Computational design of a sensitive, selective phase-changing sensor protein for the VX nerve agent.

The VX nerve agent is one of the deadliest chemical warfare agents. Specific, sensitive, real-time detection methods for this neurotoxin have not been reported. The creation of proteins that use biological recognition to fulfill these requirements using directed evolution or library screening methods has been hampered because its toxicity makes laboratory experimentation extraordinarily expensive. A pair of VX-binding proteins were designed using a supercharged scaffold that couples a large-scale phase change from unstructured to folded upon ligand binding, enabling fully internal binding sites that present the maximum surface area possible for high affinity and specificity in target recognition. Binding site residues were chosen using a new distributed evolutionary algorithm implementation in protCAD. Both designs detect VX at parts per billion concentrations with high specificity. Computational design of fully buried molecular recognition sites, in combination with supercharged phase-changing chassis proteins, enables the ready development of a new generation of small-molecule biosensors.

Effects of a More Restrictive Transfusion Trigger in Trauma Patients.

Since the Transfusion Requirements in Critical Care trial, studies have shown that acutely ill patients can drift as a low as 5 g/dL. This study reviews a transfusion trigger change to 6.5 g/dL, which we hypothesize will conserve resources and improve quality of care. This is a retrospective chart review at an urban Level I trauma center from January through December 2015 after our trauma service changed the transfusion trigger from 7 to 6.5 g/dL. Outcomes in patients before (TT7) and after (TT6.5) the change in transfusion threshold were then compared. One hundred thirty-one discrete patients were included in this trial, with 285 instances of a hemoglobin of 7 g/dL or less and 178 transfusions. Seventy-two patients were before the change in threshold and 59 after. There was no change in length of hospital stay, ICU stay, ventilator days, mortality, and organ system failure after change in the transfusion threshold. After initiation of a more conservative threshold, 72 units of blood were saved. Decreased transfusion threshold was associated with no worse outcomes associated with decreased resource utilization.

Focused apodized forked grating coupler.

The forked grating coupler (FGC) is an optical vortex interface for silicon photonics. Using the structure of a Bragg grating coupler with a calculated forked hologram, the FGC couples optical vortex modes into confined waveguide modes of a photonic integrated circuit. Design methodologies are given, as well as measured performance data from fabricated devices. Data are analyzed with a variety of metrics. The effectiveness of design features are evaluated. Advanced FGC designs are demonstrated with focused forked gratings, allowing feed length to be reduced, and with apodization improving vortex mode fidelity. Some configurations achieve over 25 dB multiplexing crosstalk isolation.

Dispersion engineering of surface plasmons.

In this work, it is shown how the shapes of surface plasmon dispersion curves can be engineered by manipulating the distribution of the electromagnetic fields in multilayer structures, which themselves are controlled by the free electron density in metal-like materials, such as doped semiconductors in the THz spectral range. By having a nonuniform free electron density profile, reduced relative to that in typical bulk metals, the electromagnetic fields of surface plasmons are distributed in different metallic materials that have different complex dielectric permittivities. As the in-plane component of surface plasmon's wave-vector increases, they become more confined to a particular layer of the multilayer structure and have energies that are predictable by considering the permittivity of the layer in which the fields are most concentrated. Unusual and arbitrary shapes of surface plasmon dispersion curves can be designed, including stair steps and dovetails shapes.

Light localization, photon sorting, and enhanced absorption in subwavelength cavity arrays.

A periodically patterned metal-dielectric composite material is designed, fabricated and characterized that spatially splits incoming microwave radiation into two spectral ranges, individually channeling the separate spectral bands to different cavities within each spatially repeating unit cell. Further, the target spectral bands are absorbed within each associated set of cavities. The photon sorting mechanism, the design methodology, and experimental methods used are all described in detail. A spectral splitting efficiency of 93-96% and absorption of 91-92% at the two spectral bands is obtained for the structure. This corresponds to an absorption enhancement over 600% as compared to the absorption in the same thickness of absorbing material. Methods to apply these concepts to other spectral bands are also described.

The light filtering and guiding properties of high finesse phase resonant compound gratings.

Phase resonances in compound gratings are studied in the frequency and time domains, with the gratings having two dissimilar grooves within the unit cell that each support waveguide cavity modes that couple. Described in this work are the dependence of the phase resonances' Q on the degree of difference between the grooves in the unit cell, their optical properties, a closed-form expression describing their dispersion, their excitation, and the extraction of energy from the phase resonances into free space and into a waveguide. Application to optical filters and corrugated surface antennas are discussed.

Polarization independent enhanced optical transmission in one-dimensional gratings and device applications.

A review and analysis is performed of various resonance effects associated with subwavelength one-dimensional (1-D) metal gratings for transverse electric (TE) and transverse magnetic (TM) polarized incident radiation. It is shown that by tuning the structural geometry (especially the groove width) and material composition of the 1-D gratings, polarization independent enhanced optical transmission (EOT) can be achieved. Three different cases of EOT have been studied for 1-D metal gratings: a) EOT for TM-polarized incident radiation b) EOT for TE-polarized incident radiation, and most importantly c) EOT for un-polarized incident light. Potential uses of these results in the design and improvement of various optoelectronic devices, such as polarizers, photodetectors and wavelength filters are discussed.

Numerical modeling of electromagnetic resonance enhanced silicon metal-semiconductor-metal photodetectors.

A rigorous method of modeling the performance of metal-semiconductor-metal photodetectors (MSM-PD) that use several electromagnetic resonance (ER) modes and optical modes to enhance performance is presented. These ER and optical modes include surface plasmons, Wood-Rayleigh anomalies and vertical cavity modes. Five modeling algorithms are integrated together in a time-dependent way to model a 256 pseudo-random bit sequence (PRBS) of 850nm wavelength TM polarized light, the electromagnetic field distribution in the MSM-PD, quasi-static electric field, the charge carrier motion, and an algorithm to construct eye diagrams and analyze responsivity, inter-symbol interference (ISI) and bit error ratio (BER). We report on the use of a combination of ER and optical modes in channeling more than 83% of the incident light into the silicon even though 60% of the Si surface area is covered with metal contacts. Also, this channeled light is localized near the Si surface below the contact window. The absorption in the metal contacts, reflection, diffraction, electromagnetic field profiles, Poynting vector, photocurrent, eye diagrams, quality factors, responsivity and BER are calculated. Designs for Si MSM-PDs with a bandwidth of 100Gb/s, responsivities in the range of 0.05?0.30A/W and BERs in the range of 10-20?10-10 are described.

Role of optical and surface plasmon modes in enhanced transmission and applications.

An analysis of several types of one-dimensional transmission gratings structures with different metal contact geometries is used to study the role of horizontally oriented surface plasmons, cavity modes and other optical modes in enhanced transmission. Several competing theories of enhanced transmission are presented and the analysis of the structures in this work clearly establishes that horizontal surface plasmons can enhance or inhibit transmission depending on whether the HSPs establish vortices of energy that circulate in a direction that enhances or inhibits the flow of energy through the center of the grooves. Also, we show that enhanced transmission can be achieved using a different mechanism than previously reported in the literature. This new mechanism is a Fabry-Perot resonance produced by small notches in the top metal surface, which concentrates the energy from the incident beam and steers it through the slit openings and into the substrate. Finally, applications of the different structures and their optical modes are discussed including chemical and biological sensors and high bandwidth, high responsivity InGaAs metal-semiconductor-metal photodetectors.