The time-resolved atomic, molecular and optical science instrument at the Linac Coherent Light Source.

The newly constructed time-resolved atomic, molecular and optical science instrument (TMO) is configured to take full advantage of both linear accelerators at SLAC National Accelerator Laboratory, the copper accelerator operating at a repetition rate of 120 Hz providing high per-pulse energy as well as the superconducting accelerator operating at a repetition rate of about 1 MHz providing high average intensity. Both accelerators power a soft X-ray free-electron laser with the new variable-gap undulator section. With this flexible light source, TMO supports many experimental techniques not previously available at LCLS and will have two X-ray beam focus spots in line. Thereby, TMO supports atomic, molecular and optical, strong-field and nonlinear science and will also host a designated new dynamic reaction microscope with a sub-micrometer X-ray focus spot. The flexible instrument design is optimized for studying ultrafast electronic and molecular phenomena and can take full advantage of the sub-femtosecond soft X-ray pulse generation program.

X-ray free-electron laser wavefront sensing using the fractional Talbot effect.

Wavefront sensing at X-ray free-electron lasers is important for quantitatively understanding the fundamental properties of the laser, for aligning X-ray instruments and for conducting scientific experimental analysis. A fractional Talbot wavefront sensor has been developed. This wavefront sensor enables measurements over a wide range of energies, as is common on X-ray instruments, with simplified mechanical requirements and is compatible with the high average power pulses expected in upcoming X-ray free-electron laser upgrades. Single-shot measurements were performed at 500 eV, 1000 eV and 1500 eV at the Linac Coherent Light Source. These measurements were applied to study both mirror alignment and the effects of undulator tapering schemes on source properties. The beamline focal plane position was tracked to an uncertainty of 0.12 mm, and the source location for various undulator tapering schemes to an uncertainty of 1 m, demonstrating excellent sensitivity. These findings pave the way to use the fractional Talbot wavefront sensor as a routine, robust and sensitive tool at X-ray free-electron lasers as well as other high-brightness X-ray sources.

Phonon-Suppressed Auger Scattering of Charge Carriers in Defective Two-Dimensional Transition Metal Dichalcogenides.

Two-dimensional transition metal dichalcogenides (TMDs) draw strong interest in materials science, with applications in optoelectronics and many other fields. Good performance requires high carrier concentrations and long lifetimes. However, high concentrations accelerate energy exchange between charged particles by Auger-type processes, especially in TMDs where many-body interactions are strong, thus facilitating carrier trapping. We report time-resolved optical pump-THz probe measurements of carrier lifetimes as a function of carrier density. Surprisingly, the lifetime reduction with increased density is very weak. It decreases only by 20% when we increase the pump fluence 100 times. This unexpected feature of the Auger process is rationalized by our time-domain ab initio simulations. The simulations show that phonon-driven trapping competes successfully with the Auger process. On the one hand, trap states are relatively close to band edges, and phonons accommodate efficiently the electronic energy during the trapping. On the other hand, trap states localize around defects, and the overlap of trapped and free carriers is small, decreasing carrier-carrier interactions. At low carrier densities, phonons provide the main charge trapping mechanism, decreasing carrier lifetimes compared to defect-free samples. At high carrier densities, phonons suppress Auger processes and lower the dependence of the trapping rate on carrier density. Our results provide theoretical insights into the diverse roles played by phonons and Auger processes in TMDs and generate guidelines for defect engineering to improve device performance at high carrier densities.

Optical Control of Non-Equilibrium Phonon Dynamics.

The light-induced selective population of short-lived far-from-equilibrium vibration modes is a promising approach for controlling ultrafast and irreversible structural changes in functional nanomaterials. However, this requires a detailed understanding of the dynamics and evolution of these phonon modes and their coupling to the excited-state electronic structure. Here, we combine femtosecond mega-electronvolt electron diffraction experiments on a prototypical layered material, MoTe2, with non-adiabatic quantum molecular dynamics simulations and ab initio electronic structure calculations to show how non-radiative energy relaxation pathways for excited electrons can be tuned by controlling the optical excitation energy. We show how the dominant intravalley and intervalley scattering mechanisms for hot and band-edge electrons leads to markedly different transient phonon populations evident in electron diffraction patterns. This understanding of how tuning optical excitations affect phonon populations and atomic motion is critical for efficiently controlling light-induced structural transitions of optoelectronic devices.

Fluorescence intensity monitors as intensity and beam-position diagnostics for X-ray free-electron lasers.

For LCLS-II, a fluorescence intensity monitor for the non-invasive, pulse-by-pulse normalization of experiments has been developed. A prototype diagnostic was constructed with a microchannel plate assembly and two photodiodes. The diagnostic was then installed in the LCLS SXR instrument Kirkpatrick-Baez mirror chamber with the detectors located above the vertically reflecting mirror. The linearity, noise and position sensitivity of the detectors have been characterized. The photodiode responsivity is suitable for high pulse energies. The microchannel plate detector shows sufficient responsivity over a wide range of pulse energies. The relative signal from the two photodiodes provides a sensitive measure of the X-ray beam position. The fluorescence intensity monitor provides intensity normalization while being compatible with high incident power, a 0.93 MHz repetition rate and ultra-high vacuum.

Laser power meters as an X-ray power diagnostic for LCLS-II.

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.

Imaging transient melting of a nanocrystal using an X-ray laser.

There is a fundamental interest in studying photoinduced dynamics in nanoparticles and nanostructures as it provides insight into their mechanical and thermal properties out of equilibrium and during phase transitions. Nanoparticles can display significantly different properties from the bulk, which is due to the interplay between their size, morphology, crystallinity, defect concentration, and surface properties. Particularly interesting scenarios arise when nanoparticles undergo phase transitions, such as melting induced by an optical laser. Current theoretical evidence suggests that nanoparticles can undergo reversible nonhomogenous melting with the formation of a core-shell structure consisting of a liquid outer layer. To date, studies from ensembles of nanoparticles have tentatively suggested that such mechanisms are present. Here we demonstrate imaging transient melting and softening of the acoustic phonon modes of an individual gold nanocrystal, using an X-ray free electron laser. The results demonstrate that the transient melting is reversible and nonhomogenous, consistent with a core-shell model of melting. The results have implications for understanding transient processes in nanoparticles and determining their elastic properties as they undergo phase transitions.

Competing Repressive Factors Control Bone Morphogenetic Protein 2 (BMP2) in Mesenchymal Cells.

The amount, timing, and location of bone morphogenetic protein 2 (BMP2) synthesis influences the differentiation of pluripotent mesenchymal cells in embryos and adults. The BMP2 3'untranslated region (3'UTR) contains a highly conserved AU-rich element (ARE) embedded in a sequence that commonly represses gene expression in mesenchymal cells. Computational analyses indicate that this site also may bind several microRNAs (miRNAs). Although miRNAs frequently target AU-rich regions, this ARE is unusual because the miRNAs directly span the ARE. We began to characterize the factors that may regulate Bmp2 expression via this complex site. The activating protein HuR (Hu antigen R, ELAVL1, HGNC:3312) directly binds this ARE and can activate gene expression. An miRNA was demonstrated to reverse HuR-mediated activation. Mutational and RNA-interference evidence also supports an AUF1 (AU-factor-1, HNRNPD, HGNC:5036) contribution to the observed repressive activity of the 3'UTR in mesenchymal cells. A limited number of studies describe how miRNAs interact with ARE-binding proteins that bind adjacent sites. This study is among the first to describe protein/miRNA interactions at the same site.

The X-ray Pump-Probe instrument at the Linac Coherent Light Source.

The X-ray Pump-Probe instrument achieves femtosecond time-resolution with hard X-ray methods using a free-electron laser source. It covers a photon energy range of 4-24 keV. A femtosecond optical laser system is available across a broad spectrum of wavelengths for generating transient states of matter. The instrument is designed to emphasize versatility and the scientific goals encompass ultrafast physical, chemical and biological processes involved in the transformation of matter and transfer of energy at the atomic scale.

Femtosecond X-ray absorption spectroscopy at a hard X-ray free electron laser: application to spin crossover dynamics.

X-ray free electron lasers (XFELs) deliver short (<100 fs) and intense (∼10(12) photons) pulses of hard X-rays, making them excellent sources for time-resolved studies. Here we show that, despite the inherent instabilities of current (SASE based) XFELs, they can be used for measuring high-quality X-ray absorption data and we report femtosecond time-resolved X-ray absorption near-edge spectroscopy (XANES) measurements of a spin-crossover system, iron(II) tris(2,2'-bipyridine) in water. The data indicate that the low-spin to high-spin transition can be modeled by single-exponential kinetics convoluted with the overall time resolution. The resulting time constant is ∼160 fs.

Quantification of urban mitigation potentials - coping with data heterogeneity.

Cities are at the forefront of European and international climate action. However, in many cities, the ever-growing urban population is putting pressure on settlement and infrastructure development, increasing attention to urban planning, infrastructure and buildings. This paper introduces a set of quantification approaches, capturing impacts of urban planning measures in three fields of action: sustainable building, transport and redensification. The quantification approaches have been developed to account for different levels of data availability, thus providing users with quantification approaches that are applicable across cities. The mitigation potentials of various measures such as a modal shift, the substitution of building materials with wood, and different redensification scenarios were calculated. The substitution of conventional building materials with wood was analyzed as having a high mitigation potential. Building construction, in combination with urban planning and design, are key drivers for mitigating climate change in cities. Given the data heterogeneity among cities, mixed quantification approaches could be defined and the measures and policy areas with the greatest climate mitigation potential identified.

Single-shot analysis of hard x-ray laser radiation using a noninvasive grating spectrometer.

We present a spectrometer setup based on grating dispersion for hard x-ray free-electron lasers. This setup consists of a focusing spectrometer grating and a charge-integrating microstrip detector. Measurement results acquired at Linac Coherent Light Source are presented, demonstrating noninvasive monitoring of single-shot spectra with a resolution of 2.0×10(-4) ±0.3×10(-4) at photon energy of 6 keV with more than 95% transmission of the main beam.

Ultrafast photovoltaic response in ferroelectric nanolayers.

We show that light drives large-amplitude structural changes in thin films of the prototypical ferroelectric PbTiO3 via direct coupling to its intrinsic photovoltaic response. Using time-resolved x-ray scattering to visualize atomic displacements on femtosecond time scales, photoinduced changes in the unit-cell tetragonality are observed. These are driven by the motion of photogenerated free charges within the ferroelectric and can be simply explained by a model including both shift and screening currents, associated with the displacement of electrons first antiparallel to and then parallel to the ferroelectric polarization direction.

An in vivo map of bone morphogenetic protein 2 post-transcriptional repression in the heart.

The Bmp2 3'untranslated region (UTR) sequence bears a sequence conserved between mammals and fishes that can post-transcriptionally activate or repress protein synthesis. We developed a map of embryonic cells in the mouse where this potent Bmp2 regulatory sequence functions by using a lacZ reporter transgene with a 3'UTR bearing two loxP sites flanking the ultra-conserved sequence. Cre-recombinase-mediated deletion of the ultra-conserved sequence caused strong ectopic expression in proepicardium, epicardium and epicardium-derived cells (EPDC) and in tissues with known epicardial contributions (coronary vessels and valves). Transient transfections of reporters in the epicardial/mesothelial cell (EMC) line confirmed this repression. Ectopic expression of the recombined transgene also occurred in the aorta, outlet septum, posterior cardiac plexus, cardiac and extracardiac nerves and neural ganglia. Bmp2 is dynamically regulated in the developing heart. 3'UTR-mediated mechanisms that restrain BMP2 synthesis may be relevant to congenital heart and vasculature malformations and to adult diseases involving aberrant BMP2 synthesis.

The cluster 1 type VI secretion system is a major virulence determinant in Burkholderia pseudomallei.

The Burkholderia pseudomallei K96243 genome encodes six type VI secretion systems (T6SSs), but little is known about the role of these systems in the biology of B. pseudomallei. In this study, we purified recombinant Hcp proteins from each T6SS and tested them as vaccine candidates in the BALB/c mouse model of melioidosis. Recombinant Hcp2 protected 80% of mice against a lethal challenge with K96243, while recombinant Hcp1, Hcp3, and Hcp6 protected 50% of mice against challenge. Hcp6 was the only Hcp constitutively produced by B. pseudomallei in vitro; however, it was not exported to the extracellular milieu. Hcp1, on the other hand, was produced and exported in vitro when the VirAG two-component regulatory system was overexpressed in trans. We also constructed six hcp deletion mutants (Δhcp1 through Δhcp6) and tested them for virulence in the Syrian hamster model of infection. The 50% lethal doses (LD(50)s) for the Δhcp2 through Δhcp6 mutants were indistinguishable from K96243 (<10 bacteria), but the LD(50) for the Δhcp1 mutant was >10(3) bacteria. The hcp1 deletion mutant also exhibited a growth defect in RAW 264.7 macrophages and was unable to form multinucleated giant cells in this cell line. Unlike K96243, the Δhcp1 mutant was only weakly cytotoxic to RAW 264.7 macrophages 18 h after infection. The results suggest that the cluster 1 T6SS is essential for virulence and plays an important role in the intracellular lifestyle of B. pseudomallei.

An autonomous BMP2 regulatory element in mesenchymal cells.

BMP2 is a morphogen that controls mesenchymal cell differentiation and behavior. For example, BMP2 concentration controls the differentiation of mesenchymal precursors into myocytes, adipocytes, chondrocytes, and osteoblasts. Sequences within the 3'untranslated region (UTR) of the Bmp2 mRNA mediate a post-transcriptional block of protein synthesis. Interaction of cell and developmental stage-specific trans-regulatory factors with the 3'UTR is a nimble and versatile mechanism for modulating this potent morphogen in different cell types. We show here, that an ultra-conserved sequence in the 3'UTR functions independently of promoter, coding region, and 3'UTR context in primary and immortalized tissue culture cells and in transgenic mice. Our findings indicate that the ultra-conserved sequence is an autonomously functioning post-transcriptional element that may be used to modulate the level of BMP2 and other proteins while retaining tissue specific regulatory elements.

The role of the phoPQ operon in the pathogenesis of the fully virulent CO92 strain of Yersinia pestis and the IP32953 strain of Yersinia pseudotuberculosis.

At the genomic level, Yersinia pestis and Yersinia pseudotuberculosis are nearly identical but cause very different diseases. Y. pestis is the etiologic agent of plague; whereas Y. pseudotuberculosis causes a gastrointestinal infection primarily after the consumption of contaminated food. In many gram-negative pathogenic bacteria, PhoP is part of a two-component global regulatory system in which PhoQ serves as the sensor kinase, and PhoP is the response regulator. PhoP is known to activate a number of genes in many bacteria related to virulence. To determine the role of the PhoPQ proteins in Yersinia infections, primarily using aerosol challenge models, the phoP gene was deleted from the chromosome of the CO92 strain of Y. pestis and the IP32953 strain of Y. pseudotuberculosis, leading to a polar mutation of the phoPQ operon. We demonstrated that loss of phoPQ from both strains leads to a defect in intracellular growth and/or survival within macrophages. These in vitro data would suggest that the phoPQ mutants would be attenuated in vivo. However, the LD(50) for the Y. pestis mutant did not differ from the calculated LD(50) for the wild-type CO92 strain for either the bubonic or pneumonic murine models of infection. In contrast, mice challenged by aerosol with the Y. pseudotuberculosis mutant had a LD(50) value 40× higher than the wild-type strain. These results demonstrate that phoPQ are necessary for full virulence by aerosol infection with the IP32953 strain of Y. pseudotuberculosis. However, the PhoPQ proteins do not play a significant role in infection with a fully virulent strain of Y. pestis.

Carrier-specific dynamics in 2H-MoTe2 observed by femtosecond soft x-ray absorption spectroscopy using an x-ray free-electron laser.

Femtosecond carrier dynamics in layered 2H-MoTe2 semiconductor crystals have been investigated using soft x-ray transient absorption spectroscopy at the x-ray free-electron laser (XFEL) of the Pohang Accelerator Laboratory. Following above-bandgap optical excitation of 2H-MoTe2, the photoexcited hole distribution is directly probed via short-lived transitions from the Te 3d 5/2 core level (M5-edge, 572-577 eV) to transiently unoccupied states in the valence band. The optically excited electrons are separately probed via the reduced absorption probability at the Te M5-edge involving partially occupied states of the conduction band. A 400 ± 110 fs delay is observed between this transient electron signal near the conduction band minimum compared to higher-lying states within the conduction band, which we assign to hot electron relaxation. Additionally, the transient absorption signals below and above the Te M5 edge, assigned to photoexcited holes and electrons, respectively, are observed to decay concomitantly on a 1-2 ps timescale, which is interpreted as electron-hole recombination. The present work provides a benchmark for applications of XFELs for soft x-ray absorption studies of carrier-specific dynamics in semiconductors, and future opportunities enabled by this method are discussed.

A conserved post-transcriptional BMP2 switch in lung cells.

An ultra-conserved sequence in the bone morphogenetic protein 2 (BMP2) 3' untranslated region (UTR) markedly represses BMP2 expression in non-transformed lung cells. In contrast, the ultra-conserved sequence stimulates BMP2 expression in transformed lung cells. The ultra-conserved sequence functions as a post-transcriptional cis-regulatory switch. A common single-nucleotide polymorphism (SNP, rs15705, +A1123C), which has been shown to influence human morphology, disrupts a conserved element within the ultra-conserved sequence and altered reporter gene activity in non-transformed lung cells. This polymorphism changed the affinity of the BMP2 RNA for several proteins including nucleolin, which has an increased affinity for the C allele. Elevated BMP2 synthesis is associated with increased malignancy in mouse models of lung cancer and poor lung cancer patient prognosis. Understanding the cis- and trans-regulatory factors that control BMP2 synthesis is relevant to the initiation or progression of pathologies associated with abnormal BMP2 levels.

Repressive BMP2 gene regulatory elements near the BMP2 promoter.

The level of bone morphogenetic protein 2 (BMP2) profoundly influences essential cell behaviors such as proliferation, differentiation, apoptosis, and migration. The spatial and temporal pattern of BMP2 synthesis, particular in diverse embryonic cells, is highly varied and dynamic. We have identified GC-rich sequences within the BMP2 promoter region that strongly repress gene expression. These elements block the activity of a highly conserved, osteoblast enhancer in response to FGF2 treatment. Both positive and negative gene regulatory elements control BMP2 synthesis. Detecting and mapping the repressive motifs is essential because they impede the identification of developmentally regulated enhancers necessary for normal BMP2 patterns and concentration.