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At least 1,027 records · Page 57

Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments

Sophisticated statistical mechanics approaches and human intuition have demonstrated the possibility of self-assembling complex lattices or finite-size constructs. However, attempts so far have mostly only been successful in silico and often fail in experiment because of unpredicted traps associated with kinetic slowing down (gelation, glass transition) and competing ordered structures. Theoretical predictions also face the difficulty of encoding the desired interparticle interaction potential with the experimentally available nano- and micrometer-sized particles. To overcome these issues, we combine SAT assembly (a patchy-particle interaction design algorithm based on constrained optimization) with coarse-grained simulations of DNA nanotechnology to experimentally realize trap-free self-assembly pathways. In this paper, we use this approach to assemble a pyrochlore three-dimensional lattice, coveted for its promise in the construction of optical metamaterials, and characterize it with small-angle x-ray scattering and scanning electron microscopy visualization.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database in which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.

59 BASIC BIOLOGICAL SCIENCES↗

Three-dimensional segmentation of luminal and adventitial borders in serial intravascular ultrasound images

Intravascular ultrasound (IVUS) provides exact anatomy of arteries, allowing accurate quantitative analysis. Automated segmentation of IVUS images is a prerequisite for routine quantitative analyses. We present a new three-dimensional (3D) segmentation technique, called active surface segmentation, which detects luminal and adventitial borders in IVUS pullback examinations of coronary arteries. The technique was validated against expert tracings by computing correlation coefficients (range 0.83-0.97) and William's index values (range 0.37-0.66). The technique was statistically accurate, robust to image artifacts, and capable of segmenting a large number of images rapidly. Active surface segmentation enabled geometrically accurate 3D reconstruction and visualization of coronary arteries and volumetric measurements.

NASA Discipline Cardiopulmonary↗

Global 3D Data Visualization and Analysis Platform With Advanced Machine Learning Capabilities in Support of Lunar Exploration

Introduction: The science goals for NASA’s Artemis program include: a) Understanding the character and origin of lunar polar volatiles, b) Conducting experimental science in the lunar environment and c) Investigating and mitigating exploration risks [1]. The permanently shadowed regions (PSRs) on the Lunar south pole are expected to host large quantities of water-ice and volatiles that are important for sustainable Lunar exploration [2]. There are several missions such as onboard Korea Pathfinder Lunar Orbiter (KPLO: Korean name Danuri) with onboard ShadowCam camera [3], Astrobotic Peregrine Mission One [4], and other efforts underway to obtain high resolution topographic, minerals, volatiles and other information on the moon. We envision a need in immediate future for platforms to integrate these data sets, provide rendering and visualization capabilities in the context of a 3D Lunar globe for easier information access and analysis. NASA's Celestial Mapping System (CMS) [5] is developed to address the need for 3D tools for planetary science investigations, mission planning, in-situ operations, in a 3D-first design constructed around a unified view of a planetary globe. At present CMS provides many critical functionalities that include: 1) equipment planning and optimized placement on Lunar surface 2) line-of-sight (LOS) analysis 3) powerful measurement tools based on 3D terrain with realistic 3D models to represent rovers, astronauts and equipment 4) visualization of derived mapping products (e.g. resource maps), and 5) a data engine for hosting new observations that are not available in other contemporary lunar data tools [5, 7]. Planetary Data Ingestion: CMS can consume and analyze data from locally hosted and external third party sources. It is compatible with Open Geospatial Consortium (OGC) data and file standards and currently integrates datasets from the Astrogeology Science Center of USGS. This includes global and local data acquired from NASA (LRO, Clementine, Lunar Orbiter) and JAXA (SELENE/Kaguya), with capability of integrating more datasets. In addition, users can specify other WMS-hosted data endpoints, which CMS can then query and stream data from automatically. To set-up an automated process for ingestion and accurate rendering, visualization and analysis of external 3rd party planetary datasets within CMS, we initiated the process of ingesting unique dataset of super-enhanced images of the permanently shadowed regions (PSRs) at the lunar poles which were produced by the Hyper-effective nOise Removal U-net Software (HORUS) tool [8]. This tool was developed to enhance the extremely low-light images of the interior of PSRs and provide the ability to see within these regions at and discern surface features (i.e. boulders and craters) down to 3 meters in size. We focused on the Nobile region on the Lunar south pole, selected site for VIPER mission and stitched several images to create a high-resolution map within one of the PSR of Nobile crater. Figure 1 shows the dark PSR zone form the original NAC layer of LRO as the base layer (left image) and the illuminated areas within that crater (center) which was created by ingesting and merging several of HORUS generated images. At present we employ a semi-automated process to ensure spatial accuracy and merger of several overlapping zones. However, we are in the process of completely automating this process by employing AI based techniques that would rank, sort, and stack the images based on their information density. The georectification of the images would employ selected features. Analysis on Ingested Planetary Datasets: Once an external planetary data-set is successfully ingested, georectified and merged seamlessly as a data-layer; CMS’ numerous analysis tools can be used on this data. A Line of Sight (LOS) tool has been developed for CMS which analyzes terrain profiles and obstructions to determine visibility for remote observers [5,6]. Figure 1 (right image) shows the viewshed analysis on the same PSR in the Nobile region. The yellow pin shows the observer location outside the PSR. The yellow area shows the visible part of PSR. The obstructed area with no visibility for the observer is shown in red. The Measurements tool allows the user to take area and distance measurements of features on the terrain using various shapes. Measurement type can be specified in a number of ways: Line, Path, Polygon, Circle, Ellipse, Square, Rectangle or Freehand. Once the shape is specified, elevation information can then be extracted along each of these shapes. Figure 2 (left) shows the measurements performed on a crater n illuminated PSR in Nobile region. The equipment placement tool allows the user to place a 3D equipment model at a desired location and analyze its coverage area. The equipment placement tool is coupled with LOS to determine the coverage. Figure 2 (right) shows an equipment placed on the Lunar terrain and it’s coverage area. The red rays are blocked sight lines and the green rays are non-obstructed sight lines with the cyan lines showing the point of intersection with the terrain. More details are provided in the video demonstrations in Reference 5. Overcoming Polar Distortions: 3D geospatial applications exhibit significant distortions in polar imagery due to several reasons: 1) distortions in the source imagery, 2) incompatible tessellation algorithms at the poles, and 3) map projections. We are leveraging new tessellation algorithms and reprojecting data using projections that are better suited for Lunar poles. The goal is to seamlessly switch to polar projections while maintaining 3D view and navigation.

Maps↗

Retina-inspired narrowband perovskite sensor array for panchromatic imaging

The retina is the essential part of the human visual system that receives light, converts it to neural signal, and transmits to brain for visual recognition. The red, green, and blue (R/G/B) cone retina cells are natural narrowband photodetectors (PDs) sensitive to R/G/B lights. Connecting with these cone cells, a multilayer neuro-network in the retina provides neuromorphic preprocessing before transmitting to brain. Inspired by this sophistication, we develop the narrowband (NB) imaging sensor combining R/G/B perovskite NB sensor array (mimicking the R/G/B photoreceptors) with a neuromorphic algorithm (mimicking the intermediate neural network) for high-fidelity panchromatic imaging. Compared to commercial sensors, we use perovskite “intrinsic” NB PD to exempt the complex optical filter array. In addition, we use an asymmetric device configuration to collect photocurrent without external bias, enabling a power-free photodetection feature. These results display a promising design for efficient and intelligent panchromatic imaging.

42 ENGINEERING↗

pnnl/sven

This is a JavaScript library for a storyline layout algorithm. Storylines are adept at communicating complex change by encoding time on the x-axis and using the proximity of lines in the y direction to represent interaction between entities. The library in this disclosure takes as input a list of objects containing an id, time, and state. The output is a data structure that can be used to conveniently render a storyline visualization. Most importantly, the library computes the y-coordinate of the entities over time that decreases layout artifacts including crossings, wiggles, and whitespace. This is accomplished through multi-objective, multi-stage optimization problem, where the output of one stage produces input and constraints for the next stage.

Arendt, Dustin↗

Towards Plume Impingement Modeling in Space Environments

After 30 years human presence in low-earth orbit, NASA is returning to the moon and eventually will go to Mars. To this end, NASA is constructing the Lunar Gateway, an ISS-like space station to act as a home base for Lunar exploration. A large space station must be assembled while in orbit, using a “piecemeal” approach. In this context, it means that the different modules will arrive at different times and attach to what is already in service. The ISS provides an excellent example of this approach, and the proposed Lunar Gateway will undergo a similar assembly process. This assembly is achieved via “docking” maneuvers between modules, which are made possible by sequential firings of the onboard reaction control system (RCS) thrusters. They work by firing hot gases to produce adverse thrust and the needed change in velocity to safely finish the docking approach. The issue is that the gas from these thrusters' forms flow structures described as “plumes” and can impinge onto the outer surfaces of the space station, causing unwanted forces and moments, heat loads, sediment deposition, and in extreme cases, even surface erosion. All mechanisms that can damage the space station and must be avoided. Both permanent and visiting modules will have these RCS thruster exhaust impingement problems. Accurately and efficiently modeling these plume is an involved multi-physics calculation but also an important tool when designing the control algorithms of approaching modules. This poster presents progress towards this simulation on two fronts. First is the verification of OpenFOAM for rarefied plume impingement calculations by direct comparison to published DAC cases. Second is the estimation of plume impingement strikes over the time scale of an entire docking event. This is done by using a simple plume source flow model and a prescribed motion visualizer—coded in Python. Together these tools help push NASA's capabilities for simulating these plume impingement effects.

Rarefied Flows↗

Fleet DNA Phase 1 Refinement & Phase 2 Implementation; NREL (National Renewable Energy Laboratory)

Fleet DNA acts as a secure data warehouse for medium- and heavy-duty vehicle data. It demonstrates that vehicle drive cycle data can be collected and stored for large-scale analysis and modeling applications. The data serve as a real-world data source for model development and validation. Storage of the results of past/present/future data collection efforts improves analysis efficiency through pooling of shared data and provides the opportunity for 'big data' type analyses. Fleet DNA shows it is possible to develop a common database structure that can store/analyze/report on data sourced from multiple parties, each with unique data formats/types. Data filtration and normalization algorithms developed for the project allow for a wide range of data types and inputs, expanding the project’s potential. Fleet DNA demonstrates the power of integrating Big Data with existing and future tools and analyses: it provides an enhanced understanding and education of users, users can explore greenhouse gases and economic opportunities via AFLEET and ADOPT modeling, drive cycles can be characterized and visualized using DRIVE, high-level vehicle modeling can be performed using real-world drive cycles via FASTSim, and data reporting through Fleet DNA Phase 1 and 2 websites provides external users access to analysis results and gives the opportunity to explore on their own.

33 ADVANCED PROPULSION SYSTEMS↗

Pure JavaScript Storyline Layout Algorithm

This is a JavaScript library for a storyline layout algorithm. Storylines are adept at communicating complex change by encoding time on the x-axis and using the proximity of lines in the y direction to represent interaction between entities. The library in this disclosure takes as input a list of objects containing an id, time, and state. The output is a data structure that can be used to conveniently render a storyline visualization. Most importantly, the library computes the y-coordinate of the entities over time that decreases layout artifacts including crossings, wiggles, and whitespace. This is accomplished through multi-objective, multi-stage optimization problem, where the output of one stage produces input and constraints for the next stage.

Source record↗

Turbulent flow characteristics in an 84-pin rod bundle for typical and damaged spacer grids

Hexagonal rod bundles arranged in a tightly packed triangular lattice are extensively used for heat transfer and energy generation applications. Staggered spacer grids are used to maintain the structural integrity of gas-cooled fast reactor (GFR) fuel assemblies, while inducing localized turbulence in flow. Damage to these spacer grids results in a disruption of flow fields within these hexagonal fuel bundles. Experimental flow visualizations are critical to identify the differences in local flow properties that the structural damage may cause. This experimental research investigates the flow-field characteristics at a near-wall and center plane in a prototypical 84-pin GFR fuel assembly. Newly installed typical spacers and spacers subject to naturally occurring damage due to material degradation over prolonged experimentation were investigated. Velocity fields were acquired by utilizing the matched-index-of-refraction method to obtain time-resolved particle image velocimetry measurements for a Reynolds number of 12 000. Reynolds decomposition statistical results divulged differences in the time-averaged velocity, velocity fluctuations, flow anisotropy, and Reynolds stress distributions. Galilean decomposition demarcated the influence of spacer grid damage on the velocity fields. To extract turbulent structures and elucidate mechanisms of flow instabilities, proper orthogonal decomposition analysis was employed. Reduced order flow reconstructions enabled the application of vortex identification algorithms to determine the spatial and statistical characteristics of vortices generated. This research work provides unique experimental data on the spacer grid condition-dependent flow. The results offer a deeper understanding of fluid dynamics behavior to support GFR rod bundle design efforts and computational fluid dynamics model validation.

36 MATERIALS SCIENCE↗

Multi-Dimensional Scaling on Groups

Leveraging the intrinsic symmetries in data for clear and efficient analysis is an important theme in signal processing and other data-driven sciences. A basic example of this is the ubiquity of the discrete Fourier transform which arises from translational symmetry (i.e. time-delay/phase-shift). Particularly important in this area is understanding how symmetries inform the algorithms that we apply to our data. In this paper we explore the behavior of the dimensionality reduction algorithm multi-dimensional scaling (MDS) in the presence of symmetry. We show that understanding the properties of the underlying symmetry group allows us to make strong statements about the output of MDS even before applying the algorithm itself. In analogy to Fourier theory, we show that in some cases only a handful of fundamental ``frequencies'' (irreducible representations derived from the corresponding group) contribute information for the MDS Euclidean embedding.

Dimensionality reduction, Representation theory, D↗

SU-E-T-02: 90Y Microspheres Dosimetry Calculation with Voxel-S-Value Method: A Simple Use in the Clinic

Purpose: To present a simple and feasible method of voxel-S-value (VSV) dosimetry calculation for daily clinical use in radioembolization (RE) with {sup 90}Y microspheres. Dose distributions are obtained and visualized over CT images. Methods: Spatial dose distributions and dose in liver and tumor are calculated for RE patients treated with Sirtex Medical miscrospheres at our center. Data obtained from the previous simulation of treatment were the basis for calculations: Tc-99m maggregated albumin SPECT-CT study in a gammacamera (Infinia, General Electric Healthcare.). Attenuation correction and ordered-subsets expectation maximization (OSEM) algorithm were applied.For VSV calculations, both SPECT and CT were exported from the gammacamera workstation and registered with the radiotherapy treatment planning system (Eclipse, Varian Medical systems). Convolution of activity matrix and local dose deposition kernel (S values) was implemented with an in-house developed software based on Python code. The kernel was downloaded from www.medphys.it. Final dose distribution was evaluated with the free software Dicompyler. Results: Liver mean dose is consistent with Partition method calculations (accepted as a good standard). Tumor dose has not been evaluated due to the high dependence on its contouring. Small lesion size, hot spots in health tissue and blurred limits can affect a lot the dose distribution in tumors. Extra work includes: export and import of images and other dicom files, create and calculate a dummy plan of external radiotherapy, convolution calculation and evaluation of the dose distribution with dicompyler. Total time spent is less than 2 hours. Conclusion: VSV calculations do not require any extra appointment or any uncomfortable process for patient. The total process is short enough to carry it out the same day of simulation and to contribute to prescription decisions prior to treatment. Three-dimensional dose knowledge provides much more information than other methods of dose calculation usually applied in the clinic.

60 APPLIED LIFE SCIENCES↗

An algorithm for automatic reduction of complex signal flow graphs

A computer algorithm is developed that provides efficient means to compute transmittances directly from a signal flow graph or a block diagram. Signal flow graphs are cast as directed graphs described by adjacency matrices. Nonsearch computation, designed for compilers without symbolic capability, is used to identify all arcs that are members of simple cycles for use with Mason's gain formula. The routine does not require the visual acumen of an interpreter to reduce the topology of the graph, and it is particularly useful for analyzing control systems described for computer analyses by means of interactive graphics.

Young, K. R.↗

Application of a Two Camera Video Imaging System to Three-Dimensional Vortex Tracking in the 80- by 120-Foot Wind Tunnel

A description is presented of two enhancements for a two-camera, video imaging system that increase the accuracy and efficiency of the system when applied to the determination of three-dimensional locations of points along a continuous line. These enhancements increase the utility of the system when extracting quantitative data from surface and off-body flow visualizations. The first enhancement utilizes epipolar geometry to resolve the stereo "correspondence" problem. This is the problem of determining, unambiguously, corresponding points in the stereo images of objects that do not have visible reference points. The second enhancement, is a method to automatically identify and trace the core of a vortex in a digital image. This is accomplished by means of an adaptive template matching algorithm. The system was used to determine the trajectory of a vortex generated by the Leading-Edge eXtension (LEX) of a full-scale F/A-18 aircraft tested in the NASA Ames 80- by 120-Foot Wind Tunnel. The system accuracy for resolving the vortex trajectories is estimated to be +/-2 inches over distance of 60 feet. Stereo images of some of the vortex trajectories are presented. The system was also used to determine the point where the LEX vortex "bursts". The vortex burst point locations are compared with those measured in small-scale tests and in flight and found to be in good agreement.

Meyn, Larry A.↗

Evolutionary Design of a Robotic Material Defect Detection System

During the post-flight inspection of SSME engines, several inaccessible regions must be disassembled to inspect for defects such as cracks, scratches, gouges, etc. An improvement to the inspection process would be the design and development of very small robots capable of penetrating these inaccessible regions and detecting the defects. The goal of this research was to utilize an evolutionary design approach for the robotic detection of these types of defects. A simulation and visualization tool was developed prior to receiving the hardware as a development test bed. A small, commercial off-the-shelf (COTS) robot was selected from several candidates as the proof of concept robot. The basic approach to detect the defects was to utilize Cadmium Sulfide (CdS) sensors to detect changes in contrast of an illuminated surface. A neural network, optimally designed utilizing a genetic algorithm, was employed to detect the presence of the defects (cracks). By utilization of the COTS robot and US sensors, the research successfully demonstrated that an evolutionarily designed neural network can detect the presence of surface defects.

Ballard, Gary↗

Software for Partly Automated Recognition of Targets

The Feature Analyst is a computer program for assisted (partially automated) recognition of targets in images. This program was developed to accelerate the processing of high-resolution satellite image data for incorporation into geographic information systems (GIS). This program creates an advanced user interface that embeds proprietary machine-learning algorithms in commercial image-processing and GIS software. A human analyst provides samples of target features from multiple sets of data, then the software develops a data-fusion model that automatically extracts the remaining features from selected sets of data. The program thus leverages the natural ability of humans to recognize objects in complex scenes, without requiring the user to explain the human visual recognition process by means of lengthy software. Two major subprograms are the reactive agent and the thinking agent. The reactive agent strives to quickly learn the user's tendencies while the user is selecting targets and to increase the user's productivity by immediately suggesting the next set of pixels that the user may wish to select. The thinking agent utilizes all available resources, taking as much time as needed, to produce the most accurate autonomous feature-extraction model possible.

Opitz, David↗

Software for Partly Automated Recognition of Targets

The Feature Analyst is a computer program for assisted (partially automated) recognition of targets in images. This program was developed to accelerate the processing of high-resolution satellite image data for incorporation into geographic information systems (GIS). This program creates an advanced user interface that embeds proprietary machine-learning algorithms in commercial image-processing and GIS software. A human analyst provides samples of target features from multiple sets of data, then the software develops a data-fusion model that automatically extracts the remaining features from selected sets of data. The program thus leverages the natural ability of humans to recognize objects in complex scenes, without requiring the user to explain the human visual recognition process by means of lengthy software. Two major subprograms are the reactive agent and the thinking agent. The reactive agent strives to quickly learn the user s tendencies while the user is selecting targets and to increase the user s productivity by immediately suggesting the next set of pixels that the user may wish to select. The thinking agent utilizes all available resources, taking as much time as needed, to produce the most accurate autonomous feature-extraction model possible.

Opitz, David↗

Visualizing dispersive features in 2D image via minimum gradient method

Here, we developed a minimum gradient based method to track ridge features in a 2D image plot, which is a typical data representation in many momentum resolved spectroscopy experiments. Through both analytic formulation and numerical simulation, we compare this new method with existing DC (distribution curve) based and higher order derivative based analyses. We find that the new method has good noise resilience and enhanced contrast especially for weak intensity features and meanwhile preserves the quantitative local maxima information from the raw image. An algorithm is proposed to extract 1D ridge dispersion from the 2D image plot, whose quantitative application to angle-resolved photoemission spectroscopy measurements on high temperature superconductors is demonstrated.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗