Data Collection to Structure Refinement and Beyond – Digital Conference
The first CCP4 Crystallographic School South Africa took place on the 22 February – 5 March 2021 hosted online due to the COVID-19 pandemic. More than 90 attendees – including 39 students and postdoctoral researchers represented by 14 different nationalities – participated in the workshop, which covered fundamental topics relating to theoretical concepts and practical approaches in protein structure solution by X-ray crystallography.
The event involved both newly emerging scientists as well as seasoned experts from across Africa, the UK, Europe, the USA, and Australia and was supported and co-hosted by the GCRF START grant, the UK’s national synchrotron – Diamond Light Source (Diamond), the Collaborative Computational Project Number 4 (CCP4), and the University of Cape Town (UCT). The workshop consisted of informal social events, formal lectures, question and answer sessions, one-on-one tutorials on data processing, case studies, and data collection where students collected data remotely from Diamond or provided their own data.
Describing the impact on the small but growing structural biology community in Africa, workshop co-organiser, Professor Trevor Sewell from UCT’s Aaron Klug Centre for Imaging and Analysis, said,
“The value of knowing a protein structure is widely appreciated by the scientific community but the knowledge and experience of how protein structures are determined is rare in Africa. The Covid-19 pandemic has shown us that we remain ignorant of this key area of science that has already led to successful vaccines and may lead to valuable drugs at our peril. The pandemic has also focused our minds on finding new ways of working and this has enabled us to hold this extraordinary workshop remotely. This has enabled African students to engage with the world’s best without the need to travel.”
“The success of the new medium was extraordinary and can potentially be extended to cover all fields. The workshop was the brainchild of Dr Carmien Tolmie from the University of the Free State here in South Africa, and it owes its success to her dedication and organizational abilities. We are grateful for the generous sponsorship from the National Research Foundation, IUPAP and the IUCr, which made this trendsetting virtual workshop possible,” Prof. Sewell added.
Three beamlines at Diamond Light Source, namely i03, i04 and i24, were dedicated to the remote data collection of students’ protein crystals, and each student was allocated to a beamline appropriate for their crystal system, as well as one-on-one assistance from beamline scientists. The workshop also had a coordinated effort involving beamline scientists from Diamond’s MX team. Diamond MX support scientists and co-hosts of the workshop – Felicity Bertram, Elliot Nelson and Marco Mazzorana – ensured the samples belonging to the workshop participants reached the correct beamline for the dedicated data collection day, in addition to organising access to the computing resources at Diamond Light Source for the data processing sessions.
Commenting on the importance of co-hosting the event from a South African perspective, Dr Carmien Tolmie said,
“It is an immense privilege to be part of the organization of this workshop and I am extremely grateful to the other members of the organization who worked extremely hard to make sure that this workshop was realized, despite the numerous setbacks we encountered because of the Covid-19 pandemic. Due to the high cost associated with traveling overseas to attend CCP4 workshops on other continents, this was a once-in-a-lifetime opportunity to learn from and engage with experts on crystallographic data processing for many of the participants attending this workshop. These are scarce skills, and this workshop will greatly aid in developing human capital in the country, as well as have a marked impact on advancing the projects of the participants who attended the workshop.”
For some of the students this was the first time attending a crystallographic workshop, including Taryn Adams, an MSc student recently starting a project in protein structure and function. Taryn heard about the workshop through her supervisor, Professor Yasien Sayed, head of the Protein Structure and Function Research Unit at the University of the Witwatersrand in South Africa. Taryn said,
“In science, success is often achieved with significant collaboration and group learning. I am looking forward to meeting scientists who are also new to the field and those with experience who could advise me as I embark on my project.”
Another participant, Dr Stanley Makumire, is a GCRF START funded Postdoctoral Research Fellow at the University of Cape Town. Stanley said,
“Being a novice in the field of structural biology attending the CCP4 workshop will equip me with the necessary skills for my research project which is to understand the mechanism of the amidase enzyme family. I am also really excited about the remote data collection and data processing tools available on CCP4.”
Commenting on the impact of the GCRF START grant on capacity building in the field of structural biology, Dr Gwyndaf Evans, START co-Investigator and Principal beamline scientist on Diamond’s VMXm beamline, said,
“We are seeing critical scientific discoveries and the emergence of a new generation of experts that have resulted directly from our training programmes in advanced methods and the use of synchrotron facilities and tools.”
Understanding biological systems is critical to the prosperity, and possibly, survival of the human race. Without it, we are threatened by disease, energy and food insecurity, pollution and climate change.
The COVID-19 pandemic has shown how important it is to have both national and international approaches to research and development with access to the right type of world class equipment, training and expertise.
Structural Biology research included SARS-CoV-2 (COVID-19), snakebite venom, HIV, tuberculosis, malaria, human papilloma virus, cardiovascular disease, as well as equine diseases, and many more. Work has also been done to create industrial enzymes for the manufacture of medicines and commodity chemicals.
“The GCRF START initiative provided an exceptional combination of expertise and experimental resources.”
Results include 80+ researchers now collaborating from multiple continents, over 50 world class papers published, and a new generation of scientists trained
A virtual event, held on Monday 7 June celebrated the many successes of the Global Challenges Research Fund (GCRF) START grant and the end of the three-year £3.7M grant provided by the UK’s Science and Technology Facilities Council (STFC) from the Global Challenges Research Fund (GCRF) in support of the Synchrotron Techniques for African Research and Technology (START) programme – a unique collaboration between scientists in the UK and Africa, and the UK’s national synchrotron, Diamond Light Source (Diamond). STFC supports the UK’s scientific community by working in partnership with universities, research organisations and government to ensure that researchers have access to large high-quality facilities.
Achievements to date have included more than 50 papers published, with dozens still in the pipeline. Nearly 20 protein structures were deposited in the global Protein Data Bank and over 230 Diamond synchrotron shifts carried out. 30 Postdoctoral Research Assistants/Fellows (PDRA’s/PDRF’s) have been funded, and numerous students introduced to synchrotron science through several workshops, secondments and visits delivered in person and remotely in Africa, the UK and beyond.
The event, hosted by Diamond, chaired by eminent scientist and grant Co-Investigator (Co-I), Professor Sir Richard Catlow, Professor at Cardiff University, University College London and Foreign Secretary at The Royal Society, was attended by START members, funders, and other stakeholders. The event featured case studies, early career impacts, and the importance of Diamond’s collaboration. Research topics included (amongst others), energy materials as catalysts for CO2 hydrogenation to reduce CO2 accelerated climate change; the development and optimisation of thin-film photovoltaic devices (solar cells) for sustainable energy; improving drug design for hypertension and blood pressure (ACE); the world’s first published nitrilaise structure and Africa’s first CryoEM results using Diamond’s eBIC facility. Professor Chris Nicklin, Science Group Leader and Principal Investigator (PI) in the GCRF START grant programme, said,
“START has been an exciting journey catalysed by the GCRF grant which has reaped fantastic results in a remarkably short space of time. By providing the new generation of synchrotron users with access to world class equipment and investing in their skills and capacity, research in the UK and Africa has been enriched and deepened. Going forward, there’s a huge appetite across the START network for a ‘START 2’, especially if the ambition of an African Light Source is to be realised. We are currently looking at ways to continue the momentum and build on START’s promising legacy.”
Dr Thandeka Moyo and Dr Carmien Tolmie are rising stars in the newly emerging Structural Biology network in South Africa. Funded as PDRF’s by the GCRF START grant, their successes stand out in fulfilling the key aims of START, including promoting equality and inclusiveness in science to challenge the under-representation of women. Carmien has made great strides in biocatalysis, investigating enzymes as drug targets for fungal infectious diseases which claim many lives, especially amongst immune-compromised patients. Recently promoted to academic staff at South Africa’s University of the Free State (UFS), she attributes her successes to the mentoring and training she received through the GCRF START grant which funded a secondment to Diamond and the University of Oxford, exposing her to cutting edge scientific techniques such as XChem fragment screening.
Thandeka’s achievements involve notable new biology in HIV (bNAbs) vaccine development projects and Covid-19 research at South Africa’s National Institute for Communicable Diseases. Highly active in mentoring young female scientists and taking part in school outreach activities, Zimbabwean Thandeka encourages the next generation to pursue STEM careers.
Dr Mohamed Fadlalla started out in 2018 as a GCRF START-funded Postdoctoral Research Fellow investigating energy materials at the University of Cape Town (UCT) and has since been promoted into a leadership role as a Research Officer. His story demonstrates how scientific development and scientist career development can work symbiotically, in this case assisted by the GCRF START grant. Mohamed said,
“As well as facilitating amazing science, the GCRF START grant played a substantial role in my career progression as a scientist. This has not only focused my interest into energy materials catalyst development, I have also learnt new energy materials characterisation techniques and conducted experiments at Diamond which were very successful. I started teaching the Catalysis Institute’s MSc. course where I now pass on my new skills to up-and-coming scientists in Africa and have recently been awarded an NRF-Thuthuka grant and UCT block grant to enable my research going forward.”
“If you don’t have this kind of network and support, it is incredibly difficult, for those who are at the start of this field,” said GCRF START Co-I, Professor Michael Claeys, from the University of Cape Town’s Centre for Catalysis and South Africa’s DST-NRF Centre of Excellence in Catalysis, c*change. “It is about building confidence, so this is where the GCRF START grant has played an incredibly important role, improving output and significantly lowering potential hesitancy to use synchrotron techniques, which can seem overwhelming to those new in the field.”
Dr Gwyndaf Evans, START Life Sciences Principal Investigator and Principal beamline scientist on Diamond’s VMXm beamline said,
“It has been rewarding to see the relatively modest investment of time and money can have such a major impact on the sustainability of research expertise, on the development of careers in Africa, on access to large scale facilities around the world, including improving our own systems at Diamond (such as remote access), and to the nurturing of collaborations and networks in South Africa. In Structural Biology, there have been valuable exchanges and collaborations especially XChem laying the foundations for drug discovery work. START is the beginning of embedding the structural research culture in South Africa and other groups around the world. We look forward to what the future holds.”
Funded by the UK’s Official Development Assistance (ODA) Global Challenges Research Fund, the GCRF START grant aims to meet key UN Sustainable Development Goals through Energy Materials for novel devices and improvements in energy efficiency, affordability, and storage (batteries and fuel cells) including renewable energy sources; and Structural Biology to better understand diseases, develop drug targets and vaccines, and drive ‘green’ biotechnology solutions.
Examples of Achievements
More than 230 Diamond synchrotron shifts; over 50 papers published, with dozens in the pipeline; 30 postdoctoral Research Assistants/Fellows (PDRA’s/PDRF’s) funded and numerous students introduced to synchrotron science; 3 ANSDAC workshops and 2 CCP4 workshops sponsored; many crystals and novel structures solved, with more than 20 protein structures deposited in the global protein bank (PDB’s); 8 PDRA’s/PDRF’s trained in Cryo-EM techniques and more than 30 students attended Cryo-EM workshops; PDRA’s involved in the development of new facilities/equipment in the UK and South Africa; 6 fully capable crystallography laboratories equipped across South Africa including in previously under-resourced universities; and multiple workshops, secondments and visits delivered in person and remotely in Africa, the UK and beyond.
Beyond GCRF START
Examples of follow on opportunities: Prof. Erick Strauss’ laboratory at the University of Stellenbosch, South Africa, winning a two year AAS Grand Challenges Africa grant focusing on Antimicrobial Resistance and drug discovery; Dr Francis Otieno from the University of the Witwatersrand, South Africa, achieving a British Council Newton Travel grant to conduct experiments on the subject of solar energy with GCRF START’s Co-I, Prof. Moritz Riede, at the University of Oxford; Prof. Dirk Opperman’s group at the University of the Orange Free State winning a Horizon 2020 ERA-NET-Cofund on Food Systems and Climate grant; and various groups able to access to other light sources and neutron sources around the world.
GCRF START collaborators
START members hail from the UK, South Africa, Lesotho, Kenya, Egypt, Zimbabwe, Tanzania, Swaziland, Namibia, the DRC, and the Sudan, amongst many other countries.
About the GCRF START grant
The GCRF START grant is a collaborative project that seeks to foster the development of Synchrotron Techniques for African Research and Technology (START). It builds partnerships between world leading scientists in Africa and the UK working together on research using synchrotron science. Funded by the UK’s Official Development Assistance (ODA) Global Challenges Research Fund, the GCRF START grant is delivered by UKRI through Diamond shareholders (the Science and Technology Facilities Council (STFC) and the Wellcome Trust). At the heart of START sits the community of co-investigators whose work in the relevant scientific disciplines is world-leading in their fields. They support a wider group of students and post-doctoral researchers whose contribution to START is vital to nurture future capacity and leadership in the African scientific research community. Working on experiments at the UK’s synchrotron, Diamond, START researchers and students will bring insights to sustainable energy and improvement in health that will have long-lasting legacies across Africa.
For further media information: please contact Diamond Communications: Isabelle Boscaro-Clarke +44 1235 778130
Nicklin, C., Stredwick, R. & Sewell, S. (2022) Synchrotron Techniques for African Research and Technology: A Step-Change in Structural Biology and Energy Materials, Synchrotron Radiation News, 35:1, 14-19, DOI: 10.1080/08940886.2022.2043684
“The GCRF START grant has been an excellent opportunity to support UK and international computational research, enabling engagement with experimentalists both within and outside of the START community. Membership of the START network enables us all to benefit from the wider networks we partner with globally, bringing scientists and research closer together, no matter where we are based. I hope to continue to build on the research links forged in Europe, Africa, Australasia, and Asia.” – Dr Michael Higham, Cardiff University (UK) and UK Catalysis Hub
Addressing emissions-linked climate change using electricity produced from renewable sources can present some complex challenges. One of these is the requirement that nations construct extensive electrical infrastructures, something which may be problematic for some developing nations. On the other hand, clean and sustainably produced liquid combustible fuels can be readily adapted for use in existing infrastructures based around gasoline fuel. To this end, scientists are conducting studies combined with carbon capture technology, photocatalytic water splitting, and catalytic processes to convert methanol to hydrocarbons. The aim is to develop a “synthetic” carbon cycle that mimics nature (albeit on much faster timescale), instead of the burning of fossil fuels which takes place at a rate which far exceeds that which nature can cope with.
Dr Michael Higham is a GCRF START Postdoctoral Research Assistant (PDRA) and an Associate of the UK Catalysis Hub – a consortium of universities involved in catalysis research led by Cardiff, Bath and Manchester universities. Based at Harwell’s Research Complex in Oxfordshire and until recently, a PDRA at Cardiff University, Michael brings his expertise in computational modelling to projects that focus on developing catalytic processes for more effective clean fuel production, minimisation and valorisation of waste byproducts, and reducing harmful gaseous emissions. These projects stretch across several research networks within the UK and further afield.
The growing global interest in developing a new carbon cycle by enabling sustainable liquid combustible fuels ties in with Sustainable Development Goals (SDGs) for Energy (SDG 7) and Climate Action (SDG 3),Industry, Innovation, and Infrastructure (SDG 9). The goal of Reduced Inequalities (SDG 10) is also supported through making clean, sustainable energy more accessible to developing nations, rather than the preserve of the wealthiest countries. By enabling the development of a range of clean energy technologies (such as synthetic combustible fuels, photovoltaics, battery technologies, and others), different nations with varying economic and geographical circumstances can aim to adopt technologies suited to their needs. This links with the Goal for Sustainable Cities and Communities (SDG 11) by making sustainability an accessible and achievable goal for all.
Providing computational insights for experimental work utilising the synchrotron facilities at the UK’s national synchrotron, Diamond Light Source (Diamond), Michael works closely with Professor Sir Richard Catlow, Foreign Secretary of the Royal Society, GCRF START Co-I and Professor at the UK’s University College London (UCL) and Cardiff University. Their aim is to gain a better understanding of catalyst systems for CO2 valorisation, which is the conversion of waste pollutant gas into clean fuels for clean and affordable energy application. This research concerns improving understanding of catalytic processes on an atomic scale by using computational methods to explore catalysts for methanol synthesis and Fischer-Tropsch synthesis, which are important processes to convert CO2 (a contributor to global warming and a product of burning fossil fuels) into combustible liquid fuels.
Michael has seen several successful publications involving his work which have been made possible through the GCRF START grant. These include a detailed and exhaustive computational investigation of the mechanism of CO2 conversion to methanol over copper surfaces, published in Dalton Transactions1 in May 2020. In this work, the powerful computational tools available in Density Functional Theory (DFT) techniques were applied to investigate all possible mechanistic routes for this reaction, elucidating the elementary processes in this reaction, thus informing, and providing an investigative framework for ongoing investigations into the more complex copper / zinc oxide (Cu/ZnO)-based systems, which is more representative of industrial methanol synthesis catalysts.
Shedding light on, and corroborating macro-scale observations – collaborations in the UK and Australia
Additionally, Michael has contributed to a joint publication with experimental colleagues from the UK’s Catalysis Hub team, the University of New South Wales (UNSW), and RMIT University, Australia, investigating thermo- and photo-catalytic processes in CO2 conversion to methanol over alumina (Al2O3) supported Cu/ZnO catalysts. Published in Nature Communications2 (March 2020), this research explores a synergistic mechanism (i.e. involving active participation of both the Cu and ZnO components of the catalyst, rather than ZnO merely acting as an inert support material) for CO2 conversion taking place at the Cu/ZnO interface, with DFT calculations being applied to assist the rationalisation of experimental valence band spectra, which can provide useful insights into the electronic structure of catalyst materials and potentially explain observed catalytic activity.
Further computational investigations have been conducted to better understand the role of reconstruction of polar ZnO surfaces in determining the morphology of supported Cu clusters, employing unbiased Monte Carlo global optimisation techniques to obtain the most stable structures for small Cu clusters supported on stable ZnO surfaces, which will enable subsequent studies to model elementary surface processes using surface models that are realistic and representative of typical Cu/ZnO catalysts. The work was published in October 2020 in the Journal of Materials Chemistry A3.
Through an ongoing collaboration with Dr Michael Stamatakis (University College London), Michael is busy extending the work published in the Dalton Transactions paper by conducting kinetic Monte Carlo simulations (which rely on random sampling of a probability distribution obtained from the previously conducted calculations published in the Dalton Transactions paper, in order to elucidate macroscopic kinetic behaviour based on atomistic simulations) for the metallic Cu systems investigated previously to obtain novel insights into the impact of reaction conditions, such as temperature and pressure, on the reaction mechanism and product distribution.
Furthermore, additional ongoing collaborations with Dr Rosa Arrigo (University of Salford) and Dr Matthew Quesne (Cardiff University) are exploring the mechanism of the electrocatalytic reduction of CO2 over bimetallic Cu/Zn systems, with computational insights supporting experimental in situ X-ray absorption spectroscopy studies undertaken at the Diamond synchrotron. It is intended that both collaborations will result in high-impact publications in leading, internationally recognised journals.
UK-Africa partnerships and atomic scale perspectives
“As long as there is funding for us to do research, we are going to build collaborations, and this provides a great deal of added value. By bringing African and UK researchers together, there is a greater opportunity for UK, European and African research networks to overlap and integrate. As we have seen from several successful collaborations, this is the wider impact of the GCRF START grant.”
Dr Michael Higham, UK Catalysis Hub and Cardiff University
Through the START network, Michael works with colleagues in Africa on studies ranging from investigating adsorption induced magnetisation changes in nickel catalysts, to research into bimetallic catalysts for CO2 hydrogenation of environmental and industrial importance. Using computer simulations and modelling to shed light on, and corroborate macro-scale observations in actual experiments, atomic scale information is possible that might otherwise be difficult to measure in situ.
One example is the experimental results from Michael’s collaboration with Professor Michael Claeys Dominic De Oliveira at UCT’s Centre for Catalysis and South Africa’s DST-NRF Centre of Excellence in Catalysis – c*Change. This collaboration began in 2019 during Michael’s GCRF START grant-funded secondment to UCT. The project explores the effect of adsorption on magnetisation of Ni surfaces and will be featured in a manuscript the team are preparing for submission in the coming months. The overarching aim is to use computational work to valorise the new techniques in Dominic’s experimental work using UCT’s Centre for Catalysis’ unique in situ magnetometer – a tool that few other institutions have access to. This work is important because it demonstrates how changes in magnetisation of catalyst nanoparticles can vary under real reactionary conditions such as high pressure and high temperature and is a good way to see what is happening on the catalyst’s surface in a way that allows the reproduction of industrial conditions.
“When it comes to computational aspects of chemistry, one has to spend a great deal of time looking at how we might model catalyst surfaces and think about what questions to ask as these are complex, multi component systems” says Michael. “We can test hypotheses for explanations of observed real-world behaviour, and on the flipside, we can use what we already know about well-studied systems to examine new, novel materials, and therefore help to direct future experimental studies.”
“We are going to focus initially on the impact of hydrogen and water species (H, O, OH, and H2O), on the surface magnetisation as Dominic already has plenty of experimental results for this from UCT’s in-situ magnetometer,” Michael adds. “The magnetometer is a really unique bit of kit andis a world’s first4. I also envisage a similar investigation looking at C-containing species relevant for Fischer-Tropsch synthesis, which we intend to result in an additional publication once we have enough experimental data.I am running a couple of additional calculations and writing my contribution to the manuscript in the coming weeks.Early indications show that there are changes in the magnetisation when conditions are varied.”
“If we can understand what is causing those changes in magnetisation, then we can investigate various species present on the catalyst’s surface, which is where the computational aspect comes in,” Michael explains. “I can look at the sort of species we might expect and test lots of different species on those surfaces and see what the calculations might suggest. Once we understand these, we can use this approach for other catalytic systems.”
Another example of UK-Africa collaboration is Michael’s work with Dr Mohamed Fadlalla and Christopher Mullins (UCT ‘s Centre of Catalysis and c*Change) on bimetallic alloy catalysts for methanol synthesis and conversion. This work also involves another UK group of catalysis researchers led by GCRF START Co-I, Dr Peter Wells from the University of Southampton’s Chemistry Department in the UK.
“In early December 2019, our team from the University of Cape Town and Southampton University visited the Diamond Light Source synchrotron and used the B18 beamline to study the influence of substituents in the ferrite structure on the reduction behaviour and carbon dioxide hydrogenation reaction to valuable products (e.g., fuels),” Mohamed Fadlalla says. “The next step is Michael’s computational work to help us to calculate certain insights from the results such as how the catalyst looks and how the reactant is interacting with the catalyst.”
The computational calculations will examine the catalytic product distributions which provide detailed insights into possible explanations for observed catalyst selectivity, as Michael explains below,
“Through modelling adsorption energies, activation energies and reaction energies we hope to shed light on what happens on the catalyst’s surface. We want to compare the observed, experimental data with the calculations. Mohamed has been doing a lot of very good experimental work. I hope to get more involved once they are in a position for me to complement their experimental work with my computational input, should they need my assistance.”
“These partnerships are important for the African and the UK research communities, not least for knowledge exchange in the search for sustainable, clean energy sources to tackle climate change.What we have seen in our interactions with our African colleagues is that they do great science and innovation on a far lower budget than most developed countries despite facing greater funding challenges than we generally do. Their expertise is world-class, and we should therefore be supporting these groups and collaborating closely with them so that the benefit from such excellent research has international as well as local impact.”
Commenting on the collaboration with Michael Higham and START, Prof. Michael Claeys, Director of c*Change said,
“Computational experts like Dr Michael Higham can predict how certain catalysts perform and we can try to confirm that with our techniques which is a reciprocal learning process. This expertise informs us, and we inform them through the results which is something a single group can’t do because very specific expertise is needed. Collaborating provides some of the most powerful learning opportunities which really shape your people.”
Developing mentoring skills and teaming up with ‘virtual’ visiting students in Germany and Singapore
Michael Higham has also teamed up with ‘virtual’ visiting students David Jurado (in Germany) and Yong Rui Poh (in Singapore) – collaborations which have worked well despite the challenges posed by the Covid-19 pandemic and remote working. Michael reports that both students have been “performing excellently”, which is promising not only due to the science but also because this is the first time Michael has mentored and supervised students. Although both students started with little experience of computational work, they have gained experience and have many interesting results5. David was able to send his calculations remotely from Germany and Yong Rui Poh could log onto UK super computers from the other side of the world without leaving Singapore. They are currently working on determining transition states for some processes, but once this is complete, should be ready to write up the manuscripts. It is hoped, given the breadth and detail of this work, that two manuscripts will be submitted.
“David has completed his Master’s thesis and will remain as a PhD student in Prof. Ingo Krossing’s group at the University of Freiburg, Germany,” Michael explains. “We intend to continue to work with David and Ingo on David’s Doctoral research, with David having prepared an ambitious proposal for his PhD studies. Meanwhile, Yong Rui has concluded his studies at the National University of Singapore and will begin his PhD studies at University of California, San Diego, USA, with the potential for more collaboration in the future.
Commenting on what he has learnt from this collaboration, Michael says,
“This has been a positive and rewarding experience for me and shows how remote collaborations can be very fruitful.Thinking about follow on opportunities for START, I would be very happy to work with students at African universities in a similar way. If there is a reliable internet and a computer terminal, there is no reason why I couldn’t also assist and mentor students in Africa.”
Michael is now embarking on a new postdoctoral appointment with Prof. Sir Richard Catlow’s group at UCL working in collaboration with Prof. Justin Hargreaves (University of Glasgow) to investigate transition metal nitride catalysts for ammonia synthesis. He will remain based largely at the Catalysis Hub at Harwell, and whilst this involves some new projects, he fully intends for there to be continuity between his current work and START collaborations.
“We have put a lot of groundwork into our collaborations through START. Although the funding for these is currently uncertain, we will always do research with the best people for the projects we work on through the Catalysis Hub and others. Prof. Claeys’ group in Cape Town is an excellent group. Whatever happens, I see no reason why we wouldn’t continue these collaborations. They are some of the best in the field!”
“In closing,” Michael adds, “I want to thank Professor Richard Catlow who has been incredible to work with through the START network, not only as an eminent scientist but also as demonstrating the importance of networking which I have benefitted a great deal from and learnt from. I have, myself, had access to Richard’s very large network of researchers who I would otherwise have not had contact with.”
Professor Sir Richard Catlow comments,
“Michael’s work, while exploring exciting fundamental scientific problems is contributing to the key challenges which must be met if we are to achieve the goal of global sustainability. His projects, which are typical of the whole START community, also illustrate how modern science is a global activity bringing together scientists at all career stages and with complementary skill sets. The GCRF START initiative can be proud of what it has achieved.”
1Mechanism of CO2 conversion to methanol over Cu(110) and Cu(100) surfaces. M. D. Higham, M. G. Quesne and C. R. A. Catlow, Dalton Trans., 2020, 49, 8478 DOI: 10.1039/D0DT00754D
2 Xie, B., Wong, R.J., Tan, T.H. et al. Synergistic ultraviolet and visible light photo-activation enables intensified low-temperature methanol synthesis over copper/zinc oxide/alumina. Nat Commun11, 1615 (2020). https://doi.org/10.1038/s41467-020-15445-z
3 Morphology of Cu clusters supported on reconstructed polar ZnO (0001) and (000) Surfaces. M. D. Higham, D. Mora-Fonz, A. A. Sokol, S. M. Woodley and C. R. A. Catlow, J. Mater. Chem. A, 2020, 8, 22840 DOI: 10.1039/D0TA08351H
4 The in situ magnetometer can analyse ferromagnetic materials under actual operating conditions, including high temperature and pressure (500°C, 50 bar) with the ability to control gas and/or liquid flows through the material. This makes it an indispensable tool for advanced research and industrial catalytic process optimisation.
5 David has focused more on the CO2 hydrogenation mechanism via HCOO*, COOH*, HCOOH*, H2COO* and OCH2OH*, whereas Yong Rui has been looking at CO2 dissociation, and subsequent hydrogenation of the resulting CO* to HCO*, HCOH*, and H2CO*, as well as the processes that are common to both mechanisms (namely H2CO* hydrogenation to either CH2OH* or CH3O*, and the subsequent hydrogenation of these two species to give the product, methanol).
“The future of all technologies is ‘smart’ and this is why Organic Solar Cells (OSCs) research is vital. OSCs can act as efficient energy sources in these contexts, given the advantages they offer over current silicon solar cells due to their unique properties – from abundant materials to scalable production processes. The goal is to meet sustainable development goals (SDGs) and the growing global demand through innovative, world class solar energy research, in which Britain is a leading player. The GCRF START grant has provided us with access to these important research opportunities.”
Dr Pascal Kaienburg, University of Oxford, UK
As countries move toward rebuilding their economies in the wake of the COVID-19 pandemic, the UN and COP26 call for recovery plans to create “a profound, systemic shift to a more sustainable economy that works for both people and the planet”. OSCs are solar cells made primarily from earth-abundant carbon-based compounds. They have great potential to significantly contribute to the COP26 vision of a “cleaner, greener, energy resilient” future through the development of the next generation of affordable renewable solar energy sources, from small scale-applications to large power stations around the world. This could be to supply the grid with electricity or integrated into off grid solutions and combined with storage to unlock novel applications which current silicon solar cells struggle to or cannot provide.
To this end, researchers from the University of the Witwatersrand (Wits) in South Africa and the University of Oxford in the UK are investigating the OSC microstructure to understand how they perform under varying conditions to find ways of enhancing the OSCs’ performance. Funded by the GCRF START grant, the aim is to gain unique insights at unprecedented resolution using state-of-the-art synchrotron techniques at the UK’s national synchrotron, Diamond Light Source (Diamond), amongst other techniques and facilities.
The UK has a strong record of solar cell research and the Department of Physics at the University of Oxford is an essential part of this research landscape. Led by Professor Moritz Riede, who is also a GCRF START Co-Investigator (Co-I), scientists in Oxford’s AFMD group conduct research into vacuum processing of OSCs. The precedent for upscaled vacuum fabrication of the related multi-billion-pound organic light-emitting diode (OLED) industry highlights the potential of vacuum-based processing for a range of ‘smart’ applications including OSCs. Indeed, leading companies commercialising OSCs apply vacuum deposition in their ‘solar film’ PV solutions.
To meet this growing demand for vacuum-based research opportunities, a National Thin-Film Cluster Facility for Advanced Functional Materials is currently being installed at the University of Oxford funded by the Engineering and Physical Sciences Research Council (EPSRC), the Wolfson Foundation and the University of Oxford, with Prof. Riede as the Technical Lead. The facility will place the UK at the centre of the development of next-generation materials and devices for applications in energy, photonics and electronics and act as an epicentre for novel thin film development within the UK.
Quantifying Organic Solar Cell charge transport
OSCs can be readily processed from solution or created by vacuum deposition. They have the advantage of being flexible, lightweight, affordable in production, and perform well under indoor lighting and elevated temperatures. With the potential to be made semi-transparent and to selectively absorb certain colors in the sun spectrum, they can, for example, enable energy-harvesting semi-transparent office windows or solar energy to be harvested and at the same time grow crops with the transmitted light. These advantages make OSCs suitable for integration into building facades and lightweight roof constructions – such as greenhouses – as well as to power sensors and transmitters for the rapidly evolving Internet of Things (IoT). However, with increasing OSC performance, the transport of charges that carry the energy absorbed from incoming light to the extracting contact in the solar cell has become a bottleneck for the technology over the past years that researchers across the world seek to tackle.
Dr Pascal Kaienburg is a GCRF START-funded Postdoctoral Research Assistant (PDRA) in Prof. Riede’s AFMD group making great strides in his research on quantifying organic solar cell charge transport, amongst other research areas. The aim of Pascal’s research is to link OSC opto-electronic characterisation with the microstructure of the light-absorbing thin films. This involves fabricating OSCs by thermal evaporation in vacuum in corresponding deposition chambers at the University of Oxford together with collaborators testing the microstructure at various synchrotron and neutron facilities worldwide including Diamond, which sits at the heart of the GCRF START grant.
“Solar energy has to be cheap enough to install where needed and useable with ‘smart’ applications, as well as large scale integrated options,” says Pascal. “Ultimately, with my research we want charges to become faster and reduce losses for better systems to make solar cells more efficient and the technology more competitive. Currently, there are silicon solar parks and silicon solar panels on buildings around the world, but to tap into new markets and applications, we need cost effective technologies with unique physical properties and organic solar cells offer these.”
This research involves quantifying and investigating different behaviours of the carbon-based, i.e., organic molecules in an OSC, such as better or worse charge transport, the nanoscale morphology in which the mix of molecules arrange, and most importantly, the interplay between the two. To gain control over the OSC’s behaviour, deposition conditions such as mixing ratio and deposition temperature are varied and optimised. Diamond in the UK, the Advanced Light Source in Berkeley, USA, the European Synchrotron Radiation Facility (ESRF) in Grenoble, France, and the UK’s ISIS neutron and muon source are being used to test OSCs in-situ and ex-situ to generate microstructural data. The data gathered in opto-electronic measurements allows Pascal to quantify the charge transport, before linking them with morphological data at Diamond regularly acquired by his colleague, Dr Thomas Derrien, who is also part of the START network; then working with chemists to design new organic solar cell molecules using this data to guide the design.
“The data looks good. I am not sure yet when we go to publication, but it won’t be long,” Pascal adds. “I’m very grateful to the GCRF START grant which has funded me to do this research and boosted my skills at the same time. Engaging with experts on microstructure characterisation has taught me and also allowed me to publish as co-author on other aspects of organic solar cells.”
Understanding how organic solar cells organise themselves and the effect on performance
Dr Thomas Derrien was a PDRA at Diamond from 2018-2021. His project focused on understanding how OSCs organise themselves and how this affects the performance of the solar cells. This work in collaboration with Prof. Riede’s group, made extensive use of an evaporation chamber, MINERVA, developed at Diamond. MINERVA enables researchers to thermally evaporate organic solar cell molecules while under synchrotron X-ray illumination enabling X-ray scattering images to be collected as the molecules are deposited on surfaces. From the X-ray scattering images, the structure, orientation, and crystallinity of the molecules can be deduced, all of which can have effects on solar cells performance. Another aspect of the project was to upgrade the MINERVA chamber to be include a third evaporation source in order to allow the study of more complex molecular mixtures and multilayer structures.
New UK-Africa solar energy research collaborations through the GCRF START grant
With the GCRF START grant, researchers like Pascal, Thomas, and Prof. Riede have teamed up with their counterparts in Africa, providing new perspectives on renewable solar energy research across different continents and research institutes. For example, the scientists from Africa contribute novel interesting materials that the UK scientists have not yet explored, and the UK scientists share knowledge about characterisation techniques with their African collaborators.
Dr Francis Otieno and Professor Daniel Wamwangi – both originally from Kenya – are based at the University of the Witwatersrand (Wits), South Africa. A member of the Energy Materials Research Group at Wits, which is led by GCRF START Co-I, Professor Dave Billing, Francis is a GCRF START funded Postdoctoral Research Fellow (PDRF) exploring the fabrication and testing of thin films-based solar cell devices including organics, perovskites and dye sensitised solar cells. In addition, he is looking into ways of enhancing their performance through nanoparticles technology such as plasmonics and spectral conversion thin films – research that is aimed at realising an efficient, cheaper source of solar energy and device-making for local and global markets. Prof. Wamwangi focuses on supplementary light management schemes and cost-effective materials, including organic molecules based on polymers and inorganic materials (metal halide perovskites – a hybrid between inorganic and organic materials, which can be solution- or vacuum-processed).
The GCRF START grant has been instrumental in exposing both scientists to expertise in the characterisation of OSC devices, such as evaporated fabrication techniques used by the AFMD Oxford University researchers, and access to synchrotron techniques at Diamond. The learning is mutual and in 2019, the grant enabled the Oxford University researchers to visit the University of Cape Town, South Africa, for a joint Energy Materials workshop. There they learnt more about African perspectives on Solar energy and other aspects of energy materials research, sharing their learning and ideas with their African colleagues.
“The GCRF START grant is very interesting because most research grants are focused exclusively on the science but START has the additional key element of capacity building both in Africa and the UK,” says Thomas. “It makes you think as a researcher about different angles on research… and allows us to build a network of collaborators. Pascal and I are in different institutions, but we have been able to work together and learn from each other through START, much like the collaborators we work with in Africa. Ultimately, the need for solar cells is huge in Africa so there is a large potential market for the UK to engage with. The potential to deploy the solar cells in Africa is much, much bigger than in Europe due to more sunlight, less existing electricity coverage and a large and growing population.”
In another example, Mohamed Abdelaal – an MSc. student from Egypt’s Ain Shams University in Cairo – was seconded in 2020 to the AFMD group in Oxford for several weeks. Despite the disruption of having to cut short his stay due to Covid-19 pandemic restrictions, he was able to conduct experiments at the University of Oxford and Diamond prior to returning home, with access provided by the GCRF START grant. Mohamed learnt new experimental techniques and applied computer modelling to explore the potential of simulating growth to better understand solar cell microstructure and how it affects performance. As a result, Mohamed has a joint publication from this work.
“The GCRF START grant allows us all to do better research, and with Daniel and Francis we collaborate on through several characterisation techniques,” Pascal explains. “By learning from each other’s knowledge and perspectives – including joint research visits and co-authoring new projects and publications – START has initiated new UK-African research opportunities which we aim to continue.”
Beyond ‘GCRF START 1’: creating a legacy of solar energy solutions for global challenges
To ensure the continuation of vital research collaborations and networks supported by ‘GCRF START’, follow-on opportunities are being explored. One option is through access to facilities like the new National Thin-Film Cluster Facility for Advanced Functional Materials, which will process a range of advanced functional materials including those for OSC and perovskite solar cells. Building on the success of the GCRF START grant, collaborators from this project and Dr Celine Omondi and Dr Victor Odari (MMUST, Kenya) – new partners from the African continent – are piloting how African countries can best benefit from these new capabilities established in Oxford.
Solar cells research investigated through START can be dominated by those with access to the best equipment, which is usually prohibitively expensive for most. With this new facility in Oxford, the goals of a newly commenced GCRF-funded UK-Africa project – ‘A Foundry for Research into emerging Photovoltaic Materials’ – are twofold: a) continue to investigate key physical questions on perovskite and organic solar cells; b) pilot a foundry model – aka “mail-order” for bespoke samples designed in Africa and made at this facility before being sent back to Africa – to see whether this concept is feasible and could be implemented in a similar pan-African research facility located on the African continent.
“I’m really excited about this project, which should demonstrate that something that is state-of-the-art in computer-chip manufacturing – the foundry model – works for research in advanced functional materials as well. We hope that such opportunities will benefit research in Africa and bring both economic and social benefits down the line, as well as being a stepping-stone to future larger projects led by a thriving and growing research community in Africa,” says Prof. Riede, the Principal Investigator of Oxford University’s Foundry project.
In another example, being part of the START collaboration has helped Francis to win a British Council Newton travel grant, allowing him to visit the AFMD group in Oxford for a period of six weeks later this year (2021). This would not have been possible without the skills and opportunities received through the GCRF START grant, enabling him to ‘give back’ to the next generation of students following in his footsteps, as Francis explains below,
“Not only has GCRF START funded my two and a half years’ Postdoctoral Research Fellowship at the University of the Witwatersrand, but it has also really exposed me to new skills, with access to advanced equipment at Diamond Light Source, the Advanced Functional Materials and Devices Group at the University of Oxford, and the Materials Physics Group at Sheffield University in the UK. As a GCRF START PDRF, I was able to buy research materials and made and strengthened South Africa-UK collaborations. But the benefit and legacy does not stop with me. Finding alternative cheaper sources using locally available materials such as organic polymers forms the basis of my research. It is this learning that I pass on to the next generation of scientists. My findings form the basis of my solar cell technology teaching for undergraduate and postgraduate students and research fellows back home in Africa.”
Post-pandemic recovery plans and ‘smart’ solar energy solutions
To address the planetary emergency, “post-pandemic recovery plans need to trigger long-term systemic shifts that will change the trajectory of CO2 levels in the atmosphere” (UN SDG 13 – Climate Action). This is where ‘smart’ solar energy solutions can play a role, says Pascal. Almost all applications use sensors in manufacturing and increasingly in domestic contexts, requiring a decentralised power source for these smart applications. The aim is to move away completely from externally charged batteries and power the sensors with solar cells, although integrated battery storage backup is possible, with batteries charged by OSCs.
Without the need for complex wiring and the frequent changing of batteries, OSCs could make the overseeing of manufacturing processes using sensors more efficient, as well as the heating of homes and workplaces, especially where hundreds of sensors are located throughout a building. From mounting OSCs on smoke detectors to integrating them into the fabric of electric vehicles to extend their travel range, to making a significant impact in the ‘power market’ – the applications of OSCs are numerous and so are the opportunities to reduce carbon footprints while improving lives and livelihoods.
“It makes sense to produce customised solutions locally which in turn creates jobs,” says Pascal. “For example, integrating OSCs into building facades requires customisation, which is an advantage as customisation increases the value. Lightweight OSCs are particularly advantageous in countries with less solidly constructed buildings and housing, particularly in sunny, warmer climates in Africa and South East Asia where thin walls may not bear the heavier loads of silicon solar cells. Another exciting option of growing interest is agricultural Photovoltaics (PV). Solar panels are located on agricultural fields, providing dual use of the area. Covering entire fields with semi-transparent or selectively absorbing OSCs, crops can still be grown while solar energy is harvested from the sunlight.”
With research progress and cost reductions due to growth of production (something that silicon solar cells, the incumbent, have well demonstrated), OSCs have the potential to eventually produce electricity at lower cost than silicon solar cells in large scale applications. This offers an exciting future of inexpensive electricity that can be scaled to the dimensions needed to make a difference in the world’s energy system.
Read more about the UN’s Sustainable Development Goals here
 The UN Secretary-General has proposed six climate-positive actions for governments to take as they build back their economies and societies. These include investing funds “in the future, not the past, and flow to sustainable sectors and projects that help the environment and the climate.” Also see: https://sdgs.un.org/2030agenda
 Thomas Derrien is a GCRF START member and in his role at Diamond was funded as a Postdoctoral Research Assistant by the GCRF START grant.
 Prof Dave Billing is Professor in the School of Chemistry and Co-PI of the Energy Materials Research Group at the University of the Witwatersrand (Wits), South Africa, and also Assistant Dean in the Faculty of Science at Wits.
“When I saw the opportunity to be a part of a GCRF START team in the UK, I was very motivated to join the group. My aim is to make connections with people and be the link between researchers in Africa and groups in the UK which brings benefit to both. START has made my dream real; it has enabled something one can’t do by oneself because you need a team, and you need funding. There is no other better way to do our research than through the START collaboration.”
Dr Khaled Mohammed, University of Southampton, UK
Our team at the University of Southampton (UK) is focussed on the application of in situ and operando methods to all aspects of catalysis; this covers all areas of a catalyst’s “life-cycle” – from formation and operational behaviour, to eventually understanding what causes it to lose performance. A catalyst is a chemical substance widely used in large-scale chemical industry to enhance reactivity and selectivity towards target products of the reaction of interest without itself being consumed in the reaction.
However, the complex nature of such material requires an advanced tool to understand its behaviour under operating conditions fundamental to the chemical industry and in the drive to increase sustainability for the future of our planet. Extensive knowledge and experience in using synchrotron radiation sources is therefore vital to understand the complex nature of catalysts and to develop new technologies here in the UK and globally. Through the START collaboration, our knowledge and hands-on-experience in this area is shared with our African partners as they develop their own catalysis and synchrotron research programmes.
My name is Khaled Mohammed, and I am a Postdoctoral Research Fellow (PDRF) in Synchrotron Methods for Catalysis within Chemistry at the University of Southampton. Funded by the GCRF START grant, I joined START in October 2019 to work with Dr Peter Wells’ team – Peter is a GCRF START Co-Investigator (Co-I) and an Associate Professor within Chemistry at Southampton, holding a joint appointment with the UK’s national synchrotron, Diamond Light Source (Diamond). I joined the START project only a matter of months before the global COVID-19 pandemic and research has been challenging in this period. Despite this, I have contributed to several published studies as a GCRF START PDRF.
Here I explain my perspectives on what START means as an African researcher in the UK. My role involves contributing to British and international research, and I see myself as an ‘ambassador’ for my country (Egypt), making connections to people and being a link between researchers in the UK and those in other African countries.
Joining the START network at the University of Southampton, UK
My experience using such facilities, with particular emphasis on operando and time-resolved X-ray absorption fine structure spectroscopy (XAFS), dates back to my PhD studies at the University of Southampton (2010 – 2014) and my previous role as a Research Associate at University College London (2013 – 2015), where our group had the opportunity to use the facilities at the Research Complex at Harwell and the Beamline Allocated Group (BAG) at Diamond. In November 2015, I decided to go back to my home country, Egypt, to start a new academic role at Sohag University as a Lecturer in chemistry. I was very keen and motivated about the role with its many teaching activities. A few months later, however, I realised that my scientific research was limited in this role by the fact that there was no access to a synchrotron, which does not exist on the African continent.
On the bright side, however, I had the opportunity to speak with my colleagues in Egypt who have no experience in using such synchrotron tools and I could share with them the knowledge I had gained in the UK. In addition, I could give lectures and seminars on the key questions about synchrotrons to the next generation of scientists: How does a synchrotron work? What type of experiments do we do with synchrotrons? Which beamlines are available to use to support our research?
My colleagues in Egypt were excited about this subject, but it was also a challenge as the facilities are good but not good enough to do the level of advanced experiments / topics that one can do with synchrotrons. People are very motivated to do these advanced topics, such as characterisation of materials for catalysts and applications, but the problem is we do not have the funding or access to these kinds of experiments. Therefore, when I saw the opportunity to be a part of a START team, I was very motivated to join the group at Southampton.
Catalysts and synchrotrons for renewable energy – the hydrogenation of furfural for biofuels
I was born in Sohag city, Egypt, where I lived for most of my childhood. I loved studying science at school, especially the physical sciences, and I dreamt about becoming a scientist to help provide power for the city where I lived – at that time access to electricity was very intermittent. Outside the city, I wanted to help people who lived in the countryside where, at that time, there was no electricity at all. Later, my dreams shifted to chemistry and I was motivated and inspired to develop pharmaceuticals. I had seen my grandfather suffering with illness and die prematurely due to lack of available medicines.
Today, I find myself inspired by these experiences working in catalysis with applications in renewable energy where waste biomass is converted to liquid biofuels (Bioenergy), or waste CO2 is converted to high value chemicals that can be used in our daily life, or as an alternative to fossil fuels. These applications rely on catalysts but to make this process more sustainable and efficient, advanced techniques are required to understand how the catalysts work under operating conditions. It is a big challenge for African researchers to access the facilities and techniques needed for this type of work. Like my dreams when I was younger, I take great pride in trying to provide something useful to society. What I love about START is that it brings these dreams to reality.
A good example of the kind of research I have collaborated on is the hydrogenation of furfural. Furfural is a bio-derived molecule and can be converted to many useful products, including the generation of liquid fuels; it is therefore a renewable energy feedstock. However, bio-derived compounds are highly functionalised, this means they have many parts of the molecular structure that can undergo chemical change. Palladium (Pd) nanoparticles are widely used as an active component in furfural hydrogenation – a specific type of reaction that involves the addition of hydrogen to a compound – however, selectivity to specific products is a big challenge. In addition, Pd is a very scarce element and there are significant concerns about the sustainability of using such elements, both from an economic perspective and the environmental impact of mining such rare materials.
In our recent paper, [ACS Catal. 2020, 10(10), 5483–5492 (https://pubs.acs.org/doi/10.1021/acscatal.0c00414)], we demonstrated that a Pd/NiO catalyst can hydrogenate furfural using a dual site process; the Pd splits the H2 molecule into adsorbed hydrogen atoms onto the Pd surface, the adsorbed hydrogen then migrates onto the NiO surface where the furfural molecule is selectively transformed. For materials like this, we need to use advanced tools at Diamond Light Source, e.g. X-ray absorption spectroscopy, to understand more about our materials and their unique properties that allow them to function as catalysts.
In the shadow of the Covid-19 pandemic – facilitating UK-African research through cross-disciplinary teamwork
“START has and continues to be a fantastic opportunity for the UK to work in concert with our African partners. Our futures are intertwined; we share the same global challenge of treading more lightly on our planet, be it to mitigate climate change or to preserve our natural world, whilst simultaneously sustaining our growing populations. New functional materials are needed to underpin the emerging sustainable technologies that allow us to tackle these challenges and START is an important gateway for sharing the tools and expertise to accelerate these advances.”
Dr Peter Wells, University of Southampton, UK
During the pandemic, the GCRF START grant has enabled us to stay productive and self-motivated, for which we are truly grateful. Although access to laboratory and synchrotron facilities has been limited, we have been able to continue our work remotely. We set goals including research activities, data reduction/analysis and submitting new beamline proposals. In addition, we participated in many on-line activities including workshops, seminars, and social activities with all participants in START.
The environment in the group here at Southampton has been excellent. There are things you can’t just learn by talking; we have learnt by doing research-based experiments together. Peter has taught me a lot. If I do an experiment, I give the idea to Peter, and then we do some tests to validate which beamline to use and what we need to adjust and optimise before we go ahead.
When I was in Egypt – before I got involved in START – I tried to do collaborations with people here in the UK. I could do the basics and prepare materials, but I couldn’t correlate the structure-performance relationship without beamtime experiments. Being here in the UK, interacting with experienced scientists, has enabled me to see what is new and to push things forward through START, sharing what I learn with my African colleagues.
A great achievement has been international collaborations across a range of disciplines. After joining START in 2019, I found the group already working with Professor Michael Claeys’ Group at the University of Cape Town (UCT) in South Africa. I soon got involved in this project working with Dr Mohamed Fadlalla and Chris Mullins on research using the B18 beamline at Diamond to assess, in situ, the effect of substituents in ferrite structure with the general formula of AB2O4. These are used in a wide range of catalytic reactions including the Haber-Bosch process, water-gas shift reaction, dehydrogenation of ethylbenzene, and Fischer-Tropsch synthesis (FTS) to produce liquid hydrocarbons/fuels.
I was able to assist Mohamed with his experiment in December 2020. We had to submit a proposal and get it accepted (to do this you have to submit initial results like a proof of concept). Once accepted, the experiment had to be done in a specific time frame. But before Mohamed came over to the UK to conduct the experiment, tests had to be carried out for optimisation of the materials. This takes time so I did this first to ensure the experiment ran smoothly when he arrived.
There are lots of other things that must be organised and managed before experiments like these, therefore my role has been to optimise as much as possible to increase the chance of success. Since then, we have assisted Mohamed and his colleagues in data analysis for publication. This successful beamtime experiment motivated us to explore new ideas, for example, in making catalysts with well-isolated active sites – mainly cobalt in tetrahedron sites to be used in preferential oxidation of carbon monoxide.
The future with START – ‘follow on’ opportunities for UK and African energy materials research
“START is a fantastic opportunity for the UK to work in concert with our African partners to tackle shared challenges. It is clear that the excitement generated can be inspirational and helps to further integrate research partnerships.” – Dr Peter Wells, University of Southampton, UK
We are discussing our new research ideas going forward with Mohamed and another colleague of his, GCRF START Postdoc – Dr Thulani Nyathi – and have set goals and tasks for two ‘follow-on’ projects currently in the pipeline. As a result, I am in the process of sending some samples to Mohamed and Thulani for the preferential oxidation of carbon monoxide. This research has the dual benefit of reducing the harmful effects of carbon monoxide and using the carbon monoxide captured to make useful chemicals for energy, such as fuel cell storage to power vehicles and other devices.
We are also very impressed with the facilities and equipment at UCT, some of which we don’t have here in the UK, and which could be beneficial to access in the future. On a practical level, routine visits are important for hands-on experience (sadly due to the Covid-19 pandemic my visit to UCT in 2020 was cancelled), therefore continuing remote options in the meantime is vital for sharing ideas.
Perspectives from our collaborators in South Africa on the impact of START
Here I want to share testimonials from Dr Thulani Nyathi and Dr Mohamed Fadlalla demonstrating their perspectives on our UK-Africa collaborations.
“I first worked with Dr Peter Wells’ group prior to the GCRF START programme through a collaboration also involving the UK Catalysis Hub (located on the Harwell Science and Innovation Campus in Oxfordshire) and with Dr Emma Gibson’s group in Chemistry at the University of Glasgow, funded by the EPSRC (grant EP/R026815/1). This included my first visit to a synchrotron facility – Diamond Light Source – and my first exposure to two in situ techniques, XAS and DRIFTS, which were used to study supported cobalt oxide catalysts for the preferential oxidation of carbon monoxide (CO-PrOx).
This collaboration proved to be highly successful as it was concluded with a very good publication in ACS Catalysis in 2019. Through the GCRF START programme (grant ST/R002754/1), I have continued to work with Peter’s group and Emma’s group, using the Block Allocation Group sessions administered by the UK Catalysis Hub, to analyse fresh and spent catalysts for the CO-PrOx reaction. I was then able to conclude my PhD thesis in September 2020 and publish a second paper in Applied Catalysis B: Environmental in June 2021.
There exists on-going work between the Southampton and UCT groups where we try to study substituted iron oxide and alloy catalysts for use in the hydrogenation of carbon dioxide (a greenhouse gas) to value-added chemicals. This work has already involved a trip to Diamond in 2019 and the results obtained will feature in a paper we aim to publish later in 2021. I hope to make more trips to Diamond and to continue working with the Southampton and Glasgow groups in the upcoming years.”
“The highly seamless collaboration with Dr Peter Wells and Dr Khaled Mohammed from the University of Southampton has led to a more profound collective understanding of the catalytic materials under activation and under working conditions using in situ and ex situ synchrotron-based techniques. Owing to the successful and harmonious collaboration between the two research groups thus far, further partnership is in the works to investigate catalyst structure/activity/selectivity correlations in the energy material field.”
START’s achievements and the future – “a great work for great value”
When I look back at what has been achieved and then look forward to the future, I ask myself the question: If there wasn’t a START network/project, how would people who don’t know about synchrotron techniques know about these opportunities? START not only transfers knowledge and enhances capacity, but it also builds awareness a bit like an advertisement. It helps us know where and how to apply to synchrotrons like Diamond for beamtime and shows us what is possible and how to do the experiments in the right way. And synchrotron techniques give unprecedented insights essential for our research. If there hadn’t been a GCRF START grant to fund these possibilities, it would have delayed our research because collaborations like START boost and speed up the process and findings.
In Africa we need the fundamental facilities to train the next generation ready to use synchrotrons. More locally, in Egypt, we need capacity-building facilities to do initial experiments and fundamental research. For example, a catalytic reactor would be very useful for scientists to do some reactions. We can do the preparation – we can buy the chemicals – but to do the catalytic reactions we need a reactor where we can do the experiments in optimised conditions.
We also need a ‘Centre for Catalysis’ in Egypt where we can teach the new generation to develop sufficient skills to collaborate with the UK and other countries for advanced experiments and push the research forward. If research hubs could be set up across Africa, like the Catalysis labs at UCT, this would be fantastic and START could be an ideal vehicle to make this happen. Another route is through funding agencies like the British Council/Newton Funding which provide travel grants and other support for researchers in developing countries.
To summarise the achievements of the GCRF START grant and what START means to me: I would describe it as “a great work for great value”, and all this despite massive setbacks caused by the Covid-19 pandemic.
START does great work that allows scientists from developing countries to gain knowledge and experience from leading scientists in the UK and to reciprocate, as my role shows. It does great work because it offers opportunities for us to work with scientists from all over the world on a level playing field. Ultimately, the greatest value from my perspective is that we work hard to provide (in a sustainable way) energy/electricity, medicines and many other applications for people who don’t have these fundamental things, enabling a better life for the future – what value is bigger or better than this?
Read more about the UN’s Sustainable Development Goals here
  ACS Catal. 2020, 10(10), 5483–5492 (https://pubs.acs.org/doi/10.1021/acscatal.0c00414) – This work has significant implications for the upgrading of bioderived feedstocks, suggesting alternative ways for promoting selective transformations and reducing the reliance on precious metals.  Phys. Chem. Chem. Phys., 2020,22, 18774-18787 (https://pubs.rsc.org/en/content/articlelanding/2020/CP/D0CP00793E#!divAbstract) – This study demonstrates the complexity of mechanochemically prepared materials and through careful choice of characterisation methods how their properties can be understood. Synchrotron techniques, such as X-ray absorption spectroscopy (XAS), have multiple benefits, which aid the in-depth understanding of chemically important yet complex systems.  Nanoscale Adv., 2019,1, 2546-2552 (https://pubs.rsc.org/en/content/articlelanding/2019/NA/C9NA00159J#!divAbstract) – Using state-of-the-art beamlines, this study demonstrates how X-ray absorption fine structure (XAFS) techniques are now able to provide accurate structural information on nano-sized colloidal Au solutions at μM concentrations.
 Author: Thulani M. Nyathi, Mohamed I. Fadlalla, Nico Fischer, Andrew P.E. York, Ezra J. Olivier, Emma K. Gibson, Peter P. Wells, Michael Claeys. Publication: Applied Catalysis B: Environmental. Publisher: Elsevier. Date: 15 November 2021. https://doi.org/10.1016/j.apcatb.2021.120450
“Abundant energy resources without adequate human resource and access to cutting edge infrastructure remains Africa’s contradiction and greatest challenge to harnessing its primary resources to useful forms. The GCRF START grant has been the vehicle towards the realisation of both, with Dr Francis Otieno being the success story to this initiative. His journey encompasses the germination to shoot culminating with the growth to a potentially giant tree visible in the horizon and useful in the vicinity” – Prof. Daniel Wamwangi, University of the Witwatersrand, South Africa.
It has been said that “The future belongs to those who believe in the beauty of their dreams”, but the truth is that so many of our dreams seem at first absolutely impossible. How do you dream of what you cannot visualise? Yet this is the story of a village boy in rural Kenya who knew nothing about experimental research laboratories or STEM, but years later became an international renewable energy researcher with a PhD in the START collaboration, with several papers published. My name is Francis Otieno and I am telling this story to inspire school kids, emerging researchers, and everyone – your dreams are possible!
From village schoolboy to PhD student – the beginnings of my renewable energy dream
My story begins as I progressed into high school and experienced the heavy environmental pollution from the congested slums of Mathare in Nairobi, Kenya. Large numbers of smoking cars in the streets and continuous electricity blackouts were the norm, especially at the slightest onset of rains. When I look back, this was the start of my dream of making a difference to society and our communities, the start of a long journey in the quest for clean, sustainable renewable energy.
Today I am a GCRF START Postdoctoral Research Fellow (PDRF) in the field of Solar Energy research. I was born in rural part of Kenya called Seme Kadero, in Kisumu County, to a big polygamous family of four mothers and 27 children. I was number 20 in our family and my father, born in 1928, was quite passionate about his kids attending school but none before me made it to university. We were allowed to go to school in the mornings but had essential chores in the afternoons. We grew up grazing cattle barefoot and cultivating land in alternation with school hours – we couldn’t even afford to buy shoes.
My father saved some money for me to attend high school but soon realised this was sufficient only to buy school uniform and other items required for admission but not school fees. I had to make do with a new school uniform, including long trousers and shoes for the first time, which I wore at home while waiting for my father to raise the fees. I didn’t know what to read during those weeks, so after putting on my school uniform each day, I would go to the newspaper vendor, and ask to read all the daily newspapers with him, and then go home in the evening.
My passion was to realise my father’s dreams one day and return home with a title earned from studying. I wanted to be a teacher and contribute immensely to society. My Physics Teacher at Eastleigh High School in Nairobi really believed in me which made a huge difference. He gave me a project using angular inclination and the concept of rectilinear propagation of light to design a device that could be used to measure the height of any building/tree from a distance without having to climb it! This kickstarted my love of science and drove my research career ambition.
I competed through the district and province and became the second best in the National Science Congress. The fire for research was then fully ignited, fuelled by the fact that I didn’t have a stable light source at night to study, in addition to the effects of environmental pollution. School and learning were vital. To avoid being mugged for our precious school books, we would walk to and from school 6 km, rising early each morning and singing on the way back home to deter anyone from stealing our text books to sell on for drugs.
My father had long retired from active business relying instead on peasant farming. Our tradition holds that our elder brothers help to cover school fees, which was a challenge as they were equally struggling to settle down in life. With all these hardships, my ambition was to improve performance at school which had back then only a 2-5% pass rate to public university. As a group of high school learners, we managed to turn this around and many secured a place at our public university where we could access government funding.
The best teacher teaches from the heart and not just the textbook, and this is what I intended when I chose a Bachelor of Education degree at Egerton University more than 100 miles northwest of Nairobi. I knew my heartfelt approach meant a lot to my father who has always urged me to do well and surpass any problems on the way. When I got my first Degree in Education teaching physics and mathematics, many of my pupils did well in my subjects. I am a proud teacher having seen them move into good careers using the physics and mathematics they had been taught.
My next thought was that the combination of research and teaching would be more impactful to society, so I enrolled for an MSc in Physics at the University of the Witwatersrand (Wits) in South Africa. Getting accepted on the course wasn’t easy, and I was rejected four times. Finally, in 2014, I joined Wits after resigning from my high school teaching job. This bold step would not have been possible without the encouragement of Prof. Daniel Wamwangi, Associate Professor in the School of Physics at Wits. I am forever grateful for the trust he had in me, the strong motivation he gave, and incredible guidance he has accorded me during my research journey at Wits.
Through his dedicated supervision I was able to successfully earn my MSc, within the time limit, and immediately enrol for a PhD, which I completed within a record time of 30 months together with an output of several publications. During my PhD journey, Prof. Daniel Wamwangi and Prof. Alex Quandt, Professor in Computational Physics in the School of Physics at Wits, formed the best team for supervision. From their immense expertise and with much hard work, I learnt so much within a record time and got exposure to advanced techniques, as well as collaborations within and beyond Africa.
I invited my then 92-year father to my graduation, and tears of joy flowed freely when he landed in Johannesburg for this happy event and throughout his three weeks stay with me in South Africa. It was his first time owning a passport and boarding an aeroplane and seeing his child graduate with the much-desired title of a Doctor of Philosophy. When my father returned to our village in Kenya, he would host sessions of storytelling about these experiences and remembers every tiny detail: his 20th child brought home his dream!
I told myself that although I was the first in the family to climb to this height of education, I would not be the last. Through this inspiration, four of my younger siblings have now earned their first degrees, and former students, friends and relatives have followed suit in South Africa and Kenya.
GCRF START Postdoctoral Research Fellowship and participation in national and international science outreach events
Through hard work with good output, I was approached by my current host, Prof. Dave Billing in the Department of Chemistry at Wits, and he suggested that I apply for a Postdoc position funded by the GCRF START grant, even before my PhD thesis examination results were back. I was highly convinced that this was the best news ever, and indeed, being accepted by START would help my career and personal growth because I needed exposure outside of Africa as well as within, to move my research forward.
START was a real blessing at the right time when I truly needed it. The GCRF START grant funded my Postdoctoral Fellowship at Wits for two and a half years. With START, I have been able to obtain lots of data results which have enabled me to publish in reputable journals. Being part of the START network has given me opportunities to collaborate with like-minded researchers at the UK’s University of Oxford, the University of Sheffield and the UK’s world-renowned national synchrotron – Diamond Light Source (Diamond). Through these interactions, I have learnt many new skills and exchanged knowledge and various perspectives.
In addition, back in South Africa and with support from the GCRF START grant to purchase the necessary kits, I participated in several community outreach programmes, including hosting an awareness and outreach activity for the 69th Lindau Nobel Laureate Meeting 2019 on Physics at the University of the Witwatersrand, which I attended in Germany. This was funded by The Academy of Science of South Africa (ASSAf), in partnership with the Department of Science and Technology (DST). The 2019 meeting – known by its Twitter hashtag #LINO19 – was dedicated to physics and was attended by 39 Nobel laureates and 580 young scientists from 89 countries. It was particularly meaningful for our South African contingent because South Africa hosted the International Day of Light that year. I also participated in the University of the Witwatersrand’s Yebo Gogga Exhibition and Focus Day, which assists young learners who need guidance into future careers such as in Physics.
Cleaner, cheaper energy sources through collaborations in cutting-edge advanced materials’ characterisation
Finding alternative cheaper energy sources using locally available materials such as organic polymers is the basis of my research. To provide clean renewable energy sources, the current market is dominated by silicon based solar cells which are high cost arising from the expense of extracting Silicon from its raw materials (sand) and due to their lower efficiency. Thin-film solar cells are known as second generation solar cell fabrication technologies to produce power electrical energy.
I focus on using nanoparticles technology such as plasmonics to realise efficient cheaper sources of energy and to find alternatives to silicon solar cells. My research interests are renewable energies and energy policy, and emerging solar technologies, with my focus under the GCRF START grant on materials’ characterisation, device fabrication and testing of thin films solar cells such as Organic Solar Cells (OSCs), perovskites, and dye sensitized solar cells. My project also explores ways to enhance the performance of these thin film devices through incorporation of nanoparticles technology and spectral conversion thin films with the ultimate goal of realising an efficient, cheaper source of solar energy and device-making for local and global markets
The GCRF START grant facilitated buying my research materials, and made and strengthened Africa-UK collaborations, with lab visits to the UK. This gave me exposure to cutting-edge opportunities and joint proposals to perform advanced materials characterisation such as Grazing Incidence Wide Angle X-ray Scattering (GIWAXs) at Diamond, and access to UK laboratories in the Materials Physics Group at the University of Sheffield with GCRF START Co-I, Professor David Lidzey, and to the Advanced Functional Materials and Devices Group (AFMD) with GCRF START Co-I, Professor Moritz Ried at the University of Oxford.
The newly acquired National Thin-Film Cluster Facility for Advanced Functional Materials based at the University of Oxford is capable of being an epicentre for novel thin film development within the UK and beyond. This facility certainly places UK at the centre of the development of next-generation materials and devices for applications in energy, photonics and electronics. Access to this facility through my on-going collaboration with Oxford will certainly revolutionise my research prospects with increased potential of producing publications in collaboration with the AFMD group, namely Dr Pascal Kaienburg and Irfan Habib.
In the Materials Physics Group at Sheffield University, Rachel Kilbride and Dr Joel Smith assisted me with carrying out GIWAXs on organic thin films. At Diamond, Dr Thomas Derrien guided me with joint beam time proposals enabling us to do measurements both at Diamond and the European Synchrotron Radiation Facility (ESRF). These collaborations and networks I aim to continue being involved in, and were made possible by Prof. Billing, who has much expertise in powder diffraction and energy materials across research networks within, and beyond Africa. I am always grateful for the faith he had to appoint me as a PDRF, and I have valued his immense support. Also, key is Prof. Wamwangi, who has been a great mentor in my research journey, from experimental techniques to manuscript preparation. As a result, I have contributed to several papers looking at solar cells materials and device-making instrumental to industries, working on improving the performance of solar cell devices highly needed in the global market.
We believe that the future of all technologies is ‘smart’ and for this reason, and Organic Solar Cells (OSCs) research is critical to realise efficient energy sources with advantages over current silicon solar cells, due to the abundance of materials and ability for scalable production processes that OSCs offer. Our aim is to contribute to the Sustainable Development Goals 7 (energy) and 3 (Climate) and the growing global demand for innovative, world class solar energy. Also, our research findings form the basis for teaching solar cell technology to undergraduate and postgraduate students as well as other Research Fellows back home.
Inspiring hope, enabling others to dream – bringing my expertise back home
Although the journey is a long one, I am excited to have embarked on making a difference in the society through our research; and I am proud that my dream of impacting young people from rural areas like my own was realised when I became a teacher. To continue investing in developing others, I have started mentoring undergraduate and postgraduate students at the University of the Witwatersrand and now at Maseno University, Kenya, where I have been offered a job as a lecturer.
The GCRF START grant exposed me to new skills and advanced equipment, and through my successes and links to START, I was able receive the British Council Newton Travel Grant which will enable me to visit Oxford for a period of six weeks, currently planned for September 2021. This exposure together with much sought after skills and strong collaborations will be very useful to me as a young researcher looking forward to supervising postgraduate students back in Kenya, upon the completion of my Postdoctoral Fellowship.
As Kenyan bush-pilot, Beryl Markham, once said, “Africa is mystic; it is wild; it is a sweltering inferno; it is a photographer’s paradise, a hunter’s Valhalla, an escapist’s Utopia. It is what you will, and it withstands all interpretations.” – one aspect of interpretation is that here, in my story and the story of START, hope does not disappoint!
Read more about the UN’s Sustainable Development Goals here
“GCRF START has been pretty awesome, in the way it’s allowed us to help accelerate some truly cutting-edge South African science with the tools we get to develop and provide at Diamond.”
Professor Frank Von Delft, GCRF START Co-I at Diamond Light Source, UK
According to the World Health Organization (WHO), antimicrobial resistance is one of the top 10 global public health threats facing humanity. In South Africa, infections caused by Staphylococcus aureus and Mycobacterium tuberculosis are an all-too-common reality. While M. tuberculosis is the causative agent of tuberculosis (TB) which shows increasing prevalence of drug-resistance, S. aureus is one of the ESKAPE pathogens  – a group of organisms that are leading causes for community- and hospital-acquired infections globally. ESKAPE pathogens are also notoriously difficult to treat and are resistant to many first line antibiotics. Considering the rise in antimicrobial-resistant organisms there is a desperate need to identify new antimicrobial compounds that work differently from those currently in clinical use.
New and exciting drug discovery initiatives
With the GCRF START grant, the Strauss Laboratory has established new, cutting edge structural biology capabilities at Stellenbosch University in South Africa to collect data onsite and remotely from Diamond. This includes embarking on an exciting approach in drug discovery initiatives to identify new antimicrobial compounds, using the UK’s world class national synchrotron, Diamond Light Source (Diamond).
Research in the Strauss Laboratory is focused on understanding the biosynthetic pathway of the central metabolic cofactor coenzyme A (CoA), as well as other enzymes that play a role in maintaining the redox balance in the human pathogen S. aureus. The Lab makes use of a number of chemical biology tools to develop novel agents for the selective inhibition of both drug-sensitive and drug-resistant strains of S. aureus by targeting enzymes involved in the biosynthesis and utilisation of CoA and other enzymes associated with its resistance to oxidative stress.
“While we would be keen to develop a new antimicrobial compound that could one day be used in a clinical setting, our current primary goal is to see if we can use small molecules to modulate the survival of S. aureus in the host–pathogen interface,” says Professor Erick Strauss, Group Leader at Stellenbosch University’s Strauss Laboratory in South Africa. “Ideally, such compounds would work synergistically with the body’s natural defences to ward off infections, thereby reducing the likelihood of antimicrobial resistance arising.”
“Through Diamond’s X-ray structure-accelerated, synthesis-aligned fragment medicinal chemistry facility, under guidance from GCRF START Co-Investigator, Prof Frank von Delft, we have been able to fast-track the identification of novel compounds that we are currently pursuing further as promising leads of such modulators of the survival of S. aureus”, adds GCRF START-funded Postdoctoral Research Fellow, Dr Blake Balcomb. “This is the first time that researchers from Stellenbosch University have used this cutting-edge technology in drug discovery initiatives.”
Diamond’s XChem workflow is geared towards automation and high-throughput screening of hundreds of compound fragments with automated structure determination of the protein of interest with each individually bound fragment, which is what enables a process that could normally take months to be fast-tracked to take just a few days.
“To explain the process in simple terms, it is like the protein represents a sponge and one by one individual compounds would be soaked into the sponge and only those compounds that have a natural propensity or chemical attraction to bind to the sponge would remain bound,” says Balcomb. “If one had to do this manually one by one it would take several months to go through each of the compounds and investigate if the compound fragment is bound to the protein of interest and, importantly, what orientation it is bound. With XChem one can obtain data and final results within a week!”
Successful experiments and new collaborations
Researchers in the Strauss Laboratory have completed two successful XChem experiments on two separate S. aureus enzymes. One enzyme is involved in the biosynthesis of CoA and a second enzyme is involved in detoxification of a host derived antimicrobial. Through XChem they have collected data on >800 crystals and obtained >150 novel crystal structures all containing different fragment compounds.
“To mitigate the usual slow progression of fragment hits to promising drug leads we are pursuing two hits in two separate approaches,” explains Prof. Strauss. “The first approach, also developed by the Frank Von Delft team, is similar to the XChem workflow and is optimized and streamlined for automation and high-throughput analysis. This technique makes use of an Opentrons pipetting robot, which is used to perform automated multi-step parallel syntheses in a checkerboard format, therefore allowing one to do combinatorial synthesis and to make many similar compounds at the same time. The added benefit is there is no need to purify the end-products, as these are soaked directly into crystals of the target enzyme to determine their inhibition potential. These experiments again would feed back into the XChem workflow.”
In a second approach, the team has initiated a new collaboration with Dr Nir London at the Weizmann Institute of Science to develop compounds that target proteins covalently (to form an irreversible attachment to proteins). This approach is also based on a high-throughput setup that screens several fragments that contain specific reactive groups. The results of the most reactive fragments are then again fed back into the XChem workflow, whereby one would be able to visualise the compound-protein complex. All of these findings help aid in the development of potent and specific compounds that could be assessed further in the drug discovery pipeline and in turn, the discovery of novel antimicrobials.
In addition to Diamond’s XChem facilities, the Strauss Laboratory also has regular access to Diamond’s MX instruments through a dedicated South African BAG . This BAG access is a highly effective means in which a consortium of other scientists can work together to share a full beamtime shift for data collection. Through the BAG access the Strauss Laboratory, has on average, sent three to four shipments of samples per year to Diamond, and has so far solved eight novel crystal structures.
Capacity building and peer training in structural biology
Alongside the cutting-edge science, the GCRF START grant has enabled the Strauss Laboratory to invest in training and capacity development in techniques like fragment screening. Dr Blake Balcomb, formally trained in structural biology, and Dr Anton Hamann originally trained as an organic chemist but now a GCRF START grant funded Postdoctoral Fellow skilled in protein X-ray crystallography, have participated in two separate CCP4 workshops as well as training on the use of XChem facilities. These skills they pass on in their research group, as well as cascade to other research groups at Stellenbosch that show interest in structural biology as a research tool.
The scientists have, in addition, transferred skills to several students and Postdoctoral students in the Strauss Laboratory, including Dr Koketso Mogwera, who is now a Post-doc at H3D at the University of Cape town (UCT), Tim Kotze (PhD), Warrick Sitzer (MSc), Karli Bothma (MSc) and Nicholas Herbert (BSc Hons), now an MSc. student at the AHRI.
The GCRF START grant has also enabled the Strauss Laboratory to call on expertise and initiate new collaborations with scientists in other African universities. For example, MSc student Warrick Sitzer is currently investigating the structure of one of the enzymes involved in CoA biosynthesis using CryoEM and is co-supervised by GCRF START Co-I, Dr Jeremy Woodward, from the University of Cape Town.
Warrick Sitzer reports below on the training and mentoring he received,
“As an MSc. student, learning about CryoEM has given me a deeper appreciation on how it is used in structural biology research as opposed to other major techniques in the field such as X-ray crystallography and NMR spectroscopy. I find that the scientific progress made in detector technology and software algorithms to unravel difficult or complex biomolecular structures at near atomic resolution without the need of crystallization to be very exciting. The ability to determine these biomolecular complexes in their native state opens up a door to a room full of possibilities that may contribute significantly to structure-based drug discovery.”
Describing the impact that GCRF START has had on his research, Anton said,
“The GCRF START grant has opened a new field for me in medicinal chemistry and has introduced me to protein crystallography. Through the GCRF START grant, I had the privilege to carry out crystallographic fragment screening experiments at Diamond’s XChem facility, which has accelerated my research in developing novel antibiotics for S. aureus. Thanks to START, I am now a better and more developed medicinal chemist.“
Commenting on the capacity building achievements supported by the GCRF START grant, Frank von Delft said,
“While a lot of Diamond’s facilities for macromolecular crystallography can be offered through remote access, our XChem facility must be attended in person; and it is only thanks to the GCRF START grant that those persons include South Africans. What’s been equally exciting is seeing those researchers being able to use those results to accelerate not only their science, but their careers.”
Read about the UN’s Sustainable Development Goals for Health and Wellbeing here
Enterococcus faecium,Staphylococcus aureus,Klebsiella pneumoniae,Acinetobacter baumannii,Pseudomonas aeruginosa, and Enterobacter species
 Front Microbiol. 2019 Apr 1;10:539. doi: 10.3389/fmicb.2019.00539. eCollection 2019
 Strauss E. Coenzyme A Biosynthesis and Enzymology, in Comprehensive Natural Products II Chemistry and Biology Vol. 7 (Eds. Lew Mander & Hung-Wen Liu) 351-410 (Elsevier, 2010).
The Agenda for Sustainable Development calls for the world to “ensure healthy lives and promoting well-being for all at all ages” by 2030 (SDG3). Although there has been progress in many health areas, the UN reported in 2020 that the rate of improvement has slowed and may not be sufficient to meet SDG 3 targets, particularly with the Covid-19 pandemic disrupting progress around the world. This also applies to related Sustainable Development Goals (SDGs), such as ensuring availability and sustainable management of water and sanitation for all (SDG 6). Currently billions of people throughout the world still lack access to safely managed water and sanitation services and basic handwashing facilities at home. The need for solutions, the UN reports, is vast and accelerating: “Countries need comprehensive health strategies and increased spending on health systems to meet urgent needs and protect health workers, while a global coordinated effort is needed to support countries in need”.
Scientists are increasingly at the forefront of global and local efforts to tackle these challenges, not least in clinical drug design and discovery and vaccine development for countries where some of the need is the greatest. This includes the small but growing community of structural biologists in Africa, many of whom are just starting out on their careers.
Established in 2013, the Structural Biology Research Group at the University of Pretoria in South Africa focuses its research on molecules involved in mechanisms of infectious diseases – primarily from Mycobacterium tuberculosis (Mtb, causing tuberculosis or TB), enterotoxigenic Escherichia coli (travellers’ diarrhoea), and Listeria monocytogenes (listeriosis). The aim is to elucidate the molecular processes that allow these microorganisms to invade and/or persist within the human body or individual cells to improve our understanding of these diseases for clinical drug design and discovery.
Collaborating with the GCRF START grant – three case studies investigating infectious diseases
In 2016, the Group moved to newly renovated laboratories in the University of Pretoria’s Agricultural Science building designed for molecular biology, protein production and structural analyses, and in 2018 commenced collaborating with the GCRF START grant programme. The benefit of being part of this international grant and research network is explained by Group leader and GCRF START Co-I, Prof. Wolf-Dieter Schubert,
“The GCRF START grant has enabled the Group to access the UK’s national synchrotron, Diamond Light Source (Diamond) for experiments using state-of-the- art synchrotron techniques not available on the African continent,” Prof. Schubert says. “It has also exposed students to international networks and workshops/training to share knowledge and build capacity in the field of structural biology for solutions to infectious diseases rife on our continent and beyond.Our Group currently includes 6 PhD students and 4 MSc students from countries as far afield as Nigeria, Cameroon, Namibia and Zimbabwe, in addition to South Africa, and we welcome two Honours students during 2021”.
The case studies below highlight the research of three emerging scientists from across Africa who are studying for their PhD’s in the Structural Biology Research Group at the University of Pretoria. Each describes how their careers and their research benefit from the collaboration between the Group and the GCRF START grant.
Clifford Manyo Ntui: Using synchrotrons in the fight against infectious diseases
My name is Clifford Manyo Ntui and I am a PhD student in Biochemistry. I was born in Ewelle village, in South West Province of Cameroon. Growing up in the village where no clear explanation was given for the cause of countless illnesses and deaths was always a nightmare to me. To seek answers, I decided to pursue a career in the field of infectious diseases. My path towards this journey gained ground when I joined the Structural Biology Research Group at the University of the Western Cape under the supervision of Prof. Wolf-Dieter Schubert in 2012 for my Honour’s degree, with a focus on the molecular basis of infectious diseases. This was followed by an MSc working on Mtb in the same group but now at the University of Pretoria. My PhD studies on Escherichia coli (ETEC), have benefited greatly from the Group’s collaboration with the GCRF START grant.
The field of Biochemistry is one of great interest and importance in Africa as attested by the need for more medicinal drugs towards the fight against infectious diseases. My training and expertise in the field of structural biology of infectious diseases makes me one of only a handful of scientists working in this area on the entire continent. I have worked with more than one synchrotron light source, which has given me skills that are scarce on the African continent. Moreover, I have a strong background and interest in communicating structural biology skills to student learners and the public.
In 2014, four years before the GCRF START collaboration, I started on my MSc studies at the University of Pretoria working on the crystals structure determination of novel drug targets of Mycobacterium tuberculosis, the bacterium that elicits tuberculosis. I was quite successful in my endeavour, solving the structure of one potential new drug target, thiamine phosphate kinase. As part of my MSc training, I twice travelled to the European Synchrotron Radiation Facility (ESRF) in Grenoble, France, to undertake diffraction experiments using highly brilliant and monochrome X‐rays. South Africa is a member of the ESRF, providing access to world class, cutting‐edge equipment. The data collected on these trips allowed me to solve the crystal structure of the protein mentioned above. In addition, I was able to collect diffraction data for a number of colleagues, again leading to the successful determination of a range of crystal structures in the field of Infection Biology as well as Microbial Ecology and Genomics. This formed the foundation of my training in synchrotron techniques which I could use in my PhD research.
For my PhD, I am working on EtpA protein from enterotoxigenic Escherichia coli (ETEC), a bacterium that causes severe diarrhoea in many African countries. This disease leads to the death of hundreds of thousands of children under the age of five all over the developing world. EtpA is an adhesin which has been found to associate with flagellin from flagella allowing for bacterial adherence and toxin delivery. Currently, there is no crystal structure of EtpA from ETEC. This research aims to structurally characterise EtpA alone, as well as in complex with flagellin from ETEC as a possible vaccine target against ETEC diarrhoeal disease.
This project has produced the first crystal structure of the secretion domain of EtpA protein from ETEC using X-ray diffraction on the beamline I04 at the Diamond Light Source synchrotron, the experiments conducted at Diamond remotely from our labs at the University of Pretoria. The project is the product of a successful research programme thanks to funding provided by the GCRF START grant which has ensured the smooth running of our molecular biology laboratory. START has also contributed to organising workshops which have been invaluable for enhancing my protein structural biology knowledge, such as the CCP4 workshop of which GCRF START is a sponsor.
Vukosi Edwin Munyai: Characterising the protein structures of Listerial adhesion protein (LAP)
My name is Vukosi Edwin Munyai. I was born and raised at Kurhuleni village, located in Limpopo Province, South Africa. Collaborating with the GCRF START grant, provides me with the opportunity to contribute to Global challenges in line with the UN’s Sustainable Development Goals for creating a better future for all. As one of the first students to enrol for a PhD in science in my village, I am so grateful to do research that impacts human lives.
The GCRF START grant has given us a platform for learning in structural biology aspects, conducting experiments, associating with other scientists, and access to the Diamond synchrotron. I have the opportunity to learn more professionally and to learn how to handle different tasks as an independent researcher. In the future, I would like to spend time in academia, teaching and influencing young people, using my own story and research to inspire them.
In 2011, I completed my BSc degree in Biochemistry and Microbiology at the University of Venda, South Africa. From 2012 to 2014, I was working at United National Breweries in South Africa as a laboratory assistant when I decided to go back to study. In 2015, I enrolled for an Honours degree in Microbiology and a year later, for a Master’s degree in Biotechnology at the University of Western Cape, which I completed in 2018. After completing my Master’s degree, I relocated to Pretoria in 2019, where I enrolled for PhD in Biochemistry and structural biology.
My main objective is to characterise the protein structures of Listerial adhesion protein (LAP) and also its complex structure with human HSP60 (‘heat shock protein’). It has been proposed recently that L. monocytogenes uses alcohol and acetaldehyde dehydrogenase/LAP interaction with human intestinal HSP60 to enable its para-cellular translocation to the sites of its pathogenicity/cause of disease. Characterising the complex structure of LAP and HSP60 will help to explain how L. monocytogenes infects its host alongside the established modes of invasion through the Internalin surface proteins. Understanding the LAP/HSP60 interaction may help in developing clinical drugs to prevent listerial infections. Dehydrogenase enzymes for industrial applications are presently in short supply. The structure of LAP will thus enhance knowledge about its roles in both disease and industrial applications.
Maria Hamuyela: Studying the functions and the structure of the ETEC EatA passenger domain
My name is Maria Hamuyela and I study the secreted EatA protein of enterotoxigenic Escherichia coli (ETEC) bacteria. I am currently employed as a technologist for the University of Namibia in Windhoek. After more than a year of searching for opportunities, I came across Prof Wolf-Dieter Schubert and he accepted me to join the Structural Biology Research Group at the University of Pretoria to carry out my PhD studies whilst retaining my job as a technologist in Namibia.
The GCRF START programme has afforded me an opportunity to study towards my PhD studies allowing me access to world class equipment and techniques like X-ray diffraction at the UK’s Diamond synchrotron and provides me with access to the reagents that I need to do my research. I am also getting scientific training, not only in the laboratory but through workshops.
ETEC commonly causes watery diarrhoea in children younger than five years old – a cause of death due to diarrhoeal diseases in this age group, as well as malnutrition and stunting in children. Lack of access to clean water and sanitation means infectious diseases such as ETEC and Shigella spread through water and food. Studying ETEC has a potential to provide knowledge needed to develop vaccines and drugs against ETEC and other related diseases in line with the WHO/UNICEF Integrated Global Action Plan for the Prevention and Control of Pneumonia and Diarrhoea (GAPPD). The GAPPD has, as a key goal, the reduction of deaths from diarrhoea in children younger than five to less than 1 per 1000 live births by 2025 (WHO/UNICEF, 2013). Hopefully designing an inhibitor for EatA will be a fundamental step in achieving this goal.
The EatA passenger domain protein is required for the virulence of ETEC. It degrades Mucin 2, a major mucin secreted by the intestinal epithelium. Previous reports show that EatA passenger domain shows potential as a candidate vaccine for ETEC and other enteric pathogens such as Shigella flexneri. The EatA passenger domain has however not been extensively studied with regards to functional and structural properties. Therefore, the main aim of my project is to characterise both the structure and functional properties of the EatA passenger domain to design an inhibitor for EatA.
Impact of the GCRF START grant – Structural Biology students trained from seven African countries
Prof Wolf-Dieter Schubert from the University of Pretoria acknowledges the dramatic impact the GCRF START programme has had from its inception in 2018:
“Overall, GCRF START has helped support the research of six PhD students, five MSc students and six BSc Honours students in our research group. In addition to supporting individual research projects, the programme also allowed them to meet and interact with international experts, provided access to internationally competitive infrastructure such as the Diamond Light Source, and supported their participation in a number of workshops and conferences.
The impact is thus clearly multidimensional. Coupled to the fact that supported students came from seven African countries with a balanced gender distribution throughout, the long-term impact will be considerable. This will apply particularly if students are able to continue on their path towards independent research careers and possibly return to their home countries. The impact of the grant so far bodes well for structural biology and health related, and as well as industrial research throughout the African continent.”
Read more about the UN’s Sustainable Development Goals here
 The Covid-19 pandemic is threatening health systems and in particular, ones with poor resources, insufficient health facilities, medical supplies and health-care workers to meet the surge in demand. For example, an estimated 10 million persons fell ill with Tuberculosis (TB) globally in 2018, and drug-resistant Tuberculosis is also a continuing threat with the goal to end TB by 2030 no longer a possibility (UN, 2020).
 Kim K-P, Jagadeesan B, Burkholder KM, Jaradat ZW, Wampler JL, Lathrop AA, Morgan MT, Bhunia AK. (2006) Adhesion characteristics of Listeria adhesion protein(LAP)-expressing Escherichia coli to Caco-2 cells and of recombinant LAP to eukaryotic receptorHsp60 as examined in a surface plasmon resonance sensor., FEMS Microbiol Lett 256, 324-332, doi:10.1111/j.1574-6968.2006.00140.x
Scientists in the UK’s University of Sheffield’s Electronic and Photonic Molecular Materials Group (EPMM) work on the development and optimisation of thin-film photovoltaic devices (solar cells) for sustainable energy solutions. The advantage of these type of devices is that they can convert sunlight to electrical power with high efficiency, with such materials being easy and cheap to process, potentially allowing ‘sustainable’ solar cells to be manufactured at high volume and low cost. This is important given the rising global energy demand and need for electrification in remote, rural areas, particularly in Africa, where national grids are often over-constrained.
The EPMM Group, which collaborates with the GCRF START grant, focuses on two classes of materials: perovskites,  and polymer fullerene blends. Industry standard silicon solar cells require very high temperature processing and expensive controlled environments (clean rooms) for their manufacture, whereas hybrid-perovskites solar can be fabricated at low temperatures using liquid-based processing which reduces costs and makes their production easily scalable. However, one of the biggest challenges with these hybrid-perovskites is their reduced stability compared to silicon. The Group is therefore investigating these materials to understand how best they can be optimised for the next generation of solar energy devices.
Investigating affordable energy solutions with the GCRF START grant
In their research, the EPMM scientists have benefitted from the GCRF START grant, enabling them to get involved in new international collaborations as well as access the UK’s national synchrotron, Diamond Light Source (Diamond), where they use synchrotron techniques such as X-ray scattering to research halide perovskites, a potential material for the next generation of low-cost photovoltaics.
“Using Diamond allows us to explore the structure of these materials at length-scales corresponding to atomic and molecular bonds, we have found that understanding the structure of these materials is absolutely critical in developing our understanding of how they ‘work’ in devices. Ultimately, this understanding helps in developing new materials or new ways to process existing materials to get optimum performance (efficiency) out of our solar cells.”
Prof. David Lidzey, GCRF START Co-I and Director of the EPMM Group
The GCRF START grant has also funded Dr Onkar Game’s one-year Postdoctoral position in the EPMM Group during which time he has both undertaken his own experiments on perovskites and worked very closely with various PhD students in the Group. Prof. Lidzey reports that Dr Game’s input has been invaluable, this flexible work-pattern maximising the amount of research using the funding available.
“The GCRF START grant provided me a unique opportunity to make use of world class structural characterisation facilities at Diamond” says Dr Game. “Working with PhD student Joel Smith, we utilised the in-situ Grazing Incidence Wide Angle X-ray Scattering (GIWAXS) facility at the I22 beamline in Diamond to identify the factors affecting the degradation of perovskite crystal commonly used in perovskite-PV devices. This helped us to tune the composition of perovskite crystal to make it more stable towards moisture and light induced degradation. I also enjoyed setting up the in-situ measurements with Joel on understanding of solvent-induced liquification and crystallisation of perovskite using GIWAXS on Diamond’s I07 beamline,” Dr Game adds.
Collaborative research on Perovskites: the effects of composition and temperature
Dr Claire Greenland completed her PhD in the EPMM Group supervised by Prof. Lidzey. She has been working on perovskites and has been particularly interested in how the structure of such materials are affected by their composition and local temperature. This work was done in close collaboration through the GCRF START network with the Energy Materials Research Group at the University of the Witwatersrand (Wits), South Africa, led by GCRF START Co-I, Prof. Dave Billing. In this research, Claire studied one type of popular perovskite called a ‘mixed cation’ perovskite, and used X-ray scattering to characterise the structure of the perovskite as it was cooled down to very low temperature (-190 °C). She also measured the ability of the perovskite to absorb and emit light over the same temperature range. In these studies, Claire was looking for changes in the crystal-phase as the temperature was changed.
Understanding such processes is important, as the temperature at which some phase changes occur are within the expected operational temperature of the solar cell and understanding the effect on the properties of the materials in the solar cell forms a critical part of the understanding of how such materials (and devices) work.
“Interestingly, the structure of the perovskite crystal is not fixed, but can vary as a function of temperature, being ‘cubic’ at room temperature and starting to change to a ‘tetragonal’ phase around -13 °C, with a second low-temperature phase identified at -180 °C,” Prof. Lidzey explains. “Through careful analysis, these changes in crystal structure could be correlated with changes in the optical properties of the perovskite.”
This research was supported with assistance from Wits University scientist, Adam Shnier. Adam met members of the Sheffield team at a GCRF START meeting in 2018, hosted by the Energy Materials Research Group at Wits.
“Adam Shnier provided us invaluable support in the analysis of the X-ray scattering data, allowing us to understand how the crystal structure changed with temperature,” Prof. Lidzey says. “With support from the GCRF START grant, Adam was able to travel to the UK in 2019 and assist us in some scattering experiments performed at Diamond and became an important part of the team.”
“At the 2018 GCRF START meeting, I met a PhD student, Joel Smith, from the University of Sheffield who works on the same type of materials,” says Adam. “Joel and his colleagues are experienced at making high quality, efficient devices; while at Wits, we are experienced in making other materials that can be used for these devices and studying their crystal structures. As the 2019 GCRF START meeting was being held in the UK, we planned a research visit where I would spend a week working with Joel and his colleague Dr Onkar Game in Prof. David Lidzey’s laboratory at Sheffield. The purpose was to share technical knowledge. They were more than happy to share their experiences with these materials which instilled me with a plenty of ideas and information to share with my colleagues at home in South Africa.”
The research was published in January 2020 and formed a very important part of Claire’s PhD thesis. Claire has since passed her PhD viva and has come back to Sheffield in the position of ‘University teacher’. While she is not currently working on perovskites, her knowledge of materials physics and experience in understanding complex phenomena are proving invaluable in teaching electromagnetism to 1st year undergraduate students and will also be useful in the 2nd year lab experiments that she is developing and running, says Prof. Lidzey.
‘The GCRF START collaboration enabled me to collaborate with academics from Wits University in South Africa, which greatly enriched my work due to their expertise in X-ray diffraction and crystal structure,” Claire explains. “I collaborated mainly with Adam Shnier, who was able to computationally model the X-ray diffraction data taken at a range of temperatures on mixed cation perovskites. This modelling revealed the temperature dependence of a variety of crystal parameters, which not only allowed us to identify phase transitions in these materials but also to correlate crystal structure with photoluminescence properties.”
“I really enjoyed working with Adam, and his insight on all things related to crystal structure and phase was invaluable to my work,” Claire adds. “These studies shed light on the fundamental properties of perovskites and how these vary as a function of temperature – such studies are a key part of solar cell optimisation, because real world solar cells must operate under a wide range of temperatures. So, it’s really cool to know that this project was part of the push towards cheap and efficient solar cell materials, which are an essential part of tackling climate change.”
Perovskite ‘healing’ for high-speed manufacture processes
PhD student Joel Smith has also been working on perovskites. Here, however, he has been interested perovskite recrystallisation processes using solvent molecules. In this process, a perovskite film is exposed to a solvent gas, with this exposure causing the solid perovskite film to melt into a different solid or liquid form. Once the gas is removed or when heated, this material crystallises back into a ‘healed’ perovskite. The advantage of this process is that the quality of the perovskite film can be substantially improved. Practically, this could be used to improve the quality of perovskite films deposited in a high-speed manufacture process such as spray coating.
The first part of this work was led by Dr Onkar Game and investigated how treatment with one type of solvent had some unexpected effects on the perovskite film microstructure. This included measurements on thin films at Diamond to understand how these changes in microstructure affected the perovskite’s ability to withstand different challenging environments3. As part of his PhD, Joel undertook experiments at Diamond where he used X-ray scattering to monitor the very rapid changes in the structure of the perovskite film as it turned into a liquid and then back into the perovskite.
“Here we were able to resolve crystal structures of new intermediate compounds that formed in the liquid, and we could evidence the improvement in crystal structure caused by the healing process,” explains Prof. Lidzey, “Importantly, we also showed that this process could be enhanced by changing the temperature at which healing took place.”
Joel is currently writing a paper on this work which has formed part of his PhD thesis. He is set to start his Postdoctoral research in Prof. Henry Snaith’s group at the University of Oxford, working on advanced perovskite solar cell devices.
“Bringing together expertise from our different institutions in the UK and Africa through collaborating with the GCRF START grant has allowed us to investigate the crystallisation behaviour and stability of perovskites in new ways at Diamond Light Source,” says Joel. “More generally, we have been able to assist each other in fabricating, characterising and understanding these materials by sharing experience and facilities. The wider START community has been valuable as a mutually supportive network for us to develop as independent researchers, and most importantly, to grow the synchrotron research community in Africa.”
Commenting on the need for affordable, renewable energy solutions in Africa and the importance of collaboration to tackle global energy challenges, Prof. Billing said,
“The synergy in GCRF START collaborations of having people from different backgrounds tackle a problem makes the solution more robust. Creativity is important to most Africans, and we needto be involved in these creative solutions. Also, if you co-develop through collaboration, you have a sense of ownership which is what we set out to do through the GCRF START grant.”
“Everything costs energy, fundamentally,” Prof. Billing adds. “Silicon uses a lot of energy in its making to make solar cells so I think the best we can do as humans is look at remediation and balance. The GCRF START grant asks us to consider questions in our research around the global challenges like: am I using components that are sustainable? Are we using elements which are abundant, affordable, and environmentally compatible? If you think about a rural village which is cooking using wood charcoal, they are energy poor and lighting will be paraffin or candles. If you can find a cheap source of energy there and you can bring in lighting, that is life changing!”
 Here, “perovskite” is a name for a class of crystalline material, and there are many different combinations of starting materials that can be used to make a perovskite. Some of these materials absorb sunlight more efficiently, and others have greater environmental stability (both important characteristics for practical applications of solar cells).
 Bishop, J.E., Read, C.D., Smith, J.A. et al. Fully Spray-Coated Triple-Cation Perovskite Solar Cells. Sci Rep10, 6610 (2020). https://doi.org/10.1038/s41598-020-63674-5. This work demonstrates the possibility for spray-coating to fabricate high efficiency and low-cost perovskite solar cells at speed.
 Onkar S. Game, Joel A. Smith et al. Solvent vapour annealing of methylammonium lead halide perovskite: what’s the catch? J. Mater. Chem. A, 8, 2020, 10943-10956 DOI: 10.1039/D0TA03023F
 Greenland, Claire, Adam Shnier, Sai K. Rajendran, Joel A. Smith, Onkar S. Game, Daniel Wamwangi, Graham A. Turnbull, Ifor DW Samuel, David G. Billing, and David G. Lidzey. “Correlating Phase Behavior with Photophysical Properties in Mixed‐Cation Mixed‐Halide Perovskite Thin Films.” Advanced Energy Materials 10, no. 4 (2020): 1901350 (https://doi.org/10.1002/aenm.201901350)