Biomimicry of quorum sensing using bacterial lifecycle model

Special issue: Proceedings of the 2012 International Conference on Intelligent Computing (ICIC 2012)Version of RecordPublishe

Nature-inspired sustainable medical materials

As life expectancy increases and health crises arise, our demand for medical materials is higher than ever. There has been, nevertheless, a concomitant increase in the reliance on traditional fabrication and disposal methods, which are environmentally harmful and energy intensive. Therefore, technologies need adaptations to ensure a more sustainable future for medicine. Such technological improvements could be designed by taking inspiration from nature, where the concept of “waste” is virtually non-existent. These nature-inspired solutions can be engineered into the lifecycle of medical materials at different points, from raw materials and fabrication to application and recycling. To achieve this, we present four technological developments as promising enablers – surface patterning, additive manufacturing, microfluidics, and synthetic biology. For each enabler, we discuss how sustainable solutions can be designed based on current understanding of, and ongoing research on, natural systems or concepts, including shark skin, decentralised manufacturing, process intensification, and synthetic biology

Application of bio-model engineering to model abstract biological behaviours

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University LondonLife in nature is defined by many characteristics. Whether something can move, communicate, response to the others, reproduce or die, indicate if it is alive or not. Among these features, communication can be considered the most basic and yet the most important as it happens both inside and outside an organism; between every molecule and every cell there are signals to be passed and to be responded to. Communication defines biology. A network of molecules or a society of organisms are both complex systems. The smallest change in this snarled network affects the whole system and changes the output significantly. Comprehending and manipulating them in detail is time and resources consuming and involves human error. But there is a way to simplify the process of inspecting the living creatures. Bio-model engineering lies at the crossroads of biology, mathematics, computer science, engineering and is a branch of systems biology. In this field of science, biological models are created and/or re-designed for simplification, abstraction and description of biological networks. Modelling these networks based on past experimental observations in silico with a set of pre-designed models and a collection of components would make this process faster and simpler. This thesis contributes to science by providing a collection of model components built in Petri nets with Snoopy. These components each describe a specific behaviour and they can be used individually or as a combination. The set of behaviours in this collection include chemotaxis, reproduction, death, communication and response. These are a few of the most basic behaviours in nature that mark something as alive. These basic behaviours choose that a piece of stone is not alive but the small microscopic bacteria on it are. Starting with small achievable steps, these components are modelled in abstract, meaning they demonstrate only the critical parts of the behaviours. Not only the models, but also the process of modelling and combining the components is provided from the adaptation and manipulation of a general protocol. The components in this library are categorised based on their complexity. In this categorisation, the models have four levels, with each level more complex than the former. The more complex levels, are built from the simpler ones in a hierarchical manner. There are two application of the models to two different microorganisms, each from one of the main biological superkingdoms to demonstrate the practicality of this collection. The chosen microorganisms are from: the domain of Prokaryotes E. coli and Eukaryotes Dictyostelium a.k.a slime mould. Each model contains a set of rate constants that define the speed of the reactions. A set of expected behaviours based on biological literature is defined for these models to be compared with the outcome result of the analysis of the models. The models are simulated by Spike, a command line programme for simulation of models built in Snoopy, and are analysed with R and Python. To achieve the expected results, optimisation methods are used to find the best rates possible in the models in order to achieve a defined behaviour. In this thesis the optimisation is applied to Dictyostelium model to achieve the best rates for the accumulation of Dictyostelium cells in one location to create fruiting bodies. Random Restart Hill Climbing and Simulated Annealing are the chosen methods for optimisation

A review of simulation and modeling approaches in microbiology

Bacterial communities are tightly interconnected systems consisting of numerous species making it challenging to analyze their structure and relations. There are several experimental techniques providing heterogeneous data concerning various aspects of this object. A recent avalanche of metagenomic data challenges not only biostatisticians but also biomodelers, since these data are essential to improve the modeling quality while simulation methods are useful to understand the evolution of microbial communities and their function in the ecosystem. An outlook on the existing modeling and simulation approaches based on different types of experimental data in the field of microbial ecology and environmental microbiology is presented. A number of approaches focusing on a description of such microbial community aspects as its trophic structure, metabolic and population dynamics, genetic diversity as well as spatial heterogeneity and expansion dynamics is considered. We also propose a classification of the existing software designed for simulation of microbial communities. It is shown that although the trend for using multiscale/hybrid models prevails, the integration between models concerning different levels of biological organization of communities still remains a problem to be solved. The multiaspect nature of integration approaches used to model microbial communities is based on the need to take into account heterogeneous data obtained from various sources by applying high-throughput genome investigation methods

Design with the living : learning to work together

Orientador: Prof. Dr. Adriano HeemannCoorientador: Prof. Dr. Aguinaldo dos SantosTese (doutorado) - Universidade Federal do Paraná, Setor de Artes, Comunicação e Design, Programa de Pós-Graduação em Design. Defesa : Curitiba, 26/05/2023Inclui referênciasResumo: A prática do biodesign parece estar se consolidando por meio de redes, concursos, exposições, e educação formal. Este estudo se baseia na definição de biodesign de Dade-Robertson, que compreende o design e a pesquisa em design que trabalhem com sistemas vivos como parte da sua produção e funcionamento. Assim, ainda numa perspectiva antropocêntrica de pesquisa, surgem novas possibilidades com as capacidades e características de várias espécies e as novas formas de construir e fazer. No entanto, vários desafios práticos e teóricos ainda limitam a difusão do biodesign. Uma lacuna parece ser a estruturação de um artefato de facilitação para o ensino e aprendizagem do processo de biodesign. A fim de contribuir para a mitigação desta lacuna, o presente trabalho procurou desenvolver e avaliar um framework para facilitar o ensino e a aprendizagem do processo de biodesign no ensino de graduação, considerando um contexto com poucos recursos, como a falta de um espaço para experimentação e um laboratório. A estratégia metodológica utilizada é a Design Science Research (DSR) conforme Dresch, Lacerda, e Antunes Jr. (2015). Esta estratégia foi adaptada às etapas: 1. Problema e Contexto; 2. Artefatos Relacionados; 3. Desenvolvimento; 4. Avaliação; e 5. Conclusão. O framework baseou-se na revisão da literatura, que inspirou 59 insights, que embasaram 17 requisitos que, por sua vez, foram estruturados em 21 objetivos de aprendizagem em acordo com a taxonomia de Bloom. O framework considera dois espaços de contexto: a sala de aula e as casas do(a)s estudantes. Ele é composto por 6 elementos principais: 1. Conceitos, 2. Repertório, 3. Metodologia de Projeto; 4. Prática; 5. Reflexões; e 6. Gestão. Exemplos das materialidades e atividades do framework são um diário de projetos e tinkering. Para além do framework, foram desenvolvidos artefatos de apoio: quatro modelos didáticos do processo de biodesign baseados em entrevistas semi-estruturadas com designers experientes - design em colaboração com (1) cogumelos, com (2) árvores, com (3) gramíneas, e com (4) bactérias. Os modelos basearam-se numa adaptação do Método Mosaico de Kim e Lee (2015), da Estrutura de Duplo Diamante do Design Council, e do Processo de Desenvolvimento de Produtos de Rozenfeld et al. (2006). A instanciação ocorreu na disciplina obrigatória Materiais e Processos III do curso de graduação de Design de Produto da Universidade Federal do Paraná. O framework foi avaliado por meio de observação aberta e da rubrica de avaliação do framework pela professora da disciplina e pelo(a)s estudantes. A triangulação e a correspondência de padrões com os objetivos de aprendizagem sugerem que 14 deles foram cumpridos, enquanto os outros 7 foram parcialmente atendidos. Ao longo do processo, o(a)s estudantes parecem ter desenvolvido novas sensibilidades em design, relacionadas com a empatia e as negociações com o outro organismo vivo com o qual trabalharam. Foi feita uma imersão no cluster de excelência "Matters of Activity. Image, Space, Material" para a discussão dos resultados. O framework deve ser testado em outros contextos. Como trabalho futuro, poderá ser desenvolvida uma versão modular para abrir as heurísticas de contingência a contextos mais amplos e diferentes tempos de aplicação.Abstract: The biodesign practice seems to consolidate through organized networks, contests, exhibitions, and formal education. This study relies on Dade-Robertson's definition of biodesign, which comprises the design and design research that work with living systems as part of their production and operation. Thus, still on an anthropocentric research perspective, new possibilities arise with the abilities and characteristics of various species and new ways of building and making. However, several practical and theoretical challenges still set back the diffusion of biodesign. One gap seems to be the structuring of a facilitation artifact for teaching and learning the biodesign process. In order to contribute to mitigate this gap, the present work aimed to develop and evaluate a framework to facilitate the teaching and learning of the biodesign process in undergraduate education, considering a context with few resources, like the lack of proper space for experimentation and a lab. The methodological strategy used is Design Science Research (DSR) following Dresch, Lacerda, and Antunes Jr. (2015). It was adapted into the steps: 1. Problem and Context; 2. Related Artifacts; 3. Development; 4. Evaluation; and 5. Conclusion. The framework drew on the literature review, which inspired 59 insights. The insights grounded 17 framework requirements, which in turn, rendered 21 learning objectives developed according to Bloom's taxonomy. The framework considers two context-spaces: the classroom and the student's homes. It consists of 6 main elements: 1. Concepts, 2. Repertoire, 3. Project Methodology; 4. Practice; 5. Reflections; and 6. Management. Examples of materialities and activities in the framework are a project journal and tinkering. Besides the framework, other support artifacts were developed in the research process: four didactic models of the biodesign process based on semi-structured interviews with experienced designers - design in collaboration with (1) mushrooms, (2) trees, (3) grass, and (4) bacteria. The models drew on an adaptation of Kim and Lee's (2015) Mosaic Method, the Design Council's Double Diamond Framework, and the Product Development Process from Rozenfeld et al. (2006). The instantiation occurred in the mandatory course Materials and Processes III of the Product Design undergraduate program of the Federal University of Paraná. The framework was evaluated through overt observation and through the framework's evaluation rubric by the course professor and by the students. Triangulation and pattern-matching to the learning objectives suggested that 14 learning objectives were met, while the other 7 were partially met. Throughout the process, students seem to have developed "new designerly sensibilities", related to empathy and negotiations with the other organism they worked with. An immersion was made at the Cluster of Excellence "Matters of Activity. Image, Space, Material" to discuss the results. The framework must be further tested in other contexts. For future work, a modular version of the framework might be developed to open its contingency heuristics to broader contexts and different application times

Chapter 34 - Biocompatibility of nanocellulose: Emerging biomedical applications

Nanocellulose already proved to be a highly relevant material for biomedical applications, ensued by its outstanding mechanical properties and, more importantly, its biocompatibility. Nevertheless, despite their previous intensive research, a notable number of emerging applications are still being developed. Interestingly, this drive is not solely based on the nanocellulose features, but also heavily dependent on sustainability. The three core nanocelluloses encompass cellulose nanocrystals (CNCs), cellulose nanofibrils (CNFs), and bacterial nanocellulose (BNC). All these different types of nanocellulose display highly interesting biomedical properties per se, after modification and when used in composite formulations. Novel applications that use nanocellulose includewell-known areas, namely, wound dressings, implants, indwelling medical devices, scaffolds, and novel printed scaffolds. Their cytotoxicity and biocompatibility using recent methodologies are thoroughly analyzed to reinforce their near future applicability. By analyzing the pristine core nanocellulose, none display cytotoxicity. However, CNF has the highest potential to fail long-term biocompatibility since it tends to trigger inflammation. On the other hand, neverdried BNC displays a remarkable biocompatibility. Despite this, all nanocelluloses clearly represent a flag bearer of future superior biomaterials, being elite materials in the urgent replacement of our petrochemical dependence

Design of aiming control strategies to enhance energy harnessing in power-generation solar systems with central receiver during cloud shading transients

Alternative technologies that have the potential to replace those based on non-renewable resources still need to grow. One of the most promising technologies is central solar towers. In central-tower thermal power plants, an array of large mirrors called heliostats redirects the solar radiation towards a receiver located at the top of a tower. Then a heat transfer fluid flowing through the receiver takes the concentrated radiation and transports the heat to a conventional thermodynamic cycle to generate power. However, at ground level, direct solar radiation mainly varies because of clouds, which is a complex phenomenon not easily predictable. This solar radiation transient variation can cause dangerous high thermal stresses over the central receiver, an unwanted condition due to the cost of these kind of devices. This dissertation proposes a novel closed loop heliostat aiming point strategy based on a multiple-input-multiple-output model predictive control (MPC) approach to maintain safe operating conditions even when the system is under the effect of solar radiation disturbances. The results reveal that the primary feedback loop aiming strategy could successfully restore the solar receiver back to its steady state after transient operations caused by clouds. However, the controlled variables showed undesired overshoots and high heating rates. These issues are overcome through a set point readjustment approach, which is temporally supported by a PI controller. Following tests indicate that the proposed aiming control strategy provides a continuous safe operation of the solar central receiver when subject to transient flux distribution due to clouds

Measuring knowledge sharing processes through social network analysis within construction organisations

The construction industry is a knowledge intensive and information dependent industry. Organisations risk losing valuable knowledge, when the employees leave them. Therefore, construction organisations need to nurture opportunities to disseminate knowledge through strengthening knowledge-sharing networks. This study aimed at evaluating the formal and informal knowledge sharing methods in social networks within Australian construction organisations and identifying how knowledge sharing could be improved. Data were collected from two estimating teams in two case studies. The collected data through semi-structured interviews were analysed using UCINET, a Social Network Analysis (SNA) tool, and SNA measures. The findings revealed that one case study consisted of influencers, while the other demonstrated an optimal knowledge sharing structure in both formal and informal knowledge sharing methods. Social networks could vary based on the organisation as well as the individuals’ behaviour. Identifying networks with specific issues and taking steps to strengthen networks will enable to achieve optimum knowledge sharing processes. This research offers knowledge sharing good practices for construction organisations to optimise their knowledge sharing processes