Quantifying the benefit of a proteome reserve in fluctuating environments.

The overexpression of proteins is a major burden for fast-growing bacteria. Paradoxically, recent characterization of the proteome of Escherichia coli found many proteins expressed in excess of what appears to be optimal for exponential growth. Here, we quantitatively investigate the possibility that this overexpression constitutes a strategic reserve kept by starving cells to quickly meet demand upon sudden improvement in growth conditions. For cells exposed to repeated famine-and-feast cycles, we derive a simple relation between the duration of feast and the allocation of the ribosomal protein reserve to maximize the overall gain in biomass during the feast

Vertex-Unfoldings of Simplicial Polyhedra

We present two algorithms for unfolding the surface of any polyhedron, all of whose faces are triangles, to a nonoverlapping, connected planar layout. The surface is cut only along polyhedron edges. The layout is connected, but it may have a disconnected interior: the triangles are connected at vertices, but not necessarily joined along edges.Comment: 10 pages; 7 figures; 8 reference

Squarepants in a Tree: Sum of Subtree Clustering and Hyperbolic Pants Decomposition

We provide efficient constant factor approximation algorithms for the problems of finding a hierarchical clustering of a point set in any metric space, minimizing the sum of minimimum spanning tree lengths within each cluster, and in the hyperbolic or Euclidean planes, minimizing the sum of cluster perimeters. Our algorithms for the hyperbolic and Euclidean planes can also be used to provide a pants decomposition, that is, a set of disjoint simple closed curves partitioning the plane minus the input points into subsets with exactly three boundary components, with approximately minimum total length. In the Euclidean case, these curves are squares; in the hyperbolic case, they combine our Euclidean square pants decomposition with our tree clustering method for general metric spaces.Comment: 22 pages, 14 figures. This version replaces the proof of what is now Lemma 5.2, as the previous proof was erroneou

Orbiter Entry Aeroheating Working Group Viscous CFD Boundary Layer Transition Trailblazer Solutions

Boundary layer transition correlations for the Shuttle Orbiter have been previously developed utilizing a two-layer boundary layer prediction technique. The particular two-layer technique that was used is limited to Mach numbers less than 20. To allow assessments at Mach numbers greater than 20, it is proposed to use viscous CFD to the predict boundary layer properties. This report addresses if the existing Orbiter entry aeroheating viscous CFD solutions, which were originally intended to be used for heat transfer rate predictions, adequately resolve boundary layer edge properties and if the existing two-layer results could be leveraged to reduce the number of needed CFD solutions. The boundary layer edge parameters from viscous CFD solutions are extracted along the wind side centerline of the Space Shuttle Orbiter at reentry conditions, and are compared with results from the two-layer boundary layer prediction technique. The differences between the viscous CFD and two-layer prediction techniques vary between Mach 6 and 18 flight conditions and Mach 6 wind tunnel conditions, and there is not a straightforward scaling between the viscous CFD and two-layer values. Therefore: it is not possible to leverage the existing two-layer Orbiter flight boundary layer data set as a substitute for a viscous CFD data set; but viscous CFD solutions at the current grid resolution are sufficient to produce a boundary layer data set suitable for applying edge-based boundary layer transition correlations

Spurious phase in a model for traffic on a bridge

We present high-precision Monte Carlo data for the phase diagram of a two-species driven diffusive system, reminiscent of traffic across a narrow bridge. Earlier studies reported two phases with broken symmetry; the existence of one of these has been the subject of some debate. We show that the disputed phase disappears for sufficiently large systems and/or sufficiently low bulk mobility.Comment: 8 pages, 3 figures, JPA styl

Nano-Aperture Array Based Optical Imaging System on a Microfluidic Chip

We report the implementation of a novel nano-aperture array based imaging technique in a microfluidic network, termed "Optofluidic Microscopy (OFM)". The OFM prototype features high resolution, compact volume and capable of high-throughput sample imaging

Optofluidic microscope and its applications in biology

In this article, we will demonstrate a novel optical imaging device that can be directly integrated into a microfluidic network, and therefore enables on-chip imaging in a microfluidic system. This micro imaging device, termed optofluidic microscope (OFM) is potentially free of bulk optics and is based on a nanohole array defined in a nontransmissive metallic layer that is patterned onto the floor of the microfluidic channel. The operation of the optofluidic microscope will be explained in details and its performance is examined by using a popular animal model, Caenorhabditis elegans (C. elegans). Images from a large population of nematode worms are efficiently acquired within a short time frame. The quality of the OFM images of C. elegans and the morphological characteristics revealed therein are evaluated. Two groups of early-stage C elegans larvae, wild-type and dpy-24 are successfully separated even though their morphological difference at the larval stage is subtle. The experimental results support our claim that the methodology described therein can be effectively used to develop a powerful tool for fulfilling high-resolution, high-throughput imaging task in microfluidics-based systems

Spitzer IRS Observations of the Galactic Center: Shocked Gas in the Radio Arc Bubble

We present Spitzer IRS spectra (R ~600, 10 - 38 micron) of 38 positions in the Galactic Center (GC), all at the same Galactic longitude and spanning plus/minus 0.3 degrees in latitude. Our positions include the Arches Cluster, the Arched Filaments, regions near the Quintuplet Cluster, the ``Bubble'' lying along the same line-of-sight as the molecular cloud G0.11-0.11, and the diffuse interstellar gas along the line-of-sight at higher Galactic latitudes. From measurements of the [O IV], [Ne II], [Ne III], [Si II], [S III], [S IV], [Fe II], [Fe III], and H_2 S(0), S(1), and S(2) lines we determine the gas excitation and ionic abundance ratios. The Ne/H and S/H abundance ratios are ~ 1.6 times that of the Orion Nebula. The main source of excitation is photoionization, with the Arches Cluster ionizing the Arched Filaments and the Quintuplet Cluster ionizing the gas nearby and at lower Galactic latitudes including the far side of the Bubble. In addition, strong shocks ionize gas to O^{+3} and destroy dust grains, releasing iron into the gas phase (Fe/H ~ 1.3 times 10^{-6} in the Arched Filaments and Fe/H ~ 8.8 times 10^{-6} in the Bubble). The shock effects are particularly noticeable in the center of the Bubble, but O$^{+3}$ is present in all positions. We suggest that the shocks are due to the winds from the Quintuplet Cluster Wolf-Rayet stars. On the other hand, the H_2 line ratios can be explained with multi-component models of warm molecular gas in photodissociation regions without the need for H_2 production in shocks.Comment: 51 pages, 17 figures To be published in the Astrophysical Journa

A compact optofluidic microscope

We demonstrate a novel optical imaging device that can be directly integrated into a microfluidic network, and therefore enables on-chip imaging in a microfluidic system. This micro imaging device, termed optofluidic microscope (OFM) is free of bulk optics and is based on a nanohole array defined in a non-transmissive metallic layer that is patterned onto the floor of the microfluidic channel. The operation of the optofluidic microscope will be explained in details and its performance is examined by using a popular animal model, Caenorhabditis elegans (C. elegans). Images from a large population of nematode worms are efficiently acquired within a short time frame. The quality of the OFM images of C. elegans and the morphological characteristics revealed therein are evaluated. Two groups of early-stage C. elegans larvae, wild-type and dpy-24 are successfully separated even though their morphological difference at the larval stage is subtle. The experimental results support our claim that the methodology described therein can be effectively used to develop a powerful tool for fulfilling high-resolution, high-throughput imaging task in microfluidics-based systems