Solution structure and dynamics of the mitochondrial-targeted GTPase-activating protein (GAP) VopE b
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Smith, Kyle P.↗
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Results for “Motion processing”
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Enriched immersed boundary method (EIBM) for interface-coupled multi-physics and applications to convective conjugate heat transfer
It is challenging to develop numerical methods that simultaneously maintain accuracy of resolving boundary conditions and mesh flexibility to handle the interface in interface-coupled multi-physics problems involving large property discontinuity. On the one hand, boundary-fitted methods possess high accuracy in capturing the interfacial phenomenon but involve complicated volumetric mesh generation, mesh-motion, and even re-meshing procedures. On the other hand, immersed boundary methods (IBM) provide mesh flexibility but sometimes suffer from inferior interface representations, leading to poor enforcement of boundary conditions. This paper presents an enriched immersed boundary method (EIBM) to overcome this challenge and demonstrates its efficacy in conjugate heat transfer, a representative example in interface-coupled multi-physics systems that have implications for many industrial processes. Further, the core technique of the method is to enhance IBM’s accuracy of the fluid–solid interface by enriching the degrees of freedom of the cut elements to enforce temperature and flux compatibilities and resolve all the physical unknowns on the background mesh to simplify the volumetric mesh generation. We implement the EIBM under the framework of a variational multiscale formulation for coupled Navier–Stokes and thermodynamics equations. The enriched DoFs enable better enforcement of temperature and flux compatibilities with large conductivity ratios across the fluid–solid interface. At the same time, the immersed nature of the proposed method still attains mesh flexibility. The EIBM’s accuracy is thoroughly evaluated through a set of examples, ranging from benchmark problems with analytical solutions to real-world cooling processes of a moving metallic structure with complex geometry.
42 ENGINEERING↗
Laboratory Measurements of Cloud Scavenging of Interstitial Aerosol in a Turbulent Environment (Final Technical Report)
The link between aerosol particles and clouds is well established. Every cloud droplet forms on a preexisting particle; clouds are the primary removal mechanism for aerosol particles with diameters in the range of 0.1 to 1 micrometer. Traditionally, those connections have been considered in the absence of the chaotic air motions (turbulence) that are ubiquitous in Earth’s atmosphere. Recent work at Michigan Tech indicates that turbulent fluctuations in temperature and water vapor, which couple aerosols and cloud droplets, play an important role in whether particles grow to the size of cloud droplets and scavenging by diffusion. In this project, we measured, in a turbulent environment, the rate at which aerosol particles are incorporated into cloud droplets through both these processes, which Michigan Tech's turbulent cloud chamber enables because we can sustain a mixing cloud almost indefinitely.
54 ENVIRONMENTAL SCIENCES↗
Time-Resolved Optical Pump-Resonant X-ray Probe Spectroscopy of 4-Thiouracil: A Simulation Study
We theoretically monitor the photoinduced ππ* → nπ* internal conversion process in 4-thiouracil (4TU), triggered by an optical pump. The element-sensitive spectroscopic signatures are recorded by a resonant X-ray probe tuned to the sulfur, oxygen, or nitrogen K-edge. We employ high-level electronic structure methods optimized for core-excited electronic structure calculation combined with quantum nuclear wavepacket dynamics computed on two relevant nuclear modes, fully accounting for their quantum nature of nuclear motions. We critically discuss the capabilities and limitations of the resonant technique. For sulfur and nitrogen, we document a pre-edge spectral window free from ground-state background and rich with ππ* and nπ* absorption features. The lowest sulfur K-edge shows strong absorption for both ππ* and nπ*. In the lowest nitrogen K-edge window, we resolve a state-specific fingerprint of the ππ* and an approximate timing of the conical intersection via its depletion. A spectral signature of the nπ* transition, not accessible by UV–vis spectroscopy, is identified. The oxygen K-edge is not sensitive to molecular deformations and gives steady transient absorption features without spectral dynamics. Here, the ππ*/nπ* coherence information is masked by more intense contributions from populations. Altogether, element-specific time-resolved resonant X-ray spectroscopy provides a detailed picture of the electronic excited-state dynamics and therefore a sensitive window into the photophysics of thiobases.
97 MATHEMATICS AND COMPUTING↗
Investigating the dislocation reactions on Σ3{111} twin boundary during deformation twin nucleation process in an ultrafine-grained high-manganese steel
Abstract Some of ultrafine-grained (UFG) metals including UFG twinning induced plasticity (TWIP) steels have been found to overcome the paradox of strength and ductility in metals benefiting from their unique deformation modes. Here, this study provides insights into the atomistic process of deformation twin nucleation at Σ3{111} twin boundaries, the dominant type of grain boundary in this UFG high manganese TWIP steel. In response to the applied tensile stresses, grain boundary sliding takes place which changes the structure of coherent Σ3{111} twin boundary from atomistically smooth to partly defective. High resolution transmission electron microscopy demonstrates that the formation of disconnection on Σ3{111} twin boundaries is associated with the motion of Shockley partial dislocations on the boundaries. The twin boundary disconnections act as preferential nucleation sites for deformation twin that is a characteristic difference from the coarse-grained counterpart, and is likely correlated with the lethargy of grain interior dislocation activities, frequently seen in UFG metals. The deformation twin nucleation behavior will be discussed based on in-situ TEM deformation experiments and nanoscale strain distribution analyses results.
36 MATERIALS SCIENCE↗
EQ_phase_detection
The EQ_phase_detection software is designed to scan continuous daily waveforms to detect earthquake phase arrivals from local to regional (150 km) events. The detections are made with a deep learning encoder-decoder model. When the model detects an earthquake in the waveforms, a second model is implemented to classify the first arriving motions. Both deep learning models are trained with the Tensorflow package using publicly available benchmark data sets. The software input is a path to a directory that contains waveforms in mseed format and the associated response files in xml format. The output is a data table of time stamped detections, signal amplitude, signal-to-noise ratio, and softmax probability of the detection in a generic format applicable to post-processing association algorithms for event locations. Additionally, the p-wave and s-wave waveforms are saved in a data table for rapid access when producing improved locations using correlation-based techniques. The software is designed for multiprocessing with multiple GPU’s for rapid processing of large data sets. The configuration file provides flexibility in the trained models implemented and allows access to multiple models trained for different sampling rates or input dimensions. This is particularly useful for regions with multiple networks that do not have the same data parameters.
Johnson, Christopher↗
Improving 3D reconstruction quality for root phenotyping: assessing the impact of camera calibration and imaging parameters
Arate 3D reconstruction is essential for high-throughput plant phenotyping, particularly for studying complex structures such as root systems. While photogrammetry and Structure from Motion (SfM) techniques have become widely used for 3D root imaging, the camera settings used are often underreported in studies, and the impact of camera calibration on model accuracyccu remains largely underexplored in plant science. In this study, we systematically evaluate the effects of focus, aperture, exposure time, and gain settings on the quality of 3D root models made with a multi-camera scanning system. We show through a series of experiments that calibration significantly improves model quality, with focus misalignment and shallow depth of field (DoF) being the most important factors affecting reconstruction accuracy. Our results further show that proper calibration has a greater effect on reducing noise than filtering it during post-processing, emphasizing the importance of optimizing image acquisition rather than relying solely on computational corrections. This work improves the repeatability and accuracy of 3D root imaging for phenotyping pipelines by giving useful calibration guidelines. This leads to better trait quantification for use in crop research and plant breeding in downstream analysis.
3D reconstruction↗
Accelerating phase-field-based microstructure evolution predictions via surrogate models trained by machine learning methods
Abstract The phase-field method is a powerful and versatile computational approach for modeling the evolution of microstructures and associated properties for a wide variety of physical, chemical, and biological systems. However, existing high-fidelity phase-field models are inherently computationally expensive, requiring high-performance computing resources and sophisticated numerical integration schemes to achieve a useful degree of accuracy. In this paper, we present a computationally inexpensive, accurate, data-driven surrogate model that directly learns the microstructural evolution of targeted systems by combining phase-field and history-dependent machine-learning techniques. We integrate a statistically representative, low-dimensional description of the microstructure, obtained directly from phase-field simulations, with either a time-series multivariate adaptive regression splines autoregressive algorithm or a long short-term memory neural network. The neural-network-trained surrogate model shows the best performance and accurately predicts the nonlinear microstructure evolution of a two-phase mixture during spinodal decomposition in seconds, without the need for “on-the-fly” solutions of the phase-field equations of motion. We also show that the predictions from our machine-learned surrogate model can be fed directly as an input into a classical high-fidelity phase-field model in order to accelerate the high-fidelity phase-field simulations by leaping in time. Such machine-learned phase-field framework opens a promising path forward to use accelerated phase-field simulations for discovering, understanding, and predicting processing–microstructure–performance relationships.
36 MATERIALS SCIENCE↗
Staircase formation by resonant and non-resonant transport of potential vorticity
The E × B staircase is a quasi-periodic pattern of pressure profile corrugations. In this work, we present a new mechanism for E × B staircase formation that involves resonant transport versus non-resonant transport. We start from a potential vorticity evolution system and use quasi-linear theory, a model dispersion relation, and a bi-Lorentzian spectrum approximation, to construct the relation between the fluxes and the profiles. With these fluxes, we close the profile evolution equations and the extended turbulence intensity evolution equation, which together constitute a turbulence-profile evolution system. In this system, the Doppler effect from the E × B mean flow can cause resonance between trapped ion precession motion and the trapped ion mode, which drives a resonant transport contribution to the fluxes. The profiles will be flattened where the resonant transport is switched on. In contrast, for the regions of non-resonant transport, profiles are steeper. A quasi-periodic pattern of profile corrugation (the E × B staircase) spontaneously emerges in this system, which is the two states mentioned above, arranged as alternating layers in space. The feedback processes during the staircase pattern formation are identified. An estimate of the critical value of the boundary heat flux is obtained, above which the staircase formation will be triggered. An estimate scaling of the step size in the staircase pattern is obtained. The resonant turbulent transport is also a mechanism for collisionless saturation of zonal flow. Furthermore, this work is related to internal transport barrier formation and suggests some new scenarios, such as an enhanced confined L mode.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Boron Nitride-Driven Strengthening of Aluminum Composites via Friction Stir Processing
Friction stir welding and processing (FSW/P) has emerged as an effective solid-state joining technique for fabricating metal matrix composites (MMCs), offering improved mechanical properties through refined microstructural evolution. In this study, an aluminum-boron nitride nanoparticle (Al-BNNP) composite was synthesized via FSW, and its indentation-based mechanical properties were systematically evaluated. Microhardness mapping across the weld cross-section revealed a progressive increase in hardness toward the stir zone (SZ), attributed to severe plastic deformation, dynamic recrystallization (DRX), and the reinforcing effect of BNNPs. Profilometry-based indentation plastometry (PIP) inferred yield strength (YS) demonstrates a 47.8% increase compared to the base metal (BM) and a 75% improvement compared to FSP pure aluminum reported in literature. This enhancement is attributed to strengthening mechanisms, including grain boundary pinning, load transfer, and increased dislocation density. The strain rate sensitivity (SRS) measurements at the nanoscale demonstrated a substantial decrease in the SZ, correlated with ultrafine grain structures and strong BNNP-matrix interactions. Activation volume analysis revealed a significant reduction in the SZ, suggesting that dislocation motion is increasingly restricted by dislocation-dislocation and dislocation-particle interactions. These findings suggest that incorporating BNNPs in FSW/P enables tailoring the microstructure without thermal degradation of the secondary particles, thereby significantly enhancing the mechanical performance of aluminum composites, particularly for structural applications in aerospace and automotive industries.
Aluminum↗
Sondheimer oscillations as a probe of non-ohmic flow in WP 2 crystals
As conductors in electronic applications shrink, microscopic conduction processes lead to strong deviations from Ohm’s law. Depending on the length scales of momentum conserving (l MC ) and relaxing (l MR ) electron scattering, and the device size (d), current flows may shift from ohmic to ballistic to hydrodynamic regimes. So far, an in situ methodology to obtain these parameters within a micro/nanodevice is critically lacking. In this context, we exploit Sondheimer oscillations, semi-classical magnetoresistance oscillations due to helical electronic motion, as a method to obtain l MR even when l MR $\gg$ d. We extract l MR from the Sondheimer amplitude in WP 2 , at temperatures up to T ~ 40 K, a range most relevant for hydrodynamic transport phenomena. Our data on μm-sized devices are in excellent agreement with experimental reports of the bulk l MR and confirm that WP 2 can be microfabricated without degradation. These results conclusively establish Sondheimer oscillations as a quantitative probe of l MR in micro-devices.
36 MATERIALS SCIENCE↗
Towards a numu CC exclusive cross section measurement with one proton and one muon in the final state at the NOvA near detector
NOvA is a long-baseline neutrino experiment at Fermilab that studies neutrino oscillations via electron neutrino appearance and muon neutrino disappearance. The NOvA Near Detector, located 1 km from the NuMI target, records a high rate of neutrino interactions in the energy range of 1-5 GeV. One of the limitations in precise extraction of oscillations is the large systematic uncertainty on neutrino-nucleus interactions. The high rate of neutrino interactions in the NOvA Near Detector provides the opportunity to probe various neutrino interaction processes and nuclear models, via the extraction of cross sections of particular final states. Nuclear models can be improved by measuring neutrino-nucleus cross sections with respect to kinematic variables which are known to be more sensitive to nuclear effects, such as transverse kinematic imbalance (TKI) variables. Usage of TKI variables allows for more direct constraints on models of neutrino scattering, as these variables can more directly investigate, for instance, effects of Fermi motion and final state interactions. In this work, we describe progress towards a method of identifying and reconstructing protons in the NOvA near detector to enable the cross section measurement of charged current neutrino interactions with a visible muon and a proton in the final state, reported in TKI variables.
Weber, Colin [Minnesota U.] (ORCID:000000031117067↗
Laser drilling and machining enhancement using gated CW and short pulsed lasers
The present disclosure relates to a laser system for processing a material. The system may make use of a laser configured to intermittently generate a first laser pulse of a first duration and a first average power, at a spot on a surface of the material being processed, and a second laser pulse having a second duration and a second peak power. The second duration may be shorter than the first duration by a factor of at least 100, and directed at the spot. The second laser pulse is generated after the first laser pulse is generated. The first laser pulse is used to heat the spot on the surface of the material, while the second laser pulse induces a melt motion and material ejection of molten material from the melt pool.
Ly, Sonny S.↗
Mg-Ion Conduction in Antiperovskite Solid Electrolytes Revealed by 25 Mg Ultrahigh Field NMR and First-Principles Calculations
Magnesium-ion batteries hold the potential to outperform the energy density of lithium-ion batteries, given the divalent charge carried by each Mg 2+ cation, but remain in an early stage of development. Here, in this study, 25 Mg solid-state nuclear magnetic resonance (ssNMR) is used to gain insight into the local structure and Mg-ion dynamics of candidate Mg-ion solid electrolytes, the antiperovskites Mg 3 SbN and Mg 3 AsN. Using the highest available magnetic field (35.2 T) for high-resolution solid-state NMR, the largest 25 Mg quadrupole coupling constants (C Q ) yet measured of up to 22 MHz are reported and corroborated by first-principles calculations. Predicted C Q values are shown to correlate with the antiperovskite’s tolerance factor; thus, 25 Mg NMR linewidths can report on lattice distortions and phase stability of these antiperovskites. Variable-temperature 25 Mg NMR spectra demonstrate changes at elevated temperatures, ascribed to Mg-ion motional effects. 25 Mg T 1 relaxometry measurements at ultrahigh field reveal a lower activation energy for the more distorted Mg 3 AsN phase, matching computational predictions of a lower energy barrier for Mg 2+ ion migration and suggesting that additional scrutiny of antiperovskites as Mg-ion conductors is warranted. Given the inherent challenges of 25 Mg NMR, this work demonstrates the benefits of combining ultrahigh field NMR spectroscopy, advanced pulse sequences, modern signal processing, and first-principles calculations to facilitate NMR of quadrupolar nuclei as a tool to probe the local structure and ion dynamics in beyond-Li battery materials.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Nanoscale defect evaluation framework combining real-time transmission electron microscopy and integrated machine learning-particle filter estimation
Observation of dynamic processes by transmission electron microscopy (TEM) is an attractive technique to experimentally analyze materials’ nanoscale phenomena and understand the microstructure-properties relationships in nanoscale. Even if spatial and temporal resolutions of real-time TEM increase significantly, it is still difficult to say that the researchers quantitatively evaluate the dynamic behavior of defects. Images in TEM video are a two-dimensional projection of three-dimensional space phenomena, thus missing information must be existed that makes image’s uniquely accurate interpretation challenging. Therefore, even though they are still a clustering high-dimensional data and can be compressed to two-dimensional, conventional statistical methods for analyzing images may not be powerful enough to track nanoscale behavior by removing various artifacts associated with experiment; and automated and unbiased processing tools for such big-data are becoming mission-critical to discover knowledge about unforeseen behavior. We have developed a method to quantitative image analysis framework to resolve these problems, in which machine learning and particle filter estimation are uniquely combined. The quantitative and automated measurement of the dislocation velocity in an Fe-31Mn-3Al-3Si autunitic steel subjected to the tensile deformation was performed to validate the framework, and an intermittent motion of the dislocations was quantitatively analyzed. The framework is successfully classifying, identifying and tracking nanoscale objects; these are not able to be accurately implemented by the conventional mean-path based analysis.
36 MATERIALS SCIENCE↗
Photochemistry sample sticks for inelastic neutron scattering
Every material experiences atomic and molecular motions that are generally termed vibrations in gases and liquids or phonons in solid state materials. Optical spectroscopy techniques, such as Raman, infrared absorption spectroscopy, or inelastic neutron scattering (INS), can be used to measure the vibrational/phonon spectrum of ground state materials properties. A variety of optical pump probe spectroscopies enable the measurement of excited states or elucidate photochemical reaction pathways and kinetics. So far, it has not been possible to study photoactive materials or processes in situ using INS due to the mismatch between neutron and photon penetration depths, differences between the flux density of photons and neutrons, cryogenic temperatures for INS measurements, vacuum conditions, and a lack of optical access to the sample space. These experimental hurdles have resulted in very limited photochemistry studies using INS. Here we report on the design of two different photochemistry sample sticks that overcome these experimental hurdles to enable in situ photochemical studies using INS, specifically at the VISION instrument at Oak Ridge National Laboratory. We demonstrate the use of these new measurement capabilities through (1) the in situ photodimerization of anthracene and (2) the in situ photopolymerization of a 405 nm photoresin using 405 nm excitation as simple test cases. Furthermore, these new measurement apparatus broaden the science enabled by INS to include photoactive materials, optically excited states, and photoinitiated reactions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Charged particle motion and radiation in strong electromagnetic fields
The dynamics of charged particles in electromagnetic fields is an essential component of understanding the most extreme environments in our Universe. In electromagnetic fields of sufficient magnitude, radiation emission dominates the particle motion and effects of quantum electrodynamics (QED) in strong fields are crucial, which triggers electron-positron pair cascades and counterintuitive particle-Trapping phenomena. As a result of recent progress in laser technology, high-power lasers provide a platform to create and probe such fields in the laboratory. With new large-scale laser facilities on the horizon and the prospect of investigating these hitherto unexplored regimes, this review explores the basic physical processes of radiation reaction and QED in strong fields, how they are treated theoretically and in simulation, the new collective dynamics they unlock, recent experimental progress and plans, and possible applications for high-flux particle and radiation sources.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Theory and Simulation of Ultrafast Multidimensional Nonlinear X-ray Spectroscopy of Molecules (Final Report)
Emerging X-ray free electron laser (XFEL) beam sources offer new types of probes of matter with unprecedented spatial and temporal resolutions. These experimental advances must be met by robust theoretical and computational tools that provide predictive modeling capacity of the underlining electronic and structural dynamics. The latter will be essential for the design of sophisticated multi-pulse experiments and for their interpretation. The proposed research effort will focus on developing cutting- edge simulation tools for nonlinear multidimensional X-ray/optical spectroscopies and aims to address key questions in Priority Research Opportunities 1 (Probing and controlling electron motion within a molecule) and 3 (Capturing rare events and intermediate states in the transformation of matter) as mentioned in the BES Roundtable Report “Opportunities for Basic Research at the Frontiers of XFEL Ultrafast Science”. XFEL multidimensional nonlinear techniques, which combine sequences of X-ray and possibly optical pulses, provide a unique experimental toolbox for probing the dynamics of core and valence electronic excitations, as well as material structure. Predictive modeling of these dynamical processes requires the combination of analytical theory for nonlinear interactions of light and matter, robust quantum-chemical methodologies for the accurate description of electronic structure of various materials, and multiscale ab initio electron and nuclear dynamics techniques operating beyond Born-Oppenheimer approximation. These challenges will be addressed with three research thrusts (i) Develop and implement theoretical apparatus for modeling a broad range of multidimensional spectroscopic techniques enabled by present and upcoming XFEL facilities. This thrust also includes the incorporation of a computational module in the DOE supported open-source NWChem computational chemistry package as well as the development of other open-source codes ready for dissemination across a broad user base; (ii) Propose and design new multi-pulse experiments that make use of the capabilities of the incoming LCLS-II facility; (iii) Perform selected applications to specific molecular systems that can be carried out at LCLS-II and demonstrate how these X-ray sources may be used to study nonadiabatic dynamics through conical interactions, electronic correlations in multi-core excitons, and charge transfer/energy transfer processes. The proposed research will be carried out by a multi-disciplinary four-institution research team which combines academia and national laboratories and spans the broad and necessary expertise in theoretical spectroscopy, nonlinear optics, quantum chemistry, molecular non-adiabatic dynamics and code development. The work will be performed in a highly interactive team environment with junior researchers shared between institutions thus cementing cross- disciplinary interactions. The developed simulation tools will be immediately deployed for XFEL facility users, both experimentalists and theorists, via freely distributed codes and databases. Altogether, this project will facilitate establishing XFEL-based multidimensional spectroscopies as a novel diagnostic tool for monitoring electronic and structural dynamics in molecular materials.
74 ATOMIC AND MOLECULAR PHYSICS↗