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At least 1,207 records · Page 67

Experimental realization of Feynman’s ratchet

Feynman's ratchet is a microscopic machine in contact with two heat reservoirs, at temperatures T A and T B , that was proposed by Richard Feynman to illustrate the second law of thermodynamics. In equilibrium (T A = T B ), thermal fluctuations prevent the ratchet from generating directed motion. When the ratchet is maintained away from equilibrium by a temperature difference (T A ≠T B ), it can operate as a heat engine, rectifying thermal fluctuations to perform work. While it has attracted much interest, the operation of Feynman's ratchet as a heat engine has not been realized experimentally, due to technical challenges. In this work, we realize Feynman's ratchet with a colloidal particle in a one dimensional optical trap in contact with two heat reservoirs: one is the surrounding water, while the effect of the other reservoir is generated by a novel feedback mechanism, using the Metropolis algorithm to impose detailed balance. We verify that the system does not produce work when T A = T B , and that it becomes a microscopic heat engine when T A ≠T B . We analyze work, heat and entropy production as functions of the temperature difference and external load. As a result, our experimental realization of Feynman's ratchet and the Metropolis algorithm can also be used to study the thermodynamics of feedback control and information processing, the working mechanism of molecular motors, and controllable particle transportation.

42 ENGINEERING↗

Coupled Cluster Green's function formulations based on the effective Hamiltonians

In this work, we demonstrate that the effective Hamiltonians obtained with the downfolding procedure based on double unitary coupled cluster (DUCC) ansatz can be used in the context of Green’s function coupled cluster (GFCC) formalism to calculate spectral functions of molecular systems. This combined approach (DUCC-GFCC) provides a significant reduction of numerical effort and good agreement with the corresponding all-orbital GFCC methods in energy windows that are consistent with the choice of active space. These features are demonstrated on the example of two benchmark systems: H 2 O and N 2 , where DUCC-GFCC calculations were performed for active spaces of various sizes.

74 ATOMIC AND MOLECULAR PHYSICS↗

Heisenberg-scaling measurement protocol for analytic functions with quantum sensor networks

Here we generalize past work on quantum sensor networks to show that, for d input parameters, entanglement can yield a factor O(d) improvement in mean-squared error when estimating an analytic function of these parameters. We show that the protocol is optimal for qubit sensors, and we conjecture an optimal protocol for photons passing through interferometers. Our protocol is also applicable to continuous variable measurements, such as one quadrature of a field operator. We outline a few potential applications, including calibration of laser operations in trapped ion quantum computing.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Metagenome-assembled genomes from topsoils along a hillslope water gradient across early snowmelt to late summer in East River, CO

Drought is changing the American Mountain West at unprecedented rates with unknown consequences to soil microbiome composition and function. As a part of LBNL Watershed Science Focus Area (SFA), we investigated shifts in microbial community and transcriptional activity on a subalpine conifer-meadow transition zone throughout the summer of 2023 as soil dried down. This work took place in Crested Butte, CO on Snodgrass mountain, using a proxy for drought conditions.Here we present metagenome assembled genomes (MAGs) for the bacterial and archaeal community at 0-10cm from three sites along a hillslope water gradient across five timepoints from early snowmelt to late summer. 42 metagenomes were sequenced at Joint Genome Institute (JGI) and can be found under the JGI GOLD (Genomes Online Database) sequencing project Gs0166660. Metagenomes were assembled through an inhouse pipeline (see methods), binned using four autobinners (concoct, maxbin2, metabat2, and vamb) and consolidated using dastool. The consolidated bins from all metagenomes were pooled, filtered by completeness (>70%) and contamination (<10%), and dereplicated at 95% ANI using drep. This dataset (1) a zip file of 157 MAGs (as fasta files, Gs0166660_bins_tar.gz), (2) sample metadata file with sample IGSNs (International Generic Sample Numbers) (samples.csv), (3) bounding box coordinates for the sampled locations (Gs0166660.kml), (4) metagenome assembly and coassembly metadata file listing IMG/M (Integrated Microbial Genomes/Metagenomes) metagenome accessions linking samples to metagenomes (EastRiver_Drought_ESSDive_Metadata.csv), (5) location metadata file (locations.csv), (6) file-level metadata file (flmd.csv) and (7) data dictionary (dd.csv) file.This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

54 ENVIRONMENTAL SCIENCES↗

Dissection of Grass Cell Wall Lignin Formation and their Associated Dirigent Protein

This Final Report describes work underway to establish why monocot (e.g. grasses) lignins are more readily (bio)degradable than their woody gymnosperm, angiosperm, and fern counterparts. Our hypothesis is that monocot specific dirigent protein (DP) sub-families are wholly or partly involved in generating these more readily (bio)degradable lignins. Three approaches are underway: metabolomics and lignin analyses of stem and leaf tissues of the grass, Brachypodium; Crispr/Cas9 gene editing of monocot specific DP sub-families in this species, and recombinant protein expression of Brachypodium’s 44 DPs. Metabolomic and lignin analyses were completed for 6 and 8 week old Brachypodium in order to establish the molecular diversity of its largely phenolic metabolites: Crispr/Cas9 gene editing has also been done on specific DPs known to be expressed in lignifying stems, and T 2 generation plant lines are now being generated, prior to establishing the effects on lignin composition and content; in the recombinant DP work (which addresses establishing the biochemical function of the monocot specific DPs and other DPOs as needed), all 44 constructs have been generated (in collaboration with DOE JGI) and are being systematically expressed in either E. coli or yeast (Pichia sp.) for future studies. Future work will be directed towards bringing the current studies to completion, and in establishing the biochemical basis as to how these more readily (bio)degradable lignins are generated/assembled.

(bio)degradability↗

Engineered mRNA–ribosome fusions for facile biosynthesis of selenoproteins

Ribosomes are often used in synthetic biology as a tool to produce desired proteins with enhanced properties or entirely new functions. However, repurposing ribosomes for producing designer proteins is challenging due to the limited number of engineering solutions available to alter the natural activity of these enzymes. In this study, we advance ribosome engineering by describing a novel strategy based on functional fusions of ribosomal RNA (rRNA) with messenger RNA (mRNA). Specifically, we create an mRNA–ribosome fusion called RiboU, where the 16S rRNA is covalently attached to selenocysteine insertion sequence (SECIS), a regulatory RNA element found in mRNAs encoding selenoproteins. When SECIS sequences are present in natural mRNAs, they instruct ribosomes to decode UGA codons as selenocysteine (Sec, U) codons instead of interpreting them as stop codons. This enables ribosomes to insert Sec into the growing polypeptide chain at the appropriate site. Our work demonstrates that the SECIS sequence maintains its functionality even when inserted into the ribosome structure. As a result, the engineered ribosomes RiboU interpret UAG codons as Sec codons, allowing easy and site-specific insertion of Sec in a protein of interest with no further modification to the natural machinery of protein synthesis. To validate this approach, we use RiboU ribosomes to produce three functional target selenoproteins in Escherichia coli by site-specifically inserting Sec into the proteins’ active sites. Overall, our work demonstrates the feasibility of creating functional mRNA–rRNA fusions as a strategy for ribosome engineering, providing a novel tool for producing Sec-containing proteins in live bacterial cells.

59 BASIC BIOLOGICAL SCIENCES↗

High‐Temperature Single‐Photon Emission From Covalently Functionalized van der Waals Heterostructures

Two-dimensional (2D) transition metal dichalcogenides (TMDs) such as tungsten diselenide (WSe 2 ) are attractive nanomaterials for quantum information applications due to single-photon emission (SPE) from intrinsic atomic defects. Defect and strain engineering techniques have been developed to produce high purity, deterministically placed SPE in WSe 2 . However, a major challenge in the application of these techniques is the low temperature required to observe defect-bound TMD exciton emission, typically limiting SPE to T < 30 K. SPE at higher temperatures either loses purity or requires integration into complex devices such as optical cavities. Here, 2D heterostructure engineering and molecular functionalization are combined to achieve high purity (>90%) SPE in strained WSe 2 persisting to over T = 90 K. Covalent diazonium functionalization of graphite in layered WSe 2 /graphite heterostructures maintains high purity up to T = 90 K and single-photon source integrity up to T = 115 K. This method preserves the best qualities of SPE from WSe 2 while increasing working temperature to more than three times the typical range. This work demonstrates the versatility of surface functionalization and heterostructure design to synergistically improve the properties of quantum emission and offers new insights into the phenomenon of SPE from 2D materials.

2D materials↗

Nonprecious Single Atom Catalyst for Methane Pyrolysis

The development of a suitable catalytic system for methane pyrolysis reactions requires a detailed investigation of the activation energy of C-H bonds on catalysts, as well as their stability against sintering and coke formation. In this work, both single-metal Ni atoms and small clusters of Ni atoms deposited on titanium nitride (TiN) plasmonic nanoparticles were characterized for the C-H bond activation of a methane pyrolysis reaction using ab initio spin-polarized density functional theory (DFT) calculations. The present work shows the complete reaction pathway, including energy barriers for C-H bond activation and dehydrogenated fragments, during the methane pyrolysis reaction on catalytic systems. Interestingly, the C-H bond activation barriers were low for both Ni single-atom and Ni-clusters, showing the energy barriers of ~1.10 eV and ~0.88 eV, respectively. Additionally, single-atom Ni-TiN showed weaker binding to adsorbates, and a net endothermic reaction pathway indicated that the single-atom Ni-TiN was expected to resist coke formation on its surface. However, these Ni single-atom catalysts can sinter, aggregate into a small cluster, and form a coke layer from the highly exothermic reaction pathway that the cluster takes despite the facile reaction pathway.

08 HYDROGEN↗

DFT-FE 1.0: A massively parallel hybrid CPU-GPU density functional theory code using finite-element discretization

In this work, we present DFT-FE 1.0, building on DFT-FE 0.6 [Comput. Phys. Commun. 246, 106853 (2020)], to conduct fast and accurate large-scale density functional theory (DFT) calculations (reaching ~ 100,000 electrons) on both many-core CPU and hybrid CPU-GPU computing architectures. This work involves improvements in the real-space formulation—via an improved treatment of the electrostatic interactions that substantially enhances the computational efficiency—as well high-performance computing aspects, including the GPU acceleration of all the key compute kernels in DFT-FE. We demonstrate the accuracy by comparing the ground-state energies, ionic forces and cell stresses on a wide-range of benchmark systems against those obtained from widely used DFT codes. Further, we demonstrate the numerical efficiency of our implementation, which yields ~ 20× CPU-GPU speed-up by using GPU acceleration on hybrid CPU-GPU nodes. Notably, owing to the parallel-scaling of the GPU implementation, we obtain wall-times of 80–140 seconds for full ground-state calculations, with stringent accuracy, on benchmark systems containing ~ 6, 000 – 15,000 electrons.

pseudopotential↗

Ultrafast Formation of Charge Transfer Trions at Molecular‐Functionalized 2D MoS 2 Interfaces

Abstract In this work, we investigate trion dynamics occurring at the heterojunction between organometallic molecules and a monolayer transition metal dichalcogenide (TMD) with transient electronic sum frequency generation (tr‐ESFG) spectroscopy. By pumping at 2.4 eV with laser pulses, we have observed an ultrafast hole transfer, succeeded by the emergence of charge‐transfer trions. This observation is facilitated by the cancellation of ground state bleach and stimulated emission signals due to their opposite phases, making tr‐ESFG especially sensitive to the trion formation dynamics. The presence of charge‐transfer trion at molecular functionalized TMD monolayers suggests the potential for engineering the local electronic structures and dynamics of specific locations on TMDs and offers a potential for transferring unique electronic attributes of TMD to the molecular layers.

Jing, Yuancheng↗

Vegetation classification map and covariates associated with NEON AOP survey, East River, CO 2018

This package includes geospatial data layers developed to investigate how environmental gradients—specifically topography and near-surface soil properties—drive the spatial arrangement of dominant plant communities in mountainous watersheds. The geospatial products, which support the analysis of these ecological relationships, are derived from airborne hyperspectral and LiDAR datasets acquired by the National Ecological Observatory Network (NEON) Airborne Observation Platform (AOP), in conjunction with an extensive ground field campaign conducted in summer 2018. This work is part of the DOE Watershed Function Science Focus Area (SFA) and features geospatial datasets developed based on observations and ground data collected at East River, Colorado, in collaboration with the National Ecological Observatory Network (NEON) Airborne Observation Platform (AOP) survey in June 2018. Classification Map: - Classification Map (PNG, GeoTIFF): Derived from hyperspectral and LiDAR airborne data using a machine learning approach. - Class Code Mapper (CSV): Associates pixel values with corresponding vegetation/non-vegetation classes. - Classification Reference Data (CSV): Reference data used in the machine learning procedure. LiDAR-Derived Products: - Topographical Metrics (GeoTIFFs): Elevation, slope, curvature, TWI, TPI, solar insolation, and canopy height model (CHM), smoothed with a 5x5 pixel window. Vegetation Indices: - GeoTIFFs of NDVI, NDNI, NDWI: Vegetation indices derived from hyperspectral data. Urban Masks: - Urban Mask (GeoTIFF): Applied to the mapping to convert bare soil classes to urban classes. Software Compatibility: GeoTIFFs: Can be visualized with GIS software or libraries that support GeoTIFF images. CSV Files: Can be opened with any software that handles comma-separated values. The FLMD file provides details and links to the source datasets used to derive the products. The manuscript (in the Method session) provides details on how each product was derived. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. Update on 2026-03-25: Since the original dataset publication date of 02/28/2020, this package has a new classification map derived by an improved methodology. This update also includes additional ground data that improved the representation of some of the communities. See the methods for further details on what has changed between versions.

2018 NEON and 2025 CHESS Campaigns↗

Elucidating Gas Reduction Effects of Organosilicon Additives in Lithium-Ion Batteries

Lithium-ion batteries (LIBs) with nonaqueous liquid electrolytes are prone to gas generation at elevated voltages and temperatures, degrading battery performance and posing serious safety risks. Organosilicon (OS) additives are an emerging candidate solution for gassing problems in LIBs, but a detailed understanding of their functional mechanisms remains elusive. In this work, we present a combined computational and experimental study to elucidate the gasreducing effects of OS additives. Cell volume measurements and gas chromatography–mass spectrometry reveal that OS additives can substantially reduce gas evolution in LIBs, particularly CO 2 regardless of source. Through density functional theory calculations, we identify multiple plausible pathways for CO 2 evolution, including (1) nucleophile-induced ring-opening of ethylene carbonate (EC) and the subsequent electro-oxidation and (2) direct electro-oxidation of lithium carbonate (Li 2 CO 3 ). Correspondingly, we find that OS additives function via two primary mechanisms: (1) scavenging of nucleophiles such as superoxide (O 2 •– ), peroxide (O 2 2– ), and carbonate ion (CO 3 2– ); (2) oligomerization with ethylene carbonate oxide ion and ethylene dicarbonate ion. Moreover, we discover that OS additives possess strong lithium coordination affinity, which helps further reduce the nucleophilic reaction energies and hence increases their nucleophile-scavenging efficiency. Finally, we provide a mechanistic interpretation for the enhanced gasreduction effects observed with fluorinated OS compounds, corroborated by surface analysis results from X-ray photoelectron spectroscopy. Our study offers the first molecular-level insights into how OS additives contribute to reduced gas formation in LIBs, paving the way for improved safety and performance of LIBs.

25 ENERGY STORAGE↗

From Bethe–Salpeter Wave functions to Generalised Parton Distributions

We review recent works on the modelling of Generalised Parton Distributions within the Dyson-Schwinger formalism. We highlight how covariant computations, using the impulse approximation, allows one to fulfil most of the theoretical constraints of the GPDs. A specific attention is brought to chiral properties and especially the so-called soft pion theorem, and its link with the Axial-Vector Ward-Takahashi identity. The limitation of the impulse approximation are also explained. Beyond impulse approximation computations are reviewed in the forward case. Finally, we stress the advantages of the overlap of lightcone wave functions, and possible ways to construct covariant GPD models within this framework, in a two-body approximation

97 MATHEMATICS AND COMPUTING↗

Local and linear chemical reactivity response functions at finite temperature in density functional theory

We explore the local and nonlocal response functions of the grand canonical potential density functional at nonzero temperature. In analogy to the zero-temperature treatment, local (e.g., the average electron density and the local softness) and nonlocal (e.g., the softness kernel) intrinsic response functions are defined as partial derivatives of the grand canonical potential with respect to its thermodynamic variables (i.e., the chemical potential of the electron reservoir and the external potential generated by the atomic nuclei). To define the local and nonlocal response functions of the electron density (e.g., the Fukui function, the linear density response function, and the dual descriptor), we differentiate with respect to the average electron number and the external potential. The well-known mathematical relationships between the intrinsic response functions and the electron-density responses are generalized to nonzero temperature, and we prove that in the zero-temperature limit, our results recover well-known identities from the density functional theory of chemical reactivity. Specific working equations and numerical results are provided for the 3-state ensemble model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Aryl Diazonium-Assisted Amidoximation of MXene for Boosting Water Stability and Uranyl Sequestration via Electrochemical Sorption

Despite that two-dimensional transition metal carbides and carbonitrides (MXenes) are burgeoning candidates for remediation of environmental pollutants, the construction of robust functionalized MXene nanosheets with a high affinity for target heavy metal ions and radionuclides remains a challenge. Here we report the successful placement of amidoxime chelating groups on Ti 3 C 2 T x MXene surface by diazonium salt grafting. The introduction of amidoxime functional groups significantly enhances the selectivity of Ti 3 C 2 T x nanosheets for uranyl ions and also greatly improves their stability in aqueous solution, enabling efficient, rapid, and recyclable uranium extraction from aqueous solutions containing competitive metal ions. Benefiting from the excellent conductivity of MXenes, the amidoxime functionalized Ti 3 C 2 T x nanosheets show outstanding electrochemical performance such that when loaded on carbon cloth the application of an electric field increases the uranium adsorption capacity from 294 to 626 mg/g, outperforming all organic electrochemical sorption materials reported previously. Finally, the present work provides an effective strategy to functionalize MXene nanosheets with fundamental implications for the design of MXene-based selective electrosorption electrode materials.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Assessment of Low-Level Pu Isotope Ratio Measurements Using Multicollector Inductively Coupled Plasma Mass Spectrometry (MC-ICP-MS/MS) Equipped with a Pre-Mass Filter

We present an initial investigation into the performance of a multicollector inductively coupled plasmamass spectrometer equipped with a pre-mass filter (Neoma MC-ICP-MS/MS) for making plutonium (Pu) isotope ratio measurements on solutions containing low level (i.e., pg mL –1 ) Pu concentrations. This assessment was achieved by comparison of the 240 Pu/ 239 Pu, 241 Pu/ 239 Pu, and 242 Pu/ 239 Pu ratios attained over a one month period on the MC-ICP-MS/MS with the long-term (∼1 year) performance observed on the predecessor MC-ICP-MS (Neptune Plus) instrument each equipped with an equipped with an APEXΩ desolvating nebulizer for repeated measurements of certified reference materials from New Brunswick Program Office (NBL PO) CRM 136a and CRM 137. The MC-ICP-MS/MS performance of repeated measurement of CRM 136a (n = 20) resulted in mean values of 240 Pu/ 239 Pu = 0.1448 ± 0.0006, 241 Pu/ 239 Pu = 0.00371 ± 0.00006, and 242 Pu/ 239 Pu = 0.00682 ± 0.00006 (k = 2). The CRM 137 (n = 20), analyzed during the same analytical sessions, produced mean values for 240 Pu/ 239 Pu = 0.2414 ± 0.0006, 241 Pu/ 239 Pu = 0.00464 ± 0.00007, and 242 Pu/ 239 Pu = 0.0157 ± 0.0001 (k = 2). These results closely align with the certificate values for CRM 136a and CRM 137 and are within the k = 2 envelopes defined by the long-term performance of the traditional MC-ICP-MS approach (Neptune Plus). Examination of the performance of the various Pu isotope ratios as a function of total Pu content revealed accurate results (<3% relative difference, or RD) above ∼50 fg total Pu. The results presented here demonstrate the capability of the MC-ICP-MS/MS making accurate and precise low level Pu isotopic measurements. While the intent of this work was not to investigate the functionality of the collision cell, the pre-mass filter was employed. Future studies are warranted to investigate the entire capability of the MC-ICP-MS/MS collision cell and pre-cell mass filter optimization for performing low level Pu isotope measurements, even in mixed matrix samples.

CRM↗

Depth-resolved sagebrush root metabolomics, rhizosphere microbial communities, and geochemistry at the East River Watershed

This data set consists of results from soil nutrient profile, untargeted metabolomics, mass spec imaging, and amplicon sequencing. Data for soil nutrient profile includes common cations (Ca, Mg, Na, and K etc.) extracted from 3 digesting steps – ammonia acetate (for exchangeable cations), nitric acid (for acid dissolved fraction), and hydrofluoric acid/perchloric acid (HF/HClO4) for whole soil digestion. It also includes concentration of organic carbon, inorganic nitrogen (ammonia and nitrate) and phosphorus (Bray-1 P and nitric acid extract), and total nitrogen and phosphorus. Data for untargeted metabolomics includes metabolomic profile for root exudate/tissues and soil extracts from depths at surface soil to saprolite, that were measured using gas chromatography – mass spectrometry (GC-MS), and liquid chromatography – tandem mass spectrometry (LC-MS/MS). Data for mass spec imaging includes spatial distribution of metabolites that were detected and annotated with Fourier transformation ion cyclotron resonance mass spectrometer (FTICR-MS). Data for amplicon sequencing includes the base paired 16S and ITS ribosomal RNA sequences from Miseq Illumina sequencing. All samples were collected from 2 sampling campaign October 2022 and June 2023. Collectively, these datasets enable a mechanistic evaluation of how nutrient acquisition, especially nitrogen and phosphorus, differs between shallow roots operating in soil and deep roots functioning within the fractured bedrock zone. All files are provided as comma-separated values (CSV) fies (.csv) and (GZIP) file (.gz). The compressed .gz FASTQ files can be read directly in R using the dada2 package as part of the amplicon sequence analysis workflow. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. This research was performed on a project award 60563 (https://dx.doi.org/10.46936/expl.proj.2022.60563/60008727) from the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility sponsored by the Biological and Environmental Research program under Contract No. DE-AC05-76RL01830.

EARTH SCIENCE > AGRICULTURE > SOILS > CARBON↗

Understanding the Role of Hydroxyl Functionalization in Linear Poly(Ethylenimine) for Oxidation‐Resistant Direct Air Capture of CO 2

Aminopolymer-based adsorbents are a prominent class of materials being used for direct air capture of CO 2 at the industrial scale. However, improving their working lifetime, specifically by increasing their resilience to oxidative degradation, remains an ongoing challenge. Toward this end, functionalization of aminopolymers with non-amine functionalities such as hydroxyls has emerged in recent years as a promising strategy toward improving adsorbent lifetime. Although there is a growing body of work demonstrating the effectiveness of this approach and investigating the origin of this improved stability, studies to date have primarily focused on branched aminopolymer systems such as branched poly(ethylenimine). In this work, hydroxyl-functionalized linear poly(ethylenimine) is used to continue to probe the underlying protective mechanism of this strategy. A combination of thermogravimetric analysis, NMR relaxometry, differential scanning calorimetry, and computational simulations is used to better understand the relationship between the extent of chemical functionalization, physical properties, and adsorbent performance.

amine-based adsorbent↗