Diamond Annual Review 2021/22

106 107 D I A M O N D L I G H T S O U R C E A N N U A L R E V I E W 2 0 2 1 / 2 2 D I A M O N D L I G H T S O U R C E A N N U A L R E V I E W 2 0 2 1 / 2 2 summer and is now fully operational in the Rosalind Franklin Institute Hub building offering state of the art capability to Franklin and Diamond scientists. Another key aspect of this collaboration is the development of the Parakeet software suite 1 that can create a comprehensive digital twin of an electron microscope, a biological sample, and a detector to perform a simulated cryo- electron tomography experiment. The simulated data can be analysed in the same way as real tomography data (see Figure 1) and allows scientists to study the relative benefits of critical decisions in sample preparation, data collection strategy and even the hardware choices in the construction of a microscope. Highlighted publication 1. Parkhurst, J. M. et al. Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography. Open Biology 11 , (2021). DO: 10.1098/ rsob.210160 Research Complex at Harwell (RCaH) TheResearchComplex at Harwell (RCaH) is a joint venturebetweenDiamond Light Source and the UK research councils, now UKRI, and provides a research hub on the Harwell campus for the physical and life sciences. It currently hosts more than 180 researchers from universities across the UK working in a mix of wet and dry laboratory space supported by research grants. In addition, there is a mix of research facilities or consortia based at RCaH e.g . Diamond’s Membrane Protein laboratory (MPL, funded by Wellcome), the Central Laser Facility (CLF), CCP4 and CCP-EM. This rich environment of research facility hubs welcomes around 500 scientific visitors and users yearly. The platform underwent a major upgrade at the start of 2022 thanks to a successful bid to the Medical Research Council (MRC) to enhance and extend the capabilities of the facility. This includes a new imaging hotel equipped with Ultra-Violet and multi-fluorescence imaging that facilitates detection of protein crystals, robotics for optimisation of crystallisation hits (the Formulatrix formulator®) and a Mosquito® Lipidic Cubic Phase (LCP) for automated crystallisation of soluble and membrane proteins. The Membrane Protein Laboratory has been successfully re-funded by Wellcome for a further five years and the first membrane protein structure determined using cryo- EM supported by access to the MPL was published by the Naismith group 1 . On the cryo-EM front, RCaH again with support from the MRC and in partnership with Diamond, have installed a ThermoFisher scientific Glacios™ 200 kV cryo- transmission electron microscope equipped with a falcon IV detector. The microscope has been installed at eBIC and provides Harwell groups with a state- of-the-art cryo-TEM for structural projects. This is complemented by dedicated facilities for cryo-EM sample preparation including the use of micropatterning to facilitate precise positioning of cells for cryo-electron tomography. Time- resolved structural biology is conducted at all five XFELs around the world, as well as at Diamond microfocus beamlines. These efforts include scientists from universities, industry, Diamond, and the XFEL Hub. A variety of strategies are available to initiate enzyme reactions within microcrystal slurries, and some of these include the use of anaerobic chambers in the Orville and Carr groups. The massive push to SARS-CoV-2 research aided by the Research Complex remaining open during the pandemic has led to further work on the SARS-CoV-2 proteases (Walsh) and the use of nanobodies directed against the SARS-CoV-2 spike protein (Naismith, Owens). The XFEL Hub (Orville) has helpedwith probing protease catalysis through a series of on-going time-resolved experiments at various XFEL sources around the globe. Finally, the XChem facility (Von Delft) continues to apply fragment-based approaches to SARS-COV-2 targets, having screened well in excess of 22,000 crystals across eight different targets at the close of 2021, following on from the success of the COVID Moonshot project which remains on track to commence preclinical trials for an orally available antiviral targeting the main protease of SARS-CoV-2. The latter initiative sprang from the very substantial fragment campaign that was rapidly executed at Diamond and the Research Complex at the start of the pandemic in 2020. Highlighted publication 1. Yang, Y. et al. The molecular basis of regulation of bacterial capsule assembly byWzc. Nat Commun 12, 4349 (2021). https://doi.org/10.1038/s41467- 021-24652-1 Catalysis Hub Since 2013 the UK Catalysis Hub has had a Block Allocation Group for X-ray Absorption Spectroscopy (XAS) at the XAS beamline (B18). The BAG aims to increase the user base within the catalysis community and is designed to encourage new users with a dedicated team at Harwell who will work with them to develop proposals and to guide and train users in the analysis of data. Through the operation of the XAS BAG, XAS has become one of the most important analytical tools available at Diamond for catalysis research. The frequent and rapid access to beamtime enables measurements to be completed on a short timescale, which is especially useful when completing publications. Over 80 publications have directly resulted from the B18 BAG with recent highlights including the study of aqueous phase reforming (APR) of glycerol which is an important reaction utilising renewable feedstocks such as biomass for the renewable production of hydrogen. These technologies are increasingly important in themove to net-zero CO 2 . Studies have included catalysis including Pt-Sn nanoparticles allowing deeper understanding of the Pt environment in active catalysts crucial to designing more active catalysts with improved lifetimes. Perovskite structured catalysts were also investigated for these reactions and it was discovered Pt/LaAlO 3 and Pt/LaNiO 3 showed higher stability and activity than other metals. XAS investigations helped show this is due to Pt redistribution and Pt/Ni alloy formation. Based on the results, intentionally prepared Pt/LaCO 3 OH catalysts were found to be active and stable in the APR reaction and the stability of materials warrants further study. The XAS BAG is managed by the UK Catalysis Hub, supported by Diamond staff, and is open to every academic working in catalysis in the UK. Time is awarded based on scientific merit and feasibility and with particular emphasis on proof-of-concept studies and exploration of new areas of catalysis science. Recently, the UK Catalysis Hub has been awarded a further BAG, this is for X-ray Pair Distribution function analysis (XPDF) at I15-1. This total scattering technique is complementary to XAS and provides both ex situ and in situ data with recently completed studies including studies of singly supported Pd atoms on MOFS and an in situ study of the formation of ruthenium nanoparticles on a silica substrate. As with the BAG for B18, the new XPDF BAG aims to introduce newusers to XPDF and to develop a broad user base fromwithin the UK Catalysis community. Active Materials Laboratory In late 2019 Diamond was awarded a grant by the Engineering and Physical Sciences Research Council (EPSRC) under the second National Nuclear User Facility scheme (NNUF II) to build a laboratory on-site to enable users to handle active samples while doing experiments at the synchrotron. The building construction finished in July 2021 and all the equipment for users has now been procured. The Active Materials Laboratory (AML) consists of four main rooms. There are two laboratories for experimental use. The wet lab has a recirculating fume cupboard, centrifuge, anaerobic Coy chamber, a small oven and high precision balances. The dry lab has two anaerobic glove boxes – one with an optical microscope and front face partially made of lead glass, the other will tolerate solvents -, a vented fume hood, a 1,200 °C tube furnace; an optical microscope; pellet press and high precision balance. Portable beamline equipment just as UV and IR spectrometers can be imported into the AML if a user has need for them. The AML has a characterisation room with a gamma spectrometer and a liquid scintillation counter and there is also a storage room, with safes, fridges and a freezer for samples to be stored when not in use in the labs or beamline. The lab is open for use in normal working hours onweekdays, though samples in the storage room can be accessed at any time. Access is designed principally for those with beamtime at Diamond, but can also be obtained without beamtime through the offline facilities scheme. Access is free for non-proprietary research via either route, but currently extra support funding is available through the NNUF II scheme. The University of Manchester at Harwell The University of Manchester at Harwell (UoMaH) is hosted by Diamond as part of the partnership. UoMaH provides the interface with the Harwell national facilities, enabling UoM researchers to access world-class research at Diamond and all the Science and Technology Facilities Council (STFC) facilities at Harwell, including the ISIS Neutron and Muon Source (ISIS), Scientific Computing Department (SCD) and the Central Laser Facility (CLF). UoMaH is comprised of core administrative and technical teams and research fellows and their groups. The core technical team specialises in developing sample environments and equipment in support of experiments, involving high riskmaterials and extreme sample environments, fielded at the national facilities. In early 2021 UoMaH expanded its core team capabilities with the recruitment of a Data Analysis manager. UoMaH plans to grow its data analysis group in the coming years. The group’s purpose will be to work with National Facilities to facilitate users' data reconstruction and analysis, with the aim to reduce the time it takes for users to publish their findings. UoMaH research fellows are affiliatedwith different departments within the University’s Faculty of Science and Engineering and pursue research in critical themes to both the University and the facilities. Currently, UoMaH has a growing contingent of fellows based at Harwell; two fellows working on resilience and catalysis are sponsored by Diamond, one fellow working on fusion is sponsored by ISIS, one fellow working on data science is sponsored by STFC/SCD and one “extreme science” fellow, currently in the recruitment stage will be sponsored by US office of Scientific research. Alongside them, six further fellows and their groups are based in Manchester. The fellows strengthen the University’s link with Harwell by bringing their research, networks and new users from industry and faculty academics to Diamond. In May 2021, UoMaH partnered with Diamond, CLF, UCL, the Health and Safety Executive (HSE) and the UK Health Security Agency (UKHSA) to support the National Core COVID-19 PROTECT Transmission and Environment Study. The research project was funded for a second year in April 2022; with the research in this last year focusing on using X-ray and laser imaging techniques to image the COVID-19 Alpha and Kappa variant. UoMaH is also being funded to programme manage, for HSE, the COVID-19 PROTECT Transmission and Environment Study during the study’s final year and transition to UKRI. InFUSE Prosperity Partnership ClimateChange is the singlebiggest threat topresent and futuregenerations. Tomeet the ambitious targets for net-zeroCO 2 set out by theUKgovernment, and in line with the Paris Climate Agreement, requires technological mobilisation on an unprecedented scale – with action required in both rapid development and deployment of new approaches. A paradigm shift in the UK’s research and development capabilities is needed to reduce time to market for novel and sustainable solutions for energy production and consumption. Successful rapid translation requires deep and coherent interactions between academia and industry, along with a shared vision and commitment. Across the range of proposed technological strategies for CO 2 reduction - either at source or via post-combustion mitigation - limitations in efficiency, stability or lifetime are associated with the role of key solid-fluid interfaces in the systems, and their evolution in the operating environments. By developing a better understanding of interfaces, researchers will be better able to design new materials, devices, and optimised processes that have reduced energy demand or longer productive lifetimes. This five-year EPSRC funded Prosperity Partnership between Imperial College London, Diamond and Shell, known as InFUSE, will examine how technologies like batteries, lubricants, chemical production, and carbon capture and storage (CCS) can be improved by understanding interfaces in these systems, enhancing sustainability and enabling a transition to a green economy. The partnership aims to increase our fundamental understanding of interface behaviours through a cross-cutting approach studying morphology, structure and chemistry from the atomic to the macroscale, and their dynamic evolution under a range of extreme operational parameters. InFUSE will prioritise engaging with diverse groups of the next generation of thinkers who will pave the way for a greener, more sustainable world. The programme will fund more than 20 new PhD studentships creating interdisciplinary cohorts working together towards the energy transition. At Diamond, three PDRA positions will help bridge the activities of this cohort with Diamond and drive exciting developments in sample environments correlative workflows and data analysis methods across the Spectroscopy, Imaging and Structures and Surfaces groups. Figure 1 (a) Digital twin of large planar lamella containing apoferritin particles. (b) Reconstruction of single apoferritin molecule from+/- 90 degree tilt series. A B