The realisation of JSD specifications in object oriented languages

Jackson System Development (JSD) is an operational software development method which addresses most of the software lifecycle either directly or by providing a framework into which more specialised techniques can fit. The method has two major phases: first an abstract specification is derived that is in principle executable; second the specification is implemented using a variety of transformations. The object oriented paradigm is based on data abstraction and encapsulation coupled to an inheritance architecture that is able to support software reuse. Its claims of improved programmer productivity and easier program maintenance make it an important technology to be considered for building complex software systems. The mapping of JSD specifications into procedural languages typified by Cobol, Ada, etc., involves techniques such as inversion and state vector separation to produce executable systems of acceptable performance. However, at present, no strategy exists to map JSD specifications into object oriented languages. The aim of this research is to investigate the relationship between JSD and the object oriented paradigm, and to identify and implement transformations capable of mapping JSD specifications into an object oriented language typified by Smalltalk-80. The direction which the transformational strategy follows is one whereby the concurrency of a specification is removed. Two approaches implementing inversion - an architectural transformation resulting in a simulated coroutine mechanism being generated - are described in detail. The first approach directly realises inversions by manipulating Smalltalk-80 system contexts. This is possible in Smalltalk-80 because contexts are first class objects and are accessible to the user like any other system object. However, problems associated with this approach are expounded. The second approach realises coroutine-like behaviour in a structure called a `followmap'. A followmap is the results of a transformation on a JSD process in which a collection of followsets is generated. Each followset represents all possible state transitions a process can undergo from the current state of the process. Followsets, together with exploitation of the class/instance mechanism for implementing state vector separation, form the basis for mapping JSD specifications into Smalltalk-80. A tool, which is also built in Smalltalk-80, supports these derived transformations and enables a user to generate Smalltalk-80 prototypes of JSD specifications.

Steps and bumps:precision extraction of discrete states of molecular machines

We report statistical time-series analysis tools providing improvements in the rapid, precision extraction of discrete state dynamics from time traces of experimental observations of molecular machines. By building physical knowledge and statistical innovations into analysis tools, we provide techniques for estimating discrete state transitions buried in highly correlated molecular noise. We demonstrate the effectiveness of our approach on simulated and real examples of steplike rotation of the bacterial flagellar motor and the F1-ATPase enzyme. We show that our method can clearly identify molecular steps, periodicities and cascaded processes that are too weak for existing algorithms to detect, and can do so much faster than existing algorithms. Our techniques represent a step in the direction toward automated analysis of high-sample-rate, molecular-machine dynamics. Modular, open-source software that implements these techniques is provided.

Canadian province-building : the state as educator and entrepreneur in Alberta

This study provides an account and analysis of the development of systems of educational provision In capitalist democracies, especially in connection with the social origin and relative autonony of those systems. Using the case study of Athabasca University, a Canadian distance-education institution in the province of Alberta, the study is a critical work of historical sociology, in which the shifting social role of a system of educational provision during two transitions of a regional political economy is analyzed. Comparative observations are made in reference to other systems of educational provision and organizations, in particular the training department of a large Company based In the same region as the Unversity. The study explores the social origin and relative autonomy of systems of educational provision In relation to educational ideologies, which are themselves associated with social ideologies. Pierre Bourdieu's theoretical construction of "fields of power'' allows for a consideration of power as a relational phenomenon in the study. In other words, power is understood as being exercised in a way that simultaneously takes account of the power of other actors and groups. Fields of power also allow for an analysis of power as it is exercised at various levels of organizations and within society. The study is organized in two phases. First, an account is developed of the historical period in which the Unlversity and the Company were created, but especially the period of establishment for the Unlversity, 1970 - 75. Conclusions are offered concerning the causal associations between the historical antecedents that gave rise to the two organlzations. It is argued that both the University and the Company were established In part to enact the AIberta government's efforts to enhance Its powers within the Canadian federation (a process called province-building), The second phase is concerned with a more recent period of three years, 1993 - 95. By this time, province-building was not as significant a concern for policy-makers, and the organizational responses of the University and the Company reflected this shift. A divergence of practice is observed at the University and the Company, with actors at the Company encouraging the development of collectivist values for employees, while at the University no such overt strategy was followed, The study concludes that a consumerist model of education developed by the University in 1970 - 75 and expanded In 1993 - 95 contributed significantly to the institution's social origin and relative autonomy. The model was used as an Ideology in the earlier period and as a strategy In the later one, serving to forestall the institution's closure during both periods of crisis, though Ieading to ambiguous social outcomes. A consumerist model may on the one hand be progressive in that expanded access to educational opportunities is made possible. On the other hand, the consumerist model will tend increasingly to provide educational services to those social segments that already have access to educational opportunities.

Nation, region and history in post-communist transitions:identity politics in Ukraine, 1991-2006

Since independence in 1991, issues of nation and identity have become highly debated topics in Ukraine. This monograph explores not only how national identity is being (re)constructed by the Ukrainian state, but also the processes by which it is negotiated through society. The central argument of this work is that too much attention, concerning identity in Ukraine, has focused on markers of ethnicity and language. Instead, the author advocates a regional approach, engaging with the issue of how Ukraine's regional differences affect nation-building processes. Following the tumultuous events of the 'Orange Revolution', the view of Ukraine as a country inherently 'divided' between 'East' and 'West' has (re)emerged to become a popular explanation for political events. The study outlines the necessity for academics, policymakers and indeed politicians to veer away from this simplistic 'West versus East' divide. The book advocates an analysis of Ukraine's unique brand of regionalism not in terms of divisions, but in terms of regional differences and diversity. The author deconstructs the concept of 'Eastern Ukraine' by focusing on three Ukrainian localities, all adjacent to the Ukrainian-Russian border. The study examines how individuals provide 'their' own understanding of the place of their region within the wider processes of nation building across Ukraine. In doing so, the book develops a 'regional' approach to the study of identity politics in Ukraine.

Controlling protein molecular dynamics:how to accelerate folding while preserving the native state

The dynamics of peptides and proteins generated by classical molecular dynamics (MD) is described by using a Markov model. The model is built by clustering the trajectory into conformational states and estimating transition probabilities between the states. Assuming that it is possible to influence the dynamics of the system by varying simulation parameters, we show how to use the Markov model to determine the parameter values that preserve the folded state of the protein and at the same time, reduce the folding time in the simulation. We investigate this by applying the method to two systems. The first system is an imaginary peptide described by given transition probabilities with a total folding time of 1 micros. We find that only small changes in the transition probabilities are needed to accelerate (or decelerate) the folding. This implies that folding times for slowly folding peptides and proteins calculated using MD cannot be meaningfully compared to experimental results. The second system is a four residue peptide valine-proline-alanine-leucine in water. We control the dynamics of the transitions by varying the temperature and the atom masses. The simulation results show that it is possible to find the combinations of parameter values that accelerate the dynamics and at the same time preserve the native state of the peptide. A method for accelerating larger systems without performing simulations for the whole folding process is outlined.

Non-Markov state model of peptide dynamics

A hidden Markov state model has been applied to classical molecular dynamics simulated small peptide in explicit water. The methodology allows increasing the time resolution of the model and describe the dynamics with the precision of 0.3 ps (comparing to 6 ps for the standard methodology). It also permits the investigation of the mechanisms of transitions between the conformational states of the peptide. The detailed description of one of such transitions for the studied molecule is presented. © 2012 Elsevier B.V. All rights reserved.

Optimised phase disposition pulse-width modulation strategy for hybrid-clamped multilevel inverters using switching state sequences

This study describes an optimised modulation strategy based on switching state sequences for the hybrid-clamped multilevel converter. Two key control variables defined as 'phase shift angle' and 'switching state change' for a five-level hybrid-clamped inverter are proposed to improve all switches' operation, and by changing their values, different control methods can be obtained for modulation optimisation purposes. Two example methods can solve the voltage imbalance problem of the dc-link capacitors and furthermore avoid two switches' simultaneous switching transitions and improve the inverter's performance as compared with the traditional phase disposition pulse-width modulation strategy. A 6 kW prototype inverter is developed and a range of simulation and experiments are carried out for validation. It is found that simulation and experimental results are in a good agreement and the proposed modulation strategy is verified in terms of low-order harmonic reduction.