P. Church, A. Goscinski

While High Performance Computing clouds allow researchers to process large amounts of genomic data, complex resource and software configuration tasks must be carried out beforehand. The current trend exposes applications and data as services, simplifying access to clouds. This paper examines commonly used cloud-based genomic analysis services, introduces the approach of exposing data as services and proposes two new solutions (HPCaaS and Uncinus) which aim to automate service development, deployment process and data provision. By comparing and contrasting these solutions, we identify key mechanisms of service creation, execution and data access required to support non-computing specialists employing clouds.

D. Yu, J. Y. Cai, J. S. Church, L. Wang

This paper introduces a novel chemical treatment for achieving sustained shrink-resist performance on natural keratin fibers. The new treatment involves the controlled reduction of keratin in the cuticle regionof the fiber, and the application of a water soluble diacrylate, namely glycerol 1,3-diglycerolate diacrylate (GDA), on the reduced keratin substrate. The acrylate groups of the GDA react with cysteine residues in the reduced keratin through thiol-ene click reactions at room temperature, leading to GDA grafting and the formation of GDA crosslinks in the keratin structure. The modified substrates were characterized by infrared spectroscopy and scanning electron microscopy, and assessed for its shrink-resistance and wet burst strength. This chemical modification has shown to alter the fiber surface morphology and hydrophilicity, resulting in substantially improved shrink-resistance with good fiber strength Retention.Possible shrink-resistance mechanisms were also discussed.

T. D. Rapson, T. D. Sutherland, J. S. Church, H. E. Trueman, H. Dacres, S. C. Trowell

To achieve the sophisticated chemistry required for life, nature uses metal containing proteins (metalloproteins). However, despite intensive research efforts, very few of these metalloproteins have been exploited for biotechnological applications. One major limiting factor is the poor stability of these proteins when they are removed from their cellular environment. To produce stable metalloproteins, we have developed an engineering strategy that uses structural proteins which can be fabricated into a number of different solid-state materials. Here we demonstrate that a recombinant silk protein (AmelF3 − Apis mellifera Fibroin 3) binds heme and other metal macrocycles in a manner reminiscent of naturally occurring metalloproteins, whereby an amino acid coordinates directly to the metal center. Our strategy affords design at four different levels: the metal center, the organic macrocycle, the protein scaffold, and the material format structure. The solid-state metalloproteins produced remained functional when stored at room temperature for over one year.

A. J. Poole, J. S. Church

The industrial utilisation of feather keratin as a biopolymer has proven difficult due to the lack of a viable extraction technique and the poor mechanical properties of the regenerated products. Here, pure keratin films were produced from chicken feathers using sodium sulphide as sole extraction reagent in a scheme that allows films to be formed without residual chemicals. In a comparison to other films, those produced using Na₂S extraction were found to be superior to other regenerated protein films and were similar to un-oriented commercial polymers. However, there was considerable variation in tensile properties between twenty repetitions of extracting and casting films which was attributed to variations in chain entanglement caused by the drying conditions. Chemical and physical treatments including crosslinking, dehydration and addition of nano-particles were investigated as means to enhance these properties. Significant increases were achieved by soaking films in isopropyl alcohol or weak acid (13 to 50 % increases) or by formaldehyde or glutaraldehyde crosslinking (24 to 40 % increases). The wide range of values across the pure keratin films indicates that the best route to further strength improvement maybe from optimising self-assembly via controlling drying conditions, rather than from chemical treatment.

M. G. Huson, J. S. Church, L. K. Hillbrick, A. L. Woodhead, M. Sridhar, A. M. L. Van De Meene

A focused ion beam has been used to mill both individual carbon fibres as well as fibres in an epoxy composite, with a view to preparing flat surfaces for nano-indentation. The milled surfaces have been assessed for damage using scanning probe microscopy nano-indentation and Raman micro-probe analysis, revealing that FIB milling damages the carbon fibre surface and covers surrounding areas with debris of disordered carbon. The debris is detected as far as 100 μm from the milling site. The energy of milling as well as the orientation of the beam was varied and shown to have an effect when assessed by Raman spectroscopy.

J. S. Church, A. S. Voda, A. Sutti, J. George, B. L. Fox, K. Magniez

In order to overcome interfacial incompatibility issues in natural fibre reinforced polymer bio-composites, surface modifications of the natural fibres using complex and environmentally unfriendly chemical methods is necessary. In this paper, we demonstrate that the interfacial properties of cellulose-based bio-composites can be tailored through surface adsorption of polyethylene glycol (PEG) based amphiphilic block copolymers using a greener alternative methodology. Mixtures of water or water/acetone were used to form amphiphilic emulsions or micro-crystal suspensions of PEG based amphiphilic block copolymers, and their deposition from solution onto the cellulosic substrate was carried out by simple dip-coating. The findings of this study evidence that, by tuning the amphiphilicity and the type of building blocks attached to the PEG unit, the flexural and dynamic thermo-mechanical properties of cellulose-based bio-composites comprised of either polylactide (PLA) or high density polyethylene (HDPE) as a matrix, can be remarkably enhanced. The trends, largely driven by interfacial effects, can be ascribed to the combined action of the hydrophilic and hydrophobic components of these amphiphiles. The nature of the interactions formed across the fibre–matrix interface is discussed. The collective outcome from this study provides a technological template to significantly improve the performance of cellulose-based bio-composite materials.

Andrew T. Church, Zak E. Hughes and Tiffany R. Walsh

A reliable description of ion pair interactions for biological systems, particularly those involving polyatomic ions such as carboxylate and divalent ions such as Ca²⁺, using biomolecular force-fields is essential for making useful predictions for a range of protein functions. In particular, the interaction of divalent ions with the double carboxylate group present in γ-carboxyglutamic acid (Gla), relevant to the function of many proteins, is relatively understudied using biomolecular force-fields. Using force-field based metadynamics simulations to predict the free energy of binding between Ca²⁺ and the carboxylate group in liquid water, we show that a widely-used biomolecular force-field, CHARMM22*, substantially over-estimates the binding strength between Ca²⁺ and the side-chains of both glutamic acid (Glu) and Gla, compared with experimental data obtained for the analogous systems of aqueous calcium–acetate and calcium–malonate. To correct for this, we propose and test a range of modifications to the σ value of the heteroatomic Lennard–Jones interaction between Ca²⁺ and the oxygen of the carboxylate group. Our revised parameter set can recover the same three association modes of this aqueous ion pair as the standard parameter set, and yields free energies of binding for the carboxylate–Ca²⁺ interaction in good agreement with experimental data. The revised parameter set recovers other structural properties of the ion pair in agreement with the standard CHARMM22* parameter set.

P. Church, A. Goscinski

Cloud-based service computing has started to change the way how research in science, in particular biology, medicine, and engineering, is being carried out. Researchers in the area of mammalian genomics have taken advantage of cloud computing technology to cost-effectively process large amounts of data and speed up discovery. Mammalian genomics is limited by the cost and complexity of analysis, which require large amounts of computational resources to analyse huge amount of data and biology specialists to interpret results. On the other hand the application of this technology requires computing knowledge, in particular programming and operations management skills to develop high performance computing (HPC) applications and deploy them on HPC clouds. We carried out a survey of cloud-based service computing solutions, as the most recent and promising instantiations of distributed computing systems, in the context their use in research of mammalian genomic analysis. We describe our most recent research and development effort which focuses on building Software as a Service (SaaS) clouds to simplify the use of HPC clouds for carrying out mammalian genomic analysis.