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Collaborative Systems Engineering in the Ascent Abort-2 Crew Module/Separation Ring Project
Generally speaking, systems engineering (SE) tool-sets face a dilemma balancing power and accessibility. High-powered SE tools (MagicDraw, Cradle, Core, etc.) tend to be specialized and are available only to highly trained Systems Engineers, and/or through the use of a 'back room' developer team making the output products available to the broader team. On the other hand, highly accessible tools (MS Word, Excel, etc.) do not have the power to implement SE in a rigorous manner. NASA has to test all aspects of the new human-rated Orion Multi-Purpose Crew Vehicle spacecraft prior to its first crewed mission. The test program includes uncrewed launch abort flight tests to demonstrate the capability to save the crew in the event that a launch failure occurs. Orion's second abort flight test will be a low-altitude flight test known as "Ascent Abort 2 (AA-2)." This test is currently scheduled to be carried out at Cape Canaveral Air Force Station's Space Launch Complex 46 (SLC-46) in Florida in 2019. NASA's in-house AA-2 Crew Module and Separation Ring (CSR) Team is producing the crew module and separation ring. Operating jointly as both an Advanced Exploration Systems (AES) Project and an Orion Project, the CSR project charter includes development of innovative, streamlined and generally more efficient practices for creation of flight hardware and software. One result of this tasking has been development of a collaborative and data-centric systems engineering environment within the team's shared web environment (Microsoft SharePoint). Through the use of built-in, 'out of the box capabilities' present in MS SharePoint, the CSR Systems Engineering team has created (with some limited developer support) a data-centric architecture for the project's SE implementation, including functional and interface analysis, requirements development and management, risk management, verification planning and management, test results, and end item management. Data elements are linked between data structures so as to define and control relationships between item types, link requirements to parents and children, and link tests to the requirements that they verify. The overall project team integration is increased by also linking SE content to project management content over the project life cycle, including team communication, action items, configuration management, decisional and meeting materials, and life cycle reviews. This presentation will provide an overview of the collaborative SE environment, showing how it provides the power for a number of SE tasks while still providing the accessibility and transparency to allow the full project team to collaborate and succeed. Given the project phase, we'll be able to present a nearly full lifecycle discussion, from concept through verification and approaching delivery.
Practical Applications of Cosmic Ray Science: Spacecraft, Aircraft, Ground-Based Computation and Control Systems, Exploration, and Human Health and Safety
In this presentation a review of galactic cosmic ray (GCR) effects on microelectronic systems and human health and safety is given. The methods used to evaluate and mitigate unwanted cosmic ray effects in ground-based, atmospheric flight, and space flight environments are also reviewed. However not all GCR effects are undesirable. We will also briefly review how observation and analysis of GCR interactions with planetary atmospheres and surfaces and reveal important compositional and geophysical data on earth and elsewhere. About 1000 GCR particles enter every square meter of Earth’s upper atmosphere every second, roughly the same number striking every square meter of the International Space Station (ISS) and every other low- Earth orbit spacecraft. GCR particles are high energy ionized atomic nuclei (90% protons, 9% alpha particles, 1% heavier nuclei) traveling very close to the speed of light. The GCR particle flux is even higher in interplanetary space because the geomagnetic field provides some limited magnetic shielding. Collisions of GCR particles with atomic nuclei in planetary atmospheres and/or regolith as well as spacecraft materials produce nuclear reactions and energetic/highly penetrating secondary particle showers. Three twentieth century technology developments have driven an ongoing evolution of basic cosmic ray science into a set of practical engineering tools needed to design, test, and verify the safety and reliability of modern complex technological systems and assess effects on human health and safety effects. The key technology developments are: 1) high altitude commercial and military aircraft; 2) manned and unmanned spacecraft; and 3) increasingly complex and sensitive solid state micro-electronics systems. Space and geophysical exploration needs drove the development of the instruments and analytical tools needed to recover compositional and structural data from GCR induced nuclear reactions and secondary particle showers. Finally, the possible role of GCR secondary particle showers in addressing an important homeland security problem, finding nuclear contraband and weapons, will be briefly reviewed.
B-Trees and Cache-Oblivious B-Trees with Different-Sized Atomic Keys
Most B-tree articles assume that all $\textit{N}$ keys have the same size $\textit{K}$, that $\textit{f = B/K}$ keys fit in a disk block, and therefore that the search cost is $O(\text{log}_{f+1}N) $ block transfers. When keys have variable size, B-tree operations have no nontrivial performance guarantees, however. This article provides B-tree-like performance guarantees on dictionaries that contain keys of different sizes in a model in which keys must be stored and compared as opaque objects. The resulting atomic-key dictionaries exhibit performance bounds in terms of the average key size and match the bounds when all keys are the same size. Atomic-key dictionaries can be built with minimal modification to the B-tree structure, simply by choosing the pivot keys properly. Further, this article describes both static and dynamic atomic-key dictionaries. In the static case, if there are $\textit{N}$ keys with average size $\textit{K}$, the search cost is $O(\lceil K/B\rceil \text{log}_{1 + \lceil K/B\rceil} N)$ expected transfers. It is not possible to transform these expected bounds into worst-case bounds. The cost to build the tree is $\textit{O(NK)}$ operations and $\textit{O(NK/B)}$ transfers if all keys are presented in sorted order. If not, the cost is the sorting cost. For the dynamic dictionaries, the amortized cost to insert a key $\textit{κ}$ of arbitrary length at an arbitrary rank is dominated by the cost to search for $\textit{κ}$. Specifically, the amortized cost to insert a key $\textit{κ}$ of arbitrary length and random rank is $O(\lceil K/B\rceil log_{1+ \lceil B/K\rceil } N + |κ|/B)$ transfers. A dynamic-programming algorithm is shown for constructing a search tree with minimal expected cost. This article also gives a cache-oblivious static atomic-key B-tree, which achieves the same asymptotic performance as the static B-tree dictionary, mentioned previously. A cache-oblivious data structure or algorithm is not parameterized by the block size $\textit{B}$ or memory size $\textit{M}$ in the memory hierarchy; rather, it is universal, working simultaneously for all possible values of $\textit{B}$ or $\textit{M}$. On a machine with block size $\textit{B}$, if there are $\textit{N}$ keys with average size $\textit{K}$, search operations costs $O(\lceil K/B \rceil log_{1+ \lceil B/K \rceil} N)$ block transfers in expectation. This cache-oblivious layout can be built in $\textit{O(N}\text{log}\textit{(NK))}$ processor operations.
Efficiency and mechanisms of Sb(III/V) removal by Fe-modified biochars using X-ray absorption spectroscopy
Fe-modified biochars (FeBC) are effective antimony (Sb) removal materials; however, the removal mechanisms require further investigation. In this study, aqueous Sb(III) and Sb(V) removal by FeBC (300, 600, and 900 °C) was evaluated, with the adsorption mechanisms investigated using X-ray absorption spectroscopy (XAS). Screening results (based on removal efficiencies) using different types of FeBC indicated the 900 °C FeCl3- modified biochar (FeCl3BC900) achieved the best Sb(III/V) removal performance. The kinetics of the Sb(III/V) removal process were best fitted by a pseudo-second-order model. Additionally, the isothermal results were described by Langmuir and Redlich-Peterson models. Aqueous analysis and X-ray absorption near-edge structure data fitting indicated Sb(III) was oxidized to Sb(V) in the Sb(III)-spiked system, and the oxidation extent increased with increasing pyrolysis temperature. The oxidation process rapidly occurred in both the solution and biochar. No Sb(V) was reduced to Sb(III) in the Sb(V)-spiked system. The XAS results of the isothermal experiment indicated the oxidation capacity of FeCl3BC900 was limited for high initial Sb(III) concentrations. The SbFe1 and Sb-Fe2 bonding distances were 3.05–3.10 and 3.47–3.54 Å, respectively, indicating inner-sphere complexes were formed during the Sb(III/V) removal processes. The Sb(III/V) removal mechanisms included electrostatic adsorption, inner-sphere complexes, and coprecipitation. Oxidation was also involved in Sb(III) removal.
sympl (v. 0.4.0) and climt (v. 0.15.3) – towards a flexible framework for building model hierarchies in Python
sympl (System for Modelling Planets) andclimt (Climate Modelling and Diagnostics Toolkit) are anattempt to rethink climate modelling frameworks from the ground up. The aimis to use expressive data structures available in the scientific Pythonecosystem along with best practices in software design to allow scientists toeasily and reliably combine model components to represent the climate systemat a desired level of complexity and to enable users to fully understandwhat the model is doing. sympl is a framework which formulates the model in terms of astate that gets evolved forward in time or modified within a specifictime by well-defined components. sympl's design facilitates buildingmodels that are self-documenting, are highly interoperable, and providefine-grained control over model components and behaviour. symplcomponents contain all relevant information about the input they expect andoutput that they provide. Components are designed to be easily interchanged,even when they rely on different units or array configurations.sympl provides basic functions and objects which could be used inany type of Earth system model. climt is an Earth system modelling toolkit that contains scientificcomponents built using sympl base objects. These include both purePython components and wrapped Fortran libraries. climt providesfunctionality requiring model-specific assumptions, such as stateinitialization and grid configuration. climt's programming interfacedesigned to be easy to use and thus appealing to a wide audience. Model building, configuration and execution are performed through a Pythonscript (or Jupyter Notebook), enabling researchers to build an end-to-endPython-based pipeline along with popular Python data analysis andvisualization tools.
Differences between nonprecipitating tropical and trade wind marine shallow cumuli
In this study, marine nonprecipitating cumulus topped boundary layers (CTBLs) observed in a tropical and in a trade wind region are contrasted based on their cloud macrophysical, dynamical, and radiative structures. Data from the Atmospheric Radiation Measurement (ARM) observational site previously operating at Manus Island, Papua New Guinea, and data collected during the deployment of ARM Mobile Facility at the island of Graciosa, in the Azores, were used in this study. The tropical marine CTBLs were deeper, had higher surface fluxes and boundary layer radiative cooling, but lower wind speeds compared to their trade wind counterparts. The radiative velocity scale was 50%-70% of the surface convective velocity scale at both locations, highlighting the prominent role played by radiation in maintaining turbulence in marine CTBLs. Despite greater thicknesses, the chord lengths of tropical cumuli were on average lower than those of trade wind cumuli, and as a result of lower cloud cover, the hourly averaged (cloudy and clear) liquid water paths of tropical cumuli were lower than the trade wind cumuli. At both locations ~70% of the cloudy profiles were updrafts, while the average amount of updrafts near cloud base stronger than 1 m s –1 was ~22% in tropical cumuli and ~12% in the trade wind cumuli. The mean in-cloud radar reflectivity within updrafts and mean updraft velocity was higher in tropical cumuli than the trade wind cumuli. Despite stronger vertical velocities and a higher number of strong updrafts, due to lower cloud fraction, the updraft mass flux was lower in the tropical cumuli compared to the trade wind cumuli. The observations suggest that the tropical and trade wind marine cumulus clouds differ significantly in their macrophysical and dynamical structures
Molecular diversity and evolution of far-red light-acclimated photosystem I
The need to acclimate to different environmental conditions is central to the evolution of cyanobacteria. Far-red light (FRL) photoacclimation, or FaRLiP, is an acclimation mechanism that enables certain cyanobacteria to use FRL to drive photosynthesis. During this process, a well-defined gene cluster is upregulated, resulting in changes to the photosystems that allow them to absorb FRL to perform photochemistry. Because FaRLiP is widespread, and because it exemplifies cyanobacterial adaptation mechanisms in nature, it is of interest to understand its molecular evolution. Here, we performed a phylogenetic analysis of the photosystem I subunits encoded in the FaRLiP gene cluster and analyzed the available structural data to predict ancestral characteristics of FRL-absorbing photosystem I. The analysis suggests that FRL-specific photosystem I subunits arose relatively late during the evolution of cyanobacteria when compared with some of the FRL-specific subunits of photosystem II, and that the order Nodosilineales, which include strains like Halomicronema hongdechloris and Synechococcus sp. PCC 7335, could have obtained FaRLiP via horizontal gene transfer. We show that the ancestral form of FRL-absorbing photosystem I contained three chlorophyll f-binding sites in the PsaB2 subunit, and a rotated chlorophyll a molecule in the A0B site of the electron transfer chain. Along with our previous study of photosystem II expressed during FaRLiP, these studies describe the molecular evolution of the photosystem complexes encoded by the FaRLiP gene cluster.
Metamesh, Version 1.0
Metamesh is a general-purpose C++ language library for creating data structures that represent meshes. An important difference between Metamesh and other "mesh" libraries is that Metamesh does not provide a specific mesh format, in the usual sense, or tools or a GUI by which users build specific meshes. Rather, it provides a mechanism by which mesh formats themselves can be built, based on their constituent parts and the relationships between them.Consider that a mesh in up to three space dimensions can, in principle, contain nodes (0d entities, or points), edges (1d entities), faces (2d entities), and cells (3d, or volumetric, entities). A node might be defined in terms of (x), (x,y), or (x,y,z) in Cartesian coordinates; or perhaps something else, in a different coordinate system. An edge is typically defined from two nodes; say, "edge E goes from node A=(ax,ay) to node B=(bx,by)." Faces can reasonably be defined in terms of nodes or edges, and cells in terms of nodes, edges, or faces. Note also that someone might wish to support general faces or cells, or only specific variants - say, triangular faces and tetrahedral cells, or quadrilateral faces and hexahedral cells. Or, perhaps, both triangular and quadrilateral faces (but no others), with prisms for each cell. Consider also that a mesh can have the same or a lesser dimension than that of its enclosing space. In 3d, for example, one could have a full 3d mesh, a 2d "sheet" mesh with no cells, a 1d "parametrized curve" with neither faces nor cells, or even a 1d "point cloud." And, in addition to defining a mesh scheme, a user might wish to place additional data onto one or more mesh entities. Imagine, for example, a velocity at each node, a flux across each edge or face, and a mass or average density per cell. Metamesh supports all of this, through the use of C++ class and function templates, and template metaprogramming techniques. Programmers begin with constructs that Metamesh provides (or, users can define their own), and assemble them in particular ways in order to create particular mesh formats. Metamesh then provides functionality automatically to meshes that are constructed in this manner. Finally, Metamesh provides very general functions for spinning, extruding, visualizing, and performing input/output of whatever meshes a user builds with it.
Understanding Strain and Failure of a Knot in Polyethylene Using Molecular Dynamics with Machine-Learned Potentials
A neural network potential (NNP) has been developed by fitting to ab initio electronic structure data on hydrocarbons and is used to study failure of linear and knotted polyethylene (PE) chains. A linear PE chain must be highly strained before breaking as the stress is equally distributed across the chain. In contrast, the stress in a PE chain with a 31 or overhand knot, accumulates at the knot’s entrance/exit. We find the strain energy is greatest when the bond length and angle are strained simultaneously, and that the knot weakens the chain by increasing the variance of the C–C–C angle, thereby allowing rupture at lower bond strains. Here, we extend our analysis to both 51 and 52 knots and find that both break at the entrance/exit of a loop. Notably, molecular scale PE knots exhibit many of the same characteristics as knots in a macroscopic rope, with stick–slip phenomena upon tightening and similar points of failure.
Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge
This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density.
The development of Nanosota-1 as anti-SARS-CoV-2 nanobody drug candidates
Combating the COVID-19 pandemic requires potent and low-cost therapeutics. We identified a series of single-domain antibodies (i.e., nanobody), Nanosota-1, from a camelid nanobody phage display library. Structural data showed that Nanosota-1 bound to the oft-hidden receptor-binding domain (RBD) of SARS-CoV-2 spike protein, blocking viral receptor angiotensin-converting enzyme 2 (ACE2). The lead drug candidate possessing an Fc tag (Nanosota-1C-Fc) bound to SARS-CoV-2 RBD ~3000 times more tightly than ACE2 did and inhibited SARS-CoV-2 pseudovirus ~160 times more efficiently than ACE2 did. Administered at a single dose, Nanosota-1C-Fc demonstrated preventive and therapeutic efficacy against live SARS-CoV-2 infection in both hamster and mouse models. Unlike conventional antibodies, Nanosota-1C-Fc was produced at high yields in bacteria and had exceptional thermostability. Pharmacokinetic analysis of Nanosota-1C-Fc documented an excellent in vivo stability and a high tissue bioavailability. As effective and inexpensive drug candidates, Nanosota-1 may contribute to the battle against COVID-19.
High‐Performance Fluorinated Fused‐Ring Electron Acceptor with 3D Stacking and Exciton/Charge Transport
Abstract A new fluorinated electron acceptor (FINIC) based on 6,6,12,12‐tetrakis(3‐fluoro‐4‐hexylphenyl)‐indacenobis(dithieno[3,2‐ b ;2 ′ ,3 ′ ‐ d ]thiophene) as the electron‐donating central core and 5,6‐difluoro‐3‐(1,1‐dicyanomethylene)‐1‐indanone as the electron‐deficient end groups is rationally designed and synthesized. FINIC shows similar absorption profile in dilute solution to the nonfluorinated analogue INIC. However, compared with INIC, FINIC film shows red‐shifted absorption, down‐shifted frontier molecular orbital energy levels, enhanced crystallinity, and more ordered molecular packing. Single‐crystal structure data show that FINIC molecules pack into closer 3D “network” motif through H‐bonding and π–π interaction, while INIC molecules pack into incompact “honeycomb” motif through only π–π stacking. Theoretical calculations reveal that FINIC has stronger electronic coupling and more molecular interactions than INIC. FINIC has higher electron mobilities in both horizontal and vertical directions than INIC. Moreover, FINIC and INIC support efficient 3D exciton transport. PBD‐SF/FINIC blend has a larger driving force for exciton splitting, more efficient charge transfer and photoinduced charge generation. Finally, the organic solar cells based on PBD‐SF/FINIC blend yield power conversion efficiency of 14.0%, far exceeding that of the PBD‐SF/INIC‐based devices (5.1%).
Operando EDXRD Study of All;#8208;Solid;#8208;State Lithium Batteries Coupling Thioantimonate Superi
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Multi‐dimensional lock‐free arrays for multithreaded mode‐directed tabling in Prolog
Summary This work proposes a new design for the supporting data structures used to implement multithreaded tabling in Prolog systems. Tabling is an implementation technique that improves the expressiveness of traditional Prolog systems in dealing with recursion and redundant computations. Mode‐directed tabling is an extension to the tabling technique that supports the definition of alternative criteria for specifying how answers are aggregated, thus being very suitable for problems where the goal is to dynamically calculate optimal or selective answers. In this work, we leverage the intrinsic potential that mode‐directed tabling has to express dynamic programming problems by creating a new design that improves the representation of multi‐dimensional arrays in the context of multithreaded tabling. To do so, we introduce a new mode for indexing arguments in mode‐directed tabled evaluations, named dim , where each dim argument features a uni‐dimensional lock‐free array. Experimental results using well‐known dynamic programming problems on a 32‐core machine show that the new design introduces less overheads and clearly improves the execution time for sequential and multithreaded tabled evaluations.
Tail queues: A multi-threaded matching architecture
As we approach exascale, computational parallelism will have to drastically increase in order to meet throughput targets. Many–core architectures have exacerbated this problem by trading reduced clock speeds, core complexity, and computation throughput for increasing parallelism. This presents two major challenges for communication libraries such as MPI: the library must leverage the performance advantages of thread level parallelism and avoid the scalability problems associated with increasing the number of processes to that scale. Hybrid programming models, such as MPI+X, have been proposed to address these challenges. MPI THREAD MULTIPLE is MPI's thread safe mode. While there has been work to optimize it, it largely remains non–performant in most implementations. While current applications avoid MPI multithreading due to performance concerns, it is expected to be utilized in future applications. One of the major synchronous data structures required by MPI is the matching engine. In this paper, we present a parallel matching algorithm that can improve MPI matching for multithreaded applications. We then perform a feasibility study to demonstrate the performance benefit of the technique.
Effects of random forest modeling decisions on biogeochemical time series predictions
Abstract Random forests (RF) are an increasingly popular machine learning approach used to model biogeochemical processes in the Earth system. While RF models are robust to many assumptions that complicate deterministic models, there are several important parameterization decisions for appropriate use and optimal model fit. We explored the role that parameter decisions, including training/testing data splitting strategies, variable selection, and hyperparameters play on RF goodness‐of‐fit by constructing models using 1296 unique parameter combinations to predict concentrations of nitrate, a key nutrient for biogeochemical cycling in aquatic ecosystems. Models were built on long‐term, publicly available water quality and meteorology time series collected by the National Estuarine Research Reserve monitoring network for two contrasting ecosystems representing freshwater and brackish estuaries. We found that accounting for temporal dependence when splitting data into training and testing subsets was key for avoiding over‐estimation of model predictive power. In addition, variable selection, the ratio of training to testing data, and to a lesser degree, variables per split and number of trees, were significant parameters for optimizing RF goodness‐of‐fit. We also explored how model parameter decisions influenced interpretation of the relative importance of predictors to the model, and model predictor‐dependent variable relationships, with results suggesting that both data structure and model parameterization influence these factors. Because much of the current RF literature is written for the computational and statistical science communities, the primary goal of this study is to provide guidelines for aquatic scientists new to machine learning to apply RF techniques appropriately to aquatic biogeochemical datasets.
Nanostructure Scaling in Semi-Dilute Triblock Copolymer Gels
Here, there is a considerable body of work that describes the scaling of diblock copolymer micelle dimensions in dilute and semi-dilute solution based upon block degrees of polymerization and copolymer concentration. However, there is a lack of analogous information for semi-dilute ABA triblock copolymer gels, which consist of ABA triblock copolymer dissolved in midblock-selective (B-selective) solvent. The present study uses small angle X-ray scattering to extract micelle dimensions for numerous triblock copolymer gels that vary in copolymer identity (and hence block lengths) and copolymer concentration, as well as gels that contain various ratios of two unique triblock copolymers. Analysis of micelle structural data subsequently translates to universal scaling expressions for the micelle core radius – r A ≈ N A 0.53 N B -0.14 $\phi$ ABA 0.16 where N A and N B are the endblock and midblock degrees of polymerization, respectively, and $\phi$ ABA is the volume fraction of triblock copolymer in the gel – and for the intermicelle spacing – l AA ≈ N A 0.09 N B 0.29 $\phi$ ABA -0.35 . Each scaling expression describes the full collection of experimental data very well. Additionally, these scaling expressions are partially in line with expectations from semi-dilute diblock copolymer solution theory.