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At least 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Numerical integration in the virtual element method with the scaled boundary cubature scheme

Abstract The virtual element method (VEM) is a stabilized Galerkin method on meshes that consist of arbitrary (convex and nonconvex) polygonal and polyhedral elements. A crucial ingredient in the implementation of low‐ and high‐order VEM is the numerical integration of monomials and nonpolynomial functions over such elements. In this article, we apply the recently proposed scaled boundary cubature (SBC) scheme to compute the weak form integrals in various virtual element formulations over polygonal and polyhedral meshes. In doing so, we demonstrate the flexibility of the approach and the accuracy that it delivers on a broad suite of boundary‐value problems in 2D and 3D over polytopes with affine faces as well as on elements with curved boundaries. In addition, the use of the SBC scheme is exemplified in an enriched Poisson formulation of the VEM in which weakly singular functions are required to be integrated. This study establishes the SBC method as a simple, accurate and efficient integration scheme for use in the VEM.

Chin, Eric B.↗
DOE OSTI2021

Correlating conductivity and Seebeck coefficient to doping within crystalline and amorphous domains in poly(3-(methoxyethoxyethoxy)thiophene)

Molecular doping of conjugated polymers (CPs) plays a vital role in optimizing organic electronic and energy applications. For the case of organic thermoelectrics, it is commonly believed that doping CPs with a strong dopant could result in higher conductivity (σ) and thus better power factor (PF). Herein, by investigating thermoelectric performance of a polar side-chain bearing CP, poly(3- (methoxyethoxyethoxy)thiophene) (P3MEET), vapor doped with fluorinatedderivative of tetracyanoquinodimethane FnTCNQ (n = 1, 2, 4), we show that using strong dopants can in fact have detrimental effects on the thermoelectric performance of CPs. Despite possessing higher electron affinity, doping P3MEET with F4TCNQ only results in a σ (27.0 S/cm) comparable to samples doped with other two weaker dopants F2TCNQ and F1TCNQ (26.4 and 20.1 S/cm). Interestingly, F4TCNQ-doped samples display a marked reduction in the Seebeck coefficient (α) compared to F1TCNQ- and F2TCNQ-doped samples from 42 to 13 μV/ K, leading to an undesirable suppression of the PF. Additionally, structural characterizations coupled with Kang-Snyder modeling of the α–σ relation show that the reduction of α in F4TCNQ-doped P3MEET samples originates from the generation of low mobility carrier within P3MEET's amorphous domain. Our results demonstrate that factors such as dopant distribution and doping efficiency within the crystalline and amorphous domains of CPs should play a crucial role in advancing rational design for organic thermoelectrics.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis

Abstract Identification of the molecular networks that facilitated the evolution of multicellular animals from their unicellular ancestors is a fundamental problem in evolutionary cellular biology. Choanoflagellates are recognized as the closest extant nonmetazoan ancestors to animals. These unicellular eukaryotes can adopt a multicellular‐like “rosette” state. Therefore, they are compelling models for the study of early multicellularity. Comparative studies revealed that a number of putative human orthologs are present in choanoflagellate genomes, suggesting that a subset of these genes were necessary for the emergence of multicellularity. However, previous work is largely based on sequence alignments alone, which does not confirm structural nor functional similarity. Here, we focus on the PDZ domain, a peptide‐binding domain which plays critical roles in myriad cellular signaling networks and which underwent a gene family expansion in metazoan lineages. Using a customized sequence similarity search algorithm, we identified 178 PDZ domains in the Monosiga brevicollis proteome. This includes 11 previously unidentified sequences, which we analyzed using Rosetta and homology modeling. To assess conservation of protein structure, we solved high‐resolution crystal structures of representative M. brevicollis PDZ domains that are homologous to human Dlg1 PDZ2, Dlg1 PDZ3, GIPC, and SHANK1 PDZ domains. To assess functional conservation, we calculated binding affinities for mbGIPC, mbSHANK1, mbSNX27, and mbDLG‐3 PDZ domains from M. brevicollis . Overall, we find that peptide selectivity is generally conserved between these two disparate organisms, with one possible exception, mbDLG‐3. Overall, our results provide novel insight into signaling pathways in a choanoflagellate model of primitive multicellularity.

Gao, Melody↗
DOE OSTI2023

Exploring novel HIV ‐1 reverse transcriptase inhibitors with drug‐resistant mutants: A double mutant surprise

Abstract HIV‐1 reverse transcriptase (RT) remains a key target for HIV drug development. As successful management of the disease requires lifelong treatment, the emergence of resistance mutations is inevitable, making development of new RT inhibitors, which remain effective against resistant variants crucial. To this end, previous computationally guided drug design efforts have resulted in catechol diether compounds, which inhibit wildtype RT with picomolar affinities and appear to be promising preclinical candidates. To confirm that these compounds remain potent against Y181C, a widespread mutation conferring resistance to first generation inhibitors, they were screened against the HIV‐1 N119 clinical isolate, reported as a Y181C single mutant. In comparison to a molecular clone with the same mutation, N119 appears less susceptible to inhibition by our preclinical candidate compounds. A more detailed sequencing effort determined that N119 was misidentified and carries V106A in combination with Y181C. While both indolizine and naphthalene substituted catechol diethers are potent against the classical Y181C single mutant, the addition of V106A confers more resistance against the indolizine derivatives than the naphthalene derivatives. Crystal structures presented in this study highlight key features of the naphthyl group, which allow these compounds to remain potent in the double mutant, including stronger interactions with F227 and less reliance on V106 for stabilization of the ethoxy‐uracil ring, which makes critical hydrogen bonds with other residues in the binding pocket.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Structural insights into the unique recognition module between α-synuclein peptide and nanobody

Nanobodies are single-domain fragments of antibodies with comparable specificity and affinity to antibodies. They are emerging as versatile tools in biology due to their relatively small size. Here, we report the crystal structure of a specific nanobody Nbα-syn01, bound to a 14 amino acid long peptide of α-synuclein (αSyn), a 140-residue protein whose aggregation is associated with Parkinson's disease. The complex structure exhibits a unique binding pattern where the αSyn peptide replaces the N-terminal region of nanobody. Recognition is mediated principally by extended main chain interaction of the αSyn peptide and specificity of the interaction lies in the central 48–52 region of αSyn peptide. Structure-guided truncation of Nbα-syn01 shows tighter binding to αSyn peptide and improved inhibition of α-synuclein aggregation. The structure of the truncated complex was subsequently determined and was indistinguishable to full length complex as the full-length form had no visible electron density for the N-terminal end. These findings reveal the molecular basis for a previously unobserved binding mode for nanobody recognition of α-synuclein, providing an explanation for the enhanced binding, and potential for an alternate framework for structure-based protein engineering of nanobodies to develop better diagnostic and therapeutic tools.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

RrA, an enzyme from Rhodospirillum rubrum , is a prototype of a new family of short‐chain L‐asparaginases

Abstract L‐Asparaginases (ASNases) catalyze the hydrolysis of L‐Asn to L‐Asp and ammonia. Members of the ASNase family are used as drugs in the treatment of leukemia, as well as in the food industry. The protomers of bacterial ASNases typically contain 300–400 amino acids (typical class 1 ASNases). In contrast, the chain of ASNase from Rhodospirillum rubrum , reported here and referred to as RrA, consists of only 172 amino acid residues. RrA is homologous to the N‐terminal domain of typical bacterial class 1 ASNases and exhibits millimolar affinity for L‐Asn. In this study, we demonstrate that RrA belongs to a unique family of cytoplasmic, short‐chain ASNases (scASNases). These proteins occupy a distinct region in the sequence space, separate from the regions typically assigned to class 1 ASNases. The scASNases are present in approximately 7% of eubacterial species, spanning diverse bacterial lineages. They seem to be significantly enriched in species that encode for more than one class 1 ASNase. Here, we report biochemical, biophysical, and structural properties of RrA, a member of scASNases family. Crystal structures of the wild‐type RrA, both with and without bound L‐Asp, as well as structures of several RrA mutants, reveal topologically unique tetramers. Moreover, the active site of one protomer is complemented by two residues (Tyr21 and Asn26) from another protomer. Upon closer inspection, these findings clearly outline scASNases as a stand‐alone subfamily of ASNases that can catalyze the hydrolysis of L‐Asn to L‐Asp despite the lack of the C‐terminal domain that is present in all ASNases described structurally to date.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

An alternative pocket for binding the N‐degrons by the UBR1 and UBR2 ubiquitin E3 ligases

The UBR family of ubiquitin ligases binds to N-termini of their targets (known as N-degron) to induce their ubiquitination and degradation via a conserved domain known as UBR-box. UBR1 and UBR2 share the highest sequence homology among the family, and substantial structural studies were previously performed for substrate binding by the UBR-boxes of UBR1 and UBR2. Here, we describe a new pocket in the UBR-boxes of UBR1 and UBR2 for binding the second residues of N-degrons through determining five co-crystal structures of the UBR-boxes with various N-degron peptides. Together with binding affinities measured by fluorescence polarization, we show that the two highly homologous UBR-boxes can interact with the second residue of an N-degron differently. In addition, the UBR-boxes undergo different conformational changes when binding N-degrons. Furthermore, we demonstrate that the sidechain of the third amino acid of an N-degron has no contribution to binding the UBR-boxes. These findings represent a new conceptual advancement for the UBR E3 ligases and the new insights described here can be leveraged for developing their selective ligands for research and potential therapies.

N-end rule↗
DOE OSTI2021

High Interfacial-Energy and Lithiophilic Janus Interphase Enables Stable Lithium Metal Anodes

The stability of solid electrolyte interphase (SEI) layers is critical for developing lithium (Li) metal batteries. However, the fabrication of stable SEI layers is plagued by un-controlled structures, properties, and functions. In this work a controllable design of an ordered LiF-rich and lithiophilic hybrid Janus interphase (LiF-HJI) is reported using organic fluorination reagent as a functional SEI precursor. The LiF-HJI with a lower crystalline LiF layer and an upper Li organosulfide layer provides high interfacial energy with the Li metal and strong Li-ion affinity, allows homogenous Li-ion distribution, fast and uniform Li-ion transport, and excellent mechanical and passivation properties, enabling stable Li metal anodes under harsh conditions, such as high deposition capacities (6 mA h cm -2 ), current densities (10 mA cm -2 ), and rates (5 C). Stable LiF-HJI@Li greatly improves cycling stability and capacity retention (80.1% after 300 cycles) of Li||LiNi 0.8 Co 0.1 Mn 0.1 O 2 cells at a commercial-level areal capacity (≈4.2 mA h cm -2 ). Even under a lean-electrolyte condition of 3 g Ah -1 , 80% capacity retention can be maintained after 100 cycles, demonstrating excellent cycling performance under such harsh conditions.

25 ENERGY STORAGE↗
DOE OSTI2023

Sequential Separation of Linear, Mono–, and Di–Branched Hexane Isomers on a Robust Coordination Polymer with Nonbonding Flexibility

Efficient separation of hexane isomers is a crucial process for upgrading gasoline. Herein, the sequential separation of linear, mono-, and di-branched hexane isomers by a robust stacked 1D coordination polymer termed as Mn-dhbq ([Mn(dhbq)(H 2 O) 2 ], H 2 dhbq = 2,5-dihydroxy-1,4-benzoquinone) is reported. The interchain space of the activated polymer is of optimal aperture size (5.58 Å) that could exclude 2,3-dimethylbutane, while the chain structure can discriminate n-hexane with high capacity (1.53 mmol g –1 at 393 K, 6.67 kPa) by high-density open metal sites (5.18 mmol g –1 ). With the temperature- and adsorbate-dependent swelling of interchain spaces, the affinity between 3-methylpentane and Mn-dhbq can be deliberately controlled from sorption to exclusion, and thus a complete separation of ternary mixture can be achieved. Column breakthrough experiments confirm the excellent separation performance of Mn-dhbq. Furthermore, the ultrahigh stability and easy scalability further highlight the application prospect of Mn-dhbq for separation of hexane isomers.

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

N‐Doping Effects On Electrocatalytic Water Splitting of Non‐Noble High‐Entropy Alloy Nanoparticles Prepared by Inert Gas Condensation

Abstract The unique catalytic activities of high‐entropy alloys (HEAs) emerge from the complex interaction among different elements in a single‐phase solid solution. As a “green” nanofabrication technique, inert gas condensation (IGC) combined with laser source opens up a highly efficient avenue to develop HEA nanoparticles (NPs) for catalysis and energy storage. In this work, the novel N‐doped non‐noble HEA NPs are designed and successfully prepared by IGC. The N‐doping effects of HEA NPs on oxygen evolution reaction (OER) and hydrogen evolution reaction (HER) are systematically investigated. The results show that N‐doping is conducive to improving the OER, but unfavorable for HER activity. The FeCoNiCrN NPs achieve an overpotential of 269.7 mV for OER at a current density of 10 mA cm −2 in 1.0 M KOH solution, which is among the best reported values for non‐noble HEA catalysts. The effects of the differences in electronegativity, ionization energy and electron affinity energy among mixed elements in N‐doped HEAs are discussed as inducing electron transfer efficiency. Combined with X‐ray photoelectron spectroscopy and the extended X‐ray absorption fine structure analysis, an element‐design strategy in N‐doped HEAs electrocatalysts is proposed to improve the intrinsic activity and ameliorate water splitting performance.

Chemistry↗
DOE OSTI2024

2D Nitrogen‐Doped Graphene Materials for Noble Gas Separation

Abstract Noble gases, notably xenon, play a pivotal role in diverse high‐tech applications. However, manufacturing xenon is an inherently challenging task, due to its unique properties and trace abundance in the Earth's atmosphere. Consequently, there is a pressing need for the development of efficient methods for the separation of noble gases. Using mild fluorographene chemistry, nitrogen‐doped graphene (GNs) materials are synthesized with abundant aromatic regions and extensive nitrogen doping within the vacancies and holes of the aromatic lattice. Due to the organized interlayer “nanochannels”, nitrogen functional groups, and defects within the two‐dimensional (2D) structures, GNs exhibits effective selectivity for Xe over Kr at low pressure. This enhanced selectivity is attributed to the stronger binding affinity of Xe to GN compared to Kr. The adsorption is governed by London dispersion forces, as revealed by theoretical calculations using symmetry‐adapted perturbation theory (SAPT). Investigation of other GNs differing in nitrogen content, surface area, and pore sizes underscores the significance of nitrogen functional groups, defects, and interlayer nanochannels over the surface area in achieving superior selectivity. This work offers a new perspective on the design and fabrication of functionalized graphene derivatives, exhibiting superior noble gas storage and separation activity exploitable in gas production technologies.

Šedajová, Veronika↗
DOE OSTI2025

Linear Dichroism of the Optical Properties of SnS and SnSe Van der Waals Crystals

Abstract Tin monochalcogenides SnS and SnSe, belonging to a family of Van der Waals crystals isoelectronic to black phosphorus, are known as environmentally friendly materials promising for thermoelectric conversion applications. However, they exhibit other desired functionalities, such as intrinsic linear dichroism of the optical and electronic properties originating from strongly anisotropic orthorhombic crystal structures. This property makes them perfect candidates for polarization‐sensitive photodetectors working in near‐infrared spectral range. A comprehensive study of the SnS and SnSe crystals is presented, performed by means of optical spectroscopy and photoemission spectroscopy, supported by ab initio calculations. The studies reveal the high sensitivity of the optical response of both materials to the incident light polarization, which is interpreted in terms of the electronic band dispersion and orbital composition of the electronic bands, dictating the selection rules. From the photoemission investigation the ionization potential, electron affinity and work function are determined, which are parameters crucial for the design of devices based on semiconductor heterostructures.

Chemistry↗
DOE OSTI2025

Nanofilm Composite Membranes of Bottlebrush Poly(1,3‐Dioxolane) Plasticized by Poly(Ethylene Glycol) for CO 2 /N 2 Separation

Abstract Poly(1,3‐dioxolane) has emerged as a leading membrane material for post‐combustion CO 2 capture due to its high ether oxygen content and strong affinity toward CO 2 . However, they are often cross‐linked to inhibit crystallization, which makes them impossible to fabricate into industrial thin‐film composite membranes. Herein, soluble and high molecular weight bottlebrush polymers ( b PDXLA) are synthesized using reversible addition‐fragmentation chain transfer polymerization and demonstrate the feasibility of fabricating nanofilm (≈100 nm) composite membranes (NCMs). Furthermore, b PDXLA can be plasticized using a miscible additive of poly(ethylene glycol) dimethyl ether (PEGDME) to improve CO 2 permeability while retaining good CO 2 /N 2 selectivity. For example, adding 20 mass% PEGDME improves CO 2 permeance from 930 to 1300 GPU and decreases CO 2 /N 2 selectivity from 74 to 53 at 25 °C; the membrane exhibits stable separation performance competitive with state‐of‐the‐art commercial membranes. This work unveils a practical approach to designing uncross‐linked, highly polar polymers for practical membrane gas separation and highlights a facile way to enhance performance by incorporating miscible plasticizers using industrial manufacturing processes.

Zhang, Gengyi [Department of Chemical and Biologic↗
DOE OSTI2023

Ag Alloying in Cu 2– y Ag y Ba(Ge,Sn)Se 4 Films and Photovoltaic Devices

Trigonal Cu 2 BaGe 1–x Sn x Se 4 (CBGTSe) has recently gained interest as a potential photovoltaic absorber to target mitigation of antisite defect formation in Cu 2 ZnSn(S,Se) 4 . This study examines partial substitution of Cu by Ag as a potential approach to tune the properties of Ag-incorporated CBGTSe in the following aspects: 1) phase stability and crystal structure as a function of Ag content; 2) film morphology and grain structure; 3) charge carrier properties; 4) band positions; and 5) charge carrier kinetics and recombination. Up to 20% of Cu can be substituted by Ag in CBGTSe, while above 20% a phase mixture appears. Increasing Ag content induces larger average grain size and reduced hole carrier densities. In contrast, photoelectron spectroscopy and photoluminescence measurements reveal negligible impact of Ag substitution on ionization potential (≈5.4 eV) and electron affinity (≈3.7 eV). Also, Ag content offers negligible impact on carrier lifetimes (few ns). Consistent with these fundamental properties, solar cells based on two different Ag/(Ag + Cu) ratios (≈0% and ≈20%) show comparable power conversion efficiencies (≈2.7–2.8%). Finally, these results indicate that CBGTSe films and solar cells may be less sensitive to Ag substitution compared to Cu 2 ZnSn(S,Se) 4 , at least at the current level of absorber and device optimization.

14 SOLAR ENERGY↗
DOE OSTI2022

On the S-matrix of Ising field theory in two dimensions

We explore the analytic structure of the non-perturbative S-matrix in arguably the simplest family of massive non-integrable quantum field theories: the Ising field theory (IFT) in two dimensions, which may be viewed as the Ising CFT deformed by its two relevant operators, or equivalently, the scaling limit of the Ising model in a magnetic field. Our strategy is that of collider physics: we employ Hamiltonian truncation method (TFFSA) to extract the scattering phase of the lightest particles in the elastic regime, and combine it with S-matrix bootstrap methods based on unitarity and analyticity assumptions to determine the analytic continuation of the 2 → 2 S-matrix element to the complex s-plane. Focusing primarily on the “high temperature” regime in which the IFT interpolates between that of a weakly coupled massive fermion and the E 8 affine Toda theory, we will numerically determine 3-particle amplitudes, follow the evolution of poles and certain resonances of the S-matrix, and exclude the possibility of unknown wide resonances up to reasonably high energies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Effective field theories as Lagrange spaces

We present a formulation of scalar effective field theories in terms of the geometry of Lagrange spaces. The horizontal geometry of the Lagrange space generalizes the Riemannian geometry on the scalar field manifold, inducing a broad class of affine connections that can be used to covariantly express and simplify tree-level scattering amplitudes. Meanwhile, the vertical geometry of the Lagrange space characterizes the physical validity of the effective field theory, as a torsion component comprises strictly higher-point Wilson coefficients. Imposing analyticity, unitarity, and symmetry on the theory then constrains the signs and sizes of derivatives of the torsion component, implying that physical theories correspond to a special class of vertical geometry.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗