Multiplexed DNA-Modified Electrodes

We report the use of silicon chips with 16 DNA-modified electrodes (DME chips) utilizing DNA-mediated charge transport for multiplexed detection of DNA and DNA-binding protein targets. Four DNA sequences were simultaneously distinguished on a single DME chip with 4-fold redundancy, including one incorporating a single base mismatch. These chips also enabled investigation of the sequence-specific activity of the restriction enzyme Alu1. DME chips supported dense DNA monolayer formation with high reproducibility, as confirmed by statistical comparison to commercially available rod electrodes. The working electrode areas on the chips were reduced to 10 μm in diameter, revealing microelectrode behavior that is beneficial for high sensitivity and rapid kinetic analysis. These results illustrate how DME chips facilitate sensitive and selective detection of DNA and DNA-binding protein targets in a robust and internally standardized multiplexed format

Synthesis and Properties of Dipyridylcyclopentenes

A short and general route to the substituted dipyridylcyclopentenes was explored and several new compounds belonging to this new group of diarylethenes were synthesized. The study of their photochromic and thermochromic properties shows that the rate of the thermal ring opening is strongly dependent on the polarity of the solvent.

DNA binding shifts the redox potential of the transcription factor SoxR

Electrochemistry measurements on DNA-modified electrodes are used to probe the effects of binding to DNA on the redox potential of SoxR, a transcription factor that contains a [2Fe-2S] cluster and is activated through oxidation. A DNA-bound potential of +200 mV versus NHE (normal hydrogen electrode) is found for SoxR isolated from Escherichia coli and Pseudomonas aeruginosa. This potential value corresponds to a dramatic shift of +490 mV versus values found in the absence of DNA. Using Redmond red as a covalently bound redox reporter affixed above the SoxR binding site, we also see, associated with SoxR binding, an attenuation in the Redmond red signal compared with that for Redmond red attached below the SoxR binding site. This observation is consistent with a SoxR-binding-induced structural distortion in the DNA base stack that inhibits DNA-mediated charge transport to the Redmond red probe. The dramatic shift in potential for DNA-bound SoxR compared with the free form is thus reconciled based on a high-energy conformational change in the SoxR–DNA complex. The substantial positive shift in potential for DNA-bound SoxR furthermore indicates that, in the reducing intracellular environment, DNA-bound SoxR is primarily in the reduced form; the activation of DNA-bound SoxR would then be limited to strong oxidants, making SoxR an effective sensor for oxidative stress. These results more generally underscore the importance of using DNA electrochemistry to determine DNA-bound potentials for redox-sensitive transcription factors because such binding can dramatically affect this key protein property

Whispering gallery mode resonator based ultra-narrow linewidth external cavity semiconductor laser

We demonstrate a miniature self-injection locked DFB laser using resonant optical feedback from a high-Q crystalline whispering gallery mode resonator. The linewidth reduction factor is greater than 10,000, with resultant instantaneous linewidth less than 200 Hz. The minimal value of the Allan deviation for the laser frequency stability is 3x10^(-12) at the integration time of 20 us. The laser possesses excellent spectral purity and good long term stability.Comment: To be published in Optics Letter

Cavity optomechanics with Si3N4 membranes at cryogenic temperatures

We describe a cryogenic cavity-optomechanical system that combines Si3N4 membranes with a mechanically-rigid Fabry-Perot cavity. The extremely high quality-factor frequency products of the membranes allow us to cool a MHz mechanical mode to a phonon occupation of less than 10, starting at a bath temperature of 5 kelvin. We show that even at cold temperatures thermally-occupied mechanical modes of the cavity elements can be a limitation, and we discuss methods to reduce these effects sufficiently to achieve ground state cooling. This promising new platform should have versatile uses for hybrid devices and searches for radiation pressure shot noise.Comment: 19 pages, 5 figures, submitted to New Journal of Physic

Multifidelity uncertainty quantification with models based on dissimilar parameters

Multifidelity uncertainty quantification (MF UQ) sampling approaches have been shown to significantly reduce the variance of statistical estimators while preserving the bias of the highest-fidelity model, provided that the low-fidelity models are well correlated. However, maintaining a high level of correlation can be challenging, especially when models depend on different input uncertain parameters, which drastically reduces the correlation. Existing MF UQ approaches do not adequately address this issue. In this work, we propose a new sampling strategy that exploits a shared space to improve the correlation among models with dissimilar parametrization. We achieve this by transforming the original coordinates onto an auxiliary manifold using the adaptive basis (AB) method~\cite{Tipireddy2014}. The AB method has two main benefits: (1) it provides an effective tool to identify the low-dimensional manifold on which each model can be represented, and (2) it enables easy transformation of polynomial chaos representations from high- to low-dimensional spaces. This latter feature is used to identify a shared manifold among models without requiring additional evaluations. We present two algorithmic flavors of the new estimator to cover different analysis scenarios, including those with legacy and non-legacy high-fidelity data. We provide numerical results for analytical examples, a direct field acoustic test, and a finite element model of a nuclear fuel assembly. For all examples, we compare the proposed strategy against both single-fidelity and MF estimators based on the original model parametrization