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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 613 records · Page 34
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Comprehensive view of microscopic interactions between DNA-coated colloids

Abstract The self-assembly of DNA-coated colloids into highly-ordered structures offers great promise for advanced optical materials. However, control of disorder, defects, melting, and crystal growth is hindered by the lack of a microscopic understanding of DNA-mediated colloidal interactions. Here we use total internal reflection microscopy to measure in situ the interaction potential between DNA-coated colloids with nanometer resolution and the macroscopic melting behavior. The range and strength of the interaction are measured and linked to key material design parameters, including DNA sequence, polymer length, grafting density, and complementary fraction. We present a first-principles model that screens and combines existing theories into one coherent framework and quantitatively reproduces our experimental data without fitting parameters over a wide range of DNA ligand designs. Our theory identifies a subtle competition between DNA binding and steric repulsion and accurately predicts adhesion and melting at a molecular level. Combining experimental and theoretical results, our work provides a quantitative and predictive approach for guiding material design with DNA-nanotechnology and can be further extended to a diversity of colloidal and biological systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Tautomerism unveils a self-inhibition mechanism of crystallization

Abstract Modifiers are commonly used in natural, biological, and synthetic crystallization to tailor the growth of diverse materials. Here, we identify tautomers as a new class of modifiers where the dynamic interconversion between solute and its corresponding tautomer(s) produces native crystal growth inhibitors. The macroscopic and microscopic effects imposed by inhibitor-crystal interactions reveal dual mechanisms of inhibition where tautomer occlusion within crystals that leads to natural bending, tunes elastic modulus, and selectively alters the rate of crystal dissolution. Our study focuses on ammonium urate crystallization and shows that the keto-enol form of urate, which exists as a minor tautomer, is a potent inhibitor that nearly suppresses crystal growth at select solution alkalinity and supersaturation. The generalizability of this phenomenon is demonstrated for two additional tautomers with relevance to biological systems and pharmaceuticals. These findings offer potential routes in crystal engineering to strategically control the mechanical or physicochemical properties of tautomeric materials.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Achieving tissue-level softness on stretchable electronics through a generalizable soft interlayer design

Soft and stretchable electronics have emerged as highly promising tools for biomedical diagnosis and biological studies, as they interface intimately with the human body and other biological systems. Most stretchable electronic materials and devices, however, still have Young’s moduli orders of magnitude higher than soft bio-tissues, which limit their conformability and long-term biocompatibility. Here, we present a design strategy of soft interlayer for allowing the use of existing stretchable materials of relatively high moduli to versatilely realize stretchable devices with ultralow tissue-level moduli. We have demonstrated stretchable transistor arrays and active-matrix circuits with moduli below 10 kPa—over two orders of magnitude lower than the current state of the art. Benefiting from the increased conformability to irregular and dynamic surfaces, the ultrasoft device created with the soft interlayer design realizes electrophysiological recording on an isolated heart with high adaptability, spatial stability, and minimal influence on ventricle pressure. In vivo biocompatibility tests also demonstrate the benefit of suppressing foreign-body responses for long-term implantation. With its general applicability to diverse materials and devices, this soft-interlayer design overcomes the material-level limitation for imparting tissue-level softness to a variety of bioelectronic devices.

42 ENGINEERING↗
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

Central transcriptional regulator controls photosynthetic growth and carbon storage in response to high light

Carbon capture and biochemical storage are some of the primary drivers of photosynthetic yield and productivity. To elucidate the mechanisms governing carbon allocation, we designed a photosynthetic light response test system for genetic and metabolic carbon assimilation tracking, using microalgae as simplified plant models. The systems biology mapping of high light-responsive photophysiology and carbon utilization dynamics between two variants of the same Picochlorum celeri species, TG1 and TG2 elucidated metabolic bottlenecks and transport rates of intermediates using instationary 13 C-fluxomics. Simultaneous global gene expression dynamics showed 73% of the annotated genes responding within one hour, elucidating a singular, diel-responsive transcription factor, closely related to the CCA1/LHY clock genes in plants, with significantly altered expression in TG2. Transgenic P. celeri TG1 cells expressing the TG2 CCA1/LHY gene, showed 15% increase in growth rates and 25% increase in storage carbohydrate content, supporting a coordinating regulatory function for a single transcription factor.

09 BIOMASS FUELS↗
DOE OSTI2024

Controlled mechanochemical coupling of anti-junctions in DNA origami arrays

Abstract Allostery is a hallmark of cellular function and important in every biological system. Still, we are only starting to mimic it in the laboratory. Here, we introduce an approach to study aspects of allostery in artificial systems. We use a DNA origami domino array structure which–upon binding of trigger DNA strands–undergoes a stepwise allosteric conformational change. Using two FRET probes placed at specific positions in the DNA origami, we zoom in into single steps of this reaction cascade. Most of the steps are strongly coupled temporally and occur simultaneously. Introduction of activation energy barriers between different intermediate states alters this coupling and induces a time delay. We then apply these approaches to release a cargo DNA strand at a predefined step in the reaction cascade to demonstrate the applicability of this concept in tunable cascades of mechanochemical coupling with both spatial and temporal control.

Science & Technology - Other Topics↗
DOE OSTI2024

Nanoscale polarization transient gratings

Light manipulation at the nanoscale is essential both for fundamental science and modern technology. The quest to shorter lengthscales, however, requires the use of light wavelengths beyond the visible. In particular, in the extreme ultraviolet regime these manipulation capabilities are hampered by the lack of efficient optics, especially for polarization control. Here, we present a method to create periodic, polarization modulations at the nanoscale using a tailored configuration of the FERMI free electron laser and demonstrate its capabilities by comparing the dynamics induced by this polarization transient grating with those driven by a conventional intensity grating on a thin ferrimagnetic alloy. While the intensity grating signal is dominated by the thermoelastic response, the polarization grating excitation minimizes it, uncovering helicity-dependent responses previously undetected. We anticipate nanoscale polarization transient gratings to become useful for the study of physical, chemical and biological systems possessing chiral symmetry.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Dense, continuous membrane labeling and expansion microscopy visualization of ultrastructure in tissues

Abstract Lipid membranes are key to the nanoscale compartmentalization of biological systems, but fluorescent visualization of them in intact tissues, with nanoscale precision, is challenging to do with high labeling density. Here, we report ultrastructural membrane expansion microscopy (umExM), which combines an innovative membrane label and optimized expansion microscopy protocol, to support dense labeling of membranes in tissues for nanoscale visualization. We validate the high signal-to-background ratio, and uniformity and continuity, of umExM membrane labeling in brain slices, which supports the imaging of membranes and proteins at a resolution of ~60 nm on a confocal microscope. We demonstrate the utility of umExM for the segmentation and tracing of neuronal processes, such as axons, in mouse brain tissue. Combining umExM with optical fluctuation imaging, or iterating the expansion process, yields ~35 nm resolution imaging, pointing towards the potential for electron microscopy resolution visualization of brain membranes on ordinary light microscopes.

Science & Technology - Other Topics↗
DOE OSTI2025

Realizing mechanical frustration at the nanoscale using DNA origami

Structural designs inspired by physical and biological systems have been previously utilized to develop mechanical metamaterials with enhanced properties based on clever geometric arrangement of constituent building blocks. Here, we use the DNA origami method to realize a nanoscale metastructure exhibiting mechanical frustration, a counterpart of the well-known phenomenon of magnetic frustration. By selectively actuating reconfigurable struts, it adopts either frustrated or non-frustrated states, each characterized by distinct free energy profiles. While the non-frustrated state distributes the strain homogeneously, the frustrated mode concentrates it at a specific location. Molecular dynamics simulations reconcile the contrasting behaviors and provide insights into underlying mechanics. We explore the design space further by tailoring responses through structural modifications. Our work combines programmable DNA self-assembly with mechanical design principles to overcome engineering limitations encountered at the macroscale to design dynamic, deformable nanostructures with potential applications in elastic energy storage, nanomechanical computation, and allosteric mechanisms in DNA-based nanomachinery.

DNA nanostructures↗
DOE OSTI2021

Accelerating phase-field-based microstructure evolution predictions via surrogate models trained by machine learning methods

Abstract The phase-field method is a powerful and versatile computational approach for modeling the evolution of microstructures and associated properties for a wide variety of physical, chemical, and biological systems. However, existing high-fidelity phase-field models are inherently computationally expensive, requiring high-performance computing resources and sophisticated numerical integration schemes to achieve a useful degree of accuracy. In this paper, we present a computationally inexpensive, accurate, data-driven surrogate model that directly learns the microstructural evolution of targeted systems by combining phase-field and history-dependent machine-learning techniques. We integrate a statistically representative, low-dimensional description of the microstructure, obtained directly from phase-field simulations, with either a time-series multivariate adaptive regression splines autoregressive algorithm or a long short-term memory neural network. The neural-network-trained surrogate model shows the best performance and accurately predicts the nonlinear microstructure evolution of a two-phase mixture during spinodal decomposition in seconds, without the need for “on-the-fly” solutions of the phase-field equations of motion. We also show that the predictions from our machine-learned surrogate model can be fed directly as an input into a classical high-fidelity phase-field model in order to accelerate the high-fidelity phase-field simulations by leaping in time. Such machine-learned phase-field framework opens a promising path forward to use accelerated phase-field simulations for discovering, understanding, and predicting processing–microstructure–performance relationships.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Genetic circuit design automation for yeast

Cells can be programmed to monitor and react to their environment using genetic circuits. Design automation software maps a desired circuit function to a DNA sequence, a process that requires units of gene regulation (gates) that are simple to connect and behave predictably. This poses a challenge for eukaryotes due to their complex mechanisms of transcription and translation. To this end, we have developed gates for yeast (Saccharomyces cerevisiae) that are connected using RNA polymerase flux as the signal carrier and are insulated from each other and host regulation. They are based on minimal constitutive promoters (~120 base pairs), for which rules are developed to insert operators for DNA-binding proteins. Using this approach, in this work we constructed nine NOT/NOR gates with nearly identical response functions and 400-fold dynamic range. In circuits, they are transcriptionally insulated from each other by placing ribozymes downstream of terminators to block nuclear export of messenger RNAs resulting from RNA polymerase readthrough. Based on these gates, Cello 2.0 was used to build circuits with up to 11 regulatory proteins. A simple dynamic model predicts the circuit response over days. Genetic circuit design automation for eukaryotes simplifies the construction of regulatory networks as part of cellular engineering projects, whether it be to stage processes during bioproduction, serve as environmental sentinels or guide living therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Nanoscale Turing patterns in a bismuth monolayer

Turing’s reaction–diffusion theory of morphogenesis has been very successful for understanding macroscopic patterns within complex objects ranging from biological systems to sand dunes. However, Turing patterns on microscopic length scales are extremely rare. Here we show that a strained atomic bismuth monolayer assembled on the surface of NbSe 2 —and subject to interatomic interactions and kinetics—displays Turing patterns. Our reaction–diffusion model produces stripe patterns with a period of five atoms (approximately 2 nm) and domain walls with Y-shaped junctions that bear a striking resemblance to what has been experimentally observed. Our work establishes that Turing patterns can occur at the atomic scale in a hard condensed-matter setting.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Imaging and spatially resolved mass spectrometry applications in nephrology

The application of spatially resolved mass spectrometry (MS) and MS imaging approaches for studying biomolecular processes in the kidney is rapidly growing. These powerful methods, which enable label-free and multiplexed detection of many molecular classes across omics domains (including metabolites, drugs, proteins and protein post-translational modifications), are beginning to reveal new molecular insights related to kidney health and disease. Further, the complexity of the kidney often necessitates multiple scales of analysis for interrogating biofluids, whole organs, functional tissue units, single cells and subcellular compartments. Various MS methods can generate omics data across these spatial domains and facilitate both basic science and pathological assessment of the kidney. Optimal processes related to sample preparation and handling for different MS applications are rapidly evolving. Emerging technology and methods, improvement of spatial resolution, broader molecular characterization, multimodal and multiomics approaches and the use of machine learning and artificial intelligence approaches promise to make these applications even more valuable in the field of nephology. Overall, spatially resolved MS and MS imaging methods have the potential to fill much of the omics gap in systems biology analysis of the kidney and provide functional outputs that cannot be obtained using genomics and transcriptomic methods.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Controlled patterning of crystalline domains by frontal polymerization

Materials with hierarchical architectures that combine soft and hard material domains with coalesced interfaces possess superior properties compared with their homogeneous counterparts. These architectures in synthetic materials have been achieved through deterministic manufacturing strategies such as 3D printing, which require an a priori design and active intervention throughout the process to achieve architectures spanning multiple length scales. Here we harness frontal polymerization spin mode dynamics to autonomously fabricate patterned crystalline domains in poly(cyclooctadiene) with multiscale organization. This rapid, dissipative processing method leads to the formation of amorphous and semi-crystalline domains emerging from the internal interfaces generated between the solid polymer and the propagating cure front. The size, spacing and arrangement of the domains are controlled by the interplay between the reaction kinetics, thermochemistry and boundary conditions. Small perturbations in the fabrication conditions reproducibly lead to remarkable changes in the patterned microstructure and the resulting strength, elastic modulus and toughness of the polymer. Furthermore, this ability to control mechanical properties and performance solely through the initial conditions and the mode of front propagation represents a marked advancement in the design and manufacturing of advanced multiscale materials. Drawing inspiration from biological systems in which structural complexity develops through dissipative reaction–diffusion processes, this study explores a transformative synthetic manufacturing strategy aimed at harnessing the principles underpinning morphogenic growth, unlocking new avenues for advanced materials design and fabrication. Synthetic coupled reaction-transport processes offer a versatile yet relatively underexplored method to manipulate the spatial attributes of synthetic materials10. Here we introduce an innovative manufacturing approach based on frontal ring-opening metathesis polymerization (FROMP) that draws parallels with morphogenic growth and development, enabling the formation of patterned microstructures within polymeric materials.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Electronic origin of reorganization energy in interfacial electron transfer

Electron transfer (ET) reactions underpin energy conversion and chemical transformations in both biological and a biological systems. The efficiency of any ET process relies on achieving a desired ET rate within an optimal driving force range. Marcus theory provides a microscopic framework for understanding the activation free energy—and therefore the rate—of ET in terms of a key parameter: the reorganization energy. For electrified solid–liquid interfaces, it has long been conventionally understood that only factors in the electrolyte phase are responsible for determining the reorganization energy and that the electronic density of states (DOS) of the electrode only serves to dictate the number of thermally accessible channels for ET. Here we show instead that the electrode DOS plays a central role in governing the reorganization energy, far outweighing its conventionally assumed role. Using atomically layered heterostructures, we tune the DOS of graphene and measure outer-sphere ET kinetics. We find the ensuing variation in ET rate arises from strong modulation in a reorganization energy associated with image potential localization in the electrode. Here we redefine the traditional paradigm of heterogeneous ET kinetics, revealing a deeper role of the electrode electronic structure in interfacial reactivity.

Electrochemistry↗
DOE OSTI2021

A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are emerging as a valuable avenue for predicting, understanding and designing microbial communities. Computation of microbial ecosystems in time and space (COMETS) extends dynamic flux balance analysis to generate simulations of multiple microbial species in molecularly complex and spatially structured environments. Here we describe how to best use and apply the most recent version of COMETS, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, evolutionary dynamics and extracellular enzyme activity modules. In addition to a command-line option, COMETS includes user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, as well as comprehensive documentation and tutorials. Overall, this protocol provides a detailed guideline for installing, testing and applying COMETS to different scenarios, generating simulations that take from a few minutes to several days to run, with broad applicability to microbial communities across biomes and scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Metagenome-assembled genome extraction and analysis from microbiomes using KBase

Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. In order to realize the hope of capturing Earth’s microbial genetic complement and to facilitate the investigation of the functional roles of specific lineages in a given ecosystem, technologies that accelerate the recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high-quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). Overall, these steps take about a day to obtain extracted genomes when starting from smaller environmental shotgun read libraries, or up to about a week from larger libraries. In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAGs, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq and others. While portions of such capabilities are available individually from other resources, the combination of the intuitive usability, data interoperability and integration of tools in a freely available computational resource makes KBase a powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended with additional MAG recovery and analysis tools, via the KBase software development kit (SDK).

59 BASIC BIOLOGICAL SCIENCES↗