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At least 253 records · Page 14

Information theory optimization of signals from small-angle scattering measurements

Small-angle X-ray scattering (SAXS) of particles in solution informs on the conformational states and assemblies of biological macromolecules (bioSAXS) outside of cryo- and solid-state conditions. In bioSAXS, the SAXS measurement under dilute conditions is resolution limited, and through an inverse Fourier transform, the measured SAXS intensities directly relate to the physical space occupied by the particles via the P (r)-distribution. Yet, this inverse transform of SAXS data has been historically cast as an ill-posed, ill-conditioned problem requiring an indirect approach. Here, we show that through the applications of matrix and information theories, the inverse transform of SAXS intensity data is a well-conditioned problem. The so-called ill-conditioning of the inverse problem is directly related to the Shannon number. By exploiting the oversampling enabled by modern detectors, a direct inverse Fourier transform of the SAXS data is possible, provided the recovered information does not exceed the Shannon number. The Shannon limit corresponds to the maximum number of significant singular values that can be recovered in a SAXS experiment, suggesting this relationship is a fundamental property of band-limited inverse integral transform problems. This correspondence reduces the complexity of the inverse problem to the Shannon limit and maximum dimension. We propose a hybrid scoring function using an information theory framework that assesses both the quality of the model-data fit as well as the quality of the recovered P (r)-distribution. The hybrid score utilizes the Akaike information criteria and Durbin-Watson statistic that considers parameter-model complexity, i.e., degrees of freedom, and the randomness of the model-data residuals. The described tests and findings extend the boundaries for bioSAXS by completing the information theory formalism initiated by Peter B. Moore to enable a quantitative measure of resolution in SAXS, robustly determine maximum dimension, and more precisely define the best parameter model appropriately representing the observed scattering data.

Rambo, Robert P. [Science and Technology Facilitie↗

[The role of the serotonin system in the stress response of various cells]

The recombinant mouse brain serotonin receptor (5HT1c) was used to study the response of plant cells and oocytes to a stress signal activated by the serotonin-serotonin receptor interaction and associated Ca2+ flow. Based on plant expression vectors, recombinant constructs were obtained to direct production of 5HT1c fused with the green fluorescent protein in plant cells. The mRNAs for hybrid proteins were synthesized in an in vitro transcription system. The expression and function of the hybrid protein and the function of the associated ion channels were electrophysiologically studied in Xenopus laevis oocytes injected with the hybrid mRNA. The hybrid protein was functional and changed the operation of the Ca2+ channel in oocytes. To study the expression of the hybrid constructs in plant cells, the in vitro transcription product was inoculated in tobacco leaves, which then fluoresced.

Non-NASA Center↗

Deep transfer operator learning for partial differential equations under conditional shift

Transfer learning enables the transfer of knowledge gained while learning to perform one task (source) to a related but different task (target), hence addressing the expense of data acquisition and labelling, potential computational power limitations and dataset distribution mismatches. Here, we propose a new transfer learning framework for task-specific learning (functional regression in partial differential equations) under conditional shift based on the deep operator network (DeepONet). Task-specific operator learning is accomplished by fine-tuning task-specific layers of the target DeepONet using a hybrid loss function that allows for the matching of individual target samples while also preserving the global properties of the conditional distribution of the target data. Inspired by conditional embedding operator theory, we minimize the statistical distance between labelled target data and the surrogate prediction on unlabelled target data by embedding conditional distributions onto a reproducing kernel Hilbert space. We demonstrate the advantages of our approach for various transfer learning scenarios involving nonlinear partial differential equations under diverse conditions due to shifts in the geometric domain and model dynamics. Our transfer learning framework enables fast and efficient learning of heterogeneous tasks despite considerable differences between the source and target domains.

42 ENGINEERING↗

Unveiling the Role of Surface Ir-Oxo Species in O 2 Evolution at IrO 2 Electrocatalysts via Embedded Cluster Multireference Calculations

Understanding the mechanisms driving the oxygen evolution reaction (OER) on iridium oxide (IrO 2 )-based catalysts is essential to improving their performance and enabling an actual scale-up of water-splitting photoelectrochemical cells. The mechanistic pathways at IrO 2 interfaces have been extensively investigated computationally using density functional theory (DFT), which predicts a high-energy barrier for the last step of the OER of molecular oxygen detachment and release from the catalyst surface. Nevertheless, surface O 2 over- and under-binding results by standard generalized gradient approximation and hybrid density functionals, respectively, call for further analysis of this crucial step via multireference methods. Aiming at unveiling the nature of such a barrier, we hereby address the formation of O 2 from the most-stable IrO 2 (110) surface with both periodic DFT and an electrostatic embedded cluster approach at the n-electron valence-state perturbation theory. With this multireference approach, we find a value for the aforementioned energy barrier that is much closer to experimental indications than DFT ones. Here, an in-depth analysis of the involved molecular orbitals suggests that the origin of this barrier is related to the breaking of a π interaction between O 2 and Ir surface atom and to a significant additional O 2 interaction with adjacent electrophilic Ir-oxo species, which is present under experimental operating conditions. Besides shedding light on the mechanism of the OER on IrO 2 , these findings point out the importance of multireference methods for dissecting complex reactions at electrocatalytic interfaces and pave the route for further investigations with effective embedding approaches.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Introduction of localized spin-state transitions in the optical absorption spectrum of Cr-doped GaN

Using a hybrid density functional, we study the electronic, magnetic, and neutral excitations of the paradigmatic Cr-doped GaN solid. Our results indicate that the ≈1% doped wurtzite GaN crystal retains the semiconducting nature of the host, associated with a magnetic moment of 3 μ B . Further, as a consequence of Cr doping, additional hybridized bands are formed within the intrinsic band gap of GaN, leading to a considerable band gap narrowing by 1.4 eV and low-energy optical transitions. Our results indicate dark Cr d-d transitions at very low energy (0.5–0.7 eV), followed by bright transitions in the visible energy range (1.8–2.2 eV). Characterization of the electron-hole pairs suggests that the latter originates from the internal transitions among hybridized Cr d –N p states. With the existence of these additional optical features within the visible energy window, one can expect an enhancement to the photoelectric conversion efficiency of GaN upon Cr doping, in addition to applications in spintronics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Version 2.0.0 - M-SPARC: Matlab-Simulation Package for Ab-initio Real-space Calculations

M-SPARC is a Matlab code for performing ab initio Kohn–Sham Density Functional Theory simulations. Version 2.0.0 of the software further extends its capability to include relativistic effects, dispersion interactions, and advanced semilocal/nonlocal exchange–correlation functionals. These features significantly increase the fidelity of first principles calculations that can be performed using M-SPARC.

97 MATHEMATICS AND COMPUTING↗

A hybrid-perturbation-Galerkin technique which combines multiple expansions

A two-step hybrid perturbation-Galerkin method for the solution of a variety of differential equations type problems is found to give better results when multiple perturbation expansions are employed. The method assumes that there is parameter in the problem formulation and that a perturbation method can be sued to construct one or more expansions in this perturbation coefficient functions multiplied by computed amplitudes. In step one, regular and/or singular perturbation methods are used to determine the perturbation coefficient functions. The results of step one are in the form of one or more expansions each expressed as a sum of perturbation coefficient functions multiplied by a priori known gauge functions. In step two the classical Bubnov-Galerkin method uses the perturbation coefficient functions computed in step one to determine a set of amplitudes which replace and improve upon the gauge functions. The hybrid method has the potential of overcoming some of the drawbacks of the perturbation and Galerkin methods as applied separately, while combining some of their better features. The proposed method is applied, with two perturbation expansions in each case, to a variety of model ordinary differential equations problems including: a family of linear two-boundary-value problems, a nonlinear two-point boundary-value problem, a quantum mechanical eigenvalue problem and a nonlinear free oscillation problem. The results obtained from the hybrid methods are compared with approximate solutions obtained by other methods, and the applicability of the hybrid method to broader problem areas is discussed.

Geer, James F.↗

A hybrid perturbation-Galerkin technique that combines multiple expansions

A two-step hybrid perturbation-Galerkin method for the solution of a variety of differential equations type problems is found to give better results when multiple perturbation expansions are employed. The method assumes that there is parameter in the problem formulation and that a perturbation method can be used to construct one or more expansions in this perturbation coefficient functions multiplied by computed amplitudes. In step one, regular and/or singular perturbation methods are used to determine the perturbation coefficient functions. The results of step one are in the form of one or more expansions each expressed as a sum of perturbation coefficient functions multiplied by a priori known gauge functions. In step two the classical Bubnov-Galerkin method uses the perturbation coefficient functions computed in step one to determine a set of amplitudes which replace and improve upon the gauge functions. The hybrid method has the potential of overcoming some of the drawbacks of the perturbation and Galerkin methods as applied separately, while combining some of their better features. The proposed method is applied, with two perturbation expansions in each case, to a variety of model ordinary differential equations problems including: a family of linear two-boundary-value problems, a nonlinear two-point boundary-value problem, a quantum mechanical eigenvalue problem and a nonlinear free oscillation problem. The results obtained from the hybrid methods are compared with approximate solutions obtained by other methods, and the applicability of the hybrid method to broader problem areas is discussed.

Geer, James F.↗

Structure, Stability, and Electronic Properties of Boron Suboxide: A Density Functional Theory Study

Boron suboxide (B 6 O) is a boron-rich compound derived from the α-rhombohedral boron lattice with extreme hardness and unusual semiconducting properties. In this work, density functional theory (DFT) was used to show that unit cell volume, mechanical strength, band gaps, and thermodynamic stabilities of B 6 O were influenced by the interstitial elements and point defects at the icosahedral sites. While the hexagonal unit cell volume (HUCV) varies with interstitial occupancy, it is the icosahedral defect that weakens the intrinsic bulk modulus of B 6 O. Using the hybrid HSE functional, we confirmed that the perfect B 6 O bulk is a p-type semiconductor with a direct band gap of 2.8 eV. Furthermore, by screening α-boron compounds systematically, we found that a simple octet rule may offer a consistent explanation for the variations in the computed electronic structures. The formation free energies calculated over a wide range of temperatures (0–2500 K) and pressures (0–80 GPa) predict that formations of interstitial defects become favorable only at higher temperatures (ca. 1800 K) in bulk B 6 O lattices. The nudged elastic band (NEB) method was employed to identify the minimum energy pathways for the diffusions of dislocated B and O atoms. The diffusion of icosahedral B atoms has an energy barrier of 0.16 eV. More complex B diffusion paths involving the reorganization of icosahedral boron atoms incur higher barriers (>1 eV). In contrast, the diffusion of interstitial O atoms is facile with a barrier of 0.4 eV. Lastly, successive O insertions into the α-B lattice were performed using DFT to generate a basic understanding of the oxidation process. Furthermore, these calculations provide fundamental atomistic insights into the growth of B 6 O crystals and control of their point defects.

36 MATERIALS SCIENCE↗

Domain Compilation for Embedded Real-Time Planning

A recently conceived approach to automated real-time control of the actions of a robotic system enables an embedded real-time planning algorithm to develop plans that are more robust than they would otherwise be, without imposing an excessive computational burden. This approach occupies a middle ground between two prior approaches known in the art as the universal-plan and hybrid approaches. Ever since discovering the performance limitations of taking a sense-plan-act approach to controlling robots, the robotics community has endeavored to follow a behavior-based approach in which a behavior includes a rapid feedback loop between state estimation and motor control. Heretofore, system architectures following this approach have been based, variously, on algorithms that implement universal plans or algorithms that function as hybrids of planners and executives. In a typical universal-plan case, a set of behaviors is merged into the plan, but the system must be restricted to relatively small problem domains to avoid having to reason about too many states and represent them in the plan. In the hybrid approach, one implements actions as small sets of behaviors, each applicable to a limited set of circumstances. Each action is intended to bring the system to a subgoal state. A planning algorithm is used to string these actions together into a sequence to traverse the state space from an initial or current state to a goal state. The hybrid approach works well in a static environment, but it is inherently brittle in a dynamic environment because a failure can occur when the environment strays beyond the region of applicability of the current activity. In the present approach, a system can vary from the hybrid approach to the universal-plan approach, depending on a single integer parameter, denoted n, which can range from 1 to a maximum domain-dependent value of M. As illustrated in the figure, n = 1 represents the hybrid approach, in which each linked action covers a small part of the state space of the system. As n increases, the portion of state space associated with each action and its subgoal grows. When n reaches M, coverage extends over the full state space, so that the system contains a universal plan.

Barrett, Anthony↗

Coarse-Grained Density Functional Theory Predictions via Deep Kernel Learning

Scalable electronic predictions are critical for soft materials design. Recently, the Electronic Coarse-Graining (ECG) method was introduced to renormalize all-atom quantum chemical (QC) predictions to coarse-grained (CG) resolutions using deep neural networks (DNNs). While DNNs can learn complex representations that prove challenging for kernel-based methods, they are susceptible to overfitting and the overconfidence of uncertainty estimations. Here, we develop ECG within a GPU-accelerated Deep Kernel Learning (DKL) framework to enable CG QC predictions using range-separated hybrid density functional theory (DFT), obtaining a 107 speedup relative to naive all-atom QC. By treating the predicted electronic properties as random Gaussian Processes, DKL incorporates CG mapping degeneracy by learning the distribution of electronic energies as a function of CG configuration. DKL-ECG accurately reproduces molecular orbital energies from range-separated DFT while facilitating efficient training via active learning using the uncertainties provided by DKL. Further, we show that while active learning algorithms enable efficient sampling of a more diverse configurational space relative to random sampling, all explored query methods exhibit comparable performance for the examined system. We attribute this result to the significant overlap of the feature space and output property distributions across multiple temperatures.

97 MATHEMATICS AND COMPUTING↗

The role of electron correlations in the electronic structure of putative Chern magnet TbMn6Sn6

Abstract A member of the RMn 6 Sn 6 rare-earth family materials, TbMn 6 Sn 6 , recently showed experimental signatures of the realization of a quantum-limit Chern magnet. In this work, we use quantum Monte Carlo (QMC) and density functional theory with Hubbard U (DFT + U ) calculations to examine the electronic structure of TbMn 6 Sn 6 . To do so, we optimize accurate, correlation-consistent pseudopotentials for Tb and Sn using coupled-cluster and configuration–interaction (CI) methods. We find that DFT + U and single-reference QMC calculations suffer from the same overestimation of the magnetic moments as meta-GGA and hybrid density functional approximations. Our findings point to the need for improved orbitals/wavefunctions for this class of materials, such as natural orbitals from CI, or for the inclusion of multi-reference effects that capture the static correlations for an accurate prediction of magnetic properties. DFT + U with Mn magnetic moments adjusted to the experiment predict the Dirac crossing in bulk to be close to the Fermi level, within ~120 meV, in agreement with the experiments. Our non-stoichiometric slab calculations show that the Dirac crossing approaches even closer to the Fermi level, suggesting the possible realization of Chern magnetism in this limit.

36 MATERIALS SCIENCE↗

Biomechanical Modeling of the Deadlift Exercise to Improve the Efficacy of Resistive Exercise Microgravity Countermeasures

During long-duration spaceflight missions, astronauts exposure to microgravity without adequate countermeasures can result in losses of muscular strength and endurance, as well as loss of bone mass. As a countermeasure to this challenge, astronauts engage in resistive exercise during spaceflight to maintain their musculoskeletal function. The Hybrid Ultimate Lifting Kit (HULK) has been designed as a prototype exercise device for an exploration-class vehicle; the HULK features a much smaller footprint than previous devices such as the Advanced Resistive Exercise Device (ARED) on the International Space Station (ISS), which makes the HULK suitable for extended spaceflight missions in vehicles with limited volume. As current ISS exercise countermeasure equipment represents an improvement over previous generations of such devices, the ARED is being employed as a benchmark of functional performance. This project involves the development of a biomechanical model of the deadlift exercise, and is novel in that it is the first exercise analyzed in this context to include the upper limbs in the loading path, in contrast to the squat, single-leg squat, and heel raise exercises also being modeled by our team. OpenSim software is employed to develop these biomechanical models of humans performing resistive exercises to assess and improve the new exercise device designs. Analyses include determining differences in joint and muscle forces when using different loading strategies with the device, comparing and contrasting with the ARED benchmark, and determining whether the loading is sufficient to maintain musculoskeletal health. During data collection, the number of repetitions, load, cadence, stance, and grip width are controlled in order to facilitate comparisons between loading configurations. To date, data have been collected for two human subjects performing the deadlift exercise on the HULK device using two different loading conditions. Recorded data include motion capture, electromyography (EMG), ground reaction forces, device load cell data, photos and videos, and anthropometric data. Work is ongoing to perform biomechanical analyses including inverse kinematics and inverse dynamics to compare different versions of the deadlift model in order to determine which provides an appropriate level of detail to study this exercise. This work is supported by the National Space Biomedical Research Institute through NCC 9-58.

physical exercise↗

Selectively accessing the hotspots of optical nanoantennas by self-aligned dry laser ablation

Plasmonic nanostructures serve as optical antennas for concentrating the energy of incoming light in localized hotspots close to their surface. By positioning nanoemitters in the antenna hotspots, energy transfer is enabled, leading to novel hybrid antenna-emitter-systems, where the antenna can be used to manipulate the optical properties of the nano-objects. The challenge remains how to precisely position emitters within the hotspots. We report a self-aligned process based on dry laser ablation of a calixarene that enables the attachment of molecules within the electromagnetic hotspots at the tips of gold nanocones. Within the laser focus, the ablation threshold is exceeded in nanoscale volumes, leading to selective access of the hotspot areas. A first indication of the site-selective functionalization process is given by attaching fluorescently labelled proteins to the nanocones. In a second example, Raman-active molecules are selectively attached only to nanocones that were previously exposed in the laser focus, which is verified by surface enhanced Raman spectroscopy. Enabling selective functionalization is an important prerequisite e.g. for preparing single photon sources for quantum optical technologies, or multiplexed Raman sensing platforms.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

The Role of Optical Phonon Confinement in the Infrared Dielectric Response of III–V Superlattices

Polar dielectrics are key materials of interest for infrared (IR) nanophotonic applications due to their ability to host phonon-polaritons that allow for low-loss, subdiffractional control of light. The properties of phonon-polaritons are limited by the characteristics of optical phonons, which are nominally fixed for most “bulk” materials. Superlattices composed of alternating atomically thin materials offer control over crystal anisotropy through changes in composition, optical phonon confinement, and the emergence of new modes. In particular, the modified optical phonons in superlattices offer the potential for so-called crystalline hybrids whose IR properties cannot be described as a simple mixture of the bulk constituents. To date, however, studies have primarily focused on identifying the presence of new or modified optical phonon modes rather than assessing their impact on the IR response. Here, this study focuses on assessing the impact of confined optical phonon modes on the hybrid IR dielectric function in superlattices of GaSb and AlSb. Using a combination of first principles theory, Raman, FTIR, and spectroscopic ellipsometry, the hybrid dielectric function is found to track the confinement of optical phonons, leading to optical phonon spectral shifts of up to 20 cm -1 . These results provide an alternative pathway toward designer IR optical materials.

36 MATERIALS SCIENCE↗

Molecular Modes of Attosecond Charge Migration

Here, first-principles calculations are employed to elucidate the modes of attosecond charge migration (CM) in halogenated hydrocarbon chains. We use constrained density functional theory (DFT) to emulate the creation of a localized hole on the halogen and follow the subsequent dynamics via time-dependent DFT. We find low-frequency CM modes (~ 1 eV) that propagate across the molecule and study their dependence on length, bond order, and halogenation. We observe that the CM speed (~ 4Å/ fs) is largely independent of molecule length, but is lower for triple-bonded versus double-bonded molecules. Additionally, as the halogen mass increases, the hole travels in a more particlelike manner as it moves across the molecule. These heuristics will be useful in identifying molecules and optimal CM detection methods for future experiments, especially for halogenated hydrocarbons which are promising targets for ionization-triggered CM.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Solvent Impregnated Polymers Loaded with Liquid-Like Nanoparticle Organic Hybrid Materials for Enhanced Kinetics of Direct Air Capture and Point Source CO 2 Capture

Hybrid CO 2 capture materials, solvent impregnated polymers (SIPs), are developed based on a simple and scalable encapsulation technique to enhance CO 2 capture kinetics of water-lean solvents with high viscosity. Liquid-like nanoparticle organic hybrid materials functionalized with polyethylenimine (NOHM-I-PEI) are incorporated into a shell material and UV-cured to produce gas-permeable solid sorbents with uniform NOHMs loading (NPEI-SIPs). The CO 2 capture kinetics of NPEI-SIPs show a remarkable 50-fold increase compared to that of neat NOHM-I-PEI due to a large increase in the NOHMs-CO 2 interfacial surface area provided by the SIP design. The optimum NOHM-I-PEI loading and sorption temperature are found to be ≈49 wt% and 50 °C, respectively, and NPEI-SIPs exhibit great thermal stability over 20 CO 2 capture/sorbent regeneration temperature swing cycles. The pseudoequilibrium CO 2 loadings of NPEI-SIPs under humid conditions are as high as 3.1 mmol CO 2 g -1 NPEI - SIPs for 15 vol% CO 2 (postcombustion capture) and 1.7 mmol CO 2 g -1 NPEI - SIPs for 400 ppm (direct air capture). Overall, these findings suggest that NPEI-SIPs can effectively capture CO 2 from a wide range of CO 2 concentrations including direct air capture while allowing the flexible design of CO 2 capture reactors by combining the benefits of liquid solvents and solid sorbents.

36 MATERIALS SCIENCE↗