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All sources NASA NTRS DOE OSTI

DOE OSTI2022

ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design

Abstract Megasynthase enzymes such as type I modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) play a central role in microbial chemical warfare because they can evolve rapidly by shuffling parts (catalytic domains) to produce novel chemicals. If we can understand the design rules to reshuffle these parts, PKSs and NRPSs will provide a systematic and modular way to synthesize millions of molecules including pharmaceuticals, biomaterials, and biofuels. However, PKS and NRPS engineering remains difficult due to a limited understanding of the determinants of PKS and NRPS fold and function. We developed ClusterCAD to streamline and simplify the process of designing and testing engineered PKS variants. Here, we present the highly improved ClusterCAD 2.0 release, available at https://clustercad.jbei.org. ClusterCAD 2.0 boasts support for PKS-NRPS hybrid and NRPS clusters in addition to PKS clusters; a vastly enlarged database of curated PKS, PKS-NRPS hybrid, and NRPS clusters; a diverse set of chemical ‘starters’ and loading modules; the new Domain Architecture Cluster Search Tool; and an offline Jupyter Notebook workspace, among other improvements. Together these features massively expand the chemical space that can be accessed by enzymes engineered with ClusterCAD.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering

Abstract CRISPR-Cas9 tools have transformed genetic manipulation capabilities in the laboratory. Empirical rules-of-thumb have been developed for only a narrow range of model organisms, and mechanistic underpinnings for sgRNA efficiency remain poorly understood. This work establishes a novel feature set and new public resource, produced with quantum chemical tensors, for interpreting and predicting sgRNA efficiency. Feature engineering for sgRNA efficiency is performed using an explainable-artificial intelligence model: iterative Random Forest (iRF). By encoding quantitative attributes of position-specific sequences for Escherichia coli sgRNAs, we identify important traits for sgRNA design in bacterial species. Additionally, we show that expanding positional encoding to quantum descriptors of base-pair, dimer, trimer, and tetramer sequences captures intricate interactions in local and neighboring nucleotides of the target DNA. These features highlight variation in CRISPR-Cas9 sgRNA dynamics between E. coli and H. sapiens genomes. These novel encodings of sgRNAs enhance our understanding of the elaborate quantum biological processes involved in CRISPR-Cas9 machinery.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes

Abstract CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Spatial Mapping of Chiral-Induced Spin Selectivity in Chiral Perovskite via Spin-Schottky Junction

Chiral halide perovskite (c-HP) semiconductors exhibit on average a large chiral-induced spin selectivity (CISS) effect. Nevertheless, the microscopic details of CISS and its integration in opto-spintronic constructs remain nascent. Reliable reporting of CISS performance characteristics represents a significant challenge in providing the necessary design rules. We show a Kelvin probe force microscopy (KPFM) method that can quantitatively evaluate and spatially map the chirality-dependent surface contact potential difference resulting from the formation of a spin-Schottky junction. We revealed inhomogeneity in the CISS response, where low-CISS regions in the c-HP films reduce the overall macroscopic average, likely serving as a key factor in optimizing macroscopic performance. We also observed that although c-HP films made from higher precursor concentrations lead to thicker films and higher carrier concentrations with subsequent larger barrier heights in the Schottky junction, stronger spin relaxation due to non-ideal film quality reduces spin polarization.

14 SOLAR ENERGY↗

DOE OSTI2022

Negative string tension of a higher-charge Schwinger model via digital quantum simulation

We study some properties of generalized global symmetry for the charge- q Schwinger model in the Hamiltonian formalism, which is the (1 + 1)D quantum electrodynamics with a charge- q Dirac fermion. This model has the |$\mathbb {Z}_q\, 1$| -form symmetry, which is a remnant of the electric |$U(1)\, 1$| -form symmetry in the pure Maxwell theory. It is known that, if we put the theory on closed space, then the Hilbert space is decomposed into q distinct sectors, called universes, and some states with higher energy density do not decay to the ground state due to the selection rule of the 1-form symmetry. Even with open boundaries, we can observe the stability of such states by seeing a negative string tension behavior, meaning that opposite charges repel each other. In order to see negative string tensions, the vacuum angle θ has to be large enough and the standard path-integral Monte Carlo method suffers from the sign problem. We develop a method based on the adiabatic state preparation to see this feature with digital quantum simulation and confirm it using a classical simulator of quantum devices. In particular, we measure the local energy density and see how it jumps between the inside and outside of the insertion of the probe charges. We explicitly see that the energy density inside is lower than that outside. This is a clear signature of the negative string tension.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Probing cosmic inflation with the LiteBIRD cosmic microwave background polarization survey

LiteBIRD, the Lite (Light) satellite for the study of B-mode polarization and Inflation from cosmic background Radiation Detection, is a space mission for primordial cosmology and fundamental physics. The Japan Aerospace Exploration Agency (JAXA) selected LiteBIRD in May 2019 as a strategic large-class (L-class) mission, with an expected launch in the late 2020s using JAXA’s H3 rocket. LiteBIRD is planned to orbit the Sun–Earth Lagrangian point L2, where it will map the cosmic microwave background polarization over the entire sky for three years, with three telescopes in 15 frequency bands between 34 and 448 GHz, to achieve an unprecedented total sensitivity of $2.2\, \mu$K-arcmin, with a typical angular resolution of 0.5° at 100 GHz. The primary scientific objective of LiteBIRD is to search for the signal from cosmic inflation, either making a discovery or ruling out well-motivated inflationary models. The measurements of LiteBIRD will also provide us with insight into the quantum nature of gravity and other new physics beyond the standard models of particle physics and cosmology. We provide an overview of the LiteBIRD project, including scientific objectives, mission and system requirements, operation concept, spacecraft and payload module design, expected scientific outcomes, potential design extensions, and synergies with other projects.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Analysis of Long-Term Quality Control Data for a 137 Cs Dosimetry Calibration Source

Strict quality assurance programs are required for many radiological applications, but these seldom exist for verifying dosimetry calibration sources. After initial characterization of a dosimetry calibration facility, quality control procedures are recommended to ensure the early detection of any changes or malfunctions. These also result in refined knowledge about average dose rate and experimental variations in dose delivery. This paper describes the implementation of a phase I quality control protocol for a 137 Cs dosimetry calibration source and includes an analysis of the resulting data collected over a 24-mo period. During this time, substantial data was collected to establish trial control limits. Air kerma rate measurements were obtained using an ion chamber and were adjusted for decay, corrected for ambient temperature, pressure and humidity, and then analyzed using quality control charts. Three variations of rational subgrouping methods were used in order to find assignable causes of error, and Nelson's Rules were followed to detect any non-random statistical variations. Measurements were subgrouped according to same-day measurements in order to detect positional errors as well as atmospheric correction errors. Additionally, measurements were subgrouped according to analogous experimental setups in order to detect failure in equipment or incorrect settings. Both were analyzed using the X-bar and R chart method. Similarly, individuals and moving ranges charts were used to carefully examine each position in order to observe any situational errors that may occur which include timing, positional, or interference errors. Each method was successful in identifying unique out-of-control data points that occurred during the phase I application of forming control limits. Furthermore, over the 24-mo period, enough data points were deemed in-control to establish reliable trial limits. Future experiments will include the phase II application of gaining more reliable measurements in order to fine-tune the limits, as well as performing a designed experiment, where variables are purposefully changed in order to test the variation of the data.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2022

Applying ALARA Principles in the Design of New Radiological Facilities

The application of ALARA (As Low As Reasonably Achievable) principles to the design of new radiological facilities at Argonne National Laboratory provides a consistent radiation safety basis for future facility operations. The Department of Energy Rule 10 CFR 835 specifies design objectives to be adopted during the design of new facilities for controlling personal radiation exposure. One is to keep exposure levels below 20% of the applicable standards in 10 CFR 835.202. For a radiation worker 20% of the standard corresponds to 5 µSv hr -1 for a 2,000 hour work year. For a member of the public the DOE design objective corresponds to 0.2 mSv in a calendar year. For a new facility worst case radionuclides and their source strengths are chosen. Local shielding is specified to reduce exposure rates to less than 50 µSv hr -1 at 30 cm from the shielding. The current version MCNP6 of the Los Alamos radiation shielding computer program MCNP is then used to calculate the exposure rates elsewhere. Design modifications are made to meet the criteria. The calculations and resulting facility design modifications are discussed for two new radiological facilities.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2022

Inferring the shape of data: a probabilistic framework for analysing experiments in the natural sciences

A critical step in data analysis for many different types of experiments is the identification of features with theoretically defined shapes in N -dimensional datasets; examples of this process include finding peaks in multi-dimensional molecular spectra or emitters in fluorescence microscopy images. Identifying such features involves determining if the overall shape of the data is consistent with an expected shape; however, it is generally unclear how to quantitatively make this determination. In practice, many analysis methods employ subjective, heuristic approaches, which complicates the validation of any ensuing results—especially as the amount and dimensionality of the data increase. Here, we present a probabilistic solution to this problem by using Bayes’ rule to calculate the probability that the data have any one of several potential shapes. This probabilistic approach may be used to objectively compare how well different theories describe a dataset, identify changes between datasets and detect features within data using a corollary method called Bayesian Inference-based Template Search; several proof-of-principle examples are provided. Altogether, this mathematical framework serves as an automated ‘engine’ capable of computationally executing analysis decisions currently made by visual inspection across the sciences.

Science & Technology - Other Topics↗

DOE OSTI2025

Hardness of Observing Strong-to-Weak Symmetry Breaking

Spontaneous symmetry breaking (SSB) is the cornerstone of our understanding of quantum phases of matter. Recent works have generalized this concept to the domain of mixed states in open quantum systems, where symmetries can be realized in two distinct ways dubbed strong and weak. Novel intrinsically mixed phases of quantum matter can then be defined by the spontaneous breaking of strong symmetry down to weak symmetry. However, proposed order parameters for strong-to-weak SSB (based on mixed-state fidelities or purities) seem to require exponentially many copies of the state, raising the question: Is it possible to efficiently detect strong-to-weak SSB, in general? In this work, we answer this question negatively in the paradigmatic cases of ℤ2 and U(1) symmetries. We construct ensembles of pseudorandom mixed states that do not break the strong symmetry yet are computationally indistinguishable from states that do. This rules out the existence of efficient state-agnostic protocols to detect strong-to-weak SSB.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2026

Selective electron-phonon coupling strength from nonequilibrium optical spectroscopy: The case of MgB 2

The coupling between quasiparticles and bosonic excitations rules the energy transfer pathways in condensed matter systems. The possibility of inferring the strength of specific coupling channels from their characteristic timescales measured in nonequilibrium experiments is still an open question. Here, in this study, we investigate MgB 2 , in which conventional superconductivity at temperatures as high as 39 K is mediated by the strong coupling between the conduction electrons and the 𝐸 2⁢𝑔 phonon mode. By means of broadband time-resolved optical spectroscopy, we show that this selective electron-phonon coupling dictates the nonequilibrium optical response of MgB 2 at early times (<100 fs) after photoexcitation. Furthermore, based on an effective temperature model analysis, we estimate its contribution to the total electron-boson coupling function extracted from complementary equilibrium spectroscopy approaches, namely, optical reflectivity and angle-resolved photoemission spectroscopy. The coupling strength with the 𝐸 2⁢𝑔 phonon modes is thus estimated to be 𝜆 ≃ 0.56, which is approximately half of the total coupling constant, in agreement with 𝑎𝑏 initio calculations from the literature. As a benchmark, broadband time-resolved optical spectroscopy is performed also on the isostructural and nonsuperconducting compound AlB 2 , showing that the nonequilibrium optical response relaxes on a slower timescale due to the lack of strongly coupled phonon modes. Our findings demonstrate the possibility to resolve and quantify selective electron-phonon coupling from nonequilibrium optical spectroscopy.

Mor, Selene [Università Cattolica del Sacro Cuore,↗

DOE OSTI2025

Evolution of structure growth during dark energy domination: Insights from the cross-correlation of DESI galaxies with CMB lensing and galaxy magnification

We use a hybrid effective field theory (HEFT) model to constrain the evolution of low-redshift (z≲0.4) matter fluctuations by cross-correlating DESI Bright Galaxy Survey (BGS) legacy imaging with the latest cosmic microwave background (CMB) lensing maps from Planck and Atacama cosmology telescope. Our tomographic BGS analysis finds that the evolution and amplitude of matter fluctuations align with CMB-conditioned Λ cold dark matter predictions. When including DESI baryon acoustic oscillation (BAO) measurements we obtain σ8=0.876-0.067+0.051 from BGS alone. Jointly analyzing BGS and luminous red galaxy (LRG) cross-correlations with the same CMB lensing maps yields σ8=0.791±0.021. As a complementary approach we isolate the galaxy magnification signal from the cross-correlation of nonoverlapping BGS and LRG photometric redshift bins, ruling out the null-magnification hypothesis at 11σ. For the first time, we constrain quasilinear structure growth from the (finite-difference calibrated) galaxy magnification signal and find σ8=0.720±0.047(stat)±0.050(sys) assuming a linear bias model and including BAO data.

Sailer, Noah↗

DOE OSTI2026

Fusion dynamics of Majorana zero modes

Braiding and fusion of Majorana zero modes are key elements of any future topological Majorana-based quantum computer. In this article, we investigate the fusion dynamics of Majorana zero modes in the spinless Kitaev model, as well as in a spinful model describing magnet-superconductor hybrid structures. We consider various scenarios allowing us to reproduce the fusion rules of the Ising anyon model. Particular emphasis is given to the charge of the fermion obtained after fusing two Majorana zero modes: as long as it remains on the superconductor, charge quantization is absent. When moving the fermion to a nonsuperconducting region, such as a quantum dot, nearly quantized charge can be measured. Our findings confirm for both platforms that fusion dynamics of Majorana zero modes can indeed be used for the readout of Majorana qubits.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2026

ϕ → 3 π and ϕ π 0 transition form factor from Khuri-Treiman equations

This work studies the ϕ → 3 π decay and the ϕ → π 0 γ * transition form factor, utilizing the Khuri-Treiman formalism to account for analyticity, crossing, and unitarity. Using once-subtracted dispersion relations, we perform a simultaneous fit to the ϕ → 3 π Dalitz plot distribution and the ϕ → π 0 γ * measurements from the KLOE collaboration, finding good agreement with these experimental data. These results reaffirm the applicability of the Khuri-Treiman approach in the analysis of three-body decays. An interesting result is that the subtraction constant appearing in the equations is similar to a sum rule expectation, in contrast to analogous studies of ω → 3 π decays and ω → π 0 γ * , which shows significant deviations. Our results also provide a reasonable description of the trend of the transition form factor data from in the e + e − → ϕ π 0 scattering region. These intriguing theoretical differences between the decays of ϕ and ω could encourage further experimental measurements to assess the discrepancies and refine the theoretical predictions.

Lorenzo, A. G. [Instituto de Física Corpuscular; U↗

DOE OSTI2025

Search for Postinflationary QCD Axions with a Quantum-Limited Tunable Microwave Receiver

A search for cosmological axions has been performed by scanning a frequency region of 38 MHz centered at about 10.2 GHz, corresponding to an axion mass 𝑚 𝑎 ≃ 42 μ ⁢eV. The QUAX experimental apparatus, a haloscope comprised of a 1-liter volume tunable cavity immersed in an 8 T magnetic field and a quantum-limited detection chain, set limits on the axion-photon coupling at the 10 −14 GeV −1 level. As no signal candidate has been observed, viable hadronic axion models are ruled out in a currently preferred postinflationary region 𝑚 𝑎 > 40 μ ⁢eV.

Sardo Infirri, Giosue [INFN, Sezione di Padova; Un↗

DOE OSTI2025

Landau-level composition of bound exciton states in magnetic field

Here, we present a theory that studies the state composition of a bound exciton in magnetic field. Using a basis set made of products of free electron and hole wave functions in Landau gauge, we derive a secular equation which shows the relation between Landau levels (LLs) of the electron and hole when a bound exciton is formed. Focusing on excitons in the light cone, we establish a scattering selection rule for the interaction of an electron in LL 𝑛 e with a hole in LL 𝑛 h . We solve the resulting secular equation and identify a simple pairing law, 𝑛 e =𝑛 h +𝑙, which informs us on the construction of a bound exciton state with magnetic quantum number 𝑙, and on the interaction of the exciton magnetic moment with magnetic field. We obtain good agreement between theory results and recent measurements of the diamagnetic shifts of exciton states in WSe 2 monolayers.

2-dimensional systems↗

DOE OSTI2025

Global QCD analysis of spin PDFs in the proton with high-𝑥 and lattice constraints

We perform a comprehensive global QCD analysis of spin-dependent parton distribution functions (PDFs), combining all available data on inclusive and semi-inclusive deep-inelastic scattering (DIS), as well as inclusive weak boson and jet production in polarized 𝑝⁢𝑝 collisions, simultaneously extracting spin-averaged PDFs and fragmentation functions. Including recent Jefferson Lab DIS data at high 𝑥, together with subleading power corrections to the leading-twist framework, allows us to verify the stability of the PDFs for 𝑊 2 ≥ 4 GeV 2 and quantify the uncertainties on the spin structure functions more reliably. We explore the use of new lattice QCD data on gluonic pseudo-Ioffe time distributions, which, together with jet production and high-𝑥 DIS data, improve the constraints on the polarized gluon PDF. The expanded kinematic reach afforded by the data into the high-𝑥 region allows us to refine the bounds on higher-twist contributions to the spin structure functions, and test the validity of the Bjorken sum rule.

Perturbative QCD↗

DOE OSTI2025

Search for 𝛾⁢𝐻 production and constraints on the Yukawa couplings of light quarks to the Higgs boson

A search for 𝛾⁢𝐻 production is performed with data from the CMS experiment at the LHC corresponding to an integrated luminosity of 138 fb −1 at a proton-proton center-of-mass collision energy of 13 TeV. The analysis focuses on the topology of a boosted Higgs boson recoiling against a high-energy photon. The final states of 𝐻 → $b\bar{b}$ and 𝐻 → 4⁢ℓ are analyzed. This study examines effective 𝐻⁡𝑍⁢𝛾 and 𝐻⁡𝛾⁢𝛾 anomalous couplings within the context of an effective field theory. In this approach, the production cross section is constrained to be 𝜎 𝛾⁢𝐻 < 16.4 fb at 95% confidence level (CL). Simultaneous constraints on four anomalous couplings involving 𝐻⁡𝑍⁢𝛾 and 𝐻⁡𝛾⁢𝛾 are provided. Additionally, the production rate for 𝐻 → 4⁢ℓ is examined to assess potential enhancements in the Yukawa couplings between light quarks and the Higgs boson. Assuming the standard model values for the Yukawa couplings of the bottom and top quarks, the following simultaneous constraints are obtained: 𝜅 𝑢 =(0.0 ± 1.5) ×10 3 , 𝜅 𝑑 = (0.0$^{+6.7}_{−6.8}$) × 10 2 , 𝜅 𝑠 = 0$^{+30}_{−32}$, and 𝜅 𝑐 =0.0$^{+2.3}_{−2.8}$. This rules out the hypothesis that up- or down-type quarks in the first or second generation have the same Yukawa couplings as those in the third generation, with a CL greater than 95%.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗