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At least 721 records · Page 40

Efficient Monte Carlo event generation for neutrino-nucleus exclusive cross sections

Modern neutrino-nucleus cross section computations need to incorporate sophisticated nuclear models to achieve greater predictive precision. However, the computational complexity of these advanced models often limits their practicality for experimental analyses. To address this challenge, we introduce a new Monte Carlo method utilizing normalizing flows to generate surrogate cross sections that closely approximate those of the original model while significantly reducing computational overhead. As a case study, we built a Monte Carlo event generator for the neutrino-nucleus cross section model developed by the Ghent group. This model employs a Hartree-Fock procedure to establish a quantum mechanical framework in which both the bound and scattering nucleon states are solutions to the mean-field nuclear potential. The surrogate cross sections generated by our method demonstrate excellent accuracy with a relative effective sample size of more than 98.4%, providing a computationally efficient alternative to traditional Monte Carlo sampling methods for differential cross sections.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Consistent Space Runtime (CSPACER) v1.0

This software provides a runtime for communication-bound applications, especially with irregular communication patterns. The target programming abstraction for the runtime is the space consistency model, which defines consistency guarantees at the granularity of memory spaces. This model has relaxed consistency semantics that enables a wide range of runtime optimizations. The runtime leverages threading to accelerate communication primitives, especially collective operations. It also allows efficient pipelining of communication operations and enable constructing a consistent state of multiple unordered communication activities targeting a memory space. The runtime uses a reduced API design that decomposes complex communication primitives in traditional general-purpose runtime into a sequence of simpler steps. To improve the productivity of using this runtime, we provide communication patterns commonly used for regular scientific computing applications and irregular data analytics. These communication patterns offer skeletons for the integration with application computation to allow efficient overlap.

Ibrahim, Khaled↗

Converging towards atomic and nuclear pressures (Final Report)

his report details the development of transformational tools and techniques, allowing the accurate characterization of matter at the most extreme conditions yet studied in the high energy density (HED) domain. Before this work, most experiments quantitatively mapping the nature of matter in the HED realm were performed using planar geometry, which allows for the isolation and measurement of variables in a single thermodynamic state. Such measurements include equation of state variables, optical conductivity, heat transport and more. However, due to a variety of plasma processes, such experiments are limited to below ~10 TPa (100 Mbar) pressures. To achieve higher pressures, convergent experiments are needed. Historically, convergent experiments have not been used for benchmark data because they are integral measurements. That is each part of a convergent target undergoes a time dependent wide range of states, making it difficult to accurately isolate any particular quantity for a given thermodynamic state. This effort developed innovative convergent HED platforms and techniques enabling the exploration of matter from atomic to nuclear scale pressures. This effort also performed pioneering experiments that yielded the first rigorous benchmark data at these extreme conditions. This funding award began with the overarching goal to understand the behavior of matter at extreme (atomic-to-nuclear scale) pressures. The motivation for these goals lie in the fact that every time scientists explore matter beyond the threshold of an atomic unit, there is a fundamental shift in science. The atomic unit for energy, mass, charge, length, and time have each been explored, and each time such a threshold was crossed, a new sequence of discoveries was made resulting in significant awards such as the Nobel Prize. The only unexplored atomic unit is pressure, and this effort set the course for exploring matter at and beyond such pressures. That most of the recently discovered extrasolar planets and stars, as well as matter in the late implosion stages of inertial fusion targets, have deep internal pressures at and beyond atomic pressures amplifies the importance of this effort. Much of the initial work in developing techniques to create these atomic-to-nuclear pressures already existed within the HED community, predominantly at large scale laser facilities such as the National Ignition Facility (NIF) and the Omega60 laser the University of Rochester and although these experiments were routinely performed the ability to extract information about the underlying physical states and processes remained elusive due to the complexity of the experiments, extreme scales in both time and space, and the integrated nature of all the measurements. This work built a rigorous framework so such measurements can routinely be made. This was done in part through the introduction of Bayesian inference techniques into the field of HED science. These techniques allow for the self-consistent extraction of the relevant variables and their explicit and implicit correlations, so as to make use of integrated experimental data to constrain physical models and provide accurate uncertainty bounds for the data. The techniques developed here are fully transparent and proved immediately useful providing quantitative rigorous benchmarks for physical states and processes at some of the most extreme conditions yet explored on Earth. This funding is directly or partly responsible for 7 publications in major peer-reviewed scientific journals, a doctoral thesis, 3 invited talks at major conferences, and the training of a post-doc, 2 graduate students, and 1 undergraduate student. Beyond the effort supported by this award launched the introduction of Bayesian inference into the HED physics community and helped push the usage if modern data-science techniques within the physics community at large.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Page curves and typical entanglement in linear optics

Bosonic Gaussian states are a special class of quantum states in an infinite dimensional Hilbert space that are relevant to universal continuous-variable quantum computation as well as to near-term quantum sampling tasks such as Gaussian Boson Sampling. In this work, we study entanglement within a set of squeezed modes that have been evolved by a random linear optical unitary. We first derive formulas that are asymptotically exact in the number of modes for the Rényi-2 Page curve (the average Rényi-2 entropy of a subsystem of a pure bosonic Gaussian state) and the corresponding Page correction (the average information of the subsystem) in certain squeezing regimes. We then prove various results on the typicality of entanglement as measured by the Rényi-2 entropy by studying its variance. Using the aforementioned results for the Rényi-2 entropy, we upper and lower bound the von Neumann entropy Page curve and prove certain regimes of entanglement typicality as measured by the von Neumann entropy. Our main proofs make use of a symmetry property obeyed by the average and the variance of the entropy that dramatically simplifies the averaging over unitaries. In this light, we propose future research directions where this symmetry might also be exploited. We conclude by discussing potential applications of our results and their generalizations to Gaussian Boson Sampling and to illuminating the relationship between entanglement and computational complexity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator

Gene activator proteins comprise distinct DNA-binding and transcriptional activation domains (ADs). Because few ADs have been described, we tested domains tiling all yeast transcription factors for activation in vivo and identified 150 ADs. By mRNA display, we showed that 73% of ADs bound the Med15 subunit of Mediator, and that binding strength was correlated with activation. AD-Mediator interaction in vitro was unaffected by a large excess of free activator protein, pointing to a dynamic mechanism of interaction. Structural modeling showed that ADs interact with Med15 without shape complementarity (‘fuzzy’ binding). ADs shared no sequence motifs, but mutagenesis revealed biochemical and structural constraints. Finally, a neural network trained on AD sequences accurately predicted ADs in human proteins and in other yeast proteins, including chromosomal proteins and chromatin remodeling complexes. These findings solve the longstanding enigma of AD structure and function and provide a rationale for their role in biology.

60 APPLIED LIFE SCIENCES↗

Structural basis for SHOC2 modulation of RAS signalling

The RAS–RAF pathway is one of the most commonly dysregulated in human cancers. Despite decades of study, understanding of the molecular mechanisms underlying dimerization and activation of the kinase RAF remains limited. Recent structures of inactive RAF monomer and active RAF dimer bound to 14-3-3 have revealed the mechanisms by which 14-3-3 stabilizes both RAF conformations via specific phosphoserine residues. Prior to RAF dimerization, the protein phosphatase 1 catalytic subunit (PP1C) must dephosphorylate the N-terminal phosphoserine (NTpS) of RAF to relieve inhibition by 14-3-3, although PP1C in isolation lacks intrinsic substrate selectivity. SHOC2 is as an essential scaffolding protein that engages both PP1C and RAS to dephosphorylate RAF NTpS, but the structure of SHOC2 and the architecture of the presumptive SHOC2–PP1C–RAS complex remain unknown. Here we present a cryo-electron microscopy structure of the SHOC2–PP1C–MRAS complex to an overall resolution of 3Å, revealing a tripartite molecular architecture in which a crescent-shaped SHOC2 acts as a cradle and brings together PP1C and MRAS. Our work demonstrates the GTP dependence of multiple RAS isoforms for complex formation, delineates the RAS-isoform preference for complex assembly, and uncovers how the SHOC2 scaffold and RAS collectively drive specificity of PP1C for RAF NTpS. Our data indicate that disease-relevant mutations affect complex assembly, reveal the simultaneous requirement of two RAS molecules for RAF activation, and establish rational avenues for discovery of new classes of inhibitors to target this pathway.

59 BASIC BIOLOGICAL SCIENCES↗

Study of Nucleon Resonance Electroexcitations at Jefferson Lab

Nucleons are the most fundamental three-body systems in Nature. During the last decade crucial progress has been achieved in the exploration of the spectrum and the structure of nucleon resonances. Studies of exclusive ?N, ?+??p, K?, and K? electroproduction off protons on the evolution of the electrocouplings with photon virtuality Q2 using the CLAS spectrometer has revealed a complex interplay between an inner core of three dressed quarks surrounded by an external meson-baryon cloud. CLAS12 is the only facility capable of extending these results on the electrocouplings into the unexplored Q2 range, spanning the domain of quark momenta where ? 50% of hadron mass is generated. The increase of the CEBAF energy and the upgrade of the CLAS12 spectrometer to measure exclusive electroproduction channels at higher luminosity and photon virtualities will offer a unique opportunity to explore how the dominant part of hadron mass and the bound three-quark structure of the resonant states emerge from QCD.

Achenbach, Patrick↗

Subtle Molecular Changes Largely Modulate Chiral Helical Assemblies of Achiral Conjugated Polymers by Tuning Solution-State Aggregation

Understanding the solution-state aggregate structure and the consequent hierarchical assembly of conjugated polymers is crucial for controlling multiscale morphologies during solid thin-film deposition and the resultant electronic properties. However, it remains challenging to comprehend detailed solution aggregate structures of conjugated polymers, let alone their chiral assembly due to the complex aggregation behavior. Herein, we present solution-state aggregate structures and their impact on hierarchical chiral helical assembly using an achiral diketopyrrolopyrrole-quaterthiophene (DPP-T4) copolymer and its two close structural analogues wherein the bithiophene is functionalized with methyl groups (DPP-T2M2) or fluorine atoms (DPP-T2F2). Combining in-depth small-angle X-ray scattering analysis with various microscopic solution imaging techniques, we find distinct aggregate in each DPP solution: (i) semicrystalline 1D fiber aggregates of DPP-T2F2 with a strongly bound internal structure, (ii) semicrystalline 1D fiber aggregates of DPP-T2M2 with a weakly bound internal structure, and (iii) highly crystalline 2D sheet aggregates of DPP-T4. These nanoscopic aggregates develop into lyotropic chiral helical liquid crystal (LC) mesophases at high solution concentrations. Intriguingly, the dimensionality of solution aggregates largely modulates hierarchical chiral helical pitches across nanoscopic to micrometer scales, with the more rigid 2D sheet aggregate of DPP-T4 creating much larger pitch length than the more flexible 1D fiber aggregates. Combining relatively small helical pitch with long-range order, the striped twist-bent mesophase of DPP-T2F2 composed of highly ordered, more rigid 1D fiber aggregate exhibits an anisotropic dissymmetry factor (g-factor) as high as 0.09. This study can be a prominent addition to our knowledge on a solution-state hierarchical assembly of conjugated polymers and, in particular, chiral helical assembly of achiral organic semiconductors that can catalyze an emerging field of chiral (opto)electronics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Half-life determination of heavy ions in a storage ring considering feeding and depleting background processes

Heavy-ion storage rings have relatively large momentum acceptance which allows for multiple ion species to circulate at the same time. This needs to be considered in radioactive decay measurements of highly charged ions, where atomic charge exchange reactions can significantly alter the intensities of parent and daughter ions. In this study, we investigate this effect using the decay curves of ion numbers in the recent 205 Tl 81+ bound-state beta decay experiment conducted using the Experimental Storage Ring at GSI Darmstadt. To understand the intricate dynamics of ion numbers, we present a set of differential equations that account for various atomic and nuclear reaction processes—bound state beta decay, atomic electron recombination and capture, and electron ionization. By incorporating appropriate boundary conditions, we develop a set of differential equations that accurately simulate the decay curves of various simultaneously stored ions in the storage ring: 205 Tl 81+ , 205 Pb 81+ , 205 Pb 82+ , 200 Hg 79+ , and 200 Hg 80+ . Through a quantitative comparison between simulations and experimental data, we provide insights into the detailed reaction mechanisms governing stored heavy ions within the storage ring. Our approach effectively models charge-changing processes, reduces the complexity of the experimental setup, and provides a simpler method for measuring the decay half-lives of highly charged ions in storage rings.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Characterizing Stress Orientations in Southern Kansas

We repot that Induced seismicity predominantly occurs along faults that are optimally oriented to the local principal compressive stress direction, and the characterization of these stress orientations is an important component of understanding seismic hazards. The seismicity rate in southern Kansas rapidly increased in 2013 primarily due to the disposal of large volumes of wastewater into the Arbuckle Group. Previously, local stress orientations in this area were poorly constrained, which limited our understanding of the complex faulting and diverse earthquake mechanisms in this region. We use shear-wave splitting and focal mechanism inversion techniques to create multiple, independent estimates of maximum horizontal stress directions (S Hmax ) and their spatial variation across the study area. We then create an integrated model of stress orientations for southern Kansas and northern Oklahoma using our local results in conjunction with previous, regional stress orientation estimates. We find that S Hmax in both southern Kansas and central Oklahoma exhibits an east-northeast (~N78°E) orientation, and these regions bound a northeast (~N59°E) rotation within a ~20km area in northern Oklahoma near the Nemaha ridge.

58 GEOSCIENCES↗

Vibrational Entropy of Crystalline Solids from Covariance of Atomic Displacements

The vibrational entropy of a solid at finite temperature is investigated from the perspective of information theory. Ab initio molecular dynamics (AIMD) simulations generate ensembles of atomic configurations at finite temperature from which we obtain the N-body distribution of atomic displacements, ρN. We calculate the information-theoretic entropy from the expectation value of lnρN. At a first level of approximation, treating individual atomic displacements independently, our method may be applied using Debye–Waller B-factors, allowing diffraction experiments to obtain an upper bound on the thermodynamic entropy. At the next level of approximation we correct the overestimation through inclusion of displacement covariances. We apply this approach to elemental body-centered cubic sodium and face-centered cubic aluminum, showing good agreement with experimental values above the Debye temperatures of the metals. Below the Debye temperatures, we extract an effective vibrational density of states from eigenvalues of the covariance matrix, and then evaluate the entropy quantum mechanically, again yielding good agreement with experiment down to low temperatures. Our method readily generalizes to complex solids, as we demonstrate for a high entropy alloy. Further, our method applies in cases where the quasiharmonic approximation fails, as we demonstrate by calculating the HCP/BCC transition in Ti.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Long-Range Allosteric Communication Modulated by Active Site Mn(II) Coordination Drives Catalysis in Xanthobacter autotrophicus Acetone Carboxylase

Acetone carboxylase (AC) from Xanthobacter autotrophicus is a 360 KDa α2β2γ2 heterohexamer that catalyzes the ATP-dependent formation of phosphorylated acetone and bicarbonate intermediates that react at Mn(II) metal active sites to form acetoacetate. Structural models of X. autotrophicus AC (XaAC) with and without nucleotides reveal that the binding and phosphorylation of the two substrates occurs ~40 Å from the Mn(II) active sites where acetoacetate is formed. Based on the crystal structures, a significant conformational change was proposed to open and close a tunnel that facilitates the passage of reaction intermediates between the sites for nucleotide binding and phosphorylation of substrates and Mn(II) sites of acetoacetate formation. We have employed electron paramagnetic resonance (EPR), kinetic assays, and hydrogen/deuterium exchange mass spectrometry (HDX-MS) of poised ligand-bound states and site-specific amino acid variants to complete an in-depth analysis of Mn(II) coordination and allosteric communication throughout the catalytic cycle. In contrast with the established paradigms for carboxylation, our analyses of XaAC suggested a carboxylate shift that couples both local and long-range structural transitions. Shifts in the coordination mode of a single carboxylic acid residue (αE89) mediate both catalysis proximal to a Mn(II) center and communication with an ATP active site in a separate subunit of a 180 kDa α2β2γ2 complex at a distance of 40 Å. This work demonstrates the power of combining structural models from X-ray crystallography with solution-phase spectroscopy and biophysical techniques to elucidate functional aspects of a multi-subunit enzyme.

Biochemistry & Molecular Biology↗

Isomer-specific, Cryogenic Ion Vibrational Spectroscopy Investigation of D2-and N2- Tagged, Protonated Formic Acid Complexes Using Two Color, IR-IR Photobleaching

Here we analyze cryogenic ion vibrational spectra of tagged protonated formic acid (PFA) with electronic structure and anharmonic vibrational calculations to establish the isomers generated by electrospray ionization (ESI) followed by buffer gas cooling to ~25 K. Two isomers are identified (the trans form (E,Z) and the cis form (E,E)) and generated in comparable abundance despite the fact that the calculated E,E structure lies 6.40 kJ mol-1 above the E,Z form. A large (~60 kJ mol-1) barrier separates them such that the E,E form can be kinetically trapped upon cooling in the ion trap. The anticooperativity between the H-bonds of the OH groups is explored by measuring the shift in the D2-bound OH fundamental when a second D2 is attached. Both isomers are observed in the N2-tagged counterparts, displaying the expected red-shifted OH bands. These results indicate that ESI generates both isomers and both must be considered when analyzing cluster spectra based on the PFA core ion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spin-selective evolution of the Zhang-Rice state in binary transition metal oxide MnO(001) film

Here, the Zhang-Rice (ZR) state is a strongly hybridized bound state formed by transition-metal and oxygen atoms. The spin fluctuations within the ZR state are known to play an important role in high-T c superconductivity in cuprates. Here, we employ a combination of angle-resolved photoemission spectroscopy (ARPES), x-ray photoemission spectroscopy (XPS), and ab initio embedded dynamical mean-field theory (eDMFT) to investigate the influence of magnetic ordering on the spectral characteristics of the valence band and Mn 2⁢p core-level in MnO (001) ultrathin films. Our results demonstrate that a complex spin-selective evolution of Mn 3⁢d-O2⁢p hybridization develops due to the long-range antiferromagnetic (AFM) ordering. This hybridization significantly alters the spectral shape and weight of the ZR state. Specifically, in the AFM phase, we observed the sharpening of the ZR state and band folding with the periodicity of the AFM unit cell of MnO(001). We also demonstrated a strong connection between the spectral evolution of the ZR state and the non-local screening channels of the photoexcited core holes. Further, our detailed temperature-dependent study reveals the presence of short-range antiferromagnetic correlations that exist at much higher temperatures than Neel temperature (T N ) and shows the evolution of the ZR state across the magnetic transitions and its implication to the core-hole screening in 3⁢d binary transition metal oxides.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Mapping the catalytic conformations of an assembly-line polyketide synthase module

Assembly-line polyketide synthases, such as the 6-deoxyerythronolide B synthase (DEBS), are large enzyme factories prized for their ability to produce specific and complex polyketide products. By channeling protein-tethered substrates across multiple active sites in a defined linear sequence, these enzymes facilitate programmed small-molecule syntheses that could theoretically be harnessed to access countless polyketide product structures. Additionally, using cryogenic electron microscopy to study DEBS module 1, we present a structural model describing this substrate-channeling phenomenon. Our 3.2- to 4.3-angstrom-resolution structures of the intact module reveal key domain-domain interfaces and highlight an unexpected module asymmetry. We also present the structure of a product-bound module that shines light on a recently described “turnstile” mechanism for transient gating of active sites along the assembly line.

59 BASIC BIOLOGICAL SCIENCES↗

Dark initial state radiation and the kinetic mixing portal

Data from Planck measurements of the cosmic microwave background (CMB) place important constraints on models with light dark matter (DM) and light mediators especially when both lie in the mass range below ~ 1 GeV. In models involving kinetic mixing where the dark photon acts as the mediator, these constraints are easily satisfied and the appropriate DM relic density achievable if the DM is, e.g., a complex scalar, where p-wave annihilation occurs, or is the lighter component of a split pseudo-Dirac state where co-annihilation dominates. In both of these cases, although higher order in the dark gauge coupling, g D , the corresponding annihilation processes including dark photon initial state radiation (ISR) will be dominantly s-wave with essentially temperature independent cross sections. The rates for these dark ISR associated processes, though not yielding cross sections large enough to contribute to the relic density, can still run into possible conflicts with the bounds arising from the CMB. In this paper we perform a preliminary study of the present and potential future constraints that the CMB imposes on the parameter spaces for both of these scenarios due to the existence of this dark ISR. Further analyses of the effects of dark ISR in DM annihilation is clearly warranted.

79 ASTRONOMY AND ASTROPHYSICS↗

Scalable semidefinite programming approach to variational embedding for quantum many-body problems

In quantum embedding theories, a quantum many-body system is divided into localized clusters of sites which are treated with an accurate ‘high-level’ theory and glued together self-consistently by a less accurate ‘low-level’ theory at the global scale. The recently introduced variational embedding approach for quantum many-body problems combines the insights of semidefinite relaxation and quantum embedding theory to provide a lower bound on the ground-state energy that improves as the cluster size is increased. The variational embedding method is formulated as a semidefinite program (SDP), which can suffer from poor computational scaling when treated with black-box solvers. Here, we exploit the interpretation of this SDP as an embedding method to develop an algorithm which alternates parallelizable local updates of the high-level quantities with updates that enforce the low-level global constraints. Moreover, we show how translation invariance in lattice systems can be exploited to reduce the complexity of projecting a key matrix to the positive semidefinite cone.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Quantum simulation of Lindbladian dynamics via repeated interactions

The Lindblad equation generalizes the Schrödinger equation to quantum systems that undergo dissipative dynamics. The quantum simulation of Lindbladian dynamics is therefore non-unitary, preventing a naive application of state-of-the-art quantum algorithms. Here, we make use of an approximate correspondence between Lindbladian dynamics and evolution based on repeated interaction (RI) CPTP maps to write down a Hamiltonian formulation of the Lindblad dynamics and derive a rigorous error bound on the master equation. Specifically, we show that the number of interactions needed to simulate the Liouvillian within error e scales in most physical scenarios as . This is significant because the error in the Lindbladian approximation to the dynamics is not explicitly bounded in existing quantum algorithms for open system simulations. We then provide quantum algorithms to simulate RI maps using an iterative qubitization approach and Trotter–Suzuki formulas, and specifically show that for iterative qubitization the number of operations needed to simulate the dynamics (for a fixed value of ?) scales as in the limit where a0 (the coefficient 1-norm for the system and bath Hamiltonians) asymptotically dominates over the corresponding factor for the interaction Hamiltonian, which is often the case in weak coupling. This scaling would appear to be optimal if the complexity of ? is not considered, which underscores the importance of considering the error in the Liouvillian that we reveal in this work.

Quantum Computing↗