Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein
Abstract not provided
Ye, Qiaozhen↗
SEARCH · Search NASA
Results for “sequence design”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Integrated Solutions for Optimized Performance (ISOP) Final Technical Report
The goal of this project was to demonstrate technical feasibility of an integrated approach for deep energy retrofits by packaging innovative technologies with smart communicating controls that represent the next generation of energy efficiency. The integrated solutions for optimized performance (ISOP) package integrates (i) advanced lighting and plug load controls; (ii) intelligent daylight harvesting through automated self-powered shades and window films; (iii) advanced HVAC controls sequences (ASHRAE Guideline (GDL) 36); and (iv) fault detection and diagnosis (FDD) and continuous commissioning (CCx) using advanced analytics. These technologies address energy use across multiple building end uses that represent more than 60% of the energy consumption in all commercial buildings. The project was structured to be implemented over three budget periods: Budget Period 1 scope included site selection, project design, site-specific customization of technology packages, procurement of technologies, initiation of installation of technologies, the development of a measurement and verification plan and collection of pre-retrofit data collection. The first year go/no-go decision was based on securing host sites representing 250,000 sq. ft. of occupied operational spaces, savings analysis, technology procurement and initiation of installation. Budget Period 2 planned to complete technology installations and initiate data collection of post-retrofit performance data. The second year go/no-go was to be the completion of technology installations and commissioning, metering and data collecting to support the requirements laid out in site specific M&V plans. Budget Period 3 planned to collect and analyze post-retrofit performance data and provide data and reporting to support energy efficiency rebate programs. After the team completed activities planned for Budget Period 1, the team reached a Go/No-Go Decision Point. At that point, TRC recommended that DOE discontinue the project without prejudice due to challenges with securing demonstration sites to meet the full 250,000 sf of occupied operational spaces and DOE concurred. In Budget Period 1, the TRC team developed criteria to recruit and evaluate potential demonstration host sites. TRC worked with Princeton University, the project demonstration partner, to identify buildings on their campus as potential candidates for the demonstration. Following the selection of demonstration sites, the TRC team customized energy technology packages according to the needs and characteristics of each site. TRC defined technology specifications, identified vendors, and conducted analysis to estimate energy and cost savings potential. The project team then developed schedules for technology procurement processes and scheduled for installation at all selected demonstration sites. The project team worked with Princeton University and DOE to develop an approach to verify energy savings achieved through measurement and verification (M&V) 2.0 methods. Princeton University initiated open bids to procure the necessary materials and installation contractors. Bid results came back higher than estimates due to a couple of factors – lack of familiarity of the bidders with the proposed technologies and lack of local trained installers to execute the installation of these new measures. Due to the higher bids, projects no longer met the internal cost-effectiveness criteria used by Princeton to proceed with procurement of the full suite of technologies as proposed in ISOP. Princeton had already procured parts of the ISOP package as part of a campus-wide initiative for FDD and lighting retrofits, but with the higher costs for other ISOP components, Princeton could no longer commit to the full ISOP package on the selected sites. Based on this, the team reached the Go/No-Go decision point, where they decided not to proceed with the project. Princeton is separately installing portions of the ISOP package where they individually meet Princeton’s payback criteria but on a different schedule than would have been needed for the DOE ISOP project. The team has learned several lessons from project progress in the first budget period. The team will utilize these lessons in future projects, as should any team which proceeds with a project around the ISOP technology. The first lesson is that more information about the proposed sites is required earlier in the process (perhaps even at the proposal stage) in order to have a successful demonstration. Technical details not evident earlier in the process (such as the TLED limitations for ALCS) can derail project execution. The second lesson is that pricing of emerging technologies is highly variable due to lack of familiarity of local installers and distributor with the proposed technologies as well as alternate bids using products they were more familiar with, but that cost more than the ones proposed by TRC. Finally, the last major lesson is that the host site’s internal project criteria is of critical importance. Based on these higher installed costs and lack of an informed installer base for the products proposed for this project, the project does not meet Princeton’s simple payback goals of five years.
32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
Utilities Perspective on Protection Challenges with High IBR Penetration
Utilities have seen rapid increase in Solar, Wind, and Battery Energy Storage Resources that interconnect to their electric system through Inverters. Inverter-Based Resources (IBRs) have fault current characteristics that are unlike the fault current response of traditional rotating-machine-based generators, which is well known and repeatable. IBR’s non-traditional fault current behavior is due to the IBR control scheme, which is configured to provide a clean AC output but also protect the inverter’s sensitive power electronics devices from damage, one source of which is overcurrent. This results in low fault current magnitude, low or no negative sequence current injection, the variability of sequence component currents, the variability of voltage with respect to current angles, and the lack of inertia. The control scheme also results in a fault current response that can vary between manufactures and between models of the same manufacturer. High penetration of IBRs can adversely affect the protection schemes applied in areas with high penetration of IBRs. With the proliferation of IBRs, utilities are finding out that conventional protection schemes are not adequately equipped to protect the electric systems. This is mainly because the existing protection elements and practices have been designed based on the fault current response of conventional rotating machines. In several cases, the available literature does not provide any clear solution for the issues when the protection scheme does not operate properly near IBRs. This presentation identifies various protection challenges due to IBRs that industry is facing, from the utility perspective. Instead of facing on one issue, we are looking broadly on all the challenges that system protection has experienced with high penetration of IBRs. Based on the IBR response from various utilities during real fault events and gathering perspective from different utility SMEs via questionnaire, the presentation summarizes on gathered data and internal experiences.
24 POWER TRANSMISSION AND DISTRIBUTION↗
Directed Synthesis of Gold Nanoparticle Superstructures Using Self-Assembling Peptoids Containing Metal-Bonding N-Heterocyclic Carbenes
N-Heterocyclic carbene (NHC) ligands, with strong metal-binding affinity, offer a robust platform for constructing organic–inorganic nanohybrids with high stability and tunable properties. However, achieving precise structural control in a simple manner remains challenging. Here, we report a one-pot synthesis of nanohybrids using self-assembling peptoids functionalized with histidine-2-ylidene, which simultaneously enable peptoid assembly and NHC–metal binding. Histidine-2-ylidene-functionalized peptoids were designed to self-assemble and provide NHC binding sites, while AuNPs served as the inorganic component due to NHCs’ strong affinity for gold surfaces. The resulting peptoid-NHC@AuNPs form well-defined vesicles that are characterized by UV–vis spectroscopy, X-ray photoelectron spectroscopy, and electron microscopy. Importantly, the vesicle size and morphology can be tuned via the peptoid sequence or environmental conditions. Further experiments highlight the crucial role of the NHC sites in the formation and stabilization of these nanohybrids. This modular strategy offers a versatile route to fabricating functional NHC-based nanohybrids for potential applications in sensing.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Hamiltonian simulation in Zeno subspaces
Here, we investigate the quantum Zeno effect as a framework for designing and analyzing quantum algorithms for Hamiltonian simulation. We show that frequent projective measurements of an ancilla qubit register can be used to simulate quantum dynamics on a target qubit register with a circuit complexity similar to randomized approaches. The classical sampling overhead in the latter approaches is traded for ancilla qubit overhead in Zeno-based approaches. A second-order Zeno sequence is developed to improve scaling and implementations through unitary kicks are discussed. We derive rigorous error bounds that allow for identifying the associated circuit complexities for the first- and second-order Zeno sequences. We show that the circuits over the combined register can be identified as a subroutine commonly used in post-Trotter Hamiltonian simulation methods. We build on this observation to reveal connections between different Hamiltonian simulation algorithms.
Hamiltonian simulation↗
Bacterial Community Members Increase Bacillus subtilis Maintenance on the Roots of Arabidopsis thaliana
Plant-growth-promoting bacteria (PGPB) are used to improve plant health and promote crop production. However, because some PGPB (including Bacillus subtilis) do not maintain substantial colonization on plant roots over time, it is unclear how effective PGPB are throughout the plant growing cycle. A better understanding of the dynamics of plant root community assembly is needed to develop and harness the potential of PGPB. Although B. subtilis is often a member of the root microbiome, it does not efficiently monoassociate with plant roots. We hypothesized that B. subtilis may require other primary colonizers to efficiently associate with plant roots. We utilized a previously designed hydroponic system to add bacteria to Arabidopsis thaliana roots and monitor their attachment over time. We inoculated seedlings with B. subtilis and individual bacterial isolates from the native A. thaliana root microbiome either alone or together. We then measured how the coinoculum affected the ability of B. subtilis to colonize and maintain on A. thaliana roots. We screened 96 fully genome-sequenced strains and identified five bacterial strains that were able to significantly improve the maintenance of B. subtilis. Three of these rhizobacteria also increased the maintenance of two strains of B. amyloliquefaciens commonly used in commercially available bioadditives. These results not only illustrate the utility of this model system to address questions about plant–microbe interactions and how other bacteria affect the ability of PGPB to maintain their relationships with plant roots but also may help inform future agricultural interventions to increase crop yields.
59 BASIC BIOLOGICAL SCIENCES↗
Natural Horizontal Gene Transfer of Antimicrobial Resistance Genes in Campylobacter spp. From Turkeys and Swine
Antibiotic-resistant Campylobacter constitutes a serious threat to public health. The clonal expansion of resistant strains and/or the horizontal spread of resistance genes to other strains and species can hinder the clinical effectiveness of antibiotics to treat severe campylobacteriosis. Still, gaps exist in our understanding of the risks of acquisition and spread of antibiotic resistance in Campylobacter. While the in vitro transfer of antimicrobial resistance genes between Campylobacter species via natural transformation has been extensively demonstrated, experimental studies have favored the use of naked DNA to obtain transformants. In this study, we used experimental designs closer to real-world conditions to evaluate the possible transfer of antimicrobial resistance genes between Campylobacter strains of the same or different species (Campylobacter coli or Campylobacter jejuni) and originating from different animal hosts (swine or turkeys). This was evaluated in vitro through co-culture experiments and in vivo with dual-strain inoculation of turkeys, followed by whole genome sequencing of parental and newly emerged strains. In vitro, we observed four independent horizontal gene transfer events leading to the acquisition of resistance to beta-lactams (blaOXA), aminoglycosides [aph(2")-If and rpsL] and tetracycline [tet(O)]. Observed events involved the displacement of resistance-associated genes by a mutated version, or the acquisition of genomic islands harboring a resistance determinant by homologous recombination; we did not detect the transfer of resistance-carrying plasmids even though they were present in some strains. In vivo, we recovered a newly emerged strain with dual-resistance pattern and identified the replacement of an existing non-functional tet(O) by a functional tet(O) in the recipient strain. Whole genome comparisons allowed characterization of the events involved in the horizontal spread of resistance genes between Campylobacter following in vitro co-culture and in vivo dual inoculation. Our study also highlights the potential for antimicrobial resistance transfer across Campylobacter species originating from turkeys and swine, which may have implications for farms hosting both species in close proximity.
59 BASIC BIOLOGICAL SCIENCES↗
Linking classical PRA models to a dynamic PRA
Here, this paper presents a series of methods designed to incorporate classical Probabilistic Risk Assessment (PRA) models such as Event Trees (ETs) and Fault Trees (FTs) into dynamic PRA. In contrast to classical PRA, dynamic PRA couples stochastic methods with system simulators to determine the risks associated with complex systems such as nuclear power plants. Compared with classical PRA methods, they can evaluate with higher resolution the safety impact of timing and sequencing of events on the progression of the accident. As part of a dynamic PRA analysis, it is not uncommon that parts of the system to be analyzed might not require a computationally expensive simulation model. These parts could be in fact modeled by employing classical PRA models (e.g., a FT). Here, we present a set of methods and tools that can be used to link the most common classical PRA models (ETs, FTs, reliability block diagrams and Markov models) to simulation codes such as RELAP5-3D: creating a “hybrid PRA.” In order to show the potential of such an hybrid PRA we employ this method to verify ET modeling assumptions (e.g., success criteria) using a large break loss of coolant accident initiating event as a test case. In this respect, we link a set of FTs from the original PRA to the RELAP5-3D code and perform a hybrid PRA. The FTs are employed to model the control logic of several safety systems and to propagate component failures throughout the system. Provided the generated dynamic PRA data, we show how conservative assumptions in the original PRA can be identified and how such original PRA can be modified by updating success criteria captured by the set of RELAP5-3D simulation runs.
97 - MATHEMATICS AND COMPUTING↗
Molecular basis of C-S bond cleavage in the glycyl radical enzyme isethionate sulfite-lyase
Desulfonation of isethionate by the bacterial glycyl radical enzyme (GRE) isethionate sulfite-lyase (IslA) generates sulfite, a substrate for respiration that in turn produces the disease-associated metabolite hydrogen sulfide. Here, we present a 2.7 Å resolution X-ray structure of wild-type IslA from Bilophila wadsworthia with isethionate bound. In comparison with other GREs, alternate positioning of the active site β strands allows for distinct residue positions to contribute to substrate binding. These structural differences, combined with sequence variations, create a highly tailored active site for the binding of the negatively charged isethionate substrate. Through the kinetic analysis of 14 IslA variants and computational analyses, we probe the mechanism by which radical chemistry is used for C-S bond cleavage. This work further elucidates the structural basis of chemistry within the GRE superfamily and will inform structure-based inhibitor design of IsIA and thus of microbial hydrogen sulfide production.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Discovery of Marburg virus neutralizing antibodies from virus-naïve human antibody repertoires using large-scale structural predictions
Marburg virus (MARV) disease is lethal, with fatality rates up to 90%. Neutralizing antibodies (Abs) are promising drug candidates to prevent or treat the disease. Current efforts are focused in part on vaccine development to induce such MARV-neutralizing Abs. We analyzed the antibody repertoire from healthy unexposed and previously MARV-infected individuals to assess if naïve repertoires contain suitable precursor antibodies that could become neutralizing with a limited set of somatic mutations. Here, we computationally searched the human Ab variable gene repertoire for predicted structural homologs of the neutralizing Ab MR78 that is specific to the receptor binding site (RBS) of MARV glycoprotein (GP). Eight Ab heavy-chain complementarity determining region 3 (HCDR3) loops from MARV-naïve individuals and one from a previously MARV-infected individual were selected for testing as HCDR3 loop chimeras on the MR78 Ab framework. Three of these chimerized antibodies bound to MARV GP. We then tested a full-length native Ab heavy chain encoding the same 17-residue-long HCDR3 loop that bound to the MARV GP the best among the chimeric Abs tested. Despite only 57% amino acid sequence identity, the Ab from a MARV-naïve donor recognized MARV GP and possessed neutralizing activity against the virus. Crystallization of both chimeric and full-length native heavy chain-containing Abs provided structural insights into the mechanism of binding for these types of Abs. Our work suggests that the MARV GP RBS is a promising candidate for epitope-focused vaccine design to induce neutralizing Abs against MARV.
59 BASIC BIOLOGICAL SCIENCES↗
Engineered mRNA–ribosome fusions for facile biosynthesis of selenoproteins
Ribosomes are often used in synthetic biology as a tool to produce desired proteins with enhanced properties or entirely new functions. However, repurposing ribosomes for producing designer proteins is challenging due to the limited number of engineering solutions available to alter the natural activity of these enzymes. In this study, we advance ribosome engineering by describing a novel strategy based on functional fusions of ribosomal RNA (rRNA) with messenger RNA (mRNA). Specifically, we create an mRNA–ribosome fusion called RiboU, where the 16S rRNA is covalently attached to selenocysteine insertion sequence (SECIS), a regulatory RNA element found in mRNAs encoding selenoproteins. When SECIS sequences are present in natural mRNAs, they instruct ribosomes to decode UGA codons as selenocysteine (Sec, U) codons instead of interpreting them as stop codons. This enables ribosomes to insert Sec into the growing polypeptide chain at the appropriate site. Our work demonstrates that the SECIS sequence maintains its functionality even when inserted into the ribosome structure. As a result, the engineered ribosomes RiboU interpret UAG codons as Sec codons, allowing easy and site-specific insertion of Sec in a protein of interest with no further modification to the natural machinery of protein synthesis. To validate this approach, we use RiboU ribosomes to produce three functional target selenoproteins in Escherichia coli by site-specifically inserting Sec into the proteins’ active sites. Overall, our work demonstrates the feasibility of creating functional mRNA–rRNA fusions as a strategy for ribosome engineering, providing a novel tool for producing Sec-containing proteins in live bacterial cells.
59 BASIC BIOLOGICAL SCIENCES↗
Multiplexing and Demultiplexing Signals for Radiography Application Using the Discrete Fourier Transform
Our goal is to develop an X-ray phase-contrast imaging system that can provide excellent soft tissue contrast of phase, attenuation, and small-angle scatter. We propose to replace the common system of G0, G1, and G2 gradings with a biprism array to replace the G1 grading and introduce a novel X-ray tube designed to replace the motion of the phase stepping grading G2. The proposed X-ray tube uses temporal multiplexing to provide simultaneous virtual “electronic phase stepping.” In this work the discrete Fourier transform is used to separate from the composite measurement individual X-ray phase contrast measurements sampled at different frequencies. The method performs a discrete Fourier transform of a composite refence sequence to obtain using the frequency amplitudes calibration factors needed to extract the X-ray phase contrast measurement amplitudes from the composite image. The composite reference sequence is the sum of the individual sequences, at different frequencies, with amplitudes of one. The method takes the discrete Fourier transform of this composite reference sequence; whereby, the amplitude of each frequency component is compared with the total sum of its stand-alone sequence amplitude. A calibration factor is determined so that the amplitude of this composite reference frequency times the calibration factor must equal the total sum of the sequence amplitude—the zero-frequency amplitude of the discrete Fourier transform of its stand-alone sequence. To demultiplex the composite measured signal these calibration factors are multiplied by the amplitudes of the frequency components of the discrete Fourier transform of the composite X-phase-contrast measurement to obtain the amplitude of each frequency encoded measurement. Using these calibration factors, we demonstrate with the discrete Fourier transform in Mathematica the extraction of individual images from a composite image that one would expect obtaining from our proposed new X-ray phase contrast imaging system. We then demonstrate as an example how using images from X-ray phase contrast data one can calculate phase, attenuation and the dark field images using grading phase step data supplied to use from Microworks, GmbH in Karlsruhe, Germany.
42 ENGINEERING↗
Multiplexed Knockouts in the Model Diatom Phaeodactylum by Episomal Delivery of a Selectable Cas9
Marine diatoms are eukaryotic microalgae that play significant ecological and biogeochemical roles in oceans. They also have significant potential as organismal platforms for exploitation to address biotechnological and industrial goals. In order to address both modes of research, sophisticated molecular and genetic tools are required. We presented here new and improved methodologies for introducing CRISPRCas9 to the model diatom Phaeodactylum tricornutum cells and a streamlined protocol for genotyping mutant cell lines with previously unknown phenotypes. First, bacterialconjugation was optimized for the delivery of Cas9 by transcriptionally fusing Cas9 to a selectable marker by the 2A peptide. An episome cloning strategy using both negative and positive selection was developed to streamline CRISPR-episome assembly. Next, cell line picking and genotyping strategies, that utilize manual sequencing curation, TIDE sequencing analysis, and a T7 endonuclease assay, were developed to shorten the time required to generate mutants. Following this new experimental pipeline, both singlegene and two-gene knockout cell lines were generated at mutagenesis efficiencies of 48% and 25%, respectively. Lastly, a protocol for precise gene insertions via CRISPRCas9 targeting was developed using particle-bombardment transformation methods. Overall, the novel Cas9 episome design and improved genotyping methods presented here allow for quick and easy genotyping and isolation of Phaeodactylum mutant cell lines (less than 3 weeks) without relying on a known phenotype to screen for mutants.
59 BASIC BIOLOGICAL SCIENCES↗
Axenisation of oleaginous microalgal cultures via anoxic photosensitisation
Growing interest in sustainable food and biofuel research has necessitated high quality axenic oleaginous microalgal strains. Unfortunately, most strains available in culture banks contain commensal microbes such as bacteria and the default decontamination method involves antibiotic treatment which has begun to exacerbate the emergence of antibiotic resistance. To overcome this problem, anoxic photosensitisation was investigated as an alternate approach. Four oleaginous microalgal species (Tetradesmus obliquus, Desmodesmus armatus, Chlorella vulgaris and Nannochloropsis limnetica) were incubated in varying concentrations of Rose Bengal (0 μM, 1 μM, 3 μM or 9 μM) either in normal (oxic) or anoxic conditions, for 72 h under light (8.85 ± 0.4 W/m 2 ) in a specially designed heterotrophic growth complex (HGC) medium, followed by 72 h in standard Bold's Basal Medium (BBM). Commonly used antibiotics-based protocol was used as the control method. Post treatment, cell numbers and percentage populations were counted with Flow Cytometry, and viability was tested using standard plating methods using BBM and LB. Additionally, the contaminating microbes in the cultures were profiled using 16Ss rRNA sequencing. Anoxic conditions were able to significantly decrease bacterial content, albeit with an equally detrimental effect on the microalgal population. Although the responses differed between the microalgae, anoxic incubation along with Rose Bengal at 3 μM was able to completely decontaminate N. limnetica and C. vulgaris, while D. armatus and T. obliquus could be decontaminated with an additional streak-plating step. None of the cultures could be decontaminated using antibiotics treatment. These results suggest that axenisation of microalgal cultures was largely due to anoxy, that was synergistically enhanced by Rose Bengal at a concentration of ≥3 μM.
59 BASIC BIOLOGICAL SCIENCES↗
Project Plan: Salt in Situ Heater Test
This project plan gives a high-level description of the US Department of Energy Office of Nuclear Energy (DOE-NE) Spent Fuel and Waste Disposition (SFWD) campaign in situ borehole heater test project planned for the Waste Isolation Pilot Plant (WIPP) site, titled the Brine Availability Test in Salt (BATS). BATS is the first stage in a planned sequence of tests to bolster the technical basis for disposal of heat generating waste in salt. This plan provides an overview of the schedule and responsibilities of the parties involved. This project is a collaborative effort by Sandia, Los Alamos, and Lawrence Berkeley National Laboratories to execute a series of small-diameter borehole heater tests in salt for the DOE-NE SFWD campaign. Design of a heater test in salt at WIPP has evolved over several years. The experiment has begun in January 2020 and the first phase will continue for several months with the possibility for follow on testing. BATS comprises a suite of modular tests, which consist of a group of adjacent horizontal boreholes in the wall of drifts at WIPP. Each test is centered around a packer-isolated heated borehole (12.2 cm [4.81 diameter) containing equipment for water-vapor collection and borehole closure monitoring, surrounded by smaller-diameter (up to 5.3 cm [2.11 diameter) satellite observation boreholes. Observation boreholes contain grouted-in temperature sensors, electrical resistivity tomography (ERT) sensors, and fiber optics; packer-isolated tracer release and sampling intervals; and acoustic emission (AE) piezoelectric sensors. A larger-diameter (12.2 cm [4.81) satellite borehole includes sorel and salt cement plugs, as part of an engineered barrier sealing test. The first two tests, to be implemented in parallel, are heated (target borehole wall temperature of 120 °C) and unheated, with similar arrays of observation borehole monitoring changes. Follow-on tests will be designed using information gathered from the first two tests, and may be conducted at other borehole wall temperatures, use multiple observation boreholes, and may include different measurement types and test designs. This 2020 update of the original 2018 project plan satisfies DOE-NE Spent Fuel and Waste Science and Technology (SFWST) milestone M3SF-205N010303034, as part of the SNL "Salt Disposal R&D" work package.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Qudit Gate Decomposition Dependence for Lattice Gauge Theories
In this work, we investigate the effect of decomposition basis on primitive qudit gates on superconducting radio-frequency cavity-based quantum computers with applications to lattice gauge theory. Three approaches are tested: SNAP & Displacement gates, ECD & single-qubit rotations $R(\theta,\phi)$, and optimal pulse control. For all three decompositions, implementing the necessary sequence of rotations concurrently rather then sequentially can reduce the primitive gate run time. The number of blocks required for the faster ECD &$R_p(\theta)$ is found to scale $\mathcal{O}(d^2)$, while slower SNAP & Displacement set scales at worst $\mathcal{O}(d)$. For qudits with $d<10$, the resulting gate times for the decompositions is similar, but strongly-dependent on experimental design choices. Optimal control can outperforms both decompositions for small $d$ by a factor of 2-12 at the cost of higher classical resources. Lastly, we find that SNAP & Displacement are slightly more robust to a simplified noise model.
Kürkçüoglu, Doga Murat↗
High-fidelity trapped-ion qubit operations with scalable photonic modulators
Abstract Experiments with trapped ions and neutral atoms typically employ optical modulators in order to control the phase, frequency, and amplitude of light directed to individual atoms. These elements are expensive, bulky, consume substantial power, and often rely on free-space I/O channels, all of which pose scaling challenges. To support many-ion systems like trapped-ion quantum computers or miniaturized deployable devices like clocks and sensors, these elements must ultimately be microfabricated, ideally monolithically with the trap to avoid losses associated with optical coupling between physically separate components. In this work we design, fabricate, and test an optical modulator capable of monolithic integration with a surface-electrode ion trap. These devices consist of piezo-optomechanical photonic integrated circuits configured as multi-stage Mach-Zehnder modulators that are used to control the intensity of light delivered to a single trapped ion on a separate chip. We use quantum tomography employing hundreds of multi-gate sequences to enhance the sensitivity of the fidelity to the types and magnitudes of gate errors relevant to quantum computing and better characterize the performance of the modulators, ultimately measuring single qubit gate fidelities that exceed 99.7%.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis -regulatory elements
Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.
59 BASIC BIOLOGICAL SCIENCES↗