Broadband energy-efficient optical modulation by hybrid integration of silicon nanophotonics and organic electro-optic polymer

Silicon-organic hybrid integrated devices have emerging applications ranging from high-speed optical interconnects to photonic electromagnetic-field sensors. Silicon slot photonic crystal waveguides (PCWs) filled with electro-optic (EO) polymers combine the slow-light effect in PCWs with the high polarizability of EO polymers, which promises the realization of high-performance optical modulators. In this paper, a broadband, power-efficient, low-dispersion, and compact optical modulator based on an EO polymer filled silicon slot PCW is presented. A small voltage-length product of V{\pi}*L=0.282Vmm is achieved, corresponding to an unprecedented record-high effective in-device EO coefficient (r33) of 1230pm/V. Assisted by a backside gate voltage, the modulation response up to 50GHz is observed, with a 3-dB bandwidth of 15GHz, and the estimated energy consumption is 94.4fJ/bit at 10Gbit/s. Furthermore, lattice-shifted PCWs are utilized to enhance the optical bandwidth by a factor of ~10X over other modulators based on non-band-engineered PCWs and ring-resonators.Comment: 12 pages, 4 figures, SPIE Photonics West Conference 201

Asymptotic Limits and Zeros of Chromatic Polynomials and Ground State Entropy of Potts Antiferromagnets

We study the asymptotic limiting function $W({G},q) = \lim_{n \to \infty}P(G,q)^{1/n}$, where $P(G,q)$ is the chromatic polynomial for a graph $G$ with $n$ vertices. We first discuss a subtlety in the definition of $W({G},q)$ resulting from the fact that at certain special points $q_s$, the following limits do not commute: $\lim_{n \to \infty} \lim_{q \to q_s} P(G,q)^{1/n} \ne \lim_{q \to q_s} \lim_{n \to \infty} P(G,q)^{1/n}$. We then present exact calculations of $W({G},q)$ and determine the corresponding analytic structure in the complex $q$ plane for a number of families of graphs ${G}$, including circuits, wheels, biwheels, bipyramids, and (cyclic and twisted) ladders. We study the zeros of the corresponding chromatic polynomials and prove a theorem that for certain families of graphs, all but a finite number of the zeros lie exactly on a unit circle, whose position depends on the family. Using the connection of $P(G,q)$ with the zero-temperature Potts antiferromagnet, we derive a theorem concerning the maximal finite real point of non-analyticity in $W({G},q)$, denoted $q_c$ and apply this theorem to deduce that $q_c(sq)=3$ and $q_c(hc) = (3+\sqrt{5})/2$ for the square and honeycomb lattices. Finally, numerical calculations of $W(hc,q)$ and $W(sq,q)$ are presented and compared with series expansions and bounds.Comment: 33 pages, Latex, 5 postscript figures, published version; includes further comments on large-q serie

Space-time Phase Transitions in Driven Kinetically Constrained Lattice Models

Kinetically constrained models (KCMs) have been used to study and understand the origin of glassy dynamics. Despite having trivial thermodynamic properties, their dynamics slows down dramatically at low temperatures while displaying dynamical heterogeneity as seen in glass forming supercooled liquids. This dynamics has its origin in an ergodic-nonergodic first-order phase transition between phases of distinct dynamical "activity". This is a "space-time" transition as it corresponds to a singular change in ensembles of trajectories of the dynamics rather than ensembles of configurations. Here we extend these ideas to driven glassy systems by considering KCMs driven into non-equilibrium steady states through non-conservative forces. By classifying trajectories through their entropy production we prove that driven KCMs also display an analogous first-order space-time transition between dynamical phases of finite and vanishing entropy production. We also discuss how trajectories with rare values of entropy production can be realized as typical trajectories of a mapped system with modified forces

Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1.

Tight binding of Gdown1 represses RNA polymerase II (Pol II) function in a manner that is reversed by Mediator, but the structural basis of these processes is unclear. Although Gdown1 is intrinsically disordered, its Pol II interacting domains were localized and shown to occlude transcription factor IIF (TFIIF) and transcription factor IIB (TFIIB) binding by perfect positioning on their Pol II interaction sites. Robust binding of Gdown1 to Pol II is established by cooperative interactions of a strong Pol II binding region and two weaker binding modulatory regions, thus providing a mechanism both for tight Pol II binding and transcription inhibition and for its reversal. In support of a physiological function for Gdown1 in transcription repression, Gdown1 co-localizes with Pol II in transcriptionally silent nuclei of early Drosophila embryos but re-localizes to the cytoplasm during zygotic genome activation. Our study reveals a self-inactivation through Gdown1 binding as a unique mode of repression in Pol II function

RASSF1A–LATS1 signalling stabilizes replication forks by restricting CDK2-mediated phosphorylation of BRCA2

Genomic instability is a key hallmark of cancer leading to tumour heterogeneity and therapeutic resistance. ​BRCA2 has a fundamental role in error-free DNA repair but also sustains genome integrity by promoting ​RAD51 nucleofilament formation at stalled replication forks. ​CDK2 phosphorylates ​BRCA2 (pS3291-​BRCA2) to limit stabilizing contacts with polymerized ​RAD51; however, how replication stress modulates ​CDK2 activity and whether loss of pS3291-​BRCA2 regulation results in genomic instability of tumours are not known. Here we demonstrate that the Hippo pathway kinase ​LATS1 interacts with ​CDK2 in response to genotoxic stress to constrain pS3291-​BRCA2 and support ​RAD51 nucleofilaments, thereby maintaining genomic fidelity during replication stalling. We also show that ​LATS1 forms part of an ​ATR-mediated response to replication stress that requires the tumour suppressor ​RASSF1A. Importantly, perturbation of the ​ATR–​RASSF1A–​LATS1 signalling axis leads to genomic defects associated with loss of ​BRCA2 function and contributes to genomic instability and ‘BRCA-ness’ in lung cancers

Antiproliferative Withanolides from Datura wrightii

A new withanolide, named withawrightolide (1), and four known withanolides (2−5) were isolated from the aerial parts of Datura wrightii. The structure of compound 1 was elucidated through 2D NMR and other spectroscopic techniques. In addition, the structure of withametelin L (2) was confirmed by X-ray crystallographic analysis. Using MTS viability assays, withanolides 1−5 showed antiproliferative activities against human glioblastoma (U251 and U87), head and neck squamous cell carcinoma (MDA-1986), and normal fetal lung fibroblast (MRC-5) cells with IC50 values in the range between 0.56 and 5.6 μM

A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry

<p>Abstract</p> <p>Background</p> <p>High-resolution tandem mass spectra can now be readily acquired with hybrid instruments, such as LTQ-Orbitrap and LTQ-FT, in high-throughput shotgun proteomics workflows. The improved spectral quality enables more accurate <it>de novo </it>sequencing for identification of post-translational modifications and amino acid polymorphisms.</p> <p>Results</p> <p>In this study, a new <it>de novo </it>sequencing algorithm, called Vonode, has been developed specifically for analysis of such high-resolution tandem mass spectra. To fully exploit the high mass accuracy of these spectra, a unique scoring system is proposed to evaluate sequence tags based primarily on mass accuracy information of fragment ions. Consensus sequence tags were inferred for 11,422 spectra with an average peptide length of 5.5 residues from a total of 40,297 input spectra acquired in a 24-hour proteomics measurement of <it>Rhodopseudomonas palustris</it>. The accuracy of inferred consensus sequence tags was 84%. According to our comparison, the performance of Vonode was shown to be superior to the PepNovo v2.0 algorithm, in terms of the number of <it>de novo </it>sequenced spectra and the sequencing accuracy.</p> <p>Conclusions</p> <p>Here, we improved <it>de novo </it>sequencing performance by developing a new algorithm specifically for high-resolution tandem mass spectral data. The Vonode algorithm is freely available for download at <url>http://compbio.ornl.gov/Vonode</url>.</p

Photochemistry of Furyl- and Thienyldiazomethanes: Spectroscopic Characterization of Triplet 3-Thienylcarbene

Photolysis (λ \u3e 543 nm) of 3-thienyldiazomethane (1), matrix isolated in Ar or N2 at 10 K, yields triplet 3-thienylcarbene (13) and α-thial-methylenecyclopropene (9). Carbene 13 was characterized by IR, UV/vis, and EPR spectroscopy. The conformational isomers of 3-thienylcarbene (s-E and s-Z) exhibit an unusually large difference in zero-field splitting parameters in the triplet EPR spectrum (|D/hc| = 0.508 cm–1, |E/hc| = 0.0554 cm–1; |D/hc| = 0.579 cm–1, |E/hc| = 0.0315 cm–1). Natural Bond Orbital (NBO) calculations reveal substantially differing spin densities in the 3-thienyl ring at the positions adjacent to the carbene center, which is one factor contributing to the large difference in D values. NBO calculations also reveal a stabilizing interaction between the sp orbital of the carbene carbon in the s-Z rotamer of 13 and the antibonding σ orbital between sulfur and the neighboring carbon—an interaction that is not observed in the s-E rotamer of 13. In contrast to the EPR spectra, the electronic absorption spectra of the rotamers of triplet 3-thienylcarbene (13) are indistinguishable under our experimental conditions. The carbene exhibits a weak electronic absorption in the visible spectrum (λmax = 467 nm) that is characteristic of triplet arylcarbenes. Although studies of 2-thienyldiazomethane (2), 3-furyldiazomethane (3), or 2-furyldiazomethane (4) provided further insight into the photochemical interconversions among C5H4S or C5H4O isomers, these studies did not lead to the spectroscopic detection of the corresponding triplet carbenes (2-thienylcarbene (11), 3-furylcarbene (23), or 2-furylcarbene (22), respectively)

An assessment of smartphone and low-cost multi-GNSS single-frequency RTK positioning for low, medium and high ionospheric disturbance periods

The emerging GNSSs make single-frequency (SF) RTK positioning possible. In this contribution two different types of low-cost (few hundred USDs) RTK receivers are analyzed, which can track L1 GPS, B1 BDS, E1 Galileo and L1 QZSS, or any combinations thereof, for a location in Dunedin, New Zealand. These SF RTK receivers can potentially give competitive ambiguity resolution and positioning performance to that of more expensive (thousands USDs) dual-frequency (DF) GPS receivers. A smartphone implementation of one of these SF receiver types is also evaluated. The least-squares variance component estimation (LS-VCE) procedure is first used to formulate a realistic stochastic model, which assures that our receivers at hand can achieve the best possible ambiguity resolution and RTK positioning performance. The best performing low-cost SF RTK receiver types are then assessed against DF GPS receivers and survey-grade antennas. Real data with ionospheric disturbances at low, medium and high levels are analyzed, while making use of the ionosphere-weighted model. It will be demonstrated that when the presence of the residual ionospheric delays increases, instantaneous RTK positioning is not possible for any of the receivers, and a multi-epoch model is necessary to use. It is finally shown that the low-cost SF RTK performance can remain competitive to that of more expensive DF GPS receivers even when the ionospheric disturbance level reaches a Kp-index of 7-, i.e. for a strong geomagnetic storm, for the baseline at hand