Omnispective Analysis and Reasoning: a framework for managing intellectual concerns in scientific workflows

Scientific workflows are extensively used to support the management of experimental and computational research by connecting together different data sources, components and processes. However, certain issues such as the ability to check the appropriateness of the processes orchestrated, management of the context of workflow components and specification, and provision for robust management of intellectual concerns are not addressed adequately. Hence, it is highly desirable to add features to uplift focus from low level details to help clarify the rationale and intent behind the choices and decisions in the workflow specifications and provide a suitable level of abstraction to capture and organize intellectual concerns and map them to the workflow specification and execution semantics. In this paper, we present Omnispective Analysis and Reasoning (OAR), a novel framework for providing the above features and enhancements in scientific workflow management systems and processes. The OAR framework is aimed at supporting effective capture and reuse of intellectual concerns in workflow management

Computational approaches for RNA structure ensemble deconvolution from structure probing data

RNA structure probing experiments have emerged over the last decade as a straightforward way to determine the structure of RNA molecules in a number of different contexts. Although powerful, the ability of RNA to dynamically interconvert between, and to simultaneously populate, alternative structural configurations, poses a nontrivial challenge to the interpretation of data derived from these experiments. Recent efforts aimed at developing computational methods for the reconstruction of coexisting alternative RNA conformations from structure probing data are paving the way to the study of RNA structure ensembles, even in the context of living cells. In this review, we critically discuss these methods, their limitations and possible future improvements

Origami surfaces for kinetic architecture

This thesis departs from the conviction that spaces that can change their formal configuration through movement may endow buildings of bigger versatility. Through kinetic architecture may be possible to generate adaptable buildings able to respond to different functional solicitations in terms of the used spaces. The research proposes the exploration of rigidly folding origami surfaces as the means to materialize reconfigurable spaces through motion. This specific kind of tessellated surfaces are the result of the transformation of a flat element, without any special structural skill, into a self-supporting element through folds in the material, which gives them the aptitude to undertake various configurations depending on the crease pattern design and welldefined rules for folding according to rigid kinematics. The research follows a methodology based on multidisciplinary, practical experiments supported on digital tools for formal exploration and simulation. The developed experiments allow to propose a workflow, from concept to fabrication, of kinetic structures made through rigidly folding regular origami surfaces. The workflow is a step-by-step process that allows to take a logical path which passes through the main involved areas, namely origami geometry and parameterization, materials and digital fabrication and mechanisms and control. The investigation demonstrates that rigidly folding origami surfaces can be used as dynamic structures to materialize reconfigurable spaces at different scales and also that the use of pantographic systems as a mechanism associated to specific parts of the origami surface permits the achievement of synchronized motion and possibility of locking the structure at specific stages of the folding.A presente tese parte da convicção de que os espaços que são capazes de mudar a sua configuração formal através de movimento podem dotar os edifícios de maior versatilidade. Através da arquitectura cinética pode ser possível a geração de edifícios adaptáveis, capazes de responder a diferentes solicitações funcionais, em termos do espaço utilizado. Esta investigação propõe a exploração de superfícies de origami, dobráveis de forma rígida, como meio de materialização de espaços reconfiguráveis através de movimento. Este tipo de superfícies tesseladas são o resultado da transformação de um elemento plano, sem capacidade estrutural que, através de dobras no material, ganha propriedades de auto-suporte. Dependendo do padrão de dobragem e segundo regras de dobragem bem definidas de acordo com uma cinemática rígida, a superfície ganha a capacidade de assumir diferentes configurações. A investigação segue uma metodologia baseada em experiências práticas e multidisciplinares apoiada em ferramentas digitais para a exploração formal e simulação. Através das experiências desenvolvidas é proposto um processo de trabalho, desde a conceptualização à construção, de estruturas cinéticas baseadas em superfícies dobráveis de origami rígido de padrão regular. O processo de trabalho proposto corresponde a um procedimento passo-apasso que permite seguir um percurso lógico que atravessa as principais áreas envolvidas, nomeadamente geometria do origami e parametrização, materiais e fabricação digital e ainda mecanismos e controle. A dissertação demonstra que as superfícies de origami dobradas de forma rígida podem ser utilizadas como estruturas dinâmicas para materializar espaços reconfiguráveis a diferentes escalas. Demonstra ainda que a utilização de sistemas pantográficos como mecanismos associados a partes específicas da superfície permite atingir um movimento sincronizado e a possibilidade de bloquear o movimento em estados específicos da dobragem

Learning without neurons in physical systems

Learning is traditionally studied in biological or computational systems. The power of learning frameworks in solving hard inverse-problems provides an appealing case for the development of `physical learning' in which physical systems adopt desirable properties on their own without computational design. It was recently realized that large classes of physical systems can physically learn through local learning rules, autonomously adapting their parameters in response to observed examples of use. We review recent work in the emerging field of physical learning, describing theoretical and experimental advances in areas ranging from molecular self-assembly to flow networks and mechanical materials. Physical learning machines provide multiple practical advantages over computer designed ones, in particular by not requiring an accurate model of the system, and their ability to autonomously adapt to changing needs over time. As theoretical constructs, physical learning machines afford a novel perspective on how physical constraints modify abstract learning theory.Comment: 25 pages, 6 figure

ORIGAMI-SCISSOR Hinged Geometry Method

The diamond origami-scissor hinged pattern marks a new type of thick origami that can not only fold and unfold, but also expand and contract (project below). This was done by applying the ‘form generation method of relative ratios’ for two-bar scissors to the thick origami. This research tests whether this method can be extended and generalized to other types of origami. The origami-scissor hinged geometry method is here applied to the waterbomb of thick panels making a waterbomb origami-scissor hinged pattern. While the waterbomb origami of thick panels has one degree of freedom, the waterbomb origami-scissor hinged pattern has two degrees of freedom as it can independently fold and unfold as an origami, and expand and contract as a scissor hinged structure. This creates a new research branch of expandable thick origami. The ‘form generation method of relative ratios’ (FGMORR) [Rivas-Adrover 17] has been applied to the ‘origami of thick panels’ [Chen et al. 15] because this method to make thick origami can be extended and generalized to different types of origami, and therefore the origami-scissor hinged geometry method can also be applied to all these different types of origami. A critical condition is that the thick origami has to be made of equal or proportional thicknesses so that when translating that geometry with scissors the end nodes match. Another condition is that the pantographs that mark the creases and join different origami faces must have an equal morphology and bilateral symmetry. Automation of this method will be investigated with Grasshopper for Rhinoceros. Origami-scissor hinged patterns provide an extra degree of freedom, therefore origami patterns that could be folded can now also contract and occupy much smaller volumes. This would be useful in applications where a high ratio of deployed-to stowed volume is required such as space applications, earthbound transportable applications, and to create adaptable spaces and transformable environments in permanent architecture