Accelerated leap methods for simulating discrete stochastic chemical kinetics

Biologists are increasingly conscious of the critical role that noise plays in cellular functions such as genetic regulation, often in connection with fluctuations in small numbers of key regulatory molecules. This has inspired the development of models that capture this fundamentally discrete and stochastic nature of cellular biology - most notably the Gillespie stochastic simulation algorithm (SSA). The SSA simulates a temporally homogeneous, discrete-state, continuous-time Markov process, and of course the corresponding probabilities and numbers of each molecular species must all remain positive. While accurately serving this purpose, the SSA can be computationally inefficient due to very small time stepping so faster approximations such as the Poisson and Binomial τ-leap methods have been suggested. This work places these leap methods in the context of numerical methods for the solution of stochastic differential equations (SDEs) driven by Poisson noise. This allows analogues of Euler-Maruyuma, Milstein and even higher order methods to be developed through the Itô-Taylor expansions as well as similar derivative-free Runge-Kutta approaches. Numerical results demonstrate that these novel methods compare favourably with existing techniques for simulating biochemical reactions by more accurately capturing crucial properties such as the mean and variance than existing methods.

'Only in the leap from the lion's head will he prove his worth':natural law and international relations

This article argues the benefits of including a theological interpretation of natural law morality within the normative discourses of international politics. It challenges the assumption of a Grotian secular natural law arguing that practical reason, in a Thomist interpretation, is better suited to the demands of international political theory. It engages with themes of agency, practical reason, and community in order to enhance the content of the post-territorial community evidenced in ethical cosmopolitan debates. Likewise, it envisions a simultaneously enhancing a rapprochement among cosmopolitan and communitarian discourses of international politics facilitated through an institutional design guided by the morality of natural law.

Leap Aided Modelling (LAM) in Blender

L'evoluzione tecnologica e l'utilizzo crescente della computer grafica in diversi settori stanno suscitando l'interesse di sempre più persone verso il mondo della modellazione 3D. I software di modellazione, tuttavia, si presentano spesso inadeguati all'utilizzo da parte di utenti senza esperienza, soprattutto a causa dei comandi di navigazione e modellazione poco intuitivi. Dal punto di vista dell'interazione uomo-computer, questi software devono infatti affrontare un grande ostacolo: il rapporto tra dispositivi di input 2D (come il mouse) e la manipolazione di una scena 3D. Il progetto presentato in questa tesi è un addon per Blender che consente di utilizzare il dispositivo Leap Motion come ausilio alla modellazione di superfici in computer grafica. L'obiettivo di questa tesi è stato quello di progettare e realizzare un'interfaccia user-friendly tra Leap e Blender, in modo da potere utilizzare i sensori del primo per facilitare ed estendere i comandi di navigazione e modellazione del secondo. L'addon realizzato per Blender implementa il concetto di LAM (Leap Aided Modelling: modellazione assistita da Leap), consentendo quindi di estendere le feature di Blender riguardanti la selezione, lo spostamento e la modifica degli oggetti in scena, la manipolazione della vista utente e la modellazione di curve e superfici Non Uniform Rational B-Splines (NURBS). Queste estensioni sono state create per rendere più veloci e semplici le operazioni altrimenti guidate esclusivamente da mouse e tastiera.

Creative design and the generative evolutionary paradigm

Design as seen from the designer's perspective is a series of amazing imaginative jumps or creative leaps. But design as seen by the design historian is a smooth progression or evolution of ideas that they seem self-evident and inevitable after the event. But the next step is anything but obvious for the artist/creator/inventor/designer stuck at that point just before the creative leap. They know where they have come from and have a general sense of where they are going, but often do not have a precise target or goal. This is why it is misleading to talk of design as a problem-solving activity - it is better defined as a problem-finding activity. This has been very frustrating for those trying to assist the design process with computer-based, problem-solving techniques. By the time the problem has been defined, it has been solved. Indeed the solution is often the very definition of the problem. Design must be creative-or it is mere imitation. But since this crucial creative leap seem inevitable after the event, the question must arise, can we find some way of searching the space ahead? Of course there are serious problems of knowing what we are looking for and the vastness of the search space. It may be better to discard altogether the term "searching" in the context of the design process: Conceptual analogies such as search, search spaces and fitness landscapes aim to elucidate the design process. However, the vastness of the multidimensional spaces involved make these analogies misguided and they thereby actually result in further confounding the issue. The term search becomes a misnomer since it has connotations that imply that it is possible to find what you are looking for. In such vast spaces the term search must be discarded. Thus, any attempt at searching for the highest peak in the fitness landscape as an optimal solution is also meaningless. Futhermore, even the very existence of a fitness landscape is fallacious. Although alternatives in the same region of the vast space can be compared to one another, distant alternatives will stem from radically different roots and will therefore not be comparable in any straightforward manner (Janssen 2000). Nevertheless we still have this tantalizing possibility that if a creative idea seems inevitable after the event, then somehow might the process be rserved? This may be as improbable as attempting to reverse time. A more helpful analogy is from nature, where it is generally assumed that the process of evolution is not long-term goal directed or teleological. Dennett points out a common minsunderstanding of Darwinism: the idea that evolution by natural selection is a procedure for producing human beings. Evolution can have produced humankind by an algorithmic process, without its being true that evolution is an algorithm for producing us. If we were to wind the tape of life back and run this algorithm again, the likelihood of "us" being created again is infinitesimally small (Gould 1989; Dennett 1995). But nevertheless Mother Nature has proved a remarkably successful, resourceful, and imaginative inventor generating a constant flow of incredible new design ideas to fire our imagination. Hence the current interest in the potential of the evolutionary paradigm in design. These evolutionary methods are frequently based on techniques such as the application of evolutionary algorithms that are usually thought of as search algorithms. It is necessary to abandon such connections with searching and see the evolutionary algorithm as a direct analogy with the evolutionary processes of nature. The process of natural selection can generate a wealth of alternative experiements, and the better ones survive. There is no one solution, there is no optimal solution, but there is continuous experiment. Nature is profligate with her prototyping and ruthless in her elimination of less successful experiments. Most importantly, nature has all the time in the world. As designers we cannot afford prototyping and ruthless experiment, nor can we operate on the time scale of the natural design process. Instead we can use the computer to compress space and time and to perform virtual prototyping and evaluation before committing ourselves to actual prototypes. This is the hypothesis underlying the evolutionary paradigm in design (1992, 1995).

Making visible the coding process : Using qualitative data software in a post-structural study

Qualitative research methods require transparency to ensure the ‘trustworthiness’ of the data analysis. The intricate processes of organizing, coding and analyzing the data are often rendered invisible in the presentation of the research findings, which requires a ‘leap of faith’ for the reader. Computer assisted data analysis software can be used to make the research process more transparent, without sacrificing rich, interpretive analysis by the researcher. This article describes in detail how one software package was used in a poststructural study to link and code multiple forms of data to four research questions for fine-grained analysis. This description will be useful for researchers seeking to use qualitative data analysis software as an analytic tool.

Hell-vetica

Helvetica (connotes Swiss typeface) has been used the most widely from street signs to government campaign posters since 1957. Helvetica represents a great leap forward for modernity: clean, sans-serif, optimistic. However in history, there was a movement against Helvetica among American artists and designers since David Carson and Paula Scher indicted Helvetica as the cause of Vietnam war. Paradoxically, we celebrated its 50th birthday in 2007. Helvetica’s message it this: “you are going to get to your destination on time; your plan will not crash; your money is safe in our vault; we will not break the package; the paperwork has been filled in; everything is going to be OK” (Finlo Rohrer, Helvetica At 50, BBC News Magazine 9 May 2007). The artwork, Hell-vetica describes its characteristic of double agent for modernism and postmodernism in this contemporary era by combination of a stylised graphical form of a heart shape in red and a typographical manipulation - Hell-vetica.

Global Lessons from Fitzgerald : From State and National to Global Integrity Systems

Tony Fitzgerald’s visionary leap was to see beyond localised, individual wrongdoing. He suggested remedies that were systemic, institutionalised, and directed at underlying structural problems that led to corruption. His report said ‘the problems with which this Inquiry is concerned are not merely associated with individuals, but are institutionalized and related to attitudes which have become entrenched’ (Fitzgerald Report 1989, 13). His response was to suggest an enmeshed system of measures to not only respond reactively to future corruption, but also to prevent its recurrence through improved integrity systems. In the two decades since that report the primary focus of corruption studies and anti-corruption activism has remained on corruption at the local level or within sovereign states. International activism was largely directed at co-ordinating national campaigns and to use international instruments to make these campaigns more effective domestically. This reflects the broader fact that, since the rise of the nation state, states have comprised the majority of the largest institutional actors and have been the most significant institution in the lives of most individuals. This made states the ‘main game in town’ for the ‘governance disciplines’ of ethics, law, political science and economics.

Modeling intrinsic noise and delays in chemical kinetics of coupled autoregulated oscillating cells

Delays are an important feature in temporal models of genetic regulation due to slow biochemical processes, such as transcription and translation. In this paper, we show how to model intrinsic noise effects in a delayed setting by either using a delay stochastic simulation algorithm (DSSA) or, for larger and more complex systems, a generalized Binomial τ-leap method (Bτ-DSSA). As a particular application, we apply these ideas to modeling somite segmentation in zebra fish across a number of cells in which two linked oscillatory genes (her1 and her7) are synchronized via Notch signaling between the cells.

Framing local stories for community consumption facilitation and evaluation in narrative driven arts-based projects

Cyclone Yasi struck the Cassowary Coast of Queensland in the early hours of Feb 3, 2011, destroying many homes sand property, including the destruction of the Cardwell and district historical society’s premises. With their own homes flattened, many were forced to live in mobile accommodation, with extended family, or leave altogether. The historical society members however were more devastated by their flattened foreshore museum and loss of their collection material. A call for assistance was made through the OHAA Qld branch, who along with QUT sponsored a trip to somehow plan how they could start to pick up the pieces to start again. This presentation highlights the need for communities to gather, preserve and present their own stories, in a way that is sustainable and meaningful to them, but that good advice and support along the way is important. Two 2 day workshops were held in March and then September, augmented by plenty of email correspondence and phone calls in between. Participants learnt that if they could conduct quality oral history interviews, they could later use these in many exhibitable ways including: documentary pieces; digital stories; photographic collections; creative short stories; audio segments –while also drawing closely together a suffering community. This story is not only about the people who were interviewed about the night Yasi struck, but the amazing women (all over 50) of the historical society who were willing to try and leap the digital divide that faces older Australians, especially those in rural Australia, so that their older local stories would not be lost and so that new stories could also be remembered.

Orchids, intersex and the auto/biographical project

Auto/biographical documentaries ask audiences to take a ‘leap of faith’, not being able to offer any real ‘proof’ of the people and events they claim to document, other than that of the film-maker’s saying this is what happened. With only memory and history seen through the distorting lens of time, ‘the authenticity of experience functions as a receding horizon of truth in which memory and testimony are articulated as modes of salvage’. Orchids: My Intersex Adventure follows a salvaging of the film-maker’s life events and experiences, being born with an intersex condition, and, via the filming and editing process, revolving around the core question: who am I? From this transformative creative documentary practice evolves a new way of embodying experience and ‘seeing’, playfully dubbed here as the ‘intersex gaze’.

New technologies for assessing the contact lens wearing eye

New technologies for examination of the anterior eye in contact lens practice don’t appear to have taken a huge leap in the past decade however there a several novel adaptations of existing technology worthy of note. In other areas of health we have self-diagnosis via smartphone or other gadgets adapted as medical devices. In practice and research in vitro and in vivo new adaptive technologies have expanded our capabilities in assessing the anterior eye, in particular corneal and conjunctival confocal microscopy.

Expressive cryptography : lattice perspectives

The invention of asymmetric encryption back in the seventies was a conceptual leap that vastly increased the expressive power of encryption of the times. For the first time, it allowed the sender of a message to designate the intended recipient in an cryptographic way, expressed as a “public key” that was related to but distinct from the “private key” that, alone, embodied the ability to decrypt. This made large-scale encryption a practical and scalable endeavour, and more than anything else—save the internet itself—led to the advent of electronic commerce as we know and practice it today.