Stochastic Simulation of Process Calculi for Biology

Biological systems typically involve large numbers of components with complex, highly parallel interactions and intrinsic stochasticity. To model this complexity, numerous programming languages based on process calculi have been developed, many of which are expressive enough to generate unbounded numbers of molecular species and reactions. As a result of this expressiveness, such calculi cannot rely on standard reaction-based simulation methods, which require fixed numbers of species and reactions. Rather than implementing custom stochastic simulation algorithms for each process calculus, we propose to use a generic abstract machine that can be instantiated to a range of process calculi and a range of reaction-based simulation algorithms. The abstract machine functions as a just-in-time compiler, which dynamically updates the set of possible reactions and chooses the next reaction in an iterative cycle. In this short paper we give a brief summary of the generic abstract machine, and show how it can be instantiated with the stochastic simulation algorithm known as Gillespie's Direct Method. We also discuss the wider implications of such an abstract machine, and outline how it can be used to simulate multiple calculi simultaneously within a common framework.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

Unsteady turbulent buoyant plumes

We model the unsteady evolution of turbulent buoyant plumes following temporal changes to the source conditions. The integral model is derived from radial integration of the governing equations expressing the conservation of mass, axial momentum and buoyancy. The non-uniform radial profiles of the axial velocity and density deficit in the plume are explicitly described by shape factors in the integral equations; the commonly-assumed top-hat profiles lead to shape factors equal to unity. The resultant model is hyperbolic when the momentum shape factor, determined from the radial profile of the mean axial velocity, differs from unity. The solutions of the model when source conditions are maintained at constant values retain the form of the well-established steady plume solutions. We demonstrate that the inclusion of a momentum shape factor that differs from unity leads to a well-posed integral model. Therefore, our model does not exhibit the mathematical pathologies that appear in previously proposed unsteady integral models of turbulent plumes. A stability threshold for the value of the shape factor is identified, resulting in a range of its values where the amplitude of small perturbations to the steady solutions decay with distance from the source. The hyperbolic character of the system allows the formation of discontinuities in the fields describing the plume properties during the unsteady evolution. We compute numerical solutions to illustrate the transient development following an abrupt change in the source conditions. The adjustment to the new source conditions occurs through the propagation of a pulse of fluid through the plume. The dynamics of this pulse are described by a similarity solution and, by constructing this new similarity solution, we identify three regimes in which the evolution of the transient pulse following adjustment of the source qualitatively differ.Comment: 41 pages, 16 figures, under consideration for publication in Journal of Fluid Mechanic

Evidence for Ubiquitous Collimated Galactic-Scale Outflows along the Star-Forming Sequence at z~0.5

We present an analysis of the MgII 2796, 2803 and FeII 2586, 2600 absorption line profiles in individual spectra of 105 galaxies at 0.3<z<1.4. The galaxies, drawn from redshift surveys of the GOODS fields and the Extended Groth Strip, fully sample the range in star formation rates (SFRs) occupied by the star-forming sequence with stellar masses log M_*/M_sun > 9.5 at 0.3<z<0.7. Using the Doppler shifts of the MgII and FeII absorption lines as tracers of cool gas kinematics, we detect large-scale winds in 66+/-5% of the galaxies. HST/ACS imaging and our spectral analysis indicate that the outflow detection rate depends primarily on galaxy orientation: winds are detected in ~89% of galaxies having inclinations (i) <30 degrees (face-on), while the wind detection rate is only ~45% in objects having i>50 degrees (edge-on). Combined with the comparatively weak dependence of the wind detection rate on intrinsic galaxy properties, this suggests that biconical outflows are ubiquitous in normal, star-forming galaxies at z~0.5. We find that the wind velocity is correlated with host galaxy M_* at 3.4-sigma significance, while the equivalent width of the flow is correlated with host galaxy SFR at 3.5-sigma significance, suggesting that hosts with higher SFR may launch more material into outflows and/or generate a larger velocity spread for the absorbing clouds. Assuming that the gas is launched into dark matter halos with simple, isothermal density profiles, the wind velocities measured for the bulk of the cool material (~200-400 km/s) are sufficient to enable escape from the halo potentials only for the lowest-M_* systems in the sample. However, the outflows typically carry sufficient energy to reach distances of >50 kpc, and may therefore be a viable source of cool material for the massive circumgalactic medium observed around bright galaxies at z~0. [abridged]Comment: Submitted to ApJ. 61 pages, 25 figures, 4 tables, 4 appendices. Uses emulateapj forma

The Slitmask Alignment Tool: robust, efficient, and astronomer-friendly software for aligning multi-object slitmasks

Multi-object spectroscopy via custom slitmasks is a key capability on three instruments at the W. M. Keck Observatory. Before observers can acquire spectra they must complete a complex procedure to align each slit with its corresponding science target. We developed the Slitmask Alignment Tool (SAT), to replace a complex, inefficient, and error-prone slitmask alignment process that often resulted in lost sky time for novice and experienced observers alike. The SAT accomplishes rapid initial mask alignment, prevents field misidentification, accurately predicts alignment box image locations, corrects for flexure-induced image displacement, verifies the instrument and exposure configuration, and accommodates both rectangular and trapezoidal alignment box shapes. The SAT is designed to lead observers through the alignment process and coordinate image acquisition with instrument and telescope moves to improve efficiencies. By simplifying the process to just a few mouse clicks, the SAT enables even novice observers to achieve robust, efficient, and accurate alignment of slitmasks on all three Keck instruments supporting multislit spectroscopy, saving substantial observing time

The Infrared Imaging Spectrograph (IRIS) for TMT: the atmospheric dispersion corrector

We present a conceptual design for the atmospheric dispersion corrector (ADC) for TMT's Infrared Imaging Spectrograph (IRIS). The severe requirements of this ADC are reviewed, as are limitations to observing caused by uncorrectable atmospheric effects. The requirement of residual dispersion less than 1 milliarcsecond can be met with certain glass combinations. The design decisions are discussed and the performance of the design ADC is described. Alternative options and their performance tradeoffs are also presented.Comment: SPIE Astronomical Instrumentation 201

Ridges, Mounds, and valleys : glacial-interglacial history of the Kaskaskia Basin, Southwestern Illinois, 55th Midwest Friends of the Pleistocene 2011 Field Conference

Geophysical surveys: two-dimensional resistivity imaging; Field trip stops: 1. Keyesport Sand and Gravel Pit; 2. Terrapin Ridge: Cores and Geophysics; 3. Ogles Creek Section; 4. Emerald Mound: Archaeology and History; 5. Pleasant Ridge Area: Cores and Geophysics; 6. Highbanks Road Section; 7. Vandalia Sand and Gravel Pit; 8. Central Illinois Materials Sand and Gravel Pit: Catfish Pond Paleoecology; 9. Pittsburg Basin: Paleoenvironmental History from Fossil Pollen and Ostracode Records in South-Central Illinois; 10. Sodium-Affected Soils in South-Central Illinois: Relationships with Relict Patterned GroundOpe

GBM heterogeneity as a function of variable epidermal growth factor receptor variant III activity.

Abnormal activation of the epidermal growth factor receptor (EGFR) due to a deletion of exons 2-7 of EGFR (EGFRvIII) is a common alteration in glioblastoma (GBM). While this alteration can drive gliomagenesis, tumors harboring EGFRvIII are heterogeneous. To investigate the role for EGFRvIII activation in tumor phenotype we used a neural progenitor cell-based murine model of GBM driven by EGFR signaling and generated tumor progenitor cells with high and low EGFRvIII activation, pEGFRHi and pEGFRLo. In vivo, ex vivo, and in vitro studies suggested a direct association between EGFRvIII activity and increased tumor cell proliferation, decreased tumor cell adhesion to the extracellular matrix, and altered progenitor cell phenotype. Time-lapse confocal imaging of tumor cells in brain slice cultures demonstrated blood vessel co-option by tumor cells and highlighted differences in invasive pattern. Inhibition of EGFR signaling in pEGFRHi promoted cell differentiation and increased cell-matrix adhesion. Conversely, increased EGFRvIII activation in pEGFRLo reduced cell-matrix adhesion. Our study using a murine model for GBM driven by a single genetic driver, suggests differences in EGFR activation contribute to tumor heterogeneity and aggressiveness

Evolution of the Near-Infrared Tully-Fisher Relation: Constraints on the Relationship Between the Stellar and Total Masses of Disk Galaxies since z=1

Using a combination of Keck spectroscopy and near-infrared imaging, we investigate the K-band and stellar mass Tully-Fisher relation for 101 disk galaxies at 0.2 < z < 1.2, with the goal of placing the first observational constraints on the assembly history of halo and stellar mass. Our main result is a lack of evolution in either the K-band or stellar mass Tully-Fisher relation from z = 0 - 1.2. Furthermore, although our sample is not statistically complete, we consider it suitable for an initial investigation of how the fraction of total mass that has condensed into stars is distributed with both redshift and total halo mass. We calculate stellar masses from optical and near-infrared photometry and total masses from maximum rotational velocities and disk scale lengths, utilizing a range of model relationships derived analytically and from simulations. We find that the stellar/total mass distribution and stellar-mass Tully-Fisher relation for z > 0.7 disks is similar to that at lower redshift, suggesting that baryonic mass is accreted by disks along with dark matter at z < 1, and that disk galaxy formation at z < 1 is hierarchical in nature. We briefly discuss the evolutionary trends expected in conventional structure formation models and the implications of extending such a study to much larger samples.Comment: ApJ, in press, 9 page

Neural responses to facial and vocal expressions of fear and disgust

Neuropsychological studies report more impaired responses to facial expressions of fear than disgust in people with amygdala lesions, and vice versa in people with Huntington's disease. Experiments using functional magnetic resonance imaging (fMRI) have confirmed the role of the amygdala in the response to fearful faces and have implicated the anterior insula in the response to facial expressions of disgust. We used fMRI to extend these studies to the perception of fear and disgust from both facial and vocal expressions. Consistent with neuropsychological findings, both types of fearful stimuli activated the amygdala. Facial expressions of disgust activated the anterior insula and the caudate-putamen; vocal expressions of disgust did not significantly activate either of these regions. All four types of stimuli activated the superior temporal gyrus. Our findings therefore (i) support the differential localization of the neural substrates of fear and disgust; (ii) confirm the involvement of the amygdala in the emotion of fear, whether evoked by facial or vocal expressions; (iii) confirm the involvement of the anterior insula and the striatum in reactions to facial expressions of disgust; and (iv) suggest a possible general role for the perception of emotional expressions for the superior temporal gyrus