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At least 1,783 records · Page 99
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DOE OSTI2014

Brownian motion of massive skyrmions in magnetic thin films

We report on the thermal effects on the motion of current-driven massive magnetic skyrmions. The reduced equation for the motion of skyrmion has the form of a stochastic generalized Thiele’s equation. We propose an ansatz for the magnetization texture of a non-rigid single skyrmion that depends linearly with the velocity. By using this ansatz it is found that the skyrmion mass tensor is closely related to intrinsic skyrmion parameters, such as Gilbert damping, skyrmion-charge and dissipative force. We have found an exact expression for the average drift velocity as well as the mean-square velocity of the skyrmion. The longitudinal and transverse mobility of skyrmions for small spin-velocity of electrons is also determined and found to be independent of the skyrmion mass.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

The effect of center-of-mass motion on photon statistics

We analyze the photon statistics of a weakly driven cavity quantum electrodynamics system and discuss the effects of photon blockade and photon-induced tunneling by effectively utilizing instead of avoiding the center-of-mass motion of a two-level atom trapped in the cavity. With the resonant interaction between atom, photon and phonon, it is shown that the bunching and anti-bunching of photons can occur with properly driving frequency. Our study shows the influence of the imperfect cooling of atom on the blockade and provides an attempt to take advantage of the center-of-mass motion.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Quantum motion of a point particle in the presence of the Aharonov–Bohm potential in curved space

The nonrelativistic quantum dynamics of a spinless charged particle in the presence of the Aharonov–Bohm potential in curved space is considered. We chose the surface as being a cone defined by a line element in polar coordinates. The geometry of this line element establishes that the motion of the particle can occur on the surface of a cone or an anti-cone. As a consequence of the nontrivial topology of the cone and also because of two-dimensional confinement, the geometric potential should be taken into account. At first, we establish the conditions for the particle describing a circular path in such a context. Because of the presence of the geometric potential, which contains a singular term, we use the self-adjoint extension method in order to describe the dynamics in all space including the singularity. Expressions are obtained for the bound state energies and wave functions. -- Highlights: •Motion of particle under the influence of magnetic field in curved space. •Bound state for Aharonov–Bohm problem. •Particle describing a circular path. •Determination of the self-adjoint extension parameter.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations

Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of {sup 15}N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S{sup 2}) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in a defined hydrated box at neutral pH were conducted and the general order parameters (S{sup 2}) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S{sup 2} values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S{sup 2} parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S{sup 2} calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S{sup 2}) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Theoretical estimate of the effect of thermal agitation on ribosome motion generated by stochastic microswimming

The effect of thermal agitation on ribosome motion is evaluated through the Péclet number, assuming that the ribosome is self-propelled along the mRNA during protein synthesis by a swimming stroke consisting of a cycle of stochastically-generated ribosome configurations involving its two subunits. The ribosome velocity probability distribution function is obtained, giving an approximately normal distribution. Its mean and variance together with an estimate of the in vivo free diffusion coefficient of the ribosome and using only configuration changes of small size, give a Péclet number similar to motor proteins and microorganisms. These results suggest the feasibility of the stochastic microswimming hypothesis to explain ribosome motion. - Highlights: • Hypothesis: the ribosome swims along the mRNA during protein synthesis. • How can withstand the thermal agitation of the particles in the surrounding fluid? • The Péclet number Pe is calculated estimating the in vivo diffusion coefficient. • With small size deformations the ribosome has speeds similar to motor proteins. • Similar Pe values for the ribosome and the motor proteins mean feasible hypothesis.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Three-dimensional phase field sintering simulations accounting for the rigid-body motion of individual grains

Sintering is a widely used powder processing technique in industrial applications. During sintering, atoms migrate to decrease the energy of the system via two main mechanisms: coarsening and densification, both of which lead to significant morphological variation of the sintered microstructure. When simulating sintering dynamics, the phase-field method has been broadly utilized because of its convenience in tracking morphology evolution. When a large number of grains is involved, it is common to use the same order parameter to describe multiple grains that are not in direct contact with one another (in order to reduce the computational memory demands). However, with this treatment it is difficult to handle the rigid-body motion of individual grains during densification. In this work, an implementation scheme is introduced to overcome the challenge of calculating individual particle motion based on existing equations. It uses a grouping algorithm and sets a cutoff radius on each grain for calculating the particle velocity during densification. This method allows for the incorporation of the densification mechanism, which has been commonly ignored in previous work, into phase-field sintering models in three-dimensional simulations with a large number of particles/grains. Moreover, through combination with the smoothed boundary method, material properties of sintered microstructures, such as the effective diffusivity and Young’s modulus, can be calculated during the sintering processes.

36 MATERIALS SCIENCE↗
DOE OSTI2011

Isotoxic Dose Escalation in the Treatment of Lung Cancer by Means of Heterogeneous Dose Distributions in the Presence of Respiratory Motion

Purpose: To test, in the presence of intrafractional respiration movement, a margin recipe valid for a homogeneous and conformal dose distribution and to test whether the use of smaller margins combined with heterogeneous dose distributions allows an isotoxic dose escalation when respiratory motion is considered. Methods and Materials: Twenty-three Stage II-III non-small-cell lung cancer patients underwent four-dimensional computed tomography scanning. The gross tumor volume and clinical target volume (CTV) were outlined in the mid-ventilation phase. The CTV-to-planning target volume (PTV) margin was calculated by use of a standard margin recipe and the patient-specific respiration pattern. Standard three-dimensional treatment plans were generated and recalculated on the remaining respiration phases. The planning was repeated for a CTV-to-PTV margin decreased by 2.5 and 5 mm relative to the initial margin in all directions. Time-averaged dose-volume histograms (four-dimensional dose-volume histograms) were calculated to evaluate the CTV-to-PTV margin. Finally, the dose was escalated in the plans with decreased PTV such that the mean lung dose (predictor of radiation-induced pneumonitis) was equal to mean lung dose in the plan by use of the initially calculated margin. Results: A reduction of the standard margin by 2.5 mm compared with the recipe resulted in too low of a minimum dose for some patients. A combination of dose escalation and use of heterogeneous dose distribution was able to increase the minimum dose to the target by approximately 10% and 20% for a CTV-to-PTV margin reduction of 2.5 mm and 5.0 mm, respectively. Conclusion: The margin recipe is valid for intrafractional respiration-induced tumor motions. It is possible to increase the dose to the target without increased mean lung dose with an inhomogeneous dose distribution.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2012

On-Line Use of Three-Dimensional Marker Trajectory Estimation From Cone-Beam Computed Tomography Projections for Precise Setup in Radiotherapy for Targets With Respiratory Motion

Purpose: To develop and evaluate accurate and objective on-line patient setup based on a novel semiautomatic technique in which three-dimensional marker trajectories were estimated from two-dimensional cone-beam computed tomography (CBCT) projections. Methods and Materials: Seven treatment courses of stereotactic body radiotherapy for liver tumors were delivered in 21 fractions in total to 6 patients by a linear accelerator. Each patient had two to three gold markers implanted close to the tumors. Before treatment, a CBCT scan with approximately 675 two-dimensional projections was acquired during a full gantry rotation. The marker positions were segmented in each projection. From this, the three-dimensional marker trajectories were estimated using a probability based method. The required couch shifts for patient setup were calculated from the mean marker positions along the trajectories. A motion phantom moving with known tumor trajectories was used to examine the accuracy of the method. Trajectory-based setup was retrospectively used off-line for the first five treatment courses (15 fractions) and on-line for the last two treatment courses (6 fractions). Automatic marker segmentation was compared with manual segmentation. The trajectory-based setup was compared with setup based on conventional CBCT guidance on the markers (first 15 fractions). Results: Phantom measurements showed that trajectory-based estimation of the mean marker position was accurate within 0.3 mm. The on-line trajectory-based patient setup was performed within approximately 5 minutes. The automatic marker segmentation agreed with manual segmentation within 0.36 {+-} 0.50 pixels (mean {+-} SD; pixel size, 0.26 mm in isocenter). The accuracy of conventional volumetric CBCT guidance was compromised by motion smearing ({<=}21 mm) that induced an absolute three-dimensional setup error of 1.6 {+-} 0.9 mm (maximum, 3.2) relative to trajectory-based setup. Conclusions: The first on-line clinical use of trajectory estimation from CBCT projections for precise setup in stereotactic body radiotherapy was demonstrated. Uncertainty in the conventional CBCT-based setup procedure was eliminated with the new method.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2013

A Comparison of Amplitude-Based and Phase-Based Positron Emission Tomography Gating Algorithms for Segmentation of Internal Target Volumes of Tumors Subject to Respiratory Motion

Purpose: To quantitatively compare the accuracy of tumor volume segmentation in amplitude-based and phase-based respiratory gating algorithms in respiratory-correlated positron emission tomography (PET). Methods and Materials: List-mode fluorodeoxyglucose-PET data was acquired for 10 patients with a total of 12 fluorodeoxyglucose-avid tumors and 9 lymph nodes. Additionally, a phantom experiment was performed in which 4 plastic butyrate spheres with inner diameters ranging from 1 to 4 cm were imaged as they underwent 1-dimensional motion based on 2 measured patient breathing trajectories. PET list-mode data were gated into 8 bins using 2 amplitude-based (equal amplitude bins [A1] and equal counts per bin [A2]) and 2 temporal phase-based gating algorithms. Gated images were segmented using a commercially available gradient-based technique and a fixed 40% threshold of maximum uptake. Internal target volumes (ITVs) were generated by taking the union of all 8 contours per gated image. Segmented phantom ITVs were compared with their respective ground-truth ITVs, defined as the volume subtended by the tumor model positions covering 99% of breathing amplitude. Superior-inferior distances between sphere centroids in the end-inhale and end-exhale phases were also calculated. Results: Tumor ITVs from amplitude-based methods were significantly larger than those from temporal-based techniques (P=.002). For lymph nodes, A2 resulted in ITVs that were significantly larger than either of the temporal-based techniques (P<.0323). A1 produced the largest and most accurate ITVs for spheres with diameters of ≥2 cm (P=.002). No significant difference was shown between algorithms in the 1-cm sphere data set. For phantom spheres, amplitude-based methods recovered an average of 9.5% more motion displacement than temporal-based methods under regular breathing conditions and an average of 45.7% more in the presence of baseline drift (P<.001). Conclusions: Target volumes in images generated from amplitude-based gating are larger and more accurate, at levels that are potentially clinically significant, compared with those from temporal phase-based gating.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

Quantification of Esophageal Tumor Motion on Cine-Magnetic Resonance Imaging

Purpose: To quantify the movement of esophageal tumors noninvasively on cine-magnetic resonance imaging (MRI) by use of a semiautomatic method to visualize tumor movement directly throughout multiple breathing cycles. Methods and Materials: Thirty-six patients with esophageal tumors underwent MRI. Tumors were located in the upper (8), middle (7), and lower (21) esophagus. Cine-MR images were collected in the coronal and sagittal plane during 60 seconds at a rate of 2 Hz. An adaptive correlation filter was used to automatically track a previously marked reference point. Tumor movement was measured in the craniocaudal (CC), left–right (LR), and anteroposterior (AP) directions and its relationship along the longitudinal axis of the esophagus was investigated. Results: Tumor registration within the individual images was typically done at a millisecond time scale. The mean (SD) peak-to-peak displacements in the CC, AP, and LR directions were 13.3 (5.2) mm, 4.9 (2.5) mm, and 2.7 (1.2) mm, respectively. The bandwidth to cover 95% of excursions from the mean position (c95) was also calculated to exclude outliers caused by sporadic movements. The mean (SD) c95 values were 10.1 (3.8) mm, 3.7 (1.9) mm, and 2.0 (0.9) mm in the CC, AP, and LR dimensions. The end-exhale phase provided a stable position in the respiratory cycle, compared with more variety in the end-inhale phase. Furthermore, lower tumors showed more movement than did higher tumors in the CC and AP directions. Conclusions: Intrafraction tumor movement was highly variable between patients. Tumor position proved the most stable during the respiratory cycle in the end-exhale phase. A better understanding of tumor motion makes it possible to individualize radiation delivery strategies accordingly. Cine-MRI is a successful noninvasive modality to analyze motion for this purpose in the future.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

Intrafractional Baseline Shift or Drift of Lung Tumor Motion During Gated Radiation Therapy With a Real-Time Tumor-Tracking System

Purpose: To investigate the frequency and amplitude of baseline shift or drift (shift/drift) of lung tumors in stereotactic body radiation therapy (SBRT), using a real-time tumor-tracking radiation therapy (RTRT) system. Methods and Materials: Sixty-eight patients with peripheral lung tumors were treated with SBRT using the RTRT system. One of the fiducial markers implanted near the tumor was used for the real-time monitoring of the intrafractional tumor motion every 0.033 seconds by the RTRT system. When baseline shift/drift is determined by the system, the position of the treatment couch is adjusted to compensate for the shift/drift. Therefore, the changes in the couch position correspond to the baseline shift/drift in the tumor motion. The frequency and amount of adjustment to the couch positions in the left-right (LR), cranio-caudal (CC), and antero-posterior (AP) directions have been analyzed for 335 fractions administered to 68 patients. Results: The average change in position of the treatment couch during the treatment time was 0.45 ± 2.23 mm (mean ± standard deviation), −1.65 ± 5.95 mm, and 1.50 ± 2.54 mm in the LR, CC, and AP directions, respectively. Overall the baseline shift/drift occurs toward the cranial and posterior directions. The incidence of baseline shift/drift exceeding 3 mm was 6.0%, 15.5%, 14.0%, and 42.1% for the LR, CC, AP, and for the square-root of sum of 3 directions, respectively, within 10 minutes of the start of treatment, and 23.0%, 37.6%, 32.5%, and 71.6% within 30 minutes. Conclusions: Real-time monitoring and frequent adjustments of the couch position and/or adding appropriate margins are suggested to be essential to compensate for possible underdosages due to baseline shift/drift in SBRT for lung cancers.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

Real-Time 3D Image Guidance Using a Standard LINAC: Measured Motion, Accuracy, and Precision of the First Prospective Clinical Trial of Kilovoltage Intrafraction Monitoring–Guided Gating for Prostate Cancer Radiation Therapy

Purpose: Kilovoltage intrafraction monitoring (KIM) is a new real-time 3-dimensional image guidance method. Unlike previous real-time image guidance methods, KIM uses a standard linear accelerator without any additional equipment needed. The first prospective clinical trial of KIM is underway for prostate cancer radiation therapy. In this paper we report on the measured motion accuracy and precision using real-time KIM-guided gating. Methods and Materials: Imaging and motion information from the first 200 fractions from 6 patient prostate cancer radiation therapy volumetric modulated arc therapy treatments were analyzed. A 3-mm/5-second action threshold was used to trigger a gating event where the beam is paused and the couch position adjusted to realign the prostate to the treatment isocenter. To quantify the in vivo accuracy and precision, KIM was compared with simultaneously acquired kV/MV triangulation for 187 fractions. Results: KIM was successfully used in 197 of 200 fractions. Gating events occurred in 29 fractions (14.5%). In these 29 fractions, the percentage of beam-on time, the prostate displacement was >3 mm from the isocenter position, reduced from 73% without KIM to 24% with KIM-guided gating. Displacements >5 mm were reduced from 16% without KIM to 0% with KIM. The KIM accuracy was measured at <0.3 mm in all 3 dimensions. The KIM precision was <0.6 mm in all 3 dimensions. Conclusions: Clinical implementation of real-time KIM image guidance combined with gating for prostate cancer eliminates large prostate displacements during treatment delivery. Both in vivo KIM accuracy and precision are well below 1 mm.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

Quantification of Intrafraction and Interfraction Tumor Motion Amplitude and Prediction Error for Different Liver Tumor Trajectories in Cyberknife Synchrony Tracking

To research the fiducial-based, real-time tracking intrafraction (during the fraction [intra-]) and interfraction (between fractions [inter-]) tumor respiration amplitude, motion trajectory, and prediction error and quantify their relationships for different types of motion trajectories during Cyberknife-based stereotactic ablation radiotherapy.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

Dosimetric Impact of Intrafraction Motion in Online-Adaptive Intensity Modulated Proton Therapy for Cervical Cancer

A method was recently developed for online-adaptive intensity modulated proton therapy (IMPT) in patients with cervical cancer. The advantage of this approach, relying on the use of tight margins, is challenged by the intrafraction target motion. The purpose of this study was to evaluate the dosimetric effect of intrafraction motion on the target owing to changes in bladder filling in patients with cervical cancer treated with online-adaptive IMPT.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2023

Deuteron off-resonance rotating frame relaxation for the characterization of slow motions in rotating and static solid-state proteins

Here, we demonstrate the feasibility of deuterium solid-state NMR off-resonance rotating frame relaxation measurements for studies of slow motions in biomolecular solids. The pulse sequence, which includes adiabatic pulses for magnetization alignment, is illustrated for static and magic-angle spinning conditions away from rotary resonances. We apply the measurements for three systems with selective deuterium labels at methyl groups: a) a model compound, Fluorenylmethyloxycarbonyl methionine-D 3 amino acid, for which the principles of the measurements and corresponding motional modeling based on rotameric interconversions are demonstrated; b) amyloid-β 1-40 fibrils labeled at a single alanine methyl group located in the disordered N-terminal domain. This system has been extensively studied in prior work and here serves as a test of the method for complex biological systems. The essential features of the dynamics consist of large-scale rearrangements of the disordered N-terminal domain and the conformational exchange between the free and bound forms of the domain, the latter one due to transient interactions with the structured core of the fibrils. and c) a 15-residue helical peptide which belongs to the predicted α-helical domain near the N-terminus of apolipoprotein B. The peptide is solvated with triolein and incorporates a selectively labeled leucine methyl groups. The method permits model refinement, indicating rotameric interconversions with a distribution of rate constants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

X-ray structure and investigation of molecular motions by dielectric, vibrational and 1H NMR methods for two organic-inorganic hybrid piperazinium compounds: (C4H12N2)2[Sb2Cl10]·2H2O and (C4H12N2)2[Sb2Br10]·2H2O

Highlights: • Bis(piperazine-1,4-diium) decabromodiantimonate(III) (PSB) dihydrate has been synthesized and characterized. • The structural phase transition for PSB at ca. 50 K has been confirmed by the dielectric and {sup 1}H NMR spectroscopy results. • The molecular motion parameters of the organic cations and water molecules have been evaluated and compared for PSB and PSC. - Abstract: Bis(piperazine-1,4-diium) decabromodiantimonate(III) dihydrate, (C{sub 4}H{sub 12}N{sub 2}){sub 2}[Sb{sub 2}Br{sub 10}]·2H{sub 2}O, (abbreviated as PSB) has been synthesized and characterized by single-crystal X-ray diffraction studies. The obtained results indicate that PSB is isostructural with a recently described chloride analogue, (C{sub 4}H{sub 12}N{sub 2}){sub 2}[Sb{sub 2}Cl{sub 10}]⋅2H{sub 2}O (PSC), crystallizing with R{sub 2}MX{sub 5}·nH{sub 2}O stoichiometry and characterized by the discrete zero-dimensional anionic species. The crystal structure of PSB is described by monoclinic symmetry in a P2{sub 1}/n space group. Dielectric measurements (down to 25 K) and IR spectral analyses (measured over a broad temperature range) suggested a much more complicated phase situation below 80 K than for that of PSC. To verify and compare the molecular motions of the organic cations in both analogues, a proton magnetic resonance ({sup 1}H NMR) technique was also applied.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Development of deformable moving lung phantom to simulate respiratory motion in radiotherapy

Radiation treatment requires high accuracy to protect healthy organs and destroy the tumor. However, tumors located near the diaphragm constantly move during treatment. Respiration-gated radiotherapy has significant potential for the improvement of the irradiation of tumor sites affected by respiratory motion, such as lung and liver tumors. To measure and minimize the effects of respiratory motion, a realistic deformable phantom is required for use as a gold standard. The purpose of this study was to develop and study the characteristics of a deformable moving lung (DML) phantom, such as simulation, tissue equivalence, and rate of deformation. The rate of change of the lung volume, target deformation, and respiratory signals were measured in this study; they were accurately measured using a realistic deformable phantom. The measured volume difference was 31%, which closely corresponds to the average difference in human respiration, and the target movement was − 30 to + 32 mm. The measured signals accurately described human respiratory signals. This DML phantom would be useful for the estimation of deformable image registration and in respiration-gated radiotherapy. This study shows that the developed DML phantom can exactly simulate the patient's respiratory signal and it acts as a deformable 4-dimensional simulation of a patient's lung with sufficient volume change.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2025

Seismic response of vertical dry storage casks under three-dimensional earthquake motions

Ensuring the long-term seismic safety of dry storage casks (DSCs) is becoming increasingly critical as these systems evolve from temporary to de facto permanent repositories for spent nuclear fuels. Traditional seismic soil–structure interaction (SSI) assessment methods use one-dimensional deconvolution or simplified boundary conditions to model incident waves. Although computationally appealing, simplifying assumptions may alter the seismic risk by neglecting the full complexity of three-dimensional (3D) wave propagation effects. To address this challenge, this paper introduces a novel high-fidelity computational framework that leverages the Domain Reduction Method (DRM) with perfectly matched layers (PML) to accurately transfer complex, 3D seismic wavefields from regional-scale fault-rupture simulations into local-scale finite element models of DSCs. Using broadband, physics-based ground motions from a generic M w 7.0 strike-slip event, both single-cask and multi-cask configurations were investigated under near- and far-field conditions. Emphasis is placed on capturing complex SSI, spatial variability in the ground motion, and nonlinear phenomena such as cask rocking and sliding. Numerical results demonstrate that near-field conditions, where forward directivity and fling-step effects dominate, lead to significantly higher DSC rocking and sliding. Far-field cases, by contrast, generally exhibit modest responses. Incorporating SSI tends to amplify or alter DSC response spectra and introduce response variability, which underscores the need for site-specific evaluations and robust modeling approaches to ensure the seismic integrity of DSCs in interim spent fuel storage installations.

Das, Tonmoy↗