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At least 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440

ABSTRACT There is growing interest in engineering Pseudomonas putida KT2440 as a microbial chassis for the conversion of renewable and waste-based feedstocks, and metabolic engineering of P. putida relies on the understanding of the functional relationships between genes. In this work, independent component analysis (ICA) was applied to a compendium of existing fitness data from randomly barcoded transposon insertion sequencing (RB-TnSeq) of P. putida KT2440 grown in 179 unique experimental conditions. ICA identified 84 independent groups of genes, which we call fModules (“functional modules”), where gene members displayed shared functional influence in a specific cellular process. This machine learning-based approach both successfully recapitulated previously characterized functional relationships and established hitherto unknown associations between genes. Selected gene members from fModules for hydroxycinnamate metabolism and stress resistance, acetyl coenzyme A assimilation, and nitrogen metabolism were validated with engineered mutants of P. putida . Additionally, functional gene clusters from ICA of RB-TnSeq data sets were compared with regulatory gene clusters from prior ICA of RNAseq data sets to draw connections between gene regulation and function. Because ICA profiles the functional role of several distinct gene networks simultaneously, it can reduce the time required to annotate gene function relative to manual curation of RB-TnSeq data sets. IMPORTANCE This study demonstrates a rapid, automated approach for elucidating functional modules within complex genetic networks. While Pseudomonas putida randomly barcoded transposon insertion sequencing data were used as a proof of concept, this approach is applicable to any organism with existing functional genomics data sets and may serve as a useful tool for many valuable applications, such as guiding metabolic engineering efforts in other microbes or understanding functional relationships between virulence-associated genes in pathogenic microbes. Furthermore, this work demonstrates that comparison of data obtained from independent component analysis of transcriptomics and gene fitness datasets can elucidate regulatory-functional relationships between genes, which may have utility in a variety of applications, such as metabolic modeling, strain engineering, or identification of antimicrobial drug targets.

09 BIOMASS FUELS↗
DOE OSTI2024

Local lattice distortions and the structural instabilities in bcc Nb–Ta–Ti–Hf high-entropy alloys: An ab initio computational study

Local lattice distortions (LLD) and structural stability of body-centered cubic (bcc) Nb–Ta–Ti–Hf high-entropy alloys (HEAs) are studied as functions of composition employing ab initio density-functional theory calculations, with specific focus on the role of the relative concentrations of group IV (Ti and Hf) versus group V (Nb and Ta) elements. Calculated results are presented as a function of composition x in Nb x Ta 0.25 Ti (0.75-x)/2 Hf (0.75-x)/2 alloys, for elastic moduli, phonon spectral functions, LLD and structural energy differences for the bcc and competing hexagonal close-packed (hcp) and ω phases. The results highlight the important role of group V elements and LLD in stabilizing the bcc structure. They further reveal how composition x can be tuned to alter both the magnitude of the LLD and structural energy differences. Specifically, the magnitude of the structural energy differences, and elastic and dynamic stability of the bcc phase, are enhanced with increasing x, while the LLD increase in magnitude as this concentration is decreased. The results also show evidence of correlated LLD at lower values of x, reflecting local structural distortions towards the ω phase, but not hcp. The degree of ω-collapse is nevertheless partial i.e., transformation towards this phase is not observed to be complete due to the presence of Ta and Nb. At lower values of x we further find an energy landscape characterized by multiple, nearly degenerate local energy minima for different values of the LLD.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Plants use molecular mechanisms mediated by biomolecular condensates to integrate environmental cues with development

This review highlights recent literature on biomolecular condensates in plant development and discusses challenges for fully dissecting their functional roles. Plant developmental biology has been inundated with descriptive examples of biomolecular condensate formation, but it is only recently that mechanistic understanding has been forthcoming. Here, we discuss recent examples of potential roles biomolecular condensates play at different stages of the plant life cycle. We group these examples based on putative molecular functions, including sequestering interacting components, enhancing dwell time, and interacting with cytoplasmic biophysical properties in response to environmental change. We explore how these mechanisms could modulate plant development in response to environmental inputs and discuss challenges and opportunities for further research into deciphering molecular mechanisms to better understand the diverse roles that biomolecular condensates exert on life.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Edge counts for the auxiliary pair graph within the graphical unitary group approach

Closed-form expressions are presented for the numbers of edges in the auxiliary pair graphs (APGs) associated with non spin-orbit and spin-orbit Shavitt graphs for full configuration interaction expansions. A Shavitt graph is a visual representation of a configuration state function expansion space constructed via the graphical unitary group approach (GUGA). An APG is an organisational aid and a programmatic tool generated from a Shavitt graph. The number of edges in an APG determines bounds on the computational scaling as a function of the total numbers of electrons, orbitals, and spin multiplicities. The edge counts extend a suite of Shavitt graph statistics based on these functional parameters. The derivation and the presentation of the formulas for the edge counts has been assisted by the bra-ket interchange symmetry and the particle-hole interchange symmetry in the GUGA formalism. Furthermore, these symmetry operators produce one-to-one correspondences between various sets of edges, and this yields identities among some edge count formulas. There are 208 possible edge types. Of these, some do not contribute to two-electron operators, some are related by bra-ket interchange symmetry, and some are related by particle-hole interchange symmetry. For the remaining unique edge types, explicit expressions are derived for the numbers of edges.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Building a Collaborative Relationship between Contractor and Oversight at SRPPF

The success of Department of Energy (DOE) projects is dependent on a functional, healthy, and collaborative relationship between the contractor and the federal oversight. A healthy relationship marked by a collaborative mindset between these two groups, can facilitate better operational safety, operational efficiency, and regulatory compliance. This paper will explore aspects of such a relationship, the roles and responsibilities of the contractor and federal oversight, the present and historical relationships in the DOE complex, and best practices considered by the contractor and federal oversight used at the Savannah River Plutonium Processing Facility (SRPPF) at the Savannah River Site (SRS). Due to the current design phase of the SRPPF, the contractor and federal oversight have a unique opportunity to begin establishing a strong relationship early in the project’s life. As a result of this dynamic, the two groups have already demonstrated their ability to successfully respond to ongoing design issues. In general, a strong criticality safety program is beginning to mature for the SRPPF alongside a developing criticality safety federal oversight group. This paper will discuss the various factors that have brought about this collaborative relationship. Lastly, a case study will be incorporated into this paper demonstrating the ability of the SRPPF contractor and federal oversight to overcome challenges relating to the SRPPF project. This case study may guide groups around the DOE Complex to create better, more functional relationships between the two parties. The case study will provide a detailed description of the issue and parties involved, highlight the factors that allowed the group to overcome the challenge via effective collaboration, and the outcome of the event. Increasing collaboration may benefit the complex, as a whole, in order to meet the mission demands of the DOE.

collaboration↗
DOE OSTI2020

Synergistic effect of dual Brønsted acidic deep eutectic solvents for oxidative desulfurization of diesel fuel

Deep eutectic solvents (DESs) are generally used as attractive solvents or extractants rather than catalysts in the field of synthesis and separation. Herein, dual Brønsted acidic DESs were prepared by mixing sulfonated quaternary ammonium and oxalic acid as extractants and catalysts for deep oxidative desulfurization. Compared to the DESs with single acidic group, the dual acidic DESs exhibited much higher catalytic activity likely due to the synergistic effect. The 1 H NMR study indicated that the weak interaction between DES and sulfur compounds led to a low extraction capacity. However, the sulfur removal could reach 97.7% under optimized reaction conditions. Density functional theory (DFT) calculations demonstrated that sulfonic group and carboxylic group are of equal importance to desulfurization performance. Further, the desulfurization efficiency was also strongly affected by the viscosity of DESs. Here, we put forward a new strategy that the reaction time could be sharply shortened to 40 min and 100 min by adding low viscous acetonitrile and polyethylene glycol into DES to form mixing reaction system, respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Molecular Insight into the Effects of Clustering on the Dynamics of Ionomers in Solutions

Ionizable groups tethered to polymers enable their many current and potential applications. However, these functionalities drive the formation of physical networks through clustering of the ionic groups, resulting in constrained dynamics of the macromolecules. Understanding the molecular origin of this hindrance remains a critical fundamental question, whose solution will directly impact the processing of ionizable polymers from molecules to viable materials. Here, in this work, using quasielastic neutron scattering accompanied by molecular dynamics simulations, segmental dynamics of slightly sulfonated polystyrene is studied in solutions as the cohesion of the ionic assemblies is tuned. We find that in cyclohexane the ionic assemblies act as centers of confinement, affecting dynamics both on macroscopic lengths and in the vicinity of the ionic assemblies. Addition of a small amount of ethanol affects the packing of the ionizable groups within the assemblies, which in turn enhances the chain dynamics.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Polymer Zwitterions for Stabilization of CsPbBr 3 Perovskite Nanoparticles and Nanocomposite Films

Abstract Functional polymers with sulfobetaine or phosphorylcholine zwitterions as pendent groups are demonstrated as both ligands and host matrices for CsPbBr 3 perovskite nanoparticles (PNPs). These polymers produce nanocomposite films with excellent NP dispersion, optical transparency, and impressive resistance to NP degradation upon exposure to water. Multidentate interactions of the zwitterion‐containing copolymers with the PNPs induce dispersed or weakly aggregated nanocomposite morphologies, depending on the extent of zwitterionic functionality in the polymer. Incorporating additional functionality into the polymers, such as benzophenone pendent groups, yields lithographically patternable films, while time‐resolved photoluminescence measurements provide insight into the electronic impact of PNPs in zwitterionic polymer matrices.

Kim, Hyunki↗
DOE OSTI2020

Polymer Zwitterions for Stabilization of CsPbBr 3 Perovskite Nanoparticles and Nanocomposite Films

Functional polymers with sulfobetaine or phosphorylcholine zwitterions as pendent groups are demonstrated as both ligands and host matrices for CsPbBr 3 perovskite nanoparticles (PNPs). These polymers produce nanocomposite films with excellent NP dispersion, optical transparency, and impressive resistance to NP degradation upon exposure to water. Multidentate interactions of the zwitterion-containing copolymers with the PNPs induce dispersed or weakly aggregated nanocomposite morphologies, depending on the extent of zwitterionic functionality in the polymer. Incorporating additional functionality into the polymers, such as benzophenone pendent groups, yields lithographically patternable films, while time-resolved photoluminescence measurements provide insight into the electronic impact of PNPs in zwitterionic polymer matrices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Alkylation of monomeric, dimeric, and polymeric lignin models through carbon-hydrogen activation using Ru-catalyzed Murai reaction

In this study, we have assessed directed carbon-hydrogen activation (CHA) for alkylation of monomeric, dimeric, and polymeric lignin models using Murai's catalyst [RuH 2 (CO)(PPh 3 ) 3 ]. Based on related work from our laboratory showing that isolated organosolv lignin bears benzylic directing groups ideal for CHA reactions, this approach could offer new methodology for the valorization of biorefinery lignin. Monomeric and dimeric models bearing a keto group at the benzylic position undergo Ru-catalyzed alkylation in good to excellent yield. Similarly, models bearing a benzylic OH group also undergo alkylation via a tandem oxidation/alkylation process enabled by the Ru catalyst. Polymeric models show low levels of functionalization as a result of the poor solubility of the starting polymer. With unsymmetrical models, functionalization occurs first at the least sterically hindered ortho-site, but a subsequent alkylation, leading to disubstituted products can occur at the more sterically hindered site, leading to hexasubstituted arenes. The reaction shows sensitivity to free phenolic OH groups, which appears to reduce the yield in some reactions, and is also a contributing factor to the low yields observed with polymeric lignin models. Finally, combining CHA methodology with lignin isolation technology able to introduce appropriate directing groups for catalytic functionalization will form the basis for improved conversion of lignin to high value chemical products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Integrated Transcriptomic and Proteomic Analysis Identifies Plasma Biomarkers of Hepatocellular Failure in Alcohol-Associated Hepatitis

Alcohol-associated hepatitis (AH) is a form of liver failure with high short-term mortality. Recent results have shown that HNF4a defective function and systemic inflammation are major disease drivers of AH. Plasma biomarkers of hepatocyte function could be useful for diagnostic and prognostic purposes. Herein an integrative analysis of hepatic RNAseq and liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed to identify plasma protein signatures for mild and severe AH patients. Alcohol-related liver disease cirrhosis (ALD)(AC), non-alcoholic fatty liver disease (NALFD), and healthy subjects (HC) were used as comparator groups. Identified proteins primarily involved in hepatocellular function were decreased in AH patients which included hepatokines, clotting factors, complement cascade components, and hepatocyte growth activators. A protein signature of AH disease severity was identified including thrombin (THRB), hepatocyte growth factor alpha (HGFA), clusterin (CLUS), human serum factor H-related protein (FHR1) and kallistatin (KAIN), which exhibited large abundance shifts between severe and non-severe AH. The combination of THRB and HGFA discriminated between severe and non-severe AH with high sensitivity and specificity. These findings were correlated with the liver expression of genes encoding secreted proteins in a similar cohort, finding a highly consistent plasma protein signature reflecting HNF4A and HNF1A functions. This unbiased proteomic-transcriptome analysis identified plasma protein signatures and pathways associated with disease severity, reflecting HNF4A/1A activity useful for diagnostic assessment in AH.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Permanent Magnets Featuring Heavy Main Group Elements for Magnetic Anisotropy

Permanent magnets are the functional component of electric motors and generators found in numerous renewable energy applications. To improve energy conversion in such applications, we require fundamentally new magnets that generate higher magnetic flux per volume while retaining the properties conferred by rare-earth elements incorporated into current technologies. We hypothesize that by engendering a covalent interaction between two elements, we can access a new regime of magnetic materials where the two components of a magnetic moment—spin and orbital angular momentum—come from two separate atoms to form a complete magnetic moment. Our previous research utilized high-pressure conditions to discover two new candidate materials ideal for assessing this hypothesis. The first material, FeBi 2 , enables the study of an unprecedented solid state metal-metal bonding interaction. The second, MnBi 2 represents the second member of the promising Mn–Bi family known for its magnetic properties. Importantly, MnBi 2 is isostructural to FeBi 2 . Together these chemically simple but magnetically rich materials provide an elegant platform for elucidating fundamental design principals of magnetic anisotropy while inspiring the synthesis of new magnetic materials. More generally, solid-state chemistry remains a synthetic black box. To fully harness the potential of such new materials, it is vital to create a window into both the structure and the properties of our high-pressure materials. One missing area of importance to energy science is high-pressure magnetometry. To this end, we assessed the magnetic structure of these materials through two objectives: (1) we performed magnetometry measurements at high-pressures, including performing high-pressure X-ray Magnetic Circular Dichroism (XMCD) experiments on these materials that are only synthesized at high-pressure and cannot be recovered to ambient conditions and (2) we targeted the recovery of these materials using dynamic compression approaches, starting with laser shock techniques. Future directions include expanding our focus to ternary phase space, employing high-throughput computational approaches to direct our search for magnetic materials across the Periodic Table. This award was originated at Northwestern, and reopened as a new grant at MIT. This is the close out for Northwestern.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Inverted c-functions in thermal states

We first compute the effect of a chiral anomaly, charge, and a magnetic field on the entanglement entropy in $\mathcal{N}$ = 4 Super-Yang-Mills theory at strong coupling via holography. Depending on the width of the entanglement strip the entanglement entropy probes energy scales from the ultraviolet to the infrared energy regime of this quantum field theory (QFT) prepared in a given state. From the entanglement entropy, we compute holographic c-functions and demonstrate an inverted c-theorem for them. That is, these c-functions in generic thermal states monotonically increase towards the infrared (IR) energy regime. This is in contrast to the c-functions in vacuum states which decrease along the renormalization group flow towards the IR regime of a renormalizable QFT. Furthermore, in thermal states and in the IR limit, the c-functions behave thermally, growing proportionally to the value of the thermal entropy. The chiral anomaly affects the c-functions more in the IR regime, and its effect is peaked at an intermediate value of the magnetic field at a fixed chemical potential and temperature.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Modeling Disorder in Pyrochlores and Other Anion-Deficient Fluorite Structural Derivative Oxides

Their very flexible chemistry gives oxide materials a richness in functionality and wide technological application. A specific group of oxides that have a structure related to fluorite but with less oxygen, termed anion-deficient fluorite structural derivatives and with pyrochlores being the most notable example, has been shown to exhibit a diversity of useful properties. For example, the possibility to undergo a transition from an ordered to disordered state allows these oxides to have high radiation tolerance. Atomistic-scale calculations in the form of molecular dynamics (MD) and density functional theory (DFT) have been extensively used to understand what drives this order/disorder transition. Here we give a brief overview of how atomistic-scale calculations are utilized in modeling disorder in pyrochlores and other anion-deficient fluorite structural derivatives. We discuss the modeling process from simple point defects to completely disordered structures, the dynamics during the disordering process, and the use of mathematical models to generate ordered solid-solution configurations. We also attempt to identify the challenges in modeling short range order and discuss future directions to more comprehensive models of the disordered structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

KBase Narrative - Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed site

Genome assemblies were imported into KBase using the Batch Import Assembly from Staging Area (v1.0.57) function. All assemblies were annotated using the Annotated Multiple Microbial Assemblies with RASTtk - v1.073 tool. Annotated genomes were grouped into sets using the Add Genomes to GenomeSet - v1.7.6 function. Individual annotated genomes can be found both below and in the Data menu to the left. Taxonomy was assigned using the Classify Microbes with GTDB-Tk-v1.7.0 tool. The results of this analysis are shown below. Analysis of the Castellaniella pangenome was performed using the Compute Pangenome (v0.0.7) tool. Using the same method, we also computed the ORR-specific and non-ORR Castellaniella pangenomes. All pangenome results (including the presence/absence matrix) can be found below.

Szink, Elizabeth↗
DOE OSTI2021

Pathways to fluorescence via restriction of intramolecular motion in substituted tetraphenylethylenes

The design of materials with enhanced luminescence properties is a fast-developing field due to the potential applicability of these materials as light-emitting diodes or for bioimaging. A transparent way to enhance the emission properties of interesting molecular candidates is blocking competing and unproductive non-radiative relaxation pathways by the restriction of intramolecular motions. Rationalized functionalization is an important possibility to achieve such restrictions. Using time-dependent density functional theory (TD-DFT) based on the ωB97XD functional and the semiempirical tight-binding method including long-range corrections (TD-LC-DFTB), this work investigates the effect of functionalization of the paradigmatic tetraphenylethylene (TPE) on achieving restricted access to conical intersections (RACI). Photodynamical surface hopping simulations have been performed on a larger set of compounds including TPE and ten functionalized TPE compounds. Functionalization has been achieved by means of electron-withdrawing groups, bulky groups which block the relaxation channels via steric hindrance and groups capable of forming strong hydrogen bonds, which restrict the motion via the formation of hydrogen bond channels. Most of the investigated functionalized TPE candidates show ultrafast deactivation to the ground state due to their still existing structural flexibility, but two examples, one containing –CN and –CF 3 groups and a second characterized by a network of hydrogen bonds, have been identified as interesting candidates for creating efficient luminescence properties in solution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Plant functional types broadly describe water use strategies in the Caatinga, a seasonally dry tropical forest in northeast Brazil

In seasonally dry tropical forests, plant functional type can be classified as deciduous low wood density, deciduous high wood density, or evergreen high wood density species. While deciduousness is often associated with drought-avoidance and low wood density is often associated with tissue water storage, the degree to which these functional types may correspond to diverging and unique water use strategies has not been extensively tested. We examined (a) tolerance to water stress, measured by predawn and mid-day leaf water potential; (b) water use efficiency, measured via foliar δ 13 C; and (c) access to soil water, measured via stem water δ 18 O. We found that deciduous low wood density species maintain high leaf water potential and low water use efficiency. Deciduous high wood density species have lower leaf water potential and variable water use efficiency. Both groups rely on shallow soil water. Evergreen high wood density species have low leaf water potential, higher water use efficiency, and access alternative water sources. These findings indicate that deciduous low wood density species are drought avoiders, with a specialized strategy for storing root and stem water. Deciduous high wood density species are moderately drought tolerant, and evergreen high wood density species are the most drought tolerant group. Our results broadly support the plant functional type framework as a way to understand water use strategies, but also highlight species-level differences.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Physical Bond Breaking in Associating Copolymer Liquids

We combine ideas from polymer and glassy liquid physics to construct a new model for the bond breaking time scale of attractive sticker groups in associating copolymer liquids that form transient networks. The activated event is argued to be a two-step process, involving first the release of the non-sticker dynamic caging constraints that defines the primary alpha relaxation, followed by attractive stickers surmounting an association free energy barrier subject to a local frictional resistance which can be strongly affected by relaxation-diffusion decoupling. Here, the ideas embedded in the model produce a consistent and good description of the bond breaking timescale for diverse polymer chemistries and architectures as a function of temperature and fraction of sticky groups. Chemically sensible values for association free energies are deduced. In strong contrast, the existing phenomenological models are shown to incur qualitative failures.

36 MATERIALS SCIENCE↗