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At least 487 records · Page 27

SU-D-207A-05: Investigating Sparse-Sampled MRI for Motion Management in Thoracic Radiotherapy

Purpose: Sparse sampling and reconstruction-based MRI techniques represent an attractive strategy to achieve sufficiently high image acquisition speed while maintaining image quality for the task of radiotherapy guidance. In this study, we examine rapid dynamic MRI using a sparse sampling sequence k-t BLAST in capturing motion-induced, cycle-to-cycle variations in tumor position. We investigate the utility of long-term MRI-based motion monitoring as a means of better characterizing respiration-induced tumor motion compared to a single-cycle 4DCT. Methods: An MRI-compatible, programmable, deformable lung motion phantom with eleven 1.5 ml water marker tubes was placed inside a 3.0 T whole-body MR scanner (Philips Ingenia). The phantom was programmed with 10 lung tumor motion traces previously recorded using the Synchrony system. 2D+t image sequences of a coronal slice were acquired using a balanced-SSFP sequence combined with k-t BLAST (accn=3, resolution=0.66×0.66×5 mm3; acquisition time = 110 ms/slice). kV fluoroscopic (ground truth) and 4DCT imaging was performed with the same phantom setup and motion trajectories. Marker positions in all three modalities were segmented and tracked using an opensource deformable image registration package, NiftyReg. Results: Marker trajectories obtained from rapid MRI exhibited <1 mm error compared to kv Fluoro trajectories in the presence of complex motion including baseline shifts and changes in respiratory amplitude, indicating the ability of MRI to monitor motion with adequate geometric fidelity for the purpose of radiotherapy guidance. In contrast, the trajectory derived from 4DCT exhibited significant errors up to 6 mm due to cycle-to-cycle variations and baseline shifts. Consequently, 4DCT was found to underestimate the range of marker motion by as much as 50%. Conclusion: Dynamic MRI is a promising tool for radiotherapy motion management as it permits for longterm, dose-free, soft-tissue-based monitoring of motion, yielding richer and more accurate information about tumor position and motion range compared to the current state-of-the-art, 4DCT. This work was partially supported through research funding from National Institutes of Health (R01CA169102).

60 APPLIED LIFE SCIENCES↗

A slip-spring framework to study relaxation dynamics of entangled wormlike micelles with kinetic Monte Carlo algorithm

Hypothesis: Wormlike micelles (WLMs) formed due to the self-assembly of amphiphiles in aqueous solution have similar viscoelastic properties as polymers. Owing to this similarity, in this work, it is postulated that kinetic Monte Carlo (kMC) sampling of slip-springs dynamics, which is able to model the rheology of polymers, can also be extended to capture the relaxation dynamics of WLMs. Theory: The proposed modeling framework considers the following relaxation mechanisms: reptation, union-scission, and constraint release. Specifically, each of these relaxation mechanisms is simulated as separate kMC events that capture the relaxation dynamics while considering the living nature of WLMs within the slip-spring framework. As a case study, the model is implemented to a system of sodium oleate and sodium chloride to predict the linear rheology and the characteristic relaxation times associated with the individual relaxation mechanisms at different pH and salt concentrations. Findings: Linear rheology predictions were found to be in good agreement with experimental data. Furthermore, the calculated relaxation times highlighted that reptation contributed to a continuous increase in viscosity while union-scission contributed to the decrease in viscosity of WLM solutions at a higher salinity and pH. Finally, this manifests the proposed model’s capability to provide insights into the key processes governing WLM’s rheology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Collective mode Brownian dynamics: A method for fast relaxation of statistical ensembles

Sampling equilibrium configurations of correlated systems of particles with long relaxation times (e.g., polymeric solutions) using conventional molecular dynamics and Monte Carlo methods can be challenging. This is especially true for systems with complicated, extended bond network topologies and other interactions that make the use and design of specialized relaxation protocols infeasible. We introduce a method based on Brownian dynamics simulations that can reduce the computational time it takes to reach equilibrium and draw decorrelated samples. Importantly, the method is completely agnostic to the particle configuration and the specifics of interparticle forces. In particular, we develop a mobility matrix that excites non-local, collective motion of N particles and can be computed efficiently in $\mathcal{O}(N)$ time. Particle motion in this scheme is computed by integrating the overdamped Langevin equation with an Euler–Maruyama scheme, in which Brownian displacements are drawn efficiently using a low-rank representation of the mobility matrix in position and wave space. We demonstrate the efficacy of the method with various examples from the realm of soft condensed matter and release a massively parallel implementation of the code as a plugin for the open-source package HOOMD-blue [J. A. Anderson et al., J. Comput. Phys. 227, 5342 (2008) and J. Glaser et al., Comput. Phys. Commun. 192, 97 (2015)] which runs on graphics processing units

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Probing viscoelastic surfaces with bimodal tapping-mode atomic force microscopy: Underlying physics and observables for a standard linear solid model

This paper presents computational simulations of single-mode and bimodal atomic force microscopy (AFM) with particular focus on the viscoelastic interactions occurring during tip–sample impact. The surface is modeled by using a standard linear solid model, which is the simplest system that can reproduce creep compliance and stress relaxation, which are fundamental behaviors exhibited by viscoelastic surfaces. The relaxation of the surface in combination with the complexities of bimodal tip–sample impacts gives rise to unique dynamic behaviors that have important consequences with regards to the acquisition of quantitative relationships between the sample properties and the AFM observables. The physics of the tip–sample interactions and its effect on the observables are illustrated and discussed, and a brief research outlook on viscoelasticity measurement with intermittent-contact AFM is provided.

36 MATERIALS SCIENCE↗

Pulse measurement apparatus and method

An embodiment of the invention is directed to a pulse measuring system that measures a characteristic of an input pulse under test, particularly the pulse shape of a single-shot, nano-second duration, high shape-contrast optical or electrical pulse. An exemplary system includes a multi-stage, passive pulse replicator, wherein each successive stage introduces a fixed time delay to the input pulse under test, a repetitively-gated electronic sampling apparatus that acquires the pulse train including an entire waveform of each replica pulse, a processor that temporally aligns the replicated pulses, and an averager that temporally averages the replicated pulses to generate the pulse shape of the pulse under test. An embodiment of the invention is directed to a method for measuring an optical or an electrical pulse shape. The method includes the steps of passively replicating the pulse under test with a known time delay, temporally stacking the pulses, and temporally averaging the stacked pulses. An embodiment of the invention is directed to a method for increasing the dynamic range of a pulse measurement by a repetitively-gated electronic sampling device having a rated dynamic range capability, beyond the rated dynamic range of the sampling device; e.g., enhancing the dynamic range of an oscilloscope. The embodied technique can improve the SNR from about 300:1 to 1000:1. A dynamic range enhancement of four to seven bits may be achieved.

47 OTHER INSTRUMENTATION↗

Measurement of Passive Uptake Rates for Volatile Organic Compounds on Commercial Thermal Desorption Tubes and the Effect of Ozone on Sampling

Diffusive or passive sampling methods using commercially filled axial-sampling thermal desorption tubes are widely used for measuring volatile organic compounds (VOCs) in air. The passive sampling method provides a robust, cost effective way to measure air quality with time-averaged concentrations spanning up to a week or more. Sampling rates for VOCs can be calculated using tube geometry and Fick’s Law for ideal diffusion behavior or measured experimentally. There is evidence that uptake rates deviate from ideal and may not be constant over time. Therefore, experimentally measured sampling rates are preferred. In this project, a calibration chamber with a continuous stirred tank reactor design and constant VOC source was combined with active sampling to generate a controlled dynamic calibration environment for passive samplers. The chamber air was augmented with a continuous source of 45 VOCs ranging from pentane to diethyl phthalate representing a variety of chemical classes and physiochemical properties. Both passive and active samples were collected on commercially filled Tenax TA thermal desorption tubes over an 11-day period and used to calculate passive sampling rates. A second experiment was designed to determine the impact of ozone on passive sampling by using the calibration chamber to passively load five terpenes on a set of Tenax tubes and then exposing the tubes to different ozone environments with and without ozone scrubbers attached to the tube inlet. During the sampling rate experiment, the measured diffusive uptake was constant for up to seven days for most of the VOCs tested but deviated from linearity for some of the more volatile compounds between seven and eleven days. In the ozone experiment, both exposed and unexposed tubes showed a similar decline in terpene mass over time indicating back diffusion when uncapped tubes were transferred to a clean environment but there was no indication of significant loss by ozone reaction.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Solvent Dynamics Are Critical to Understanding Carbon Dioxide Dissolution and Hydration in Water

Simulations of carbon dioxide (CO 2 ) in water may aid in understanding the impact of its accumulation in aquatic environments and help advance technologies for carbon capture and utilization (via, e.g., mineralization). Quantum mechanical (QM) simulations based on static molecular models with polarizable continuum solvation poorly reproduce the energetics of CO 2 hydration to form carbonic acid in water, independent of the level of QM theory employed. Only with density-functional-theory-based molecular dynamics and rare-event sampling, followed by energy corrections based on embedded correlated wavefunction theory (in conjunction with density functional embedding theory), can a close agreement between theory and experiment be achieved. Such multilevel simulations can serve as benchmarks for simpler, less costly models, giving insight into potential errors of the latter. The strong influence of sampling/averaging over dynamical solvent configurations on the energetics stems from the difference in polarity of both the transition state and product (both polar) versus the reactant (nonpolar). When a solute undergoes a change in polarity during reaction, affecting its interaction with the solvent, careful assessment of the energetic contribution of the solvent response to this change is critical. Here, we show that static models (without structural sampling) that incorporate three explicit water molecules can yield far superior results than models with more explicit water molecules because fewer water molecules yield less configurational artifacts. Static models intelligently incorporating both explicit (molecules directly participating in the reaction) and implicit solvation, along with a proper QM theory, e.g., CCSD(T) for closed-shell systems, can close the accuracy gap between static and dynamic models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Size and shape fluctuations of ultrasoft colloids

An ultrasoft colloidal particle fluctuates due to its flexibility. Such fluctuation is essential for colloidal structure and dynamics, but is challenging to quantify experimentally. We use dendrimers as a model system to study the fluctuation of ultrasoft colloids. By considering the dynamic polydispersity in the small-angle neutron scattering (SANS) model and introducing the fluctuation of invasive water into the contrast in SANS, we reveal the fluctuating amplitudes of the size and shape of the dendrimer of generation 6 at finite concentrations. The size fluctuation is suppressed while the shape fluctuation increases as the weight fraction of dendrimers passes 11%. With neutron spin echo data, we suggest that such a crossover originates from the competition between the inter- and intraparticle dynamics. Further investigation on lower-generation samples shows a contrary result, which suggests a structural basis for these dynamic phenomena.

42 ENGINEERING↗

Comparison of greenhouse gas emission estimates from six hydropower reservoirs using modeling versus field surveys

As with most aquatic ecosystems, reservoirs play an important role in the global carbon (C) cycle and emit greenhouse gases (GHG) as carbon dioxide (CO 2 ) and methane (CH 4 ). However, GHG emissions from reservoirs are poorly quantified, especially in temperate systems, resulting in high uncertainty. We compared reservoir C emission estimates and uncertainty of diffusive, ebullitive, and degassing pathways in six hydropower reservoirs in the southeastern United States among four data sources: two field-based surveys and two models (including the GHG Reservoir “G-res” Tool). We found that CH 4 diffusion was most similar across data sources (modeled minus observed, bias = - 21 g CO 2-eq m -2 y -1 ) and had low relative uncertainty (coefficient of variation, CV = 0.98). On the other hand, CO 2 diffusion was least consistent across data sources (bias = - 518 g CO 2-eq m -2 y -1 ). Both field surveys indicated strong negative CO 2 diffusion (i.e., CO 2 uptake) at all reservoirs, while G-res estimated positive CO 2 diffusion. By extension, total C emissions showed similar discrepancies, leading to high uncertainty in upscaling and interpreting reservoir source-sink dynamics. Finally, CH 4 ebullition had the highest relative uncertainty (CV = 2.77) due to high variability across sites. We discuss limitations of field surveys and these models, including temperature-based annualization methods, varying definitions of ebullition zones, low sampling resolution, and lack of dynamism. Future field efforts focused on capturing variability in CO 2 diffusion and CH 4 ebullition will be especially valuable in reducing uncertainty and improving models to advance our understanding reservoir GHG emissions.

54 ENVIRONMENTAL SCIENCES↗

Non-equilibrium approach to prediction of microstructure evolution for metals undergoing severe plastic deformation

Highlights: • New consistent physically-based model of dynamic recrystallization. • The model is based on evolution of fraction of high-angle grain boundaries. • Possibility to predict the evolution of dislocation cells and grain boundaries. • The model is implemented for FEM simulations. • Results demonstrate inhomogeneous distribution of strain within the sample. - Abstract: Available models of dynamic recrystallization have a number of disadvantages that in most cases make them inapplicable for practical predictions of material microstructure evolution. Both the microstructural and the empirically based approaches do not reflect physical processes leading to evolution of material defect structure in the process of plastic deformation. This work presents an attempt to develop a consistent physically-based model of dynamic recrystallization. This model, accounting for physical nature of processes of material defect structure evolution, should provide a possibility to predict evolution of several different experimentally measurable parameters of material microstructure without introduction of big number of fitting parameters. It is suggested that such a model should be based on equation for evolution of fraction of high-angle grain boundaries (HAGBs) in the process of deformation. It is shown, that the new model gives a possibility to predict the evolution of dislocation cells and grain boundaries in copper-based alloys providing good coincidence with experimental observations. Full 3-dimensional numerical simulation of multidirectional forging of copper is performed utilizing the developed dynamic recrystallization model. The same 3D simulations demonstrate new noteworthy effects connected to inhomogeneous distribution of plastic strain within the bulk of the material and material strain hardening.

36 MATERIALS SCIENCE↗

Chapter 4.2 - Preparation of nanoparticles for surface analysis

A variety of methods used to prepare nano-objects for surface analysis are described along with information about when they might be best applied. Intrinsic properties of NPs that complicate their characterization and need to be considered when planning for surface or other analyses of NPs are identified, including challenges associated with reproducible synthesis and functionalization of the particles as well as their dynamic nature. Information about the sample preparation processes, along with analysis data, that need to be added to the collection of material provenance information is identified and examples of protocols that have been successfully used for preparation of nano-objects for surface analysis are included in an annex.

characterization challenges↗

Induced polarization restricts the conformational distribution of a light-harvesting molecular triad in the ground state

The light-harvesting molecular triad consisting of carotenoid polyene (C), diaryl-porphyrin (P) and pyrrole-fullerene (C60) is a donor–acceptor molecule capable of absorbing incident light in the visible range. Its ability to convert solar energy to electrical excitation and charge separation energy suggests a great potential in real-world applications. The ensemble of its conformations under ambient conditions varies widely according to its electronic state. In previous work, we applied a non-polarizable model to study the conformational distribution of the molecular triad in the ground and charge separated states. However, due to the lack of polarization, which imparts subtle changes in the charge distribution on atoms, molecular simulations fail to produce accurate average dipole moments. We developed the first polarizable model for a molecular triad to investigate the structural and dynamic properties of a molecular triad in the ground state in an explicit organic solvent, tetrahydrofuran (THF). We performed first-principles electronic structure calculations of the individual components in the triad as well as THF and then fit the partial atomic charges to the electrostatic potential using the i-RESP methodology. We validated these force field parameters by comparing the thermodynamic and dynamic properties obtained from molecular dynamics simulations with those from experiments. We enhanced the sampling of the triad conformations with replica exchange molecular dynamics simulations. We characterized the effects of induced polarization on the structural stability of the triad by analyzing the free energy landscapes constructed with polarizable force fields. Furthermore, by using principal component analysis, we found that the molecular triad conformations adopted a small range of torsional angles with induced polarization. The triad conformation solvated in polar solvent with a polarizable force field qualitatively agrees with that obtained from nuclear magnetic resonance spectroscopy.

Starovoytov, Oleg N.↗

Coherent diffractive imaging of time-evolving samples with improved temporal resolution

Bragg coherent x-ray diffractive imaging is a powerful technique for investigating dynamic nanoscale processes in nanoparticles immersed in reactive, realistic environments. Its temporal resolution is limited, however, by the oversampling requirements of three-dimensional phase retrieval. Here, we show that incorporating the entire measurement time series, which is typically a continuous physical process, into phase retrieval allows the oversampling requirement at each time step to be reduced, leading to a subsequent improvement in the temporal resolution by a factor of 2-20 times. The increased time resolution will allow imaging of faster dynamics and of radiation-dose-sensitive samples. Furthermore, this approach, which we call "chrono CDI," may find use in improving the time resolution in other imaging techniques.

36 MATERIALS SCIENCE↗

Simulated XUV photoelectron spectra of THz-pumped liquid water

Highly intense, sub-picosecond terahertz (THz) pulses can be used to induce ultrafast temperature jumps (T-jumps) in liquid water. A supercritical state of gas-like water with liquid density is established, and the accompanying structural changes are expected to give rise to time-dependent chemical shifts. We investigate the possibility of using extreme ultraviolet photoelectron spectroscopy as a probe for ultrafast dynamics induced by sub-picosecond THz pulses of varying intensities and frequencies. To this end, we use ab initio methods to calculate photoionization cross sections and photoelectron energies of (H 2 O) 20 clusters embedded in an aqueous environment represented by point charges. The cluster geometries are sampled from ab initio molecular dynamics simulations modeling the THz-water interactions. Here we find that the peaks in the valence photoelectron spectrum are shifted by up to 0.4 eV after the pump pulse and that they are broadened with respect to unheated water. The shifts can be connected to structural changes caused by the heating, but due to saturation effects they are not sensitive enough to serve as a thermometer for T-jumped water.

74 ATOMIC AND MOLECULAR PHYSICS↗

Estimating groundwater dynamics at a Colorado River floodplain site using historical hydrological data and climate information

Long-term prediction of groundwater dynamics is important for assessing water resources and their impacts on biogeochemical cycling. However, estimating future groundwater dynamics is challenging due to the wide range of spatiotemporal scales in hydrological processes and uncertainty in future climate conditions. In this study, we develop a Bayesian model to combine small-scale historical hydrological data with large-scale climate information to estimate groundwater dynamics at a floodplain site in Rifle, Colorado. Although we have only a few years of groundwater elevation measurements, we have 47 years of streamflow data from a gaging station approximately 43 km upstream and long-term climate prediction on the Upper Colorado River Basin. To estimate future daily groundwater dynamics, we first develop a time series model to downscale the monthly streamflow derived from climate information to daily streamflow, and then transform the daily streamflow to groundwater dynamics at the downstream floodplain site. We use Monte Carlo methods to estimate future groundwater dynamics at the site through sampling from the joint posterior probability distribution. The results suggest that although future groundwater levels are expected to be similar to the current levels, the timing of the high groundwater levels is predicted to occur about 1 month earlier. The developed framework is extendable to other sites to estimate future groundwater dynamics given disparate data sets and climate projections. Additionally, the obtained estimates are being used as input to a site-specific watershed reactive transport models to predict how climate-induced changes will influence future biogeochemical cycling relevant to a variety of ecosystem services.

58 GEOSCIENCES↗

Restoring the discontinuous heat equation source using sparse boundary data and dynamic sensors

Abstract This study focuses on addressing the inverse source problem associated with the parabolic equation. We rely on sparse boundary flux data as our measurements, which are acquired from a restricted section of the boundary. While it has been established that utilizing sparse boundary flux data can enable source recovery, the presence of a limited number of observation sensors poses a challenge for accurately tracing the inverse quantity of interest. To overcome this limitation, we introduce a sampling algorithm grounded in Langevin dynamics that incorporates dynamic sensors to capture the flux information. Furthermore, we propose and discuss two distinct dynamic sensor migration strategies. Remarkably, our findings demonstrate that even with only two observation sensors at our disposal, it remains feasible to successfully reconstruct the high-dimensional unknown parameters.

Mathematics↗

Hot-carrier dynamics in InAs/AlAsSb multiple-quantum wells

A type-II InAs/AlAs 0.16 Sb 0.84 multiple-quantum well sample is investigated for the photoexcited carrier dynamics as a function of excitation photon energy and lattice temperature. Time-resolved measurements are performed using a near-infrared pump pulse, with photon energies near to and above the band gap, probed with a terahertz probe pulse. The transient terahertz absorption is characterized by a multi-rise, multi-decay function that captures long-lived decay times and a metastable state for an excess-photon energy of >100 meV. For sufficient excess-photon energy, excitation of the metastable state is followed by a transition to the long-lived states. Excitation dependence of the long-lived states map onto a nearly-direct band gap (E g ) density of states with an Urbach tail below E g . As temperature increases, the long-lived decay times increase < E g , due to the increased phonon interaction of the unintentional defect states, and by phonon stabilization of the hot carriers > E g . Additionally, Auger (and/or trap-assisted Auger) scattering above the onset of the plateau may also contribute to longer hot-carrier lifetimes. Meanwhile, the initial decay component shows strong dependence on excitation energy and temperature, reflecting the complicated initial transfer of energy between valence-band and defect states, indicating methods to further prolong hot carriers for technological applications.

14 SOLAR ENERGY↗

PLASTIC BEHAVIOR OF POLYCRYSTALLINE TANTALUM IN THE 5 x 10^7/s REGIME

The goal of this experiment is to investigate the plastic response of Tantalum to dynamic loading at high strain rates. The samples used were derived from high purity rolled plate, polished down to thicknesses in the range 25-100 {micro}m. Dynamic loading was applied by direct laser ablation of the sample, with pulses up to 10 ns long, at the Jupiter Laser Facility. The elastic-plastic wave structure was measured using two line VISAR systems of different sensitivity, and strain rates were inferred from the rise time of the waves. The elastic wave amplitudes indicated flow stresses between 2 and 3 GPa, depending on the sample thickness. Samples were recovered for post-shot metallographic analysis.

36 MATERIALS SCIENCE↗