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At least 973 records · Page 54

Recovering hidden dynamical modes from the generalized Langevin equation

In studying large molecular systems, insights can better be extracted by selecting a limited number of physical quantities for analysis rather than treating every atomic coordinate in detail. Some information may, however, be lost by projecting the total system onto a small number of coordinates. For such problems, the generalized Langevin equation (GLE) is shown to provide a useful framework to examine the interaction between the observed variables and their environment. Starting with the GLE obtained from the time series of the observed quantity, we perform a transformation to introduce a set of variables that describe dynamical modes existing in the environment. The introduced variables are shown to effectively recover the essential information of the total system that appeared to be lost by the projection.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dynamical origin of near- and below-threshold harmonic generation of Cs in an intense mid-infrared laser field

Near- and below-threshold harmonic generation provides a potential approach to generate vacuum-ultraviolet frequency comb. However, the dynamical origin of in these lower harmonics is less understood and largely unexplored. Here we perform an ab initio quantum study of the near- and below-threshold harmonic generation of caesium (Cs) atoms in an intense 3,600-nm mid-infrared laser field. Combining with a synchrosqueezing transform of the quantum time-frequency spectrum and an extended semiclassical analysis, the roles of multiphoton and multiple rescattering trajectories on the near- and below-threshold harmonic generation processes are clarified. We find that the multiphoton-dominated trajectories only involve the electrons scattered off the higher part of the combined atom-field potential followed by the absorption of many photons in near- and below-threshold regime. Furthermore, only the near-resonant below-threshold harmonic is exclusive to exhibit phase locked features. Our results shed light on the dynamic origin of the near- and below-threshold harmonic generation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Jet formation in cerium metal to examine material strength

Examining the evolution of material properties at extreme conditions advances our understanding of numerous high-pressure phenomena from natural events like meteorite impacts to general solid mechanics and fluid flow behavior. Recent advances in synchrotron diagnostics coupled with dynamic compression platforms have introduced new possibilities for examining in-situ, spatially resolved material response with nanosecond time resolution. In this work, we examined jet formation from a Richtmyer-Meshkov instability in cerium initially shocked into a transient, high-pressure phase, and then released to a low-pressure, higher-temperature state. Cerium's rich phase diagram allows us to study the yield stress following a shock induced solid-solid phase transition. X-ray imaging was used to obtain images of jet formation and evolution with 2–3 μm spatial resolution. From these images, an analytic method was used to estimate the post-shock yield stress, and these results were compared to continuum calculations that incorporated an experimentally validated equation-of-state (EOS) for cerium coupled with a deviatoric strength model. Reasonable agreement was observed between the calculations and the data illustrating the sensitivity of jet formation on the yield stress values. The data and analysis shown here provide insight into material strength during dynamic loading which is expected to aid in the development of strength aware multi-phase EOS required to predict the response of matter at extreme conditions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Analysis of current-driven oscillatory dynamics of single-layer homoepitaxial islands on crystalline conducting substrates

Here we report results of a systematic study on the complex oscillatory current-driven dynamics of single-layer homoepitaxial islands on crystalline substrate surfaces and the dependence of this driven dynamical behavior on important physical parameters, including island size, substrate surface orientation, and direction of externally applied electric field. The analysis is based on a nonlinear model of driven island edge morphological evolution that accounts for curvature-driven edge diffusion, edge electromigration, and edge diffusional anisotropy. Using a linear theory of island edge morphological stability, we calculate a critical island size at which the island’s equilibrium edge shape becomes unstable, which sets a lower bound for the onset of time-periodic oscillatory dynamical response. Using direct dynamical simulations, we study the edge morphological dynamics of current-driven single-layer islands at larger-than-critical size, and determine the actual island size at which the migrating islands undergo a transition from steady to time-periodic asymptotic states through a subcritical Hopf bifurcation. At the highest symmetry of diffusional anisotropy examined, on {111} surfaces of face-centered cubic crystalline substrates, we find that more complex stable oscillatory states can be reached through period-doubling bifurcation at island sizes larger than those at the Hopf points. We characterize in detail the island morphology and dynamical response at the stable time-periodic asymptotic states, determine the range of stability of these oscillatory states terminated by island breakup, and explain the morphological features of the stable oscillating islands on the basis of linear stability theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DeepLearnMOR: a deep-learning framework for fluorescence image-based classification of organelle morphology

Abstract The proper biogenesis, morphogenesis, and dynamics of subcellular organelles are essential to their metabolic functions. Conventional techniques for identifying, classifying, and quantifying abnormalities in organelle morphology are largely manual and time-consuming, and require specific expertise. Deep learning has the potential to revolutionize image-based screens by greatly improving their scope, speed, and efficiency. Here, we used transfer learning and a convolutional neural network (CNN) to analyze over 47,000 confocal microscopy images from Arabidopsis wild-type and mutant plants with abnormal division of one of three essential energy organelles: chloroplasts, mitochondria, or peroxisomes. We have built a deep-learning framework, DeepLearnMOR (Deep Learning of the Morphology of Organelles), which can rapidly classify image categories and identify abnormalities in organelle morphology with over 97% accuracy. Feature visualization analysis identified important features used by the CNN to predict morphological abnormalities, and visual clues helped to better understand the decision-making process, thereby validating the reliability and interpretability of the neural network. This framework establishes a foundation for future larger-scale research with broader scopes and greater data set diversity and heterogeneity.

Plant Sciences↗

Enhanced PDV waveform search and analysis method using parallel circular-convolution / cross-correlation for improved dynamic surface velocity extraction [Poster]

Previous work on exhaustive search methodologies for extracting best-match parameters pertaining to dynamic surface quantities from PDV was done by cross-correlating synthetically generated PDV waveforms with observed counterparts using the circular-convolution theorem. This work was further developed into an open-source PDV analysis toolkit called CCPDVANALYSIS which expands upon and enhances the previously tested methods by parallelizing serial algorithmic components and incorporating a comprehensive script library for different flavors of instantaneous frequency functions utilized in generating synthetic PDV waveforms. Results of these enhancements have been shown to markedly decrease execution times of exhaustive search and extraction algorithms and produce improved velocity recoveries for low-velocity and dynamically varying velocity signals. The CCPDVANALYSIS script library demonstrates an advanced method for extracting velocities from low-velocity and non-constant velocity signals further extending and improving the methods beyond capabilities of traditional frequency domain tools.

97 MATHEMATICS AND COMPUTING↗

GenomeGraphR: A user-friendly open-source web application for foodborne pathogen whole genome sequencing data integration, analysis, and visualization

Food safety risk assessments and large-scale epidemiological investigations have the potential to provide better and new types of information when whole genome sequence (WGS) data are effectively integrated. Today, the NCBI Pathogen Detection database WGS collections have grown significantly through improvements in technology, coordination, and collaboration, such as the GenomeTrakr and PulseNet networks. However, high-quality genomic data is not often coupled with high-quality epidemiological or food chain metadata. We have created a set of tools for cleaning, curation, integration, analysis and visualization of microbial genome sequencing data. It has been tested using Salmonella enterica and Listeria monocytogenes data sets provided by NCBI Pathogen Detection (160,000 sequenced isolates in 2018). GenomeGraphR presents foodborne pathogen WGS data and associated curated metadata in a user-friendly interface that allows a user to query a variety of research questions such as, transmission sources and dynamics, global reach, and persistence of genotypes associated with contamination in the food supply and foodborne illness across time or space. The application is freely available (https://fda-riskmodels.foodrisk.org/ genomegraphr/).

60 APPLIED LIFE SCIENCES↗

Analysis of operator splitting errors for near-limit flame simulations

High-fidelity simulations of ignition, extinction and oscillatory combustion processes are of practical interest in a broad range of combustion applications. Splitting schemes, widely employed in reactive flow simulations, could fail for stiff reaction–diffusion systems exhibiting near-limit flame phenomena. The present work first employs a model perfectly stirred reactor (PSR) problem with an Arrhenius reaction term and a linear mixing term to study the effects of splitting errors on the near-limit combustion phenomena. Analysis shows that the errors induced by decoupling of the fractional steps may result in unphysical extinction or ignition. The analysis is then extended to the prediction of ignition, extinction and oscillatory combustion in unsteady PSRs of various fuel/air mixtures with a 9-species detailed mechanism for hydrogen oxidation and an 88-species skeletal mechanism for n-heptane oxidation, together with a Jacobian-based analysis for the time scales. The tested schemes include the Strang splitting, the balanced splitting, and a newly developed semi-implicit midpoint method. Results show that the semi-implicit midpoint method can accurately reproduce the dynamics of the near-limit flame phenomena and it is second-order accurate over a wide range of time step size. For the extinction and ignition processes, both the balanced splitting and midpoint method can yield accurate predictions, whereas the Strang splitting can lead to significant shifts on the ignition/extinction processes or even unphysical results. With an enriched H radical source in the inflow stream, a delay of the ignition process and the deviation on the equilibrium temperature are observed for the Strang splitting. On the contrary, the midpoint method that solves reaction and diffusion together matches the fully implicit accurate solution. The balanced splitting predicts the temperature rise correctly but with an over-predicted peak. For the sustainable and decaying oscillatory combustion from cool flames, both the Strang splitting and the midpoint method can successfully capture the dynamic behavior, whereas the balanced splitting scheme results in significant errors.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Magnetism and finite-temperature effects in UZr 2 : A density functional theory analysis

The structure and the thermophysical properties of d-UZr 2 are investigated using 0 K density functional theory and ab initio molecular dynamics (AIMD). Modeling the true paramagnetic state of this intermetallic compound has been challenging using first-principles calculations. For the first time, we find that the generalized gradient approximation method without applying an on-site Coulomb interaction term (Hubbard U) can result in a ground state that is antiferromagnetic (AFM). We believe that this weak AFM ground state is the closest to the real paramagnetic state. We found that structure optimization at finite temperatures using AIMD is necessary to achieve this ground state instead of the non-magnetic and ferromagnetic states previously reported in the literature. Our findings indicate that applying the Hubbard U on uranium f-orbitals in this metallic system is unnecessary and not recommended, as it leads to a large overestimation of the volume and introduces an unphysical strong spin polarization. Finally, our approach results in atomic volume, thermal expansion, and heat capacities that have strong agreement with experiments.

36 MATERIALS SCIENCE↗

A device for volatile organic compound (VOC) analysis from skin using heated dynamic headspace sampling

Abstract Human skin is an important source of volatile organic compounds (VOCs) offering noninvasive methods to gain clinical metabolite information. This work was focused on the development of a skin sampling device based on a dynamic headspace sampling method with the addition of temperature to increase VOC metabolite recovery. The device preconcentrates skin VOC emissions onto a sorbent substrate, which can either be preserved for offline analysis or attached to a real time sensor downstream. In this work, skin VOC samples were analyzed offline using thermal desorption-gas chromatography-mass spectrometry. A list of 10 common skin VOCs was pre-selected to optimize parameters of sampling time, sampling temperature, and sorbent selection. Overall, this study highlights an effective skin VOC sampling technology with a heating dimension (40 °C, rather than 30 °C or no heating) with a sampling time of 15 min (rather than 5 or 30 mins) and onto Tenax TA sorbent (rather than PDMS), which collectively increases the recovery of compounds with lower vapor pressure and decreases the observed variability in skin VOC measurements. Finally, a list of 79 skin VOC compounds were detected and identified within a cohort of 20 young, healthy volunteers.

Biochemistry & Molecular Biology↗

Microscopic theory of onset of decaging and bond-breaking activated dynamics in ultradense fluids with strong short-range attractions

We theoretically study thermally activated “in cage” elementary dynamical processes that precede full structural relaxation in ultra-dense particle liquids interacting via strong short range attractive forces. The analysis is based on a microscopic theory formulated at the particle trajectory level built on the dynamic free energy concept and an explicit treatment of how attractive forces control the formation and lifetime of physical bonds. Mean time scales for bond breaking, the early stage of cage escape, and non-Fickian displacement by a fixed amount are analyzed in the repulsive glass, bonded repulsive (attractive) glass, fluid, and dense gel regimes. The theory predicts a strong length-scale-dependent growth of these time scales with attractive force strength at fixed packing fraction, a much weaker slowing down with density at fixed attraction strength, and a strong decoupling of the shorter bond breaking time with the other two time scales that are controlled mainly by perturbed steric caging. All results are in good accord with simulations, and additional testable predictions are made. In conclusion, the classic statistical mechanical projection approximation of replacing all bare attractive and repulsive forces with a single effective force determined by pair structure incurs major errors for describing processes associated with thermally activated escape from transiently localized states.

36 MATERIALS SCIENCE↗

High-Performance Computing Based EMT Simulation of Large PV or Hybrid PV Plants

Faults in the transmission grid have led to reduced power generation from power electronics resources that are typically not connected to the faulted transmission line. In many of the cases, partial loss of power is observed within the power electronics resources like large photovoltaic (PV) power plants. This phenomena is not captured in existing simulation models and/or simulators. High-fidelity switched system electromagnetic transient (EMT) dynamic models of PV power plants can improve the fidelity of models available for accurate analysis of the impact on PV plants during simulation of faults. However, these models are extremely computationally expensive and take a long time to simulate. Long simulation times limit the ability to use these models as larger regions are studied in EMT simulations with more power electronics resources. In this paper, numerical simulation algorithms are combined with high-performance computing techniques and applied to the high-fidelity switched system EMT model of PV plants. Using these techniques, a speed-up of up to 58x is obtained, while preserving the accuracy of the simulation at greater than 98%.

Debnath, Suman↗

Regional and correlative sweat analysis using high-throughput microfluidic sensing patches toward decoding sweat

Recent technological advancements in wearable sensors have made it easier to detect sweat components, but our limited understanding of sweat restricts its application. A critical bottleneck for temporal and regional sweat analysis is achieving uniform, high-throughput fabrication of sweat sensor components, including microfluidic chip and sensing electrodes. To overcome this challenge, we introduce microfluidic sensing patches mass fabricated via roll-to-roll (R2R) processes. The patch allows sweat capture within a spiral microfluidic for real-time measurement of sweat parameters including [Na + ], [K + ], [glucose], and sweat rate in exercise and chemically induced sweat. The patch is demonstrated for investigating regional sweat composition, predicting whole-body fluid/electrolyte loss during exercise, uncovering relationships between sweat metrics, and tracking glucose dynamics to explore sweat-to-blood correlations in healthy and diabetic individuals. By enabling a comprehensive sweat analysis, the presented device is a crucial tool for advancing sweat testing beyond the research stage for point-of-care medical and athletic applications.

47 OTHER INSTRUMENTATION↗

Block Island Noise Modeling Data

Noise propagation near Block Island was simulated to assess environmental impacts of impact pile driving during wind turbine construction. Computational models complement field-recorded acoustic data, providing insights into sound attenuation, spectral variability, and propagation dynamics. The dataset includes: 1. Propagation Models: Simulated underwater sound fields documenting sound pressure and directional variability across frequency bands and distances. 2. Spectral Analysis (LTSA): Long-term averages and processed outputs calculating acoustic intensity over time. 3. Visualization Files: Graphs, 2D/3D simulation results, and reference calculations used in sound modeling.

17 WIND ENERGY↗

MULTIFRACTAL SOLAR EUV INTENSITY FLUCTUATIONS AND THEIR IMPLICATIONS FOR CORONAL HEATING MODELS

We investigate the scaling properties of the long-range temporal evolution and intermittency of Atmospheric Imaging Assembly/ Solar Dynamics Observatory intensity observations in four solar environments: an active region core, a weak emission region, and two core loops. We use two approaches: the probability distribution function (PDF) of time series increments and multifractal detrended fluctuation analysis (MF-DFA). Noise taints the results, so we focus on the 171 Å waveband, which has the highest signal-to-noise ratio. The lags between pairs of wavebands distinguish between coronal versus transition region (TR) emission. In all physical regions studied, scaling in the range of 15–45 minutes is multifractal, and the time series are anti-persistent on average. The degree of anti-correlation in the TR time series is greater than that for coronal emission. The multifractality stems from long-term correlations in the data rather than the wide distribution of intensities. Observations in the 335 Å waveband can be described in terms of a multifractal with added noise. The multiscaling of the extreme-ultraviolet data agrees qualitatively with the radiance from a phenomenological model of impulsive bursts plus noise, and also from ohmic dissipation in a reduced magnetohydrodynamic model for coronal loop heating. The parameter space must be further explored to seek quantitative agreement. Thus, the observational “signatures” obtained by the combined tests of the PDF of increments and the MF-DFA offer strong constraints that can systematically discriminate among models for coronal heating.

79 ASTRONOMY AND ASTROPHYSICS↗

3D multi-system Bayesian calibration with energy conservation to study rapidity-dependent dynamics of nuclear collisions

Considerable information about the early-stage dynamics of heavy ion collisions is encoded in the rapidity dependence of measurements. To leverage the large amount of experimental data, we perform a systematic analysis using three-dimensional hydrodynamic simulations of multiple collision systems — large and small, symmetric and asymmetric. Specifically, we perform fully 3D multi-stage hydrodynamic simulations initialized by a parameterized model for rapidity-dependent energy deposition, which we calibrate on the hadron multiplicity and anisotropic flow coefficients. We utilize Bayesian inference to constrain properties of the early- and late-time dynamics of the system, and highlight the impact of enforcing global energy conservation in our 3D model.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Simulation-Based Recovery Action Analysis Using the EMRALD Dynamic Risk Assessment Tool

A recovery action is defined as the action that prevents deviant conditions from producing unwanted effects. It generally indicates a kind of countermeasure performed in response to a failure of human action. The recovery actions especially play an important role in complex systems like nuclear power plants (NPPs), which consist of highly sophisticated controllers to ensure that desired performance and safety must be achieved and maintained. This is because a combination of human error and its recovery failure may be able to cause a catastrophic effect on a system. Analyzing recovery actions has been a critical part of HRA, which is a technique to evaluate human errors and provide human error probabilities (HEPs) for application in probabilistic safety assessment (PSA). If recovery actions are not adequately analyzed and applied to PSA models, the PSA results may be under-estimated or be not able to reasonably account for the failure of human actions in the context of PSA. For this reason, some regulatory documents such as ASME/ANS RA-Sb-2013 by the American Society for Mechanical Engineers and the American Nuclear Society and NUREG-1792 by U.S. Nuclear Regulatory Commission have emphasized the importance of recovery analysis within the HRA. A couple of existing HRA methods, such as the Technique for Human Error-Rate Prediction (THERP), the Cause-Based Decision Tree (CBDT), and the Korean Standard HRA (K-HRA), have respectively suggested their own approaches to the HRA recovery analysis. However, there are a couple of limitations to treating recovery actions using only the current HRA methods available. The biggest limitation is that the existing recovery analysis does not explicitly consider a variety of recovery action types and recovery sequences as they occur in actual NPPs. To handle the limitations of existing recovery analysis, this study proposes a simulation-based recovery analysis method using the Event Modeling Risk Assessment Using Linked Diagram (EMRALD) software. The EMRALD software is a dynamic simulation tool for PSA. It supports realistic and dynamic modeling of human actions as they would be performed at NPPs. It is also favorable to simultaneously model the specific moment at which an action is performed, the time it takes to perform the action, and the failure probability of that action. In this paper, a detailed methodology for modeling recovery actions in the simulation platform is proposed with a couple of examples. Then, outputs from the simulation are discussed as reviewing if this novel approach can complement the challenges of existing recovery analyses.

99 GENERAL AND MISCELLANEOUS↗

Real-time neutron multiplicity and source localization for criticality safety during fuel debris removal

Advancing neutron detection and analysis techniques for complex radiation environments is an ongoing focus in nuclear instrumentation and monitoring. This proposal presents research and development of a generalized real-time neutron monitoring and analysis system, applicable to any detector capable of producing time-tagged neutron count data. While the work is demonstrated using the Neutron Multiplication Analysis Detector (NoMAD), a modular 15-tube helium-3 (He-3) array, due to its availability, spatial resolution, and flexible deployment, the methods developed are extensible to other systems, including organic scintillators and fast digital detectors. This research investigates two complementary analytical techniques for real-time characterization of neutron emitting sources: neutron multiplicity estimation based on the Hage-Cifarelli formalism and spatial localization using supervised machine learning applied to spatial count rate patterns. These methods are designed to operate under dynamic, evolving conditions such as fuel debris retrieval or reactor startup, where neutron-emitting material geometries may be partially unknown or changing over time. By integrating statistical neutron emission data with spatial localization, this research aims to develop and evaluate methods for real time neutron monitoring, source characterization, and material verification. Key contributions include implementation of a low-latency data pipeline for continuous neutron multiplicity analysis, development and validation of machine learning models for spatial inference, and experimental evaluation of system performance under variable measurement conditions. The outcomes are intended to support applications in nuclear safeguards, verification, emergency response, and reactor startup.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗