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At least 1,531 records · Page 85

Single or functionalized fullerenes interacting with heme group

The heme group is responsible for iron transportation through the bloodstream, where iron participates in redox reactions, electron transfer, gases detection etc. The efficiency of such processes can be reduced if the whole heme molecule or even the iron is somehow altered from its original oxidation state, which can be caused by interactions with nanoparticles as fullerenes. To verify how such particles alter the geometry and electronic structure of heme molecule, here we report first principles calculations based on density functional theory of heme group interacting with single C{sub 60} fullerene or with C{sub 60} functionalized with small functional groups (−CH{sub 3}, −COOH, −NH{sub 2}, −OH). The calculations shown that the system heme + nanoparticle has a different spin state in comparison with heme group if the fullerene is functionalized. Also a functional group can provide a stronger binding between nanoparticle and heme molecule or inhibit the chemical bonding in comparison with single fullerene results. In addition heme molecule loses electrons to the nanoparticles and some systems exhibited a geometry distortion in heme group, depending on the binding energy. Furthermore, one find that such nanoparticles induce a formation of spin up states in heme group. Moreover, there exist modifications in density of states near the Fermi energy. Although of such changes in heme electronic structure and geometry, the iron atom remains in the heme group with the same oxidation state, so that processes that involve the iron might not be affected, only those that depend on the whole heme molecule.

36 MATERIALS SCIENCE↗

Bimodal Control of Heat Transport at Graphene–Metal Interfaces Using Disorder in Graphene

Thermal energy transport across the interfaces of physically and chemically modified graphene with two metals, Al and Cu, was investigated by measuring thermal conductance using the time-domain thermoreflectance method. Graphene was processed using a He 2+ ion-beam with a Gaussian distribution or by exposure to ultraviolet/O 3 , which generates structural or chemical disorder, respectively. Hereby, we could monitor changes in the thermal conductance in response to varying degrees of disorder. We find that the measured conductance increases as the density of the physical disorder increases, but undergoes an abrupt modulation with increasing degrees of chemical modification, which decreases at first and then increases considerably. Moreover, we find that the conductance varies inverse proportionally to the average distance between the structural defects in the graphene, implying a strong in-plane influence of phonon kinetics on interfacial heat flow. We attribute the bimodal results to an interplay between the distinct effects on graphene’s vibrational modes exerted by graphene modification and by the scattering of modes.

Science & Technology - Other Topics↗

Structural basis of substrate recognition by a bacterial deubiquitinase important for dynamics of phagosome ubiquitination

Manipulation of the host’s ubiquitin network is emerging as an important strategy for counteracting and repurposing the posttranslational modification machineries of the host by pathogens. Ubiquitin E3 ligases encoded by infectious agents are well known, as are a variety of viral deubiquitinases (DUBs). Bacterial DUBs have been discovered, but little is known about the structure and mechanism underlying their ubiquitin recognition. In this report, we found that members of the Legionella pneumophila SidE effector family harbor a DUB module important for ubiquitin dynamics on the bacterial phagosome. Structural analysis of this domain alone and in complex with ubiquitin vinyl methyl ester (Ub-VME) reveals unique molecular contacts used in ubiquitin recognition. Instead of relying on the Ile44 patch of ubiquitin, as commonly used in eukaryotic counterparts, the SdeA Dub module engages Gln40 of ubiquitin. The architecture of the active-site cleft presents an open arrangement with conformational plasticity, permitting deubiquitination of three of the most abundant polyubiquitin chains, with a distinct preference for Lys63 linkages. We have shown that this preference enables efficient removal of Lys63 linkages from the phagosomal surface. Remarkably, the structure reveals by far the most parsimonious use of molecular contacts to achieve deubiquitination, with less than 1,000 Å 2 of accessible surface area buried upon complex formation with ubiquitin. In conclusion, this type of molecular recognition appears to enable dual specificity toward ubiquitin and the ubiquitin-like modifier NEDD8.

59 BASIC BIOLOGICAL SCIENCES↗

Direct tunneling through high-κ amorphous HfO{sub 2}: Effects of chemical modification

We report first principles modeling of quantum tunneling through amorphous HfO{sub 2} dielectric layer of metal-oxide-semiconductor (MOS) nanostructures in the form of n-Si/HfO{sub 2}/Al. In particular, we predict that chemically modifying the amorphous HfO{sub 2} barrier by doping N and Al atoms in the middle region—far from the two interfaces of the MOS structure—can reduce the gate-to-channel tunnel leakage by more than one order of magnitude. Several other types of modification are found to enhance tunneling or induce substantial band bending in the Si, both are not desired from leakage point of view. By analyzing transmission coefficients and projected density of states, the microscopic physics of electron traversing the tunnel barrier with or without impurity atoms in the high-κ dielectric is revealed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Variable-spectrum mode control of high poloidal beta discharges

DIII-D experiments demonstrate that high pressure, broad current profile equilibria can be accessed in the high poloidal beta regime by optimizing the MHD mode control poloidal spectrum. A novel, variable spectrum (VS) magnetic feedback scheme implemented using the DIII-D internal non-axisymmetric coils (I-coils) facilitated access to reduced internal inductance $l$ i operation above the no-wall beta limit compared with both no feedback and fixed spectrum feedback. In addition, the VS feedback helped avoid beta collapses caused by marginally unstable resistive wall mode activity. The lower and upper I-coil rows were configured in two independent feedback loops, allowing the feedback field's poloidal spectrum to vary and track changes in the plasma mode structure as the edge safety factor q 95 varied from 11 to 6 during the discharges. The q 95 dependence of the measured phase difference between the lower and upper I-coil rows during VS feedback is qualitatively compatible with ideal MHD simulations of the least-stable plasma kink mode and with plasma response simulations that included kinetic modifications to ideal MHD. The VS feedback approach is a straightforward way to improve resilience to variations in mode structure that occur as plasma parameters change. The demonstrated expansion of the operating space to lower $l$ i is expected to improve the coupling of the plasma kink mode to external fields and beneficial wall eddy currents, and is compatible with high bootstrap fraction operation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Lignin valorization reshapes sustainable biomass refining

As the largest natural reservoir of aromatics, lignin offers significant potential for bioproduct manufacturing through advances in valorization technologies. However, the intrinsically complex structures of lignin pose significant challenges for its fractionization and downstream valorization. Overcoming challenges in lignin chemistry modification is crucial for achieving effective lignin valorization and establishing sustainable biorefinery industries. This review explores the potential of tailoring lignin reactivity to enable functional bioproduct manufacturing thereby contributing to profitable biorefining. The intrinsic characteristics of lignin are first summarized, highlighting their roles in both fractionization and valorization. The latest progress in lignin fractionation is then presented, emphasizing their potential to tailor lignin chemistry, reactivity, and processibility. Furthermore, advancements in lignin valorization are covered, recognizing that tailored lignin reactivity is key to defining bioproduct functionality. By examining these chemical mechanisms, this review sheds on the structure-function relationships between lignin and its derived products. To address the dilemma of lignin valorization and biorefineries, a promising synergistic biorefinery is proposed. This involves redesigning biomass fractionation strategies, tailoring lignin chemistry, and upgrading both carbohydrate and lignin streams across the entire biorefinery chain—from feedstock to application. Altogether, a deeper understanding of tailored lignin chemistry is crucial for decoding the reaction mechanisms in biomass processing. A synergistic biorefinery could harness lignin's intrinsic properties to improve product functionality and address key challenges, paving the way for cost-effective, sustainable biorefinery solutions.

09 BIOMASS FUELS↗

Morphology engineering of iridium electrodes via modifying titanium substrates with controllable pillar structures for highly efficient oxygen evolution reaction

Nowadays, Ti is the well-chosen anode substrate material for proton exchange membrane electrolyzer cells (PEMECs) and modifications of the substrate surfaces are essential for the fabrication of highly efficient electrodes. Herein, we introduce the morphology engineering of Ir/Ti electrodes with different acid treatments of hydrochloric acid (HCl) and oxalic acid (OA), and the comparative benefits of these two acid treatment methods are studied from the aspects of their impacts on the morphology, interfacial contact resistance (ICR), and oxygen evolution reaction (OER) performances of resultant electrodes. Notably, compared to the flat surface from OA treatment, Ti substrates with the pillar structure could be successfully achieved via HCl etching. Further, the HCl and the oxalic acid (OA) treatments would reduce the interfacial contact resistance (ICR) to 15.2% and 5.5% of the pristine Ti substrate at 1.38 MPa, respectively. By iridium electrodeposition on Ti substrates, Ir/Ti electrodes with different catalyst loadings are fabricated. With similar low-loadings of about 0.05 mgIr cm –2 , an Ir/Ti electrode with HCl treated substrate exhibits a lower overpotential of ~283 mV at 10 mA cm –2 current density than 305 mV from OA treatment, due to the boosted reaction areas from HCl treatment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hierarchically structured MoO 2 /dopamine-derived carbon spheres as intercalation electrodes for lithium-ion batteries

A hydrogen peroxide initiated sol-gel process involving molybdenum transformation in the presence of dopamine (Dopa) hydrochloride excess produced the metastable precipitate composed of polydopamine (PDopa) spheres coated with Dopa preintercalated molybdenum oxide, (Dopa) x MoO y @PDopa. The hydrothermal treatment (HT) of the (Dopa) x MoO y @PDopa precursor resulted in the simultaneous carbonization of Dopa and molybdenum reduction generating MoO 2 nanoplatelets distributed and confined on the surface of the Dopa-derived carbon matrix (HT-MoO 2 /C). The consecutive annealing (An) of the HT-MoO 2 /C sample at 600 °C under Ar atmosphere led to the formation of MoO 2 with increased Mo oxidation state and improved structural stability (AnHT-MoO 2 /C). Annealing had also further facilitated interaction between the molybdenum-derived and Dopa-derived components resulting in the modification of the carbon matrix confirmed by Raman spectroscopy. Morphology of both materials is best described as Dopa-derived carbon spheres decorated with MoO 2 nanoplatelets. These integrated metal oxide and carbon structures were tested as electrodes for lithium-ion batteries in the potential window that corresponds to the intercalation mechanism of charge storage. The AnHT-MoO 2 /C electrode showed enhanced electrochemical activity, with an initial specific discharge capacity of 260 mAh/g and capacity retention of 67% after 50 cycles, compared to the HT-MoO 2 /C electrode which exhibited an initial specific discharge capacity of 235 mAh g –1 and capacity retention of 47% after 50 cycles. The rate capability experiments revealed that the capacity of 93 mAh/g and 120 mAh/g was delivered by the HT-MoO 2 /C and AnHT-MoO 2 /C electrodes, respectively, when the current density was increased to 100 mA/g. Here, the improved specific capacity, electrochemical stability, and rate capability achieved after annealing were attributed to higher crystallinity of MoO 2 , increased oxidation state of Mo, and formation of the tighter MoO 2 /carbon contact accompanied by the annealing assisted interaction between MoO 2 and Dopa-derived carbon.

25 ENERGY STORAGE↗

TREAT neutronics analysis and design support, Part II: Multi-SERTTA-CAL

Experiment vehicle design is necessary in preparation for Transient Reactor Test (TREAT) facility restart and the resumption of transient testing to support Accident Tolerant Fuel (ATF) characterization and other future fuels testing requirements. Currently the most mature vehicle design is the Multi-SERTTA (Static Environments Rodlet Transient Test Apparatuses), which can accommodate up to four concurrent rodlet-sized specimens under separate environmental conditions. Robust test vehicle design requires neutronics analyses to support design development, optimization of the power coupling factor (PCF) to efficiently maximize energy generation in the test fuel rodlets, and experiment safety analyses. An integral aspect of prior TREAT transient testing was the incorporation of calibration experiments to experimentally evaluate and validate test conditions in preparation of the actual fuel testing. The calibration experiment package established the test parameter conditions to support fine-tuning of the computational models to deliver the required energy deposition to the fuel samples. The calibration vehicle was designed to be as near neutronically equivalent to the experiment vehicle as possible to minimize errors between the calibration and final tests. The Multi-SERTTA-CAL vehicle was designed to serve as the calibration vehicle supporting Multi-SERTTA experimentation. Models of the Multi-SERTTA-CAL vehicle containing typical PWR-fuel rodlets were prepared and neutronics calculations were performed using MCNP6.1 with ENDF/B-VII.1 nuclear data libraries; these results were then compared against those performed for Multi-SERTTA to determine the similarity and possible design modification necessary prior to construction of these experiment vehicles. The estimated reactivity insertion worth into the TREAT core is very similar between the two vehicle designs, with the primary physical difference being a hollow Inconel tube running down the length of the calibration vehicle. Calculations of PCF indicate that on average there is a reduction of approximately 6 % for PWR fuel rodlets irradiated under both wet and dry conditions. Changes to the primary or secondary vessel structure in the calibration vehicle can be performed to offset this discrepancy and maintain neutronic equivalency. Current possible modifications to the calibration vehicle include reduction of the primary vessel wall thickness, swapping Zircaloy-4 for stainless steel 316 in the secondary containment, or slight modification to the temperature and pressure of the water environment within the primary vessel. Removal of some of the instrumentation within the calibration vehicle can also serve to slightly increase the PCF. Future efforts include further modification and optimization of the Multi-SERTTA and Multi-SERTTA-CAL designs in preparation of actual TREAT transient testing. Experimental results from both test vehicles will be compared against calculational results and methods to provide validation and support additional neutronics analyses. (authors)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Innate immune restriction and antagonism of viral RNA lacking 2'-O methylation

N-7 and 2′-O methylation of host cell mRNA occurs in the nucleus and results in the generation of cap structures (cap 0, m{sup 7}GpppN; cap 1, m{sup 7}GpppNm) that control gene expression by modulating nuclear export, splicing, turnover, and protein synthesis. Remarkably, RNA cap modification also contributes to mammalian cell host defense as viral RNA lacking 2′-O methylation is sensed and inhibited by IFIT1, an interferon (IFN) stimulated gene (ISG). Accordingly, pathogenic viruses that replicate in the cytoplasm have evolved mechanisms to circumvent IFIT1 restriction and facilitate infection of mammalian cells. These include: (a) generating cap 1 structures on their RNA through cap-snatching or virally-encoded 2′-O methyltransferases, (b) using cap-independent means of translation, or (c) using RNA secondary structural motifs to antagonize IFIT1 binding. This review will discuss new insights as to how specific modifications at the 5′-end of viral RNA modulate host pathogen recognition responses to promote infection and disease.

60 APPLIED LIFE SCIENCES↗

Structure‐based control of the rate limitation of photosynthetic electron transport

The 2.5 Å structure of the cytochrome (cyt) b 6 f complex provides a basis for control of the rate‐limiting electron transfer step of oxygenic photosynthesis associated with the plastoquinol/quinone exchange pathway. Here, a structural change was made at a site containing two proline residues which border the intra‐cyt pathway for plastoquinol/quinone exchange. The proline side chains confer a larger aperture for passage of plastoquinol/quinone. Change of these prolines to alanine in the cyanobacterium Synechococcus sp. PCC 7002 results in attenuation of this rate‐limiting step, observed by a two‐fold reduction in the rate of cell growth, O 2 evolution, and plastoquinol‐mediated reduction of cyt f . This study demonstrates modification by site‐directed mutagenesis of photosynthetic energy transduction based on rational application of information in the atomic structure.

Ness, Jillian↗

TREAT Neutronics Analysis and Design Support, Part II: Multi-SERTTA-CAL

Experiment vehicle design is necessary in preparation for Transient Reactor Test (TREAT) facility restart and the resumption of transient testing to support Accident Tolerant Fuel (ATF) characterization and other future fuels testing requirements. Currently the most mature vehicle design is the Multi-SERTTA (Static Environments Rodlet Transient Test Apparatuses), which can accommodate up to four concurrent rodlet-sized specimens under separate environmental conditions. Robust test vehicle design requires neutronics analyses to support design development, optimization of the power coupling factor (PCF) to efficiently maximize energy generation in the test fuel rodlets, and experiment safety analyses. In integral aspect of prior TREAT transient testing was the incorporation of calibration experiments to experimentally evaluate and validate test conditions in preparation of the actual fuel testing. The calibration experiment package established the test parameter conditions to support fine-tuning of the computational models to deliver the required energy deposition to the fuel samples. The calibration vehicle was designed to be as near neutronically equivalent to the experiment vehicle as possible to minimize errors between the calibration and final tests. The Multi-SERTTA-CAL vehicle was designed to serve as the calibration vehicle supporting Multi-SERTTA experimentation. Models of the Multi-SERTTA-CAL vehicle containing typical PWR-fuel rodlets were prepared and neutronics calculations were performed using MCNP6.1 with ENDF/B-VII.1 nuclear data libraries; these results were then compared against those performed for Multi-SERTTA to determine the similarity and possible design modification necessary prior to construction of these experiment vehicles. The estimated reactivity insertion worth into the TREAT core is very similar between the two vehicle designs, with the primary physical difference being a hollow Inconel tube running down the length of the calibration vehicle. Calculations of PCF indicate that on average there is a reduction of approximately 6.3 and 12.6%, respectively, for PWR fuel rodlets irradiated under wet and dry conditions. Changes to the primary or secondary vessel structure in the calibration vehicle can be performed to offset this discrepancy and maintain neutronic equivalency. Current possible modifications to the calibration vehicle include reduction of the primary vessel wall thickness, swapping Zircaloy-4 for stainless steel 316 in the secondary containment, or slight modification to the temperature and pressure of the water environment within the primary vessel. Removal of some of the instrumentation within the calibration vehicle can also serve to slightly increase the PCF. Future efforts include further modification and optimization of the Multi-SERTTA and Multi-SERTTA-CAL designs in preparation of actual TREAT transient testing. Experimental results from both test vehicles will be compared against calculational results and methods to provide validation and support additional neutronics analyses.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Interdomain and Intermodule Organization in Epimerization Domain Containing Nonribosomal Peptide Synthetases

Nonribosomal peptide synthetases are large, complex multidomain enzymes responsible for the biosynthesis of a wide range of peptidic natural products. Inherent to synthetase chemistry is the thioester templated mechanism that relies on protein/protein interactions and interdomain dynamics. Several questions related to structure and mechanism remain to be addressed, including the incorporation of accessory domains and intermodule interactions. The inclusion of nonproteinogenic d-amino acids into peptide frameworks is a common and important modification for bioactive nonribosomal peptides. Epimerization domains, embedded in nonribosomal peptide synthetases assembly lines, catalyze the l- to d-amino acid conversion. Here we report the structure of the epimerization domain/peptidyl carrier protein didomain construct from the first module of the cyclic peptide antibiotic gramicidin synthetase. Both holo (phosphopantethiene post-translationally modified) and apo structures were determined, each representing catalytically relevant conformations of the two domains. The structures provide insight into domain–domain recognition, substrate delivery during the assembly line process, in addition to the structural organization of homologous condensation domains, canonical players in all synthetase modules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dielectric function in the spectral range (0.5–8.5)eV of an (Al{sub x}Ga{sub 1−x}){sub 2}O{sub 3} thin film with continuous composition spread

We determined the dielectric function of the alloy system (Al{sub x}Ga{sub 1−x}){sub 2}O{sub 3} by spectroscopic ellipsometry in the wide spectral range from 0.5 eV to 8.5 eV and for Al contents ranging from x = 0.11 to x = 0.55. For the composition range x < 0.4, we observe single phase material in the β-modification and for larger Al content also the occurrence of γ-(Al,Ga){sub 2}O{sub 3}. We derived spectra of the refractive index and the absorption coefficient as well as energy parameters of electronic band-band transitions by model analysis of the dielectric function. The dependence of the dielectric functions lineshape and the energy parameters on x is highly continuous, reflecting theoretical expectations. The data presented here provide a basis for a deeper understanding of the electronic properties of this material system and may be useful for device engineering.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Recrystallization and modification of the stainless-steel surface relief under photonic heat load in powerful plasma discharges

Targets made of ITER-grade 316L(N)-IG stainless steel and Russian-grade 12Cr18Ni10Ti stainless steel with a close composition were exposed at the QSPA-T plasma gun to plasma photonic radiation pulses simulating conditions of disruption mitigation in ITER. After a large number of pulses, modification of the stainless-steel surface was observed, such as the formation of a wavy structure, irregular roughness, and cracks on the target surface. X-ray and optic microscopic analyses of targets revealed changes in the orientation and dimensions of crystallites (grains) over a depth of up to 20 μm for 316L(N)-IG stainless steel after 200 pulses and up to 40 μm for 12Cr18Ni10Ti stainless steel after 50 pulses, which is significantly larger than the depth of the layer melted in one pulse (∼10 μm). In a series of 200 tests of ITER-grade 316L(N)-IG ITER stainless steel, a linear increase in the height of irregularity (roughness) with increasing number of pulses at a rate of up to ∼1 μm per pulse was observed. No alteration in the chemical composition of the stainless-steel surface in the series of tests was revealed. A model is developed that describes the formation of wavy irregularities on the melted metal surface with allowance for the nonlinear stage of instability of the melted layer with a vapor/plasma flow above it. A decisive factor in this case is the viscous flow of the melted metal from the troughs to tops of the wavy structure. The model predicts saturation of the growth of the wavy structure when its amplitude becomes comparable with its wavelength. Approaches to describing the observed stochastic relief and roughness of the stainless-steel surface formed in the series of tests are considered. The recurrence of the melting-solidification process in which mechanisms of the hill growth compete with the spreading of the material from the hills can result in the formation of a stochastic relief.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗