Simbiotics: a multi-scale integrative platform for 3D modeling of bacterial populations

Simbiotics is a spatially explicit multiscale modeling platform for the design, simulation and analysis of bacterial populations. Systems ranging from planktonic cells and colonies, to biofilm formation and development may be modeled. Representation of biological systems in Simbiotics is flexible, and user-defined processes may be in a variety of forms depending on desired model abstraction. Simbiotics provides a library of modules such as cell geometries, physical force dynamics, genetic circuits, metabolic pathways, chemical diffusion and cell interactions. Model defined processes are integrated and scheduled for parallel multithread and multi-CPU execution. A virtual lab provides the modeler with analysis modules and some simulated lab equipment, enabling automation of sample interaction and data collection. An extendable and modular framework allows for the platform to be updated as novel models of bacteria are developed, coupled with an intuitive user interface to allow for model definitions with minimal programming experience. Simbiotics can integrate existing standards such as SBML, and process microscopy images to initialize the 3D spatial configuration of bacteria consortia. Two case studies, used to illustrate the platform flexibility, focus on the physical properties of the biosystems modeled. These pilot case studies demonstrate Simbiotics versatility in modeling and analysis of natural systems and as a CAD tool for synthetic biology

Modeling and characterization of thermo-oxidative behavior of bismaleimide composites

High-temperature polymer matrix composites (HTPMCs) are susceptible to thermo-oxidation, which accelerates the composites\u27 degradation and reduces the service life. Mechanical properties of HTPMCs deteriorate due to coupled thermo-oxidation and cross-linking mechanisms. Bismaleimides (BMIs) are commonly used high-temperature resins for aerospace applications. This work presents the viability of using experimental weight loss to model the spatial distribution of oxidation when the oxidized polymer matrix is not discernible. Three tasks are introduced: (1) Anisotropic oxidation prediction using optimized weight loss behavior of bismaleimide composites, (2) A multi-scale modeling of thermo-oxidative effects on the flexural behavior of cross-ply bismaleimide composites, and (3) Thermo-oxidative induced damage in polymer composites: microstructure image-based multi-scale modeling and experimental validation. Task 1 deals with simulating the weight loss and oxidized layer evolution in unidirectional BMI composites exposed to a service temperature in the operating range, 176.67 °C (350 °F) and 200 °C (392 °F). In task 2, microstructural changes of the cross-ply BMIs composites were characterized using microscopy. A multiscale approach for modeling flexural modulus degradation was proposed. In Task 3, a multi-scale modeling approach is presented to simulate and validate thermo-oxidation shrinkage and cracking damage. The micro-scale shrinkage deformation and cracking damage are simulated and validated using 2D and 3D simulations. The meso-scale geometrical domain and the micro-scale geometry and mesh are developed using the object oriented finite element (OOF). The macro-scale shrinkage and weight loss are measured using unidirectional coupons and used to build the macro-shrinkage model --Abstract, page iv

3D scene modeling and understanding from image sequences

A new method for 3D modeling is proposed, which generates a content-based 3D mosaic (CB3M) representation for long video sequences of 3D, dynamic urban scenes captured by a camera on a mobile platform. In the first phase, a set of parallel-perspective (pushbroom) mosaics with varying viewing directions is generated to capture both the 3D and dynamic aspects of the scene under the camera coverage. In the second phase, a unified patch-based stereo matching algorithm is applied to extract parametric representations of the color, structure and motion of the dynamic and/or 3D objects in urban scenes, where a lot of planar surfaces exist. Multiple pairs of stereo mosaics are used for facilitating reliable stereo matching, occlusion handling, accurate 3D reconstruction and robust moving target detection. The outcome of this phase is a CB3M representation, which is a highly compressed visual representation for a dynamic 3D scene, and has object contents of both 3D and motion information. In the third phase, a multi-layer based scene understanding algorithm is proposed, resulting in a planar surface model for higher-level object representations. Experimental results are given for both simulated and several different real video sequences of large-scale 3D scenes to show the accuracy and effectiveness of the representation. We also show the patch-based stereo matching algorithm and the CB3M representation can be generalized to 3D modeling with perspective views using either a single camera or a stereovision head on a ground mobile platform or a pedestrian. Applications of the proposed method include airborne or ground video surveillance, 3D urban scene modeling, traffic survey, transportation planning and the visual aid for perception and navigation of blind people

Spatial distribution of radionuclides in 3D models of SN 1987A and Cas A

Fostered by the possibilities of multi-dimensional computational modeling, in particular the advent of three-dimensional (3D) simulations, our understanding of the neutrino-driven explosion mechanism of core-collapse supernovae (SNe) has experienced remarkable progress over the past decade. First self-consistent, first-principle models have shown successful explosions in 3D, and even failed cases may be cured by moderate changes of the microphysics inside the neutron star (NS), better grid resolution, or more detailed progenitor conditions at the onset of core collapse, in particular large-scale perturbations in the convective Si and O burning shells. 3D simulations have also achieved to follow neutrino-driven explosions continuously from the initiation of the blast wave, through the shock breakout from the progenitor surface, into the radioactively powered evolution of the SN, and towards the free expansion phase of the emerging remnant. Here we present results from such simulations, which form the basis for direct comparisons with observations of SNe and SN remnants in order to derive constraints on the still disputed explosion mechanism. It is shown that predictions based on hydrodynamic instabilities and mixing processes associated with neutrino-driven explosions yield good agreement with measured NS kicks, light-curve properties of SN 1987A, and asymmetries of iron and 44Ti distributions observed in SN 1987A and Cassiopeia A.Comment: 9 pages, 6 figures; submitted to: "SN 1987A, 30 years later", Proceedings IAU Symposium No. 331, 2017; eds. M. Renaud et a

Collaborative multi-scale 3D city and infrastructure modeling and simulation

Computer-aided collaborative and multi-scale 3D planning are challenges for complex railway and subway track infrastructure projects in the built environment. Many legal, economic, environmental, and structural requirements have to be taken into account. The stringent use of 3D models in the different phases of the planning process facilitates communication and collaboration between the stake holders such as civil engineers, geological engineers, and decision makers. This paper presents concepts, developments, and experiences gained by an interdisciplinary research group coming from civil engineering informatics and geo-informatics banding together skills of both, the Building Information Modeling and the 3D GIS world. New approaches including the development of a collaborative platform and 3D multi-scale modelling are proposed for collaborative planning and simulation to improve the digital 3D planning of subway tracks and other infrastructures. Experiences during this research and lessons learned are presented as well as an outlook on future research focusing on Building Information Modeling and 3D GIS applications for cities of the future