The instrument will help British scientists in fields such as advanced materials and power generation, and is expected to lead to breakthroughs benefiting health and the environment.
The £3.7 million Nion Hermes Scanning Transmission Electron Microscope, to be sited at a laboratory in Daresbury, near Warrington, allows researchers to identify atoms and observe the strength of the bonds between them.
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This is expected to improve understanding of their electronic properties when in bulk and how they may perform when used.
Minister for universities, science and cities, Greg Clark, said: “The UK is a world leader in the development and application of Stem (Scanning Transition Electron Microscope) techniques, and this new super-powerful microscope will ensure we remain world-class.
“From developing new materials for space travel to creating a better, cheaper treatment for anaemia, this new super-powerful microscope lets UK scientists examine how materials behave at a level a million times smaller than a human hair.
“This exciting research will help lead to breakthroughs that will benefit not only our health but the environment too.”
The microscope, one of only three in the world - the others have been at universities in the United States for about a year - will be at the the Engineering and Physical Sciences Research Council (EPSRC) SuperStem facility at the Daresbury laboratory complex, which is part of the Science and Technology Facilities Council .
ESPRC chief executive Professor Philip Nelson said: “This EPSRC investment in state-of-the-art equipment is an investment in UK science and engineering.
“It will give scientists access to a tool that can delve into the heart of materials, discoveries made using this microscope will aid research and lead to innovations that benefit society and our economy.
“The EPSRC SuperStem facility at Daresbury has already delivered us new knowledge and applications and this new equipment will continue that pedigree.”
SuperStem is supported by a network of collaborating universities - Leeds, Glasgow, Liverpool, Manchester and Oxford, and a steering committee.
The EPSRC is the UK’s main agency for funding research in engineering and physical sciences. It invests around £800m a year in research and postgraduate training, to help the nation handle the next generation of technological change.