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DOE OSTI2022

NASMDR: a framework for miRNA-drug resistance prediction using efficient neural architecture search and graph isomorphism networks

Abstract As a frontier field of individualized therapy, microRNA (miRNA) pharmacogenomics facilitates the understanding of different individual responses to certain drugs and provides a reasonable reference for clinical treatment. However, the known drug resistance-associated miRNAs are not yet sufficient to support precision medicine. Although existing methods are effective, they all focus on modelling miRNA-drug resistance interaction graphs, making their performance bounded by the interaction density. In this study, we propose a framework for miRNA-drug resistance prediction through efficient neural architecture search and graph isomorphism networks (NASMDR). NASMDR uses attribute information instead of the commonly used interactive graph information. In the cross-validation experiment, the proposed framework can achieve an AUC of 0.9468 on the ncDR dataset, which is 2.29% higher than the state-of-the-art method. In addition, we propose a novel sequence characterization approach, k-mer Sparse Nonnegative Matrix Factorization (KSNMF). The results show that NASMDR provides novel insights for integrating efficient neural architecture search and graph isomorphic networks into a unified framework to predict drug resistance-related miRNAs. The codes for NASMDR are available at https://github.com/kaizheng-academic/NASMDR.

Zheng, Kai↗

DOE OSTI2021

Bound Constrained Partial DifferentialEquation Inverse Problem Solution by theSemi-Smooth Newton Method

We present the mathematical derivation, software implementation details, and computational results for a semi-smooth Newton method applied to two inverse problems governed by partial differential equations with bound constraints. The two problems share mathematical structural similarities to density-based topology optimization problems. The semi-smooth Newton method provides a mesh independent solution computation for the two test problems. A key step is that the complementarity part of the necessary optimality conditions are reformulated with the use of a complementarity functionφsuch that the complementarity conditions are satisfied if and only if a zero of a nonsmooth function has been obtained. The modular finite element package MFEM is utilized for the software implementation. In addition we constructed a matrix-free Operator to enable the use of efficient Krylov subspace IterativeSolver of MFEM for the solution of our two target problems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Physics-Informed Machine Learning Model for Ceramic Matrix Composite Creep

A physics-informed recurrent neural network (RNN) based surrogate model is developed to emulate the nonlinear, time-dependent constitutive behavior of ceramic matrix composites (CMCs) driven by matrix damage and constituent creep at the microscale. Physics-informed constraints are introduced into the surrogate model through regularization to ground the prediction in physics and improve its predictive capabilities. Training data is generated using the high-fidelity generalized method of cells (HFGMC) approach which calls appropriate creep and damage models for each of the constituents. This coupling permits simulating the nonlinear behavior of CMCs based on constituent response at the microscale along with microstructural features such as fiber and porosity volume fraction and fiber radius. The microscale repeating unit cell is loaded under creep fatigue conditions to replicate the material loading experienced in a turbine engine. Therefore, the RNN-based surrogate model is tasked with predicting, as a function of variable input stress sequence, temperature, and microstructural features, the resulting strain history response while satisfying physical constraints related to creep rate, isochoric inelastic deformation, and strain energy density. The trained surrogate model is shown to effectively match the strain history over quantified distributions of microstructural features and relevant loading regimes and temperatures. Neural network based surrogate models can offer efficient alternatives to running computationally intensive multiscale material models to simulate the nonlinear response of large structural models. Therefore, the presented work provides evidence towards the feasibility of developing, training, and running such models for CMCs with complex microstructures, nonlinear time-dependent material response, and under non-monotonic loading conditions.

ceramic matrix composites↗

DOE OSTI2026

Ab initio calculation of atomic solid hydrogen phases based on Gutzwiller many-body wave functions

We apply two ab initio many-body methods based on Gutzwiller wave functions, i.e., correlation matrix renormalization theory (CMRT) and Gutzwiller conjugate gradient minimization (GCGM), to the study of crystalline phases of atomic hydrogen. Both methods avoid empirical Hubbard U parameters and are free from double-counting issues. CMRT employs a Gutzwiller-type approximation that enables efficient calculations, while GCGM goes beyond this approximation to achieve higher accuracy at higher computational cost. By benchmarking against available quantum Monte Carlo (QMC) results, we demonstrate that while both methods are more accurate than the widely used density-functional theory, GCGM systematically captures additional correlation energy missing in CMRT, leading to significantly improved total energy predictions. We also show that by including the correlation energy Ec from local density approximation in the CMRT calculation, CMRT + E c produces energy in better agreement with the QMC results in these hydrogen lattice systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Surface modification of ZIF ‐90 with triptycene for enhanced interfacial interaction in mixed‐matrix membranes for gas separation

Abstract Zeolite imidazole framework (ZIF‐90) nanoparticles were chemically modified by grafting triptycene moieties. The modified nanoparticles were introduced into a triptycene‐based polyimide as fillers to generate mixed matrix membranes (MMMs) for gas separation. The incorporation of “hook‐like” triptycene moieties in both dispersed and continuous phases led to intimate contact between the two phases and thus defect‐free interfacial morphology, due to the supramolecular interlocking and π–π stacking interaction between triptycene units presented in both phases. The filler/polymer solution showed shear thickening behavior due to such strong interfacial interaction. The separation performance of the prepared composite membranes was investigated as a function of filler loading and particle surface grafting density. Pure‐gas permeation results showed that the gas permeabilities increased expectedly as the filler loading increased, with stable or improved selectivities. The reduced permeability relative to pristine polyimide film is likely due to the pore blockage of ZIF‐90 upon grafting triptycene moieties on the particle surface. Reducing the grafting density of triptycene moieties led to improved permeability and selectivity suggesting good tunability of this series of new composite membranes. Overall, modification of nanofiller with hierarchical triptycene moieties offers a fundamentally new avenue for creation of composite membranes with unique properties in gas separations.

Zhang, Qinnan↗

DOE OSTI2022

The importance of maldistribution matching for thermal performance of compact heat exchangers

Compact heat exchangers have gained increased attention in recent years, particularly in demanding applications where high temperatures, high pressures, and/or high power densities are required. For decades, the heat exchanger (HX) community believes that flow maldistribution is a key factor for HX effectiveness, that is, reducing the degree of flow maldistribution (MALD) can help increase the HX effectiveness. Therefore, significant efforts have been devoted in the past to optimizing the header geometry to minimize flow maldistribution. This work was initially motivated by this, and the original goal was to figure out a HX header design with the lowest maldistribution. However, by systematically constructing a comprehensive maldistribution matrix, the analysis revealed that the HX effectiveness is not actually determined by the MALD, but instead dominated by the degree of maldistribution mismatch (MISM). This conclusion was also theoretically generalized, which indicated that matching of the local heat capacity rate is key for achieving maximum performance. The MISM provides a local means of tracking this information, while the MALD only provides a global approximation of the maldistribution itself. With this new perspective, flow maldistribution needs not necessarily be avoided, but instead matched between two fluid streams, to improve the HX performance. We demonstrated that by carefully designing the header geometry to match the velocity profiles of the two fluids in a 2 MW PCHE with molten salt and supercritical carbon dioxide (sCO2) as the heat transfer fluids, the HX could achieve a higher effectiveness even when the maldistribution increased. Finally, a technoeconomic study using a CSP system as an example revealed that the use of this new HX design paradigm could result in CSP capital cost savings as large as 16.6%.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

Classical and quantum simulations of 1+1-dimensional ${\mathbb{Z}}_{2}$ gauge theory at finite temperature and density

Simulating strongly coupled gauge theories at finite temperature and density is a longstanding challenge in nuclear and high-energy physics with fundamental implications for condensed matter physics. Here, we simulate such systems using minimally entangled typical thermal state (METTS) approaches, which combine classical random sampling with imaginary-time evolution, implementable on either classical or quantum computers, to estimate thermal averages of observables. We study 1+1-dimensional ${\mathbb{Z}}_{2}$ gauge theory coupled to spinless fermionic matter, which maps onto a local quantum spin chain. We benchmark both a classical matrix-product-state implementation of METTS and a recently proposed adaptive variational approach for near-term quantum devices, focusing on the equation of state and measures of fermion confinement. Of particular importance is the choice of basis for METTS sampling, which impacts both the sampling overhead and quantum circuit complexity. Our work sets the stage for future studies of strongly coupled gauge theories using classical and quantum hardware.

Chen, I-Chi [Iowa State Univ., Ames, IA (United St↗

DOE OSTI2020

Testing general relativity on cosmological scales at redshift z ∼ 1.5 with quasar and CMB lensing

ABSTRACT We test general relativity (GR) at the effective redshift $\bar{z} \sim 1.5$ by estimating the statistic EG, a probe of gravity, on cosmological scales $19 - 190\, h^{-1}{\rm Mpc}$. This is the highest redshift and largest scale estimation of EG so far. We use the quasar sample with redshifts 0.8 < z < 2.2 from Sloan Digital Sky Survey IV extended Baryon Oscillation Spectroscopic Survey Data Release 16 as the large-scale structure (LSS) tracer, for which the angular power spectrum $C_\ell ^{qq}$ and the redshift-space distortion parameter β are estimated. By cross-correlating with the Planck 2018 cosmic microwave background (CMB) lensing map, we detect the angular cross-power spectrum $C_\ell ^{\kappa q}$ signal at $12\, \sigma$ significance. Both jackknife resampling and simulations are used to estimate the covariance matrix (CM) of EG at five bins covering different scales, with the later preferred for its better constraints on the covariances. We find EG estimates agree with the GR prediction at $1\, \sigma$ level over all these scales. With the CM estimated with 300 simulations, we report a best-fitting scale-averaged estimate of $E_G(\bar{z})=0.30\pm 0.05$, which is in line with the GR prediction $E_G^{\rm GR}(\bar{z})=0.33$ with Planck 2018 CMB + BAO matter density fraction Ωm = 0.31. The statistical errors of EG with future LSS surveys at similar redshifts will be reduced by an order of magnitude, which makes it possible to constrain modified gravity models.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Chiral effective field theory calculations of weak transitions in light nuclei

In this work, we report quantum Monte Carlo calculations of weak transitions in A≤10 nuclei, based on the Norfolk two- and three-nucleon chiral interactions, and associated one- and two-body axial currents. Furthermore, we find that the contribution from two-body currents is at the 2–3% level, with the exception of matrix elements entering the rates of 8Li, 8B, and 8He β decay. These matrix elements are suppressed in impulse approximation based on the (leading order) Gamow Teller transition operator alone; two-body currents provide a 20–30% correction, which is, however, insufficient to bring theory in agreement with experimental data. For the other transitions, the agreement with the data is satisfactory, and the results exhibit a negligible to mild model dependence when different combinations of Norfolk interactions are utilized to construct the nuclear wave functions. We report a complete study of two-body weak transition densities which reveals the expected universal behavior of two-body currents at short distances throughout the range of A=3 to A=10 systems considered here.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Bobfinchite, Na[(UO2)8O3(OH)11]·10H2O, a new Na-bearing member of the schoepite family

Abstract The new mineral bobfinchite (IMA2020-082), Na[(UO2)8O3(OH)11]·10H2O, was found in the Burro mine, Slick Rock district, San Miguel County, Colorado, U.S.A., where it occurs as an oxidation product of uraninite on asphaltite matrix in intimate association with gypsum, natrozippeite, metaschoepite, and uranopilite. Bobfinchite crystals are transparent to translucent, yellow, lozenge-shaped disks up to 0.3 mm wide. Crystals are flattened on [100] and exhibit the forms {100}, {011}, {021}, {021}, and {011}. Bobfinchite has a pale-yellow streak and emits very dim yellow fluorescence under 365 nm ultraviolet illumination. The crystals are brittle with very good {100} cleavage and irregular, stepped fracture. The Mohs hardness is ca. 2 based on scratch tests. The calculated density is 5.044 g/cm3 based on the empirical formula and 5.036 g/cm3 for the ideal formula. Bobfinchite is optically biaxial (–), with α = 1.690(5), β = 1.7205(5), and γ = 1.730(5) (white light). The measured 2V, estimated from the interference figure, is 55(5)° and the calculated value is 59.1°. Dispersion is moderate, r > v; orientation: X = a, Y = b, Z = c; pleochroism: X nearly colorless, Y yellow, Z yellow; X < Y ≈Z. Electron microprobe analysis provided the empirical formula (Na0.99Pb0.02)[(UO2)7.99O3(OH)11]·10H2O. The five strongest X-ray powder diffraction lines are [dobs in Å(I)(hkl)]: 7.34(100)(200), 3.59(50)(024), 3.23(60)(224), 3.18(36)(240), and 2.01(23)(624,551,208,640,346). Bobfinchite is orthorhombic, Pbcn, a = 14.6249(9), b = 14.0389(10), c = 16.6923(10) Å, V = 3427.2(4) Å3, and Z = 4. The structure of bobfinchite (R1 = 0.0330 for 3770 I > 4σI) is built from uranyl oxide-hydroxide sheets that adopt the fourmarierite topology, with interlayer Na+ and H2O groups. Both the sheet and interlayer topology mimic those observed in natural and synthetic Na-metaschoepites studied previously, and as seen in other uranyl oxide hydrate minerals, charge balance is achieved at specific sites in the sheet through the substitution O2– ↔ (OH)–.

Geochemistry & Geophysics↗

DOE OSTI2022

Surface Functionalized Barium Titanate Nanoparticles: A Combined Experimental and Computational Study

Barium titanate (BTO) nanoparticles show great potential for use in electrostatic capacitors with high energy density. This includes both polymer composite and sintered capacitors. However, questions about the nanoparticles' size distribution, amount of agglomeration, and surface ligand effect on performance properties remain. Reducing particle agglomeration is a crucial step to understanding the properties of nanoscale particles, as agglomeration has significant effects on the composite dielectric constant. BTO surface functionalization using phosphonic acids is known reduce BTO nanoparticle agglomeration. We explore solution synthesized 10 nm BTO particles with tert-butylphosphonic acid ligands. Recent methods to quantifying agglomeration using an epoxy matrix before imaging shows that tert-butylphosphonic acid ligands reduce BTO agglomeration by 33%. Thermometric, spectroscopic, and computational methods provide confirmation of ligand binding and provide evidence of multiple ligand binding modes on the BTO particle surface.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Competition between charge-density-wave and superconducting orders on eight-leg square Hubbard cylinders

The issue of whether d-wave superconductivity (SC) occurs in the square-lattice Hubbard model with U of order of the bandwidth has been one of the most debated issues to emerge from the study of high temperature SC. Here, we report variational results on eight-leg cylinders with next-nearest-neighbor hopping in the range $-0.5t\le t^{\prime} \le 0.25t$ with U = 8t and 12t and doped hole concentrations δ = 1/12 and 1/8. For $t^{\prime} \le 0$, the ground-state appears to be a charge-density wave (CDW) of one sort or another with SC correlations that are extremely short-ranged. In contrast, in some cases, the local magnetic order has a correlation length greater than half the cylinder width - suggestive that magnetic order might also arise in the 2D limit. For $t^{\prime} \le 0$, our results depend more strongly on boundary conditions (periodic vs antiperiodic), making it still harder to correctly guess whether SC or CDW correlations dominate in the 2D limit. These results were obtained employing matrix-product states with bond dimensions large enough that energy differences as small as 10 −3 t per site can be resolved.

materials science↗

DOE OSTI2025

Real-time scattering in Ising field theory using matrix product states

We study scattering in Ising field theory (IFT) using matrix product states and the time-dependent variational principle. IFT is a one-parameter family of strongly coupled nonintegrable quantum field theories in 1+1 dimensions, interpolating between massive free fermion theory and Zamolodchikov's integrable massive 𝐸 8 theory. Particles in IFT may scatter either elastically or inelastically. In the postcollision wave function, particle tracks from all final-state channels occur in superposition; processes of interest can be isolated by projecting the wave function onto definite particle sectors, or by evaluating energy density correlation functions. Using numerical simulations we determine the time delay of elastic scattering and the probability of inelastic particle production as a function of collision energy. We also study the mass and width of the lightest resonance near the 𝐸 8 point in detail. Close to both the free fermion and 𝐸 8 theories, our results for both elastic and inelastic scattering are in good agreement with expectations from form-factor perturbation theory. Using numerical computations to go beyond the regime accessible by perturbation theory, we find that the high-energy behavior of the two-to-two particle scattering probability in IFT is consistent with a conjecture of Zamolodchikov. Our results demonstrate the efficacy of tensor-network methods for simulating the real-time dynamics of strongly coupled quantum field theories in 1+1 dimensions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

Structural response reconstruction using a system-equivalent singular vector basis

Here, this paper develops a novel method for reconstructing the full-field response of structural dynamic systems using sparse measurements. The singular value decomposition is applied to a frequency response matrix relating the structural response to physical loads, base motion, or modal loads. The left singular vectors form a non-physical reduced basis that can be used for response reconstruction with far fewer sensors than existing methods. The contributions of the singular vectors to measured response are termed singular-vector loads (SVLs) and are used in a regularized Bayesian framework to generate full-field response estimates and confidence intervals. The reconstruction framework is applicable to the estimation of single data records and power spectral densities from multiple records. Reconstruction is successfully performed in configurations where the number of SVLs to identify is less than, equal to, and greater than the number of sensors used for reconstruction. In a simulation featuring a seismically excited shear structure, SVL reconstruction significantly outperforms modal FRF-based reconstruction and successfully estimates full-field responses with as few as two uniaxial accelerometers. SVL reconstruction is further verified in a simulation featuring an acoustically excited cylinder. Finally, response reconstruction and uncertainty quantification are performed on an experimental structure with three shaker inputs and 27 triaxial accelerometer outputs.

42 ENGINEERING↗

DOE OSTI2020

Microcomputed X-Ray Tomographic Imaging and Image Processing for Microstructural Characterization of Explosives

Microstructural characterization of composite high explosives (HEs) has become increasingly important over the last several decades in association with the development of high fidelity mesoscale modeling and an improved understanding of ignition and detonation processes. HE microstructure influences not only typical material properties (e.g., thermal, mechanical) but also reactive behavior (e.g., shock sensitivity, detonation wave shape). A detailed nondestructive 3D examination of the microstructure has generally been limited to custom-engineered samples or surrogates due to poor contrast between the composite constituents. Highly loaded (>90 wt%) HE composites such as plastic-bonded explosives (PBX) are especially difficult. Here, we present efforts to improve measurement quality by using single and dual-energy microcomputed X-ray tomography and state-of-the-art image processing techniques to study a broad set of HE materials. Some materials, such as PBX 9502, exhibit suitable contrast and resolution for an automatic segmentation of the HE from the polymer binder and the voids. Other composite HEs had varying levels of success in segmentation. Post-processing techniques that used commercially available algorithms to improve the segmentation quality of PBX 9501 as well as zero-density defects such as cracks and voids could be easily segmented for all samples. Aspects of the materials that lend themselves well to this type of measurement are discussed.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Plasma and X-ray radiation-induced damage mechanisms in a tungsten heavy alloy

Tungsten-based materials are among the main candidate plasma-facing materials for future fusion reactors where extreme conditions of thermomechanical stresses, radiation, and energetic particles must be withstood. Here a hybrid X-pinch platform combined with a pulsed power machine was used to study damage mechanisms in 90W–4Cu–6Ni tungsten heavy alloy as a result of exposure to high energy density plasma, X-ray radiation, and the resulting thermal shock. It was found that the plasma-facing surface of the material undergoes severe melting and ablation with the extent of ablation being higher in the Cu–Ni phase than the W particles. Rapid melting and solidification transform the W particles into fine dendrite morphologies embedded in the Cu–Ni solid solution. Cracking was also observed in the subsurface layers at the interfaces between the W particles and the Cu-rich phase of the Cu–Ni matrix. X-ray radiation, on the other hand, cause slight melting on the surface without significant ablation and no cracking.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Utilizing integrated neutron diffraction and elastoplastic self-consistent crystal plasticity model to quantitatively assess the strengthening mechanism in Al–12.5Ce and Al–12.5Ce–0.4Mg alloys

An integrated in-situ neutron diffraction and elastic plastic self-consistent crystal plasticity (EPSC-CP) modeling scheme is performed on a binary Al–12Ce alloy and a ternary Al–12Ce–0.4Mg alloys. Using this scheme, the constitutive parameters, i.e. elastic constants and slip system parameters of individual phases can be calibrated which can be used in microstructure-based CP models to predict materials performance. From this study, it is shown that the elastic constants of Al 11 Ce 3 intermetallics calculated from density function theory calculation in the literature are rather accurate. When applied to the EPSC-CP model, the lattice strains of both the binary and ternary alloys are correctly predicted as compared with experiments, and large lattice strain differences between Al (100) plane and Al 11 Ce 3 (010) plane are demonstrated. The slip system parameters calibrated by the scheme shows that the addition of 0.4 wt% Mg in the alloy has little influence on the critical resolved shear stress of initial dislocation glide in the Al matrix which caused plastic yield in the material. This can be explained by the very dilute Mg solute content in the Al solid solution, causing large spacing of Al–Mg lattice misfit sites and little impact on resistance of dislocation glide at initial yield. The 0.4 wt% Mg addition, on the other hand, has a large influence on the hardening term in the slip system parameters, indicating those Al–Mg misfit sites do help dislocation accumulation during the deformation. The impact of dilute Mg addition on the Al slip system parameters is also reflected in the flow behavior of the ternary alloy: little impact on the yield stress, but a large impact on working hardening and tensile strength of the materials which is consistent with the literature.

36 MATERIALS SCIENCE↗

DOE OSTI2021

$t\bar{t}b\bar{b}$ at the LHC: on the size of corrections and b -jet definitions

We report on the calculation of the next-to-leading order QCD corrections to the production of a $t\bar t$ pair in association with two heavy-flavour jets. We concentrate on the di-lepton $t\bar t$ decay channel at the LHC with $\sqrt{s}$ = 13 TeV. The computation is based on pp → $e^+ν_eμ^-\bar{ν}_μb\bar{b}b\bar{b}$ matrix elements and includes all resonant and non-resonant diagrams, interferences and off-shell effects of the top quark and the W gauge boson. As it is customary for such studies, results are presented in the form of inclusive and differential fiducial cross sections. We extensively investigate the dependence of our results upon variation of renormalisation and factorisation scales and parton distribution functions in the quest for an accurate estimate of the theoretical uncertainties. We additionally study the impact of the contributions induced by the bottom-quark parton density. Results presented here are particularly relevant for measurements of $t\bar{t}H(H → b\bar{b})$ and the determination of the Higgs coupling to the top quark. In addition, they might be used for precise measurements of the top-quark fiducial cross sections and to investigate top-quark decay modelling at the LHC.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗