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At least 343 records · Page 19

The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics

Abstract While many aspects of archaeal cell biology remain relatively unexplored, systems biology approaches like mass spectrometry (MS) based proteomics offer an opportunity for rapid advances. Unfortunately, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools and field-specific biological expertise for data interpretation. Here we present the initiation of the Archaeal Proteome Project (ArcPP), a community-based effort to comprehensively analyze archaeal proteomes. Starting with the model archaeon Haloferax volcanii , we reanalyze MS datasets from various strains and culture conditions. Optimized peptide spectrum matching, with strict control of false discovery rates, facilitates identifying > 72% of the reference proteome, with a median protein sequence coverage of 51%. These analyses, together with expert knowledge in diverse aspects of cell biology, provide meaningful insights into processes such as N-terminal protein maturation, N -glycosylation, and metabolism. Altogether, ArcPP serves as an invaluable blueprint for comprehensive prokaryotic proteomics.

59 BASIC BIOLOGICAL SCIENCES↗

Supercharging simulation-based inference for Bayesian optimal experimental design

Abstract Bayesian optimal experimental design (BOED) seeks to maximize the expected information gain (EIG) of experiments. This requires a likelihood estimate, which in many settings is intractable. Simulation-based inference (SBI) provides powerful tools for this regime. However, existing work explicitly connecting SBI and BOED is restricted to a single contrastive EIG bound. We show that the EIG admits multiple formulations which can directly leverage modern SBI density estimators, encompassing neural posterior, likelihood, and ratio estimation. Building on this perspective, we define a novel EIG estimator using neural likelihood estimation. Further, we identify optimization as a key bottleneck of gradient based EIG maximization and show that a simple multi-start parallel gradient ascent procedure can substantially improve reliability and performance. With these innovations, our SBI-based BOED methods are able to match or outperform by up to 22% existing state-of-the-art approaches across standard BOED benchmarks.

97 MATHEMATICS AND COMPUTING↗

Final Cooling with Thick Wedges for a Muon Collider

A muon collider is a particle accelerator that collides muons rather than protons or electrons. An important component of such a collider is cooling, in which the emittance of the muon beam is reduced to make it suitable for use in a collider. In the last stage of this process, called final 4D cooling, emittance in the transverse axes is reduced while emittance in the longitudinal axis is allowed to grow. In previous studies, Final 4-D cooling used absorbers within very high field solenoids to cool low-momentum muons. Simulations of the systems did not reach the desired cooling design goals. In this study, we develop and optimize a different conceptual design for the final 4D cooling channel, which is based on single thick wedges. We used G4Beamline to simulate the channel and Python to generate and analyze particle distributions. We characterized the effects of various parameters on the performance of this system, including the initial emittances and Twiss parameters, the length and angle of the wedges, the length of the drift channel, and the length, frequency, gradient, and phase of the RF cavities. We optimized the design parameters of the cooling channel and produced two conceptual designs (corresponding to two possible starting points for the input beam) which achieve transverse cooling in both x and y by a factor of ≈ 3.5. These channels achieve a lower transverse and longitudinal emittance than the best design previously published.

43 PARTICLE ACCELERATORS↗

Designing the Space Transfer Vehicle (STV)

The most significant challenges facing the Space Transfer Vehicle (STV) program are making space basing affordable and developing an easily evolvable STV. Study efforts try minimizing the high cost of astronauts activities and Space Station modification to enhance affordability. Modularity, design margins, and simple interfaces are being evaluated to develop an evolutionary approach for space basing starting in the 1990's. In this STV study, the concept definition approach is presented, including concept optimization trades as well as concept selection and sensitivity analyses.

Austin, Gene↗

Determination of design and operation parameters for upper atmospheric research instrumentation to yield optimum resolution with deconvolution, appendix 3

The Always-Convergent Iterative Noise Removal and Deconvolution Method of Ioup is applied as a single-filter in the transform domain to deconvolution with both narrow and wide Gaussian impulse response functions. The wraparound error for both cases is also studied. A method is developed by which one can find the optimum iteration number for single-filter iterative deconvolution of sampled data. The method employs the mean square error (MSE), the square of the difference between the deconvolved result and the input, for optimization. The MSE decreases as the deconvolution iterations proceed, but at the optimum iteration number, the MSE starts to increase. This procedure is repeated for signal-to-noise ratio of 10 to 150. The optimum iteration number and the MSE are plotted vs SNR. By knowing the SNR for a particular experiment, one can find the optimum iteration number and MSE.

Ioup, George E.↗

Multi-Configuration and Aeroelastic Shape Design

This presentation describes the advances being made with the Aerodynamic Shape Optimization (ASO) and high-fidelity Multidisciplinary Optimization (MDO) software used in the High Speed Research Program at NASA Ames Research Center. The description starts with the motivation for continued ASO/MDO development. Objectives of the current work are then presented. A list of ingredients deemed necessary for a flexible design environment is discussed, and the HSR requirement for different geometries at different design points is explained. Multiple design disciplines within a high-fidelity design environment are demonstrated. Finally, progress so far is summarized and planned future work is outlined.

Reuther, James↗

Bridging the Gap Between Microscale Modeling and Additive Manufacturing for TPS

An overview of the now open-source NASA ARC software PuMA will be provided. On top of the well-documented ability to import and compute material properties from micro-CT images, PuMA has the ability to design microstructures and compute/predict material properties such as: porosity, permeability, tortuosity, thermal and electrical conductivity, tensile strength, etc. Therefore, a whole new range of capabilities is available, and provides users with the ability to build TPS materials (both fibrous and woven types) and optimize their properties based on missions and requirements. This talk will aim to provide a seed to start bridging the gap between microscale modeling of TPS materials and additive manufacturing.

Conductivity↗

Waste Management Project Success - Regulatory Assurance Systems - 20118

Waste management (WM) and remediation projects are essential within a restorative environmental culture. Despite years of experience, challenges and obstacles associated with efficient and effective WM project execution remain. Although some obstacles are project specific, a common challenge is navigating the regulatory landscape from planning through execution, particularly with first of a kind (FOAK) and first in a while (FIAW) projects. The absence of a comprehensive regulatory assurance strategy places significant hurdles in the path of project success. To clear a path for the successful execution of increasingly complex WM projects, this paper focuses on development of a comprehensive regulatory assurance strategy and implementation plan that effectively engages stakeholders, agencies, and performers to produce project plans that fully and cost effectively integrate applicable regulatory requirements. The most reliable way to align regulatory processes and decisions needed for mission success is through a regulatory assurance system. This system establishes a healthy interface with regulatory decision makers, to work in a collaborative manner, to create a common vision for regulatory decisions on an agreed upon schedule. A regulatory assurance system consists of several elements. Although the mission may vary from cleanup to site closure to nuclear component production, the elements of a regulatory assurance system remain essentially constant and must include: 1) identifying a common vision or end state, 2) developing a long-term, integrated strategy and schedule, 3) establishing a regulatory partnering team consisting of key decision-makers, 4) regular and frequent communication with decision-makers, 5) ensuring consistent surveillance for early identification of issues and changes that may impact the project, 6) quick resolution of emerging issues to prevent schedule impact, 7) identifying core compliance functions, 8) periodically assessing progress of the project as it relates to regulatory assurance and, 9) providing constructive feedback to improve the process. A regulatory assurance system provides a living, multi-faceted approach to planning, visioning, communicating and tracking to avoid surprises and ensure smooth and timely progress to the project. The overall success measures will be whether the system produces common sense regulatory decisions supporting the vision on time without appeal. Effective regulatory frameworks rarely happen on their own. Balanced, common-sense regulatory decisions stem from teams that are trained to work together to achieve shared goals. In this paper, particular attention is placed on the importance of starting with a shared vision for a regulatory assurance and execution strategy that leverages experience to establish optimal approaches. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

An efficient approach to explore the solution space of a wind turbine rotor design process

This study proposes a novel approach to explore the solution space of a wind turbine rotor design process. The goal is to offer to blade designers the possibility to select an optimal rotor for given market conditions, assessing trade-offs and alternatives in a matter of minutes. The design process consists of sequential aerodynamic-structural optimizations, where the two loops are linked via a blade-loading parameter that can be varied by the user. A design study is performed starting from the IEA Wind Task 37 land-based reference wind turbine. The solution space is characterized for rotor diameters in the range of 130–160 m, rated generator power values in the range of 3.0–6.0 MW, and tip-speed ratios in the range of 7.5–12.5. Results are discussed highlighting optimal design decisions and trade-offs.

17 WIND ENERGY↗

ATLAST and JWST Segmented Telescope Design Considerations

To the extent it makes sense, leverage JWST (James Webb Space Telescope) knowledge, designs, architectures. GSE (Ground Support Equipment) good starting point. Develop a full end-to-end architecture that closes. Try to avoid recreating the wheel except where needed. Optimize from there (mainly for stability and coronagraphy). Develop a scalable design reference mission (9.2 meters). Do just enough work to understand launch break points in aperture size Demonstrate 10 pm (phase modulation) stability is achievable on a design reference mission. A really key design driver is the most robust stability possible!!! Make design compatible with starshades. While segmented coronagraphs with high throughput and large bandpasses are important, make the system serviceable so you can evolve the instruments. Keep it room temperature to minimize the costs associated with cryo. Focus resources on the contrast problem. Start with the architecture and connect it to the technology needs.

Feinberg, Lee↗

Transcriptome architecture of the three main lineages of agrobacteria

ABSTRACT Agrobacteria are a diverse, polyphyletic group of prokaryotes with multipartite genomes capable of transferring DNA into the genomes of host plants, making them an essential tool in plant biotechnology. Despite their utility in plant transformation, genome-wide transcriptional regulation is not well understood across the three main lineages of agrobacteria. Transcription start sites (TSSs) are a necessary component of gene expression and regulation. In this study, we used differential RNA-seq and a TSS identification algorithm optimized on manually annotated TSS, then validated with existing TSS to identify thousands of TSS with nucleotide resolution for representatives of each lineage. We extend upon the 356 TSSs previously reported in Agrobacterium fabrum C58 by identifying 1,916 TSSs. In addition, we completed genomes and phenotyping of Rhizobium rhizogenes C16/80 and Allorhizobium vitis T60/94, identifying 2,650 and 2,432 TSSs, respectively. Parameter optimization was crucial for an accurate, high-resolution view of genome and transcriptional dynamics, highlighting the importance of algorithm optimization in genome-wide TSS identification and genomics at large. The optimized algorithm reduced the number of TSSs identified internal and antisense to the coding sequence on average by 90.5% and 91.9%, respectively. Comparison of TSS conservation between orthologs of the three lineages revealed differences in cell cycle regulation of ctrA as well as divergence of transcriptional regulation of chemotaxis-related genes when grown in conditions that simulate the plant environment. These results provide a framework to elucidate the mechanistic basis and evolution of pathology across the three main lineages of agrobacteria. IMPORTANCE Transcription start sites (TSSs) are fundamental for understanding gene expression and regulation. Agrobacteria, a group of prokaryotes with the ability to transfer DNA into the genomes of host plants, are widely used in plant biotechnology. However, the genome-wide transcriptional regulation of agrobacteria is not well understood, especially in less-studied lineages. Differential RNA-seq and an optimized algorithm enabled identification of thousands of TSSs with nucleotide resolution for representatives of each lineage. The results of this study provide a framework for elucidating the mechanistic basis and evolution of pathology across the three main lineages of agrobacteria. The optimized algorithm also highlights the importance of parameter optimization in genome-wide TSS identification and genomics at large.

59 BASIC BIOLOGICAL SCIENCES↗

Automated Generation of Finite-Element Meshes for Aircraft Conceptual Design

This paper presents a novel approach for automated generation of fully connected finite-element meshes for all internal structural components and skins of a given wing-body geometry model, controlled by a few conceptual-level structural layout parameters. Internal structural components include spars, ribs, frames, and bulkheads. Structural layout parameters include spar/rib locations in wing chordwise/spanwise direction and frame/bulkhead locations in longitudinal direction. A simple shell thickness optimization problem with two load conditions is used to verify versatility and robustness of the automated meshing process. The automation process is implemented in ModelCenter starting from an OpenVSP geometry and ending with a NASTRAN 200 solution. One subsonic configuration and one supersonic configuration are used for numerical verification. Two different structural layouts are constructed for each configuration and five finite-element meshes of different sizes are generated for each layout. The paper includes various comparisons of solutions of 20 thickness optimization problems, as well as discussions on how the optimal solutions are affected by the stress constraint bound and the initial guess of design variables.

Li, Wu↗

A Framework for Robust Multivariable Optimization of Integrated Circuits in Space Applications

Application Specific Integrated Circuit (ASIC) design for space applications involves multiple challenges of maximizing performance, minimizing power and ensuring reliable operation in extreme environments. This is a complex multidimensional optimization problem which must be solved early in the development cycle of a system due to the time required for testing and qualification severely limiting opportunities to modify and iterate. Manual design techniques which generally involve simulation at one or a small number of corners with a very limited set of simultaneously variable parameters in order to make the problem tractable are inefficient and not guaranteed to achieve the best possible results within the performance envelope defined by the process and environmental requirements. What is required is a means to automate design parameter variation, allow the designer to specify operational constraints and performance goals, and to analyze the results in a way which facilitates identifying the tradeoffs defining the performance envelope over the full set of process and environmental corner cases. The system developed by the Mixed Signal ASIC Group (MSAG) at the Goddard Space Flight Center is implemented as framework of software modules, templates and function libraries. It integrates CAD tools and a mathematical computing environment, and can be customized for new circuit designs with only a modest amount of effort as most common tasks are already encapsulated. Customization is required for simulation test benches to determine performance metrics and for cost function computation. Templates provide a starting point for both while toolbox functions minimize the code required. Once a test bench has been coded to optimize a particular circuit, it is also used to verify the final design. The combination of test bench and cost function can then serve as a template for similar circuits or be re-used to migrate the design to different processes by re-running it with the new process specific device models. The system has been used in the design of time to digital converters for laser ranging and time-of-flight mass spectrometry to optimize analog, mixed signal and digital circuits such as charge sensitive amplifiers, comparators, delay elements, radiation tolerant dual interlocked (DICE) flip-flops and two of three voter gates.

DuMonthier, Jeffrey↗

A novel open-source cultivation system helps establish the first full cycle chemosynthetic symbiosis model system involving the giant ciliate Zoothamnium niveum

Symbiotic interactions drive species evolution, with nutritional symbioses playing vital roles across ecosystems. Chemosynthetic symbioses are globally distributed and ecologically significant, yet the lack of model systems has hindered research progress. The giant ciliate Zoothamnium niveum and its sulfur-oxidizing symbionts represent the only known chemosynthetic symbiosis with a short life span that has been transiently cultivated in the laboratory. While it is experimentally tractable and presents a promising model system, it currently lacks an open-source, simple, and standardized cultivation setup. Following the FABricated Ecosystems (EcoFABs) model, we leveraged 3D printing and polydimethylsiloxane (PDMS) casting to develop simple flow-through cultivation chambers that can be produced and adopted by any laboratory. The streamlined manufacturing process reduces production time by 86% and cuts cost by tenfold compared to the previous system. Benchmarking using previously established optimal growth conditions, the new open-source cultivation system proves stable, efficient, more autonomous, and promotes a more prolific growth of the symbiosis. For the first time, starting from single cells, we successfully cultivated the symbiosis in flow-through chambers for 20 days, spanning multiple generations of colonies that remained symbiotic. They were transferred from chamber to chamber enabling long-term cultivation and eliminating the need for continuous field sampling. The chambers, optimized for live imaging, allowed detailed observation of the synchronized growth between the host and symbiont. Highlighting the benefit of this new system, we here describe a new step in the first hours of development where the host pauses growth, expels a coat, before resuming growth, hinting at a putative symbiont selection mechanism early in the colony life cycle. With this simple, open-source, cultivation setup, Z. niveum holds promises for comparative studies, standardization of research and wide adoption by the symbiosis research community.

59 BASIC BIOLOGICAL SCIENCES↗

Alternatives for jet engine control

General goals of the research were classified into two categories. The first category involves the use of modern multivariable frequency domain methods for control of engine models in the neighborhood of a quiescent point. The second category involves the use of nonlinear modelling and optimization techniques for control of engine models over a more extensive part of the flight envelope. In the frequency domain category, works were published in the areas of low-interaction design, polynomial design, and multiple setpoint studies. A number of these ideas progressed to the point at which they are starting to attract practical interest. In the nonlinear category, advances were made both in engine modelling and in the details associated with software for determination of time optimal controls. Nonlinear models for a two spool turbofan engine were expanded and refined; and a promising new approach to automatic model generation was placed under study. A two time scale scheme was developed to do two-dimensional dynamic programming, and an outward spiral sweep technique has greatly speeded convergence times in time optimal calculations.

Leake, R. J.↗

The role of photographic parameters in laser speckle or particle image displacement velocimetry

The parameters involved in obtaining the multiple exposure photographs in the laser speckle velocimetry method (to record the light scattering by the seeding particles) were optimized. The effects of the type, concentration, and dimensions of the tracer, the exposure conditions (time between exposures, exposure time, and number of exposures), and the sensitivity and resolution of the film on the quality of the final results were investigated, photographing an experimental flow behind an impulsively started circular cylinder. The velocity data were acquired by digital processing of Young's fringes, produced by point-by-point scanning of a photographic negative. Using the optimal photographing conditions, the errors involved in the estimation of the fringe angle and spacing were of the order of 1 percent for the spacing and +/1 deg for the fringe orientation. The resulting accuracy in the velocity was of the order of 2-3 percent of the maximum velocity in the field.

Lourenco, L.↗

Implicit Formulation of Muscle Dynamics in OpenSim

Astronauts lose bone and muscle mass during spaceflight. Exercise countermeasure is the primary method for counteracting bone and muscle mass loss in space. New spacecraft exercise device concepts are currently being developed for the NASAs new crew exploration vehicle. The NASA Digital Astronaut Project (DAP) uses computational modeling to help determine if the new exercise devices will be effective as countermeasures. The NASA Digital Astronaut Project is developing the ability to utilize predictive simulation to provide insight into the change in kinematics and kinetics with a change in device and gravitational environment (1-g versus 0-g). For example, in space exercise the subject's body weight is applied in addition to the loads prescribed for musculoskeletal maintenance. How and where these loads are applied obviously directly impacts bone and tissue loads. Additionally, due to space vehicle structural requirements, exercise devices are often placed on vibration isolation systems. This changes the apparent impedance or stiffness of the device as seen by the user. Data collection under these conditions is often impractical and limited. Predictive modeling provides a means to have a virtual subject to test hypotheses. Predictive simulation provides a virtual subject for which we are able to perform studies such as sensitivity to device loading and vibration isolation without the need for laboratory kinematic or kinetic test data.Direct Collocation optimization provides an efficient means to perform task based optimization and predictive modeling. It is relatively straight forward to structure a physical exercise task in a Direct Collocation mathematical formulation: perform a motion such that you start at an initial pose, achieve a given amount of deflection i.e a squat, return to the initial pose, and minimize muscle activation cost. Direct Collocation is advantageous in that it does not require numerical integration to evaluate the objective function. Instead, the system dynamics are transformed to discrete time and the optimizer is constrained such that the solution is not considered to be a valid unless the dynamic equations are satisfied at all time points. The simulation and optimization are effectively done simultaneously. Due to the implicit integration, time steps can be more coarse than in a differential equation solver. In a gait scenario this means that that the model constraints and cost function are evaluated at 100 nodes in the gait cycle versus 10,000 integration steps in a variable-step forward dynamic simulation. Furthermore, no time is wasted on accurate simulations of movements that are far from the optimum. Constrained optimization algorithms require a Jacobian matrix that contains the partial derivatives of each of the dynamic constraints with respect to of each of the state and control variables at all time points. This is a large but sparse matrix. An implicit dynamics formulation requires computation of the dynamic residuals f as a function of the states x and their derivatives, and controls u:f(x, dxdt, u) 0If the dynamics of musculoskeletal system are formulated implicitly, the Jacobian elements are often available analytically, eliminating the need for numerical differentiation; this is obviously computationally advantageous. Additionally, implicit formulation of musculoskeletal dynamics do not suffer from singularities from low mass bodies, zero muscle activation, or other stiff system or

physical exercise↗

Future of Fuel Savings

Using automation to free up controllers for more strategic management of air traffic is one approach being studied by NASA as it seeks to boost airspace system capacity and efficiency, thereby saving fuel. Heinz Erzberger, a NASA Ames Research Center senior scientist, says the Advanced Airspace Concept (AAC) has been studied for several years. It could increase efficiency 15% by providing optimal routes that cut airlines direct operating costs. A 25% increase in landings on existing runways could follow an important benefit. AAC is one of the efforts to be reviewed by the Joint Planning and Development Organization, an FAA-led initiative by six federal agencies to redesign the U.S. air transportation system by 2025. The main goal is to triple air traffic capacity within 20 years to avert the sort of gridlock that would make fuel consumption only one of many travel nightmares. The automated system approach would allow aircraft to fly optimal trajectories. A trajectory would be defined in the standard three dimensions and eventually include the fourth, time. The management of air traffic by the data-linked exchange of trajectories would start at high altitude and eventually move down to lower altitudes. The automated concept is an outgrowth of the type of tools developed by NASA for use by FAA controllers in managing traffic flows over the years, including ones that optimize routings for the best fuel burn. But AAC would push automation further to reduce workload so controllers can focus on "solving strategic control problems, managing traffic flow during changing weather and ... other unusal events." One key component, the automated trajectory server (ATS), is a ground systems that would rely on software to manage flight path requests from aircrews and controllers. But, Erzberger acknowledges, "The FAA's current plan for upgrades to air traffic services does not include [allowing] the future ground system to issue separation-critical clearances of trajectory changes autonomously to aircraft via data link without explicit approval of a controller," as the AAC proposes. The AAC enables pilots or controllers to data link requests for a trajectory change to the ATS for approval after they are deconflicted with the paths of other aircraft. To divert around storms, for example, pilots could data link their trajectory preference to the ATS. Since several aircraft might request similar routes, the computer would then have to suggest alternatives. This could be accomplished without pilot-controller radio calls, a big bottleneck now. The ATS would have a built-in conflict monitor to call for a resolution (turn, climb or descend), when loss of separation is likely in 1-20 min. The AAC system would reduce controller errors by 90%, according to NASA Ames estimates. The AAC would have a back-up program to assure separation-Tactical Separation Assurance (TSAFE). It s designed to detect short-term traffic conflicts within 3-4 min. of loss of separation. The last line of defense would still be provided by traffic alert & collision avoidance systems (TCAS).

Hughes, David↗