Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Expression systems”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 613 records · Page 34
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A Pilot Study of Whole-Blood Transcriptomic Analysis to Identify Genes Associated with Repetitive Low-Level Blast Exposure in Career Breachers

Repetitive low-level blast exposure is one of the major occupational health concerns among US military service members and law enforcement. This study seeks to identify gene expression using microRNA and RNA sequencing in whole-blood samples from experienced breachers and unexposed controls. We performed experimental RNA sequencing using Illumina’s HiSeq 2500 Sequencing System, and microRNA analysis using NanoString Technology nCounter miRNA expression panel in whole-blood total RNA samples from 15 experienced breachers and 14 age-, sex-, and race-matched unexposed controls. We identified 10 significantly dysregulated genes between experienced breachers and unexposed controls, with FDR corrected <0.05: One upregulated gene, LINC00996 (long intergenic non-protein coding RNA 996); and nine downregulated genes, IGLV3-16 (immunoglobulin lambda variable 3-16), CD200 (CD200 molecule), LILRB5 (leukocyte immunoglobulin-like receptor B5), ZNF667-AS1 (ZNF667 antisense RNA 1), LMOD1 (leiomodin 1), CNTNAP2 (contactin-associated protein 2), EVPL (envoplakin), DPF3 (double PHD fingers 3), and IGHV4-34 (immunoglobulin heavy variable 4-34). The dysregulated gene expressions reported here have been associated with chronic inflammation and immune response, suggesting that these pathways may relate to the risk of lasting neurological symptoms following high exposures to blast over a career.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2011

AutoBayes Program Synthesis System System Internals

This lecture combines the theoretical background of schema based program synthesis with the hands-on study of a powerful, open-source program synthesis system (Auto-Bayes). Schema-based program synthesis is a popular approach toward program synthesis. The lecture will provide an introduction into this topic and discuss how this technology can be used to generate customized algorithms. The synthesis of advanced numerical algorithms requires the availability of a powerful symbolic (algebra) system. Its task is to symbolically solve equations, simplify expressions, or to symbolically calculate derivatives (among others) such that the synthesized algorithms become as efficient as possible. We will discuss the use and importance of the symbolic system for synthesis. Any synthesis system is a large and complex piece of code. In this lecture, we will study Autobayes in detail. AutoBayes has been developed at NASA Ames and has been made open source. It takes a compact statistical specification and generates a customized data analysis algorithm (in C/C++) from it. AutoBayes is written in SWI Prolog and many concepts from rewriting, logic, functional, and symbolic programming. We will discuss the system architecture, the schema libary and the extensive support infra-structure. Practical hands-on experiments and exercises will enable the student to get insight into a realistic program synthesis system and provides knowledge to use, modify, and extend Autobayes.

Statistical Algorithms↗
NASA NTRS1987

A framework for qualitative reasoning about solid objects

Predicting the behavior of a qualitatively described system of solid objects requires a combination of geometrical, temporal, and physical reasoning. Methods based upon formulating and solving differential equations are not adequate for robust prediction, since the behavior of a system over extended time may be much simpler than its behavior over local time. A first-order logic, in which one can state simple physical problems and derive their solution deductively, without recourse to solving the differential equations, is discussed. This logic is substantially more expressive and powerful than any previous AI representational system in this domain.

Davis, E.↗
NASA NTRS1960

Vacancy Relaxation in Cubic Crystals

The configuration of the atoms surrounding a vacancy in four face-centered cubic and three body-centered cubic metals has been computed, using a pairwise, central-force model in which the energy of interaction between two atoms was taken to have the form of a Morse function. Only radial relaxations were considered. The first and second nearest-neighbor relaxations for the face-centered systems were found to be: Pb (1.42,−0.43), Ni (2.14,−0.39), Cu(2.24,−0.40) and Ca (2.73,−0.41, expressed in percentages of normal distances. For the body-centered systems the relaxations out to the fourth nearest neighbors to the vacancy were: Fe (6.07,−2.12, −0.25, −), Ba (7.85, −2.70, 0.70, −0.33) and Na (10.80, −3.14, 3.43, −0.20). The positive signs indicate relaxation toward the vacancy and the negative signs indicate relaxation away from the vacancy. The energies of relaxation (eV) are: Pb (0.162), Ni (0.626), Cu (0.560), Ca (0.400), Fe (1.410), Ba (0.950) and Na (0.172).

Girifalco, L. A.↗
NASA NTRS1999

Arabidopsis alcohol dehydrogenase expression in both shoots and roots is conditioned by root growth environment

It is widely accepted that the Arabidopsis Adh (alcohol dehydrogenase) gene is constitutively expressed at low levels in the roots of young plants grown on agar media, and that the expression level is greatly induced by anoxic or hypoxic stresses. We questioned whether the agar medium itself created an anaerobic environment for the roots upon their growing into the gel. beta-Glucuronidase (GUS) expression driven by the Adh promoter was examined by growing transgenic Arabidopsis plants in different growing systems. Whereas roots grown on horizontal-positioned plates showed high Adh/GUS expression levels, roots from vertical-positioned plates had no Adh/GUS expression. Additional results indicate that growth on vertical plates closely mimics the Adh/GUS expression observed for soil-grown seedlings, and that growth on horizontal plates results in induction of high Adh/GUS expression that is consistent with hypoxic or anoxic conditions within the agar of the root zone. Adh/GUS expression in the shoot apex is also highly induced by root penetration of the agar medium. This induction of Adh/GUS in shoot apex and roots is due, at least in part, to mechanisms involving Ca2+ signal transduction.

NASA Discipline Plant Biology↗
NASA NTRS2013

SynGenics Optimization System (SynOptSys)

The SynGenics Optimization System (SynOptSys) software application optimizes a product with respect to multiple, competing criteria using statistical Design of Experiments, Response-Surface Methodology, and the Desirability Optimization Methodology. The user is not required to be skilled in the underlying math; thus, SynOptSys can help designers and product developers overcome the barriers that prevent them from using powerful techniques to develop better pro ducts in a less costly manner. SynOpt-Sys is applicable to the design of any product or process with multiple criteria to meet, and at least two factors that influence achievement of those criteria. The user begins with a selected solution principle or system concept and a set of criteria that needs to be satisfied. The criteria may be expressed in terms of documented desirements or defined responses that the future system needs to achieve. Documented desirements can be imported into SynOptSys or created and documented directly within SynOptSys. Subsequent steps include identifying factors, specifying model order for each response, designing the experiment, running the experiment and gathering the data, analyzing the results, and determining the specifications for the optimized system. The user may also enter textual information as the project progresses. Data is easily edited within SynOptSys, and the software design enables full traceability within any step in the process, and facilitates reporting as needed. SynOptSys is unique in the way responses are defined and the nuances of the goodness associated with changes in response values for each of the responses of interest. The Desirability Optimization Methodology provides the basis of this novel feature. Moreover, this is a complete, guided design and optimization process tool with embedded math that can remain invisible to the user. It is not a standalone statistical program; it is a design and optimization system.

Ventresca, Carol↗
NASA NTRS2003

Parallel Signal Processing and System Simulation using aCe

Recently, networked and cluster computation have become very popular for both signal processing and system simulation. A new language is ideally suited for parallel signal processing applications and system simulation since it allows the programmer to explicitly express the computations that can be performed concurrently. In addition, the new C based parallel language (ace C) for architecture-adaptive programming allows programmers to implement algorithms and system simulation applications on parallel architectures by providing them with the assurance that future parallel architectures will be able to run their applications with a minimum of modification. In this paper, we will focus on some fundamental features of ace C and present a signal processing application (FFT).

Dorband, John E.↗
DOE OSTI2022

Machine learning of consistent thermodynamic models using automatic differentiation

In this study, we propose a data-driven method to describe consistent equations of state (EOS) for arbitrary systems. Complex EOS are traditionally obtained by fitting suitable analytical expressions to thermophysical data. A key aspect of EOS is that the relationships between state variables are given by derivatives of the system free energy. In this work, we model the free energy with an artificial neural network and utilize automatic differentiation to directly learn the derivatives of the free energy. We demonstrate this approach on two different systems, the analytic van der Waals EOS and published data for the Lennard-Jones fluid, and we show that it is advantageous over direct learning of thermodynamic properties (i.e., not as derivatives of the free energy but as independent properties), in terms of both accuracy and the exact preservation of the Maxwell relations. Furthermore, the method implicitly provides the free energy of a system without explicit integration.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS1987

Flexible system model reduction and control system design based upon actuator and sensor influence functions

A model reduction technique based on aggregation with respect to sensor and actuator influence functions rather than modes is presented for large systems of coupled second-order differential equations. Perturbation expressions which can predict the effects of spillover on both the reduced-order plant model and the neglected plant model are derived. For the special case of collocated actuators and sensors, these expressions lead to the derivation of constraints on the controller gains that are, given the validity of the perturbation technique, sufficient to guarantee the stability of the closed-loop system. A case study demonstrates the derivation of stabilizing controllers based on the present technique. The use of control and observation synthesis in modifying the dimension of the reduced-order plant model is also discussed. A numerical example is provided for illustration.

Yam, Yeung↗
DOE OSTI2025

Leveraging CRISPR Cas9 RNPs and Cre- loxP in Picochlorum celeri for generation of field deployable strains and selection marker recycling

As new highly productive strains of algae are discovered and developed to meet the energy, chemical, and food requirements of the future, genetic engineering of those strains in a manner that yields deployable transformants is paramount. This study introduces the novel CRoxP ($\underline{\textrm{C}}$$\textrm{as9}$ $\underline{\textrm{R}}$$\textrm{NPs}$ coupled with an inducible $\underline{\textrm{CR}}$$\textrm{e}$-$\textrm{l}\underline{\textrm{oxP}}$) system for rapid generation of marker- and transgene-free strains of Picochlorum celeri. The CRoxP system allows reuse of selection markers without Cas9 expression in vivo, eliminating many of the bottlenecks associated with conventional CRISPR Cas9 use for precise genome editing. In P. celeri, transformants were generated with a turnaround time as short as 21 days between transformation and being ready for another round of transformation with the same selection marker by using the CRoxP system. As a use-case for CRoxP, depigmented strains of P. celeri were generated by multiplexed Cas9 disruption of major LHCII genes followed by either a second round of LHCII targeting, or knockout of an LHCI gene. One transformant tested in flask culture (R6) exhibited similar biomass production to the wild type with 46% less Chl a + b on a biomass basis. In photobioreactors and under diel light simulating a solar day, a transformant (LhcBM31) exhibited 34 g AFDW m –2 d –1 with 54% less Chl a + b on a biomass basis vs. wild type.

09 BIOMASS FUELS↗
NASA NTRS1972

Computerized optimal control system design for reusable and expendable boost vehicles.

An optimization technique has been developed which combines the practical features of hybrid simulation of the dynamic system under study with the systematic approach of modern control theory where a mathematically formulated design criterion is optimized by functional minimization. Standard hybrid computer optimization methods using high-speed repetitive simulations and gradient minimization schemes have been extended to obtain time-varying optimal gain schedules and reduce the sensitivity of the optimized system to parameter and disturbance uncertainties. In this approach the performance index is expressed in meaningful engineering terms that reflect the interactions among all major disciplines, structures, control/actuation system design, aerodynamics and performance. The basic optimization technique is developed and its application to current aerospace control problems including the space shuttle is presented in detail. In the discussion of the application, the controllers resulting from the technique are compared with controllers developed by conventional methods. The paper concludes with a review of the advantages and disadvantages of the technique and plans for future applications.

Connor, C. L.↗
DOE OSTI2021

Transforming a Simple Structure Model to Represent a Complex Dynamic System with Unknown Boundary Restraints

Imposing a boundary condition on a structure can significantly alter its dynamic properties. However, sometimes the specifics of the new boundary conditions are not known. When the effects of a boundary condition are uncertain or there is not enough information, engineers need to excite the complex structure to obtain these modified properties. In order to experimentally obtain the new properties, engineers need multiple experiments and many outputs for interpolation in order to sufficiently represent the entire structure. In this study, the researchers attached a stinger to a cantilever beam, acting as a new transverse restraint of unknown properties. This paper presents a conversion expression that predicts the dynamic behavior of any point in the system with the new boundary condition. This expression relies only on one impact hammer experiment with one output and the model of the stinger-free cantilever beam, referred to as the simple structure. Researchers estimated the Transfer Function (TRF) of the beam and compared it with an experimentally measured TRF to validate the method. The mean absolute error of the estimated TRF compared to the experimental TRF is 1.99 dB. This demonstrates the use of the proposed method for estimating unmeasured TRFs in a system with an uncertain boundary condition using a single input, single output (SISO) test and a model of the simple structure.

42 ENGINEERING↗
DOE OSTI2020

Thermodynamic Modeling of Aqueous LiCl, LiBr, LiI, and LiNO 3 Solutions

Thermodynamic models are essential to facilitate the advancement of process design, optimization, and operation of electrolyte systems. In this work, a comprehensive thermodynamic framework based on the Electrolyte Nonrandom Two-Liquid model is developed to calculate phase equilibria behavior and salt solubility of aqueous LiCl, LiBr, LiI, and LiNO 3 solutions. The model describes the non-ideality of the electrolyte solutions by using two binary interaction parameters for each electrolyte-molecule pair in the system. Each binary interaction parameter is further expressed with up to three temperature coefficients which are regressed from experimental data. To take into account the hydration of lithium ion, two separate chemistries for the dissociation of lithium salts are investigated. In the first case, the lithium ion is considered as a bare ion, Li + , while in the second case hydration of the lithium ion from Li + to Li(H 2 O) + is considered. Here, the calculated thermodynamic properties compare adequately with the experimental data for both sets of chemistries for concentrations up to saturation and temperatures from 273.15 K up to 623.15 K. Moderate to significant improvements are observed with the incorporation of the hydration chemistry for aqueous LiCl, LiBr, and LiI solutions when compared to the non-hydrated lithium ion model results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Modified Energy Span Analysis Reveals Heterogeneous Catalytic Kinetics

Mechanistic modeling is a cornerstone of catalyst development generally conducted with microkinetic models or density functional theory-based energy profiles. We extend the energy span model of homogeneous catalysis to heterogeneous systems by introducing the modified energy span analysis (MESA) model by implementing collision theory and gas-phase concentration effects. We determine analytically turnover frequencies, coverages, rate-determining steps, apparent activation energies, and reaction orders in agreement with microkinetic and kinetic Monte Carlo simulations. The model applies to discrete catalyst state systems, including single-atom catalysts, homogeneous systems, and microporous materials. A generalizable rate expression is derived for reactor modeling or mechanistic insights from solely experimentally measured reaction orders. Here, we illustrate MESA on three published mechanisms and reveal unexpected phenomena absent in traditional energy span profiles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate

Abstract Microbial predators such as choanoflagellates are key players in ocean food webs. Choanoflagellates, which are the closest unicellular relatives of animals, consume bacteria and also exhibit marked biological transitions triggered by bacterial compounds, yet their native microbiomes remain uncharacterized. Here we report the discovery of a ubiquitous, uncultured bacterial lineage we name Candidatus Comchoanobacterales ord. nov., related to the human pathogen Coxiella and physically associated with the uncultured marine choanoflagellate Bicosta minor . We analyse complete ‘Comchoano’ genomes acquired after sorting single Bicosta cells, finding signatures of obligate host-dependence, including reduction of pathways encoding glycolysis, membrane components, amino acids and B-vitamins. Comchoano encode the necessary apparatus to import energy and other compounds from the host, proteins for host-cell associations and a type IV secretion system closest to Coxiella’s that is expressed in Pacific Ocean metatranscriptomes. Interactions between choanoflagellates and their microbiota could reshape the direction of energy and resource flow attributed to microbial predators, adding complexity and nuance to marine food webs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Single Crystal Plasticity Model with Deformation Twinning for the High Rate Deformation of β-HMX

Deformation twinning is an active deformation mechanism during loading along certain crystallographic directions of β-cyclotetramethylene tetranitramine (β-HMX). In this work, a finite strain thermomechanical model is extended to include twinning as a deformation mechanism in addition to plastic slip. The stress is derived from the free energy expression including a term representing the equation of state. The crystal plasticity framework is used to divide the total strain into inelastic and elastic component, where the elastic part is used in the expression for the free energy. The twin systems are treated as pseudo slip systems and the shear rate on the twin systems is evaluated in terms of the twin resistance and the projection of the stress tensor. The model parameters were calibrated against a set of plate impact experiments performed on β-HMX by Dick et al. The remaining plate impact experiments are used to evaluate the predictive capability of the model. The quality of the model fits and predictions is discussed from a physical and modeling perspective. Particularly, the role of twin modeling on results is highlighted. Finally, the model is used to explore the relationship between the propensity for twinning and crystal orientation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Unexpected Scaling of Peak Acceleration for a Yielding Mass-Spring System Subjected to a Triangular Base Acceleration Pulse

The use of bounding scenarios is a common practice that greatly simplifies the design and qualification of structures. However, this approach implicitly assumes that the quantities of interest increase monotonically with the input to the structure, which is not necessarily true for nonlinear structures. This paper surveys the literature for observations of nonmonotonic behavior of nonlinear systems and finds such observations in both the earthquake engineering and applied mechanics literature. Numerical simulations of a single degree-of-freedom mass-spring system with an elastic–plastic spring subjected to a triangular base acceleration pulse are then presented, and it is shown that the relative acceleration of this system scales nonmonotonically with the input magnitude in some cases. The equation of motion for this system is solved symbolically and an approximate expression for the relative acceleration is developed, which qualitatively agrees with the nonmonotonic behavior seen in the numerical results. The nonmonotonicity is investigated and found to be a result of dynamics excited by the discontinuous derivative of the base acceleration pulse, the magnitude of which scales nonmonotonically with the input magnitude due to the fact that the first yield of the spring occurs earlier as the input magnitude is increased. The relevance of this finding within the context of defining bounding scenarios is discussed, and it is recommended that modeling be used to perform a survey of the full range of possible inputs prior to defining bounding scenarios.

42 ENGINEERING↗
DOE OSTI2021

A consensus-based ensemble approach to improve transcriptome assembly

Systems-level analyses, such as differential gene expression analysis, co-expression analysis, and metabolic pathway reconstruction, depend on the accuracy of the transcriptome. Multiple tools exist to perform transcriptome assembly from RNAseq data. However, assembling high quality transcriptomes is still not a trivial problem. This is especially the case for non-model organisms where adequate reference genomes are often not available. Different methods produce different transcriptome models and there is no easy way to determine which are more accurate. Furthermore, having alternative-splicing events exacerbates such difficult assembly problems. While benchmarking transcriptome assemblies is critical, this is also not trivial due to the general lack of true reference transcriptomes. In this study, we first provide a pipeline to generate a set of the simulated benchmark transcriptome and corresponding RNAseq data. Using the simulated benchmarking datasets, we compared the performance of various transcriptome assembly approaches including both de novo and genome-guided methods. The results showed that the assembly performance deteriorates significantly when alternative transcripts (isoforms) exist or for genome-guided methods when the reference is not available from the same genome. To improve the transcriptome assembly performance, leveraging the overlapping predictions between different assemblies, we present a new consensus-based ensemble transcriptome assembly approach, ConSemble. Without using a reference genome, ConSemble using four de novo assemblers achieved an accuracy up to twice as high as any de novo assemblers we compared. When a reference genome is available, ConSemble using four genome-guided assemblies removed many incorrectly assembled contigs with minimal impact on correctly assembled contigs, achieving higher precision and accuracy than individual genome-guided methods. Furthermore, ConSemble using de novo assemblers matched or exceeded the best performing genome-guided assemblers even when the transcriptomes included isoforms. We thus demonstrated that the ConSemble consensus strategy both for de novo and genome-guided assemblers can improve transcriptome assembly. The RNAseq simulation pipeline, the benchmark transcriptome datasets, and the script to perform the ConSemble assembly are all freely available from: http://bioinfolab.unl.edu/emlab/consemble/.

59 BASIC BIOLOGICAL SCIENCES↗