Experimental and computational investigation of confined laser-induced breakdown spectroscopy

This paper presents an experimental and computational study on laser-induced breakdown spectroscopy (LIBS) for both unconfined flat surface and confined cavity cases. An integrated LIBS system is employed to acquire the shockwave and plasma plume images. The computational model consists of the mass, momentum, and energy conservation equations, which are necessary to describe shockwave behaviors. The numerical predictions are validated against shadowgraphic images in terms of shockwave expansion and reflection. The three-dimensional (3D) shockwave morphology and velocity fields are displayed and discussed

Atlas Toolkit: Fast registration of 3D morphological datasets in the absence of landmarks

Image registration is a gateway technology for Developmental Systems Biology, enabling computational analysis of related datasets within a shared coordinate system. Many registration tools rely on landmarks to ensure that datasets are correctly aligned; yet suitable landmarks are not present in many datasets. Atlas Toolkit is a Fiji/ImageJ plugin collection offering elastic group-wise registration of 3D morphological datasets, guided by segmentation of the interesting morphology. We demonstrate the method by combinatorial mapping of cell signalling events in the developing eyes of chick embryos, and use the integrated datasets to predictively enumerate Gene Regulatory Network states

1D-3D hybrid modeling—from multi-compartment models to full resolution models in space and time

Investigation of cellular and network dynamics in the brain by means of modeling & simulation has evolved into a highly interdisciplinary field, that uses sophisticated modeling & simulation approaches to understand distinct areas of brain function. Depending on the underlying complexity, these models vary in level of detail to cope with the attached computational cost. Hence for large network simulations, single neurons are typically reduced to time-dependent signal processors, dismissing spatial aspects of the cells. For single cell or small-world networks, general purpose simulators allow for space and time-dependent simulations of electrical signal processing, based on the cable equation theory. An emerging field in Computational Neuroscience encompasses a new level of detail by incorporating the 3D morphology of cells and organelles into 3D space and time-dependent simulations. Every approach has its advantages and limitations, such as computational cost, integrated and methods-spanning simulation approaches, depending on the network size could establish new ways to investigate the brain. We present a hybrid simulation approach, that makes use of reduced 1D-models using e.g. the NEURON which couples to fully resolved models for simulating cellular and sub-cellular dynamics, including the detailed 3D-morphology of neurons and organelles. To couple 1D- & 3D-simulations, we present a geometry and membrane potential mapping framework, with which graph-based morphologies, e.g. in swc-/hoc-format, are mapped to full surface and volume representations of the neuron; membrane potential data from 1D-simulations are used as boundary conditions for full 3D simulations. Thus, established models and data, based on general purpose 1D-simulators, can be directly coupled to the emerging field of fully resolved highly detailed 3D-modeling approaches. The new framework is applied to investigate electrically active neurons and their intracellular spatio-temporal Calcium Dynamics

Three-Dimensional Simulations of Core-Collapse Supernovae: From Shock Revival to Shock Breakout

We present 3D simulations of core-collapse supernovae from blast-wave initiation by the neutrino-driven mechanism to shock breakout from the stellar surface, considering two 15 Msun red supergiants (RSG) and two blue supergiants (BSG) of 15 Msun and 20 Msun. We demonstrate that the metal-rich ejecta in homologous expansion still carry fingerprints of asymmetries at the beginning of the explosion, but the final metal distribution is massively affected by the detailed progenitor structure. The most extended and fastest metal fingers and clumps are correlated with the biggest and fastest-rising plumes of neutrino-heated matter, because these plumes most effectively seed the growth of Rayleigh-Taylor (RT) instabilities at the C+O/He and He/H composition-shell interfaces after the passage of the SN shock. The extent of radial mixing, global asymmetry of the metal-rich ejecta, RT-induced fragmentation of initial plumes to smaller-scale fingers, and maximal Ni and minimal H velocities do not only depend on the initial asphericity and explosion energy (which determine the shock and initial Ni velocities) but also on the density profiles and widths of C+O core and He shell and on the density gradient at the He/H transition, which lead to unsteady shock propagation and the formation of reverse shocks. Both RSG explosions retain a great global metal asymmetry with pronounced clumpiness and substructure, deep penetration of Ni fingers into the H-envelope (with maximum velocities of 4000-5000 km/s for an explosion energy around 1.5 bethe) and efficient inward H-mixing. While the 15 Msun BSG shares these properties (maximum Ni speeds up to ~3500 km/s), the 20 Msun BSG develops a much more roundish geometry without pronounced metal fingers (maximum Ni velocities only ~2200 km/s) because of reverse-shock deceleration and insufficient time for strong RT growth and fragmentation at the He/H interface.Comment: 21 pages, 15 figures; revised version with minor changes in Sect.1; accepted by Astron. Astrophy