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 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Inhibition of PTEN activity promotes IB4‐positive sensory neuronal axon growth

Abstract Traumatic nerve injuries have become a common clinical problem, and axon regeneration is a critical process in the successful functional recovery of the injured nervous system. In this study, we found that peripheral axotomy reduces PTEN expression in adult sensory neurons; however, it did not alter the expression level of PTEN in IB4‐positive sensory neurons. Additionally, our results indicate that the artificial inhibition of PTEN markedly promotes adult sensory axon regeneration, including IB4‐positive neuronal axon growth. Thus, our results provide strong evidence that PTEN is a prominent repressor of adult sensory axon regeneration, especially in IB4‐positive neurons.

Zhou, Li‐Yu↗
DOE OSTI2024

Synchronization for CXL Based Memory

Compute Express Link (CXL) is an important emerging standard for disaggregated memory. While this standard provisions coherency across numerous hosts and devices, implementing hardware support for type three devices is challenging. In this work, we look at the overhead of software synchronization and using software-based coherency. Moreover, we discuss the limits of software-based coherency in fully expressing modern synchronization techniques for a CXL-based disaggregate memory system. We demonstrate our approach using a CXL hardware prototype and running a version of the famous Peterson Lock (enhanced to run with more than two threads). We analyze its performance and share how more advanced synchronization techniques might interact with software-based coherence CXL hardware and program execution models.

High Performance Computing (HPC)↗
DOE OSTI2023

Biological insights from multi-omics analysis strategies: Complex pleotropic effects associated with autophagy

Research strategies that combine molecular data from multiple levels of genome expression (i.e., multi-omics data), often referred to as a systems biology strategy, has been advocated as a route to discovering gene functions. In this study we conducted an evaluation of this strategy by combining lipidomics, metabolite mass-spectral imaging and transcriptomics data from leaves and roots in response to mutations in two AuTophaGy-related ( ATG ) genes of Arabidopsis . Autophagy is an essential cellular process that degrades and recycles macromolecules and organelles, and this process is blocked in the atg7 and atg9 mutants that were the focus of this study. Specifically, we quantified abundances of ~100 lipids and imaged the cellular locations of ~15 lipid molecular species and the relative abundance of ~26,000 transcripts from leaf and root tissues of WT, atg7 and atg9 mutant plants, grown either in normal (nitrogen-replete) and autophagy-inducing conditions (nitrogen-deficient). The multi-omics data enabled detailed molecular depiction of the effect of each mutation, and a comprehensive physiological model to explain the consequence of these genetic and environmental changes in autophagy is greatly facilitated by the a priori knowledge of the exact biochemical function of the ATG7 and ATG9 proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

CompLaB v1.0: a scalable pore-scale model for flow, biogeochemistry, microbial metabolism, and biofilm dynamics

Abstract. Microbial activity and chemical reactions in porous media depend on the local conditions at the pore scale and can involve complex feedback with fluid flow and mass transport. We present a modeling framework that quantitatively accounts for the interactions between the bio(geo)chemical and physical processes and that can integrate genome-scale microbial metabolic information into a dynamically changing, spatially explicit representation of environmental conditions. The model couples a lattice Boltzmann implementation of Navier–Stokes (flow) and advection–diffusion-reaction (mass conservation) equations. Reaction formulations can include both kinetic rate expressions and flux balance analysis, thereby integrating reactive transport modeling and systems biology. We also show that the use of surrogate models such as neural network representations of in silico cell models can speed up computations significantly, facilitating applications to complex environmental systems. Parallelization enables simulations that resolve heterogeneity at multiple scales, and a cellular automaton module provides additional capabilities to simulate biofilm dynamics. The code thus constitutes a platform suitable for a range of environmental, engineering and – potentially – medical applications, in particular ones that involve the simulation of microbial dynamics.

58 GEOSCIENCES↗
DOE OSTI2021

Self-powered Heating: Efficiency Analysis

Conventional fuel-fired heating devices such as furnaces, boilers, and water heaters have fuel efficiency less than 100% on the basis of higher heating value. They also require electricity from the electric grid to power parasitic loads such as blowers, pumps, fans, and ignitors. The primary energy efficiency of the device accounts for both fuel used on-site and primary energy used off-site to produce electric power used by the device. This work compares conventional fuel-fired heating devices to two types of self-powered devices. A self-powered device (SPD) integrates a power cycle onboard to eliminate consumption of grid electricity. We assume that all heat rejected by the onboard power cycle is added to the process fluid, so that, compared with a conventional device, the same amount of heat is provided to the process fluid and the same amount of fuel is consumed, but grid electricity consumption is eliminated. The first SPD type is the basic one: exactly the electricity required is generated. The second type considered is the SPD with heat pump (SPD-HP), in which the power cycle generates more electricity than needed for parasitic loads, and the excess electricity is used to power a heat pump. The heat pump extracts additional heat from the ambient to boost efficiency. Both SPD and SPD-HP self-consume all the generated electricity, in contrast to combined heat and power (CHP) systems that export electricity. In this work, equations are derived to express the efficiency of three classes of heating devices: conventional (consuming grid electricity), self-powered (consuming no grid electricity), and self-powered with heat pump. The efficiency of each is derived as a function of up to six factors: (1) the fraction of combustion heat captured, (2) the rate of parasitic power consumption, (3) the fraction of electric energy dissipated as useful heat, (4) the power cycle conversion efficiency, (5) the grid efficiency, when applicable, and (6) the heat pump COP, when applicable. Scenarios are identified in which it is possible to achieve efficiency greater than 100% on a higher heating value basis. Plausible configurations using existing technology options are outlined.

Gluesenkamp, Kyle↗
DOE OSTI2022

Real-Time Seismic System for Monitoring, Imaging, and Characterization (RT-SEISMIC)

The goal of this Laboratory Directed Research and Development (LDRD) project was to develop a borehole seismic source and sensor array to enable real-time seismic imaging at scales and conditions relevant to the energy industry including both fossil-energy and geothermal. In FY21 and FY22, we designed, built, and tested both a prototype impulse source module for generating seismic energy and a sensing module for recording ground motions generated by the source module array. A pneumatically driven vibratory source was also designed. The source modules were fabricated with all high temperature components and the team has worked to incorporate the current RT-SEISMIC electronics design into a commercially available, high temperature silicon-on-insulator chip integrated circuit. Several issues were identified during fabrication and lab testing that led to redesign of several system components and subsequent retesting. The final round of testing showed that while metal/graphite-based seals worked quite well for static seals, they were unable to provide an adequate gas seal for dynamic, reciprocating part movements which necessitated a final redesign using Kalrez. This change will result in a continuous temperature rating of approximately 275 degrees C for the system. While a field test of the RT-SEISMIC system was targeted in FY22, due to the extended lab testing and redesign efforts, field testing was not achieved. As a result of this LDRD investment, several sponsors have expressed interest in RT-SEISMIC and we expect to continue towards a field demonstration of the full system in the future.

58 GEOSCIENCES↗
DOE OSTI2026

Expansion-driven Weibel instability in magnetohydrodynamics: Linear theory for static systems

The Weibel dispersion relation is obtained in the magnetohydrodynamic (MHD) approximation by including a tensor expression for temperature. MHD gives an upper cutoff wavenumber for Weibel growth identical to kinetic theory if the electron drift velocity is included in the evolution of the electron temperature. MHD overestimates growth rates compared to kinetic theory and gives maximum growth at larger wavenumbers, but it only leads to divergent results as temperature anisotropy tends to infinity. Thermal conduction in MHD lowers the growth rates and shifts maximum growth to smaller wavenumbers, but flux-limited or nonlocal thermal conduction is found to significantly limit these effects. The results are used as a first step in evaluating the potential of MHD to simulate expansion-driven Weibel instability, which occurs due to the temperature tensor only cooling in the direction of expansion. Finally, the small temperature anisotropy found in expansion-driven Weibel instability means that MHD could be an adequate model because growth rates are much less than the electron plasma frequency, and wavelengths are much greater than the Debye length.

Davies, J. R. [Univ. of Rochester, NY (United Stat↗
DOE OSTI2021

Transcription initiation as a control point in plastid gene expression

The extensive processing and protein-assisted stabilization of transcripts have been taken as evidence for a viewpoint that the control of gene expression had shifted entirely in evolution from transcriptional in the bacterial endosymbiont to posttranscriptional in the plastid. This suggestion is however at odds with many observations on plastid gene transcription. Chloroplasts of flowering plants and mosses contain two or more RNA polymerases with distinct promoter preference and division of labor for the coordinated synthesis of plastid RNAs. Plant and algal plastids further possess multiple nonredundant sigma factors that function as transcription initiation factors. The controlled accumulation of plastid sigma factors and modification of their activity by sigma-binding proteins and phosphorylation constitute additional transcriptional regulatory strategies. Plant and algal plastids also contain dedicated one- or two-component transcriptional regulators. Finally, transcription initiation thus continues to form a critical control point at which varied developmental and environmental signals intersect with plastid gene expression.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Cell-Free-Based Thermophilic Biocatalyst for the Synthesis of Amino Acids from One-Carbon Feedstocks

Bioproduction from one-carbon compounds, such as formate, is an attractive prospect due to reduced energy requirements and the possibility for using CO 2 as a sustainable feedstock. Formate-fixing pathways engineered using Escherichia coli lysate-based cell-free expression (CFE) biocatalysts have the potential to route 100% of feedstock carbon toward chemical synthesis but are undermined by siphoning of in-pathway metabolites and cofactors by the CFE background metabolism. To address this limitation, we engineer a CFE-based thermophilic multienzyme biocatalyst for the synthesis of serine and glycine from formate, bicarbonate, and ammonia. After expression of the thermophilic formate-to-serine pathway in a one-pot reaction, the mesophilic E. coli CFE background machinery is removed by simple heat denaturation, eliminating the siphoning of cofactors, inpathway metabolites, and products. After bioprocess optimization, including pathway gene expression duration and chemical synthesis temperature, we achieve near stoichiometric conversion of formate and bicarbonate to serine and glycine, reaching 97% of stoichiometric yield. The use of a moderately thermophilic biocatalyst allowed chemical synthesis to take place at mesophilic temperatures, enabling the balance of optimal enzyme activity with minimal metabolite/cofactor thermal degradation. In a fed-batch experiment, the biocatalyst shows sustained chemical synthesis rates for 8 h, paving the way toward a continuous bioprocess. Finally, a sensitivity analysis of cofactor usage revealed that the most expensive cofactors, THF and NADPH, can be reduced by 5-fold without significantly lowering product yields. To the best of our knowledge, this is the first instance of expressing a thermophilic pathway in an E. coli lysate-based CFE system to generate a thermophilic biocatalyst for use at mesophilic temperatures. The CFEbased thermophilic formate-to-serine biocatalyst triples the combined serine and glycine yield previously obtained by a CFE-based mesophilic formate-to-serine biocatalyst (30%), and quadruple the yield obtained by a purified enzyme system (22%). Ultimately, this work opens the door to using E. coli lysate-based CFE for thermophilic biocatalyst generation to achieve high chemical synthesis yields.

bacteria↗
DOE OSTI2022

N-dependent dynamics of root growth and nitrate and ammonium uptake are altered by the bacterium Herbaspirillum seropedicae in the cereal model Brachypodium distachyon

Nitrogen (N) fixation in cereals by root-associated bacteria is a promising solution for reducing use of chemical N fertilizers in agriculture. However, plant and bacterial responses are unpredictable across environments. We hypothesized that cereal responses to N-fixing bacteria are dynamic, depending on N supply and time. To quantify the dynamics, a gnotobiotic, fabricated ecosystem (EcoFAB) was adapted to analyse N mass balance, to image shoot and root growth, and to measure gene expression of Brachypodium distachyon inoculated with the N-fixing bacterium Herbaspirillum seropedicae. Phenotyping throughput of EcoFAB-N was 25–30 plants h -1 with open software and imaging systems. Herbaspirillum seropedicae inoculation of B. distachyon shifted root and shoot growth, nitrate versus ammonium uptake, and gene expression with time; directions and magnitude depended on N availability. Primary roots were longer and root hairs shorter regardless of N, with stronger changes at low N. At higher N, H. seropedicae provided 11% of the total plant N that came from sources other than the seed or the nutrient solution. The time-resolved phenotypic and molecular data point to distinct modes of action: at 5 mM NH 4 NO 3 the benefit appears through N fixation, while at 0.5 mM NH 4 NO 3 the mechanism appears to be plant physiological, with H. seropedicae promoting uptake of N from the root medium.Future work could fine-tune plant and root-associated microorganisms to growth and nutrient dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Imaging of Fibroblast Activation Protein Alpha Expression in a Preclinical Mouse Model of Glioma Using Positron Emission Tomography

Glioblastoma multiforme (GBM) is the most aggressive glioma of the primary central nervous system. Due to the lack of effective treatment options, the prognosis for patients remains bleak. Fibroblast activation protein alpha (FAP), a 170 kDa type II transmembrane serine protease was observed to be expressed on glioma cells and within the glioma tumor microenvironment. To understand the utility of targeting FAP in this tumor type, the immuno-PET radiopharmaceutical [ 89 Zr]Zr-Df-Bz-F19 mAb was prepared and Lindmo analysis was used for its in vitro evaluation using the U87MG cell line, which expresses FAP endogenously. Lindmo analysis revealed an association constant (K a ) of 10 -8 M -1 and an immunoreactivity of 52%. Biodistribution studies in U87MG tumor-bearing mice revealed increasing radiotracer retention in tumors over time, leading to average tumor-to-muscle ratios of 3.1, 7.3, 7.2, and 8.3 at 2, 24, 48 and 72 h, respectively. Small animal PET corroborated the biodistribution studies; tumor-to-muscle ratios at 2, 24, 48, and 72 h were 2.0, 5.0, 6.1 and 7.8, respectively. Autoradiography demonstrated accumulated activity throughout the interior of FAP + tumors, while sequential tumor sections stained positively for FAP expression. Conversely, FAP - tissues retained minimal radioactivity and were negative for FAP expression by immunohistochemistry. These results demonstrate FAP as a promising biomarker that may be exploited to diagnose and potentially treat GBM and other neuroepithelial cancers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Cost Model for Pumped Storage Hydropower Geomembrane Lining Systems

The Cost Model for Pumped Storage Hydropower Geomembrane Lining Systems offers an approximation of geomembrane lining system costs for pumped storage hydropower (PSH) reservoirs. Geomembrane lining systems have been used around the world for over 60 years for the construction of dams and reservoirs. Although geomembrane lining systems have found widespread use in the construction of canals and waste containment systems, they have not been utilized in the construction of new PSH facilities in the United States since the Mount Elbert PSH powerplant in Colorado. For this reason, PSH developers in the United States expressed the need for a tool that would allow them to estimate the costs of geomembrane lining systems for their PSH projects. To meet this need, the Cost Model for Pumped Storage Hydropower Geomembrane Lining Systems was developed by Oak Ridge National Laboratory with support from Argonne National Laboratory and Stantec, Inc. This Cost Model will enable PSH developers to develop a preliminary estimate of the cost of geomembrane lining systems and to better understand different reservoir lining options and their cost and performance characteristics, thus enabling them to make informed decisions related to preferred reservoir lining systems for their PSH projects.

DeNeale, Scott [Oak Ridge National Laboratory (ORN↗
DOE OSTI2026

Molecular concentration field design using closed-form steady-state solutions

Control over spatial concentration fields represents a fundamental challenge in designing synthetic biological systems and programmable soft materials. While nature creates morphogen gradients that orchestrate complex developmental processes, synthetic approaches have largely relied on empirical optimization and computationally intensive simulations. Here, we present an analytical framework for steady-state concentration fields generated by finite-sized localized sources in diffusion–degradation systems and derive closed-form solutions for one-, two-, and three-dimensional geometries. By expressing these solutions in dimensionless form, we show that gradient steepness and spatial structure are organized by the Thiele modulus, which captures the competition between diffusion and degradation length scales. The analysis reveals distinct design regimes: in degradation-dominated systems, gradient shape is governed by exponential decay and becomes dimension-independent, whereas in diffusion-dominated systems, gradient magnitude and extent follow dimension-dependent power-law scaling. Building on these results, we introduce a quantitative design strategy that uses threshold-based criteria to program concentration ranges by tuning physically accessible parameters, most directly the production rate, while holding transport and degradation properties fixed. Comparisons with numerical solutions and reported experimental systems demonstrate consistency with the predicted scaling behavior. Together, this work provides a generalizable and physically transparent framework for designing steady-state concentration fields in synthetic biological and soft matter systems, enabling predictive control of gradient-mediated organization without reliance on extensive numerical optimization.

Kim, Dong Woo [Johns Hopkins University, Baltimore↗
DOE OSTI2021

Identification and widespread environmental distribution of a gene cassette implicated in anaerobic dichloromethane degradation

Anthropogenic activities and natural processes release dichloromethane (DCM, methylene chloride), a toxic chemical with substantial ozone-depleting capacity. Specialized anaerobic bacteria metabolize DCM; however, the genetic basis for this process has remained elusive. Comparative genomics of the three known anaerobic DCM-degrading bacterial species revealed a homologous gene cluster, designated the methylene chloride catabolism (mec) gene cassette, comprising 8–10 genes encoding proteins with 79.6%–99.7% amino acid identities. Functional annotation identified genes encoding a corrinoid-dependent methyltransferase system, and shotgun proteomics applied to two DCM-catabolizing cultures revealed high expression of proteins encoded on the mec gene cluster during anaerobic growth with DCM. In a DCM-contaminated groundwater plume, the abundance of mec genes strongly correlated with DCM concentrations (R 2 = 0.71–0.85) indicating their potential value as process-specific bioremediation biomarkers. mec gene clusters were identified in metagenomes representing peat bogs, the deep subsurface, and marine ecosystems including oxygen minimum zones (OMZs), suggesting a capacity for DCM degradation in diverse habitats. Here, the broad distribution of anaerobic DCM catabolic potential infers a role for DCM as an energy source in various environmental systems, and implies that the global DCM flux (i.e., the rate of formation minus the rate of consumption) might be greater than emission measurements suggest.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Complex field reversal dynamics in nanomagnetic systems

Nanomagnetic materials, built from thin, patterned films of ferromagnetic materials, began as analogues to frustrated magnetism. Their low energy of operation and emergent properties make them strong candidates for physics-based devices. A recent model of how nanomagnetic domains flip, the Glauber mean-field model, is used here to understand how systems of nanomagnets evolve when opposed by external field. This reversal can be expressed in an analytical form in the case of one-dimensional chains and trees at zero temperature, where the cascade of spin flips gives rise to harmonic power spectra. Finally, the same cascades in two and three dimensions form fractal field reversal clusters whose shape depends on the strength of the field and the tuning of interactions between nanomagnets.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Derivation of K-matrix reaction theory in a discrete basis formalism

The usual derivations of the S and K matrices for two-particle reactions proceed through the Lippmann–Schwinger equation with formal definitions of the incoming and outgoing scattering states. Here we present a simpler alternative derivation that is carried out completely in the Hamiltonian representation, using a discrete basis of configurations for the scattering channels as well as the quasi-bound configurations of the combined fragments. We use matrix algebra to derive an explicit expression for the K matrix in terms of the Hamiltonian of the internal states of the compound system and the coupling between the channels and the internal states. The formula for the K matrix includes explicitly a real dispersive shift matrix to the internal Hamiltonian that is easily computed in the formalism. That expression is applied to derive the usual form of the S matrix as a sum over poles in the complex energy plane. Some extensions and limitations of the discrete-basis Hamiltonian formalism are discussed in the concluding remarks and in the Appendix.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Exact Maps to Second Order for Selected Elements in MAD-X Variables

This report presents calculations for exact maps to second order about an arbitrary orbit for certain elements: drifts, solenoids, and rotations about a transverse axis. These expressions were used in recent updates to MAD-X, and thus the phase space variables used are those of MAD-X. Formulas are given here for the final orbit and its first and second derivatives with respect to the incoming phase space coordinates for a drift, solenoid, and coordinate system rotations about transverse axes. I do not claim these results to be new: these expressions are well-known and are presented here only for reference. This document does not collect all maps that could be expressed exactly, in particular dipoles are omitted.

43 PARTICLE ACCELERATORS↗
DOE OSTI2022

Impact of the optical parametric amplification phase on laser pulse compression

Optical parametric chirped-pulse amplification (OPCPA) is an effective way to generate ultrashort pulses that has been used extensively for a variety of applications requiring high peak intensities. Precise control and measurement of a system’s spectral and spatial phases are required for Fourier transform–limited pulse compression and diffraction-limited focusing. Phase accumulated during optical parametric amplification (OPA) can degrade the compressibility and focusability of the pulse, reducing peak intensity. We used analytic and numerical analysis of OPA to study the influence of crystal parameters, wavefront of the pump and signal, and their relative optical alignment on the accumulated phase. Here, we show that the accumulated signal phase is largely independent of amplifier saturation and, with significant local wavefront gradients in the signal or pump beam, the quality of the compressed pulses can be degraded. We use first-order expressions for the pump- and signal-angle sensitivity to evaluate an OPCPA system consisting of a highly deuterated potassium dihydrogen phosphate (DKDP) amplifier designed to support bandwidth for 15 fs pulses centered at 920 nm.

47 OTHER INSTRUMENTATION↗