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At least 1,135 records · Page 63

High-throughput feedback-enabled optogenetic stimulation and spectroscopy in microwell plates

Abstract The ability to perform sophisticated, high-throughput optogenetic experiments has been greatly enhanced by recent open-source illumination devices that allow independent programming of light patterns in single wells of microwell plates. However, there is currently a lack of instrumentation to monitor such experiments in real time, necessitating repeated transfers of the samples to stand-alone analytical instruments, thus limiting the types of experiments that could be performed. Here we address this gap with the development of the optoPlateReader (oPR), an open-source, solid-state, compact device that allows automated optogenetic stimulation and spectroscopy in each well of a 96-well plate. The oPR integrates an optoPlate illumination module with a module called the optoReader, an array of 96 photodiodes and LEDs that allows 96 parallel light measurements. The oPR was optimized for stimulation with blue light and for measurements of optical density and fluorescence. After calibration of all device components, we used the oPR to measure growth and to induce and measure fluorescent protein expression in E. coli . We further demonstrated how the optical read/write capabilities of the oPR permit computer-in-the-loop feedback control, where the current state of the sample can be used to adjust the optical stimulation parameters of the sample according to pre-defined feedback algorithms. The oPR will thus help realize an untapped potential for optogenetic experiments by enabling automated reading, writing, and feedback in microwell plates through open-source hardware that is accessible, customizable, and inexpensive.

59 BASIC BIOLOGICAL SCIENCES↗

Tunable bandgap in halogen doped 2D nitrogenated microporous materials

The quest for new materials with extraordinary electronic, magnetic, and optical properties leads to the synthesis of 2D nitrogenated microporous materials with the hole diameter of 1.16 nm. We computationally study the evolution of the energy bandgaps, optical, and transport properties with the following substituents: hydrogen, fluorine, chlorine, and iodine. We find that such a small perturbation by these atoms has a tremendous impact on the electronic properties of these materials. Indeed, the direct energy bandgaps can be tuned from 1.64 to 0.96 eV by the substituents from hydrogen to iodine. The optical gaps demonstrate similar dependence. From the transport properties, we calculate the effective masses of π-conjugated microporous polymers and find that the conduction electron effective masses are insensitive to halogen substituents while for some low-lying energy valence bands the effective masses can be drastically increased from 0.71 to 2.98 m e and 0.28 to 0.58 m e for the heavy and light holes, respectively. The application of the nitrogenated microporous materials is very broad. They can be useful as sensitizers in solar cells, for water splitting catalysis, in biomedicine, and for gas and energy storage.

36 MATERIALS SCIENCE↗

Deep Learning and Natural Language Processing for Accelerated Inverse Design of Optical Metamaterials

Optical metamaterial device design has enjoyed a long track of success over the past 50 years leading to the manipulation of light over a wide range of wavelengths spanning the ultraviolet to the far infrared. The manipulation of light over such wavelengths has already led to many technological advancements such as the design of selective radiative absorbers for solar energy, daytime passive cooling using deep space, and optical invisibility cloaks for defense applications. Further disruptive advancements in energy, defense, computing, and biomedical fields could be enabled or enhanced by future optical metamaterial devices. These technologies could lead to increased energy efficiency and hence reduced national primary energy consumption, cheap long duration energy storage, and next generation solid-state heat engines. But historically the methods to invent and develop all of these devices have been time- consuming and based mostly on intuition and iteration. Finding an optimal design can take years. In this project we developed a machine learning-based algorithm capable of automatically generating device designs to produce desired optical properties, reducing the design cycle life in certain situations to be almost instantaneous.

36 MATERIALS SCIENCE↗

Thermal-stress modeling of an optical microphone at high temperature.

To help determine the capability range of a MEMS optical microphone design in harsh conditions computer simulations were carried out. Thermal stress modeling was performed up to temperatures of 1000 C. Particular concern was over stress and strain profiles due to the coefficient of thermal expansion mismatch between the polysilicon device and alumina packaging. Preliminary results with simplified models indicate acceptable levels of deformation within the device.

42 ENGINEERING↗

A Modified Model Dielectric Function for Analyzing Optical Spectra of InGaN Nanofilms on Sapphire Substrates

Due to a lower InN bandgap energy Eg~0.7 eV, InxGa1−xN/Sapphire epifilms are considered valuable in the development of low-dimensional heterostructure-based photonic devices. Adjusting the composition x and thickness d in epitaxially grown films has offered many possibilities of light emission across a wide spectral range, from ultraviolet through visible into near-infrared regions. Optical properties have played important roles in making semiconductor materials useful in electro-optic applications. Despite the efforts to grow InxGa1−xN/Sapphire samples, no x- and d-dependent optical studies exist for ultrathin films. Many researchers have used computationally intensive methods to study the electronic band structures Ejk→, and subsequently derive optical properties. By including inter-band transitions at critical points from Ejk→, we have developed a semiempirical approach to comprehend the optical characteristics of InN, GaN and InxGa1−xN. Refractive indices of InxGa1−xN and sapphire substrate are meticulously integrated into a transfer matrix method to simulate d- and x-dependent reflectivity RE and transmission TE spectra of nanostructured InxGa1−xN/Sapphire epifilms. Analyses of RE and TE have offered accurate x-dependent shifts of energy gaps for InxGa1−xN (x = 0.5, 0.7) in excellent agreement with the experimental data.

Talwar, Devki N. (ORCID:0000000202723195)↗

Collapse events of two-color optical beams

Here in this work, we study optical self-focusing that leads to collapse events for the time-independent model of copropagating beams with different wavelengths. We show that collapse events depend on the combined critical power of two beams for fundamental, vortex, and mixed configurations as well as on the ratio of their individual powers.

74 ATOMIC AND MOLECULAR PHYSICS↗

An Efficient Holographic Huygens? Metasurface based on Dielectric Resonant Meta-Atoms.

Subwavelength-thin metasurfaces have shown great promises for the control of optical wavefronts, thus opening new pathways for the development of efficient flat optics. In particular, Huygens’ metasurfaces based on all-dielectric resonant meta-atoms have already shown a huge potential for practical applications with their polarization insensitivity and high transmittance efficiency. Here, we experimentally demonstrate a holographic Huygens’ metasurface based on dielectric resonant meta-atoms capable of complex wavefront control at telecom wavelengths. Our metasurface produces a hologram image in the far-field with 82% transmittance efficiency and 40% imaging efficiency. Such efficient complex wavefront control shows that Huygens’ metasurfaces based on resonant dielectric meta-atoms are a big step towards practical applications of metasurfaces in wavefront design related technologies, including computer-generated holograms, ultra-thin optics, security and data storage devices.

47 OTHER INSTRUMENTATION↗

Deep Learning and Natural Language Processing for Accelerated Inverse Design of Optical Metamaterials

Optical metamaterial device design has enjoyed a long track of success over the past 50 years leading to the manipulation of light over a wide range of wavelengths spanning the ultraviolet to the far infrared. The manipulation of light over such wavelengths has already led to many technological advancements such as the design of selective radiative absorbers for solar energy, daytime passive cooling using deep space, and optical invisibility cloaks for defense applications. Further disruptive advancements in energy, defense, computing, and biomedical fields could be enabled or enhanced by future optical metamaterial devices. These technologies could lead to increased energy efficiency and hence reduced national primary energy consumption, cheap long duration energy storage, and next generation solid-state heat engines. But historically the methods to invent and develop all of these devices have been time- consuming and based mostly on intuition and iteration. Finding an optimal design can take years.

36 MATERIALS SCIENCE↗

Improvement of the Simulation of Cloud Longwave Scattering in Broadband Radiative Transfer Models

Abstract Cloud longwave scattering is generally neglected in general circulation models (GCMs), but it plays a significant and highly uncertain role in the atmospheric energy budget as demonstrated in recent studies. To reduce the errors caused by neglecting cloud longwave scattering, two new radiance adjustment methods are developed that retain the computational efficiency of broadband radiative transfer simulations. In particular, two existing scaling methods and the two new adjustment methods are implemented in the Rapid Radiative Transfer Model (RRTM). The results are then compared with those based on the Discrete Ordinate Radiative Transfer model (DISORT) that explicitly accounts for multiple scattering by clouds. The two scaling methods are shown to improve the accuracy of radiative transfer simulations for optically thin clouds but not effectively for optically thick clouds. However, the adjustment methods reduce computational errors over a wide range, from optically thin to thick clouds. With the adjustment methods, the errors resulting from neglecting cloud longwave scattering are reduced to less than 2 W m−2 for the upward irradiance at the top of the atmosphere and less than 0.5 W m−2 for the surface downward irradiance. The adjustment schemes prove to be more accurate and efficient than a four-stream approximation that explicitly accounts for multiple scattering. The neglect of cloud longwave scattering results in an underestimate of the surface downward irradiance (cooling effect), but the errors are almost eliminated by the adjustment methods (warming effect).

54 ENVIRONMENTAL SCIENCES↗

Experimental characterization and modeling of optical tweezer particle handling dynamics [Modeling and Simulation of Optical Tweezer Particle Handling Dynamics]

Here, we report a new framework for a quantitative understanding of optical trapping (OT) particle handling dynamics. We present a novel three-dimensional particle-based model that includes optical, hydrodynamic, and inter-particle forces. This semi-empirical colloid model is based on an open-source simulation code known as LAMMPS (large-scale atomic/molecular massively parallel simulator) and properly recapitulates the full OT force profile beyond the typical linear approximations valid near the trap center. Simulations are carried out with typical system parameters relevant for our experimental holographic optical trapping (HOT) system, including varied particle sizes, trap movement speeds, and beam powers. Furthermore, we present a new experimental method for measuring both the stable and metastable boundaries of the optical force profile to inform or validate the model’s underlying force profile. We show that our framework is a powerful tool for accurately predicting particle behavior in a practical experimental OT setup and can be used to characterize and predict particle handling dynamics within any arbitrary OT force profile.

36 MATERIALS SCIENCE↗

NEAR-INFRARED REVERBERATION BY DUSTY CLUMPY TORI IN ACTIVE GALACTIC NUCLEI

According to recent models, the accretion disk and black hole in active galactic nuclei (AGNs) are surrounded by a clumpy torus. We investigate the NIR flux variation of the torus in response to a UV flash for various geometries. Anisotropic illumination by the disk and the torus self-occultation contrast our study with earlier works. Both the waning effect of each clump and the torus self-occultation selectively reduce the emission from the region with a short delay. Therefore, the NIR delay depends on the viewing angle (where a more inclined angle leads to a longer delay), and the time response shows an asymmetric profile with negative skewness, opposing the results for optically thin tori. The range of the computed delay coincides with the observed one, suggesting that the viewing angle is primarily responsible for the scatter of the observed delay. We also propose that the red NIR-to-optical color of type 1.8/1.9 objects is caused not only by the dust extinction but also the intrinsically red color. Compared with the modest torus thickness, both a thick and a thin tori display weaker NIR emission. A selection bias is thus expected such that NIR-selected AGNs tend to possess moderately thick tori. A thicker torus shows a narrower and more heavily skewed time profile, while a thin torus produces a rapid response. A super-Eddington accretion rate leads to much weaker NIR emission due to the disk self-occultation and the disk truncation by self-gravity. A long delay is expected from an optically thin and/or a largely misaligned torus. Very weak NIR emission, such as in hot-dust-poor active nuclei, can arise from a geometrically thin torus, a super-Eddington accretion rate, or a slightly misaligned torus.

79 ASTRONOMY AND ASTROPHYSICS↗

Optical properties of transition metal oxide quantum wells

Fabrication of a quantum well, a structure that confines the electron motion along one or more spatial directions, is a powerful method of controlling the electronic structure and corresponding optical response of a material. For example, semiconductor quantum wells are used to enhance optical properties of laser diodes. The ability to control the growth of transition metal oxide films to atomic precision opens an exciting opportunity of engineering quantum wells in these materials. The wide range of transition metal oxide band gaps offers unprecedented control of confinement while the strong correlation of d-electrons allows for various cooperative phenomena to come into play. Here, we combine density functional theory and tight-binding model Hamiltonian analysis to provide a simple physical picture of transition metal oxide quantum well states using a SrO/SrTiO{sub 3}/SrO heterostructure as an example. The optical properties of the well are investigated by computing the frequency-dependent dielectric functions. The effect of an external electric field, which is essential for electro-optical devices, is also considered.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Some constraints on a greenhouse atmosphere for Triton

The possibility that a thick atmosphere exists around Neptune's satellite Triton is examined. The IR optical depth in the gray atmosphere approximation is computed for a range of possible surface compositions, albedos, and gravities. It is found that a self-sustaining optically-thick atmosphere is possible if molecular nitrogen and/or hydrogen are present. It is suggested that bimodal behavior of Triton's atmosphere is possible as seasonal effects and volatile distribution alter the distribution of thermal emission.

Nolan, Michael C.↗

The Vision Machines

The thoughts of computer scientists at LeRC on the direction that computer development is taking and future implications are explored. Experts discuss the coming information superhighway and technologies such as fiber optics and neural networks. The impact of future computers on education, laboratory research, telecommunications, and science visualization.

Source record↗

A Fast Infrared Radiative Transfer Model for Overlapping Clouds

A fast infrared radiative transfer model (FIRTM2) appropriate for application to both single-layered and overlapping cloud situations is developed for simulating the outgoing infrared spectral radiance at the top of the atmosphere (TOA). In FIRTM2 a pre-computed library of cloud reflectance and transmittance values is employed to account for one or two cloud layers, whereas the background atmospheric optical thickness due to gaseous absorption can be computed from a clear-sky radiative transfer model. FIRTM2 is applicable to three atmospheric conditions: 1) clear-sky, 2) single-layered ice or water cloud, and 3) two simultaneous cloud layers in a column (e.g., ice cloud overlying water cloud). Moreover, FIRTM2 outputs the derivatives (i.e., Jacobians) of the TOA brightness temperature with respect to cloud optical thickness and effective particle size. Sensitivity analyses have been carried out to assess the performance of FIRTM2 for two spectral regions, namely the longwave (LW) band (587.3 - 1179.5/cm) and the short-to-medium wave (SMW) band (1180.1 - 2228.9/cm). The assessment is carried out in terms of brightness temperature differences (BTD) between FIRTM2 and the well-known discrete ordinates radiative transfer model (DISORT), henceforth referred to as BTD (F-D). The BTD (F-D) values for single-layered clouds are generally less than 0.8 K. For the case of two cloud layers (specifically ice cloud over water cloud), the BTD(F-D) values are also generally less than 0.8 K except for the SMW band for the case of a very high altitude (>15 km) cloud comprised of small ice particles. Note that for clear-sky atmospheres, FIRTM2 reduces to the clear-sky radiative transfer model that is incorporated into FIRTM2, and the errors in this case are essentially those of the clear-sky radiative transfer model.

Niu, Jianguo↗

Analysis of the DFP/AFCS Systems for Compensating Gravity Distortions on the 70-Meter Antenna

This paper presents the theoretical computations showing the expected performances for both systems. The basic analysis tool is a Physical Optics reflector analysis code that was ported to a parallel computer for faster execution times. There are several steps involved in computing the RF performance of the various systems. 1 . A model of the RF distortions of the main reflector is required. This model is based upon measured holography maps of the 70-meter antenna obtained at 3 elevation angles. The holography maps are then processed (using an appropriate gravity mechanical model of the dish) to provide surface distortion maps at all elevation angles. 2. From the surface distortion maps, ray optics is used to determine the theoretical shape of the DFP that will exactly phase compensate the distortions. 3. From the theoretical shape and a NASTRAN mechanical model of the plate, the actuator positions that generate a surface that provides the best RMS fit to the theoretical model are selected. Using the actuator positions and the NASTRAN model provides an accurate description of the actual mirror shape. 4. Starting from the mechanical drawings of the feed, a computed RF feed pattern is generated. This pattern is expanded into a set of spherical wave modes so that a complete near field analysis of the reflector system can be obtained. 5. For the array feed, the excitation coefficients that provide the maximum gain are computed using a phase conjugate technique. The basic experimental geometry consisted of a dual shaped 70-meter antenna system; a refocusing ellipse, a DFP and an array feed system. To provide physical insight to the systems performance, focal plane field plots are presented at several elevations. Curves of predicted performance are shown for the DFP system, monopulse tracking system, AFCS and combined DFP/AFCS system. The calculated results show that the combined DFP/AFCS system is capable of recovering the majority of the gain lost due to gravity distortion.

Imbriale, William A.↗

Quantification of Porosity in Ceramic Matrix Composites Using Thermography

Thermography is one of the Non-Destructive Evaluation methods used to qualitatively estimate the amount of porosity in as-manufactured ceramic matrix composite (CMC) parts. Through-transmission (TT) thermography allows for comparison of thermal diffusivity caused by differences in material density and porosity at different locations in the part. In this study, volume fraction of pores and its distribution in CMC samples containing different amounts of porosity was quantified using optical microscopy and X-ray computed tomography scans. TT thermography was done on the same specimens and images were analyzed to determine the distribution of thermal diffusivity. Comparison of porosity measurements and thermal diffusivity images shows an inverse correlation. A simple two-phase analytical model describing this relationship is derived for composites and its solution is shown to compare favorably with experimental data. In the absence of porosity data, the model can be used to estimate porosity directly from thermal diffusivity data.

36 MATERIALS SCIENCE↗