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FAST-PT: a novel algorithm to calculate convolution integrals in cosmological perturbation theory
We present a novel algorithm, FAST-PT, for performing convolution or mode-coupling integrals that appear in nonlinear cosmological perturbation theory. The algorithm uses several properties of gravitational structure formation—the locality of the dark matter equations and the scale invariance of the problem—as well as Fast Fourier Transforms to describe the input power spectrum as a superposition of power laws. This yields extremely fast performance, enabling mode-coupling integral computations fast enough to embed in Monte Carlo Markov Chain parameter estimation. We describe the algorithm and demonstrate its application to calculating nonlinear corrections to the matter power spectrum, including one-loop standard perturbation theory and the renormalization group approach. We also describe our public code (in Python) to implement this algorithm. The code, along with a user manual and example implementations, is available at https://github.com/JoeMcEwen/FAST-PT.
Craspase is a CRISPR RNA-guided, RNA-activated protease
The CRISPR-Cas type III-E RNA-targeting effector complex gRAMP/Cas7-11 is associated with a caspase-like protein (TPR-CHAT/Csx29) to form Craspase (CRISPR-guided caspase). Here, we use cryo–electron microscopy snapshots of Craspase to explain its target RNA cleavage and protease activation mechanisms. Target-guide pairing extending into the 5' region of the guide RNA displaces a gating loop in gRAMP, which triggers an extensive conformational relay that allosterically aligns the protease catalytic dyad and opens an amino acid side-chain–binding pocket. We further define Csx30 as the endogenous protein substrate that is site-specifically proteolyzed by RNA-activated Craspase. This protease activity is switched off by target RNA cleavage by gRAMP and is not activated by RNA targets containing a matching protospacer flanking sequence. We thus conclude that Craspase is a target RNA–activated protease with self-regulatory capacity.
Evaluation of Vacuum Pumps for Low-Tritium Applications
As fusion and other applications that require tritium processing capabilities become more prominent worldwide, it begins to strain the supply of tritium compatible pumps. In order to help alleviate the supply chain bottleneck, alternatives need to be identified that can help reduce the required number of tritium compatible pumps to strictly the primary process loop where tritium concentrations are high. This research is aimed at identifying vacuum pumps that can be used in low tritium environments (e.g., glovebox stripper systems, adsorbent regeneration, flush gas/inert line evacuation, etc.)
Surveillance for Western equine encephalitis St. Louis encephalitis and West Nile viruses using reverse transcription loop-mediated isothermal amplification
In this study, collection of mosquitoes and testing for vector-borne viruses is a key surveillance activity that directly influences the vector control efforts of public health agencies, including determining when and where to apply insecticides. Vector control districts in California routinely monitor for three human pathogenic viruses including West Nile virus (WNV), Western equine encephalitis virus (WEEV), and St. Louis encephalitis virus (SLEV). Reverse transcription quantitative polymerase chain reaction (RT-qPCR) offers highly sensitive and specific detection of these three viruses in a single multiplex reaction, but this technique requires costly, specialized equipment that is generally only available in centralized public health laboratories. We report the use of reverse transcription loop-mediated isothermal amplification (RT-LAMP) to detect WNV, WEEV, and SLEV RNA extracted from pooled mosquito samples collected in California, including novel primer sets for specific detection of WEEV and SLEV, targeting the nonstructural protein 4 (nsP4) gene of WEEV and the 3’ untranslated region (3’-UTR) of SLEV. Our WEEV and SLEV RT-LAMP primers allowed detection of <0.1 PFU/reaction of their respective targets in <30 minutes, and exhibited high specificity without cross reactivity when tested against a panel of alphaviruses and flaviviruses. Furthermore, the SLEV primers do not cross-react with WNV, despite both viruses being closely related members of the Japanese encephalitis virus complex. The SLEV and WEEV primers can also be combined in a single RT-LAMP reaction, with discrimination between amplicons by melt curve analysis. Although RT-qPCR is approximately one order of magnitude more sensitive than RT-LAMP for all three targets, the RT-LAMP technique is less instrumentally intensive than RT-qPCR and provides a more cost-effective method of vector-borne virus surveillance.
OBSERVATIONAL SIGNATURES OF CORONAL LOOP HEATING AND COOLING DRIVEN BY FOOTPOINT SHUFFLING
The evolution of a coronal loop is studied by means of numerical simulations of the fully compressible three-dimensional magnetohydrodynamic equations using the HYPERION code. The footpoints of the loop magnetic field are advected by random motions. As a consequence, the magnetic field in the loop is energized and develops turbulent nonlinear dynamics characterized by the continuous formation and dissipation of field-aligned current sheets: energy is deposited at small scales where heating occurs. Dissipation is nonuniformly distributed so that only a fraction of the coronal mass and volume gets heated at any time. Temperature and density are highly structured at scales that, in the solar corona, remain observationally unresolved: the plasma of our simulated loop is multithermal, where highly dynamical hotter and cooler plasma strands are scattered throughout the loop at sub-observational scales. Numerical simulations of coronal loops of 50,000 km length and axial magnetic field intensities ranging from 0.01 to 0.04 T are presented. To connect these simulations to observations, we use the computed number densities and temperatures to synthesize the intensities expected in emission lines typically observed with the Extreme Ultraviolet Imaging Spectrometer on Hinode. These intensities are used to compute differential emission measure distributions using the Monte Carlo Markov Chain code, which are very similar to those derived from observations of solar active regions. We conclude that coronal heating is found to be strongly intermittent in space and time, with only small portions of the coronal loop being heated: in fact, at any given time, most of the corona is cooling down.
Integrated data-driven and experimental approaches to accelerate lead optimization targeting SARS-CoV- 2 main protease
Identification of potential therapeutic candidates can be expedited by integrating computational modeling with domain aware machine learning (ML) approaches followed by experimental validation. Generative deep learning models have been recently developed that can generate thousands of new candidates, but their physiochemical properties are typically not optimized. Using our deep learning models and a scaffold as a starting point, we generated tens of thousands of compounds for SARS-CoV-2 M pro that preserve the core scaffold. Here we utilized and implemented several computational tools such as structural alert and toxicity analysis, high throughput virtual screening, ML-based 3D quantitative structure–activity relationships, multi-parameter optimization, and graph neural networks on libraries of generated candidates to predict biological activity and binding affinity a priori. From these collective computational results, eight promising candidates were identified and tested experimentally using Native Mass Spectrometry (MS) and FRET-based functional assays. Two compounds, with quinazoline-2-thiol and acetylpiperidine core moiety showed IC 50 values in the low micromolar range: 2.95±0.0017 µM and 3.41±0.0015 µM, respectively. The molecular dynamics simulations further highlight that binding of these compounds results in allosteric modulations in the chain B and the interface domains of the M pro . The key fragments from these top hits can be used as input for closed loop lead optimization in the integrated pipeline.
Easy-Processable and Aging-Free All-Polymer Polysiloxane Composites
In this work, we report all-polymer polysiloxane composites that overcome the long-standing processing problems of silica-reinforced silicone rubbers. Polystyrene fillers are dispersed with styrene/dimethylsiloxane symmetric diblock and triblock copolymers that control the filler morphology, filler–matrix interactions, and filler–filler interactions. Surprisingly, the composites not only rival the traditional silica-reinforced polysiloxane in mechanical properties of cured materials but also have better processability and stability than the silica-filled compound before curing. Large amplitude oscillatory shear experiments demonstrate that the triblock copolymer addition strongly affects the rheological properties. We hypothesize that the bridges and entangled loops that were formed by the triblock copolymer can connect different PS domains to provide additional reinforcement. The aging effect that originates from PDMS chain adsorption on the filler particle surface is also avoided because of the thermodynamic repulsion between PS and PDMS phases.
Framework for assessment of magnetic equilibrium controller performance on the MAST upgrade spherical tokamak
Here, in this work we present the assessment framework for magnetic equilibrium controllers on MAST Upgrade spherical tokamak (MAST-U) spherical tokamak. Such controllers are essential for the MAST-U since exhaust physics and core-edge integration studies require advanced divertor plasma configurations. The developed framework is based on the TokSys suite of plasma control codes, which was adapted and upgraded for MAST-U. However, extra capabilities were added on top of TokSys to support the development of new control algorithms, deployment of controllers to the plasma control system (PCS) and evaluation of their performance. The controller assessment was realized via closed-loop integrated control simulations with the actual MAST-U PCS and different physics-based plasma models. Since all components of the assessment chain were experimentally validated, these simulations provide qualified controllers applicable for direct use in the experiment. This resulted in the successful experimental demonstration of advanced plasma shape control on MAST-U with minimal on-machine development time. A similar methodology would be beneficial to other tokamaks, both existing and future.
Neutrino Dipole Moments and Radiative Signatures from Partial Compositeness
We investigate composite neutrino models where heavy neutrinos emerge as bound states from a near-conformal strongly coupled sector. Standard Model neutrinos mix with these composite singlets via an inverse seesaw mechanism, where the anomalous scaling dimensions of the composite-sector operators naturally suppress light neutrino masses to sub-eV scales. Matching the conformal dynamics onto low-energy theory yields enhanced electromagnetic transition dipole operators with couplings $d_{μN} \sim 10^{-6}$-$10^{-8}\,\mathrm{GeV}^{-1}$, parametrically larger than the loop-level predictions of minimal Dirac or Majorana models. We carry out a dedicated event-level simulation of the production-and-decay chain $νX \to \mathcal{U} X \to νγX$ and compute the resulting event rates at MiniBooNE and MINERvA within the model, accounting for the composite production cross section and decay kinematics in detail. We further present predictions for the photon energy, angular, and multiplicity distributions. For the benchmark scenarios accessible at these experiments the radiative signal is predominantly single-photon; the composite structure additionally permits fragmentation of the up-scattered state into multiple heavy neutrinos, each decaying as $N\toνγ$, with multi-photon final states emerging for lighter compositeness scales or higher beam energies as a qualitatively new probe of the composite dynamics.
Voltage Service Limits Smart Contract Using Distributed Ledger Technology for Electrical Utility Grid with Customer-Owned Generator
Modern electrical grids face growing stability risks from customer-owned generators, especially at points of common couplings (PCCs). Disruptive behavior from power-electronic sources can cause protective relays to isolate problematic generators, making measurement integrity critical. This article presents a distributed ledger technology (DLT) approach that uses smart contracts to evaluate PCC voltage measurements and trigger backup breaker operations. The approach is framed as a verifiable, multi-organization attestation and audit layer, not as a real-time control security mechanism. In the proposed architecture, voltage measurements from a hardware protective relay are anchored on a DLT through the Cyber Grid Guard (CGG) system for attestation by both the grid utility and customer-owned generator. A Voltage Service Limits (VSLs) smart contract evaluates the on-chain measurements against allowable phase-voltage limits derived from the ANSI C84.1 standard. The framework is validated in a hardware-relay-in-the-loop test bed under sustained-undervoltage, sustained-overvoltage, and transient line-to-line fault scenarios. The results show that the VSL smart contract can process these measurements and issue backup breaker actions consistent with the defined service-limit criteria, demonstrating the DLT potential as a verifiable audit layer at the PCC that complements primary protection.
Programmable design of orthogonal protein heterodimers
Specificity of interactions between two DNA strands, or between protein and DNA, is often achieved by varying bases or side chains coming off the DNA or protein backbone—for example, the bases participating in Watson–Crick pairing in the double helix, or the side chains contacting DNA in TALEN–DNA complexes. By contrast, specificity of protein–protein interactions usually involves backbone shape complementarity1, which is less modular and hence harder to generalize. Coiled-coil heterodimers are an exception, but the restricted geometry of interactions across the heterodimer interface (primarily at the heptad a and d positions2) limits the number of orthogonal pairs that can be created simply by varying side-chain interactions3,4. Here we show that protein–protein interaction specificity can be achieved using extensive and modular side-chain hydrogen-bond networks. We used the Crick generating equations5 to produce millions of four-helix backbones with varying degrees of supercoiling around a central axis, identified those accommodating extensive hydrogen-bond networks, and used Rosetta to connect pairs of helices with short loops and to optimize the remainder of the sequence. Of 97 such designs expressed in Escherichia coli, 65 formed constitutive heterodimers, and the crystal structures of four designs were in close agreement with the computational models and confirmed the designed hydrogen-bond networks. In cells, six heterodimers were fully orthogonal, and in vitro—following mixing of 32 chains from 16 heterodimer designs, denaturation in 5 M guanidine hydrochloride and reannealing—almost all of the interactions observed by native mass spectrometry were between the designed cognate pairs. The ability to design orthogonal protein heterodimers should enable sophisticated protein-based control logic for synthetic biology, and illustrates that nature has not fully explored the possibilities for programmable biomolecular interaction modalities.
Rice Cellulose SynthaseA8 Plant-Conserved Region Is a Coiled-Coil at the Catalytic Core Entrance
The crystallographic structure of a rice (Oryza sativa) cellulose synthase, OsCesA8, plant-conserved region (P-CR), one of two unique domains in the catalytic domain of plant CesAs, was solved to 2.4 Å resolution. Two antiparallel α-helices form a coiled-coil domain linked by a large extended connector loop containing a conserved trio of aromatic residues. The P-CR structure was fit into a molecular envelope for the P-CR domain derived from small-angle X-ray scattering data. The P-CR structure and molecular envelope, combined with a homology-based chain trace of the CesA8 catalytic core, were modeled into a previously determined CesA8 small-angle X-ray scattering molecular envelope to produce a detailed topological model of the CesA8 catalytic domain. The predicted position for the P-CR domain from the molecular docking models places the P-CR connector loop into a hydrophobic pocket of the catalytic core, with the coiled-coil aligned near the entrance of the substrate UDP-glucose into the active site. In this configuration, the P-CR coiled-coil alone is unlikely to regulate substrate access to the active site, but it could interact with other domains of CesA, accessory proteins, or other CesA catalytic domains to control substrate delivery.
Conversion Rules for Weyl Points and Nodal Lines in Topological Media
According to a widely held paradigm, a pair of Weyl points with opposite chirality mutually annihilate when brought together. In contrast, we show that such a process is strictly forbidden for Weyl points related by a mirror symmetry, provided that an effective two-band description exists in terms of orbitals with opposite mirror eigenvalue. Instead, such a pair of Weyl points convert into a nodal loop inside a symmetric plane upon the collision. Similar constraints are identified for systems with multiple mirrors, facilitating previously unreported nodal-line and nodal-chain semimetals that exhibit both Fermi-arc and drumhead surface states. Additionally, we further find that Weyl points in systems symmetric under a π rotation composed with time reversal are characterized by an additional integer charge that we call helicity. A pair of Weyl points with opposite chirality can annihilate only if their helicities also cancel out. We base our predictions on topological crystalline invariants derived from relative homotopy theory, and we test our predictions on simple tight-binding models. Finally, the outlined homotopy description can be directly generalized to systems with multiple bands and other choices of symmetry.
3D domain swapping in the TIM barrel of the α subunit of Streptococcus pneumoniae tryptophan synthase
Tryptophan synthase catalyzes the last two steps of tryptophan biosynthesis in plants, fungi and bacteria. It consists of two protein chains, designated α and β, encoded by trpA and trpB genes, that function as an αββα complex. Structural and functional features of tryptophan synthase have been extensively studied, explaining the roles of individual residues in the two active sites in catalysis and allosteric regulation. TrpA serves as a model for protein-folding studies. In 1969, Jackson and Yanofsky observed that the typically monomeric TrpA forms a small population of dimers. Dimerization was postulated to take place through an exchange of structural elements of the monomeric chains, a phenomenon later termed 3D domain swapping. The structural details of the TrpA dimer have remained unknown. Here, the crystal structure of the Streptococcus pneumoniae TrpA homodimer is reported, demonstrating 3D domain swapping in a TIM-barrel fold for the first time. The N-terminal domain comprising the H0–S1–H1–S2 elements is exchanged, while the hinge region corresponds to loop L2 linking strand S2 to helix H2′. The structural elements S2 and L2 carry the catalytic residues Glu52 and Asp63. As the S2 element is part of the swapped domain, the architecture of the catalytic apparatus in the dimer is recreated from two protein chains. The homodimer interface overlaps with the α–β interface of the tryptophan synthase αββα heterotetramer, suggesting that the 3D domain-swapped dimer cannot form a complex with the β subunit. In the crystal, the dimers assemble into a decamer comprising two pentameric rings.
Human cytochrome P450 17A1 structures with metabolites of prostate cancer drug abiraterone reveal substrate-binding plasticity and a second binding site
Abiraterone acetate is a first-line therapy for castration-resistant prostate cancer. This prodrug is deacetylated in vivo to abiraterone, which is a potent and specific inhibitor of cytochrome P450 17A1 (CYP17A1). CYP17A1 performs two sequential steps that are required for the biosynthesis of androgens that drive prostate cancer proliferation, analogous to estrogens in breast cancer. Abiraterone can be further metabolized in vivo on the steroid A ring to multiple metabolites that also inhibit CYP17A1. Despite its design as an active-site-directed substrate analog, abiraterone and its metabolites demonstrate mixed competitive/noncompetitive inhibition. To understand their binding, we solved the X-ray structures of CYP17A1 with three primary abiraterone metabolites. Despite different conformations of the steroid A ring and substituents, all three bound in the CYP17A1 active site with the steroid core packed against the I helix and the A ring C3 keto or hydroxyl oxygen forming a hydrogen bond with N202 similar to abiraterone itself. The structure of CYP17A1 with 3-keto, 5α-abiraterone was solved to 2.0 Å, the highest resolution to date for a CYP17A1 complex. This structure had additional electron density near the F/G loop, which is likely a second molecule of the inhibitor and which may explain the noncompetitive inhibition. Mutation of the adjacent Asn52 to Tyr positions its side chain in this space, maintains enzyme activity, and prevents binding of the peripheral ligand. Collectively, our findings provide further insight into abiraterone metabolite binding and CYP17A1 function.
Magnetization dynamics and frustration in the multiferroic double perovskite Lu 2 MnCoO 6
Here, we investigate the magnetic ordering and the magnetization dynamics (from kHz to THz time scales) of the double perovskite Lu 2 MnCoO 6 using elastic neutron diffraction, muon spin relaxation, and micro-Hall magnetization measurements. This compound is known to be a type II multiferroic with the interesting feature that a ferromagneticlike magnetization hysteresis loop couples to an equally hysteretic electric polarization in the bulk of the material despite a zero-field magnetic ordering of the type ↑↑↓↓ along Co-Mn spin chains. Here we explore the unusual dynamics of this compound and find extremely strong fluctuations, consistent with the axial next-nearest-neighbor Ising (ANNNI) model for frustrated spin chains. We identify three temperature scales in Lu 2 MnCoO 6 corresponding to the onset of highly fluctuating long-range order below T N = 50±3 K identified from neutron scattering, the onset of magnetic and electric hysteresis, with change in kHz magnetic and electric dynamics below a 30 K temperature scale, and partial freezing of ~MHz spin fluctuations in the muon spin relaxation data below 12 ± 3 K. Our results provide a framework for understanding the multiferroic behavior of this compound and its hysteresis and dynamics.
A green closed-loop process for selective recycling of lithium from spent lithium-ion batteries
As the economy started to recover from the COVID pandemic, the price of Li 2 CO 3 skyrocketed to its highest. This situation has aggravated concerns about the supply chain for lithium-ion batteries (LIBs). Recycling spent LIBs is a potential solution to alleviate the bottleneck of the supply chain and prevent environmental pollution, and has attracted lots of attention. However, lithium recycling is generally disregarded because of the complex recycling process and its low recycling efficiency. Here, in this work we developed a sustainable lithium recovery process, which can selectively leach and recover lithium with formic acid before recycling valuable metals. With the reported method, lithium can be 99.8% recovered from layered oxide cathode materials with 99.994% purity. In addition, this lithium recovery process is affordable, compared to the typical hydrometallurgical process, by saving 11.15% per kilogram of spent LIBs. Therefore, this research provided a new solution to eliminating the effects of lithium ions on valuable metal separation and the co-precipitation reaction and precluding the influence of other metal ions on lithium recovery. Finally, this simplified lithium recovery process provides new opportunities for sustainable recycling of LIBs and economical restoration of the lithium supply chain.