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Results for “Structure and Interactions”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants

The serotonin transporter (SERT) is a member of the SLC6 neurotransmitter transporter family that mediates serotonin reuptake at presynaptic nerve terminals. SERT is the target of both therapeutic antidepressant drugs and psychostimulant substances such as cocaine and methamphetamines, which are small molecules that perturb normal serotonergic transmission by interfering with serotonin transport. Despite decades of studies, important functional aspects of SERT such as the oligomerization state of native SERT and its interactions with potential proteins remain unresolved. Here, we develop methods to isolate SERT from porcine brain (pSERT) using a mild, nonionic detergent, utilize fluorescence-detection size-exclusion chromatography to investigate its oligomerization state and interactions with other proteins, and employ single-particle cryo-electron microscopy to elucidate the structures of pSERT in complexes with methamphetamine or cocaine, providing structural insights into psychostimulant recognition and accompanying pSERT conformations. Methamphetamine and cocaine both bind to the central site, stabilizing the transporter in an outward open conformation. We also identify densities attributable to multiple cholesterol or cholesteryl hemisuccinate (CHS) molecules, as well as to a detergent molecule bound to the pSERT allosteric site. Under our conditions of isolation, we find that pSERT is best described as a monomeric entity, isolated without interacting proteins, and is ensconced by multiple cholesterol or CHS molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Final-state interactions and spin structure in E 1 breakup of Li 11 in halo effective field theory

In this work, we calculate the E1 breakup of the 2n halo nucleus 11 Li in halo effective field theory (Halo EFT) at leading order. In Halo EFT, 11 Li is treated as a three-body system of a 9 Li core and two neutrons. We present a detailed investigation of final-state interactions (FSIs) in the neutron-neutron (nn) and neutron-core (nc) channels. We employ Møller operators to formulate an expansion scheme that satisfies the non-energy-weighted cluster sum rule and successively includes higher-order terms in the multiple-scattering series for the FSI. Computing the E1 strength up to third order in this scheme, we observe apparent convergence and good agreement with experiment. The neutron-neutron FSI is by far the most important contribution and largely determines the maximum value of the E1 distribution. However, inclusion of nc FSI does shift the peak position to slightly lower energies. Moreover, we investigate the sensitivity of the E1 response to the spin structure of the neutron- 9 Li interaction. We contrast results for an interaction that is the same in the spin-1 and spin-2 channels with one that is only operative in the spin-2 channel, and find that good agreement with experimental data is only obtained if the interaction is present in both spin channels. The latter case is shown to be equivalent to a calculation in which the spin of 9 Li is neglected.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Acetylcholinesterase: Structure, dynamics, and interactions with organophosphorus compounds

Acetylcholinesterase (AChE) is an enzyme that hydrolyzes the neurotransmitter acetylcholine (ACh), removing it from the synaptic cleft after the transmission of an electrical signal, making it an essential component of chemical neurotransmission. AChE is a serine hydrolase, containing a catalytic triad of Ser/His/Glu. AChE is a prime target for pharmaceuticals treating a variety of neurological disorders. It is also the target of synthetic organophosphorus (OP) compounds that have been used as pesticides and chemical warfare agents. OP compounds contain a potent leaving group, such as fluorine, and act by forming a covalent adduct with the catalytic serine of the AChE active site. A wealth of structural information is available for AChE, including over 300 structures, including a subset of structures in complex with drugs as well as OP compounds. This review will highlight the interactions between OP compounds and AChE from a structural and computational perspective, with a discussion of access to the active site, as well as side reactions that lead to dealkylation of the OP-catalytic serine adduct, a process known as aging. We conclude that while the majority of the conformational changes needed to accommodate the OP compounds are localized to the acyl loop in the crystal structures, molecular dynamics simulations highlight the potential for a far more dynamic enzyme.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Magnetic structure and exchange interactions in the Heisenberg pyrochlore antiferromagnet Gd 2 Pt 2 O 7

In this report the Heisenberg pyrochlore antiferromagnet Gd 2 Pt 2 O 7 is one of a series of gadolinium pyrochlore compounds with a variety of B-site cations. Despite the expected simplicity of a spin-only Gd 3+ Heisenberg interaction model, the gadolinium pyrochlore series exhibits various complex magnetic ground states at low temperature. Gd 2 Pt 2 O 7 displays the highest temperature magnetic order of the series with $T_N$=1.6 K, which has been attributed to enhanced superexchange pathways facilitated by empty $5d$ $e_g$ Pt orbitals. In this study, we use various neutron scattering techniques on an isotopically enriched polycrystalline 160 Gd 2 Pt 2 O 7 sample to examine the magnetic structure and spin-wave excitation spectrum below $T_N$ in order to extract the dominant exchange interactions. We find that the ground-state magnetic structure is the Palmer-Chalker state previously seen in Gd 2 Sn 2 O 7 with an associated gapped excitation spectrum consistent with enhanced exchange interactions between further near-neighbor Gd 3+ ions. We confirm this exchange model with analysis of the magnetic diffuse scattering in the paramagnetic regime using polarized neutrons.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Impact of Noncovalent Interactions on the Structural Chemistry of Thorium(IV)-Aquo-Chloro Complexes

Five novel tetravalent thorium (Th) compounds that consist of Th(H 2 O) x Cl y structural units were isolated from acidic aqueous solutions using a series of nitrogen-containing heterocyclic hydrogen (H) bond donors. Taken together with three previously reported phases, the compounds provide a series of monomeric Th IV complexes wherein the effects of noncovalent interactions (and H-bond donor identity) on Th structural chemistry can be examined. Seven distinct structural units of the general formulas [Th(H 2 O) x Cl 8–x ] x-4 (x = 2, 4) and [Th(H 2 O) x Cl 9–x] x-5 (x = 5–7) are described. The complexes range from chloride-deficient [Th(H 2 O) 7 Cl 2 ] 2+ to chloride-rich [Th(H 2 O) 2 Cl 6 ] 2– species, and theory was used to understand the relative energies that separate complexes within this series via the stepwise chloride addition to an aquated Th cation. Electronic structure theory predicted the reaction energies of chloride addition and release of water through a series of transformations, generally highlighting an energetic driving force for chloride complexation. To probe the role of the counterion in the stabilization of these complexes, electrostatic potential (ESP) surfaces were calculated. Finally, the ESP surfaces indicated a dependence of the chloride distribution about the Th metal center on the pK a of the countercation, highlighting the directing effects of noncovalent interactions (e.g., Hbonding) on Th speciation.

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

Experimental measurement of the effective contact angle for solvent/packing interactions in a structured packed column for CO 2 capture

The contact angle is a critical factor for determining the effective mass transfer area for carbon dioxide (CO 2 ) capture via the chemical absorption process in a packed column, and thus the overall capture efficiency of the packed column. Many widely used commercial packings involve microscale features (perforation, corrugation, etc.) that may also affect the wetting behavior. This study proposes a systematic method of using a modified Wilhelmy plate to measure the effective contact angle to characterize the solvent and featured packing interaction. In lieu of computational efforts relying on assumptions guided by semi-informed correlation, the proposed method directly measures the effective contact angle as a function of the solvent and packing thermophysical and hydrodynamic properties. The characterization of the effective contact angle is then integrated in the computational fluid dynamics modeling to reduce uncertainty in the prediction of effective mas transfer area. Experiments were conducted for stainless steel coupons using water and aqueous sodium hydroxide (NaOH) solvent for verification of the proposed experimental protocol. The surface tension of the aqueous NaOH solvent was altered using surfactant and antifoam. The effective contact angle increases with the increased value of the surface tension for flat stainless steel sheets. On the other hand, effective contact angles do not vary in Mellapak coupons for aqueous monoethanolamine (MEA) and NaOH solvent. In this case, surface textures and sheet design play a dominant role in the surface tension of solvents. Furthermore, CO 2 loading has a significant effect on the contact angle for Mellapak coupons. As expected, the contact angle decreases with the increasing temperature of CO 2 capture solvents (MEA, EEMPA). The effective contact angle measurement using the Wilhelmy plate method can provide more accurate and efficient solvents for characterizing the solvent-packing surface interactions. Subsequently, the present method enhances the accuracy of the prediction of the effective mass transfer area in carbon capture by solvent absorption.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Structure, Hydration, and Interactions of Native and Hydrophobically Modified Phytoglycogen Nanoparticles

Phytoglycogen is a highly branched polymer of glucose produced as soft, compact nanoparticles by sweet corn. Properties such as softness, porosity, and mechanical integrity, combined with nontoxicity and biodegradability, make phytoglycogen nanoparticles ideal for applications involving the human body, ranging from skin moisturizing and rejuvenation agents in personal care formulations to functional therapeutics in biomedicine. To further broaden the range of applications, phytoglycogen nanoparticles can be chemically modified with hydrophobic species such as octenyl succinic anhydride (OSA). In this study, we present a self-consistent model of the particle structure, water content, and degree of chemical modification of the particles, as well as the emergence of well-defined interparticle spacings in concentrated dispersions, based on small-angle neutron scattering (SANS) measurements of aqueous dispersions of native phytoglycogen nanoparticles and particles that were hydrophobically modified using octenyl succinic anhydride (OSA) in both its protiated (pOSA) and deuterated (dOSA) forms. Measurements on native particles with reduced polydispersity have allowed us to refine the particle morphology, which is well described by a hairy particle (core-chain) geometry with short chains decorating the surface of the particles. The isotopic variants of OSA-modified particles enhanced the scattering contrast for neutrons, revealing lightly modified hairy chains for small degrees of substitution (DS) of OSA, and a raspberry particle geometry for the largest DS value, where the OSA-modified hairy chains collapse to form small seeds on the surface of the particles. This refined model of native and OSA-modified phytoglycogen nanoparticles establishes a quantitative basis for the development of new applications of this promising sustainable nanotechnology.

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

Bringing function to structure: Root–soil interactions shaping phosphatase activity throughout a soil profile in Puerto Rico

Abstract Large areas of highly productive tropical forests occur on weathered soils with low concentrations of available phosphorus (P). In such forests, root and microbial production of acid phosphatase enzymes capable of mineralizing organic phosphorus is considered vital to increasing available P for plant uptake. We measured both root and soil phosphatase throughout depth and alongside a variety of root and soil factors to better understand the potential of roots and soil biota to increase P availability and to constrain estimates of the biochemical mineralization within ecosystem models. We measured soil phosphatase down to 1 m, root phosphatase to 30 cm, and collected data on fine‐root mass density, specific root length, soil P, bulk density, and soil texture using soil cores in four tropical forests within the Luquillo Experimental Forest in Puerto Rico. We found that soil phosphatase decreased with soil depth, but not root phosphatase. Furthermore, when both soil and root phosphatase were expressed per soil volume, soil phosphatase was 100‐fold higher that root phosphatase. Both root and soil factors influenced soil and root phosphatase. Soil phosphatase increased with fine‐root mass density and organic P, which together explained over 50% of the variation in soil phosphatase. Over 80% of the variation in root phosphatase per unit root mass was attributed to specific root length (positive correlation) and available (resin) P (negative correlation). Synthesis : Fine‐root traits and soil P data are necessary to understand and represent soil and root phosphatase activity throughout the soil column and across sites with different soil conditions and tree species. These findings can be used to parameterize or benchmark estimates of biochemical mineralization in ecosystem models that contain fine‐root biomass and soil P distributions throughout depth.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater

Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant. By creating a co-occurrence network with thousands of time-resolved microbial populations from over 100 samples spanning four operating configurations, known and novel microbial consortia with potential to drive methane production were identified. Interactions between these populations were further resolved in relation to specific process configurations by mapping metagenome assembled genomes and cognate gene expression data onto the network. Prominent interactions included transcriptionally active Methanolinea methanogens and syntrophic benzoate oxidizing Syntrophorhabdus , as well as a Methanoregulaceae population and putative syntrophic acetate oxidizing bacteria affiliated with Bateroidetes (Tenuifilaceae) expressing the glycine cleavage bypass of the Wood–Ljungdahl pathway.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The role of H–H interactions and impurities on the structure and energetics of H/Pd(111)

Understanding hydrogen incorporation into palladium requires detailed knowledge of surface and subsurface structure and atomic interactions as surface hydrogen is being embedded. Using density functional theory (DFT), we examine the energies of hydrogen layers of varying coverage adsorbed on Pd(111). Here we find that H–H and H–Pd interactions promote the formation of the well-known ($\sqrt{3}$ x $\sqrt{3}$) phases but also favor an unreported (3 × 3) phase at high H coverages for which we present experimental evidence. We relate the stability of isolated H vacancies of the (3 × 3) phase to the need of H 2 molecules to access bare Pd before they can dissociate. Following higher hydrogen dosage, we observe initial steps of hydride formation, starting with small clusters of subsurface hydrogen. The interaction between H and Pd is complicated by the persistent presence of carbon at the surface. X-ray photoelectron spectroscopy experiments show that trace amounts of carbon, emerging from the Pd bulk despite many surface cleaning cycles, become mobile enough to repopulate the C-depleted surface at temperatures above 200 K. When exposed to hydrogen, these surface carbon atoms react to form benzene, as evidenced by scanning tunneling microscopy observations interpreted with DFT.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Control of light-matter interactions in hybrid structured environments with novel nanomaterials of different dimensionalities

The project calls for exploration of individual nanomaterials and the ability to fabricate functional structures without degrading the properties of components. The rich photophysics of novel semiconductors like transition metal dichalcogenides (TMDs), lead halide perovskites (LHPs) and nanocrystal quantum dots (NQDs) can be gainfully exploited in integrated photonic structures alongside conventional semiconducting and dielectric materials. Realization of the prospects of such hybrid structures crucially depends on the ability to fabricate these “designer” assemblies while preserving and enhancing the optoelectronic properties of individual components. We study emission properties of these materials at both bulk and single particles levels to elucidate their intrinsic photophysical properties in order to minimize energy losses and facilitate their judicious integration via control of energy/charge flows and photon-exciton interconversions.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Improving estimates of sub-daily gross primary production from solar-induced chlorophyll fluorescence by accounting for light distribution within canopy

Solar-induced chlorophyll fluorescence (SIF) has long been regarded as a proxy for photosynthesis and has shown superiority in estimating gross primary production (GPP) compared to traditional vegetation indices, especially in evergreen ecosystems. However, current SIF-based GPP estimations regard the canopy as a large leaf and seldom consider the impact of interactions among light, canopy structure, and leaf physiology. In this study, we proposed GPP estimation models with different descriptions of light–structure–physiology interactions (including the layered model, the two-leaf model, and the layered two-leaf model) and compared their performances with the big-leaf model using half-hourly (or hourly) observations at evergreen needleleaf forest sites. First, we found that the big-leaf model underestimated GPP, especially at noon. All models showed higher accuracy than that of the big-leaf model. Second, we investigated the diurnal dynamics of GPP estimations in each canopy layer and found that models with a two-leaf assumption captured the diurnal variations in GPP better than that with the layered assumption. Here we also deduced that the poor performance of the big-leaf model was related to its overestimation of the overall light stress on the redox state of PSII reaction centers (qL). Finally, we noticed that the qL at the canopy scale had lower sensitivity to light change than the single-leaf qL and that the light response of canopy-scale qL was influenced by the leaf area index during seasonal cycles. Overall, this study describes methods to accurately estimate sub-daily GPP from SIF in evergreen needleleaf forests and demonstrates that the interactions among light, canopy structure, and leaf physiology regulate the SIF-GPP relationship at the canopy scale. Further, it indicates the need to consider the description of light distribution within the canopy in next-generation terrestrial biosphere models, even if they incorporate SIF to constrain their parameterization. Thus, upscaling the established leaf-scale mechanistic SIF-GPP relationship or findings to canopy-scale applications still requires much work, especially when there are significant changes in environmental conditions and their within-canopy distributions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Weak entanglement approximation for nuclear structure

The interacting shell model, a configuration-interaction method, is a venerable approach for low-lying nuclear structure calculations, but it is hampered by the exponential growth of its basis dimension as one increases the single-particle space and/or the number of active particles. Recent, quantum-information-inspired work has demonstrated that the proton and neutron sectors of a nuclear wave function are weakly entangled. Furthermore, the entanglement is smaller for nuclides away from N = Z, such as heavy, neutron-rich nuclides. Here, in this study, we implement a weak entanglement approximation to bipartite configuration-interaction wave functions, approximating low-lying levels by coupling a relatively small number of many-proton and many-neutron states. This truncation scheme, which we present in the context of past approaches, reduces the basis dimension by many orders of magnitude while preserving essential features of nuclear spectra.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Magnetic ground states of a model for M Nb 3 S 6 ( M = Co, Fe, Ni)

The transition-metal-intercalated dichalcogenide CoNb 3 S 6 is a triangular antiferromagnet (AFM) that has recently been shown to exhibit a large anomalous Hall effect (AHE) below the Neel temperature, even though the response to an external field is very small. This suggests that there is an interesting magnetic structure that interacts with the electronic structure to yield the AHE, as collinear AFMs cannot exhibit a nonzero AHE. We propose a model for magnetic transition-metal-intercalated dichalcogenides and examine its ground state as a function of interaction parameters. The model exhibits transitions between planar spin spirals, nonplanar spin spirals, and a particular noncoplanar so-called 3q state. Finally, this latter state must exhibit a nonzero AHE, while the spin spirals do not.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Affinity-matured homotypic interactions induce spectrum of PfCSP structures that influence protection from malaria infection

The generation of high-quality antibody responses to Plasmodium falciparum (Pf) circumsporozoite protein (PfCSP), the primary surface antigen of Pf sporozoites, is paramount to the development of an effective malaria vaccine. Here we present an in-depth structural and functional analysis of a panel of potent antibodies encoded by the immunoglobulin heavy chain variable (IGHV) gene IGHV3-33, which is among the most prevalent and potent antibody families induced in the anti-PfCSP immune response and targets the Asn-Ala-Asn-Pro (NANP) repeat region. Cryo-electron microscopy (cryo-EM) reveals a remarkable spectrum of helical antibody-PfCSP structures stabilized by homotypic interactions between tightly packed fragments antigen binding (Fabs), many of which correlate with somatic hypermutation. We demonstrate a key role of these mutated homotypic contacts for high avidity binding to PfCSP and in protection from Pf malaria infection. Together, these data emphasize the importance of anti-homotypic affinity maturation in the frequent selection of IGHV3–33 antibodies and highlight key features underlying the potent protection of this antibody family.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Harvest legacies and climate change interact to shape forest structure and biomass through time

Forest structural change driven by climate trends has been observed worldwide and is expected to increase in the future. Management of forest structure has been an important tool for mitigating the impacts of climate change but forest structure may shift independently of management goals as it interacts with climate change. Here, we investigated the long-term impacts of harvest-based management strategies on structure and resistance to climate-induced biomass loss using a process-based ecosystem model for a midwestern USA hardwood forest. We identified aboveground biomass loss events and compared the cumulative number of these events following a five-year period of active management under four management strategies and two climate change scenarios. Management legacy had the clearest impact on climate-driven biomass loss over the mid-term (∼25 years) with the shelterwood scenario experiencing no loss events during this period. However, by the end of the century legacy effects faded and climate change severity became the driver of differences as greater warming scenarios experienced twice the loss events, and end-of-century loss events were 3–10 times more frequent than mid-century events. We found that while structure was distinct among harvest scenarios through the mid-century, differences were negligible by the end-of-century; identical to when management correlated with loss event frequency. Here, we found that loss events were preceded by a drop in precipitation two years prior, while no specific forest structure preceded a loss event. However, the structures preceding a biomass loss event were distinct across different legacies, implying additional influences of past management.

54 ENVIRONMENTAL SCIENCES↗