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At least 433 records · Page 24

Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering

One of the most challenging tasks in biological science is to understand how a protein folds. In theoretical studies, the hypothesis adopting a funnel-like free-energy landscape has been recognized as a prominent scheme for explaining protein folding in views of both internal energy and conformational heterogeneity of a protein. Despite numerous experimental efforts, however, comprehensively studying protein folding with respect to its global conformational changes in conjunction with the heterogeneity has been elusive. Here we investigate the redox-coupled folding dynamics of equine heart cytochrome c (cyt-c) induced by external electron injection by using time-resolved X-ray solution scattering. A systematic kinetic analysis unveils a kinetic model for its folding with a stretched exponential behavior during the transition toward the folded state. With the aid of the ensemble optimization method combined with molecular dynamics simulations, we found that during the folding the heterogeneously populated ensemble of the unfolded state is converted to a narrowly populated ensemble of folded conformations. These observations obtained from the kinetic and the structural analyses of X-ray scattering data reveal that the folding dynamics of cyt-c accompanies many parallel pathways associated with the heterogeneously populated ensemble of unfolded conformations, resulting in the stretched exponential kinetics at room temperature. This finding provides direct evidence with a view to microscopic protein conformations that the cyt-c folding initiates from a highly heterogeneous unfolded state, passes through still diverse intermediate structures, and reaches structural homogeneity by arriving at the folded state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Theory for time-resolved resonant inelastic x-ray scattering

Time-resolved measurements of materials provide a wealth of information on quasiparticle dynamics, and have been the focus of optical studies for decades. In this paper, we develop a theory for explicitly evaluating time-resolved resonant inelastic x-ray scattering (tr-RIXS). We apply the theory to a noninteracting electronic system and reveal the particle-hole spectrum and its evolution during the pump pulse. With a high-frequency pump, the frequency and amplitude dependence analysis of the spectra agrees well with the steady-state assumptions and Floquet excitations. When the pump frequency is low, the spectrum extracts real-time dynamics of the particle-hole continuum in momentum space. These results verify the correctness of our theory and demonstrate the breadth of physical problems that tr-RIXS could shed light on.

36 MATERIALS SCIENCE↗

Ultrafast optical observation of spin-pumping induced dynamic exchange coupling in ferromagnetic semiconductor/metal bilayer

Abstract Spin angular momentum transfer in magnetic bilayers offers the possibility of ultrafast and low-loss operation for next-generation spintronic devices. We report the field- and temperature- dependent measurements on the magnetization precessions in Co 2 FeAl/(Ga,Mn)As by time-resolved magneto-optical Kerr effect. Analysis of the effective Gilbert damping and phase shift indicates a clear signature of an enhanced dynamic exchange coupling between the two ferromagnetic (FM) layers due to the reinforced spin pumping at resonance. The temperature dependence of the dynamic exchange-coupling reveals a primary contribution from the ferromagnetism in (Ga,Mn)As.

30 DIRECT ENERGY CONVERSION↗

Identifying Water–Anion Correlated Motion in Aqueous Solutions through Van Hove Functions

Electrolyte solutions are ubiquitous in materials in daily use and in biological systems. However, the understanding of their molecular and ionic dynamics, particularly those of their correlated motions, are elusive despite extensive experimental, theoretical, and numerical studies. Here we report the real-space observations of the molecular/ionic-correlated dynamics of aqueous salt (NaCl, NaBr, and NaI) solutions using the Van Hove functions obtained by high-resolution inelastic X-ray scattering measurement and molecular dynamics simulation. Our results directly depict the distance-dependent dynamics of aqueous salt solutions on the picosecond time scale and identify the changes in the anion–water correlations. This study demonstrates the capability of the real-space Van Hove function analysis to describe the local correlated dynamics in aqueous salt solutions.

Shinohara, Yuya↗

Mesoporous layered aluminosilicates prepared from protozeolitic nanoclusters: Synthesis, physicochemical and catalytic properties

Mesoporous layered aluminosilicates were prepared by a two-stage route using tetrapropylammonium hydroxide (TPAOH) and hexadecylamine (HAD). First, aluminosilicate sols were prepared from very dilute solutions under mild conditions. The sols contained aluminosilicate nanoclusters of the average size 4 – 5 nm. 27Al NMR studies demonstrated that tumbling alone of the small aluminosilicate nanoclusters due to Brownian motions was removing effectively chemical shift anisotropy, dipolar interactions and narrowing quadrupolar interactions; thus, magic-angle-spinning was not required for obtaining good quality 27Al and 29Si NMR spectra of the sols studied. Quantitative analysis of 29Si NMR spectra allowed following evolution of the signals in time, providing insight into dynamical behavior during formation of sols. Second, the sols with the Si/Al ratios of 12 – 70 were used for preparation of the X-ray amorphous aluminosilicate materials. The samples exhibited good sorption properties due to the presence of the ca. 3 nm slit mesopores, coupled with the presence of Brønsted and Lewis acid sites. The initial reaction rate in the liquid-phase isomerization of ?-pinene and the turnover frequency (TOF) were estimated at relatively low temperature of 348 K. The mesoporous aluminosilicate materials turned out to be very active catalytically; the initial reaction rate was surpassing the rate measured over the reference zeolitic and non-zeolitic materials. TOF on mesoporous materials was also high, 0.15 and 0.27 s-1, in comparison with ZSM-5 (0.02 s-1) and ferrierite type zeolites (0.06 – 0.09 s-1).

Onik, Katarzyna↗

Tip-Enhanced Raman Nanospectroscopy of Smooth Spherical Gold Nanoparticles

We record nanoscale-resolved chemical images of thiobenzonitrile (TBN)-functionalized smooth gold nanospheres on silicon via tip-enhanced Raman (TER) nano-spectroscopy. The recorded images trace the nascence of the familiar doughnut-shaped scattering profile of nanoparticles on silicon at its origin (the particle surface), which appears as a horseshoe-shaped scattering pattern under our experimental conditions. The local optical field maps are in agreement with their simulated finite-difference time-domain analogues. Analysis of the recorded spectra with the aid of ab initio molecular dynamics-based Raman spectral simulations further suggests that optical rectification and molecular charging take place throughout the course of atomic force microscopy-based TER nanoscale chemical imaging.

Bhattarai, Ashish↗

Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

Viruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health, and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in soil, 1 of the most complex microbial systems. Here, we assembled 48 individual metatranscriptomes from 4 habitats within a planted soil sampled over a 22-d time series: Rhizosphere alone, detritosphere alone, rhizosphere with added root detritus, and unamended soil (4 time points and 3 biological replicates). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker genes. Based on viral phylogeny, much of the diversity was Narnaviridae that may parasitize fungi or Leviviridae , which may infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral and host communities were structured based on the presence of root litter. Clear temporal dynamics by Leviviridae and their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant, and active in soil. When viral infection causes host cell death, it may mobilize cell carbon in a process that may represent an overlooked component of soil carbon cycling.

54 ENVIRONMENTAL SCIENCES↗

Electromagnetic waves near the proton cyclotron frequency: Stereo observations

Transverse, near-circularly polarized, parallel-propagating electromagnetic waves around the proton cyclotron frequency were found sporadically in the solar wind throughout the inner heliosphere. They could play an important role in heating and accelerating the solar wind. These low-frequency waves (LFWs) are intermittent but often occur in prolonged bursts lasting over 10 minutes, named 'LFW storms'. Through a comprehensive survey of them from Solar Terrestrial Relations Observatory A using dynamic spectral wave analysis, we have identified 241 LFW storms in 2008, present 0.9% of the time. They are left-hand (LH) or right-hand (RH) polarized in the spacecraft frame with similar characteristics, probably due to Doppler shift of the same type of waves or waves of intrinsically different polarities. In rare cases, the opposite polarities are observed closely in time or even simultaneously. Having ruled out interplanetary coronal mass ejections, shocks, energetic particles, comets, planets, and interstellar ions as LFW sources, we discuss the remaining generation scenarios: LH ion cyclotron instability driven by greater perpendicular temperature than parallel temperature or by ring-beam distribution, and RH ion fire hose instability driven by inverse temperature anisotropy or by cool ion beams. The investigation of solar wind conditions is compromised by the bias of the one-dimensional Maxwellian fit used for plasma data calibration. However, the LFW storms are preferentially detected in rarefaction regions following fast winds and when the magnetic field is radial. This preference may be related to the ion cyclotron anisotropy instability in fast wind and the minimum in damping along the radial field.

79 ASTRONOMY AND ASTROPHYSICS↗

DeepGrid: Robust Deep Reinforcement Learning-based Contingency Management

Increasing uncertainty raised by the integration of renewable energy resources requires an enormous number of simulations to be carried out for the security assessment of the power grid. However, it is challenging to assess the steady-state and dynamic security indices for different system contingency events by doing an exhaustive analysis in real-time due to the computational and communication constraints. One promising solution is using data-driven techniques along with the system models to train an intelligent contingency management framework to better handle the contingencies in real-time. Nevertheless, implementing a data-driven technique to obtain the best remedial actions necessitates to account for the effect of the measurement noise on the performance of the contingency management. To tackle these challenges, we leverage a robust deep reinforcement learning (DRL) algorithm called Double Deep Q-Network (DDQN) to design a recommender system capable of prescribing optimal control actions with the help of the real-time digital simulator (RTDS). The use of RTDS system in combination with the advanced DRL algorithm allows to explore a wide variety of system contingencies in order to derive better remedial actions. The performance of the proposed algorithm is evaluated in IEEE 9-bus system under different loading conditions, and different network configurations in presence of noisy measurements.

Ghasemkhani, Amir↗

304L Can Crush Validation Studies

Accurate prediction of ductile behavior of structural alloys up to and including failure is essential in component or system failure assessment, which is necessary for nuclear weapons alteration and life extensions programs of Sandia National Laboratories. Modeling such behavior requires computational capabilities to robustly capture strong nonlinearities (geometric and material), rate- dependent and temperature-dependent properties, and ductile failure mechanisms. This study's objective is to validate numerical simulations of a high-deformation crush of a stainless steel can. The process consists of identifying a suitable can geometry and loading conditions, conducting the laboratory testing, developing a high-quality Sierra/SM simulation, and then drawing comparisons between model and measurement to assess the fitness of the simulation in regards to material model (plasticity), finite element model construction, and failure model. Following previous material model calibration, a J 2 plasticity model with a microstructural BCJ failure model is employed to model the test specimen made of 304L stainless steel. Simulated results are verified and validated through mesh and mass-scaling convergence studies, parameter sensitivity studies, and a comparison to experimental data. The converged mesh and degree of mass-scaling are the mesh discretization with 140,372 elements, and a mass scaling with a target time increment of 1.0e-6 seconds and time step scale factor of 0.5, respectively. Results from the coupled thermal-mechanical explicit dynamic analysis are comparable to the experimental data. Simulated global force vs displacement (F/D) response predicts key points such as yield, ultimate, and kinks of the experimental F/D response. Furthermore, the final deformed shape of the can and field data predicted from the analysis are similar to that of the deformed can, as measured by 3D optical CMM scans and DIC data from the experiment.

36 MATERIALS SCIENCE↗

Arboreal Epiphytes in the Soil-Atmosphere Interface: How Often Are the Biggest “Buckets” in the Canopy Empty?

Arboreal epiphytes (plants residing in forest canopies) are present across all major climate zones and play important roles in forest biogeochemistry. The substantial water storage capacity per unit area of the epiphyte “bucket” is a key attribute underlying their capability to influence forest hydrological processes and their related mass and energy flows. It is commonly assumed that the epiphyte bucket remains saturated, or near-saturated, most of the time; thus, epiphytes (particularly vascular epiphytes) can store little precipitation, limiting their impact on the forest canopy water budget. We present evidence that contradicts this common assumption from (i) an examination of past research; (ii) new datasets on vascular epiphyte and epi-soil water relations at a tropical montane cloud forest (Monteverde, Costa Rica); and (iii) a global evaluation of non-vascular epiphyte saturation state using a process-based vegetation model, LiBry. All analyses found that the external and internal water storage capacity of epiphyte communities is highly dynamic and frequently available to intercept precipitation. Globally, non-vascular epiphytes spend <20% of their time near saturation and regionally, including the humid tropics, model results found that non-vascular epiphytes spend ~1/3 of their time in the dry state (0–10% of water storage capacity). Even data from Costa Rican cloud forest sites found the epiphyte community was saturated only 1/3 of the time and that internal leaf water storage was temporally dynamic enough to aid in precipitation interception. Analysis of the epi-soils associated with epiphytes further revealed the extent to which the epiphyte bucket emptied—as even the canopy soils were often <50% saturated (29–53% of all days observed). Results clearly show that the epiphyte bucket is more dynamic than currently assumed, meriting further research on epiphyte roles in precipitation interception, redistribution to the surface and chemical composition of “net” precipitation waters reaching the surface.

Hargis, Hailey↗

Predicting Initial Trans-Membrane Pressure for Optimized Operations in UF Unit Using Random Forest

With the growing scarcity of freshwater, innovative process design mechanisms like Reverse Osmosis (RO) are increasingly gaining attention among water treatment utilities to address the rising demand. Ensuring reliable water production necessitates efficient resource utilization, minimizing downtime in (ultra-filtration) UF systems. Recent advancements in machine learning (ML) have enabled the development of accurate data-driven models for Model Predictive Control (MPC), often requiring minimal prior knowledge of underlying physical processes. In this study, we present predictive regression models based on Random Forest (RF) and Auto-Regressive (AR) approaches to forecast the initial Trans-Membrane Pressure (TMP) for each filtration cycle in data generated by Direct Potable Reuse (DPR) systems. The proposed RF-based model demonstrates superior performance compared to baseline methods, including historical mean, Last Observation Carried Forward (LOCF), and naïve AR models, across various forecasting horizons in terms of root mean square error (RMSE) metric. To evaluate how different classes of process variables contribute to TMP dynamics over time, we examine the feature importance of independent covariates across multiple forecast horizons. This analysis provides insight into the temporal relevance of operational and sensor-derived features, guiding control and monitoring strategies. Additionally, the impact of hyperparameter tuning on TMP prediction performance is studied for both direct and recursive RF modelling approaches across increasing forecast horizons. Accurate prediction of initial TMP is critical for optimizing RO operations, as it enables the development of robust modelling frameworks by accurately estimating membrane fouling trends, thereby enhancing process efficiency and long-term reliability. The demonstrated efficacy of the RF-based approach highlights its potential as a tool for real-time decision-making in water treatment systems, paving the way for advanced process optimization and sustainable water resource management.

Mukherjee, Subrata [ORNL] (ORCID:0000000309930338)↗

Dispatchable Virtual Oscillator Control for Decentralized Inverter-Dominated Power Systems: Analysis and Experiments: Preprint

This paper presents an analysis and experimental validation of dispatchable virtual oscillator control (dVOC) for inverter-dominated power systems. dVOC is a promising decentralized control strategy that requires only local measurements to induce grid-forming behavior with programmable droop characteristics. It is dispatchable -- i.e., the inverters can vary their power generation via user-defined power set-points and guarantees strong stability. To verify its feasibility, a testbed comprising multiple dVOC-programmed inverters with transmission line impedances is designed. With an embedded synchronization strategy, the dVOC inverters are capable of dynamic synchronization, black start operation, and transient grid voltage regulation with dynamic load sharing, and real-time-programmable droop characteristics for backward compatibility. All these features are experimentally verified.

14 SOLAR ENERGY↗

Modal dynamics of wind turbine wake meandering from lidar observations

Horizontal scans from nacelle-mounted lidars provide time series measurements of wind turbine wakes across diverse atmospheric conditions, enabling analysis of coherent turbulent structures that influence wake meandering through proper orthogonal decomposition (POD). While low-order modes capture the most energetic turbulent structures, our analysis reveals that they do not necessarily dominate wake meandering dynamics. We evaluate more than 16,000 combinatorial reconstructions of the flow field for each inflow case, demonstrating that mode relevance depends on mode symmetry, turbulent kinetic energy content, and inflow characteristics. Cases with low turbulence intensity and large integral timescales show stronger correlations between POD modes and wake meandering, whereas higher turbulence conditions (turbulence intensity > 7%) are less effectively described by reduced-order models. However, the qualitative similarity of POD modes across varied atmospheric conditions suggests the potential existence of a semi-universal basis for representing wind turbine wakes, with implications for improving engineering wake models.

17 WIND ENERGY↗

A hierarchical gray-box dynamic modeling methodology for direct-expansion cooling systems to support control stability analysis; Méthodologie de modélisation dynamique hiérarchique de type boîte grise pour les systèmes de refroidissement à détente directe afin de soutenir l'analyse de stabilité de la commande

In this paper, a gray-box dynamic modeling approach for direct-expansion cooling systems is presented. The overall approach incorporates a multi-stage training procedure that consists of 1) identification of component sub-models from quasi-steady-state performance data, 2) system model integration with estimation of refrigerant charge and 3) fine tuning of thermal capacitances of the evaporator and condenser to capture the system dynamic responses. Compared to traditional physics-based models, the proposed modeling approach has advantages including reduced engineering efforts in the model development phase, improved computational efficiency and enhanced prediction accuracy. The modeling method was validated using a 3-ton variable-speed heat pump and proved to be capable of accurately predicting the system transient behaviors over a wide range of operating conditions. The established dynamic model was then applied for control stability analysis, with a specific goal of determining a proper control execution time step. The case study results showed that the stable control execution time step could change significantly, from 3 sec to 19 sec, as the operating conditions and control settings vary, and a proper selection of the execution time step is critical to ensure stable and reliable operations.

42 ENGINEERING↗

Phase-Space Detection of Cyber Events

Energy Delivery Systems (EDS) are a network of processes that produce, transfer and distribute energy. EDS are increasingly dependent on networked computing assets, as are many Industrial Control Systems. Consequently, cyber-attacks pose a real and pertinent threat, as evidenced by Stuxnet, Shamoon and Dragonfly. Hence, there is a critical need for novel methods to detect, prevent, and mitigate effects of such attacks. To detect cyber-attacks in EDS, we developed a framework for gathering and analyzing timing data that involves establishing a baseline execution profile and then capturing the effect of perturbations in the state from injecting various malware. The data analysis was based on nonlinear dynamics and graph theory to improve detection of anomalous events in cyber applications. The goal was the extraction of changing dynamics or anomalous activity in the underlying computer system. Takens' theorem in nonlinear dynamics allows reconstruction of topologically invariant, time-delay-embedding states from the computer data in a sufficiently high-dimensional space. The resultant dynamical states were nodes, and the state-to-state transitions were links in a mathematical graph. Alternatively, sequential tabulation of executing instructions provides the nodes with corresponding instruction-to-instruction links. Graph theorems guarantee graph-invariant measures to quantify the dynamical changes in the running applications. Results showed a successful detection of cyber events.

cyber anomaly detection↗

Systematic characterization of unknown compounds via dimensionality reduction of time series

Analysis of ambient aerosols provides valuable insight into particle sources and formation chemistry. However, due to the complexity of atmospheric data and the dynamic nature of aerosol composition, a substantial fraction of data often become discarded by conventional analysis methods. Furthermore, a large fraction of chemical species within those data are unidentifiable due to a lack of matching spectral information, resulting in suboptimal characterization of chemical composition. Previous work has demonstrated techniques for cataloging analytes in a chromatographic dataset by deconvolution of mass spectra, but integration of these analytes throughout a large dataset remains time consuming. Here, we present a method to automatically identify an ion for quantitation for single-ion chromatogram based peak fitting and integration, enabling comprehensive integration of analytes with minimal user interaction. The resulting time series are clustered with a machine-learning based dimensionality reduction technique to systematically investigate the underlying characteristics of the categorized analytes and gain new insights into the chemical composition and physicochemical properties of the unidentifiable analytes. We apply these methods to existing atmospheric datasets collected in Manacapuru, Brazil during the GoAmazon2014/5 campaign to identify new analytes and interpret their variability and transformations in the atmosphere. The analysis results generate 408 time series from cataloged analytes of interest, and the clustering of those time series with spherical k-means results in 8 distinct clusters. We find the analytes form clusters based on their distinct physicochemical properties, demonstrating the method’s ability to systematically identify and selectively filter contaminants and instrumental analytes and characterize the unidentifiable analytes.

54 ENVIRONMENTAL SCIENCES↗

Characterization of multielectron dynamics in molecules: A multiconfiguration time-dependent Hartree-Fock picture

Using the framework of multiconfiguration theory, where the wavefunction Φ(t) of a many-electron system at time t is expanded as Φ(t)=∑{sub I}C{sub I}(t)Φ{sub I}(t) in terms of electron configurations (Φ{sub I}(t)), we divided the total electronic energy E(t) as E(t)=∑{sub I}|C{sub I}(t)|{sup 2}E{sub I}(t) . Here E{sub I}(t) is the instantaneous phase changes of C{sub I}(t) regarded as a configurational energy associated with Φ{sub I}(t). We then newly defined two types of time-dependent states: (i) a state at which the rates of population transfer among configurations are all zero; (ii) a state at which (E{sub I}(t)) associated with the quantum phases of C{sub I}(t) are all the same. We call the former time-dependent state a classical stationary state by analogy with the stationary (steady) states of classical reaction rate equations and the latter one a quantum stationary state. The conditions (i) and (ii) are satisfied simultaneously for the conventional stationary state in quantum mechanics. We numerically found for a LiH molecule interacting with a near-infrared (IR) field ε(t) that the condition (i) is satisfied whenever the average velocity of electrons is zero and the condition (ii) is satisfied whenever the average acceleration is zero. We also derived the chemical potentials μ{sub j}(t) for time-dependent natural orbitals ϕ{sub j}(t) of a many-electron system. The analysis of the electron dynamics of LiH indicated that the temporal change in Δμ{sub j}(t) ≡ μ{sub j}(t) + ε(t) · d{sub j}(t) − μ{sub j}(0) correlates with the motion of the dipole moment of ϕ{sub j}(t), d{sub j}(t). The values Δμ{sub j}(t) are much larger than the energy ζ{sub j}(t) directly supplied to ϕ{sub j}(t) by the field, suggesting that valence electrons exchange energy with inner shell electrons. For H{sub 2} in an intense near-IR field, the ionization efficiency of ϕ{sub j}(t) is correlated with Δμ{sub j}(t). Comparing Δμ{sub j}(t) to ζ{sub j}(t), we found that energy accepting orbitals of Δμ{sub j}(t) > ζ{sub j}(t) indicate high ionization efficiency. The difference between Δμ{sub j}(t) and ζ{sub j}(t) is significantly affected by electron-electron interactions in real time.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗