Second-Shell Amino Acid R266 Helps Determine N-Succinylamino Acid Racemase Reaction Specificity in P
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Truong, Dat P.↗
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Static Subspace Approximation for Random Phase Approximation Correlation Energies: Implementation and Performance
Developing theoretical understanding of complex reactions and processes at interfaces requires using methods that go beyond semilocal density functional theory to accurately describe the interactions between solvent, reactants and substrates. Methods based on many-body perturbation theory, such as the random phase approximation (RPA), have previously been limited due to their computational complexity. However, this is now a surmountable barrier due to the advances in computational power available, in particular through modern GPU-based supercomputers. In this work, we describe the implementation of RPA calculations within BerkeleyGW and show its favorable computational performance on large complex systems relevant for catalysis and electrochemistry applications. Our implementation builds off of the static subspace approximation which, by employing a compressed representation of the frequency dependent polarizability, enables the evaluation of the RPA correlation energy with significant acceleration and systematically controllable accuracy. We find that the computational cost of calculating the RPA correlation energy scales only linearly with system size for systems containing up to 50 thousand bands, and is expected to scale quadratically thereafter. We also show excellent strong scaling results across several supercomputers, demonstrating the performance and portability of this implementation.
algorithmic development↗
Static Subspace Approximation for Random Phase Approximation Correlation Energies: Applications to Materials for Catalysis and Electrochemistry
Modeling complex materials using high-fidelity, ab initio methods at low cost is a fundamental goal for quantum chemical software packages. The GW approximation and random phase approximation (RPA) provide a unified description of both electronic structure and total energies using the same physics in a many-body perturbative approach that can be more accurate than generalized-gradient density functional theory (DFT) methods. However, GW/RPA implementations have historically been limited to either specific materials classes or application toward small chemical systems. Here, the static subspace approximation allows for reduced cost full-frequency GW/RPA calculations and has previously been benchmarked thoroughly for GW calculations. Here, we describe our approach to including partial occupations of electronic orbitals in full-frequency GW and RPA calculations for the study of electrocatalysts. We benchmarked RPA total energy calculations using the subspace approximation across a diverse test suite of materials for a variety of computational parameters. The benchmarking quantifies the impact of different extrapolation procedures for representing the static polarizability at infinite screened cutoff, and shows that using screened cutoffs above 20-25 Ryd result in diminishing accuracy returns for predicting RPA total energies. Additionally, for moderately sized electrocatalytic models, 2-3 times fewer computational resources are used to compute RPA total energies by representing the static polarizability with 20-30% of the static subspace basis, with an error of approximately 0.01 eV or better in RPA adsorption energy calculations. Finally, we show that for these electrochemical models RPA can shift DFT adsorption energy shifts by up to 0.5 eV and that GW can frequently shift DFT eigenvalues of surface and adsorbate states by approximately 0.5-1 eV.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Identification of Potent and Selective Inhibitors of Acanthamoeba : Structural Insights into Sterol 14α-Demethylase as a Key Drug Target
Acanthamoeba are free-living pathogenic protozoa that cause blinding keratitis, disseminated infection, and granulomatous amebic encephalitis, which is generally fatal. The development of efficient and safe drugs is a critical unmet need. Acanthamoeba sterol 14α-demethylase (CYP51) is an essential enzyme of the sterol biosynthetic pathway. Repurposing antifungal azoles for amoebic infections has been reported, but their inhibitory effects on Acanthamoeba CYP51 enzymatic activity have not been studied. Here, we report catalytic properties, inhibition, and structural characterization of CYP51 from Acanthamoeba castellanii. The enzyme displays a 100-fold substrate preference for obtusifoliol over lanosterol, supporting the plant-like cycloartenol-based pathway in the pathogen. The strongest inhibition was observed with voriconazole (1 h IC 50 0.45 μM), VT1598 (0.25 μM), and VT1161 (0.20 μM). The crystal structures of A. castellanii CYP51 with bound VT1161 (2.24 Å) and without an inhibitor (1.95 Å), presented here, can be used in the development of azole-based scaffolds to achieve optimal amoebicidal effectiveness.
60 APPLIED LIFE SCIENCES↗
Theoretical Investigations on the Plasmon-Mediated Dissociation of Small Molecules in the Presence of Silver Atomic Wires
Plasmonic nanoparticles can promote bond activation in adsorbed molecules under relatively benign conditions via excitation of the nanoparticle’s plasmon resonance. As the plasmon resonance often falls within the visible light region, plasmonic nanomaterials are a promising class of catalysts. However, the exact mechanisms through which plasmonic nanoparticles activate the bonds of nearby molecules are still unclear. Herein, we evaluate Ag 8 –X 2 (X = N, H) model systems via real-time time-dependent density functional theory (RT-TDDFT), linear response time-dependent density functional theory (LR-TDDFT), and Ehrenfest dynamics in order to better understand the bond activation processes of N 2 and H 2 facilitated by the presence of the atomic silver wire under excitation at the plasmon resonance energies. We find that dissociation is possible for both small molecules at high electric field strength. Activation of each adsorbate is symmetry- and electric field-dependent, and H 2 activates at lower electric field strengths than N 2 . Furthermore, this work serves as a step toward understanding the complex time-dependent electron and electron–nuclear dynamics between plasmonic nanowires and adsorbed small molecules.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Time-Resolved X-ray Emission Spectroscopy and Resonant Inelastic X-ray Scattering Spectroscopy of Laser Irradiated Carbon
The existence of liquid carbon as an intermediate phase preceding the formation of novel carbon materials has been a point of contention for several decades. Experimental observation of such a liquid state requires nonthermal melting of solid carbon materials at various laser fluences and pulse properties. Reflectivity experiments performed in the mid-1980s reached opposing conclusions regarding the metallic or insulating properties of the purported liquid state. Time-resolved X-ray absorption studies showed shortening of C–C bonds and increasing diffraction densities, thought to evidence a liquid or glassy carbon state, respectively. Nevertheless, none of these experiments provided information on the electronic structure of the proposed liquid state. Herein, we report the results of time-resolved resonant inelastic X-ray scattering (RIXS) and time-resolved X-ray emission spectroscopy (XES) studies on amorphous carbon (a-C) and ultrananocrystalline diamond (UNCD) as a function of delay time between the irradiating pulse and X-ray probe. For both a-C and UNCD, we attribute decreases in RIXS or XES signals to transition blocking, relaxation, and finally, ablation. Increased signal at 20 ps following the irradiation of the UNCD is attributed to the probable formation of nanoscale structures in the ablation plume. Further, differences in the amount of signal observed between a-C and UNCD are explained by the difference in sample thickness and, specifically, incomplete melting of the UNCD film. Comparisons to spectral simulations based on MD trajectories at extreme conditions indicate that the carbon state in our experiments is crystalline. Normal mode analysis confirmed that symmetrical bending or stretching of the C–C bonds in the diamond lattice results in XES spectra with small intensity differences. Overall, we observed no evidence of melting to a liquid state, as determined by the lack of changes in the spectral properties for up to 100 ps delays following the melting pulses.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Performance of Spherical Quantum Well Down Converters in Solid State Lighting
We report the color conversion performance of amber and red emitting quantum dots (QDs) on InGaN solid-state lighting (SSL) light emitting diode (LED) packages. Spherical quantum well (SQW) architectures (CdS/CdSe 1- x S x /CdS) were prepared using a library of thio- and selenourea synthesis reagents and high throughput synthesis robotics. CdS/CdSe 1- x S x QDs with narrow luminescence bands were coated with thick CdS shells (thickness = 1.6-7.5 nm) to achieve photoluminescence quantum yields (PLQY) up to 88% at amber and red emission wavelengths (λ max = 600-642 nm, FWHM < 45 nm). The photoluminescence from SQWs encapsulated in silicone and deposited on LED packages was monitored under accelerated aging conditions (oven temperature = 85 °C, relative humidity = 5-85%, blue optical power density = 3-45 W/cm 2 ) by monitoring the red photon output over several hundred hours of continuous operation. The growth of a ZnS shell on the SQW surface increases the stability under long-term operation but also reduces the PLQY, especially of SQWs with thick CdS shells. The results illustrate that the outer ZnS shell layer is key to optimizing the PLQY and the long-term stability of QDs during operation on SSL packages.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Nutrient Recovery from Algae Using Mild Oxidative Treatment and Ion Exchange
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Multipoint Observations of Dispersive Scale Alfvénic Field‐Line Resonances Associated With Substorm Auroral Beads
We present a case study of the field-aligned current (FAC) systems that transpire within the high-altitude auroral acceleration region of an “auroral bead” initiated double oval substorm observed on 23 February 2001 by the Cluster fleet. Conjunctive Cluster measurements and auroral images from IMAGE reveal that auroral bead current system formation and evolution is a multi-scale, injection-mediated process. The FACs at large scales vary on substorm evolution time scales (~minutes) in response to the injection and evolution of hotter denser magnetospheric plasma. Embedded within the large-scale FACs are intense short-scale (≲ few 10s of km) currents comprising dispersive scale Alfvén wave (DAW) fluctuations. The DAWs are a complex mixture of ingoing and reflected components that regularly interfere to form a broad spectrum of kinetic (dispersive) scale Alfvénic field-line resonances (KFLRs). The Alfvénic currents appear as a nested series of upward and downward FAC densities with amplitudes reaching a few 100 nA/m 2 . Energized field-aligned or counterstreaming electrons near keV energies and below are observed with parallel skews that vary in concert with variations in the DAW current sense. Positive correlations between DAW electric field energy densities and the energies of energized H + , He + , and O + outflow are observed, indicative of ion energization within the DAW fields. Due to their L-shell location (L~5.8–7.0) and associations with injections, the KFLRs are interpreted as the high-altitude auroral zone analog of KFLRs observed in the equatorial inner magnetosphere.
79 ASTRONOMY AND ASTROPHYSICS↗
Global River Topology (GRIT): A Bifurcating River Hydrography
Existing global river networks underpin a wide range of hydrological applications but do not represent channels with divergent river flows (bifurcations, multi‐threaded channels, canals), as these features defy the convergent flow assumption that elevation‐derived networks (e.g., HydroSHEDS, MERIT Hydro) are based on. Yet, bifurcations are important features of the global river drainage system, especially on large floodplains and river deltas, and are also often found in densely populated regions. Here we developed the first raster and vector‐based Global RIver Topology that not only represents the tributaries of the global drainage network but also the distributaries, including multi‐threaded rivers, canals and deltas. We achieve this by merging a 30 m Landsat‐based river mask with elevation‐generated streams to ensure a homogeneous drainage density outside of the river mask for rivers narrower than approximately 30 m. Crucially, we employ the new 30 m digital terrain model, FABDEM, based on TanDEM‐X, which shows greater accuracy over the traditionally used SRTM derivatives. After vectorization and pruning, directionality is assigned by a series of elevation, flow angle and continuity approaches. The new global network and its attributes are validated using gauging stations, comparison with existing networks, and randomized manual checks. The new network represents 19.6 million km of streams and rivers with drainage areas greater than 50 km 2 and includes 67,495 bifurcations. With the advent of hyper‐resolution modeling and artificial intelligence, GRIT is expected to greatly improve the accuracy of many river‐based applications such as flood forecasting, water availability and quality simulations, or riverine habitat mapping.
54 ENVIRONMENTAL SCIENCES↗
Negative linear compressibility and complex phase behaviour in 7 Li 2 CO 3
We present a combination of neutron powder-diffraction measurements demonstrating negative linear compressibility and irregular thermal expansion in 7 Li 2 CO 3 . This is shown to be due to an interplay between the tilting of the rigid carbonate group and the shear strain in the unit cell, which leads to a first-order transition from monoclinic to hexagonal symmetry. The phase evolution is shown to be highly sensitive to the level of hydrostaticity in the sample. Under hydrostatic conditions, the sample begins transformation at 8.5 GPa leading to a change from tetrahedral to octahedral Li coordination. Symmetry adapted basis mode analysis, combined with density functional theoretical (DFT) calculations and Raman spectroscopy, is used to show that this transition is reverse proper ferroelastic in nature.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The occurrence and impact of carbon-oxygen shell mergers in massive stars
In their final stages before undergoing a core-collapse supernova, massive stars may experience mergers between internal shells where carbon (C) and oxygen (O) are consumed as fuels for nuclear burning. This interaction, known as a C-O shell merger, can dramatically alter the internal structure of the star, leading to peculiar nucleosynthesis and potentially influencing the supernova explosion and the propagation of the subsequent supernova shock. Our understanding of the frequency and consequences of C-O shell mergers remains limited. This study aims to identify, for the first time, early diagnostics in the stellar structure that lead to C-O shell mergers in more advanced stages. We also assess their role in shaping the chemical abundances in the most metal poor stars of the Galaxy. We analyzed a set of 209 stellar evolution models available in the literature, with different initial progenitor masses and metallicities. We then compared the nucleosynthetic yields from a subset of these models with the abundances of odd-Z elements in metal-poor stars. We find that the occurrence of C-O shell mergers in stellar models can be predicted with a good approximation based on the outcomes of the central He burning phase, specifically, from the CO core mass (M CO ) and the 12 C central mass fraction (X C12 ): 90% of models with a C-O merger have X C12 <0.277 and M CO <4.90 M ⊙ , with average values of M CO = 4.02 M ⊙ and X C12 = 0.176. The quantities X C12 and M CO are indirectly affected from several stellar properties, including the initial stellar mass and metallicity. Additionally, we confirm that the Sc-rich and K-rich yields from models with C-O mergers would solve the long-standing underproduction of these elements in massive stars. Our results emphasize the crucial role of C-O shell mergers in enriching the interstellar medium, particularly in the production of odd-Z elements. This highlights the necessity of further investigations to refine their influence on presupernova stellar properties and their broader impact on Galactic chemical evolution.
79 ASTRONOMY AND ASTROPHYSICS↗
Interface formation and Schottky barrier height for Y, Nb, Au, and Pt on Ge as determined by hard x-ray photoelectron spectroscopy
Development of a robust, thin, hole-blocking (n+) contact on high purity germanium (HPGe) has been the main challenge in the development of Ge-based radiation sensors. Yttrium has been reported to be a viable hole-blocking contact on HPGe, and detectors with low leakage have been fabricated. Niobium has also been considered as a potential hole-blocking contact due to its low work function. Here, we investigate interface chemistry and the Schottky barrier height of Y and Nb, as well as electron-blocking contacts Au and Pt, on Ge(100) surfaces using hard x-ray photoelectron spectroscopy. We find a barrier height of 1.05 ± 0.10 eV for Y/HPGe, confirming the formation of a hole-blocking barrier. For Nb/HPGe, the barrier height of 0.13 ± 0.10 eV demonstrates that the interface is not hole-blocking. The Schottky barrier of Au and Pt was found to be 0.45 ± 0.10 and 0.51 ± 0.10 eV, respectively.
36 MATERIALS SCIENCE↗
An in vitro BRAF activation assay elucidates molecular mechanisms driving disassembly of the autoinhibited BRAF state
The RAF kinases (ARAF, BRAF, and CRAF) are essential components of the RAS-ERK signaling pathway, which controls vital cellular processes and is frequently dysregulated in human disease. Notably, mutations that alter BRAF function are prominent drivers of human cancer and certain RASopathy disorders, making BRAF an important target for therapeutic intervention. Despite extensive research, several aspects of BRAF regulation remain unclear. In this study, we developed an in vitro BRAF activation assay using purified autoinhibited BRAF:14-3-3 2 :MEK complexes. Our results show that fully processed, active-state KRAS alone can promote dimer-dependent BRAF activation. Moreover, we found that phosphatidylserine (PS)-containing liposomes synergized with KRAS to promote BRAF activation, achieving activity levels comparable to those observed with BRAF proteins that constitutively dimerize. In contrast, the SMP phosphatase complex had only a minimal effect on BRAF catalytic activity in this system but mediated the dephosphorylation of the negative regulatory pS365 14-3-3 binding site in a manner that was accelerated by the presence of KRAS alone or KRAS and 30% PS liposomes. Finally, we show that inhibitors blocking the BRAF RBD:KRAS interaction were able to suppress the in vitro activation of BRAF, underscoring the critical role of RAS binding in initiating the disassembly of the BRAF autoinhibited state. Thus, this assay provides valuable insights into the steps required for BRAF activation and can serve as an effective screening tool for identifying compounds that may inhibit this process and have therapeutic potential.
BRAF↗
Optimization of a Lethal, Combat-Relevant Model of Sterile Inflammation in Mice for Drug Candidate Screening
ABSTRACT Introduction Extensive trauma, commonly seen in wounded military Service Members, often leads to a severe sterile inflammation termed systemic inflammatory response syndrome (SIRS), which can progress to multiple organ dysfunction syndrome (MODS) and death. MODS is a serious threat to wounded Service Members, historically causing 10% of all deaths in trauma admissions at a forward deployed combat hospital. The importance of this problem will be exacerbated in large-scale combat operations, in which evacuation will be delayed and care of complex injuries at lower echelons of care may be prolonged. The main goal of this study was to optimize an existing mouse model of lethal SIRS/MODS as a therapeutic screening platform for the evaluation of immunomodulatory drugs. Materials and Methods Male C57BL/6 mice were euthanized, and the bones and muscles were collected and blended into a paste termed tissue–bone matrix (TBX). The TBX at 12.5%–20% relative to body weight of each recipient mouse was implanted into subcutaneous pouches created on the dorsum of anesthetized animals. Mice were observed for clinical scores for up to 48 hours postimplantation and euthanized at the preset point of moribundity. To test effects of anesthetics on TBX-induced mortality, animals received isoflurane or ketamine/xylazine (K/X). In a separate set of studies, mice received TBX followed by intraperitoneal injection with 20 mg/kg or 40 mg/kg Eritoran or a placebo carrier. All Eritoran studies were performed in a blinded fashion. Results We observed that K/X anesthesia significantly increased the lethality of the implanted TBX in comparison to inhaled anesthetics. Although all the mice anesthetized with isoflurane and implanted with 12.5% TBX survived for 24 hours, 60% of mice anesthetized with K/X were moribund by 24 hours postimplantation. To mimic more closely the timing of lethal SIRS/MODS following polytrauma in human patients, we extended observation to 48 hours. We performed TBX dose–response studies and found that as low as 15%, 17.5%, and 20% TBX caused moribundity/mortality in 50%, 80%, and 100% mice, respectively, over a 48-hour time period. With 17.5% TBX, we tested if moribundity/mortality could be rescued by anti-inflammatory drug Eritoran, a toll-like receptor 4 antagonist. Neither 20 mg/kg nor 40 mg/kg doses of Eritoran were found to be effective in this model. Conclusions We optimized a TBX mouse model of SIRS/MODS for the purpose of evaluating novel therapeutic interventions to prevent trauma-related pathophysiologies in wounded Service Members. Negative effects of K/X on lethality of TBX should be further evaluated, particularly in the light of widespread use of ketamine in treatment of pain. By mimicking muscle crush, bone fracture, and necrosis, the TBX model has pleiotropic effects on physiology and immunology that make it uniquely valuable as a screening tool for the evaluation of novel therapeutics against trauma-induced SIRS/MODS.
General & Internal Medicine↗
LDIP cooperates with SEIPIN and LDAP to facilitate lipid droplet biogenesis in Arabidopsis
Cytoplasmic lipid droplets (LDs) are evolutionarily conserved organelles that store neutral lipids and play critical roles in plant growth, development, and stress responses. However, the molecular mechanisms underlying their biogenesis at the endoplasmic reticulum (ER) remain obscure. Here we show that a recently identified protein termed LD-associated protein [LDAP]-interacting protein (LDIP) works together with both endoplasmic reticulum-localized SEIPIN and the LD-coat protein LDAP to facilitate LD formation in Arabidopsis thaliana. Heterologous expression in insect cells demonstrated that LDAP is required for the targeting of LDIP to the LD surface, and both proteins are required for the production of normal numbers and sizes of LDs in plant cells. LDIP also interacts with SEIPIN via a conserved hydrophobic helix in SEIPIN and LDIP functions together with SEIPIN to modulate LD numbers and sizes in plants. Further, the co-expression of both proteins is required to restore normal LD production in SEIPIN-deficient yeast cells. These data, combined with the analogous function of LDIP to a mammalian protein called LD Assembly Factor 1, are discussed in the context of a new model for LD biogenesis in plant cells with evolutionary connections to LD biogenesis in other eukaryotes.
59 BASIC BIOLOGICAL SCIENCES↗
Patulin Inhibition of Specific Apple Microbiome Members Uncovers Hanseniaspora uvarum as a Potential Biocontrol Agent
Penicillium expansum is a major postharvest pathogen of apples, causing loss in fruits through tissue damage, as well as in apple products due to contamination with the mycotoxin patulin. During infections, patulin is a cultivar-dependent virulence factor that facilitates apple lesion development. Patulin also has characterized antimicrobial activity and is important for inhibiting other competitive phytopathogens, but the role of this inhibitory activity has not been investigated in the context of the apple microbiome. Here, in our current study, we isolated 68 apple microbiota and characterized their susceptibility to P. expansum extracts. We found gram-negative bacteria and basidiomycete yeast to demonstrate largely patulin-specific growth inhibition compared with gram-positive and ascomycete isolates. From co-cultures, we identified a Hanseniaspora and Gluconobacter pairing that reduced P. expansum biomass and found that H. uvarum alone is sufficient to reduce apple disease progression in vivo. We investigated possible mechanisms of H. uvarum biocontrol activity and found modest inhibition on apple puree plates, as well as a trend toward lower patulin levels at the wound site. Active biocontrol activity required live yeast, which was also effective in controlling Botrytis cinerea apple infections. Lastly, we explored the breadth of H. uvarum biocontrol activity with over 30 H. uvarum isolates and found consistent inhibition of P. expansum apple disease.
Hanseniaspora uvarum↗