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Abstract: Eight potential monochromator crystal designs were
subjected to a combination of three different beam powers
on two different footprints. The temperature and thermal
deformation were determined for each. It was found that
thermal deformation of the lattice is negligible compared
to the surface curvature, and that while the thinnest crystal
wafer showed the smallest temperature increase, crystals
cooled from the bottom alone demonstrated a far
more uniform thermal deformation and a larger radius of
curvature.
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Jun 2017
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I20-Scanning-X-ray spectroscopy (XAS/XES)
Mechanical Engineering
Optics
Theoretical Physics
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Abstract: Abstract. An analytical model was constructed of a single silicon crystal monochromator. This model was used to examine
the heat transfer processes within the monochromator. It was discovered that extracting heat from the top surface of the
monochromator could cause the peak temperature to be below the surface of the crystal; this dislocation was shown to be
approximately 10% of the thickness of the crystal when 20% of the input power was extracted from the top surface.
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Jul 2016
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Franklin D
Fuller
,
Sheraz
Gul
,
Ruchira
Chatterjee
,
E. Sethe
Burgie
,
Iris D.
Young
,
Hugo
Lebrette
,
Vivek
Srinivas
,
Aaron
Brewster
,
Tara
Michels-clark
,
Jonathan A
Clinger
,
Babak
Andi
,
Mohamed
Ibrahim
,
Ernest
Pastor
,
Casper
De Lichtenberg
,
Rana
Hussein
,
Christopher J
Pollock
,
Miao
Zhang
,
Claudiu A
Stan
,
Thomas
Kroll
,
Thomas
Fransson
,
Clemens
Weninger
,
Markus
Kubin
,
Pierre
Aller
,
Louise
Lassalle
,
Philipp
Braeuer
,
Mitchell D.
Miller
,
Muhamed
Amin
,
Sergey
Koroidov
,
Christian G.
Roessler
,
Marc
Allaire
,
Raymond G
Sierra
,
Peter T.
Docker
,
James M.
Glownia
,
Silke
Nelson
,
Jason E
Koglin
,
Diling
Zhu
,
Matthieu
Chollet
,
Sanghoon
Song
,
Henrik
Lemke
,
Mengning
Liang
,
Dimosthenis
Sokaras
,
Roberto
Alonso-mori
,
Athina
Zouni
,
Johannes
Messinger
,
Uwe
Bergmann
,
Amie K.
Boal
,
J. Martin
Bollinger
,
Carsten
Krebs
,
Martin
Högbom
,
George N.
Phillips
,
Richard D.
Vierstra
,
Nicholas K
Sauter
,
Allen M.
Orville
,
Jan
Kern
,
Vittal K
Yachandra
,
Junko
Yano
Abstract: 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 into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.
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Feb 2017
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I24-Microfocus Macromolecular Crystallography
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Open Access
Abstract: Macromolecular Crystallography is a powerful and valuable technique to assess protein structures. Samples are commonly cryogenically cooled to minimise radiation damage effects from the X-ray beam, but low temperatures hinder normal protein functions and this procedure can introduce structural artefacts. Previous experiments utilising acoustic levitation for beamline science have focused on Langevin horns which deliver significant power to the confined droplet and are complex to set up accurately. In this work, the low power, portable TinyLev acoustic levitation system is used in combination with an approach to dispense and contain droplets, free of physical sample support to aid protein crystallography experiments. This method facilitates efficient X-ray data acquisition in ambient conditions compatible with dynamic studies. Levitated samples remain free of interference from fixed sample mounts, receive negligible heating, do not suffer significant evaporation and since the system occupies a small volume, can be readily installed at other light sources.
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Aug 2019
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I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[14493, 19458]
Open Access
Abstract: Efficient sample delivery is an essential aspect of serial crystallography at both synchrotrons and X-ray free-electron lasers. Rastering fixed target chips through the X-ray beam is an efficient method for serial delivery from the perspectives of both sample consumption and beam time usage. Here, an approach for loading fixed targets using acoustic drop ejection is presented that does not compromise crystal quality, can reduce sample consumption by more than an order of magnitude and allows serial diffraction to be collected from a larger proportion of the crystals in the slurry.
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Sep 2019
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Iris D.
Young
,
Mohamed
Ibrahim
,
Ruchira
Chatterjee
,
Sheraz
Gul
,
Franklin D.
Fuller
,
Sergey
Koroidov
,
Aaron S.
Brewster
,
Rosalie
Tran
,
Roberto
Alonso-mori
,
Thomas
Kroll
,
Tara
Michels-clark
,
Hartawan
Laksmono
,
Raymond G.
Sierra
,
Claudiu A.
Stan
,
Rana
Hussein
,
Miao
Zhang
,
Lacey
Douthit
,
Markus
Kubin
,
Casper
De Lichtenberg
,
Long
Vo Pham
,
Håkan
Nilsson
,
Mun Hon
Cheah
,
Dmitriy
Shevela
,
Claudio
Saracini
,
Mackenzie A.
Bean
,
Ina
Seuffert
,
Dimosthenis
Sokaras
,
Tsu-chien
Weng
,
Ernest
Pastor
,
Clemens
Weninger
,
Thomas
Fransson
,
Louise
Lassalle
,
Philipp
Bräuer
,
Pierre
Aller
,
Peter T.
Docker
,
Babak
Andi
,
Allen M.
Orville
,
James M.
Glownia
,
Silke
Nelson
,
Marcin
Sikorski
,
Diling
Zhu
,
Mark S.
Hunter
,
Thomas J.
Lane
,
Andy
Aquila
,
Jason E.
Koglin
,
Joseph
Robinson
,
Mengning
Liang
,
Sébastien
Boutet
,
Artem Y.
Lyubimov
,
Monarin
Uervirojnangkoorn
,
Nigel W.
Moriarty
,
Dorothee
Liebschner
,
Pavel V.
Afonine
,
David G.
Waterman
,
Gwyndaf
Evans
,
Philippe
Wernet
,
Holger
Dobbek
,
William I.
Weis
,
Axel T.
Brunger
,
Petrus H.
Zwart
,
Paul D.
Adams
,
Athina
Zouni
,
Johannes
Messinger
,
Uwe
Bergmann
,
Nicholas K.
Sauter
,
Jan
Kern
,
Vittal K.
Yachandra
,
Junko
Yano
Abstract: 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)1, in which S1 is the dark-stable state and S3 is the last semi-stable state before O–O bond formation and O2 evolution2, 3. 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 site4, 5, 6. 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-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL7 provided a damage-free view of the S1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions8, 9, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states10. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site10, 11, 12, 13. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O–O bond formation mechanisms.
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Nov 2016
|
|
I24-Microfocus Macromolecular Crystallography
|
Open Access
Abstract: As the pressure continues to grow on Diamond and the world’s synchrotrons for higher throughput of diffraction experiments, new and novel techniques are required for presenting micron dimension crystals to the X ray beam. Currently this task is both labour intensive and primarily a serial process. Diffraction measurements typically take milliseconds but sample preparation and presentation can reduce throughput down to 4 measurements an hour.
With beamline waiting times as long as two years it is of key importance for researchers to capitalize on available beam time, generating as much data as possible. Other approaches detailed in the literature [1] [2] [3] are very much skewed towards automating, with robotics, the actions of a human protocols. The work detailed here is the development and discussion of a bottom up approach relying on SSAW self assembly, including material selection, microfluidic integration and tuning of the acoustic cavity to order the protein crystals.
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Jun 2015
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Data acquisition
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Abstract: As the world’s synchrotrons and X-FELs endeavour to meet the need to analyse ever-smaller protein crystals, there grows a requirement for a new technique to present nano-dimensional samples to the beam for X-ray diffraction experiments.The nano tweezers are very much a bottom up approach and facilitate self-assembly, alignment and subsequently automation. They also offer the potential to inform the user that a crystal has been trapped prior to interrogation. This paper details crystal trapping experiments that have been carried out proving ‘typical’ protein crystals the system will be required to trap in service can indeed be trapped. Modified chip architecture has been developed as the standard chips attenuated too much of the X-ray beam. Early tests with the next generation of chips have shown the modified chips can trap 500nm protein crystals. Trials to confirm the reduced beam attenuation have been completed and early diffraction experiments are also showing great promise.This novel approach of assembling, aligning and ultimately automating the presentation of nano dimensional protein crystals for X-ray diffraction experiments will prove potentially game changing for the structural biology community.
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Jun 2015
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Mechanical Engineering
|
Abstract: Circular dichroism (CD) is the differential absorption of left- and right-handed circularly polarized light. It is a form of spectroscopy used to determine the optical isomerism and secondary structure of molecules, and to study a wide variety of chiral materials in solution, particularly biologically important molecules such as proteins, nucleic acids, carbohydrates, lipids and drugs. The benefit of carrying out such experiments using synchrotron radiation is that the light available is several orders of magnitude higher in intensity than that available using conventional CD instruments, thereby providing a much higher signal-to-noise ratio over a wide wavelength range (140-700 nm). This paper will detail the development of a technique for rapidly producing 3D printed microfluidic channels in transparent polymer flow cells that enables the rapid and low-cost evaluation and iteration of microfluidic channel geometries. Permitting the flow through novel microfluidic devices to be interrogated thoroughly and the design optimized prior to making the significant financial and most crucially time commitment to the UV compatible flow cell for presentation to the synchrotron.
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Jun 2015
|
|
Optics
|
Open Access
Abstract: The work detailed here describes how a novel approach has been applied to overcome the challenging task of cryo-cooling the first monochromator crystals of many of the world's synchrotrons' more challenging beam lines. The beam line configuration investigated in this work requires the crystal to diffract 15 Watts of 4-34 keV X-ray wavelength and dissipate the additional 485 watts of redundant X-ray power without significant deformation of the crystal surface. In this case the beam foot print is 25 mm by 25 mm on a crystal surface measuring 38 mm by 25 mm and maintain a radius of curvature of more than 50 km. Currently the crystal is clamped between two copper heat exchangers which have LN2 flowing through them. There are two conditions that must be met simultaneously in this scenario: the crystal needs to be clamped strongly enough to prevent the thermal deformation developing whilst being loose enough not to mechanically deform the diffracting surface. An additional source of error also occurs as the configuration is assembled by hand, leading to human error in the assembly procedure. This new approach explores making the first crystal cylindrical with a sleeve heat exchanger. By manufacturing the copper sleeve to be slightly larger than the silicon crystal at room temperature the sleeve can be slid over the silicon and when cooled will form an interference fit. This has the additional advantage that the crystal and its heat exchanger become a single entity and will always perform the same way each time it is used, eliminating error due to assembly. Various fits have been explored to investigate the associated crystal surface deformations under such a regime.
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Dec 2017
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