Jason Koglin
Stanford University, SLAC National Accelerator Laboratory, Department Member
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The Nuclear Spectroscopic Telescope Array (NuSTAR) is a small explorer (SMEX) mission currently under an extended Phase A study by NASA. NuSTAR will be the first satellite mission to employ focusing optics in the hard X-ray band (8-80... more
The Nuclear Spectroscopic Telescope Array (NuSTAR) is a small explorer (SMEX) mission currently under an extended Phase A study by NASA. NuSTAR will be the first satellite mission to employ focusing optics in the hard X-ray band (8-80 keV). Its design eliminates high detector backgrounds, allows true imaging, and permits the use of compact high performance detectors. The result: a combination of clarity, sensitivity, and spectral resolution surpassing the largest observatories that have operated in this band by orders of magnitude. We present an overview of the NuSTAR optics design and production process. We also describe the progress of several components of our independent optics development program that are beginning to reach maturity and could possibly be incorporated into the NuSTAR production scheme. We then present environmental test results that are being conducted in preparation of full space qualification of the NuSTAR optics.
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The Nuclear Spectroscopic Telescope Array (NuSTAR) will be the first focusing telescope on orbit to operate in the high energy X-ray band (6 - 79 keV). This Small Explorer Mission is currently under development, and is scheduled for... more
The Nuclear Spectroscopic Telescope Array (NuSTAR) will be the first focusing telescope on orbit to operate in the high energy X-ray band (6 - 79 keV). This Small Explorer Mission is currently under development, and is scheduled for launch in 2011. In this poster we describe the detailed performance characteristics the hard X-ray multilayer optics and shielded solid state focal plane detectors. We describe the expected throughput, spectroscopy and imaging properties of the observatory, as well as the planned data analysis and archiving plans.
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ABSTRACT The Nuclear Spectroscopic Telescope ARray (NuSTAR) was launched in June 2012 carrying the first focusing hard X-ray (5-80keV) optics to orbit. The multilayer coating was carried out at the Technical University of Denmark (DTU... more
ABSTRACT The Nuclear Spectroscopic Telescope ARray (NuSTAR) was launched in June 2012 carrying the first focusing hard X-ray (5-80keV) optics to orbit. The multilayer coating was carried out at the Technical University of Denmark (DTU Space). In this article we introduce the NuSTAR multilayer reference database and its implementation in the NuSTAR optic response model. The database and its implementation is validated using on-ground effective area calibration data and used to estimate in-orbit performance.
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Abstract The Nuclear Spectroscopic Telescope ARray (NuSTAR) is a NASA Small Explorer mission that will carry the first focusing hard X-ray (580 keV) telescope to orbit. The ground calibration of the optics posed a challenge as the need... more
Abstract The Nuclear Spectroscopic Telescope ARray (NuSTAR) is a NASA Small Explorer mission that will carry the first focusing hard X-ray (580 keV) telescope to orbit. The ground calibration of the optics posed a challenge as the need to suppress finite source distance ...
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ABSTRACT The Nuclear Spectroscopic Telescope Array (NuSTAR) is a NASA Small Explorer mission that will carry the first focusing hard X-ray (5− 80 keV) telescope to orbit. The ground calibration of the three flight optics was carried out... more
ABSTRACT The Nuclear Spectroscopic Telescope Array (NuSTAR) is a NASA Small Explorer mission that will carry the first focusing hard X-ray (5− 80 keV) telescope to orbit. The ground calibration of the three flight optics was carried out at the Rainwater Memorial ...
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ABSTRACT The Nuclear Spectroscopic Telescope Array (NuSTAR) launched in June 2012 carries the first focusing hard Xray (5 - 80 keV) telescope to orbit. The on-ground calibration was performed at the RaMCaF facility at Nevis, Columbia... more
ABSTRACT The Nuclear Spectroscopic Telescope Array (NuSTAR) launched in June 2012 carries the first focusing hard Xray (5 - 80 keV) telescope to orbit. The on-ground calibration was performed at the RaMCaF facility at Nevis, Columbia University. During the assembly of the telescopes, mechanical surface metrology provided surface maps of the reflecting surfaces. Several flight coated mirrors were brought to BNL for scattering measurements. The information from both sources is fed to a raytracing code that is tested against the on-ground calibration data. The code is subsequently used for predicting the imaging properties for X-ray sources at infinite distance.
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This paper outlines an in-depth study of the W/Si coated mirrors for the High Energy Focusing Telescope (HEFT). We present data taken at 8, 40 and 60 keV obtained at the Danish Space Research Institute and the European Synchrotron... more
This paper outlines an in-depth study of the W/Si coated mirrors for the High Energy Focusing Telescope (HEFT). We present data taken at 8, 40 and 60 keV obtained at the Danish Space Research Institute and the European Synchrotron Radiation Facility in Grenoble. The set of samples were chosen to cover the parameter space of sample type, sample size and
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Research Interests: Mechanical Engineering, Near Field Optics, Atomic Force Microscopy, Near-field scanning optical microscopy, Optical microscopy, and 8 moreElectromagnetic Field, Applied Optics, Optical physics, Atomic Force Microscope, Rayleigh Scattering, Electrical And Electronic Engineering, Optical Microscope, and Near Field
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... more
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 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4), in which S1 is the dark-stable state and S3 is the last semi-stable state before O-O bond formation and O2 evolution. A detailed understanding of the O-O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S1), two-fla...
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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... more
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 internalized mature toxin, and finally to toxic oligomeric pores. The small size of the crystals-50 unit cells per edge, on average-has impeded structural characterization by conventional means. Here we report the structure of Lysinibacillus sphaericus BinAB solved de novo by serial-femtosecond crystallography at an X-ray free-electron laser. The structure reveals tyrosine- and carboxylate-mediated contacts acting as pH switches to release soluble protoxin in the alkaline larval midgut. An enormous heterodimeric interface appears to be responsible for anchoring BinA to receptor-bound BinB for co-internalization. Remarkably, this interface...
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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... more
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 agonist ergotamine, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH2, the human smoothened receptor in complex with an antagonist cyclopamine, and finally the human angiotensin II type 1 receptor in complex with the selective antagonist ZD7155. All four datasets have been deposited, with minimal processing, in an HDF5-based file format, which can be used directly for crystallographic processing with CrystFEL or other software. We have provided processing scripts and supporting files for recent versions of CrystFEL, which can be used to validate the data.
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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... more
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 information required for quick decision making in the face of extreme rates of data collection. In addition, a set of modules, functions and algorithms that allow developers to modify the provided monitors or develop new ones are provided. The emphasis here is on simple, modular and scalable code that is based on open-source libraries and protocols. OnDA monitors have already proven to be invaluable tools in several experiments, especially for scoring and monitoring of diffraction data during serial crystallography experiments at both free-electron laser and synchrotron facilities. It is felt that in the future the kind of fast feedback that ...
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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... more
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 shock waves, produced by X-ray laser pulses, at the internal surface of drops of water. Depending on the X-ray pulse energy, a range of cavitation phenomena occurred, including the rupture and detachment, or spallation, of thin liquid layers at the surface of the drop. When spallation occurred, we evaluated that negative pressures below -100 MPa were reached in the drops. We model the negative pressures from shock reflection experiments using a nucleation-and-growth model that explains how rapid decompression could outrun heterogeneous cavitation in water, and enable the study of stretched water close to homogeneous cavitation pressures.
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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 datade... more
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 datade novois complicated by the inherent inaccuracy of SFX data, and only a few successful examples, mostly based on exceedingly strong anomalous or isomorphous difference signals, have been reported. Here, it is shown that SFX data from thaumatin microcrystals can be successfully phased using only the weak anomalous scattering from the endogenous S atoms. Moreover, a step-by-step investigation is presented of the particular problems of SAD phasing of SFX data, analysing data from a derivative with a strong anomalous signal as well as the weak signal from endogenous S atoms.
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... more
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 resolution with which to solve the crystal structure. The observation that crystals with reduced unit-cell volumes and tighter macromolecular packing often produce higher-resolution Bragg peaks suggests that crystallographic resolution for some macromolecules may be limited not by their heterogeneity, but by a deviation of strict positional ordering of the crystalline lattice. Such displacements of molecules from the ideal lattice give rise to a continuous diffraction pattern that is equal to the incoherent sum of diffraction from rigid individual molecular complexes aligned along several discrete crystallographic orientations and that, consequent...
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Free-electron lasers (FELs) are pushing back the limits of possibility in protein crystallography. Using the high-intensity, femtosecond duration pulses afforded by FELs allow data collection from micrometer-sized crystals while... more
Free-electron lasers (FELs) are pushing back the limits of possibility in protein crystallography. Using the high-intensity, femtosecond duration pulses afforded by FELs allow data collection from micrometer-sized crystals while outrunning radiation damage. Moreover, FELs may be used for pump-probe experiments with unprecedented time resolution. However, the intricacies of FEL data collection pose specific challenges: as every FEL pulse destroys the sample, data are mostly collected from a stream of microcrystals and averaged to remove the variations in crystal size and quality as well as shot-to-shot variations in beam parameters. This technique is called serial femtosecond crystallography (SFX). In SFX, several tens of thousands of images typically need to be averaged to obtain reasonably accurate structure factor amplitudes. We previously showed that SFX yields structure factor amplitudes accurate enough to detect the weak anomalous signal of endogenous sulfur atoms. Now we show ...
Intense femtosecond x-ray pulses produced at the Linac Coherent Light Source (LCLS) were used for simultaneous x-ray diffraction (XRD) and x-ray emission spectroscopy (XES) of microcrystals of photosystem II (PS II) at room temperature.... more
Intense femtosecond x-ray pulses produced at the Linac Coherent Light Source (LCLS) were used for simultaneous x-ray diffraction (XRD) and x-ray emission spectroscopy (XES) of microcrystals of photosystem II (PS II) at room temperature. This method probes the overall protein structure and the electronic structure of the Mn4CaO5 cluster in the oxygen-evolving complex of PS II. XRD data are presented from both the dark state (S1) and the first illuminated state (S2) of PS II. Our simultaneous XRD-XES study shows that the PS II crystals are intact during our measurements at the LCLS, not only with respect to the structure of PS II, but also with regard to the electronic structure of the highly radiation-sensitive Mn4CaO5 cluster, opening new directions for future dynamics studies.
Research Interests: Physics, Chemistry, Crystallography, Water, Free Electron Lasers, and 18 moreStructural Biology, Science, Cyanobacteria, Electrospinning, Multidisciplinary, Macromolecular X-Ray Crystallography, Physical sciences, Light, Temperature, X-ray free electron laser, CHEMICAL SCIENCES, Electrons, X ray diffraction, Protein Conformation, Serial Femtosecond Crystallography, Oxides, Manganese Compounds, and Oxidation-Reduction
We describe the design, construction and performance of the PIBETA detector built for the precise measurement of the branching ratio of pion beta decay, π+→ π0e+ νe, at the Paul Scherrer Institute. The central part of the detector is a... more
We describe the design, construction and performance of the PIBETA detector built for the precise measurement of the branching ratio of pion beta decay, π+→ π0e+ νe, at the Paul Scherrer Institute. The central part of the detector is a 240-module spherical pure CsI ...
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Nearly 30 years ago, the Einstein observatory introduced grazing incidence focusing optics for soft X-rays ( 0.1-10 keV), completely changing our view of the X-ray sky. The Nuclear Spectroscopic Telescope Array (NuSTAR), a NASA satellite... more
Nearly 30 years ago, the Einstein observatory introduced grazing incidence focusing optics for soft X-rays ( 0.1-10 keV), completely changing our view of the X-ray sky. The Nuclear Spectroscopic Telescope Array (NuSTAR), a NASA satellite mission, is poised to similarly open the next energy decade - the hard X-ray band from 6 to 80 keV. Using focusing optics with multilayer coating for enhanced reflectivity at high energies, NuSTAR will provide a combination of clarity, sensitivity and spectral resolution surpassing the largest observatories in this band by orders of magnitude. This advance will allow NuSTAR to test theories of how heavy elements are born, discover collapsed stars and black holes on all scales and explore the most extreme physical environments. We will present an overview of the NuSTAR optics design and production process and detail the optics performance. We will also describe our optics calibration plans. As part of this discussion, we will include ground and in-fl...
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X-ray free-electron laser sources such as the Linac Coherent Light Source offer very exciting possibilities for unique research. However, beam time at such facilities is very limited and in high demand. This has led to significant efforts... more
X-ray free-electron laser sources such as the Linac Coherent Light Source offer very exciting possibilities for unique research. However, beam time at such facilities is very limited and in high demand. This has led to significant efforts towards beam multiplexing of various forms. One such effort involves re-using the so-called spent beam that passes through the hole in an area detector after a weak interaction with a primary sample. This beam can be refocused into a secondary interaction region and used for a second, independent experiment operating in series. The beam profile of this refocused beam was characterized for a particular experimental geometry at the Coherent X-ray Imaging instrument at LCLS. A demonstration of this multiplexing capability was performed with two simultaneous serial femtosecond crystallography experiments, both yielding interpretable data of sufficient quality to produce electron density maps.
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Serial femtosecond crystallography (SFX) is an emerging method for data collection at free-electron lasers (FELs) in which single diffraction snapshots are taken from a large number of crystals. The partial intensities collected in this... more
Serial femtosecond crystallography (SFX) is an emerging method for data collection at free-electron lasers (FELs) in which single diffraction snapshots are taken from a large number of crystals. The partial intensities collected in this way are then combined in a scheme called Monte Carlo integration, which provides the full diffraction intensities. However, apart from having to perform this merging, the Monte Carlo integration must also average out all variations in crystal quality, crystal size, X-ray beam properties and other factors, necessitating data collection from thousands of crystals. Because the pulses provided by FELs running in the typical self-amplified spontaneous emission (SASE) mode of operation have very irregular, spiky spectra that vary strongly from pulse to pulse, it has been suggested that this is an important source of variation contributing to inaccuracies in the intensities, and that, by using monochromatic pulses produced through a process called self-seeding, fewer images might be needed for Monte Carlo integration to converge, resulting in more accurate data. This paper reports the results of two experiments performed at the Linac Coherent Light Source in which data collected in both SASE and self-seeded mode were compared. Importantly, no improvement attributable to the use of self-seeding was detected. In addition, other possible sources of variation that affect SFX data quality were investigated, such as crystal-to-crystal variations reflected in the unit-cell parameters; however, these factors were found to have no influence on data quality either. Possibly, there is another source of variation as yet undetected that affects SFX data quality much more than any of the factors investigated here.
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The Nuclear Spectroscopic Telescope Array (NuSTAR) is a NASA Small Explorer (SMEX) mission which employs two focusing optics. The optics are composed of stacks of thin mirror shells and spacers. Epoxy is used to bond the mirror shells to... more
The Nuclear Spectroscopic Telescope Array (NuSTAR) is a NASA Small Explorer (SMEX) mission which employs two focusing optics. The optics are composed of stacks of thin mirror shells and spacers. Epoxy is used to bond the mirror shells to the spacers and is a crucial component in determining the structural and optical performance of the telescopes. We describe the epoxy
Hard X-ray/soft gamma-ray astrophysics is on the verge of a major advance with the practical realization of technologies capable of efficiently focusing X-rays above 10 keV. Hard X-ray focusing telescopes can achieve orders of magnitude... more
Hard X-ray/soft gamma-ray astrophysics is on the verge of a major advance with the practical realization of technologies capable of efficiently focusing X-rays above 10 keV. Hard X-ray focusing telescopes can achieve orders of magnitude improvements in sensitivity compared to the instruments based on coded apertures and collimated detectors that have traditionally been employed in this energy band. Compact focal
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We report on recent work on the General Antiparticle Spectrometer Experiment (GAPS). GAPS is a balloon-based search for antideuterons generated in the annihilation of weakly interacting massive particles. Antideuterons provide an... more
We report on recent work on the General Antiparticle Spectrometer Experiment (GAPS). GAPS is a balloon-based search for antideuterons generated in the annihilation of weakly interacting massive particles. Antideuterons provide an extremely clean signature of dark matter. It is difficult to produce backgrounds that mimic the annihilation antideuterons. GAPS consists of a time-of-flight system combined with a multi-layer particle tracker
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Proteins that contain metal cofactors are expected to be highly radiation sensitive since the degree of X-ray absorption correlates with the presence of high-atomic-number elements and X-ray energy. To explore the effects of local damage... more
Proteins that contain metal cofactors are expected to be highly radiation sensitive since the degree of X-ray absorption correlates with the presence of high-atomic-number elements and X-ray energy. To explore the effects of local damage in serial femtosecond crystallography (SFX), Clostridium ferredoxin was used as a model system. The protein contains two [4Fe-4S] clusters that serve as sensitive probes for radiation-induced electronic and structural changes. High-dose room-temperature SFX datasets were collected at the Linac Coherent Light Source of ferredoxin microcrystals. Difference electron density maps calculated from high-dose SFX and synchrotron data show peaks at the iron positions of the clusters, indicative of decrease of atomic scattering factors due to ionization. The electron density of the two [4Fe-4S] clusters differs in the FEL data, but not in the synchrotron data. Since the clusters differ in their detailed architecture, this observation is suggestive of an influ...
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It has long been known that toxins produced by Bacillus thuringiensis (Bt) are stored in the bacterial cells in crystalline form. Here we describe the structure determination of the Cry3A toxin found naturally crystallized within Bt... more
It has long been known that toxins produced by Bacillus thuringiensis (Bt) are stored in the bacterial cells in crystalline form. Here we describe the structure determination of the Cry3A toxin found naturally crystallized within Bt cells. When whole Bt cells were streamed into an X-ray free-electron laser beam we found that scattering from other cell components did not obscure diffraction from the crystals. The resolution limits of the best diffraction images collected from cells were the same as from isolated crystals. The integrity of the cells at the moment of diffraction is unclear; however, given the short time (∼ 5 µs) between exiting the injector to intersecting with the X-ray beam, our result is a 2.9-Å-resolution structure of a crystalline protein as it exists in a living cell. The study suggests that authentic in vivo diffraction studies can produce atomic-level structural information.
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NuSTAR is a hard X-ray satellite experiment to be launched in 2012. Two optics with 10.15 m focal length focus Xrays with energies between 5 and 80 keV onto CdZnTe detectors located at the end of a deployable mast. The FM1 and FM2 flight... more
NuSTAR is a hard X-ray satellite experiment to be launched in 2012. Two optics with 10.15 m focal length focus Xrays with energies between 5 and 80 keV onto CdZnTe detectors located at the end of a deployable mast. The FM1 and FM2 flight optics were built at the same time based on the same design and with very similar
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Serial femtosecond crystallography using ultrashort pulses from x-ray free electron lasers (XFELs) enables studies of the light-triggered dynamics of biomolecules. We used microcrystals of photoactive yellow protein (a bacterial blue... more
Serial femtosecond crystallography using ultrashort pulses from x-ray free electron lasers (XFELs) enables studies of the light-triggered dynamics of biomolecules. We used microcrystals of photoactive yellow protein (a bacterial blue light photoreceptor) as a model system and obtained high-resolution, time-resolved difference electron density maps of excellent quality with strong features; these allowed the determination of structures of reaction intermediates to a resolution of 1.6 angstroms. Our results open the way to the study of reversible and nonreversible biological reactions on time scales as short as femtoseconds under conditions that maximize the extent of reaction initiation throughout the crystal.