Experimental demonstration of a light-ray-direction-flipping METATOY based on confocal lenticular arrays

We show, theoretically and experimentally, that a sheet formed by two confocal lenticular arrays can flip one component of the local light-ray direction. Ray-optically, such a sheet is equivalent to a Dove-prism sheet, an example of a METATOY (metamaterial for light rays), a structure that changes the direction of transmitted light rays in a way that cannot be performed perfectly wave-optically.Comment: 5 pages, 6 figure

Hardware acceleration of reaction-diffusion systems:a guide to optimisation of pattern formation algorithms using OpenACC

Reaction Diffusion Systems (RDS) have widespread applications in computational ecology, biology, computer graphics and the visual arts. For the former applications a major barrier to the development of effective simulation models is their computational complexity - it takes a great deal of processing power to simulate enough replicates such that reliable conclusions can be drawn. Optimizing the computation is thus highly desirable in order to obtain more results with less resources. Existing optimizations of RDS tend to be low-level and GPGPU based. Here we apply the higher-level OpenACC framework to two case studies: a simple RDS to learn the ‘workings’ of OpenACC and a more realistic and complex example. Our results show that simple parallelization directives and minimal data transfer can produce a useful performance improvement. The relative simplicity of porting OpenACC code between heterogeneous hardware is a key benefit to the scientific computing community in terms of speed-up and portability

Visual simulation of soil-microbial system using GPGPU technology

General Purpose (use of) Graphics Processing Units (GPGPU) is a promising technology for simulation upscaling; in particular for bottom–up modelling approaches seeking to translate micro-scale system processes to macro-scale properties. Many existing simulations of soil ecosystems do not recover the emergent system scale properties and this may be a consequence of “missing” information at finer scales. Interpretation of model output can be challenging and we advocate the “built-in” visual simulation afforded by GPGPU implementations. We apply this GPGPU approach to a reaction–diffusion soil ecosystem model with the intent of linking micro (micron) and core (cm) spatial scales to investigate how microbes respond to changing environments and the consequences on soil respiration. The performance is evaluated in terms of computational speed up, spatial upscaling and visual feedback. We conclude that a GPGPU approach can significantly improve computational efficiency and offers the potential added benefit of visual immediacy. For massive spatial domains distribution over GPU devices may still be required

Emergent behavior of soil fungal dynamics:influence of soil architecture and water distribution

Macroscopic measurements and observations in two-dimensional soil-thin sections indicate that fungal hyphae invade preferentially the larger, air-filled pores in soils. This suggests that the architecture of soils and the microscale distribution of water are likely to influence significantly the dynamics of fungal growth. Unfortunately, techniques are lacking at present to verify this hypothesis experimentally, and as a result, factors that control fungal growth in soils remain poorly understood. Nevertheless, to design appropriate experiments later on, it is useful to indirectly obtain estimates of the effects involved. Such estimates can be obtained via simulation, based on detailed micron-scale X-ray computed tomography information about the soil pore geometry. In this context, this article reports on a series of simulations resulting from the combination of an individual-based fungal growth model, describing in detail the physiological processes involved in fungal growth, and of a Lattice Boltzmann model used to predict the distribution of air-liquid interfaces in soils. Three soil samples with contrasting properties were used as test cases. Several quantitative parameters, including Minkowski functionals, were used to characterize the geometry of pores, air-water interfaces, and fungal hyphae. Simulation results show that the water distribution in the soils is affected more by the pore size distribution than by the porosity of the soils. The presence of water decreased the colonization efficiency of the fungi, as evinced by a decline in the magnitude of all fungal biomass functional measures, in all three samples. The architecture of the soils and water distribution had an effect on the general morphology of the hyphal network, with a "looped" configuration in one soil, due to growing around water droplets. These morphologic differences are satisfactorily discriminated by the Minkowski functionals, applied to the fungal biomass

Characterising the tumour morphological response to therapeutic intervention:an ex vivo model

In cancer, morphological assessment of histological tissue samples is a fundamental part of both diagnosis and prognosis. Image analysis offers opportunities to support that assessment through quantitative metrics of morphology. Generally, morphometric analysis is carried out on two dimensional tissue section data and so only represents a small fraction of any tumour. We present a novel application of three-dimensional (3D) morphometrics for 3D imaging data obtained from tumours grown in a culture model. Minkowski functionals, a set of measures that characterise geometry and topology in n-dimensional space, are used to quantify tumour topology in the absence of and in response to therapeutic intervention. These measures are used to stratify the morphological response of tumours to therapeutic intervention. Breast tumours are characterised by estrogen receptor (ER) status, human epidermal growth factor receptor (HER)2 status and tumour grade. Previously, we have shown that ER status is associated with tumour volume in response to tamoxifen treatment ex vivo. Here, HER2 status is found to predict the changes in morphology other than volume as a result of tamoxifen treatment ex vivo. Finally, we show the extent to which Minkowski functionals might be used to predict tumour grade.Minkowski functionals are generalisable to any 3D data set, including in vivo and cellular systems. This quantitative topological analysis can provide a valuable link among biomarkers, drug intervention and tumour morphology that is complementary to existing, non-morphological measures of tumour response to intervention and could ultimately inform patient treatment

Quantification of the pore size distribution of soils:assessment of existing software using tomographic and synthetic 3D images

The pore size distribution (PSD) of the void space is widely used to predict a range of processes in soils. Recent advances in X-ray computed tomography (CT) now afford novel ways to obtain exact data on pore geometry, which has stimulated the development of algorithms to estimate the pore size distribution from 3D data sets. To date there is however no clear consensus on how PSDs should be estimated, and in what form PSDs are best presented. In this article, we first review the theoretical principles shared by the various methods for PSD estimation. Then we select methods that are widely adopted in soil science and geoscience, and we use a robust statistical method to compare their application to synthetic image samples, for which analytical solutions of PSDs are available, and X-ray CT images of soil samples selected from different treatments to obtain wide ranging PSDs. Results indicate that, when applied to the synthetic images, all methods presenting PSDs as pore volume per class size (i.e., Avizo, CTAnalyser, BoneJ, Quantim4, and DTM), perform well. Among them, the methods based on Maximum Inscribed Balls (Bone J, CTAnalyser, Quantim4) also produce similar PSDs for the soil samples, whereas the Delaunay Triangulation Method (DTM) produces larger estimates of the pore volume occupied by small pores, and Avizo yields larger estimates of the pore volume occupied by large pores. By contrast, the methods that calculate PSDs as object population fraction per volume class (Avizo, 3DMA, DFS-FIJI) perform inconsistently on the synthetic images and do not appear well suited to handle the more complex geometries of soils. It is anticipated that the extensive evaluation of method performance carried out in this study, together with the recommendations reached, will be useful to the porous media community to make more informed choices relative to suitable PSD estimation methods, and will help improve current practice, which is often ad hoc and heuristic

Local-Oscillator Noise Coupling in Balanced Homodyne Readout for Advanced Gravitational Wave Detectors

The second generation of interferometric gravitational wave detectors are quickly approaching their design sensitivity. For the first time these detectors will become limited by quantum back-action noise. Several back-action evasion techniques have been proposed to further increase the detector sensitivity. Since most proposals rely on a flexible readout of the full amplitude- and phase-quadrature space of the output light field, balanced homodyne detection is generally expected to replace the currently used DC readout. Up to now, little investigation has been undertaken into how balanced homodyne detection can be successfully transferred from its ubiquitous application in table-top quantum optics experiments to large-scale interferometers with suspended optics. Here we derive implementation requirements with respect to local oscillator noise couplings and highlight potential issues with the example of the Glasgow Sagnac Speed Meter experiment, as well as for a future upgrade to the Advanced LIGO detectors.Comment: 7 pages, 5 figure

Effects of static and dynamic higher-order optical modes in balanced homodyne readout for future gravitational waves detectors

With the recent detection of Gravitational waves (GW), marking the start of the new field of GW astronomy, the push for building more sensitive laser-interferometric gravitational wave detectors (GWD) has never been stronger. Balanced homodyne detection (BHD) allows for a quantum noise (QN) limited readout of arbitrary light field quadratures, and has therefore been suggested as a vital building block for upgrades to Advanced LIGO and third generation observatories. In terms of the practical implementation of BHD, we develop a full framework for analyzing the static optical high order modes (HOMs) occurring in the BHD paths related to the misalignment or mode matching at the input and output ports of the laser interferometer. We find the effects of HOMs on the quantum noise limited sensitivity is independent of the actual interferometer configuration, e.g. Michelson and Sagnac interferometers are effected in the same way. We show that misalignment of the output ports of the interferometer (output misalignment) only effects the high frequency part of the quantum noise limited sensitivity (detection noise). However, at low frequencies, HOMs reduce the interferometer response and the radiation pressure noise (back action noise) by the same amount and hence the quantum noise limited sensitivity is not negatively effected in that frequency range. We show that the misalignment of laser into the interferometer (input misalignment) produces the same effect as output misalignment and additionally decreases the power inside the interferometer. We also analyze dynamic HOM effects, such as beam jitter created by the suspended mirrors of the BHD. Our analyses can be directly applied to any BHD implementation in a future GWD. Moreover, we apply our analytical techniques to the example of the speed meter proof of concept experiment under construction in Glasgow. We find that for our experimental parameters, the performance of our seismic isolation system in the BHD paths is compatible with the design sensitivity of the experiment

Local light-ray rotation

We present a sheet structure that rotates the local ray direction through an arbitrary angle around the sheet normal. The sheet structure consists of two parallel Dove-prism sheets, each of which flips one component of the local direction of transmitted light rays. Together, the two sheets rotate transmitted light rays around the sheet normal. We show that the direction under which a point light source is seen is given by a Mobius transform. We illustrate some of the properties with movies calculated by ray-tracing software.Comment: 9 pages, 6 figure