Modelling tools and methodologies for rapid protocell prototyping

The field of unconventional computing considers the possibility of implementing computational devices using novel paradigms and materials to produce computers which may be more efficient, adaptable and robust than their silicon based counterparts. The integration of computation into the realms of chemistry and biology will allow the embedding of engineered logic into living systems and could produce truly ubiquitous computing devices. Recently, advances in synthetic biology have resulted in the modification of microorganism genomes to create computational behaviour in living cells, so called “cellular computing”. The cellular computing paradigm offers the possibility of intelligent bacterial agents which may respond and communicate with one another according to chemical signals received from the environment. However, the high levels of complexity when altering an organism which has been well adapted to certain environments over millions of years of evolution suggests an alternative approach in which chemical computational devices can be constructed completely from the bottom up, allowing the designer exquisite control and knowledge about the system being created. This thesis presents the development of a simulation and modelling framework to aid the study and design of bottom-up chemical computers, involving the encapsulation of computational re-actions within vesicles. The new “vesicle computing” paradigm is investigated using a sophisticated multi-scale simulation framework, developed from mesoscale, macroscale and executable biology techniques

Meta-stochastic simulation for systems and synthetic biology using classification

PhD ThesisTo comprehend the immense complexity that drives biological systems, it is necessary to generate hypotheses of system behaviour. This is because one can observe the results of a biological process and have knowledge of the molecular/genetic components, but not directly witness biochemical interaction mechanisms. Hypotheses can be tested in silico which is considerably cheaper and faster than “wet” lab trialand- error experimentation. Bio-systems are traditionally modelled using ordinary differential equations (ODEs). ODEs are generally suitable for the approximation of a (test tube sized) in vitro system trajectory, but cannot account for inherent system noise or discrete event behaviour. Most in vivo biochemical interactions occur within small spatially compartmentalised units commonly known as cells, which are prone to stochastic noise due to relatively low intracellular molecular populations. Stochastic simulation algorithms (SSAs) provide an exact mechanistic account of the temporal evolution of a bio-system, and can account for noise and discrete cellular transcription and signalling behaviour. Whilst this reaction-by-reaction account of system trajectory elucidates biological mechanisms more comprehensively than ODE execution, it comes at increased computational expense. Scaling to the demands of modern biology requires ever larger and more detailed models to be executed. Scientists evaluating and engineering tissue-scale and bacterial colony sized biosystems can be limited by the tractability of their computational hypothesis testing techniques. This thesis evaluates a hypothesised relationship between SSA computational performance and biochemical model characteristics. This relationship leads to the possibility of predicting the fastest SSA for an arbitrary model - a method that can provide computational headroom for more complex models to be executed. The research output of this thesis is realised as a software package for meta-stochastic simulation called ssapredict. Ssapredict uses statistical classification to predict SSA performance, and also provides high performance stochastic simulation implementations to the wider community.Newcastle University & University of Nottingham Computing Science department

Never Too Old To Learn: On-line Evolution of Controllers in Swarm- and Modular Robotics

Eiben, A.E. [Promotor

Compendium of Directors Colloquia 1999-2012

The Director s colloquium series was established primarily to provide a mechanism to bring high profile individuals to the Center to present new and innovative ideas to the entire Ames staff. More focused lecture series are arranged by specific divisions or departments. Before the year 1999, there is only a fragmentary record of who spoke in this series. Announcements to the staff were sent via land mail, and tickets were required to attend the colloquium. In 1999, the notification to attend colloquia became electronic and the entire resident staff was invited to attend. The centerwide announcement archive established in this timeframe created a lasting record of the Director s colloquia. The "Office of the Chief Scientist" at Ames had the responsibility for administering the colloquium series. When I became Chief Scientist on June 29, 1998, the program was not being used extensively and this continued to be the case through the years 1999-2002 of Harry McDonald s tenure as Director (see graph below). During Scott Hubbard s tenure as Director (September 19, 2002- February 15, 2006), the Director's colloquium series was used exclusively for high profile speakers from outside Ames whom he selected, such as lab directors from other research organizations around the Bay Area. During Pete Worden s tenure as Ames Director (May 4, 2006 -present) the colloquium series gained far greater use. First, I had greater discretion to select speakers for the colloquium series. Secondly, beginning in 2007, we established a 10-week Director's Colloquium Summer Series focused on enriching the experience of our many summer interns, and giving our top researchers within Ames Research Center an opportunity to present their work to the Center. The summer program has received rave reviews. This compendium contains a compilation of one-page descriptions (title, abstract and speaker biographies) for all of the 171 colloquia presented from the beginning of 1999 to October of 2012. The list of speakers includes four Nobel Laureates, six astronauts, three current or former Ames Center Directors, as well as many CEOs and other lab directors. Other featured speakers include famous mountain climbers, historians, movie stars, and former FBI agents and directors. Finally, the list includes world-class scientists and engineers representing a wide range of disciplines. It has been my privilege to host almost all of the colloquia presented in this compendium

Enhancing Free-text Interactions in a Communication Skills Learning Environment

Learning environments frequently use gamification to enhance user interactions.Virtual characters with whom players engage in simulated conversations often employ prescripted dialogues; however, free user inputs enable deeper immersion and higher-order cognition. In our learning environment, experts developed a scripted scenario as a sequence of potential actions, and we explore possibilities for enhancing interactions by enabling users to type free inputs that are matched to the pre-scripted statements using Natural Language Processing techniques. In this paper, we introduce a clustering mechanism that provides recommendations for fine-tuning the pre-scripted answers in order to better match user inputs

Design, Mathematical Modelling, Construction and Testing of Synthetic Gene Network Oscillators to Establish Roseobacter Clade Bacteria and the Protozoan Trypanosoma brucei as Synthetic Biology Chassis.

The aim of this project is to establish Roseobacter marine bacteria and Trypanosoma brucei (T. brucei) protozoa as synthetic biology chassis. This work addresses the gap within synthetic biology resulting from the limited choice of host cells available for use in practice. This was done by developing synthetic bacterial and trypanosomal genetic regulatory networks (GRNs) which function as an oscillator as well as by developing the necessary protocols and set-ups to allow for the analysis of GRN dynamics within the host. Roseobacter clade bacteria are naturally found in diverse oceanic habitats and have an important ecological role in balancing global carbon levels. This makes Roseobacter an ideal chassis for future efforts to apply synthetic biology to bioremediation and geo-engineering challenges. The aim of this investigation was to establish straight-forward molecular biology procedures in Roseobacter bacteria followed by characterisation and modelling of an E. coli oscillator in Roseobacter. Results showed that Roseobacter synthetic biology is non-trivial. Protozoa are exploited as host cells for industrial production of biotherapeutics due to fast doubling times and host proteins’ mammalian-like post-translational glycosylation. As an established model organism for studying protozoa, T. brucei provided a test case for establishing synthetic biology in this phylum for the first time. T. brucei is highly divergent from eukaryotes commonly used in synthetic biology and possesses a sophisticated genomic machinery to evade host immune systems. The establishment of standard synthetic biology approaches in mathematical modelling and gene network design in T. brucei will underpin application of synthetic biology to enhance the industrial capability of the protozoa as a chassis and to probe its pathobiology. This investigation involved design and assembly of a Goodwin oscillator, followed by characterisation and modelling of the network and the development of a novel experimental set-up for live-cell imaging of single motile trypanosomes. Results showed that T. brucei is a promising novel synthetic biology chassi

CIMODE 2016: 3º Congresso Internacional de Moda e Design: proceedings

O CIMODE 2016 é o terceiro Congresso Internacional de Moda e Design, a decorrer de 9 a 12 de maio de 2016 na cidade de Buenos Aires, subordinado ao tema : EM--‐TRAMAS. A presente edição é organizada pela Faculdade de Arquitetura, Desenho e Urbanismo da Universidade de Buenos Aires, em conjunto com o Departamento de Engenharia Têxtil da Universidade do Minho e com a ABEPEM – Associação Brasileira de Estudos e Pesquisa em Moda.info:eu-repo/semantics/publishedVersio