T-cell epitope prediction and immune complex simulation using molecular dynamics:state of the art and persisting challenges

Atomistic Molecular Dynamics provides powerful and flexible tools for the prediction and analysis of molecular and macromolecular systems. Specifically, it provides a means by which we can measure theoretically that which cannot be measured experimentally: the dynamic time-evolution of complex systems comprising atoms and molecules. It is particularly suitable for the simulation and analysis of the otherwise inaccessible details of MHC-peptide interaction and, on a larger scale, the simulation of the immune synapse. Progress has been relatively tentative yet the emergence of truly high-performance computing and the development of coarse-grained simulation now offers us the hope of accurately predicting thermodynamic parameters and of simulating not merely a handful of proteins but larger, longer simulations comprising thousands of protein molecules and the cellular scale structures they form. We exemplify this within the context of immunoinformatics.

Aggregation and caking processes of granular materials:continuum model and simulation with application to sugar

Aggregation and caking of particles are common severe problems in many operations and processing of granular materials, where granulated sugar is an important example. Prevention of aggregation and caking of granular materials requires a good understanding of moisture migration and caking mechanisms. In this paper, the modeling of solid bridge formation between particles is introduced, based on moisture migration of atmospheric moisture into containers packed with granular materials through vapor evaporation and condensation. A model for the caking process is then developed, based on the growth of liquid bridges (during condensation), and their hardening and subsequent creation of solid bridges (during evaporation). The predicted caking strengths agree well with some available experimental data on granulated sugar under storage conditions.

Using DEA and simulation in guiding operating units to improved performance

The potential for the use of DEA and simulation in a mutually supporting role in guiding operating units to improved performance is presented. An analysis following a three-stage process is suggested. Stage one involves obtaining the data for the DEA analysis. This can be sourced from historical data, simulated data or a combination of the two. Stage two involves the DEA analysis that identifies benchmark operating units. In the third stage simulation can now be used in order to offer practical guidance to operating units towards improved performance. This can be achieved by the use of sensitivity analysis of the benchmark unit using a simulation model to offer direct support as to the feasibility and efficiency of any variations in operating practices to be tested. Alternatively, the simulation can be used as a mechanism to transmit the practices of the benchmark unit to weaker performing units by building a simulation model of the weaker unit to the process design of the benchmark unit. The model can then compare performance of the current and benchmark process designs. Quantifying improvement in this way provides a useful driver to any process change initiative that is required to bring the performance of weaker units up to the best in class. © 2005 Operational Research Society Ltd. All rights reserved.

The valuation of travel time savings in least developed countries:theoretical and empirical challenges and results from a field study

In developed countries travel time savings can account for as much as 80% of the overall benefits arising from transport infrastructure and service improvements. In developing countries they are generally ignored in transport project appraisals, notwithstanding their importance. One of the reasons for ignoring these benefits in the developing countries is that there is insufficient empirical evidence to support the conventional models for valuing travel time where work patterns, particularly of the poor, are diverse and it is difficult to distinguish between work and non-work activities. The exclusion of time saving benefits may lead to a bias against investment decisions that benefit the poor and understate the poverty reduction potential of transport investments in Least Developed Countries (LDCs). This is because the poor undertake most travel and transport by walking and headloading on local roads, tracks and paths and improvements of local infrastructure and services bring large time saving benefits for them through modal shifts. The paper reports on an empirical study to develop a methodology for valuing rural travel time savings in the LDCs. Apart from identifying the theoretical and empirical issues in valuing travel time savings in the LDCs, the paper presents and discusses the results of an analysis of data from Bangladesh. Some of the study findings challenge the conventional wisdom concerning the time saving values. The Bangladesh study suggests that the western concept of dividing travel time savings into working and non-working time savings is broadly valid in the developing country context. The study validates the use of preference methods in valuing non-working time saving values. However, stated preference (SP) method is more appropriate than revealed preference (RP) method.

Analysis and simulation of computer controlled cellular mobile radio systems

Cellular mobile radio systems will be of increasing importance in the future. This thesis describes research work concerned with the teletraffic capacity and the canputer control requirements of such systems. The work involves theoretical analysis and experimental investigations using digital computer simulation. New formulas are derived for the congestion in single-cell systems in which there are both land-to-mobile and mobile-to-mobile calls and in which mobile-to-mobile calls go via the base station. Two approaches are used, the first yields modified forms of the familiar Erlang and Engset formulas, while the second gives more complicated but more accurate formulas. The results of computer simulations to establish the accuracy of the formulas are described. New teletraffic formulas are also derived for the congestion in multi -cell systems. Fixed, dynamic and hybrid channel assignments are considered. The formulas agree with previously published simulation results. Simulation programs are described for the evaluation of the speech traffic of mobiles and for the investigation of a possible computer network for the control of the speech traffic. The programs were developed according to the structured progranming approach leading to programs of modular construction. Two simulation methods are used for the speech traffic: the roulette method and the time-true method. The first is economical but has some restriction, while the second is expensive but gives comprehensive answers. The proposed control network operates at three hierarchical levels performing various control functions which include: the setting-up and clearing-down of calls, the hand-over of calls between cells and the address-changing of mobiles travelling between cities. The results demonstrate the feasibility of the control netwvork and indicate that small mini -computers inter-connected via voice grade data channels would be capable of providing satisfactory control

CFD-modeling and experiments of insulation debris transport phenomena in water flow

The investigation of insulation debris generation, transport, and sedimentation becomes more important with regard to reactor safety research for pressurized water reactors and boiling water reactors when considering the long-term behavior of emergency core coolant systems during all types of loss-of-coolant accidents (LOCAs). The insulation debris released near the break during a LOCA incident consists of a mixture of disparate particle populations that varies with size, shape, consistency, and other properties. Some fractions of the released insulation debris can be transported into the reactor sump, where it may perturb/impinge on the emergency core cooling systems. Open questions of generic interest are, for example, the particle load on strainers and corresponding pressure drop, the sedimentation of the insulation debris in a water pool, and its possible resuspension and transport in the sump water flow. A joint research project on such questions is being performed in cooperation with the University of Applied Sciences Zittau/Görlitz. The project deals with the experimental investigation and the development of computational fluid dynamics (CFD) models for the description of particle transport phenomena in coolant flow. While the experiments are performed at the University of Applied Sciences Zittau/Görlitz, the theoretical work is concentrated at Forschungszentrum Dresden-Rossendorf. In the current paper the basic concepts for CFD modeling are described and feasibility studies including the conceptual design of the experiments are presented.

Design, modeling and construction of a novel ablative fast pyrolysis reactor and product collection system

The objective of this work was to design, construct and commission a new ablative pyrolysis reactor and a high efficiency product collection system. The reactor was to have a nominal throughput of 10 kg/11r of dry biomass and be inherently scalable up to an industrial scale application of 10 tones/hr. The whole process consists of a bladed ablative pyrolysis reactor, two high efficiency cyclones for char removal and a disk and doughnut quench column combined with a wet walled electrostatic precipitator, which is directly mounted on top, for liquids collection. In order to aid design and scale-up calculations, detailed mathematical modelling was undertaken of the reaction system enabling sizes, efficiencies and operating conditions to be determined. Specifically, a modular approach was taken due to the iterative nature of some of the design methodologies, with the output from one module being the input to the next. Separate modules were developed for the determination of the biomass ablation rate, specification of the reactor capacity, cyclone design, quench column design and electrostatic precipitator design. These models enabled a rigorous design protocol to be developed capable of specifying the required reactor and product collection system size for specified biomass throughputs, operating conditions and collection efficiencies. The reactor proved capable of generating an ablation rate of 0.63 mm/s for pine wood at a temperature of 525 'DC with a relative velocity between the heated surface and reacting biomass particle of 12.1 m/s. The reactor achieved a maximum throughput of 2.3 kg/hr, which was the maximum the biomass feeder could supply. The reactor is capable of being operated at a far higher throughput but this would require a new feeder and drive motor to be purchased. Modelling showed that the reactor is capable of achieving a reactor throughput of approximately 30 kg/hr. This is an area that should be considered for the future as the reactor is currently operating well below its theoretical maximum. Calculations show that the current product collection system could operate efficiently up to a maximum feed rate of 10 kg/Fir, provided the inert gas supply was adjusted accordingly to keep the vapour residence time in the electrostatic precipitator above one second. Operation above 10 kg/hr would require some modifications to the product collection system. Eight experimental runs were documented and considered successful, more were attempted but due to equipment failure had to be abandoned. This does not detract from the fact that the reactor and product collection system design was extremely efficient. The maximum total liquid yield was 64.9 % liquid yields on a dry wood fed basis. It is considered that the liquid yield would have been higher had there been sufficient development time to overcome certain operational difficulties and if longer operating runs had been attempted to offset product losses occurring due to the difficulties in collecting all available product from a large scale collection unit. The liquids collection system was highly efficient and modeling determined a liquid collection efficiency of above 99% on a mass basis. This was validated due to the fact that a dry ice/acetone condenser and a cotton wool filter downstream of the collection unit enabled mass measurements of the amount of condensable product exiting the product collection unit. This showed that the collection efficiency was in excess of 99% on a mass basis.

Going green: prospects for SME's to attain ISO 14001 and the challenges they face in the process

This research aimed to identify any common factors that have enabled and/or motivated SMEs to successfully implement ISO 14001 whilst the majority have not. It also identified what challenges and barriers SMEs face in doing so and how some have overcome these. The existing literature suggests that the majority of SMEs perceive their environmental impacts to be proportional to their size; have a poor understanding of environmental issues; have a poor awareness of environmental regulations; do that have the necessary expertise or leadership to address environmental issues and that SMEs with an environmental management system such as ISO 14001 are very much the minority. The main factors that influenced whether an SME had implemented ISO 14001 were: competitive advantage, regulatory compliance, supply chain pressures, leadership, expertise, resources and external support. This research used qualitative analysis of interviews with managers and directors from 8 SMEs with ISO 14001 and 4 without. All of the SMEs were based in the West Midlands or Staffordshire. Interviews were also conducted with 3 organisations offering support to businesses on environmental issues and with 1 large business who was engaging their suppliers (which included SMEs within this sample) on environmental issues. The research found that there were four main factors that enabled or motivated the SMEs to implement ISO 14001, these were: leadership, supply chain pressures, external support and SMEs' history and experience of accredited management systems. The main challenges that these business had to overcome and that prevented the other SMEs from achieving ISO 14001 were: achieving regulatory compliance, perceived financial cost, lack of perceived competitive advantage, access to relevant and affordable support and for those SMEs without ISO 14001 there was very little perceived external pressure or need for them to do so.

Scale-up of human mesenchymal stem cell culture:current technologies and future challenges

Regenerative medicine technologies have the potential to revolutionise human healthcare. However, whilst science has revealed the potential, and early products have shown the power of such therapies, there is now a need for the long-term supply of human stem cells in sufficient numbers to create reproducible and cost effective therapeutic products. The industrial platforms to be developed for human cell culture are in some ways analogous to those already developed for biopharmaceutical production using mammalian cells at large scales. However, there are a number of unique challenges that need to be addressed, largely because the quality of the cell is paramount, rather than the proteins that they express. © 2013 Elsevier Ltd.