Multiscale metabolic modeling of C4 plants: connecting nonlinear genome-scale models to leaf-scale metabolism in developing maize leaves

C4 plants, such as maize, concentrate carbon dioxide in a specialized compartment surrounding the veins of their leaves to improve the efficiency of carbon dioxide assimilation. Nonlinear relationships between carbon dioxide and oxygen levels and reaction rates are key to their physiology but cannot be handled with standard techniques of constraint-based metabolic modeling. We demonstrate that incorporating these relationships as constraints on reaction rates and solving the resulting nonlinear optimization problem yields realistic predictions of the response of C4 systems to environmental and biochemical perturbations. Using a new genome-scale reconstruction of maize metabolism, we build an 18000-reaction, nonlinearly constrained model describing mesophyll and bundle sheath cells in 15 segments of the developing maize leaf, interacting via metabolite exchange, and use RNA-seq and enzyme activity measurements to predict spatial variation in metabolic state by a novel method that optimizes correlation between fluxes and expression data. Though such correlations are known to be weak in general, here the predicted fluxes achieve high correlation with the data, successfully capture the experimentally observed base-to-tip transition between carbon-importing tissue and carbon-exporting tissue, and include a nonzero growth rate, in contrast to prior results from similar methods in other systems. We suggest that developmental gradients may be particularly suited to the inference of metabolic fluxes from expression data.Comment: 57 pages, 14 figures; submitted to PLoS Computational Biology; source code available at http://github.com/ebogart/fluxtools and http://github.com/ebogart/multiscale_c4_sourc

Small Chvatal rank

We propose a variant of the Chvatal-Gomory procedure that will produce a sufficient set of facet normals for the integer hulls of all polyhedra {xx : Ax <= b} as b varies. The number of steps needed is called the small Chvatal rank (SCR) of A. We characterize matrices for which SCR is zero via the notion of supernormality which generalizes unimodularity. SCR is studied in the context of the stable set problem in a graph, and we show that many of the well-known facet normals of the stable set polytope appear in at most two rounds of our procedure. Our results reveal a uniform hypercyclic structure behind the normals of many complicated facet inequalities in the literature for the stable set polytope. Lower bounds for SCR are derived both in general and for polytopes in the unit cube.Comment: 24 pages, 3 figures, v3. Major revision: additional author, new application to stable-set polytopes, reorganization of sections. Accepted for publication in Mathematical Programmin

Solar Meridional Flow in the Shallow Interior during the Rising Phase of Cycle 24

Solar subsurface zonal and meridional-flow profiles during the rising phase of solar cycle 24 are studied using time-distance helioseismology technique. The faster zonal bands in the torsional-oscillation pattern show strong hemispheric asymmetries and temporal variations in both width and speed. The faster band in the northern hemisphere is located closer to the equator than the band in the southern hemisphere, and migrates past the equator when the magnetic activity in the southern hemisphere is reaching maximum. The meridional-flow speed decreases substantially with the increase of magnetic activity, and the flow profile shows two zonal structures in each hemisphere. The residual meridional flow, after subtracting a mean meridional-flow profile, converges toward the activity belts and shows faster and slower bands like the torsional-oscillation pattern. More interestingly, the meridional-flow speed above latitude 30 degree shows an anti-correlation with the poleward-transporting magnetic flux, slower when the following-polarity flux is transported and faster when the leading-polarity flux is transported. It is expected that this phenomenon slows the process of magnetic cancellation and polarity reversal in the high-latitude areas.Comment: Accepted by ApJ Letter

The role of modeling in troubleshooting: an example from electronics

Troubleshooting systems is integral to experimental physics in both research and instructional laboratory settings. The recently adopted AAPT Lab Guidelines identify troubleshooting as an important learning outcome of the undergraduate laboratory curriculum. We investigate students' model-based reasoning on a troubleshooting task using data collected in think-aloud interviews during which pairs of students attempted to diagnose and repair a malfunctioning circuit. Our analysis scheme is informed by the Experimental Modeling Framework, which describes physicists' use of mathematical and conceptual models when reasoning about experimental systems. We show that this framework is a useful lens through which to characterize the troubleshooting process.Comment: 4 pages, 2 figures; Submitted to 2015 PERC Proceeding

Ages of D/d,n/He sup 3 and T/d,n/He sup 4 neutrons in water and tungsten-water mixtures

Ages for D-D and D-T neutrons in water and tungsten-water mixture

Plasma enhanced chemical vapor deposition of SiO_2 using novel alkoxysilane precursors

This communication describes our results using these novel alkoxysilane precursors for PECVD of SiO_2 films in an inductively coupled rf plasma reactor. The effects of deposition time, rf power, and organosilane pressure on the films’ characteristics are described

Investigating the role of model-based reasoning while troubleshooting an electric circuit

We explore the overlap of two nationally-recognized learning outcomes for physics lab courses, namely, the ability to model experimental systems and the ability to troubleshoot a malfunctioning apparatus. Modeling and troubleshooting are both nonlinear, recursive processes that involve using models to inform revisions to an apparatus. To probe the overlap of modeling and troubleshooting, we collected audiovisual data from think-aloud activities in which eight pairs of students from two institutions attempted to diagnose and repair a malfunctioning electrical circuit. We characterize the cognitive tasks and model-based reasoning that students employed during this activity. In doing so, we demonstrate that troubleshooting engages students in the core scientific practice of modeling.Comment: 20 pages, 6 figures, 4 tables; Submitted to Physical Review PE

Global-scale equatorial Rossby waves as an essential component of solar internal dynamics

The Sun's complex dynamics is controlled by buoyancy and rotation in the convection zone and by magnetic forces in the atmosphere and corona. While small-scale solar convection is well understood, the dynamics of large-scale flows in the solar convection zone is not explained by theory or simulations. Waves of vorticity due to the Coriolis force, known as Rossby waves, are expected to remove energy out of convection at the largest scales. Here we unambiguously detect and characterize retrograde-propagating vorticity waves in the shallow subsurface layers of the Sun at angular wavenumbers below fifteen, with the dispersion relation of textbook sectoral Rossby waves. The waves have lifetimes of several months, well-defined mode frequencies below 200 nHz in a co-rotating frame, and eigenfunctions of vorticity that peak at the equator. Rossby waves have nearly as much vorticity as the convection at the same scales, thus they are an essential component of solar dynamics. We find a transition from turbulence-like to wave-like dynamics around the Rhines scale of angular wavenumber of twenty; this might provide an explanation for the puzzling deficit of kinetic energy at the largest spatial scales.Comment: This is the submitted version of the paper published in Nature Astronomy. 23 pages, 8 figures, 1 tabl