Multi-scale approaches to Food Sciences: computational QM and MM explorations at the microscopic level

L'obiettivo principale della politica di sicurezza alimentare è quello di garantire la salute dei consumatori attraverso regole e protocolli di sicurezza specifici. Al fine di rispondere ai requisiti di sicurezza alimentare e standardizzazione della qualità, nel 2002 il Parlamento Europeo e il Consiglio dell'UE (Regolamento (CE) 178/2002 (CE, 2002)), hanno cercato di uniformare concetti, principi e procedure in modo da fornire una base comune in materia di disciplina degli alimenti e mangimi provenienti da Stati membri a livello comunitario. La formalizzazione di regole e protocolli di standardizzazione dovrebbe però passare attraverso una più dettagliata e accurata comprensione ed armonizzazione delle proprietà globali (macroscopiche), pseudo-locali (mesoscopiche), ed eventualmente, locali (microscopiche) dei prodotti alimentari. L'obiettivo principale di questa tesi di dottorato è di illustrare come le tecniche computazionali possano rappresentare un valido supporto per l'analisi e ciò tramite (i) l’applicazione di protocolli e (ii) miglioramento delle tecniche ampiamente applicate. Una dimostrazione diretta delle potenzialità già offerte dagli approcci computazionali viene offerta nel primo lavoro in cui un virtual screening basato su docking è stato applicato al fine di valutare la preliminare xeno-androgenicità di alcuni contaminanti alimentari. Il secondo e terzo lavoro riguardano lo sviluppo e la convalida di nuovi descrittori chimico-fisici in un contesto 3D-QSAR. Denominata HyPhar (Hydrophobic Pharmacophore), la nuova metodologia così messa a punto è stata usata per esplorare il tema della selettività tra bersagli molecolari strutturalmente correlati e ha così dimostrato di possedere i necessari requisiti di applicabilità e adattabilità in un contesto alimentare. Nel complesso, i risultati ci permettono di essere fiduciosi nel potenziale impatto che le tecniche in silico potranno avere nella identificazione e chiarificazione di eventi molecolari implicati negli aspetti tossicologici e nutrizionali degli alimenti.

Theory and application of inverse problems in groundwater: numerical, laboratory and field studies.

Aquifers are a vital water resource whose quality characteristics must be safeguarded or, if damaged, restored. The extent and complexity of aquifer contamination is related to characteristics of the porous medium, the influence of boundary conditions, and the biological, chemical and physical processes. After the nineties, the efforts of the scientists have been increased exponentially in order to find an efficient way for estimating the hydraulic parameters of the aquifers, and thus, recover the contaminant source position and its release history. To simplify and understand the influence of these various factors on aquifer phenomena, it is common for researchers to use numerical and controlled experiments. This work presents some of these methods, applying and comparing them on data collected during laboratory, field and numerical tests. The work is structured in four parts which present the results and the conclusions of the specific objectives.

Techniques to improve forecasting models: applications to energy demand and price

This thesis is a study of three techniques to improve performance of some standard fore-casting models, application to the energy demand and prices. We focus on forecasting demand and price one-day ahead. First, the wavelet transform was used as a pre-processing procedure with two approaches: multicomponent-forecasts and direct-forecasts. We have empirically compared these approaches and found that the former consistently outperformed the latter. Second, adaptive models were introduced to continuously update model parameters in the testing period by combining ?lters with standard forecasting methods. Among these adaptive models, the adaptive LR-GARCH model was proposed for the fi?rst time in the thesis. Third, with regard to noise distributions of the dependent variables in the forecasting models, we used either Gaussian or Student-t distributions. This thesis proposed a novel algorithm to infer parameters of Student-t noise models. The method is an extension of earlier work for models that are linear in parameters to the non-linear multilayer perceptron. Therefore, the proposed method broadens the range of models that can use a Student-t noise distribution. Because these techniques cannot stand alone, they must be combined with prediction models to improve their performance. We combined these techniques with some standard forecasting models: multilayer perceptron, radial basis functions, linear regression, and linear regression with GARCH. These techniques and forecasting models were applied to two datasets from the UK energy markets: daily electricity demand (which is stationary) and gas forward prices (non-stationary). The results showed that these techniques provided good improvement to prediction performance.

Raman amplification and performance altering effects

This thesis presents an experimental investigation into several applications of the Raman scattering effect in communication optical fibres as well as how some of these applications can be modified to enhance the resulting performance. The majority of the work contained within is based on laboratory results using many commercially available components. The results can be divided into and presented in three main parts: Firstly, a novel application of a known effect is used to broaden Raman pump light in order to achieve a more continuous distribution of gain with respect to wavelength. Multiple experimental results are presented, all based around the prior spreading of the pump spectrum before being used in the desired transmission fibre. Gathered results show that a notable improvement can be obtained from applying such a technique along with the scope for further optimisation work. Secondly, an investigation into the interaction between the well known effect of Four Wave Mixing (FWM) and Raman scattering is provided. The work provides an introduction to the effect as well commenting on previous literature regarding the effect and its mitigation. In response to existing research experimental results are provided detailing some limitations of proposed schemes along with concepts of how further alleviation from the deleterious effects maybe obtained. Lastly, the distributed nature of the Raman gain process is explored. A novel technique on how a near constant distribution of gain can be employed is implemented practically. The application of distributed gain is then applied to the generation of optical pulses with special mathematical properties within a laboratory setting and finally the effect of pump noise upon distributed gain techniques is acknowledged.

Characterisation and modification of hydrogel polymers

The work described in this thesis can be broadly divided into two sections. The first being the characterisation of hydrogel polymers in both their hydrated and dehydrated states and the second some aspects of the structural modification of polymers. The characterisation of hydrogel polymers in their dehydrated state (xerogels) involves such techniques as elemental analysis, pyrolysis gas liquid chromatography, infra-red spectroscopy, density determination and surface characterisation by contact angle measurements. The characterisation of some commercially available hydrogel materials was undertaken using such techniques and the results obtained were compared to laboratory synthesised systems in an attempt to assess the value of the combination of techniques employed. In the characterisation of hydrated polymers the amoumt and nature of water present is the single most important factor. The most convenient method of characterising this water involves the use of differential scanning calorimetry (DSC), coupled with total equilibrium water content measurements. DSC distinguishes between non-freezing and freezing water but in addition provides some information on the continuum of states in the freezing water fraction. Two aspects of the structural modification of hydrogel polymers were studied. The first involved the incorporation of acrylamide and substituted acryamide monomers into a copolymer system and an examination of the effect of this on the amino acid interaction of the polymers. The second was the attempted synthesis of cell surface analogues by the attachment of sugar type molecules to the polymer using a variety of reaction methods.

Effect of pulsed current on the electrodeposition of chromium and copper

This research was concerned with the effects of pulsed current on the electrodeposition of chromium and copper. In the case of the latter metal, a novel application has been studied and a theory proposed for the ability to improve throwing power by the joint use of organic additives and pulsed reverse current. During the course of the research, several improvements were made to the pulse plating unit.Chromium. A study was made of the effect of square wave pulsed current on various physical properties of deposits from three hard chromium plating electrolytes. The effect of varying frequency at a duty cycle of 50% on the mean bulk internal stress, visual appearance, hardness, crack characteristics and surface topography of the electrodeposits was determined. X-ray diffraction techniques were used to study the phases present in the deposits. The effect of varying frequency on the cathodic efficiencies of the electrolytes was also determined. It was found that pulsed current reduced the internal stress of deposits from the sulphate catalysed electrolyte. It also reduced or eliminated cracking of deposits and reduced deposit brightness. Under certain conditions, pulsed current was found to induce the co-deposition of hydrides of chromium. Deposit hardness was found to be reduced by the use of pulsed current. Cathodic efficiencies of the high efficiency electrolytes were reduced by use of pulsed current although this effect was minimised at high frequencies. The sulphate catalysed electrolyte showed an increase in efficiency over the frequency range where hydrides were co-deposited.Copper. The polarisation behaviour of acid copper solutions containing polyethers, sulphopropyl sulphides and chloride ions was studied using both direct and pulse reverse current. The effect of these additives on the rest potentials of copper deposits immersed in the electrolyte was also studied. Hole Throwing Power on printed circuit boards was determined using a specially designed test cell. The effect of pulsed reverse current on the hole throwing power of commercially produced printed circuit boards was also studied. Polyethers were found to have an inhibiting effect on the deposition of copper whereas the sulphopropyl sulphides produced a stimulating (i.e. depolarising) effect. Studies of rest potentials made when both additives were present indicated that the sulphopropyl sulphide was preferentially adsorbed. The use of pulsed reverse current in solutions containing both polyether and sulphopropyl sulphide was found to cause desorption of the sulphopropyl sulphide at the cathode surface. Thus, at higher current densities, the inhibiting effect of the polyether produced an increase in the cathodic polarisation potential. At lower current densities, the depolarisation effect of the sulphopropyl sulphide could still occur. On printed circuit boards, this effect was found to produce an increase in the `hole throwing power' due to depolarisation of the holes relative to the surface of the boards. Typically, using direct current, hole/surface thickness ratios of 40% were obtained when plating 0.6 mm holes in a 3.2 mm thick board at a current density of 3 A/dm2 whereas using pulsed reverse current, ratios of 80% could be obtained at an equivalent rate of deposition. This was observed both in laboratory tests and on commercially plated boards.

A combination of cyclone and vert techniques for the management of construction projects

Many planning and control tools, especially network analysis, have been developed in the last four decades. The majority of them were created in military organization to solve the problem of planning and controlling research and development projects. The original version of the network model (i.e. C.P.M/PERT) was transplanted to the construction industry without the consideration of the special nature and environment of construction projects. It suited the purpose of setting up targets and defining objectives, but it failed in satisfying the requirement of detailed planning and control at the site level. Several analytical and heuristic rules based methods were designed and combined with the structure of C.P.M. to eliminate its deficiencies. None of them provides a complete solution to the problem of resource, time and cost control. VERT was designed to deal with new ventures. It is suitable for project evaluation at the development stage. CYCLONE, on the other hand, is concerned with the design and micro-analysis of the production process. This work introduces an extensive critical review of the available planning techniques and addresses the problem of planning for site operation and control. Based on the outline of the nature of site control, this research developed a simulation based network model which combines part of the logics of both VERT and CYCLONE. Several new nodes were designed to model the availability and flow of resources, the overhead and operating cost and special nodes for evaluating time and cost. A large software package is written to handle the input, the simulation process and the output of the model. This package is designed to be used on any microcomputer using MS-DOS operating system. Data from real life projects were used to demonstrate the capability of the technique. Finally, a set of conclusions are drawn regarding the features and limitations of the proposed model, and recommendations for future work are outlined at the end of this thesis.

The sedimentology and diagenesis of the Pendleside limestone group in the Craven Basin of Northern England. Available in 2 volumes.

This thesis describes the stratigraphy, sedimentology and diagenesis of the Pendleside Limestone (Asbian age), a sequence of limestones, shales and dolostones in the Clitheroe area of N. W. England. Field study of 19 measured sections indicates that it was deposited in a rhythmically subsiding basin (Craven Basin) because of movements on the Mid-Craven Fault which was active in Dinantian times. The sequence is up to 190m thick and consists mostly of distal turbidite deposits which have been reworked at horizons when sediment accumulation built up to the wave base. The original depositional fabric and mineralogy of the Pendleside Limestone Group has been extensively modified by diagenetic processes including cementation, authi­genesis, dolomitization and silicification. These processes have been studied using a wide variety of laboratory techniques. The carbonate cements of the PendIeside Limestone consist predominantly of ferroan calcite and non-ferroan calcite with microdolomite incIusions. The former is probably a stable replacement of original-high-magnesian calcite. Cementation was accompanied by the formation of authigenic albite and quartz. Much of the upper part of the Pendleside Limestone has been extensively dolomitized and chertified. Several distinct zones of dolomitization are found which increase in thickness and intensity towards the top of the Pendleside Limestone Group. The dolostone horizons correspond to coarser-grained lithologies deposited during periods of shallow water sedimentation. The composition of the dolomites changes from ferroan dolomite in the lower part of the Group to non-ferroan dolomite in the upper part. The low strontium and sodium content of the dolostones in association with the other evidence suggests that the dolomitization was brought about in an open system by the mixing of marine and fresh water in phreatic lens which were established at periodic intervals. The dolomitization was closely associated with chertification although this was initiated by the dissolution of siliceous spicules which provided the necessary source of silica.

Practical and cost-effective high-fidelity optical carrier dissemination using coherent communication techniques

We report a unidirectional frequency dissemination scheme for high-fidelity optical carriers deployable over telecommunication networks. For the first time, a 10 Gb/s Binary Phase Shift Keying (BPSK) signal from an ultra-narrow linewidth laser was transmitted through a field-installed optical fibre with round-trip length of 124 km between Cork City and town of Clonakilty, without inline optical amplification. At the receiver, using coherent communication techniques and optical injection-locking the carrier was recovered with noise suppression. The beat signal between the original carrier at the transmitter and recovered carrier at the receiver shows a linewidth of 2.8 kHz. Long term stability measurements revealed fractional instabilities (True Allan deviation) of 3.3 × 10-14 for 1 s averaging time, prior to phase noise cancellation.

Foundational forensic techniques for cellular and ad hoc multi-hop networks

The Internet has become an integral part of our nation’s critical socio-economic infrastructure. With its heightened use and growing complexity however, organizations are at greater risk of cyber crimes. To aid in the investigation of crimes committed on or via the Internet, a network forensics analysis tool pulls together needed digital evidence. It provides a platform for performing deep network analysis by capturing, recording and analyzing network events to find out the source of a security attack or other information security incidents. Existing network forensics work has been mostly focused on the Internet and fixed networks. But the exponential growth and use of wireless technologies, coupled with their unprecedented characteristics, necessitates the development of new network forensic analysis tools. This dissertation fostered the emergence of a new research field in cellular and ad-hoc network forensics. It was one of the first works to identify this problem and offer fundamental techniques and tools that laid the groundwork for future research. In particular, it introduced novel methods to record network incidents and report logged incidents. For recording incidents, location is considered essential to documenting network incidents. However, in network topology spaces, location cannot be measured due to absence of a ‘distance metric’. Therefore, a novel solution was proposed to label locations of nodes within network topology spaces, and then to authenticate the identity of nodes in ad hoc environments. For reporting logged incidents, a novel technique based on Distributed Hash Tables (DHT) was adopted. Although the direct use of DHTs for reporting logged incidents would result in an uncontrollably recursive traffic, a new mechanism was introduced that overcome this recursive process. These logging and reporting techniques aided forensics over cellular and ad-hoc networks, which in turn increased their ability to track and trace attacks to their source. These techniques were a starting point for further research and development that would result in equipping future ad hoc networks with forensic components to complement existing security mechanisms.

Orthogonal frequency division multiplexing based air interfaces and multiple input multiple output techniques in cooperative satellite communications for 4th generation mobile systems

Recently, wireless network technology has grown at such a pace that scientific research has become a practical reality in a very short time span. Mobile wireless communications have witnessed the adoption of several generations, each of them complementing and improving the former. One mobile system that features high data rates and open network architecture is 4G. Currently, the research community and industry, in the field of wireless networks, are working on possible choices for solutions in the 4G system. 4G is a collection of technologies and standards that will allow a range of ubiquitous computing and wireless communication architectures. The researcher considers one of the most important characteristics of future 4G mobile systems the ability to guarantee reliable communications from 100 Mbps, in high mobility links, to as high as 1 Gbps for low mobility users, in addition to high efficiency in the spectrum usage. On mobile wireless communications networks, one important factor is the coverage of large geographical areas. In 4G systems, a hybrid satellite/terrestrial network is crucial to providing users with coverage wherever needed. Subscribers thus require a reliable satellite link to access their services when they are in remote locations, where a terrestrial infrastructure is unavailable. Thus, they must rely upon satellite coverage. Good modulation and access technique are also required in order to transmit high data rates over satellite links to mobile users. This technique must adapt to the characteristics of the satellite channel and also be efficient in the use of allocated bandwidth. Satellite links are fading channels, when used by mobile users. Some measures designed to approach these fading environments make use of: (1) spatial diversity (two receive antenna configuration); (2) time diversity (channel interleaver/spreading techniques); and (3) upper layer FEC. The author proposes the use of OFDM (Orthogonal Frequency Multiple Access) for the satellite link by increasing the time diversity. This technique will allow for an increase of the data rate, as primarily required by multimedia applications, and will also optimally use the available bandwidth. In addition, this dissertation approaches the use of Cooperative Satellite Communications for hybrid satellite/terrestrial networks. By using this technique, the satellite coverage can be extended to areas where there is no direct link to the satellite. For this purpose, a good channel model is necessary.

Headspace analysis of smokeless powders: Development of mass calibration methods using microdrop printing for chromatographic and ion mobility spectrometric detection

Smokeless powder additives are usually detected by their extraction from post-blast residues or unburned powder particles followed by analysis using chromatographic techniques. This work presents the first comprehensive study of the detection of the volatile and semi-volatile additives of smokeless powders using solid phase microextraction (SPME) as a sampling and pre-concentration technique. Seventy smokeless powders were studied using laboratory based chromatography techniques and a field deployable ion mobility spectrometer (IMS). The detection of diphenylamine, ethyl and methyl centralite, 2,4-dinitrotoluene, diethyl and dibutyl phthalate by IMS to associate the presence of these compounds to smokeless powders is also reported for the first time. A previously reported SPME-IMS analytical approach facilitates rapid sub-nanogram detection of the vapor phase components of smokeless powders. A mass calibration procedure for the analytical techniques used in this study was developed. Precise and accurate mass delivery of analytes in picoliter volumes was achieved using a drop-on-demand inkjet printing method. Absolute mass detection limits determined using this method for the various analytes of interest ranged between 0.03–0.8 ng for the GC-MS and between 0.03–2 ng for the IMS. Mass response graphs generated for different detection techniques help in the determination of mass extracted from the headspace of each smokeless powder. The analyte mass present in the vapor phase was sufficient for a SPME fiber to extract most analytes at amounts above the detection limits of both chromatographic techniques and the ion mobility spectrometer. Analysis of the large number of smokeless powders revealed that diphenylamine was present in the headspace of 96% of the powders. Ethyl centralite was detected in 47% of the powders and 8% of the powders had methyl centralite available for detection from the headspace sampling of the powders by SPME. Nitroglycerin was the dominant peak present in the headspace of the double-based powders. 2,4-dinitrotoluene which is another important headspace component was detected in 44% of the powders. The powders therefore have more than one headspace component and the detection of a combination of these compounds is achievable by SPME-IMS leading to an association to the presence of smokeless powders.

Thioredoxin and Jab1 control estrogen- and antiestrogen-mediated progression of the cell cycle through p27 interactions

A major problem with breast cancer treatment is the prevalence of antiestrogen resistance, be it de novo or acquired after continued use. Many of the underlying mechanisms of antiestrogen resistance are not clear, although estrogen receptor-mediated actions have been identified as a pathway that is blocked by antiestrogens. Selective estrogen receptor modulators (SERMs), such as tamoxifen, are capable of producing reactive oxygen species (ROS) through metabolic activation, and these ROS, at high levels, can induce irreversible growth arrest that is similar to the growth arrest incurred by SERMs. This suggests that SERM-mediated growth arrest may also be through ROS accumulation. Breast cancer receiving long-term antiestrogen treatment appears to adapt to this increased, persistent level of ROS. This, in turn, leads to the disruption of reversible redox signaling that involves redox-sensitive phosphatases and protein kinases and transcription factors. This has downstream consequences for apoptosis, cell cycle progression, and cell metabolism. For this dissertation, we explored if altering the ROS formed by tamoxifen also alters sensitivity of the drug in resistant cells. We explored an association with a thioredoxin/Jab1/p27 pathway, and a possible role of dysregulation of thioredoxin-mediated redox regulation contributing to the development of antiestrogen resistance in breast cancer. We used standard laboratory techniques to perform proteomic assays that showed cell proliferation, protein concentrations, redox states, and protein-protein interactions. We found that increasing thioredoxin reductase levels, and thus increasing the amount of reduced thioredoxin, increased tamoxifen sensitivity in previously resistant cells, as well as altered estrogen and tamoxifen-induced ROS. We also found that decreasing levels of Jab1 protein also increased tamoxifen sensitivity, and that the downstream effects showed a decrease p27 phosphorylation in both cases. We conclude that the chronic use of tamoxifen can lead to an increase in ROS that alters cell signaling and causing cell growth in the presence of tamoxifen, and that this resistant cell growth can be reversed with an alteration to the thioredoxin/Jab1 pathway.

Computational evaluation of wind loads on low- and highrise buildings

Buildings and other infrastructures located in the coastal regions of the US have a higher level of wind vulnerability. Reducing the increasing property losses and causalities associated with severe windstorms has been the central research focus of the wind engineering community. The present wind engineering toolbox consists of building codes and standards, laboratory experiments, and field measurements. The American Society of Civil Engineers (ASCE) 7 standard provides wind loads only for buildings with common shapes. For complex cases it refers to physical modeling. Although this option can be economically viable for large projects, it is not cost-effective for low-rise residential houses. To circumvent these limitations, a numerical approach based on the techniques of Computational Fluid Dynamics (CFD) has been developed. The recent advance in computing technology and significant developments in turbulence modeling is making numerical evaluation of wind effects a more affordable approach. The present study targeted those cases that are not addressed by the standards. These include wind loads on complex roofs for low-rise buildings, aerodynamics of tall buildings, and effects of complex surrounding buildings. Among all the turbulence models investigated, the large eddy simulation (LES) model performed the best in predicting wind loads. The application of a spatially evolving time-dependent wind velocity field with the relevant turbulence structures at the inlet boundaries was found to be essential. All the results were compared and validated with experimental data. The study also revealed CFD's unique flow visualization and aerodynamic data generation capabilities along with a better understanding of the complex three-dimensional aerodynamics of wind-structure interactions. With the proper modeling that realistically represents the actual turbulent atmospheric boundary layer flow, CFD can offer an economical alternative to the existing wind engineering tools. CFD's easy accessibility is expected to transform the practice of structural design for wind, resulting in more wind-resilient and sustainable systems by encouraging optimal aerodynamic and sustainable structural/building design. Thus, this method will help ensure public safety and reduce economic losses due to wind perils.

Effects of Management-Development Practices on Hospitality Management Graduates' Job Satisfaction and Intention to Stay

Companies have long recognized the importance of training and developing their managers to prepare them for their short- and long-term careers. Formal management-development programs and other less formal means of management development abound in the hospitality industry. Therefore, one may ask whether the entry-level managers for whom these programs are designed perceive them to be effective. The present study explores management-development practices, procedures, and techniques, and their effects on job satisfaction and organizational commitment