Revisiting the anomalous bending elasticity of sharply bent DNA

Several recent experiments suggest that sharply bent DNA has a surprisingly high bending flexibility, but the cause of this flexibility is poorly understood. Although excitation of flexible defects can explain these results, whether such excitation can occur with the level of DNA bending in these experiments remains unclear. Intriguingly, the DNA contained preexisting nicks in most of these experiments but whether nicks might play a role in flexibility has never been considered in the interpretation of experimental results. Here, using full-atom molecular dynamics simulations, we show that nicks promote DNA basepair disruption at the nicked sites, which drastically reduces DNA bending energy. In addition, lower temperatures suppress the nick-dependent basepair disruption. In the absence of nicks, basepair disruption can also occur but requires a higher level of DNA bending. Therefore, basepair disruption inside B-form DNA can be suppressed if the DNA contains preexisting nicks. Overall, our results suggest that the reported mechanical anomaly of sharply bent DNA is likely dependent on preexisting nicks, therefore the intrinsic mechanisms of sharply bent nick-free DNA remain an open question.Comment: 39 pages, 11 figures, 1 supporting materia

An ASCA Study of the High Luminosity SNR G349.7+0.2

We present ASCA observations of supernova remnant (SNR) G349.7+0.2. The remnant has an irregular shell morphology and is interacting with a molecular cloud, evident from the presence of OH(1720 MHz) masers and shocked molecular gas. The X-ray morphology is consistent with that at radio wavelengths, with a distinct enhancement in the south. The X-ray emission from the SNR is well described by a model of a thermal plasma which has yet to reach ionization equilibrium. The hydrogen column of ~6.0 X 10^{22} cm^{-2} is consistent with the large distance to the remnant of ~22 kpc estimated from the maser velocities. We derive an X-ray luminosity of L_x(0.5-10.0 keV)= 1.8 X 10^{37} d_{22}^2 erg/s, which makes G349.7+0.2 one of the most X-ray luminous shell-type SNRs known in the Galaxy. The age of the remnant is estimated to be about 2800 yrs. The ambient density and pressure conditions appear similar to those inferred for luminous compact SNRs found in starburst regions of other galaxies, and provides support for the notion that these may be the result of SNR evolution in the vicinity of dense molecular clouds.Comment: 5 pages, 3 figures. Accepted for publication in Ap

Anomaly-safe discrete groups

We show that there is a class of finite groups, the so-called perfect groups, which cannot exhibit anomalies. This implies that all non-Abelian finite simple groups are anomaly-free. On the other hand, non-perfect groups generically suffer from anomalies. We present two different ways that allow one to understand these statements.Comment: 11 page

Synthesis of Nonspherical Microcapsules through Controlled Polyelectrolyte Coating of Hydrogel Templates

We report a simple approach to fabricate custom-shape microcapsules using hydrogel templates synthesized by stop flow lithography. Cargo-containing microcapsules were made by coating hydrogel particles with a single layer of poly-l-lysine followed by a one-step core degradation and capsule cross-linking procedure. We determined appropriate coating conditions by investigating the effect of pH, ionic strength, and prepolymer composition on the diffusion of polyelectrolytes into the oppositely charged hydrogel template. We also characterized the degradation of the templating core by tracking the diffusivity of nanoparticles embedded within the hydrogel. Unlike any other technique, this approach allows for easy fabrication of microcapsules with internal features (e.g., toroids) and selective surface modification of Janus particles using any polyelectrolyte. These soft, flexible capsules may be useful for therapeutic applications as well as fundamental studies of membrane mechanics.United States. Army Research Office (Institute for Collaborative Biotechnologies. Grant W911NF-09-0001)National Science Foundation (U.S.) (Grants CMMI-1120724 and DMR-1006147

Decentralized Data Fusion and Active Sensing with Mobile Sensors for Modeling and Predicting Spatiotemporal Traffic Phenomena

The problem of modeling and predicting spatiotemporal traffic phenomena over an urban road network is important to many traffic applications such as detecting and forecasting congestion hotspots. This paper presents a decentralized data fusion and active sensing (D2FAS) algorithm for mobile sensors to actively explore the road network to gather and assimilate the most informative data for predicting the traffic phenomenon. We analyze the time and communication complexity of D2FAS and demonstrate that it can scale well with a large number of observations and sensors. We provide a theoretical guarantee on its predictive performance to be equivalent to that of a sophisticated centralized sparse approximation for the Gaussian process (GP) model: The computation of such a sparse approximate GP model can thus be parallelized and distributed among the mobile sensors (in a Google-like MapReduce paradigm), thereby achieving efficient and scalable prediction. We also theoretically guarantee its active sensing performance that improves under various practical environmental conditions. Empirical evaluation on real-world urban road network data shows that our D2FAS algorithm is significantly more time-efficient and scalable than state-of-the-art centralized algorithms while achieving comparable predictive performance.Comment: 28th Conference on Uncertainty in Artificial Intelligence (UAI 2012), Extended version with proofs, 13 page

Synthesis of a 2,4,6,8,10-dodecapentanoic acid thioester as a substrate for biosynthesis of heat stable antifungal factor (HSAF)

The N-acetylcystamine (SNAC) thioester of dodecapentaenoic acid, an analog of a putative intermediate in the biosynthesis of Heat Stable Antifungal Factor (HSAF), is synthesized. Key steps include sequential Horner–Emmons homologations with the Weinreb amide of diethylphosponoacetic acid, and thioesterification of an aldol-derived 3-hydroxyalkanoate, which serves as a stable precursor of the sensitive polyenoate. The thioester was investigated as a biosynthetic substrate using a purified nonribosomal peptide synthetase and was not incorporated in the observed products

A Search for Nitrogen Enriched Quasars in the Sloan Digital Sky Survey Early Data Release

A search for nitrogen-rich quasars in the Sloan Digital Sky Survey Early Data Release (SDSS EDR) catalog has yielded 16 candidates, including five with very prominent emission, but no cases with nitrogen emission as strong as in Q0353-383. The quasar Q0353-383 has long been known to have extremely strong nitrogen intercombination lines at lambda 1486 and lambda 1750 Angstroms, implying an anomalously high nitrogen abundance of about 15 times solar. It is still the only one of its kind known. A preliminary search through the EDR using the observed property of the weak C IV emission seen in Q0353-383 resulted in a sample of 23 objects with unusual emission or absorption-line properties, including one very luminous redshift 2.5 star-forming galaxy. We present descriptions, preliminary emission-line measurements, and spectra for all the objects discussed here.Comment: 20 pages, 5 figures, submitted to AJ; final refereed versio

First Operation of a Resistive Shell Liquid Argon Time Projection Chamber -- A new Approach to Electric-Field Shaping

We present a new technology for the shaping of the electric field in Time Projection Chambers (TPCs) using a carbon-loaded polyimide foil. This technology allows for the minimisation of passive material near the active volume of the TPC and thus is capable to reduce background events originating from radioactive decays or scattering on the material itself. Furthermore, the high and continuous electric resistivity of the foil limits the power dissipation per unit area and minimizes the risks of damages in the case of an electric field breakdown. Replacing the conventional field cage with a resistive plastic film structure called 'shell' decreases the number of components within the TPC and therefore reduces the potential points of failure when operating the detector. A prototype liquid argon (LAr) TPC with such a resistive shell and with a cathode made of the same material was successfully tested for long term operation with electric field values up to about 1.5 kV/cm. The experiment shows that it is feasible to successfully produce and shape the electric field in liquefied noble-gas detectors with this new technology.Comment: 13 page