24 results on '"Erik McKee"'
Search Results
2. TEXTAL: Crystallographic Protein Model Building Using AI and Pattern Recognition.
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Kreshna Gopal, Tod D. Romo, Erik McKee, Reetal Pai, Jacob N. Smith, James C. Sacchettini, and Thomas R. Ioerger
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- 2006
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3. TEXTAL: AI-Based Structural Determination for X-ray Protein Crystallography.
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Tod D. Romo, Kreshna Gopal, Erik McKee, Lalji Kanbi, Reetal Pai, Jacob N. Smith, James C. Sacchettini, and Thomas R. Ioerger
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- 2005
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4. Crystallographic protein model-building on the web.
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Kreshna Gopal, Erik McKee, Tod D. Romo, Reetal Pai, Jacob N. Smith, James C. Sacchettini, and Thomas R. Ioerger
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- 2007
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5. Design and optimization of a liner-on-target injector for staged Z-pinch experiments using computational fluid dynamics and MHD simulations
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Erik McKee, Frank Wessel, Paul Ney, Jeff Narkis, H. U. Rahman, J. C. Valenzuela, V. Fadeev, F. N. Beg, F. Conti, I. Krasheninnikov, Aaron Covington, and T. Darling
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Physics ,business.industry ,Current driver ,Injector ,Mechanics ,Plasma ,Computational fluid dynamics ,law.invention ,Nuclear physics ,law ,Z-pinch ,Energy density ,Neutron ,Magnetohydrodynamics ,business - Abstract
Previous Staged Z-pinch experiments have demonstrated that gas liners (or puffs) can efficiently couple energy to a target plasma and implode uniformly, producing plasmas in High Energy Density (HED) regimes. In these experiments, a 50 kJ, 1.5 MA, 1 μs current driver was used to implode a magnetized, Kr liner onto a D+ target, producing 1010 neutrons per shot. Time-of-flight data suggested that primary and secondary neutrons were produced.
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- 2016
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6. Characterization of a compact gas-puff nozzle and plasma gun assembly for staged Z-pinch experiments
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Erik McKee, Paul Ney, Aaron Covington, F. N. Beg, Jeff Narkis, F. Conti, I. Krasheninnikov, Frank Wessel, V. Fadeev, H. U. Rahman, T. Darling, and J. C. Valenzuela
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Physics ,Dense plasma focus ,Z-pinch ,Nuclear engineering ,Electric breakdown ,Nozzle ,Implosion ,Plasma ,Characterization (materials science) - Abstract
We discuss the design and characterization of a compact gas-puff nozzle and plasma gun assembly that will be used in Staged Z-pinch experiments1, where gas liners are imploded onto an on-axis target-plasma column. Previous work on the Staged Z-pinch demonstrated that gas liners can efficiently couple the energy and produce a uniform implosion on a target-plasma.2
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- 2016
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7. Fusion in a staged Z-pinch
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F. N. Beg, Frank Wessel, H. U. Rahman, T. Darling, Erik McKee, Paul Ney, and J. C. Valenzuela
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Engineering ,business.industry ,Z-pinch ,Electrical engineering ,Pinch ,business - Abstract
This paper is dedicated to Norman Rostoker, our (FJW and HUR) mentor and long-term collaborator, who will always be remembered for the incredible inspiration that he has provided us. Norman’s illustrious career dealt with a broad range of fundamental-physics problems and we were fortunate to have worked with him on many important topics: intense-charged-particle beams, field-reversed configurations, and Z-pinches. Rostoker ’s group at the University of CA, Irvine was well known for having implemented many refinements to the Z-pinch, that make it more stable, scalable, and efficient, including the development of: the gas-puff Z-pinch [1], which provides for the use of an expanded range of pinch-load materials; the gas-mixture Z-pinch [2], which enhances the pinch stability and increases its radiation efficiency; e-beam pre-ionization [3], which enhances the uniformity of the initial-breakdown process in a gas pinch; magnetic-flux-compression [4, 5], which allows for the amplification of an axial-magnetic f...
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- 2016
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8. Filamentation and Pulse Self-compression in the Anomalous Dispersion Region of Glasses
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Arnaud Couairon, Matthias Baudisch, Nicolas Forget, I. Gražulevičiūtė, Aurélien Houard, Alexandre Thai, Vytautas Jukna, Martin Richardson, D. Majus, Audrius Dubietis, S. Grabielle, Magali Durand, André Mysyrowicz, Gintaras Valiulis, Michael Hemmer, Matthieu Baudelet, Francisco Silva, Gintaras Tamošauskas, J. Darginavičius, Amélie Jarnac, Khan Lim, Yi Liu, Jens Biegert, D. Faccio, Dane R. Austin, Erik McKee, Anne Durécu, N. Garejev, Centre de Physique Théorique [Palaiseau] (CPHT), Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X), Department of Quantum Electronics [Vilnius], Vilnius University [Vilnius], Institut de Ciencies Fotoniques [Castelldefels] (ICFO), School of Engineering and Physical Sciences, Heriot-Watt University [Edinburgh] (HWU), Interaction Laser-Matière (ILM), Laboratoire d'optique appliquée (LOA), École Nationale Supérieure de Techniques Avancées (ENSTA Paris)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure de Techniques Avancées (ENSTA Paris)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), FASTLITE, ONERA - The French Aerospace Lab [Palaiseau], ONERA-Université Paris Saclay (COmUE), The College of Optics and Photonics [Orlando] (CREOL), University of Central Florida [Orlando] (UCF), Andre D. Bandrauk, Emmanuel Lorin, and Jerome V. Moloney
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anomalous dispersion ,Infrared ,medicine.disease_cause ,01 natural sciences ,Molecular physics ,law.invention ,010309 optics ,Optics ,Filamentation ,law ,0103 physical sciences ,medicine ,High harmonic generation ,010306 general physics ,femtosecond pulse ,Physics ,[PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics] ,business.industry ,Conical surface ,Laser ,laser ,Pulse (physics) ,filamentation ,business ,Ultraviolet ,Doppler broadening - Abstract
The propagation of near-infrared ultra-short laser pulses in the regime of anomalous dispersion of transparent solids is associated with a host of self-induced effects including a significant spectral broadening extending from the ultraviolet into the infrared region, pulse self-compression down to few-cycle pulse durations, free and driven third harmonic generation, conical emission and the formation of stable filaments over several \(\mathop{\mathrm{cm}}\nolimits\) showing the emergence of conical light bullets. We review measurements performed in different experimental conditions and results of numerical simulations of unidirectional propagation models showing that the interpretation of all these phenomena proceeds from the formation of non-spreading conical light bullets during filamentation.
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- 2016
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9. Effects of a Demonstration Laboratory on Student Learning
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Vickie M. Williamson, Laura E. Ruebush, and Erik McKee
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Chemistry education ,Computer science ,education ,Significant difference ,General Engineering ,Educational technology ,Academic achievement ,Science education ,Education ,Concept learning ,ComputingMilieux_COMPUTERSANDEDUCATION ,Mathematics education ,Cognitive skill ,Student learning - Abstract
Laboratory and demonstration have long been used to supplement lecture in chemistry education. Current research indicates that students are better served by laboratories which exercise the higher-order cognitive skills, such as inquiry-based laboratories. However, the time and the resources available to perform these recommended types of laboratories are continually shrinking. Due to these factors, a demonstration-laboratory was designed to allow students to make observations through demonstration rather then through hands-on laboratory. For this study, the hands-on procedures of an inquiry style laboratory were replaced by an instructor demonstration of these same procedures. A significant difference was found between student conceptual understanding before and after the experiment, indicating that students performing the laboratory experiment and students viewing the demonstration-laboratory had an increase in conceptual understanding. However, no significant difference was found between the conceptual understanding of the two groups after the experiment, indicating that students learn roughly the same from both methods and that the demonstration-laboratory at least does no harm to the students conceptually. Long-term effects on student understanding were not measured. Student opinions comparing the demonstration laboratory to a hands-on laboratory were also collected and analyzed.
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- 2007
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10. Note: Infrared laser diagnostics for deuterium gas puff Z pinches
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T. Darling, B. D. Hammel, Erik McKee, Aaron Covington, K. J. Swanson, and V. V. Ivanov
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Materials science ,Far-infrared laser ,Plasma ,Laser ,01 natural sciences ,010305 fluids & plasmas ,law.invention ,Physics::Fluid Dynamics ,Deuterium ,Physics::Plasma Physics ,law ,Z-pinch ,0103 physical sciences ,Pinch ,Neutron ,Plasma diagnostics ,Physics::Atomic Physics ,Atomic physics ,Nuclear Experiment ,010306 general physics ,Instrumentation - Abstract
Deuterium gas puff Z pinches have been used for generation of strong neutron fluxes on the MA class pulse power machines. Due to the low electron density of deuterium Z-pinch plasma, regular laser diagnostics in the visible range cannot be used for observation and study of the pinch. Laser probing at the wavelength of 1064 nm was used for visualization of deuterium plasma. Infrared schlieren and interferometry diagnostics showed the deuterium gas puff plasma dynamics, instabilities, and allowed for the reconstruction of the profile of the plasma density.
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- 2017
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11. Neutron yield detectors characterized with MCNP
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Timothy W. Darling and Erik McKee
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Bonner sphere ,Physics ,Nuclear physics ,Astrophysics::High Energy Astrophysical Phenomena ,Nuclear Theory ,Neutron cross section ,Neutron detection ,Neutron source ,Neutron ,Neutron scattering ,Nuclear Experiment ,Neutron time-of-flight scattering ,Neutron temperature - Abstract
In preparation for measuring neutrons generated in experiments on the Zebra 1-MA Z-pinch generator at the Nevada Terawatt Facility, we use the Monte Carlo N-Particles (MCNP) radiation transport code to characterize neutron activation detectors. For reasonable assumptions regarding the emitted neutron pulse characteristics, the MCNP code is used to predict the expected neutron signal taking into account scattering events and thermalization effects from the neutron scatter. These effects can bolster neutron yield derivations via unique room geometries and, in general, higher absorption cross-section values for lower neutron energies. We report on neutron yield detector characterization, calibrated against NSTec's dense plasma focus for a known neutron yield, and the build-up factors calculated with MCNP necessary for a measurement of a correct neutron yield at NTF.
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- 2014
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12. Helical Filaments
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Nicholas Barbieri, Zahra Hosseinimakarem, Khan Lim, Magali Durand, Benjamin Webb, Joshua Bradford, Erik McKee, Nathan Bodnar, Lawrence Shah, Matthieu Baudelet, Eric Johnson, and Martin Richardson
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- 2014
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13. Compact 10 TW laser to generate multi-filament arrays
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Martin Richardson, Nathan Bodnar, Erik McKee, Andreas Vaupel, Matthieu Baudelet, Benjamin Webb, Joshua Bradford, Magali Durand, Khan Lim, and Lawrence Shah
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Materials science ,business.industry ,Stray light ,Ti:sapphire laser ,Laser ,law.invention ,Protein filament ,Optics ,Regenerative amplification ,law ,Sapphire ,Optoelectronics ,Laser beam quality ,business - Abstract
The design and construction of a compact 10 TW Ti:sapphire CPA system for the generation of filament arrays is presented. The design and implementation challenges are discussed, in particular the optimization of beam quality.
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- 2014
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14. Crystallographic protein model-building on the web
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Reetal Pai, Kreshna Gopal, Thomas R. Ioerger, James C. Sacchettini, Erik McKee, Jacob Smith, and Tod D. Romo
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Models, Molecular ,Statistics and Probability ,Electron density ,Protein Conformation ,Computer science ,Biochemistry ,Protein structure ,Sequence Analysis, Protein ,Side chain ,Computer Simulation ,Molecular Biology ,Throughput (business) ,chemistry.chemical_classification ,Internet ,Crystallography ,Protein molecules ,Process (computing) ,Proteins ,Computer Science Applications ,Amino acid ,Computational Mathematics ,Models, Chemical ,Computational Theory and Mathematics ,chemistry ,Protein model ,User interface ,Algorithms ,Software - Abstract
Summary: X-ray crystallography is the most widely used method to determine the 3D structure of protein molecules. One of the most difficult steps in protein crystallography is model-building, which consists of constructing a backbone and then amino acid side chains into an electron density map. Interpretation of electron density maps represents a major bottleneck in protein structure determination pipelines, and thus, automated techniques to interpret maps can greatly improve the throughput. We have developed WebTex, a simple and yet powerful web interface to TEXTAL, a program that automates this process of fitting atoms into electron density maps. TEXTAL can also be downloaded for local installation.Availability: Web interface, downloadable binaries and documentation atContact: textal@tamu.edu
- Published
- 2006
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15. Blueshifted continuum peaks from filamentation in the anomalous dispersion regime
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Erik McKee, Magali Durand, Aurélien Houard, Matthieu Baudelet, Martin Richardson, Arnaud Couairon, Vytautas Jukna, André Mysyrowicz, Khan Lim, The College of Optics and Photonics [Orlando] (CREOL), University of Central Florida [Orlando] (UCF), Laboratoire d'optique appliquée (LOA), École Nationale Supérieure de Techniques Avancées (ENSTA Paris)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Centre de Physique Théorique [Palaiseau] (CPHT), and Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)
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Optical amplifier ,Physics ,[PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics] ,Continuum (measurement) ,business.industry ,Physics::Optics ,Conical surface ,01 natural sciences ,Molecular physics ,Atomic and Molecular Physics, and Optics ,Supercontinuum ,010309 optics ,Protein filament ,Optics ,Filamentation ,Quantum mechanics ,Dispersion (optics) ,0103 physical sciences ,010306 general physics ,business ,Self-phase modulation ,Phase matching - Abstract
International audience; Filamentation in the anomalous dispersion regime is experimentally shown to give rise to an extreme blueshifted continuum peak in the visible region even when the filament is formed by near-infrared pulses. Measurements and numerical simulations allow us to identify this peak as an axial component of the conical emission. Its features are characterized and quantitatively reproduced by the effective three-wave mixing model.
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- 2013
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16. Influence of the anomalous dispersion on the supercontinuum generation by femtosecond laser filamentation
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Erik McKee, André Mysyrowicz, Khan Lim, Arnaud Couairon, Matthieu Baudelet, Vytautas Jukna, Aurélien Houard, Martin Richardson, and Magali Durand
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Materials science ,Computer simulation ,business.industry ,Physics::Optics ,Ultrafast optics ,Astrophysics::Cosmology and Extragalactic Astrophysics ,Conical surface ,Laser ,Supercontinuum ,law.invention ,Optics ,Filamentation ,law ,Femtosecond ,Dispersion (optics) ,business ,Astrophysics::Galaxy Astrophysics - Abstract
Measurements and numerical simulations of the continuum created by laser filamentation in anomalous dispersion regime of fused silica allow us to identify the extreme blueshifted peak as an axial component of the conical emission.
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- 2013
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17. Highly polarized all-fiber thulium laser with femtosecond-laser-written fiber Bragg gratings
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Stefan Nolte, Ria G. Krämer, Christian Voigtländer, Martin Richardson, Pascal Böswetter, Erik McKee, Andreas Tünnermann, Joshua Bradford, Alex Sincore, Lawrence Shah, Jens Thomas, Christina C. C. Willis, and Publica
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PHOSFOS ,Materials science ,Physics::Optics ,Polarization-maintaining optical fiber ,fibers ,polarization maintaining ,law.invention ,fiber Bragg grating ,Molecular Imprinting ,Optics ,Fiber Bragg grating ,law ,Fiber laser ,Fiber Optic Technology ,Birefringence ,business.industry ,Equipment Design ,Laser ,Atomic and Molecular Physics, and Optics ,Equipment Failure Analysis ,Refractometry ,Thulium ,Femtosecond ,Optoelectronics ,business ,lasers ,Photonic-crystal fiber - Abstract
We demonstrate and characterize a highly linearly polarized (18.8 dB) narrow spectral emission (80 pm) from an all-fiber Tm laser utilizing femtosecond-laser-written fiber Bragg gratings. Thermally-dependent anisotropic birefringence is observed in the FBG transmission, the effects of which enable both the generation and elimination of highly linearly polarized output. To our knowledge, this is the first detailed study of such thermal anisotropic birefringence in femtosecond-written FBGs.
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- 2013
18. Study of implosion dynamics, the x-ray yield and plasma interpenetration in star wire arrays with gates in the inner cylinder
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Erik McKee, Brent Manley Jones, A. L. Astanovitskiy, Dóra Papp, Simon Bland, V. V. Ivanov, and S. D. Altemara
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Physics ,business.industry ,Implosion ,Plasma ,Shadowgraphy ,Computer Science::Emerging Technologies ,Optics ,Physics::Plasma Physics ,Z-pinch ,Logic gate ,Pinch ,Cylinder ,Plasma diagnostics ,business - Abstract
Star wire arrays with two closely located wires (“gates”) on the inner cylinder of star wire arrays were studied. The gate wires were used to study plasma interpenetration and reproduce transparent and non-transparent regimes of propagation of the imploding plasma through the gates. The non-transparent mode of collision is typical for regular star wire arrays and it was also observed in Al stars with gate wires of regular length. Gated star arrays demonstrate similar x-ray yield but slightly different delay of x-ray generation compared to regular stars. Double length wires were applied as gate wires to increase their inductance and resistance and to increase transparency for the imploding plasma. The wires of the gates were made of Al or high atomic number elements, while the rest of the arrays were regular length Al wires. An intermediate semi-transparent mode of collision was observed in Al stars with long Al gate wires. Arrays with long heavy-element gate wires demonstrated transparency to plasma passing through. Shadowgraphy at the wavelength of 266 nm showed that plasma moved through the gate wires. Double implosions, generating a double-peak keV X-ray pulse, were observed in star arrays when the gates were made of high atomic number elements. A new laser diagnostic beampath for vertical probing of the Z-pinch was built to test how wires could be used to redirect plasma flow. This setup was designed to test gated arrays and further configurations to create a rotating pinch. Results on plasma flow control obtained are discussed, and compared to numerical calculations.
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- 2010
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19. Development of high resolution UV laser probing for 1-MA z-pinches
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A. L. Astanovitskiy, S. D. Altemara, Erik McKee, G. S. Sarkisov, Dóra Papp, and V. V. Ivanov
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Physics ,Dense plasma focus ,business.industry ,Implosion ,Plasma ,Shadowgraphy ,Laser ,law.invention ,Wavelength ,Optics ,law ,Z-pinch ,Plasma diagnostics ,business - Abstract
Laser probing diagnostics at the wavelength of 266 nm have been developed at the 1-MA pulsed power Zebra facility. Due to the smaller absorption and refraction at 266 nm, UV radiation penetrates deeper into the dense Z-pinch plasma. This allows the observation of fine details and structures of the Z-pinch plasma at the implosion and stagnation phases. UV interferograms and shadowgrams of the z-pinch plasma were compared to regular interferograms and shadowgrams at 532 nm. The UV laser shadowgraphy was shown to be a significant improvement in probing of wire array plasmas. Plasma distribution and dynamics in compact cylindrical, star, and planar wire arrays were studied at the wavelength of 266 nm. An electron density N e >5.1019 cm-3 was measured directly in the stagnated Z-pinch with the 266nm differential interferometer. Two-color shadowgraphy shows low density "corona" plasma with the 532 nm laser and dense plasma structures with the 266 nm laser in wire arrays.
- Published
- 2010
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20. Automated structure solution with the PHENIX suite
- Author
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Peter H, Zwart, Pavel V, Afonine, Ralf W, Grosse-Kunstleve, Li-Wei, Hung, Thomas R, Ioerger, Airlie J, McCoy, Erik, McKee, Nigel W, Moriarty, Randy J, Read, James C, Sacchettini, Nicholas K, Sauter, Laurent C, Storoni, Thomas C, Terwilliger, and Paul D, Adams
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Models, Molecular ,Automation ,Proteins ,Crystallization ,Crystallography, X-Ray ,Algorithms ,Software - Abstract
Significant time and effort are often required to solve and complete a macromolecular crystal structure. The development of automated computational methods for the analysis, solution, and completion of crystallographic structures has the potential to produce minimally biased models in a short time without the need for manual intervention. The PHENIX software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution, and good quality data. This achievement has been made possible by the development of new algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template- and pattern-based automated model-building (RESOLVE, TEXTAL), automated macromolecular refinement (phenix. refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that have been built and made available to the community. The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI.
- Published
- 2008
21. Automated Structure Solution with the PHENIX Suite
- Author
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Paul D. Adams, Li-Wei Hung, Nigel W. Moriarty, Airlie J. McCoy, Thomas C. Terwilliger, Peter H. Zwart, Nicholas K. Sauter, Ralf W. Grosse-Kunstleve, Erik McKee, James C. Sacchettini, Pavel V. Afonine, Randy J. Read, Laurent C. Storoni, and Thomas R. Ioerger
- Subjects
Set (abstract data type) ,Structure (mathematical logic) ,Computer science ,Suite ,Molecular replacement ,Crystal structure ,Resolution (logic) ,Bioinformatics ,Macromolecule ,Computational science - Abstract
Significant time and effort are often required to solve and complete a macromolecular crystal structure. The development of automated computational methods for the analysis, solution, and completion of crystallographic structures has the potential to produce minimally biased models in a short time without the need for manual intervention. The PHENIX software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution, and good quality data. This achievement has been made possible by the development of new algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template- and pattern-based automated model-building (RESOLVE, TEXTAL), automated macromolecular refinement (phenix. refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that have been built and made available to the community. The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI.
- Published
- 2008
- Full Text
- View/download PDF
22. Automated structure determination with phenix
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Ralf W. Grosse-Kunstleve, Peter H. Zwart, Nicholas K. Sauter, Pavel V. Afonine, Tod D. Romo, Lalji Kanbi, Airlie J. McCoy, Kreshna Gopal, Erik McKee, Li-Wei Hung, Thomas R. Ioerger, Nigel W. Moriarty, Paul D. Adams, Reetal Pai, Randy J. Read, Thomas C. Terwilliger, Laurent C. Storoni, James C. Sacchettini, and Thiru Radhakannan
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Crystallography ,Computer science ,business.industry ,Reduced intensity ,Software system ,User interface ,Python (programming language) ,business ,Automation ,computer ,Computational science ,computer.programming_language - Abstract
A new software system called PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) has been developed for the automation of crystallographic structure solution. This provides algorithms to go from reduced intensity data to a refined molecular model, and facilitates structure solution for both the novice and expert crystallographer. Here, we review the major features of PHENIX, including the different user interfaces, and briefly describe the recent advances in infrastructure and algorithms.
- Published
- 2007
- Full Text
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23. FINDMOL: automated identification of macromolecules in electron-density maps
- Author
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Lalji Kanbi, James C. Sacchettini, Ralf W. Grosse-Kunstleve, Erik McKee, Paul D. Adams, Kevin L. Childs, and Thomas R. Ioerger
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Models, Molecular ,Electron density ,Parsing ,Computer science ,Macromolecular Substances ,Low resolution ,Electrons ,General Medicine ,computer.software_genre ,Crystallography, X-Ray ,Rendering (computer graphics) ,Biological unit ,Crystallography ,Structural Biology ,Alpha-Globulins ,Cluster Analysis ,Model building ,Algorithm ,computer ,Prior information ,Algorithms ,Macromolecule - Abstract
Automating the determination of novel macromolecular structures via X-ray crystallographic methods involves building a model into an electron-density map. Unfortunately, the conventional crystallographic asymmetric unit volumes are usually not well matched to the biological molecular units. In most cases, the facets of the asymmetric unit cut the molecules into a number of disconnected fragments, rendering interpretation by the crystallographer significantly more difficult. The FINDMOL algorithm is designed to quickly parse the arrangement of trace points (pseudo-atoms) derived from a skeletonized electron-density map without requiring higher level prior information such as sequence information or number of molecules in the asymmetric unit. The algorithm was tested with a variety of density-modified maps computed with medium- to low-resolution data. Typically, the resulting volume resembles the biological unit. In the remaining cases the number of disconnected fragments is very small. In all examples, secondary-structural elements such as alpha-helices or beta-sheets are easily identifiable in the defragmented arrangement. FINDMOL can greatly assist a crystallographer during manual model building or in cases where automatic model building can only build partial models owing to limitations of the data such as low resolution and/or poor phases.
- Published
- 2005
24. Filamentation as a diagnostic to measure molecular alignment
- Author
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Magali Durand, Tamar Seideman, Matthieu Baudelet, Erik McKee, Khan Lim, Ramakrishna Sesha Shankar, and Martin Richardson
- Subjects
Physics ,business.industry ,Measure (physics) ,Physics::Optics ,Plasma ,Laser ,law.invention ,Protein filament ,Optics ,Filamentation ,law ,Femtosecond ,Molecular alignment ,business ,Refractive index - Abstract
The properties of a femtosecond laser filament (the initial collapse distance and plasma length) have been studied in a pre-aligned gas and prove to be an effective diagnostic for molecular alignment.
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