Visualising and controlling the flow in biomolecular systems at and between multiple scales:from atoms to hydrodynamics at different locations in time and space

A novel framework for modelling biomolecular systems at multiple scales in space and time simultaneously is described. The atomistic molecular dynamics representation is smoothly connected with a statistical continuum hydrodynamics description. The system behaves correctly at the limits of pure molecular dynamics (hydrodynamics) and at the intermediate regimes when the atoms move partly as atomistic particles, and at the same time follow the hydrodynamic flows. The corresponding contributions are controlled by a parameter, which is defined as an arbitrary function of space and time, thus, allowing an effective separation of the atomistic 'core' and continuum 'environment'. To fill the scale gap between the atomistic and the continuum representations our special purpose computer for molecular dynamics, MDGRAPE-4, as well as GPU-based computing were used for developing the framework. These hardware developments also include interactive molecular dynamics simulations that allow intervention of the modelling through force-feedback devices.

Meta level component-based framework for distributed computing applications

Adaptability for distributed object-oriented enterprise frameworks is a critical mission for system evolution. Today, building adaptive services is a complex task due to lack of adequate framework support in the distributed computing environment. In this thesis, we propose a Meta Level Component-Based Framework (MELC) which uses distributed computing design patterns as components to develop an adaptable pattern-oriented framework for distributed computing applications. We describe our novel approach of combining a meta architecture with a pattern-oriented framework, resulting in an adaptable framework which provides a mechanism to facilitate system evolution. The critical nature of distributed technologies requires frameworks to be adaptable. Our framework employs a meta architecture. It supports dynamic adaptation of feasible design decisions in the framework design space by specifying and coordinating meta-objects that represent various aspects within the distributed environment. The meta architecture in MELC framework can provide the adaptability for system evolution. This approach resolves the problem of dynamic adaptation in the framework, which is encountered in most distributed applications. The concept of using a meta architecture to produce an adaptable pattern-oriented framework for distributed computing applications is new and has not previously been explored in research. As the framework is adaptable, the proposed architecture of the pattern-oriented framework has the abilities to dynamically adapt new design patterns to address technical system issues in the domain of distributed computing and they can be woven together to shape the framework in future. We show how MELC can be used effectively to enable dynamic component integration and to separate system functionality from business functionality. We demonstrate how MELC provides an adaptable and dynamic run time environment using our system configuration and management utility. We also highlight how MELC will impose significant adaptability in system evolution through a prototype E-Bookshop application to assemble its business functions with distributed computing components at the meta level in MELC architecture. Our performance tests show that MELC does not entail prohibitive performance tradeoffs. The work to develop the MELC framework for distributed computing applications has emerged as a promising way to meet current and future challenges in the distributed environment.

Multimodal 'Eyes-Free' interaction techniques for mobile devices

Mobile and wearable computers present input/output prob-lems due to limited screen space and interaction techniques. When mobile, users typically focus their visual attention on navigating their environment - making visually demanding interface designs hard to operate. This paper presents two multimodal interaction techniques designed to overcome these problems and allow truly mobile, 'eyes-free' device use. The first is a 3D audio radial pie menu that uses head gestures for selecting items. An evaluation of a range of different audio designs showed that egocentric sounds re-duced task completion time, perceived annoyance, and al-lowed users to walk closer to their preferred walking speed. The second is a sonically enhanced 2D gesture recognition system for use on a belt-mounted PDA. An evaluation of the system with and without audio feedback showed users' ges-tures were more accurate when dynamically guided by au-dio-feedback. These novel interaction techniques demon-strate effective alternatives to visual-centric interface de-signs on mobile devices.

Reproducible computing with Tzar and Docker

The potential for sharing environmental data and models is huge, but can be challenging for experts without specific programming expertise. We built an open-source, cross-platform framework (‘Tzar’) to run models across distributed machines. Tzar is simple to set up and use, allows dynamic parameter generation and enhances reproducibility by accessing versioned data and code. Combining Tzar with Docker helps us lower the entry barrier further by versioning and bundling all required modules and dependencies, together with the database needed to schedule work.

Meta level component-based framework for distributed computing systems

Adaptability for distributed object-oriented enterprise frameworks in multimedia technology is a critical mission for system evolution. Today, building adaptive services is a complex task due to lack of adequate framework support in the distributed computing systems. In this paper, we propose a Metalevel Component-Based Framework which uses distributed computing design patterns as components to develop an adaptable pattern-oriented framework for distributed computing applications. We describe our approach of combining a meta-architecture with a pattern-oriented framework, resulting in an adaptable framework which provides a mechanism to facilitate system evolution. This approach resolves the problem of dynamic adaptation in the framework, which is encountered in most distributed multimedia applications. The proposed architecture of the pattern-oriented framework has the abilities to dynamically adapt new design patterns to address issues in the domain of distributed computing and they can be woven together to shape the framework in future. © 2011 Springer Science+Business Media B.V.

An integrative framework for determining cross-national human resource management practices

Currently, debate in the area of cross-national human resource management (HRM) suggests that both “culture-bound” and “culture-free” factors and variables are important determinants of HRM policies and practices. HRM is presented as being context-specific and it is argued that with the growth of new markets world-wide, and increased levels of competition and globalization of business, there is a strong need for more cross-national HRM studies. However, the literature shows the absence of an integrated framework, which can help to highlight the different role that context-specific facets of HRM practices play. The nature of different determinants in different national and regional settings is rarely analyzed. This paper develops an integrated framework. It delineates the main distinctive facets associated with national factors, contingent variables, and organizational and human resource (HR) strategies and policies, that may be used to evaluate cross-national comparative HRM policies and practices.

A design environment for deadlock-free concurrent software

Using current software engineering technology, the robustness required for safety critical software is not assurable. However, different approaches are possible which can help to assure software robustness to some extent. For achieving high reliability software, methods should be adopted which avoid introducing faults (fault avoidance); then testing should be carried out to identify any faults which persist (error removal). Finally, techniques should be used which allow any undetected faults to be tolerated (fault tolerance). The verification of correctness in system design specification and performance analysis of the model, are the basic issues in concurrent systems. In this context, modeling distributed concurrent software is one of the most important activities in the software life cycle, and communication analysis is a primary consideration to achieve reliability and safety. By and large fault avoidance requires human analysis which is error prone; by reducing human involvement in the tedious aspect of modelling and analysis of the software it is hoped that fewer faults will persist into its implementation in the real-time environment. The Occam language supports concurrent programming and is a language where interprocess interaction takes place by communications. This may lead to deadlock due to communication failure. Proper systematic methods must be adopted in the design of concurrent software for distributed computing systems if the communication structure is to be free of pathologies, such as deadlock. The objective of this thesis is to provide a design environment which ensures that processes are free from deadlock. A software tool was designed and used to facilitate the production of fault-tolerant software for distributed concurrent systems. Where Occam is used as a design language then state space methods, such as Petri-nets, can be used in analysis and simulation to determine the dynamic behaviour of the software, and to identify structures which may be prone to deadlock so that they may be eliminated from the design before the program is ever run. This design software tool consists of two parts. One takes an input program and translates it into a mathematical model (Petri-net), which is used for modeling and analysis of the concurrent software. The second part is the Petri-net simulator that takes the translated program as its input and starts simulation to generate the reachability tree. The tree identifies `deadlock potential' which the user can explore further. Finally, the software tool has been applied to a number of Occam programs. Two examples were taken to show how the tool works in the early design phase for fault prevention before the program is ever run.

Reconfigurable service-oriented architecture for autonomic computing

Almost a decade has passed since the objectives and benefits of autonomic computing were stated, yet even the latest system designs and deployments exhibit only limited and isolated elements of autonomic functionality. In previous work, we identified several of the key challenges behind this delay in the adoption of autonomic solutions, and proposed a generic framework for the development of autonomic computing systems that overcomes these challenges. In this article, we describe how existing technologies and standards can be used to realise our autonomic computing framework, and present its implementation as a service-oriented architecture. We show how this implementation employs a combination of automated code generation, model-based and object-oriented development techniques to ensure that the framework can be used to add autonomic capabilities to systems whose characteristics are unknown until runtime. We then use our framework to develop two autonomic solutions for the allocation of server capacity to services of different priorities and variable workloads, thus illustrating its application in the context of a typical data-centre resource management problem.

General-purpose autonomic computing

The success of mainstream computing is largely due to the widespread availability of general-purpose architectures and of generic approaches that can be used to solve real-world problems cost-effectively and across a broad range of application domains. In this chapter, we propose that a similar generic framework is used to make the development of autonomic solutions cost effective, and to establish autonomic computing as a major approach to managing the complexity of today’s large-scale systems and systems of systems. To demonstrate the feasibility of general-purpose autonomic computing, we introduce a generic autonomic computing framework comprising a policy-based autonomic architecture and a novel four-step method for the effective development of self-managing systems. A prototype implementation of the reconfigurable policy engine at the core of our architecture is then used to develop autonomic solutions for case studies from several application domains. Looking into the future, we describe a methodology for the engineering of self-managing systems that extends and generalises our autonomic computing framework further.

Resource-definition policies for autonomic computing

The paper introduces a framework for the formal specification of autonomic computing policies, and uses it to define a new type of autonomic computing policy termed a resource-definition policy. We describe the semantics of resource-definition policies, explain how they can be used as a basis for the development of autonomic system of systems, and present a sample data-centre application built using the new policy type.

A shape-based decomposition of the yield adjustment term in the arbitrage-free Nelson and Siegel (AFNS) model of the yield curve

The appealing feature of the arbitrage-free Nelson-Siegel model of the yield curve is the ability to capture movements in the yield curve through readily interpretable shifts in its level, slope or curvature, all within a dynamic arbitrage-free framework. To ensure that the level, slope and curvature factors evolve so as not to admit arbitrage, the model introduces a yield-adjustment term. This paper shows how the yield-adjustment term can also be decomposed into the familiar level, slope and curvature elements plus some additional readily interpretable shape adjustments. This means that, even in an arbitrage-free setting, it continues to be possible to interpret movements in the yield curve in terms of level, slope and curvature influences. © 2014 © 2014 Taylor & Francis.

CLAE to move to online format

Editorial: The 2015 BCLA annual conference was another fantastic affair. It was the first time the conference was held in the beautiful city of Liverpool. The venue was great and the programme was excellent. The venue overlooked the River Mersey and many of the hotels were local boutique hotels. I stayed in one which was formerly the offices of White Star Liners—where the RMS Titanic was originally registered. The hotel decor was consistent with its historic significance. The BCLA gala dinner was held in the hugely impressive Anglican Cathedral with entertainment from a Beatles tribute band. That will certainly be a hard act to follow at the next conference in 2017. Brian Tompkins took the reigns as the new BCLA president. Professor Fiona Stapleton was the recipient of the BCLA Gold Medal Award. The winner of the poster competition was Dorota Szczesna-Iskander with a poster entitled ‘Dry Contact lens poor wettability and visual performance’. Second place was Renee Reeder with her poster entitled ‘Abnormal Rosacea as a differential diagnosis in corneal scarring’. And third place was Maria Jesus Gonzalez-Garcia with her poster entitled ‘Dry Effect of the Environmental Conditions on Tear Inflammatory Mediators Concentration in Contact Lens Wearers’. The photographic competition winner was Professor Wolfgang Sickenberger from Jena in Germany. The Editorial Panel of CLAE met at the BCLA conference for their first biannual meeting. The journal metrics were discussed. In terms of number of submissions of new papers CLAE seems to have plateaued after seeing a rapid growth in the number of submissions over the last few years. The increase over the last few years could be attributed to the fact that CLAE was awarded an impact factor for the first time in 2012. This year it seems that impact factors across nearly all ophthalmic related journals has dropped. This could in part be due to the fact that last year was a ‘Research Exercise Framework (REF) year for UK universities, where they are judged on quality of their research output. The next REF is in 2020 so we may see changes nearing that time. Looking at article downloads, there seems to be a continued rise in figures. Currently CLAE attracts around 85,000 downloads per year (this is an increase of around 10,000 per year for the last few years) and the 2015 prediction is 120,000! With this in mind and with other contributing factors too, the BCLA has decided to move to online delivery of CLAE to its members starting from issue 5 of 2015. Some members do like to flick through the pages of a hard copy of the journal so members will still have the option of receiving a hard copy through the post but the default journal delivery method will now be online. The BCLA office will send various alerts and content details to members email addresses. To access CLAE online you will need to log in via the BCLA web page, currently you then click on ‘Resources’ and then under ‘Free and Discounted Publications’ you will see CLAE. This actually takes you to CLAE’s own webpage (www.contactlensjournal.com) but you need to log in via the BCLA web page. The BCLA plans to change these weblinks so that from the BCLA web page you can link to the journal website much more easily and you have the choice of going directly into the general website for CLAE or straight to the current issue. In 2016 you will see an even easier way of accessing CLAE online as the BCLA will launch a CLAE application for mobile devices where the journal can be downloaded as a ‘flick-book’. This is a great way of bringing CLAE into the modern era where people access their information in newer ways. For many the BCLA conference was part of a very busy conference week as it was preceded by the International Association of Contact Lens Educators’ (IACLE) Third World Congress, held in Manchester on the 4 days before the BCLA conference. The first and second IACE World Congresses were held in Waterloo, Canada in 1994 and 2000 respectively and hosted by Professor Des Fonn. Professor Fonn was the recipient of the first ever IACLE lifetime achievement award. The Third IACLE World Congress saw more than 100 contact lens educators and industry representatives from around 30 countries gather in the UK for the four-day event, hosted by The University of Manchester. Delegates gained hands-on experience of innovations in teaching, such as learning delivery systems, the use of iPads in the classroom and for creating ePub content, and augmented and virtual reality technologies. IACLE members around the world also took part via a live online broadcast. The Third IACLE World Congress was made possible by the generous support of Sponsors Alcon, CooperVision and Johnson & Johnson Vision Care., for more information look at the IACLE web page (www.iacle.org).

Architectural aspects of self-aware and self-expressive computing systems:from psychology to engineering

Work on human self-Awareness is the basis for a framework to develop computational systems that can adaptively manage complex dynamic tradeoffs at runtime. An architectural case study in cloud computing illustrates the framework's potential benefits.

Smoke rings:towards a comprehensive tobacco free policy for the Olympic Games

Background The tobacco industry has long sought affiliation with major sporting events, including the Olympic Games, for marketing, advertising and promotion purposes. Since 1988, each Olympic Games has adopted a tobacco-free policy. Limited study of the effectiveness of the smoke-free policy has been undertaken to date, with none examining the tobacco industry's involvement with the Olympics or use of the Olympic brand. Methods and Findings A comparison of the contents of Olympic tobacco-free policies from 1988 to 2014 was carried out by searching the websites of the IOC and host NOCs. The specific tobacco control measures adopted for each Games were compiled and compared with measures recommended by the WHO Tobacco Free Sports Initiative and Article 13 of the Framework Convention on Tobacco Control (FCTC). This was supported by semi-structured interviews of key informants involved with the adoption of tobacco-free policies for selected games. To understand the industry's interests in the Olympics, the Legacy Tobacco Documents Library (http://legacy.library.ucsf.edu) was systematically searched between June 2013 and August 2014. Company websites, secondary sources and media reports were also searched to triangulate the above data sources. This paper finds that, while most direct associations between tobacco and the Olympics have been prohibited since 1988, a variety of indirect associations undermine the Olympic tobacco-free policy. This is due to variation in the scope of tobacco-free policies, limited jurisdiction and continued efforts by the industry to be associated with Olympic ideals. Conclusions The paper concludes that, compatible with the IOC's commitment to promoting healthy lifestyles, a comprehensive tobacco-free policy with standardized and binding measures should be adopted by the International Olympic Committee and all national Olympic committees.

The framework of the virtual laser tracker - A systematic approach to the assessment of error sources and uncertainty in laser tracker measurement

Laser trackers have been widely used in many industries to meet increasingly high accuracy requirements. In laser tracker measurement, it is complex and difficult to perform an accurate error analysis and uncertainty evaluation. This paper firstly reviews the working principle of single beam laser trackers and state-of- The- Art of key technologies from both industrial and academic efforts, followed by a comprehensive analysis of uncertainty sources. A generic laser tracker modelling method is formulated and the framework of the virtual tracker is proposed. The VLS can be used for measurement planning, measurement accuracy optimization and uncertainty evaluation. The completed virtual laser tracking system should take all the uncertainty sources affecting coordinate measurement into consideration and establish an uncertainty model which will behave in an identical way to the real system. © Springer-Verlag Berlin Heidelberg 2010.