Visualization in spatial modeling

This chapter deals with issues arising from a central theme in contemporary computer modeling - visualization. We first tie visualization to varieties of modeling along the continuum from iconic to symbolic and then focus on the notion that our models are so intrinsically complex that there are many different types of visualization that might be developed in their understanding and implementation. This focuses the debate on the very way of 'doing science' in that patterns and processes of any complexity can be better understood through visualizing the data, the simulations, and the outcomes that such models generate. As we have grown more sensitive to the problem of complexity in all systems, we are more aware that the twin goals of parsimony and verifiability which have dominated scientific theory since the 'Enlightenment' are up for grabs: good theories and models must 'look right' despite what our statistics and causal logics tell us. Visualization is the cutting edge of this new way of thinking about science but its styles vary enormously with context. Here we define three varieties: visualization of complicated systems to make things simple or at least explicable, which is the role of pedagogy; visualization to explore unanticipated outcomes and to refine processes that interact in unanticipated ways; and visualization to enable end users with no prior understanding of the science but a deep understanding of the problem to engage in using models for prediction, prescription, and control. We illustrate these themes with a model of an agricultural market which is the basis of modern urban economics - the von Thünen model of land rent and density; a model of urban development based on interacting spatial and temporal processes of land development - the DUEM model; and a pedestrian model of human movement at the fine scale where control of such movements to meet standards of public safety is intrinsically part of the model about which the controllers know intimately. © Springer-Verlag Berlin Heidelberg 2006

Segue: Overviewing Evolution Patterns of Egocentric Networks by Interactive Construction of Spatial Layouts

Getting the overall picture of how a large number of ego-networks evolve is a common yet challenging task. Existing techniques often require analysts to inspect the evolution patterns of ego-networks one after another. In this study, we explore an approach that allows analysts to interactively create spatial layouts in which each dot is a dynamic ego-network. These spatial layouts provide overviews of the evolution patterns of ego-networks, thereby revealing different global patterns such as trends, clusters and outliers in evolution patterns. To let analysts interactively construct interpretable spatial layouts, we propose a data transformation pipeline, with which analysts can adjust the spatial layouts and convert dynamic egonetworks into event sequences to aid interpretations of the spatial positions. Based on this transformation pipeline, we developed Segue, a visual analysis system that supports thorough exploration of the evolution patterns of ego-networks. Through two usage scenarios, we demonstrate how analysts can gain insights into the overall evolution patterns of a large collection of ego-networks by interactively creating different spatial layouts.Comment: Published at IEEE Conference on Visual Analytics Science and Technology (IEEE VAST 2018

Nonlinear dynamics and pattern formation in turbulent wake transition

Results are reported on direct numerical simulations of transition from two-dimensional to three-dimensional states due to secondary instability in the wake of a circular cylinder. These calculations quantify the nonlinear response of the system to three-dimensional perturbations near threshold for the two separate linear instabilities of the wake: mode A and mode B. The objectives are to classify the nonlinear form of the bifurcation to mode A and mode B and to identify the conditions under which the wake evolves to periodic, quasi-periodic, or chaotic states with respect to changes in spanwise dimension and Reynolds number. The onset of mode A is shown to occur through a subcritical bifurcation that causes a reduction in the primary oscillation frequency of the wake at saturation. In contrast, the onset of mode B occurs through a supercritical bifurcation with no frequency shift near threshold. Simulations of the three-dimensional wake for fixed Reynolds number and increasing spanwise dimension show that large systems evolve to a state of spatiotemporal chaos, and suggest that three-dimensionality in the wake leads to irregular states and fast transition to turbulence at Reynolds numbers just beyond the onset of the secondary instability. A key feature of these ‘turbulent’ states is the competition between self-excited, three-dimensional instability modes (global modes) in the mode A wavenumber band. These instability modes produce irregular spatiotemporal patterns and large-scale ‘spot-like’ disturbances in the wake during the breakdown of the regular mode A pattern. Simulations at higher Reynolds number show that long-wavelength interactions modulate fluctuating forces and cause variations in phase along the span of the cylinder that reduce the fluctuating amplitude of lift and drag. Results of both two-dimensional and three-dimensional simulations are presented for a range of Reynolds number from about 10 up to 1000

Two-phase flow dynamics in a micro hydrophilic channel: A theoretical and experimental study

In this paper, two-phase flow dynamics in a micro hydrophilic channel are experimentally and theoretically investigated. Flow patterns of annulus, wavy, and slug are observed in the range of operating condition. A set of empirical models based on the Lockhart-Martinelli parameter and a two-fluid model using several correlations of the relative permeability are adopted; and their predictions are compared with experimental data. It shows that for low liquid flow rates most model predictions show acceptable agreement with experimental data, while in the regime of high liquid flow rate only a few of them exhibit a good match. Correlation optimization is conducted for individual flow pattern. Through theoretical analysis of flows in a circular and 2-D channel, respectively, we obtain correlations close to the experimental observation. Real-time pressure measurement shows that different flow patterns yield different pressure evolutions. © 2013 Elsevier Ltd. All rights reserved

mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data

<p>Motivation: Stable isotope-labelling experiments have recently gained increasing popularity in metabolomics studies, providing unique insights into the dynamics of metabolic fluxes, beyond the steady-state information gathered by routine mass spectrometry. However, most liquid chromatography–mass spectrometry data analysis software lacks features that enable automated annotation and relative quantification of labelled metabolite peaks. Here, we describe mzMatch–ISO, a new extension to the metabolomics analysis pipeline mzMatch.R.</p> <p>Results: Targeted and untargeted isotope profiling using mzMatch–ISO provides a convenient visual summary of the quality and quantity of labelling for every metabolite through four types of diagnostic plots that show (i) the chromatograms of the isotope peaks of each compound in each sample group; (ii) the ratio of mono-isotopic and labelled peaks indicating the fraction of labelling; (iii) the average peak area of mono-isotopic and labelled peaks in each sample group; and (iv) the trend in the relative amount of labelling in a predetermined isotopomer. To aid further statistical analyses, the values used for generating these plots are also provided as a tab-delimited file. We demonstrate the power and versatility of mzMatch–ISO by analysing a 13C-labelled metabolome dataset from trypanosomal parasites.</p&gt

Dynamical systems analysis of fluid transport in time-periodic vortex ring flows

It is known that the stable and unstable manifolds of dynamical systems theory provide a powerful tool for understanding Lagrangian aspects of time-periodic flows. In this work we consider two time-periodic vortex ring flows. The first is a vortex ring with an elliptical core. The manifolds provide information about entrainment and detrainment of irrotational fluid into and out of the volume transported with the ring. The likeness of the manifolds with features observed in flow visualization experiments of turbulent vortex rings suggests that a similar process might be at play. However, what precise modes of unsteadiness are responsible for stirring in a turbulent vortex ring is left as an open question. The second situation is that of two leapfrogging rings. The unstable manifold shows striking agreement with even the fine features of smoke visualization photographs, suggesting that fluid elements in the vicinity of the manifold are drawn out along it and begin to reveal its structure. We suggest that interpretations of these photographs that argue for complex vorticity dynamics ought to be reconsidered. Recently, theoretical and computational tools have been developed to locate structures analogous to stable and unstable manifolds in aperiodic, or finite-time systems. The usefulness of these analogs is demonstrated, using vortex ring flows as an example, in the paper by Shadden, Dabiri, and Marsden [Phys. Fluids 18, 047105 (2006)]