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At least 577 records · Page 32
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DOE OSTI2024

Fermentation Practices Select for Thermostable Endolysins in Phages

Endolysins are produced by (bacterio)phages and play a crucial role in degrading the bacterial cell wall and the subsequent release of new phage progeny. These lytic enzymes exhibit a remarkable diversity, often occurring in a multimodular form that combines different catalytic and cell wall-binding domains, even in phages infecting the same species. Yet, our current understanding lacks insight into how environmental factors and ecological niches may have influenced the evolution of these enzymes. In this study, we focused on phages infecting Streptococcus thermophilus, as this bacterial species has a well-defined and narrow ecological niche, namely, dairy fermentation. Among the endolysins found in phages targeting this species, we observed limited diversity, with a singular structural type dominating in most of identified S. thermophilus phages. Within this prevailing endolysin type, we discovered a novel and highly conserved calcium-binding motif. This motif proved to be crucial for the stability and activity of the enzyme at elevated temperatures. Ultimately, we demonstrated its positive selection within the host's environmental conditions, particularly under the temperature profiles encountered in the production of yogurt, mozzarella, and hard cheeses that rely on S. thermophilus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

SODAs: sparse optimization for the discovery of differential and algebraic equations

Differential-algebraic equations (DAEs) integrate ordinary differential equations (ODEs) with algebraic constraints, providing a fundamental framework for developing models of dynamical systems characterized by time-scale separation, conservation laws and physical constraints. While sparse optimization has revolutionized model development by allowing data-driven discovery of parsimonious models from a library of possible equations, existing approaches for dynamical systems assume DAEs can be reduced to ODEs by eliminating variables before model discovery. This assumption limits the applicability of such methods for DAE systems with unknown constraints and time scales. We introduce sparse optimization for differential-algebraic systems (SODAs), a data-driven method for the identification of DAEs in their explicit form. By discovering the algebraic and dynamic components sequentially without prior identification of the algebraic variables, this approach leads to a sequence of convex optimization problems. It has the advantage of discovering interpretable models that preserve the structure of the underlying physical system. To this end, SODAs improves since SODAs is singular numerical stability when handling high correlations between library terms, caused by near-perfect algebraic relationships, by iteratively refining the conditioning of the candidate library. We demonstrate the performance of our method on biological, mechanical and electrical systems, showcasing its robustness to noise in both simulated time series and real-time experimental data.

DAE↗
DOE OSTI2024

BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA

Gene prediction has remained an active area of bioinformatics research for a long time. Still, gene prediction in large eukaryotic genomes presents a challenge that must be addressed by new algorithms. The amount and significance of the evidence available from transcriptomes and proteomes vary across genomes, between genes, and even along a single gene. User-friendly and accurate annotation pipelines that can cope with such data heterogeneity are needed. The previously developed annotation pipelines BRAKER1 and BRAKER2 use RNA-seq or protein data, respectively, but not both. A further significant performance improvement integrating all three data types was made by the recently released GeneMark-ETP. We here present the BRAKER3 pipeline that builds on GeneMark-ETP and AUGUSTUS, and further improves accuracy using the TSEBRA combiner. BRAKER3 annotates protein-coding genes in eukaryotic genomes using both short-read RNA-seq and a large protein database, along with statistical models learned iteratively and specifically for the target genome. We benchmarked the new pipeline on genomes of 11 species under an assumed level of relatedness of the target species proteome to available proteomes. BRAKER3 outperforms BRAKER1 and BRAKER2. The average transcript-level F1-score is increased by about 20 percentage points on average, whereas the difference is most pronounced for species with large and complex genomes. BRAKER3 also outperforms other existing tools, MAKER2, Funannotate, and FINDER. The code of BRAKER3 is available on GitHub and as a ready-to-run Docker container for execution with Docker or Singularity. Overall, BRAKER3 is an accurate, easy-to-use tool for eukaryotic genome annotation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Revisiting the three-kaon interaction and its relation with 𝐾⁡(1460)

Here, we test the hypothesis of 𝐾⁡(1460) being a hadronic 𝐽 𝑃 = 0 − molecule through nonperturbative 𝑆-wave $KK\bar{⁢K}$, 𝐾⁢𝜋⁢𝜋, 𝐾⁢𝜋⁢𝜂 coupled-channel dynamics in a three-body unitary isobar approach. The scalar two-body coupled-channel resonances 𝑓 0 ⁡(500), 𝑓 0 ⁡(980), 𝑎 0 ⁡(980), and 𝐾$^*_0$⁡(700) are generated in the subsytems in amplitudes that match phase shifts from experiment. In a first step, previous results in the limit of mass-degenerate, stable 𝑓 0 and 𝑎 0 isobars are reproduced. Once the full seven-coupled channel model is switched on, other 𝑆-matrix effects obscure and modify the resonance signal, including complex thresholds, a two-body cusp, and a triangle singularity at threshold.

Döring, M. [George Washington Univ., Washington, D↗
DOE OSTI2025

Field Induced Density Wave in a Kagome Superconductor

On the kagome lattice, electrons benefit from the simultaneous presence of band topology, flat electronic bands, and Van Hove singularities, forming competing or cooperating orders. Understanding the interrelation between these distinct order parameters remains a significant challenge, leaving much of the associated physics unexplored. In the kagome superconductor KV 3 Sb 5 , which exhibits a charge density wave (CDW) state below T ≃ 78 K, we uncover an unpredicted field-induced phase transition below 6 K. The observed transition is marked by a hysteretic anomaly in the resistivity, nonlinear electrical transport, and a change in the symmetry of the electronic response as probed via the angular dependence of the magnetoresistivity. These observations surprisingly suggest the emergence of an unanticipated broken symmetry state coexisting with the original CDW. To understand this experimental observation, we developed a theoretical minimal model for the normal state inside the high-temperature parent CDW phase, where an incommensurate CDW order emerges as an instability subleading to superconductivity. Here, the incommensurate CDW emerges when superconducting fluctuations become fully suppressed by large magnetic fields. Our results suggest that, in kagome superconductors, quantum states can either coexist or are nearly degenerate in energy, indicating that these are rich platforms to expose new correlated phenomena.

Charge density waves↗
DOE OSTI2026

Electronic structure of the kagome compound CaTi 3⁢ Bi 4 using high-field torque magnetometry and density functional theory

Here, we report systematic torque magnetometry measurements to investigate the electronic properties of the newly discovered kagome compound CaTi 3 ⁢Bi 4 . Electrical transport, magnetic susceptibility, and thermal measurements reveal no evidence of a magnetic ground state in this material. Torque data obtained in magnetic fields up to 41.5 T exhibit clear de Haas–van Alphen (dHvA) oscillations, with nine distinct frequencies ranging from 13 to 6164 T. Angular-dependent dHvA measurements show that, with the exception of the lowest frequency (13 T), all observed frequencies nearly follow a 1/cos ⁡𝜃 dependence, where 𝜃 is the angle between the crystallographic 𝑐 axis and the magnetic field direction. This behavior is characteristic of quasi-two-dimensional Fermi-surface sheets with nearly circular cross sections. To further elucidate the electronic structure, we performed density functional theory (DFT) calculations of the band structure and Fermi surface. The calculated bands reveal the presence of multiple Dirac points (DP), flat bands (FB), and van Hove singularities (VHS) near the Fermi level. The resulting Fermi surface consists of several quasi-two-dimensional cylindrical sheets, consistent with the experimentally observed 1/cos⁡ 𝜃 dependence. Notably, the theoretical dHvA frequencies, derived from extremal Fermi-surface cross-sectional areas, agree well with the experimental values and reproduce their angular dependence. Remarkably, all experimentally observed frequencies are captured by the DFT predictions. Pressure-dependent calculations up to 10 GPa show that the electronic features—DP, FB, and VHS—evolve systematically with pressure. In particular, the VHS shifts closer to the Fermi level, demonstrating that pressure acts as an effective tuning parameter in this material. These combined experimental and theoretical results provide a comprehensive understanding of the electronic structure of CaTi 3 ⁢Bi 4 and demonstrate how pressure can be used to tune its key electronic features, offering valuable guidance for exploring related kagome materials.

Shtefiienko, Kyryl [West Texas A & M University, C↗
DOE OSTI2025

Factorization and resummation of QED radiative corrections for neutron beta decay

Details of the two-loop analysis of long-distance QED radiative corrections to neutron beta decay are presented. Explicit expressions are given for hard, jet, and soft functions appearing in the factorization formula that describes the limit of small electron mass and large electron energy. Numerical enhancements from the infrared region are resummed using renormalization group methods. Power corrections, cancellation of singularities in the small-mass expansion, renormalization scheme dependence, and bound-state effects are also discussed. These results provide the most precise determination of long-distance radiative corrections to neutron beta decay and impact the determination of |𝑉 𝑢⁢𝑑 | from the measured neutron lifetime and thus set a target for uncertainty reductions in the experimental and short-distance inputs.

Beta decay↗
DOE OSTI2025

Cosmological perturbations from a new approach to inflation

In a previous paper, we proposed a new approach to the beginning of inflation—a lingering universe [Melcher et al. Phys. Rev. D 110, 063517 (2024).]—that is a quasistatic phase prior to inflation. The Universe begins in a lingering state with a nearly vanishing Hubble parameter. This calls into question the absolute age of the Universe, as the Hubble time can be nearly infinite. It also provides promise for addressing the initial singularity of inflation and issues with quantum field theory in de Sitter spacetime. Such models arise in classical cosmologies with nonvanishing spatial curvature (inspired by PLANCK 2018 data) and independently by models that arise in string cosmology. Here, in this paper, we consider the importance of cosmological perturbations for the stability of the lingering phase and how this influences cosmological observations. Our goal is to establish observables in this new paradigm for the origin of inflation, which is in contrast to eternal inflation and cyclic cosmologies. We also address questions of stability and the transition to inflation.

cosmology↗
DOE OSTI2025

Interacting spin and charge density waves in the kagome metal FeGe

Unveiling the interplay between spin density wave (SDW) and charge density wave (CDW) orders in correlated electron materials is important in obtaining a comprehensive understanding of their electronic, structural, and magnetic properties. Kagome lattice materials are interesting because their flat electronic bands, Dirac points, and Van Hove singularities can enable a variety of exotic electronic and magnetic phenomena. The kagome metal FeGe (the B35 phase), which exhibits a CDW order deep within an A-type antiferromagnetic (AFM) phase, was found to respond dramatically to postgrowth annealing—with the ability to tune the CDW repeatedly from long-range order to negligible order. Additionally, neutron scattering studies suggest that incommensurate magnetic peaks that onset at 𝑇 Canting = 𝑇 SDW ≈ 60 K in the system arise from a SDW order instead of the AFM double-cone structure. Here, in this study, we use inelastic neutron scattering to show that two distinct spin excitations exist below 𝑇 Canting corresponding to two coexisting magnetic orders in the system in both sets of annealed samples with and without CDW. While CDW order or negligible order can dramatically affect the onset temperature of 𝑇 Canting and elastic incommensurate magnetic scattering, its impact on low-energy spin fluctuations is more limited. In both samples, a pair of gapless incommensurate spin excitations arising from the SDW order wave vector coexist with gapped commensurate spin waves from the A-type AFM order across 𝑇 Canting . The low-energy spin excitations for both samples couple dynamically to the lattice through enhanced magnetic scattering intensity on cooling below 𝑇 CDW , regardless of the status of the static long-range CDW order. The incommensurate SDW order in the long-range CDW ordered sample also induces a tiny in-plane lattice distortion of the kagome lattice that is absent in the negligible CDW ordered sample, in a way that is different from the previously known SDW and CDW ordering materials.

charge density waves↗
DOE OSTI2021

Scaling functions for eigenstate entanglement crossovers in harmonic lattices

For quantum matter, eigenstate entanglement entropies obey an area law or log-area law at low energies and small subsystem sizes and cross over to volume laws for high energies and large subsystems. This transition is captured by crossover functions, which assume a universal scaling form in quantum critical regimes. We demonstrate this for the harmonic lattice model, which describes quantized lattice vibrations and is a regularization for free scalar field theories, modeling, e.g., spin-0 bosonic particles. In one dimension, the ground-state entanglement obeys a log-area law. For dimensions d ≥ 2, it displays area laws, even at criticality. The distribution of excited-state entanglement entropies is found to be sharply peaked around subsystem entropies of corresponding thermodynamic ensembles in accordance with the eigenstate thermalization hypothesis. Numerically, we determine crossover scaling functions for the quantum critical regime of the model and do a large-deviation analysis. We show how infrared singularities of the system can be handled and how to access the thermodynamic limit using a perturbative trick for the covariance matrix. Eigenstates for quasi-free bosonic systems are not Gaussian. Here, we resolve this problem by considering appropriate squeezed states instead. For these, entanglement entropies can be evaluated efficiently.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

van der Waals interaction as the starting point for an effective field theory

We consider the system of three 4 He atoms to assess whether a pure van der Waals potential can be used as a starting point for an effective field theory to describe three-body processes in ultracold atomic systems. Using a long-range van der Waals interaction in combination with short-distance two-body counterterms, we analyze the dependence of two- and three-body observables on the short-distance regulator that is required due to the singular nature of the van der Waals interaction. We benchmark our approach with results obtained with the realistic 4 He- 4 He LM2M2 potential and find good agreement. We furthermore show that in this effective field theory approach no three-body force is required at leading order and that universal van der Waals physics leads to a universal correlation between three-body observables in the absence of an Efimov three-body parameter.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Quantum algorithms for open lattice field theory

Certain aspects of some unitary quantum systems are well described by evolution via a non-Hermitian effective Hamiltonian, as in the Wigner-Weisskopf theory for spontaneous decay. Conversely, any non-Hermitian Hamiltonian evolution can be accommodated in a corresponding unitary system + environment model via a generalization of Wigner-Weisskopf theory. This demonstrates the physical relevance of novel features such as exceptional points in quantum dynamics, and opens up avenues for studying many-body systems in the complex plane of coupling constants. In the case of lattice field theory, sparsity lends these channels the promise of efficient simulation on standardized quantum hardware. We thus consider quantum operations that correspond to Suzuki-Lie-Trotter approximation of lattice field theories undergoing nonunitary time evolution, with potential applicability to studies of spin or gauge models at finite chemical potential, with topological terms, to quantum phase transitions—a range of models with sign problems. We develop non-Hermitian quantum circuits and explore their promise on a benchmark, the quantum one-dimensional Ising model with complex longitudinal magnetic field, showing that observables can probe the Lee-Yang edge singularity. The development of attractors past critical points in the space of complex couplings indicates a potential for study on near-term noisy hardware.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Quantum state preparation and nonunitary evolution with diagonal operators

Realizing nonunitary transformations on unitary-gate-based quantum devices is critically important for simulating a variety of physical problems, including open quantum systems and subnormalized quantum states. Here, we present a dilation-based algorithm to simulate nonunitary operations using probabilistic quantum computing with only one ancilla qubit. We utilize the singular-value decomposition (SVD) to decompose any general quantum operator into a product of two unitary operators and a diagonal nonunitary operator, which we show can be implemented by a diagonal unitary operator in a one-qubit dilated space. While dilation techniques increase the number of qubits in the calculation, and thus the gate complexity, our algorithm limits the operations required in the dilated space to a diagonal unitary operator, which has known circuit decompositions. We use this algorithm to prepare random subnormalized two-level states on a quantum device with high fidelity. Furthermore, we present the accurate nonunitary dynamics of two-level open quantum systems in a dephasing channel and an amplitude-damping channel computed on a quantum device. The algorithm presented will be most useful for implementing general nonunitary operations when the SVD can be readily computed, which is the case for most operators in the noisy intermediate-scale quantum computing era.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Radiative properties of an artificial atom coupled to a Josephson-junction array

We study the radiative properties—the Lamb shift, Purcell decay rate, and spontaneous emission dynamics—of an artificial atom coupled to a long, multimode cavity formed by an array of Josephson junctions. Introducing a tunable coupling element between the atom and the array, we demonstrate that such a system can exhibit a crossover from a perturbative to a nonperturbative regime of light-matter interaction as one strengthens the coupling between the atom and the Josephson-junction array. As a consequence, the concept of spontaneous emission as the occupation of the local atomic site being governed by a single complex-valued exponent breaks down. This breakdown, we show, can be interpreted in terms of formation of hybrid atom-resonator modes with radiative losses that are nontrivially related to the effective coupling between individual modes. We develop a singular function expansion approach for the description of the open quantum system dynamics in such a multimode nonperturbative regime. This modal framework generalizes the normal-mode description of quantum fields in a finite volume, incorporating exact radiative losses and incident quantum noise at the delimiting surface. Our results are pertinent to recent experiments with Josephson atoms coupled to high-impedance Josephson-junction arrays.

42 ENGINEERING↗
DOE OSTI2023

Perturbative model of noisy quantum signal processing

Recent progress in quantum signal processing (QSP) and its generalization, quantum singular value transformation, has led to a grand unification of quantum algorithms. However, inherent experimental noise in quantum devices severely limits the length of realizable QSP sequences. Here, we consider a model of QSP with generic perturbative noise in the signal processing basis and present a diagrammatic notation useful for analyzing such errors. To demonstrate our technique, we study a specific coherent error, that of under- or overrotation of the signal processing operator parametrized by ε<<1. For this coherent error model, it is shown that while Pauli Z errors are not recoverable without additional resources, Pauli X and Y errors can be arbitrarily suppressed by coherently appending a noisy recovery QSP without the use of additional resources or ancillas. Furthermore, through a careful accounting of errors using our diagrammatic tools, we provide an upper and lower bound on the length of this recovery QSP operator. We anticipate that the perturbative technique and the diagrammatic notation proposed here will facilitate future study of generic noise in QSP and quantum algorithms.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Toward precision Fermi-liquid theory in two dimensions

The ultracold and weakly coupled Fermi gas in two spatial dimensions is studied in an effective field theory framework. It has long been observed that universal corrections to the energy density to two orders in the interaction strength do not agree with Monte Carlo simulations in the weak-coupling regime. Here, universal corrections to three orders in the interaction strength are obtained, and are shown to provide agreement between theory and simulation. Special consideration is given to the scale ambiguity associated with the nontrivial renormalization of the singular contact interactions. Further, the isotropic superfluid gap is obtained to next-to-leading order, and nonuniversal contributions to the energy density due to effective range effects, p -wave interactions, and three-body forces are computed. Results are compared with precise Monte Carlo simulations of the energy density and the contact in the weakly coupled attractive and repulsive Fermi-liquid regimes. In addition, the known all-orders sum of ladder and ring diagrams is compared with Monte Carlo simulations at weak coupling and beyond.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Pairing instability on a Luttinger surface: A non-Fermi liquid to superconductor transition and its Sachdev-Ye-Kitaev dual

Superconductivity results from an instability of the Fermi surface—contour of poles of the single-particle propagator—to an infinitesimally small attraction between electrons. Here, we instead discuss the analogous problem on a model Luttinger surface, or contour of zeros of the Green function. At zero temperature ($β → \infty$) and a critical interaction strength ($u_{c∞}$) characterized by the residue of self-energy pole, we find that the pair susceptibility diverges leading to a superconducting instability. We evaluate the pair fluctuation partition function and find that the spectral density in the normal state has an interaction-driven, power-law $\frac{1}{\sqrt{ω}}$ type, van-Hove singularity (vHS), indicating non-Fermi liquid (NFL) physics. Crucially, in the strong coupling limit ($βu \gg 1$), the leading-order fluctuation free-energy terms in the normal state of this NFL-SC transition resembles the equivalent [$\textit{O}(1)$] terms of the Sachdev-Ye-Kitaev (SYK) model. This free-energy contribution takes a simple form $–βF = βu_{c∞} – γ \text{ln}(βu_{c∞}$), where $\gamma$ is a constant equal to $\frac{1}{2}$. Weak impurity scattering ($τ \gg β^{–1}$) leaves the low-energy spectral density unaffected but leads to an interaction-driven enhancement of superconductivity. Our results in this work shed light on the role played by order-parameter fluctuations in providing the key missing link between Mott physics and strongly coupled toy models exhibiting gravity duals.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Nematic superconductivity in twisted bilayer graphene

Twisted bilayer graphene displays insulating and superconducting phases caused by exceptional flattening of its lowest energy bands. Superconductivity with highest T c appears near half filling of the valence band (n ≈ –2). The data show that in the large part of the superconducting dome near n = –2, threefold lattice rotation symmetry is broken in the superconducting phase, i.e., a superconductor is also a nematic. We perform a comprehensive analysis of superconductivity in twisted-bilayer graphene within an itinerant approach and present a mechanism for nematic superconductivity. We take as an input the fact that at dopings, where superconductivity has been observed, the Fermi energy lies in the vicinity of twist-induced Van Hove singularities in the density of states. We argue that the low-energy physics can be properly described by patch models with either six or twelve Van Hove points. We obtain pairing interactions for the patch models in terms of parameters of the microscopic model for the flat bands, which contains both local and twist-induced nonlocal interactions. Here, we show that the latter give rise to attraction in different superconducting channels. For six Van Hove points, there is just one attractive d-wave channel, and we find chiral d ± id superconducting order, which breaks time-reversal symmetry but leaves the lattice rotation symmetry intact. For twelve Van Hove points, we find two attractive channels, g and i waves, with almost equal coupling constants. We show that both order parameters are nonzero in the ground state and explicitly demonstrate that in this co-existence state the threefold lattice rotation symmetry is broken, i.e., the superconducting state is also a nematic. We find two possible nematic states, one is time-reversal symmetric, the other additionally breaks time-reversal symmetry. We apply our scenario to twisted bilayer graphene near n = –2 and argue that it is applicable also to other systems with two (or more) attractive channels with similar couplings as our reasoning for a nematic superconductivity is based on generic symmetry considerations.

36 MATERIALS SCIENCE↗