| 1. |
- Echelmeier, A., et al.
(författare)
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Segmented flow generator for serial crystallography at the European X-ray free electron laser
- 2020
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Ingår i: Nature Communications. - : Nature Research. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) allows structure determination of membrane proteins and time-resolved crystallography. Common liquid sample delivery continuously jets the protein crystal suspension into the path of the XFEL, wasting a vast amount of sample due to the pulsed nature of all current XFEL sources. The European XFEL (EuXFEL) delivers femtosecond (fs) X-ray pulses in trains spaced 100 ms apart whereas pulses within trains are currently separated by 889 ns. Therefore, continuous sample delivery via fast jets wastes >99% of sample. Here, we introduce a microfluidic device delivering crystal laden droplets segmented with an immiscible oil reducing sample waste and demonstrate droplet injection at the EuXFEL compatible with high pressure liquid delivery of an SFX experiment. While achieving ~60% reduction in sample waste, we determine the structure of the enzyme 3-deoxy-D-manno-octulosonate-8-phosphate synthase from microcrystals delivered in droplets revealing distinct structural features not previously reported.
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| 2. |
- Wiedorn, Max O., et al.
(författare)
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Megahertz serial crystallography
- 2018
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 9
-
Tidskriftsartikel (refereegranskat)abstract
- The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a beta-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.
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| 3. |
- Wunderer, C. B., et al.
(författare)
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Detector developments at DESY
- 2016
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Ingår i: Journal of Synchrotron Radiation. - 0909-0495 .- 1600-5775. ; 23, s. 111-117
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Tidskriftsartikel (refereegranskat)abstract
- With the increased brilliance of state-of-the-art synchrotron radiation sources and the advent of free-electron lasers (FELs) enabling revolutionary science with EUV to X-ray photons comes an urgent need for suitable photon imaging detectors. Requirements include high frame rates, very large dynamic range, single-photon sensitivity with low probability of false positives and (multi)-megapixels. At DESY, one ongoing development project-in collaboration with RAL/STFC, Elettra Sincrotrone Trieste, Diamond, and Pohang Accelerator Laboratory-is the CMOS-based soft X-ray imager PERCIVAL. PERCIVAL is a monolithic active-pixel sensor back-thinned to access its primary energy range of 250 eV to 1 keV with target efficiencies above 90%. According to preliminary specifications, the roughly 10 cm × 10 cm, 3.5k × 3.7k monolithic sensor will operate at frame rates up to 120 Hz (commensurate with most FELs) and use multiple gains within 27 μm pixels to measure 1 to ∼ 100000 (500 eV) simultaneously arriving photons. DESY is also leading the development of the AGIPD, a high-speed detector based on hybrid pixel technology intended for use at the European XFEL. This system is being developed in collaboration with PSI, University of Hamburg, and University of Bonn. The AGIPD allows singlepulse imaging at 4.5 MHz frame rate into a 352-frame buffer, with a dynamic range allowing single-photon detection and detection of more than 10000 photons at 12.4 keV in the same image. Modules of 65k pixels each are configured to make up (multi)megapixel cameras. This review describes the AGIPD and the PERCIVAL concepts and systems, including some recent results and a summary of their current status. It also gives a short overview over other FEL-relevant developments where the Photon Science Detector Group at DESY is involved. © 2016 International Union of Crystallography.
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| 4. |
- Allahgholi, A., et al.
(författare)
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AGIPD 1.0 : The high-speed high dynamic range readout ASIC for the adaptive gain integrating pixel detector at the European XFEL
- 2014
-
Ingår i: 2014 IEEE Nuclear Science Symposium and Medical Imaging Conference, NSS/MIC 2014. - : Institute of Electrical and Electronics Engineers (IEEE). - 9781479960972
-
Konferensbidrag (refereegranskat)abstract
- AGIPD is a hybrid pixel X-ray detector developed by a collaboration between Deutsches Elektronen-Synchrotron (DESY), Paul-Scherrer-Institute (PSI), University of Hamburg and the University of Bonn. The detector is designed to comply with the requirements of the European XFEL. The radiation tolerant Application Specific Integrated Circuit (ASIC) is designed with the following highlights: high dynamic range, spanning from single photon sensitivity up to 104 × 12.4 keV photons, achieved by the use of dynamic gain switching, auto-selecting one of 3 gains of the charge sensitive pre-amplifier. To cope with the unique features of the European XFEL source, image data is stored in 352 analogue memory cells per pixel. The selected gain is stored in the same way and depth, encoded as one of 3 voltage levels. These memories are operated in random-access mode at 4.5MHz frame rate. Data is read out on a row-by-row basis via multiplexers to the DAQ system for digitisation during the 99.4ms gap between the bunch trains of the European XFEL. The AGIPD 1.0 ASIC features 64×64 pixels with a pixel area of 200×200 μm2. It is bump-bonded to a 500 μm thick silicon sensor. The principles of the chip architecture were proven in different experiments and the ASIC characterization was performed with a series of development prototypes. The mechanical concept of the detector system was developed in close contact with the XFEL beamline scientists to ensure a seamless integration into the beamline setup and is currently being manufactured. The first single module system was successfully tested at APS1 the high dynamic range allows imaging of the direct synchrotron beam along with single photon sensitivity and burst imaging of 352 subsequent frames synchronized to the source.
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| 5. |
- Allahgholi, A., et al.
(författare)
-
AGIPD, a high dynamic range fast detector for the European XFEL
- 2015
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Ingår i: Journal of Instrumentation. - 1748-0221. ; 10:1
-
Tidskriftsartikel (refereegranskat)abstract
- AGIPD-(Adaptive Gain Integrating Pixel Detector) is a hybrid pixel X-ray detector developed by a collaboration between Deutsches Elektronen-Synchrotron (DESY), Paul-Scherrer-Institut (PSI), University of Hamburg and the University of Bonn. The detector is designed to comply with the requirements of the European XFEL. The radiation tolerant Application Specific Integrated Circuit (ASIC) is designed with the following highlights: high dynamic range, spanning from single photon sensitivity up to 10(4) 12.5keV photons, achieved by the use of the dynamic gain switching technique using 3 possible gains of the charge sensitive preamplifier. In order to store the image data, the ASIC incorporates 352 analog memory cells per pixel, allowing also to store 3 voltage levels corresponding to the selected gain. It is operated in random-access mode at 4.5MHz frame rate. The data acquisition is done during the 99.4ms between the bunch trains. The AGIPD has a pixel area of 200 x 200 m m(2) and a 500 m m thick silicon sensor is used. The architecture principles were proven in different experiments and the ASIC characterization was done with a series of development prototypes. The mechanical concept was developed in the close contact with the XFEL beamline scientists and is now being manufactured. A first single module system was successfully tested at APS.
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| 6. |
- Allahgholi, A., et al.
(författare)
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AGIPD, the electronics for a high speed X-ray imager at the Eu-XFEL
- 2014
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Ingår i: Proceedings of Science. - : Proceedings of Science (PoS).
-
Konferensbidrag (refereegranskat)abstract
- The AGIPD (Adaptive Gain Integrated Pixel Detector) X-ray imaging camera will be operated at the X-ray Free Electron Laser, Eu-XFEL, under construction in Hamburg, Germany. Key parameters are 1 million 200 μm square pixels, single 12.4 keV photon detection and a dynamic range to 10 000/pixel/image. The developed sensors, ASICs, PCB-electronics and FPGA firmware acquire individual images per bunch at 27 000 bunches/s, packed into 10 bunch-trains/s with a bunch separation of 222 ns. Bunch-trains are handled by 352 analogue storage cells within each pixel of the ASIC and written during the 0.6msec train delivery. Therefore AGIPD can store 3520 images/s from the delivered 27 000 bunches/s. Random addressing provides reusability of each cell after an image has been declared as low-quality, so that good images can be selected. Digitization is performed between trains (99.4 msec). In the paper all functional blocks are introduced. The details concentrate on the DAQ-chain PCB-electronics and the slow control. A dense area of 1024 ADC-channels, each with a pickup-noise filtering and sampling of up to 50 MS/s/ADC and a serial output of 700 Mbit/s/ADC. FPGAs operate the ASICs synchronized to the bunch structure and collect the bit streams from 64 ADCs/FPGA. Pre-sorted data is transmitted on 10 GbE links out of the camera head using the time between trains. The control and monitoring of the camera with 600 A current consumption is based on a micro-controller and I2C bus with an addressing architecture allowing many devices and identical modules. The high currents require planned return paths at the system level. First experimental experience with the constructed components will be presented.
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| 7. |
- Allahgholi, A., et al.
(författare)
-
Front end ASIC for AGIPD, a high dynamic range fast detector for the European XFEL
- 2016
-
Ingår i: Journal of Instrumentation. - 1748-0221. ; 11:1
-
Tidskriftsartikel (refereegranskat)abstract
- The Adaptive Gain Integrating Pixel Detector (AGIPD) is a hybrid pixel X-ray detector for the European-XFEL. One of the detector's important parts is the radiation tolerant front end ASIC fulfilling the European-XFEL requirements: high dynamic range-from sensitivity to single 12.5keV-photons up to 104 photons. It is implemented using the dynamic gain switching technique with three possible gains of the charge sensitive preamplifier. Each pixel can store up to 352 images in memory operated in random-access mode at >= 4.5MHz frame rate. An external vetoing may be applied to overwrite unwanted frames.
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| 8. |
- Allahgholi, A., et al.
(författare)
-
The adaptive gain integrating pixel detector
- 2016
-
Ingår i: Journal of Instrumentation. - 1748-0221. ; 11:2
-
Tidskriftsartikel (refereegranskat)abstract
- The adaptive gain integrating pixel detector (AGIPD) is a development of a collaboration between Deustsches Elektronen-Synchrotron (DESY), the Paul-Scherrer-Institute (PSI), the University of Hamburg and the University of Bonn. The detector is designed to cope with the demanding challenges of the European XFEL. Therefore it comes along with an adaptive gain stage allowing a high dynamic range, spanning from single photon sensitivity to 10(4) x 12.4 keV photons and 352 analogue memory cells per pixel. The aim of this report is to briefly explain the concepts of the AGIPD electronics and mechanics and then present recent experiments demonstrating the functionality of its key features.
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| 9. |
- Allahgholi, A., et al.
(författare)
-
The AGIPD 1.0 ASIC : Random access high frame rate, high dynamic range X-ray camera readout for the European XFEL
- 2015
-
Ingår i: 2015 IEEE Nuclear Science Symposium and Medical Imaging Conference, NSS/MIC 2015. - : Institute of Electrical and Electronics Engineers (IEEE). - 9781467398626
-
Konferensbidrag (refereegranskat)abstract
- The European XFEL is an extremely brilliant Free Electron Laser Source with a very demanding pulse structure: trains of 2700 X-Ray pulses are repeated at 10 Hz. The pulses inside the train are spaced by 220 ns and each one contains up to 1012 photons of 12.4 keV, while being ≤ 100 fs in length. AGIPD (Adaptive Gain Integrating Pixel Detector) is a hybrid 1M-pixel detector developed by DESY, PSI, and the Universities of Bonn and Hamburg to cope with these properties. Thus the readout ASIC has to provide not only single photon sensitivity and a dynamic range ≳ 104 photons/pixel in the same image but also a memory for as many images of a pulse train as possible for delayed readout prior to the next train. The AGIPD 1.0 ASIC uses a 130 nm CMOS technology and radiation tolerant techniques to withstand the radiation damage incurred by the high impinging photon flux. Each ASIC contains 64 × 64 pixels of 200μmχ200μm. The circuit of each pixel contains a charge sensitive preamplifier with threefold switchable gain, a discriminator for an adaptive gain selection, and a correlated double sampling (CDS) stage to remove reset and low-frequency noise components. The output of the CDS, as well as the dynamically selected gain is sampled in a capacitor-based analogue memory for 352 samples, which occupies about 80% of a pixels area. For readout each pixel features a charge sensitive buffer. A control circuit with a command based interface provides random access to the memory and controls the row-wise readout of the data via multiplexers to four differential analogue ports. The AGIPD 1.0 full scale ASIC has been received back from the foundry in fall of 2013. Since then it has been extensively characterised also with a sensor as a single chip and in 2 × 8-chip modules for the AGIPD 1 Mpix detector. We present the design of the AGIPD 1.0 ASIC along with supporting results, also from beam tests at PETRA III and APS, and show changes incorporated in the recently taped out AGIPD 1.1 ASIC upgrade.
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| 10. |
- Correa, J., et al.
(författare)
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On the Charge Collection Efficiency of the PERCIVAL Detector
- 2016
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Ingår i: Journal of Instrumentation. - : IOP. - 1748-0221. ; 11:12
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Tidskriftsartikel (refereegranskat)abstract
- The PERCIVAL soft X-ray imager is being developed by DESY, RAL, Elettra, DLS, and PAL to address the challenges at high brilliance Light Sources such as new-generation Synchrotrons and Free Electron Lasers. Typical requirements for detector systems at these sources are high frame rates, large dynamic range, single-photon counting capability with low probability of false positives, high quantum efficiency, and (multi)-mega-pixel arrangements. PERCIVAL is a monolithic active pixel sensor, based on CMOS technology. It is designed for the soft X-ray regime and, therefore, it is post-processed in order to achieve high quantum efficiency in its primary energy range (250 eV to 1 keV) . This work will report on the latest experimental results on charge collection efficiency obtained for multiple back-side-illuminated test sensors during two campaigns, at the P04 beam-line at PETRA III, and the CiPo beam-line at Elettra, spanning most of the primary energy range as well as testing the performance for photon-energies below 250 eV . In addition, XPS surface analysis was used to cross-check the obtained results.
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| 11. |
- Marras, A., et al.
(författare)
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Vertically integrated circuits : Example of an application to an x-ray detector
- 2014
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Ingår i: 2014 21st IEEE International Conference on Electronics, Circuits and Systems, ICECS 2014. - 9781479942428 ; , s. 243-246
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Konferensbidrag (refereegranskat)abstract
- Replacing planar circuits with vertically integrated ones allows to increment circuit functionalities on a given silicon area, while avoiding some of the problems associated with aggressively scaled technology nodes. This is particularly true for applications likely to subject circuits to high doses of ionizing radiation (such of x-ray detectors to be used in synchrotron rings and Free Electron Lasers), since the degradation mechanisms of some of the innovative materials to be used in most recent nodes have not been fully characterized yet. In this paper, an evolution is presented for the readout ASIC of a pixelated x-ray detector to be used for such applications. The readout circuit is distributed in a stack of two vertically interconnected tiers, thus doubling the circuitry resident in each pixel without increasing the pixel pitch (and thus compromising spatial resolution of the detector). A first prototype has been designed and manufactured, using a commercial 130 nm CMOS technology. Design issues are discussed, along with preliminary characterization results. © 2014 IEEE.
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| 12. |
- Mezza, D., et al.
(författare)
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Characterization of AGIPD1.0 : The full scale chip
- 2016
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 838, s. 39-46
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Tidskriftsartikel (refereegranskat)abstract
- The AGIPD (adaptive gain integrating pixel detector) detector is a high frame rate (4.5 MHz) and high dynamic range (up to 104 ·12.4 keV photons) detector with single photon resolution (down to 4 keV taking 5σ as limit and lowest noise settings) developed for the European XFEL (XFEL.EU). This work is focused on the characterization of AGIPD1.0, which is the first full scale version of the chip. The chip is 64×64 pixels and each pixel has a size of 200×200 μm2. Each pixel can store up to 352 images at a rate of 4.5 MHz (corresponding to 220 ns). A detailed characterization of the AGIPD1.0 chip has been performed in order to assess the main performance of the ASIC in terms of gain, noise, speed and dynamic range. From the measurements presented in this paper a good uniformity of the gain, a noise around 320 e− (rms) in standard mode and around 240 e− (rms) in high gain mode has been measured. Furthermore a detailed discussion about the non-linear behavior after the gain switching is presented with both experimental results and simulations.
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| 13. |
- Mezza, D., et al.
(författare)
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Characterization of the AGIPD1.1 readout chip and improvements with respect to AGIPD1.0
- 2019
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 945
-
Tidskriftsartikel (refereegranskat)abstract
- AGIPD, the Adaptive Gain Integrating Pixel Detector, is a hybrid detector with a frame rate of 4.5 MHz, a dynamic range up to 104⋅ 12.4 keV photons, as well as single photon resolution, developed for the European XFEL (Eu.XFEL). The final 1 Mpixel detector system consists of 16 tiled modules each one with 16 readout chips. The single ASIC is 64 x 64 pixels, each with a size of 200 x 200 μm2. Each pixel can store up to 352 images. This work is focused on the characterization of AGIPD1.1, the second version of the full scale ASIC, and the improvements with respect to AGIPD1.0. From the measurements presented in this paper we show that the flaws observed in AGIPD1.0 (i.e. ghosting, crosstalk, slow readout speed) have been fixed in AGIPD1.1. In addition the main performance parameters such as noise, dynamic range and so on were measured for the new version of the ASIC and will be summarized.
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| 14. |
- Mezza, D., et al.
(författare)
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New calibration circuitry and concept for AGIPD
- 2016
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Ingår i: Journal of Instrumentation. - 1748-0221. ; 11:11
-
Tidskriftsartikel (refereegranskat)abstract
- AGIPD (adaptive gain integrating pixel detector) is a detector system developed for the European XFEL (XFEL.EU), which is currently being constructed in Hamburg, Germany. The XFEL.EU will operate with bunch trains at a repetition rate of 10 Hz. Each train consists of 2700 bunches with a temporal separation of 220 ns corresponding to a rate of 4.5 MHz. Each photon pulse has a duration of < 100 fs (rms) and contains up to 1012 photons in an energy range between 0.25 and 25 keV . In order to cope with the large dynamic range, the first stage of each bump-bonded AGIPD ASIC is a charge sensitive preamplifier with three different gain settings that are dynamically switched during the charge integration. Dynamic gain switching allows single photon resolution in the high gain stage and can cover a dynamic range of 104 × 12.4 keV photons in the low gain stage. The burst structure of the bunch trains forces to have an intermediate in-pixel storage of the signals. The full scale chip has 352 in-pixel storage cells inside the pixel area of 200 × 200 μm2. This contribution will report on the measurements done with the new calibration circuitry of the AGIPD1.1 chip (without sensor). These results will be compared with the old version of the chip (AGIPD1.0). A new calibration method (that is not AGIPD specific) will also be shown.
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| 15. |
- Trunk, Ulrich, et al.
(författare)
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AGIPD : A multi megapixel, multi megahertz X-ray camera for the European XFEL
- 2017
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Ingår i: Proceedings of SPIE - The International Society for Optical Engineering. - : SPIE - International Society for Optical Engineering. - 9781510611009
-
Konferensbidrag (refereegranskat)abstract
- AGIPD is a hybrid pixel detector developed by DESY, PSI, and the Universities of Bonn and Hamburg. It is targeted for use at the European XFEL, a source with unique properties: a train of up to 2700 pulses is repeated at 10 Hz rate. The pulses inside a train are ≤100fs long and separated by 220 ns, containing up to 1012 photons of 12.4 keV each. The readout ASICs with 64 x 64 pixels each have to cope with these properties: Single photon sensitivity and a dynamic range up to 104 photons/pixel in the same image as well as storage for as many as possible images of a pulse train for delayed readout, prior to the next train. The high impinging photon flux also requires a very radiation hard design of sensor and ASIC, which uses 130 nm CMOS technology and radiation tolerant techniques. The signal path inside a pixel of the ASIC consists of a charge sensitive preamplifier with 3 individual gains, adaptively selected by a subsequent discriminator. The preamp also feeds to a correlated double sampling stage, which writes to an analogue memory to record 352 frames. It is random-access, so it can be used most efficiently by overwriting bad or empty images. Encoded gain information is stored to a similar memory. Readout of these memories is via a common charge sensitive amplifier in each pixel, and multiplexers on four differential ports. Operation of the ASIC is controlled via a command interface, using 3 LVDS lines. It also serves to configure the chip's operational parameters and timings.
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| 16. |
- Greiffenberg, D., et al.
(författare)
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Towards AGIPD1.0 : Optimization of the dynamic range and investigation of a pixel input protection
- 2014
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Ingår i: Journal of Instrumentation. - 1748-0221. ; 9:6, s. Art. no. P06001-
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Tidskriftsartikel (refereegranskat)abstract
- AGIPD is a charge integrating, hybrid pixel readout ASIC, which is under development for the European XFEL [1,2]. A dynamic gain switching logic at the output of the preamplifier (preamp) is used to provide single photon resolution as well as covering a dynamic range of at least 104·12.4 keV photons [3,4]. Moreover, at each point of the dynamic range the electronics noise should be lower than the Poisson fluctuations, which is especially challenging at the points of gain switching. This paper reports on the progress of the chip design on the way to the first full-scale chip AGIPD1.0, focusing on the optimization of the dynamic range and the implementation of protection circuits at the preamplifier input to avoid pixel destruction due to high intense spots. © 2014 IOP Publishing Ltd and Sissa Medialab srl.
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| 17. |
- Allahgholi, Leila, et al.
(författare)
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Exploring a novel β-1,3-glucanosyltransglycosylase, MlGH17B, from a marine Muricauda lutaonensis strain for modification of laminari-oligosaccharides
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Ingår i: Glycobiology. - 1460-2423.
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Tidskriftsartikel (refereegranskat)abstract
- The marine environment, contains plentiful renewable resources, e.g. macroalgae with unique polysaccharides, motivating search for enzymes from marine microorganisms to explore conversion possibilities of the polysaccharides. In this study, the first GH17 glucanosyltransglycosylase, MlGH17B, from a marine bacterium (Muricauda lutaonensis), was characterized. The enzyme was moderately thermostable with Tm at 64.4 °C and 73.2 °C, but an activity optimum at 20 °C, indicating temperature sensitive active site interactions. MlGH17B uses β-1,3 laminari-oligosaccharides with a degree of polymerization (DP) of 4 or higher as donors. Two glucose moieties (bound in the aglycone +1 and + 2 subsites) are cleaved off from the reducing end of the donor while the remaining part (bound in the glycone subsites) is transferred to an incoming β-1,3 glucan acceptor, making a β-1,6-linkage, thereby synthesizing branched or kinked oligosaccharides. Synthesized oligosaccharides up to DP26 were detected by mass spectrometry analysis, showing that repeated transfer reactions occurred, resulting in several β-1,6-linked branches. The modelled structure revealed an active site comprising five subsites: three glycone (-3, -2 and - 1) and two aglycone (+1 and + 2) subsites, with significant conservation of substrate interactions compared to the only crystallized 1,3-β-glucanosyltransferase from GH17 (RmBgt17A from the compost thriving fungus Rhizomucor miehei), suggesting a common catalytic mechanism, despite different phylogenetic origin, growth environment, and natural substrate. Both enzymes lacked the subdomain extending the aglycone subsites, found in GH17 endo-β-glucanases from plants, but this extension was also missing in bacterial endoglucanases (modelled here), showing that this feature does not distinguish transglycosylation from hydrolysis, but may rather relate to phylogeny.
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| 18. |
- Allahgholi, Leila, et al.
(författare)
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Fermentation of the Brown Seaweed Alaria esculenta by a Lactic Acid Bacteria Consortium Able to Utilize Mannitol and Laminari-Oligosaccharides
- 2023
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Ingår i: Fermentation. - 2311-5637. ; 9:6
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Tidskriftsartikel (refereegranskat)abstract
- The brown seaweed Alaria esculenta is the second most cultivated species in Europe, and it is therefore of interest to expand its application by developing food products. In this study, a lactic acid bacteria consortium (LAB consortium) consisting of three Lactiplantibacillus plantarum strains (relative abundance ~94%) and a minor amount of a Levilactobacillus brevis strain (relative abundance ~6%) was investigated for its ability to ferment carbohydrates available in brown seaweed. The consortium demonstrated the ability to ferment glucose, mannitol, galactose, mannose, and xylose, of which glucose and mannitol were the most favored substrates. No growth was observed on fucose, mannuronic and guluronic acid. The consortium used different pathways for carbohydrate utilization and produced lactic acid as the main metabolite. In glucose fermentation, only lactic acid was produced, but using mannitol as a carbohydrate source resulted in the co-production of lactic acid, ethanol, and succinate. Xylose fermentation resulted in acetate production. The consortium was also able to utilize laminari-oligosaccharides (DP2-4), obtained after enzymatic hydrolysis of laminarin, and produced lactic acid as a metabolite. The consortium could grow directly on A. esculenta, resulting in a pH decrease to 3.8 after 7 days of fermentation. Incubation of the same seaweed in corresponding conditions without inoculation resulted in spoilage of the seaweed by endogenous bacteria.
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| 19. |
- Daugbjerg Christensen, Monica, et al.
(författare)
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Cloning and Characterization of a Novel N-Acetyl-D-galactosamine-4-O-sulfate Sulfatase, SulA1, from a Marine Arthrobacter Strain
- 2024
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Ingår i: Marine Drugs. - 1660-3397. ; 22:3
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Tidskriftsartikel (refereegranskat)abstract
- Sulfation is gaining increased interest due to the role of sulfate in the bioactivity of many polysaccharides of marine origin. Hence, sulfatases, enzymes that control the degree of sulfation, are being more extensively researched. In this work, a novel sulfatase (SulA1) encoded by the gene sulA1 was characterized. The sulA1-gene is located upstream of a chondroitin lyase encoding gene in the genome of the marine Arthrobacter strain (MAT3885). The sulfatase was produced in Escherichia coli. Based on the primary sequence, the enzyme is classified under sulfatase family 1 and the two catalytic residues typical of the sulfatase 1 family—Cys57 (post-translationally modified to formyl glycine for function) and His190—were conserved. The enzyme showed increased activity, but not improved stability, in the presence of Ca2+, and conserved residues for Ca2+ binding were identified (Asp17, Asp18, Asp277, and Asn278) in a structural model of the enzyme. The temperature and pH activity profiles (screened using p-nitrocatechol sulfate) were narrow, with an activity optimum at 40–50 °C and a pH optimum at pH 5.5. The Tm was significantly higher (67 °C) than the activity optimum. Desulfation activity was not detected on polymeric substrates, but was found on GalNAc4S, which is a sulfated monomer in the repeated disaccharide unit (GlcA–GalNAc4S) of, e.g., chondroitin sulfate A. The position of the sulA1 gene upstream of a chondroitin lyase gene and combined with the activity on GalNAc4S suggests that there is an involvement of the enzyme in the chondroitin-degrading cascade reaction, which specifically removes sulfate from monomeric GalNAc4S from chondroitin sulfate degradation products.
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