On the hydrophobicity of peptides:comparing empirical predictions of peptide log P values

Peptides are of great therapeutic potential as vaccines and drugs. Knowledge of physicochemical descriptors, including the partition coefficient logP, is useful for the development of predictive Quantitative Structure-Activity Relationships (QSARs). We have investigated the accuracy of available programs for the prediction of logP values for peptides with known experimental values obtained from the literature. Eight prediction programs were tested, of which seven programs were fragment-based methods: XLogP, LogKow, PLogP, ACDLogP, AlogP, Interactive Analysis's LogP and MlogP; and one program used a whole molecule approach: QikProp. The predictive accuracy of the programs was assessed using r(2) values, with ALogP being the most effective (r( 2) = 0.822) and MLogP the least (r(2) = 0.090). We also examined three distinct types of peptide structure: blocked, unblocked, and cyclic. For each study (all peptides, blocked, unblocked and cyclic peptides) the performance of programs rated from best to worse is as follows: all peptides - ALogP, QikProp, PLogP, XLogP, IALogP, LogKow, ACDLogP, and MlogP; blocked peptides - PLogP, XLogP, ACDLogP, IALogP, LogKow, QikProp, ALogP, and MLogP; unblocked peptides - QikProp, IALogP, ALogP, ACDLogP, MLogP, XLogP, LogKow and PLogP; cyclic peptides - LogKow, ALogP, XLogP, MLogP, QikProp, ACDLogP, IALogP. In summary, all programs gave better predictions for blocked peptides, while, in general, logP values for cyclic peptides were under-predicted and those of unblocked peptides were over-predicted.

Simultaneous chemical reaction and distillation of formaldehyde

The thesis is concerned with the development and testing of a mathematical model of a distillation process in which the components react chemically. The formaldehyde-methanol-water system was selected and only the reversible reactions between formaldehyde and water giving methylene glycol and between formaldehyde and methanol producing hemiformal were assumed to occur under the distillation conditions. Accordingly the system has been treated as a five component system. The vapour-liquid equilibrium calculations were performed by solving iteratively the thermodynamic relationships expressing the phase equilibria with the stoichiometric equations expressing the chemical equilibria. Using optimisation techniques, the Wilson single parameters and Henry's constants were calculated for binary systems containing formaldehyde which was assumed to be a supercritical component whilst Wilson binary parameters were calculated for the remaining binary systems. Thus the phase equilibria for the formaldehyde system could be calculated using these parameters and good accuracy was obtained when calculated values were compared with experimental values. The distillation process was modelled using the mass and energy balance equations together with the phase equilibria calculations. The plate efficiencies were obtained from a modified A.I.Ch.E. Bubble Tray method. The resulting equations were solved by an iterative plate to plate calculation based on the Newton Raphson method. Experiments were carried out in a 76mm I.D., eight sieve plate distillation column and the results were compared with the mathematical model calculations. Overall, good agreement was obtained but some discrepancies were observed in the concentration profiles and these may have been caused by the effect of limited physical property data and a limited understanding of the reactions mechanism. The model equations were solved in the form of modular computer programs. Although they were written to describe the steady state distillation with simultaneous chemical reaction of the formaldehyde system, the approach used may be of wider application.

Separation of n-paraffins by selective adsorption

A study has been undertaken of the vapor-phase adsorptive separation of n-alkanes from Kuwait kerosene (Kuwait National Petroleum Company, heavy kerosene) using zeolite molecular sieves. Due to the shortage of information on the adsorption of multicomponent systems in the open literature, the present investigation was initiated to study the effect of feed flowrate, temperature, and zeolite particle size on the height of mass transfer zone (MTZ) and the dynamic capacity of the adsorbent for multicomponent n-alkanes adsorption on a fixed-bed of zeolite type-5A. The optimum operating conditions for separation of the n-alkanes has been identified so that the effluent would also be of marketable quality. The effect of multicycle adsorption-desorption stages on the dynamic behaviour of zeolite using steam as a desorbing agent has been studied and compared with n-pentane and n-hexane as desorbing agents. The separation process comprised one cycle of adsorption using a fixed-bed of zeolite type-5A. The bed was fed with vaporized kerosene until saturation had been achieved whereby the n-alkanes were adsorbed and the denormalized material eluted. The process of adsorption-desorption was carried out isobarically at one atmosphere. A mathematical model has been developed to predict the breakthrough time using the method of characteristics. The results were in a reasonable agreement with the experimental values. This model has also been utilized to develop the equilibrium isotherm. Optimum operating conditions were achieved at a feed flowrate of 33.33 x 10-9 m3/s, a temperature of 643 K, and a particle size of (1.0 - 2.0) x 10-3 m. This yielded an HMTZ value and a dynamic capacity of 0.206 m and 9.6S3 x 10-2 kg n-alkanes/kg of zeolite respectively. These data will serve as a basis for design of a commercial plant. The purity of liquid-paraffin product desorbed using steam was 83.24 wt%. The dynamic capacity was noticed to decrease sharply with the cycle number, without intermediate reactivation of zeolite, while it was kept unchanged by intermediate reactivation. Normal hexane was found to be the best desorbing agent, the efficiency of which was mounted to 88.2%.

Modelling and measurements on a condensing counter-flow heat exchanger

Experimental investigations and computer modelling studies have been made on the refrigerant-water counterflow condenser section of a small air to water heat pump. The main object of the investigation was a comparative study between the computer modelling predictions and the experimental observations for a range of operating conditions but other characteristics of a counterflow heat exchanger are also discussed. The counterflow condenser consisted of 15 metres of a thermally coupled pair of copper pipes, one containing the R12 working fluid and the other water flowing in the opposite direction. This condenser was mounted horizontally and folded into 0.5 metre straight sections. Thermocouples were inserted in both pipes at one metre intervals and transducers for pressure and flow measurement were also included. Data acquisition, storage and analysis was carried out by a micro-computer suitably interfaced with the transducers and thermocouples. Many sets of readings were taken under a variety of conditions, with air temperature ranging from 18 to 26 degrees Celsius, water inlet from 13.5 to 21.7 degrees, R12 inlet temperature from 61.2 to 81.7 degrees and water mass flow rate from 6.7 to 32.9 grammes per second. A Fortran computer model of the condenser (originally prepared by Carrington[1]) has been modified to match the information available from experimental work. This program uses iterative segmental integration over the desuperheating, mixed phase and subcooled regions for the R12 working fluid, the water always being in the liquid phase. Methods of estimating the inlet and exit fluid conditions from the available experimental data have been developed for application to the model. Temperature profiles and other parameters have been predicted and compared with experimental values for the condenser for a range of evaporator conditions and have shown that the model gives a satisfactory prediction of the physical behaviour of a simple counterflow heat exchanger in both single phase and two phase regions.

The role of oxidation in the protection of sliding metal surfaces

This study is concerned with the mechanisms of growth and wear of protective oxide films formed under various tribological conditions. In the study three different tribological systems are examined in each of which oxidational wear is the dominant equilibrium mode. These are an unlubricated steel on steel system sliding at low and elevated temperatures, a boundary lubricated aluminium bronze on steel system and an unlubricated reciprocating sliding 9% Cr steel system operated at elevated temperature, in an atmosphere of carbon dioxide. The results of mechanical measurements of wear and friction are presented for a range of conditions of load, speed and temper.ature for the systems, together with the results of extensive examinations of the surfaces and sub­ surfaces by various physical methods of analysis. The major part of the thesis, however, is devoted to the development and application of surface models and theoretical quantative expressions in order to explain the observed oxidational wear phenomena. In this work, the mechanisms of formation of load bearing ox ide plateaux are described and are found to be dependent on system geometry and environment. The relative importance of ''in contact" and "out of contact" oxidation is identified together with growth rate constants appropriate to the two situations. Hypotheses are presented to explain the mechanisms of removal of plateaux to form wear debris. The latter hypotheses include the effects of cyclic stressing and dislocation accumulation, together with effects associated with the kinetics of growth and physical properties of the various oxides. The proposed surf ace mode1s have led to the develop­ ment of quantitative expressions for contact temperature, unlubricated wear rates, boundary lubricated wear rates and the wear of rna ter ial during the transition from severe to mild wear. In general theoretical predictions from these expressions are in very good agreement with experimental values.

Phase equilibrium studies at moderate pressures

The theory of vapour-liquid equilibria is reviewed, as is the present status or prediction methods in this field. After discussion of the experimental methods available, development of a recirculating equilibrium still based on a previously successful design (the modified Raal, Code and Best still of O'Donnell and Jenkins) is described. This novel still is designed to work at pressures up to 35 bar and for the measurement of both isothermal and isobaric vapour-liquid equilibrium data. The equilibrium still was first commissioned by measuring the saturated vapour pressures of pure ethanol and cyclohexane in the temperature range 77-124°C and 80-142°C respectively. The data obtained were compared with available literature experimental values and with values derived from an extended form of the Antoine equation for which parameters were given in the literature. Commissioning continued with the study of the phase behaviour of mixtures of the two pure components as such mixtures are strongly non-ideal, showing azeotopic behaviour. Existing data did not exist above one atmosphere pressure. Isothermal measurements were made at 83.29°C and 106.54°C, whilst isobaric measurements were made at pressures of 1 bar, 3 bar and 5 bar respectively. The experimental vapour-liquid equilibrium data obtained are assessed by a standard literature method incorporating a themodynamic consistency test that minimises the errors in all the measured variables. This assessment showed that reasonable x-P-T data-sets had been measured, from which y-values could be deduced, but that the experimental y-values indicated the need for improvements in the design of the still. The final discussion sets out the improvements required and outlines how they might be attained.

Why are MD simulated protein folding times wrong?

The question of significant deviations of protein folding times simulated using molecular dynamics from experimental values is investigated. It is shown that in the framework of Markov State Model (MSM) describing the conformational dynamics of peptides and proteins, the folding time is very sensitive to the simulation model parameters, such as forcefield and temperature. Using two peptides as examples, we show that the deviations in the folding times can reach an order of magnitude for modest variations of the molecular model. We, therefore, conclude that the folding rate values obtained in molecular dynamics simulations have to be treated with care.

A knowledge-based system for process planning in a seamless steel tube plant

The thesis describes the work carried out to develop a prototype knowledge-based system 'KBS-SETUPP' to generate process plans for the manufacture of seamless tubes. The work is specifically related to a plant in which hollows are made from solid billets using a rotary piercing process and then reduced to required size and finished properties using the fixed plug cold drawing process. The thesis first discusses various methods of tube production in order to give a general background of tube manufacture. Then a review of the automation of the process planning function is presented in terms of its basic sub-tasks and the techniques and suitability of a knowledge-based system is established. In the light of such a review and a case study, the process planning problem is formulated in the domain of seamless tube manufacture, its basic sub-tasks are identified and capabilities and constraints of the available equipment in the specific plant are established. The task of collecting and collating the process planning knowledge in seamless tube manufacture is discussed and is mostly fulfilled from domain experts, analysing of existing manufacturing records specific to plant, textbooks and applicable Standards. For the cold drawing mill, tube-drawing schedules have been rationalised to correspond with practice. The validation of such schedules has been achieved by computing the process parameters and then comparing these with the drawbench capacity to avoid over-loading. The existing models cannot be simulated in the computer program as such, therefore a mathematical model has been proposed which estimates the process parameters which are in close agreement with experimental values established by other researchers. To implement the concepts, a Knowledge-Based System 'KBS- SETUPP' has been developed on Personal Computer using Turbo- Prolog. The system is capable of generating process plans, production schedules and some additional capabilities to supplement process planning. The system generated process plans have been compared with the actual plans of the company and it has been shown that the results are satisfactory and encouraging and that the system has the capabilities which are useful.

The effect of elevated temperature on the wear of stainless steel in contact with tungsten carbide

The bearings in the air motors of modern jet aircraft engines must operate dry in hostile conditions at temperatures up to 500° C, where the thrust races in the actuators operate at temperatures up to 300° C. One of the few metallurgical combinations which can function efficiently under these conditions is martensitic stainless steel on tungsten carbide. The work described was initiated to isolate the wear mechanisms of two such steels in contact with tungsten carbide at temperatures up to 500° C. Experiments were carried out on angular contact bearings similar to these used in service, where both rolling and sliding is present and also for pure sliding conditions using a pin-on-disc apparatus. Wear measurements of the bearings were obtained with wear rates, friction and surface temperatures from the pin-on-disc machine for a series of loads and speeds. Extensive X-ray diffraction analysis was carried out on the wear debris, with also S.E.M. analysis and hardness tests on the worn surfaces along with profilometry measurements of the disc. The oxidational parameters of the steel were obtained from measurements of oxide growth rates by ellipsometry. Three distinct mechanisms of wear were established and the latter two were found to be present in both configurations. These involve an oxidational-abrasive mechanism at loads below 40 N with pin surface temperatures up to about 300 °C, with the mechanism changing to severe wear for higher loads. As the temperature increases a third wear mechanism appears due to transfer of relatively soft oxide films to the steel surface reducing the wear rate. Theoretical K factors were derived and compared with experimental values which were found to be in good agreement for the severe wear mechanism. The pin-on-disc experiments may be useful as a screening test for material selection, without the considerable cost of producing the angular contact bearings.

Empirical prediction of peptide octanol-water partition coefficients

Peptides are of great therapeutic potential as vaccines and drugs. Knowledge of physicochemical descriptors, including the partition coefficient P (commonly expressed in logarithm form: logP), is useful for screening out unsuitable molecules and also for the development of predictive Quantitative Structure-Activity Relationships (QSARs). In this paper we develop a new approach to the prediction of LogP values for peptides based on an empirical relationship between global molecular properties and measured physical properties. Our method was successful in terms of peptide prediction (total r2 = 0.641). The final model consisted of 5 physicochemical descriptors (molecular weight, number of single bonds, 2D-VDW volume, 2D-VSA hydrophobic and 2D-VSA polar). The approach is peptide specific and its predictive accuracy was high. Overall, 67% of the peptides were able to be predicted within +/-0.5 log units from the experimental values. Our method thus represents a novel prediction method with proven predictive ability.

Leadership development: the role of developmental readiness, personality dispositions, and individual values

Increased awareness of the crucial role of leadership as a competitive advantage for organisations (McCall, 1998; Petrick, Scherer, Brodzinski, Quinn, & Ainina, 1999) has led to billions spent on leadership development programmes and training (Avolio & Hannah, 2008). However, research reports confusing and contradictory evidence regarding return on investment and developmental outcomes, and a lot of variance has been observed across studies (Avolio, Reichard, Hannah, Walumbwa, & Chan, 2009). The purpose of this thesis is to understand the mechanisms underlying this variability in leadership development. Of the many factors at play in the process, such as programme design and delivery, organisational support, and perceptions of relevance (Mabey, 2002; Day, Harrison, & Halpin, 2009), individual differences and characteristics stand out. One way in which individuals differ is in their Developmental Readiness (DR), a concept recently introduced in the literature that may well explain this variance and which has been proposed to accelerate development (Avolio & Hannah, 2008, 2009). Building on previous work, DR is introduced and conceptualised somewhat differently. In this study, DR is construed of self-awareness, self-regulation, and self-motivation, proposed by Day (2000) to be the backbones of leadership development. DR is suggested to moderate the developmental process. Furthermore, personality dispositions and individual values are proposed to be precursors of DR. The empirical research conducted uses a pre-test post-test quasi-experimental design. Before conducting the study, though, both a measure of Developmental Readiness and a competency profiling measure are tested in two pilot studies. Results do not find evidence of a direct effect of leadership development programmes on development, but do support an interactive effect between DR and leadership development programmes. Personality dispositions Agreeableness, Conscientiousness, and Openness to Experience and value orientations Conservation, Open, and Closed Orientation are found to significantly predict DR. Finally, the theoretical and practical implications of findings are discussed.

An experimental analysis of operating conditions in cold roll-forming

A detailed literature survey confirmed cold roll-forming to be a complex and little understood process. In spite of its growing value, the process remains largely un-automated with few principles used in set-up of the rolling mill. This work concentrates on experimental investigations of operating conditions in order to gain a scientific understanding of the process. The operating conditions are; inter-pass distance, roll load, roll speed, horizontal roll alignment. Fifty tests have been carried out under varied operating conditions, measuring section quality and longitudinal straining to give a picture of bending. A channel section was chosen for its simplicity and compatibility with previous work. Quality measurements were measured in terms of vertical bow, twist and cross-sectional geometric accuracy, and a complete method of classifying quality has been devised. The longitudinal strain profile was recorded, by the use of strain gauges attached to the strip surface at five locations. Parameter control is shown to be important in allowing consistency in section quality. At present rolling mills are constructed with large tolerances on operating conditions. By reduction of the variability in parameters, section consistency is maintained and mill down-time is reduced. Roll load, alignment and differential roll speed are all shown to affect quality, and can be used to control quality. Set-up time is reduced by improving the design of the mill so that parameter values can be measured and set, without the need for judgment by eye. Values of parameters can be guided by models of the process, although elements of experience are still unavoidable. Despite increased parameter control, section quality is variable, if only due to variability in strip material properties. Parameters must therefore be changed during rolling. Ideally this can take place by closed-loop feedback control. Future work lies in overcoming the problems connected with this control.

PPD v1.0 - an integrated, web-accessible database of experimentally determined protein pKa values

The Protein pKa Database (PPD) v1.0 provides a compendium of protein residue-specific ionization equilibria (pKa values), as collated from the primary literature, in the form of a web-accessible postgreSQL relational database. Ionizable residues play key roles in the molecular mechanisms that underlie many biological phenomena, including protein folding and enzyme catalysis. The PPD serves as a general protein pKa archive and as a source of data that allows for the development and improvement of pKa prediction systems. The database is accessed through an HTML interface, which offers two fast, efficient search methods: an amino acid-based query and a Basic Local Alignment Search Tool search. Entries also give details of experimental techniques and links to other key databases, such as National Center for Biotechnology Information and the Protein Data Bank, providing the user with considerable background information.

Experimental full duplex simultaneous transmission of LTE over a DWDM directly modulated RoF system

In this paper, we experimentally demonstrate the seamless integration of full duplex system frequency division duplex (FDD) long-term evolution (LTE) technology with radio over fiber (RoF) for eNodeB (eNB) coverage extension. LTE is composed of quadrature phase-shift keying (QPSK), 16-quadrature amplitude modulation (16-QAM) and 64-QAM, modulated onto orthogonal frequency division multiplexing (OFDM) and single-carrier-frequency division multiplexing for downlink (DL) and uplink (UL) transmissions, respectively. The RoF system is composed of dedicated directly modulated lasers for DL and UL with dense wavelength division multiplexing (DWDM) for instantaneous connections and for Rayleigh backscattering and nonlinear interference mitigation. DL and UL signals have varying carrier frequencies and are categorized as broad frequency spacing (BFS), intermediate frequency spacing (IFS), and narrow frequency spacing (NFS). The adjacent channel leakage ratio (ACLR) for DL and UL with 64-QAM are similar for all frequency spacings while cross talk is observed for NFS. For the best case scenario for DL and UL transmissions we achieve error vector magnitude (EVM) values of ~2.30%, ~2.33%, and ~2.39% for QPSK, 16-QAM, and 64-QAM, respectively, while for the worst case scenario with a NFS EVM is increased by 0.40% for all schemes. © 2009-2012 OSA.

Superfocusing of high-M2 semiconductor laser beams:experimental demonstration

The focusing of multimode laser diode beams is probably the most significant problem that hinders the expansion of the high-power semiconductor lasers in many spatially-demanding applications. Generally, the 'quality' of laser beams is characterized by so-called 'beam propagation parameter' M2, which is defined as the ratio of the divergence of the laser beam to that of a diffraction-limited counterpart. Therefore, M2 determines the ratio of the beam focal-spot size to that of the 'ideal' Gaussian beam focused by the same optical system. Typically, M2 takes the value of 20-50 for high-power broad-stripe laser diodes thus making the focal-spot 1-2 orders of magnitude larger than the diffraction limit. The idea of 'superfocusing' for high-M2 beams relies on a technique developed for the generation of Bessel beams from laser diodes using a cone-shaped lens (axicon). With traditional focusing of multimode radiation, different curvatures of the wavefronts of the various constituent modes lead to a shift of their focal points along the optical axis that in turn implies larger focal-spot sizes with correspondingly increased values of M2. In contrast, the generation of a Bessel-type beam with an axicon relies on 'self-interference' of each mode thus eliminating the underlying reason for an increase in the focal-spot size. For an experimental demonstration of the proposed technique, we used a fiber-coupled laser diode with M2 below 20 and an emission wavelength in ~1μm range. Utilization of the axicons with apex angle of 140deg, made by direct laser writing on a fiber tip, enabled the demonstration of an order of magnitude decrease of the focal-spot size compared to that achievable using an 'ideal' lens of unity numerical aperture. © 2014 SPIE.