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Journal of Physics. Conference Series

Isseki Yu, Michael Feig, Yuji Sugita
The inside of a cell is highly crowded with a large number of macromolecules together with solvents and metabolites. To know the molecular-level behaviour of biomolecules in such dense crowding environment, we constructed full atomistic model of the cytoplasm of bacteria, and performed massive all-atom molecular dynamics (MD) simulations. On the other hand, to analyse such big MD data, we need significant computational power and efficient calculation methodology. Here, we introduce what and how we analyse the biomolecule properties from the big trajectory data produced by cellular scale all-atom MD simulations...
2018: Journal of Physics. Conference Series
Michael Feig, Grzegorz Nawrocki, Isseki Yu, Po-Hung Wang, Yuji Sugita
Computer simulations are widely used to study molecular systems, especially in biology. As simulations have greatly increased in scale reaching cellular levels there are now significant challenges in managing, analyzing, and interpreting such data in comparison with experiments that are being discussed. Management challenges revolve around storing and sharing terabyte to petabyte scale data sets whereas the analysis of simulations of highly complex systems will increasingly require automated machine learning and artificial intelligence approaches...
2018: Journal of Physics. Conference Series
B Ravel, M Newville
We propose a standard data format for the interchange of XAFS data. The XAFS Data Interchange (XDI) standard is meant to encapsulate a single spectrum of XAFS along with relevant metadata. XDI is a text-based format with a simple syntax which clearly delineates metadata from the data table in a way that is easily interpreted both by a computer and by a human. The metadata header is inspired by the format of an electronic mail header, representing metadata names and values as an associative array. The data table is represented as columns of numbers...
2016: Journal of Physics. Conference Series
Kazuki Maeda, Tim Colonius, Wayne Kreider, Adam Maxwell, Bryan Cunitz, Michael Bailey
A combined modeling and experimental study of acoustic cavitation bubbles that are initiated by focused ultrasound waves is reported. Focused ultrasound waves of frequency 335 kHz and peak negative pressure 8 MPa are generated in a water tank by a piezoelectric transducer to initiate cavitation. The resulting pressure field is obtained by direct numerical simulation (DNS) and used to simulate single bubble oscillation. The characteristics of cavitation bubbles observed by high-speed photography qualitatively agree withs the simulation result...
December 2015: Journal of Physics. Conference Series
Kang K L Liu, Ronny P Bartsch, Qianli D Y Ma, Plamen Ch Ivanov
The human organism is a complex network of interconnected organ systems, where the behavior of one system affects the dynamics of other systems. Identifying and quantifying dynamical networks of diverse physiologic systems under varied conditions is a challenge due to the complexity in the output dynamics of the individual systems and the transient and non-linear characteristics of their coupling. We introduce a novel computational method based on the concept of time delay stability and major component analysis to investigate how organ systems interact as a network to coordinate their functions...
2015: Journal of Physics. Conference Series
C B Trame, M Dragovic, H-J Chiu
Radiation damage is one of the bottlenecks in the field of structural biology. Cryo-cooling of protein crystals provided a breakthrough in the 1980s and resulted in significant reductions in radiation damage. Other factors positively influencing the progression of damage include the application of radical scavengers and reductions in the experimental beam size. Here we study the impact on radiation damage of applying static magnetic and electric fields during protein diffraction experiments, ultimately probing the Lorenz force effect on primary photoelectrons and secondary Auger electrons, which both contribute to the damage process...
June 2014: Journal of Physics. Conference Series
O Kizilkaya, R W Jiles, M C Patterson, C A Thibodeaux, E D Poliakoff, P T Sprunger, R L Kurtz, E Morikawa
A 5 meter toroidal grating (5m-TGM) beamline has been commissioned to deliver 28 mrad of bending magnet radiation to an ultrahigh vacuum endstation chamber to facilitate angle resolved photoelectron spectroscopy. The 5m-TGM beamline is equipped with Au-coated gratings with 300, 600 and 1200 lines/mm providing monochromatized synchrotron radiation in the energy ranges 25-70 eV, 50-120 eV and 100-240 eV, respectively. The beamline delivers excellent flux (~10(14)-10(17) photons/sec/100mA) and a combined energy resolution of 189 meV for the beamline (at 1...
2014: Journal of Physics. Conference Series
S Khan, A Borsic, Preston Manwaring, Alexander Hartov, Ryan Halter
Electrical Impedance Tomography (EIT) systems are used to image tissue bio-impedance. EIT provides a number of features making it attractive for use as a medical imaging device including the ability to image fast physiological processes (>60 Hz), to meet a range of clinical imaging needs through varying electrode geometries and configurations, to impart only non-ionizing radiation to a patient, and to map the significant electrical property contrasts present between numerous benign and pathological tissues...
March 1, 2013: Journal of Physics. Conference Series
M Niebanck, T Juang, J Newton, J Adamovics, Z Wang, M Oldham
Stereotactic radiosurgery has become a widely used technique to treat solid tumors and secondary metastases of the brain. Multiple targets can be simultaneously treated with a single isocenter in order to reduce the set-up time to improve patient comfort and workflow. In this study, a 5-arc multifocal RapidArc treatment was delivered to multiple PRESAGE(®) dosimeters in order to explore the repeatability of the treatment. The three delivery measurements agreed well with each other, with less than 3% standard deviation of dose in the target...
2013: Journal of Physics. Conference Series
A Thomas, H Yan, M Oldham, T Juang, J Adamovics, F F Yin
Six base of skull IMRT treatment plans were delivered to 3D dosimeters within the RPC Head and Neck Phantom for QA verification. Isotropic 2mm 3D data was obtained using the DLOS-PRESAGE system and compared to an Eclipse (Varian) treatment plan. Normalized Dose Distribution pass rates were obtained for a number of criteria. High quality 3D dosimetry data was observed from the DLOS system, illustrated here through colormaps, isodose lines, profiles, and NDD 3D maps. Excellent agreement with the planned dose distributions was also observed with NDD analysis revealing > 90% NDD pass rates [3%, 2mm], noise < 0...
2013: Journal of Physics. Conference Series
Y Yuan, S Chen, S C Gleber, B Lai, K Brister, C Flachenecker, B Wanzer, T Paunesku, S Vogt, G E Woloschak
The targeted delivery of Fe3O4@TiO2 nanoparticles to cancer cells is an important step in their development as nanomedicines. We have synthesized nanoparticles that can bind the Epidermal Growth Factor Receptor, a cell surface protein that is overexpressed in many epithelial type cancers. In order to study the subcellular distribution of these nanoparticles, we have utilized the sub-micron resolution of X-ray Fluorescence Microscopy to map the locationof Fe3O4@TiO2 NPs and other trace metal elements within HeLa cervical cancer cells...
2013: Journal of Physics. Conference Series
P A Schulte, C L Geraci, L L Hodson, R D Zumwalde, E D Kuempel, V Murashov, K F Martinez, D S Heidel
Occupational exposure to engineered nanomaterials (ENMs) is considered a new and challenging occurrence. Preliminary information from laboratory studies indicates that workers exposed to some kinds of ENMs could be at risk of adverse health effects. To protect the nanomaterial workforce, a precautionary risk management approach is warranted and given the newness of ENMs and emergence of nanotechnology, a naturalistic view of risk management is useful. Employers have the primary responsibility for providing a safe and healthy workplace...
2013: Journal of Physics. Conference Series
S Tsuruoka, K Takeuchi, K Koyama, T Noguchi, M Endo, F Tristan, M Terrones, H Matsumoto, N Saito, Y Usui, D W Porter, V Castranova
Carbon nanotubes (CNTs) are important materials in advanced industries. It is a concern that pulmonary exposure to CNTs may induce carcinogenic responses. It has been recently reported that CNTs scavenge ROS though non-carbon fibers generate ROS. A comprehensive evaluation of ROS scavenging using various kinds of CNTs has not been demonstrated well. The present work specifically investigates ROS scavenging capabilities with a series of CNTs and their derivatives that were physically treated, and with the number of commercially available CNTs...
2013: Journal of Physics. Conference Series
Robert F Fischetti, Derek Yoder, Shenglan Xu, Oleg Makarov, Craig Ogata, Janet L Smith
GM/CA at the APS has developed microcrystallography capabilities for structural biology applications. The robust, quad, mini-beam collimators, which enable users to rapidly select between a 5, 10 or 20 micron diameter beam or a scatter guard for the full focused beam, are coupled with several powerful automated software tools that are built into the beamline control system JBluIce-EPICS. Recent successes at beamlines around the world in solving structures from microcrystals (2 - 10 microns) have led to increased demand for high-intensity micro-focus beams...
2013: Journal of Physics. Conference Series
A Thomas, J O'Daniel, J Adamovics, G Ibbott, M Oldham
Six base of skull IMRT treatment plans were delivered to Presage dosimeters within the RPC Head and Neck Phantom for quality assurance (QA) verification. Isotropic 2mm 3D data were acquired by optical-CT scanning with the DLOS system (Duke Large Optical-CT Scanner) and compared to the Eclipse (Varian) treatment plan. Normalized Dose Distribution (NDD) pass rates were obtained for a number of criteria. High quality 3D dosimetry data was observed from the DLOS system, illustrated here through colormaps, isodose lines, and profiles...
2013: Journal of Physics. Conference Series
T Juang, J Newton, M Niebanck, R Benning, J Adamovics, M Oldham
PRESAGE(®) is a solid radiochromic dosimeter consisting of a polyurethane matrix, a triarylmethane leuco dye, and a trihalomethane initiator. Varying the composition and/or relative amounts of these constituents can affect the dose sensitivity, post-irradiation stability, and physical properties of the dosimeter. This allows customisation of PRESAGE(®) to meet application-specific requirements, such as low sensitivity for high dose applications, stability for remote dosimetry, optical clearing for reusability, and tissue-like elasticity for deformable dosimetry...
2013: Journal of Physics. Conference Series
Bipin Singh, Stuart R Miller, Harish B Bhandari, Rita Graceffa, Thomas C Irving, Vivek V Nagarkar
There are a growing number of high brightness synchrotron sources that require high-frame-rate detectors to provide the time-scales required for performing time-resolved diffraction experiments. We report on the development of a very high frame rate CMOS X-ray detector for time-resolved muscle diffraction and time-resolved solution scattering experiments. The detector is based on a low-afterglow scintillator, provides a megapixel resolution with frame rates of up to 120,000 frames per second, an effective pixel size of 64 µm, and can be adapted for various X-ray energies...
2013: Journal of Physics. Conference Series
J Adamson, Y Yang, L Rankine, J Newton, J Adamovics, O Craciunescu, M Oldham
We describe a method to directly measure the radial dose and anisotropy functions of brachytherapy sources using polyurethane based dosimeters read out with optical CT. We measured the radial dose and anisotropy functions for a Cs-137 source using a PRESAGE® dosimeter (9.5cm diameter, 9.2cm height) with a 0.35cm channel drilled for source placement. The dosimeter was immersed in water and irradiated to 5.3Gy at 1cm. Pre- and post-irradiation optical CT scans were acquired with the Duke Large field of view Optical CT Scanner (DLOS) and dose was reconstructed with 0...
2013: Journal of Physics. Conference Series
T Juang, J Newton, S Das, J Adamovics, M Oldham
Deformable 3D dosimeters have potential applications in validating deformable dose mapping algorithms. This study evaluates a novel deformable PRESAGE(®) dosimeter and its application toward validating the deformable algorithm employed by VelocityAI. The deformable PRESAGE(®) dosimeter exhibited a linear dose response with a sensitivity of 0.0032 ΔOD/(Gy/cm). Comparison of an experimental dosimeter irradiated with an MLC pencilbeam checkerboard pattern under lateral compression up to 27% to a non-deformed control dosimeter irradiated with the same pattern verified dose tracking under deformation...
2013: Journal of Physics. Conference Series
M Oldham, J Newton, L Rankine, J Adamovics, D Kirsch, S Das
There is significant interest in delivering precisely targeted small-volume radiation treatments, in the pre-clinical setting, to study dose-volume relationships with tumor control and normal tissue damage. In this work we investigate the IGRT targeting accuracy of the XRad225Cx system from Precision x-Ray using high resolution 3D dosimetry techniques. Initial results revealed a significant targeting error of about 2.4mm. This error was reduced to within 0.5mm after the IGRT hardware and software had been recalibrated...
2013: Journal of Physics. Conference Series
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