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Accuracy in contouring of small and low contrast lesions: Comparison between diagnostic quality computed tomography scanner and computed tomography simulation scanner-A phantom study
To evaluate the accuracy in detection of small and low-contrast regions using a high-definition diagnostic computed tomography (CT) scanner compared with a radiotherapy CT simulation scanner. A custom-made phantom with cylindrical holes of diameters ranging from 2-9 mm was filled with 9 different concentrations of contrast solution. The phantom was scanned using a 16-slice multidetector CT simulation scanner (LightSpeed RT16, General Electric Healthcare, Milwaukee, WI) and a 64-slice high-definition diagnostic CT scanner (Discovery CT750 HD, General Electric Healthcare). The low-contrast regions of interest (ROIs) were delineated automatically upon their full width at half maximum of the CT number profile in Hounsfield units on a treatment planning workstation. Two conformal indexes, CI{sub in}, and CI{sub out}, were calculated to represent the percentage errors of underestimation and overestimation in the automated contours compared with their actual sizes. Summarizing the conformal indexes of different sizes and contrast concentration, the means of CI{sub in} and CI{sub out} for the CT simulation scanner were 33.7% and 60.9%, respectively, and 10.5% and 41.5% were found for the diagnostic CT scanner. The mean differences between the 2 scanners' CI{sub in} and CI{sub out} were shown to be significant with p < 0.001. A descending trend of the index values was observed as the ROI size increases for both scanners, which indicates an improved accuracy when the ROI size increases, whereas no observable trend was found in the contouring accuracy with respect to the contrast levels in this study. Images acquired by the diagnostic CT scanner allow higher accuracy on size estimation compared with the CT simulation scanner in this study. We recommend using a diagnostic CT scanner to scan patients with small lesions (<1 cm in diameter) for radiotherapy treatment planning, especially for those pending for stereotactic radiosurgery in which accurate delineation of small-sized, low-contrast regions is important for dose calculation.
Dosimetric comparison of lung stereotactic body radiotherapy treatment plans using averaged computed tomography and end-exhalation computed tomography images: Evaluation of the effect of different dose-calculation algorithms and prescription methods
The purpose of this article is to quantitatively evaluate differences in dose distributions calculated using various computed tomography (CT) datasets, dose-calculation algorithms, and prescription methods in stereotactic body radiotherapy (SBRT) for patients with early-stage lung cancer. Data on 29 patients with early-stage lung cancer treated with SBRT were retrospectively analyzed. Averaged CT (Ave-CT) and expiratory CT (Ex-CT) images were reconstructed for each patient using 4-dimensional CT data. Dose distributions were initially calculated using the Ave-CT images and recalculated (in the same monitor units [MUs]) by employing Ex-CT images with the same beam arrangements. The dose-volume parameters, including D{sub 95}, D{sub 90}, D{sub 50}, and D{sub 2} of the planning target volume (PTV), were compared between the 2 image sets. To explore the influence of dose-calculation algorithms and prescription methods on the differences in dose distributions evident between Ave-CT and Ex-CT images, we calculated dose distributions using the following 3 different algorithms: x-ray Voxel Monte Carlo (XVMC), Acuros XB (AXB), and the anisotropic analytical algorithm (AAA). We also used 2 different dose-prescription methods; the isocenter prescription and the PTV periphery prescription methods. All differences in PTV dose-volume parameters calculated using Ave-CT and Ex-CT data were within 3 percentage points (%pts) employing the isocenter prescription method, and within 1.5%pts using the PTV periphery prescription method, irrespective of which of the 3 algorithms (XVMC, AXB, and AAA) was employed. The frequencies of dose-volume parameters differing by >1%pt when the XVMC and AXB were used were greater than those associated with the use of the AAA, regardless of the dose-prescription method employed. All differences in PTV dose-volume parameters calculated using Ave-CT and Ex-CT data on patients who underwent lung SBRT were within 3%pts, regardless of the dose-calculation algorithm or the dose-prescription method employed.
New method for analysis of X-ray computed tomography scans of TRISO fuel forms
X-ray computed tomography (XCT) is a powerful characterization tool that has been used for examination of both tristructural-isotropic (TRISO) coated particles and fuel forms. Rapid, nondestructive imaging of complete specimens by XCT provides significant characterization advantages in both speed and comprehensiveness over traditional materialographic methods. This paper discusses a method that has been developed to analyze XCT images of pebble fuel forms containing ~18,000 TRISO particles each. The XCT images are three-dimensional with contrast based on relative x-ray transparency. In the case of TRISO fuel forms, XCT image intensity distinguishes between the high-density kernel, the medium-density SiC, and the low-density matrix and carbon layers. Image analysis software has been developed to process XCT data sets to extract spatial distribution information, including particle nearest-neighbor distances, local packing fraction, and fuel-free zone thickness in TRISO fuel forms. Finally, although this type of high-resolution XCT analysis is likely not feasible as a quality control measurement for commercial TRISO fuel, it is highly useful in generating feedback for the development of fuel form fabrication processes.
I/O-aware bandwidth allocation for petascale computing systems
In the Big Data era, the gap between the storage performance and an appli- cation's I/O requirement is increasing. I/O congestion caused by concurrent storage accesses from multiple applications is inevitable and severely harms the performance. Conventional approaches either focus on optimizing an ap- plication's access pattern individually or handle I/O requests on a low-level storage layer without any knowledge from the upper-level applications. In this paper, we present a novel I/O-aware bandwidth allocation framework to coordinate ongoing I/O requests on petascale computing systems. The motivation behind this innovation is that the resource management system has a holistic view of both the system state and jobs' activities and can dy- namically control the jobs' status or allocate resource on the y during their execution. We treat a job's I/O requests as periodical subjobs within its lifecycle and transform the I/O congestion issue into a classical scheduling problem. Based on this model, we propose a bandwidth management mech- anism as an extension to the existing scheduling system. We design several bandwidth allocation policies with different optimization objectives either on user-oriented metrics or system performance. We conduct extensive trace- based simulations using real job traces and I/O traces from a production IBM Blue Gene/Q system at Argonne National Laboratory. Experimental results demonstrate that our new design can improve job performance by more than 30%, as well as increasing system performance.
Combined Experimental and Computational Investigation of the Elementary Reaction of Ground State Atomic Carbon (C; 3 P j ) with Pyridine (C 5 H 5 N; X 1 A 1 ) via Ring Expansion and Ring Degradation Pathways
In t his work, we explored the elementary reaction of atomic carbon (C; 3 P j ) with pyridine (C 5 H 5 N; X 1 A 1 ) at a collision energy of 34 ± 4 kJ mol-1 utilizing the crossed molecular beams technique. Forwardconvolution fitting of the data was combined with high-level electronic structure calculations and statistical (RRKM) calculations on the triplet C 6 H 5 N potential energy surface (PES). These investigations reveal that the reaction dynamics are indirect and dominated by large range reactive impact parameters leading via barrier-less addition to the nitrogen atom and to two chemically non-equivalent ‘aromatic’ carbon-carbon bonds forming three distinct collision complexes. At least two reaction pathways through atomic hydrogen loss were identified on the triplet surface. These channels involve multiple isomerization steps of the initial collision complexes via ring-opening and ring expansion forming an acyclic 1-ethynyl-3-isocyanoallyl radical (P1; 2 A”) and a hitherto unreported seven-membered 1-aza-2-dehydrocyclohepta-2,4,6-trien-4-yl radical isomer (P3; 2 A), respectively. For RRKM calculations at zero collision energy, representing conditions in cold molecular clouds, the ring expansion product P3 is formed nearly exclusively for the atomic hydrogen loss channel. Based on the computations, the molecular fragmentation channel eliminating acetylene (C 2 H 2 ) plus 3-cyano-2-propen-1-ylidene (P6; 3 A”) plays also an important role the reaction of atomic carbon with pyridine proposing a probable destruction pathway of interstellar pyridine. Lastly, these results are also discussed in light of the isoelectronic carbon – benzene (C 6 H 6 ; X 1 A 1 ) system with important implications to the rapid degradation of nitrogen-bearing polycyclic aromatic hydrocarbons (NPAHs) in the interstellar medium compared to mass growth processes of PAH counterparts through ring expansion.
Validation of Methods for Computational Catalyst Design: Geometries, Structures, and Energies of Neutral and Charged Silver Clusters
We report a systematic study of small silver clusters, Agn, Agn+, and Agn–, n = 1–7. We studied all possible isomers of clusters with n = 5–7. We tested 42 exchange–correlation functionals, and we assess these functionals for their accuracy in three respects: geometries (quantitative prediction of internuclear distances), structures (the nature of the lowest-energy structure, for example, whether it is planar or nonplanar), and energies. We find that the ingredients of exchange–correlation functionals are indicators of their success in predicting geometries and structures: local exchange–correlation functionals are generally better than hybrid functionals for geometries; functionals depending on kinetic energy density are the best for predicting the lowest-energy isomer correctly, especially for predicting two-dimensional to three-dimenstional transitions correctly. The accuracy for energies is less sensitive to the ingredient list. Our findings could be useful for guiding the selection of methods for computational catalyst design.
Strategies for Computer-Aided Discovery of Novel Open-Shell Polymers
Organic π-conjugated polymers with a triplet ground state have been the focus of recent research for their interesting and unique electronic properties, arising from the presence of the two unpaired electrons. These compounds are usually built from alternating electron-donating and electron-accepting monomer pairs which lower the HOMO–LUMO gap and yield a triplet state instead of the typical singlet ground state. In this paper, we use density functional theory calculations to explore the design rules that govern the creation of a ground-state triplet conjugated polymer and find that a small HOMO–LUMO gap in the singlet state is the best predictor for the existence of a triplet ground state, compared to previous use of a pro-quinoidal bonding character. Furthermore, this work can accelerate the discovery of new stable triplet materials by reducing the computational resources needed for electronic-state calculations and the number of potential candidates for synthesis.
A Combined Experimental and Computational Study on Selected Physical Properties of Aminosilicones
A number of physical properties of aminosilicones have been determined experimentally and predicted computationally. It was found that COSMO-RS predicted the densities of the materials under study to within about 4% of the experimentally determined values. Vapor pressure measurements were performed, and all of the aminosilicones of interest were found to be significantly less volatile than the benchmark MEA material. COSMO-RS was reasonably accurate for predicting the vapor pressures for aminosilicones that were thermally stable. The heat capacities of all aminosilicones tested were between 2.0 and 2.3 J/(g.degrees C); again substantially lower than a benchmark 30% aqueous MEA solution. Surface energies for the aminosilicones were found to be 23.3-28.3 dyne/cm and were accurately predicted using the parachor method.
Structural, NMR Spectroscopic, and Computational Investigation of Hemin Loading in the Hemophore HasAp from Pseudomonas aeruginosa
Abstract not provided
Large-Scale Computational Screening of Zeolites for Ethane/Ethene Separation
Large-scale computational screening of thirty thousand zeolite structures was conducted to find optimal structures for seperation of ethane/ethene mixtures. Efficient grand canonical Monte Carlo (GCMC) simulations were performed with graphics processing units (GPUs) to obtain pure component adsorption isotherms for both ethane and ethene. We have utilized the ideal adsorbed solution theory (LAST) to obtain the mixture isotherms, which were used to evaluate the performance of each zeolite structure based on its working capacity and selectivity. In our analysis, we have determined that specific arrangements of zeolite framework atoms create sites for the preferential adsorption of ethane over ethene. The majority of optimum separation materials can be identified by utilizing this knowledge and screening structures for the presence of this feature will enable the efficient selection of promising candidate materials for ethane/ethene separation prior to performing molecular simulations.
Comprehensive Thermodynamics of Nickel Hydride Bis(Diphosphine) Complexes: A Predictive Model through Computations
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A combined crossed molecular beams and computational study on the formation of distinct resonantly stabilized C 5 H 3 radicals via chemically activated C 5 H 4 and C 6 H 6 intermediates
The crossed molecular beams technique was utilized to investigate the formation of three isomers of resonantly stabilized (C 5 H 3 ) radicals along with their d 2 -substituted counterparts via the bimolecular reactions of singlet/triplet dicarbon [C 2 (X 1 Σ + g /a 3 Π u )] with methylacetylene [CH 3 CCH(X 1 A 1 )], d 3 -methylacetylene [CD 3 CCH(X 1 A 1 )], and 1-butyne [C 2 H 5 CCH(X 1 A')] at collision energies up to 26 kJ mol -1 via chemically activated singlet/triplet C 5 H 4 /C 5 D 3 H and C 6 H 6 intermediates. These studies exploit a newly developed supersonic dicarbon [C 2 (X 1 Σ + g /a 3 Π u )] beam generated via photolysis of tetrachloroethylene [C 2 Cl 4 (X 1 A g )] by excluding interference from carbon atoms, which represent the dominating (interfering) species in ablation-based dicarbon sources. We assessed the performance of the dicarbon [C 2 (X 1 Σ + g /a 3 Π u )] beam in reactions with methylacetylene [CH 3 CCH(X 1 A 1 )] and d 3 -methylacetylene [CD 3 CCH(X 1 A 1 )]; the investigations demonstrate that the reaction dynamics match previous studies in our laboratory utilizing ablation-based dicarbon sources involving the synthesis of 1,4-pentadiynyl-3 [HCCCHCCH(X 2 B 1 )] and 2,4-pentadiynyl-1 [H 2 CCCCCH(X 2 B 1 )] radicals via hydrogen (deuterium) atom elimination. Considering the C 2 (X 1 Σ + g /a 3 Π u )–1-butyne [C 2 H 5 CCH(X 1 A')] reaction, the hitherto elusive methyl-loss pathway was detected. This channel forms the previously unknown resonantly stabilized penta-1-yn-3,4-dienyl-1 [H 2 CCCHCC(X 2 A)] radical along with the methyl radical [CH 3 (X 2 A 2 ")] and is open exclusively on the triplet surface with an overall reaction energy of -86 ± 10 kJ mol -1 . The preferred reaction pathways proceed first by barrierless addition of triplet dicarbon to the π-electronic system of 1-butyne, either to both acetylenic carbon atoms or to the sterically more accessible carbon atom, to form the methyl-bearing triplet C 6 H 6 intermediates [ i4 1b ] and [ i8 1b ], respectively, with the latter decomposing via a tight exit transition state to penta-1-yn-3,4-dienyl-1 [(H 2 CCCHCC(X 2 A)] plus the methyl radical [CH 3 (X 2 A 2 ")]. The successful unraveling of this methyl-loss channel – through collaborative experimental and computational efforts – underscores the viability of the photolytically generated dicarbon beam as an unprecedented tool to access reaction dynamics underlying the formation of resonantly stabilized free radicals (RSFR) that are vital to molecular mass growth processes that ultimately lead to polycyclic aromatic hydrocarbons (PAHs)
Photoelectron spectroscopic and computational study of [EDTA•M(III)]- complexes (M = H3, Al, Sc, V-Co)
Metal-EDTA complexes are commonly existed as biological redox reagents. We havegenerated a series of such complexes, [EDTA•M(III)]- (M = Al, Sc, V-Co), via electrospray ionization and characterized them by cryogenic mass-selected negative ion photoelectron spectroscopy (NIPES) and theoretical calculations. Experiments clearly revealed one more spectral band at low electron binding energy for transition metal complexes with d electrons (M = V-Co) than those without d electrons (M = Al and Sc). Quantum chemical calculations suggested that all of the metal-complexes possess hexacoordinated metal-ligand binding motifs, from which the calculated adiabatic/vertical detachment energy (ADE/VDE) and band gaps are in good agreement with experimental values. Direct spectrum and electronic structure analyses indicted that [EDTA•V(III)]- can be easily oxidized to [EDTA•V(IV)] with the smallest ADE/VDE of 3.95/4.40 eV among these metal-complexes, but further oxidation is hindered by the existence of a 2.30 eV band gap, a fact that accords with the special redox behavior of vanadium-containing species in biology cells. Spin density and molecular orbital analyses reveal that [EDTA•V(III)]- was overwhelmingly detached from vanadium atom, in a stark contrast to [EDTA•Sc(III)/Al(III)]- where the detachment occurred from the EDTA ligand. For all other metal complex anions, from M = Cr to Co, the detachment process is derived from contributions from both the metal and ligand. The intrinsic electronic and geometric structures of these complexes, obtained in this work, provide a molecular foundation to better understand their redox chemistries and specific metal bindings in condensed phases and biology cells.
Structure and proton conduction in sulfonated poly(ether ether ketone) semi-permeable membranes: a multi-scale computational approach.
The design of polymeric membranes for proton or ionic exchange highly depends on the fundamental understanding of the physical and molecular mechanisms that control the formation of the conduction channels. There is an inherent relation between the dynamical structure of the polymeric membrane and the electrostatic forces that drive membrane segregation and proton transport. Here, we used a multi-scale computational approach to analyze the morphology of sulfonated poly(ether ether ketone) membranes at the mesoscale. A self-consistent description of the electrostatic phenomenon was adopted, where discrete polymer chains and a continuum proton field were embedded in a continuum fluid. Brownian dynamics was used for the evolution of the suspended polymer molecules, while a convection-diffusion transport equation, including the Nernst-Planck diffusion mechanism, accounted for the dynamics of the proton concentration field. We varied the polymer concentration, the degree of sulfonation and the level of confinement to find relationships between membrane structure and proton conduction. Our results indicate that the reduced mobility of polymer chains, at concentrations above overlap, and a moderate degree of sulfonation -i.e., 30% - are essential elements for membrane segregation and proton domain connectivity. These conditions also ensure that the membrane structure is not affected by size or by potential gradients. Importantly, our analysis shows that membrane conductivity and current are linearly dependent on polymer concentration and quadratically dependent on the degree of sulfonation. We found that the optimal polymeric membrane design requires a polymer concentration above overlap and a degree of sulfonation around 50%. These conditions promote a dynamical membrane morphology with a constant density of proton channels. Our results and measurements agree with previous experimental works, thereby validating our model and observations.
Interfacial analysis of a PEM electrolyzer using X-ray computed tomography
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Computational and experimental search for potential polyanionic K-ion cathode materials
Discovering high-energy cathode materials is critical to construct K-ion batteries for practical applications. Owing to the great success of layered oxides in Li- and Na-ion systems, K layered cathodes have also been investigated in recent years. However, the much larger size of K + compared to Li or Na introduces strong K + –K + interaction within the layer, which results in a sloped voltage profile thereby limiting the specific capacity and operating voltage. In contrast, polyanionic materials with a three-dimensional K + arrangement can effectively mitigate K + –K + interaction. In this work, ten K polyanionic compounds with theoretical capacity >100 mA h g –1 are screened from the Inorganic Crystal Structure Database as potential cathode materials for K-ion batteries. Among the ten proposed compounds, K 2 MnP 2 O 7 , K 2 Mn 2 P 2 O 7 F 2 , K 2 Fe 2 P 2 O 7 F 2 , and K 6 V 2 (PO 4 ) 4 with average voltage <4.5 V are synthesized and evaluated electrochemically. While the re-insertion of K into these compounds is not fully reversible, it may be related to the very high migration barrier that we compute for K ions. In addition, we show the successful synthesis of a series of K 3 V 3–x Cr x (PO 4 ) 4 (x = 0, 1, 2, 3) compounds. Among these, K 3 V 2 Cr(PO 4 ) 4 exhibits the largest reversible capacity, as revealed by the in situ investigation. Lastly, we find that the redox couples in many of these compounds sit at remarkably high potential, even higher than in equivalent Li compounds, which brings both opportunities and challenges in the future research of K polyanion cathodes.