Indefinite waitings in MIRELA systems

MIRELA is a high-level language and a rapid prototyping framework dedicated to systems where virtual and digital objects coexist in the same environment and interact in real time. Its semantics is given in the form of networks of timed automata, which can be checked using symbolic methods. This paper shows how to detect various kinds of indefinite waitings in the components of such systems. The method is experimented using the PRISM model checker.Comment: In Proceedings ESSS 2015, arXiv:1506.0325

Adaptive wall wind tunnels: A selected, annotated bibliography

This bibliography, with abstracts, consists of 257 citations arranged in chronological order. Selection of the citations was made for their value to researchers working to solve problems associated with reducing wall interference by the design, development, and operation of adaptive wall test sections. Author, source, and subject indexes are included

Automated reasoning for attributed graph properties

Graphs are ubiquitous in computer science. Moreover, in various application fields, graphs are equipped with attributes to express additional information such as names of entities or weights of relationships. Due to the pervasiveness of attributed graphs, it is highly important to have the means to express properties on attributed graphs to strengthen modeling capabilities and to enable analysis. Firstly, we introduce a new logic of attributed graph properties, where the graph part and attribution part are neatly separated. The graph part is equivalent to first-order logic on graphs as introduced by Courcelle. It employs graph morphisms to allow the specification of complex graph patterns. The attribution part is added to this graph part by reverting to the symbolic approach to graph attribution, where attributes are represented symbolically by variables whose possible values are specified by a set of constraints making use of algebraic specifications. Secondly, we extend our refutationally complete tableau-based reasoning method as well as our symbolic model generation approach for graph properties to attributed graph properties. Due to the new logic mentioned above, neatly separating the graph and attribution parts, and the categorical constructions employed only on a more abstract level, we can leave the graph part of the algorithms seemingly unchanged. For the integration of the attribution part into the algorithms, we use an oracle, allowing for flexible adoption of different available SMT solvers in the actual implementation. Finally, our automated reasoning approach for attributed graph properties is implemented in the tool AutoGraph integrating in particular the SMT solver Z3 for the attribute part of the properties. We motivate and illustrate our work with a particular application scenario on graph database query validation.Peer ReviewedPostprint (author's final draft

A study of free-form shape rationalization using biomimicry as inspiration

Bridging the gap between the material and geometrical aspects of a structure is critical in lightweight construction. Throughout the history of structural development, shape rationalization has been of prime focus for designers and architects, with biological forms being a major source of inspiration. In this work, an attempt is made to integrate different phases of design, construction, and fabrication under a single framework of parametric modeling with the help of visual programming. The idea is to offer a novel free-form shape rationalization process that can be realized with unidirectional materials. Taking inspiration from the growth of a plant, we established a relationship between form and force, which can be translated into different shapes using mathematical operators. Different prototypes of generated shapes were constructed using a combination of existing manufacturing processes to test the validity of the concept in both isotropic and anisotropic material domains. Moreover, for each material/manufacturing combination, generated geometrical shapes were compared with other equivalent and more conventional geometrical constructions, with compressive load-test results being the qualitative measure for each use case. Eventually, a 6-axis robot emulator was integrated with the setup, and corresponding adjustments were made such that a true free-form geometry could be visualized in a 3D space, thus closing the loop of digital fabrication

A new computational framework for the classification and function prediction of long non-coding RNAs

Long non-coding RNAs (lncRNAs) are known to play a significant role in several biological processes. These RNAs possess sequence length greater than 200 base pairs (bp), and so are often misclassified as protein-coding genes. Most Coding Potential Computation (CPC) tools fail to accurately identify, classify and predict the biological functions of lncRNAs in plant genomes, due to previous research being limited to mammalian genomes. In this thesis, an investigation and extraction of various sequence and codon-bias features for identification of lncRNA sequences has been carried out, to develop a new CPC Framework. For identification of essential features, the framework implements regularisation-based selection. A novel classification algorithm is implemented, which removes the dependency on experimental datasets and provides a coordinate-based solution for sub-classification of lncRNAs. For imputing the lncRNA functions, lncRNA-protein interactions have been first determined through co-expression of genes which were re-analysed by a sequence similaritybased approach for identification of novel interactions and prediction of lncRNA functions in the genome. This integrates a D3-based application for visualisation of lncRNA sequences and their associated functions in the genome. Standard evaluation metrics such as accuracy, sensitivity, and specificity have been used for benchmarking the performance of the framework against leading CPC tools. Case study analyses were conducted with plant RNA-seq datasets for evaluating the effectiveness of the framework using a cross-validation approach. The tests show the framework can provide significant improvements on existing CPC models for plant genomes: 20-40% greater accuracy. Function prediction analysis demonstrates results are consistent with the experimentally-published findings

Simulating rare events using a Weighted Ensemble-based string method

We introduce an extension to the Weighted Ensemble (WE) path sampling method to restrict sampling to a one dimensional path through a high dimensional phase space. Our method, which is based on the finite-temperature string method, permits efficient sampling of both equilibrium and non-equilibrium systems. Sampling obtained from the WE method guides the adaptive refinement of a Voronoi tessellation of order parameter space, whose generating points, upon convergence, coincide with the principle reaction pathway. We demonstrate the application of this method to several simple, two-dimensional models of driven Brownian motion and to the conformational change of the nitrogen regulatory protein C receiver domain using an elastic network model. The simplicity of the two-dimensional models allows us to directly compare the efficiency of the WE method to conventional brute force simulations and other path sampling algorithms, while the example of protein conformational change demonstrates how the method can be used to efficiently study transitions in the space of many collective variables