Predicting residue-wise contact orders in proteins by support vector regression

Background: The residue-wise contact order (RWCO) describes the sequence separations between the residues of interest and its contacting residues in a protein sequence. It is a new kind of one-dimensional protein structure that represents the extent of long-range contacts and is considered as a generalization of contact order. Together with secondary structure, accessible surface area, the B factor, and contact number, RWCO provides comprehensive and indispensable important information to reconstructing the protein three-dimensional structure from a set of one-dimensional structural properties. Accurately predicting RWCO values could have many important applications in protein three-dimensional structure prediction and protein folding rate prediction, and give deep insights into protein sequence-structure relationships. Results: We developed a novel approach to predict residue-wise contact order values in proteins based on support vector regression (SVR), starting from primary amino acid sequences. We explored seven different sequence encoding schemes to examine their effects on the prediction performance, including local sequence in the form of PSI-BLAST profiles, local sequence plus amino acid composition, local sequence plus molecular weight, local sequence plus secondary structure predicted by PSIPRED, local sequence plus molecular weight and amino acid composition, local sequence plus molecular weight and predicted secondary structure, and local sequence plus molecular weight, amino acid composition and predicted secondary structure. When using local sequences with multiple sequence alignments in the form of PSI-BLAST profiles, we could predict the RWCO distribution with a Pearson correlation coefficient (CC) between the predicted and observed RWCO values of 0.55, and root mean square error (RMSE) of 0.82, based on a well-defined dataset with 680 protein sequences. Moreover, by incorporating global features such as molecular weight and amino acid composition we could further improve the prediction performance with the CC to 0.57 and an RMSE of 0.79. In addition, combining the predicted secondary structure by PSIPRED was found to significantly improve the prediction performance and could yield the best prediction accuracy with a CC of 0.60 and RMSE of 0.78, which provided at least comparable performance compared with the other existing methods. Conclusion: The SVR method shows a prediction performance competitive with or at least comparable to the previously developed linear regression-based methods for predicting RWCO values. In contrast to support vector classification (SVC), SVR is very good at estimating the raw value profiles of the samples. The successful application of the SVR approach in this study reinforces the fact that support vector regression is a powerful tool in extracting the protein sequence-structure relationship and in estimating the protein structural profiles from amino acid sequences.

Supra-assembly of siliceous vesicles

We report a new approach to produce macroporous (110 nm in diameter) ordered siliceous foams (MOSF) by using block copolymers as templates in the absence of any organic cosolvent. The fine three-dimensional honeycomb structure of MOSF was determined by electron tomography. A formation mechanism of MOSF that spans from the atomic to macroscopic scale is proposed, which involves the cooperative self-assembly of unilamellar vesicles followed by the supra-assembly of vesicles. The fusion of soft vesicles finally leads to MOSF with well-ordered and defined honeycomb structures.

Edge-coloured cube decompositions

An edge-colored graph is a graph H together with a function f:E(H) → C where C is a set of colors. Given an edge-colored graph H, the graph induced by the edges of color c C is denoted by H(c). Let G, H, and J be graphs and let μ be a positive integer. A (J, H, G, μ) edge-colored graph decomposition is a set S = {H 1,H 2,...,H t} of edge-colored graphs with color set C = {c 1, c 2,..., c k} such that Hi ≅ H for 1 ≤ i ≤ t; Hi (cj) ≅ G for 1 ≤ i ≤ t and ≤ j ≤ k; and for j = 1, 2,..., k, each edge of J occurs in exactly μ of the graphs H 1(c j ), H 2(c j ),..., H t (c j ). Let Q 3 denote the 3-dimensional cube. In this paper, we find necessary and sufficient conditions on n, μ and G for the existence of a (K n ,Q 3,G, μ) edge-colored graph decomposition. © Birkhäuser Verlag, Basel 2007.

Anisotropic viscous models of large-deformation Mohr-Coulomb failure

We have developed a way to represent Mohr-Coulomb failure within a mantle-convection fluid dynamics code. We use a viscous model of deformation with an orthotropic viscoplasticity (a different viscosity is used for pure shear to that used for simple shear) to define a prefered plane for slip to occur given the local stress field. The simple-shear viscosity and the deformation can then be iterated to ensure that the yield criterion is always satisfied. We again assume the Boussinesq approximation, neglecting any effect of dilatancy on the stress field. An additional criterion is required to ensure that deformation occurs along the plane aligned with maximum shear strain-rate rather than the perpendicular plane, which is formally equivalent in any symmetric formulation. We also allow for strain-weakening of the material. The material can remember both the accumulated failure history and the direction of failure. We have included this capacity in a Lagrangian-integration-point finite element code and show a number of examples of extension and compression of a crustal block with a Mohr-Coulomb failure criterion. The formulation itself is general and applies to 2- and 3-dimensional problems.

Approximate Bayesian techniques for inference in stochastic dynamical systems

This thesis is concerned with approximate inference in dynamical systems, from a variational Bayesian perspective. When modelling real world dynamical systems, stochastic differential equations appear as a natural choice, mainly because of their ability to model the noise of the system by adding a variant of some stochastic process to the deterministic dynamics. Hence, inference in such processes has drawn much attention. Here two new extended frameworks are derived and presented that are based on basis function expansions and local polynomial approximations of a recently proposed variational Bayesian algorithm. It is shown that the new extensions converge to the original variational algorithm and can be used for state estimation (smoothing). However, the main focus is on estimating the (hyper-) parameters of these systems (i.e. drift parameters and diffusion coefficients). The new methods are numerically validated on a range of different systems which vary in dimensionality and non-linearity. These are the Ornstein-Uhlenbeck process, for which the exact likelihood can be computed analytically, the univariate and highly non-linear, stochastic double well and the multivariate chaotic stochastic Lorenz '63 (3-dimensional model). The algorithms are also applied to the 40 dimensional stochastic Lorenz '96 system. In this investigation these new approaches are compared with a variety of other well known methods such as the ensemble Kalman filter / smoother, a hybrid Monte Carlo sampler, the dual unscented Kalman filter (for jointly estimating the systems states and model parameters) and full weak-constraint 4D-Var. Empirical analysis of their asymptotic behaviour as a function of observation density or length of time window increases is provided.

A study of magnetic non-linearity and finite length effects in solid iron subjected to a travelling MMF wave

This thesis describes an experimental and analytic study of the effects of magnetic non-linearity and finite length on the loss and field distribution in solid iron due to a travelling mmf wave. In the first half of the thesis, a two-dimensional solution is developed which accounts for the effects of both magnetic non-linearity and eddy-current reaction; this solution is extended, in the second half, to a three-dimensional model. In the two-dimensional solution, new equations for loss and flux/pole are given; these equations contain the primary excitation, the machine parameters and factors describing the shape of the normal B-H curve. The solution applies to machines of any air-gap length. The conditions for maximum loss are defined, and generalised torque/frequency curves are obtained. A relationship between the peripheral component of magnetic field on the surface of the iron and the primary excitation is given. The effects of magnetic non-linearity and finite length are combined analytically by introducing an equivalent constant permeability into a linear three-dimensional analysis. The equivalent constant permeability is defined from the non-linear solution for the two-dimensional magnetic field at the axial centre of the machine to avoid iterative solutions. In the linear three-dimensional analysis, the primary excitation in the passive end-regions of the machine is set equal to zero and the secondary end faces are developed onto the air-gap surface. The analyses, and the assumptions on which they are based, were verified on an experimental machine which consists of a three-phase rotor and alternative solid iron stators, one with copper end rings, and one without copper end rings j the main dimensions of the two stators are identical. Measurements of torque, flux /pole, surface current density and radial power flow were obtained for both stators over a range of frequencies and excitations. Comparison of the measurements on the two stators enabled the individual effects of finite length and saturation to be identified, and the definition of constant equivalent permeability to be verified. The penetration of the peripheral flux into the stator with copper end rings was measured and compared with theoretical penetration curves. Agreement between measured and theoretical results was generally good.

Simulation based knowledge elicitation:effect of visual representation and model parameters

Since much knowledge is tacit, eliciting knowledge is a common bottleneck during the development of knowledge-based systems. Visual interactive simulation (VIS) has been proposed as a means for eliciting experts’ decision-making by getting them to interact with a visual simulation of the real system in which they work. In order to explore the effectiveness and efficiency of VIS based knowledge elicitation, an experiment has been carried out with decision-makers in a Ford Motor Company engine assembly plant. The model properties under investigation were the level of visual representation (2-dimensional, 2½-dimensional and 3-dimensional) and the model parameter settings (unadjusted and adjusted to represent more uncommon and extreme situations). The conclusion from the experiment is that using a 2-dimensional representation with adjusted parameter settings provides the better simulation-based means for eliciting knowledge, at least for the case modelled.

A CFD approach on the effect of particle size on char entrainment in bubbling fluidised bed reactors

The fluid – particle interaction inside a 41.7 mg s-1 fluidised bed reactor is modelled. Three char particles of sizes 500 µm, 250 µm, and 100 µm are injected into the fluidised bed and the momentum transport from the fluidising gas and fluidised sand is modelled. Due to the fluidising conditions and reactor design the char particles will either be entrained from the reactor or remain inside the bubbling bed. The particle size is the factor that differentiates the particle motion inside the reactor and their efficient entrainment out of it. A 3-Dimensional simulation has been performed with a completele revised momentum transport model for bubble three-phase flow according to the literature as an extension to the commercial finite volume code FLUENT 6.2.

Future of contact lens usage

I was recently part of a small committee looking at higher qualifications in contact lens practice and the discussion turned to future technologies. There was mention of different materials and different applications of contact lenses. Drug delivery with contact lenses was discussed as this has been talked about in the literature for a while. The first paper I could find that talked about using contact lenses for drug delivery dates back over 40 years. There was a review paper in CLAE in 2008 that looked specifically at this too [1]. However, where are these products? Why are we not seeing them in the market place? Maybe the technology is not quite there yet, or maybe patents are prohibiting usage or maybe the market is not big enough to develop such products? We do have lenses on the market with slow release of lubricating agents but not therapeutic agents used for ocular or systemic conditions. Contact lenses with pathogen detectors may be part of our contact lens armoury of the future and again we can already see papers in the literature that have trialled this technology for glucose monitoring in diabetics or lactate concentration in the tear film. Future contact lenses may incorporate better optics based on aberration control and we see this starting to emerge with aspheric designs designed to minimise spherical aberration. Irregular corneas can be fitted with topography based designs and again this technology exists and is being used by some manufacturers in their designs already. Moreover, the topography based fitting of irregular corneas is certainly something we see a lot of today and CLAE has seen many articles related to this over the last decade or so. What about further into the future? Well one interesting area must the 3-dimensional contact lenses, or contact lenses with electronic devices built in that simulate a display screen. A little like the virtual display spectacles that are already sold by electronics companies. It does not take much of a stretch of the imagination to see a large electronic company taking this technology on and making it viable. Will we see people on the train watching movies on these electronic virtual reality contact lenses? I think we will, but when is harder to know.

On Structural Resource of Monotone Recognition

Algorithmic resources are considered for elaboration and identification of monotone functions and some alternate structures are brought, which are more explicit in sense of structure and quantities and which can serve as elements of practical identification algorithms. General monotone recognition is considered on multi- dimensional grid structure. Particular reconstructing problem is reduced to the monotone recognition through the multi-dimensional grid partitioning into the set of binary cubes.

Thermal processing of miscanthus, sugarcane bagasse, sugarcane trash and their acid hydrolysis residues

The research presented in this thesis was developed as part of DIBANET, an EC funded project aiming to develop an energetically self-sustainable process for the production of diesel miscible biofuels (i.e. ethyl levulinate) via acid hydrolysis of selected biomass feedstocks. Three thermal conversion technologies, pyrolysis, gasification and combustion, were evaluated in the present work with the aim of recovering the energy stored in the acid hydrolysis solid residue (AHR). Mainly consisting of lignin and humins, the AHR can contain up to 80% of the energy in the original feedstock. Pyrolysis of AHR proved unsatisfactory, so attention focussed on gasification and combustion with the aim of producing heat and/or power to supply the energy demanded by the ethyl levulinate production process. A thermal processing rig consisting on a Laminar Entrained Flow Reactor (LEFR) equipped with solid and liquid collection and online gas analysis systems was designed and built to explore pyrolysis, gasification and air-blown combustion of AHR. Maximum liquid yield for pyrolysis of AHR was 30wt% with volatile conversion of 80%. Gas yield for AHR gasification was 78wt%, with 8wt% tar yields and conversion of volatiles close to 100%. 90wt% of the AHR was transformed into gas by combustion, with volatile conversions above 90%. 5volO2%-95vol%N2 gasification resulted in a nitrogen diluted, low heating value gas (2MJ/m3). Steam and oxygen-blown gasification of AHR were additionally investigated in a batch gasifier at KTH in Sweden. Steam promoted the formation of hydrogen (25vol%) and methane (14vol%) improving the gas heating value to 10MJ/m3, below the typical for steam gasification due to equipment limitations. Arrhenius kinetic parameters were calculated using data collected with the LEFR to provide reaction rate information for process design and optimisation. Activation energy (EA) and pre-exponential factor (ko in s-1) for pyrolysis (EA=80kJ/mol, lnko=14), gasification (EA=69kJ/mol, lnko=13) and combustion (EA=42kJ/mol, lnko=8) were calculated after linearly fitting the data using the random pore model. Kinetic parameters for pyrolysis and combustion were also determined by dynamic thermogravimetric analysis (TGA), including studies of the original biomass feedstocks for comparison. Results obtained by differential and integral isoconversional methods for activation energy determination were compared. Activation energy calculated by the Vyazovkin method was 103-204kJ/mol for pyrolysis of untreated feedstocks and 185-387kJ/mol for AHRs. Combustion activation energy was 138-163kJ/mol for biomass and 119-158 for AHRs. The non-linear least squares method was used to determine reaction model and pre-exponential factor. Pyrolysis and combustion of biomass were best modelled by a combination of third order reaction and 3 dimensional diffusion models, while AHR decomposed following the third order reaction for pyrolysis and the 3 dimensional diffusion for combustion.

Cohomology of the G-Hilbert Scheme for 1/r(1,1,R−1)

2000 Mathematics Subject Classification: Primary 14E15; Secondary 14C05,14L30.

Complete Integrability of a Nonlinear Elliptic System, Generating Bi-umbilical Foliated Semi-symmetric Hypersurfaces in R^4

Николай Кутев, Величка Милушева - Намираме експлицитно всичките би-омбилични фолирани полусиметрични повърхнини в четиримерното евклидово пространство R^4

On the impact of Cu dispersion on CO2 photoreduction over Cu/TiO2

A family of Cu/TiO2 catalysts was prepared using a refined sol–gel method, and tested in the photocatalytic reduction of CO2 by H2O to CH4 using a stirred batch, annular reactor. The resulting photoactivity was benchmarked against pure TiO2 nanoparticles (synthesised by an identical sol–gel route). CO2 photoreduction exhibited a strong volcano dependence on Cu loading, reflecting the transition from 2-dimensional CuOx nanostructures to 3-dimensional crystallites, with optimum CH4 production observed for 0.03 wt.% Cu/TiO2.

3D printed sensing patches with embedded polymer optical fibre Bragg gratings

The first demonstration of a polymer optical fibre Bragg grating (POFBG) embedded in a 3-D printed structure is reported. Its cyclic strain performance and temperature characteristics are examined and discussed. The sensing patch has a repeatable strain sensitivity of 0.38 pm/μepsilon. Its temperature behaviour is unstable, with temperature sensitivity values varying between 30-40 pm/°C.