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At least 415 records · Page 23

Molecular dynamics simulations of Zika virus NS3 helicase: Insights into RNA binding site activity

America is still suffering with the outbreak of Zika virus (ZIKV) infection. Congenital ZIKV syndrome has already caused a public health emergency of international concern. However, there are still no vaccines to prevent or drugs to treat the infection caused by ZIKV. The ZIKV NS3 helicase (NS3h) protein is a promising target for drug discovery due to its essential role in viral genome replication. NS3h unwinds the viral RNA to enable the replication of the viral genome by the NS5 protein. NS3h contains two important binding sites: the NTPase binding site and the RNA binding site. Here, we used molecular dynamics (MD) simulations to study the molecular behavior of ZIKV NS3h in the presence and absence of ssRNA and the potential implications for NS3h activity and inhibition. Although there is conformational variability and poor electron densities of the RNA binding loop in various apo flaviviruses NS3h crystallographic structures, the MD trajectories of NS3h-ssRNA demonstrated that the RNA binding loop becomes more stable when NS3h is occupied by RNA. Our results suggest that the presence of RNA generates important interactions with the RNA binding loop, and these interactions stabilize the loop sufficiently that it remains in a closed conformation. This closed conformation likely keeps the ssRNA bound to the protein for a sufficient duration to enable the unwinding/replication activities of NS3h to occur. In addition, conformational changes of this RNA binding loop can change the nature and location of the optimal ligand binding site, according to ligand binding site prediction results. These are important findings to help guide the design and discovery of new inhibitors of NS3h as promising compounds to treat the ZIKV infection. - Highlights: • Ligand binding site predictions could provide useful insights into design of compounds to block ZIKV helicase activities. • Insights into dynamic features of NS3h and its interactions with ssRNA are provided through molecular dynamics simulations. • Presence of RNA generates stabilizing interactions with RNA binding loop of NS3h, which holds it in a closed conformation. • Closed conformation of the RNA binding loop keeps the ssRNA bound to the protein to enable the activity of NS3h.

60 APPLIED LIFE SCIENCES↗

Bypassing the yellow phase for extremely stable formamidinium lead iodide perovskite solar cells

INTRODUCTION Formamidinium lead iodide (FAPI) emerged as an ideal material for single-junction perovskite solar cells owing to its near optimal bandgap of 1.45 to 1.5 eV and outstanding thermal stability. However, the photoactive cubic α-phase (3C-FAPI) of FAPI is structurally unstable and undergoes a reconstructive phase transition to the nonperovskite yellow hexagonal δ-phase (2H-FAPI) at ambient temperature. The phase reconstruction from 3C-FAPI to 2H-FAPI could be prevented by alloying methylammonium (MA) or Cs or both at the A-site and Br at the halide site, but this limits long-term durability owing to phase segregation or materials instability. Addressing these challenges requires a rational design strategy to stabilize 3C-FAPI by restricting lattice reconstruction without compromising thermal stability. RATIONALE Two main strategies have emerged to improve the phase stability and film quality of FAPI. Here, the first is a lattice-templating approach, which enables the slow formation of perovskite but it eventually degrades through the formation of yellow phases. The second approach, which has been widely explored, involves additive engineering, using alkyl ammonium halide or mostly chloride-based additives, which provide better control over the crystallization route. However, the FAPI films fabricated using these additives are often alloyed and compromise long-term stability. Moreover, the exact role of Cl has been unclear and speculative, specifically when Cl-based additives are used. Even after using a high additive concentration, the incorporation of Cl in perovskite lattice is rare. RESULTS Guided by synergistic modeling and experimental studies, we developed a coadditive strategy using 15 mol % FACl and 0.5 mol % BA 2 PbI 4 perovskites in combination (where BA is butylammonium) to enable a highly oriented (100) Cl-doped FAPI film with exceptional durability. Synchrotron-based in situ wide-angle x-ray scattering revealed a favorable transition for the coadditive-treated FAPI (FAPI-CA) to the corner-sharing 3C black phase through a progressive transformation through the 2H, 4H, 6H, and 8H phases. Moreover, solid-state 35 Cl nuclear magnetic resonance (NMR) revealed Cl incorporation in the perovskite lattice and, as predicted by modeling, indicated that Cl plays a key role in altering the energetics of both the formation and degradation pathways. The Cl-doped perovskite can completely bypass the expected and energetically favorable degradation pathway via the yellow phase or the 2H-PbI 2 phase. Instead, it undergoes degradation only upon exposure to harsh conditions such as 15-sun illumination and 90°C through the energetically uphill 3R-PbI 2 phase path. A p-i-n device fabricated with FAPI-CA film demonstrated a power conversion efficiency (PCE) of 25.1% with an average of 24.1% (40 devices). The notable film stability translated to other devices and retained 98% of its initial PCE under open-circuit conditions at 85° ± 5°C for 1200 hours. CONCLUSION Our study highlights the decisive role of chloride in regulating both the formation and degradation pathways. This regulation is critical for creating a perovskite film with commercially relevant durability.

Garai, Rabindranath [Rice Univ., Houston, TX (Unit↗

Hybrid data-driven cement-stabilized soil design: An integration of machine learning, multi-objective optimization, and life cycle assessment

Soil stabilization is crucial in geotechnical engineering, yet conventional methods are often time-consuming, resource-intensive, and environmentally unsustainable. Despite growing interest in Machine Learning (ML) and optimization tools for mix design, few studies integrate these methods with decision-making techniques and environmental assessment to support practical implementation. This study proposes a hybrid data-driven framework for predicting strength, optimizing mix compositions, and evaluating environmental impacts via life cycle assessment of cement-stabilized soft soils. Six ML models were evaluated, and the top-performing eXtreme Gradient Boosting (XGB) model was further improved using the Grey Wolf Optimizer (GWO). The optimized XGB-GWO model, integrated with a polynomial cost function, served as the objective function in a multi-objective optimization problem solved via the Non-Dominated Sorting Genetic Algorithm II (NSGA-II), with final mix selection guided by the entropy-weighted TOPSIS method. Validation through a case study produced mix designs offering superior strength-cost trade-offs, with the optimal mix achieving 2243.2 kPa unconfined compressive strength and a 16.07 % reduction in carbon emissions compared to the highest-cost design. In conclusion, this study offers a sustainable, scalable approach to soil stabilization and supports informed decision-making in construction.

Life cycle assessment↗

Intrinsic and Stable Conjugation of Thiolated Mesoporous Silica Nanoparticles with Radioarsenic

The development of new image-guided drug delivery tools to improve the therapeutic efficacy of chemotherapeutics remains an important goal in nanomedicine. Using labeling strategies that involve radioelements that have theranostic pairs of diagnostic positron-emitting isotopes and therapeutic electron-emitting isotopes has promise in achieving this goal and further enhancing drug performance through radiotherapeutic effects. The isotopes of radioarsenic offer such theranostic potential and would allow for the use of positron emission tomography (PET) for image-guided drug delivery studies of the arsenic-based chemotherapeutic arsenic trioxide (ATO). Thiolated mesoporous silica nanoparticles (MSN) are shown to effectively and stably bind cyclotron-produced radioarsenic. Labeling studies elucidate that this affinity is a result of specific binding between trivalent arsenic and nanoparticle thiol surface modification. Serial PET imaging of the in vivo murine biodistribution of radiolabeled silica nanoparticles shows very good stability toward dearsenylation that is directly proportional to silica porosity. Thiolated MSNs are found to have a macroscopic arsenic loading capacity of 20 mg of ATO per gram of MSN, sufficient for delivery of chemotherapeutic quantities of the drug. In conclusion, these results show the great potential of radioarsenic-labeled thiolated MSN for the preparation of theranostic radiopharmaceuticals and image-guided drug delivery of ATO-based chemotherapeutics.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site

The host cell factor cyclophilin A (CypA) interacts directly with the HIV-1 capsid and regulates viral infectivity. Although the crystal structure of CypA in complex with the N-terminal domain of the HIV-1 capsid protein (CA) has been known for nearly two decades, how CypA interacts with the viral capsid and modulates HIV-1 infectivity remains unclear. We determined the cryoEM structure of CypA in complex with the assembled HIV-1 capsid at 8-Å resolution. The structure exhibits a distinct CypA-binding pattern in which CypA selectively bridges the two CA hexamers along the direction of highest curvature. EM-guided all-atom molecular dynamics simulations and solid-state NMR further reveal that the CypA-binding pattern is achieved by single-CypA molecules simultaneously interacting with two CA subunits, in different hexamers, through a previously uncharacterized non-canonical interface. These results provide new insights into how CypA stabilizes the HIV-1 capsid and is recruited to facilitate HIV-1 infection.

Science & Technology - Other Topics↗

Computational Design of Interlayers for Thermally Stable Compositionally Graded Coatings on Nickel Alloys

To extend the service life of Ni-based superalloys, refractory metal coatings are often used. However, direct bonding between metals with dissimilar crystal structure promotes brittle intermetallic phase formation. This work presents a computational thermodynamic framework for high throughput design of functionally graded interlayers to suppress deleterious phases that may form at the interlayer. The Thermo-Calc software package was used to screen candidate metallic interlayer elements based on stability of solid-solution phases. Vanadium was identified as a promising interlayer due to its consistent suppression of intermetallic phases. Temperature-dependent phase diagram mapping between 600 and 1000 °C guided selection of a compositional pathway that significantly reduced intermetallic formation compared to directly joining the Ni-based and Nb refractory alloys. Time–temperature–transformation analysis was performed to assess whether equilibrium-predicted phases are kinetically accessible along regions of the graded path where non-solid-solution phases are not fully suppressed. The methodology was further applied to additional Ni-based alloy and coating systems, illustrating its transferability as an approach for rapid computational design of graded interlayers in dissimilar high-temperature materials.

36 MATERIALS SCIENCE↗

Imaging Strain-Localized Single-Photon Emitters in Layered GaSe below the Diffraction Limit

Nanoscale strain control of exciton funneling is an increasingly critical tool for the scalable production of single photon emitters (SPEs) in two-dimensional materials. However, conventional far-field optical microscopies remain constrained in spatial resolution by the diffraction limit and thus can provide only a limited description of nanoscale strain localization of SPEs. Here, we quantify the effects of nanoscale heterogeneous strain on the energy and brightness of GaSe SPEs on nanopillars with correlative cathodoluminescence, photoluminescence, and atomic force microscopy, supported by density functional theory simulations. We report the strain-localized SPEs have a broad range of emission wavelengths from 620 to 900 nm. We reveal substantial strain-controlled SPE wavelength tunability over a ~100 nm spectral range and 2 orders of magnitude enhancement in the SPE brightness at the pillar center due to Type-I exciton funneling. In addition, we show that radiative biexciton cascade processes contribute to observed CL photon superbunching. Also, the GaSe SPEs show excellent stability, where their properties remain unchanged after electron beam exposure. Importantly, we anticipate that this comprehensive study on the nanoscale strain control of two-dimensional SPEs will provide key insights to guide the development of truly deterministic quantum photonics.

2D materials↗

Stable tuning of photorefractive microcavities using an auxiliary laser

Cavity nonlinear optics enables intriguing physical phenomena to occur at micro- or nano-scales with modest input powers. While this enhances capabilities in applications such as comb generation, frequency conversion, and quantum optics, undesired nonlinear effects including photorefraction and thermal bistability are exacerbated. In this Letter, we propose and demonstrate a highly effective method of achieving cavity stabilization using an auxiliary laser for controlling photorefraction in a z-cut periodically poled lithium niobate (LN) microcavity system. Our numerical study accurately models the photorefractive effect under high input powers, guiding future analyses and development of LN microcavity systems.

42 ENGINEERING↗

Hot planets around cool stars – two short-period mini-Neptunes transiting the late K-dwarf TOI-1260

We present the discovery and characterization of two sub-Neptunes in close orbits, as well as a tentative outer planet of a similar size, orbiting TOI-1260 – a low metallicity K6 V dwarf star. Photometry from Transiting Exoplanet Survey Satellite(TESS) yields radii of R(b) = 2.33 ± 0.10 and R(c) = 2.82 ± 0.15 Rꚛ, and periods of 3.13 and 7.49 d for TOI-1260 b and TOI-1260 c, respectively. We combined the TESS data with a series of ground-based follow-up observations to characterize the planetary system. From HARPS-N high-precision radial velocities we obtain M(b) = 8.6(+1.4,−1.5) and M(c) = 11.8(+3.4,−3.2) Mꚛ. The star is moderately active with a complex activity pattern, which necessitated the use of Gaussian process regression for both the light-curve detrending and the radial velocity modelling, in the latter case guided by suitable activity indicators. We successfully disentangle the stellar-induced signal from the planetary signals, underlining the importance and usefulness of the Gaussian process approach. We test the system’s stability against atmospheric photoevaporation and find that the TOI-1260 planets are classic examples of the structure and composition ambiguity typical for the 2–3 Rꚛ range.

I Y Georgieva↗

Silk Flexible Electronics: From Bombyx mori Silk Ag Nanoclusters Hybrid Materials to Mesoscopic Memristors and Synaptic Emulators

Functionalization of flexible materials based on mesoscopic reconstruction is a key strategy in fabricating biocompatible flexible electronics. This work is to acquire new mesoscopic bioelectronic hybrid materials of silk fibroin (SF)-Ag nanoclusters (AgNCs@BSA; BSA: bovine serum albumin), which enhance significantly the performance of silk memristors. It is to build AgNCs@BSA into SF mesoscopic networks by templated ß-crystallization. Atomic force microscopy potential probing indicates that AgNCs@BSA serve as electronic potential wells that change completely the transport behavior of charge particles within the SF films. This leads to significant enhancement in the switching speed (˜10 ns), very good switching stability, extremely low set/reset voltages (0.3/-0.18 V) of SF meso-hybrid memristors, compared with the original and other organic memristors, and displays unique synapse characteristics and the capability of synapse learning. Classical density functional theory Poisson–Nernst–Planck simulations indicate that the enhanced performance is subject to the low potential paths interconnecting the AgNCs@BSA, which guide charges' transport (Ag+) and deposition in SF films.

Shi, Chenyang↗

Theory-Guided Synthesis of a Metastable Lead-Free Piezoelectric Polymorph

Many technologically critical materials are metastable under ambient conditions, yet the understanding of how to rationally design and guide the synthesis of these materials is limited. This paper presents an integrated approach that targets a metastable lead-free piezoelectric polymorph of SrHfO 3 . First-principles calculations predict that the previous experimentally unrealized, metastable P4mm phase of SrHfO 3 should exhibit a direct piezoelectric response (d 33 ) of 36.9 pC N -1 (compared to d 33 = 0 for the ground state). Combining computationally optimized substrate selection and synthesis conditions lead to the epitaxial stabilization of the polar P4mm phase of SrHfO 3 on SrTiO 3 . The films are structurally consistent with the theory predictions. A ferroelectric-induced large signal effective converse piezoelectric response of 5.2 pm V -1 for a 35 nm film is observed, indicating the ability to predict and target multifunctionality. Finally, this illustrates a coupled theory-experimental approach to the discovery and realization of new multifunctional polymorphs.

36 MATERIALS SCIENCE↗

Selective non-oxidative dehydrogenation of ethanol to acetaldehyde and hydrogen on highly dilute NiCu alloys

The non-oxidative dehydrogenation of ethanol to acetaldehyde has long been considered as an important method to produce acetaldehyde and clean hydrogen gas. Although monometallic Cu nanoparticles have high activity in the non-oxidative dehydrogenation of ethanol, they quickly deactivate due to sintering of Cu. In this paper, we show that adding a small amount of Ni (Ni 0.01 Cu - Ni 0.001 Cu) into Cu to form highly dilute NiCu alloys dramatically increases the catalytic activity and increases their long-term stability. The kinetic studies show that the apparent activation energy decreases from ~70 kJ/mol over Cu to ~45 kJ/mol over the dilute NiCu alloys. The improved performance is observed both for nanoparticles and nanoporous NiCu alloys. The improvement in the long-term stability of the catalysts is attributed to the stabilization of Cu against sintering. Our characterization data show that Ni is atomically dispersed in Cu. The comparison of the catalytic performance of highly dilute alloy nanoparticles with nanoporous materials is useful to guide the design of novel mesoporous catalyst architectures for selective dehydrogenation reactions.

36 MATERIALS SCIENCE↗

Evidence for prevalent Z = 6 magic number in neutron-rich carbon isotopes

Here, the nuclear shell structure, which originates in the nearly independent motion of nucleons in an average potential, provides an important guide for our understanding of nuclear structure and the underlying nuclear forces. Its most remarkable fingerprint is the existence of the so-called magic numbers of protons and neutrons associated with extra stability. Although the introduction of a phenomenological spin–orbit (SO) coupling force in 1949 helped in explaining the magic numbers, its origins are still open questions. Here, we present experimental evidence for the smallest SO-originated magic number (subshell closure) at the proton number six in C obtained from systematic analysis of point-proton distribution radii, electromagnetic transition rates and atomic masses of light nuclei. Performing ab initio calculations on C, we show that the observed proton distribution radii and subshell closure can be explained by the state-of-the-art nuclear theory with chiral nucleon–nucleon and three-nucleon forces, which are rooted in the quantum chromodynamics.

74 ATOMIC AND MOLECULAR PHYSICS↗

Small-molecule modulation of β-arrestins

β-Arrestins are multifunctional regulators of G-protein-coupled receptor (GPCR) signalling and orchestrate diverse downstream signalling events and physiological responses across the GPCR superfamily. Although GPCR pharmacology has advanced to target orthosteric and allosteric sites, as well as G proteins and GPCR kinases, direct chemical tools to modulate β-arrestin activities have remained conspicuously absent. Here we report the identification of small-molecule inhibitors that selectively target β-arrestins and delineate their mechanism of action through integrated pharmacological, biochemical, biophysical and structural analyses. These inhibitors disrupt β-arrestin engagement with agonist-activated GPCRs, impairing desensitization, internalization and β-arrestin-dependent physiological functions while sparing G protein–receptor coupling. Cryo-electron microscopy, molecular dynamics simulations and structure-guided mutagenesis reveal that one modulator, Cmpd-5, engages a pocket within the central crest of β-arrestin1 formed by the middle, C and lariat loops, a critical receptor-binding interface, stabilizing a distinct conformation that is incompatible with full β-arrestin–receptor engagement. Together, these findings establish a mechanistic framework for β-arrestin modulation, reveal a novel allosteric site for structure-based drug design, and open new avenues for transducer-targeted, pathway-specific GPCR therapeutic agents.

Kahsai, Alem W. [Duke University, Durham, NC (Unit↗

Development of Advanced Casing Treatments for Flow Control

Under the Base R&T and Ultra Efficient Engine Technology programs, the NASA-Goddard Space Flight Center Compressor Branch is investigating flow control strategies required to increase the loading and efficiency of core compressors while maintaining current levels of operability. Flow-control strategies being studied include advanced casing treatments, wall jet injection, and blade-tip injection for compressor stability enhancement, directed jets for surface boundary layer control, and vortex-generating devices. The use of computational fluid dynamics (CFD) simulations to assess the effectiveness of flow-control devices and to guide their design is a key element in this research. CFD simulations serve to screen potential flow-control concepts at a lower cost than executing physical experiments in turbomachinery facilities. CFD simulations also provide guidance in designing physical experiments for those flow control concepts, which appear promising.

Keith, Theo G., Jr.↗

The Evaluation of Composite Energy Absorbers for Use in UAM EVTOL Vehicle Impact Attenuation

The demand for new personal air-taxi services is leading to the development of lightweight Vertical Take-off and Landing (eVTOL) vehicles with electric propulsion for the Urban Air Mobility (UAM) industry. Manufacturers (OEMs) are considering many different designs to develop a vehicle that is able to take-off, cruise, and land autonomously with seating arrangements ranging between 2 and 15 passengers. It is unclear at present how the eventual market will mature; however, one of the common design characteristics noted by many of the OEMs is the use of advanced materials such as composites. A test and analysis program was initiated at NASA Langley Research Center (LaRC) in 2018 to evaluate the impact attenuation capabilities of various composite material systems with the goal of eventual implementation into an eVTOL vehicle. A series of 3-inch diameter by 6-inch length tubular specimens were fabricated from different material systems which included both traditional carbon and hybrid woven layers of fibers. Additionally, a subset of specimens were filled with closed-cell polyisocyanurate foam to help both with stabilization and crush response. The ultimate goal of the test program was to design a specimen capable of limiting the sustained crush acceleration to 20 g through a stable crush progression. After a series of material tests, these specimens were evaluated under both static and dynamic conditions for impact energy attenuation characteristics and crush stability. Additionally, a series of simulation models were developed in parallel to the test efforts. It is anticipated that the models developed using the component level test efforts can be used to help guide the development of a design for use in full-scale eVTOL vehicle applications.

Littell, Justin↗

Using the 18-Electron Rule To Understand the Nominal 19-Electron Half-Heusler NbCoSb with Nb Vacancies

The 18-electron rule is a widely used criterion in the search for new half-Heusler thermoelectric materials. However, several 19-electron compounds such as NbCoSb have been found to be stable and exhibit thermoelectric properties rivaling state-of-the art materials. Using synchrotron X-ray diffraction and density functional theory calculations, we show that samples with nominal (19-electron) composition NbCoSb actually contain a half-Heusler phase with composition Nb0.84CoSb. The large amount of stable Nb vacancies reduces the overall electron count, which brings the stoichiometry of the compound close to an 18-electron count, and stabilizes the material. Excess electrons beyond 18 electrons provide heavy doping needed to make these good thermoelectric materials. This work demonstrates that considering possible defect chemistry and allowing small variation of electron counting leads to extra degrees of freedom for tailoring thermoelectric properties and exploring new compounds. Here we discuss the 18-electron rule as a guide to find defect-free half-Heusler semiconductors. Other electron counts such as 19-electron NbCoSb can also be expected to be stable as n-type metals, perhaps with cation vacancy defects to reduce the electron count.

36 MATERIALS SCIENCE↗