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At least 1,207 records · Page 67

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DOE OSTI2026

Probing the limits of genetic recoding using multi-omics-guided evolution

Engineering the genetic code—by reassigning multiple of the 64 natural codons—enables making organisms resistant to all viruses, preventing genetic information exchange, and allowing the biosynthesis of genetically encoded unnatural polymers. However, synonymous codon replacement—recoding—is frequently lethal, and how recoding impacts fitness remains poorly explored. Here, we explore these effects using genome synthesis, directed evolution, and genome-transcriptome-translatome-proteome co-profiling on multiple synthetic Escherichia coli genomes. We construct six partially recoded E. coli strains bearing up to 45.8% of a synthetic genome with a deleterious 57-codon genetic code. As our analyses revealed widespread defects—including unassigned codons in Syn61 and Syn57—we apply multi-omics to revise our genome design and mitigate defects. Using multi-omics, we show that recoding induces transcriptional and translational changes leading to fitness defects under hundreds of conditions. Finally, we develop a multi-omics-guided evolution strategy that rapidly restores fitness, enabling genome synthesis with radical changes.

Nyerges, Akos [Harvard Medical School, Boston, MA ↗

DOE OSTI2025

Soft X-ray tomography reveals variations in B. subtilis biofilm structure upon tasA deletion

Bacterial biofilms are complex cell communities within a self-produced extracellular matrix, crucial in various fields but challenging to analyze in 3D. We developed a "biofilm-in-capillary" growth method compatible with full-rotation soft X-ray tomography, enabling high-resolution 3D imaging of bacterial cells and their matrix during biofilm formation. This approach offers 50 nm isotropic spatial resolution, rapid imaging, and quantitative native analysis of biofilm structure. Using Bacillus subtilis biofilms, we detected coherent alignment and chaining of wild-type cells towards the oxygen-rich capillary tip. In contrast, the ΔtasA genetic knock-out showed a loss of cellular orientation and changes in the extracellular matrix. Adding TasA protein to the ΔtasA strain restored matrix density and led to cell assembly compaction, but without the chaining observed in wild-type biofilms. This scalable and transferable approach opens new avenues for examining biofilm structure and function across various species, including mixed biofilms, and response to genetic and environmental factors.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Nuclear spin assisted magnetic field angle sensing

Abstract Quantum sensing exploits the strong sensitivity of quantum systems to measure small external signals. The nitrogen-vacancy (NV) center in diamond is one of the most promising platforms for real-world quantum sensing applications, predominantly used as a magnetometer. However, its magnetic field sensitivity vanishes when a bias magnetic field acts perpendicular to the NV axis. Here, we introduce a different sensing strategy assisted by the nitrogen nuclear spin that uses the entanglement between the electron and nuclear spins to restore the magnetic field sensitivity. This, in turn, allows us to detect small changes in the magnetic field angle relative to the NV axis. Furthermore, based on the same underlying principle, we show that the NV coupling strength to magnetic noise, and hence its coherence time, exhibits a strong asymmetric angle dependence. This allows us to uncover the directional properties of the local magnetic environment and to realize maximal decoupling from anisotropic noise.

Physics↗

DOE OSTI2021

Electric-field-driven octahedral rotation in perovskite

Rotation of MO 6 (M = transition metal) octahedra is a key determinant of the physical properties of perovskite materials. Therefore, tuning physical properties, one of the most important goals in condensed matter research, may be accomplished by controlling octahedral rotation (OR). In this study, it is demonstrated that OR can be driven by an electric field in Sr 2 RuO 4 . Rotated octahedra in the surface layer of Sr2RuO4 are restored to the unrotated bulk structure upon dosing the surface with K. Theoretical investigation shows that OR in Sr 2 RuO 4 originates from the surface electric field, which can be tuned via the screening effect of the overlaid K layer. This work establishes not only that variation in the OR angle can be induced by an electric field, but also provides a way to control OR, which is an important step toward in situ control of the physical properties of perovskite oxides.

36 MATERIALS SCIENCE↗

DOE OSTI2022

The impact of bilateral injuries on the pathophysiology and functional outcomes of volumetric muscle loss

Volumetric muscle loss (VML)—defined as the irrecoverable loss of skeletal muscle tissue with associated persistent functional deficits—is among the most common and highly debilitating combat-related extremity injuries. This is particularly true in cases of severe polytrauma wherein multiple extremities may be involved as a result of high energy wounding mechanisms. As such, significant investment and effort has been made toward developing a clinically viable intervention capable of restoring the form and function of the affected musculature. While these investigations conducted to date have varied with respect to the species, breed, and sex of the chosen pre-clinical in-vivo model system, the majority of these studies have been performed in unilateral injury models, an aspect which may not fully exemplify the clinical representation of the multiply injured patient. Furthermore, while various components of the basal pathophysiology of VML (e.g., fibrosis and inflammation) have been investigated, relatively little effort has focused on how the pathophysiology and efficacy of pro-regenerative technologies is altered when there are multiple VML injuries. Thus, the purpose of this study was two-fold: (1) to investigate if/how the pathophysiology of unilateral VML injuries differs from bilateral VML injuries and (2) to interrogate the effect of bilateral VML injuries on the efficacy of a well-characterized regenerative therapy, minced muscle autograft (MMG). In contrast to our hypothesis, we show that bilateral VML injuries exhibit a similar systemic inflammatory response and improved muscle functional recovery, compared to unilateral injured animals. Furthermore, MMG treatment was found to only be effective at promoting an increase in functional outcomes in unilateral VML injuries. The findings presented herein add to the growing knowledge base of the pathophysiology of VML, and, importantly, reiterate the importance of comprehensively characterizing preclinical models which are utilized for early-stage screening of putative therapies as they can directly influence the translational research pipeline.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Rejuvenating dead lithium supply in lithium metal anodes by iodine redox

Inactive lithium (more frequently called dead lithium) in the forms of solid-electrolyte interphase and electrically isolated metallic lithium is principally responsible for the performance decay commonly observed in lithium metal batteries. A fundamental solution of recovering dead lithium is urgently needed to stabilize lithium metal batteries. In this paper, we quantify the solid-electrolyte interphase components, and determine their relation with the formation of electrically isolated dead lithium metal. We present a lithium restoration method based on a series of iodine redox reactions mainly involving I 3 - /I - . Using a biochar capsule host for iodine, we show that the I 3 - /I - redox takes place spontaneously, effectively rejuvenating dead lithium to compensate the lithium loss. Through this design, a full-cell using a very limited lithium metal anode exhibits an excellent lifespan of 1,000 cycles with a high Coulombic efficiency of 99.9%. We also demonstrate the design with a commercial cathode in pouch cells. Cycling lithium batteries often results in inactive lithium that no longer participates in redox reactions, leading to performance deterioration. Here the authors use an iodic species to react with inactive lithium, bringing it back to life and thus making batteries last longer.

25 ENERGY STORAGE↗

DOE OSTI2024

Mild pH-decoupling aqueous flow battery with practical pH recovery

Establishing a pH difference between the two electrolytes (pH decoupling) of an aqueous redox flow battery (ARFB) enables cell voltages exceeding the 1.23 V thermodynamic water-splitting window, but acid–base crossover penalizes efficiency and lifetime. Here we employ mildly acidic and mildly alkaline electrolytes to mitigate crossover, achieving high round-trip energy efficiency with open circuit voltage >1.7 V. We implemented an acid–base regeneration system to periodically restore electrolytes to their initial pH values. The combined system exhibited capacity fade rate <0.07% per day, round-trip energy efficiency >85% and approximately 99% Coulombic efficiency during stable operation for over a week. Cost analysis shows that the tolerance of acid–base crossover could be increased if the pH-decoupling ARFB achieved a higher voltage output and lower resistance. Finally, this work demonstrates principles for improving lifespan, rate capability and energy efficiency in high-voltage pH-decoupling ARFBs and pH recovery concepts applicable for pH-decoupling systems.

25 ENERGY STORAGE↗

DOE OSTI2021

Photocurrent-driven transient symmetry breaking in the Weyl semimetal TaAs

Symmetry plays a central role in conventional and topological phases of matter, making the ability to optically drive symmetry changes a critical step in developing future technologies that rely on such control. Topological materials, like topological semimetals, are particularly sensitive to a breaking or restoring of time-reversal and crystalline symmetries, which affect both bulk and surface electronic states. While previous studies have focused on controlling symmetry via coupling to the crystal lattice, we demonstrate here an all-electronic mechanism based on photocurrent generation. Using second harmonic generation spectroscopy as a sensitive probe of symmetry changes, we observe an ultrafast breaking of time-reversal and spatial symmetries following femtosecond optical excitation in the prototypical type-I Weyl semimetal TaAs. Here, our results show that optically driven photocurrents can be tailored to explicitly break electronic symmetry in a generic fashion, opening up the possibility of driving phase transitions between symmetry-protected states on ultrafast timescales.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Manipulating the insulator–metal transition through tip-induced hydrogenation

Manipulating the insulator–metal transition in strongly correlated materials has attracted a broad range of research activity due to its promising applications in, for example, memories, electrochromic windows and optical modulators. Electric-field-controlled hydrogenation using ionic liquids and solid electrolytes is a useful strategy to obtain the insulator–metal transition with corresponding electron filling, but faces technical challenges for miniaturization due to the complicated device architecture. Here, in this work, we demonstrate reversible electric-field control of nanoscale hydrogenation into VO 2 with a tunable insulator–metal transition using a scanning probe. The Pt-coated probe serves as an efficient catalyst to split hydrogen molecules, while the positive-biased voltage accelerates hydrogen ions between the tip and sample surface to facilitate their incorporation, leading to non-volatile transformation from insulating VO 2 into conducting H x VO 2 . Remarkably, a negative-biased voltage triggers dehydrogenation to restore the insulating VO 2 . This work demonstrates a local and reversible electric-field-controlled insulator–metal transition through hydrogen evolution and presents a versatile pathway to exploit multiple functional devices at the nanoscale.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Environmental stress mediates groundwater microbial community assembly

Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and ‘drift’ related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. As a result, our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Bioorthogonal catalytic patch

The toxicity and complicated administration procedures of transition metal catalysts have hampered the applications of bioorthogonal catalysis in vivo. Here the authors fill the needles of a microneedle array patch with palladium nanoparticles deposited on titanium nanosheets and show that the device, applied locally on the skin of mouse models bearing melanoma, promotes intratumoural conversion of systemically injected caged doxorubicin into the active drug, reducing its toxicity and side effects. Bioorthogonal catalysis mediated by transition metals has inspired a new subfield of artificial chemistry complementary to enzymatic reactions, enabling the selective labelling of biomolecules or in situ synthesis of bioactive agents via non-natural processes. However, the effective deployment of bioorthogonal catalysis in vivo remains challenging, mired by the safety concerns of metal toxicity or complicated procedures to administer catalysts. Here, we describe a bioorthogonal catalytic device comprising a microneedle array patch integrated with Pd nanoparticles deposited on TiO 2 nanosheets. This device is robust and removable, and can mediate the local conversion of caged substrates into their active states in high-level living systems. In particular, we show that such a patch can promote the activation of a prodrug at subcutaneous tumour sites, restoring its parent drug's therapeutic anticancer properties. Finally, this in situ applied device potentiates local treatment efficacy and eliminates off-target prodrug activation and dose-dependent side effects in healthy organs or distant tissues.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2024

Dimensionality crossover to a two-dimensional vestigial nematic state from a three-dimensional antiferromagnet in a honeycomb van der Waals magnet

The effects of fluctuations and disorder, which are substantially enhanced in reduced dimensional-ities, can play a crucial role in producing nontrivial phases of matter such as vestigial orders char-acterized by a composite order parameter. However, fluctuation-driven magnetic phases in low dimensions have remained relatively unexplored. Here we demonstrate a phase transition from the zigzag antiferromagnetic order in the three-dimensional bulk to a Z 3 vestigial Potts-nematicity in two-dimensional few-layer samples of van der Waals magnet NiPS 3 . Our spin relaxometry and op-tical spectroscopy measurements reveal that the spin fluctuations are enhanced over the gigahertz to terahertz range as the layer number of NiPS 3 reduces. Monte Carlo simulations corroborate the experimental finding of 3-fold rotational symmetry breaking, but show that translational symmetry is restored in thin layers of NiPS 3 . Furthermore, our results show that strong quantum fluctuations can stabilize an unconventional magnetic phase after destroying a more conventional one.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Liquid-induced topological transformations of cellular microstructures

The fundamental topology of cellular structures—the location, number and connectivity of nodes and compartments—can profoundly affect their acoustic, electrical5, chemical, mechanical and optical properties, as well as heat, fluid and particle transport. Approaches that harness swelling, electromagnetic actuation and mechanical instabilities in cellular materials have enabled a variety of interesting wall deformations and compartment shape alterations, but the resulting structures generally preserve the defining connectivity features of the initial topology. Achieving topological transformation presents a distinct challenge for existing strategies: it requires complex reorganization, repacking, and coordinated bending, stretching and folding, particularly around each node, where elastic resistance is highest owing to connectivity. Here we introduce a two-tiered dynamic strategy that achieves systematic reversible transformations of the fundamental topology of cellular microstructures, which can be applied to a wide range of materials and geometries. Our approach requires only exposing the structure to a selected liquid that is able to first infiltrate and plasticize the material at the molecular scale, and then, upon evaporation, form a network of localized capillary forces at the architectural scale that ‘zip’ the edges of the softened lattice into a new topological structure, which subsequently restiffens and remains kinetically trapped. Reversibility is induced by applying a mixture of liquids that act separately at the molecular and architectural scales (thus offering modular temporal control over the softening–evaporation–stiffening sequence) to restore the original topology or provide access to intermediate modes. Guided by a generalized theoretical model that connects cellular geometries, material stiffness and capillary forces, we demonstrate programmed reversible topological transformations of various lattice geometries and responsive materials that undergo fast global or localized deformations. In conclusion, we then harness dynamic topologies to develop active surfaces with information encryption, selective particle trapping and bubble release, as well as tunable mechanical, chemical and acoustic properties.

42 ENGINEERING↗

DOE OSTI2025

Aqueous-based recycling of perovskite photovoltaics

Abstract Cumulative silicon photovoltaic (PV) waste highlights the importance of considering waste recycling before the commercialization of emerging PV technologies 1,2 . Perovskite PVs are a promising next-generation technology 3 , in which recycling their end-of-life waste can reduce the toxic waste and retain resources 4,5 . Here we report a low-cost, green-solvent-based holistic recycling strategy to restore all valuable components from perovskite PV waste. We develop an efficient aqueous-based perovskite recycling approach that can also rejuvenate degraded perovskites. We further extend the scope of recycling to charge-transport layers, substrates, cover glasses and metal electrodes. After repeated degradation–recycling processes, the recycled devices show similar efficiency and stability compared with the fresh devices. Our holistic recycling strategy reduces by 96.6% resource depletion and by 68.8% human toxicity (cancer effects) impacts associated with perovskite PVs compared with the landfill treatment. With recycling, the levelized cost of electricity also decreases for both utility-scale and residential systems. This study highlights unique opportunities of perovskite PVs for holistic recycling and paves the way for a sustainable perovskite solar economy.

Science & Technology - Other Topics↗

DOE OSTI2023

Soil microbiome engineering for sustainability in a changing environment

Recent advances in microbial ecology and synthetic biology have the potential to mitigate damage caused by anthropogenic activities that are deleteriously impacting Earth’s soil ecosystems. Here, we discuss challenges and opportunities for harnessing natural and synthetic soil microbial communities, focusing on plant growth promotion under different scenarios. We explore current needs for microbial solutions in soil ecosystems, how these solutions are being developed and applied, and the potential for new biotechnology breakthroughs to tailor and target microbial products for specific applications. We highlight several scientific and technological advances in soil microbiome engineering, including characterization of microbes that impact soil ecosystems, directing how microbes assemble to interact in soil environments, and the developing suite of gene-engineering approaches. This Review underscores the need for an interdisciplinary approach to understand the composition, dynamics and deployment of beneficial soil microbiomes to drive efforts to mitigate or reverse environmental damage by restoring and protecting healthy soil ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Fourier-based three-dimensional multistage transformer for aberration correction in multicellular specimens

High-resolution tissue imaging is often compromised by sample-induced optical aberrations that degrade resolution and contrast. Although wavefront sensor-based adaptive optics (AO) can measure these aberrations, such hardware solutions are typically complex, expensive to implement and slow when serially mapping spatially varying aberrations across large fields of view. Here we introduce AOViFT (adaptive optical vision Fourier transformer)—a machine learning-based aberration sensing framework built around a three-dimensional multistage vision transformer that operates on Fourier domain embeddings. AOViFT infers aberrations and restores diffraction-limited performance in puncta-labeled specimens with substantially reduced computational cost, training time and memory footprint compared to conventional architectures or real-space networks. We validated AOViFT on live gene-edited zebrafish embryos, demonstrating its ability to correct spatially varying aberrations using either a deformable mirror or postacquisition deconvolution. By eliminating the need for the guide star and wavefront sensing hardware and simplifying the experimental workflow, AOViFT lowers technical barriers for high-resolution volumetric microscopy across diverse biological samples.

Alshaabi, Thayer [Howard Hughes Medical Institute,↗

DOE OSTI2026

Adaptive optical correction for in vivo two-photon fluorescence microscopy with neural fields

Adaptive optics restore ideal imaging performance in complex samples by measuring and correcting optical aberrations but often require custom-built microscopes with carefully aligned wavefront sensing/shaping devices and can be susceptible to sample motion. Here we describe NeAT, a computational framework using neural fields for adaptive optics two-photon fluorescence microscopy. NeAT estimates wavefront aberration and recovers sample structure from a 3D image stack without requiring external datasets for training. Incorporating motion correction in learning and correcting conjugation errors commonly found in commercial microscopes, NeAT is designed for deployment in biological laboratories for in vivo imaging. We validate NeAT’s performance using a custom-built microscope with a wavefront sensor under varying signal-to-noise ratios, aberration and motion conditions. With a commercial microscope, we demonstrate real-time aberration correction for in vivo morphological and functional imaging in the living mouse brain, with NeAT improving the signal and accuracy of glutamate and calcium imaging of synapses and neurons.

Kang, Iksung↗

DOE OSTI2020

Sustainability of soil organic carbon in consolidated gully land in China’s Loess Plateau

Massive gully land consolidation projects, launched in China’s Loess Plateau, aim to restore 2667 km 2 agricultural lands in total by consolidating 2026 highly eroded gullies. This effort represents a social engineering project where the economic development and livelihood of the farming families are closely tied to the ability of these emergent landscapes to provide agricultural services. Whether these ‘time zero’ landscapes have the resilience to provide a sustainable soil condition such as soil organic carbon (SOC) content remains unknown. By studying two watersheds, one of which is a control site, we show that the consolidated gully serves as an enhanced carbon sink, where the magnitude of SOC increase rate (1.0 gC/m 2 /year) is about twice that of the SOC decrease rate (-0.5 gC/m 2 /year) in the surrounding natural watershed. Over a 50-year co-evolution of landscape and SOC turnover, we find that the dominant mechanisms that determine the carbon cycling are different between the consolidated gully and natural watersheds. In natural watersheds, the flux of SOC transformation is mainly driven by the flux of SOC transport; but in the consolidated gully, the transport has little impact on the transformation. Furthermore, we find that extending the surface carbon residence time has the potential to efficiently enhance carbon sequestration from the atmosphere with a rate as high as 8 gC/m 2 /year compared to the current 0.4 gC/m 2 /year. The success for the completion of all gully consolidation would lead to as high as 26.67 GgC/year sequestrated into soils. This work, therefore, not only provides an assessment and guidance of the long-term sustainability of the ‘time zero’ landscapes but also a solution for sequestration CO 2 into soils.

54 ENVIRONMENTAL SCIENCES↗