Structured neural network modelling of multi-valued functions for wind retrieval from scatterometer measurements

A conventional neural network approach to regression problems approximates the conditional mean of the output vector. For mappings which are multi-valued this approach breaks down, since the average of two solutions is not necessarily a valid solution. In this article mixture density networks, a principled method to model conditional probability density functions, are applied to retrieving Cartesian wind vector components from satellite scatterometer data. A hybrid mixture density network is implemented to incorporate prior knowledge of the predominantly bimodal function branches. An advantage of a fully probabilistic model is that more sophisticated and principled methods can be used to resolve ambiguities.

Structured neural network modelling of multi-valued functions for wind retrieval from scatterometer measurements

A conventional neural network approach to regression problems approximates the conditional mean of the output vector. For mappings which are multi-valued this approach breaks down, since the average of two solutions is not necessarily a valid solution. In this article mixture density networks, a principled method to model conditional probability density functions, are applied to retrieving Cartesian wind vector components from satellite scatterometer data. A hybrid mixture density network is implemented to incorporate prior knowledge of the predominantly bimodal function branches. An advantage of a fully probabilistic model is that more sophisticated and principled methods can be used to resolve ambiguities.

Mean sea surface modelling from multi-satellite altimetry utilising frequency domain techniques

A technique is presented for the development of a high precision and resolution Mean Sea Surface (MSS) model. The model utilises Radar altimetric sea surface heights extracted from the geodetic phase of the ESA ERS-1 mission. The methodology uses a modified Le Traon et al. (1995) cubic-spline fit of dual ERS-1 and TOPEX/Poseidon crossovers for the minimisation of radial orbit error. The procedure then uses Fourier domain processing techniques for spectral optimal interpolation of the mean sea surface in order to reduce residual errors within the model. Additionally, a multi-satellite mean sea surface integration technique is investigated to supplement the first model with additional enhanced data from the GEOSAT geodetic mission.The methodology employs a novel technique that combines the Stokes' and Vening-Meinsz' transformations, again in the spectral domain. This allows the presentation of a new enhanced GEOSAT gravity anomaly field.

Improved production of industrially relevant recombinant proteins: application of multi-factorial design of experiments and scalable process modelling

The work described in this thesis focuses on the use of a design-of-experiments approach in a multi-well mini-bioreactor to enable the rapid establishments of high yielding production phase conditions in yeast, which is an increasingly popular host system in both academic and industrial laboratories. Using green fluorescent protein secreted from the yeast, Pichia pastoris, a scalable predictive model of protein yield per cell was derived from 13 sets of conditions each with three factors (temperature, pH and dissolved oxygen) at 3 levels and was directly transferable to a 7 L bioreactor. This was in clear contrast to the situation in shake flasks, where the process parameters cannot be tightly controlled. By further optimisating both the accumulation of cell density in batch and improving the fed-batch induction regime, additional yield improvement was found to be additive to the per cell yield of the model. A separate study also demonstrated that improving biomass improved product yield in a second yeast species, Saccharomyces cerevisiae. Investigations of cell wall hydrophobicity in high cell density P. pastoris cultures indicated that cell wall hydrophobin (protein) compositional changes with growth phase becoming more hydrophobic in log growth than in lag or stationary phases. This is possibly due to an increased occurrence of proteins associated with cell division. Finally, the modelling approach was validated in mammalian cells, showing its flexibility and robustness. In summary, the strategy presented in this thesis has the benefit of reducing process development time in recombinant protein production, directly from bench to bioreactor.

Analysis and modelling of muscles motion during whole body vibration

The aim of the study is to characterize the local muscles motion in individuals undergoing whole body mechanical stimulation. In this study we aim also to evaluate how subject positioning modifies vibration dumping, altering local mechanical stimulus. Vibrations were delivered to subjects by the use of a vibrating platform, while stimulation frequency was increased linearly from 15 to 60Hz. Two different subject postures were here analysed. Platform and muscles motion were monitored using tiny MEMS accelerometers; a contra lateral analysis was also presented. Muscle motion analysis revealed typical displacement trajectories: motion components were found not to be purely sinusoidal neither in phase to each other. Results also revealed a mechanical resonant-like behaviour at some muscles, similar to a second-order system response. Resonance frequencies and dumping factors depended on subject and his positioning. Proper mechanical stimulation can maximize muscle spindle solicitation, which may produce a more effective muscle activation. © 2010 M. Cesarelli et al.

Multi-threaded parallel numerical modelling of femtosecond pulse propagation in laser machining

Femtosecond laser microfabrication has emerged over the last decade as a 3D flexible technology in photonics. Numerical simulations provide an important insight into spatial and temporal beam and pulse shaping during the course of extremely intricate nonlinear propagation (see e.g. [1,2]). Electromagnetics of such propagation is typically described in the form of the generalized Non-Linear Schrdinger Equation (NLSE) coupled with Drude model for plasma [3]. In this paper we consider a multi-threaded parallel numerical solution for a specific model which describes femtosecond laser pulse propagation in transparent media [4, 5]. However our approach can be extended to similar models. The numerical code is implemented in NVIDIA Graphics Processing Unit (GPU) which provides an effitient hardware platform for multi-threded computing. We compare the performance of the described below parallel code implementated for GPU using CUDA programming interface [3] with a serial CPU version used in our previous papers [4,5]. © 2011 IEEE.

Multi-modes approach to modelling of vortex-induced vibration

Acknowledgements A.P. would like to acknowledge the support of the National Subsea Research Institute (NSRI) UK. E.P. and M.W. are grateful for partial support provided by the Italian Ministry of Education, University and Research (MIUR) by the PRIN funded program 2010/11 N.2010MBJK5B

Modelling of stiffness degradation due to cracking in laminates subjected to multi-axial loading

Funding Financial support of this research by the Engineering and Physical Sciences Research Council (EPSRC/GR/L51348) and the British Ministry of Defence is gratefully acknowledged.

A Force-Balanced Control Volume Finite Element Method for Multi-Phase Porous Media Flow Modelling

Peer reviewed

Determination of a Total Body Model of Efficiency Applied to a Rowing Movement in Humans

Efficiency represents the ratio of work done to energy expended. In human movement, it is desirable to maximise the work done or minimise the energy expenditure. Whilst research has examined the efficiency of human movement for the lower and upper body, there is a paucity of research which considers the efficiency of a total body movement. Rowing is a movement which encompasses all parts of the body to generate locomotion and is a useful modality to measure total body efficiency. It was the aim of this research to develop a total body model of efficiency and explore how skill level of participants and assumptions of the modelling process affected the efficiency estimates Three studies were used to develop and evaluate the efficiency model. Firstly, the efficiency of ten healthy males was established using rowing, cycling and arm cranking. The model included internal work from motion capture and efficiency estimates were comparable to published literature, indicating the suitability of the model to estimate efficiency. Secondly, the model was developed to include a multi-segmented trunk and twelve novice and twelve skilled participants were assessed for efficiency. Whilst the efficiency estimates were similar to published results, novice participants were assessed as more efficient. Issues such as the unique physiology of trained rowers and a lack of energy transfers in the model were considered contributing factors. Finally the model was redeveloped to account for energy transfers, where skilled participants had higher efficiency at large workloads. This work presents a novel model for estimating efficiency during a rowing motion. The specific inclusion of energy transfers expands previous knowledge of internal work and efficiency, demonstrating a need to include energy transfers in the assessment of efficiency of a total body action.

Analysis and modelling of immune cell behaviour in lymph nodes based on multi-photon imaging

This thesis presents quantitative studies of T cell and dendritic cell (DC) behaviour in mouse lymph nodes (LNs) in the naive state and following immunisation. These processes are of importance and interest in basic immunology, and better understanding could improve both diagnostic capacity and therapeutic manipulations, potentially helping in producing more effective vaccines or developing treatments for autoimmune diseases. The problem is also interesting conceptually as it is relevant to other fields where 3D movement of objects is tracked with a discrete scanning interval. A general immunology introduction is presented in chapter 1. In chapter 2, I apply quantitative methods to multi-photon imaging data to measure how T cells and DCs are spatially arranged in LNs. This has been previously studied to describe differences between the naive and immunised state and as an indicator of the magnitude of the immune response in LNs, but previous analyses have been generally descriptive. The quantitative analysis shows that some of the previous conclusions may have been premature. In chapter 3, I use Bayesian state-space models to test some hypotheses about the mode of T cell search for DCs. A two-state mode of movement where T cells can be classified as either interacting to a DC or freely migrating is supported over a model where T cells would home in on DCs at distance through for example the action of chemokines. In chapter 4, I study whether T cell migration is linked to the geometric structure of the fibroblast reticular network (FRC). I find support for the hypothesis that the movement is constrained to the fibroblast reticular cell (FRC) network over an alternative 'random walk with persistence time' model where cells would move randomly, with a short-term persistence driven by a hypothetical T cell intrinsic 'clock'. I also present unexpected results on the FRC network geometry. Finally, a quantitative method is presented for addressing some measurement biases inherent to multi-photon imaging. In all three chapters, novel findings are made, and the methods developed have the potential for further use to address important problems in the field. In chapter 5, I present a summary and synthesis of results from chapters 3-4 and a more speculative discussion of these results and potential future directions.

MULTI-BAND BOSE HUBBARD MODELS AND EFFECTIVE THREE-BODY INTERACTIONS

Experiments with ultracold atoms in optical lattice have become a versatile testing ground to study diverse quantum many-body Hamiltonians. A single-band Bose-Hubbard (BH) Hamiltonian was first proposed to describe these systems in 1998 and its associated quantum phase-transition was subsequently observed in 2002. Over the years, there has been a rapid progress in experimental realizations of more complex lattice geometries, leading to more exotic BH Hamiltonians with contributions from excited bands, and modified tunneling and interaction energies. There has also been interesting theoretical insights and experimental studies on “un- conventional” Bose-Einstein condensates in optical lattices and predictions of rich orbital physics in higher bands. In this thesis, I present our results on several multi- band BH models and emergent quantum phenomena. In particular, I study optical lattices with two local minima per unit cell and show that the low energy states of a multi-band BH Hamiltonian with only pairwise interactions is equivalent to an effec- tive single-band Hamiltonian with strong three-body interactions. I also propose a second method to create three-body interactions in ultracold gases of bosonic atoms in a optical lattice. In this case, this is achieved by a careful cancellation of two contributions in the pair-wise interaction between the atoms, one proportional to the zero-energy scattering length and a second proportional to the effective range. I subsequently study the physics of Bose-Einstein condensation in the second band of a double-well 2D lattice and show that the collision aided decay rate of the con- densate to the ground band is smaller than the tunneling rate between neighboring unit cells. Finally, I propose a numerical method using the discrete variable repre- sentation for constructing real-valued Wannier functions localized in a unit cell for optical lattices. The developed numerical method is general and can be applied to a wide array of optical lattice geometries in one, two or three dimensions.

An allometric modelling approach to identify the optimal body shape sssociated with, and differences between brazilian and peruvian youth motor performance

Children fromdevelopedanddevelopingcountriesdifferintheirbodysizeandshapedueto markeddifferencesacrosstheirlifehistorycausedbysocial,economicandculturaldifferenceswhicharealsolinkedtotheirmotorperformance(MP).Weusedallometricmodelsto identifysize/shapecharacteristicsassociatedwithMPtestsbetweenBrazilianandPeruvianschoolchildren.Atotalof4,560subjects,2,385girlsand2,175boysaged9–15years werestudied.Heightandweightweremeasured;biological maturation wasestimated with thematurityoffsettechnique;MPmeasuresincludedthe12minuterun(12MR),handgrip strength(HG),standinglongjump(SLJ)andtheshuttlerunspeed(SR)tests;physicalactivity(PA)wasassessedusingtheBaeckequestionnaire.Amultiplicativeallometricmodel wasadoptedtoadjustforbodysizedifferencesacrosscountries.Reciprocalponderalindex (RPI)wasfoundtobethemostsuitablebodyshapeindicatorassociatedwiththe12MR, SLJ,HGandSRperformance.Apositivematurationoffset parameterwasalsoassociated withabetterperformanceinSLJ,HGandSRtests.Sexdifferenceswerefoundinallmotor tests.BrazilianyouthshowedbetterscoresinMPthantheirPeruvianpeers,evenwhen controlling fortheirbodysizedifferencesThecurrentstudyidentifiedthekeybodysize associatedwithfourbodymass-dependentMPtests.Biological maturationandPAwere associatedwithstrengthandmotorperformance.Sexdifferenceswerefoundinallmotor tests,aswellasacrosscountriesfavoringBrazilianchildrenevenwhenaccountingfortheir bodysize/shapedifferences.