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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.

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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Evolutionary engineering reveals amino acid substitutions in Ato2 and Ato3 that allow improved growth of Saccharomyces cerevisiae on lactic acid

ABSTRACT In Saccharomyces cerevisiae, the complete set of proteins involved in transport of lactic acid across the cell membrane has not been determined. In this study, we aimed to identify transport proteins not previously described to be involved in lactic acid transport via a combination of directed evolution, whole-genome resequencing and reverse engineering. Evolution of a strain lacking all known lactic acid transporters on lactate led to the discovery of mutated Ato2 and Ato3 as two novel lactic acid transport proteins. When compared to previously identified S. cerevisiae genes involved in lactic acid transport, expression of ATO3T284C was able to facilitate the highest growth rate (0.15 ± 0.01 h-1) on this carbon source. A comparison between (evolved) sequences and 3D models of the transport proteins showed that most of the identified mutations resulted in a widening of the narrowest hydrophobic constriction of the anion channel. We hypothesize that this observation, sometimes in combination with an increased binding affinity of lactic acid to the sites adjacent to this constriction, are responsible for the improved lactic acid transport in the evolved proteins.

Baldi, Nicolò↗
DOE OSTI2024

A reversible four-electron Sn metal aqueous battery

Sn is a promising metal anode for aqueous batteries, with up to four-electron redox available per atom (903 mAh g −1 Sn ). However, practically harnessing the four-electron Sn(OH) 6 2− /Sn reversibility remains challenging due to limited mechanistic understanding. Here, in this study, we reveal a kinetically asymmetric redox pathway involving a successive four-electron plating and a stepwise 2 + 2 electron stripping through a Sn(OH) 3 − intermediate. The crossover of Sn(OH) 3 − induces a reversible self-discharge that reduces Coulombic efficiency but does not impact cyclability, demonstrated by four-electron Sn-Ni full cells that sustain >800 h of stable cycling. By tuning the ion selectivity of the separator to suppress Sn(OH) 3 − crossover while allowing OH − transport, we further demonstrate high Sn utilization (67%) and high energy density (143.1 Wh L −1 cell). The results provide key understandings of the tradeoffs in engineering reversible multi-electron metal anodes and define a new benchmark for practical energy density that exceeds any Sn-based aqueous batteries to date.

SN anode↗
DOE OSTI2022

Disentangling direct from indirect relationships in association networks

Networks are vital tools for understanding and modeling interactions in complex systems in science and engineering, and direct and indirect interactions are pervasive in all types of networks. However, quantitatively disentangling direct and indirect relationships in networks remains a formidable task. Here, we present a framework, called iDIRECT (Inference of Direct and Indirect Relationships with Effective Copula-based Transitivity), for quantitatively inferring direct dependencies in association networks. Using copula-based transitivity, iDIRECT eliminates/ameliorates several challenging mathematical problems, including ill-conditioning, self-looping, and interaction strength overflow. With simulation data as benchmark examples, iDIRECT showed high prediction accuracies. Application of iDIRECT to reconstruct gene regulatory networks in Escherichia coli also revealed considerably higher prediction power than the best-performing approaches in the DREAM5 (Dialogue on Reverse Engineering Assessment and Methods project, #5) Network Inference Challenge. In addition, applying iDIRECT to highly diverse grassland soil microbial communities in response to climate warming showed that the iDIRECT-processed networks were significantly different from the original networks, with considerably fewer nodes, links, and connectivity, but higher relative modularity. Further analysis revealed that the iDIRECT-processed network was more complex under warming than the control and more robust to both random and target species removal ( P < 0.001). As a general approach, iDIRECT has great advantages for network inference, and it should be widely applicable to infer direct relationships in association networks across diverse disciplines in science and engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Adaptive laboratory evolution and genetic engineering improved terephthalate utilization in Pseudomonas putida KT2440

Poly(ethylene terephthalate) (PET) is one of the most ubiquitous plastics and can be depolymerized through biological and chemo-catalytic routes to its constituent monomers, terephthalic acid (TPA) and ethylene glycol (EG). TPA and EG can be re-synthesized into PET for closed-loop recycling or microbially converted into higher-value products for open-loop recycling. Here, in this study, we expand on our previous efforts engineering and applying Pseudomonas putida KT2440 for PET conversion by employing adaptive laboratory evolution (ALE) to improve TPA catabolism. Three P. putida strains with varying degrees of metabolic engineering for EG catabolism underwent an automation-enabled ALE campaign on TPA, a TPA and EG mixture, and glucose as a control. ALE increased the growth rate on TPA and TPA-EG mixtures by 4.1- and 3.5-fold, respectively, in approximately 350 generations. Evolved isolates were collected at the midpoints and endpoints of 39 independent ALE experiments, and growth rates were increased by 0.15 and 0.20 h -1 on TPA and a TPA-EG, respectively, in the best performing isolates. Whole-genome re-sequencing identified multiple converged mutations, including loss-of-function mutations to global regulators gacS, gacA, and turA along with large duplication and intergenic deletion events that impacted the heterologously-expressed tphAB II catabolic genes. Reverse engineering of these targets confirmed causality, and a strain with all three regulators deleted and second copies of tphAB II and tpaK displayed improved TPA utilization compared to the base strain. Taken together, an iterative strain engineering process involving heterologous pathway engineering, ALE, whole genome sequencing, and genome editing identified five genetic interventions that improve P. putida growth on TPA, aimed at developing enhanced whole-cell biocatalysts for PET upcycling.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Precision genome editing in plants using gene targeting and prime editing: existing and emerging strategies

Precise modification of plant genomes, such as seamless insertion, deletion, or replacement of DNA sequences at a predefined site, is a challenging task. Gene targeting (GT) and prime editing are currently the best approaches for this purpose. However, these techniques are inefficient in plants, which limits their applications for crop breeding programs. Recently, substantial developments have been made to improve the efficiency of these techniques in plants. Several strategies, such as RNA donor templating, chemically modified donor DNA template, and tandem-repeat homology-directed repair, are aimed at improving GT. Additionally, improved prime editing gRNA design, use of engineered reverse transcriptase enzymes, and splitting prime editing components have improved the efficacy of prime editing in plants. These emerging strategies and existing technologies are reviewed along with various perspectives on their future improvement and the development of robust precision genome editing technologies for plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Explaining and predicting human behavior and social dynamics in simulated virtual worlds: reproducibility, generalizability, and robustness of causal discovery methods

Ground Truth program was designed to evaluate social science modeling approaches using simulation test beds with ground truth intentionally and systematically embedded to understand and model complex Human Domain systems and their dynamics Lazer et al. (Science 369:1060–1062, 2020). Our multidisciplinary team of data scientists, statisticians, experts in Artificial Intelligence (AI) and visual analytics had a unique role on the program to investigate accuracy, reproducibility, generalizability, and robustness of the state-of-the-art (SOTA) causal structure learning approaches applied to fully observed and sampled simulated data across virtual worlds. In addition, we analyzed the feasibility of using machine learning models to predict future social behavior with and without causal knowledge explicitly embedded. In this paper, we first present our causal modeling approach to discover the causal structure of four virtual worlds produced by the simulation teams—Urban Life, Financial Governance, Disaster and Geopolitical Conflict. Our approach adapts the state-of-the-art causal discovery (including ensemble models), machine learning, data analytics, and visualization techniques to allow a human-machine team to reverse-engineer the true causal relations from sampled and fully observed data. We next present our reproducibility analysis of two research methods team’s performance using a range of causal discovery models applied to both sampled and fully observed data, and analyze their effectiveness and limitations. We further investigate the generalizability and robustness to sampling of the SOTA causal discovery approaches on additional simulated datasets with known ground truth. Our results reveal the limitations of existing causal modeling approaches when applied to large-scale, noisy, high-dimensional data with unobserved variables and unknown relationships between them. We show that the SOTA causal models explored in our experiments are not designed to take advantage from vasts amounts of data and have difficulty recovering ground truth when latent confounders are present; they do not generalize well across simulation scenarios and are not robust to sampling; they are vulnerable to data and modeling assumptions, and therefore, the results are hard to reproduce. Finally, when we outline lessons learned and provide recommendations to improve models for causal discovery and prediction of human social behavior from observational data, we highlight the importance of learning data to knowledge representations or transformations to improve causal discovery and describe the benefit of causal feature selection for predictive and prescriptive modeling.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

An active learning high-throughput microstructure calibration framework for solving inverse structure–process problems in materials informatics

Determining a process–structure–property relationship is the holy grail of materials science, where both computational prediction in the forward direction and materials design in the inverse direction are essential. Problems in materials design are often considered in the context of process–property linkage by bypassing the materials structure, or in the context of structure–property linkage as in microstructure-sensitive design problems. However, there is a lack of research effort in studying materials design problems in the context of process–structure linkage, which has a great implication in reverse engineering. In this paper, given a target microstructure, we propose an active learning high-throughput microstructure calibration framework to derive a set of processing parameters, which can produce an optimal microstructure that is statistically equivalent to the target microstructure. The proposed framework is formulated as a noisy multi-objective optimization problem, where each objective function measures a deterministic or statistical difference of the same microstructure descriptor between a candidate microstructure and a target microstructure. Furthermore, to significantly reduce the physical waiting wall-time, we enable the high-throughput feature of the microstructure calibration framework by adopting an asynchronously parallel Bayesian optimization to exploit high-performance computing resources. Case studies in additive manufacturing and grain growth are used to demonstrate the applicability of the proposed framework, where kinetic Monte Carlo (kMC) simulation is used as a forward predictive model, such that for a given target microstructure, the target processing parameters that produced this microstructure are successfully recovered.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Evaluating the performance of random forest and iterative random forest based methods when applied to gene expression data

Gene-to-gene networks, such as Gene Regulatory Networks (GRN) and Predictive Expression Networks (PEN) capture relationships between genes and are beneficial for use in downstream biological analyses. There exists multiple network inference tools to produce these gene-to-gene networks from matrices of gene expression data. Random Forest-Leave One Out Prediction (RF-LOOP) is a method that has been shown to be efficient at producing these gene-to-gene networks, frequently known as GEne Network Inference with Ensemble of trees (GENIE3). Random Forest can be replaced in this process by iterative Random Forest (iRF), which performs variable selection and boosting. Here we validate that iterative Random Forest-Leave One Out Prediction (iRF-LOOP) produces higher quality networks than GENIE3 (RF-LOOP). We use both synthetic and empirical networks from the Dialogue for Reverse Engineering Assessment and Methods (DREAM) Challenges by Sage Bionetworks, as well as two additional empirical networks created from Arabidopsis thaliana and Populus trichocarpa expression data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Towards generic memory forensic framework for programmable logic controllers

A Programmable Logic Controller (PLC) is a microprocessor-based controller that is used to automate physical processes in critical infrastructure and various other industries and manufacturing sectors. Initially, PLCs were completely isolated from the Internet, and cyber security was not incorporated at the time of development. The introduction of industry 4.0 and the evolution of ICS systems to communicate over public IP addresses from the Internet enhanced productivity and efficiency, but Internet connectivity exposed the systems and their vulnerabilities, which led to an increase in cyber attacks. When a system is sabotaged/compromised, security analysts need to get to the root cause of the attack as quickly as possible to recover the system. To do so, memory forensic analysis is critical to provide a unique insight into the run-time memory activities and extract a reliable source of evidence. In this paper, we analyze the memory structure of the Schneider Electric Modicon M221 PLC. To build a memory profile, we reverse engineer the communication protocol and conduct differential analysis to gain knowledge about the structure of the memory and the low-level representation of control logic instructions. We then identify dynamic and static memory regions by modifying different project fields and conducting differential analysis, which allows us to identify boundaries of critical memory structures and extract important forensic artifacts that can be found in the memory. The Python implementation of the memory profile can help reduce the time and effort required for manual analysis in case of cyber incident or system failure.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Cutting force and stability for inserted cutters using structured light metrology

This paper describes force and stability prediction for inserted end and face mills using a reverse engineering approach. Structured light scanning is used to identify the spatial coordinates of the points that define the multiple insert cutting edges. These points are used to extract the cutting edge radius and angle and are then incorporated in a time domain simulation that predicts cutting force and tool/workpiece deflection for user-selected operating parameters. Good agreement between predicted and measured cutting forces is demonstrated. The process stability is then predicted using the validated force model and measured structural dynamics.

Machining↗
DOE OSTI2020

Cutting force and stability prediction for inserted cutters

Here, this paper presents an approach for inserted end/face mill force and stability predictions using a reverse engineering approach. Structured light scanning is implemented to identify the spatial coordinates of the points that define the multiple insert cutting edges. These points are analyzed to extract the cutting edge radius and angle values, which are then incorporated in a time domain simulation that predicts cutting force and tool/workpiece deflection for user-selected operating parameters. Good agreement between predicted and measured cutting forces is first demonstrated. The process stability is then predicted using the validated force model and measured structural dynamics. Observations about the stability dependence on insert geometry are finally presented for a selected end mill.

Machining↗
DOE OSTI2021

Aging mechanisms of filled cross-linked polyethylene (XLPE) cable insulation material exposed to simultaneous thermal and gamma radiation

Thermal and simultaneous thermal and gamma radiation aging experiments were conducted on an industry grade cross-linked polyethylene (XLPE) cable insulation material, which is a composite material with XLPE as polymer matrix and various additives and fillers. Reverse engineering was conducted to identify and quantify the material composition given that this information was not revealed by the cable manufacture. Samples were then aged at temperatures of 60, 90, and 115 °C, exposed to gamma radiation for total doses of 0 to 324 kGy, and at dose rates of 0 to 540 Gy/h. Aging mechanisms were studied using various materials characterization techniques including pyrolysis gas chromatography mass spectrometry (Py-GCMS), differential scanning calorimetry (DSC), nuclear magnetic resonance spectroscopy (NMR), and gel-fraction tests. Results show that the flame-retardant components were decomposed into smaller molecules when the material was exposed to gamma radiation, while no changes were observed when the samples were aged thermally without gamma radiation. With exposure to gamma radiation, the crystalline phase of the XLPE were damaged by gamma radiation introducing defects in the crystals, resulting in smaller and less perfect crystals. The dominance of chain scission or chain reformation process largely depends on the chain mobility, which is decided by the aging temperature. Chain scission was seen to dominate when the material was exposed to gamma radiation at 60 °C. Chain cross-linking slightly dominated when the material was exposed to gamma radiation at 90 °C and became more dominant with exposure to gamma radiation at 115 °C. No significant change to the XLPE polymer matrix was observed when the samples were exposed to thermal aging without gamma radiation. Finally, antioxidant is more effective in protecting the XLPE polymer matrix under thermal aging, but less effective with sample exposure to gamma radiation.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2020

Empirically verified analysis of dual pre-cooling system for hydrogen refuelling station

The dual cooling system at the California State University Los Angeles Hydrogen Research and Fueling Facility is analysed to predict the output hydrogen temperature in different ambient conditions. Initially, the facility was built with a coil chiller T20 cooling, sufficient for occasional fuelings. A flat plate evaporator system was added in series to resolve any issues for multiple fuelings even in the hottest weather. This study was commenced to verify the set points and determine the control requirements for the dual setup in order to inform future designs. A numerical-empirical model of the cooling system was developed by reverse engineering, using the station experimental measurements and database records. The subsystems are characterized separately but validated as a whole system imposing specific and standard operating conditions. The cooling model is tested with different inputs to validate the pre-set parameter variation of the cooling components. Ten scenarios were investigated to evaluate the fueling output parameters, testing two hydrogen temperature input trends (according to the facility initial conditions) and five ambient temperatures (from 15 °C to 35 °C). In closing, the simulation results have confirmed that the hydrogen output temperature remains within the range imposed by the SAE J2601 for each scenario studied, around -22 °C and -25 °C.

08 HYDROGEN↗
DOE OSTI2026

Elucidation of odd-chain dicarboxylate metabolism in Acinetobacter baylyi and application to polyethylene upcycling

Polyethylene (PE) is a versatile polymer, but its end-of-life management is challenging due to its recalcitrant structure. We present a promising approach combining chemical degradation and bio-upcycling to convert postconsumer PE waste into a value-added bioproduct. Specifically, PE was degraded into acetic acid and C 4 –C 7 dicarboxylic acids by nitric acid. We then elucidated the catabolic pathways for glutarate (C 5 ) and pimelate (C 7 ) in the nonmodel bacterium Acinetobacter baylyi ADP1 through RNA sequencing, phenotyping, and enzymatic assays. Whole-genome sequencing of evolved isolates also identified a crucial IclR family transcriptional regulator, DcaS, which acts as a repressor of dicarboxylate metabolism. The reverse-engineered strain exhibited enhanced substrate utilization compared to the wild-type strain. Using rational metabolic engineering, the PE deconstruction products were bioconverted into the valuable chemical lycopene, highlighting the potential of this microbial chassis to produce value-added bioproducts from postconsumer PE waste, thus promoting a circular economy for plastics.

metabolic engineering↗
DOE OSTI2021

Spectroscopic Signatures of MQ-Resins in Silicone Elastomers

Polysiloxane elastomers have a large application space due to their versatile cross-linking chemistry and highly tunable physical and mechanical properties. One approach for improving the mechanical integrity of commercial polysiloxane “silicone” elastomers while maintaining their optical transparency is the addition of small, silicone-resin molecules to the network. However, both the poly(dimethylsiloxane) (PDMS) network and the silicone-resin particles have an amorphous structure and complex chemistry, which makes the characterization of their structural properties and segmental network dynamics difficult. Here, we report the synthesis and characterization of a series of model silicone networks modified with a specific class of silicone-resin known as MQ-resin using Raman and advanced nuclear magnetic resonance (NMR) spectroscopy methods. Raman spectroscopy was successfully used to quantify the contribution of the MQ-resin to the network, to determine the type of MQ-resin present in the network, and to investigate the completeness of the network cross-linking reaction. Furthermore, solid-state and 1H double-quantum (DQ) NMR spectroscopies were used not only as a detection method for the MQ-resins but also to quantify changes in the segmental dynamics of the network as a function of MQ-resin concentration. The combination of Raman and NMR spectroscopies describes a series of samples where the MQ-resin particles and PDMS chains maintain their independent segmental dynamics up to high concentrations of MQ-resins (40–50% MQ), where the physical properties of the resin dominate the physical properties of the overall network. The results from our spectroscopic analyses are consistent with the results from macroscopic characterization techniques such as solvent uptake and mechanical testing. The spectroscopic insights into the structure–property relationships of PDMS-MQ composites presented in this study are a valuable tool not only for the synthesis and reverse engineering of future generations of commercial silicone elastomers but also for understanding the mechanisms of aging and degradation over the material lifetime.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Modeling Structural Colors from Disordered One-Component Colloidal Nanoparticle-Based Supraballs Using Combined Experimental and Simulation Techniques

Bright, saturated structural colors in birds have inspired synthesis of self-assembled, disordered arrays of assembled nanoparticles with varied particle spacings and refractive indices. However, predicting colors of assembled nanoparticles, and thereby guiding their synthesis, remains challenging due to the effects of multiple scattering and strong absorption. In this work, we use a computational approach to first reconstruct the nanoparticles’ assembled structures from small-angle scattering measurements and then input the reconstructed structures to a finite-difference time-domain method to predict their color and reflectance. This computational approach is successfully validated by comparing its predictions against experimentally measured reflectance and provides a pathway for reverse engineering colloidal assemblies with desired optical and photothermal properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Tutorial: Machine-Learning-Based CREASE-2D Analysis of 2D SAXS Profiles to Characterize Anisotropic Nanostructures in Soft Materials

We present a tutorial to guide users on how to extend the Computational Reverse Engineering Analysis of Scattering Experiments-2D (CREASE-2D) framework to interpret their experimental two-dimensional small-angle scattering (SAS) data from soft materials (e.g., polymers, peptide amphiphiles, biomolecular fibrils). Unlike most traditional SAS analysis approaches, which typically rely on azimuthally averaged onedimensional (1D) profiles, CREASE-2D utilizes the complete 2D scattering profile to reveal information about anisotropy in the structure. In past applications, CREASE has provided insights into complex structural features, including the cross-sectional shapes of assembled nanostructures and dispersity in these features, which are difficult to discern with existing analytical models. While (1D- ) CREASE has been applied to SANS and SAXS data, this tutorial shares the steps for implementing CREASE-2D using an example of a dipeptide solution system, for which we have SAXS data. We present details for these steps involved in using CREASE-2D to interpret SAXS profiles: how to preprocess SAXS data, define relevant structural features, generate three-dimensional real-space structures for specific values of these features, train a machine learning (ML) surrogate model to predict scattering profiles for given structural features, and optimize these features using genetic algorithms (GA). Then, we use these steps to interpret complex 2DSAXS data collected from dipeptide solutions that, in microscopy images, exhibit nanoscale structures that could be elliptical tubes/ flat tapes/cylinders or a combination of these cross sections. Open-source codes, computational hardware, and software requirements, as well as the strengths and limitations of this protocol, are also presented. We expect researchers working with (soft) biomaterials, peptide amphiphiles, amphiphilic polymer solutions, polymer nanocomposites, and blends of particles/polymers will find this CREASE-2D method and this tutorial of use.

CREASE↗
DOE OSTI2022

Hardware functional obfuscation with ferroelectric active interconnects

Existing circuit camouflaging techniques to prevent reverse engineering increase circuit-complexity with significant area, energy, and delay penalty. In this paper, we propose an efficient hardware encryption technique with minimal complexity and overheads based on ferroelectric field-effect transistor (FeFET) active interconnects. By utilizing the threshold voltage programmability of the FeFETs, run-time reconfigurable inverter-buffer logic, utilizing two FeFETs and an inverter, is enabled. Judicious placement of the proposed logic makes it act as a hardware encryption key and enable encoding and decoding of the functional output without affecting the critical path timing delay. Additionally, a peripheral programming scheme for reconfigurable logic by reusing the existing scan chain logic is proposed, obviating the need for specialized programming logic and circuitry for keybit distribution. Our analysis shows an average encryption probability of 97.43% with an increase of 2.24%/ 3.67% delay for the most critical path/ sum of 100 critical paths delay for ISCAS85 benchmarks.

42 ENGINEERING↗