Numerical calculation of strong-field laser-atom interaction: An approach with perfect reflection-free radiation boundary conditions

The time-dependent, single-particle Schrodinger equation with a finite-range potential is solved numerically on a three-dimensional spherical domain. In order to correctly account for outgoing waves, perfect reflection-free radiation boundary conditions are used on the surface of a sphere. These are computationally most effective if the particle wavefunction is expanded in the set of spherical harmonics and computations are performed in the Kramers-Henneberger accelerated frame. The method allows one to solve the full ionization dynamics in intense laser fields within a small region of atomic dimensions

Rational engineering of recombinant picornavirus capsids to produce safe, protective vaccine antigen

Foot-and-mouth disease remains a major plague of livestock and outbreaks are often economically catastrophic. Current inactivated virus vaccines require expensive high containment facilities for their production and maintenance of a cold-chain for their activity. We have addressed both of these major drawbacks. Firstly we have developed methods to efficiently express recombinant empty capsids. Expression constructs aimed at lowering the levels and activity of the viral protease required for the cleavage of the capsid protein precursor were used; this enabled the synthesis of empty A-serotype capsids in eukaryotic cells at levels potentially attractive to industry using both vaccinia virus and baculovirus driven expression. Secondly we have enhanced capsid stability by incorporating a rationally designed mutation, and shown by X-ray crystallography that stabilised and wild-type empty capsids have essentially the same structure as intact virus. Cattle vaccinated with recombinant capsids showed sustained virus neutralisation titres and protection from challenge 34 weeks after immunization. This approach to vaccine antigen production has several potential advantages over current technologies by reducing production costs, eliminating the risk of infectivity and enhancing the temperature stability of the product. Similar strategies that will optimize host cell viability during expression of a foreign toxic gene and/or improve capsid stability could allow the production of safe vaccines for other pathogenic picornaviruses of humans and animals

In cellulo structure determination of a novel cypovirus polyhedrin.

This work demonstrates that with the use of a microfocus synchrotron beam the structure of a novel viral polyhedrin could be successfully determined from microcrystals within cells, removing the preparatory step of sample isolation and maintaining a favourable biological environment. The data obtained are of high quality, comparable to that obtained from isolated crystals, and enabled a facile structure determination. A small but significant difference is observed between the unit-cell parameters and the mosaic spread of in cellulo and isolated crystals, suggesting that even these robust crystals are adversely affected by removal from the cell

The development of an optofluidic evanescent field sample trapping and loading solution for time resolved protein crystallography experiments

X-ray crystallography is the leading technique for determining the atomic structure of biological molecules. The developers of this technique have maintained this position by continuously pushing the hardware and software boundaries such that data-collection from micron sized crystals are now possible. However, to break through the micron barrier will require a paradigm shift. Currently, the majority of samples are mounted on cryo-cooled pins. Mounting and aligning a micron and nano metre sized crystal to an X-ray incident beam is beyond the limits of electromechanical goniometers whose inherent limitations such as movement backlash impair practicable manipulation and alignment on this scale. Currently proposed alternatives have had varying degrees of success, but have yet to unlock the coveted submicron sample-loading domain. We propose a novel sample loading methodology, which combines elements from microfluidics and optical tweezing. The device is an optofluidic chip and nano-tweezers system that traps samples via evanescent fields emitted from silicon nitride waveguides transmitting a 1064 nm laser beam. Crystals can be aligned in solution, negating the need for pins and cryo-cooling systems. This paper presents a further development of the system's application. The highly beneficial implementation of microfluidics was further exploited by upgrading the system to allow for the control of one or more microfluidic ports and flow streams. This not only improved the tweezing process but it also created the ability to introduce multiple samples and reagents. Combining these during both the sample feeding and tweezing stages has allowed for the possibility of using the x-ray crystallographic method to capture ongoing reactions as they occur. These 'time resolved' nano crystal experiments are currently beyond the capabilities of the crystallographic method but remain the ultimate quest of many structural biology projects as they could reveal the complex structural changes of enzymes as they react in real time with their substrates. The optofluidic chip is currently being used to explore the mechanism of the beta-lactamases; several families of proteins which catalyse the hydrolysis of beta-lactam antibiotics. These proteins are ideal for this task, not only because the biological question is exceptionally relevant in a post-antibiotic world [1], but also several substrates undergo a colorimetric change during catalysis so the X-ray diffraction data can be obtained whilst monitoring the activity of the enzyme. These optofluidic chips have potential application for both synchrotrons light sources and X-FEL beamlines