Projects

 

I am extremely grateful for generous funding from EPSRC, BBSRC, MRC, the Royal Society and the Kirkwood Memorial Fund.

 

Seeing how polymer chains organise with torsional tapping atomic force microscopy

EPSRC EP/J013005/1 - PI

Our understanding of semicrystalline polymers, the class of polymers that by far and away dominates usage in modern society, is surprisingly poor. At a molecular scale we rely on cartoons and inference, unable to reach the certainty obtained in other areas of material science by direct, atomic or molecular scale imaging, and by diffraction from macroscopic crystals. Yet in polymers the structure at this level is arguably more important as it determines the properties from mechanical behaviour to the oxygen barrier performance through the adhesive behaviour to the aesthetic appeal. Recently we developed a new form of atomic force microscopy, torsional tapping AFM (TTAFM) capable of robustly and routinely obtaining images with true molecular resolution on the most frequently used polymers (polyolefins, that include polyethylene and polypropylene) in essentially any sample. This step change in performance is based on the improved dynamics and signal-to-noise performance that comes from the cantilever geometry and drive mechanism. Perfecting the cantilever design is predicted to lead to even greater performance, and to allow the technique to be used in a wide range of instruments. At the same time as developing the technology we will use it to answer a string of questions that underpin our understanding of polymer crystals, questions that will lead to both greatly enhanced fundamental understanding and real application from the development of new materials and applications to problem solving during processing. We aim to directly reveal how crystallization temperature, variations in chain chemistry, chain branching, re-enforcing fibres and particles, control the organisation of polymer chains within the crystal and at the interface between the crystal and the non-crystalline material. While doing this we will perfect the sample preparation methods for molecular scale imaging, and enhance the cantilever design to improve performance, allowing the technique to be widely adopted both in polymer science and across molecular nanoscience.


 

The Exclusion Force Microscope

Royal Society Paul Instrument Fund - PI

The “atomic hypothesis” lies at the heart of our understanding of matter. Super resolution microscopy techniques (STM, AFM and TEM) have turned this hypothesis into fact, allowing visualization and manipulation of individual atoms. However, it is still not possible to obtain atomic resolution under ambient conditions. To do so would lay bare a myriad of questions in diverse areas from semiconductor physics to plastic electronics to biology. A microscope that could view everyday samples at atomic resolution would simply change our view of the world. Our aim is to build a new form of scanning force microscope, the Exclusion Force Microscope (ExFM), a microscope capable of differentiating between different types of interaction with different time dependences, so as to cross the barrier to molecular and even atomic resolution in air.

 

From molecules to systems: Towards an integrated heuristic for understanding the physics of life

EPSRC EP/K000594/1 - coI, PI Prof Graham Leggett

The last fifty years have seen enormous strides in our understanding of biology at the most basic level, the molecular scale. For example, the structure of DNA has been discovered, and the genetic information encoded in its structure has begun to be worked out. We know that many biological molecules are associated with particular types of behaviour in larger organisms: for example some people have a genetic predisposition to particular diseases. However, understanding the complex links in the chain between a single molecule inside a cell and the behaviour of a person is a very difficult challenge. We can focus in on individual molecules and understand their structures and behaviour in great detail, but every human body contains vast numbers of molecules of many different types, and the challenge is to try to put together the complex systems of interactions between molecules that go on inside each cell; the relationships between cells that lead to the function of tissue; and the way that tissues and organs are integrated into a whole person. When a person discovers they have cancer, for example, there is a strong chance that the disease began with a change in a single molecule; but this will have initiated a staggeringly complex cascade of knock-on chains of cause-and-effect that led to the formation of the disease, and modern epigenetics is also suggesting that a complex chain of cause-and-effect may very well have preceded that initial change. Untangling this web of interactions is an enormous challenge but it is undoubtedly the most important problem facing biology at present.

Read more at www.physicsoflife.org.uk



Low dimensional chemistry

EPSRC EP/I012060/1 - coI, PI Prof Graham Leggett

Miniaturisation has become a familiar aspect of modern technology: every year, laptops get thinner, mobile phones get smaller, and computers get faster as more and more components can be accommodated on their chips. The emergence of nanoscience as a scientific discipline has been driven by the relentless quest by the electronic device industry over the past four decades for ever-faster chips. The importance of miniaturisation is not just in the fact that smaller devices can be packed more closely together, however: when objects become very small indeed, they sometimes acquire entirely new properties that larger objects formed from the same materials do not normally exhibit. Catalysts have been used for over a century to accelerate chemical reactions, and many catalysts consist of metal particles supported on ceramics. For several decades, catalytic converters in car exhausts have used metallic nanoparticles - particles a few billionths of a metre in size - to clean the exhaust gas because the catalytic activity has been found to be dramatically increased by the small size of the active metal. When semiconductors are formed into structures of the same size, they acquire entirely new optical properties purely as a consequence of their small size - for example, they glow brightly when stimulated by electrical current, and the colour of the light emitted is determined by the size of the particle (and can thus be controlled with high precision). These phenomena are referred to as low-dimensional ones: they are new, unexpected phenomena that result only from the small size of the active objects.There is a very important sense in which biological objects may also be said to be low-dimensional. Cells are tiny objects that are driven by processes that involve small numbers of molecules. Biologists have recognised that single molecules are quite different from large groups of molecules, and there has therefore been a lot of interest in studying them, because they may help us to understand much better how larger systems work. However, there are no established tools for building systems of interacting single molecules, what might be called low-dimensional systems . New tools are required to achieve this, and the goal of this programme will be to develop them.We wish to build a synthetic low-dimensional system, which will incorporate biological molecules and synthetic models for them, that replicates the photosynthetic pathway of a bacterium. Photosynthesis is the basis for all life on earth, so it has fundamental importance. However, there are important other motivations for studying the marvellously efficient processes by which biological organisms collect sunlight and use it to live, grow and reproduce. The current concerns about shortage of fossil fuels, and the problems associated with the carbon dioxide produced by burning them, make solar energy a highly attractive solution to many pressing problems. To best exploit the huge amount of solar energy that falls on the earth, even in colder climates like the UK, we may do well to learn from Nature. By building a ship-based system that replicates the photosynthetic behaviour of a biological organism, we will gain new insights into how Natural photosynthesis works. More than that, however, we will develop entirely new, biologically-inspired design principles that may be useful in understanding many other scientific and engineering problems. At a fundamental level, biological systems work quite differently from electronic devices: they are driven by complex signals, they are fuzzy and probabilistic, where microsystems are based on binary logic and are precisely determined. The construction of a functioning low-dimensional system that replicates a cellular pathway will require the adoption, in a man-made structure, of these very different design principles. If we can achieve this it may yield important new insights into how similar principles could be applied to other technologies.

 

Super resolution fluorescence atomic force microscopy

BBSRC BB/I023518/1- coI, PI Prof Simon Foster

Bacteria are microscopic organisms of immense importance to humans. Given their diminutive size much of our understanding of how they grow and divide has been determined by a variety of microscopy approaches. Since the earliest microscopes many important discoveries have been made and continued technological developments have permitted new and exciting revelations. Bacterial cell biology and the ability to determine the subcellular localization of components have been largely driven by fluorescence microscopy, whereby individual components are labelled with fluorescent markers. However the limit of detection, coupled with the small dimensions of bacteria has limited the true potential of this approach. Very recently new techniques have allowed fluorescence microscopy to traverse this barrier to attain a level of resolution approaching single molecules. However due to the technical difficulties, lack of commercial availability and expense of some of these developments they have not as yet made a great impact. We have been using a complementary approach called atomic force microscopy, which gives very high resolution of surfaces. We have applied this to the study of bacterial cell walls (the site of action of important antibiotics such as penicillin). This has revealed many important new insights. The aim of the project is to build a new type of microscope coupling super resolution fluorescence and atomic force. We will use our existing microscopy set up as a scaffold to rapidly and efficiently develop the new machine, given the interdisciplinary expertise of the investigator team. The new machine will be tested and further developed within our current bacterial cell wall architecture and dynamics research area. This will provide an ideal framework to develop a new microscope, which can then be utilized and duplicated more widely to allow the rapid uptake of a novel and exciting approach.

 

Bacterial cell wall architecture and dynamics

BBSRC BB/H011005/1 - coI, PI Prof Simon Foster

Bacteria are able to assume a myriad of different shapes, a property governed by their cell wall. The cell wall is like an external skeleton not only required for shape determination but also for keeping the cell alive as it is able to withstand the considerable internal forces which would otherwise rupture the cell. The major structural element of the cell wall for most bacteria is a polymer called peptidoglycan (PG). PG is unique to the bacteria and is essential for keeping the bacteria alive. This importance of PG is illustrated by the incredibly wide use of cell wall antibiotics such as penicillin and vancomycin, which prevent PG production. PG is a single large, bag-like molecule that surrounds the cell and whilst very strong is also dynamic to allow the cells to grow and divide. Even though PG is chemically only made of relatively simple building blocks how these are assembled to produce an architecture able to fulfil the many functions of PG has remained largely elusive. We have used a high-resolution microscopy technique that has provided exciting new and unexpected information as to the architecture of the PG. Initially in the rod shaped bacterium Bacillus subtilis we have found cables of material running round the cylinder of the cell providing strength. Also where the cell divides, a complex plate of material is laid down in an apparent spiral. Our further work in the round bacterium Staphylococcus aureus has shown a very different architecture of whorls and small knobbles. It is these features, which allow the cells to solve their engineering problems of maintaining cell integrity whilst allowing growth. The proposed project will take an integrated approach across the biological, chemical and physical disciplines to determine the architecture of PG from the molecular to the cellular level. We will address fundamental questions in microbiology that lie at the heart of the ability of bacteria to grow and proliferate.