Toward the atomistic simulation of T cell epitopes automated construction of MHC:peptide structures for free energy calculations

Epitopes mediated by T cells lie at the heart of the adaptive immune response and form the essential nucleus of anti-tumour peptide or epitope-based vaccines. Antigenic T cell epitopes are mediated by major histocompatibility complex (MHC) molecules, which present them to T cell receptors. Calculating the affinity between a given MHC molecule and an antigenic peptide using experimental approaches is both difficult and time consuming, thus various computational methods have been developed for this purpose. A server has been developed to allow a structural approach to the problem by generating specific MHC:peptide complex structures and providing configuration files to run molecular modelling simulations upon them. A system has been produced which allows the automated construction of MHC:peptide structure files and the corresponding configuration files required to execute a molecular dynamics simulation using NAMD. The system has been made available through a web-based front end and stand-alone scripts. Previous attempts at structural prediction of MHC:peptide affinity have been limited due to the paucity of structures and the computational expense in running large scale molecular dynamics simulations. The MHCsim server (http://igrid-ext.cryst.bbk.ac.uk/MHCsim) allows the user to rapidly generate any desired MHC:peptide complex and will facilitate molecular modelling simulation of MHC complexes on an unprecedented scale.

Re-engineering construction communication in distance management framework

In an exploding and fluctuating construction market, managers are facing a challenge, which is how to manage business on a wider scale and to utilize modern developments in information technology to promote productivity. The extraordinary development of telecommunications and computer technology makes it possible for people to plan, lead, control, organize and manage projects from a distance without the need to be on site on a daily basis. A modern management known as distance management (DM) or remote management is emerging. Physical distance no longer determines the boundary of management since managers can now operate projects through virtual teams that organize manpower, material and production without face-to-face communication. What organization prototype could overcome psychological and physical barriers to reengineer a successful project through information technology? What criteria distinguishes the adapted way of communication of individual activities in a teamwork and assist the integration of an efficient and effective communication between face-to-face and a physical distance? The entire methodology has been explained through a case application on refuse incineration plant projects in Taiwan.

Project time risk analysis through simulation

An inherent weakness in the management of large scale projects is the failure to achieve the scheduled completion date. When projects are planned with the objective of time achievement, the initial planning plays a vital role in the successful achievement of project deadlines. Cost and quality are additional priorities when such projects are being executed. This article proposes a methodology for achieving time duration of a project through risk analysis with the application of a Monte Carlo simulation technique. The methodology is demonstrated using a case application of a cross-country petroleum pipeline construction project.

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

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.

Evaluation and development of drainage and pipeline construction processes

In 1974 Dr D M Bramwell published his research work at the University of Aston a part of which was the establishment of an elemental work study data base covering drainage construction. The Transport and Road Research Laboratory decided to, extend that work as part of their continuing research programme into the design and construction of buried pipelines by placing a research contract with Bryant Construction. This research may be considered under two broad categories. In the first, site studies were undertaken to validate and extend the data base. The studies showed good agreement with the existing data with the exception of the excavation trench shoring and pipelaying data which was amended to incorporate new construction plant and methods. An inter-active on-line computer system for drainage estimating was developed. This system stores the elemental data, synthesizes the standard time of each drainage operation and is used to determine the required resources and construction method of the total drainage activity. The remainder of the research was into the general topic of construction efficiency. An on-line command driven computer system was produced. This system uses a stochastic simulation technique, based on distributions of site efficiency measurements to evaluate the effects of varying performance levels. The analysis of this performance data quantities the variability inherent in construction and demonstrates how some of this variability can be reconciled by considering the characteristics of a contract. A long term trend of decreasing efficiency with contract duration was also identified. The results obtained from the simulation suite were compared to site records collected from current contracts. This showed that this approach will give comparable answers, but these are greatly affected by the site performance parameters.

Agent-based simulation of lock-in dynamics in a duopoly

Lock-in is observed in real world markets of experience goods; experience goods are goods whose characteristics are difficult to determine in advance, but ascertained upon consumption. We create an agent-based simulation of consumers choosing between two experience goods available in a virtual market. We model consumers in a grid representing the spatial network of the consumers. Utilising simple assumptions, including identical distributions of product experience and consumers having a degree of follower tendency, we explore the dynamics of the model through simulations. We conduct simulations to create a lock-in before testing several hypotheses upon how to break an existing lock-in; these include the effect of advertising and free give-away. Our experiments show that the key to successfully breaking a lock-in required the creation of regions in a consumer population. Regions arise due to the degree of local conformity between agents within the regions, which spread throughout the population when a mildly superior competitor was available. These regions may be likened to a niche in a market, which gains in popularity to transition into the mainstream.

Towards asphalt mixture morphology evaluation with the virtual specimen approach

The morphology of asphalt mixture can be defined as a set of parameters describing the geometrical characteristics of its constituent materials, their relative proportions as well as spatial arrangement in the mixture. The present study is carried out to investigate the effect of the morphology on its meso- and macro-mechanical response. An analysis approach is used for the meso-structural characterisation based on the X-ray computed tomography (CT) data. Image processing techniques are used to systematically vary the internal structure to obtain different morphology structures. A morphology framework is used to characterise the average mastic coating thickness around the main load carrying structure in the structures. The uniaxial tension simulation shows that the mixtures with the lowest coating thickness exhibit better inter-particle interaction with more continuous load distribution chains between adjacent aggregate particles, less stress concentrations and less strain localisation in the mastic phase.