Hybrid modelling of time-variant heterogeneous objects.

The physical world consists of a wide range of objects of a diverse constitution. Past research was mainly focussed on the modelling of simple homogeneous objects of a uniform constitution. Such research resulted in the development of a number of advanced theoretical concepts and practical techniques for describing such physical objects. As a result, the process of modelling and animating certain types of homogeneous objects became feasible. In fact most physical objects are not homogeneous but heterogeneous in their constitution and it is thus important that one is able to deal with such heterogeneous objects that are composed of diverse materials and may have complex internal structures. Heterogeneous object modelling is still a very new and evolving research area, which is likely to prove useful in a wide range of application areas. Despite its great promise, heterogeneous object modelling is still at an embryonic state of development and there is a dearth of extant tools that would allow one to work with static and dynamic heterogeneous objects. In addition, the heterogeneous nature of the modelled objects makes it appealing to employ a combination of different representations resulting in the creation of hybrid models. In this thesis we present a new dynamic Implicit Complexes (IC) framework incorporating a number of existing representations and animation techniques. This framework can be used for the modelling of dynamic multidimensional heterogeneous objects. We then introduce an Implicit Complexes Application Programming Interface (IC API). This IC API is designed to provide various applications with a unified set of tools allowing these to model time-variant heterogeneous objects. We also present a new Function Representation (FRep) API, which is used for the integration of FReps into complex time-variant hybrid models. This approach allows us to create a practical multilevel modelling system suited for complex multidimensional hybrid modelling of dynamic heterogeneous objects. We demonstrate the advantages of our approach through the introduction of a novel set of tools tailored to problems encountered in simulation applications, computer animation and computer games. These new tools empower users and amplify their creativity by allowing them to overcome a large number of extant modelling and animation problems, which were previously considered difficult or even impossible to solve

Hybrid modelling of time-variant heterogeneous objects

The physical world consists of a wide range of objects of a diverse constitution. Past research was mainly focussed on the modelling of simple homogeneous objects of a uniform constitution. Such research resulted in the development of a number of advanced theoretical concepts and practical techniques for describing such physical objects. As a result, the process of modelling and animating certain types of homogeneous objects became feasible. In fact most physical objects are not homogeneous but heterogeneous in their constitution and it is thus important that one is able to deal with such heterogeneous objects that are composed of diverse materials and may have complex internal structures. Heterogeneous object modelling is still a very new and evolving research area, which is likely to prove useful in a wide range of application areas. Despite its great promise, heterogeneous object modelling is still at an embryonic state of development and there is a dearth of extant tools that would allow one to work with static and dynamic heterogeneous objects. In addition, the heterogeneous nature of the modelled objects makes it appealing to employ a combination of different representations resulting in the creation of hybrid models. In this thesis we present a new dynamic Implicit Complexes (IC) framework incorporating a number of existing representations and animation techniques. This framework can be used for the modelling of dynamic multidimensional heterogeneous objects. We then introduce an Implicit Complexes Application Programming Interface (IC API). This IC API is designed to provide various applications with a unified set of tools allowing these to model time-variant heterogeneous objects. We also present a new Function Representation (FRep) API, which is used for the integration of FReps into complex time-variant hybrid models. This approach allows us to create a practical multilevel modelling system suited for complex multidimensional hybrid modelling of dynamic heterogeneous objects. We demonstrate the advantages of our approach through the introduction of a novel set of tools tailored to problems encountered in simulation applications, computer animation and computer games. These new tools empower users and amplify their creativity by allowing them to overcome a large number of extant modelling and animation problems, which were previously considered difficult or even impossible to solve.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Visual-auditory visualisation of dynamic multi-scale heterogeneous objects.

The multi-scale phenomena analysis is an area of active research that is connecting simulations with experiments to get a correct insight into the compound dynamic structure. Visualisation is a challenging task due to a large amount of data and a wide range of complex data representations. The analysis of dynamic multi-scale phenomena requires a combination of geometric modelling and rendering techniques for the analysis of the changes in the internal structure in the case of data coming from different sources of various nature. Moreover, the area often addresses the limitations of solely visual data representation and considers the introduction of other sensory stimuli as a well-known tool to enhance visual analysis. However, there is a lack of software tools allowing perform an advanced real-time analysis of heterogeneous phenomena properties. The hardware-accelerated volume rendering allows getting insight into the internal structure of complex multi-scale phenomena. The technique is convenient for detailed visual analysis and highlights the features of interest in complex structures and is an area of active research. However, the conventional volume visualisation is limited to the use of transfer functions that operate on homogeneous material and, as a result, does not provide flexibility in geometry and material distribution modelling that is crucial for the analysis of heterogeneous objects. Moreover, the extension to visual-auditory analysis emphasises the necessity to review the entire conventional volume visualisation pipeline. The multi-sensory feedback highly depends on the use of modern hardware and software advances for real-time modelling and evaluation. In this work, we explore the aspects of the design of visual-auditory pipelines for the analysis of dynamic multi-scale properties of heterogeneous objects that can allow overcoming well-known problems of complex representations solely visual analysis. We consider the similarities between light and sound propagation as a solution to the problem. The approach benefits from a combination of GPU accelerated ray-casting, geometry, optical and auditory properties modelling. We discuss how the modern GPU techniques application in those areas allows introducing a unified approach to the visual-auditory analysis of dynamic multi-scale heterogeneous objects. Similarly to the conventional volume rendering technique based on light propagation, we model auditory feedback as a result of initial impulse propagation through 3D space and its digital representation as a sampled sound wave obtained with the ray-casting procedure. The auditory stimuli can complement visual ones in the analysis of the dynamic multi-scale heterogeneous object. We propose a framework that facilitates the design of dynamic multi-scale heterogeneous objects visual-auditory pipeline and discuss the framework application for two case studies. The first is a molecular phenomena study that is a result of molecular dynamics simulation and quantum simulation. The second explores microstructures in digital fabrication with an arbitrary irregular lattice structure. For considered case studies, the visual-auditory techniques facilitate the interactive analysis of both spatial structure and internal multi-scale properties of volume nature in complex heterogeneous objects. A GPU-accelerated framework for visual-auditory analysis of heterogeneous objects can be applied and extend beyond this research. Thus, to specify the main direction of such extension from the point of view of the potential users, strengthen the value of this research as well as to evaluate the vision of the application of the techniques described above, we carry out a preliminary evaluation. The user study aims to compare our expectations on the visual-auditory approach with the views of the potential users of this system if it is implemented as a software product. A preliminary evaluation study was carried out with limitations imposed by 2020/2021 restrictions. However, it confirms that the main direction for the visual-auditory analysis of heterogeneous objects has been identified correctly and visual and auditory stimuli can complement each other in the analysis of both volume and spatial distribution properties of heterogeneous phenomena. The user reviews also highlight the necessary enhancements that should be introduced to the approach in terms of the design of more complex user interfaces and consideration of additional application cases. To provide a more detailed picture on evaluation results and recommendations introduced, we also identify the key factors that define the user vision of the approach further enhancement and its possible application areas, such as users experience in the area of complex physical phenomena analysis or multi-sensory area. The discussed in this work aspects of heterogeneous objects analysis task, theoretical and practical solutions allow considering the application, further development and enhancement of the results in multidisciplinary areas of GPU accelerated High-performance visualisation pipelines design and multi-sensory analysis

Geospatial Data Management Research: Progress and Future Directions

Without geospatial data management, today´s challenges in big data applications such as earth observation, geographic information system/building information modeling (GIS/BIM) integration, and 3D/4D city planning cannot be solved. Furthermore, geospatial data management plays a connecting role between data acquisition, data modelling, data visualization, and data analysis. It enables the continuous availability of geospatial data and the replicability of geospatial data analysis. In the first part of this article, five milestones of geospatial data management research are presented that were achieved during the last decade. The first one reflects advancements in BIM/GIS integration at data, process, and application levels. The second milestone presents theoretical progress by introducing topology as a key concept of geospatial data management. In the third milestone, 3D/4D geospatial data management is described as a key concept for city modelling, including subsurface models. Progress in modelling and visualization of massive geospatial features on web platforms is the fourth milestone which includes discrete global grid systems as an alternative geospatial reference framework. The intensive use of geosensor data sources is the fifth milestone which opens the way to parallel data storage platforms supporting data analysis on geosensors. In the second part of this article, five future directions of geospatial data management research are presented that have the potential to become key research fields of geospatial data management in the next decade. Geo-data science will have the task to extract knowledge from unstructured and structured geospatial data and to bridge the gap between modern information technology concepts and the geo-related sciences. Topology is presented as a powerful and general concept to analyze GIS and BIM data structures and spatial relations that will be of great importance in emerging applications such as smart cities and digital twins. Data-streaming libraries and “in-situ” geo-computing on objects executed directly on the sensors will revolutionize geo-information science and bridge geo-computing with geospatial data management. Advanced geospatial data visualization on web platforms will enable the representation of dynamically changing geospatial features or moving objects’ trajectories. Finally, geospatial data management will support big geospatial data analysis, and graph databases are expected to experience a revival on top of parallel and distributed data stores supporting big geospatial data analysis

Visualizing Biological Membrane Organization and Dynamics

International audienc

A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins

Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. The computational studies of membrane proteins are usually much more complicated than those of globular proteins. Here we propose a new continuum model for Poisson-Boltzmann calculations of membrane channel proteins. Major improvements over the existing continuum slab model are as follows: 1) The location and thickness of the slab model are fine-tuned based on explicit-solvent MD simulations. 2) The highly different accessibility in the membrane and water regions are addressed with a two-step, two-probe grid labeling procedure, and 3) The water pores/channels are automatically identified. The new continuum membrane model is optimized (by adjusting the membrane probe, as well as the slab thickness and center) to best reproduce the distributions of buried water molecules in the membrane region as sampled in explicit water simulations. Our optimization also shows that the widely adopted water probe of 1.4 {\AA} for globular proteins is a very reasonable default value for membrane protein simulations. It gives an overall minimum number of inconsistencies between the continuum and explicit representations of water distributions in membrane channel proteins, at least in the water accessible pore/channel regions that we focus on. Finally, we validate the new membrane model by carrying out binding affinity calculations for a potassium channel, and we observe a good agreement with experiment results.Comment: 40 pages, 6 figures, 5 table