DNA: From rigid base-pairs to semiflexible polymers

The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have been obtained from all-atom MD simulation and from high-resolution structural data. On the scale of a hundred nm, DNA is successfully described by a continuous worm-like chain model with homogeneous elastic properties characterized by a set of four elastic constants, which have been directly measured in single-molecule experiments. We present here a theory that links these experiments on different scales, by systematically coarse-graining the rigid base-pair model for random sequence DNA to an effective worm-like chain description. The average helical geometry of the molecule is exactly taken into account in our approach. We find that the available microscopic parameters sets predict qualitatively similar mesoscopic parameters. The thermal bending and twisting persistence lengths computed from MD data are 42 and 48 nm, respectively. The static persistence lengths are generally much higher, in agreement with cyclization experiments. All microscopic parameter sets predict negative twist-stretch coupling. The variability and anisotropy of bending stiffness in short random chains lead to non-Gaussian bend angle distributions, but become unimportant after two helical turns.Comment: 13 pages, 6 figures, 6 table

High nutrient transport and cycling potential revealed in the microbial metagenome of australian sea lion (neophoca cinerea) faeces

Metagenomic analysis was used to examine the taxonomic diversity and metabolic potential of an Australian sea lion (Neophoca cinerea) gut microbiome. Bacteria comprised 98% of classifiable sequences and of these matches to Firmicutes (80%) were dominant, with Proteobacteria and Actinobacteria representing 8% and 2% of matches respectively. The relative proportion of Firmicutes (80%) to Bacteriodetes (2%) is similar to that in previous studies of obese humans and obese mice, suggesting the gut microbiome may confer a predisposition towards the excess body fat that is needed for thermoregulation within the cold oceanic habitats foraged by Australian sea lions. Core metabolic functions, including carbohydrate utilisation (14%), protein metabolism (9%) and DNA metabolism (7%) dominated the metagenome, but in comparison to human and fish gut microbiomes there was a significantly higher proportion of genes involved in phosphorus metabolism (2.4%) and iron scavenging mechanisms (1%). When sea lions defecate at sea, the relatively high nutrient metabolism potential of bacteria in their faeces may accelerate the dissolution of nutrients from faecal particles, enhancing their persistence in the euphotic zone where they are available to stimulate marine production. © 2012 Lavery et al

Probing the Evolution of the Galaxy Interaction/Merger Rate Using Collisional Ring Galaxies

We present the results from our program to determine the evolution of the galaxy interaction/merger rate with redshift using the unique star-forming characteristics of collisional ring galaxies. We have identified 25 distant collisional ring galaxy candidates (CRGCs) in a total of 162 deep Hubble Space Telescope Wide Field/Planetary Camera-2 images obtained from the HST Archives. Based on measured and estimated redshifts, these 25 CRGCs all lie in the redshift interval of 0.1 < z < 1. Using the local collisional ring galaxy volume density and the new ``standard'' cosmology, we find that in order to account for the number of identified CRGCs in our surveyed fields, the galaxy interaction/merger rate, parameterized as (1 + z)^m, must increase steeply with redshift.We determine a minimum value of m = 5.2 $\pm$ 0.7, though m could be as high as 7 or 8. We can rule out a non-evolving (m = 0) and weakly evolving (m = 1-2) galaxy interaction/merger rate at greater than the 4 sigma level of confidence.Comment: Accepted in the Astrophysical Journal (11 pages, 4 figures). Higher resolution version of the figures is available at http://www.astro.cornell.edu/~vassilis/papers

Rotational Doppler velocimetry to probe the angular velocity of spinning microparticles

Laser Doppler velocimetry is a technique used to measure linear velocity, ranging from that of exhaust gases to blood flow. A rotational analog of laser Doppler velocimetry was recently demonstrated, using a rotationally symmetric interference pattern to probe the angular velocity of a spinning object. In this work, we demonstrate the use of a diffraction-limited structured illumination pattern to measure the angular velocity of a micron-sized particle trapped and spinning at tens of Hz in an optical trap. The technique requires no detailed knowledge of the shape of the particle, or the distribution of scatterers within it, and is independent of the particle's chirality, transparency, and birefringence. The particle is also subjected to Brownian motion, which complicates the signal by affecting the rotation rate and the rotation axis. By careful consideration of these influences, we show how the measurement is robust to both, representing a technique with which to probe the rotational motion of microscale particles

Optical Fiber Communication Systems Based on End-to-End Deep Learning: (Invited Paper)

We investigate end-to-end optimized optical transmission systems based on feedforward or bidirectional recurrent neural networks (BRNN) and deep learning. In particular, we report the first experimental demonstration of a BRNN auto-encoder, highlighting the performance improvement achieved with recurrent processing for communication over dispersive nonlinear channels

Transition From Laparoscopic to Robotic Partial Nephrectomy: the Learning Curve for an Experienced Laparoscopic Surgeon

The transition from laparoscopic partial nephrectomy to robotic partial nephrectomy was found to be too rapid for an experienced laparoscopic surgeon