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At least 271 records · Page 15

Technological developments and accelerator improvements for the FRIB beam power ramp-up

The Facility for Rare Isotope Beams (FRIB) began operation with 1 kW beam power for scientific users in May 2022 upon completion of 8 years of project construction. The ramp-up to the ultimate beam power of 400 kW, planned over a 6-year period, will enable the facility to reach its full potential for scientific discovery in isotope science and applications. In December 2023, a record-high beam power of 10.4 kW uranium was delivered to the target. Technological developments and accelerator improvements are being made over the entire facility and are key to completion of the power ramp-up. Major technological developments entail the phased deployment of high-power beam-intercepting systems, including the charge strippers, the charge selection systems, the production target, and the beam dump, along with support systems, including non-conventional utilities (NCU) and remote handling facilities. Major accelerator improvements include renovations to aging legacy systems associated with experimental beam lines and system automation for improved operational efficiency and better machine availability. Experience must be gained to safely handle the increased radiological impacts associated with high beam power; extensive machine studies and advanced beam tuning procedures are needed to minimize uncontrolled beam losses for the desired operating conditions. This paper discusses the technological developments and accelerator improvements with emphasis on major R&D efforts.

43 PARTICLE ACCELERATORS↗

Phage-based delivery of CRISPR-associated transposases for targeted bacterial editing

Phage λ, a well-characterized temperate phage, has been recently leveraged for bacterial genome editing by selectively delivering base editors into targeted bacterial species. We extend this concept by engineering phage λ to deliver CRISPR-guided transposases, accomplishing large insertions and targeted gene disruptions. To achieve this, we engineered phage λ using homologous recombination paired with Cas13a-based counterselection for precise phage modifications. Initially, we established the utility of Cas13a in phage λ by conducting minimal recoding edits, deletions, and insertions. Subsequently, we scaled up the engineering to embed the comprehensive DNA-editing CRISPR-Cas transposase (DART) system within the phage genome, creating λ-DART phages. These modified λ-DART phages were then employed to infectEscherichia coli, generating CRISPR RNA-guided transposition events in the host genome. Applying our engineered λ-DART phages to monocultures and a mixed bacterial community comprising three genera led to efficient, precise, and specific gene knockouts and insertions in the targetedE. colicells, achieving editing efficiencies surpassing 50% of the population. This research enhances phage-mediated genome editing by enabling efficient in situ gene integrations in bacteria, offering an avenue for further application in microbial community contexts. This scalable method enables flexible microbial genome editing in situ to manipulate the function and composition of diverse ecosystems.

Science & Technology - Other Topics↗

Bench-Scale Testing of a High Efficiency, Ultra-Compact Process for Pre-Combustion CO 2 Capture (Final Report)

The overarching objective of this bench-scale study is to field-validate the technical feasibility of a membrane- and adsorption-enhanced water gas shift (WGS) reaction process that employs a carbon molecular sieve (CMS) membrane reactor (MR) followed by an adsorption reactor (AR) for pre-combustion CO 2 capture while demonstrating progress towards achievement of the overall performance goals of CO 2 capture with 95% CO 2 purity at a cost of electricity (COE) of 30% less than the baseline capture approaches. The main goal of this bench-scale project is to advance the proposed MR-AR transformative CO 2 capture technology to a sufficient maturity level so that our present industrial partners (M&PT and Worley) can potentially adapt the technology for further small pilot-scale testing. The project began at TRL 4, as the system prototype had already been validated in the laboratory on simulated syngas (as part of project DE-FE0026423). The project ended at TRL 5, via scaling-up of the prototype system and testing it on actual syngas at a host site (CAER at the University of Kentucky (UKy)). The project was carried-out in two different phases: In Phase I (during BP1 of the project), the team designed, constructed, and assembled the bench-scale experimental MR-AR system, prepared the membranes, adsorbents, and catalysts, tested the bench-scale unit with simulated syngas to validate functionality, and prepared a preliminary TEA of the technology. In Phase II (during BP2 of the project), the team installed the unit at the test site at the UKy site and completed all utility connections and hookups, field-tested the novel MR-AR process in the bench-scale system using real syngas, collected and analyzed experimental data, and completed a detailed TEA of the technology. A key aim of the project was to identify and address the technical and process risks and to generate information to advance the technology to the next stage of development. All project milestones and success criteria were met. Specifically, the team: (i) designed, constructed and assembled a bench scale system that handled 1 – 5 scfm syngas and tested its functionality with simulated syngas; (ii) prepared high performance CMS membrane tubes (ID: 3.5 mm, OD: 5.7 mm, 30” long) that meet the target H 2 permeance ( > 1 m 3 /(m 2 .hr.bar) or (> 370.3 GPU)) and a target H 2 /CO selectivity >80 at the relevant temperature (up to 300oC) and pressure conditions (up to 25 bar) with a <10% decline in performance over each 250 hr. testing period (iii) procured commercial sour-shift catalyst in sufficient quantity and prepared up to 10 kg of pelletized adsorbent for use at relevant conditions (250oC 2.5wt.% and target sorbent attrition rate < 0.2; (iv) installed the bench-scale unit at the test site (UKy) and tested the MR-AR technology using real syngas for over 250 hr. for both static and flow experiments; (v) updated the TEA analysis based on bench-scale data and met CO 2 capture goals of 95% CO 2 purity at a cost of electricity 30% less than baseline capture approaches. The CMS membranes, HTC adsorbents and catalysts employed all exhibited very robust and stable performance during the long-term run (over a >250 hr live syngas run). Furthermore, the proposed MR-AR IGCC system achieved a LCOE with a N 2 sale price of $\$$ 30/ton, with N 2 compression (no N 2 compression) of 101.2 $\$$/MWh (95.3 $\$$/MWh), which represents a 29.8% (33.9%) LCOE reduction in the baseline IGCC with carbon capture of 144.2 $\$$/MWh. The proposed MR-AR IGCC delivers a CO 2 capture cost of 44.8 $\$$/tonne (39.9 $\$$/tonne) vs 98.1 $\$$/tonne of the baseline capture case and a net power production of 586 MWe (623 MWe) vs 556 MWe of the baseline capture case.

01 COAL, LIGNITE, AND PEAT↗

Structure and Stability of the Ionic Liquid Clusters [EMIM]n[BF4]n+1- (n = 1 – 9): Implications for Electrochemical Separations

Precise functionalization of electrodes with size-selected ionic liquid (IL) clusters may improve the application of ILs in electrochemical separations. Herein, we report our combined experimental and theoretical investigation of the IL clusters [EMIM]????[BF4]????+1- (n = 1 – 9) and demonstrate their selectivity and efficiency towards targeted adsorption of molecules from solution. The structures and energies of the IL clusters, predicted with global optimization, agree with and help interpret the ion abundances and stabilities measured by high mass resolution electrospray ionization mass spectrometry and collision induced dissociation experiments. The [EMIM][BF4]2- cluster, which was identified as the most stable IL cluster, was selectively soft landed onto a working electrode. Electrochemical impedance spectroscopy revealed a lower charge transfer resistance on the soft-landed electrode containing [EMIM] [BF_4 ]_2^- compared to an electrode prepared by drop casting of IL solution, which contains the full range of IL clusters. Our findings indicate that specific IL clusters may be used to increase the efficiency of electrochemical separations by lowering the overpotentials involved.

Zhang, Jun↗

Treatment of Prostate Cancer with CD46-targeted 225 Ac Alpha Particle Radioimmunotherapy

Radiopharmaceutical therapy is changing the standard of care in prostate cancer and other malignancies. We previously reported high CD46 expression in prostate cancer and developed an antibody–drug conjugate and immunoPET agent based on the YS5 antibody, which targets a tumor-selective CD46 epitope. Here, we present the preparation, preclinical efficacy, and toxicity evaluation of [ 225 Ac]DOTA-YS5, a radioimmunotherapy agent based on the YS5 antibody. [ 225 Ac]DOTA-YS5 was developed, and its therapeutic efficiency was tested on cell-derived (22Rv1, DU145), and patient-derived (LTL-545, LTL484) prostate cancer xenograft models. Biodistribution studies were carried out on 22Rv1 tumor xenograft models to confirm the targeting efficacy. Toxicity analysis of the [ 225 Ac]DOTA-YS5 was carried out on nu/nu mice to study short-term (acute) and long-term (chronic) toxicity. Biodistribution study shows that [ 225 Ac]DOTA-YS5 agent delivers high levels of radiation to the tumor tissue (11.64% ± 1.37%ID/g, 28.58% ± 10.88%ID/g, 29.35% ± 7.76%ID/g, and 31.78% ± 5.89%ID/g at 24, 96, 168, and 408 hours, respectively), compared with the healthy organs. [ 225 Ac]DOTA-YS5 suppressed tumor size and prolonged survival in cell line–derived and patient-derived xenograft models. Toxicity analysis revealed that the 0.5 μCi activity levels showed toxicity to the kidneys, likely due to redistribution of daughter isotope 213 Bi. [ 225 Ac]DOTA-YS5 suppressed the growth of cell-derived and patient-derived xenografts, including prostate-specific membrane antigen–positive and prostate-specific membrane antigen–deficient models. Overall, this preclinical study confirms that [ 225 Ac]DOTA-YS5 is a highly effective treatment and suggests feasibility for clinical translation of CD46-targeted radioligand therapy in prostate cancer.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Human TRPV1 structure and inhibition by the analgesic SB-366791

Pain therapy has remained conceptually stagnant since the opioid crisis, which highlighted the dangers of treating pain with opioids. An alternative addiction-free strategy to conventional painkiller-based treatment is targeting receptors at the origin of the pain pathway, such as transient receptor potential (TRP) ion channels. Thus, a founding member of the vanilloid subfamily of TRP channels, TRPV1, represents one of the most sought-after pain therapy targets. The need for selective TRPV1 inhibitors extends beyond pain treatment, to other diseases associated with this channel, including psychiatric disorders. Here we report the cryo-electron microscopy structures of human TRPV1 in the apo state and in complex with the TRPV1-specific nanomolar-affinity analgesic antagonist SB-366791. SB-366791 binds to the vanilloid site and acts as an allosteric hTRPV1 inhibitor. SB-366791 binding site is supported by mutagenesis combined with electrophysiological recordings and can be further explored to design new drugs targeting TRPV1 in disease conditions.

59 BASIC BIOLOGICAL SCIENCES↗

Photonics in Multimaterial Lateral Heterostructures Combining Group IV Chalcogenide van der Waals Semiconductors

Abstract Lateral heterostructures combining two multilayer group IV chalcogenide van der Waals semiconductors have attracted interest for optoelectronics, twistronics, and valleytronics, owing to their structural anisotropy, bulk‐like electronic properties, enhanced optical thickness, and vertical interfaces enabling in‐plane charge manipulation/separation, perpendicular to the trajectory of incident light. Group IV monochalcogenides support propagating photonic waveguide modes, but their interference gives rise to complex light emission patterns throughout the visible/near‐infrared range both in uniform flakes and single‐interface lateral heterostructures. Here, this work demonstrates the judicious integration of pure and alloyed monochalcogenide crystals into multimaterial heterostructures with unique photonic properties, notably the ability to select photonic modes with targeted discrete energies through geometric factors rather than band engineering. SnS‐GeS 1− x Se x ‐GeSe‐GeS 1− x Se x heterostructures with a GeS 1− x Se x active layer sandwiched laterally between GeSe and SnS, semiconductors with similar optical constants but smaller bandgaps, were designed and realized via sequential vapor transport synthesis. Raman spectroscopy, electron microscopy/diffraction, and energy‐dispersive X‐ray spectroscopy confirm a high crystal quality of the laterally stitched components with sharp interfaces. Nanometer‐scale cathodoluminescence spectroscopy provides evidence for a facile transfer of electron–hole pairs across the lateral interfaces and demonstrates the selection of photon emission at discrete energies in the laterally embedded active (GeS 1− x Se x ) part of the heterostructure.

2D layered crystals↗

Performance analysis and comparison of data-driven models for predicting indoor temperature in multi-zone commercial buildings

Building thermal models, which characterize the properties of a building’s envelope and thermal mass, are essential for accurate indoor temperature and cooling/heating demand prediction. Because of their flexibility and ease of use, data-driven models are increasingly used. Here, this study compared and analyzed the performance of gray-box (resistance-capacitance) and black-box (recurrent neural network) models for predicting indoor air temperature in a real multi-zone commercial building. The developed resistance-capacitance model served as a benchmark model for which full sets of temporal data and building information were used as inputs. The recurrent neural network models were trained and tested assuming various available types and amounts of temporal data and known building physical information to investigate the effects of data and information availability. Feature importance analysis was conducted to select the key variables for different prediction targets under different scenarios. This research provides guidance in selecting an appropriate building thermal response modeling method based on the measured data availability, building physical information, and application.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Host cell and viral protease targets of human SERPINs identified by in silico docking

Serine protease inhibitors (SERPINs) are involved in various physiological processes and diseases, such as inflammation, cancer metastasis, and neurodegeneration. Their role in viral infections is poorly understood, as their expression patterns during infection and the range of proteases they target have yet to be fully characterized. Here, we show widespread expression of human SERPINs in response to respiratory virus infections, both in bronchioalveolar lavages from COVID-19 patients and in polarized human airway epithelial cultures. Using in silico docking of 10 SERPINs to 48 host proteases, we confirm known targets and predict new interactions. Protease activity assays validated selected interactions, confirming the newly predicted host targets for PAI-1 (SERPINE1) and PAI-2 (SERPINB2). PAI-1 inhibits cathepsin L, essential for SARS-CoV-2 maturation, and suppresses multi-cycle replication of both ancestral SARS-CoV-2 WA-1 and its variant Omicron BA.1. In addition, we identify PAI-2 as an antiviral SERPIN that reduces infectivity of human adenovirus 5 by directly inhibiting the adenoviral protease. Our study leverages in silico docking using full-length 3D protein structures to uncover new SERPIN targets, offering a range of candidate targets for therapeutic interventions.

59 BASIC BIOLOGICAL SCIENCES↗

Measuring Vibronic Coupling and Ultrafast Charge Delocalization on Nanocrystal Surfaces Using Ligand-Specific Vibrational Probes

The primary goal of this proposal was to measure and quantify how vibronic ligand-exciton interactions at the inorganic-organic interface of semiconductor nanocrystals (NCs) govern femtosecond non-radiative relaxation and charge delocalization mechanisms as a function of nanocrystal and ligand structures – including NC size, shape, and ligand identity. Molecular-scale chemical and physical properties and interactions of surface ligands dictate nanocrystal exciton dynamics on the femto-to-microsecond timescales. Improvements in synthesis, experimental, and theoretical characterizations have enhanced our understanding of NC photophysics. However, quantitative descriptions of complex ligand-exciton interactions at the NC surface have remained elusive, which limits elucidation of relaxation mechanisms that determine overall carrier transfer dynamics at the exciton-ligand interface. Thus, the central motivation for this proposal was to fill a significant knowledge gap for judicious selection of ligand-functionalized nanocrystals for targeted isolation and capture of charge carriers to drive selective organic photocatalytic transformations in NC photocatalysts and NC-assembled photonic materials. Our unique two-pronged experimental approach combining nanocrystal synthesis and ligand-specific nonlinear spectroscopy has resulted in (i) four peer-reviewed publications; (ii) 12+ invited and contributed posters and talks at national and international scientific meetings and seminars, (iii) two completed PhD theses, (iv) training of two postdoctoral researchers, three PhD students, and two undergraduate students, and (v) two manuscripts under preparation.

36 MATERIALS SCIENCE↗

Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP15

Abstract Estimating the accuracy of quaternary structural models of protein complexes and assemblies (EMA) is important for predicting quaternary structures and applying them to studying protein function and interaction. The pairwise similarity between structural models is proven useful for estimating the quality of protein tertiary structural models, but it has been rarely applied to predicting the quality of quaternary structural models. Moreover, the pairwise similarity approach often fails when many structural models are of low quality and similar to each other. To address the gap, we developed a hybrid method (MULTICOM_qa) combining a pairwise similarity score (PSS) and an interface contact probability score (ICPS) based on the deep learning inter‐chain contact prediction for estimating protein complex model accuracy. It blindly participated in the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) in 2022 and performed very well in estimating the global structure accuracy of assembly models. The average per‐target correlation coefficient between the model quality scores predicted by MULTICOM_qa and the true quality scores of the models of CASP15 assembly targets is 0.66. The average per‐target ranking loss in using the predicted quality scores to rank the models is 0.14. It was able to select good models for most targets. Moreover, several key factors (i.e., target difficulty, model sampling difficulty, skewness of model quality, and similarity between good/bad models) for EMA are identified and analyzed. The results demonstrate that combining the multi‐model method (PSS) with the complementary single‐model method (ICPS) is a promising approach to EMA.

59 BASIC BIOLOGICAL SCIENCES↗

Deep learning uncertainty quantification for clinical text classification

Machine learning algorithms are expected to work side-by-side with humans in decision-making pipelines. Thus, the ability of classifiers to make reliable decisions is of paramount importance. Deep neural networks (DNNs) represent the state-of-the-art models to address real-world classification. Although the strength of activation in DNNs is often correlated with the network’s confidence, in-depth analyses are needed to establish whether they are well calibrated. In this paper, we demonstrate the use of DNN-based classification tools to benefit cancer registries by automating information extraction of disease at diagnosis and at surgery from electronic text pathology reports from the US National Cancer Institute (NCI) Surveillance, Epidemiology, and End Results (SEER) population-based cancer registries. In particular, we introduce multiple methods for selective classification to achieve a target level of accuracy on multiple classification tasks while minimizing the rejection amount—that is, the number of electronic pathology reports for which the model’s predictions are unreliable. We evaluate the proposed methods by comparing our approach with the current in-house deep learning-based abstaining classifier. Overall, all the proposed selective classification methods effectively allow for achieving the targeted level of accuracy or higher in a trade-off analysis aimed to minimize the rejection rate. On in-distribution validation and holdout test data, with all the proposed methods, we achieve on all tasks the required target level of accuracy with a lower rejection rate than the deep abstaining classifier (DAC). Interpreting the results for the out-of-distribution test data is more complex; nevertheless, in this case as well, the rejection rate from the best among the proposed methods achieving 97% accuracy or higher is lower than the rejection rate based on the DAC. We show that although both approaches can flag those samples that should be manually reviewed and labeled by human annotators, the newly proposed methods retain a larger fraction and do so without retraining—thus offering a reduced computational cost compared with the in-house deep learning-based abstaining classifier.

59 BASIC BIOLOGICAL SCIENCES↗

Domesticating a food spoilage yeast into an organic acid–tolerant metabolic engineering host: Lactic acid production by engineered Zygosaccharomyces bailii

Lactic acid represents an important class of commodity chemicals, which can be produced by microbial cell factories. However, due to the toxicity of lactic acid at lower pH, microbial production requires the usage of neutralizing agents to maintain neutral pH. Zygosaccharomyces bailii, a food spoilage yeast, can grow under the presence of organic acids used as food preservatives. This unique trait of the yeast might be useful for producing lactic acid. With the goal of domesticating the organic acid!tolerant yeast as a metabolic engineering host, seven Z. bailii strains were screened in a minimal medium with 10 g/L of acetic, or 60 g/L of lactic acid at pH 3. The Z. bailii NRRL Y7239 strain was selected as the most robust strain to be en- gineered for lactic acid production. By applying a PAN!ARS!based CRISPR!Cas9 system consisting of a transfer RNA promoter and NAT selection, we demonstrated the targeted deletion of ADE2 and site!specific integration of Rhizopus oryzae ldhA coding for lactate dehydrogenase into the PDC1 locus. The resulting pdc1::ldhA strain produced 35 g/L of lactic acid without ethanol production. Here, this study de- monstrates the feasibility of the CRISPR!Cas9 system in Z. bailii, which can be applied for a fundamental study of the species.

59 BASIC BIOLOGICAL SCIENCES↗

Development of a VRC01-class germline targeting immunogen derived from anti-idiotypic antibodies

An effective HIV-1 vaccine will likely need to elicit broadly neutralizing antibodies (bNAbs). Broad and potent VRC01-class bNAbs have been isolated from multiple infected individuals, suggesting that they could be reproducibly elicited by vaccination. Several HIV-1 envelope-derived germline-targeting immunogens have been designed to engage naive VRC01-class precursor B cells. However, they also present off-target epitopes that could hinder development of VRC01-class bNAbs. We characterize a panel of anti-idiotypic monoclonal antibodies (ai-mAbs) raised against inferred-germline (iGL) VRC01-class antibodies. By leveraging binding, structural, and B cell sorting data, we engineered a bispecific molecule derived from two aimAbs; one specific for VRC01-class heavy chains and one specific for VRC01-class light chains. The bispecific molecule preferentially activates iGL-VRC01 B cells in vitro and induces specific antibody responses in a murine adoptive transfer model with a diverse polyclonal B cell repertoire. This molecule represents an alternative non-envelope-derived germline-targeting immunogen that can selectively activate VRC01-class precursors in vivo.

59 BASIC BIOLOGICAL SCIENCES↗

MADHAT: Model-Agnostic Dark Halo Analysis Tool

We present the Model-Agnostic Dark Halo Analysis Tool (MADHAT), a numerical tool which implements a Fermi-LAT data-driven, model-independent analysis of gamma-ray emission from dwarf satellite galaxies and dwarf galaxy candidates due to dark matter annihilation, dark matter decay, or other nonstandard or unknown astrophysics. This tool efficiently provides statistical upper bounds on the number of observed photons in excess of the number expected, based on empirical determinations of foregrounds and backgrounds, using a stacked analysis of any selected set of dwarf targets. It also calculates the resulting bounds on the properties of dark matter under any assumptions the user makes regarding dark sector particle physics or astrophysics. As an application, we determine new bounds on Sommerfeld-enhanced dark matter annihilation in a set of eight dwarfs. MADHAT v1.0 includes 58 dwarfs and dwarf candidate targets, and we discuss future planned developments. MADHAT is available and will be maintained at https://github.com/MADHATdm.

79 ASTRONOMY AND ASTROPHYSICS↗

Motif-centric phosphoproteomics to target kinase-mediated signaling pathways

Identifying cellular phosphorylation pathways based on kinase-substrate relationships is a critical step to understanding the regulation of physiological functions in cells. Mass spectrometry-based phosphoproteomics workflows have made it possible to comprehensively collect information on individual phosphorylation sites in a variety of samples. However, there is still no generic approach to uncover phosphorylation networks based on kinase-substrate relationships in rare cell populations. Here, we describe a motif-centric phosphoproteomics approach combined with multiplexed isobaric labeling, in which in vitro kinase reactions are used to generate targeted phosphopeptides, which are spiked into one of the isobaric channels to increase detectability. Proof-of-concept experiments demonstrate selective and comprehensive quantification of targeted phosphopeptides by using multiple kinases for motif-centric channels. More than 7,000 tyrosine phosphorylation sites were quantified from several tens of micrograms of starting materials. This approach enables the quantification of multiple phosphorylation pathways under physiological or pathological regulation in a motif-centric manner.

59 BASIC BIOLOGICAL SCIENCES↗

Understanding Self-Assembly and the Stabilization of Liquid/Liquid Interfaces: The Importance of Ligand Tail Branching and Oil-Phase Solvation

Organophosphorus-based ligands represent a versatile set of solvent extraction reagents whose chemical makeup plays an important role in extraction mechanism. We hypothesize that the branching of the extractant hydrophobic tail and its oil-phase solvation affect the liquid/liquid interfacial structure. Understanding the structure mediated adsorption and interfacial ordering becomes key in designing ligands with enhanced selectivity and efficiency for targeted extractions. We employed vibrational sum frequency generation spectroscopy and interfacial tension measurements to extract thermodynamic adsorption energies, map interfacial ordering, and rationalize disparate behaviors of model di-(2-ethylhexyl) phosphoric acid and dioctyl phosphoric acid ligands at the hexadecane water interface. With increased surface loading, ligands with branched hydrophobic tails formed stable interfaces at much lower concentrations than those observed for ligands with linear alkyl tails. The lack of an oil phase and associated solvation results in markedly different interfacial properties, and thus measurements made at air/liquid surfaces cannot be assumed to correlate with the processes occurring at buried liquid/liquid interfaces. Here, we attribute these differences in the surface mediated self-assembly to key variations in hydrophobic interactions and tail solvation taking place in the oil phase demonstrating that interactions in both the polar and nonpolar phases are essential to understand self-assembly and function.

36 MATERIALS SCIENCE↗