee...

This study explores the capabilities of the Coherent X-ray Imaging Instrument at the Linac Coherent Light Source to image small biological samples. The weak signal from small samples puts a significant demand on the experiment. Aerosolized Omono River virus particles of ∼40 nm in diameter were injected into the submicrometre X-ray focus at a reduce...

X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights i...

We present a catalog of hard X-ray sources in a square-degree region surveyed by NuSTAR in the direction of the Norma spiral arm. This survey has a total exposure time of 1.7 Ms, and typical and maximum exposure depths of 50 ks and 1 Ms, respectively. In the area of deepest coverage, sensitivity limits of $5\times10^{-14}$ and $4\times10^{-14}$ erg...

The distribution of elements produced in the inner-most layers of a supernova explosion is a key diagnostic for studying the collapse of massive stars. Here we present the results of a 2.4 Ms \textit{NuSTAR} observing campaign aimed at studying the supernova remnant Cassiopeia A (Cas A). We perform spatially-resolved spectroscopic analyses of the $...

Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn4CaO5 clu...

We present the 3–8 keV and 8–24 keV number counts of active galactic nuclei (AGNs) identified in the Nuclear Spectroscopic Telescope Array (NuSTAR) extragalactic surveys. NuSTAR has now resolved 33%–39% of the X-ray background in the 8–24 keV band, directly identifying AGNs with obscuring columns up to ~10²⁵ cm⁻². In the softer 3–8 keV band the numb...

Supplementary Figures 1-4, Supplementary Tables 1-2, Supplementary Note 1 and Supplementary References.

Structural information about biological macromolecules near the atomic scale provides important insight into the functions of these molecules. To date, X-ray crystallography has been the predominant method used for macromolecular structure determination. However, challenges exist when solving structures with X-rays, including the phase problem and...

BinAB is a naturally occurring paracrystalline larvicide distributed worldwide to combat the devastating diseases borne by mosquitoes. These crystals are composed of homologous molecules, BinA and BinB, which play distinct roles in the multi-step intoxication process, transforming from harmless, robust crystals, to soluble protoxin heterodimers, to...

We report the first hard X-ray observations with NuSTAR of the BL Lac type blazar PKS 2155-304, augmented with soft X-ray data from XMM-Newton and gamma-ray data from the Fermi Large Area Telescope, obtained in April 2013 when the source was in a very low flux state. A joint NuSTAR and XMM spectrum, covering the energy range 0.5 - 60 keV, is best d...

Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with...

Supplementary Figures 1-5.

The movie illustrates enhancement of the M state features in the electron density when increasing fractions (0 to 0.87) of the dark state are subtracted from the bR1ms data (nFobs(bR1ms)-mFobs(dark_bR)). Bacteriorhodopsin is shown in dark state (purple C atoms, PDB code: 5J7A) and M state (pink C atoms, PDB code: 1DZE). The electron density was dra...

We describe the deposition of four datasets consisting of X-ray diffraction images acquired using serial femtosecond crystallography experiments on microcrystals of human G protein-coupled receptors, grown and delivered in lipidic cubic phase, at the Linac Coherent Light Source. The receptors are: the human serotonin receptor 2B in complex with an...

This article describes a free and open-source data analysis utility designed for fast online feedback during serial X-ray diffraction and scattering experiments: OnDA (online data analysis). Three complete real-time monitors for common types of serial X-ray imaging experiments are presented. These monitors are capable of providing the essential inf...

Explosions are spectacular and intriguing phenomena that expose the dynamics of matter under extreme conditions. We investigated, using time-resolved imaging, explosions induced by ultraintense X-ray laser pulses in water drops and jets. Our observations revealed an explosive vaporization followed by high-velocity interacting flows of liquid and va...

Most experimental studies of cavitation in liquid water at negative pressures reported cavitation at tensions significantly smaller than those expected for homogeneous nucleation, suggesting that achievable tensions are limited by heterogeneous cavitation. We generated tension pulses with nanosecond rise times in water by reflecting cylindrical sho...

We present the first survey results of hard X-ray point sources in the Galactic Center (GC) region by NuSTAR. We have discovered 70 hard (3-79 keV) X-ray point sources in a 0.6 deg^2 region around Sgr A* with a total exposure of 1.7 Ms, and 7 sources in the Sgr B2 field with 300 ks. We identify clear Chandra counterparts for 58 NuSTAR sources and a...

Visualizing a response to light Many biological processes depend on detecting and responding to light. The response is often mediated by a structural change in a protein that begins when absorption of a photon causes isomerization of a chromophore bound to the protein. Pande et al. used x-ray pulses emitted by a free electron laser source to conduc...

Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) offers unprecedented possibilities for macromolecular structure determination of systems that are prone to radiation damage. However, phasing XFEL data de novo is complicated by the inherent inaccuracy of SFX data, and only a few successful examples, mostly based on exce...

The three-dimensional structures of macromolecules and their complexes are mainly elucidated by X-ray protein crystallography. A major limitation of this method is access to high-quality crystals, which is necessary to ensure X-ray diffraction extends to sufficiently large scattering angles and hence yields information of sufficiently high resoluti...

In condensed matter systems, strong optical excitations can induce phonon-driven processes that alter their mechanical properties. We report on a new phenomenon where a massive electronic excitation induces a collective change in the bond character that leads to transient lattice contraction. Single large van der Waals clusters were isochorically h...

Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with...

The three-dimensional structures of macromolecules and their complexes are mainly elucidated by X-ray protein crystallography. A major limitation of this method is access to high-quality crystals, which is necessary to ensure X-ray diffraction extends to sufficiently large scattering angles and hence yields information of sufficiently high resoluti...

We present coordinated multiwavelength observations of the bright, nearby BL Lac object Mrk 421 taken in 2013 January-March, involving GASP-WEBT, Swift, NuSTAR, Fermi-LAT, MAGIC, VERITAS, and other collaborations and instruments, providing data from radio to very-high-energy (VHE) gamma-ray bands. NuSTAR yielded previously unattainable sensitivity...