A Proactive–Reactive Methodology for Cyber-Resilient Inverter Control System
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Abstract Transcription rates are regulated by the interactions between RNA polymerase, sigma factor, and promoter DNA sequences in bacteria. However, it remains unclear how non-canonical sequence motifs collectively control transcription rates. Here, we combine massively parallel assays, biophysics, and machine learning to develop a 346-parameter model that predicts site-specific transcription initiation rates for any σ 70 promoter sequence, validated across 22132 bacterial promoters with diverse sequences. We apply the model to predict genetic context effects, design σ 70 promoters with desired transcription rates, and identify undesired promoters inside engineered genetic systems. The model provides a biophysical basis for understanding gene regulation in natural genetic systems and precise transcriptional control for engineering synthetic genetic systems.
We examined phylogeographic structure in gray fox (Urocyon cinereoargenteus) across the United States to identify the location of secondary contact zone(s) between eastern and western lineages and investigate the possibility of additional cryptic intraspecific divergences. We generated and analyzed complete mitochondrial genome sequence data from 75 samples and partial control region mitochondrial DNA sequences from 378 samples to investigate levels of genetic diversity and structure through population- and individual-based analyses including estimates of divergence (FST and SAMOVA), median joining networks, and phylogenies. We used complete mitochondrial genomes to infer phylogenetic relationships and date divergence times of major lineages of Urocyon in the United States. Despite broad-scale sampling, we did not recover additional major lineages of Urocyon within the United States, but identified a deep east-west split (~0.8 million years) with secondary contact at the Great Plains Suture Zone and confirmed the Channel Island fox (Urocyon littoralis) is nested within U. cinereoargenteus. Genetic diversity declined at northern latitudes in the eastern United States, a pattern concordant with post-glacial recolonization and range expansion. Beyond the east-west divergence, morphologically-based subspecies did not form monophyletic groups, though unique haplotypes were often geographically limited. Gray foxes in the United States displayed a deep, cryptic divergence suggesting taxonomic revision is needed. Secondary contact at a common phylogeographic break, the Great Plains Suture Zone, where environmental variables show a sharp cline, suggests ongoing evolutionary processes may reinforce this divergence. Follow-up study with nuclear markers should investigate whether hybridization is occurring along the suture zone and characterize contemporary population structure to help identify conservation units. Comparative work on other wide-ranging carnivores in the region should test whether similar evolutionary patterns and processes are occurring.
Synthetic nucleic acids are a key input to modern biotechnology, yet they represent dual-use materials that require robust screening to mitigate biosecurity risks. The prevailing screening paradigm, which identifies sequences of concern (SoCs) through sequence similarity to controlled pathogens and toxins, may not fully capture risks posed by AI tools that can decouple biomolecular function from reliance on known sequences. Rapidly advancing biodesign capabilities enable the generation of genes and proteins that might evade sequence-based detection. We highlight the critical need for function-based screening approaches that can detect sequences capable of hazardous biological functions, regardless of similarity to known SoCs. We examine the feasibility of function-based screening with an initial focus on proteins, arguing that, while protein sequence space is vast, biologically functional proteins are significantly constrained by biophysical and biochemical requirements that can be learned and modeled. We propose a concrete implementation framework organized along a continuum of complexity, starting with toxins as the most tractable targets before expanding to more complex pathogenic functions. We then discuss open challenges and describe a research and development strategy to address them.
The Aerojet General Nucleonics (AGN) model 201-Modified, known as the AGN-201M reactor, plays an essential role in the educational and research activities at Idaho State University (ISU). The ISU AGN-201M's original Control Rod Drive Mechanism (CRDM) has been in operation for more than fifty years with no large-scale redesigns. The CRDM is required to eject the fuel rods within one second during a SCRAM event (also known as a 'reactor trip') and adjust the control rods' insertion speed, and keeps the rod insertion sequence correct. The existing control rod drive mechanisms meet these criteria but experience a few concerns due to aging. Concerns include complex maintenance and costly repairs for old electromechanical components, rod position feedback errors, and the impediment of the plate during a SCRAM due to binding of the lead screws of the existing mechanism. During a binding event, the drive mechanism becomes locked, preventing the control rod's magnetic plate from moving in or out under the reactor's normal and emergency operating conditions. Although, the binding has no effect on the ability of the rod to exit the core during the SCRAM. To counteract the concerns and issues with the current CRDM, a new design has been proposed using newer components and a simplified design. The new design utilizes more advanced electric and mechanical components that are commercially available. The new CRDM system is divided into four main aspects: (1) control rod movement design (motor, lead screw, guide rods), (2) control rod ejection (springs, electromagnet), (3) control rod position and feedback (position transducer, microswitches), and (4) material selection and structural analysis. The new design aims to reduce the overall complexity and probability of failure to improve the reactor's overall reliability. With proper material selection and improved structural design, the new drives are lighter with little to no change in structural integrity. The new control rod drive mechanism eliminates binding scenarios by using a single lead screw and implementing additional guide rods. An advanced linear position sensor and microswitches replace the existing and aging synchro system for accurate rod position feedback resulting in better reactivity control. The new design meets the reactor's operational limits by having an average reactivity insertion of 0.065% Δk/k per second, which corresponds to a total control rod insertion time of 19.23 s, while the control rod's ejection time remains less than one second during a SCRAM event. The new design ensures the reactor's long-term viability for educational and research activities by increasing the reliability and safety of operation for years to come.
An electronic device handles accesses of a branch prediction functional block when executing instructions in program code. The electronic device includes a processor having the branch prediction functional block that provides branch prediction information for control transfer instructions (CTIs) in the program code and a minimum predictor use (MPU) functional block. The MPU functional block determines, based on a record associated with a given fetch group of instructions, that a specified number of subsequent fetch groups of instructions that were previously determined to include no CTIs or conditional CTIs that were not taken are to be fetched for execution in sequence following the given fetch group. The MPU functional block then, when each of the specified number of the subsequent fetch groups is fetched and prepared for execution, prevents corresponding accesses of the branch prediction functional block for acquiring branch prediction information for instructions in that subsequent fetch group.
Advanced simulations and calculations on quantum computers require high-fidelity implementations of quantum operations. The universal gateset approach builds complex unitaries from a small set of primitive gates, often resulting in a long gate sequence, which is typically a leading factor in the total accumulated error. Compiling a complex unitary for processors with higher-dimensional logical elements, such as qutrits, exacerbates the accumulated error per unitary, since an even longer gate sequence is required. Optimal control methods promise time- and resource-efficient compact gate sequences and, therefore, higher fidelity. These methods generate pulses that can directly implement any complex unitary on a quantum device. In this work, we demonstrate that any arbitrary qubit and qutrit gate can be realized with high fidelity, which can significantly reduce the length of a gate sequence. We generate and test pulses for a large set of randomly selected arbitrary unitaries on several quantum processing units (QPUs): the Lawrence Livermore National Laboratory Quantum Device and Integration Testbed’s (QuDIT’s) standard QPU and three of Rigetti’s QPUs: Ankaa-2, Ankaa-9Q-1, and Aspen-M-3. On the QuDIT platform’s standard QPU, the average fidelity of random qutrit gates is 97.9 ± 0.5% measured with conventional QPT and 98.8 ± 0.6% from QPT with gate folding. Rigetti’s Ankaa-2 achieves random qubit gates with an average fidelity of 98.4 ± 0.5% (conventional QPT) and 99.7 ± 0.1% (QPT with gate folding). On Ankaa-9Q-1 and Aspen-M-3, the average fidelities with conventional qubit QPT measurements were higher than 99% (see Appendix). Here we show that optimal control gates are robust to drift for at least 3 h and that the same calibration parameters can be used for all implemented gates. Our work promises that the calibration overheads for optimal control gates can be made small enough to enable efficient quantum circuits based on this technique.
SUMMARY Monoterpene synthases (MTSs) catalyze the first committed step in the biosynthesis of monoterpenoids, a class of specialized metabolites with particularly high chemical diversity in angiosperms. In addition to accomplishing a rate enhancement, these enzymes manage the formation and turnover of highly reactive carbocation intermediates formed from a prenyl diphosphate substrate. At each step along the reaction path, a cationic intermediate can be subject to cyclization, migration of a proton, hydride, or alkyl group, or quenching to terminate the sequence. However, enzymatic control of ligand folding, stabilization of specific intermediates, and defined quenching chemistry can maintain the specificity for forming a signature product. This review article will discuss our current understanding of how angiosperm MTSs control the reaction environment. Such knowledge allows inferences about the origin and regulation of chemical diversity, which is pertinent for appreciating the role of monoterpenoids in plant ecology but also for aiding commercial efforts that harness the accumulation of these specialized metabolites for the food, cosmetic, and pharmaceutical industries.
Suzuki catalyst transfer polymerization (SCTP) has emerged as an effective method for accessing length-controlled π-conjugated poly(p-phenylene). Regio-controlled functional group sequencing along the backbone and the chain ends of synthetic polymers remains a challenge for the successful integration of organic semiconductors in sensors and electronic devices. Here, we report a bidirectional SCTP system based on dinuclear palladium(II) initiators. Functional groups transferred during the initiation and termination steps unlock independently addressable synthetic handles at the polymer core and respective chain ends. These functional groups open opportunities for late-stage regio-controlled and chemoselective derivatizations. Control over key polymer parameters, including molecular weight (M n ), dispersity ( Đ = M w /M n ), degree of polymerization ( DP ), termination efficiency, and functional group interconversion, is corroborated by size exclusion chromatography (SEC) and NMR spectroscopy. The modular design of SCTP initiators, in combination with commercially available terminating groups, represents a highly flexible toolbox for late-stage polymer conjugation, e.g., chemoselective anchoring groups for integration with functional electronics or bioorthogonal conjugation for molecular sensing.
We herein report the reactivity and regioselectivity of 2-pyrenyl as a coupling unit in Scholl reactions. On the basis of the Scholl reactions of hexaarylbenzene substrates, we have found that pyrenyl units are preferably oxidized over naphthyl and phenyl units under appropriate Scholl reaction conditions, allowing divergent synthesis through a highly controllable intramolecular coupling sequence. We find that the C1 and C3 positions of the 2-pyrenyl unit are the favorable sites for intramolecular coupling while C4 is not reactive to allow further coupling. The reactivity and regioselectivity pattern can be explained by the spin density distribution, which shows that carbon–carbon bonds preferably form at sites with higher positive spin density. Guided by these findings, we successfully synthesized a double helicene and a sextuple helicene through the controlled Scholl reactions of 2-pyrenyl units.
ABSTRACT Below-ground carbon transformations that contribute to healthy soils represent a natural climate change mitigation, but newly acquired traits adaptive to climate stress may alter microbial feedback mechanisms. To better define microbial evolutionary responses to long-term climate warming, we study microorganisms from an ongoing in situ soil warming experiment where, for over three decades, temperate forest soils are continuously heated at 5°C above ambient. We hypothesize that across generations of chronic warming, genomic signatures within diverse bacterial lineages reflect adaptations related to growth and carbon utilization. From our bacterial culture collection isolated from experimental heated and control plots, we sequenced genomes representing dominant taxa sensitive to warming, including lineages of Actinobacteria, Alphaproteobacteria, and Betaproteobacteria. We investigated genomic attributes and functional gene content to identify signatures of adaptation. Comparative pangenomics revealed accessory gene clusters related to central metabolism, competition, and carbon substrate degradation, with few functional annotations explicitly associated with long-term warming. Trends in functional gene patterns suggest genomes from heated plots were relatively enriched in central carbohydrate and nitrogen metabolism pathways, while genomes from control plots were relatively enriched in amino acid and fatty acid metabolism pathways. We observed that genomes from heated plots had less codon bias, suggesting potential adaptive traits related to growth or growth efficiency. Codon usage bias varied for organisms with similar 16S rrn operon copy number, suggesting that these organisms experience different selective pressures on growth efficiency. Our work suggests the emergence of lineage-specific trends as well as common ecological-evolutionary microbial responses to climate change. IMPORTANCE Anthropogenic climate change threatens soil ecosystem health in part by altering below-ground carbon cycling carried out by microbes. Microbial evolutionary responses are often overshadowed by community-level ecological responses, but adaptive responses represent potential changes in traits and functional potential that may alter ecosystem function. We predict that microbes are adapting to climate change stressors like soil warming. To test this, we analyzed the genomes of bacteria from a soil warming experiment where soil plots have been experimentally heated 5°C above ambient for over 30 years. While genomic attributes were unchanged by long-term warming, we observed trends in functional gene content related to carbon and nitrogen usage and genomic indicators of growth efficiency. These responses may represent new parameters in how soil ecosystems feedback to the climate system.
Poly(ethylene terephthalate) (PET) oligomers derived from glycolysis depolymerization were converted into multiblock copolymers through diisocyanate-mediated coupling with dihydroxy-terminated oligomers, enabling precise control over copolymer sequence distribution, connectivity, and mechanical performance. Here, we demonstrate that telechelic PET oligomers isolated directly from depolymerized consumer waste can serve as reactive building blocks for the formation of segmented multiblock copolymers, eliminating the need to revert to monomeric feedstocks. Dihydroxy-terminated PET oligomers (Mw ≈ 8 kg mol−1) were coupled with poly(ethylene oxide) (PEO, Mw ≈ 4 kg mol−1) to form PET-PEO multiblock copolymers with high molar mass (Mw ≈ 160 kg mol−1). We further show that the timing of end-capping reactions provides a key control parameter that governs the competition between chain extension and termination, thereby dictating the resulting multiblock architecture and molecular-weight evolution. Evaluation of their mechanical properties reveals that virgin PET exhibits high modulus (∼3 GPa) and strength (43 MPa) but limited ductility (<10% elongation). In contrast, PET–PEO multiblock copolymers retain comparable tensile strength (44 MPa), albeit while exhibiting dramatically enhanced ductility (>90% elongation), forming tougher materials with efficient stress transfer between the rigid PET domains and the flexible PEO segments. When incorporated into PET/PEO blends at low loadings, the multiblock copolymers serve as effective compatibilizers, yielding materials with an intermediate modulus (1.1–1.2 GPa) and improved elongation compared to uncompatibilized blends. Furthermore, the presence of PEO blocks increases water uptake and gas permeability relative to virgin PET, reflecting the tunability of molecular transport through the copolymeric blocks. To our knowledge, this represents the first report of PET–PEO multiblock copolymers derived from post-consumer PET for gas transport applications. These results demonstrate that multiblock copolymer formation from telechelic PET oligomers provides a versatile platform for tailoring the mechanical and transport behavior of polyester-based materials through controlled macromolecular design and establishes a generalizable strategy for transforming consumer plastic waste into functional segmented polymers without requiring complete depolymerization to monomers.
Here, we present an iterative scheme to estimate the minimal duration in which a quantum gate can be realized while satisfying hardware constraints on the control pulse amplitudes. The scheme performs a sequence of unconstrained numerical optimal control cycles that each minimize the gate fidelity for a given gate duration alongside an additional penalty term for the control pulse amplitudes. After each cycle, the gate duration is adjusted based on the inverse of the resulting maximum control pulse amplitudes by re-scaling the dynamics to a new duration where control pulses satisfy the amplitude constraints. Those scaled controls then serve as an initial guess for the next unconstrained optimal control cycle, using the adjusted gate duration. We provide multiple numerical examples that each demonstrate fast convergence of the scheme toward a gate duration that is close to the quantum speed limit, given the control pulse amplitude bound. The proposed technique is agnostic to the underlying system and control Hamiltonian models, as well as the target unitary gate operation, making the time-scaling iteration an easy to implement and practically useful scheme for reducing the durations of quantum gate operations.
Most off-highway constructions and agriculture equipment use hydraulics, which has unmatched power density, for power transmission and throttling as a means for control. A novel hybrid hydraulic-electric architecture (HHEA) has recently been proposed to improve efficiency for high-power machines that would have been cost-prohibitive to electrify directly. HHEA uses a set of common pressure rails (CPRs) to transmit the majority of power hydraulically and small electric motor drives to modulate that power and to achieve precise control. This article proposes a computationally efficient Lagrange multiplier method (LMM) for computing the optimal sequence of pressure rail selections to minimize energy use. This is needed to evaluate HHEA's energy-saving potential and for iterative architecture design and sizing. An interesting complication is that the cost function is not fully defined until the candidate control sequence is fully specified. This issue is dealt with by decomposing the original problem into a set of sub-problems with additional constraints that can be solved efficiently. Computational effort can be further reduced if actuators are optimized individually instead of together. However, additional steps are required to prevent the constraint functions from becoming discontinuous with respect to the Lagrange multipliers, which is necessary for meeting the constraints. Lastly, a case study of a construction machine demonstrates the efficacy of the method and shows that the HHEA reduces energy consumption by 68%-73% compared to the baseline load-sensing architecture.
Natural organisms make a wide variety of exquisitely complex, nano-, micro-, and macroscale structured materials in an energy-efficient and highly reproducible manner. During these processes, the information-carrying biomolecules (e.g., proteins, peptides, and carbohydrates) enable (1) hierarchical organization to assemble scaffold materials and execute high-level functions and (2) exquisite control over inorganic materials synthesis, generating biominerals whose properties are optimized for their functions. Inspired by nature, significant efforts have been devoted to developing functional materials that can rival those natural molecules by mimicking in vivo functions using engineered proteins, peptides, DNAs, sequence-defined synthetic molecules (e.g., peptoids), and other biomimetic polymers. Among them, peptoids, a new type of synthetic mimetics of peptides and proteins, have received particular attention because they combine the merits of both synthetic polymers (e.g., high chemical stability and efficient synthesis) and biomolecules (e.g., sequence programmability and biocompatibility). The lack of both chirality and hydrogen bonds in their backbone results in a highly designable peptoid-based system with reduced structural complexity and side chain-chemistry-dominated properties. Here in this Account, we present our recent efforts in this field by programming amphiphilic peptoid sequences for (1) the controlled self-assembly into different hierarchically structured nanomaterials with favorable properties and (2) manipulating inorganic (nano)crystal nucleation, growth, and assembly into superstructures. First, we designed a series of amphiphilic peptoids with controlled side chain chemistries that self-assembled into 1D highly stiff and dynamic nanotubes, 2D membrane-mimetic nanosheets, hexagonally patterned nanoribbons, and 3D nanoflowers. These crystalline nanostructures exhibited sequence-dependent properties and showed promise for different applications. The corresponding peptoid self-assembly pathways and mechanisms were also investigated by leveraging in situ atomic force microscopy studies and molecular dynamics simulations, which showed precise sequence dependency. Second, inspired by peptide- and protein-controlled formation of hierarchical inorganic nanostructures in nature, we developed peptoid-based biomimetic approaches for controlled synthesis of inorganic materials (e.g., noble metals and calcite), in which we took advantage of the substantial side chain chemistry of peptoids and investigated the relationship between the peptoid sequences and the morphology and growth kinetics of inorganic materials. For example, to overcome the challenges (e.g., complexity of protein- and peptide-folding, poor thermal and chemical stabilities) facing the area of protein- and peptide-controlled synthesis of inorganic materials, we recently reported the design of sequence-defined peptoids for controlled synthesis of highly branched plasmonic gold particles. Moreover, we developed a rule of thumb for designing peptoids that predictively enabled the morphological evolution from spherical to coral-shaped gold nanoparticles (NPs). With this Account, we hope to stimulate the research interest of chemists and materials scientists and promote the predictive synthesis of functional and robust materials through the design of sequence-defined synthetic molecules.
ABSTRACT Bacteriophages (phages) are ubiquitous entities present in every conceivable habitat as a result of their bacterial parasitism. Their prevalence and impact in the ecology of bacterial communities and their ability to control pathogens make their characterization essential, particularly of new phages, improving knowledge and potential application. The isolation and characterization of a new lytic phage against Sphaerotilus natans strain DSM 6575, named vB_SnaP-R1 (SnaR1), is here described. Besides being the first sequenced genome of a Sphaerotilus natans infecting phage, 99% of its 41507 bp genome lacks homology with any other sequenced phage, revealing its uniqueness and previous lack of knowledge. Moreover, SnaR1 is the first Podoviridae phage described infecting this bacterium. Sphaerotilus natans is an important filamentous bacterium due to its deleterious effect on wastewater treatment plants (WWTP) and thus, phages may play a role as novel biotechnological tools against filamentous overgrowth in WWTP. The lytic spectrum of SnaR1 was restricted to its host strain, infecting only one out of three S. natans strains and infection assays revealed its ability to reduce bacterial loads. Results suggest SnaR1 as the prototype of a new phage genus and demonstrates its potential as a non-chemical alternative to reduce S. natans DSM 6575 cells.
Highlights: • 4996 mRNAs and 2942 circRNAs were identified differentially expressed in platelets of AS patients. • Several platelet-derived immune mediators were upregulated to regulate the interaction between platelets and immune cells. • Two downregulated circRNA were identified, and the corresponding circRNA-miRNA-mRNA regulatory network was constructed. • mRNAs and circRNAs found herein could be used as diagnostic biomarkers or new therapeutic targets. Ankylosing spondylitis (AS) is a chronic inflammatory disease significantly decreasing the quality of life. Platelets play an important and active role in the development of AS. Accumulating evidence demonstrated platelets contain diverse RNA repository inherited from megakaryocytes or microvesicles. Platelet RNAs are dynamically affected by pathological conditions and could be used as diagnostic or prognostic biomarkers. However, the role of the platelet RNAs in AS is elusive. In this study, we compared mRNA and circRNA profiles in platelets between AS patients and healthy controls using RNA sequencing and bioinformatic analysis, and found 4996 mRNAs and 2942 circRNAs were differently expressed. The significantly over-expressed mRNAs in AS patients are involved in platelet activity, gap junction, focal adhesion, rap1 and toll and Imd signaling pathway. The previous identified platelet-derived immune mediators such as P2Y1, P2Y12, PF4, GPIbα, CD40L, ICAM2, CCL5 (RANTES), TGF-β (TGF-β1 and TGF-β2) and PDGF (PDGFB and PDGFA) are also included in these over expressed mRNAs, implying these factors may trigger inflammatory cascades and promote the development of AS. Additionally, we found two down-regulated circRNA (circPTPN22 and circFCHSD2) from the intersection analyses of platelets and spinal ligament tissues of AS patients. The circRNA-miRNA-mRNA regulatory network of these two circRNAs was constructed, and the target mRNAs were enriched in Th17 cell differentiation, inflammatory bowel disease, cell adhesion molecules, cytokine-cytokine receptor interaction, Jak-STAT and Wnt signaling pathway, all these pathways participate in the bone remodeling and pro/anti-inflammatory immune regulation in AS. Then, qRT-PCR was performed to validate the expression of selected key mRNAs and circRNAs and the results demonstrated that the expression levels of P2Y12, GPIbα, circPTPN22 and circFCHSD2 were consistent with the sequencing analysis. In addition, the high expression of five predicted miRNAs interacting with circPTPN22 and circFCHSD2 were also detected in AS by qRT-PCR. Taken together, our study presents a comprehensive overview of mRNAs and circRNAs in platelets in AS patients and offers new insight into the mechanisms of platelet involving in the pathogenesis of AS. The mRNAs and circRNAs identified in this study may serve as candidates for diagnosis and targeted treatment of AS.
Achieving the long-term stability of perovskite solar cells is arguably the most important challenge required to enable widespread commercialization. Understanding the perovskite crystallization process and its direct impact on device stability is critical to achieving this goal. The commonly employed dimethyl-formamide/dimethyl-sulfoxide solvent preparation method results in a poor crystal quality and microstructure of the polycrystalline perovskite films. In this work, we introduce a high-temperature dimethyl-sulfoxide-free processing method that utilizes dimethylammonium chloride as an additive to control the perovskite intermediate precursor phases. By controlling the crystallization sequence, we tune the grain size, texturing, orientation (corner-up versus face-up) and crystallinity of the formamidinium (FA)/caesium (FA) y Cs 1-y Pb(I x Br 1-x )3 perovskite system. A population of encapsulated devices showed improved operational stability, with a median T80 lifetime (the time over which the device power conversion efficiency decreases to 80% of its initial value) for the steady-state power conversion efficiency of 1,190 hours, and a champion device showed a T80 of 1,410 hours, under simulated sunlight at 65 degrees C in air, under open-circuit conditions. In conclusion, this work highlights the importance of material quality in achieving the long-term operational stability of perovskite optoelectronic devices.