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At least 1,567 records · Page 87
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Tuning charge carrier dynamics through spacer cation functionalization in layered halide perovskites: an ab initio quantum dynamics study

Dion–Jacobson (DJ) phase two-dimensional (2D) hybrid halide perovskites are promising for environmentally stable optoelectronic device applications due to their attractive photophysical properties, including long charge carrier lifetime and partially suppressed non-radiative losses. However, the atomistic details of the structure–property relationship are severely limited, which substantially restricts the strategic materials designed for these layered halide perovskites (LHPs). Here, we combine nonadiabatic molecular dynamics and time-domain density functional theory to understand the effects of spacer cation functionalization on the ground and excited-state charge carrier dynamics in DJ phase LHPs. Our in-depth study reveals that the fluorination of spacer cations considerably restricts the thermal motions of LHPs at ambient conditions. The compact structure weakens the overall electron–phonon interactions and reduces the thermal fluctuations of the band edges in real-time. These dynamic modifications partially mitigate the non-radiative recombination, prolonging the lifetime of photogenerated charge carriers. The suppressed carrier loss mechanism strongly suggests that the fluorinated spacer cation-based LHPs would exhibit enhanced performance as optoelectronic materials. These systematic simulations of excited state carrier dynamics elaborate that chemically viable functionalization of the spacer cations is a robust approach to improve the photophysical properties of 2D halide perovskites strategically. These insights also guide us to propose a few potential strategies to design highly beneficial spacer cations of LHPs that can be introduced in next-generation optoelectronic devices.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Resolving local ordering and structure in Mn x Ge 1- x Te alloys through thermodynamic ensembles of pair distribution functions

Characterizing local bonding environments in complex materials is essential for understanding and optimizing their properties. Equally as important is the ability to predict local motifs as a function of synthesis conditions, enhancing chemists’ ability to design properties into materials. In this study, we present an approach to leverage statistical mechanics to generate temperature- and energy-informed ensemble averaged pair distribution functions (PDFs). This method, which we have named Thermodynamic Ensemble Averages of PDFs for Ordering and Transformations (TEAPOT), utilizes density functional theory (DFT) to relax supercells while incorporating energetic penalties for local order, enabling accurate and computationally efficient analysis of local structure. We apply this method to the neutron PDF measurements of the pseudobinary MnTe–GeTe (MGT) alloy, demonstrating its capability to resolve complex local distortions and chemical ordering. Our results reveal detailed insights into phase transformations and local distortions driven by Mn substitution. For compositions that globally present as rock salt, our analysis reveals that Ge coordination geometry is heavily impacted by synthesis temperature. We propose that high temperature synthesis conditions promote a lowered Ge polyhedra distortion, promoting high charge carrier mobility due to the alignment of local and global structure. Incorporating statistical mechanics and computation into experimental analysis thus guides synthesis of tailored local structure.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Strengthening poly(lactic acid) composites with poly(methyl methacrylate) functionalized flax nanofibrils

Biobased reinforcements for poly(lactic acid) (PLA) are needed for more additive manufacturing applications requiring higher strength and sustainability. Flax nanofibrils (FNFs) produced through mechanical refining were explored as a lower energy alternative to cellulose nanofibril (CNF) reinforcements. To compatibilize the FNFs for the PLA matrix, a grafting-through surfactant free emulsion polymerization (SFEP) was performed to functionalize the FNF surface with poly(methyl methacrylate) (PMMA). FNFs produced using different refining energy were functionalized under varying solid contents in suspension. Polymerizations performed at 0.7 wt% FNFs in water yielded the highest degree of PMMA functionality. These optimal conditions were scaled up and the PMMA modified FNFs melt compounded into PLA yielding a 12% increase in tensile strength and 92% increase in the modulus of elasticity as compared to the original PLA. Interestingly, the FNFs with the lowest refining energy yielded the strongest composites using these methods, surpassing the higher refining energy CNF reinforcements. This increase was attributed to improved dispersion of the FNF reinforcements in the PLA matrix that was enabled by the PMMA coating on the FNF surface preventing interfibrillar adhesion and aggregation within the PLA matrix.

Mulligan, Abigail [University of Maine]↗
DOE OSTI2020

Experimental determination of the temperature-dependent Van Hove function in a Zr 80 Pt 20 liquid

Even though the viscosity is one of the most fundamental properties of liquids, the connection with the atomic structure of the liquid has proven elusive. By combining inelastic neutron scattering with the electrostatic levitation technique, the time-dependent pair-distribution function (i.e., the Van Hove function) has been determined for liquid Zr 80 Pt 20 . We show that the decay time of the first peak of the Van Hove function is directly related to the Maxwell relaxation time of the liquid, which is proportional to the shear viscosity. This result demonstrates that the local dynamics for increasing or decreasing the coordination number of local clusters by one determines the viscosity at high temperature, supporting earlier predictions from molecular dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

A light weight regularization for wave function parameter gradients in quantum Monte Carlo

The parameter derivative of the expectation value of the energy, ∂E/∂p, is a key ingredient in variational Monte Carlo (VMC) wave function optimization methods. In some cases, a naïve estimate of this derivative suffers from an infinite variance, which inhibits the efficiency of optimization methods that rely on a stable estimate of the derivative. In this work, we derive a simple regularization of the naïve estimator, which is trivial to implement in existing VMC codes, has finite variance, and a negligible bias, which can be extrapolated to zero bias with no extra cost. We use this estimator to construct an unbiased, finite variance estimation of ∂E/∂p for a multi-Slater–Jastrow trial wave function on the LiH molecule and in the optimization of a multi-Slater–Jastrow trial wave function on the CuO molecule. This regularized estimator is a simple and efficient estimator of ∂E/∂p for VMC optimization techniques.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Accuracy of Kohn–Sham density functional theory for warm- and hot-dense matter equation of state

We study the accuracy of Kohn–Sham density functional theory (DFT) for warm- and hot-dense matter (WDM and HDM). Specifically, considering a wide range of systems, we perform accurate ab initio molecular dynamics simulations with temperature-independent local/semilocal density functionals to determine the equations of state at compression ratios of 3x–7x and temperatures near 1 MK. We find very good agreement with path integral Monte Carlo benchmarks, while having significantly smaller error bars and smoother data, demonstrating the accuracy of DFT for the study of WDM and HDM at such conditions. In addition, using a Δ-machine learned force field scheme, we confirm that the DFT results are insensitive to the choice of exchange-correlation functional, whether local, semilocal, or nonlocal.

Suryanarayana, Phanish (ORCID:0000000151720049)↗
DOE OSTI2020

Fc-mediated effector function contributes to the in vivo antiviral effect of an HIV neutralizing antibody

Significance Neutralizing antibodies (NAbs) against HIV-1 are under clinical development. Despite demonstrated antiviral activity when used as treatment in HIV-infected people, the mechanism of action of NAbs remains controversial. Quantification of the relative contribution of Fab-mediated (neutralization of free virus) and Fc-mediated functions such as antibody-dependent cellular cytotoxicity (ADCC), phagocytosis, and complement fixation is essential to develop better therapies. Here, we treated chronically SHIV-infected rhesus macaques with a single dose of NAb VRC07-523LS with or without Fc modifications. Fc function contributes 21% to the antiviral activity of VRC07-523LS with an unmodified Fc region, when compared to NAb with Fc knockout mutations. However, NAbs with improved ADCC function in vitro did not show enhanced antiviral activity in vivo.

Asokan, Mangaiarkarasi↗
DOE OSTI2020

Structure-function analysis of microRNA 3'-end trimming by Nibbler

Nibbler (Nbr) is a 3'-to-5' exoribonuclease whose catalytic 3'-end trimming activity impacts microRNA (miRNA) and PIWI-interacting RNA (piRNA) biogenesis. Here, we report on structural and functional studies to decipher the contributions of Nbr’s N-terminal domain (NTD) and exonucleolytic domain (EXO) in miRNA 3'-end trimming. We have solved the crystal structures of the NTD core and EXO domains of Nbr, both in the apo-state. The NTD-core domain of Aedes aegypti Nbr adopts a HEAT-like repeat scaffold with basic patches constituting an RNA-binding surface exhibiting a preference for binding double-strand RNA (dsRNA) over single-strand RNA (ssRNA). Structure-guided functional assays in Drosophila S2 cells confirmed a principal role of the NTD in exonucleolytic miRNA trimming, which depends on basic surface patches. Gain-of-function experiments revealed a potential role of the NTD in recruiting Nbr to Argonaute-bound small RNA substrates. The EXO domain of A. aegypti and Drosophila melanogaster Nbr adopt a mixed α/β-scaffold with a deep pocket lined by a DEDDy catalytic cleavage motif. We demonstrate that Nbr’s EXO domain exhibits Mn2+-dependent ssRNA-specific 3'-to-5' exoribonuclease activity. Modeling of a 3' terminal Uridine into the catalytic pocket of Nbr EXO indicates that 2'-O-methylation of the 3'-U would result in a steric clash with a tryptophan side chain, suggesting that 2'-O-methylation protects small RNAs from Nbr-mediated trimming. Overall, our data establish that Nbr requires its NTD as a substrate recruitment platform to execute exonucleolytic miRNA maturation, catalyzed by the ribonuclease EXO domain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean

Enzymes catalyze key reactions within Earth’s life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO 2 , NO, methanethiol, and methylamines were most abundant in the upwelling region. Here, we identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Pervasive alterations to snow-dominated ecosystem functions under climate change

Climate change projections consistently demonstrate that warming temperatures and dwindling seasonal snowpack will elicit cascading effects on ecosystem function and water resource availability. Despite this consensus, little is known about potential changes in the variability of ecohydrological conditions, which is also required to inform climate change adaptation and mitigation strategies. Considering potential changes in ecohydrological variability is critical to evaluating the emergence of trends, assessing the likelihood of extreme events such as floods and droughts, and identifying when tipping points may be reached that fundamentally alter ecohydrological function. Using a single-model Large Ensemble with sophisticated terrestrial ecosystem representation, we characterize projected changes in the mean state and variability of ecohydrological processes in historically snow-dominated regions of the Northern Hemisphere. Widespread snowpack reductions, earlier snowmelt timing, longer growing seasons, drier soils, and increased fire risk are projected for this century under a high-emissions scenario. In addition to these changes in the mean state, increased variability in winter snowmelt will increase growing-season water deficits and increase the stochasticity of runoff. Thus, with warming, declining snowpack loses its dependable buffering capacity so that runoff quantity and timing more closely reflect the episodic characteristics of precipitation. This results in a declining predictability of annual runoff from maximum snow water equivalent, which has critical implications for ecosystem stress and water resource management. So our results suggest that there is a strong likelihood of pervasive alterations to ecohydrological function that may be expected with climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Structural insights reveal interplay between LAG-3 homodimerization, ligand binding, and function

Lymphocyte activation gene-3 (LAG-3) is an inhibitory receptor expressed on activated T cells and an emerging immunotherapy target. Domain 1 (D1) of LAG-3, which has been purported to directly interact with major histocompatibility complex class II (MHCII) and fibrinogen-like protein 1 (FGL1), has been the major focus for the development of therapeutic antibodies that inhibit LAG-3 receptor-ligand interactions and restore T cell function. Here, we present a high-resolution structure of glycosylated mouse LAG-3 ectodomain, identifying that cis-homodimerization, mediated through a network of hydrophobic residues within domain 2 (D2), is critically required for LAG-3 function. Additionally, we found a previously unidentified key protein-glycan interaction in the dimer interface that affects the spatial orientation of the neighboring D1 domain. Mutation of LAG-3 D2 residues reduced dimer formation, dramatically abolished LAG-3 binding to both MHCII and FGL1 ligands, and consequentially inhibited the role of LAG-3 in suppressing T cell responses. Intriguingly, we showed that antibodies directed against D1, D2, and D3 domains are all capable of blocking LAG-3 dimer formation and MHCII and FGL-1 ligand binding, suggesting a potential allosteric model of LAG-3 function tightly regulated by dimerization. Furthermore, our work reveals unique epitopes, in addition to D1, that can be targeted for immunotherapy of cancer and other human diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Lanthanide-dependent alcohol dehydrogenases require an essential aspartate residue for metal coordination and enzymatic function

The lanthanide elements (Ln 3+ ), those with atomic numbers 57–63 (excluding promethium, Pm 3+ ), form a cofactor complex with pyrroloquinoline quinone (PQQ) in bacterial XoxF methanol dehydrogenases (MDHs) and ExaF ethanol dehydrogenases (EDHs), expanding the range of biological elements and opening novel areas of metabolism and ecology. Other MDHs, known as MxaFIs, are related in sequence and structure to these proteins, yet they instead possess a Ca 2+ -PQQ cofactor. An important missing piece of the Ln 3+ puzzle is defining what features distinguish enzymes that use Ln 3+ -PQQ cofactors from those that do not. In this work, using XoxF1 MDH from the model methylotrophic bacterium Methylorubrum extorquens AM1, we investigated the functional importance of a proposed lanthanide-coordinating aspartate residue. We report two crystal structures of XoxF1, one with and another without PQQ, both with La 3+ bound in the active-site region and coordinated by Asp 320 . Using constructs to produce either recombinant XoxF1 or its D320A variant, we show that Asp 320 is needed for in vivo catalytic function, in vitro activity, and La 3+ coordination. XoxF1 and XoxF1 D320A, when produced in the absence of La 3+ , coordinated Ca 2+ but exhibited little or no catalytic activity. We also generated the parallel substitution in ExaF to produce ExaF D319S and found that this variant loses the capacity for efficient ethanol oxidation with La 3+ . These results provide evidence that a Ln 3+ -coordinating aspartate is essential for the enzymatic functions of XoxF MDHs and ExaF EDHs, supporting the notion that sequences of these enzymes, and the genes that encode them, are markers for Ln 3+ metabolism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

The structural and functional integrities of porcine myocardium are mostly preserved by cryopreservation

Structural and functional studies of heart muscle are important to gain insights into the physiological bases of cardiac muscle contraction and the pathological bases of heart disease. While fresh muscle tissue works best for these kinds of studies, this is not always practical to obtain, especially for heart tissue from large animal models and humans. Conversely, tissue banks of frozen human hearts are available and could be a tremendous resource for translational research. It is not well understood, however, how liquid nitrogen freezing and cryostorage may impact the structural integrity of myocardium from large mammals. In this study, we directly compared the structural and functional integrity of never-frozen to previously frozen porcine myocardium to investigate the consequences of freezing and cryostorage. X-ray diffraction measurements from hydrated tissue under near-physiological conditions and electron microscope images from chemically fixed porcine myocardium showed that prior freezing has only minor effects on structural integrity of the muscle. Furthermore, mechanical studies similarly showed no significant differences in contractile capabilities of porcine myocardium with and without freezing and cryostorage. These results demonstrate that liquid nitrogen preservation is a practical approach for structural and functional studies of myocardium.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Exploring metastable states in UO 2 using hybrid functionals and dynamical mean field theory

A detailed exploration of the f-atomic orbital occupancy space for UO2 is performed using a first principles approach based on density functional theory (DFT), employing a full hybrid functional within a systematic basis set. Specifically, the PBE0 functional is combined with an occupancy biasing scheme implemented in a wavelet-based algorithm which is adapted to large supercells. The results are compared with previous DFT + U calculations reported in the literature, while dynamical mean field theory is also performed to provide a further base for comparison. This work shows that the computational complexity of the energy landscape of a correlated f-electron oxide is much richer than has previously been demonstrated. The resulting calculations provide evidence of the existence of multiple previously unexplored metastable electronic states of UO 2 , including those with energies which are lower than previously reported ground states.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Quasinormal modes, echoes and the causal structure of the Green's function

Quasinormal modes describe the return to equilibrium of a perturbed system, in particular the ringdown phase of a black hole merger. But as globally-defined quantities, the quasinormal spectrum can be highly sensitive to global structure, including distant small perturbations to the potential. In what sense are quasinormal modes a property of the resulting black hole? We explore this question for the linearized perturbation equation with two potentials having disjoint bounded support. We give a composition law for the Wronskian that determines the quasinormal frequencies of the combined system. We show that over short time scales the evolution is governed by the quasinormal frequencies of the individual potentials, while the sensitivity to global structure can be understood in terms of echoes. We introduce an echo expansion of the Green’s function and show that, as expected on general grounds, at any finite time causality limits the number of echoes that can contribute. We illustrate our results with the soluble example of a pair of -function potentials. We explicate the causal structure of the Green’s function, demonstrating under what conditions two very different quasinormal spectra give rise to very similar ringdown waveforms.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Aemulus ν: precision halo mass functions in wνCDM cosmologies

Precise and accurate predictions of the halo mass function for cluster mass scales in wνCDM cosmologies are crucial for extracting robust and unbiased cosmological information from upcoming galaxy cluster surveys. Here, we present a halo mass function emulator for cluster mass scales (≳ 1013 M ⊙/h) up to redshift z = 2 with comprehensive support for the parameter space of wνCDM cosmologies allowed by current data. Based on the Aemulus ν suite of simulations, the emulator marks a significant improvement in the precision of halo mass function predictions by incorporating both massive neutrinos and non-standard dark energy equation of state models. This allows for accurate modeling of the cosmology dependence in large-scale structure and galaxy cluster studies. We show that the emulator, designed using Gaussian Process Regression, has negligible theoretical uncertainties compared to dominant sources of error in future cluster abundance studies. Our emulator is publicly available (https://github.com/DelonShen/aemulusnu_hmf), providing the community with a crucial tool for upcoming cosmological surveys such as LSST and Euclid.

cluster counts↗
DOE OSTI2026

Monte Carlo simulation methodology for characterizing the energy response function and resolving power of a digital Flat Panel Detector (FPD) assembly

The use of high-resolution, digital flat panel detectors (FPDs) makes quantitative assessments of radiographic and 3D tomographic representations feasible. However, the energy response function and spatial resolving power of the detector must be known. Here, we present a methodology for characterizing an FPD assembly using Monte Carlo simulations. The detector assembly modeled here was fielded in the 3-Ring Flash X-ray Imaging System designed and built at Lawrence Livermore National Laboratory (LLNL), which employs fifteen Carestream ® HPX-DR3543 FPDs enclosed in protective housings. Detailed Monte Carlo (MCNP6) simulations of an as-fielded detector assembly were performed to estimate its energy response function in terms of analog-to-digital unit (ADU) “counts” per pixel per incident x-ray as a function of energy up to ∼ 500 keV and its theoretical (idealized) resolving power. The practical resolving power of the FPD assembly in a realistic scenario was then estimated by simulating radiographic images of a variant of the United Kingdom (U.K.) “Kaleidoscope” resolution target.

Physics↗
DOE OSTI2021

Differentiable programming for online training of a neural artificial viscosity function within a staggered grid Lagrangian hydrodynamics scheme

Lagrangian methods to solve the inviscid Euler equations produce numerical oscillations near shock waves. A common approach to reducing these oscillations is to add artificial viscosity (AV) to the discrete equations. The AV term acts as a dissipative mechanism that attenuates oscillations by smearing the shock across a finite number of computational cells. However, AV introduces several control parameters that are not determined by the underlying physical model, and hence, in practice are tuned to the characteristics of a given problem. We seek to improve the standard quadratic-linear AV form by replacing it with a learned neural function that reduces oscillations relative to exact solutions of the Euler equations, resulting in a hybrid numerical-neural hydrodynamic solver. Because AV is an artificial construct that exists solely to improve the numerical properties of a hydrodynamic code, there is no offline ‘viscosity data’ against which a neural network can be trained before inserting into a numerical simulation, thus requiring online training. We achieve this via differentiable programming, i.e. end-to-end backpropagation or adjoint solution through both the neural and differential equation code, using automatic differentiation of the hybrid code in the Julia programming language to calculate the necessary loss function gradients. A novel offline pre-training step accelerates training by initializing the neural network to the default numerical AV scheme, which can be learned rapidly by space-filling sampling over the AV input space. We find that online training over early time steps of simulation is sufficient to learn a neural AV function that reduces numerical oscillations in long-term hydrodynamic shock simulations. These results offer an early proof-of-principle that online differentiable training of hybrid numerical schemes with novel neural network components can improve certain performance aspects existing in purely numerical schemes.

97 MATHEMATICS AND COMPUTING↗