Recent lbnl_lab_ld items

Building Inclusive Educational and Career Pathways in Fusion Energy

Thu, 21 May 2026 00:00:00 +0000

This paper was written in preparation for the Workforce Accelerator for Fusion Energy Development conference, which was funded by the National Science Foundation. Prior to the conference, participants from academia, government, industry, national laboratories, and nonprofit organizations worked together to write White papers. Held in Hampton, Virginia, in May 2024, the conference convened participants to discuss various topics in support of workforce development in fusion energy. As the fusion industry expands, efforts to recruit and retain a diverse workforce, ensure equitable access to fusion education, and gain public support will be critical to meeting workforce needs in this field. We outline strategic recommendations across three vital areas: improving diversity data collection; supporting career advancement and retention with a diversity, equity, inclusion, accessibility, and belonging focus; and strengthening community engagement and education in fusion energy.

Validated ligand geometries for macromolecular refinement restraints and molecular‐mechanics force fields

Wed, 22 Apr 2026 00:00:00 +0000

In macromolecular structure refinement, the low observation-to-parameter ratio and the lack of high-resolution data are countered by using a priori information in the form of restraints. Having accurate geometries of the chemical entities in the sample is paramount for generating accurate chemical restraints and, therefore, accurate macromolecular structures. In particular, it is desirable to have accurate restraints for known and novel ligand entities. Quantum mechanics (QM) can minimize the energy of a ligand by adjusting its geometry, and these geometries can be used to generate restraints for macromolecular refinement. This article describes a library of approximately 37 000 small molecules extracted from the Chemical Component Dictionary in the Protein Data Bank and minimized by density-functional QM. The library includes restraint files for use in crystallography or cryo-EM refinement, along with files suitable for molecular-dynamics simulation. Because the geometries are...

Agnostic capture of pathogens for the detection and diagnostics of emerging threats

Thu, 2 Apr 2026 00:00:00 +0000

The continued emergence of pathogens, whether novel, re-emerging, or engineered, poses a persistent global biosecurity and public health challenge. Recent outbreaks, including COVID-19, Lassa fever, Marburg virus, mpox, and avian influenza, underscore the urgent need for robust systems that enable rapid surveillance, early diagnosis, and timely countermeasures before widespread human transmission occurs. In this article, we focus on early detection technologies and systematically evaluate current diagnostic and sensing modalities. We highlight sequencing and spectroscopy as two complementary approaches capable of providing broad, agnostic detection and rich biological insight. Our analysis emphasizes that scientific innovation alone is insufficient: effective preparedness also requires improved data curation, integration, and sharing to build AI-ready resources that accelerate future responses. We argue for coordinated advances in both technological capabilities and supporting...

Recent advances in probing electron delocalization in conjugated molecules by attached infrared reporter groups for energy conversion and storage

Tue, 20 Jan 2026 00:00:00 +0000

Recent advances in probing electron delocalization in conjugated molecules by attached infrared reporter groups for energy conversion and storage

Ultraselective sequestration of Li+ and Mg2+ from brines via a reusable polyoxoniobate-based ion sponge

Mon, 12 Jan 2026 00:00:00 +0000

Lithium (Li) and magnesium (Mg) are designated as critical mineral materials (CMM) due to their essential roles in clean energy technologies. However, extracting high-purity Li⁺ from brine remains a formidable challenge owing to the presence of Mg²⁺, a physicochemical similar ion that often exists in excess. Here, we introduce a polyoxoniobate-based "Mg-PONb sponge" that enables ultraselective and rapid Li⁺/Mg²⁺ separation across an exceptionally broad range of Mg/Li ratios (0.02 to 200.63). This framework achieves >99.9% Mg²⁺ removal with negligible Li⁺ loss in under 1 min, yielding Li⁺/Mg²⁺ selectivity values exceeding 5000. The sponge demonstrates excellent recyclability, maintaining >99% Mg²⁺ rejection and Li⁺ permeability across five regeneration cycles without structural degradation. Mechanistic investigations reveal that selective Mg²⁺ capture originates...

Predictive CRISPR-mediated gene downregulation for enhanced production of sustainable aviation fuel precursor in Pseudomonas putida

Tue, 16 Dec 2025 00:00:00 +0000

CRISPR interference (CRISPRi) has emerged as a valuable tool for redirecting metabolic flux to enhance bioproduction. However, its application is often constrained by two challenges: (i) rationally identifying effective gene targets for downregulation and (ii) efficiently constructing multiplexed CRISPRi systems. In this study, we address both challenges by integrating a computational prioritization tool with a versatile assembly method for building multiplexed CRISPRi systems. FluxRETAP (Flux-Reaction Target Prioritization) accurately identified gene targets whose knockdown led to substantial increase of isoprenol titers in Pseudomonas putida KT2440, outperforming a conventional non-computational, pathway-guided target selection. The highest isoprenol titer of nearly 1.5 g/L was achieved by knocking down PP_4118 (a gene encoding α-ketoglutarate dehydrogenase). The use of VAMMPIRE (Versatile Assembly Method for MultiPlexing CRISPRi-mediated downREgulation) enabled accurate...

Advantages of the Samarskii-type schemes on the Shishkin mesh

Fri, 21 Nov 2025 00:00:00 +0000

The schemes of the Samarskii type are simple modifications of the upwind scheme. We use them on the Shishkin mesh and discuss their advantages over the upwind scheme when applied to the linear one-dimensional singularly perturbed convection–diffusion problem. One of the advantages is that the Samarskii-type schemes have exact first-order accuracy uniform in the perturbation parameter, as opposed to the upwind scheme which is almost first-order uniformly accurate because its accuracy is diminished by logarithmic factors. Although this is not a new result, we re-emphasize it in the paper. We also demonstrate another advantage, that the Samarskii-type schemes are almost second-order uniformly accurate on the layer component of the solution. Motivated by this fact, we present a further improvement of the numerical method.

Accelerating the fusion workforce in the USA

Fri, 21 Nov 2025 00:00:00 +0000

The fusion energy research and development landscape has seen significant advances in recent years, with important scientific and technological breakthroughs and a rapid rise of investment in the private sector. The workforce needs of the nascent fusion industry are growing at a rate that academic workforce development programs are not currently able to match. This paper presents the findings of the Workforce Accelerator for Fusion Energy Development Conference held in Hampton, Virginia, United States of America (USA), on 29–30 May 2024, which was funded by the National Science Foundation of the USA. A major goal of the conference was to focus on bringing public and private stakeholders together to identify opportunities for partnership in fusion research and education with the goal of meeting the needs for a talented and diverse workforce. Representatives from industry, academia, and national laboratories participated in the conference through the preparation of white papers,...

Biosensor-driven strain engineering reveals key cellular processes for maximizing isoprenol production in Pseudomonas putida

Tue, 18 Nov 2025 00:00:00 +0000

Synthetic biology generates vast combinatorial designs, yet high-throughput analytical methods to screen them are poorly matched to interrogate this search space. We address this challenge by developing a biosensor-driven, growth-coupled selection strategy in Pseudomonas putida for isoprenol, a potential aviation fuel precursor. We found and characterized a noncanonical signaling pathway, revealing a functional and physical complex between a hybrid histidine kinase and an alcohol dehydrogenase, whose activity is tuned by heterodimerization. Leveraging this biosensor in a pooled CRISPRi library selection, we identified key host limitations. Iterative combinatorial strain engineering derived from these hits yielded a 36-fold titer increase to ~900 milligrams per liter. Integrated omics analysis revealed that metabolic rewiring toward amino acid catabolism was crucial for this improvement. This observation was found to be beneficial by technoeconomic analysis. Our modular...

Huge ensembles – Part 2: Properties of a huge ensemble of hindcasts generated with spherical Fourier neural operators

Mon, 17 Nov 2025 00:00:00 +0000

Abstract. In Part 1, we created an ensemble based on spherical Fourier neural operators. As initial condition perturbations, we used bred vectors, and as model perturbations, we used multiple checkpoints trained independently from scratch. Based on diagnostics that assess the ensemble's physical fidelity, our ensemble has comparable performance to operational weather forecasting systems. However, it requires orders-of-magnitude fewer computational resources. Here in Part 2, we generate a huge ensemble (HENS), with 7424 members initialized each day of summer 2023. We enumerate the technical requirements for running huge ensembles at this scale. HENS precisely samples the tails of the forecast distribution and presents a detailed sampling of internal variability. HENS has two primary applications: (1) as a large dataset with which to study the statistics and drivers of extreme weather and (2) as a weather forecasting system. For extreme climate statistics, HENS samples...

High-Throughput Microfluidic Electroporation (HTME): A Scalable, 384-Well Platform for Multiplexed Cell Engineering

Tue, 29 Jul 2025 00:00:00 +0000

Electroporation-mediated gene delivery is a cornerstone of synthetic biology, offering several advantages over other methods: higher efficiencies, broader applicability, and simpler sample preparation. Yet, electroporation protocols are often challenging to integrate into highly multiplexed workflows, owing to limitations in their scalability and tunability. These challenges ultimately increase the time and cost per transformation. As a result, rapidly screening genetic libraries, exploring combinatorial designs, or optimizing electroporation parameters requires extensive iterations, consuming large quantities of expensive custom-made DNA and cell lines or primary cells. To address these limitations, we have developed a High-Throughput Microfluidic Electroporation (HTME) platform that includes a 384-well electroporation plate (E-Plate) and control electronics capable of rapidly electroporating all wells in under a minute with individual control of each well. Fabricated using scalable...

Graphene-driven correlated electronic states in one dimensional defects within WS2

Tue, 29 Jul 2025 00:00:00 +0000

Tomonaga-Luttinger liquid (TLL) behavior in one-dimensional systems has been predicted and shown to occur at semiconductor-to-metal transitions within two-dimensional materials. Reports of one-dimensional defects hosting a Fermi liquid or a TLL have suggested a dependence on the underlying substrate, however, unveiling the physical details of electronic contributions from the substrate require cross-correlative investigation. Here, we study TLL formation within defectively engineered WS2 atop graphene, where band structure and the atomic environment is visualized with nano angle-resolved photoelectron spectroscopy, scanning tunneling microscopy and spectroscopy, and non-contact atomic force microscopy. Correlations between the local density of states and electronic band dispersion elucidated the electron transfer from graphene into a TLL hosted by one-dimensional metal (1DM) defects. It appears that the vertical heterostructure with graphene and the induced charge transfer from...

ALS-ENABLE: creating synergy and opportunity at the Advanced Light Source synchrotron structural biology beamlines

Tue, 29 Jul 2025 00:00:00 +0000

ALS-ENABLE is an integrated NIH P30 resource at the Advanced Light Source synchrotron at Lawrence Berkeley National Laboratory in Berkeley, California, USA. The resource provides a single portal to the combined mature structural biology technologies of macromolecular crystallography, small-angle X-ray scattering and X-ray footprinting mass spectrometry, and includes beamlines 2.0.1, 3.3.1, 4.2.2, 5.0.1, 5.0.2, 5.0.3, 8.2.1, 8.2.2, 8.3.1 and 12.3.1. This paper describes the organizational structure and the technologies of ALS-ENABLE. A case study showcasing the main technologies of the resource applied to the characterization of the SpyCatcher-SpyTag protein system is presented.

Thermodynamic phase transitions of nematic order in magnetic helices

Mon, 21 Jul 2025 00:00:00 +0000

A nematic phase lacks translation order but has orientational order. Nematic phases have been discovered in a variety of systems, including liquid crystals, correlated materials, and superconductors. Here, we report on a magnetic nematic phase, where the basis components are composed of magnetic helices. We directly probed the order parameters associated with the magnetic helices using resonant soft x-ray scattering and find two distinct nematic phases with complex spatiotemporal signatures. Using x-ray correlation spectroscopy, we find that near the phase boundary between the two nematic phases, fluctuations coexist on multiple disparate timescales. Our micromagnetic simulations and density functional theory calculations show that the fluctuations occur concomitantly with a reorientation of the magnetic helices, indicating spontaneous symmetry breaking and the emergence of additional degrees of freedom. Our results provide a framework for characterizing exotic phases that can...

Accelerated data-driven materials science with the Materials Project

Tue, 15 Jul 2025 00:00:00 +0000

The Materials Project was launched formally in 2011 to drive materials discovery forwards through high-throughput computation and open data. More than a decade later, the Materials Project has become an indispensable tool used by more than 600,000 materials researchers around the world. This Perspective describes how the Materials Project, as a data platform and a software ecosystem, has helped to shape research in data-driven materials science. We cover how sustainable software and computational methods have accelerated materials design while becoming more open source and collaborative in nature. Next, we present cases where the Materials Project was used to understand and discover functional materials. We then describe our efforts to meet the needs of an expanding user base, through technical infrastructure updates ranging from data architecture and cloud resources to interactive web applications. Finally, we discuss opportunities to better aid the research community, with the...

Non-DNA radiosensitive targets that initiate persistent behavioral deficits in rats exposed to space radiation

Tue, 15 Jul 2025 00:00:00 +0000

Predicting future CNS risks for astronauts during deep-space missions will rely substantially on ground-based rodent data with space-relevant ions and behaviors. For rats, the accumulated evidence indicates that less densely ionizing radiation, such as ⁴He and ¹²C ions, induce behavior deficits at lower doses than densely ionizing ions, such as ⁴⁸Ti and ⁵⁶Fe. However, this observation conflicts with standard somatic radiobiology, in which densely ionizing ions are generally more effective than less densely ionizing ions, and where the DNA/nucleus is the accepted target for radiation-induced tumorigenesis, cytogenetic aberrations, genetic mutations, and reproductive cell death. To gain deeper insight into the subcellular nature of the radiation targets for behavior risks, we compared the effects of dose, fluence, and linear energy transfer (LET) of ⁴He and ⁵⁶Fe particles using existing datasets for four distinct...

Multimodal correlative study of Hall transport and magnetic phases in Fe/Gd multilayer systems

Tue, 17 Jun 2025 00:00:00 +0000

The Fe/Gd multilayer system hosts a number of magnetic phases, such as stripe, mixed stripe and skyrmion, skyrmion lattice, and isolated skyrmions for a wide range of temperature and magnetic field. We report different Hall transport signals in a Fe/Gd system through multimodal correlative resonant soft x-ray scattering (RSXS), Hall effect, magneto-optic Kerr effect, and transmission x-ray microscopy measurements. The simultaneous nature of the RSXS and Hall transport measurements allowed us to accurately connect various features in the transport data with the specific magnetic phases. We found that the topological Hall effect (THE) shows peaks with opposite signs, which we attribute to two different mechanisms. Our multimodal correlative study indicates that the sign reversal in THE occurs when the system transforms to and from a skyrmion lattice and low density isolated skyrmion phases. We propose that the skyrmion lattice contributes to the THE through a Berry phase induced...

The Reliability of Hybrid Functionals for Accurate Fundamental and Optical Gap Prediction of Bulk Solids and Surfaces

Tue, 20 May 2025 00:00:00 +0000

Hybrid functionals have been considered insufficiently reliable for the prediction of band gaps in solids and surfaces. We revisit this issue with a new generation of optimally tuned range-separated hybrid functionals, focusing on the reconstructed Si(111)-(2×1) and Ge(111)-(2×1) surfaces. We show that certain hybrid functionals can accurately predict the surface-state and bulk fundamental and optical gaps, as well as projected band structures of these surfaces, by combining ground-state and time-dependent density functional theory.

A polyketide-based biosynthetic platform for diols, amino alcohols and hydroxy acids

Tue, 13 May 2025 00:00:00 +0000

Medium- and branched-chain diols and amino alcohols are important industrial solvents, polymer building blocks, cosmetics and pharmaceutical ingredients, yet biosynthetically challenging to produce. Here we present an approach that uses a modular polyketide synthase (PKS) platform for the efficient production of these compounds. This platform takes advantage of a versatile loading module from the rimocidin PKS and nicotinamide adenine dinucleotide phosphate-dependent terminal thioester reductases. Reduction of the terminal aldehyde with alcohol dehydrogenases enables the production of diols, oxidation enables the production of hydroxy acids and specific transaminases allow the production of various amino alcohols. Furthermore, replacement of the malonyl-coenzyme A-specific acyltransferase in the extension module with methyl- or ethylmalonyl-coenzyme A-specific acyltransferase enables the production of branched-chain diols, amino alcohols and carboxylic acids in high titres. Use...

Modest functional diversity decline and pronounced composition shifts of microbial communities in a mixed waste-contaminated aquifer

Fri, 9 May 2025 00:00:00 +0000

BackgroundMicrobial taxonomic diversity declines with increased environmental stress. Yet, few studies have explored whether phylogenetic and functional diversities track taxonomic diversity along the stress gradient. Here, we investigated microbial communities within an aquifer in Oak Ridge, Tennessee, USA, which is characterized by a broad spectrum of stressors, including extremely high levels of nitrate, heavy metals like cadmium and chromium, radionuclides such as uranium, and extremely low pH (< 3).ResultsBoth taxonomic and phylogenetic α-diversities were reduced in the most impacted wells, while the decline in functional α-diversity was modest and statistically insignificant, indicating a more robust buffering capacity to environmental stress. Differences in functional gene composition (i.e., functional β-diversity) were pronounced in highly contaminated wells, while convergent functional gene composition was observed in uncontaminated wells. The relative abundances of...

Correction: “When I talk about it, my eyes light up!” Impacts of a national laboratory internship on community college student success

Wed, 7 May 2025 00:00:00 +0000

[This corrects the article DOI: 10.1371/journal.pone.0317403.].

Environmental stress mediates groundwater microbial community assembly

Tue, 22 Apr 2025 00:00:00 +0000

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. Our...

Enzymatic cleavage of model lignin dimers depends on pH, enzyme, and bond type

Mon, 7 Apr 2025 00:00:00 +0000

Lignin is composed of phenylpropanoid monomers linked by ether and carbon-carbon bonds to form a complex heterogeneous structure. Bond-specific studies of lignin-modifying enzymes (LMEs; e.g., laccases and peroxidases) are limited by the polymerization of model lignin substrates and repolymerization of cleavage products. Here we present a high throughput platform to screen LME activities on four tagged model lignin compounds that represent the β-O-4’, β-β’, 5–5’, and 4-O-5’ linkages in lignin. We utilized nanostructure-initiator mass spectrometry (NIMS) and model lignin compounds with tags containing perfluorinated and cationic moieties, which effectively limit polymerization and condensation of the substrates and their degrading products. Sub-microliter sample droplets were printed on the NIMS chip with a novel robotics method. This rapid platform enabled characterization of LMEs across a range of pH 3–10 and relative quantification of modified (typically oxidized), cleaved,...

Modal focal adaptive optics for Bessel-focus two-photon fluorescence microscopy

Mon, 31 Mar 2025 00:00:00 +0000

Adaptive optics (AO) improves the spatial resolution of microscopy by correcting optical aberrations. While its application has been well established in microscopy modalities utilizing a circular pupil, its adaptation to systems with non-circular pupils, such as Bessel-focus two-photon fluorescence microscopy (2PFM) with an annular pupil, remains relatively uncharted. Herein, we present a modal focal AO (MFAO) method for Bessel-focus 2PFM. Measuring and correcting aberration using a spatial light modulator placed in conjugation with the focal plane of the microscope objective, MFAO employs Zernike annular polynomials - a first in AO implementation - to achieve performance on par with a previous zonal AO method, but with a notably simplified optical configuration. We validated the performance of MFAO in correcting artificial and sample-induced aberrations, as well as in in vivo imaging of zebrafish larvae and mouse brains. By expanding the application of modal AO to annular...

“When I talk about it, my eyes light up!” Impacts of a national laboratory internship on community college student success

Thu, 23 Jan 2025 00:00:00 +0000

Participation in technical/research internships may improve undergraduate graduation rates and persistence in science, technology, engineering, and mathematics (STEM), yet little is known about the benefits of these activities a) for community college students, b) when hosted by national laboratories, and c) beyond the first few years after the internship. We applied Social Cognitive Career Theory (SCCT) to investigate alumni perspectives about how CCI at Lawrence Berkeley National Laboratory (LBNL) impacted their academic/career activities. We learned that alumni had low confidence and expectations of success in STEM as community college students. Participation in CCI increased their professional networks, expectations of success, and STEM skills, identity, and self-efficacy/confidence. Hispanic/Latinx alumni recalled the positive impact of mentors who prioritized personal connections, and women valued "warm" social environments. We propose several additions to the SCCT model,...

Electronic structure and optical properties of halide double perovskites from a Wannier-localized optimally-tuned screened range-separated hybrid functional

Mon, 6 Jan 2025 00:00:00 +0000

Halide double perovskites are a chemically diverse and growing class of compound semiconductors that are promising for optoelectronic applications. However, the prediction of their fundamental gaps and optical properties with density functional theory (DFT) and ab initio many-body perturbation theory has been a significant challenge. Recently, a nonempirical Wannier-localized optimally tuned screened range-separated hybrid (WOT-SRSH) functional has been shown to accurately produce the fundamental band gaps of a wide set of semiconductors and insulators, including lead halide perovskites. Here, we apply the WOT-SRSH functional to five halide double perovskites and compare the results with those obtained from other known functionals and previous GW calculations. We also use the approach as a starting point for GW calculations and we compute the band structures and optical absorption spectrum for Cs2AgBiBr6, using both time-dependent DFT and the GW-Bethe-Salpeter equation approach....

Automated Flow-Based/Digital Microfluidic Platform Integrated with Onsite Electroporation Process for Multiplex Genetic Engineering Applications

Wed, 11 Dec 2024 00:00:00 +0000

We present a novel automated flow-based/digital microfluidic platform integrated with onsite electroporation function. In addition to high-throughput arraying of microdroplets and mixing of DNA parts and cells, proposed platform is capable of multiplexed electroporation process and dual optical detection of expressed fluorescence on chip. Unlike conventional microtiter plate based reactions, our platform would allow completely automated and robust genetic engineering steps using drastically smaller amounts of reagents and can be useful for gene editing processes such as CRISPRlCas9 for synthetic biology applications.

The crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase reveals active site features controlling catalytic specificity

Mon, 2 Dec 2024 00:00:00 +0000

Diterpenoid natural products serve critical functions in plant development and ecological adaptation and many diterpenoids have economic value as bioproducts. The family of class II diterpene synthases catalyzes the committed reactions in diterpenoid biosynthesis, converting a common geranylgeranyl diphosphate precursor into different bicyclic prenyl diphosphate scaffolds. Enzymatic rearrangement and modification of these precursors generate the diversity of bioactive diterpenoids. We report the crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase, GrTPS2, at 2.1 Å of resolution. GrTPS2 catalyzes the committed reaction in the biosynthesis of grindelic acid, which represents the signature metabolite in species of gumweed (Grindelia spp., Asteraceae). Grindelic acid has been explored as a potential source for drug leads and biofuel production. The GrTPS2 crystal structure adopts the conserved three-domain fold of class II diterpene synthases featuring a functional...

Characterization of lignin-degrading enzyme PmdC, which catalyzes a key step in the synthesis of polymer precursor 2-pyrone-4,6-dicarboxylic acid

Wed, 13 Nov 2024 00:00:00 +0000

Pyrone-2,4-dicarboxylic acid (PDC) is a valuable polymer precursor that can be derived from the microbial degradation of lignin. The key enzyme in the microbial production of PDC is 4-carboxy-2-hydroxymuconate-6-semialdehyde (CHMS) dehydrogenase, which acts on the substrate CHMS. We present the crystal structure of CHMS dehydrogenase (PmdC from Comamonas testosteroni) bound to the cofactor NADP, shedding light on its three-dimensional architecture, and revealing residues responsible for binding NADP. Using a combination of structural homology, molecular docking, and quantum chemistry calculations, we have predicted the binding site of CHMS. Key histidine residues in a conserved sequence are identified as crucial for binding the hydroxyl group of CHMS and facilitating dehydrogenation with NADP. Mutating these histidine residues results in a loss of enzyme activity, leading to a proposed model for the enzyme's mechanism. These findings are expected to help guide efforts in protein...

EcoFAB 3.0: a sterile system for studying sorghum that replicates previous field and greenhouse observations

Tue, 5 Nov 2024 00:00:00 +0000

Introduction: Studying plant-microbe interactions is one of the key elements in understanding the path to sustainable agricultural practices. These interactions play a crucial role in ensuring survival of healthy plants, soil and microbial communities. Many platforms have been developed over the years to isolate these highly complex interactions however, these are designed for small model plants. This creates a need for complementary devices for larger plants, such as sorghum. Methods: This work introduces a novel platform, EcoFAB 3.0, which is designed to enable studying bioenergy plants such as sorghum for up to 4 weeks in a controlled sterile environment. Several other advantages of this platform such as dark root chambers and user-friendly assembly are also discussed in this work. Results and discussion: EcoFAB 3.0 was found to replicate previous greenhouse and field observations when comparing an engineered sorghum line overproducing 4-hydroxybenzoic acid (4-HBA) and wildtype...

Protonation of histidine rings using quantum-mechanical methods

Mon, 19 Aug 2024 00:00:00 +0000

Histidine can be protonated on either or both of the two N atoms of the imidazole moiety. Each of the three possible forms occurs as a result of the stereochemical environment of the histidine side chain. In an atomic model, comparing the possible protonation states in situ, looking at possible hydrogen bonding and metal coordination, it is possible to predict which is most likely to be correct. A more direct method is described that uses quantum-mechanical methods to calculate, also in situ, the minimum geometry and energy for comparison, and therefore to more accurately identify the most likely protonation state.

Correction: CO 2 induced phase transitions in diamine-appended metal–organic frameworks

Sun, 18 Aug 2024 00:00:00 +0000

[This corrects the article DOI: 10.1039/C5SC01828E.].

An automatically curated first-principles database of ferroelectrics.

Sun, 18 Aug 2024 00:00:00 +0000

Ferroelectric materials have technological applications in information storage and electronic devices. The ferroelectric polar phase can be controlled with external fields, chemical substitution and size-effects in bulk and ultrathin film form, providing a platform for future technologies and for exploratory research. In this work, we integrate spin-polarized density functional theory (DFT) calculations, crystal structure databases, symmetry tools, workflow software, and a custom analysis toolkit to build a library of known, previously-proposed, and newly-proposed ferroelectric materials. With our automated workflow, we screen over 67,000 candidate materials from the Materials Project database to generate a dataset of 255 ferroelectric candidates, and propose 126 new ferroelectric materials. We benchmark our results against experimental data and previous first-principles results. The data provided includes atomic structures, output files, and DFT values of band gaps, energies,...

Back-to-back high category atmospheric river landfalls occur more often on the west coast of the United States

Fri, 2 Aug 2024 00:00:00 +0000

The catastrophic December 2022-January 2023 nine atmospheric rivers in California underscore the urgent need to better understand such high-risk weather extremes. Here we applied a machine learning clustering tool to understand the activity of atmospheric river clusters. Reanalysis results show that clusters with high density, that is the time fraction under atmospheric river conditions within a cluster, exhibit more frequent high-category atmospheric rivers, alongside an increased likelihood for extreme precipitation and severe land surface responses. The key circulation patterns of atmospheric river clusters are primarily attributed to subseasonal variability. Furthermore, the occurrence and density of atmospheric river clusters are modulated by the daily variability of the geopotential height field. Climate model projections suggest that atmospheric river clusters with higher density and higher categories will be more frequent as warming level increases. Our findings emphasize...

Identifying atmospheric rivers and their poleward latent heat transport with generalizable neural networks: ARCNNv1

Mon, 29 Jul 2024 00:00:00 +0000

Abstract. Atmospheric rivers (ARs) are extreme weather events that can alleviate drought or cause billions of US dollars in flood damage. By transporting significant amounts of latent energy towards the poles, they are crucial to maintaining the climate system's energy balance. Since there is no first-principle definition of an AR grounded in geophysical fluid mechanics, AR identification is currently performed by a multitude of expert-defined, threshold-based algorithms. The variety of AR detection algorithms has introduced uncertainty into the study of ARs, and the thresholds of the algorithms may not generalize to new climate datasets and resolutions. We train convolutional neural networks (CNNs) to detect ARs while representing this uncertainty; we name these models ARCNNs. To detect ARs without requiring new labeled data and labor-intensive AR detection campaigns, we present a semi-supervised learning framework based on image style transfer. This framework generalizes ARCNNs...

Monoterpene production by the carotenogenic yeast Rhodosporidium toruloides

Sun, 21 Jul 2024 00:00:00 +0000

BackgroundDue to their high energy density and compatible physical properties, several monoterpenes have been investigated as potential renewable transportation fuels, either as blendstocks with petroleum or as drop-in replacements for use in vehicles (both heavy and light-weight) or in aviation. Sustainable microbial production of these biofuels requires the ability to utilize cheap and readily available feedstocks such as lignocellulosic biomass, which can be depolymerized into fermentable carbon sources such as glucose and xylose. However, common microbial production platforms such as the yeast Saccharomyces cerevisiae are not naturally capable of utilizing xylose, hence requiring extensive strain engineering and optimization to efficiently utilize lignocellulosic feedstocks. In contrast, the oleaginous red yeast Rhodosporidium toruloides is capable of efficiently metabolizing both xylose and glucose, suggesting that it may be a suitable host for the production of lignocellulosic...

The DECOVALEX international collaboration on modeling of coupled subsurface processes and its contribution to confidence building in radioactive waste disposal

Thu, 11 Jul 2024 00:00:00 +0000

Abstract The long-lived radiotoxicity of the high-level radioactive waste generated by nuclear power plants requires safe isolation from the biosphere for many hundreds of thousands of years. An international consensus has emerged that such isolation can best be provided by disposal in mined geologic repositories, a strategy that today is pursued by most countries dealing with radioactive waste. However, the need to predict the performance of such repositories over very long time periods generates large uncertainties that have to be accounted for in safety assessments. The findings from such safety assessments need to be conveyed to all stakeholders in a clear way, such that public confidence in geologic disposal solutions can be achieved. It is suggested here that close international collaboration on the technical aspects of geologic waste disposal has helped, and will continue to help, building trust and increasing confidence. This paper discusses a particular international...

Protecting scientific integrity in an age of generative AI

Wed, 10 Jul 2024 00:00:00 +0000

Protecting scientific integrity in an age of generative AI

The mitochondrial unfolded protein response regulates hippocampal neural stem cell aging

Mon, 24 Jun 2024 00:00:00 +0000

Aging results in a decline in neural stem cells (NSCs), neurogenesis, and cognitive function, and evidence is emerging to demonstrate disrupted adult neurogenesis in the hippocampus of patients with several neurodegenerative disorders. Here, single-cell RNA sequencing of the dentate gyrus of young and old mice shows that the mitochondrial protein folding stress is prominent in activated NSCs/neural progenitors (NPCs) among the neurogenic niche, and it increases with aging accompanying dysregulated cell cycle and mitochondrial activity in activated NSCs/NPCs in the dentate gyrus. Increasing mitochondrial protein folding stress results in compromised NSC maintenance and reduced neurogenesis in the dentate gyrus, neural hyperactivity, and impaired cognitive function. Reducing mitochondrial protein folding stress in the dentate gyrus of old mice improves neurogenesis and cognitive function. These results establish the mitochondrial protein folding stress as a driver of NSC aging and...

Systematic engineering for production of anti-aging sunscreen compound in Pseudomonas putida

Tue, 18 Jun 2024 00:00:00 +0000

Sunscreen has been used for thousands of years to protect skin from ultraviolet radiation. However, the use of modern commercial sunscreen containing oxybenzone, ZnO, and TiO₂ has raised concerns due to their negative effects on human health and the environment. In this study, we aim to establish an efficient microbial platform for production of shinorine, a UV light absorbing compound with anti-aging properties. First, we methodically selected an appropriate host for shinorine production by analyzing central carbon flux distribution data from prior studies alongside predictions from genome-scale metabolic models (GEMs). We enhanced shinorine productivity through CRISPRi-mediated downregulation and utilized shotgun proteomics to pinpoint potential competing pathways. Simultaneously, we improved the shinorine biosynthetic pathway by refining its design, optimizing promoter usage, and altering the strength of ribosome binding sites. Finally, we conducted amino acid feeding...

Assessment of energy and thermal resilience performance to inform climate mitigation of multifamily buildings in disadvantaged communities

Tue, 21 May 2024 00:00:00 +0000

The compound impacts of heatwaves and power outages pose a serious indoor heat-related health risk for residents living in disadvantaged communities (DACs) with limited or no air conditioning. In this study we selected 13 heat vulnerable multifamily buildings in El Monte, in Los Angeles County, and employed CityBES to evaluate their energy and thermal resilience performance. A retrofit package with seven passive and low-power active measures—cool roof, cool wall, window solar film, air sealing, internal blinds, natural ventilation, and ceiling fan—was evaluated under 2018 weather conditions and projected 2058 future weather conditions. Results show: (1) under the 2018 weather conditions, the retrofit package reduces the peak electricity load by 19 % and reduces the annual energy cost by $183 per housing unit; (2) the housing units without air conditioning would face heat danger conditions throughout the heatwave period. Although the retrofit package could reduce the heat danger...

Cooperative Carbon Dioxide Adsorption in Alcoholamine‐ and Alkoxyalkylamine‐Functionalized Metal–Organic Frameworks

Sun, 25 Feb 2024 00:00:00 +0000

Abstract A series of structurally diverse alcoholamine‐ and alkoxyalkylamine‐functionalized variants of the metal–organic framework Mg 2 (dobpdc) are shown to adsorb CO 2 selectively via cooperative chain‐forming mechanisms. Solid‐state NMR spectra and optimized structures obtained from van der Waals‐corrected density functional theory calculations indicate that the adsorption profiles can be attributed to the formation of carbamic acid or ammonium carbamate chains that are stabilized by hydrogen bonding interactions within the framework pores. These findings significantly expand the scope of chemical functionalities that can be utilized to design cooperative CO 2 adsorbents, providing further means of optimizing these powerful materials for energy‐efficient CO 2 separations.

Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix

Sun, 25 Feb 2024 00:00:00 +0000

The refinement of biomolecular crystallographic models relies on geometric restraints to help to address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models. Here, an integration of the full all-atom Amber molecular-dynamics force field into Phenix crystallographic refinement is presented, which enables more complete modeling of biomolecular chemistry. The advantages of the force field include a carefully derived set of torsion-angle potentials, an extensive and flexible set of atom types, Lennard-Jones treatment of nonbonded interactions and a full treatment of crystalline electrostatics. The new combined method was tested against conventional geometry restraints for over 22 000 protein structures. Structures refined with the new method show substantially improved model quality. On average, Ramachandran and rotamer scores are somewhat better, clashscores and MolProbity scores are...

Improved joint X-ray and neutron refinement procedure in Phenix

Wed, 7 Feb 2024 00:00:00 +0000

Neutron diffraction is one of the three crystallographic techniques (X-ray, neutron and electron diffraction) used to determine the atomic structures of molecules. Its particular strengths derive from the fact that H (and D) atoms are strong neutron scatterers, meaning that their positions, and thus protonation states, can be derived from crystallographic maps. However, because of technical limitations and experimental obstacles, the quality of neutron diffraction data is typically much poorer (completeness, resolution and signal to noise) than that of X-ray diffraction data for the same sample. Further, refinement is more complex as it usually requires additional parameters to describe the H (and D) atoms. The increase in the number of parameters may be mitigated by using the `riding hydrogen' refinement strategy, in which the positions of H atoms without a rotational degree of freedom are inferred from their neighboring heavy atoms. However, this does not address the issues...

Sparse Approximate Multifrontal Factorization with Composite Compression Methods

Fri, 12 Jan 2024 00:00:00 +0000

This article presents a fast and approximate multifrontal solver for large sparse linear systems. In a recent work by Liu et al., we showed the efficiency of a multifrontal solver leveraging the butterfly algorithm and its hierarchical matrix extension, HODBF (hierarchical off-diagonal butterfly) compression to compress large frontal matrices. The resulting multifrontal solver can attain quasi-linear computation and memory complexity when applied to sparse linear systems arising from spatial discretization of high-frequency wave equations. To further reduce the overall number of operations and especially the factorization memory usage to scale to larger problem sizes, in this article we develop a composite multifrontal solver that employs the HODBF format for large-sized fronts, a reduced-memory version of the nonhierarchical block low-rank format for medium-sized fronts, and a lossy compression format for small-sized fronts. This allows us to solve sparse linear systems...

Importance of nonuniform Brillouin zone sampling for ab initio Bethe-Salpeter equation calculations of exciton binding energies in crystalline solids

Mon, 8 Jan 2024 00:00:00 +0000

Excitons are prevalent in semiconductors and insulators, and their binding energies are critical for optoelectronic applications. The state-of-the-art method for first-principles calculations of excitons in extended systems is the ab initio GW-Bethe-Salpeter equation (BSE) approach, which can require a fine sampling of reciprocal space to accurately resolve solid-state exciton properties. Here we show, for a range of semiconductors and insulators, that the commonly employed approach of uniformly sampling the Brillouin zone can lead to underconverged exciton binding energies, as impractical grid sizes are required to achieve adequate convergence. We further show that nonuniform sampling of the Brillouin zone, focused on the region of reciprocal space where the exciton wave function resides, enables efficient rapid numerical convergence of exciton binding energies at a given level of theory. We propose a well-defined convergence procedure, which can be carried out at relatively...

Cell type-specific long-range connections of basal forebrain circuit

Sun, 24 Dec 2023 00:00:00 +0000

The basal forebrain (BF) plays key roles in multiple brain functions, including sleep-wake regulation, attention, and learning/memory, but the long-range connections mediating these functions remain poorly characterized. Here we performed whole-brain mapping of both inputs and outputs of four BF cell types - cholinergic, glutamatergic, and parvalbumin-positive (PV+) and somatostatin-positive (SOM+) GABAergic neurons - in the mouse brain. Using rabies virus -mediated monosynaptic retrograde tracing to label the inputs and adeno-associated virus to trace axonal projections, we identified numerous brain areas connected to the BF. The inputs to different cell types were qualitatively similar, but the output projections showed marked differences. The connections to glutamatergic and SOM+ neurons were strongly reciprocal, while those to cholinergic and PV+ neurons were more unidirectional. These results reveal the long-range wiring diagram of the BF circuit with highly convergent inputs...

A Membrane‐Associated Light‐Harvesting Model is Enabled by Functionalized Assemblies of Gene‐Doubled TMV Proteins

Wed, 13 Dec 2023 00:00:00 +0000

Photosynthetic light harvesting requires efficient energy transfer within dynamic networks of light-harvesting complexes embedded within phospholipid membranes. Artificial light-harvesting models are valuable tools for understanding the structural features underpinning energy absorption and transfer within chromophore arrays. Here, a method for attaching a protein-based light-harvesting model to a planar, fluid supported lipid bilayer (SLB) is developed. The protein model consists of the tobacco mosaic viral capsid proteins that are gene-doubled to create a tandem dimer (dTMV). Assemblies of dTMV break the facial symmetry of the double disk to allow for differentiation between the disk faces. A single reactive lysine residue is incorporated into the dTMV assemblies for the site-selective attachment of chromophores for light absorption. On the opposing dTMV face, a cysteine residue is incorporated for the bioconjugation of a peptide containing a polyhistidine tag...

Comparing simulated demand flexibility against actual performance in commercial office buildings

Thu, 30 Nov 2023 00:00:00 +0000

Commercial building energy benchmarking has been used as a mechanism to evaluate energy use of a single building over time, relative to other similar buildings, or to simulations of a reference building conforming to various energy standards. Lack of empirical demand flexibility data and consistent flexibility metrics has limited the ability to compare demand flexibility performance with estimated demand flexibility in buildings. In this study, we collected demand response performance data for a total of 831 demand response events from 192 sites as a first step to build such a building demand flexibility dataset, and propose a standard core data schema to consolidate field data from different sources. We also performed parametric simulations of a control strategy called “global temperature adjustment” using commercial office prototype building models. We then compared the simulated demand flexibility performance against the actual data for offices with global temperature adjustment...

The Relationship Between African Easterly Waves and Tropical Cyclones in Historical and Future Climates in the HighResMIP‐PRIMAVERA Simulations

Thu, 30 Nov 2023 00:00:00 +0000

Abstract The deadly and destructive nature of tropical cyclones (TCs) makes understanding their response to future climate change of the utmost importance. TC genesis hinges on multiple factors, including an initial disturbance. African easterly waves (AEWs) have been shown to serve as such disturbances for TCs developing in the North Atlantic. It is therefore crucial to understand the relationship between AEWs and TCs and how this relationship may be affected by climate change. In this study, we examine the AEW‐TC relationship in historical and future climates using three models from the HighResMIP PRIMAVERA simulations. The AEWs and TCs were tracked in the model data using objective tracking algorithms, and AEW and TC tracks were then matched together if they were close to each other in space and time. The strength of the AEWs was measured using the eddy kinetic energy and the curvature vorticity of the waves. TC strength and intensity were measured using potential intensity...

A positively tuned voltage indicator for extended electrical recordings in the brain

Fri, 17 Nov 2023 00:00:00 +0000

Genetically encoded voltage indicators (GEVIs) enable optical recording of electrical signals in the brain, providing subthreshold sensitivity and temporal resolution not possible with calcium indicators. However, one- and two-photon voltage imaging over prolonged periods with the same GEVI has not yet been demonstrated. Here, we report engineering of ASAP family GEVIs to enhance photostability by inversion of the fluorescence–voltage relationship. Two of the resulting GEVIs, ASAP4b and ASAP4e, respond to 100-mV depolarizations with ≥180% fluorescence increases, compared with the 50% fluorescence decrease of the parental ASAP3. With standard microscopy equipment, ASAP4e enables single-trial detection of spikes in mice over the course of minutes. Unlike GEVIs previously used for one-photon voltage recordings, ASAP4b and ASAP4e also perform well under two-photon illumination. By imaging voltage and calcium simultaneously, we show that ASAP4b and ASAP4e can identify place cells and...

Simultaneous carbon catabolite repression governs sugar and aromatic co-utilization in Pseudomonas putida M2

Fri, 3 Nov 2023 00:00:00 +0000

Pseudomonas putida have emerged as promising biocatalysts for the conversion of sugars and aromatic compounds obtained from lignocellulosic biomass. Understanding the role of carbon catabolite repression (CCR) in these strains is critical to optimize biomass conversion to fuels and chemicals. The CCR functioning in P. putida M2, a strain capable of consuming both hexose and pentose sugars as well as aromatic compounds, was investigated by cultivation experiments, proteomics, and CRISPRi-based gene repression. Strain M2 co-utilized sugars and aromatic compounds simultaneously; however, during cultivation with glucose and aromatic compounds (p-coumarate and ferulate) mixture, intermediates (4-hydroxybenzoate and vanillate) accumulated, and substrate consumption was incomplete. In contrast, xylose-aromatic consumption resulted in transient intermediate accumulation and complete aromatic consumption, while xylose was incompletely consumed. Proteomics analysis...

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures

Sun, 22 Oct 2023 00:00:00 +0000

Structures of biomolecular systems are increasingly computed by integrative modeling. In this approach, a structural model is constructed by combining information from multiple sources, including varied experimental methods and prior models. In 2019, a Workshop was held as a Biophysical Society Satellite Meeting to assess progress and discuss further requirements for archiving integrative structures. The primary goal of the Workshop was to build consensus for addressing the challenges involved in creating common data standards, building methods for federated data exchange, and developing mechanisms for validating integrative structures. The summary of the Workshop and the recommendations that emerged are presented here.

Cryo‐EM map interpretation and protein model‐building using iterative map segmentation

Sun, 15 Oct 2023 00:00:00 +0000

A procedure for building protein chains into maps produced by single-particle electron cryo-microscopy (cryo-EM) is described. The procedure is similar to the way an experienced structural biologist might analyze a map, focusing first on secondary structure elements such as helices and sheets, then varying the contour level to identify connections between these elements. Since the high density in a map typically follows the main-chain of the protein, the main-chain connection between secondary structure elements can often be identified as the unbranched path between them with the highest minimum value along the path. This chain-tracing procedure is then combined with finding side-chain positions based on the presence of density extending away from the main path of the chain, allowing generation of a C_α model. The C_α model is converted to an all-atom model and is refined against the map. We show that this procedure is as effective as other existing methods...

Comparing time-dependent density functional theory with many-body perturbation theory for semiconductors: Screened range-separated hybrids and the GW plus Bethe-Salpeter approach

Tue, 26 Sep 2023 00:00:00 +0000

We present band structure and optical absorption spectra obtained from density functional theory (DFT) and linear response time-dependent DFT (TDDFT) calculations using a screened range-separated hybrid (SRSH) functional, including spin-orbit coupling, for seven prototypical semiconductors. The results are compared to those obtained from highly converged many-body perturbation theory calculations using the GW approximation and the GW plus Bethe-Salpeter equation (GW-BSE) approaches. We use a single empirical parameter for our SRSH calculations, fit such that the SRSH band gap reproduces the GW band gap at the Γ point. We then find that ground-state generalized Kohn-Sham SRSH eigenvalues accurately reproduce the band structure obtained from GW calculations, typically to within 0.1–0.2 eV, and optical absorption spectra obtained using TDDFT with the SRSH functional agree well with those of GW-BSE, with a mean deviation of 0.03 and 0.11 eV for the location of the first and second...

Cryo_fit: Democratization of flexible fitting for cryo-EM

Thu, 21 Sep 2023 00:00:00 +0000

Cryo-electron microscopy (cryo-EM) is becoming a method of choice for describing native conformations of biomolecular complexes at high resolution. The rapid growth of cryo-EM in recent years has created a high demand for automated solutions, both in hardware and software. Flexible fitting of atomic models to three-dimensional (3D) cryo-EM reconstructions by molecular dynamics (MD) simulation is a popular technique but often requires technical expertise in computer simulation. This work introduces cryo_fit, a package for the automatic flexible fitting of atomic models in cryo-EM maps using MD simulation. The package is integrated with the Phenix software suite. The module was designed to automate the multiple steps of MD simulation in a reproducible manner, as well as facilitate refinement and validation through Phenix. Through the use of cryo_fit, scientists with little experience in MD simulation can produce high quality atomic models automatically and better exploit the potential...

Correction: Enhancement of CO 2 binding and mechanical properties upon diamine functionalization of M 2 (dobpdc) metal–organic frameworks

Thu, 21 Sep 2023 00:00:00 +0000

[This corrects the article DOI: 10.1039/C7SC05217K.].

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)

Wed, 20 Sep 2023 00:00:00 +0000

This letter announces that PDBx/mmCIF format files will become mandatory for crystallographic depositions to the Protein Data Bank (PDB).

Monitoring Methane Emissions from Oil and Gas Operations

Tue, 19 Sep 2023 00:00:00 +0000

The atmospheric concentration of methane has more than doubled since the start of the Industrial Revolution. Methane is the second-most-Abundant greenhouse gas created by human activities and a major driver of climate change. This APS-Optica report provides a technical assessment of the current state of monitoring U.S. methane emissions from oil and gas operations, which accounts for roughly 30% of U.S. anthropogenic methane emissions. The report identifies current technological and policy gaps and makes recommendations for the federal government in three key areas: methane emissions detection, reliable and systematized data and models to support mitigation measures, and effective regulation.

Spray‐induced gene silencing to identify powdery mildew gene targets and processes for powdery mildew control

Tue, 5 Sep 2023 00:00:00 +0000

Spray-induced gene silencing (SIGS) is an emerging tool for crop pest protection. It utilizes exogenously applied double-stranded RNA to specifically reduce pest target gene expression using endogenous RNA interference machinery. In this study, SIGS methods were developed and optimized for powdery mildew fungi, which are widespread obligate biotrophic fungi that infect agricultural crops, using the known azole-fungicide target cytochrome P450 51 (CYP51) in the Golovinomyces orontii-Arabidopsis thaliana pathosystem. Additional screening resulted in the identification of conserved gene targets and processes important to powdery mildew proliferation: apoptosis-antagonizing transcription factor in essential cellular metabolism and stress response; lipid catabolism genes lipase a, lipase 1, and acetyl-CoA oxidase in energy production; and genes involved in manipulation of the plant host via abscisic acid metabolism (9-cis-epoxycarotenoid dioxygenase, xanthoxin dehydrogenase, and a...

Extended radiation source imaging with a prototype Compton imager

Wed, 30 Aug 2023 00:00:00 +0000

This paper reports results from a prototype Compton imager (PCI) which consists of three planes of silicon pixel detectors as a scattering detector followed by an array of CsI(Tl) crystals as an absorbing detector. The CsI(Tl) array is mounted directly behind the silicon detectors. Simple back-projection algorithms are not sufficient to resolve extended shapes, but iterative algorithms provide the necessary de-convolution. List-mode maximum likelihood expectation maximization (LM-MLEM) is an iterative algorithm that reconstructs the most probable source distribution for a given data set. LM-MLEM attempts to reconstruct an image by finding successive approximations to the true source data. Each data set imaged is different, but the number of iterations required for convergence is typically 10-30 for the PCI. In this paper, reconstructed images of point and extended sources using measured PCI data are presented. Data are corroborated using GEANT4 simulations.

Mobile, hybrid Compton/coded aperture imaging for detection, identification and localization of gamma-ray sources at stand-off distances

Wed, 30 Aug 2023 00:00:00 +0000

The Stand-off Radiation Detection System (SORDS) program is an Advanced Technology Demonstration (ATD) project through the Department of Homeland Security’s Domestic Nuclear Detection Office (DNDO) with the goal of detection, identification and localization of weak radiological sources in the presence of large dynamic backgrounds. The Raytheon-SORDS Tri-Modal Imager (TMI) is a mobile truckbased, hybrid gamma-ray spectroscopic and imaging system able to quickly detect, identify and localize, radiation sources at standoff distances through improved sensitivity provided by multiple detection modes while minimizing the false alarm rate. Reconstruction of gamma-ray sources is performed using a combination of gamma-ray spectroscopy and two imaging modalities; coded aperture and Compton scatter imaging. The TMI consists of 35 sodium iodide (NaI) crystals (5x5x2 in3 each), arranged in a random coded aperture mask array (CA), followed by 30 position sensitive NaI iv bars (24x2.5x3 in3...

A simple algorithm for estimation of source-to-detector distance in Compton imaging

Wed, 30 Aug 2023 00:00:00 +0000

Compton imaging is used to predict the location of gamma-emitting radiation sources. The X and Y coordinates of the source can be obtained using a back-projected image and a two-dimensional peak-finding algorithm. The emphasis of this work is to estimate the source-to-detector distance (Z). The algorithm presented uses the solid angle subtended by the reconstructed image at various source-to-detector distances. This algorithm was validated using both measured data from the prototype Compton imager (PCI) constructed at the Los Alamos National Laboratory and simulated data of the same imager. Results show this method can be applied successfully to estimate Z, and it provides a way of determining Z without prior knowledge of the source location. This method is faster than the methods that employ maximum likelihood method because it is based on simple back projections of Compton scatter data.

Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format

Tue, 8 Aug 2023 00:00:00 +0000

Plate-based proteomic sample preparation offers a solution to the large sample throughput demands in the biotechnology field where hundreds or thousands of engineered microbes are constructed for testing is routine. Meanwhile, sample preparation methods that work efficiently on broader microbial groups are desirable for new applications of proteomics in other fields, such as microbial communities. Here, we detail a step-by-step protocol that consists of cell lysis in an alkaline chemical buffer (NaOH/SDS) followed by protein precipitation with high-ionic strength acetone in 96-well format. The protocol works for a broad range of microbes (e.g., Gram-negative bacteria, Gram-positive bacteria, non-filamentous fungi) and the resulting proteins are ready for tryptic digestion for bottom-up quantitative proteomic analysis without the need for desalting column cleanup. The yield of protein using this protocol increases linearly with respect to the amount of starting biomass from 0.5-2.0...

A combinatorial droplet microfluidic device integrated with mass spectrometry for enzyme screening

Mon, 31 Jul 2023 00:00:00 +0000

Mass spectrometry (MS) enables detection of different chemical species with a very high specificity; however, it can be limited by its throughput. Integrating MS with microfluidics has a tremendous potential to improve throughput and accelerate biochemical research. In this work, we introduce Drop-NIMS, a combination of a passive droplet loading microfluidic device and a matrix-free MS laser desorption ionization technique called nanostructure-initiator mass spectrometry (NIMS). This platform combines different droplets at random to generate a combinatorial library of enzymatic reactions that are deposited directly on the NIMS surface without requiring additional sample handling. The enzyme reaction products are then detected with MS. Drop-NIMS was used to rapidly screen enzymatic reactions containing low (on the order of nL) volumes of glycoside reactants and glycoside hydrolase enzymes per reaction. MS "barcodes" (small compounds with unique masses) were added to the droplets...

Structural evidence for intermediates during O2 formation in photosystem II

Sat, 15 Jul 2023 00:00:00 +0000

In natural photosynthesis, the light-driven splitting of water into electrons, protons and molecular oxygen forms the first step of the solar-to-chemical energy conversion process. The reaction takes place in photosystem II, where the Mn4CaO5 cluster first stores four oxidizing equivalents, the S0 to S4 intermediate states in the Kok cycle, sequentially generated by photochemical charge separations in the reaction center and then catalyzes the O–O bond formation chemistry1–3. Here, we report room temperature snapshots by serial femtosecond X-ray crystallography to provide structural insights into the final reaction step of Kok’s photosynthetic water oxidation cycle, the S3→[S4]→S0 transition where O2 is formed and Kok’s water oxidation clock is reset. Our data reveal a complex sequence of events, which occur over micro- to milliseconds, comprising changes at the Mn4CaO5 cluster, its ligands and water pathways as well as controlled proton release through the hydrogen-bonding network...

Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2

Fri, 14 Jul 2023 00:00:00 +0000

Direct-acting antivirals are needed to combat coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The papain-like protease (PLpro) domain of Nsp3 from SARS-CoV-2 is essential for viral replication. In addition, PLpro dysregulates the host immune response by cleaving ubiquitin and interferon-stimulated gene 15 protein from host proteins. As a result, PLpro is a promising target for inhibition by small-molecule therapeutics. Here we design a series of covalent inhibitors by introducing a peptidomimetic linker and reactive electrophile onto analogs of the noncovalent PLpro inhibitor GRL0617. The most potent compound inhibits PLpro with kinact/KI = 9,600 M−1 s−1, achieves sub-μM EC50 values against three SARS-CoV-2 variants in mammalian cell lines, and does not inhibit a panel of human deubiquitinases (DUBs) at >30 μM concentrations of inhibitor. An X-ray co-crystal structure of the compound bound to PLpro validates...

In situ ligand restraints from quantum-mechanical methods

Tue, 11 Jul 2023 00:00:00 +0000

In macromolecular crystallographic structure refinement, ligands present challenges for the generation of geometric restraints due to their large chemical variability, their possible novel nature and their specific interaction with the binding pocket of the protein. Quantum-mechanical approaches are useful for providing accurate ligand geometries, but can be plagued by the number of minima in flexible molecules. In an effort to avoid these issues, the Quantum Mechanical Restraints (QMR) procedure optimizes the ligand geometry in situ, thus accounting for the influence of the macromolecule on the local energy minima of the ligand. The optimized ligand geometry is used to generate target values for geometric restraints during the crystallographic refinement. As demonstrated using a sample of >2330 ligand instances in >1700 protein-ligand models, QMR restraints generally result in lower deviations from the target stereochemistry compared with conventionally generated restraints....

Increasing reactivity by incorporating π-acceptor ligands into coordinatively unsaturated thiolate-ligated iron(II) complexes

Wed, 21 Jun 2023 00:00:00 +0000

Reported herein is the structural, spectroscopic, redox, and reactivity properties of a series of iron complexes containing both a π-donating thiolate, and π-accepting N-heterocycles in the coordination sphere, in which we systematically vary the substituents on the N-heterocycle, the size of the N-heterocycle, and the linker between the imine nitrogen and tertiary amine nitrogen. In contrast to our primary amine/thiolate-ligated Fe(II) complex, [Fe^II(S^Me2N₄(tren))]⁺ (1), the Fe(II) complexes reported herein are intensely colored, allowing us to visually monitor reactivity. Ferrous complexes with R = H substituents in the 6-position of the pyridines, [Fe^II(S^Me2N₄(6-H-DPPN)]⁺ (6) and [Fe^II(S^Me2N₄(6-H-DPEN))(MeOH)]⁺ (8-MeOH) are shown to readily bind neutral ligands, and all of the Fe(II) complexes are shown...

Quasiparticle and Optical Properties of Carrier-Doped Monolayer MoTe2 from First Principles

Sun, 11 Jun 2023 00:00:00 +0000

The intrinsic weak and highly nonlocal dielectric screening of two-dimensional materials is well-known to lead to high sensitivity of their optoelectronic properties to environment. Less studied theoretically is the role of free carriers in those properties. Here, we use ab initio GW and Bethe-Salpeter equation calculations, with a rigorous treatment of dynamical screening and local-field effects, to study the doping dependence of the quasiparticle and optical properties of a monolayer transition-metal dichalcogenide, 2H MoTe₂. We predict a quasiparticle band gap renormalization of several hundreds of meV for experimentally attainable carrier densities and a similarly sizable decrease in the exciton binding energy. This results in an almost constant excitation energy for the lowest-energy exciton resonance with an increasing doping density. Using a newly developed and generally applicable plasmon-pole model and a self-consistent solution of the Bethe-Salpeter equation,...

Chapter Eleven What are the current limits on determination of protonation state using neutron macromolecular crystallography?

Wed, 7 Jun 2023 00:00:00 +0000

The rate of deposition of models determined by neutron diffraction, or a hybrid approach that combines X-ray and neutron diffraction, has increased in recent years. The benefit of neutron diffraction is that hydrogen atom (H) positions are detectable, allowing for the determination of protonation state and water molecule orientation. This study analyses all neutron models deposited in the Protein Data Bank to date, focusing on protonation state and properties of H (or deuterium, D) atoms as well as the details of water molecules. In particular, clashes and hydrogen bonds involving H or D atoms are investigated. As water molecules are typically the least reproducible part of a structural model, their positions in neutron models were compared to those in homologous high-resolution X-ray structures. For models determined by joint refinement against X-ray and neutron data, the water structure comparison was also carried out for models re-refined against the X-ray data alone. The homologues...

Implementation of the riding hydrogen model in CCTBX to support the next generation of X-ray and neutron joint refinement in Phenix

Wed, 7 Jun 2023 00:00:00 +0000

A fundamental prerequisite for implementing new procedures of atomic model refinement against neutron diffraction data is the efficient handling of hydrogen atoms. The riding hydrogen model, which constrains hydrogen atom parameters to those of the non-hydrogen atoms, is a plausible parameterization for refinements. This work describes the implementation of the riding hydrogen model in the Computational Crystallography Toolbox and in Phenix. Riding hydrogen atoms can be found in several different configurations that are characterized by specific geometries. For each configuration, the hydrogen atom parameterization and the expressions for the gradients of refinement target function with respect to non-hydrogen parameters are described.

Characteristics and Variability of Winter Northern Pacific Atmospheric River Flavors

Tue, 6 Jun 2023 00:00:00 +0000

Abstract Atmospheric rivers (ARs) are intensive poleward moisture transport events that are essential to the global hydrological cycle and are often linked to extreme weather events. We categorize the winter North Pacific ARs into two “flavors”: wind‐dominated (windy ARs) and moisture‐dominated (wet ARs) using 40 years of hourly data from fifth generation of the European Centre for Medium‐Range Weather Forecasts Interim Reanalysis. We compare the differences between windy ARs and wet ARs including the lifecycle characteristics (such as genesis locations and changes of meteorological elements through the lifecycle), overall AR frequency, landfall impacts, and variability. The windy ARs are more likely to occur in the midlatitudes, while wet ARs are more active in the subtropics. Windy ARs are associated with intensive surface pressure lows, where the strong pressure gradient can support the strong wind within ARs. Due to larger size and longer lifetime, wet ARs are more likely...

Chronic Implantation of Multiple Flexible Polymer Electrode Arrays

Fri, 2 Jun 2023 00:00:00 +0000

Simultaneous recordings from large populations of individual neurons across distributed brain regions over months to years will enable new avenues of scientific and clinical development. The use of flexible polymer electrode arrays can support long-lasting recording, but the same mechanical properties that allow for longevity of recording make multiple insertions and integration into a chronic implant a challenge. Here is a methodology by which multiple polymer electrode arrays can be targeted to a relatively spatially unconstrained set of brain areas. The method utilizes thin-film polymer devices, selected for their biocompatibility and capability to achieve long-term and stable electrophysiologic recording interfaces. The resultant implant allows accurate and flexible targeting of anatomically distant regions, physical stability for months, and robustness to electrical noise. The methodology supports up to sixteen serially inserted devices across eight different anatomic...

High-Density, Long-Lasting, and Multi-region Electrophysiological Recordings Using Polymer Electrode Arrays

Wed, 24 May 2023 00:00:00 +0000

The brain is a massive neuronal network, organized into anatomically distributed sub-circuits, with functionally relevant activity occurring at timescales ranging from milliseconds to years. Current methods to monitor neural activity, however, lack the necessary conjunction of anatomical spatial coverage, temporal resolution, and long-term stability to measure this distributed activity. Here we introduce a large-scale, multi-site, extracellular recording platform that integrates polymer electrodes with a modular stacking headstage design supporting up to 1,024 recording channels in freely behaving rats. This system can support months-long recordings from hundreds of well-isolated units across multiple brain regions. Moreover, these recordings are stable enough to track large numbers of single units for over a week. This platform enables large-scale electrophysiological interrogation of the fast dynamics and long-timescale evolution of anatomically distributed circuits, and thereby...

How Do Ring Size and π‑Donating Thiolate Ligands Affect Redox-Active, α‑Imino‑N‑heterocycle Ligand Activation?

Mon, 22 May 2023 00:00:00 +0000

Considerable effort has been devoted to the development of first-row transition-metal catalysts containing redox-active imino-pyridine ligands that are capable of storing multiple reducing equivalents. This property allows abundant and inexpensive first-row transition metals, which favor sequential one-electron redox processes, to function as competent catalysts in the concerted two-electron reduction of substrates. Herein we report the syntheses and characterization of a series of iron complexes that contain both π-donating thiolate and π-accepting (α-imino)-N-heterocycle redox-active ligands, with progressively larger N-heterocycle rings (imidazole, pyridine, and quinoline). A cooperative interaction between these complementary redox-active ligands is shown to dictate the properties of these complexes. Unusually intense charge-transfer (CT) bands, and intraligand metrical parameters, reminiscent of a reduced (α-imino)-N-heterocycle ligand (L^•-), initially suggested...

Metal-Assisted Oxo Atom Addition to an Fe(III) Thiolate

Mon, 22 May 2023 00:00:00 +0000

Cysteinate oxygenation is intimately tied to the function of both cysteine dioxygenases (CDOs) and nitrile hydratases (NHases), and yet the mechanisms by which sulfurs are oxidized by these enzymes are unknown, in part because intermediates have yet to be observed. Herein, we report a five-coordinate bis-thiolate ligated Fe(III) complex, [Fe^III(S₂^Me2N₃(Pr,Pr))]⁺ (2), that reacts with oxo atom donors (PhIO, IBX-ester, and H₂O₂) to afford a rare example of a singly oxygenated sulfenate, [Fe^III(η²-S^Me2O)(S^Me2)N₃(Pr,Pr)]⁺ (5), resembling both a proposed intermediate in the CDO catalytic cycle and the essential NHase Fe-S(O)^Cys114 proposed to be intimately involved in nitrile hydrolysis. Comparison of the reactivity of 2 with that of a more electron-rich, crystallographically characterized derivative, [Fe^IIIS₂^Me2N^MeN₂^amide(Pr,Pr)]^-...

Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge

Sat, 20 May 2023 00:00:00 +0000

A recently-developed method for identifying a compact, contiguous region representing the unique part of a density map was applied to 218 Cryo-EM maps with resolutions of 4.5 Å or better. The key elements of the segmentation procedure are (1) identification of all regions of density above a threshold and (2) choice of a unique set of these regions, taking symmetry into consideration, that maximize connectivity and compactness. This segmentation approach was then combined with tools for automated map sharpening and model-building to generate models for the 12 maps in the 2016 Cryo-EM Model Challenge in a fully automated manner. The resulting models have completeness from 24% to 82% and RMS distances from reference interpretations of 0.6 Å-2.1 Å.

Evaluation system and web infrastructure for the second cryo-EM model challenge

Sat, 20 May 2023 00:00:00 +0000

An evaluation system and a web infrastructure were developed for the second cryo-EM model challenge. The evaluation system includes tools to validate stereo-chemical plausibility of submitted models, check their fit to the corresponding density maps, estimate their overall and per-residue accuracy, and assess their similarity to reference cryo-EM or X-ray structures as well as other models submitted in this challenge. The web infrastructure provides a convenient interface for analyzing models at different levels of detail. It includes interactively sortable tables of evaluation scores for different subsets of models and different sublevels of structure organization, and a suite of visualization tools facilitating model analysis. The results are publicly accessible at http://model-compare.emdatabank.org.

Chapter One MacroBac: New Technologies for Robust and Efficient Large-Scale Production of Recombinant Multiprotein Complexes

Thu, 11 May 2023 00:00:00 +0000

Recombinant expression of large, multiprotein complexes is essential and often rate limiting for determining structural, biophysical, and biochemical properties of DNA repair, replication, transcription, and other key cellular processes. Baculovirus-infected insect cell expression systems are especially well suited for producing large, human proteins recombinantly, and multigene baculovirus systems have facilitated studies of multiprotein complexes. In this chapter, we describe a multigene baculovirus system called MacroBac that uses a Biobricks-type assembly method based on restriction and ligation (Series 11) or ligation-independent cloning (Series 438). MacroBac cloning and assembly is efficient and equally well suited for either single subcloning reactions or high-throughput cloning using 96-well plates and liquid handling robotics. MacroBac vectors are polypromoter with each gene flanked by a strong polyhedrin promoter and an SV40 poly(A) termination signal that minimize...

Structure of the OsSERK2 leucine-rich repeat extracellular domain

Sat, 29 Apr 2023 00:00:00 +0000

Somatic embryogenesis receptor kinases (SERKs) are leucine-rich repeat (LRR)-containing integral membrane receptors that are involved in the regulation of development and immune responses in plants. It has recently been shown that rice SERK2 (OsSERK2) is essential for XA21-mediated resistance to the pathogen Xanthomonas oryzae pv. oryzae. OsSERK2 is also required for the BRI1-mediated, FLS2-mediated and EFR-mediated responses to brassinosteroids, flagellin and elongation factor Tu (EF-Tu), respectively. Here, crystal structures of the LRR domains of OsSERK2 and a D128N OsSERK2 mutant, expressed as hagfish variable lymphocyte receptor (VLR) fusions, are reported. These structures suggest that the aspartate mutation does not generate any significant conformational change in the protein, but instead leads to an altered interaction with partner receptors.

Ab initio study of hot electrons in GaAs

Thu, 27 Apr 2023 00:00:00 +0000

Hot carrier dynamics critically impacts the performance of electronic, optoelectronic, photovoltaic, and plasmonic devices. Hot carriers lose energy over nanometer lengths and picosecond timescales and thus are challenging to study experimentally, whereas calculations of hot carrier dynamics are cumbersome and dominated by empirical approaches. In this work, we present ab initio calculations of hot electrons in gallium arsenide (GaAs) using density functional theory and many-body perturbation theory. Our computed electron-phonon relaxation times at the onset of the Γ, L, and X valleys are in excellent agreement with ultrafast optical experiments and show that the ultrafast (tens of femtoseconds) hot electron decay times observed experimentally arise from electron-phonon scattering. This result is an important advance to resolve a controversy on hot electron cooling in GaAs. We further find that, contrary to common notions, all optical and acoustic modes contribute substantially...

Biochemical and Structural Studies of NADH-Dependent FabG Used To Increase the Bacterial Production of Fatty Acids under Anaerobic Conditions

Thu, 27 Apr 2023 00:00:00 +0000

Major efforts in bioenergy research have focused on producing fuels that can directly replace petroleum-derived gasoline and diesel fuel through metabolic engineering of microbial fatty acid biosynthetic pathways. Typically, growth and pathway induction are conducted under aerobic conditions, but for operational efficiency in an industrial context, anaerobic culture conditions would be preferred to obviate the need to maintain specific dissolved oxygen concentrations and to maximize the proportion of reducing equivalents directed to biofuel biosynthesis rather than ATP production. A major concern with fermentative growth conditions is elevated NADH levels, which can adversely affect cell physiology. The purpose of this study was to identify homologs of Escherichia coli FabG, an essential reductase involved in fatty acid biosynthesis, that display a higher preference for NADH than for NADPH as a cofactor. Four potential NADH-dependent FabG variants were identified through bioinformatic...

Fast and flexible analysis of direct dark matter search data with machine learning

Tue, 25 Apr 2023 00:00:00 +0000

We present the results from combining machine learning with the profile likelihood fit procedure, using data from the Large Underground Xenon (LUX) dark matter experiment. This approach demonstrates reduction in computation time by a factor of 30 when compared with the previous approach, without loss of performance on real data. We establish its flexibility to capture nonlinear correlations between variables (such as smearing in light and charge signals due to position variation) by achieving equal performance using pulse areas with and without position-corrections applied. Its efficiency and scalability furthermore enables searching for dark matter using additional variables without significant computational burden. We demonstrate this by including a light signal pulse shape variable alongside more traditional inputs, such as light and charge signal strengths. This technique can be exploited by future dark matter experiments to make use of additional information, reduce computational...

Phonon-Induced Localization of Excitons in Molecular Crystals from First Principles

Fri, 21 Apr 2023 00:00:00 +0000

The spatial extent of excitons in molecular systems underpins their photophysics and utility for optoelectronic applications. Phonons are reported to lead to both exciton localization and delocalization. However, a microscopic understanding of phonon-induced (de)localization is lacking, in particular, how localized states form, the role of specific vibrations, and the relative importance of quantum and thermal nuclear fluctuations. Here, we present a first-principles study of these phenomena in solid pentacene, a prototypical molecular crystal, capturing the formation of bound excitons, exciton-phonon coupling to all orders, and phonon anharmonicity, using density functional theory, the ab initio GW-Bethe-Salpeter equation approach, finite-difference, and path integral techniques. We find that for pentacene zero-point nuclear motion causes uniformly strong localization, with thermal motion providing additional localization only for Wannier-Mott-like excitons. Anharmonic effects...

Far-infrared surface emissivity and climate

Fri, 21 Apr 2023 00:00:00 +0000

Presently, there are no global measurement constraints on the surface emissivity at wavelengths longer than 15 μm, even though this surface property in this far-IR region has a direct impact on the outgoing longwave radiation (OLR) and infrared cooling rates where the column precipitable water vapor (PWV) is less than 1 mm. Such dry conditions are common for high-altitude and high-latitude locations, with the potential for modeled climate to be impacted by uncertain surface characteristics. This paper explores the sensitivity of instantaneous OLR and cooling rates to changes in far-IR surface emissivity and how this unconstrained property impacts climate model projections. At high latitudes and altitudes, a 0.05 change in emissivity due to mineralogy and snow grain size can cause a 1.8-2.0 W m(-2) difference in the instantaneous clear-sky OLR. A variety of radiative transfer techniques have been used to model the far-IR spectral emissivities of surface types defined by the International...

Diffuse X-Ray Scattering to Model Protein Motions

Wed, 5 Apr 2023 00:00:00 +0000

Problems in biology increasingly need models of protein flexibility to understand and control protein function. At the same time, as they improve, crystallographic methods are marching closer to the limits of what can be learned from Bragg data in isolation. It is thus inevitable that mainstream protein crystallography will turn to diffuse scattering to model protein motions and improve crystallographic models. The time is ripe to make it happen.

Scalable single-mode surface-emitting laser via open-Dirac singularities

Tue, 7 Mar 2023 00:00:00 +0000

Single-aperture cavities are a key component of lasers that are instrumental for the amplification and emission of a single light mode. However, the appearance of high-order transverse modes as the size of the cavities increases has frustrated efforts to scale-up cavities while preserving single-mode operation since the invention of the laser six decades ago1–8. A suitable physical mechanism that allows single-mode lasing irrespective of the cavity size—a ‘scale invariant’ cavity or laser—has not been identified yet. Here we propose and demonstrate experimentally that open-Dirac electromagnetic cavities with linear dispersion—which in our devices are realized by a truncated photonic crystal arranged in a hexagonal pattern—exhibit unconventional scaling of losses in reciprocal space, leading to single-mode lasing that is maintained as the cavity is scaled up in size. The physical origin of this phenomenon lies in the convergence of the complex part of the free spectral range in...

Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction

Mon, 27 Feb 2023 00:00:00 +0000

BackgroundPlant cell walls are interwoven structures recalcitrant to degradation. Native and adapted microbiomes can be particularly effective at plant cell wall deconstruction. Although most understanding of biological cell wall deconstruction has been obtained from isolates, cultivated microbiomes that break down cell walls have emerged as new sources for biotechnologically relevant microbes and enzymes. These microbiomes provide a unique resource to identify key interacting functional microbial groups and to guide the design of specialized synthetic microbial communities.ResultsTo establish a system assessing comparative microbiome performance, parallel microbiomes were cultivated on sorghum (Sorghum bicolor L. Moench) from compost inocula. Biomass loss and biochemical assays indicated that these microbiomes diverged in their ability to deconstruct biomass. Network reconstructions from gene expression dynamics identified key groups and potential interactions within the adapted...

Rapid quantification of alcohol production in microorganisms based on nanostructure-initiator mass spectrometry (NIMS)

Mon, 27 Feb 2023 00:00:00 +0000

We described a mass spectrometry-based assay to rapidly quantify the production of primary alcohols directly from cell cultures. This novel assay used the combination of TEMPO-based oxidation chemistry and oxime ligation, followed by product analysis based on Nanostructure-Initiator Mass Spectrometry. This assay enables quantitative monitor both C5 to C18 alcohols as well as glucose and gluconate in the growth medium to support strain characterization and optimization. We find that this assay yields similar results to gas chromatography for isoprenol production but required much less acquisition time per sample. We applied this assay to gain new insights into P. Putida's utilization of alcohols and find that this strain largely could not grow on heptanol and octanol.

Addressing solar photochemistry durability with an amorphous nickel antimonate photoanode

Tue, 21 Feb 2023 00:00:00 +0000

Renewable generation of fuels using solar energy is a promising technology whose deployment hinges on the discovery of materials with a combination of durability and solar-to-chemical conversion efficiency that has yet to be demonstrated. Stable operation of photoanodes has been demonstrated with wide-gap semiconductors, as well as protected visible gap semiconductors. Visible photoresponse from electrochemically stable materials is quite rare. In this paper, we report the high-throughput discovery of an amorphous Ni-Sb (1:1) oxide photoanode that meets the requirements of operational stability, visible photoresponse, and appreciable photovoltage. X-ray absorption characterization of Ni and Sb establishes a structural connection to rutile NiSb2O6, guiding electronic structure characterization via X-ray photoelectron experiments and density functional theory. This amorphous photoanode opens avenues for photoelectrode development due to the lack of crystal anisotropy combined with...

The Influence of Ocean Coupling on Simulated and Projected Tropical Cyclone Precipitation in the HighResMIP–PRIMAVERA Simulations

Thu, 22 Dec 2022 00:00:00 +0000

Abstract This study aims to quantify the impacts of atmosphere–ocean coupling on simulated and projected tropical cyclone (TC) precipitation globally. We used global climate model (GCM) simulations over 1950–2050 from the High Resolution Model Intercomparison Project (HighResMIP) and compared its fully coupled atmosphere–ocean GCMs (AOGCMs) with atmosphere‐only GCMs (AGCMs). We find that ocean coupling generally leads to decreased TC precipitation over ocean and land. Large‐scale sea surface temperature (SST) biases are critical drivers of the precipitation difference, with secondary contributions from local TC–ocean feedbacks via SST cold wakes. The two driving factors, attributed to ocean coupling in the AOGCMs, influence TC precipitation in association with decreased TC intensity and specific humidity. The AOGCMs and AGCMs consistently project TC precipitation increases in 2015–2050 relative to 1950–2014 over ocean for all basins, and for landfalling TCs in the North Atlantic...

Potential bill impacts of dynamic electricity pricing on California utility customers

Mon, 19 Dec 2022 00:00:00 +0000

The rapid growth of renewable generation is creating challenges for the California grid in the form of the “duck curve,” with increasingly steep ramping required for conventional generation resources in the morning and evening, and growing curtailment of solar resources in midday periods. Time-varying electricity tariffs have received considerable attention as a tool to address these challenges, with a renewed recent focus on the potential for dynamic tariffs that vary to reflect conditions on the grid in near-real time. Consideration of dynamic tariffs may raise concerns about the financial impact on utility customers, especially for those who have limited flexibility to modify their electricity consumption in response. Specific areas of concern include electricity bills, bill volatility, and equity implications related to cost shifting among customer groups. In this paper we leverage smart meter data for more than 400,000 California utility customers, spanning residential, commercial,...

Rats use memory confidence to guide decisions

Fri, 18 Nov 2022 00:00:00 +0000

Memory enables access to past experiences to guide future behavior. Humans can determine which memories to trust (high confidence) and which to doubt (low confidence). How memory retrieval, memory confidence, and memory-guided decisions are related, however, is not understood. In particular, how confidence in memories is used in decision making is unknown. We developed a spatial memory task in which rats were incentivized to gamble their time: betting more following a correct choice yielded greater reward. Rat behavior reflected memory confidence, with higher temporal bets following correct choices. We applied machine learning to identify a memory decision variable and built a generative model of memories evolving over time that accurately predicted both choices and confidence reports. Our results reveal in rats an ability thought to exist exclusively in primates and introduce a unified model of memory dynamics, retrieval, choice, and confidence.

Phylogenomically Guided Identification of Industrially Relevant GH1 β‑Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry

Tue, 15 Nov 2022 00:00:00 +0000

Harnessing the biotechnological potential of the large number of proteins available in sequence databases requires scalable methods for functional characterization. Here we propose a workflow to address this challenge by combining phylogenomic guided DNA synthesis with high-throughput mass spectrometry and apply it to the systematic characterization of GH1 β-glucosidases, a family of enzymes necessary for biomass hydrolysis, an important step in the conversion of lignocellulosic feedstocks to fuels and chemicals. We synthesized and expressed 175 GH1s, selected from over 2000 candidate sequences to cover maximum sequence diversity. These enzymes were functionally characterized over a range of temperatures and pHs using nanostructure-initiator mass spectrometry (NIMS), generating over 10,000 data points. When combined with HPLC-based sugar profiling, we observed GH1 enzymes active over a broad temperature range and toward many different β-linked disaccharides. For some GH1s we also...

Asymmetric emergence of low-to-no snow in the midlatitudes of the American Cordillera

Tue, 15 Nov 2022 00:00:00 +0000

Societies and ecosystems within and downstream of mountains rely on seasonal snowmelt to satisfy their water demands. Anthropogenic climate change has reduced mountain snowpacks worldwide, altering snowmelt magnitude and timing. Here the global warming level leading to widespread and persistent mountain snowpack decline, termed low-to-no snow, is estimated for the world’s most latitudinally contiguous mountain range, the American Cordillera. We show that a combination of dynamical, thermodynamical and hypsometric factors results in an asymmetric emergence of low-to-no-snow conditions within the midlatitudes of the American Cordillera. Low-to-no-snow emergence occurs approximately 20 years earlier in the southern hemisphere, at a third of the local warming level, and coincides with runoff efficiency declines (8% average) in both dry and wet years. The prevention of a low-to-no-snow future in either hemisphere requires the level of global warming to be held to, at most, +2.5 °C.

Structural plasticity enables evolution and innovation of RuBisCO assemblies

Mon, 24 Oct 2022 00:00:00 +0000

Oligomerization is a core structural feature that defines the form and function of many proteins. Most proteins form molecular complexes; however, there remains a dearth of diversity-driven structural studies investigating the evolutionary trajectory of these assemblies. Ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) is one such enzyme that adopts multiple assemblies, although the origins and distribution of its different oligomeric states remain cryptic. Here, we retrace the evolution of ancestral and extant form II RuBisCOs, revealing a complex and diverse history of oligomerization. We structurally characterize a newly discovered tetrameric RuBisCO, elucidating how solvent-exposed surfaces can readily adopt new interactions to interconvert or give rise to new oligomeric states. We further use these principles to engineer and demonstrate how changes in oligomerization can be mediated by relatively few mutations. Our findings yield insight into how structural plasticity...

Defining and applying an electricity demand flexibility benchmarking metrics framework for grid-interactive efficient commercial buildings

Tue, 4 Oct 2022 00:00:00 +0000

Building demand flexibility (DF) research has recently gained attention. To unlock building DF as a predictable grid resource, we must establish a quantitative understanding of the resource size, performance variability, and predictability based on large empirical datasets. Researchers have proposed various sets of theoretical metrics to measure this performance. Some metrics have been applied to simulation results, but most fall short of exploring the complexities in real building applications. There are practical metrics used in individual demand response field studies but they alone cannot fulfil the job of DF benchmarking across a diverse group of buildings. The electrical grid's geographically diverse and changing nature presents challenges to comparing building DF performance measured under different conditions (i.e., benchmarking DF). To address this challenge, a novel DF benchmarking framework focused on load shedding and shifting is presented; the foundation is a set...

Iron L2,3-Edge X‑ray Absorption and X-ray Magnetic Circular Dichroism Studies of Molecular Iron Complexes with Relevance to the FeMoco and FeVco Active Sites of Nitrogenase

Tue, 27 Sep 2022 00:00:00 +0000

Herein, a systematic study of a series of molecular iron model complexes has been carried out using Fe L_2,3-edge X-ray absorption (XAS) and X-ray magnetic circular dichroism (XMCD) spectroscopies. This series spans iron complexes of increasing complexity, starting from ferric and ferrous tetrachlorides ([FeCl₄]^-/2-), to ferric and ferrous tetrathiolates ([Fe(SR)₄]^-/2-), to diferric and mixed-valent iron-sulfur complexes [Fe₂S₂R₄]^2-/3-. This test set of compounds is used to evaluate the sensitivity of both Fe L_2,3-edge XAS and XMCD spectroscopy to oxidation state and ligation changes. It is demonstrated that the energy shift and intensity of the L_2,3-edge XAS spectra depends on both the oxidation state and covalency of the system; however, the quantitative information that can be extracted from these data is limited. On the other hand, analysis of the Fe XMCD...

Experimental and theoretical correlations between vanadium K-edge X-ray absorption and Kβ emission spectra

Tue, 27 Sep 2022 00:00:00 +0000

A series of vanadium compounds was studied by K-edge X-ray absorption (XAS) and K[Formula: see text] X-ray emission spectroscopies (XES). Qualitative trends within the datasets, as well as comparisons between the XAS and XES data, illustrate the information content of both methods. The complementary nature of the chemical insight highlights the success of this dual-technique approach in characterizing both the structural and electronic properties of vanadium sites. In particular, and in contrast to XAS or extended X-ray absorption fine structure (EXAFS), we demonstrate that valence-to-core XES is capable of differentiating between ligating atoms with the same identity but different bonding character. Finally, density functional theory (DFT) and time-dependent DFT calculations enable a more detailed, quantitative interpretation of the data. We also establish correction factors for the computational protocols through calibration to experiment. These hard X-ray methods can probe...