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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 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering

Abstract CRISPR-Cas9 tools have transformed genetic manipulation capabilities in the laboratory. Empirical rules-of-thumb have been developed for only a narrow range of model organisms, and mechanistic underpinnings for sgRNA efficiency remain poorly understood. This work establishes a novel feature set and new public resource, produced with quantum chemical tensors, for interpreting and predicting sgRNA efficiency. Feature engineering for sgRNA efficiency is performed using an explainable-artificial intelligence model: iterative Random Forest (iRF). By encoding quantitative attributes of position-specific sequences for Escherichia coli sgRNAs, we identify important traits for sgRNA design in bacterial species. Additionally, we show that expanding positional encoding to quantum descriptors of base-pair, dimer, trimer, and tetramer sequences captures intricate interactions in local and neighboring nucleotides of the target DNA. These features highlight variation in CRISPR-Cas9 sgRNA dynamics between E. coli and H. sapiens genomes. These novel encodings of sgRNAs enhance our understanding of the elaborate quantum biological processes involved in CRISPR-Cas9 machinery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Three-dimensional structure-guided evolution of a ribosome with tethered subunits

We report RNA-based macromolecular machines, such as the ribosome, have functional parts reliant on structural interactions spanning sequence-distant regions. These features limit evolutionary exploration of mutant libraries and confound three-dimensional structure-guided design. To address these challenges, we describe Evolink (evolution and linkage), a method that enables high-throughput evolution of sequence-distant regions in large macromolecular machines, and library design guided by computational RNA modeling to enable exploration of structurally stable designs. Using Evolink, we evolved a tethered ribosome with a 58% increased activity in orthogonal protein translation and a 97% improvement in doubling times in SQ171 cells compared to a previously developed tethered ribosome, and reveal new permissible sequences in a pair of ribosomal helices with previously explored biological function. The Evolink approach may enable enhanced engineering of macromolecular machines for new and improved functions for synthetic biology.

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

Constructing O2/O3 homogeneous hybrid stabilizes Li-rich layered cathodes

With the advantages of high energy density and low manufacture cost, lithium-rich layered oxides (LLOs), typically with a layered O3-type structure, are regarded as promising cathodes for lithium-ion batteries (LIBs), but their broad usages are hindered by severe voltage decay over cycling. Although recent progress in O2-type LLOs has aroused interest for their less voltage decay, the critical barrier of unsatisfactory capacity retention has not been overcome yet. In this work, to tackle these handicaps, we design a new type of LLO (O2/O3-type LLO) with a homogeneous hybrid structure, where the O2 and O3 lattice stacking sequences are arranged alternatively. Benefitting from this novel O2/O3 hybrid structure, the designed material shows greatly improved voltage and capacity stability than that of pure O2- and O3-type LLOs. Revealed by in-situ synchrotron X-ray diffraction and operando differential electrochemical mass spectra, the O2/O3-hybrid LLO cathode shows a more reversible structural evolution, smaller volume change and suppressed oxygen loss during the electrochemical processes. Our approach has initiated a new way to reduce the capacity and voltage decay of LLOs, which endows great promise to the development of high-energy-density LIBs.

25 ENERGY STORAGE↗
DOE OSTI2021

jialiu232/MetaFunPrimer_paper_info

Genes belonging to the same functional group may include numerous and variable gene sequences, making characterizing and quantifying difficult. Therefore, high-throughput design tools are needed to simultaneously create primers for improved quantification of target genes. We developed MetaFunPrimer, a bioinformatic pipeline, to design primers for numerous genes of interest. This tool also enables gene target prioritization based on ranking the presence of genes in user-defined references, such as environment-specific metagenomes. Given inputs of protein and nucleotide sequences for gene targets of interest and an accompanying set of reference metagenomes or genomes, MetaFunPrimer generates primers for ranked genes of interest. To demonstrate the usage and benefits of MetaFunPrimer, a total of 78 primer pairs were designed to target observed ammonia monooxygenase subunit A (amoA) genes of ammonia-oxidizing bacteria (AOB) in 1,550 publicly available soil metagenomes. We demonstrate computationally that these amoA-AOB primers can cover 94% of the amoA-AOB genes observed in the 1,550 soil metagenomes compared with a 49% estimated coverage by previously published primers. Finally, we verified the utility of these primer sets in incubation experiments that used long-term nitrogen fertilized or unfertilized soils. High-throughput quantitative PCR (qPCR) results and statistical analyses showed significant differences in relative quantification patterns between the two soils, and subsequent absolute quantifications also confirmed that target genes enumerated by six selected primer pairs were significantly more abundant in the nitrogen-fertilized soils. This new tool gives microbial ecologists a new approach to assess functional gene abundance and related microbial community dynamics quickly and affordably.

Liu, Jia↗
DOE OSTI2023

Gate-based quantum computing for protein design

Protein design is a technique to engineer proteins by permuting amino acids in the sequence to obtain novel functionalities. However, exploring all possible combinations of amino acids is generally impossible due to the exponential growth of possibilities with the number of designable sites. The present work introduces circuits implementing a pure quantum approach, Grover’s algorithm, to solve protein design problems. Our algorithms can adjust to implement any custom pair-wise energy tables and protein structure models. Moreover, the algorithm’s oracle is designed to consist of only adder functions. Quantum computer simulators validate the practicality of our circuits, containing up to 234 qubits. However, a smaller circuit is implemented on real quantum devices. Our results show that using iterations, the circuits find the correct results among all N possibilities, providing the expected quadratic speed up of Grover’s algorithm over classical methods (i.e.,).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

SynopFrame: Multiscale time-dependent visual abstraction framework for analyzing DNA nanotechnology simulations

We present an open-source framework, SynopFrame, that allows DNA nanotechnology (DNA-nano) experts to analyze and understand molecular dynamics simulation trajectories of their designs. We use a multiscale multi-dimensional abstraction space, connect the representations to a projected conformational space plot of the structure’s temporal sequence, and thus enable experts to analyze the dynamics of their structural designs and, specifically, failure cases of the assembly. In addition, our time-dependent abstraction representation allows the biologists, for the first time in a smooth and structurally clear way, to identify and observe temporal transitions of a DNA-nano design from one configuration to another, and to highlight important periods of the simulation for further analysis. We realize SynopFrame as a dashboard of the different synchronized 3D spatial and 2D schematic visual representations, with a color overlay to show essential properties such as the status of hydrogen bonds. The linking of the spatial, schematic, and abstract views ensures that users can effectively analyze the high-frequency motion. We also categorize the status of the hydrogen bonds into a new format to allow us to color-encode it and overlay it on the representations. To demonstrate the utility of SynopFrame, we describe example usage scenarios and report user feedback.

Abstraction space↗
DOE OSTI2024

Assembly of short amphiphilic peptoids into nanohelices with controllable supramolecular chirality

Abstract A long-standing challenge in bioinspired materials is to design and synthesize synthetic materials that mimic the sophisticated structures and functions of natural biomaterials, such as helical protein assemblies that are important in biological systems. Herein, we report the formation of a series of nanohelices from a type of well-developed protein-mimetics called peptoids. We demonstrate that nanohelix structures and supramolecular chirality can be well-controlled through the side-chain chemistry. Specifically, the ionic effects on peptoids from varying the polar side-chain groups result in the formation of either single helical fiber or hierarchically stacked helical bundles. We also demonstrate that the supramolecular chirality of assembled peptoid helices can be controlled by modifying assembling peptoids with a single chiral amino acid side chain. Computational simulations and theoretical modeling predict that minimizing exposure of hydrophobic domains within a twisted helical form presents the most thermodynamically favorable packing of these amphiphilic peptoids and suggests a key role for both polar and hydrophobic domains on nanohelix formation. Our findings establish a platform to design and synthesize chiral functional materials using sequence-defined synthetic polymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Assessment of the errors of high-fidelity two-qubit gates in silicon quantum dots

Achieving high-fidelity entangling operations between qubits consistently is essential for the performance of multi-qubit systems. Solid-state platforms are particularly exposed to errors arising from materials-induced variability between qubits, which leads to performance inconsistencies. Here we study the errors in a spin qubit processor, tying them to their physical origins. We use this knowledge to demonstrate consistent and repeatable operation with above 99% fidelity of two-qubit gates in the technologically important silicon metal-oxide-semiconductor quantum dot platform. Analysis of the physical errors and fidelities in multiple devices over extended periods allows us to ensure that we capture the variation and the most common error types. Physical error sources include the slow nuclear and electrical noise on single qubits and contextual noise that depends on the applied control sequence. Furthermore, we investigate the impact of qubit design, feedback systems and robust gate design to inform the design of future scalable, high-fidelity control strategies. Our results highlight both the capabilities and challenges for the scaling-up of silicon spin-based qubits into full-scale quantum processors.

Quantum dots↗
DOE OSTI2022

Sequentially regular polymer acceptors featuring flexible spacers for high-performance and mechanically robust all-polymer solar cells

Developing high-performance and mechanically robust polymer solar cells (PSCs) is crucial for realizing wearable power sources. While efficient all-polymer solar cells (all-PSCs) can be fabricated from polymerized small-molecule acceptors (PSMAs) with high optical absorption and electron mobilities, they still show limited mechanical robustness. Here, we achieve highly efficient and mechanically robust all-PSCs by designing a PSMA (PYFS-Reg) containing sequence-regular flexible spacers (FSs). The regular incorporation of the FS units into PSMAs is essential in simultaneously improving the electrical and mechanical properties of blend films. As a result, all-PSCs featuring PYFS-Reg achieve a high power conversion efficiency (PCE = 16.1%) and stretchability (crack onset strain (COS) = 22.4%), outperforming PSMAs without FSs (i.e., PYBDT, PCE = 12.6% and COS = 11.7%) or with randomly distributed FSs (i.e., PYFS-Ran, PCE = 12.2% and COS = 18.1%). Importantly, these all-PSCs are fabricated by an environmentally benign, non-halogenated solvent process. To further demonstrate their feasible applications in wearable devices, we construct intrinsically stretchable (IS) all-PSCs by using PYFS-Reg-based active layers, which exhibit a high PCE (10.6%) and excellent device stretchability (strain at PCE 80% = 36.7%).

14 SOLAR ENERGY↗
DOE OSTI2021

Solid-Binding Proteins: Bridging Synthesis, Assembly, and Function in Hybrid and Hierarchical Materials Fabrication

There is considerable interest in the development of hybrid organic–inorganic materials because of the potential for harvesting the unique capabilities that each system has to offer. Proteins are an especially attractive organic component owing to the high amount of chemical information encoded in their amino acid sequence, their amenability to molecular and computational (re)design, and the many structures and functions they specify. Genetic installation of solid-binding peptides (SBPs) within protein frameworks affords control over the position and orientation of adhesive and morphogenetic segments, and a path toward predictive synthesis and assembly of functional materials and devices, all while harnessing the built-in properties of the host scaffold. Furthermore, we review the current understanding of the mechanisms through which SBPs bind to technologically relevant interfaces, with an emphasis on the variables that influence the process, and highlight the last decade of progress in the use of solid-binding proteins for hybrid and hierarchical materials synthesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Constraining Kick Signals Through Advanced Multi-Phase Data

<ul><li>Re-designed ambient experimental apparatus constructed and operational</li><li>Finalized design of elevated experiments w/ LSU</li><li>Shakedown reveals that current sensors do not respond to changes in gas content</li><li>Designing surrogate sensor(s) w/ LSU</li><li>Implemented a sequence anomaly detection algorithm to identify kicks</li></ul>

Carney, Janine↗
DOE OSTI2024

Merefa Community Microgrid: Supporting Distributed Energy Resource Deployment in Ukraine

A conceptual design is described for a community microgrid in Ukraine. Microgrid resources include solar photovoltaics, battery energy storage, and conventional natural gas fueled reciprocating engine generators. The conceptual architecture was informed by the microgrid developer, NREL subject matter experts, and the application of REopt, an NREL-developed software tool created for identification of least-cost combination of resources for achieving cost savings, resilience, and renewable energy goals. This fact sheet is a summary of a previously published technical report; see NREL/TP-7A40-89527, which includes conceptual architecture, estimates of key summary financial metrics, and sequence of operations.

battery storage↗
DOE OSTI2022

Fast Evaluation of Viral Emerging Risks (FEVER): A computational tool for biosurveillance, diagnostics, and mutation typing of emerging viral pathogens

Viral pathogens can rapidly evolve, adapt to novel hosts, and evade human immunity. The early detection of emerging viral pathogens through biosurveillance coupled with rapid and accurate diagnostics are required to mitigate global pandemics. However, RNA viruses can mutate rapidly, hampering biosurveillance and diagnostic efforts. Here, we present a novel computational approach called FEVER (Fast Evaluation of Viral Emerging Risks) to design assays that simultaneously accomplish: 1) broad-coverage biosurveillance of an entire group of viruses, 2) accurate diagnosis of an outbreak strain, and 3) mutation typing to detect variants of public health importance. We demonstrate the application of FEVER to generate assays to simultaneously 1) detect sarbecoviruses for biosurveillance; 2) diagnose infections specifically caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); and 3) perform rapid mutation typing of the D614G SARS-CoV-2 spike variant associated with increased pathogen transmissibility. These FEVER assays had a high in silico recall (predicted positive) up to 99.7% of 525,708 SARS-CoV-2 sequences analyzed and displayed sensitivities and specificities as high as 92.4% and 100% respectively when validated in 100 clinical samples. The D614G SARS-CoV-2 spike mutation PCR test was able to identify the single nucleotide identity at position 23,403 in the viral genome of 96.6% SARS-CoV-2 positive samples without the need for sequencing. This study demonstrates the utility of FEVER to design assays for biosurveillance, diagnostics, and mutation typing to rapidly detect, track, and mitigate future outbreaks and pandemics caused by emerging viruses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Computational evolution of high-performing unfused non-fullerene acceptors for organic solar cells

Materials optimization for organic solar cells (OSCs) is a highly active field, with many approaches using empirical experimental synthesis, computational brute force to screen a subset of chemical space, or generative machine learning methods that often require significant training sets. While these methods may find high-performing materials, they can be inefficient and time-consuming. Genetic algorithms (GAs) are an alternative approach, allowing for the “virtual synthesis” of molecules and a prediction of their “fitness” for some property, with new candidates suggested based on good characteristics of previously generated molecules. In this work, a GA is used to discover high-performing unfused non-fullerene acceptors (NFAs) based on an empirical prediction of power conversion efficiency (PCE) and provides design rules for future work. The electron-withdrawing/donating strength, as well as the sequence and symmetry, of those units are examined. The utilization of a GA over a brute-force approach resulted in speedups up to 1.8 × 10 12 . New types of units, not frequently seen in OSCs, are suggested, and in total 5426 NFAs are discovered with the GA. Of these, 1087 NFAs are predicted to have a PCE greater than 18%, which is roughly the current record efficiency. While the symmetry of the sequence showed no correlation with PCE, analysis of the sequence arrangement revealed that higher performance can be achieved with a donor core and acceptor end groups. Future NFA designs should consider this strategy as an alternative to the current A-D-A'-D-A architecture.

14 SOLAR ENERGY↗
DOE OSTI2023

Model-based data center cooling controls comparative co-design

This article presents a comparative simulation-based control logic design process. It uses the Control Description Language (CDL) and the ASHRAE Guideline 36 high-performing building control sequences with the Modelica Buildings Library (MBL) to demonstrate a comparative analysis of two control designs for a data center chilled water plant. Details include a description of the closed-loop plant and control design methodology, including sizing and parameterization, base and alternative (Guideline 36) control logic with software implementation structure, and outline of the simulation experimentation process. The selected control designs are paired with comparable chilled water plant configurations. The models include a chiller, a water-side economizer, and an evaporative cooling tower. The plant provides cooling at 27ºC zone supply air temperature to a data center in Sacramento, CA. The comparative simulation results examined the impacts of a selected control logic detail, and present an example model-based design application. Overall, the simulation results showed a 25% annual and a 18% summer energy use reduction for alternative controls. This shows that simulation-based control logic design performance evaluation can improve energy efficiency and resilience aspects of system controls at large.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

Uncovering supramolecular chirality codes for the design of tunable biomaterials

In neurodegenerative diseases, polymorphism and supramolecular assembly of β-sheet amyloids are implicated in many different etiologies and may adopt either a left- or right-handed supramolecular chirality. Yet, the underlying principles of how sequence regulates supramolecular chirality remains unknown. Here, we characterize the sequence specificity of the central core of amyloid-β 42 and design derivatives which enable chirality inversion at biologically relevant temperatures. We further find that C-terminal modifications can tune the energy barrier of a left-to-right chiral inversion. Leveraging this design principle, we demonstrate how temperature-triggered chiral inversion of peptides hosting therapeutic payloads modulates the dosed release of an anticancer drug. These results suggest a generalizable approach for fine-tuning supramolecular chirality that can be applied in developing treatments to regulate amyloid morphology in neurodegeneration as well as in other disease states.

60 APPLIED LIFE SCIENCES↗