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X-RAY RUNS: Apply for Beamtime

2017  Nov 1 - Dec 21

2018  Feb 7 - Apr 3
2018  Proposal/BTR deadline: 12/1/17

2018  Apr 11 - Jun 4
2018  Proposal/BTR deadline: 2/1/18


Poster Abstracts

"Spoked Channel Arrays for confocal x-ray fluorescence microscopy"

David Agyeman-Budu1, Arthur R Woll2 and Joel D Brock2,3
1Department of Materials Science and Engineering, Cornell University, Ithaca NY 14853; 2Cornell High Energy Synchrotron Source, Ithaca NY 14853; 3Department of Applied & Engineering Physics, Cornell University, Ithaca NY 14853

Abstract: This project builds on the development of nanofabricated x-ray optics - in particular, Spoked Channel Arrays (SCA) development for Confocal X-ray Fluorescence (CXRF). CXRF is a depth resolved probe technique employed to interrogate the “chemical composition vs depth” information of thin films or virtual cross sections of bulk materials using fluorescent x-rays from a micro focused probe source. Two optics are therefore required for this technique - a focusing optic and a collection optic. The overlap of the focus of the collector and focusing optic creates the 3D excitation volume which is utilized as a scanning microprobe. SCAs are excellent collection optics in this regard since they have a nearly energy independent resolution and are more flexible to design.

The SCAs are nanofabricated by deep reactive ion etching of germanium substrates. The use of germanium is the natural progression from our previous efforts [1, 2] with silicon optics where the useful range of operating energies was limited by attenuation losses at higher energies. Germanium optics as an alternative operate well up to 30 keV compared to 12 keV with silicon optics.

The etch chemistry of germanium with SF6 is comparable to that of silicon and as such, deep reactive ion etch recipes for silicon also work well with germanium substrates. The etch recipe however is morphed to compensate for loading and aspect ratio dependent etching effects. This was accomplished by gradually increasing the forward power and etch time steps for each loop cycle where there is fast switching between etching and passivation.

[1] A R. Woll, D. Agyeman-Budu, D. H. Bilderback, D. Dale, A. Y. Kazimirov, M. Pfeifer, T. Plautz, T. Szebenyi, and G. Untracht, SPIE Optical Engineering + Applications, 8502, 85020K-85021-85014 (2012).
[2] AR Woll, D Agyeman-Budu, S Choudhury, I Coulthard, AC Finnefrock, R Gordon, E Hallin and J Mass, Journal of Physics: Conference Series, 493 (1), 012028 (2014).


"Structure of the DMPC Ripple Phase"

Kiyotaka Akabori and John. F. Nagle
Carnegie Mellon University

Abstract: High resolution structure is presented for the ripple phase of DMPC. Low angle X-ray scattering from oriented samples yielded 57 orders, more than twice as many as recorded previously. The determined electron density map has a saw tooth profile similar to the result from lower resolution data, but the features are sharper allowing better estimates for the modulated bilayer profile and the distribution of headgroups along the aqueous interface. Analysis of high resolution wide angle X-ray data shows that the hydrocarbon chains in the longer, major side of the asymmetric sawtooth are packed similarly to the gel phase, with chains in both monolayers coupled and tilted by 18o in the same direction. The absence of Bragg rods that could be associated with the minor side is consistent with disordered chains, as often suggested in the literature. However, the new high resolution bilayer profile strongly suggests that the chains in the two monolayers in the minor side and the curved region are not in registry. This staggered monolayer modulated melting suggests a direction for improving theories of the ripple phase. Soft Matter (2015) 11, 918-26.


"The Mixed-Mode Pixel Array Detector Family"

Julian Beckera, Katherine S. Shanksa, Hugh T. Philippa, Mark W. Tatea, Joel T. Weissa, Prafull Purohita, Darol Chamberlainb, & Sol M. Grunera,b
aLaboratory of Atomic and Solid State Physics, Physics Department, Cornell University, Ithaca, NY; bCornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY

Abstract: We summarize progress on development of the Mixed-Mode Pixel Array Detector (MM-PAD) family of photon-integrating Pixel Array Detectors. The MM-PAD readout chip is optimized for experiments requiring a high frame rate (1 kHz) and/or wide dynamic range (1 to > 107 x-rays/pix/frame). The MM-PAD progenitor of the family, in the form of a 2x3 module (= 256 x 384 pixel) detector, has been used successfully in experiments at CHESS, APS, PETRA III and the ESRF. This detector utilizes 500 micron thick silicon sensors whose x-ray stopping power becomes limiting for x-ray energies above ~20keV. To overcome this limitation, MM-PAD modules were recently equipped with CdTe sensors to extend the energy range from ~20 keV to ~80 keV.

A single module (= 128 x128 pixel) variant (EM-PAD) has been adapted and installed in an atomic resolution electron microscope and is currently being used for experimental investigations of several materials.

The MM-PAD readout chip was designed for storage ring applications and is not suitable when all the x-rays arrive in a single pulse, as it is the case at X-ray Free-Electron Laser (XFEL) sources. An MM-PAD variant suitable for use at XFELs, named the High Dynamic Range Pixel Array Detector (HDR-PAD), is under development.


"In situ x-ray scattering study of a Cellulose Nano Crystal suspensions under shear: Evidence of flow-aligning behavior"

Lina Sanchez Botero
Cornell University


"X-ray study of polypropylene non-woven fabrics"

Naigeng Chen, Margaret Koker, Meredith Silberstein
Cornell University

Abstract: Non-woven fabrics have been widely used in the industry due to their good properties, including high surface area, high damage tolerance, high porosity and low cost. However, because of geometry complexity, their mechanical behavior is still poorly understood. This work aims at elucidate deformation mechanisms of non-wovens and the effects of microstructure on mechanical properties. A commercial polypropylene based geotextile, Dupont Typar SF, was used for this investigation.

The mechanical behaviors of this geotextile and its constituent fiber were characterized by monotonic tensile tests and relaxation tests. The macroscopic behavior is highly dependent on initial material area weight, with higher stiffness, higher strength and longer relaxation time for higher area weight material. Single fibers were extracted from the geotextile by tweezers. The yielding process starts at small strain level and continues to moderate deformation status. Non-woven microstructure information was captured by in-sitµ X-ray diffraction (XRD) and Micro Computed Tomography (µCT) experiments. A customized setup was built at Cornell High Energy Synchrotron Source (CHESS), which enables XRD and µCT during uniaxial deformation. Fiber reorientation during loading was captured by XRD. 3D microstructure images at 6 different strains were reconstructed through µCT projections. The strain points were chosen to span the elastic regime, small scale damage, yield, and large scale damage. The deformation process was then analyzed. As tensile stress is applied, initially 2D fiber network starts to contract in width accompany with bond breakage and fiber realignment. The contraction leads to fiber bending and material bulging on the surface. In the later stage of the deformation, when significant macroscopic damage has occurred, thickness increases significantly due to interlayer bonds and fibers breakages. Some axial fibers are still carrying loads while portions of the material separate apart from the original specimen plane.


"Differential dependencies on [Ca2+] and temperature of the monolayer spontaneous curvatures of DOPE, DOPA and cardiolipin: effects of modulating the strength of the inter-headgroup repulsion"

Yi-Fan Chen
National Central University, Taiwan


"Revealing transient structures of nucleosomes as DNA unwinds"

Yujie Chen
Cornell University


"Capturing Carbon Dioxide in Bacterial β-Carbonic Anhydrase using Pressure Cryocooling Technique"

Teck Khiang Chua
MacCHESS, Cornell University

Abstract: High-pressure cryo-cooling is a technique that was developed by Kim et. al to eliminate the need for penetrative cryoprotectants in protein crystals. To reduce damage during cryo-cooling, high pressure up to 200 Mpa, using helium gas was applied prior to rapidly cooling the protein crystal in liquid nitrogen. The development of pressure cryo-cooling opened up new possibilities in structural biology research. One application is to trap reactants or reaction intermediates in protein crystals using biologically active gases in pressurized form. Here, we show that applying pressurized carbon dioxide gas (CO2) on bacterial β-class carbonic anhydrase (bCA) protein crystals could successfully trap its substrate CO2.


"Your New CHESS User Portal – Userdb"

Kathleen Dedrick1, Ted Caldwell2, Ernest Fontes1, Barbara Herrman1, John Sammis2 and Tess Tuttle1
1Cornell High Energy Synchrotron Source, Cornell University; 2Gorges, Inc.


"Tuning the dynamics of DNA-AuNP adsorption at the silicon-water interface"

Thomas Derrien
Cornell University

Abstract: The ability to control the deposition of nanoparticles silicon surfaces is imperative to the fabrication of devices ranging in applications from electronics, optics, and biosensing. In order to optimize this process the solution phase parameters governing the deposition rate in solution must be elucidated. Here, using quartz crystal microbalance with dissipation we monitor the adsorption kinetics of variously functionalized DNA-gold nanoparticle on functionalized silica in solutions of various ionic strengths. It is found that both the DNA ligand and the solution ionic strength can serve to tune the kinetics of the nanoparticle adsorption. A dual exponential model is proposed to describe the adsorption kinetics. Finally, and the structure of the resulting nanoparticle monolayers are characterized using grazing incidence small angle X-ray scattering and scanning electron microscopy.


"Synchrotron Metrology for emerging Metal Oxide Semiconductor Devices"

Sonal Dey


"UV induced change in electronic structure of a photocatalyst observed with X ray Emission Spectroscopy"

Rohit Garg
Cornell University

Abstract: SrTiO3 is a catalyst for photo-assisted water splitting. X ray Emission Spectroscopy (XES) is a hard x ray spectroscopic probe which can provide high energy resolution in in-situ environments from a source with poor spatial and temporal coherence. We perform XES measurements of SrTiO3 close to top of valence band with and without applied UV radiation and further use Markov Chain Monte Carlo analysis to measure UV induced changes in electronic structure. We find that in presence of UV, the XES intensity from top of valence band increases. Since an increase cannot be explained by UV driven migration of electrons from valence band to conduction band, we conclude that application of UV induces changes in electronic structure, which are observable with XES.


"Spontaneous Formation of High-Index Planes in Single Domain Gold Nanocrystal Superlattices"

Nicolas Goubet
University Pierre et Marie Curie

Abstract: Crystals of nanocrystals, also called supracrystals and nanocrystal superlattices, are expected to exhibit specific properties that differ from both the corresponding bulk material and nanosized elementary units. Here, we describe the spontaneous formation of upper vicinal surfaces of gold supracrystals grown on a sublayer of ordered cobalt nanocrystals. The formation of such high-index planes is explained by a heteroepitaxial relationship between both Co and Au nanocrystal superlattice.


"Reconfigurable Nanorod Films: An in Situ Study of the Relationship between the Tunable Nanorod Orientation and the Optical Properties of Their Self-Assembled Thin Films"

Tobias Hanrath
Cornell University

Abstract: We investigated the self-assembly, disordering, and re-assembly of colloidal CdSe/CdS dot/rod nanorods (NR) films in real time using in-situ grazing incidence small-angle and wide-angle X-ray scattering. Multi-probe optical and structural experiments allowed us to directly correlate the NR superlattice structure and optical absorption. Structure and optical properties of NR films can be reconfigured through adjustment of solvent vapor concentration.


"High Pressure Cryocooling Improves Protein Crystal Diffraction Quality"

Qingqiu Huang, Chaeun Kim and Doletha M. E. Szebenyi
MacCHESS, Cornell University, Ithaca, NY 14853, USA

Abstract: High pressure cryocooling has been developed as an alternative method for cryopreservation of macromolecular crystals in which crystals are pressurized at around 200MPa and cooled to liquid nitrogen temperature. Here we found high pressure cryocooling could improve X-ray diffraction quality of protein crystals in two aspects. Firstly, high pressure cryocooling dramatically improved the diffraction resolution of three protein crystals. After being pressurized at 200MPa for 30 minutes, the resolutions of crystal #1 and crystal #2 have been improved from <4Å to 2.4Å and from 2.4Å to 1.6Å, respectively. The resolution of crystal #3 has been improved from <2.3Å to 1.5Å after being pressurized at 380MPa for 30 minutes. Secondly, high pressure cryocooling at pressure over 300MPa transformed non-merohedral twinned-crystal to single-crystal for three protein crystals. Pressure lower than 250MPa could not induce the transformation. For crystal #3, more than a dozen of diffraction data sets have been collected from different crystals at ambient pressure, but none of them could be processed because of non-merohedral twinning. After being pressurized at 380MPa for 30 minutes and then cooled to liquid nitrogen temperature, the crystal has been transformed from twinned-crystal to single-crystal and the resolution was improved dramatically at the same time.


"Potential of Quantitative X-Ray Fluorescence Computed Tomography for trace element detections"

Rong Huang1 & Karin E. Limburg2
1CHESS, Cornell University; 2SUNY College of Environmental Science and Forestry

Abstract: The filtered backprojection algorithm for X-Ray absorption/emission computed tomography (CT) has been well developed, and robust software is available in many platforms and packages. For X-ray fluorescence (XRF) tomography, if the sample is very small and its absorption of XRF is negligible, any software based on filtered backprojection can be used. However this is not often the case, therefore various kind of software based on Algebraic Reconstruction Techniques (ART) has been developed. This kind of software is not as easily available, therefore less well tested.

At CHESS F3 beamline, with a 4 mm diameter fish eye lens as test sample, we demonstrated that almost all the interesting trace elements (such as Br, Se, Zn, Cu, Ni and even Fe) can be reconstructed with CT software (Tomopy) based on filtered backprojection. Simulation of XRF absorption demonstrated that such absorption will not alter the reconstructed “pattern” of trace elements. The error in overall concentration and inner concentration by reconstruction can be corrected with absorption simulations. Such quantitative XRF tomography of trace elements is doable even for the elements with absorption length many times smaller than sample dimensions.


"Effect of surface structure of SrTiO3 on the Catalysis of Photo-Assisted Water Splitting"

Xin Huang
A&EP, Cornell University

Abstract: SrTiO3 (STO) is a promising semiconductor material for the water splitting reaction since its valence and conduction bands lie at appropriate energy positions for the simultaneous photo-induced evolution of hydrogen and oxygen even at zero applied bias. While much is known about the bulk electronic structure of STO as well as its surface structure in vacuum, much less is known about the atomic structure of the catalytically active surface, especially how changes in the surface structure and comp...


"Sub-microsecond x-ray diffraction during dynamic deformation of metals"

Todd Hufnagel, Caleb Hustedt, and Paul Lambert
Department of Materials Science and Engineering, Johns Hopkins University

K.T. Ramesh and Vignesh Kannan
Department of Mechanical Engineering, Johns Hopkins University

Sol Gruner, Mark Tate, Hugh Philipp, Prafull Purohit, and Joel Weiss
Department of Physics, Cornell University

Arthur Woll
Cornell High Energy Synchrotron Source (CHESS)

Dan Casem and Emily Huskins
U.S. Army Research Laboratory, Aberdeen Proving Grounds

Abstract: The response of materials to high-strain-rate mechanical deformation is important in many fields including the automotive, aerospace, and defense industries. Information about structural evolution in these experiments is usually inferred from the starting and ending microstructures, or by performing recovery experiments at various levels of strain. However, post-mortem microstructures may be different from the non-equilibrated structures present during the dynamic event. Time-resolved x-ray diffraction can provide important insights into the evolution of the structure of a material during dynamic loading, such as the elastic strains in individual phases, crystallographic texture, and the development of new (possibly metastable) phases. We present first-of-a-kind experiments performed at CHESS whereby changes in a magnesium alloy are tracked upon impact from a gas-gun driven projectile using a unique time-resolving Keck Pixel Array Detector.


"Experimental Assessment of Tilt-Dependent Thermal Fluctuations in Lipid Bilayers"

Michael S. Jablin, Kiyotaka Akabori, and John. F. Nagle
Carnegie Mellon University

Abstract: For length scales shorter than several membrane thicknesses, many molecular dynamics simulations of single component lipid bilayers have reported significant deviations in the measured height-height fluctuation spectrum compared to predictions from the Helfrich free energy. Recently, others have posited membrane models that depend on molecular tilt and that have been shown to be consistent with the aforementioned deviations. We present the first experimental support for a tilt-dependent theory for biomembrane mechanics. X-ray scattering from a liquid crystalline stack of oriented fluid phase lipid bilayers was collected and compared to the predictions of tilt-dependent and tilt-independent membrane models. Both tilt-dependent and -independent models satisfactorily fit the X-ray data dominated by in-plane correlation lengths much greater than membrane thickness (> 100 Å), but only a tilt-dependent model accounts for X-ray data primarily attributable to shorter length correlations. By fitting the measured X-ray scattering intensity, both the bending modulus Kc = 8.3 ± 0.6×10-20 J and the tilt modulus Kθ = 95 ± 7 mN/m were determined for DOPC lipid bilayers at 30 °C. Our experimental results support the enrichment of the classic Helfrich continuum model to include molecular tilt. Since the size of many biomembrane related molecules is similar to tilt-dependent length scales, the tilt modulus may be highly sensitive to various membrane-biomolecule interactions. Phys. Rev. Lett. 113, 248102 (2014)


"PS-b-PMMA Ordering Kinetics Determination by Laser Induced Millisecond Heating and micro-GISAXS"

Alan G. Jacobs
Cornell University

Abstract: Self-assembly dynamics of (PS-b-PMMA) during millisecond thermal anneals has been probed utilizing ex-situ μ-GISAXS. At temperatures exceeding the order-disorder transition, blocks exhibit mixing in the milliseconds establishing fast dynamics of the underlying segregation. The onset of mixing was characterized for dwells of 0.25 to 10 ms, reaching an asymptote by 10 ms. The order after rapid quench from high temperatures was independent of temperature, but varied with the quench rate.


"WAXS studies of interactions between nucleic acids and multivalent counter ions"

Andrea M. Katz1, Suzette A. Pabit1, Igor S. Tolokh2, Alexey V. Onufriev2,3, and Lois Pollack1
1School of Applied and Engineering Physics, Cornell University, Ithaca NY; 2Department of Computer Science, Virginia Tech, Blacksburg VA; 3Department of Physics, Virginia Tech, Blacksburg VA

Abstract: Wide-angle x-ray scattering (WAXS) is a sensitive probe of small conformational changes in biomolecules. It can provide structural information that is higher in spatial resolution than small-angle x-ray scattering, highlighting features that are on the order of tens of angstroms. Here, we use WAXS to probe the interactions between DNA, RNA, and small multivalent counterions. Understanding how counter ions associate to different nucleic acid forms, as well detecting potential counterion-induced conformational changes gives insight into why the condensation propensities of RNA and DNA helices differ. These experimental data can be used to validate and assess results from molecular dynamics simulations.


"Potential Application of Expand-Maximize-Compress (EMC) Algorithm on Synchrotron-based Serial Crystallography"

Ti-Yen Lan(a), Jennifer L. Wierman(b,c), Mark W. Tate(a), Hugh T. Philipp(a), Veit Elser(a) and Sol M. Gruner(a,c)
(a) Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA; (b) Field of Biophysics, Cornell University, Ithaca, NY 14853, USA; (c) Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA

Abstract: The launch of X-ray Free Electron Lasers (XFELs) has inspired several ingenious experiments such as serial femtosecond crystallography (SFX), where datasets are collected from a series of microcrystals injected across ultrafast X-ray pulses to outrun radiation damage. This has stoked interest in performing serial microcrystallography at storage ring sources. However, serial crystallography of micron-sized crystals at synchrotrons is challenging because the brilliance at synchrotrons is several orders of magnitude lower than that at XFELs, and the diffraction patterns become so ‘sparse’ that conventional indexing methods fail. Here, we demonstrate a successful reconstruction from such unoriented sparse frames with our EMC algorithm. In this proof-of-principle experiment, a hen egg white lysozyme (HEWL) crystal rotating about a single axis is illuminated by an attenuated beam from a rotating anode to simulate the diffraction patterns of microcrystals from synchrotron radiation. Millions of such sparse frames are taken and the average photon number per frame is less than 200. We show that reconstruction is possible even in this extreme and the reconstructed intensity can be phased to solve the protein structure. This success suggests that synchrotron-based serial crystallography of micron-sized crystals can be practical with the aid of the EMC algorithm.


"Flash cooling for protein crystallography"

David Moreau
Cornell University

Abstract: The properties of a protein-solvent system are strongly temperature dependent and undergo a kinetic glass transition near 200K. Depending on the cooling rate and the kinetics of transitions between conformational substates, the distribution of structures within a crystal at low temperature may deviate significantly from the biologically relevant ensemble. A computer controlled device has been constructed that allows cooling to 100K at rates up to 20,000 K/s.


"Probing the Origins of PbSe Quantum Dots: In-situ Mechanistic Characterization of Nucleation and Growth"

Douglas Neversa, James Stevensona, Amanda Preskeb, Jacob Ruffc, Todd Kraussb, Paulette Clancya, and Tobias Hanratha
aSchool of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY; bDepartment of Chemistry, University of Rochester, Rochester, NY; cCornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY

Abstract: Efforts to scale-up and commercialize nanocrystal quantum dot (QD) syntheses have accentuated a glaring need to understand the formation mechanism of colloidally synthesized QDs. Specifically, both the identity and structure of initial QD nuclei and their active growth species (i.e. monomer) have not been investigated, likely due to difficult in isolating and characterizing these short-lived, small reaction intermediates. Total X-ray scattering methods provide a novel, powerful, and in-situ analytical tool to characterize these crucial, but fleeting initial structures and their growth mechanism, as well as fully characterize the QD reaction—from reagents to final QD products. In this work, we used a magic-sized nanocluster QD (e.g. PbSe) reaction, which is air-stable and slow growing, in order to realistically probe the QD intermediates using in-situ total scattering analysis.


"Quantitative analysis of crystal scale deformation heterogeneity during cyclic plasticity using high-energy X-ray diffraction and finite-element simulation"

M. Obstalecki1, S. Wong2, P. R. Dawson1, M. P. Miller1
1Cornell University, Ithaca, NY, USA; 2Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany

Abstract: Modern high-energy X-ray diffraction (HEXD) experiments coupled with a crystal-based finite-element model employing forward projection of virtual X-rays through each element is applied to study cyclic plasticity. An Okegawa mold copper specimen was cyclically deformed in situ at the Advanced Photon Source. The strain amplitudes of the cyclic experiments reached well into the plastic regime and diffraction images were generated at several points in the loading history using a HEXD methodology. Four grains within the bulk of a polycrystalline sample were tracked and interrogated with X-rays. Diffraction peak data were reduced to center of mass (COM) and full width at half maximum (FWHM) values in the detector coordinates 2θ (radial) and η (azimuthal). The peaks evolved with cycles and changed significantly when the plastic strain amplitude was increased. Large changes in the peaks (especially the azimuthal FWHM values) were also observed during the course of one loading cycle; larger FWHM values were seen at the compressive end of the cycles. This trend was reversed when the sample was initially loaded in compression. Diffracted intensity distributions were also seen to change significantly from one grain to the next. Using a virtual diffractometer model, COM and FWHM values were computed from the modeling results by projecting virtual X-rays through the finite-element mesh and compared to the experimental data. The finite-element polycrystal model serves as the final step in the data reduction process, revealing significant spatial heterogeneity of orientation, stress and plastic strain rate distributions. Studying these distributions collectively will be necessary to fully understand the detailed elastic–plastic deformation behavior within each grain and to explore problems such as microcrack initiation hypotheses in polycrystalline materials.


"Finding the Solution: Ions and Water around Nucleic Acids"

Suzette A. Pabit, Steve P. Meisburger and Lois Pollack
Cornell University

Abstract: Nucleic acids are highly negatively charged biomolecules and therefore always surrounded by charge compensating cations and hydration water in solution. Solution-based structural methods like Small Angle X-ray Scattering (SAXS) are useful tools in uncovering relationships between the macromolecules, the ions and the solvent. Here, we describe tools we use in our group to probe the ion atmosphere and the water layer around nucleic acids. We compare Anomalous Small Angle X-ray Scattering (ASAXS) data to models based on liquid-state statistical mechanics that computes the solvent distribution around the nucleic acid, including both water and ions [1]. We also discuss the most recent work from our group that uses SAXS with heavy-atom isomorphous replacement to vary the scattering strength of the ion atmosphere and deconvolute contributions from DNA and ions [2]. We elaborate on the practical aspects of the measurements and data analysis and highlight the importance of taking data with absolute calibration [3] to gain quantitative information.

[1] H. T. Nguyen, S. A. Pabit, S. P. Meisburger, L. Pollack, and D. A. Case, “Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids,” J. Chem. Phys., vol. 141, no. 22, p. 22D508, 2014.
[2] S. P. Meisburger, S. A. Pabit, and L. Pollack, “Determining the locations of ions and water around DNA from X-ray scattering measurements,” Biophys. J., 2015.
[3] D. Orthaber, A. Bergmann, and O. Glatter, “SAXS experiments on absolute scale with Kratky systems using water as a secondary standard,” J. Appl. Crystallogr., vol. 33, no. 2, pp. 218–225, 2000.


"High-Speed X-ray Imaging Pixel Array Detector (Keck-PAD) for Time-Resolved Experiments at Synchrotron Sources"

Hugh T. Philippa, Mark W. Tatea, Prafull Purohita, Darol Chamberlainb, Katherine S. Shanksa, Joel T. Weissa & Sol M. Grunera,b
aLaboratory of Atomic and Solid State Physics, Physics Department, Cornell University, Ithaca, NY; bCornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY

Abstract: Modern storage rings are readily capable of providing intense x-ray pulses tens of picoseconds in duration millions of times per second. Exploiting the temporal structure of these x-ray sources opens avenues for the study of rapid structural changes in materials. Many processes (e.g. crack propagation, deformation on impact, turbulence, etc.) differ in detail from one sample trial to the next and would benefit from the ability to record successive x-ray images with single x-ray sensitivity while framing at 5 to 10 MHz frame rates. To this end, we have pursued the development fast x-ray imaging detectors capable of collecting bursts of images that enable the isolation of single synchrotron bunches and/or bunch trains. The detector technology used is the hybrid pixel array detector (PAD) with a charge integrating front-end, and high-speed, in-pixel signal storage elements. A 384 x 256 pixel version, the Keck-PAD, with 150 x 150 micron pixels and 8 dedicated in-pixel storage elements is operational, has been tested at CHESS, and has collected data for shockwave studies. An updated version with 27 dedicated storage capacitors and similar pixel size has been fabricated. The capabilities of the Keck-PADs will be presented.


"Reproducibility of Diffuse X-ray Scatter In Lysozyme Crystals"

Veronica Pillar, David Schuller, Marian Szebenyi, Michael Wall, Jennifer Wierman, Sol Gruner
Cornell University

Abstract: Just as Bragg peaks contain information about the static structure of crystalline macromolecules, diffuse x-ray scatter contains information about macromolecular dynamics. However, due to the weak intensity of diffuse scatter as compared to Bragg peaks, collecting quality diffuse data requires x-ray detector technology that has only recently been developed. The fundamental experimental properties of diffuse scatter are therefore yet to be fully determined. Here we begin the investigation by comparing the diffuse scattering data from several crystals of hen egg white lysozyme with and without a bound inhibitor.


"Geometric and electronic structure of the Fe-V cofactor in vanadium nitrogenase determined by X-ray spectroscopy"

Julian Rees
Max-Planck-Institute for Chemical Energy Conversion

Abstract: The nitrogenase enzyme is responsible for the fixation of aerial nitrogen to bioavailable ammonia. This reaction is catalyzed by a complex, M-7Fe-9S-C cofactor (M-cluster) where M = Mo or V. While the Mo variant of the enzyme is a far more efficient catalyst for N2 reduction, the V nitrogenase has recently been shown to perform reductive C-C bond coupling at rates ~700 faster than the Mo analogue. The complete atomic structure of the Mo M-cluster was determined in 2011, with definitive identification of the central carbide provided by Valence-to-Core X-ray Emission Spectroscopy. Through a similar study we provide novel evidence for a structurally-analogous M-cluster in V nitrogenase. Using complementary high energy resolution fluorescence-detected (HERFD) XANES, we further demonstrate differences in cofactor electronic structure which should provide insight into the disparate reactivities of these enzymes.


"Ferroquadrupole order in YbRu2Ge2"

Elliott Rosenberg
Stanford University

Abstract: The tetragonal compound YbRu2Ge2 exhibits a nonmagnetic transition at 10,2K which is believed to arise from ferroquadrupole order. The corresponding structural transition to an orthorhombic phase was observed at the same temperature as the quadrupolar transition, shown by the splitting of the (6 6 0) Bragg peak into four new Bragg peaks.


"What's New at MacCHESS"

D. Szebenyi, R. Cerione, T.K. Chua, M. Cook, R. Gillilan, Q. Huang, I. Kriksunov, T. Lukk, W. Miller, D. Schuller, and S. Smith
MacCHESS, Cornell University, Ithaca, New York 14853

Abstract: MacCHESS conducts both core and collaborative research projects, and supports users doing "Macromolecular diffraction at CHESS". In 2014-2015, users employed CHESS facilities to collect crystallographic and small-angle solution scattering (BioSAXS) data on numerous molecules and complexes of biological interest. A sampling of users' important structural results, reported here, provides insight into how synthesis of the sweetener aspartame can be made more efficient, how viruses used for gene therapy can be optimized, and how ribonucleoprotein complexes work.

Developments in the major focus areas of MacCHESS include:

BioSAXS – installation of new undulator has resulted in improved flux at G1; in-line SEC-SAXS-DLS-MALS is routinely available; development of cryo-SAXS is continuing; time-resolved work is starting.

Pressure Cryocooling (HPC) – upgrades to the apparatus, to allow use of gases other than He, are in the design phase; pressure-induced detwinning is being investigated; new users are seeing improved cryocooling using HPC.

Microcrystallography – fluorescence of mounted crystals is being used to see them more clearly; development of on-line confocal microscopy is continuing; a current priority is dealing with a stream of microcrystals: transporting them into the X-ray beam, and extracting useful diffraction data from the very weak images produced.

Dynamics – extensive diffuse scattering data have been collected and are being processed to evaluate how diffuse scattering is related to molecular motions in crystals.

Facility Upgrades – a Pilatus 6M detector, installed at A1 in fall 2014 and moved to F1 in spring 2015, produces excellent data and is very popular with users; F1 hutch equipment has been upgraded for stability and flexibility; reliability and speed of A1 automounter have been improved.


"Assembly of PbSe Nanocrystals on Polyethleneglycol Brushes"

Ben Treml
Cornell University

Abstract: Confined-but-connected nanocrystal assemblies show enhanced transport properties as well as the potential for band-like transport. However, these films are formed on ethylene glycol subphases and require transfer to solid substrates for characterization or integration into prototype devices. In this work, we explore polyethlyene glycol brushes as a replacement for the liquid subphase that presents the same chemical environment to the NCs.


"Exploring Highly Covalent Metal Ligand Interactions through X-Ray Absorption Spectroscopy"

Richard Walroth
Cornell University

Abstract: Pre-edge features in X-ray absorption spectroscopy (XAS) have long been used to study metal oxidation state and coordination environment.1 Canonically these features arise from transitions from metal 1s to metal based LUMOs. Using high energy resolved fluorescence detected X-ray absorption spectroscopy (HERFD-XAS) we have evaluated a number of Cu(I) complexes, which should have no pre-edge features based on this formalism. Observed features are thus assigned to MLCT transitions, and their energies are correlated to other experimental properties to confirm this assignment. We applied this technique towards identifying species in catalytic mixtures, specifically a Cu/TEMPO based alcohol oxidation system reported by Stahl et al.2 We have identified the primary components of the precatalytic system, as well as the resting state within the catalytic reaction itself. Finally, we used HERFD-XAS to study the nature of Cu-NO interactions.


"Recovering protein crystal orientation and reconstructing structure factors from sparse data frames"

Jennifer L. Wierman(a,b,d), Ti-Yen Lan(c,d), Mark W. Tate(c,d), Hugh T. Philipp(c,d), Veit Elser(c,d), & Sol M. Gruner(b,c,d)
(a)Field of Biophysics, (b)Cornell High Energy Synchrotron Source, (c)Physics Department, (d)Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY

Abstract: In determining structure from protein crystals, the number of diffracted rays available, prior to irreversible radiation damage, decreases with crystal size. We consider a data frame to be “sparse” when too few x-rays are collected per frame to determine the orientation of a small crystal using traditional methods, thus setting a lower limit to the size of microcrystals that may be indexed with a given source fluence. The EMC algorithm (Loh & Elser, 2009) has previously been applied to reconstruct structure from sparse noncrystalline data of objects with unknown orientations (Philipp et al., 2012; Ayyer et al., 2015). To simulate the conditions of a small crystal on a brighter beam at a synchrotron, we reconstructed the 3-dimensional diffraction intensity of a larger lysozyme crystal using a lower dose from a rotating anode, with as few as 190 photons per frame and no requirement for a priori knowledge of the orientation of the crystal yielding the data frame. We reconstructed structure factors, and used molecular replacement to rebuild the original protein structure. The results suggest that serial microcrystallography is not limited by the fluence of the x-ray source and collection of complete data sets from sparse data frames of microcrystals is feasible at, e.g., storage ring x-ray sources.


"Nanocrystal Superlattices that Exhibit Improved Order On Heating: An Example of Inverse Melting?"

Yixuan Yua, Avni Jaina, Adrien Guillaussiera, Vikas Reddy Voggua, Thomas M. Trusketta, Detlef-M. Smilgiesb, and Brian A. Korgela
aMcKetta Department of Chemical Engineering, Texas Materials Institute, Center for Nano- and Molecular Science and Technology, The University of Texas at Austin, Austin, TX 78712-1062, USA; bCornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA

Abstract: Generally in nature, a matter melts at a temperature above its melting point and solidifies at a temperature below this point. Nanocrystal superlattices, also known as “artificial solid”, generally speaking, also exhibit an order-to-disorder structural transition during heating, similar to that of natural solids. Here, we show that thiol-capped sub-2nm gold nanocrystal superlattices exhibit a reversible heating-induced ordering, similar to the inverse melting. Capping ligands configuration, a internal freedom of nanocrystals, is considered as the cause of such superlattice structural transitions.