Part I. Electric birefringence studies of deoxyribonucleic acids. Part II. Selective dissociation of nucleohistone complexes

Part I

The electric birefringence of dilute DNA solutions has been studied in considerable detail and on a large number of samples, but no new and reliable information was discovered concerning the tertiary structure of DNA. The large number of variables which effect the birefringence results is discussed and suggestions are made for further work on the subject.

The DNA molecules have been aligned in a rapidly alternating (10 to 20 kc/sec) square wave field confirming that the orientation mechanism is that of counterion polarization. A simple empirical relation between the steady state birefringence, Δn_st, and the square of the electric field, E, has been found: Δn_st = E²/(a E² + b), where a = 1/Δn_s and b = (E²/Δn_st)_E→o. Δn_s is the birefringence extrapolated to infinite field strength.

The molecules show a distribution of relaxation times from 10^-4 to 0.2 sec, which is consistent with expectations for flexible coil molecules. The birefringence and the relaxation times decrease with increasing salt concentrations. They also depend on the field strength and pulse duration in a rather non-reproducible manner, which may be due in part to changes in the composition of the solution or in the molecular structure of the DNA (other than denaturation). Further progress depends on the development of some control over these effects.

Part II

The specificity of the dissociation of reconstituted and native deoxyribonucleohistones (DNH) by monovalent salt solutions has been investigated. A novel zone ultracentrifugation method is used in which the DNH is sedimented as a zone through a preformed salt gradient, superimposed on a stabilizing D₂O (sucrose) density gradient. The results, obtained by scanning the quartz sedimentation tubes in a spectrophotometer, were verified by the conventional, preparative sedimentation technique. Procedures are discussed for the detection of microgram quantities of histones, since low concentrations must be used to prevent excessive aggregation of the DNH.

The data show that major histone fractions are selectively dissociated from DNH by increasing salt concentrations: Lysine rich histone (H I) dissociates gradually between 0.1 and 0.3 F, slightly lysine rich histone (H II) dissociates as a narrow band between 0.35 and 0.5 F, and arginine rich histone (H III, H IV) dissociates gradually above 0.5 F NaClO₄.

The activity of the partially dissociated, native DNH in sustaining RNA synthesis, their mobility and their unusual heat denaturation and renaturation behavior are described. The two-step melting behavior of the material indicates that the histones are non-randomly distributed along the DNA, but the implications are that the uncovered regions are not of gene-size length.

Calibration of Grassholme Channels, 1982

Adjustment of experimental channels to give any specified pattern of water depth or velocity is complex and tedious because it involves a number of variables. Since some variables are not controllable and variables may interact, valve settings of the Grassholme channels were initially determined on an ad hoc basis to suit individual experiments. This method was used during 1982 but additional observations were made in order to gain more detailed understanding of the channel system and, as far as possible, to develop a guide to future short-cuts in attaining suitable channel settings for any given purpose. This report describes calibration of the Grassholme channels (using water of the Grassholme Reservoir) for the biological experiments of spring - summer 1982. The main variables that are discussed are valve turns and discharge and velocity and depth. It also seeks to establish relationships which will be of value in future managment of the channels for experimental purposes.

Wave induced oscillations in harbors of arbitrary shape

Theoretical and experimental studies were conducted to investigate the wave induced oscillations in an arbitrary shaped harbor with constant depth which is connected to the open-sea.

A theory termed the “arbitrary shaped harbor” theory is developed. The solution of the Helmholtz equation, ∇²f + k²f = 0, is formulated as an integral equation; an approximate method is employed to solve the integral equation by converting it to a matrix equation. The final solution is obtained by equating, at the harbor entrance, the wave amplitude and its normal derivative obtained from the solutions for the regions outside and inside the harbor.

Two special theories called the circular harbor theory and the rectangular harbor theory are also developed. The coordinates inside a circular and a rectangular harbor are separable; therefore, the solution for the region inside these harbors is obtained by the method of separation of variables. For the solution in the open-sea region, the same method is used as that employed for the arbitrary shaped harbor theory. The final solution is also obtained by a matching procedure similar to that used for the arbitrary shaped harbor theory. These two special theories provide a useful analytical check on the arbitrary shaped harbor theory.

Experiments were conducted to verify the theories in a wave basin 15 ft wide by 31 ft long with an effective system of wave energy dissipators mounted along the boundary to simulate the open-sea condition.

Four harbors were investigated theoretically and experimentally: circular harbors with a 10° opening and a 60° opening, a rectangular harbor, and a model of the East and West Basins of Long Beach Harbor located in Long Beach, California.

Theoretical solutions for these four harbors using the arbitrary shaped harbor theory were obtained. In addition, the theoretical solutions for the circular harbors and the rectangular harbor using the two special theories were also obtained. In each case, the theories have proven to agree well with the experimental data.

It is found that: (1) the resonant frequencies for a specific harbor are predicted correctly by the theory, although the amplification factors at resonance are somewhat larger than those found experimentally,(2) for the circular harbors, as the width of the harbor entrance increases, the amplification at resonance decreases, but the wave number bandwidth at resonance increases, (3) each peak in the curve of entrance velocity vs incident wave period corresponds to a distinct mode of resonant oscillation inside the harbor, thus the velocity at the harbor entrance appears to be a good indicator for resonance in harbors of complicated shape, (4) the results show that the present theory can be applied with confidence to prototype harbors with relatively uniform depth and reflective interior boundaries.

Valuation of Wind Energy Projects: A Real Options Approach

We address the valuation of an operating wind farm and the finite-lived option to invest in it under different reward/support schemes: a constant feed-in tariff, a premium on top of the electricity market price (either a fixed premium or a variable subsidy such as a renewable obligation certificate or ROC), and a transitory subsidy, among others. Futures contracts on electricity with ever longer maturities enable market-based valuations to be undertaken. The model considers up to three sources of uncertainty: the electricity price, the level of wind generation, and the certificate (ROC) price where appropriate. When analytical solutions are lacking, we resort to a trinomial lattice combined with Monte Carlo simulation; we also use a two-dimensional binomial lattice when uncertainty in the ROC price is considered. Our data set refers to the UK. The numerical results show the impact of several factors involved in the decision to invest: the subsidy per MWh generated, the initial lump-sum subsidy, the maturity of the investment option, and electricity price volatility. Different combinations of variables can help bring forward investments in wind generation. One-off policies, e.g., a transitory initial subsidy, seem to have a stronger effect than a fixed premium per MWh produced.

Lakes - Classification & Monitoring: a strategy for the classification of lakes

This is the report on Lakes – Classification and Monitoring, a strategy for the classification of lakes by the National Rivers Authority. This report describes a scheme for the assessment and monitoring of water and ecological quality in standing waters, greater than about 1ha in area, in England and Wales although it is generally relevant to Northwest Europe. Thirteen hydrological, chemical and biological variables are used to characterize the standing water body in any current sampling. Statistical testing on the chemical variables showed that at least six samples during a year would be needed to produce a representative sampling mean; but in this scheme the choice of variables minimizes logistic cost by not using boat sampling and time costs by not demanding extensive taxonomic work. Standing waters are classified in a state-changed system in which the contemporary values of the variables are compared with a reference baseline state and then placed in categories of percentage change from this baseline. The scheme is presently designed for use at about five year intervals on all lakes greater than 2ha area plus additional lakes of significant amenity or conservation interest.

Determinants of small-scale fishermen's income on Oman's Batinah Coast

The small-scale fishing industry of Oman is responsible for almost 90 percent of the total marine fishery production. It is also the main supplier of fish for Omani households. This study analyzes the factors that determine small-scale fishermen’s income on Oman’s Batinah Coast, which has almost 30 percent of Oman’s population and more than one-third of the small-scale fishermen. We find that fishermen’s income here can be explained broadly under four major blocks of variables: geographical region, fishing inputs and catch, socioeconomic and demographic characteristics, and the nature of the relationship with fisheries extension services. In general, the Wilayat (local administrative units) failed to make any significant impact on fishermen’s income. The variable “Fishing inputs and catch,” such as increases in engine power, boat length, weekly catch, and number of weekly trips, positively impacted fishermen’s income while increases in weekly fishing costs, number of crew members, and difficulty in getting ice had a significantly negative effect on the income. Furthermore, socioeconomic and demographic characteristics also contributed significantly in determining the fishermen’s income level. The other important findings were related to extension services. The variables “Fishermen’s exchange of information and cooperation with the ministry” and “Fishermen’s involvement in the extension activities” were found to have positive effects on fishermen’s income levels. Capitalizing on these findings could improve fishermen’s incomes and their lives across the region, as well as nationally.

Introduction to the development of an information management system for soil mix technology using artificial neural networks

This paper introduces current work in collating data from different projects using soil mix technology and establishing trends using artificial neural networks (ANNs). Variation in unconfined compressive strength as a function of selected soil mix variables (e.g., initial soil water content and binder dosage) is observed through the data compiled from completed and on-going soil mixing projects around the world. The potential and feasibility of ANNs in developing predictive models, which take into account a large number of variables, is discussed. The main objective of the work is the management and effective utilization of salient variables and the development of predictive models useful for soil mix technology design. Based on the observed success in the predictions made, this paper suggests that neural network analysis for the prediction of properties of soil mix systems is feasible. © ASCE 2011.

Making a shallow network deep: Conversion of a boosting classifier into a decision tree by boolean optimisation

This paper presents a novel way to speed up the evaluation time of a boosting classifier. We make a shallow (flat) network deep (hierarchical) by growing a tree from decision regions of a given boosting classifier. The tree provides many short paths for speeding up while preserving the reasonably smooth decision regions of the boosting classifier for good generalisation. For converting a boosting classifier into a decision tree, we formulate a Boolean optimization problem, which has been previously studied for circuit design but limited to a small number of binary variables. In this work, a novel optimisation method is proposed for, firstly, several tens of variables i.e. weak-learners of a boosting classifier, and then any larger number of weak-learners by using a two-stage cascade. Experiments on the synthetic and face image data sets show that the obtained tree achieves a significant speed up both over a standard boosting classifier and the Fast-exit-a previously described method for speeding-up boosting classification, at the same accuracy. The proposed method as a general meta-algorithm is also useful for a boosting cascade, where it speeds up individual stage classifiers by different gains. The proposed method is further demonstrated for fast-moving object tracking and segmentation problems. © 2011 Springer Science+Business Media, LLC.

A Structured Model of Video Reproduces Primary Visual Cortical Organisation

The visual system must learn to infer the presence of objects and features in the world from the images it encounters, and as such it must, either implicitly or explicitly, model the way these elements interact to create the image. Do the response properties of cells in the mammalian visual system reflect this constraint? To address this question, we constructed a probabilistic model in which the identity and attributes of simple visual elements were represented explicitly and learnt the parameters of this model from unparsed, natural video sequences. After learning, the behaviour and grouping of variables in the probabilistic model corresponded closely to functional and anatomical properties of simple and complex cells in the primary visual cortex (V1). In particular, feature identity variables were activated in a way that resembled the activity of complex cells, while feature attribute variables responded much like simple cells. Furthermore, the grouping of the attributes within the model closely parallelled the reported anatomical grouping of simple cells in cat V1. Thus, this generative model makes explicit an interpretation of complex and simple cells as elements in the segmentation of a visual scene into basic independent features, along with a parametrisation of their moment-by-moment appearances. We speculate that such a segmentation may form the initial stage of a hierarchical system that progressively separates the identity and appearance of more articulated visual elements, culminating in view-invariant object recognition.

Tailored seeding geometries for the multi-fidelity design of compression systems

Design optimisation of compressor systems is a computationally expensive problem due to the large number of variables, complicated design space and expense of the analysis tools. One approach to reduce the expense of the process and make it achievable in industrial timescales is to employ multi-fidelity techniques, which utilise more rapid tools in conjunction with the highest fidelity analyses. The complexity of the compressor design landscape is such that the starting point for these optimisations can influence the achievable results; these starting points are often existing (optimised) compressor designs, which form a limited set in terms of both quantity and diversity of the design. To facilitate the multi-fidelity optimisation procedure, a compressor synthesis code was developed which allowed the performance attributes (e.g. stage loadings, inlet conditions) to be stipulated, enabling the generation of a variety of compressors covering a range of both design topology and quality to act as seeding geometries for the optimisation procedures. Analysis of the performance of the multi-fidelity optimisation system when restricting its exploration space to topologically different areas of the design space indicated little advantage over allowing the system to search the design space itself. However, comparing results from optimisations started from seed designs with different aerodynamic qualites indicated an improved performance could be achieved by starting an optimisation from a higher quality point, and thus that the choice of starting point did affect the final outcome of the optimisations. Both investigations indicated that the performance gains through the optimisation were largely defined by the early exploration of the design space where the multi-fidelity speedup could be exploited, thus extending this region is likely to have the greatest effect on performance of the optimisation system. © 2013 by the American Institute of Aeronautics and Astronautics, Inc. All rights reserved.

Tailored seeding geometries for the multi-fidelity design of compression systems

Design optimisation of compressor systems is a computationally expensive problem due to the large number of variables, complicated design space and expense of the analysis tools. One approach to reduce the expense of the process and make it achievable in industrial timescales is to employ multi-fidelity techniques, which utilise more rapid tools in conjunction with the highest fidelity analyses. The complexity of the compressor design landscape is such that the starting point for these optimisations can influence the achievable results; these starting points are often existing (optimised) compressor designs, which form a limited set in terms of both quantity and diversity of the design. To facilitate the multi-fidelity optimisation procedure, a compressor synthesis code was developed which allowed the performance attributes (e.g. stage loadings, inlet conditions) to be stipulated, enabling the generation of a variety of compressors covering a range of both design topology and quality to act as seeding geometries for the optimisation procedures. Analysis of the performance of the multi-fidelity optimisation system when restricting its exploration space to topologically different areas of the design space indicated little advantage over allowing the system to search the design space itself. However, comparing results from optimisations started from seed designs with different aerodynamic qualites indicated an improved performance could be achieved by starting an optimisation from a higher quality point, and thus that the choice of starting point did affect the final outcome of the optimisations. Both investigations indicated that the performance gains through the optimisation were largely defined by the early exploration of the design space where the multi-fidelity speedup could be exploited, thus extending this region is likely to have the greatest effect on performance of the optimisation system. © 2012 AIAA.

Impact of hydrated magnesium carbonate additives on the carbonation of reactive MgO cements

Reactive magnesia (MgO) cements have emerged as a potentially more sustainable and technically superior alternative to Portland cement due to their lower production temperature and ability to sequester significant quantities of CO2. Porous blocks containing MgO were found to achieve higher strength values than PC blocks. A number of variables are investigated to achieve maximum carbonation and associated high strengths. This paper focuses on the impact of four different hydrated magnesium carbonates (HMCs) as cement replacements of either 20 or 50%. Accelerated carbonation (20 C, 70-90% RH, 20% CO2) is compared with natural curing (20 C, 60-70% RH, ambient CO2). SEM, TG/DTA, XRD, and HCl acid digestion are utilized to provide a thorough understanding of the performance of MgO-cement porous blocks. The presence of HMCs resulted in the formation of larger size carbonation products with a different morphology than those in the control mix, leading to significantly enhanced carbonation and strength. © 2013 Elsevier Ltd.

Strength correlations of cement-mixed soils using data mapping

Development of comparisons and correlations between the unconfined compressive strength (UCS) and the undrained triaxial compressive strength, qu, is essential for generalising performance and optimising the design of cement-stabilised soils. This paper introduces current work in collecting and collating data from a number of research projects involving both laboratory strength tests performed on identical cement-stabilised soil samples. The research project on cement-stabilised Singapore marine clays at the National University of Singapore has been used as an example to explain the work on comparing and correlating results from both tests by normalising data and constructing contour plots. The effect of variables on strength comparison and correlations was evaluated. The variation in strength correlations was found to be dependent on a number of factors including: soil properties, cement content, curing time and stress, total water/cement ratio, confining stress and strain rate. The results showed that at ~ 100 kPa confining stress, UCS and qu, had similar magnitudes. Correlations between strengths and other design variables are discussed and presented.

On the radiation and diffraction of linear water waves by an infinitely long rectangular structure submerged in oblique seas

The radiation and diffraction of linear water waves by an infinitely long rectangular structure submerged in oblique seas of finite depth is investigated. The analytical expressions for the radiated and diffracted potentials are derived as infinite series by use of the method of separation of variables. The unknown coefficients in the series are determined by the eigenfunction expansion matching method. The expressions for wave forces, hydrodynamic coefficients and reflection and transmission coefficients are given and verified by the boundary element method. Using the present analytical solution, the hydrodynamic influences of the angle of incidence, the submergence, the width and the thickness of the structure on the wave forces, hydrodynamic coefficients, and reflection and transmission coefficients are discussed in detail.

Scattering of linear water waves by a fixed and infinitely long rectangular structure parallel to a vertical wall in oblique seas

The scattering of linear water waves by an infinitely long rectangular structure parallel to a vertical wall in oblique seas is investigated. Analytical expressions for the diffracted potentials are derived using the method of separation of variables. The unknown coefficients in the expressions are determined through the application of the eigenfunction expansion matching method. The expressions for wave forces on the structure are given. The calculated results are compared with those obtained by the boundary element method. In addition, the influences of the wall, the angle of wave incidence, the width of the structure, and the distance between the structure and the wall on wave forces are discussed. The method presented here can be easily extended to the study of the diffraction of obliquely incident waves by multiple rectangular structures.