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DOE OSTI2023

pmartR 2.0 : A Quality Control, Visualization, and Statistics Pipeline for Multiple Omics Datatypes

The pmartR (https://github.com/pmartR/pmartR) package was designed for the quality control (QC) and analysis of mass spectrometry (MS) data, tailored to specific characteristics of proteomic (isobaric or labelled), metabolomic, and lipidomic datasets. Since its initial release, the tool has been expanded to address the needs of its growing userbase and now includes QC and statistics for nuclear magnetic resonance (NMR) metabolomic data, and leverages the DESeq2, edgeR, and limma-voom R packages for some transcriptomic data analyses. These improvements have made progress towards a unified omics processing pipeline for ease of reporting and streamlined statistical purposes. The package’s statistics and visualization capabilities have also been expanded by adding support for paired data and by integrating pmartR with the trelliscopejs R package for the quick creation of trellis displays (https://github.com/hafen/trelliscopejs). Here, we present relevant examples of each of these enhancements to pmartR and highlight how each new feature benefits the omics community.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Trends in spatial correlations, two-phase coexistence, and criticality in a class of type-2 Schloegl models for autocatalysis

A class of type-2 Schloegl models is considered for particles on a square lattice with variable-range cooperativity. These models involve: (i) spontaneous particle annihilation at rate p; (ii) autocatalytic particle creation at unoccupied sites (i, j) with n ⩾ 2 particles within a specified neighborhood, Ω 𝑁 (i, j), of sites at rate $k_n$ = $\frac{^{(^n_2)}}{_{(^N_2)}}$ = $\frac{n{(n-1)}}{_{N(N-1)}}$; and (iii) possible spontaneous particle creation at unoccupied sites at “small” rate ɛ ⩾ 0. In some cases, Ω 𝑁 just includes all symmetry-equivalent sites at a single specific distance 𝑑 (in units of lattice constants) from the unoccupied site, e.g., 𝑑 = 1 (nearest-neighbor sites) where 𝑁 = 4, or 𝑑 = √5 (or √13 or…) where 𝑁 = 8. In other cases, Ω 𝑁 includes sites multiple distances from the unoccupied site, e.g., 𝑑 = {1,√2}, where 𝑁 = 8. Kinetic Monte Carlo (KMC) simulation reveals that these models exhibit a nonequilibrium discontinuous phase transition between high- and low-density states below a critical point, ɛ < ɛ c , with generic two-phase coexistence (2PC) at least for smaller 𝑁. With some exceptions, there is an approach toward mean-field behavior with increasing 𝑁 (so the regime of generic 2PC shrinks, and ɛ c approaches the mean-field value of 1/27). Additional insight into trends is provided by analysis of the exact master equations for the models via hierarchical truncation. These truncations utilize suitably tailored pair approximations which reflect the dominant nonequilibrium spatial correlations. These correlations in turn are shown to reflect the details of the autocatalytic particle creation process. For spatially heterogeneous states, the truncations produce coupled sets of lattice differential equations (LDE) which can describe orientation-dependent propagation of an interface between high- and low-density steady states for ɛ < ɛ c . Pair approximation values of 𝑝 = 𝑝 eq where the interface is stationary, and its orientation-dependence, are in semiquantitative agreement with KMC results. In conclusion, this comparison accounts for propagation failure in the LDE which complicates interpretation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Production of b b ¯ at forward rapidity in p + p collisions at s = 510 GeV

The cross section of bottom quark-antiquark ( b b ¯ ) production in p + p collisions at s = 510 GeV is measured with the PHENIX detector at the Relativistic Heavy Ion Collider. The results are based on the yield of high mass, like-sign muon pairs measured within the PHENIX muon arm acceptance ( 1.2 < | y | < 2.2 ). The b b ¯ signal is extracted from like-sign dimuons by utilizing the unique properties of neutral B meson oscillation. We report a differential cross section of d σ b b ¯ → μ ± μ ± / d y = 0.16 ± 0.01 ( stat ) ± 0.02 ( syst ) ± 0.02 ( global ) nb for like-sign muons in the rapidity and p T ranges 1.2 < | y | < 2.2 and p T > 1 GeV / c , and dimuon mass of 5 – 10 GeV / c 2 . The extrapolated total cross section at this energy for b b ¯ production is 13.1 ± 0.6 ( stat ) ± 1.5 ( syst ) ± 2.7 ( global ) μ b . The total cross section is compared to a perturbative quantum chromodynamics calculation and is consistent within uncertainties. The azimuthal opening angle between muon pairs from b b ¯ decays and their p T distributions are compared to distributions generated using ps pythia 6, which includes next-to-leading order processes. The azimuthal correlations and pair p T distribution are not very well described by pythia calculations, but are still consistent within uncertainties. Flavor creation and flavor excitation subprocesses are favored over gluon splitting.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Quantum chromodynamics resolution of the ATOMKI anomaly in 4 He nuclear transitions

Observations of anomalous angular correlations in electron-positron pairs produced from excited states of 4 He, 8 Be, and 12 C nuclei have been suggested as being due to the creation and subsequent decay of a new light particle of mass ~17MeV. In this work, we investigate the possibility that the source of the observed signals is a set of new excitation channels created by the 12-quark hidden-color Fock state within the 4 He nuclear wave function dubbed the “hexadiquark.” We calculate the invariant e + ⁢ e - mass spectrum for the electromagnetic transition from a new excitation of 4 He, estimating its differential and total decay width. We find that we can fit the shape of the anomalous signal with the QCD Fock state at excitation energy E* = 17.9 ± 1MeV and a Gaussian form factor for the electromagnetic decay. We address the physical issues with the fit parameters using properties of the hexadiquark state, in particular the three weakly repulsive 6 C interactions of SU⁡(3) C between diquark pairs. Experimental tests of our model are described in detail. In light of this work, we emphasize the need for independent experimental confirmation or refutation of the ATOMKI results as well as dedicated experiments to search for the proposed new excitations of 4 He and other a-cluster nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Anomalous Interlayer Exciton Diffusion in WS 2 /WSe 2 Moiré Heterostructure

Stacking van der Waals crystals allows for the on-demand creation of a periodic potential landscape to tailor the transport of quasiparticle excitations. We investigate the diffusion of photoexcited electron-hole pairs, or excitons, at the interface of WS 2 /WSe 2 van der Waals heterostructure over a wide range of temperatures. We observe the appearance of distinct interlayer excitons for parallel and antiparallel stacking and track their diffusion through spatially and temporally resolved photoluminescence spectroscopy from 30 to 250 K. While the measured exciton diffusivity decreases with temperature, it surprisingly plateaus below 90 K. Our observations cannot be explained by classical models like hopping in the moiré potential. A combination of ab initio theory and molecular dynamics simulations suggests that low-energy phonons arising from the mismatched lattices of moiré heterostructures, also known as phasons, play a key role in describing and understanding this anomalous behavior of exciton diffusion. Our observations indicate that the moiré potential landscape is dynamic down to very low temperatures and that the phason modes can enable efficient transport of energy in the form of excitons.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Sensitivity Analysis for the Component Design App: Analysis of Success Assured Data

A new tool has been developed to perform variance-based global sensitivity analysis (VBGSA) on data from a set-based concurrent engineering software called Success Assured (SA). The tool is part of a digital component design app, which is currently in production as an Accelerated Digital Engineering Pathfinder at Sandia National Laboratories. When working with complex digital models, it is important to understand relationships between inputs and outputs, i.e., how “sensitive” model outputs are to changes in model inputs. After extensive research and trials of various sensitivity analysis methods, it was determined that estimation of Sobol’ indices for VBGSA with Monte Carlo simulation, paired with simple surrogate models, produces the best results for SA data. This tool increases understanding of SA models and streamlines the creation of SA datasets. This report details the methodology and implementation of this sensitivity analysis tool so others can understand it and implement it.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Proximity-induced collective modes in an unconventional superconductor heterostructure

Unconventional superconductors have been long sought for their potential applications in quantum technologies and devices. A key challenge impeding this effort is the difficulty associated with probing and characterizing candidate materials and establishing their order parameter. Here we present a platform that allows one to spectroscopically probe unconventional superconductivity in thin-layer materials via the proximity effect. Here we show that inducing an s-wave gap in a sample with an intrinsic d-wave instability leads to the formation of bound states of quasiparticle pairs, which manifest as a collective mode in the d-wave channel. This finding provides a way to study the underlying pairing interactions vicariously through the collective mode spectrum of the system. Upon further cooling of the system we observe that this mode softens considerably and may even condense, signaling the onset of time-reversal symmetry-breaking superconductivity. Therefore, our proposal also allows for the creation and study of these elusive unconventional states.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Anion-dependent phase behavior of methylimidazolium-based ionic liquids mixed with water: Correlation between local molecular structure and mesoscale behaviors

The mesoscopic phase behavior of decylmethylimidazolium (C 10 mim) ionic liquids (ILs) bearing three monovalent anions—thiocyanate (SCN − ), nitrate (NO 3 − ), and chloride (Cl − )—mixed with water at relatively high IL contents (50–95 wt%) was investigated. Small-angle and wide-angle X-ray scattering (SAXS/WAXS) were employed to follow the evolution of both local and mesoscale structures across this composition range. In the absence of water, C 10 mimSCN and C 10 mimCl behaved as disordered liquids, whereas C 10 mimNO 3 spontaneously formed a hexagonally ordered cylindrical mesophase and displayed a sticky-solid macroscopic appearance. Upon addition of water, C 10 mimSCN remained a viscous liquid and only weakly ordered lamellar domains were observed. This limited ordering is attributed to the lack of hydrogen bonding and weak interaction energy between SCN − anions and C 10 mim + cations. In contrast, the trigonal-planar NO 3 − and point-like Cl − anions promoted the formation of well-defined hexagonal mesophases up to 35–45 wt% water. The formation of hydrogen bonding of the two anions with imidazolium ring protons likely enabled the creation of compact ion clusters that effectively exclude water molecules from the immediate vicinity of the IL aggregates. These findings demonstrate that the interaction energy between ion pairs dictate IL-water interactions and therefore control the transition from disordered liquids to ordered mesophases in IL/water mixtures with high IL contents. In conclusion, the combined SAXS/WAXS analysis reveals a correlation between local intermolecular structure and the emergence of mesoscopic order, providing a systematic framework for tailoring mesoscale structures in alkylimidazolium-based IL/water systems.

36 MATERIALS SCIENCE↗

NASA NTRS2011

Ionic Liquids to Replace Hydrazine

A method for developing safe, easy-to-handle propellants has been developed based upon ionic liquids (ILs) or their eutectic mixtures. An IL is a binary combination of a typically organic cation and anion, which generally produces an ionic salt with a melting point below 100 deg C. Many ILs have melting points near, or even below, room temperature (room temperature ionic liquids, RTILs). More importantly, a number of ILs have a positive enthalpy of formation. This means the thermal energy released during decomposition reactions makes energetic ILs ideal for use as propellants. In this specific work, to date, a baseline set of energetic ILs has been identified, synthesized, and characterized. Many of the ILs in this set have excellent performance potential in their own right. In all, ten ILs were characterized for their enthalpy of formation, density, melting point, glass transition point (if applicable), and decomposition temperature. Enthalpy of formation was measured using a microcalorimeter designed specifically to test milligram amounts of energetic materials. Of the ten ILs characterized, five offer higher Isp performance than hydrazine, ranging between 10 and 113 seconds higher than the state-of-the-art propellant. To achieve this level of performance, the energetic cations 4- amino-l,2,4-triazolium and 3-amino-1,2,4-triazolium were paired with various anions in the nitrate, dicyanamide, chloride, and 3-nitro-l,2,4-triazole families. Protonation, alkylation, and butylation synthesis routes were used for creation of the different salts.

Koelfgen, Syri↗

DOE OSTI2025

Control and synchronization of rapid nanoscale DNA heat engine by local heating

To further activate devices based on DNA nanotechnology, we introduce an approach that notably enhances both the speed and force of DNA powered machines and artificial hinge machine. A microheater, with millisecond response, heats or recools DNA origami constructs, hybridizing or dehybridizing sticky ends. Because anything within 20 micrometers of the heater equilibrates to a programmed temperature change in milliseconds, sticky ends of a compound DNA origami machine can open and close synchronously and operate cooperatively, in phase, additively increasing the drive force compared to single pair of sticky ends DNA machine (the six-helix bundle DNA origami hinge machine). In our demonstrations, we fold and unfold two square origami with 10 pairs of complementary sticky ends to drive a bead on the end of a rod like origami to speeds exceeding 30 micrometers per second. Our device envisions the creation of complex, synchronized DNA machines.

Science & Technology - Other Topics↗

DOE OSTI2022

Positrons for Our Future

JLab Users want beams of polarized (and unpolarized) positrons, with beam qualities and modes of operation similar to those provided in the electron beams at CEBAF today [Gra19]. The creation of positrons with a high degree of spin polarization is however very challenging – limited to beta decay, self-polarization in rings, or via e+/e- pair-production, a process requiring a source of polarized gamma rays. At JLab we have a unique source of polarized gamma rays – the bremsstrahlung radiation produced when the spin polarized electron beams of CEBAF interacts with matter – called Polarized Electrons for Polarized Positrons (or PEPPo) [Abb04]. This project sought to extend the PEPPo concept by exploring a possible layout and parameter space for a polarized positron injector at CEBAF based on this approach.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2023

Auger spectroscopy beyond the ultra-short core-hole relaxation time approximation

Abstract We present a time-dependent computational approach to study Auger electron spectroscopy (AES) beyond the ultra-short core-hole relaxation time approximation and, as a test case, we apply it to the paradigmatic example of a one-dimensional Mott insulator represented by a half-filled Hubbard chain. The Auger spectrum is usually calculated by assuming that, after the creation of a core-hole, the system thermalizes almost instantaneously. This leads to a relatively simple analytical expression that uses the ground-state with a core-hole as a reference state and ignores all the transient dynamics related to the screening of the core-hole. In this picture, the response of the system can be associated to the pair spectral function. On the other hand, in our numerical calculations, the core hole is created by a light pulse, allowing one to study the transient dynamics of the system in terms of the pulse duration and in the non-perturbative regime. Time-dependent density matrix renormalization group calculations reveal that the relaxation process involves the creation of a polarization cloud of doublon excitations that have an effect similar to photo-doping. As a consequence, there is a leak of spectral weight to higher energies into what otherwise would be the Mott gap. For longer pulses, these excited states, mostly comprised of doublons, can dominate the spectrum. By changing the duration of the light-pulse, the entire screening process can be resolved in time.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Neutrino condensation from a new Higgs-like interaction

In this work, we revisit the scenario of having a new interaction between neutrinos and a Higgs-like scalar suggested by short-baseline neutrino anomalies. We find that there are two possible attractive channels in the resulting effective 4-Fermi theory which lead to a neutrino condensation in cosmic neutrinos and the creation of a neutrino superfluid at low temperatures and finite chemical potential. We find that at the minimum of the effective potential V the condensates are mostly made up of pairs of left-left + right-right composites, with a tiny admixture of left-right + right-left composites which differs from the scenario of Kapusta which focused on the energetically unfavored left-right + right-left scenario. We obtain an approximate equation for the gap Δ 2 = 4 m H ( μ - m ) Exp [ - π 2 G eff μ μ 2 - m 2 ] , where m H is the mass of the Higgs scalar, and G eff is the effective (renormalized) 4- Fermi interaction. Recent constraints on cosmological neutrinos suggest the possibility that log 10 ( G eff MeV 2 ) = - 1.72 which would lead to an exponentially small gap.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS1982

Relativistic thermal plasmas - Pair processes and equilibria

The work of Bisnovatyi-Kogan, Zel'dovich and Sunyaev (1971) is extended and generalized, through the inclusion of pair-producing photon processes and effects due to the finite size of the plasma, in an investigation of the equilibria of relativistic thermal plasmas which takes into account electron-positron creation and annihilation and photons produced within the plasma. It is shown that the bridge between an effectively thin plasma and an effectively thick plasma occurs in the transrelativistic region, where the dimensionless temperature value is between 0.1 and 1.0 and the temperature remains in this region over a great luminosity range.

Lightman, A. P.↗

DOE OSTI2022

Strategies for Computer-Aided Discovery of Novel Open-Shell Polymers

Organic π-conjugated polymers with a triplet ground state have been the focus of recent research for their interesting and unique electronic properties, arising from the presence of the two unpaired electrons. These compounds are usually built from alternating electron-donating and electron-accepting monomer pairs which lower the HOMO–LUMO gap and yield a triplet state instead of the typical singlet ground state. In this paper, we use density functional theory calculations to explore the design rules that govern the creation of a ground-state triplet conjugated polymer and find that a small HOMO–LUMO gap in the singlet state is the best predictor for the existence of a triplet ground state, compared to previous use of a pro-quinoidal bonding character. Furthermore, this work can accelerate the discovery of new stable triplet materials by reducing the computational resources needed for electronic-state calculations and the number of potential candidates for synthesis.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Designing high-power, octave spanning entangled photon sources for quantum spectroscopy

Entangled photon spectroscopy is a nascent field that has important implications for measurement and imaging across chemical, biology, and materials fields. Entangled photon spectroscopy potentially offers improved spatial and temporal-frequency resolutions, increased cross sections for multiphoton and nonlinear measurements, and new abilities in inducing or measuring quantum correlations. A critical step in enabling entangled photon spectroscopies is the creation of high-flux entangled sources that can use conventional detectors as well as provide redundancy for the losses in realistic samples. Here, we report a periodically poled, chirped, lithium tantalate platform that generates entangled photon pairs with ~10 -7 efficiency. For a near watt level diode laser, this results in a near μW-level flux. The single photon per mode limit that is necessary to maintain non-classical photon behavior is still satisfied by distributing this power over up to an octave-spanning bandwidth. The spectral–temporal photon correlations are observed via a Michelson-type interferometer that measures the broadband Hong–Ou–Mandel two-photon interference. A coherence time of 245 fs for a 10 nm bandwidth in the collinear case and a coherence time of 62 fs for a 125 nm bandwidth in the non-collinear case are measured using a CW pump laser and, essentially, collecting the full photon cone. We outline in detail the numerical methods used for designing and tailoring the entangled photons source, such as changing center wavelength or bandwidth, with the ultimate aim of increasing the availability of high-flux UV–Vis entangled photon sources in the optical spectroscopy community.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Lightweight and effective tensor sensitivity for atomistic neural networks

Atomistic machine learning focuses on the creation of models that obey fundamental symmetries of atomistic configurations, such as permutation, translation, and rotation invariances. In many of these schemes, translation and rotation invariance are achieved by building on scalar invariants, e.g., distances between atom pairs. There is growing interest in molecular representations that work internally with higher rank rotational tensors, e.g., vector displacements between atoms, and tensor products thereof. Here, we present a framework for extending the Hierarchically Interacting Particle Neural Network (HIP-NN) with Tensor Sensitivity information (HIP-NN-TS) from each local atomic environment. Crucially, the method employs a weight tying strategy that allows direct incorporation of many-body information while adding very few model parameters. We show that HIP-NN-TS is more accurate than HIP-NN, with negligible increase in parameter count, for several datasets and network sizes. As the dataset becomes more complex, tensor sensitivities provide greater improvements to model accuracy. In particular, HIP-NN-TS achieves a record mean absolute error of 0.927 $\frac{\text{kcal}}{\text{mol}}$ for conformational energy variation on the challenging COMP6 benchmark, which includes a broad set of organic molecules. We also compare the computational performance of HIP-NN-TS to HIP-NN and other models in the literature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2015

Aram Chaos: a Long Lived Subsurface Aqueous Environment with Strong Water Resources Potential for Human Missions on Mars

Aram Chaos, Mars is a crater 280 kilometers in diameter with elevations circa. minus 2 to minus 3 kilometers below datum that provides a compelling landing site for future human explorers as it features multiple scientific regions of interest (ROI) paired with a rich extensible Resource ROI that features poly-hydrated sulfates [1]. The geologic history of Aram Chaos suggests several past episodes of groundwater recharge and infilling by liquid water, ice, and other materials [1-3]. The creation of the fractured region with no known terrestrial equivalent may have been caused by melting of deep ice reservoirs that triggered the collapse of terrain followed by catastrophic water outflows over the region. Aram Chaos is of particular scientific interest because it is hypothesized that the chaotic terrain may be the source of water that contributed to the creation of nearby valleys such as Ares Vallis flowing toward Chryse Planitia. The liquid water was likely sourced as groundwater and therefore represents water derived from a protected subsurface environment making it a compelling astrobiological site [2]. The past history of water is also represented by high concentrations of hematite, Fe-oxyhydroxides, mono-hydrated and poly-hydrated sulfates [1, 2]. Poly-hydrated sulfates are likely to contain abundant water that evolves at temperatures below 500 degrees Centigrade thus conferring Aram Chaos a potentially high value for early in-situ resource utilization (ISRU) [4]. The geologic history also calls for future prospecting of deep ice deposits and possibly liquid water via deep drilling. The most recent stratigraphic units in the central part of Aram Chaos are not fractured, and are part of a dome-shaped formation that features bright, poorly-consolidated material that contains both hydrated sulfates and ferric oxides according to OMEGA (Observatoire pour la Minéralogie, l'Eau, les Glaces et l'Activité) data [5]. These surface material characteristics are preliminary indications of their potential use in civil engineering activities that involve regolith moving and hauling, while further study is needed to assess traverse-ability challenges. The widespread distribution of sulfates is also of interest as a resource for the use of sulfur as a binding compound in regolith-based concrete for constructions. The terrain depressions caused by the rock fracturing events may challenge surface mobility but also suggest the possibility of using such natural features for additional shielding from space radiation and as emplacement of nuclear surface power reactors for the same reason. The high concentration of hematite (up to 16 percent) in some of the smoother recent terrains of the central part of Aram Chaos [2] is a favorable attribute for metal extraction ISRU to create iron-based feedstock for in-situ fabrication of replacement parts or their repairs. Preliminary data on Aram Chaos indicate that it offers a combination of many critical criteria for human missions to the surface of Mars: equatorial region at low Mars Orbiter Laser Altimeter (MOLA), evidence of hydrated minerals over large areas and at high concentrations tied to historic evidence of liquid water over long periods.

Sibille, L.↗