Buckling of a growing tissue and the emergence of two-dimensional patterns

The process of biological growth and the associated generation of residual stress has previously been considered as a driving mechanism for tissue buckling and pattern selection in numerous areas of biology. Here, we develop a two-dimensional thin plate theory to simulate the growth of cultured intestinal epithelial cells on a deformable substrate, with the goal of elucidating how a tissue engineer might best recreate the regular array of invaginations (crypts of Lieberkühn) found in the wall of the mammalian intestine. We extend the standard von Kármán equations to incorporate inhomogeneity in the plate’s mechanical properties and surface stresses applied to the substrate by cell proliferation. We determine numerically the configurations of a homogeneous plate under uniform cell growth, and show how tethering to an underlying elastic foundation can be used to promote higher-order buckled configurations. We then examine the independent effects of localised softening of the substrate and spatial patterning of cellular growth, demonstrating that (within a two-dimensional framework, and contrary to the predictions of one-dimensional models) growth patterning constitutes a more viable mechanism for control of crypt distribution than does material inhomogeneity

An analytically linearized helicopter model with improved modeling accuracy

An analytically linearized model for helicopter flight response including rotor blade dynamics and dynamic inflow, that was recently developed, was studied with the objective of increasing the understanding, the ease of use, and the accuracy of the model. The mathematical model is described along with a description of the UH-60A Black Hawk helicopter and flight test used to validate the model. To aid in utilization of the model for sensitivity analysis, a new, faster, and more efficient implementation of the model was developed. It is shown that several errors in the mathematical modeling of the system caused a reduction in accuracy. These errors in rotor force resolution, trim force and moment calculation, and rotor inertia terms were corrected along with improvements to the programming style and documentation. Use of a trim input file to drive the model is examined. Trim file errors in blade twist, control input phase angle, coning and lag angles, main and tail rotor pitch, and uniform induced velocity, were corrected. Finally, through direct comparison of the original and corrected model responses to flight test data, the effect of the corrections on overall model output is shown

Bayesian variable selection and data integration for biological regulatory networks

A substantial focus of research in molecular biology are gene regulatory networks: the set of transcription factors and target genes which control the involvement of different biological processes in living cells. Previous statistical approaches for identifying gene regulatory networks have used gene expression data, ChIP binding data or promoter sequence data, but each of these resources provides only partial information. We present a Bayesian hierarchical model that integrates all three data types in a principled variable selection framework. The gene expression data are modeled as a function of the unknown gene regulatory network which has an informed prior distribution based upon both ChIP binding and promoter sequence data. We also present a variable weighting methodology for the principled balancing of multiple sources of prior information. We apply our procedure to the discovery of gene regulatory relationships in Saccharomyces cerevisiae (Yeast) for which we can use several external sources of information to validate our results. Our inferred relationships show greater biological relevance on the external validation measures than previous data integration methods. Our model also estimates synergistic and antagonistic interactions between transcription factors, many of which are validated by previous studies. We also evaluate the results from our procedure for the weighting for multiple sources of prior information. Finally, we discuss our methodology in the context of previous approaches to data integration and Bayesian variable selection.Comment: Published in at http://dx.doi.org/10.1214/07-AOAS130 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Learning a Static Analyzer from Data

To be practically useful, modern static analyzers must precisely model the effect of both, statements in the programming language as well as frameworks used by the program under analysis. While important, manually addressing these challenges is difficult for at least two reasons: (i) the effects on the overall analysis can be non-trivial, and (ii) as the size and complexity of modern libraries increase, so is the number of cases the analysis must handle. In this paper we present a new, automated approach for creating static analyzers: instead of manually providing the various inference rules of the analyzer, the key idea is to learn these rules from a dataset of programs. Our method consists of two ingredients: (i) a synthesis algorithm capable of learning a candidate analyzer from a given dataset, and (ii) a counter-example guided learning procedure which generates new programs beyond those in the initial dataset, critical for discovering corner cases and ensuring the learned analysis generalizes to unseen programs. We implemented and instantiated our approach to the task of learning JavaScript static analysis rules for a subset of points-to analysis and for allocation sites analysis. These are challenging yet important problems that have received significant research attention. We show that our approach is effective: our system automatically discovered practical and useful inference rules for many cases that are tricky to manually identify and are missed by state-of-the-art, manually tuned analyzers

Mobile remote manipulator vehicle system

A mobile remote manipulator system is disclosed for assembly, repair and logistics transport on, around and about a space station square bay truss structure. The vehicle is supported by a square track arrangement supported by guide pins integral with the space station truss structure and located at each truss node. Propulsion is provided by a central push-pull drive mechanism that extends out from the vehicle one full structural bay over the truss and locks drive rods into the guide pins. The draw bar is now retracted and the mobile remote manipulator system is pulled onto the next adjacent structural bay. Thus, translation of the vehicle is inchworm style. The drive bar can be locked onto two guide pins while the extendable draw bar is within the vehicle and then push the vehicle away one bay providing bidirectional push-pull drive. The track switches allow the vehicle to travel in two orthogonal directions over the truss structure which coupled with the bidirectional drive, allow movement in four directions on one plane. The top layer of this trilayered vehicle is a logistics platform. This platform is capable of 369 degees of rotation and will have two astronaut foot restraint platforms and a space crane integral

Passive phloem loading and long-distance transport in a synthetic tree-on-a-chip

Vascular plants rely on differences of osmotic pressure to export sugars from regions of synthesis (mature leaves) to sugar sinks (roots, fruits). In this process, known as M\"unch pressure flow, the loading of sugars from photosynthetic cells to the export conduit (the phloem) is crucial, as it sets the pressure head necessary to power long-distance transport. Whereas most herbaceous plants use active mechanisms to increase phloem concentration above that of the photosynthetic cells, in most tree species, for which transport distances are largest, loading seems to occur via passive symplastic diffusion from the mesophyll to the phloem. Here, we use a synthetic microfluidic model of a passive loader to explore the nonlinear dynamics that arise during export and determine the ability of passive loading to drive long-distance transport. We first demonstrate that in our device, phloem concentration is set by the balance between the resistances to diffusive loading from the source and convective export through the phloem. Convection-limited export corresponds to classical models of M\"unch transport, where phloem concentration is close to that of the source; in contrast, diffusion-limited export leads to small phloem concentrations and weak scaling of flow rates with the hydraulic resistance. We then show that the effective regime of convection-limited export is predominant in plants with large transport resistances and low xylem pressures. Moreover, hydrostatic pressures developed in our synthetic passive loader can reach botanically relevant values as high as 10 bars. We conclude that passive loading is sufficient to drive long-distance transport in large plants, and that trees are well suited to take full advantage of passive phloem loading strategies

The Frequency Dependence of Critical-velocity Behavior in Oscillatory Flow of Superfluid Helium-4 Through a 2-micrometer by 2-micrometer Aperture in a Thin Foil

The critical-velocity behavior of oscillatory superfluid Helium-4 flow through a 2-micrometer by 2-micrometer aperture in a 0.1-micrometer-thick foil has been studied from 0.36 K to 2.10 K at frequencies from less than 50 Hz up to above 1880 Hz. The pressure remained less than 0.5 bar. In early runs during which the frequency remained below 400 Hz, the critical velocity was a nearly-linearly decreasing function of increasing temperature throughout the region of temperature studied. In runs at the lowest frequencies, isolated 2 Pi phase slips could be observed at the onset of dissipation. In runs with frequencies higher than 400 Hz, downward curvature was observed in the decrease of critical velocity with increasing temperature. In addition, above 500 Hz an alteration in supercritical behavior was seen at the lower temperatures, involving the appearance of large energy-loss events. These irregular events typically lasted a few tens of half-cycles of oscillation and could involve hundreds of times more energy loss than would have occurred in a single complete 2 Pi phase slip at maximum flow. The temperatures at which this altered behavior was observed rose with frequency, from ~ 0.6 K and below, at 500 Hz, to ~ 1.0 K and below, at 1880 Hz.Comment: 35 pages, 13 figures, prequel to cond-mat/050203