WorldWideScience

Sample records for beam based alignment

  1. Simulator for beam-based LHC collimator alignment

    Science.gov (United States)

    Valentino, Gianluca; Aßmann, Ralph; Redaelli, Stefano; Sammut, Nicholas

    2014-02-01

    In the CERN Large Hadron Collider, collimators need to be set up to form a multistage hierarchy to ensure efficient multiturn cleaning of halo particles. Automatic algorithms were introduced during the first run to reduce the beam time required for beam-based setup, improve the alignment accuracy, and reduce the risk of human errors. Simulating the alignment procedure would allow for off-line tests of alignment policies and algorithms. A simulator was developed based on a diffusion beam model to generate the characteristic beam loss signal spike and decay produced when a collimator jaw touches the beam, which is observed in a beam loss monitor (BLM). Empirical models derived from the available measurement data are used to simulate the steady-state beam loss and crosstalk between multiple BLMs. The simulator design is presented, together with simulation results and comparison to measurement data.

  2. Beam-based alignment of CLIC drive beam decelerator using girders movers

    CERN Document Server

    Sterbini, G

    2011-01-01

    The CLIC drive beams will provide the rf power to accelerate the colliding beams: in order to reach the design performance, an efficient transport of the drive beam has to be ensured in spite of its challenging energy spread and large current intensity. As shown in previous studies, the specifications can be met by coupling a convenient optics design with the state-of-the-art of pre-alignment and beambased alignment techniques. In this paper we consider a novel beam-based alignment scheme that does not require quadrupole movers or dipole correctors but uses the motors already foreseen for the pre-alignment system. This implies potential savings in terms of complexity and cost at the expense of the alignment flexibility: the performance, limitations and sensitivity to pre-alignment tolerances of this method are discussed.

  3. Comparison of LHC collimator beam-based alignment to BPM-Interpolated centers

    CERN Document Server

    Valentino, G; Assmann, R W; Bruce, R; Muller, G J; Redaelli, S; Rossi, A; Lari, L

    2012-01-01

    The beam centers at the Large Hadron Collider collimators are determined by beam-based alignment, where both jaws of a collimator are moved in separately until a loss spike is detected on a Beam LossMonitor downstream. Orbit drifts of more than a few hundred micrometers cannot be tolerated, as they would compromise the performance of the collimation system. Beam Position Monitors (BPMs) are installed at various locations around the LHC ring, and a linear interpolation of the orbit can be obtained at the collimator positions. In this paper, the results obtained from beam-based alignment are compared with the orbit interpolated from the BPM data throughout the 2011 and 2012 LHC proton runs.

  4. Beam based alignment at the KEK accelerator test facility

    International Nuclear Information System (INIS)

    Ross, M.; Nelson, J.; Woodley, M.; Wolski, A.

    2002-01-01

    The KEK Accelerator Test Facility (ATF) damping ring is a prototype low emittance source for the NLC/JLC linear collider. To achieve the goal normalized vertical emittance gey = 20 nm-rad, magnet placement accuracy better than 30 mm must be achieved. Accurate beam-based alignment (BBA) is required. The ATF arc optics uses a FOBO cell with two horizontally focusing quadrupoles, two sextupoles and a horizontally defocusing gradient dipole, all of which must be aligned with BBA. BBA at ATF uses the quadrupole and sextupole trim windings to find the trajectory through the center of each magnet. The results can be interpreted to assess the accuracy of the mechanical alignment and the beam position monitor offsets

  5. Tests of beam-based alignement at FACET

    CERN Document Server

    Latina, A; Schulte, D; Adli, E

    2014-01-01

    The performance of future linear colliders will depend critically on beam-based alignment (BBA) and feedback systems, which will play a crucial role in guaranteeing the low emittance transport throughout such machines. BBA algorithms designed to improve the beam transmission in a linac by simultaneously optimising the trajectory and minimising the residual dispersion, have thoughtfully been studied in theory over the last years, and successfully verified experimentally. One such technique is called Dispersion-Free Steering (DFS). A careful study of the DFS performance at the SLAC test facility FACET lead us to design a beam-based technique specifically targeted to reduce the impact of transverse short-range wakefields, rather than of the dispersion, being the wakefields the limiting factor to the FACET performance. This technique is called Wakefield-Free Steering (WFS). The results of the first tests of WFS at FACET are presented in this paper.

  6. Beam-based alignment at the KEK-ATF damping ring

    International Nuclear Information System (INIS)

    Woodley, Mark D.; Nelson, Janice; Ross, Marc; Turner, James; Wolski, A.; Kubo, Kiyoshi

    2004-01-01

    The damping rings of a future linear collider will have demanding alignment and stability requirements in order to achieve the low vertical emittance necessary for high luminosity. The Accelerator Test Facility (ATF) at KEK has successfully demonstrated the vertical emittance below 5 pm that is specified for the GLC/NLC Main Damping Rings. One contribution to this accomplishment has been the use of Beam Based Alignment (BBA) techniques. The mode of operation of the ATF presents particular challenges for BBA, and we describe here how we have deduced the offsets of the BPMs with respect to the quadrupoles. We also discuss a technique that allows for direct measurements of the beam-to-quad offsets

  7. Mechanical alignment based on beam diagnostics

    International Nuclear Information System (INIS)

    Farvacque, L.; Martin, D.; Nagaoka, R.

    1999-01-01

    This article studies the consequences of misalignment of the different components on the displacement of the beam. 3 types of motion have been investigated: quadrupole vertical displacement, quadrupole tilt and sextupole vertical displacement. For each shift a response matrix has been designed and from this formulation, aligning quadrupoles means inverting this matrix. The strategy for correction depends on the accuracy of the response matrix and on the quality of the beam position measurements. A modelling of the corrections is proposed. (A.C.)

  8. Beam-based alignment of C-shaped quadrupole magnets

    International Nuclear Information System (INIS)

    Portmann, G.; Robin, D.

    1998-06-01

    Many storage rings have implemented a method of finding the positional offset between the electrical center of the beam position monitors (BPM) and the magnetic center of the adjacent quadrupole magnets. The algorithm for accomplishing this is usually based on modulating the current in the quadrupole magnet and finding the beam position that minimizes the orbit perturbation. When the quadrupole magnet is C-shaped, as it is for many light sources, the modulation method can produce an erroneous measurement of the magnetic center in the horizontal plane. When the current in a C-shaped quadrupole is changed, there is an additional dipole component in the vertical field. Due to nonlinearities in the hysteresis cycle of the C-magnet geometry, the beam-based alignment technique at the Advanced Light Source (ALS) deviated horizontally by .5 mm from the actual magnetic center. By modifying the technique, the offsets were measured to an accuracy of better than 50 microm

  9. Generation and application of Bessel beam in alignment works

    International Nuclear Information System (INIS)

    Gale, D. M.

    2009-01-01

    The divergence of a Gaussian laser beam is a limiting factor for optical alignment tasks at large distances. Bessel beams have almost zero divergence but are still not widely used. We discuss the construction of an alignment telescope based on Bessel beam generation using a commercial laser diode module. The Bessel beam is generated with conical or plano-convex lenses, and projected using a commercial CCD camera lens to extend the useful range of the beam. Our Bessel beams have diameters of between 0.5 - 1mm over beam lengths of 15m, representing a six-fold improvement compared to Gaussian beams, while the transverse beam structure (Bessel pattern) provides an excellent alignment aid for use with beam target. Another advantage of Bessel beams is their self-regeneration property, which allows the use of multiple beam targets with minimum beam degradation. We are using our crosshair targets with crosshair targets to align optical components in a large astronomical telescope, and can achieve precisions of tens of microns over distances of 20m using purely visual methods. (Author)

  10. Antares beam-alignment-system performance

    International Nuclear Information System (INIS)

    Appert, Q.D.; Bender, S.C.

    1983-01-01

    The beam alignment system for the 24-beam-sector Antares CO 2 fusion laser automatically aligns more than 200 optical elements. A visible-wavelength alignment technique is employed which uses a telescope/TV system to view point-light sources appropriately located down the beamline. The centroids of the light spots are determined by a video tracker, which generates error signals used by the computer control system to move appropriate mirrors in a closed-loop system. Final touch-up alignment is accomplished by projecting a CO 2 alignment laser beam through the system and sensing its position at the target location. The techniques and control algorithms employed have resulted in alignment accuracies exceeding design requirements. By employing video processing to determine the centroids of diffraction images and by averaging over multiple TV frames, we achieve alignment accuracies better than 0.1 times system diffraction limits in the presence of air turbulence

  11. Reducing beam shaper alignment complexity: diagnostic techniques for alignment and tuning

    Science.gov (United States)

    Lizotte, Todd E.

    2011-10-01

    Safe and efficient optical alignment is a critical requirement for industrial laser systems used in a high volume manufacturing environment. Of specific interest is the development of techniques to align beam shaping optics within a beam line; having the ability to instantly verify by a qualitative means that each element is in its proper position as the beam shaper module is being aligned. There is a need to reduce these types of alignment techniques down to a level where even a newbie to optical alignment will be able to complete the task. Couple this alignment need with the fact that most laser system manufacturers ship their products worldwide and the introduction of a new set of variables including cultural and language barriers, makes this a top priority for manufacturers. Tools and methodologies for alignment of complex optical systems need to be able to cross these barriers to ensure the highest degree of up time and reduce the cost of maintenance on the production floor. Customers worldwide, who purchase production laser equipment, understand that the majority of costs to a manufacturing facility is spent on system maintenance and is typically the largest single controllable expenditure in a production plant. This desire to reduce costs is driving the trend these days towards predictive and proactive, not reactive maintenance of laser based optical beam delivery systems [10]. With proper diagnostic tools, laser system developers can develop proactive approaches to reduce system down time, safe guard operational performance and reduce premature or catastrophic optics failures. Obviously analytical data will provide quantifiable performance standards which are more precise than qualitative standards, but each have a role in determining overall optical system performance [10]. This paper will discuss the use of film and fluorescent mirror devices as diagnostic tools for beam shaper module alignment off line or in-situ. The paper will also provide an overview

  12. Electron Beam Alignment Strategy in the LCLS Undulators

    International Nuclear Information System (INIS)

    Nuhn, H

    2007-01-01

    The x-ray FEL process puts very tight tolerances on the straightness of the electron beam trajectory (2 (micro)m rms) through the LCLS undulator system. Tight but less stringent tolerances of 80 (micro)m rms vertical and 140 (micro)m rms horizontally are to be met for the placement of the individual undulator segments with respect to the beam axis. The tolerances for electron beam straightness can only be met through beam-based alignment (BBA) based on electron energy variations. Conventional alignment will set the start conditions for BBA. Precision-fiducialization of components mounted on remotely adjustable girders and the use of beam-finder wires (BFW) will satisfy placement tolerances. Girder movement due to ground motion and temperature changes will be monitored continuously by an alignment monitoring system (ADS) and remotely corrected. This stabilization of components as well as the monitoring and correction of the electron beam trajectory based on BPMs and correctors will increase the time between BBA applications. Undulator segments will be periodically removed from the undulator Hall and measured to monitor radiation damage and other effects that might degrade undulator tuning

  13. ACCELERATORS: Beam based alignment of the SSRF storage ring

    Science.gov (United States)

    Zhang, Man-Zhou; Li, Hao-Hu; Jiang, Bo-Cheng; Liu, Gui-Min; Li, De-Ming

    2009-04-01

    There are 140 beam position monitors (BPMs) in the Shanghai Synchrotron Radiation Facility (SSRF) storage ring used for measuring the closed orbit. As the BPM pickup electrodes are assembled directly on the vacuum chamber, it is important to calibrate the electrical center offset of the BPM to an adjacent quadrupole magnetic center. A beam based alignment (BBA) method which varies individual quadrupole magnet strength and observes its effects on the orbit is used to measure the BPM offsets in both the horizontal and vertical planes. It is a completely automated technique with various data processing methods. There are several parameters such as the strength change of the correctors and the quadrupoles which should be chosen carefully in real measurement. After several rounds of BBA measurement and closed orbit correction, these offsets are set to an accuracy better than 10 μm. In this paper we present the method of beam based calibration of BPMs, the experimental results of the SSRF storage ring, and the error analysis.

  14. Beam alignment based on two-dimensional power spectral density of a near-field image.

    Science.gov (United States)

    Wang, Shenzhen; Yuan, Qiang; Zeng, Fa; Zhang, Xin; Zhao, Junpu; Li, Kehong; Zhang, Xiaolu; Xue, Qiao; Yang, Ying; Dai, Wanjun; Zhou, Wei; Wang, Yuanchen; Zheng, Kuixing; Su, Jingqin; Hu, Dongxia; Zhu, Qihua

    2017-10-30

    Beam alignment is crucial to high-power laser facilities and is used to adjust the laser beams quickly and accurately to meet stringent requirements of pointing and centering. In this paper, a novel alignment method is presented, which employs data processing of the two-dimensional power spectral density (2D-PSD) for a near-field image and resolves the beam pointing error relative to the spatial filter pinhole directly. Combining this with a near-field fiducial mark, the operation of beam alignment is achieved. It is experimentally demonstrated that this scheme realizes a far-field alignment precision of approximately 3% of the pinhole size. This scheme adopts only one near-field camera to construct the alignment system, which provides a simple, efficient, and low-cost way to align lasers.

  15. Successive approximation algorithm for beam-position-monitor-based LHC collimator alignment

    Science.gov (United States)

    Valentino, Gianluca; Nosych, Andriy A.; Bruce, Roderik; Gasior, Marek; Mirarchi, Daniele; Redaelli, Stefano; Salvachua, Belen; Wollmann, Daniel

    2014-02-01

    Collimators with embedded beam position monitor (BPM) button electrodes will be installed in the Large Hadron Collider (LHC) during the current long shutdown period. For the subsequent operation, BPMs will allow the collimator jaws to be kept centered around the beam orbit. In this manner, a better beam cleaning efficiency and machine protection can be provided at unprecedented higher beam energies and intensities. A collimator alignment algorithm is proposed to center the jaws automatically around the beam. The algorithm is based on successive approximation and takes into account a correction of the nonlinear BPM sensitivity to beam displacement and an asymmetry of the electronic channels processing the BPM electrode signals. A software implementation was tested with a prototype collimator in the Super Proton Synchrotron. This paper presents results of the tests along with some considerations for eventual operation in the LHC.

  16. Resolution and systematic limitations in beam based alignment

    Energy Technology Data Exchange (ETDEWEB)

    Tenenbaum, P.G.

    2000-03-15

    Beam based alignment of quadrupoles by variation of quadrupole strength is a widely-used technique in accelerators today. The authors describe the dominant systematic limitation of this technique, which arises from the change in the center position of the quadrupole as the strength is varied, and derive expressions for the resulting error. In addition, the authors derive an expression for the statistical resolution of such techniques in a periodic transport line, given knowledge of the line's transport matrices, the resolution of the beam position monitor system, and the details of the strength variation procedure. These results are applied to the Next Linear Collider main linear accelerator, an 11 kilometer accelerator containing 750 quadrupoles and 5,000 accelerator structures. The authors find that in principle a statistical resolution of 1 micron is easily achievable but the systematic error due to variation of the magnetic centers could be several times larger.

  17. Beam-Based Alignment of Magnetic Field in the Fermilab Electron Cooler Cooling Section

    International Nuclear Information System (INIS)

    Seletskiy, S. M.; Tupikov, V.

    2006-01-01

    The Fermilab Electron Cooling Project requires low effective anglular spread of electrons in the cooling section. One of the main components of the effective electron angles is an angle of electron beam centroid with respect to antiproton beam. This angle is caused by the poor quality of magnetic field in the 20 m long cooling section solenoid and by the mismatch of the beam centroid to the entrance of the cooling section. This paper focuses on the beam-based procedure of the alignment of the cooling section field and beam centroid matching. The discussed procedure allows to suppress the beam centroid angles below the critical value of 0.1 mrad

  18. Successive approximation algorithm for beam-position-monitor-based LHC collimator alignment

    Directory of Open Access Journals (Sweden)

    Gianluca Valentino

    2014-02-01

    Full Text Available Collimators with embedded beam position monitor (BPM button electrodes will be installed in the Large Hadron Collider (LHC during the current long shutdown period. For the subsequent operation, BPMs will allow the collimator jaws to be kept centered around the beam orbit. In this manner, a better beam cleaning efficiency and machine protection can be provided at unprecedented higher beam energies and intensities. A collimator alignment algorithm is proposed to center the jaws automatically around the beam. The algorithm is based on successive approximation and takes into account a correction of the nonlinear BPM sensitivity to beam displacement and an asymmetry of the electronic channels processing the BPM electrode signals. A software implementation was tested with a prototype collimator in the Super Proton Synchrotron. This paper presents results of the tests along with some considerations for eventual operation in the LHC.

  19. Beam based alignment of the SLC final focus sextupoles

    International Nuclear Information System (INIS)

    Emma, P.; Irwin, J.; Phinney, N.; Raimondi, P.; Toge, N.; Walker, N.J.; Ziemann, V.

    1993-05-01

    The strong demagnification inherent in final focus systems requires local cancellation of the resulting chromaticty. Strong sextupole pair separated by a -I transform are positioned π/2 in the betatron phase away from the Interaction Point (IP) in order to cancel chromatic aberrations primarily due to the final quadrupoles. Sextupole alignment is critical in order to provide orthogonal tuning of the chromaticty and, in the case of the SLC, to limit the third and higher order optical aberrations generated from misaligned and 'nested' horizontal and vertical sextupole pairs. Reported here is a novel technique for aligning the beam centroid to the sextupole centers, which uses measurements of the criticality dependent parameter - the beam size at the IP. Results for the SLC final focus sextupoles are presented, where a resolution of <50 μm is achieved

  20. Laser beam alignment and profilometry using diagnostic fluorescent safety mirrors

    Science.gov (United States)

    Lizotte, Todd E.

    2011-03-01

    There are a wide range of laser beam delivery systems in use for various purposes; including industrial and medical applications. Virtually all such beam delivery systems for practical purposes employ optical systems comprised of mirrors and lenses to shape, focus and guide the laser beam down to the material being processed. The goal of the laser beam delivery is to set the optimum parameters and to "fold" the beam path to reduce the mechanical length of the optical system, thereby allowing a physically compact system. In many cases, even a compact system can incorporate upwards of six mirrors and a comparable number of lenses all needing alignment so they are collinear. One of the major requirements for use of such systems in industry is a method of safe alignment. The alignment process requires that the aligner determine where the beam strikes each element. The aligner should also preferably be able to determine the shape or pattern of the laser beam at that point and its relative power. These alignments are further compounded in that the laser beams generated are not visible to the unaided human eye. Such beams are also often of relatively high power levels, and are thereby a significant hazard to the eyes of the aligner. Obvious an invisible beam makes it nearly impossible to align laser system without some form of optical assistance. The predominant method of visually aligning the laser beam delivery is the use of thermal paper, paper cards or fluorescing card material. The use of paper products which have limited power handling capability or coated plastics can produce significant debris and contaminants within the beam line that ultimately damage the optics. The use of the cards can also create significant laser light scatter jeopardizing the safety of the person aligning the system. This paper covers a new safety mirror design for use with at various UV and Near IR wavelengths (193 nm to 1064 nm) within laser beam delivery systems and how its use can

  1. An optimal beam alignment method for large-scale distributed space surveillance radar system

    Science.gov (United States)

    Huang, Jian; Wang, Dongya; Xia, Shuangzhi

    2018-06-01

    Large-scale distributed space surveillance radar is a very important ground-based equipment to maintain a complete catalogue for Low Earth Orbit (LEO) space debris. However, due to the thousands of kilometers distance between each sites of the distributed radar system, how to optimally implement the Transmitting/Receiving (T/R) beams alignment in a great space using the narrow beam, which proposed a special and considerable technical challenge in the space surveillance area. According to the common coordinate transformation model and the radar beam space model, we presented a two dimensional projection algorithm for T/R beam using the direction angles, which could visually describe and assess the beam alignment performance. Subsequently, the optimal mathematical models for the orientation angle of the antenna array, the site location and the T/R beam coverage are constructed, and also the beam alignment parameters are precisely solved. At last, we conducted the optimal beam alignment experiments base on the site parameters of Air Force Space Surveillance System (AFSSS). The simulation results demonstrate the correctness and effectiveness of our novel method, which can significantly stimulate the construction for the LEO space debris surveillance equipment.

  2. Strategy for alignment of electron beam trajectory in LEReC cooling section

    Energy Technology Data Exchange (ETDEWEB)

    Seletskiy, S. [Brookhaven National Lab. (BNL), Upton, NY (United States); Blaskiewicz, M. [Brookhaven National Lab. (BNL), Upton, NY (United States); Fedotov, A. [Brookhaven National Lab. (BNL), Upton, NY (United States); Kayran, D. [Brookhaven National Lab. (BNL), Upton, NY (United States); Kewisch, J. [Brookhaven National Lab. (BNL), Upton, NY (United States); Michnoff, R. [Brookhaven National Lab. (BNL), Upton, NY (United States); Pinayev, I. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2016-09-23

    We considered the steps required to align the electron beam trajectory through the LEReC cooling section. We devised a detailed procedure for the beam-based alignment of the cooling section solenoids. We showed that it is critical to have an individual control of each CS solenoid current. Finally, we modeled the alignment procedure and showed that with two BPM fitting the solenoid shift can be measured with 40 um accuracy and the solenoid inclination can be measured with 30 urad accuracy. These accuracies are well within the tolerances of the cooling section solenoid alignment.

  3. CLIC main beam quadrupole active pre-alignment based on cam movers

    CERN Document Server

    Kemppinen, J; Leuxe, R; Mainaud Durand, H; Sandomierski, J; Sosin, M

    2012-01-01

    Compact Linear Collider (CLIC) is a study for a future 48 km long linear electron-positron collider in the multi TeV range. Its target luminosity can only be reached if the main beam quadrupoles (MB quads) are actively pre-aligned within 17 µm in sliding windows of 200 m with respect to a straight reference line. In addition to the positioning requirement, the pre-alignment system has to provide a rigid support for the nano-stabilization system to ensure that the first eigenfrequency is above 100 Hz. Re-adjustment based on cam movers was chosen for detailed studies to meet the stringent pre-alignment requirements. There are four different types of MB quads in CLIC. Their lengths and masses vary so that at least two types of cam movers have to be developed. The validation of the cams with less stringent space restrictions has proceeded to a test setup in 5 degrees of freedom (DOF). Prototypes of the more demanding, smaller cams have been manufactured and they are under tests in 1 DOF. This paper describes the...

  4. Beam-based alignment technique for the SLC [Stanford Linear Collider] linac

    International Nuclear Information System (INIS)

    Adolphsen, C.E.; Lavine, T.L.; Atwood, W.B.

    1989-03-01

    Misalignment of quadrupole magnets and beam position monitors (BPMs) in the linac of the SLAC Linear Collider (SLC) cause the electron and positron beams to be steered off-center in the disk-loaded waveguide accelerator structures. Off-center beams produce wakefields which limit the SLC performance at high beam intensities by causing emittance growth. Here, we present a general method for simultaneously determining quadrupole magnet and BPM offsets using beam trajectory measurements. Results from the application of the method to the SLC linac are described. The alignment precision achieved is approximately 100 μm, which is significantly better than that obtained using optical surveying techniques. 2 refs., 4 figs

  5. Beam based alignment and its relevance in Indus-2

    Energy Technology Data Exchange (ETDEWEB)

    Jena, Saroj Kumar; Husain, Riyasat; Gandhi, M. L.; Agrawal, R. K.; Yadav, S.; Ghodke, A. D. [Raja Ramanna Centre for Advanced Technology, Indore (India)

    2015-09-15

    Initially in the Indus-2 storage ring, the closed orbit distortion (COD) could be best corrected to 1.3 mm rms in the horizontal and 0.43 mm rms in the vertical plane. The strength of the corrector magnets required high values for COD correction. This revealed that offsets in COD readout by the beam position monitors (BPMs) played a role in not achieving a rms COD lower than the above value. Thus, the offset between the electrical center of BPMs and the magnetic center of the nearest quadrupole magnet could be estimated using the beam based alignment (BBA) method. It prefers that the quadrupole magnet is able to be controlled individually and active shunt power supply (ASPS) system was designed for this purpose that works efficiently. This paper describes the methodology of BBA, topology of ASPS and its performance, and COD minimization using the measured BPM offsets. After BBA, the COD could be reduced to 0.45 mm rms and 0.2 mm rms in horizontal and vertical planes, respectively.

  6. Beam based alignment and its relevance in Indus-2

    Science.gov (United States)

    Jena, Saroj Kumar; Husain, Riyasat; Gandhi, M. L.; Agrawal, R. K.; Yadav, S.; Ghodke, A. D.

    2015-09-01

    Initially in the Indus-2 storage ring, the closed orbit distortion (COD) could be best corrected to 1.3 mm rms in the horizontal and 0.43 mm rms in the vertical plane. The strength of the corrector magnets required high values for COD correction. This revealed that offsets in COD readout by the beam position monitors (BPMs) played a role in not achieving a rms COD lower than the above value. Thus, the offset between the electrical center of BPMs and the magnetic center of the nearest quadrupole magnet could be estimated using the beam based alignment (BBA) method. It prefers that the quadrupole magnet is able to be controlled individually and active shunt power supply (ASPS) system was designed for this purpose that works efficiently. This paper describes the methodology of BBA, topology of ASPS and its performance, and COD minimization using the measured BPM offsets. After BBA, the COD could be reduced to 0.45 mm rms and 0.2 mm rms in horizontal and vertical planes, respectively.

  7. The beam based alignment technique for the measurements of beam position monitors offsets and beam offsets from quadrupoles in the Pohang Light Source

    International Nuclear Information System (INIS)

    Kim, K.H.; Huang, J.Y.; Ko, I.S.

    1999-01-01

    The beam based alignment (BBA) technique is applied to the 2-GeV storage ring of the Pohang Light Source to measure the offsets of beam position monitors. This measurement is particularly necessary for beam position monitors (BPMs) plugged into a long (∼10 m) aluminum chamber, since the mechanical deformation of the vacuum chamber is experienced after repeated heating for the outgassing process, and the BPM positions are changed accordingly. A part of the excitation current of each quadrupole magnet is shunted through an electronic shunt circuit. Then, the closed orbit receives a perturbation due to the current reduction. Using two quadrupole magnets, we can measure the offset of each BPM. Also, the BBA technique is applied to measure the beam offsets from the center of quadrupole magnets, and gives information to the survey team about which quadrupole magnets should be aligned mostly. In this process, we introduce the merit function to reduce various errors such as BPM characteristic changes and the lattice imperfection. By minimizing the merit function, we can get the beam offset as the maximized expectation value. This paper presents the BBA technique used and experimental results taken from the 2-GeV Pohang Light Source (PLS) storage ring. When the BPM offset is measured, it is observed that a 3% of the shunt current is suitable. (author)

  8. Development of an Eccentric CAM Based Active Pre-Alignment System for the CLIC Main Beam Quadrupole Magnet

    CERN Document Server

    Lackner, F; Collette, C; Mainaud Durand, H; Hauviller, C; Kemppinen, J; Leuxe, R

    2010-01-01

    CLIC (Compact Linear Collider) is a study for a future electron-positron collider that would allow physicists to explore a new energy region beyond the capabilities of today's particle accelerators. The demanding transverse and vertical beam sizes and emittance specifications are resulting in stringent alignment and a nanometre stability requirement. In the current feasibility study, the main beam quadrupole magnets have to be actively pre-aligned with a precision of 1 µm in 5 degrees of freedom (d.o.f.) before being mechanically stabilized to the nm scale above 1 Hz. This contribution describes the approach of performing this active pre-alignment based on an eccentric cam system. In order to limit the amplification of the vibration sources at resonant frequencies a sufficiently high Eigenfrequency is required. Therefore the contact region between cam and support was optimized for adequate stiffness based on the Hertzian theory. Furthermore, practical tests performed on a single degree of freedom mock-up wil...

  9. Beam-based alignment and tuning procedures for e+e- collider final focus systems

    International Nuclear Information System (INIS)

    Bulos, F.; Burke, D.; Helm, R.; Irwin, J.; Odian, A.; Roy, G.; Ruth, R.; Yamamoto

    1991-01-01

    For future linear colliders, with very small emittances and beam sizes and demanding tolerances on final focus system alignment and magnet errors, it becomes increasingly important to use the beam as a diagnostic tool. The authors report here procedures they have identified and will be implemented in the Final Focus Test Beam at SLAC incorporating (1) quadrupole strength changes, (2) central orbit modifications, (3) spot size measurements, and (4) beam stability monitoring

  10. Beam-based alignment and tuning procedures for e+e- collider final focus systems

    International Nuclear Information System (INIS)

    Bulos, F.; Burke, D.; Helm, R.; Irwin, J.; Odian, A.; Roy, G.; Ruth, R.; Yamamoto, N.

    1991-05-01

    For future linear colliders, with very small emittances and beam sizes and demanding tolerances on final focus system alignment and magnet errors, it becomes increasingly important to use the beam as a diagnostic tool. We report here procedures we have identified and will be implemented in the Final Focus Test Beam at SLAC incorporating (1) quadrupole strength changes, (2) central orbit modifications, (3) spot size measurements, and (4) beam stability monitoring. 3 refs., 4 figs., 3 tabs

  11. Fast Beam-Based BPM Calibration

    International Nuclear Information System (INIS)

    Bertsche, Kirk

    2012-01-01

    The Alignment Diagnostic System (ADS) of the LCLS undulator system indicates that the 33 undulator quadrupoles have extremely high position stability over many weeks. However, beam trajectory straightness and lasing efficiency degrade more quickly than this. A lengthy Beam Based Alignment (BBA) procedure must be executed every two to four weeks to re-optimize the X-ray beam parameters. The undulator system includes RF cavity Beam Position Monitors (RFBPMs), several of which are utilized by an automatic feedback system to align the incoming electron-beam trajectory to the undulator axis. The beam trajectory straightness degradation has been traced to electronic drifts of the gain and offset of the BPMs used in the beam feedback system. To quickly recover the trajectory straightness, we have developed a fast beam-based procedure to recalibrate the BPMs. This procedure takes advantage of the high-precision monitoring capability of the ADS, which allows highly repeatable positioning of undulator quadrupoles. This report describes the ADS, the position stability of the LCLS undulator quadrupoles, and some results of the new recovery procedure.

  12. A beam-based alignment technique for correction of accelerator structure misalignments

    International Nuclear Information System (INIS)

    Kubo, K.; Raubenheimer, T.O.

    1994-08-01

    This paper describes a method of reducing the transverse emittance dilution in linear colliders due to transverse wakefields arising-from misaligned accelerator structures. The technique is a generalization of the Wake-Free correction algorithm. The structure alignment errors are measured locally by varying the bunch charge and/or bunch length and measuring the change in the beam trajectory. The misalignments can then be corrected by varying the beam trajectory or moving structures. The results of simulations are presented demonstrating the viability of the technique

  13. Antares automatic beam alignment system

    International Nuclear Information System (INIS)

    Appert, Q.; Swann, T.; Sweatt, W.; Saxman, A.

    1980-01-01

    Antares is a 24-beam-line CO 2 laser system for controlled fusion research, under construction at Los Alamos Scientific Laboratory (LASL). Rapid automatic alignment of this system is required prior to each experiment shot. The alignment requirements, operational constraints, and a developed prototype system are discussed. A visible-wavelength alignment technique is employed that uses a telescope/TV system to view point light sources appropriately located down the beamline. Auto-alignment is accomplished by means of a video centroid tracker, which determines the off-axis error of the point sources. The error is nulled by computer-driven, movable mirrors in a closed-loop system. The light sources are fiber-optic terminations located at key points in the optics path, primarily at the center of large copper mirrors, and remotely illuminated to reduce heating effects

  14. Alignment of the eight beams Octal 82 laser

    International Nuclear Information System (INIS)

    Josse, Michel.

    1982-10-01

    The OCTAL 82 laser facility is a Neodymium glass laser system, recently put in operation at Limeil, France. It is designed to create high energy light beams during very short periods of time in the nanosecond range and shorter, in order to irradiate and compress microscopic fusion targets to extremely high densities. The alignment is undertaken in two stages, each using a telescope with vidicon detectors connected to a real time computer named ''CENTROIDE'' which displays the digitized image on a color TV screen. First, a refracting telescope is used to inject the front-end beam into the preamplifier assembly and to align all its optical components. Second, a reflecting telescope and ten insertable mirrors are used to align the eight individual power chains and the beam splitter arrays. The alignment method works with a manually controlled closed loop which is the most flexible approach that can meet our dual objectives of reliability and accuracy. The over all alignment of OCTAL 82 was first completed in may 1982 and since that time only minor routine realignments have been made, thereby proving the feasibility of the method

  15. Initial alignment method for free space optics laser beam

    Science.gov (United States)

    Shimada, Yuta; Tashiro, Yuki; Izumi, Kiyotaka; Yoshida, Koichi; Tsujimura, Takeshi

    2016-08-01

    The authors have newly proposed and constructed an active free space optics transmission system. It is equipped with a motor driven laser emitting mechanism and positioning photodiodes, and it transmits a collimated thin laser beam and accurately steers the laser beam direction. It is necessary to introduce the laser beam within sensible range of the receiver in advance of laser beam tracking control. This paper studies an estimation method of laser reaching point for initial laser beam alignment. Distributed photodiodes detect laser luminescence at respective position, and the optical axis of laser beam is analytically presumed based on the Gaussian beam optics. Computer simulation evaluates the accuracy of the proposed estimation methods, and results disclose that the methods help us to guide the laser beam to a distant receiver.

  16. A Dynamic Alignment System for the Final Focus Test Beam

    International Nuclear Information System (INIS)

    Ruland, R.E.; Bressler, V.E.; Fischer, G.; Plouffe, D.; SLAC

    2005-01-01

    The Final Focus Test Beam (FFTB) was conceived as a technological stepping stone on the way to the next linear collider. Nowhere is this more evident than with the alignment subsystems. Alignment tolerances for components prior to beam turn are almost an order of magnitude smaller than for previous projects at SLAC. Position monitoring systems which operate independent of the beam are employed to monitor motions of the components locally and globally with unprecedented precision. An overview of the FFTB alignment system is presented herein

  17. Quadrupole beam-based alignment in the RHIC interaction regions

    International Nuclear Information System (INIS)

    Ziegler, J.; Satogata, T.

    2011-01-01

    Continued beam-based alignment (BBA) efforts have provided significant benefit to both heavy ion and polarized proton operations at RHIC. Recent studies demonstrated previously unknown systematic beam position monitor (BPM) offset errors and produced accurate measurements of individual BPM offsets in the experiment interaction regions. Here we describe the algorithm used to collect and analyze data during the 2010 and early 2011 RHIC runs and the results of these measurements. BBA data has been collected over the past two runs for all three of the active experimental IRs at RHIC, updating results from the 2005 run which were taken with incorrectly installed offsets. The technique was successfully applied to expose a systematic misuse of the BPM survey offsets in the control system. This is likely to benefit polarized proton operations as polarization transmission through acceleration ramps depends on RMS orbit control in the arcs, but a quantitative understanding of its impact is still under active investigation. Data taking is ongoing as are refinements to the BBA technique aimed at reducing systematic errors and properly accounting for dispersive effects. Further development may focus on non-triplet BPMs such as those located near snakes, or arc quadrupoles that do not have individually shunted power supplies (a prerequisite for the current method) and as such, will require a modified procedure.

  18. SRF cavity alignment detection method using beam-induced HOM with curved beam orbit

    Science.gov (United States)

    Hattori, Ayaka; Hayano, Hitoshi

    2017-09-01

    We have developed a method to obtain mechanical centers of nine cell superconducting radio frequency (SRF) cavities from localized dipole modes, that is one of the higher order modes (HOM) induced by low-energy beams. It is to be noted that low-energy beams, which are used as alignment probes, are easy to bend in fringe fields of accelerator cavities. The estimation of the beam passing orbit is important because only information about the beam positions measured by beam position monitors outside the cavities is available. In this case, the alignment information about the cavities can be obtained by optimizing the parameters of the acceleration components over the beam orbit simulation to consistently represent the position of the beam position monitors measured at every beam sweep. We discuss details of the orbit estimation method, and estimate the mechanical center of the localized modes through experiments performed at the STF accelerator. The mechanical center is determined as (x , y) =(0 . 44 ± 0 . 56 mm , - 1 . 95 ± 0 . 40 mm) . We also discuss the error and the applicable range of this method.

  19. Minimal-effort planning of active alignment processes for beam-shaping optics

    Science.gov (United States)

    Haag, Sebastian; Schranner, Matthias; Müller, Tobias; Zontar, Daniel; Schlette, Christian; Losch, Daniel; Brecher, Christian; Roßmann, Jürgen

    2015-03-01

    In science and industry, the alignment of beam-shaping optics is usually a manual procedure. Many industrial applications utilizing beam-shaping optical systems require more scalable production solutions and therefore effort has been invested in research regarding the automation of optics assembly. In previous works, the authors and other researchers have proven the feasibility of automated alignment of beam-shaping optics such as collimation lenses or homogenization optics. Nevertheless, the planning efforts as well as additional knowledge from the fields of automation and control required for such alignment processes are immense. This paper presents a novel approach of planning active alignment processes of beam-shaping optics with the focus of minimizing the planning efforts for active alignment. The approach utilizes optical simulation and the genetic programming paradigm from computer science for automatically extracting features from a simulated data basis with a high correlation coefficient regarding the individual degrees of freedom of alignment. The strategy is capable of finding active alignment strategies that can be executed by an automated assembly system. The paper presents a tool making the algorithm available to end-users and it discusses the results of planning the active alignment of the well-known assembly of a fast-axis collimator. The paper concludes with an outlook on the transferability to other use cases such as application specific intensity distributions which will benefit from reduced planning efforts.

  20. A technique for aligning sextupole systems using beam optics

    International Nuclear Information System (INIS)

    Chao, Yu-Chiu.

    1992-03-01

    A technique for beam based alignment of sextupole system is developed exploiting the enhancement effect of orbit differences by the sextupoles. This technique can in principle be applied to sextupole or sextupole strings with controlled orbit pattern and BPM configurations. This paper will discuss the theoretical basis, special optimization considerations and expected accuracy. Application to the SLC final focus is also discussed

  1. Laser alignment measurement model with double beam

    Science.gov (United States)

    Mo, Changtao; Zhang, Lili; Hou, Xianglin; Wang, Ming; Lv, Jia; Du, Xin; He, Ping

    2012-10-01

    Double LD-Double PSD schedule.employ a symmetric structure and there are a laser and a PSD receiver on each axis. The Double LD-Double PSD is used, and the rectangular coordinate system is set up by use of the relationship of arbitrary two points coordinates, and then the parameter formula is deduced by the knowledge of solid geometry. Using the data acquisition system and the data processing model of laser alignment meter with double laser beam and two detector , basing on the installation parameter of the computer, we can have the state parameter between the two shafts by more complicated calculation and correction. The correcting data of the four under chassis of the adjusted apparatus moving on the level and the vertical plane can be calculated using the computer. This will instruct us to move the apparatus to align the shafts.

  2. Opto-mechanical devices for the Antares automatic beam alignment system

    International Nuclear Information System (INIS)

    Swann, T.; Combs, C.; Witt, J.

    1981-01-01

    Antares is a 24-beam CO 2 laser system for controlled fusion research, under construction at Los Alamos National Laboratory. Rapid automatic alignment of this system is required prior to each experimental shot. Unique opto-mechanical alignment devices, which have been developed specifically for this automatic alignment system, are discussed. A variable focus alignment telescope views point light sources. A beam expander/spatial filter processes both a visible Krypton Ion and a 10.6 μm CO 2 alignment laser. The periscope/carousel device provides the means by which the alignment telescope can sequentially view each of twelve optical trains in each power amplifier. The polyhedron alignment device projects a point-light source for both centering and pointing alignment at the polyhedron mirror. The rotating wedge alignment device provides a sequencing point-light source and also compensates for dispersion between visible and 10.6 μm radiation. The back reflector flip in remotely positions point-light sources at the back reflector mirrors. A light source box illuminates optic fibers with high intensity white light which is distributed to the various point-light sources in the system

  3. Angular momentum alignment in molecular beam scattering

    International Nuclear Information System (INIS)

    Treffers, M.A.

    1985-01-01

    It is shown how the angular momentum alignment in a molecular beam can be determined using laser-induced fluorescence in combination with precession of the angular momenta in a magnetic field. After a general analysis of the method, some results are presented to illustrate the possibilities of the method. Experimental data are presented on the alignment production for Na 2 molecules that made a collision induced angular momentum transition. Magnitude as well as direction of the alignment have been determined for scattering with several scattering partners and for a large number of scattering angles and transitions. The last chapter deals with the total alignment production in a final J-state, i.e. without state selection of the initial rotational state. (orig.)

  4. UV beam shaper alignment sensitivity: grayscale versus binary designs

    Science.gov (United States)

    Lizotte, Todd E.

    2008-08-01

    What defines a good flat top beam shaper? What is more important; an ideal flat top profile or ease of alignment and stability? These are the questions designers and fabricators can not easily define, since they are a function of experience. Anyone can generate a theoretical beam shaper design and model it until it is clear that on paper the design looks good and meets the general needs of the end customer. However, the method of fabrication can add a twist that is not fully understood by either party until the beam shaper is actually tested for the first time in a system and also produced in high volume. This paper provides some insight into how grayscale and binary fabrication methods can produce the same style of beam shaper, with similar beam shaping performance; however provide a result wherein each fabricated design has separate degrees of sensitivity for alignment and stability. The paper will explain the design and fabrication approach for the two units and present alignment and testing data to provide a contrast comparison. Further data will show that over twenty sets of each fabricated design there is a consistency to the sensitivity issue. An understanding of this phenomenon is essential when considering the use of beam shapers on production equipment that is dedicated to producing micron-precision features within high value microelectronic and consumer products. We will present our findings and explore potential explanations and solutions.

  5. Beam-Based Procedures for RF Guns

    CERN Document Server

    Krasilnikov, Mikhail; Grabosch, H J; Hartrott, Michael; Hui Han, Jang; Miltchev, Velizar; Oppelt, Anne; Petrosyan, Bagrat; Staykov, Lazar; Stephan, Frank

    2005-01-01

    A wide range of rf photo injector parameters has to be optimized in order to achieve an electron source performance as required for linac based high gain FELs. Some of the machine parameters can not be precisely controlled by direct measurements, whereas the tolerance on them is extremely tight. Therefore, this should be met with beam-based techniques. Procedures for beam-based alignment (BBA) of the laser on the photo cathode as well as solenoid alignment have been developed. They were applied at the Photo Injector Test facility at DESY Zeuthen (PITZ) and at the photo injector of the VUV-FEL at DESY Hamburg. A field balance of the accelerating mode in the 1 ½ cell gun cavity is one of the key beam dynamics issues of the rf gun. Since no direct field measurement in the half and full cell of the cavity is available for the PITZ gun, a beam-based technique to determine the field balance has been proposed. A beam-based rf phase monitoring procedure has been developed as well.

  6. Image-guided small animal radiation research platform: calibration of treatment beam alignment

    International Nuclear Information System (INIS)

    Matinfar, Mohammad; Iordachita, Iulian; Kazanzides, Peter; Ford, Eric; Wong, John

    2009-01-01

    Small animal research allows detailed study of biological processes, disease progression and response to therapy with the potential to provide a natural bridge to the clinical environment. The small animal radiation research platform (SARRP) is a portable system for precision irradiation with beam sizes down to approximately 0.5 mm and optimally planned radiation with on-board cone-beam CT (CBCT) guidance. This paper focuses on the geometric calibration of the system for high-precision irradiation. A novel technique for the calibration of the treatment beam is presented, which employs an x-ray camera whose precise positioning need not be known. Using the camera system we acquired a digitally reconstructed 3D 'star shot' for gantry calibration and then developed a technique to align each beam to a common isocenter with the robotic animal positioning stages. The calibration incorporates localization by cone-beam CT guidance. Uncorrected offsets of the beams with respect to the calibration origin ranged from 0.4 mm to 5.2 mm. With corrections, these alignment errors can be reduced to the sub-millimeter range. The calibration technique was used to deliver a stereotactic-like arc treatment to a phantom constructed with EBT Gafchromic films. All beams were shown to intersect at a common isocenter with a measured beam (FWHM) of approximately 1.07 mm using the 0.5 mm collimated beam. The desired positioning accuracy of the SARRP is 0.25 mm and the results indicate an accuracy of 0.2 mm. To fully realize the radiation localization capabilities of the SARRP, precise geometric calibration is required, as with any such system. The x-ray camera-based technique presented here provides a straightforward and semi-automatic method for system calibration.

  7. Alignment of dipole magnet in micro-beam line of HIRFL

    International Nuclear Information System (INIS)

    Wang Shaoming; Chen Wenjun; Yang Shengli; Cai Guozhu; Guo Yizhen; Zhou Guangming; Man Kaidi; Song Mingtao

    2010-01-01

    Microbeam irradiation facility is an experiment platform, which can reduce the beam-spot on the irradiated sample to micrometer level, and can accurately locate and count the radioactive particles. It is a powerful research tool for the irradiation material science, irradiation biology, irradiation biomedicine and micro mechanical machining. The microbeam irradiation facility requires the precise work for installation and alignment. These conditions make magnet's change for directions and positions because the location space of dipole magnets in micro-beam line of HIRFL (Heavy Ion Research Facility in Lanzhou) is very small. It is a challenge for the installation and alignment work of magnets. It was solved by transforming coordinates of benchmarks of magnets, which controlled the error of magnet setup within error tolerance range. (authors)

  8. Alignment of the CMS Muon System with Cosmic-Ray and Beam-Halo Muons

    CERN Document Server

    Chatrchyan, S; Sirunyan, A M; Adam, W; Arnold, B; Bergauer, H; Bergauer, T; Dragicevic, M; Eichberger, M; Erö, J; Friedl, M; Frühwirth, R; Ghete, V M; Hammer, J; Hänsel, S; Hoch, M; Hörmann, N; Hrubec, J; Jeitler, M; Kasieczka, G; Kastner, K; Krammer, M; Liko, D; Magrans de Abril, I; Mikulec, I; Mittermayr, F; Neuherz, B; Oberegger, M; Padrta, M; Pernicka, M; Rohringer, H; Schmid, S; Schöfbeck, R; Schreiner, T; Stark, R; Steininger, H; Strauss, J; Taurok, A; Teischinger, F; Themel, T; Uhl, D; Wagner, P; Waltenberger, W; Walzel, G; Widl, E; Wulz, C E; Chekhovsky, V; Dvornikov, O; Emeliantchik, I; Litomin, A; Makarenko, V; Marfin, I; Mossolov, V; Shumeiko, N; Solin, A; Stefanovitch, R; Suarez Gonzalez, J; Tikhonov, A; Fedorov, A; Karneyeu, A; Korzhik, M; Panov, V; Zuyeuski, R; Kuchinsky, P; Beaumont, W; Benucci, L; Cardaci, M; De Wolf, E A; Delmeire, E; Druzhkin, D; Hashemi, M; Janssen, X; Maes, T; Mucibello, L; Ochesanu, S; Rougny, R; Selvaggi, M; Van Haevermaet, H; Van Mechelen, P; Van Remortel, N; Adler, V; Beauceron, S; Blyweert, S; D'Hondt, J; De Weirdt, S; Devroede, O; Heyninck, J; Kalogeropoulos, A; Maes, J; Maes, M; Mozer, M U; Tavernier, S; Van Doninck, W; Van Mulders, P; Villella, I; Bouhali, O; Chabert, E C; Charaf, O; Clerbaux, B; De Lentdecker, G; Dero, V; Elgammal, S; Gay, A P R; Hammad, G H; Marage, P E; Rugovac, S; Vander Velde, C; Vanlaer, P; Wickens, J; Grunewald, M; Klein, B; Marinov, A; Ryckbosch, D; Thyssen, F; Tytgat, M; Vanelderen, L; Verwilligen, P; Basegmez, S; Bruno, G; Caudron, J; Delaere, C; Demin, P; Favart, D; Giammanco, A; Grégoire, G; Lemaitre, V; Militaru, O; Ovyn, S; Piotrzkowski, K; Quertenmont, L; Schul, N; Beliy, N; Daubie, E; Alves, G A; Pol, M E; Souza, M H G; Carvalho, W; De Jesus Damiao, D; De Oliveira Martins, C; Fonseca De Souza, S; Mundim, L; Oguri, V; Santoro, A; Silva Do Amaral, S M; Sznajder, A; Fernandez Perez Tomei, T R; Ferreira Dias, M A; Gregores, E M; Novaes, S F; Abadjiev, K; Anguelov, T; Damgov, J; Darmenov, N; Dimitrov, L; Genchev, V; Iaydjiev, P; Piperov, S; Stoykova, S; Sultanov, G; Trayanov, R; Vankov, I; Dimitrov, A; Dyulendarova, M; Kozhuharov, V; Litov, L; Marinova, E; Mateev, M; Pavlov, B; Petkov, P; Toteva, Z; Chen, G M; Chen, H S; Guan, W; Jiang, C H; Liang, D; Liu, B; Meng, X; Tao, J; Wang, J; Wang, Z; Xue, Z; Zhang, Z; Ban, Y; Cai, J; Ge, Y; Guo, S; Hu, Z; Mao, Y; Qian, S J; Teng, H; Zhu, B; Avila, C; Baquero Ruiz, M; Carrillo Montoya, C A; Gomez, A; Gomez Moreno, B; Ocampo Rios, A A; Osorio Oliveros, A F; Reyes Romero, D; Sanabria, J C; Godinovic, N; Lelas, K; Plestina, R; Polic, D; Puljak, I; Antunovic, Z; Dzelalija, M; Brigljevic, V; Duric, S; Kadija, K; Morovic, S; Fereos, R; Galanti, M; Mousa, J; Papadakis, A; Ptochos, F; Razis, P A; Tsiakkouri, D; Zinonos, Z; Hektor, A; Kadastik, M; Kannike, K; Müntel, M; Raidal, M; Rebane, L; Anttila, E; Czellar, S; Härkönen, J; Heikkinen, A; Karimäki, V; Kinnunen, R; Klem, J; Kortelainen, M J; Lampén, T; Lassila-Perini, K; Lehti, S; Lindén, T; Luukka, P; Mäenpää, T; Nysten, J; Tuominen, E; Tuominiemi, J; Ungaro, D; Wendland, L; Banzuzi, K; Korpela, A; Tuuva, T; Nedelec, P; Sillou, D; Besancon, M; Chipaux, R; Dejardin, M; Denegri, D; Descamps, J; Fabbro, B; Faure, J L; Ferri, F; Ganjour, S; Gentit, F X; Givernaud, A; Gras, P; Hamel de Monchenault, G; Jarry, P; Lemaire, M C; Locci, E; Malcles, J; Marionneau, M; Millischer, L; Rander, J; Rosowsky, A; Rousseau, D; Titov, M; Verrecchia, P; Baffioni, S; Bianchini, L; Bluj, M; Busson, P; Charlot, C; Dobrzynski, L; Granier de Cassagnac, R; Haguenauer, M; Miné, P; Paganini, P; Sirois, Y; Thiebaux, C; Zabi, A; Agram, J L; Besson, A; Bloch, D; Bodin, D; Brom, J M; Conte, E; Drouhin, F; Fontaine, J C; Gelé, D; Goerlach, U; Gross, L; Juillot, P; Le Bihan, A C; Patois, Y; Speck, J; Van Hove, P; Baty, C; Bedjidian, M; Blaha, J; Boudoul, G; Brun, H; Chanon, N; Chierici, R; Contardo, D; Depasse, P; Dupasquier, T; El Mamouni, H; Fassi, F; Fay, J; Gascon, S; Ille, B; Kurca, T; Le Grand, T; Lethuillier, M; Lumb, N; Mirabito, L; Perries, S; Vander Donckt, M; Verdier, P; Djaoshvili, N; Roinishvili, N; Roinishvili, V; Amaglobeli, N; Adolphi, R; Anagnostou, G; Brauer, R; Braunschweig, W; Edelhoff, M; Esser, H; Feld, L; Karpinski, W; Khomich, A; Klein, K; Mohr, N; Ostaptchouk, A; Pandoulas, D; Pierschel, G; Raupach, F; Schael, S; Schultz von Dratzig, A; Schwering, G; Sprenger, D; Thomas, M; Weber, M; Wittmer, B; Wlochal, M; Actis, O; Altenhöfer, G; Bender, W; Biallass, P; Erdmann, M; Fetchenhauer, G; Frangenheim, J; Hebbeker, T; Hilgers, G; Hinzmann, A; Hoepfner, K; Hof, C; Kirsch, M; Klimkovich, T; Kreuzer, P; Lanske, D; Merschmeyer, M; Meyer, A; Philipps, B; Pieta, H; Reithler, H; Schmitz, S A; Sonnenschein, L; Sowa, M; Steggemann, J; Szczesny, H; Teyssier, D; Zeidler, C; Bontenackels, M; Davids, M; Duda, M; Flügge, G; Geenen, H; Giffels, M; Haj Ahmad, W; Hermanns, T; Heydhausen, D; Kalinin, S; Kress, T; Linn, A; Nowack, A; Perchalla, L; Poettgens, M; Pooth, O; Sauerland, P; Stahl, A; Tornier, D; Zoeller, M H; Aldaya Martin, M; Behrens, U; Borras, K; Campbell, A; Castro, E; Dammann, D; Eckerlin, G; Flossdorf, A; Flucke, G; Geiser, A; Hatton, D; Hauk, J; Jung, H; Kasemann, M; Katkov, I; Kleinwort, C; Kluge, H; Knutsson, A; Kuznetsova, E; Lange, W; Lohmann, W; Mankel, R; Marienfeld, M; Meyer, A B; Miglioranzi, S; Mnich, J; Ohlerich, M; Olzem, J; Parenti, A; Rosemann, C; Schmidt, R; Schoerner-Sadenius, T; Volyanskyy, D; Wissing, C; Zeuner, W D; Autermann, C; Bechtel, F; Draeger, J; Eckstein, D; Gebbert, U; Kaschube, K; Kaussen, G; Klanner, R; Mura, B; Naumann-Emme, S; Nowak, F; Pein, U; Sander, C; Schleper, P; Schum, T; Stadie, H; Steinbrück, G; Thomsen, J; Wolf, R; Bauer, J; Blüm, P; Buege, V; Cakir, A; Chwalek, T; De Boer, W; Dierlamm, A; Dirkes, G; Feindt, M; Felzmann, U; Frey, M; Furgeri, A; Gruschke, J; Hackstein, C; Hartmann, F; Heier, S; Heinrich, M; Held, H; Hirschbuehl, D; Hoffmann, K H; Honc, S; Jung, C; Kuhr, T; Liamsuwan, T; Martschei, D; Mueller, S; Müller, Th; Neuland, M B; Niegel, M; Oberst, O; Oehler, A; Ott, J; Peiffer, T; Piparo, D; Quast, G; Rabbertz, K; Ratnikov, F; Ratnikova, N; Renz, M; Saout, C; Sartisohn, G; Scheurer, A; Schieferdecker, P; Schilling, F P; Schott, G; Simonis, H J; Stober, F M; Sturm, P; Troendle, D; Trunov, A; Wagner, W; Wagner-Kuhr, J; Zeise, M; Zhukov, V; Ziebarth, E B; Daskalakis, G; Geralis, T; Karafasoulis, K; Kyriakis, A; Loukas, D; Markou, A; Markou, C; Mavrommatis, C; Petrakou, E; Zachariadou, A; Gouskos, L; Katsas, P; Panagiotou, A; Evangelou, I; Kokkas, P; Manthos, N; Papadopoulos, I; Patras, V; Triantis, F A; Bencze, G; Boldizsar, L; Debreczeni, G; Hajdu, C; Hernath, S; Hidas, P; Horvath, D; Krajczar, K; Laszlo, A; Patay, G; Sikler, F; Toth, N; Vesztergombi, G; Beni, N; Christian, G; Imrek, J; Molnar, J; Novak, D; Palinkas, J; Szekely, G; Szillasi, Z; Tokesi, K; Veszpremi, V; Kapusi, A; Marian, G; Raics, P; Szabo, Z; Trocsanyi, Z L; Ujvari, B; Zilizi, G; Bansal, S; Bawa, H S; Beri, S B; Bhatnagar, V; Jindal, M; Kaur, M; Kaur, R; Kohli, J M; Mehta, M Z; Nishu, N; Saini, L K; Sharma, A; Singh, A; Singh, J B; Singh, S P; Ahuja, S; Arora, S; Bhattacharya, S; Chauhan, S; Choudhary, B C; Gupta, P; Jain, S; Jha, M; Kumar, A; Ranjan, K; Shivpuri, R K; Srivastava, A K; Choudhury, R K; Dutta, D; Kailas, S; Kataria, S K; Mohanty, A K; Pant, L M; Shukla, P; Topkar, A; Aziz, T; Guchait, M; Gurtu, A; Maity, M; Majumder, D; Majumder, G; Mazumdar, K; Nayak, A; Saha, A; Sudhakar, K; Banerjee, S; Dugad, S; Mondal, N K; Arfaei, H; Bakhshiansohi, H; Fahim, A; Jafari, A; Mohammadi Najafabadi, M; Moshaii, A; Paktinat Mehdiabadi, S; Rouhani, S; Safarzadeh, B; Zeinali, M; Felcini, M; Abbrescia, M; Barbone, L; Chiumarulo, F; Clemente, A; Colaleo, A; Creanza, D; Cuscela, G; De Filippis, N; De Palma, M; De Robertis, G; Donvito, G; Fedele, F; Fiore, L; Franco, M; Iaselli, G; Lacalamita, N; Loddo, F; Lusito, L; Maggi, G; Maggi, M; Manna, N; Marangelli, B; My, S; Natali, S; Nuzzo, S; Papagni, G; Piccolomo, S; Pierro, G A; Pinto, C; 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Dykstra, D; Eartly, D P; Elias, J E; Elvira, V D; Evans, D; Feng, L; Fischler, M; Fisk, I; Foulkes, S; Freeman, J; Gartung, P; Gottschalk, E; Grassi, T; Green, D; Guo, Y; Gutsche, O; Hahn, A; Hanlon, J; Harris, R M; Holzman, B; Howell, J; Hufnagel, D; James, E; Jensen, H; Johnson, M; Jones, C D; Joshi, U; Juska, E; Kaiser, J; Klima, B; Kossiakov, S; Kousouris, K; Kwan, S; Lei, C M; Limon, P; Lopez Perez, J A; Los, S; Lueking, L; Lukhanin, G; Lusin, S; Lykken, J; Maeshima, K; Marraffino, J M; Mason, D; McBride, P; Miao, T; Mishra, K; Moccia, S; Mommsen, R; Mrenna, S; Muhammad, A S; Newman-Holmes, C; Noeding, C; O'Dell, V; Prokofyev, O; Rivera, R; Rivetta, C H; Ronzhin, A; Rossman, P; Ryu, S; Sekhri, V; Sexton-Kennedy, E; Sfiligoi, I; Sharma, S; Shaw, T M; Shpakov, D; Skup, E; Smith, R P; Soha, A; Spalding, W J; Spiegel, L; Suzuki, I; Tan, P; Tanenbaum, W; Tkaczyk, S; Trentadue, R; Uplegger, L; Vaandering, E W; Vidal, R; Whitmore, J; Wicklund, E; Wu, W; Yarba, J; Yumiceva, F; Yun, J C; Acosta, D; Avery, P; Barashko, V; Bourilkov, D; Chen, M; Di Giovanni, G P; Dobur, D; Drozdetskiy, A; Field, R D; Fu, Y; Furic, I K; Gartner, J; Holmes, D; Kim, B; Klimenko, S; Konigsberg, J; Korytov, A; Kotov, K; Kropivnitskaya, A; Kypreos, T; Madorsky, A; Matchev, K; Mitselmakher, G; Pakhotin, Y; Piedra Gomez, J; Prescott, C; Rapsevicius, V; Remington, R; Schmitt, M; Scurlock, B; Wang, D; Yelton, J; Ceron, C; Gaultney, V; Kramer, L; Lebolo, L M; Linn, S; Markowitz, P; Martinez, G; Rodriguez, J L; Adams, T; Askew, A; Baer, H; Bertoldi, M; Chen, J; Dharmaratna, W G D; Gleyzer, S V; Haas, J; Hagopian, S; Hagopian, V; Jenkins, M; Johnson, K F; Prettner, E; Prosper, H; Sekmen, S; Baarmand, M M; Guragain, S; Hohlmann, M; Kalakhety, H; Mermerkaya, H; Ralich, R; Vodopiyanov, I; Abelev, B; Adams, M R; Anghel, I M; Apanasevich, L; Bazterra, V E; Betts, R R; Callner, J; Castro, M A; Cavanaugh, R; Dragoiu, C; Garcia-Solis, E J; Gerber, C E; Hofman, D J; Khalatian, S; Mironov, C; Shabalina, E; Smoron, A; Varelas, N; Akgun, U; Albayrak, E A; Ayan, A S; Bilki, B; Briggs, R; Cankocak, K; Chung, K; Clarida, W; Debbins, P; Duru, F; Ingram, F D; Lae, C K; McCliment, E; Merlo, J P; Mestvirishvili, A; Miller, M J; Moeller, A; Nachtman, J; Newsom, C R; Norbeck, E; Olson, J; Onel, Y; Ozok, F; Parsons, J; Schmidt, I; Sen, S; Wetzel, J; Yetkin, T; Yi, K; Barnett, B A; Blumenfeld, B; Bonato, A; Chien, C Y; Fehling, D; Giurgiu, G; Gritsan, A V; Guo, Z J; Maksimovic, P; Rappoccio, S; Swartz, M; Tran, N V; Zhang, Y; Baringer, P; Bean, A; Grachov, O; Murray, M; Radicci, V; Sanders, S; Wood, J S; Zhukova, V; Bandurin, D; Bolton, T; Kaadze, K; Liu, A; Maravin, Y; Onoprienko, D; Svintradze, I; Wan, Z; Gronberg, J; Hollar, J; Lange, D; Wright, D; Baden, D; Bard, R; Boutemeur, M; Eno, S C; Ferencek, D; Hadley, N J; Kellogg, R G; Kirn, M; Kunori, S; Rossato, K; Rumerio, P; Santanastasio, F; Skuja, A; Temple, J; Tonjes, M B; Tonwar, S C; Toole, T; Twedt, E; Alver, B; Bauer, G; Bendavid, J; Busza, W; Butz, E; Cali, I A; Chan, M; D'Enterria, D; Everaerts, P; Gomez Ceballos, G; Hahn, K A; Harris, P; Jaditz, S; Kim, Y; Klute, M; Lee, Y J; Li, W; Loizides, C; Ma, T; Miller, M; Nahn, S; Paus, C; Roland, C; Roland, G; Rudolph, M; Stephans, G; Sumorok, K; Sung, K; Vaurynovich, S; Wenger, E A; Wyslouch, B; Xie, S; Yilmaz, Y; Yoon, A S; Bailleux, D; Cooper, S I; Cushman, P; Dahmes, B; De Benedetti, A; Dolgopolov, A; Dudero, P R; Egeland, R; Franzoni, G; Haupt, J; Inyakin, A; Klapoetke, K; Kubota, Y; Mans, J; Mirman, N; Petyt, D; Rekovic, V; Rusack, R; Schroeder, M; Singovsky, A; Zhang, J; Cremaldi, L M; Godang, R; Kroeger, R; Perera, L; Rahmat, R; Sanders, D A; Sonnek, P; Summers, D; Bloom, K; Bockelman, B; Bose, S; Butt, J; Claes, D R; Dominguez, A; Eads, M; Keller, J; Kelly, T; Kravchenko, I; Lazo-Flores, J; Lundstedt, C; Malbouisson, H; Malik, S; Snow, G R; Baur, U; Iashvili, I; Kharchilava, A; Kumar, A; Smith, K; Strang, M; Alverson, G; Barberis, E; Boeriu, O; Eulisse, G; Govi, G; McCauley, T; Musienko, Y; Muzaffar, S; Osborne, I; Paul, T; Reucroft, S; Swain, J; Taylor, L; Tuura, L; Anastassov, A; Gobbi, B; Kubik, A; Ofierzynski, R A; Pozdnyakov, A; Schmitt, M; Stoynev, S; Velasco, M; Won, S; Antonelli, L; Berry, D; Hildreth, M; Jessop, C; Karmgard, D J; Kolberg, T; Lannon, K; Lynch, S; Marinelli, N; Morse, D M; Ruchti, R; Slaunwhite, J; Warchol, J; Wayne, M; Bylsma, B; Durkin, L S; Gilmore, J; Gu, J; Killewald, P; Ling, T Y; Williams, G; Adam, N; Berry, E; Elmer, P; Garmash, A; Gerbaudo, D; Halyo, V; Hunt, A; Jones, J; Laird, E; Marlow, D; Medvedeva, T; Mooney, M; Olsen, J; Piroué, P; Stickland, D; Tully, C; Werner, J S; Wildish, T; Xie, Z; Zuranski, A; Acosta, J G; Bonnett Del Alamo, M; Huang, X T; Lopez, A; Mendez, H; Oliveros, S; Ramirez Vargas, J E; Santacruz, N; Zatzerklyany, A; Alagoz, E; Antillon, E; Barnes, V E; Bolla, G; Bortoletto, D; Everett, A; Garfinkel, A F; Gecse, Z; Gutay, L; Ippolito, N; Jones, M; Koybasi, O; Laasanen, A T; Leonardo, N; Liu, C; Maroussov, V; Merkel, P; Miller, D H; Neumeister, N; Sedov, A; Shipsey, I; Yoo, H D; Zheng, Y; Jindal, P; Parashar, N; Cuplov, V; Ecklund, K M; Geurts, F J M; Liu, J H; Maronde, D; Matveev, M; Padley, B P; Redjimi, R; Roberts, J; Sabbatini, L; Tumanov, A; Betchart, B; Bodek, A; Budd, H; Chung, Y S; de Barbaro, P; Demina, R; Flacher, H; Gotra, Y; Harel, A; Korjenevski, S; Miner, D C; Orbaker, D; Petrillo, G; Vishnevskiy, D; Zielinski, M; Bhatti, A; Demortier, L; Goulianos, K; Hatakeyama, K; Lungu, G; Mesropian, C; Yan, M; Atramentov, O; Bartz, E; Gershtein, Y; Halkiadakis, E; Hits, D; Lath, A; Rose, K; Schnetzer, S; Somalwar, S; Stone, R; Thomas, S; Watts, T L; Cerizza, G; Hollingsworth, M; Spanier, S; Yang, Z C; York, A; Asaadi, J; Aurisano, A; Eusebi, R; Golyash, A; Gurrola, A; Kamon, T; Nguyen, C N; Pivarski, J; Safonov, A; Sengupta, S; Toback, D; Weinberger, M; Akchurin, N; Berntzon, L; Gumus, K; Jeong, C; Kim, H; Lee, S W; Popescu, S; Roh, Y; Sill, A; Volobouev, I; Washington, E; Wigmans, R; Yazgan, E; Engh, D; Florez, C; Johns, W; Pathak, S; Sheldon, P; Andelin, D; Arenton, M W; Balazs, M; Boutle, S; Buehler, M; Conetti, S; Cox, B; Hirosky, R; Ledovskoy, A; Neu, C; Phillips II, D; Ronquest, M; Yohay, R; Gollapinni, S; Gunthoti, K; Harr, R; Karchin, P E; Mattson, M; Sakharov, A; Anderson, M; Bachtis, M; Bellinger, J N; Carlsmith, D; Crotty, I; Dasu, S; Dutta, S; Efron, J; Feyzi, F; Flood, K; Gray, L; Grogg, K S; Grothe, M; Hall-Wilton, R; Jaworski, M; Klabbers, P; Klukas, J; Lanaro, A; Lazaridis, C; Leonard, J; Loveless, R; Magrans de Abril, M; Mohapatra, A; Ott, G; Polese, G; Reeder, D; Savin, A; Smith, W H; Sourkov, A; Swanson, J; Weinberg, M; Wenman, D; Wensveen, M; White, A

    2010-01-01

    The CMS muon system has been aligned using cosmic-ray muons collected in 2008 and beam-halo muons from the 2008 LHC circulating beam tests. After alignment, the resolution of the most sensitive coordinate is 80 microns for the relative positions of superlayers in the same barrel chamber and 270 microns for the relative positions ofendcap chambers in the same ring structure. The resolution on the position of the central barrel chambers relative to the tracker is comprised between two extreme estimates, 200 and 700 microns, provided by two complementary studies. With minor modifications, the alignment procedures can be applied using muons from LHC collisions, leading to additional significant improvements.

  9. Anomalous foreshock field-aligned beams observed by Cluster

    Directory of Open Access Journals (Sweden)

    K. Meziane

    2011-10-01

    Full Text Available We report occasional observations of two simultaneously distinct ion foreshock components recorded by the Cluster spacecraft upstream of the Earth's bow shock. In most occurrences, the lower-energy population originates as a field-aligned beam (FAB associated with quasi-perpendicular regions, which loses energy as the IMF rotates into oblique geometries. A second beam, with energies in excess of ~10 keV, appears sometimes in association with the onset of ultra-low frequency (ULF waves, and sometimes ahead of the appearance of the latter. Measurements from the mass spectrometer indicate that both beams consist of protons. While the lower-speed beam is well-accounted for by a known reflection mechanism, the non-radial IMF orientations as well as other arguments seem to rule out magnetosheath or magnetospheric sources for the higher energy component. The wave characteristics are typical of the oblique foreshock and we have found that they are in cyclotron-resonance with the low speed beam (FAB. These observations constitute a theoretical challenge since conventional mechanisms described in the literature cannot account for the production of beams at two different energies.

  10. Beam geometry, alignment, and wavefront aberration effects on interferometric differential wavefront sensing

    International Nuclear Information System (INIS)

    Yu, Xiangzhi; Gillmer, S R; Ellis, J D

    2015-01-01

    Heterodyne interferometry is a widely accepted methodology with high resolution in many metrology applications. As a functionality enhancement, differential wavefront sensing (DWS) enables simultaneous measurement of displacement, pitch, and yaw using a displacement interferometry system and a single beam incident on a plane mirror target. The angular change is measured using a weighted phase average between symmetrically adjacent quadrant photodiode pairs. In this paper, we present an analytical model to predict the scaling of differential phase signals based on fundamental Gaussian beams. Several numerical models are presented to discuss the effects of physical beam parameters, detector size, system alignment errors, and beam wavefront aberrations on the DWS technique. The results of our modeling predict rotational scaling factors and a usable linear range. Furthermore, experimental results show the analytically predicted scaling factor is in good agreement with empirical calibration. Our three degree-of-freedom interferometer can achieve a resolution of 0.4 nm in displacement and 0.2 μrad in pitch and yaw simultaneously. (paper)

  11. Study and Development of a Laser Based Alignment System

    CERN Multimedia

    Stern, G

    2014-01-01

    CLIC (Compact Linear Collider) has tight requirements regarding pre-alignment of beam related components: 10 µm accuracy over a sliding window of 200 m along the 20 km of linac. To perform such an alignment, a new system is proposed combining laser beam as straight line reference and camera/shutter assemblies as sensors. The poster describes the alignment system and shows results regarding laser pointing stability with respect to time, shutter type, distance and environment. These results give a frame for future building and calibrating of sensors.

  12. Alignment of Duke free electron laser storage ring and optical beam delivery system

    International Nuclear Information System (INIS)

    Emamian, M.; Hower, N.

    1999-01-01

    Duke Free Electron Laser Laboratory (DFELL) hosts a 1.1 GeV electron beam storage ring facility which is capable of generating beams in the range of nearly monochromatic gamma rays to high peak power infra red (IR) laser. In this report specifications and procedures for alignment of OK-4 /Duke storage ring FEL wiggler and optical cavity mirrors will be discussed. The OK-4 FEL lasing has demonstrated a series of world record in the last few years. In August of this year the OK-4 FEL successfully commissioned to laser at 193.7 nm. Also in this article, alignment of the γ-ray and UV optical beam delivery system that is currently in progress will be described. (authors)

  13. Scattering of field-aligned beam ions upstream of Earth's bow shock

    Directory of Open Access Journals (Sweden)

    A. Kis

    2007-03-01

    Full Text Available Field-aligned beams are known to originate from the quasi-perpendicular side of the Earth's bow shock, while the diffuse ion population consists of accelerated ions at the quasi-parallel side of the bow shock. The two distinct ion populations show typical characteristics in their velocity space distributions. By using particle and magnetic field measurements from one Cluster spacecraft we present a case study when the two ion populations are observed simultaneously in the foreshock region during a high Mach number, high solar wind velocity event. We present the spatial-temporal evolution of the field-aligned beam ion distribution in front of the Earth's bow shock, focusing on the processes in the deep foreshock region, i.e. on the quasi-parallel side. Our analysis demonstrates that the scattering of field-aligned beam (FAB ions combined with convection by the solar wind results in the presence of lower-energy, toroidal gyrating ions at positions deeper in the foreshock region which are magnetically connected to the quasi-parallel bow shock. The gyrating ions are superposed onto a higher energy diffuse ion population. It is suggested that the toroidal gyrating ion population observed deep in the foreshock region has its origins in the FAB and that its characteristics are correlated with its distance from the FAB, but is independent on distance to the bow shock along the magnetic field.

  14. Accurate Alignment of Plasma Channels Based on Laser Centroid Oscillations

    International Nuclear Information System (INIS)

    Gonsalves, Anthony; Nakamura, Kei; Lin, Chen; Osterhoff, Jens; Shiraishi, Satomi; Schroeder, Carl; Geddes, Cameron; Toth, Csaba; Esarey, Eric; Leemans, Wim

    2011-01-01

    A technique has been developed to accurately align a laser beam through a plasma channel by minimizing the shift in laser centroid and angle at the channel outptut. If only the shift in centroid or angle is measured, then accurate alignment is provided by minimizing laser centroid motion at the channel exit as the channel properties are scanned. The improvement in alignment accuracy provided by this technique is important for minimizing electron beam pointing errors in laser plasma accelerators.

  15. Development and Beam Tests of an Automatic Algorithm for Alignment of LHC Collimators with Embedded BPMs

    CERN Document Server

    Valentino, G; Gasior, M; Mirarchi, D; Nosych, A A; Redaelli, S; Salvachua, B; Assmann, R W; Sammut, N

    2013-01-01

    Collimators with embedded Beam Position Monitor (BPM) buttons will be installed in the LHC during the upcoming long shutdown period. During the subsequent operation, the BPMs will allow the collimator jaws to be kept centered around the beam trajectory. In this manner, the best possible beam cleaning efficiency and machine protection can be provided at unprecedented higher beam energies and intensities. A collimator alignment algorithm is proposed to center the jaws automatically around the beam. The algorithm is based on successive approximation, as the BPM measurements are affected by non-linearities, which vary with the distance between opposite buttons, as well as the difference between the beam and the jaw centers. The successful test results, as well as some considerations for eventual operation in the LHC are also presented.

  16. Progress in ETA-II magnetic field alignment using stretched wire and low energy electron beam techniques

    International Nuclear Information System (INIS)

    Griffith, L.V.; Deadrick, F.J.

    1991-01-01

    Flux line alignment of the solenoidal focus magnets used on the ETA-II linear induction accelerator is a key element leading to a reduction of beam corkscrew motion. Two techniques have been used on the ETA-II accelerator to measure and establish magnet alignment. A low energy electron beam has been used to directly map magnetic field lines, and recent work has utilized a pulsed stretched wire technique to measure magnet tilts and offsets with respect to a reference axis. This paper reports on the techniques used in the ETA-II accelerator alignment, and presents results from those measurements which show that accelerator is magnetically aligned to within ∼ ± 200 microns

  17. High-resolution accelerator alignment using x-ray optics

    Directory of Open Access Journals (Sweden)

    Bingxin Yang

    2006-03-01

    Full Text Available We propose a novel alignment technique utilizing the x-ray beam of an undulator in conjunction with pinholes and position-sensitive detectors for positioning components of the accelerator, undulator, and beam line in an x-ray free-electron laser. Two retractable pinholes at each end of the undulator define a stable and reproducible x-ray beam axis (XBA. Targets are precisely positioned on the XBA using a pinhole camera technique. Position-sensitive detectors responding to both x-ray and electron beams enable direct transfer of the position setting from the XBA to the electron beam. This system has the potential to deliver superior alignment accuracy (1–3   μm for target pinholes in the transverse directions over a long distance (200 m or longer. It can be used to define the beam axis of the electron-beam–based alignment, enabling high reproducibility of the latter. This x-ray–based concept should complement the electron-beam–based alignment and the existing survey methods to raise the alignment accuracy of long accelerators to an unprecedented level. Further improvement of the transverse accuracy using x-ray zone plates will be discussed. We also propose a concurrent measurement scheme during accelerator operation to allow real-time feedback for transverse position correction.

  18. Alignment of the Pixel and SCT Modules for the 2004 ATLAS Combined Test Beam

    Energy Technology Data Exchange (ETDEWEB)

    ATLAS Collaboration; Ahmad, A.; Andreazza, A.; Atkinson, T.; Baines, J.; Barr, A.J.; Beccherle, R.; Bell, P.J.; Bernabeu, J.; Broklova, Z.; Bruckman de Renstrom, P.A.; Cauz, D.; Chevalier, L.; Chouridou, S.; Citterio, M.; Clark, A.; Cobal, M.; Cornelissen, T.; Correard, S.; Costa, M.J.; Costanzo, D.; Cuneo, S.; Dameri, M.; Darbo, G.; de Vivie, J.B.; Di Girolamo, B.; Dobos, D.; Drasal, Z.; Drohan, J.; Einsweiler, K.; Elsing, M.; Emelyanov, D.; Escobar, C.; Facius, K.; Ferrari, P.; Fergusson, D.; Ferrere, D.; Flick,, T.; Froidevaux, D.; Gagliardi, G.; Gallas, M.; Gallop, B.J.; Gan, K.K.; Garcia, C.; Gavrilenko, I.L.; Gemme, C.; Gerlach, P.; Golling, T.; Gonzalez-Sevilla, S.; Goodrick, M.J.; Gorfine, G.; Gottfert, T.; Grosse-Knetter, J.; Hansen, P.H.; Hara, K.; Hartel, R.; Harvey, A.; Hawkings, R.J.; Heinemann, F.E.W.; Henss, T.; Hill, J.C.; Huegging, F.; Jansen, E.; Joseph, J.; Unel, M. Karagoz; Kataoka, M.; Kersten, S.; Khomich, A.; Klingenberg, R.; Kodys, P.; Koffas, T.; Konstantinidis, N.; Kostyukhin, V.; Lacasta, C.; Lari, T.; Latorre, S.; Lester, C.G.; Liebig, W.; Lipniacka, A.; Lourerio, K.F.; Mangin-Brinet, M.; Marti i Garcia, S.; Mathes, M.; Meroni, C.; Mikulec, B.; Mindur, B.; Moed, S.; Moorhead, G.; Morettini, P.; Moyse, E.W.J.; Nakamura, K.; Nechaeva, P.; Nikolaev, K.; Parodi, F.; Parzhitskiy, S.; Pater, J.; Petti, R.; Phillips, P.W.; Pinto, B.; Poppleton, A.; Reeves, K.; Reisinger, I.; Reznicek, P.; Risso, P.; Robinson, D.; Roe, S.; Rozanov, A.; Salzburger, A.; Sandaker, H.; Santi, L.; Schiavi, C.; Schieck, J.; Schultes, J.; Sfyrla, A.; Shaw, C.; Tegenfeldt, F.; Timmermans, C.J.W.P.; Toczek, B.; Troncon, C.; Tyndel, M.; Vernocchi, F.; Virzi, J.; Anh, T. Vu; Warren, M.; Weber, J.; Weber, M.; Weidberg, A.R.; Weingarten, J.; Wellsf, P.S.; Zhelezkow, A.

    2008-06-02

    A small set of final prototypes of the ATLAS Inner Detector silicon tracking system(Pixel Detector and SemiConductor Tracker), were used to take data during the 2004 Combined Test Beam. Data were collected from runs with beams of different flavour (electrons, pions, muons and photons) with a momentum range of 2 to 180 GeV/c. Four independent methods were used to align the silicon modules. The corrections obtained were validated using the known momenta of the beam particles and were shown to yield consistent results among the different alignment approaches. From the residual distributions, it is concluded that the precision attained in the alignmentof the silicon modules is of the order of 5 mm in their most precise coordinate.

  19. Precision alignment device

    Science.gov (United States)

    Jones, N.E.

    1988-03-10

    Apparatus for providing automatic alignment of beam devices having an associated structure for directing, collimating, focusing, reflecting, or otherwise modifying the main beam. A reference laser is attached to the structure enclosing the main beam producing apparatus and produces a reference beam substantially parallel to the main beam. Detector modules containing optical switching devices and optical detectors are positioned in the path of the reference beam and are effective to produce an electrical output indicative of the alignment of the main beam. This electrical output drives servomotor operated adjustment screws to adjust the position of elements of the structure associated with the main beam to maintain alignment of the main beam. 5 figs.

  20. Nova laser alignment control system

    International Nuclear Information System (INIS)

    Van Arsdall, P.J.; Holloway, F.W.; McGuigan, D.L.; Shelton, R.T.

    1984-01-01

    Alignment of the Nova laser requires control of hundreds of optical components in the ten beam paths. Extensive application of computer technology makes daily alignment practical. The control system is designed in a manner which provides both centralized and local manual operator controls integrated with automatic closed loop alignment. Menudriven operator consoles using high resolution color graphics displays overlaid with transport touch panels allow laser personnel to interact efficiently with the computer system. Automatic alignment is accomplished by using image analysis techniques to determine beam references points from video images acquired along the laser chain. A major goal of the design is to contribute substantially to rapid experimental turnaround and consistent alignment results. This paper describes the computer-based control structure and the software methods developed for aligning this large laser system

  1. Effect of upflowing field-aligned electron beams on the electron ...

    Indian Academy of Sciences (India)

    The role of low density upflowing field-aligned electron beams (FEBs) on the growth rate of the electron cyclotron waves at the frequencies r < e, propagating downward in the direction of the Earth's magnetic field, has been analysed in the auroral region at e/e < 1 where e is the plasma frequency and e is the ...

  2. Feasibility study of multipoint based laser alignment system for CLIC

    CERN Document Server

    Stern, G; Mainaud-Durand, H; Piedigrossi, D; Geiger, A

    2012-01-01

    CLIC (Compact LInear Collider) is a study for a future electron-positron collider that would allow physicists to explore a new energy region beyond the capabilities oftoday’s particle accelerators. Alignment is one of the major challenges within the CLIC study in order to achieve the high requirement of a multi-TeV center of mass colliding beam energy range (nominal 3 TeV). To reach this energy in a realistic and cost efficient scenario all accelerator components have to be aligned with an accuracy of 10 μm over a sliding window of 200 m. The demand for a straight line reference is so far based on stretched wires coupled with Wire Positioning Sensors (WPS). These solutions are currently further developed inorder to reduce the drawbacks which are mainly given by their costs and difficult implementation. However, it should be validated through inter-comparison with a solution ideally based on a different physical principle. Therefore, a new metrological approach is proposed using a laser beam as straight lin...

  3. Propagation and stability characteristics of a 500-m-long laser-based fiducial line for high-precision alignment of long-distance linear accelerators.

    Science.gov (United States)

    Suwada, Tsuyoshi; Satoh, Masanori; Telada, Souichi; Minoshima, Kaoru

    2013-09-01

    A laser-based alignment system with a He-Ne laser has been newly developed in order to precisely align accelerator units at the KEKB injector linac. The laser beam was first implemented as a 500-m-long fiducial straight line for alignment measurements. We experimentally investigated the propagation and stability characteristics of the laser beam passing through laser pipes in vacuum. The pointing stability at the last fiducial point was successfully obtained with the transverse displacements of ±40 μm level in one standard deviation by applying a feedback control. This pointing stability corresponds to an angle of ±0.08 μrad. This report contains a detailed description of the experimental investigation for the propagation and stability characteristics of the laser beam in the laser-based alignment system for long-distance linear accelerators.

  4. Effect of upflowing field-aligned electron beams on the electron ...

    Indian Academy of Sciences (India)

    Abstract. The role of low density upflowing field-aligned electron beams (FEBs) on the growth rate of the electron cyclotron waves at the frequencies ωr < Ωe, propagating downward in the direction of the Earth's magnetic field, has been analysed in the auroral region at ωe/Ωe < 1 where ωe is the plasma frequency and Ωe is ...

  5. Automatic laser beam alignment using blob detection for an environment monitoring spectroscopy

    Science.gov (United States)

    Khidir, Jarjees; Chen, Youhua; Anderson, Gary

    2013-05-01

    This paper describes a fully automated system to align an infra-red laser beam with a small retro-reflector over a wide range of distances. The component development and test were especially used for an open-path spectrometer gas detection system. Using blob detection under OpenCV library, an automatic alignment algorithm was designed to achieve fast and accurate target detection in a complex background environment. Test results are presented to show that the proposed algorithm has been successfully applied to various target distances and environment conditions.

  6. Development and Validation of a Multipoint Based Laser Alignment System for CLIC

    CERN Document Server

    Stern, G; Lackner, F; Mainaud-Durand, H; Piedigrossi, D; Sandomierski, J; Sosin, M; Geiger, A; Guillaume, S

    2013-01-01

    Alignment is one of the major challenges within CLIC study, since all accelerator components have to be aligned with accuracy up to 10 μm over sliding windows of 200 m. So far, the straight line reference concept has been based on stretched wires coupled with Wire Positioning Sensors. This concept should be validated through inter-comparison with an alternative solution. This paper proposes an alternative concept where laser beam acts as straight line reference and optical shutters coupled with cameras visualise the beam. The principle was first validated by a series of tests using low-cost components. Yet, in order to further decrease measurement uncertainty in this validation step, a high-precision automatised micrometric table and reference targets have been added to the setup. The paper presents the results obtained with this new equipment, in terms of measurement precision. In addition, the paper gives an overview of first tests done at long distance (up to 53 m), having emphasis on beam divergence

  7. Beam plug replacement and alignment under high radiation conditions for cold neutron facilities at Hanaro

    International Nuclear Information System (INIS)

    Yeong-Garp, Cho; Jin-Won, Shin; Jung-Hee, Lee; Jeong-Soo, Ryu

    2010-01-01

    Full text : The HANARO, an open-tank-in-pool type research reactor of a 30 MWth power in Korea, has been operating for 15 years since its initial criticality in February 1995. The beam port assigned for the cold neutron at HANARO had been used for an 8-m SANS without neutron guides until it was replaced by a cold neutron guide system in 2008. It was developed a cold neutron guide system for the delivery of cold neutrons from the cold neutron source in the reactor to the neutron scattering instruments in the guide hall. Since the HANARO has been operated from 1995, it was a big challenge to replace the existing plug and shutter with the new facilities under high radiation conditions. When the old plug was removed from the beam port in 2008, the radiation level was 230 mSv/hr at the end of beam port. In addition to that, there were more difficult situations such as the poor as-built dimensions of the beam port, limited work space and time constraint due to other constructions in parallel in the reactor hall. Before the removal of the old plug the level of the radiation was measured coming out through a small hole of the plug to estimate the radiation level during the removal of the old plug and installation of a new plug. Based on the measurement and analysis results, special tools and various shielding facilities were developed for the removal of old in-pile plug and the installation of the new in-pile plug assembly safely. In 2008, the old plug and shutter were successfully replaced by the new plug and shutter as shown in this article with a minimum exposure to the workers. A laser tracker system was also one of the main factors in our successful installation and alignment under high radiation conditions and limited work space. The laser tracker was used to measure and align all the mechanical facilities and the neutron guides with a minimum radiation exposure to workers. The alignment of all the guides and accessories were possible during reactor operation because

  8. Scattering of field-aligned beam ions upstream of Earth's bow shock

    Directory of Open Access Journals (Sweden)

    A. Kis

    2007-03-01

    Full Text Available Field-aligned beams are known to originate from the quasi-perpendicular side of the Earth's bow shock, while the diffuse ion population consists of accelerated ions at the quasi-parallel side of the bow shock. The two distinct ion populations show typical characteristics in their velocity space distributions. By using particle and magnetic field measurements from one Cluster spacecraft we present a case study when the two ion populations are observed simultaneously in the foreshock region during a high Mach number, high solar wind velocity event. We present the spatial-temporal evolution of the field-aligned beam ion distribution in front of the Earth's bow shock, focusing on the processes in the deep foreshock region, i.e. on the quasi-parallel side. Our analysis demonstrates that the scattering of field-aligned beam (FAB ions combined with convection by the solar wind results in the presence of lower-energy, toroidal gyrating ions at positions deeper in the foreshock region which are magnetically connected to the quasi-parallel bow shock. The gyrating ions are superposed onto a higher energy diffuse ion population. It is suggested that the toroidal gyrating ion population observed deep in the foreshock region has its origins in the FAB and that its characteristics are correlated with its distance from the FAB, but is independent on distance to the bow shock along the magnetic field.

  9. The proposed alignment system for the Final Focus Test Beam at SLAC

    International Nuclear Information System (INIS)

    Ruland, R.E.; Fischer, G.E.

    1990-09-01

    This report describes the current state of work in progress with respect to the geometry, alignment requirements, scenarios, and hardware for meeting the tolerances of the Final Focus Test Beam (FFTB) at SLAC. The methods and systems proposed acknowledge that component motion at the micron level, from whatever cause (ground motion, thermal effects, etc.) must be measured on-line and compensated for on relatively short time scales. To provide an integrated alignment/positioning package, some unique designs for reference systems, calibration of effect electric and magnetic centers, and component movers are introduced. 24 refs., 28 figs

  10. SU-E-J-24: Image-Guidance Using Cone-Beam CT for Stereotactic Body Radiotherapy (SBRT) of Lung Cancer Patients: Bony Alignment or Soft Tissue Alignment?

    Science.gov (United States)

    Wang, L; Turaka, A; Meyer, J; Spoka, D; Jin, L; Fan, J; Ma, C

    2012-06-01

    To assess the reliability of soft tissue alignment by comparing pre- and post-treatment cone-beam CT (CBCT) for image guidance in stereotactic body radiotherapy (SBRT) of lung cancers. Our lung SBRT procedures require all patients undergo 4D CT scan in order to obtain patient-specific target motion information through reconstructed 4D data using the maximum-intensity projection (MIP) algorithm. The internal target volume (ITV) was outlined directly from the MIP images and a 3-5 mm margin expansion was then applied to the ITV to create the PTV. Conformal treatment planning was performed on the helical images, to which the MIP images were fused. Prior to each treatment, CBCT was used for image guidance by comparing with the simulation CT and for patient relocalization based on the bony anatomy. Any displacement of the patient bony structure would be considered as setup errors and would be corrected by couch shifts. Theoretically, as the PTV definition included target internal motion, no further shifts other than setup corrections should be made. However, it is our practice to have treating physicians further check target localization within the PTV. Whenever the shifts based on the soft-tissue alignment (that is, target alignment) exceeded a certain value (e.g. 5 mm), a post-treatment CBCT was carried out to ensure that the tissue alignment is reliable by comparing between pre- and post-treatment CBCT. Pre- and post-CBCT has been performed for 7 patients so far who had shifts beyond 5 mm despite bony alignment. For all patients, post CBCT confirmed that the visualized target position was kept in the same position as before treatment after adjusting for soft-tissue alignment. For the patient population studied, it is shown that soft-tissue alignment is necessary and reliable in the lung SBRT for individual cases. © 2012 American Association of Physicists in Medicine.

  11. Alignment tools used to locate a wire and a laser beam in the VISA undulator project

    Energy Technology Data Exchange (ETDEWEB)

    Wolf, Z.; Ruland, R.; Dix, B.; Arnett, D. [Stanford Linear Accelerator Center, Menlo Park, CA (United States)

    1999-07-01

    Within the framework of the LCLS (Linac Coherent Light Source), a small experiment VISA (Visual to Infrared SASE (Self Amplified Stimulated Emission) Amplifier) is being performed at Brookhaven National Laboratory. VISA consists of four wiggler segments, each 0.99 m long. The four segments are required to be aligned to the beam axis with an rms error less than 50 {mu}m. This very demanding alignment is carried out in two steps. First the segments are fiducialized using a pulsed wire system. Then the wiggler segments are placed along a reference laser beam which coincides with the electron beam axis. In the wiggler segment fiducialization, a wire is stretched through a wiggler segment and a current pulse is sent down the wire. The deflection of the wire is monitored. The deflection gives information about the electron beam trajectory. The wire is moved until its x position, the coordinate without wire sag, is on the ideal beam trajectory. (The y position is obtained by rotating the wiggler 90 deg C.) Once the wire is on the ideal beam trajectory, the wire's location is measured relative to tooling balls on the wiggler segment. To locate the wire, a device was constructed which measures the wire position relative to tooling balls on the device. The device is called the wire finder. It will be discussed in this paper. To place the magnets along the reference laser beam, the position of the laser beam must be determined. A device which can locate the laser beam relative to tooling balls was constructed and is also discussed in this paper. This device is called the laser finder. With a total alignment error budget less than 50 {mu}m, both the fiducialization and magnet placement must be performed with errors much smaller than 50 {mu}m. It is desired to keep the errors from the wire finder and laser finder at the few {mu}m level. (authors)

  12. Laser shaft alignment measurement model

    Science.gov (United States)

    Mo, Chang-tao; Chen, Changzheng; Hou, Xiang-lin; Zhang, Guoyu

    2007-12-01

    Laser beam's track which is on photosensitive surface of the a receiver will be closed curve, when driving shaft and the driven shaft rotate with same angular velocity and rotation direction. The coordinate of arbitrary point which is on the curve is decided by the relative position of two shafts. Basing on the viewpoint, a mathematic model of laser alignment is set up. By using a data acquisition system and a data processing model of laser alignment meter with single laser beam and a detector, and basing on the installation parameter of computer, the state parameter between two shafts can be obtained by more complicated calculation and correction. The correcting data of the four under chassis of the adjusted apparatus moving on the level and the vertical plane can be calculated. This will instruct us to move the apparatus to align the shafts.

  13. Method to evaluate steering and alignment algorithms for controlling emittance growth

    International Nuclear Information System (INIS)

    Adolphsen, C.; Raubenheimer, T.

    1993-04-01

    Future linear colliders will likely use sophisticated beam-based alignment and/or steering algorithms to control the growth of the beam emittance in the linac. In this paper, a mathematical framework is presented which simplifies the evaluation of the effectiveness of these algorithms. As an application, a quad alignment that uses beam data taken with the nominal linac optics, and with a scaled optics, is evaluated in terms of the dispersive emittance growth remaining after alignment

  14. Conception and realisation of a system for the automatic alignment of a CO2 laser beam

    International Nuclear Information System (INIS)

    Mardon, Nathalie

    1983-01-01

    The present paper deals with the continuous control of the direction of a CO 2 laser beam, with a view to laser machining. Slow deviations, due to the cavity instability, move away the beam from the focusing system axis. An automatic alignment device acting on the last flat mirror of the optical line has been designed. This mirror is actuated by 2 motors which vary its inclination in 2 directions x,y. The first part of the present paper deals with the alignment principle worked according to the specific constraints to be faced and to the characteristics of the beam. It uses the revolution symmetry of the energy distribution of the beam: 4 thermocouples surrounding the beam on a same circumference yield equals signals if the beam is centered onto the 4 sensors. An angular displacement is characterised by the difference between the signals of 2 opposed detectors. The second part presents the digital feedback system: the divergence or the beam is computed from the differential signal by a coefficient K experimentally valued. The motor commands proceed from optical geometry laws. The filtering of the thermocouple signals is necessary in order to sort the slowly changing signal related to the beam displacement, from the higher frequency signal related to the laser system instability. The system has been implemented on a 16 bit microprocessor. (author) [fr

  15. Novel method for the production of spin-aligned RI beams in projectile fragmentation reaction with the dispersion matching technique

    Energy Technology Data Exchange (ETDEWEB)

    Ichikawa, Y., E-mail: yuichikawa@phys.titech.ac.jp [Tokyo Institute of Technology, Department of Physics (Japan); Ueno, H. [RIKEN Nishina Center (Japan); Ishii, Y. [Tokyo Institute of Technology, Department of Physics (Japan); Furukawa, T. [Tokyo Metropolitan University, Department of Physics (Japan); Yoshimi, A. [Okayama University, Research Core for Extreme Quantum World (Japan); Kameda, D.; Watanabe, H.; Aoi, N. [RIKEN Nishina Center (Japan); Asahi, K. [Tokyo Institute of Technology, Department of Physics (Japan); Balabanski, D. L. [Bulgarian Academy of Sciences, Institute for Nuclear Research and Nuclear Energy (Bulgaria); Chevrier, R.; Daugas, J. M. [CEA, DAM, DIF (France); Fukuda, N. [RIKEN Nishina Center (Japan); Georgiev, G. [CSNSM, IN2P3-CNRS, Universite Paris-sud (France); Hayashi, H.; Iijima, H. [Tokyo Institute of Technology, Department of Physics (Japan); Inabe, N. [RIKEN Nishina Center (Japan); Inoue, T. [Tokyo Institute of Technology, Department of Physics (Japan); Ishihara, M.; Kubo, T. [RIKEN Nishina Center (Japan); and others

    2013-05-15

    A novel method to produce spin-aligned rare-isotope (RI) beam has been developed, that is the two-step projectile fragmentation method with a technique of dispersion matching. The present method was verified in an experiment at the RIKEN RIBF, where an RI beam of {sup 32}Al with spin alignment of 8(1) % was successfully produced from a primary beam of {sup 48}Ca, with {sup 33}Al as an intermediate nucleus. Figure of merit of the present method was found to be improved by a factor larger than 50 compared with a conventional method employing single-step projectile fragmentation.

  16. Fast Automatic Beam-Based Alignment of the LHC Collimator Jaws

    CERN Document Server

    AUTHOR|(CDS)2080813; Assmann, R W

    2014-01-01

    The CERN Large Hadron Collider (LHC) in Geneva, Switzerland is the largest and most powerful particle accelerator ever built. With a circumference of 27 km, it is designed to collide particles in two counter-rotating beams at a centre-of-mass energy of 14 TeV to explore the fundamental forces and constituents of matter. Due to its potentially destructive high energy particle beams, the LHC is equipped with several machine protection systems. The LHC collimation system is tasked with scattering and absorbing beam halo particles before they can quench the superconducting magnets. The 108 collimators also protect the machine from damage in the event of very fast beam losses, and shields sensitive devices in the tunnel from radiation over years of operation. Each collimator is made up of two blocks or ‘jaws’ of carbon, tungsten or copper material. The collimator jaws need be placed symmetrically on either side of the beam trajectory, to clean halo particles with maximum efficiency. The beam orbit and beam siz...

  17. Validation of the CLIC alignment strategy on short range

    CERN Document Server

    Mainaud Durand, H; Griffet, S; Kemppinen, J; Rude, V; Sosin, M

    2012-01-01

    The pre-alignment of CLIC consists of aligning the components of linacs and beam delivery systems (BDS) in the most accurate possible way, so that a first pilot beam can circulate and allow the implementation of the beam based alignment. Taking into account the precision and accuracy needed: 10 µm rms over sliding windows of 200m, this pre-alignment must be active and it can be divided into two parts: the determination of a straight reference over 20 km, thanks to a metrological network and the determination of the component positions with respect to this reference, and their adjustment. The second part is the object of the paper, describing the steps of the proposed strategy: firstly the fiducialisation of the different components of CLIC; secondly, the alignment of these components on common supports and thirdly the active alignment of these supports using sensors and actuators. These steps have been validated on a test setup over a length of 4m, and the obtained results are analysed.

  18. Proposal for an alignment method of the CLIC linear accelerator - From geodesic networks to the active pre-alignment

    International Nuclear Information System (INIS)

    Touze, T.

    2011-01-01

    The compact linear collider (CLIC) is the particle accelerator project proposed by the european organization for nuclear research (CERN) for high energy physics after the large hadron collider (LHC). Because of the nano-metric scale of the CLIC leptons beams, the emittance growth budget is very tight. It induces alignment tolerances on the positions of the CLIC components that have never been achieved before. The last step of the CLIC alignment will be done according to the beam itself. It falls within the competence of the physicists. However, in order to implement the beam-based feedback, a challenging pre-alignment is required: 10 μm at 3σ along a 200 m sliding window. For such a precision, the proposed solution must be compatible with a feedback between the measurement and repositioning systems. The CLIC pre-alignment will have to be active. This thesis does not demonstrate the feasibility of the CLIC active pre-alignment but shows the way to the last developments that have to be done for that purpose. A method is proposed. Based on the management of the Helmert transformations between Euclidean coordinate systems, from the geodetic networks to the metrological measurements, this method is likely to solve the CLIC pre-alignment problem. Large scale facilities have been built and Monte-Carlo simulations have been made in order to validate the mathematical modeling of the measurement systems and of the alignment references. When this is done, it will be possible to extrapolate the modeling to the entire CLIC length. It will be the last step towards the demonstration of the CLIC pre-alignment feasibility. (author)

  19. 2D kV orthogonal imaging with fiducial markers is more precise for daily image guided alignments than soft-tissue cone beam computed tomography for prostate radiation therapy

    Directory of Open Access Journals (Sweden)

    Peter H. Goff, MD, PhD

    2017-07-01

    Conclusions: The kV-FM–based daily IG alignment for IMRT of prostate cancer is more precise than ST-CBCT, as assessed by a physician's ability to reproducibly align images. Given the magnitude of the error introduced by inconsistency in making ST-CBCT alignments, these data support a role for daily kV imaging of FM to enhance the precision of external beam dose delivery to the prostate.

  20. Centroid stabilization for laser alignment to corner cubes: designing a matched filter

    Energy Technology Data Exchange (ETDEWEB)

    Awwal, Abdul A. S.; Bliss, Erlan; Brunton, Gordon; Kamm, Victoria Miller; Leach, Richard R.; Lowe-Webb, Roger; Roberts, Randy; Wilhelmsen, Karl

    2016-11-08

    Automation of image-based alignment of National Ignition Facility high energy laser beams is providing the capability of executing multiple target shots per day. One important alignment is beam centration through the second and third harmonic generating crystals in the final optics assembly (FOA), which employs two retroreflecting corner cubes as centering references for each beam. Beam-to-beam variations and systematic beam changes over time in the FOA corner cube images can lead to a reduction in accuracy as well as increased convergence durations for the template-based position detector. A systematic approach is described that maintains FOA corner cube templates and guarantees stable position estimation.

  1. Alignment of CEBAF cryomodules

    International Nuclear Information System (INIS)

    Schneider, W.J.; Bisognano, J.J.; Fischer, J.

    1993-06-01

    CEBAF, the Continuous Electron Beam Accelerator Facility, when completed, will house a 4 GeV recirculating accelerator. Each of the accelerator's two linacs contains 160 superconducting radio frequency (SRF) 1497 MHz niobium cavities in 20 cryomodules. Alignments of the cavities within the cryomodule with respect to beam axis is critical to achieving the optimum accelerator performance. This paper discusses the rationale for the current specification on cavity mechanical alignment: 2 mrad (rms) applied to the 0.5 m active length cavities. We describe the tooling that was developed to achieve the tolerance at the time of cavity pair assembly, to preserve and integrate alignment during cryomodule assembly, and to translate alignment to appropriate installation in the beam line

  2. Development and commissioning of an x-ray beam alignment flag for NSLS-II

    Energy Technology Data Exchange (ETDEWEB)

    Kosciuk, B., E-mail: bkosciuk@bnl.gov; Hu, Y.; Keister, J.; Seletskiy, S. [National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, New York 11973 (United States)

    2016-07-27

    The NSLS-II Synchrotron Light Source is a 3 GeV electron storage ring recently commissioned and is now entering operations at Brookhaven National Laboratory. One of the major tasks was to commission the six project beamline front ends which required a diagnostic to resolve x-ray beam position for the purpose of beam alignment at low current. Since none of the front ends were outfitted with any x-ray diagnostics in the baseline design, an x-ray beam profile monitor or “flag” that could be easily installed into existing front end vacuum chambers was proposed to satisfy this requirement. Here we present the development of this novel device which utilizes a polycrystalline CVD diamond luminescent screen to produce a visible image of the x-ray beam cross-section and is then captured with a CCD camera.

  3. LHCb: Experience with LHCb alignment software on first data

    CERN Multimedia

    Deissenroth, M

    2009-01-01

    We report results obtained with different track-based algorithms for the alignment of the LHCb detector with first data. The large-area Muon Detector and Outer Tracker have been aligned with a large sample of tracks from cosmic rays. The three silicon detectors --- VELO, TT-station and Inner Tracker --- have been aligned with beam-induced events from the LHC injection line. We compare the results from the track-based alignment with expectations from detector survey.

  4. Spike Pattern Recognition for Automatic Collimation Alignment

    CERN Document Server

    Azzopardi, Gabriella; Salvachua Ferrando, Belen Maria; Mereghetti, Alessio; Redaelli, Stefano; CERN. Geneva. ATS Department

    2017-01-01

    The LHC makes use of a collimation system to protect its sensitive equipment by intercepting potentially dangerous beam halo particles. The appropriate collimator settings to protect the machine against beam losses relies on a very precise alignment of all the collimators with respect to the beam. The beam center at each collimator is then found by touching the beam halo using an alignment procedure. Until now, in order to determine whether a collimator is aligned with the beam or not, a user is required to follow the collimator’s BLM loss data and detect spikes. A machine learning (ML) model was trained in order to automatically recognize spikes when a collimator is aligned. The model was loosely integrated with the alignment implementation to determine the classification performance and reliability, without effecting the alignment process itself. The model was tested on a number of collimators during this MD and the machine learning was able to output the classifications in real-time.

  5. The CMS Muon System Alignment

    CERN Document Server

    Martinez Ruiz-Del-Arbol, P

    2009-01-01

    The alignment of the muon system of CMS is performed using different techniques: photogrammetry measurements, optical alignment and alignment with tracks. For track-based alignment, several methods are employed, ranging from a hit and impact point (HIP) algorithm and a procedure exploiting chamber overlaps to a global fit method based on the Millepede approach. For start-up alignment as long as available integrated luminosity is still significantly limiting the size of the muon sample from collisions, cosmic muon and beam halo signatures play a very strong role. During the last commissioning runs in 2008 the first aligned geometries have been produced and validated with data. The CMS offline computing infrastructure has been used in order to perform improved reconstructions. We present the computational aspects related to the calculation of alignment constants at the CERN Analysis Facility (CAF), the production and population of databases and the validation and performance in the official reconstruction. Also...

  6. On the origin of field-aligned beams at the quasi-perpendicular bow shock: multi-spacecraft observations by Cluster

    Directory of Open Access Journals (Sweden)

    H. Kucharek

    2004-07-01

    Full Text Available Two distinct populations of reflected and accelerated ions are known to originate from quasi-perpendicular shocks, gyrating ions and reflected ion beams. Recent observations under such bow shock conditions with Cluster have shown strong evidence that both particle distributions appear to emerge from the same reflection process. In this paper the basic production mechanism of field-aligned beams has been investigated by using CLUSTER multi-spacecraft measurements. We have analyzed several quasi-perpendicular shocks with the Cluster Ion Spectrometry experiment (CIS and followed the spatial and temporal evolution of the reflected and transmitted ion populations across the shock. These observations show that the field-aligned beams most likely result from effective scattering in pitch angle during reflection in the shock ramp. Investigating a low Mach number shock, leakage of a fraction of the thermalized ion distribution in the downstream region does not appear to be the source as the volume in phase space occupied by beam ions is empty downstream of the shock ramp.

  7. A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law

    Science.gov (United States)

    Yan, Rui; Edwards, Thomas J.; Pankratz, Logan M.; Kuhn, Richard J.; Lanman, Jason K.; Liu, Jun; Jiang, Wen

    2015-01-01

    In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography. PMID:26455556

  8. A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law.

    Science.gov (United States)

    Yan, Rui; Edwards, Thomas J; Pankratz, Logan M; Kuhn, Richard J; Lanman, Jason K; Liu, Jun; Jiang, Wen

    2015-11-01

    In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Vacuum mechatronic laser alignment system on the Nova laser

    International Nuclear Information System (INIS)

    Holliday, M.; Wong, K.; Shelton, R.

    1991-11-01

    The experiments conducted on NOVA are done to investigate inertially confined laser fusion reactions. To this end, the ten beams of the laser are aligned to within 30mm. The target chamber employs a vacuum mechatronic based reticle/target positioning system to accomplish this. It is a five degree-of-freedom chamber resident system, known as the Alignment Aids Positioner or AAP. The AAP aids in beam and diagnostic alignment by accurately positioning a reticle at target chamber center to with 7mm. The AAP system increases target positioning and alignment flexibility and accuracy through the use of a computer controlled multi degree-of-freedom stage assembly. This device uses microstepping DC stepper motors with encoders to achieve closed loop control in a 10 -6 torr vacuum. The AAP has two positioning regimes to move the alignment reticle and do beam alignment. One is course positioning in the Y-Z plane that moves a high resolution stage assembly to target chamber center. The other regime is high resolution movement in the X,Y,Z and q directions. 5 refs., 9 figs

  10. Fiber‐free coupling between bulk laser beams and on‐chip polymer‐based multimode waveguides

    DEFF Research Database (Denmark)

    Jensen, Thomas Glasdam; Nielsen, Lars Bue; Kutter, Jörg Peter

    2011-01-01

    light from a bulk beam to on‐chip waveguides and back into a bulk beam again. Using this setup, as much as 20% of the light coming from the source can be retrieved after passing through the on‐chip waveguides. The proposed setup is based on a pin‐aided alignment system that makes it possible to change...

  11. An Alignment of J-PARC Linac

    CERN Document Server

    Morishita, Takatoshi; Hasegawa, Kazuo; Ikegami, Masanori; Ito, Takashi; Kubota, Chikashi; Naito, Fujio; Takasaki, Eiichi; Tanaka, Hirokazu; Ueno, Akira; Yoshino, Kazuo

    2005-01-01

    J-PARC linear accelerator components are now being installed in the accelerator tunnel, whose total length is more than 400 m including the beam transport line to RCS (Rapid Cycling Synchrotron). A precise alignment of accelerator components is essential for a high quality beam acceleration. In this paper, planned alignment schemes for the installation of linac components, the fine alignment before beam acceleration, and watching the long term motion of the building are described. Guide points are placed on the floor, which acts as a reference for the initial alignment at the installation and also as a relay point for the long surveying network linking at the fine alignment. For a straight line alignment, the wire position sensor is placed on the offset position with respect to the beam center by a target holder, then a single wire can cover the accelerator cavities and the focusing magnets at the DTL-SDTL section (120m). The hydrostatic levering system (HLS) is used for watching the floor elevation (changes)...

  12. Automatic Angular alignment of LHC Collimators

    CERN Document Server

    Azzopardi, Gabriella; Salvachua Ferrando, Belen Maria; Mereghetti, Alessio; Bruce, Roderik; Redaelli, Stefano; CERN. Geneva. ATS Department

    2017-01-01

    The LHC is equipped with a complex collimation system to protect sensitive equipment from unavoidable beam losses. Collimators are positioned close to the beam using an alignment procedure. Until now they have always been aligned assuming no tilt between the collimator and the beam, however, tank misalignments or beam envelope angles at large-divergence locations could introduce a tilt limiting the collimation performance. Three different algorithms were implemented to automatically align a chosen collimator at various angles. The implementation was tested on a number of collimators during this MD and no human intervention was required.

  13. Ultracompact high-efficiency polarising beam splitter based on silicon nanobrick arrays.

    Science.gov (United States)

    Zheng, Guoxing; Liu, Guogen; Kenney, Mitchell Guy; Li, Zile; He, Ping'an; Li, Song; Ren, Zhi; Deng, Qiling

    2016-03-21

    Since the transmission of anisotropic nano-structures is sensitive to the polarisation of an incident beam, a novel polarising beam splitter (PBS) based on silicon nanobrick arrays is proposed. With careful design of such structures, an incident beam with polarisation direction aligned with the long axis of the nanobrick is almost totally reflected (~98.5%), whilst that along the short axis is nearly totally transmitted (~94.3%). More importantly, by simply changing the width of the nanobrick we can shift the peak response wavelength from 1460 nm to 1625 nm, covering S, C and L bands of the fiber telecommunications windows. The silicon nanobrick-based PBS can find applications in many fields which require ultracompactness, high efficiency, and compatibility with semiconductor industry technologies.

  14. Beam Techniques - Beam Control and Manipulation

    International Nuclear Information System (INIS)

    Minty, Michiko G

    2003-01-01

    We describe commonly used strategies for the control of charged particle beams and the manipulation of their properties. Emphasis is placed on relativistic beams in linear accelerators and storage rings. After a brief review of linear optics, we discuss basic and advanced beam control techniques, such as transverse and longitudinal lattice diagnostics, matching, orbit correction and steering, beam-based alignment, and linac emittance preservation. A variety of methods for the manipulation of particle beam properties are also presented, for instance, bunch length and energy compression, bunch rotation, changes to the damping partition number, and beam collimation. The different procedures are illustrated by examples from various accelerators. Special topics include injection and extraction methods, beam cooling, spin transport and polarization

  15. Beam Techniques - Beam Control and Manipulation

    Energy Technology Data Exchange (ETDEWEB)

    Minty, Michiko G

    2003-04-24

    We describe commonly used strategies for the control of charged particle beams and the manipulation of their properties. Emphasis is placed on relativistic beams in linear accelerators and storage rings. After a brief review of linear optics, we discuss basic and advanced beam control techniques, such as transverse and longitudinal lattice diagnostics, matching, orbit correction and steering, beam-based alignment, and linac emittance preservation. A variety of methods for the manipulation of particle beam properties are also presented, for instance, bunch length and energy compression, bunch rotation, changes to the damping partition number, and beam collimation. The different procedures are illustrated by examples from various accelerators. Special topics include injection and extraction methods, beam cooling, spin transport and polarization.

  16. Simultaneous AFM and fluorescence imaging: A method for aligning an AFM-tip with an excitation beam using a 2D galvanometer

    Science.gov (United States)

    Moores, A. N.; Cadby, A. J.

    2018-02-01

    Correlative fluorescence and atomic force microscopy (AFM) imaging is a highly attractive technique for use in biological imaging, enabling force and mechanical measurements of particular structures whose locations are known due to the specificity of fluorescence imaging. The ability to perform these two measurements simultaneously (rather than consecutively with post-processing correlation) is highly valuable because it would allow the mechanical properties of a structure to be tracked over time as changes in the sample occur. We present an instrument which allows simultaneous AFM and fluorescence imaging by aligning an incident fluorescence excitation beam with an AFM-tip. Alignment was performed by calibrating a 2D galvanometer present in the excitation beam path and using it to reposition the incident beam. Two programs were developed (one manual and one automated) which correlate sample features between the AFM and fluorescence images, calculating the distance required to translate the incident beam towards the AFM-tip. Using this method, we were able to obtain beam-tip alignment (and therefore field-of-view alignment) from an offset of >15 μm to within one micron in two iterations of the program. With the program running alongside data acquisition for real-time feedback between AFM and optical images, this offset was maintained over a time period of several hours. Not only does this eliminate the need to image large areas with both techniques to ensure that fields-of-view overlap, but it also raises the possibility of using this instrument for tip-enhanced fluorescence applications, a technique in which super-resolution images have previously been achieved.

  17. Linear collider accelerator physics issues regarding alignment

    International Nuclear Information System (INIS)

    Seeman, J.T.

    1990-01-01

    The next generation of linear colliders will require more stringent alignment tolerances than those for the SLC with regard to the accelerating structures, quadrupoles, and beam position monitors. New techniques must be developed to achieve these tolerances. A combination of mechanical-electrical and beam-based methods will likely be needed

  18. Beam Dynamics Simulation for the CTF3 Drive Beam Accelerator

    CERN Document Server

    Schulte, Daniel

    2000-01-01

    A new CLIC Test Facility (CTF3) at CERN will serve to study the drive beam generation for the Compact Linear Collider (CLIC). CTF3 has to accelerate a 3.5 A electron beam in almost fully-loaded structures. The pulse contains more than 2000 bunches, one in every second RF bucket, and has a length of more than one microsecond. Different options for the lattice of the drive-beam accelerator are presented, based on FODO-cells and triplets as well as solenoids. The transverse stability is simulated, including the effects of beam jitter, alignment and beam-based correction.

  19. Utilization of cone-beam CT for offline evaluation of target volume coverage during prostate image-guided radiotherapy based on bony anatomy alignment.

    Science.gov (United States)

    Paluska, Petr; Hanus, Josef; Sefrova, Jana; Rouskova, Lucie; Grepl, Jakub; Jansa, Jan; Kasaova, Linda; Hodek, Miroslav; Zouhar, Milan; Vosmik, Milan; Petera, Jiri

    2012-01-01

    To assess target volume coverage during prostate image-guided radiotherapy based on bony anatomy alignment and to assess possibility of safety margin reduction. Implementation of IGRT should influence safety margins. Utilization of cone-beam CT provides current 3D anatomic information directly in irradiation position. Such information enables reconstruction of the actual dose distribution. Seventeen prostate patients were treated with daily bony anatomy image-guidance. Cone-beam CT (CBCT) scans were acquired once a week immediately after bony anatomy alignment. After the prostate, seminal vesicles, rectum and bladder were contoured, the delivered dose distribution was reconstructed. Target dose coverage was evaluated by the proportion of the CTV encompassed by the 95% isodose. Original plans employed a 1 cm safety margin. Alternative plans assuming a smaller 7 mm margin between CTV and PTV were evaluated in the same way. Rectal and bladder volumes were compared with the initial ones. Rectal and bladder volumes irradiated with doses higher than 75 Gy, 70 Gy, 60 Gy, 50 Gy and 40 Gy were analyzed. In 12% of reconstructed plans the prostate coverage was not sufficient. The prostate underdosage was observed in 5 patients. Coverage of seminal vesicles was not satisfactory in 3% of plans. Most of the target underdosage corresponded to excessive rectal or bladder filling. Evaluation of alternative plans assuming a smaller 7 mm margin revealed 22% and 11% of plans where prostate and seminal vesicles coverage, respectively, was compromised. These were distributed over 8 and 7 patients, respectively. Sufficient dose coverage of target volumes was not achieved for all patients. Reducing of safety margin is not acceptable. Initial rectal and bladder volumes cannot be considered representative for subsequent treatment.

  20. Alignment of Ion Accelerator for Surface Analysis using Theodolite and Laser Tracker

    Energy Technology Data Exchange (ETDEWEB)

    Ahn, Tae Sung; Seo, Dong Hyuk; Kim, Dae Il; Kim, Han Sung; Kwon, Hyeok Jung; Cho, Yong Sub [KAERI, Daejeon (Korea, Republic of)

    2016-05-15

    The method of ion accelerator alignment is used two ways which are a theodolite and laser tracker. For the alignment and maintenance of the proton linear accelerator, the laser tracker is typically used at KOMAC. While the device for alignment by using laser tracker is not installed in all ion accelerator components, it was used in parallel in two methods. In this paper, alignment methods are introduced and the result and comparison of each alignment method are presented. The ion accelerator for surface analysis has aligned using theodolite and laser tracker. The two ways for alignment have advantage as well as weakness. But alignment using laser tracker is stronger than using theodolite. Because it is based on alignment and position data and it is more detailed. Also since the beam distribution is smaller than accelerator component that is direction of beam progress, main component (ex. Magnet, Chamber, Pelletron tank, etc.) alignment using laser tracker is enough to align the ion accelerator.

  1. NOVA integrated alignment/diagnostic sensors

    International Nuclear Information System (INIS)

    1978-01-01

    Under Contract 3772003 to the Lawrence Livermore Laboratory, Aerojet ElectroSystems Company has investigated a number of alignment system design topics for the NOVA and SHIVA upgrade lasers. Prior reports dealt with the Main Beam Alignment System, and with Multipass Amplifier Alignment Concepts. This report, which completes the contract, examines ways in which the Return Beam Diagnostic (RBD) package and Incident Beam Diagnostic (IBD) packages may be reconfigured to a more integrated package. In particular, the report shows that the RBD optics may be directly integrated in the Pointing Focus and Centering (PFC) sensor, and that the IBD optics may use the same basic common configuration as the PFC/RBD package

  2. CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

    Directory of Open Access Journals (Sweden)

    Genki Terashi

    Full Text Available Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align, which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1 agreement with the gold standard alignment, (2 alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3 consistency of the multiple alignments, and (4 classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins

  3. CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

    Science.gov (United States)

    Terashi, Genki; Takeda-Shitaka, Mayuko

    2015-01-01

    Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D) coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align), which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1) agreement with the gold standard alignment, (2) alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3) consistency of the multiple alignments, and (4) classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite) using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins in both

  4. Comparative genomics beyond sequence-based alignments

    DEFF Research Database (Denmark)

    Þórarinsson, Elfar; Yao, Zizhen; Wiklund, Eric D.

    2008-01-01

    Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA structure--frequent compensating base changes--is increasingly likely to cause sequence-based alignment me...

  5. Modified alignment CGHs for aspheric surface test

    Science.gov (United States)

    Song, Jae-Bong; Yang, Ho-Soon; Rhee, Hyug-Gyo; Lee, Yun-Woo

    2009-08-01

    Computer Generated Holograms (CGH) for optical test are commonly consisted of one main pattern for testing aspheric surface and some alignment patterns for aligning the interferometer, CGH, and the test optics. To align the CGH plate and the test optics, we designed the alignment CGHs modified from the cat's eye alignment method, which are consisted of a couple of CGH patterns. The incident beam passed through the one part of the alignment CGH pattern is focused onto the one radius position of the test aspheric surface, and is reflected to the other part, and vice versa. This method has several merits compared to the conventional cat's eye alignment method. First, this method can be used in testing optics with a center hole, and the center part of CGH plate can be assigned to the alignment pattern. Second, the alignment pattern becomes a concentric circular arc pattern. The whole CGH patterns including the main pattern and alignment patterns are consisted of only concentric circular fringes. This concentric circular pattern can be easily made by the polar coordinated writer with circular scanning. The required diffraction angle becomes relatively small, so the 1st order diffraction beams instead of the 3rd order diffraction beam can be used as alignment beams, and the visibility can be improved. This alignment method also is more sensitive to the tilt and the lateral shift of the test aspheric surface. Using this alignment pattern, a 200 mm diameter F/0.5 aspheric mirror and a 600 mm diameter F/0.9 mirror were tested.

  6. Beam feasibility study of a collimator with in-jaw beam position monitors

    Science.gov (United States)

    Wollmann, Daniel; Nosych, Andriy A.; Valentino, Gianluca; Aberle, Oliver; Aßmann, Ralph W.; Bertarelli, Alessandro; Boccard, Christian; Bruce, Roderik; Burkart, Florian; Calvo, Eva; Cauchi, Marija; Dallocchio, Alessandro; Deboy, Daniel; Gasior, Marek; Jones, Rhodri; Kain, Verena; Lari, Luisella; Redaelli, Stefano; Rossi, Adriana

    2014-12-01

    At present, the beam-based alignment of the LHC collimators is performed by touching the beam halo with both jaws of each collimator. This method requires dedicated fills at low intensities that are done infrequently and makes this procedure time consuming. This limits the operational flexibility, in particular in the case of changes of optics and orbit configuration in the experimental regions. The performance of the LHC collimation system relies on the machine reproducibility and regular loss maps to validate the settings of the collimator jaws. To overcome these limitations and to allow a continuous monitoring of the beam position at the collimators, a design with jaw-integrated Beam Position Monitors (BPMs) was proposed and successfully tested with a prototype (mock-up) collimator in the CERN SPS. Extensive beam experiments allowed to determine the achievable accuracy of the jaw alignment for single and multi-turn operation. In this paper, the results of these experiments are discussed. The non-linear response of the BPMs is compared to the predictions from electromagnetic simulations. Finally, the measured alignment accuracy is compared to the one achieved with the present collimators in the LHC.

  7. Automatic alignment of double optical paths in excimer laser amplifier

    Science.gov (United States)

    Wang, Dahui; Zhao, Xueqing; Hua, Hengqi; Zhang, Yongsheng; Hu, Yun; Yi, Aiping; Zhao, Jun

    2013-05-01

    A kind of beam automatic alignment method used for double paths amplification in the electron pumped excimer laser system is demonstrated. In this way, the beams from the amplifiers can be transferred along the designated direction and accordingly irradiate on the target with high stabilization and accuracy. However, owing to nonexistence of natural alignment references in excimer laser amplifiers, two cross-hairs structure is used to align the beams. Here, one crosshair put into the input beam is regarded as the near-field reference while the other put into output beam is regarded as the far-field reference. The two cross-hairs are transmitted onto Charge Coupled Devices (CCD) by image-relaying structures separately. The errors between intersection points of two cross-talk images and centroid coordinates of actual beam are recorded automatically and sent to closed loop feedback control mechanism. Negative feedback keeps running until preset accuracy is reached. On the basis of above-mentioned design, the alignment optical path is built and the software is compiled, whereafter the experiment of double paths automatic alignment in electron pumped excimer laser amplifier is carried through. Meanwhile, the related influencing factors and the alignment precision are analyzed. Experimental results indicate that the alignment system can achieve the aiming direction of automatic aligning beams in short time. The analysis shows that the accuracy of alignment system is 0.63μrad and the beam maximum restoration error is 13.75μm. Furthermore, the bigger distance between the two cross-hairs, the higher precision of the system is. Therefore, the automatic alignment system has been used in angular multiplexing excimer Main Oscillation Power Amplification (MOPA) system and can satisfy the requirement of beam alignment precision on the whole.

  8. Alignment system for SGII-Up laser facility

    Science.gov (United States)

    Gao, Yanqi; Cui, Yong; Li, Hong; Gong, Lei; Lin, Qiang; Liu, Daizhong; Zhu, Baoqiang; Ma, Weixin; Zhu, Jian; Lin, Zunqi

    2018-03-01

    The SGII-Up laser facility in Shanghai is one of the most important high-power laser facilities in China. It is designed to obtain 24 kJ (3ω) of energy with a square pulse of 3 ns using eight laser beams (two bundles). To satisfy the requirements for the safety, efficiency, and quality, an alignment system is developed for this facility. This alignment system can perform automatic alignment of the preamplifier system, main amplifier system, and harmonic conversion system within 30 min before every shot during the routine operation of the facility. In this article, an overview of the alignment system is first presented. Then, its alignment characteristics are discussed, along with the alignment process. Finally, experimental results, including the alignment results and the facility performance, are reported. The results show that the far-field beam pointing alignment accuracy is better than 3 μrad, and the alignment error of the near-field beam centering is no larger than 1 mm. These satisfy the design requirements very well.

  9. Triangular Alignment (TAME). A Tensor-based Approach for Higher-order Network Alignment

    Energy Technology Data Exchange (ETDEWEB)

    Mohammadi, Shahin [Purdue Univ., West Lafayette, IN (United States); Gleich, David F. [Purdue Univ., West Lafayette, IN (United States); Kolda, Tamara G. [Sandia National Laboratories (SNL-CA), Livermore, CA (United States); Grama, Ananth [Purdue Univ., West Lafayette, IN (United States)

    2015-11-01

    Network alignment is an important tool with extensive applications in comparative interactomics. Traditional approaches aim to simultaneously maximize the number of conserved edges and the underlying similarity of aligned entities. We propose a novel formulation of the network alignment problem that extends topological similarity to higher-order structures and provide a new objective function that maximizes the number of aligned substructures. This objective function corresponds to an integer programming problem, which is NP-hard. Consequently, we approximate this objective function as a surrogate function whose maximization results in a tensor eigenvalue problem. Based on this formulation, we present an algorithm called Triangular AlignMEnt (TAME), which attempts to maximize the number of aligned triangles across networks. We focus on alignment of triangles because of their enrichment in complex networks; however, our formulation and resulting algorithms can be applied to general motifs. Using a case study on the NAPABench dataset, we show that TAME is capable of producing alignments with up to 99% accuracy in terms of aligned nodes. We further evaluate our method by aligning yeast and human interactomes. Our results indicate that TAME outperforms the state-of-art alignment methods both in terms of biological and topological quality of the alignments.

  10. Principles of alignment of multibeam lasers for thermonuclear purposes

    International Nuclear Information System (INIS)

    Basovy, N.G.; Ol'shevskii, Y.N.; Belyan, V.F.

    1980-01-01

    The concrete object of the investigation is the alignment of the high-power 12-channel ''Del'fin'' neodymium-glass laser facilaity. The objects of the alignment are the optical channel of the laser installation, the system for pointing and focusing the laser radiation on the target, the system for positioning the target in the focal volume, and the system for monitoring the optical quality of the elements of the laser installation and laser beams and also the conditions of the target irradiation in the vacuum chamber. The list of requirements that must be satisfied by the alignment beams, the possible sources of alignment beams, the makeup of the apparatus, and the methods of aligning the laser facility are considered. The principles and the actual systems of automatic alignment of the optical elements are described, as are the operating models of the automatized units. The problem of simulating the working laser beams by the alignment beams and the possibility of automatizing the control of the spatial and angular characteristics of the laser radiation are discussed. The system for controlling the alignment processes by means of a laser is considered, as it also a scheme for incorporating the automatized alignment subsystem in the overall system for the automation of the ''Del'fin'' facility

  11. Neural-network-directed alignment of optical systems using the laser-beam spatial filter as an example

    Science.gov (United States)

    Decker, Arthur J.; Krasowski, Michael J.; Weiland, Kenneth E.

    1993-01-01

    This report describes an effort at NASA Lewis Research Center to use artificial neural networks to automate the alignment and control of optical measurement systems. Specifically, it addresses the use of commercially available neural network software and hardware to direct alignments of the common laser-beam-smoothing spatial filter. The report presents a general approach for designing alignment records and combining these into training sets to teach optical alignment functions to neural networks and discusses the use of these training sets to train several types of neural networks. Neural network configurations used include the adaptive resonance network, the back-propagation-trained network, and the counter-propagation network. This work shows that neural networks can be used to produce robust sequencers. These sequencers can learn by example to execute the step-by-step procedures of optical alignment and also can learn adaptively to correct for environmentally induced misalignment. The long-range objective is to use neural networks to automate the alignment and operation of optical measurement systems in remote, harsh, or dangerous aerospace environments. This work also shows that when neural networks are trained by a human operator, training sets should be recorded, training should be executed, and testing should be done in a manner that does not depend on intellectual judgments of the human operator.

  12. Evolution of shiva laser alignment systems

    International Nuclear Information System (INIS)

    Boyd, R.D.

    1980-07-01

    The Shiva oscillator pulse is preamplified and divided into twenty beams. Each beam is then amplified, spatially filtered, directed, and focused onto a target a few hundred micrometers in size producing optical intensities up to 10 16 W/cm 2 . The laser was designed and built with three automatic alignment systems: the oscillator alignment system, which aligns each of the laser's three oscillators to a reference beamline; the chain input pointing system, which points each beam into its respective chain; and the chain output pointing, focusing and centering system which points, centers and focuses the beam onto the target. Recently the alignment of the laser's one hundred twenty spatial filter pinholes was also automated. This system uses digitized video images of back-illuminated pinholes and computer analysis to determine current positions. The offset of each current position from a desired center point is then translated into stepper motor commands and the pinhole is moved the proper distance. While motors for one pinhole are moving, the system can digitize, analyze, and send commands to other motors, allowing the system to efficiently align several pinholes in parallel

  13. Three wavelength optical alignment of the Nova laser

    International Nuclear Information System (INIS)

    Swift, C.D.; Bliss, E.S.; Jones, W.A.; Seppala, L.G.

    1983-01-01

    The Nova laser, presently under construction at Lawrence Livermore National Laboratory, will be capable of delivering more than 100 kJ of focused energy to an Inertial Confinement Fusion (ICF) target. Operation at the fundamental wavelength of the laser (1.05 μm) and at the second and third harmonic will be possible. This paper will discuss the optical alignment systems and techniques being implemented to align the laser output to the target at these wavelengths prior to each target irradiation. When experiments require conversion of the laser light to wavelengths of 0.53 μm and 0.35 μm prior to target irradiation, this will be accomplished in harmonic conversion crystals located at the beam entrances to the target chamber. The harmonic alignment system will be capable of introducing colinear alignment beams of all three wavelengths into the laser chains at the final spatial filter. The alignment beam at 1.05 μm will be about three cm in diameter and intense enough to align the conversion crystals. Beams at 0.53 μm and 0.35 μm will be expanded by the spatial filter to full aperture (74 cm) and used to illuminate the target and other alignment aids at the target chamber focus. This harmonic illumination system will include viewing capability as well. A final alignment sensor will be located at the target chamber. It will view images of the chamber focal plane at all three wavelengths. In this way, each beam can be aligned at the desired wavelength to produce the focal pattern required for each target irradiation. The design of the major components in the harmonic alignment system will be described, and a typical alignment sequence for alignment to a target will be presented

  14. Electronics and Algorithms for HOM Based Beam Diagnostics

    Science.gov (United States)

    Frisch, Josef; Baboi, Nicoleta; Eddy, Nathan; Nagaitsev, Sergei; Hensler, Olaf; McCormick, Douglas; May, Justin; Molloy, Stephen; Napoly, Olivier; Paparella, Rita; Petrosyan, Lyudvig; Ross, Marc; Simon, Claire; Smith, Tonee

    2006-11-01

    The signals from the Higher Order Mode (HOM) ports on superconducting cavities can be used as beam position monitors and to do survey structure alignment. A HOM-based diagnostic system has been installed to instrument both couplers on each of the 40 cryogenic accelerating structures in the DESY TTF2 Linac. The electronics uses a single stage down conversion from the 1.7 GHz HOM spectral line to a 20MHz IF which has been digitized. The electronics is based on low cost surface mount components suitable for large scale production. The analysis of the HOM data is based on Singular Value Decomposition. The response of the OM modes is calibrated using conventional BPMs.

  15. Alignment control of GEO 600

    International Nuclear Information System (INIS)

    Grote, H; Heinzel, G; Freise, A; Gossler, S; Willke, B; Lueck, H; Ward, H; Casey, M M; Strain, K A; Robertson, D I; Hough, J; Danzmannx, K

    2004-01-01

    We give an overview of the automatic mirror alignment system of the gravitational wave detector GEO 600. In order to achieve the required sensitivity of the Michelson interferometer, the axes of interfering beams have to be superimposed with a residual angle of the order 10 -8 rad. The beam spots have to be centred on the mirrors to minimize coupling of alignment noise into longitudinal signals. We present the actual control topology and results from the system in operation, which controls all alignment degrees of the power-recycled Michelson. With this system continuous lock stretches of more than 121 h duration were achieved

  16. Feature-based Alignment of Volumetric Multi-modal Images

    Science.gov (United States)

    Toews, Matthew; Zöllei, Lilla; Wells, William M.

    2014-01-01

    This paper proposes a method for aligning image volumes acquired from different imaging modalities (e.g. MR, CT) based on 3D scale-invariant image features. A novel method for encoding invariant feature geometry and appearance is developed, based on the assumption of locally linear intensity relationships, providing a solution to poor repeatability of feature detection in different image modalities. The encoding method is incorporated into a probabilistic feature-based model for multi-modal image alignment. The model parameters are estimated via a group-wise alignment algorithm, that iteratively alternates between estimating a feature-based model from feature data, then realigning feature data to the model, converging to a stable alignment solution with few pre-processing or pre-alignment requirements. The resulting model can be used to align multi-modal image data with the benefits of invariant feature correspondence: globally optimal solutions, high efficiency and low memory usage. The method is tested on the difficult RIRE data set of CT, T1, T2, PD and MP-RAGE brain images of subjects exhibiting significant inter-subject variability due to pathology. PMID:24683955

  17. Alignment of the drift tube detector at the neutrino oscillation experiment OPERA; Alignment des Driftroehrendetektors am Neutrino-Oszillationsexperiment OPERA

    Energy Technology Data Exchange (ETDEWEB)

    Goellnitz, Christoph

    2012-09-15

    The present thesis was composed during the course of the OPERA experiment, which aims to give a direct evidence for neutrino oscillations in the channel {nu}{sub {mu}} {yields} {nu}{sub {tau}}. The OPERA detector is designed to observe the appearance of tau neutrinos in an originally pure muon neutrino beam, the CNGS beam. As important part of the detector the precision tracker (PT), a drift tube detector, consists of 9504 drift tubes in 198 modules. In this thesis, several parts of the slow control of the PT are developed and implemented to ensure operation during data taking over several years. The main part is the geometric calibration, the alignment of the detector. The alignment procedure contains both hardware and software parts, the software methods are developed and applied. Using straight particle tracks, the detector components are geometrically corrected. A special challenge for the alignment for the PT is the fact that at this kind of low-rate experiment only a small number of particle tracks is available. With software-based corrections of the module rotation, a systematic error of 0.2 mrad has been attained, for corrections of translation, a systematic error of 32 {mu}m is reached. For the alignment between two adjacent PT walls, the statistical error is less than 8 {mu}m. All results of the position monitoring system are considered. All developed methods are tested with Monte Carlo simulations. The detector requirements ({Delta}p/p {<=} 0.25 below 25 GeV) are met. The analysis of the momentum measurement for high energies above 25 GeV demonstrates the resulting improvement. The mean momentum is falling significantly using the new alignment values. The significance of the detector alignment becomes most evident in the analysis of cosmic particles. The muon charge ratio R{sub {mu}} is expected not to be angular dependent. The {chi}{sup 2} probability of the measured distribution improves up to 58%. The muon charge ratio was also investigated in

  18. Beam electron microprobe

    CERN Document Server

    Stoller, D; Muterspaugh, M W; Pollock, R E

    1999-01-01

    A beam profile monitor based on the deflection of a probe electron beam by the electric field of a stored, electron-cooled proton beam is described and first results are presented. Electrons were transported parallel to the proton beam by a uniform longitudinal magnetic field. The probe beam may be slowly scanned across the stored beam to determine its intensity, position, and size. Alternatively, it may be scanned rapidly over a narrow range within the interior of the stored beam for continuous observation of the changing central density during cooling. Examples of a two dimensional charge density profile obtained from a raster scan and of a cooling alignment study illustrate the scope of measurements made possible by this device.

  19. MICA: Multiple interval-based curve alignment

    Science.gov (United States)

    Mann, Martin; Kahle, Hans-Peter; Beck, Matthias; Bender, Bela Johannes; Spiecker, Heinrich; Backofen, Rolf

    2018-01-01

    MICA enables the automatic synchronization of discrete data curves. To this end, characteristic points of the curves' shapes are identified. These landmarks are used within a heuristic curve registration approach to align profile pairs by mapping similar characteristics onto each other. In combination with a progressive alignment scheme, this enables the computation of multiple curve alignments. Multiple curve alignments are needed to derive meaningful representative consensus data of measured time or data series. MICA was already successfully applied to generate representative profiles of tree growth data based on intra-annual wood density profiles or cell formation data. The MICA package provides a command-line and graphical user interface. The R interface enables the direct embedding of multiple curve alignment computation into larger analyses pipelines. Source code, binaries and documentation are freely available at https://github.com/BackofenLab/MICA

  20. A feature alignment score for online cone-beam CT-based image-guided radiotherapy for prostate cancer.

    Science.gov (United States)

    Hargrave, Catriona; Deegan, Timothy; Poulsen, Michael; Bednarz, Tomasz; Harden, Fiona; Mengersen, Kerrie

    2018-05-17

    To develop a method for scoring online cone-beam CT (CBCT)-to-planning CT image feature alignment to inform prostate image-guided radiotherapy (IGRT) decision-making. The feasibility of incorporating volume variation metric thresholds predictive of delivering planned dose into weighted functions, was investigated. Radiation therapists and radiation oncologists participated in workshops where they reviewed prostate CBCT-IGRT case examples and completed a paper-based survey of image feature matching practices. For 36 prostate cancer patients, one daily CBCT was retrospectively contoured then registered with their plan to simulate delivered dose if (a) no online setup corrections and (b) online image alignment and setup corrections, were performed. Survey results were used to select variables for inclusion in classification and regression tree (CART) and boosted regression trees (BRT) modeling of volume variation metric thresholds predictive of delivering planned dose to the prostate, proximal seminal vesicles (PSV), bladder, and rectum. Weighted functions incorporating the CART and BRT results were used to calculate a score of individual tumor and organ at risk image feature alignment (FAS TV _ OAR ). Scaled and weighted FAS TV _ OAR were then used to calculate a score of overall treatment compliance (FAS global ) for a given CBCT-planning CT registration. The FAS TV _ OAR were assessed for sensitivity, specificity, and predictive power. FAS global thresholds indicative of high, medium, or low overall treatment plan compliance were determined using coefficients from multiple linear regression analysis. Thirty-two participants completed the prostate CBCT-IGRT survey. While responses demonstrated consensus of practice for preferential ranking of planning CT and CBCT match features in the presence of deformation and rotation, variation existed in the specified thresholds for observed volume differences requiring patient repositioning or repeat bladder and bowel

  1. Permanent bending and alignment of ZnO nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Borschel, Christian; Spindler, Susann; Oertel, Michael; Ronning, Carsten [Institut fuer Festkoerperphysik, Friedrich-Schiller-Universitaet Jena, Max-Wien-Platz 1, 07743 Jena (Germany); Lerose, Damiana [MPI fuer Mikrostrukturphysik, Weinberg 2, 06120 Halle/Saale (Germany); Institut fuer Photonische Technologien, Albert-Einstein-Strasse 9, 07745 Jena (Germany); Bochmann, Arne [Institut fuer Photonische Technologien, Albert-Einstein-Strasse 9, 07745 Jena (Germany); Christiansen, Silke H. [Institut fuer Photonische Technologien, Albert-Einstein-Strasse 9, 07745 Jena (Germany); MPI fuer die Physik des Lichts, Guenther-Scharowsky-Str. 1, 91058 Erlangen (Germany); Nietzsche, Sandor [Zentrum fuer Elektronenmikroskopie, Friedrich-Schiller-Universitaet Jena, Ziegelmuehlenweg 1, 07743 Jena (Germany)

    2011-07-01

    Ion beams can be used to bend or re-align nanowires permanently, after they have been grown. We have irradiated ZnO nanowires with ions of different species and energy, achieving bending and alignment in various directions. We study the bending of single nanowires as well as the simultaneous alignment of large ensembles of ZnO nanowires in detail. Computer simulations show that the bending is initiated by ion beam induced damage. Dislocations are identified to relax stresses and make the bending and alignment permanent and resistant against annealing procedures.

  2. General beam position controlling method for 3D optical systems based on the method of solving ray matrix equations

    Science.gov (United States)

    Chen, Meixiong; Yuan, Jie; Long, Xingwu; Kang, Zhenglong; Wang, Zhiguo; Li, Yingying

    2013-12-01

    A general beam position controlling method for 3D optical systems based on the method of solving ray matrix equations has been proposed in this paper. As a typical 3D optical system, nonplanar ring resonator of Zero-Lock Laser Gyroscopes has been chosen as an example to show its application. The total mismatching error induced by Faraday-wedge in nonplanar ring resonator has been defined and eliminated quite accurately with the error less than 1 μm. Compared with the method proposed in Ref. [14], the precision of the beam position controlling has been improved by two orders of magnitude. The novel method can be used to implement automatic beam position controlling in 3D optical systems with servo circuit. All those results have been confirmed by related alignment experiments. The results in this paper are important for beam controlling, ray tracing, cavity design and alignment in 3D optical systems.

  3. Drift tube alignment and beam emittance codes in use at the SuperHILAC

    International Nuclear Information System (INIS)

    Spence, D.A.

    1974-01-01

    Two Fortran-IV codes in use at the SuperHILAC are of significant value in optimizing the geometry of the accelerator and in evaluating the performance of the heavy ion beams. The first routine described is used to determine the existing root mean square deviation of the 210 internal drift tube quadrupoles fitted to a straight line or to a second-order quadratic. It then predicts the minimum number of drift tubes, and their identities, to be moved in order to attain a user-elected margin of error fit. Brief mention is made of the pulsed-wire alignment technique for the quadrupole positioning. The second program described is part of a data system which utilizes a PDP-8/I as a control device for the manipulation of beam-scanning hardware and a CDC-6600 in an off-line interactive mode which gives the user maximum versatility in treating the raw data and displaying the results of calculations. The code portrays the transverse beam emittance figures and their transmission through the accelerator and transport lines. Also discussed are future plans which include on-line data reduction and CRT display by the PDP-8/I to enable the operators to optimize the tuning of the HILAC. (U.S.)

  4. Search for Anisotropic Light Propagation as a Function of Laser Beam Alignment Relative to the Earth's Velocity Vector

    Directory of Open Access Journals (Sweden)

    Navia C. E.

    2007-01-01

    Full Text Available A laser diffraction experiment was conducted to study light propagation in air. The experiment is easy to reproduce and it is based on simple optical principles. Two optical sensors (segmented photo-diodes are used for measuring the position of diffracted light spots with a precision better than 0.1 μ m. The goal is to look for signals of anisotropic light propagation as function of the laser beam alignment to the Earth’s motion (solar barycenter motion obtained by COBE. Two raster search techniques have been used. First, a laser beam fixed in the laboratory frame scans in space due to Earth’s rotation. Second, a laser beam mounted on a turntable system scans actively in space by turning the table. The results obtained with both methods show that the course of light rays are affected by the motion of the Earth, and a predominant first order quantity with a Δ c/c = − β (1 + 2 a cos θ signature with ˉ a = − 0.393 ± 0.032 describes well the experimental results. This result differs in amount of 21% from the Special Relativity Theory prediction and that supplies the value of a = − 1 2 (isotropy.

  5. Alignment of the Thomson scattering diagnostic on NSTX

    International Nuclear Information System (INIS)

    LeBlanc, B P; Diallo, A

    2013-01-01

    The Thomson scattering diagnostic can provide profile measurement of the electron temperature, T e , and density, n e , in plasmas. Proper laser beam path and optics arrangement permits profiles T e (R) and n e (R) measurement along the major radius R. Keeping proper alignment between the laser beam path and the collection optics is necessary for an accurate determination of the electron density. As time progresses the relative position of the collection optics field of view with respect to the laser beam path will invariably shift. This can be kept to a minimum by proper attention to the physical arrangement of the collection and laser-beam delivery optics. A system has been in place to monitor the relative position between laser beam and collection optics. Variation of the alignment can be detected before it begins to affect the quality of the profile data. This paper discusses details of the instrumentation and techniques used to maintain alignment during NSTX multi-month experimental campaigns

  6. NIF pointing and centering systems and target alignment using a 351 nm laser source

    International Nuclear Information System (INIS)

    Boege, S.J.; Bliss, E.S.; Chocol, C.J.; Holdener, F.R.; Miller, J.L.; Toeppen, J.S.; Vann, C.S.; Zacharias, R.A.

    1996-10-01

    The operational requirements of the National Ignition Facility (NIF) place tight constraints upon its alignment system. In general, the alignment system must establish and maintain the correct relationships between beam position, beam angle, laser component clear apertures, and the target. At the target, this includes adjustment of beam focus to obtain the correct spot size. This must be accomplished for all beamlines in a time consistent with planned shot rates and yet, in the front end and main laser, beam control functions cannot be initiated until the amplifiers have sufficiently cooled so as to minimize dynamic thermal distortions during and after alignment and wavefront optimization. The scope of the task dictates an automated system that implements parallel processes. We describe reticle choices and other alignment references, insertion of alignment beams, principles of operation of the Chamber Center Reference System 2048 and Target Alignment Sensor, and the anticipated alignment sequence that will occur between shots

  7. Magnetic Field Measurements in Beam Guiding Magnets

    CERN Document Server

    Henrichsen, K N

    1998-01-01

    Electromagnets used as beam guiding elements in particle accelerators and colliders require very tight tole-rances on their magnetic fields and on their alignment along the particle path. This article describes the methods and equipment used for magnetic measurements in beam transport magnets. Descriptions are given of magnetic resonance techniques, various induction coil methods, Hall generator measurements, the fluxgate magnetometer as well as the recently developed method of beam based alignment. References of historical nature as well as citations of recent work are given. The present commercial availability of the different sensors and asso-ciated equipment is indicated. Finally we shall try to analyze possible future needs for developments in those fields.

  8. Laser diagnostics for picosecond e-beams

    International Nuclear Information System (INIS)

    Pogorelsky, I.; Ben-Zvi, I.

    1992-01-01

    We propose a novel approach to picosecond e-bunch/laser pulse synchronization and spatial alignment based upon refraction and reflection of a laser beam on a plasma column created by relativistic electrons traveling through a gas or solid optical material. The technique may be used in laser accelerators and for general subpicosecond e-beam diagnostics

  9. A user-friendly nano-CT image alignment and 3D reconstruction platform based on LabVIEW

    International Nuclear Information System (INIS)

    Wang Shenghao; Wang Zhili; Gao Kun; Wu Zhao; Zhang Kai; Zhu Peiping; Wu Ziyu

    2015-01-01

    X-ray computed tomography at the nanometer scale (nano-CT) offers a wide range of applications in scientific and industrial areas. Here we describe a reliable, user-friendly, and fast software package based on LabVIEW that may allow us to perform all procedures after the acquisition of raw projection images in order to obtain the inner structure of the investigated sample. A suitable image alignment process to address misalignment problems among image series due to mechanical manufacturing errors, thermal expansion, and other external factors has been considered, together with a novel fast parallel beam 3D reconstruction procedure that was developed ad hoc to perform the tomographic reconstruction. We have obtained remarkably improved reconstruction results at the Beijing Synchrotron Radiation Facility after the image calibration, the fundamental role of this image alignment procedure was confirmed, which minimizes the unwanted blurs and additional streaking artifacts that are always present in reconstructed slices. Moreover, this nano-CT image alignment and its associated 3D reconstruction procedure are fully based on LabVIEW routines, significantly reducing the data post-processing cycle, thus making the activity of the users faster and easier during experimental runs. (authors)

  10. Quality control methods for linear accelerator radiation and mechanical axes alignment.

    Science.gov (United States)

    Létourneau, Daniel; Keller, Harald; Becker, Nathan; Amin, Md Nurul; Norrlinger, Bernhard; Jaffray, David A

    2018-06-01

    The delivery accuracy of highly conformal dose distributions generated using intensity modulation and collimator, gantry, and couch degrees of freedom is directly affected by the quality of the alignment between the radiation beam and the mechanical axes of a linear accelerator. For this purpose, quality control (QC) guidelines recommend a tolerance of ±1 mm for the coincidence of the radiation and mechanical isocenters. Traditional QC methods for assessment of radiation and mechanical axes alignment (based on pointer alignment) are time consuming and complex tasks that provide limited accuracy. In this work, an automated test suite based on an analytical model of the linear accelerator motions was developed to streamline the QC of radiation and mechanical axes alignment. The proposed method used the automated analysis of megavoltage images of two simple task-specific phantoms acquired at different linear accelerator settings to determine the coincidence of the radiation and mechanical isocenters. The sensitivity and accuracy of the test suite were validated by introducing actual misalignments on a linear accelerator between the radiation axis and the mechanical axes using both beam steering and mechanical adjustments of the gantry and couch. The validation demonstrated that the new QC method can detect sub-millimeter misalignment between the radiation axis and the three mechanical axes of rotation. A displacement of the radiation source of 0.2 mm using beam steering parameters was easily detectable with the proposed collimator rotation axis test. Mechanical misalignments of the gantry and couch rotation axes of the same magnitude (0.2 mm) were also detectable using the new gantry and couch rotation axis tests. For the couch rotation axis, the phantom and test design allow detection of both translational and tilt misalignments with the radiation beam axis. For the collimator rotation axis, the test can isolate the misalignment between the beam radiation axis

  11. An improved Hough transform-based fingerprint alignment approach

    CSIR Research Space (South Africa)

    Mlambo, CS

    2014-11-01

    Full Text Available An improved Hough Transform based fingerprint alignment approach is presented, which improves computing time and memory usage with accurate alignment parameter (rotation and translation) results. This is achieved by studying the strengths...

  12. THE ATLAS INNER DETECTOR TRACK BASED ALIGNMENT

    CERN Document Server

    Marti i Garcia, Salvador; The ATLAS collaboration

    2018-01-01

    The alignment of the ATLAS Inner Detector is performed with a track-based alignment algorithm. Its goal is to provide an accurate description of the detector geometry such that track parameters are accurately determined and free from biases. Its software implementation is modular and configurable, with a clear separation of the alignment algorithm from the detector system specifics and the database handling. The alignment must cope with the rapid movements of the detector as well as with the slow drift of the different mechanical units. Prompt alignment constants are derived for every run at the calibration stage. These sets of constants are then dynamically split from the beginning of the run in many chunks, allowing to describe the tracker geometry as it evolves with time. The alignment of the Inner Detector is validated and improved by studying resonance decays (Z and J/psi to mu+mu-), as well as using information from the calorimeter system with the E/p method with electrons. A detailed study of these res...

  13. The magnetized electron-acoustic instability driven by a warm, field-aligned electron beam

    International Nuclear Information System (INIS)

    Sooklal, A.; Mace, R.L.

    2004-01-01

    The electron-acoustic instability in a magnetized plasma having three electron components, one of which is a field-aligned beam of intermediate temperature, is investigated. When the plasma frequency of the cool electrons exceeds the electron gyrofrequency, the electron-acoustic instability 'bifurcates' at sufficiently large propagation angles with respect to the magnetic field to yield an obliquely propagating, low-frequency electron-acoustic instability and a higher frequency cyclotron-sound instability. Each of these instabilities retains certain wave features of its progenitor, the quasiparallel electron-acoustic instability, but displays also new magnetic qualities through its dependence on the electron gyrofrequency. The obliquely propagating electron-acoustic instability requires a lower threshold beam speed for its excitation than does the cyclotron-sound instability, and for low to intermediate beam speeds has the higher maximum growth rate. When the plasma is sufficiently strongly magnetized that the plasma frequency of the cool electrons is less than the electron gyrofrequency, the only instability in the electron-acoustic frequency range is the strongly magnetized electron-acoustic instability. Its growth rate and real frequency exhibit a monotonic decrease with wave propagation angle and it grows at small to intermediate wave numbers where its parallel phase speed is approximately constant. The relevance of the results to the interpretation of cusp auroral hiss and auroral broadband electrostatic noise is briefly discussed

  14. Automatic beam centering at the SSC interaction regions

    International Nuclear Information System (INIS)

    Joestlein, H.

    1984-01-01

    In the SSC interaction regions, the two colliding beams, each only a few microns in size, will have to be centered and maintained in good alignment over many hours, in order to provide the maximum possible luminosity and to minimize off-center beam-beam focussing effects. It is unlikely that sufficiently good alignment can be achieved without some kind of active feedback system, based on the beam-beam interaction rate. This memo describes such a system. In the proposed scheme, one of the beams is moved continuously and in a circular fashion about its mean transverse position. The radius of this motion is approximately 0.01 of the rms beam size at the interaction point. The motion is achieved with two sets of crossed high frequency dipole magnets, one on each side of the interaction region, suitably phased. As a consequence of this motion, the beam-beam interaction rate is modulated in synchronism with the beam motion when the beams are not centered on one another. The amplitude and phase of this modulation yields information on the magnitude and direction of the misalignment between the beams, allowing continuous display and automatic correction of any misalignment

  15. HIE ISOLDE Alignment and monitoring system technical design and project status

    CERN Document Server

    Gayde, J C; Kautzmann, G; Leclercq, Y; Waniorek, S; Williams, L

    2012-01-01

    In the frame of the HIE ISOLDE project most of the existing ISOLDE REX line will be replaced by a superconducting linac in order to upgrade the energy and intensity of the REX ISOLDE facility at CERN. Beam-physics simulations show that the optimum linac working conditions are obtained when the main axes of the active components, RF cavities and solenoid placed inside the cryostats, are aligned and permanently monitored on the REX Nominal Beam Line (NBL) within a precision of 0.3 mm for the cavities and 0.15 mm for the solenoids at one sigma level along directions perpendicular to the beam axis. This paper presents the proposed adjustment and alignment system based on opto-electronic sensors, optics and precise mechanic elements which are used, for some of them, in various non-standard environmental conditions such as high vacuum, cryogenic temperatures.

  16. L-GRAAL: Lagrangian graphlet-based network aligner.

    Science.gov (United States)

    Malod-Dognin, Noël; Pržulj, Nataša

    2015-07-01

    Discovering and understanding patterns in networks of protein-protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary conserved pathways, protein complexes and functional orthologs. A few methods have been proposed for global PPI network alignments, but because of NP-completeness of underlying sub-graph isomorphism problem, producing topologically and biologically accurate alignments remains a challenge. We introduce a novel global network alignment tool, Lagrangian GRAphlet-based ALigner (L-GRAAL), which directly optimizes both the protein and the interaction functional conservations, using a novel alignment search heuristic based on integer programming and Lagrangian relaxation. We compare L-GRAAL with the state-of-the-art network aligners on the largest available PPI networks from BioGRID and observe that L-GRAAL uncovers the largest common sub-graphs between the networks, as measured by edge-correctness and symmetric sub-structures scores, which allow transferring more functional information across networks. We assess the biological quality of the protein mappings using the semantic similarity of their Gene Ontology annotations and observe that L-GRAAL best uncovers functionally conserved proteins. Furthermore, we introduce for the first time a measure of the semantic similarity of the mapped interactions and show that L-GRAAL also uncovers best functionally conserved interactions. In addition, we illustrate on the PPI networks of baker's yeast and human the ability of L-GRAAL to predict new PPIs. Finally, L-GRAAL's results are the first to show that topological information is more important than sequence information for uncovering functionally conserved interactions. L-GRAAL is coded in C++. Software is available at: http://bio-nets.doc.ic.ac.uk/L-GRAAL/. n.malod-dognin@imperial.ac.uk Supplementary data are available at

  17. Autonomous monitoring of control hardware to predict off-normal conditions using NIF automatic alignment systems

    International Nuclear Information System (INIS)

    Awwal, Abdul A.S.; Wilhelmsen, Karl; Leach, Richard R.; Miller-Kamm, Vicki; Burkhart, Scott; Lowe-Webb, Roger; Cohen, Simon

    2012-01-01

    Highlights: ► An automatic alignment system was developed to process images of the laser beams. ► System uses processing to adjust a series of control loops until alignment criteria are satisfied. ► Monitored conditions are compared against nominal values with an off-normal alert. ► Automated health monitoring system trends off-normals with a large image history. - Abstract: The National Ignition Facility (NIF) is a high power laser system capable of supporting high-energy-density experimentation as a user facility for the next 30 years. In order to maximize the facility availability, preventive maintenance enhancements are being introduced into the system. An example of such an enhancement is a camera-based health monitoring system, integrated into the automated alignment system, which provides an opportunity to monitor trends in measurements such as average beam intensity, size of the beam, and pixel saturation. The monitoring system will generate alerts based on observed trends in measurements to allow scheduled pro-active maintenance before routine off-normal detection stops system operations requiring unscheduled intervention.

  18. Autonomous monitoring of control hardware to predict off-normal conditions using NIF automatic alignment systems

    Energy Technology Data Exchange (ETDEWEB)

    Awwal, Abdul A.S., E-mail: awwal1@llnl.gov [Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States); Wilhelmsen, Karl; Leach, Richard R.; Miller-Kamm, Vicki; Burkhart, Scott; Lowe-Webb, Roger; Cohen, Simon [Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States)

    2012-12-15

    Highlights: Black-Right-Pointing-Pointer An automatic alignment system was developed to process images of the laser beams. Black-Right-Pointing-Pointer System uses processing to adjust a series of control loops until alignment criteria are satisfied. Black-Right-Pointing-Pointer Monitored conditions are compared against nominal values with an off-normal alert. Black-Right-Pointing-Pointer Automated health monitoring system trends off-normals with a large image history. - Abstract: The National Ignition Facility (NIF) is a high power laser system capable of supporting high-energy-density experimentation as a user facility for the next 30 years. In order to maximize the facility availability, preventive maintenance enhancements are being introduced into the system. An example of such an enhancement is a camera-based health monitoring system, integrated into the automated alignment system, which provides an opportunity to monitor trends in measurements such as average beam intensity, size of the beam, and pixel saturation. The monitoring system will generate alerts based on observed trends in measurements to allow scheduled pro-active maintenance before routine off-normal detection stops system operations requiring unscheduled intervention.

  19. Precise rotational alignment of x-ray transmission diffraction gratings

    International Nuclear Information System (INIS)

    Hill, S.L.

    1988-01-01

    Gold transmission diffraction gratings used for x-ray spectroscopy must sometimes be rotationally aligned to the axis of a diagnostic instrument to within sub-milliradian accuracy. We have fabricated transmission diffraction gratings with high line-densities (grating period of 200 and 300 nm) using uv holographic and x-ray lithography. Since the submicron features of the gratings are not optically visible, precision alignment is time consuming and difficult to verify in situ. We have developed a technique to write an optically visible alignment pattern onto these gratings using a scanning electron microscope (SEM). At high magnification (15000 X) several submicron lines of the grating are observable in the SEM, making it possible to write an alignment pattern parallel to the grating lines in an electron-beam-sensitive coating that overlays the grating. We create an alignment pattern by following a 1-cm-long grating line using the SEM's joystick-controlled translation stage. By following the same grating line we are assured the traveled direction of the SEM electron beam is parallel to the grating to better than 10 μradian. The electron-beam-exposed line-width can be large (5 to 15 μm wide) depending on the SEM magnification, and is therefore optically visible. The exposed pattern is eventually made a permanent feature of the grating by ion beam etching or gold electroplating. The pattern can be used to accurately align the grating to the axis of a diagnostic instrument. More importantly, the alignment of the grating can be quickly verified in situ

  20. Two-Stream Transformer Networks for Video-based Face Alignment.

    Science.gov (United States)

    Liu, Hao; Lu, Jiwen; Feng, Jianjiang; Zhou, Jie

    2017-08-01

    In this paper, we propose a two-stream transformer networks (TSTN) approach for video-based face alignment. Unlike conventional image-based face alignment approaches which cannot explicitly model the temporal dependency in videos and motivated by the fact that consistent movements of facial landmarks usually occur across consecutive frames, our TSTN aims to capture the complementary information of both the spatial appearance on still frames and the temporal consistency information across frames. To achieve this, we develop a two-stream architecture, which decomposes the video-based face alignment into spatial and temporal streams accordingly. Specifically, the spatial stream aims to transform the facial image to the landmark positions by preserving the holistic facial shape structure. Accordingly, the temporal stream encodes the video input as active appearance codes, where the temporal consistency information across frames is captured to help shape refinements. Experimental results on the benchmarking video-based face alignment datasets show very competitive performance of our method in comparisons to the state-of-the-arts.

  1. Alignment of the drift tube detector at the neutrino oscillation experiment OPERA

    International Nuclear Information System (INIS)

    Goellnitz, Christoph

    2012-09-01

    The present thesis was composed during the course of the OPERA experiment, which aims to give a direct evidence for neutrino oscillations in the channel ν μ → ν τ . The OPERA detector is designed to observe the appearance of tau neutrinos in an originally pure muon neutrino beam, the CNGS beam. As important part of the detector the precision tracker (PT), a drift tube detector, consists of 9504 drift tubes in 198 modules. In this thesis, several parts of the slow control of the PT are developed and implemented to ensure operation during data taking over several years. The main part is the geometric calibration, the alignment of the detector. The alignment procedure contains both hardware and software parts, the software methods are developed and applied. Using straight particle tracks, the detector components are geometrically corrected. A special challenge for the alignment for the PT is the fact that at this kind of low-rate experiment only a small number of particle tracks is available. With software-based corrections of the module rotation, a systematic error of 0.2 mrad has been attained, for corrections of translation, a systematic error of 32 μm is reached. For the alignment between two adjacent PT walls, the statistical error is less than 8 μm. All results of the position monitoring system are considered. All developed methods are tested with Monte Carlo simulations. The detector requirements (Δp/p ≤ 0.25 below 25 GeV) are met. The analysis of the momentum measurement for high energies above 25 GeV demonstrates the resulting improvement. The mean momentum is falling significantly using the new alignment values. The significance of the detector alignment becomes most evident in the analysis of cosmic particles. The muon charge ratio R μ is expected not to be angular dependent. The χ 2 probability of the measured distribution improves up to 58%. The muon charge ratio was also investigated in dependence of particle energy in terms of the alignment

  2. Optical grid alignment system for portable radiography and portable radiography apparatus incorporating same

    International Nuclear Information System (INIS)

    MacMahon, H.

    1993-01-01

    A grid alignment system is described for use in a portable radiographic apparatus for aligning x-ray film with an x-ray source within said portable radiographic apparatus, comprising: a grid cassette, movable relative to said x-ray source, including an x-ray film holding portion, an anti-scatter grid substantially fixed relative to said x-ray film holding portion and positioned between said x-ray film holding portion and said x-ray source, and a reflector element substantially fixed relative to said grid, said reflector element including a reflective surface for reflecting said incident light beam to produce a reflected light beam, and an imaging surface for producing images of said incident light beam and said reflected light beam, said images providing an indication of alignment between said grid cassette and said x-ray source; and a light beam projector substantially fixed relative to said x-ray source, said light-beam projector projecting said incident light beam upon said reflector element to provide said indication of alignment between said grid cassette and said x-ray source

  3. A rank-based sequence aligner with applications in phylogenetic analysis.

    Directory of Open Access Journals (Sweden)

    Liviu P Dinu

    Full Text Available Recent tools for aligning short DNA reads have been designed to optimize the trade-off between correctness and speed. This paper introduces a method for assigning a set of short DNA reads to a reference genome, under Local Rank Distance (LRD. The rank-based aligner proposed in this work aims to improve correctness over speed. However, some indexing strategies to speed up the aligner are also investigated. The LRD aligner is improved in terms of speed by storing [Formula: see text]-mer positions in a hash table for each read. Another improvement, that produces an approximate LRD aligner, is to consider only the positions in the reference that are likely to represent a good positional match of the read. The proposed aligner is evaluated and compared to other state of the art alignment tools in several experiments. A set of experiments are conducted to determine the precision and the recall of the proposed aligner, in the presence of contaminated reads. In another set of experiments, the proposed aligner is used to find the order, the family, or the species of a new (or unknown organism, given only a set of short Next-Generation Sequencing DNA reads. The empirical results show that the aligner proposed in this work is highly accurate from a biological point of view. Compared to the other evaluated tools, the LRD aligner has the important advantage of being very accurate even for a very low base coverage. Thus, the LRD aligner can be considered as a good alternative to standard alignment tools, especially when the accuracy of the aligner is of high importance. Source code and UNIX binaries of the aligner are freely available for future development and use at http://lrd.herokuapp.com/aligners. The software is implemented in C++ and Java, being supported on UNIX and MS Windows.

  4. Unsupervised image matching based on manifold alignment.

    Science.gov (United States)

    Pei, Yuru; Huang, Fengchun; Shi, Fuhao; Zha, Hongbin

    2012-08-01

    This paper challenges the issue of automatic matching between two image sets with similar intrinsic structures and different appearances, especially when there is no prior correspondence. An unsupervised manifold alignment framework is proposed to establish correspondence between data sets by a mapping function in the mutual embedding space. We introduce a local similarity metric based on parameterized distance curves to represent the connection of one point with the rest of the manifold. A small set of valid feature pairs can be found without manual interactions by matching the distance curve of one manifold with the curve cluster of the other manifold. To avoid potential confusions in image matching, we propose an extended affine transformation to solve the nonrigid alignment in the embedding space. The comparatively tight alignments and the structure preservation can be obtained simultaneously. The point pairs with the minimum distance after alignment are viewed as the matchings. We apply manifold alignment to image set matching problems. The correspondence between image sets of different poses, illuminations, and identities can be established effectively by our approach.

  5. An X-ray beam position monitor based on the photoluminescence of helium gas

    Science.gov (United States)

    Revesz, Peter; White, Jeffrey A.

    2005-03-01

    A new method for white beam position monitoring for both bend magnet and wiggler synchrotron X-ray radiation has been developed. This method utilizes visible light luminescence generated as a result of ionization by the intense X-ray flux. In video beam position monitors (VBPMs), the luminescence of helium gas at atmospheric pressure is observed through a view port using a CCD camera next to the beam line. The beam position, profile, integrated intensity and FWHM are calculated from the distribution of luminescence intensity in each captured image by custom software. Misalignment of upstream apertures changes the image profile making VBPMs helpful for initial alignment of upstream beam line components. VBPMs can thus provide more information about the X-ray beam than most beam position monitors (BPMs). A beam position calibration procedure, employing a tilted plane-parallel glass plate placed in front of the camera lens, has also been developed. The accuracy of the VBPM system was measured during a bench-top experiment to be better than 1 μm. The He-luminescence-based VBPM system has been operative on three CHESS beam lines (F hard-bend and wiggler, A-line wiggler and G-line wiggler) for about a year. The beam positions are converted to analog voltages and used as feedback signals for beam stabilization. In our paper we discuss details of VBPM construction and describe further results of its performance.

  6. Relay telescope for high power laser alignment system

    Science.gov (United States)

    Dane, C. Brent; Hackel, Lloyd; Harris, Fritz B.

    2006-09-19

    A laser system includes an optical path having an intracavity relay telescope with a telescope focal point for imaging an output of the gain medium between an image location at or near the gain medium and an image location at or near an output coupler for the laser system. A kinematic mount is provided within a vacuum chamber, and adapted to secure beam baffles near the telescope focal point. An access port on the vacuum chamber is adapted for allowing insertion and removal of the beam baffles. A first baffle formed using an alignment pinhole aperture is used during alignment of the laser system. A second tapered baffle replaces the alignment aperture during operation and acts as a far-field baffle in which off angle beams strike the baffle a grazing angle of incidence, reducing fluence levels at the impact areas.

  7. CMS Muon Alignment: System Description and first results

    CERN Document Server

    Sobron, M

    2008-01-01

    The CMS detector has been instrumented with a precise and complex opto-mechanical alignment subsystem that provides a common reference frame between Tracker and Muon detection systems by means of a net of laser beams. The system allows a continuous and accurate monitoring of the muon chambers positions with respect to the Tracker body. Preliminary results of operation during the test of the CMS 4T solenoid magnet, performed in 2006, are presented. These measurements complement the information provided by the use of survey techniques and the results of alignment algorithms based on muon tracks crossing the detector.

  8. Aligning molecules with intense nonresonant laser fields

    DEFF Research Database (Denmark)

    Larsen, J.J.; Safvan, C.P.; Sakai, H.

    1999-01-01

    Molecules in a seeded supersonic beam are aligned by the interaction between an intense nonresonant linearly polarized laser field and the molecular polarizability. We demonstrate the general applicability of the scheme by aligning I2, ICl, CS2, CH3I, and C6H5I molecules. The alignment is probed...... by mass selective two dimensional imaging of the photofragment ions produced by femtosecond laser pulses. Calculations on the degree of alignment of I2 are in good agreement with the experiments. We discuss some future applications of laser aligned molecules....

  9. Automatic target alignment of the Helios laser system

    International Nuclear Information System (INIS)

    Liberman, I.; Viswanathan, V.K.; Klein, M.; Seery, B.D.

    1980-01-01

    An automatic target-alignment technique for the Helios laser facility is reported and verified experimentally. The desired alignment condition is completely described by an autocollimation test. A computer program examines the autocollimated return pattern from the surrogate target and correctly describes any changes required in mirror orientation to yield optimum targe alignment with either aberrated or misaligned beams. Automated on-line target alignment is thus shown to be feasible

  10. Base-By-Base: single nucleotide-level analysis of whole viral genome alignments.

    Science.gov (United States)

    Brodie, Ryan; Smith, Alex J; Roper, Rachel L; Tcherepanov, Vasily; Upton, Chris

    2004-07-14

    With ever increasing numbers of closely related virus genomes being sequenced, it has become desirable to be able to compare two genomes at a level more detailed than gene content because two strains of an organism may share the same set of predicted genes but still differ in their pathogenicity profiles. For example, detailed comparison of multiple isolates of the smallpox virus genome (each approximately 200 kb, with 200 genes) is not feasible without new bioinformatics tools. A software package, Base-By-Base, has been developed that provides visualization tools to enable researchers to 1) rapidly identify and correct alignment errors in large, multiple genome alignments; and 2) generate tabular and graphical output of differences between the genomes at the nucleotide level. Base-By-Base uses detailed annotation information about the aligned genomes and can list each predicted gene with nucleotide differences, display whether variations occur within promoter regions or coding regions and whether these changes result in amino acid substitutions. Base-By-Base can connect to our mySQL database (Virus Orthologous Clusters; VOCs) to retrieve detailed annotation information about the aligned genomes or use information from text files. Base-By-Base enables users to quickly and easily compare large viral genomes; it highlights small differences that may be responsible for important phenotypic differences such as virulence. It is available via the Internet using Java Web Start and runs on Macintosh, PC and Linux operating systems with the Java 1.4 virtual machine.

  11. The Laser Alignment System for the CMS silicon strip tracker

    CERN Document Server

    Olzem, Jan

    2009-01-01

    The Laser Alignment System (LAS) of the CMS silicon strip Tracker has been designed for surveying the geometry of the large-scale Tracker support structures. It uses 40 laser beams ($\\lambda$ = 1075 nm) that induce signals on a subset of the Tracker silicon sensors. The positions in space of the laser spots on the sensors are reconstructed with a resolution of 30 $\\mu$m. From this, the LAS is capable of permanent in-time monitoring of the different Tracker components relative to each other with better than 30 $\\mu$m precision. Additionally, it can provide an absolute measurement of the Tracker mechanical structure with an accuracy better than 70 $\\mu$m, thereby supplying additional input to the track based alignment at detector startup. 31 out of the 40 LAS beams have been successfully operated during the CMS cosmic muon data taking campaign in autumn 2008. The alignment of the Tracker Endcap Discs and of the discs with respect to the Tracker Inner Barrel and Tracker Outer Barrel subdetectors was measured w...

  12. Alignment Challenges for a Future Linear Collider

    CERN Document Server

    Durand, H; Stern, G

    2013-01-01

    The preservation of ultra-low emittances in the main linac and Beam Delivery System area is one of the main challenges for linear colliders. This requires alignment tolerances never achieved before at that scale, down to the micrometre level. As a matter of fact, in the LHC, the goal for the smoothing of the components was to obtain a 1σ deviation with respect to a smooth curve of 0.15 mm over a 150 m long sliding window, while for the CLIC project for example, it corresponds to 10 μm over a sliding window of 200 m in the Beam Delivery System area. Two complementary strategies are being studied to fulfil these requirements: the development and validation of long range alignment systems over a few hundreds of metres and short range alignment systems over a few metres. The studies undertaken, with associated tests setups and the latest results will be detailed, as well as their application for the alignment of both CLIC and ILC colliders.

  13. NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction

    DEFF Research Database (Denmark)

    Nielsen, Morten; Lund, Ole

    2009-01-01

    this binding event. RESULTS: Here, we present a novel artificial neural network-based method, NN-align that allows for simultaneous identification of the MHC class II binding core and binding affinity. NN-align is trained using a novel training algorithm that allows for correction of bias in the training data...

  14. The use of an intermediate wavelength laser for alignment to inertial confinement fusion targets

    International Nuclear Information System (INIS)

    English, R.E. Jr.; Seppala, L.G.; Vann, C.S.; Bliss, E.S.

    1995-01-01

    The conceptual design of the National Ignition Facility (NIF) 192 beam laser incorporates a low-power alignment beam injected in the pinhole plane of the final spatial filter with a wave length intermediate between the 1053 mn laser output and the 351 mn frequency-converted beam that illuminates the target Choosing the specific wavelength for which the spatial filter plane is reimaged in the same target chamber plane as the frequency-converted main laser pulse, achieves optimum accuracy without the need for additional means to insure precise overlap between the two beams. Insertion of the alignment beam after the last laser amplifier also allows alignment to the target while the amplifiers are still cooling from a previous shot

  15. An Improved Measurement Method for the Strength of Radiation of Reflective Beam in an Industrial Optical Sensor Based on Laser Displacement Meter.

    Science.gov (United States)

    Bae, Youngchul

    2016-05-23

    An optical sensor such as a laser range finder (LRF) or laser displacement meter (LDM) uses reflected and returned laser beam from a target. The optical sensor has been mainly used to measure the distance between a launch position and the target. However, optical sensor based LRF and LDM have numerous and various errors such as statistical errors, drift errors, cyclic errors, alignment errors and slope errors. Among these errors, an alignment error that contains measurement error for the strength of radiation of returned laser beam from the target is the most serious error in industrial optical sensors. It is caused by the dependence of the measurement offset upon the strength of radiation of returned beam incident upon the focusing lens from the target. In this paper, in order to solve these problems, we propose a novel method for the measurement of the output of direct current (DC) voltage that is proportional to the strength of radiation of returned laser beam in the received avalanche photo diode (APD) circuit. We implemented a measuring circuit that is able to provide an exact measurement of reflected laser beam. By using the proposed method, we can measure the intensity or strength of radiation of laser beam in real time and with a high degree of precision.

  16. BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks

    DEFF Research Database (Denmark)

    Alkan, Ferhat; Erten, Cesim

    2014-01-01

    MOTIVATION: Global many-to-many alignment of biological networks has been a central problem in comparative biological network studies. Given a set of biological interaction networks, the informal goal is to group together related nodes. For the case of protein-protein interaction networks...... of execution speed and memory requirements is more reasonable than the competing algorithms. AVAILABILITY AND IMPLEMENTATION: Supplementary material including code implementations in LEDA C++, experimental data and the results are available at http://webprs.khas.edu.tr/~cesim/BEAMS.tar.gz....

  17. Cryo-EM image alignment based on nonuniform fast Fourier transform

    International Nuclear Information System (INIS)

    Yang Zhengfan; Penczek, Pawel A.

    2008-01-01

    In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform fast Fourier transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis

  18. Cryo-EM image alignment based on nonuniform fast Fourier transform.

    Science.gov (United States)

    Yang, Zhengfan; Penczek, Pawel A

    2008-08-01

    In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform fast Fourier transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis.

  19. Spent fuel container alignment device and method

    Science.gov (United States)

    Jones, Stewart D.; Chapek, George V.

    1996-01-01

    An alignment device is used with a spent fuel shipping container including a plurality of fuel pockets for spent fuel arranged in an annular array and having a rotatable cover including an access opening therein. The alignment device includes a lightweight plate which is installed over the access opening of the cover. A laser device is mounted on the plate so as to emit a laser beam through a laser admittance window in the cover into the container in the direction of a pre-established target associated with a particular fuel pocket. An indexing arrangement on the container provides an indication of the angular position of the rotatable cover when the laser beam produced by the laser is brought into alignment with the target of the associated fuel pocket.

  20. A Kalman Filter for SINS Self-Alignment Based on Vector Observation.

    Science.gov (United States)

    Xu, Xiang; Xu, Xiaosu; Zhang, Tao; Li, Yao; Tong, Jinwu

    2017-01-29

    In this paper, a self-alignment method for strapdown inertial navigation systems based on the q -method is studied. In addition, an improved method based on integrating gravitational apparent motion to form apparent velocity is designed, which can reduce the random noises of the observation vectors. For further analysis, a novel self-alignment method using a Kalman filter based on adaptive filter technology is proposed, which transforms the self-alignment procedure into an attitude estimation using the observation vectors. In the proposed method, a linear psuedo-measurement equation is adopted by employing the transfer method between the quaternion and the observation vectors. Analysis and simulation indicate that the accuracy of the self-alignment is improved. Meanwhile, to improve the convergence rate of the proposed method, a new method based on parameter recognition and a reconstruction algorithm for apparent gravitation is devised, which can reduce the influence of the random noises of the observation vectors. Simulations and turntable tests are carried out, and the results indicate that the proposed method can acquire sound alignment results with lower standard variances, and can obtain higher alignment accuracy and a faster convergence rate.

  1. Transparent silicon strip sensors for the optical alignment of particle detector systems

    International Nuclear Information System (INIS)

    Blum, W.; Kroha, H.; Widmann, P.

    1995-05-01

    Modern large-area precision tracking detectors require increasing accuracy for the alignment of their components. A novel multi-point laser alignment system has been developed for such applications. The position of detector components with respect to reference laser beams is monitored by semi-transparent optical position sensors which work on the principle of silicon strip photodiodes. Two types of custom designed transparent strip sensors, based on crystalline and on amorphous silicon as active material, have been studied. The sensors are optimised for the typical diameters of collimated laser beams of 3-5 mm over distances of 10-20 m. They provide very high position resolution, on the order of 1 μm, uniformly over a wide measurement range of several centimeters. The preparation of the sensor surfaces requires special attention in order to achieve high light transmittance and minimum distortion of the traversing laser beams. At selected wavelengths, produced by laser diodes, transmission rates above 90% have been achieved. This allows to position more than 30 sensors along one laser beam. The sensors will be equipped with custom designed integrated readout electronics. (orig.)

  2. Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments

    Directory of Open Access Journals (Sweden)

    Tcherepanov Vasily

    2004-07-01

    Full Text Available Abstract Background With ever increasing numbers of closely related virus genomes being sequenced, it has become desirable to be able to compare two genomes at a level more detailed than gene content because two strains of an organism may share the same set of predicted genes but still differ in their pathogenicity profiles. For example, detailed comparison of multiple isolates of the smallpox virus genome (each approximately 200 kb, with 200 genes is not feasible without new bioinformatics tools. Results A software package, Base-By-Base, has been developed that provides visualization tools to enable researchers to 1 rapidly identify and correct alignment errors in large, multiple genome alignments; and 2 generate tabular and graphical output of differences between the genomes at the nucleotide level. Base-By-Base uses detailed annotation information about the aligned genomes and can list each predicted gene with nucleotide differences, display whether variations occur within promoter regions or coding regions and whether these changes result in amino acid substitutions. Base-By-Base can connect to our mySQL database (Virus Orthologous Clusters; VOCs to retrieve detailed annotation information about the aligned genomes or use information from text files. Conclusion Base-By-Base enables users to quickly and easily compare large viral genomes; it highlights small differences that may be responsible for important phenotypic differences such as virulence. It is available via the Internet using Java Web Start and runs on Macintosh, PC and Linux operating systems with the Java 1.4 virtual machine.

  3. Engineering of automated assembly of beam-shaping optics

    Science.gov (United States)

    Haag, Sebastian; Sinhoff, Volker; Müller, Tobias; Brecher, Christian

    2014-03-01

    Beam-shaping is essential for any kind of laser application. Assembly technologies for beam-shaping subassemblies are subject to intense research and development activities and their technical feasibility has been proven in recent years while economic viability requires more efficient engineering tools for process planning and production ramp up of complex assembly tasks for micro-optical systems. The work presented in this paper aims for significant reduction of process development and production ramp up times for the automated assembly of micro-optical subassemblies for beam-collimation and beam-tilting. The approach proposed bridges the gap between the product development phase and the realization of automation control through integration of established software tools such as optics simulation and CAD modeling as well as through introduction of novel software tools and methods to efficiently describe active alignment strategies. The focus of the paper is put on the methodological approach regarding the engineering of assembly processes for beam-shaping micro-optics and the formal representation of assembly objectives similar to representation in mechanical assemblies. Main topic of the paper is the engineering methodology for active alignment processes based on the classification of optical functions for beam-shaping optics and corresponding standardized measurement setups including adaptable alignment algorithms. The concepts are applied to industrial use-cases: (1) integrated collimation module for fast- and slow-axis and (2) beam-tilting subassembly consisting of a fast-axis collimator and micro-lens array. The paper concludes with an overview of current limitations as well as an outlook on the next development steps considering adhesive bonding processes.

  4. An Improved Measurement Method for the Strength of Radiation of Reflective Beam in an Industrial Optical Sensor Based on Laser Displacement Meter

    OpenAIRE

    Youngchul Bae

    2016-01-01

    An optical sensor such as a laser range finder (LRF) or laser displacement meter (LDM) uses reflected and returned laser beam from a target. The optical sensor has been mainly used to measure the distance between a launch position and the target. However, optical sensor based LRF and LDM have numerous and various errors such as statistical errors, drift errors, cyclic errors, alignment errors and slope errors. Among these errors, an alignment error that contains measurement error for the stre...

  5. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez.

    Since June of 2009, the muon alignment group has focused on providing new alignment constants and on finalizing the hardware alignment reconstruction. Alignment constants for DTs and CSCs were provided for CRAFT09 data reprocessing. For DT chambers, the track-based alignment was repeated using CRAFT09 cosmic ray muons and validated using segment extrapolation and split cosmic tools. One difference with respect to the previous alignment is that only five degrees of freedom were aligned, leaving the rotation around the local x-axis to be better determined by the hardware system. Similarly, DT chambers poorly aligned by tracks (due to limited statistics) were aligned by a combination of photogrammetry and hardware-based alignment. For the CSC chambers, the hardware system provided alignment in global z and rotations about local x. Entire muon endcap rings were further corrected in the transverse plane (global x and y) by the track-based alignment. Single chamber track-based alignment suffers from poor statistic...

  6. Study and development of a laser based alignment system for the compact linear collider

    CERN Document Server

    AUTHOR|(CDS)2083149

    The first objective of the PhD thesis is to develop a new type of positioning sensor to align components at micrometre level over 200 m with respect to a laser beam as straight line reference. The second objective is to estimate the measurement accuracy of the total alignment system over 200 m. The context of the PhD thesis is the Compact Linear Collider project, which is a study for a future particle accelerator. The proposed positioning sensor is made of a camera and an open/close shutter. The sensor can measure the position of the laser beam with respect to its own coordinate system. To do a measurement, the shutter closes, a laser spot appears on it, the camera captures a picture of the laser spot and the coordinates of the laser spot centre are reconstructed in the sensor coordinate system with image processing. Such a measurement requires reference targets on the positioning sensor. To reach the rst objective of the PhD thesis, we used laser theory...

  7. Study on Dynamic Alignment Technology of COIL Resonator

    International Nuclear Information System (INIS)

    Xiong, M D; Zou, X J; Guo, J H; Jia, S N; Zhang, Z B

    2006-01-01

    The performance of great power chemical oxygen-iodine laser (COIL) beam is decided mostly by resonator mirror maladjustment and environment vibration. To improve the performance of light beam, an auto-alignment device is used in COIL resonator, the device can keep COIL resonator collimating by adjusting the optical components of resonator. So the coupling model of COIL resonator is present. The multivariable self study fuzzy uncoupling arithmetic and six-dimensional micro drive technology are used to design a six-input-three-output uncoupling controller, resulting in the realization of the high precision dynamic alignment. The experiments indicate that the collimating range of this system is 8 mrad, precision is 5 urad and frequency response is 20Hz, which meet the demand of resonator alignment system

  8. Magnetic field alignment for a 20 MeV linear induction accelerator

    International Nuclear Information System (INIS)

    Zhang Wenwei; Pan Haifeng; Li Hong; Liu Yunlong; Zhang Linwen

    2002-01-01

    'Dragon-1' accelerator now is being constructed in CAEP. It will produce high current pulse electron beams. The main components of the accelerator include 72 induction accelerating cells and 18 connection cells with ports for beam di gnostic hardware and vacuum pump. In order to acquire high quality beams, a lot of problems have to be addressed such as to reduce the emittance, to control the increase of corkscrew and so on. The alignment of the focus magnetic field is the most concerned. A laser track has been used for mechanical alignment, magnetic alignment is performed by using pulsed-wire technique, and the natural tilt errors is corrected by a pair of steering coil, which is located inside the cell

  9. Moving State Marine SINS Initial Alignment Based on High Degree CKF

    Directory of Open Access Journals (Sweden)

    Yong-Gang Zhang

    2014-01-01

    Full Text Available A new moving state marine initial alignment method of strap-down inertial navigation system (SINS is proposed based on high-degree cubature Kalman filter (CKF, which can capture higher order Taylor expansion terms of nonlinear alignment model than the existing third-degree CKF, unscented Kalman filter and central difference Kalman filter, and improve the accuracy of initial alignment under large heading misalignment angle condition. Simulation results show the efficiency and advantage of the proposed initial alignment method as compared with existing initial alignment methods for the moving state SINS initial alignment with large heading misalignment angle.

  10. Alignment Compensation for Bending Radius in TI 2 Transfer Line Magnets

    CERN Document Server

    Weterings, W

    2004-01-01

    The optics file for the TI 2 transfer lines specifies the position of the bending magnets assuming that the beam enters and exists at the centre of the vacuum pipe. In order to disbribute the deflected beam evenly inside the vacuum tube, the alignment has to be compensated by moving the magnets half of the beam deflection away from the centre of the bending radius. In this note the saggitas of the various TI 2 magnets are calculated and the alignment displacements tabulated for future reference.

  11. Design of a divergence and alignment indicator

    International Nuclear Information System (INIS)

    Brenizer, J.S. Jr.; Raine, D.A.; Gao, J.; Chen, J.

    1996-01-01

    The divergence and alignment indicator (DAI) is an extension of the ASTM E803 L/D thermal neutron radiography L/D device that allows the user to determine both the beam centerline and the beam divergence. The DAI was made using aluminium plate and rods, and incorporated cadmium wire for contrast. Circular symmetry was utilized to simplify manufacture. The DAI was placed with the five posts against the film cassette or radioscopic imaging device in the physical center of the beam. The DAI was perpendicular to the selected beam radius when the front and back center Cd wire images overlap. The degree of misalignment was indicated by their image positions. After the DAI was aligned, analysis of the cadmium wire ''+'' image spacing yielded the beam divergence. The DAI was tested in a neutron beam which has an L/D of 30 but a small degree of divergence. The DAI was also imaged using an X-ray source. The point source predictions of Cd wire image locations showed good agreement with those measured from the X-ray radiograph. The neutron radiographic locations could be predicted using the point source equations, even though the neutron beam was a complex distributed source. (orig.)

  12. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    2010-01-01

    The main developments in muon alignment since March 2010 have been the production, approval and deployment of alignment constants for the ICHEP data reprocessing. In the barrel, a new geometry, combining information from both hardware and track-based alignment systems, has been developed for the first time. The hardware alignment provides an initial DT geometry, which is then anchored as a rigid solid, using the link alignment system, to a reference frame common to the tracker. The “GlobalPositionRecords” for both the Tracker and Muon systems are being used for the first time, and the initial tracker-muon relative positioning, based on the link alignment, yields good results within the photogrammetry uncertainties of the Tracker and alignment ring positions. For the first time, the optical and track-based alignments show good agreement between them; the optical alignment being refined by the track-based alignment. The resulting geometry is the most complete to date, aligning all 250 DTs, ...

  13. The Stonehenge technique. A method for aligning coherent bremsstrahlung radiators

    International Nuclear Information System (INIS)

    Livingston, Ken

    2009-01-01

    This paper describes a technique for the alignment of crystal radiators used to produce high energy, linearly polarized photons via coherent bremsstrahlung scattering at electron beam facilities. In these experiments the crystal is mounted on a goniometer which is used to adjust its orientation relative to the electron beam. The angles and equations which relate the crystal lattice, goniometer and electron beam direction are presented here, and the method of alignment is illustrated with data taken at MAMI (the Mainz microtron). A practical guide to setting up a coherent bremsstrahlung facility and installing new crystals using this technique is also included.

  14. The Stonehenge technique. A method for aligning coherent bremsstrahlung radiators

    Energy Technology Data Exchange (ETDEWEB)

    Livingston, Ken [Department of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ (United Kingdom)], E-mail: k.livingston@physics.gla.ac.uk

    2009-05-21

    This paper describes a technique for the alignment of crystal radiators used to produce high energy, linearly polarized photons via coherent bremsstrahlung scattering at electron beam facilities. In these experiments the crystal is mounted on a goniometer which is used to adjust its orientation relative to the electron beam. The angles and equations which relate the crystal lattice, goniometer and electron beam direction are presented here, and the method of alignment is illustrated with data taken at MAMI (the Mainz microtron). A practical guide to setting up a coherent bremsstrahlung facility and installing new crystals using this technique is also included.

  15. The Stonehenge technique. A method for aligning coherent bremsstrahlung radiators

    Science.gov (United States)

    Livingston, Ken

    2009-05-01

    This paper describes a technique for the alignment of crystal radiators used to produce high energy, linearly polarized photons via coherent bremsstrahlung scattering at electron beam facilities. In these experiments the crystal is mounted on a goniometer which is used to adjust its orientation relative to the electron beam. The angles and equations which relate the crystal lattice, goniometer and electron beam direction are presented here, and the method of alignment is illustrated with data taken at MAMI (the Mainz microtron). A practical guide to setting up a coherent bremsstrahlung facility and installing new crystals using this technique is also included.

  16. An Improved Measurement Method for the Strength of Radiation of Reflective Beam in an Industrial Optical Sensor Based on Laser Displacement Meter

    Directory of Open Access Journals (Sweden)

    Youngchul Bae

    2016-05-01

    Full Text Available An optical sensor such as a laser range finder (LRF or laser displacement meter (LDM uses reflected and returned laser beam from a target. The optical sensor has been mainly used to measure the distance between a launch position and the target. However, optical sensor based LRF and LDM have numerous and various errors such as statistical errors, drift errors, cyclic errors, alignment errors and slope errors. Among these errors, an alignment error that contains measurement error for the strength of radiation of returned laser beam from the target is the most serious error in industrial optical sensors. It is caused by the dependence of the measurement offset upon the strength of radiation of returned beam incident upon the focusing lens from the target. In this paper, in order to solve these problems, we propose a novel method for the measurement of the output of direct current (DC voltage that is proportional to the strength of radiation of returned laser beam in the received avalanche photo diode (APD circuit. We implemented a measuring circuit that is able to provide an exact measurement of reflected laser beam. By using the proposed method, we can measure the intensity or strength of radiation of laser beam in real time and with a high degree of precision.

  17. Proposition d'une méthode d'alignement de l'accélérateur linéaire CLIC

    CERN Document Server

    Touzé, Thomas; Mainaud-Durand, H

    2011-01-01

    The compact linear collider (CLIC) is the particles accelerator project proposed by the european organization for nuclear research (CERN) for high energy physics after the large hadron collider (LHC). Because of the nanometric scale of the CLIC leptons beams, the emittance growth budget is very tight. It induces alignment tolerances on the positions of the CLIC components that have never been achieved. The last step of the CLIC alignment will be done according to the beam itself. It falls within the competence of the physicists. However, in order to implement the beam-based feedback, a challenging pre-alignment is required : 10 μm at 3σ along a 200 m sliding window. For such a precision, the proposed solution must be compatible with a feedback between the measurement and repositioning systems. The CLIC pre-alignment will have to be active. This thesis does not demonstrate the feasibility of the CLIC active prealignment but shows the way to the last developments that have to be done for that purpose. A metho...

  18. PACMAN Project: A New Solution for the High-accuracy Alignment of Accelerator Components

    CERN Document Server

    Mainaud Durand, Helene; Buzio, Marco; Caiazza, Domenico; Catalán Lasheras, Nuria; Cherif, Ahmed; Doytchinov, Iordan; Fuchs, Jean-Frederic; Gaddi, Andrea; Galindo Munoz, Natalia; Gayde, Jean-Christophe; Kamugasa, Solomon; Modena, Michele; Novotny, Peter; Russenschuck, Stephan; Sanz, Claude; Severino, Giordana; Tshilumba, David; Vlachakis, Vasileios; Wendt, Manfred; Zorzetti, Silvia

    2016-01-01

    The beam alignment requirements for the next generation of lepton colliders have become increasingly challenging. As an example, the alignment requirements for the three major collider components of the CLIC linear collider are as follows. Before the first beam circulates, the Beam Position Monitors (BPM), Accelerating Structures (AS)and quadrupoles will have to be aligned up to 10 μm w.r.t. a straight line over 200 m long segments, along the 20 km of linacs. PACMAN is a study on Particle Accelerator Components' Metrology and Alignment to the Nanometre scale. It is an Innovative Doctoral Program, funded by the EU and hosted by CERN, providing high quality training to 10 Early Stage Researchers working towards a PhD thesis. The technical aim of the project is to improve the alignment accuracy of the CLIC components by developing new methods and tools addressing several steps of alignment simultaneously, to gain time and accuracy. The tools and methods developed will be validated on a test bench. This paper pr...

  19. Construction and calibration of the laser alignment system for the CMS tracker

    International Nuclear Information System (INIS)

    Adolphi, R.

    2006-01-01

    A robust and reliable optical system able to measure and control the large CMS tracker geometry with high accuracy has been developed and validated. The construction and integration of the LAS fulfilling the requirements, as well as its calibration and performance are described in this thesis. The working principle is based on the partial transparency of silicon for light wavelengths in the near infrared region. The absorbed part of the laser beam generates a signal in the corresponding silicon strip module serving to reconstruct its position. The transmitted part reaches the subsequent module layer generating an optical link between the two layers. Investigation of the light generation and distribution led to a definition of the optical components and their optimization for Laser Alignment purposes. Laser diodes have been qualified as light sources and singlemode optical fibres, terminated by special connectors, distribute the light to the CMS tracker detector. The beamsplitting device, a key component of the LAS light distribution inside the CMS tracker, has been studied in detail. The challenge of splitting one collimated beam into two back-to-back beams inside a small available volume has been solved by using the polarization principle. Special test setups were developed to determine the collinearity of the two outgoing beams with a precision better than 50 μrad and it has been shown that their relative orientation remains constant under working conditions. The interface between the tracker and the LAS is given by the silicon sensors which are responsible both for particle detection and for the determination of the position of the laser spot. An anti-reflex-coating has been applied on the backside of all alignment sensors to improve their optical properties without deterioration of their tracking performance. A test setup has been developed to simultaneously study the transmission and reflection properties of the alignment sensors. The working principle of the

  20. Construction and calibration of the laser alignment system for the CMS tracker

    Energy Technology Data Exchange (ETDEWEB)

    Adolphi, R.

    2006-11-28

    A robust and reliable optical system able to measure and control the large CMS tracker geometry with high accuracy has been developed and validated. The construction and integration of the LAS fulfilling the requirements, as well as its calibration and performance are described in this thesis. The working principle is based on the partial transparency of silicon for light wavelengths in the near infrared region. The absorbed part of the laser beam generates a signal in the corresponding silicon strip module serving to reconstruct its position. The transmitted part reaches the subsequent module layer generating an optical link between the two layers. Investigation of the light generation and distribution led to a definition of the optical components and their optimization for Laser Alignment purposes. Laser diodes have been qualified as light sources and singlemode optical fibres, terminated by special connectors, distribute the light to the CMS tracker detector. The beamsplitting device, a key component of the LAS light distribution inside the CMS tracker, has been studied in detail. The challenge of splitting one collimated beam into two back-to-back beams inside a small available volume has been solved by using the polarization principle. Special test setups were developed to determine the collinearity of the two outgoing beams with a precision better than 50 {mu}rad and it has been shown that their relative orientation remains constant under working conditions. The interface between the tracker and the LAS is given by the silicon sensors which are responsible both for particle detection and for the determination of the position of the laser spot. An anti-reflex-coating has been applied on the backside of all alignment sensors to improve their optical properties without deterioration of their tracking performance. A test setup has been developed to simultaneously study the transmission and reflection properties of the alignment sensors. The working principle of

  1. The stonehenge technique: a new method of crystal alignment for coherent bremsstrahlung experiments

    Science.gov (United States)

    Livingston, Kenneth

    2005-08-01

    In the coherent bremsstrahlung technique a thin diamond crystal oriented correctly in an electron beam can produce photons with a high degree of linear polarization.1 The crystal is mounted on a goniometer to control its orientation and it is necessary to measure the angular offsets a) between the crystal axes and the goniometer axes and b) between the goniometer and the electron beam axis. A method for measuring these offsets and aligning the crystal was developed by Lohman et al, and has been used successfully in Mainz.2 However, recent attempts to investigate new crystals have shown that this approach has limitations which become more serious at higher beam energies where more accurate setting of the crystal angles, which scale with l/Ebeam, is required. (Eg. the recent installation of coherent bremsstrahlung facility at Jlab, with Ebeam = 6 GeV ) This paper describes a new, more general alignment technique, which overcomes these limitations. The technique is based on scans where the horizontal and vertical rotation axes of the goniometer are adjusted in a series of steps to make the normal to the crystal describe a cone of a given angle. For each step in the scan, the photon energy spectrum is measured using a tagging spectrometer, and the offsets between the electron beam and the crystal lattice are inferred from the resulting 2D plot. Using this method, it is possible to align the crystal with the beam quickly, and hence to set any desired orientation of the crystal relative to the beam. This is essential for any experiment requiring linearly polarized photons produced via coherent bremsstrahlung, and is also required for a systematic study of the channeling radiation produced by the electron beam incident on the crystal.

  2. Automatic alignment device for focal spot measurements in the center of the field for mammography

    International Nuclear Information System (INIS)

    Vieira, Marcelo A.C.; Watanabe, Alex O.; Oliveira Junior, Paulo D.; Schiabel, Homero

    2010-01-01

    Some quality control procedures used for mammography, such as focal spot evaluation, requires previous alignment of the measurement equipment with the X-ray central beam. However, alignment procedures are, in general, the most difficult task and the one that needs more time to be performed. Moreover, the operator sometimes is exposed to radiation during this procedure. This work presents an automatic alignment system for mammographic equipment that allows locating the central ray of the radiation beam and, immediately, aligns with it by dislocating itself automatically along the field. The system consists on a bidirectional moving device, connected to a CCD sensor for digital radiographic image acquisition. A computational analysis of a radiographic image, acquired at any position on the field, is performed in order to determine its positioning under the X-ray beam. Finally, a mechanical system for two moving directions, electronically controlled by a microcontroller under USB communication, makes the system to align automatically with the radiation beam central ray. The alignment process is fully automatic, fast and accurate, with no operator exposure to radiation, which allows a considerable time saving for quality control procedures achievement for mammography. (author)

  3. Automated alignment of a 10-kJ laser

    International Nuclear Information System (INIS)

    Partridge, R.E.

    1979-01-01

    The complex task of aligning helios, the 10-kilojoule carbon-dioxide laser, built for fusion research at the Los Alamos Scientific Laboratory, requires computer control of steering mirrors and error sensors. The control system is a three-level minicomputer and microprocessor hierarchy which automatically aligns each of the 40 beam-line sections

  4. Shocklets, SLAMS, and Field-Aligned Ion Beams in the Terrestrial Foreshock

    Science.gov (United States)

    Wilson, L. B.; Koval, A.; Sibeck, D. G.; Szabo, A.; Cattell, C. A.; Kasper, J. C.; Maruca, B. A.; Pulupa, M.; Salem, C. S.; Wilber, M.

    2012-01-01

    We present Wind spacecraft observations of ion distributions showing field- aligned beams (FABs) and large-amplitude magnetic fluctuations composed of a series of shocklets and short large-amplitude magnetic structures (SLAMS). The FABs are found to have T(sub k) approx 80-850 eV, V(sub b)/V(sub sw) approx 1.3-2.4, T(sub perpendicular,b)/T(sub paralell,b) approx 1-8, and n(sub b)/n(sub o) approx 0.2-11%. Saturation amplitudes for ion/ion resonant and non-resonant instabilities are too small to explain the observed SLAMS amplitudes. We show two examples where groups of SLAMS can act like a local quasi-perpendicular shock reflecting ions to produce the FABs, a scenario distinct from the more-common production at the quasi-perpendicular bow shock. The SLAMS exhibit a foot-like magnetic enhancement with a leading magnetosonic whistler train, consistent with previous observations. Strong ion and electron heating are observed within the series of shocklets and SLAMS with temperatures increasing by factors approx > 5 and approx >3, respectively. Both the core and halo electron components show strong perpendicular heating inside the feature.

  5. Fiducialisation and initial alignment of CLIC component with micrometric accuracy

    CERN Document Server

    Mainaud Durand, Helene; Buzio, Marco; Caiazza, Domenico; Catalan Lasheras, Nuria; Cherif, Ahmed; Doytchinov, Iordan Petrov; Fuchs, Jean-Frederic; Gaddi, Andrea; Galindo Munoz, Natalia; Gayde, Jean-Christophe; Kamugasa, Solomon William; Modena, Michele; Novotny, Peter; Sanz, Claude; Severino, Giordana; Russenschuck, Stephan; Tshilumba, David; Vlachakis, Vasileios; Wendt, Manfred; Zorzetti, Silvia; CERN. Geneva. ATS Department

    2016-01-01

    We propose a new solution to fiducialise the three major components of the CLIC collider: quadrupoles, beam-position monitors (BPM), and accelerating structures (AS). This solution is based on the use of a copper-beryllium (CuBe) wire to locate the reference position, i.e. the symmetry axes of the components (their magnetic, respectively electromagnetic centre axis), and to determine their position in the common support assembly defining a local coordinate system, with respect to the fiducials. These alignment targets will be used later to align the support assembly in the tunnel. With such a method, several accelerator components of different types, supported by a dedicated adjustment system, can be simultaneously fiducialised and pre-aligned using the same wire, enabling a micrometric accuracy with help of a 3D coordinate measurement machine (CMM). Alternative solutions based on frequency scanning interferometry (FSI) and micro-triangulation are also under development, to perform such fiducialisation and in...

  6. Cell Based Meniscal Repair Using an Aligned Bioactive Nanofibrous Sheath

    Science.gov (United States)

    2017-07-01

    to subsequently guide tissue regeneration , for example, by seeded tissue progenitor cells . To achieve this objective, the first step is to develop...AWARD NUMBER: W81XWH-15-1-0104 TITLE: Cell -Based Meniscal Repair Using an Aligned Bioactive Nanofibrous Sheath PRINCIPAL INVESTIGATOR...SUBTITLE 5a. CONTRACT NUMBER Cell -Based Meniscal Repair Using an Aligned Bioactive Nanofibrous Sheath 5b. GRANT NUMBER W81XWH-15-1-0104 5c. PROGRAM

  7. Emittance growth rates for displaced beams

    International Nuclear Information System (INIS)

    Anderson, O.A.

    1993-05-01

    Emittance growth rates have been previously analyzed for nonuniform beams in linear channels and for initially uniform mismatched beams in nonlinear channels. These studies were for centered beams. Additional emittance growth can arise in cases where the beam is initially displaced. The purpose of this study is to obtain growth rates for displaced beams. This work differs from studies involving random displacement of electrodes. Our analysis assumes instead that the focusing system is perfectly aligned but that the beam is initially displaced with respect to the equilibrium axis. If the focusing force is slightly nonlinear, we find a gradual transfer of the potential energy of beam displacement into kinetic energy associated with emittance growth. We present explicit results for the emittance growth distance as a function of the nonlinearity of the channel. These results will have practical importance for designers of accelerators and transport systems when setting realistic tolerances for initial beam alignment. These tolerances will depend on the nonlinearity and the length of the system

  8. A new correlation based alignment technique for use in electron tomography

    International Nuclear Information System (INIS)

    Jones, S.D.; Härting, M.

    2013-01-01

    In this paper we present a new correlation based method for the alignment of a single axis tilt series. Rather than performing the pairwise correlation procedure with the central image as the starting point, the method presented here calculates the optimal starting position within the tilt series and proceeds towards both ends. The starting position is determined by maximisation of a viability function, J, which rewards cumulative series correlation and penalises both cumulative series shift and distance from the centre of the image series. - Highlights: • Pairwise correlation based alignment is investigated as a function of seed position. • It is shown that the convention of using the central image as the seed is not optimal. • A function is proposed which improves alignment by finding the optimal seed position. • The method is found to produce alignment with lower residual scores with the phantom data. • Superior alignment is produced vs the standard method with the experimental data

  9. Relevance-based evaluation of alignment approaches: The OAEI2007 food task revisited

    NARCIS (Netherlands)

    Hage, W.R. van; Kolb, H.; Schreiber, G.

    2008-01-01

    Current state-of-the-art ontology-alignment evaluation methods are based on the assumption that alignment relations come in two flavors: correct and incorrect. Some alignment systems find more correct mappings than others and hence, by this assumption, they perform better. In practical applications

  10. Alignment Fixtures For Vacuum-Plasma-Spray Gun

    Science.gov (United States)

    Woodford, William H.; Mckechnie, Timothy N.; Power, Christopher A.; Daniel, Ronald L., Jr.

    1993-01-01

    Fixtures for alignment of vacuum-plasma-spray guns built. Each fixture designed to fit specific gun and holds small, battery-powered laser on centerline of gun. Laser beam projects small red dot where centerline intersects surface of workpiece to be sprayed. After laser beam positioned on surface of workpiece, fixture removed from gun and spraying proceeds.

  11. SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics.

    Science.gov (United States)

    Will, Sebastian; Otto, Christina; Miladi, Milad; Möhl, Mathias; Backofen, Rolf

    2015-08-01

    RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of [Formula: see text]. Subsequently, numerous faster 'Sankoff-style' approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity ([Formula: see text] quartic time). Breaking this barrier, we introduce the novel Sankoff-style algorithm 'sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)', which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff's original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics. © The Author 2015. Published by Oxford University Press.

  12. Final focus test beam alignment: A draft proposal

    International Nuclear Information System (INIS)

    Fischer, G.E.; Ruland, R.E.

    1989-03-01

    The Final Focus Test Beam is a transport line designed to transmit 50 GeV electron beams of SLC emittance (3 x 10 -10 radian-meters) straight through the central arm of the Beam Switchyard (BSY C line) with a final focus point out in the Research Yard but relatively near the end of the switchyard tunnel. The hardware, methods and procedures outlined in this proposal are dedicated to measuring the placement of mechanical objects with respect to certain defined geometric axes. We wish to emphasize that the very difficult problems of locating the effective magnetic axes of focusing elements, the effective electrical center of beam position monitors and even the effective axis of the incident beam relative to mechanical reference surfaces is outside the scope of this work. Further, this proposal is restricted to the act of measurement and does not consider the vital task of on-line mechanical repositioning of elements that will, in likelihood, be called upon during operation of the system. 16 refs., 16 figs., 4 tabs

  13. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez and J. Pivarski

    2011-01-01

    Alignment efforts in the first few months of 2011 have shifted away from providing alignment constants (now a well established procedure) and focussed on some critical remaining issues. The single most important task left was to understand the systematic differences observed between the track-based (TB) and hardware-based (HW) barrel alignments: a systematic difference in r-φ and in z, which grew as a function of z, and which amounted to ~4-5 mm differences going from one end of the barrel to the other. This difference is now understood to be caused by the tracker alignment. The systematic differences disappear when the track-based barrel alignment is performed using the new “twist-free” tracker alignment. This removes the largest remaining source of systematic uncertainty. Since the barrel alignment is based on hardware, it does not suffer from the tracker twist. However, untwisting the tracker causes endcap disks (which are aligned ...

  14. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    Gervasio Gomez

    The main progress of the muon alignment group since March has been in the refinement of both the track-based alignment for the DTs and the hardware-based alignment for the CSCs. For DT track-based alignment, there has been significant improvement in the internal alignment of the superlayers inside the DTs. In particular, the distance between superlayers is now corrected, eliminating the residual dependence on track impact angles, and good agreement is found between survey and track-based corrections. The new internal geometry has been approved to be included in the forthcoming reprocessing of CRAFT samples. The alignment of DTs with respect to the tracker using global tracks has also improved significantly, since the algorithms use the latest B-field mapping, better run selection criteria, optimized momentum cuts, and an alignment is now obtained for all six degrees of freedom (three spatial coordinates and three rotations) of the aligned DTs. This work is ongoing and at a stage where we are trying to unders...

  15. Accelerator Technology: Geodesy and Alignment for Particle Accelerators

    CERN Document Server

    Missiaen, D

    2013-01-01

    This document is part of Subvolume C 'Accelerators and Colliders' of Volume 21 'Elementary Particles' of Landolt-Börnstein - Group I 'Elementary Particles, Nuclei and Atoms'. It contains the the Section '8.9 Geodesy and Alignment for Particle Accelerators' of the Chapter '8 Accelerator Technology' with the content: 8.9 Geodesy and Alignment for Particle Accelerators 8.9.1 Introduction 8.9.2 Reference and Co-ordinate Systems 8.9.3 Definition of the Beam Line on the Accelerator Site 8.9.4 Geodetic Network 8.9.5 Tunnel Preliminary Works 8.9.6 The Alignment References 8.9.7 Alignment of Accelerator Components 8.9.8 Permanent Monitoring and Remote Alignment of Low Beta Quadrupoles 8.9.9 Alignment of Detector Components

  16. T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life.

    Science.gov (United States)

    Carbone, Ignazio; White, James B; Miadlikowska, Jolanta; Arnold, A Elizabeth; Miller, Mark A; Kauff, Frank; U'Ren, Jana M; May, Georgiana; Lutzoni, François

    2017-04-15

    High-quality phylogenetic placement of sequence data has the potential to greatly accelerate studies of the diversity, systematics, ecology and functional biology of diverse groups. We developed the Tree-Based Alignment Selector (T-BAS) toolkit to allow evolutionary placement and visualization of diverse DNA sequences representing unknown taxa within a robust phylogenetic context, and to permit the downloading of highly curated, single- and multi-locus alignments for specific clades. In its initial form, T-BAS v1.0 uses a core phylogeny of 979 taxa (including 23 outgroup taxa, as well as 61 orders, 175 families and 496 genera) representing all 13 classes of largest subphylum of Fungi-Pezizomycotina (Ascomycota)-based on sequence alignments for six loci (nr5.8S, nrLSU, nrSSU, mtSSU, RPB1, RPB2 ). T-BAS v1.0 has three main uses: (i) Users may download alignments and voucher tables for members of the Pezizomycotina directly from the reference tree, facilitating systematics studies of focal clades. (ii) Users may upload sequence files with reads representing unknown taxa and place these on the phylogeny using either BLAST or phylogeny-based approaches, and then use the displayed tree to select reference taxa to include when downloading alignments. The placement of unknowns can be performed for large numbers of Sanger sequences obtained from fungal cultures and for alignable, short reads of environmental amplicons. (iii) User-customizable metadata can be visualized on the tree. T-BAS Version 1.0 is available online at http://tbas.hpc.ncsu.edu . Registration is required to access the CIPRES Science Gateway and NSF XSEDE's large computational resources. icarbon@ncsu.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  17. Laser application for nuclear reaction product detecting system alignment

    International Nuclear Information System (INIS)

    Grantsev, V.I.; Dryapachenko, I.P.; Kornilov, V.A.; Nemets, O.F.; Rudenko, B.A.; Sokolov, M.V.; Struzhko, B.G.; Gnatovskij, A.V.; Bojchuk, V.N.

    1982-01-01

    A method for optical alignment of nuclear particle detector system using a laser beam and hologram is described. The method permits to arrange detectors very precisely in accordance with any chosen space coordinate values. The results of modelling the geometry of an experiment based on using the suggested method on cyclotron beams are described. A gas helium-neon laser with wavelength of 0.63 μm radiation power of an order of 2 MW and angular beam divergence less than 10 angular minutes is used for modelling. It is concluded that the laser and hologram application provides large possibilities for the modelling the geometry of experiments on nuclear reaction investigation. When necessary it is possible to obtain small nonius scale of reference beams by means of multiplicating properties of the wave front modulator-hologram system. It is also possible to record holograms shaping the reference beams in two or several planes crossing along the central beam direction. Such holograms can be used for modelling the noncoplanar geometry of correlation experiments [ru

  18. Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner.

    Science.gov (United States)

    Lu, David V; Brown, Randall H; Arumugam, Manimozhiyan; Brent, Michael R

    2009-07-01

    The most accurate way to determine the intron-exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary determinant of alignment accuracy, while heuristics that prevent consideration of certain alignments are a primary determinant of runtime and memory usage. Both accuracy and speed are important considerations in choosing an alignment algorithm, but scoring systems have received much less attention than heuristics. We present Pairagon, a pair hidden Markov model based cDNA-to-genome alignment program, as the most accurate aligner for sequences with high- and low-identity levels. We conducted a series of experiments testing alignment accuracy with varying sequence identity. We first created 'perfect' simulated cDNA sequences by splicing the sequences of exons in the reference genome sequences of fly and human. The complete reference genome sequences were then mutated to various degrees using a realistic mutation simulator and the perfect cDNAs were aligned to them using Pairagon and 12 other aligners. To validate these results with natural sequences, we performed cross-species alignment using orthologous transcripts from human, mouse and rat. We found that aligner accuracy is heavily dependent on sequence identity. For sequences with 100% identity, Pairagon achieved accuracy levels of >99.6%, with one quarter of the errors of any other aligner. Furthermore, for human/mouse alignments, which are only 85% identical, Pairagon achieved 87% accuracy, higher than any other aligner. Pairagon source and executables are freely available at http://mblab.wustl.edu/software/pairagon/

  19. SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics

    Science.gov (United States)

    Will, Sebastian; Otto, Christina; Miladi, Milad; Möhl, Mathias; Backofen, Rolf

    2015-01-01

    Motivation: RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of O(n6). Subsequently, numerous faster ‘Sankoff-style’ approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity (≥ quartic time). Results: Breaking this barrier, we introduce the novel Sankoff-style algorithm ‘sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)’, which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff’s original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics. Availability and implementation: SPARSE is freely available at http://www.bioinf.uni-freiburg.de/Software/SPARSE. Contact: backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25838465

  20. Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences.

    Science.gov (United States)

    Tan, Yen Hock; Huang, He; Kihara, Daisuke

    2006-08-15

    Aligning distantly related protein sequences is a long-standing problem in bioinformatics, and a key for successful protein structure prediction. Its importance is increasing recently in the context of structural genomics projects because more and more experimentally solved structures are available as templates for protein structure modeling. Toward this end, recent structure prediction methods employ profile-profile alignments, and various ways of aligning two profiles have been developed. More fundamentally, a better amino acid similarity matrix can improve a profile itself; thereby resulting in more accurate profile-profile alignments. Here we have developed novel amino acid similarity matrices from knowledge-based amino acid contact potentials. Contact potentials are used because the contact propensity to the other amino acids would be one of the most conserved features of each position of a protein structure. The derived amino acid similarity matrices are tested on benchmark alignments at three different levels, namely, the family, the superfamily, and the fold level. Compared to BLOSUM45 and the other existing matrices, the contact potential-based matrices perform comparably in the family level alignments, but clearly outperform in the fold level alignments. The contact potential-based matrices perform even better when suboptimal alignments are considered. Comparing the matrices themselves with each other revealed that the contact potential-based matrices are very different from BLOSUM45 and the other matrices, indicating that they are located in a different basin in the amino acid similarity matrix space.

  1. A novel laser alignment system for tracking detectors using transparent silicon strip sensors

    International Nuclear Information System (INIS)

    Blum, W.; Kroha, H.; Widmann, P.

    1995-02-01

    Modern large-area precision tracking detectors require increasing accuracy of the geometrical alignment over large distances. A novel optical multi-point alignment system has been developed for the muon spectrometer of the ATLAS detector at the Large Hadron Collider. The system uses collimated laser beams as alignment references which are monitored by semi-transparent optical position sensors. The custom designed sensors provide very precise and uniform position information on the order of 1 μm over a wide measurement range. At suitable laser wavelengths, produced by laser diodes, transmission rates above 90% have been achieved which allow to align more than 30 sensors along one laser beam. With this capability and equipped with integrated readout electronics, the alignment system offers high flexibility for precision applications in a wide range of detector systems. (orig.)

  2. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    2011-01-01

    The Muon Alignment work now focuses on producing a new track-based alignment with higher track statistics, making systematic studies between the results of the hardware and track-based alignment methods and aligning the barrel using standalone muon tracks. Currently, the muon track reconstruction software uses a hardware-based alignment in the barrel (DT) and a track-based alignment in the endcaps (CSC). An important task is to assess the muon momentum resolution that can be achieved using the current muon alignment, especially for highly energetic muons. For this purpose, cosmic ray muons are used, since the rate of high-energy muons from collisions is very low and the event statistics are still limited. Cosmics have the advantage of higher statistics in the pT region above 100 GeV/c, but they have the disadvantage of having a mostly vertical topology, resulting in a very few global endcap muons. Only the barrel alignment has therefore been tested so far. Cosmic muons traversing CMS from top to bottom are s...

  3. The LACARA Vacuum Laser Accelerator Experiment: Beam Positioning and Alignment in a Strong Magnetic Field

    International Nuclear Information System (INIS)

    Shchelkunov, Sergey V.; Marshall, T. C.; Hirshfield, J. L.; Wang, Changbiao; LaPointe, M. A.

    2006-01-01

    LACARA (laser cyclotron auto-resonance accelerator) is a vacuum laser accelerator of electrons that is under construction at the Accelerator Test Facility (ATF), Brookhaven National Laboratory. It is expected that the experiment will be assembled by September 2006; this paper presents progress towards this goal. According to numerical studies, as an electron bunch moves along the LACARA solenoidal magnetic field (∼5.2 T, length ∼1 m), it will be accelerated from 50 to ∼75 MeV by interacting with a 0.8 TW Gaussian-mode circularly polarized optical pulse provided by the ATF CO2 10.6μm laser system. The LACARA laser transport optics must handle 10 J and be capable of forming a Gaussian beam inside the solenoid with a 1.4 mm waist and a Rayleigh range of 60 cm. The electron optics must transport a bunch having input emittance of 0.015 mm-mrad and 100 μm waist through the magnet. Precision alignment between the electron beam and the solenoid magnetic axis is required, and a method to achieve this is described in detail. Emittance- filtering may be necessary to yield an accelerated bunch having a narrow (∼1%) energy-spread

  4. Alignment and focusing device for a multibeam laser system

    International Nuclear Information System (INIS)

    Sweatt, W.C.

    1980-01-01

    Large inertial confinement fusion laser systems have many beams focusing on a small target. The Antares system is a 24-beam CO 2 pulse laser. To produce uniform illumination, the 24 beams must be individually focused on (or near) the target's surface in a symmetric pattern. To assess the quality of a given beam, we will locate a Smartt (point diffraction) interferometer at the desired focal point and illuminate it with an alignment laser. The resulting fringe pattern shows defocus, lateral misalignment, and beam aberrations; all of which can be minimized by tilting and translating the focusing mirror and the preceding flat mirror. The device described in this paper will remotely translate the Smartt interferometer to any position in the target space and point it in any direction using a two-axis gimbal. The fringes produced by the interferometer are relayed out of the target vacuum shell to a vidicon by a train or prisms. We are designing four separate snap-in heads to mount on the gimbal; two of which are Smartt interferometers (for 10.6 μm and 633 nm) and two for pinholes, should we wish to put an alignment beam backwards through the system

  5. Codebook-based interference alignment for uplink MIMO interference channels

    KAUST Repository

    Lee, Hyun Ho; Park, Kihong; Ko, Youngchai; Alouini, Mohamed-Slim

    2014-01-01

    In this paper, we propose a codebook-based interference alignment (IA) scheme in the constant multiple-input multipleoutput (MIMO) interference channel especially for the uplink scenario. In our proposed scheme, we assume cooperation among base

  6. Magnetic Alignment of Pulsed Solenoids Using the Pulsed Wire Method

    International Nuclear Information System (INIS)

    Arbelaez, D.; Madur, A.; Lipton, T.M.; Waldron, W.L.; Kwan, J.W.

    2011-01-01

    A unique application of the pulsed-wire measurement method has been implemented for alignment of 2.5 T pulsed solenoid magnets. The magnetic axis measurement has been shown to have a resolution of better than 25 (micro)m. The accuracy of the technique allows for the identification of inherent field errors due to, for example, the winding layer transitions and the current leads. The alignment system is developed for the induction accelerator NDCX-II under construction at LBNL, an upgraded Neutralized Drift Compression experiment for research on warm dense matter and heavy ion fusion. Precise alignment is essential for NDCX-II, since the ion beam has a large energy spread associated with the rapid pulse compression such that misalignments lead to corkscrew deformation of the beam and reduced intensity at focus. The ability to align the magnetic axis of the pulsed solenoids to within 100 pm of the induction cell axis has been demonstrated.

  7. TMRG studies on spin alignment in molecule-based ferrimagnetics [rapid communication

    Science.gov (United States)

    Liu, Q. M.; Yao, K. L.; Liu, Z. L.

    2005-05-01

    A physical picture of spin alignment in organic molecule-based ferrimagnets is presented from studying the thermal effective magnetic moment of the sublattice by use of the transfer matrix renormalization group. We conclude that the classical antiparallel spin alignment is not the most stable state. The three-spin system tends to parallel alignment when the exchange interaction between the biradical and the monoradical molecules is much weaker than that within the biradical, which can result in the decrease of the effective magnetic moment upon lowering the temperature. More importantly, we give the theoretical evidence that even the antiparallel spin alignment in the biradical monoradical alternating chain does not necessarily lead to ferrimagnetic spin ordering due to the formation of the spin singlet pairs, which suppresses the ferrimagnetic spin alignment.

  8. Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

    Directory of Open Access Journals (Sweden)

    Toh Hiroyuki

    2008-04-01

    Full Text Available Abstract Background Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs. Recent studies, mainly based on various approximations of the Sankoff algorithm, have resulted in considerable improvement in the accuracy of pairwise structural alignment. In contrast, for the cases with more than two sequences, the practical merit of structural alignment remains unclear as compared to traditional sequence-based methods, although the importance of multiple structural alignment is widely recognized. Results We took a different approach from a straightforward extension of the Sankoff algorithm to the multiple alignments from the viewpoints of accuracy and time complexity. As a new option of the MAFFT alignment program, we developed a multiple RNA alignment framework, X-INS-i, which builds a multiple alignment with an iterative method incorporating structural information through two components: (1 pairwise structural alignments by an external pairwise alignment method such as SCARNA or LaRA and (2 a new objective function, Four-way Consistency, derived from the base-pairing probability of every sub-aligned group at every multiple alignment stage. Conclusion The BRAliBASE benchmark showed that X-INS-i outperforms other methods currently available in the sum-of-pairs score (SPS criterion. As a basis for predicting common secondary structure, the accuracy of the present method is comparable to or rather higher than those of the current leading methods such as RNA Sampler. The X-INS-i framework can be used for building a multiple RNA alignment from any combination of algorithms for pairwise RNA alignment and base-pairing probability. The source code is available at the webpage found in the Availability and requirements section.

  9. Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment

    Directory of Open Access Journals (Sweden)

    Daniels Noah M

    2012-10-01

    Full Text Available Abstract Background The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult. Results We present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular HOMSTRAD benchmark. For the SABMark twilight zone benchmark set that captures more remote homology, Formatt and Matt outperform other programs; depending on choice of embedded sequence aligner, Formatt produces either better sequence and structural alignments with a smaller core size than Matt, or similarly sized alignments with better sequence similarity, for a small cost in average RMSD. Conclusions Considering sequence information as well as purely geometric information seems to improve quality of multiple structure alignments, though defining what constitutes the best alignment when sequence and structural measures would suggest different alignments remains a difficult open question.

  10. High-precision laser microcutting and laser microdrilling using diffractive beam-splitting and high-precision flexible beam alignment

    Science.gov (United States)

    Zibner, F.; Fornaroli, C.; Holtkamp, J.; Shachaf, Lior; Kaplan, Natan; Gillner, A.

    2017-08-01

    High-precision laser micro machining gains more importance in industrial applications every month. Optical systems like the helical optics offer highest quality together with controllable and adjustable drilling geometry, thus as taper angle, aspect ratio and heat effected zone. The helical optics is based on a rotating Dove-prism which is mounted in a hollow shaft engine together with other optical elements like wedge prisms and plane plates. Although the achieved quality can be interpreted as extremely high the low process efficiency is a main reason that this manufacturing technology has only limited demand within the industrial market. The objective of the research studies presented in this paper is to dramatically increase process efficiency as well as process flexibility. During the last years, the average power of commercial ultra-short pulsed laser sources has increased significantly. The efficient utilization of the high average laser power in the field of material processing requires an effective distribution of the laser power onto the work piece. One approach to increase the efficiency is the application of beam splitting devices to enable parallel processing. Multi beam processing is used to parallelize the fabrication of periodic structures as most application only require a partial amount of the emitted ultra-short pulsed laser power. In order to achieve highest flexibility while using multi beam processing the single beams are diverted and re-guided in a way that enables the opportunity to process with each partial beam on locally apart probes or semimanufactures.

  11. Beam diagnostics based on virtual instrument technology for HLS

    International Nuclear Information System (INIS)

    Sun Baogen; Lu Ping; Wang Xiaohui; Wang Baoyun; Wang Junhua; Gu Liming; Fang Jia; Ma Tianji

    2009-01-01

    The paper introduce the beam diagnostics system using virtual instrument technology for Hefei Light Source (HLS), which includes a GPIB bus-based DCCT measurement system to measure the beam DC current and beam life, a VXIbus-based closed orbit measurement system to measure the beam position, a PCIbus-based beam profile measurement system to measure the beam profile and emittance, a GPIB-LAN based bunch length system using photoelectric method, and a Ethernet-based photon beam position measurement system. The software is programmed by LabVIEW, which reduces much developing work. (authors)

  12. Probing the liquid crystal alignment interface and switching dynamics in a slab waveguide architecture

    Science.gov (United States)

    Gotjen, Henry G.; Kolacz, Jakub; Myers, Jason D.; Frantz, Jesse A.; Bekele, Robel Y.; Naciri, Jawad; Spillmann, Christopher M.

    2018-02-01

    A non-mechanical refractive laser beam steering device has been developed to provide continuous, two-dimensional steering of infrared beams. The technology implements a dielectric slab waveguide architecture with a liquid crystal (LC) cladding. With voltage control, the birefringence of the LC can be leveraged to tune the effective index of the waveguide under an electrode. With a clever prism electrode design a beam coupled into the waveguide can be deflected continuously in two dimensions as it is coupled out into free space. The optical interaction with LC in this beamsteerer is unique from typical LC applications: only the thin layer of LC (100s of nm) near the alignment interface interacts with the beam's evanescent field. Whereas most LC interactions take place over short path lengths (microns) in the bulk of the material, here we can interrogate the behavior of LC near the alignment interface over long path lengths (centimeters). In this work the beamsteerer is leveraged as a tool to study the behavior of LC near the alignment layer in contrast to the bulk material. We find that scattering is substantially decreased near the alignment interface due to the influence of the surface anchoring energy to suppress thermal fluctuations. By tracking the position of the deflected beam with a high speed camera, we measure response times of the LC near the interface in off-to-on switching ( ms) and on-to-off switching ( 100ms). Combined, this work will provide a path for improved alignment techniques, greater optical throughput, and faster response times in this unique approach to non-mechanical beamsteering.

  13. Beam collimator for a particle accelerator. [German patent

    Energy Technology Data Exchange (ETDEWEB)

    Benedetti, R

    1977-12-01

    The beam collimator for the electron beam coming from an electron accelerator consists of aperture plates and penumbra trimmers aligned parallel to them. To protect the patient from scattered radiation, additional tube plates are arranged between the radiation source and the patient. Continuous matching of the radiation field to the dimensions of a focus is achieved by providing a support plate outside the beam path which holds the tube plates. In this arrangement, the tube plates are aligned parallel to the edges of the aperture plates limiting the beam cone. The tube plates have different widths. They can be moved out of the beam path. Lining the inner walls of the tube plates with acrylic glass prevents the generation of secondary electrons and X-rays.

  14. Alignment Compensation for Bending Radius in TT40 and TI 8 Transfer Line Magnets

    CERN Document Server

    Weterings, W

    2003-01-01

    The BEATCH file for the TI 8 transfer lines specifies the position of the bending magnets assuming that the beam enters and exits at the centre of the vacuum pipe. In order to distribute the deflected beam evenly inside the vacuum tube, the alignment has to be compensated by moving the magnets half of the beam deflection away from the centre of the bending radius. In this note the saggitas of the various TT40 and TI 8 magnets are calculated and the alignment displacements tabulated for future reference.

  15. Incremental Ontology-Based Extraction and Alignment in Semi-structured Documents

    Science.gov (United States)

    Thiam, Mouhamadou; Bennacer, Nacéra; Pernelle, Nathalie; Lô, Moussa

    SHIRIis an ontology-based system for integration of semi-structured documents related to a specific domain. The system’s purpose is to allow users to access to relevant parts of documents as answers to their queries. SHIRI uses RDF/OWL for representation of resources and SPARQL for their querying. It relies on an automatic, unsupervised and ontology-driven approach for extraction, alignment and semantic annotation of tagged elements of documents. In this paper, we focus on the Extract-Align algorithm which exploits a set of named entity and term patterns to extract term candidates to be aligned with the ontology. It proceeds in an incremental manner in order to populate the ontology with terms describing instances of the domain and to reduce the access to extern resources such as Web. We experiment it on a HTML corpus related to call for papers in computer science and the results that we obtain are very promising. These results show how the incremental behaviour of Extract-Align algorithm enriches the ontology and the number of terms (or named entities) aligned directly with the ontology increases.

  16. Compression of Ultrafast Laser Beams

    Science.gov (United States)

    2016-03-01

    Copyright 2003, AIP Publishing LLC. DOI: http://dx.doi.org/10.1063/1.1611998.) When designing the pulse shaper, the laser beam must completely fill the...for the design of future versions of this device. The easiest way to align the pulse shaper is to use the laser beam that will be shaped, without...Afterward, an ultrafast thin beam splitter is placed into the system after the diameter of the laser beam is reduced; this is done to monitor the beam

  17. Survey, alignment, and beam stability at the Advanced Light Source

    International Nuclear Information System (INIS)

    Krebs, G.F.

    1997-10-01

    This paper describes survey and alignment at the Lawrence Berkeley Laboratories Advanced Light Source (ALS) accelerators from 1993 to 1997. The ALS is a third generation light source requiring magnet alignment to within 150 microns. To accomplish this, a network of monuments was established and maintained. Monthly elevation surveys show the movement of the floor over time. Inclinometers have recently been employed to give real time information about magnet, vacuum tank and magnet girder motion in the ALS storage ring

  18. ALCBEAM - Neutral beam formation and propagation code for beam-based plasma diagnostics

    Science.gov (United States)

    Bespamyatnov, I. O.; Rowan, W. L.; Liao, K. T.

    2012-03-01

    ALCBEAM is a new three-dimensional neutral beam formation and propagation code. It was developed to support the beam-based diagnostics installed on the Alcator C-Mod tokamak. The purpose of the code is to provide reliable estimates of the local beam equilibrium parameters: such as beam energy fractions, density profiles and excitation populations. The code effectively unifies the ion beam formation, extraction and neutralization processes with beam attenuation and excitation in plasma and neutral gas and beam stopping by the beam apertures. This paper describes the physical processes interpreted and utilized by the code, along with exploited computational methods. The description is concluded by an example simulation of beam penetration into plasma of Alcator C-Mod. The code is successfully being used in Alcator C-Mod tokamak and expected to be valuable in the support of beam-based diagnostics in most other tokamak environments. Program summaryProgram title: ALCBEAM Catalogue identifier: AEKU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKU_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 66 459 No. of bytes in distributed program, including test data, etc.: 7 841 051 Distribution format: tar.gz Programming language: IDL Computer: Workstation, PC Operating system: Linux RAM: 1 GB Classification: 19.2 Nature of problem: Neutral beams are commonly used to heat and/or diagnose high-temperature magnetically-confined laboratory plasmas. An accurate neutral beam characterization is required for beam-based measurements of plasma properties. Beam parameters such as density distribution, energy composition, and atomic excited populations of the beam atoms need to be known. Solution method: A neutral beam is initially formed as an ion beam which is extracted from

  19. Specification and R and D Program on Magnet Alignment Tolerances for NSLS-II

    International Nuclear Information System (INIS)

    Kramer, S.L.; Jain, A.K.

    2009-01-01

    The NSLS-II light source is a proposed 3 GeV storage ring, with the potential for ultra-low emittance. Despite the reduced emittance goal for the bare lattice, the closed orbit amplification factors are on average >55 in both planes, for random quadrupole alignment errors. The high chromaticity will also require strong sextupoles and the low 3 GeV energy will require large dynamic and momentum aperture to insure adequate lifetime. This will require tight alignment tolerances (∼ 30(micro)m) on the multipole magnets during installation. By specifying tight alignment tolerances of the magnets on the support girders, the random alignment tolerances of the girders in the tunnel can be significantly relaxed. Using beam based alignment to find the golden orbit through the quadrupole centers, the closed orbit offsets in the multipole magnets will then be reduced to essentially the alignment errors of the magnets, restoring much of the dynamic aperture and lifetime of the bare lattice. Our R and D program to achieve these tight alignment tolerances of the magnets on the girders using a vibrating wire technique, will be discussed and initial results presented.

  20. Amorphous Silicon Position Detectors for the Link Alignment System of the CMS Detector: Users Handbook

    International Nuclear Information System (INIS)

    Calderon, A.; Gomez, G.; Gonzalez-Sanchez, F. J.; Martinez-Rivero, C.; Matorras, F.; Rodrigo, T.; Ruiz-Arbol, P.; Scodellaro, L.; Vila, I.; Virto, A. L.; Alberdi, J.; Arce, P.; Barcala, J.M.; Calvo, E.; Ferrando, A.; Josa, M. I.; Molinero, A.; Navarrete, J.; Oller, J. C.; Yuste, C.

    2007-01-01

    We present the general characteristics, calibration procedures and measured performance of the Amorphous Silicon Position Detectors installed in the Link Alignment System of the CMS Detector for laser beam detection and reconstruction and give the Data Base to be used as a Handbook during CMS operation. (Author) 10 refs

  1. Amorphous Silicon Position Detectors for the Link Alignment System of the CMS Detector: Users Handbook

    Energy Technology Data Exchange (ETDEWEB)

    Calderon, A.; Gomez, G.; Gonzalez-Sanchez, F. J.; Martinez-Rivero, C.; Matorras, F.; Rodrigo, T.; Ruiz-Arbol, P.; Scodellaro, L.; Vila, I.; Virto, A. L.; Alberdi, J.; Arce, P.; Barcala, J.M.; Calvo, E.; Ferrando, A.; Josa, M. I.; Molinero, A.; Navarrete, J.; Oller, J. C.; Yuste, C.

    2007-07-01

    We present the general characteristics, calibration procedures and measured performance of the Amorphous Silicon Position Detectors installed in the Link Alignment System of the CMS Detector for laser beam detection and reconstruction and give the Data Base to be used as a Handbook during CMS operation. (Author) 10 refs.

  2. Aligning ERP systems with companies' real needs: an `Operational Model Based' method

    Science.gov (United States)

    Mamoghli, Sarra; Goepp, Virginie; Botta-Genoulaz, Valérie

    2017-02-01

    Enterprise Resource Planning (ERP) systems offer standard functionalities that have to be configured and customised by a specific company depending on its own requirements. A consistent alignment is therefore an essential success factor of ERP projects. To manage this alignment, an 'Operational Model Based' method is proposed. It is based on the design and the matching of models, and conforms to the modelling views and constructs of the ISO 19439 and 19440 enterprise-modelling standards. It is characterised by: (1) a predefined design and matching order of the models; (2) the formalisation, in terms of modelling constructs, of alignment and misalignment situations; and (3) their association with a set of decisions in order to mitigate the misalignment risk. Thus, a comprehensive understanding of the alignment management during ERP projects is given. Unlike existing methods, this one includes decisions related to the organisational changes an ERP system can induce, as well as criteria on which the best decision can be based. In this way, it provides effective support and guidance to companies implementing ERP systems, as the alignment process is detailed and structured. The method is applied on the ERP project of a Small and Medium Enterprise, showing that it can be used even in contexts where the ERP project expertise level is low.

  3. A comprehensive method for evaluating precision of transfer alignment on a moving base

    Science.gov (United States)

    Yin, Hongliang; Xu, Bo; Liu, Dezheng

    2017-09-01

    In this study, we propose the use of the Degree of Alignment (DOA) in engineering applications for evaluating the precision of and identifying the transfer alignment on a moving base. First, we derive the statistical formula on the basis of estimations. Next, we design a scheme for evaluating the transfer alignment on a moving base, for which the attitude error cannot be directly measured. Then, we build a mathematic estimation model and discuss Fixed Point Smoothing (FPS), Returns to Scale (RTS), Inverted Sequence Recursive Estimation (ISRE), and Kalman filter estimation methods, which can be used when evaluating alignment accuracy. Our theoretical calculations and simulated analyses show that the DOA reflects not only the alignment time and accuracy but also differences in the maneuver schemes, and is suitable for use as an integrated evaluation index. Furthermore, all four of these algorithms can be used to identify the transfer alignment and evaluate its accuracy. We recommend RTS in particular for engineering applications. Generalized DOAs should be calculated according to the tactical requirements.

  4. Design of a magnetic field alignment diagnostic for the MFTF-B magnet system

    International Nuclear Information System (INIS)

    Deadrick, F.J.; House, P.A.; Frye, R.W.

    1985-01-01

    Magnet alignment in tandem mirror fusion machines plays a crucial role in achieving and maintaining plasma confinement. Various visual alignment tools have been described by Post et al. to align the Tara magnet system. We have designed and installed a remotely operated magnetic field alignment (MFA) diagnostic system as a part of the Mirror Fusion Test Facility (MFTF-B). It measures critical magnetic field alignment parameters of the MFTF-B coil set while under full-field operating conditions. The MFA diagnostic employs a pair of low-energy, electron beam guns on a remotely positionable probe to trace and map selected magnetic field lines. An array of precision electrical detector paddles locates the position of the electron beam, and thus the magnetic field line, at several critical points. The measurements provide a means to compute proper compensating currents to correct for mechanical misalignments of the magnets with auxiliary trim coils if necessary. This paper describes both the mechanical and electrical design of the MFA diagnostic hardware

  5. A vertically aligned carbon nanotube-based impedance sensing biosensor for rapid and high sensitive detection of cancer cells.

    Science.gov (United States)

    Abdolahad, Mohammad; Taghinejad, Mohammad; Taghinejad, Hossein; Janmaleki, Mohsen; Mohajerzadeh, Shams

    2012-03-21

    A novel vertically aligned carbon nanotube based electrical cell impedance sensing biosensor (CNT-ECIS) was demonstrated for the first time as a more rapid, sensitive and specific device for the detection of cancer cells. This biosensor is based on the fast entrapment of cancer cells on vertically aligned carbon nanotube arrays and leads to mechanical and electrical interactions between CNT tips and entrapped cell membranes, changing the impedance of the biosensor. CNT-ECIS was fabricated through a photolithography process on Ni/SiO(2)/Si layers. Carbon nanotube arrays have been grown on 9 nm thick patterned Ni microelectrodes by DC-PECVD. SW48 colon cancer cells were passed over the surface of CNT covered electrodes to be specifically entrapped on elastic nanotube beams. CNT arrays act as both adhesive and conductive agents and impedance changes occurred as fast as 30 s (for whole entrapment and signaling processes). CNT-ECIS detected the cancer cells with the concentration as low as 4000 cells cm(-2) on its surface and a sensitivity of 1.7 × 10(-3)Ω cm(2). Time and cell efficiency factor (TEF and CEF) parameters were defined which describe the sensor's rapidness and resolution, respectively. TEF and CEF of CNT-ECIS were much higher than other cell based electrical biosensors which are compared in this paper.

  6. Aligned electromagnetic excitations of a black hole and their impact on its quantum horizon

    Energy Technology Data Exchange (ETDEWEB)

    Burinskii, Alexander [Gravity Research Group, NSI, Russian Academy of Sciences, B. Tulskaya 52, Moscow 115191 (Russian Federation)], E-mail: bur@ibrae.ac.ru; Elizalde, Emilio [Instituto de Ciencias del Espacio (CSIC) and Institut d' Estudis Espacials de Catalunya (IEEC/CSIC), Campus UAB, Facultat de Ciencies, Torre C5-Parell-2a planta, 08193 Bellaterra, Barcelona (Spain)], E-mail: elizalde@ieec.uab.es; Hildebrandt, Sergi R. [Instituto de Astrofisica de Canarias, C/Via Lactea s/n, La Laguna, Tenerife 38200 (Spain)], E-mail: srh@iac.es; Magli, Giulio [Dipartimento di Matematica del Politecnico di Milano, Piazza Leonardo Da Vinci 32, 20133 Milano (Italy)], E-mail: magli@mate.polimi.it

    2009-02-02

    We show that elementary aligned electromagnetic excitations of black holes, as coming from exact Kerr-Schild solutions, represent light-like beams pulses which have a very strong back reaction on the metric and change the topology of the horizon. Based on York's proposal, that elementary deformations of the BH horizon are related with elementary vacuum fluctuations, we analyze deformations of the horizon caused by the beam-like vacuum fluctuations and obtain a very specific feature of the topological deformations of the horizon. In particular, we show how the beams pierce the horizon, forming a multitude of micro-holes in it. A conjecture is taken into consideration, that these specific excitations are connected with the conformal-analytic properties of the Kerr geometry and are at the base of the emission mechanism.

  7. Initial Alignment for SINS Based on Pseudo-Earth Frame in Polar Regions.

    Science.gov (United States)

    Gao, Yanbin; Liu, Meng; Li, Guangchun; Guang, Xingxing

    2017-06-16

    An accurate initial alignment must be required for inertial navigation system (INS). The performance of initial alignment directly affects the following navigation accuracy. However, the rapid convergence of meridians and the small horizontalcomponent of rotation of Earth make the traditional alignment methods ineffective in polar regions. In this paper, from the perspective of global inertial navigation, a novel alignment algorithm based on pseudo-Earth frame and backward process is proposed to implement the initial alignment in polar regions. Considering that an accurate coarse alignment of azimuth is difficult to obtain in polar regions, the dynamic error modeling with large azimuth misalignment angle is designed. At the end of alignment phase, the strapdown attitude matrix relative to local geographic frame is obtained without influence of position errors and cumbersome computation. As a result, it would be more convenient to access the following polar navigation system. Then, it is also expected to unify the polar alignment algorithm as much as possible, thereby further unifying the form of external reference information. Finally, semi-physical static simulation and in-motion tests with large azimuth misalignment angle assisted by unscented Kalman filter (UKF) validate the effectiveness of the proposed method.

  8. Alignment system for large high-power CO2 laser fusion systems

    International Nuclear Information System (INIS)

    Bausman, M.D.; Liberman, I.; Manning, J.P.; Singer, S.

    1977-01-01

    Aligning a pulsed CO 2 laser fusion system involves control systems which insure that the centers of beams follow a prescribed path to within 1 mm, that the pointing of the beams is correct to approximately 20 microradians, and that focal spot at the location of the experimental fusion target be placed to accuracies of 10 to 20 micrometers laterally and approximately 50 micrometers axially. These alignments are accomplished by a variety of sensing techniques which include thermal pinholes and quadrant detectors, Seebeck effect silicon detectors, and imaging autocollimating Hartmann test procedures employing ir vidicon systems

  9. Improving beam set-up using an online beam optics tool

    International Nuclear Information System (INIS)

    Richter, S.; Barth, W.; Franczak, B.; Scheeler, U.; Wilms, D.

    2004-01-01

    The GSI accelerator facility [1] consists of the Universal Linear Accelerator (Unilac), the heavy ion synchrotron SIS, and the Experimental Storage Ring (ESR). Two Unilac injectors with three ion source terminals provide ion species from the lightest such as hydrogen up to uranium. The High Current Injector (HSI) for low charge state ion beams provides mostly high intense but short pulses, whereas the High Charge State Injector (HLI) supplies long pulses with a high duty factor of up to 27%. Before entering the Alvarez section of the Unilac the ion beam from the HSI is stripped in a supersonic gas jet. Up to three different ion species can be accelerated for up to five experiments in a time-sharing mode. Frequent changes of beam energy and intensity during a single beam time period may result in time consuming set-up and tuning especially of the beam transport lines. To shorten these changeover times an online optics tool (MIRKO EXPERT) had been developed. Based on online emittance measurements at well-defined locations the beam envelopes are calculated using the actual magnet settings. With this input improved calculated magnet settings can be directly sent to the magnet power supplies. The program reads profile grid measurements, such that an atomized beam alignment is established and that steering times are minimized. Experiences on this tool will be reported. At the Unilac a special focus is put on high current operation with short but intense beam pulses. Limitations like missing non-destructive beam diagnostics, insufficient longitudinal beam diagnostics, insufficient longitudinal beam matching, and influence of the hard edged model for magnetic fields will be discussed. Special attention will be put on the limits due to high current effects with bunched beams. (author)

  10. Track based alignment of the Mu3e detector

    Energy Technology Data Exchange (ETDEWEB)

    Hartenstein, Ulrich [Institut fuer Kernphysik, Universitaet Mainz (Germany)

    2016-07-01

    The Mu3e experiment searches for the lepton flavor violating decay μ{sup +} → e{sup +}e{sup -}e{sup +} with a sensitivity goal for the branching fraction of better than 10{sup -16}. This process is heavily supressed in the standard model of particle physics (BR < 10{sup -50}) which makes an observation of this decay a clear indication of new physics. For track reconstruction, four barrel shaped layers consisting of about 3000 high-voltage monolithic active pixel sensors (HV-MAPS) are used. The position, orientation and possible deformations of these sensors must be known to greater precision than the assembly tolerances. A track based alignment via the General Broken Lines fit and the Millepede-II algorithm will be used to achieve this precision in the final detector. The talk discusses a study of the required alignment precision and preparations for aligning the detector using a detailed simulation.

  11. Video-based beam position monitoring at CHESS

    Science.gov (United States)

    Revesz, Peter; Pauling, Alan; Krawczyk, Thomas; Kelly, Kevin J.

    2012-10-01

    CHESS has pioneered the development of X-ray Video Beam Position Monitors (VBPMs). Unlike traditional photoelectron beam position monitors that rely on photoelectrons generated by the fringe edges of the X-ray beam, with VBPMs we collect information from the whole cross-section of the X-ray beam. VBPMs can also give real-time shape/size information. We have developed three types of VBPMs: (1) VBPMs based on helium luminescence from the intense white X-ray beam. In this case the CCD camera is viewing the luminescence from the side. (2) VBPMs based on luminescence of a thin (~50 micron) CVD diamond sheet as the white beam passes through it. The CCD camera is placed outside the beam line vacuum and views the diamond fluorescence through a viewport. (3) Scatter-based VBPMs. In this case the white X-ray beam passes through a thin graphite filter or Be window. The scattered X-rays create an image of the beam's footprint on an X-ray sensitive fluorescent screen using a slit placed outside the beam line vacuum. For all VBPMs we use relatively inexpensive 1.3 Mega-pixel CCD cameras connected via USB to a Windows host for image acquisition and analysis. The VBPM host computers are networked and provide live images of the beam and streams of data about the beam position, profile and intensity to CHESS's signal logging system and to the CHESS operator. The operational use of VBPMs showed great advantage over the traditional BPMs by providing direct visual input for the CHESS operator. The VBPM precision in most cases is on the order of ~0.1 micron. On the down side, the data acquisition frequency (50-1000ms) is inferior to the photoelectron based BPMs. In the future with the use of more expensive fast cameras we will be able create VBPMs working in the few hundreds Hz scale.

  12. Alignment of CT images of skull dysmorphology using anatomy-based perpendicular axes

    International Nuclear Information System (INIS)

    Yoo, Sun K; Kim, Yong O; Kim, Hee-Joung; Kim, Nam H; Jang, Young Beom; Kim, Kee-Deog; Lee, Hye-Yeon

    2003-01-01

    Rigid body registration of 3D CT scans, based on manual identification of homologous landmarks, is useful for the visual analysis of skull dysmorphology. In this paper, a robust and simple alignment method was proposed to allow for the comparison of skull morphologies, within and between individuals with craniofacial anomalies, based on 3D CT scans, and the minimum number of anatomical landmarks, under rigidity and uniqueness constraints. Three perpendicular axes, extracted from anatomical landmarks, define the absolute coordinate system, through a rigid body transformation, to align multiple CT images for different patients and acquisition times. The accuracy of the alignment method depends on the accuracy of the localized landmarks and target points. The numerical simulation generalizes the accuracy requirements of the alignment method. Experiments using a human dried skull specimen, and ten sets of skull CT images (the pre- and post-operative CT scans of four plagiocephaly, and one fibrous dysplasia patients), demonstrated the feasibility of the technique in clinical practice

  13. High performance electronics for alignment regulation on the CLIC 30GHz modules

    International Nuclear Information System (INIS)

    Carrica, D.; Coosemans, W.; Pittin, R.

    1999-01-01

    CERN is studying a linear collider (CLIC) to obtain electron-positron collisions with centre-of-mass energies in the TeV range. To demonstrate the feasibility of CLIC, a test facility (CTF2) is being constructed. CTF2 consists of 4 identical modules, each 1.4 m long module consists of 2 linac with a girder and a doublet or a triplet quadrupole. Girders are elements that support mechanically the cavities of the accelerator while the main objective of the quadrupole is to focus particle beams. The alignment system has 2 principal utilities. The first is to pre-align the elements to make the beam pass through the aperture and produce signals in beam position monitors. In respect to these signals the girders and the quadrupoles are moved for making the definitive alignment. The second utility is to maintain the elements in this position. The alignment control system of CTF2 must regulate the position of the girders and quadrupoles with a precision < 10 μm. In fact an accuracy of 1 μ has been obtained on CTF2. Thanks to its flexibility and its simplicity, the system is expected to adapt easily to CLIC even if it means to control modules that involve up to a maximum of 384 motors and 896 sensors

  14. Beam based systems and controls

    CERN Document Server

    Jacquet, D

    2012-01-01

    This presentation will give a review from the operations team of the performance and issues of the beam based systems, namely RF, ADT, beam instrumentation, controls and injection systems. For each of these systems, statistics on performance and availability will be presented with the main issues encountered in 2012. The possible improvements for operational efficiency and safety will be discussed, with an attempt to answer the question "Are we ready for the new challenges brought by the 25ns beam and increased energy after LSI? ".

  15. Coarse Alignment Technology on Moving base for SINS Based on the Improved Quaternion Filter Algorithm.

    Science.gov (United States)

    Zhang, Tao; Zhu, Yongyun; Zhou, Feng; Yan, Yaxiong; Tong, Jinwu

    2017-06-17

    Initial alignment of the strapdown inertial navigation system (SINS) is intended to determine the initial attitude matrix in a short time with certain accuracy. The alignment accuracy of the quaternion filter algorithm is remarkable, but the convergence rate is slow. To solve this problem, this paper proposes an improved quaternion filter algorithm for faster initial alignment based on the error model of the quaternion filter algorithm. The improved quaternion filter algorithm constructs the K matrix based on the principle of optimal quaternion algorithm, and rebuilds the measurement model by containing acceleration and velocity errors to make the convergence rate faster. A doppler velocity log (DVL) provides the reference velocity for the improved quaternion filter alignment algorithm. In order to demonstrate the performance of the improved quaternion filter algorithm in the field, a turntable experiment and a vehicle test are carried out. The results of the experiments show that the convergence rate of the proposed improved quaternion filter is faster than that of the tradition quaternion filter algorithm. In addition, the improved quaternion filter algorithm also demonstrates advantages in terms of correctness, effectiveness, and practicability.

  16. FSO tracking and auto-alignment transceiver system

    Science.gov (United States)

    Cap, Gabriel A.; Refai, Hakki H.; Sluss, James J., Jr.

    2008-10-01

    Free-space optics (FSO) technology utilizes a modulated light beam to transmit information through the atmosphere. Due to reduced size and cost, and higher data rates, FSO can be more effective than wireless communication. Although atmospheric conditions can affect FSO communication, a line-of-sight connection between FSO transceivers is a necessary condition to maintain continuous exchange of data, voice, and video information. To date, the primary concentration of mobile FSO research and development has been toward accurate alignment between two transceivers. This study introduces a fully automatic, advanced alignment system that will maintain a line of sight connection for any FSO transceiver system. A complete transceiver system includes a position-sensing detector (PSD) to receive the signal, a laser to transmit the signal, a gimbal to move the transceiver to maintain alignment, and a computer to coordinate the necessary movements during motion. The FSO system was tested for mobility by employing one gimbal as a mobile unit and establishing another as a base station. Tests were performed to establish that alignment between two transceivers could be maintained during a given period of experiments and to determine the maximum speeds tolerated by the system. Implementation of the transceiver system can be realized in many ways, including vehicle-to-base station communication or vehicle-to-vehicle communication. This study is especially promising in that it suggests such a system is able to provide high-speed data in many applications where current wireless technology may not be effective. This phenomenon, coupled with the ability to maintain an autonomously realigned connection, opens the possibility of endless applications for both military and civilian use.

  17. Kinematic analysis and experimental verification of a eccentric wheel based precision alignment mechanism for LINAC

    International Nuclear Information System (INIS)

    Mundra, G.; Jain, V.; Singh, K.K.; Saxena, P.; Khare, R.K.; Bagre, M.

    2011-01-01

    Eccentric wheel based precision alignment system was designed for the remote motorized alignment of proposed proton injector LINAC (SFDTL). As a part of the further development for the alignment and monitoring scheme, a menu driven alignment system is being developed. The paper describes a general kinematic equation (with base line tilt correction) based on the various parameters of the mechanism like eccentricity, wheel diameter, distance between the wheels and the diameter of the cylindrical accelerator component. Based on this equation the extent of the alignment range for the 4 degree of freedom is evaluated and analysis on some of the parameters variation and the theoretical accuracy/resolution is computed. For the same a computer program is written which can compute the various points for the each discrete position of the two motor combinations. The paper also describes the experimentally evaluated values of these positions (for the full extent of area) and the matching/comparison of the two data. These data now can be used for the movement computation required for alignment of the four motors (two front and two rear motors of the support structure). (author)

  18. Alignment of global supply networks based on strategic groups of supply chains

    Directory of Open Access Journals (Sweden)

    Nikos G. Moraitakis

    2017-09-01

    Full Text Available Background: From a supply chain perspective, often big differences exist between global raw material suppliers’ approaches to supply their respective local markets. The progressing complexity of large centrally managed global supply networks and their often-unknown upstream ramifications increase the likelihood of undetected bottlenecks and inefficiencies. It is therefore necessary to develop an approach to strategically master the upstream complexity of such networks from a holistic supply chain perspective in order to align regional competitive priorities and supply chain structures. The objective of this research is hence to develop an approach for the supply-chain-based alignment of complex global supply networks. Method: We review existing literature from the fields of supply chain and network management, strategic sourcing, and strategic management. Based on the literature review and theoretical and practical considerations we deduce a conceptual approach to consider upstream supply chain structures in supply network alignment initiatives. Results: On the basis of these considerations and current empirical literature we transfer strategic group theory to the supply network management context. The proposed approach introduces strategic groups of supply chains as a segmentation criterion for complex global supply networks which enables the network-wide alignment of competitive priorities. Conclusion: Supply-chain-based segmentation of global supply network structures can effectively reduce the complexity, firms face when aiming to strategically align their supply chains on a holistic level. The results of this research are applicable for certain types of global supply networks and can be used for network alignment and strategy development. The approach can furthermore generate insights useable for negotiation support with suppliers.

  19. AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences

    Directory of Open Access Journals (Sweden)

    Claros M Gonzalo

    2010-06-01

    Full Text Available Abstract Background Multiple sequence alignments are used to study gene or protein function, phylogenetic relations, genome evolution hypotheses and even gene polymorphisms. Virtually without exception, all available tools focus on conserved segments or residues. Small divergent regions, however, are biologically important for specific quantitative polymerase chain reaction, genotyping, molecular markers and preparation of specific antibodies, and yet have received little attention. As a consequence, they must be selected empirically by the researcher. AlignMiner has been developed to fill this gap in bioinformatic analyses. Results AlignMiner is a Web-based application for detection of conserved and divergent regions in alignments of conserved sequences, focusing particularly on divergence. It accepts alignments (protein or nucleic acid obtained using any of a variety of algorithms, which does not appear to have a significant impact on the final results. AlignMiner uses different scoring methods for assessing conserved/divergent regions, Entropy being the method that provides the highest number of regions with the greatest length, and Weighted being the most restrictive. Conserved/divergent regions can be generated either with respect to the consensus sequence or to one master sequence. The resulting data are presented in a graphical interface developed in AJAX, which provides remarkable user interaction capabilities. Users do not need to wait until execution is complete and can.even inspect their results on a different computer. Data can be downloaded onto a user disk, in standard formats. In silico and experimental proof-of-concept cases have shown that AlignMiner can be successfully used to designing specific polymerase chain reaction primers as well as potential epitopes for antibodies. Primer design is assisted by a module that deploys several oligonucleotide parameters for designing primers "on the fly". Conclusions AlignMiner can be used

  20. Optimal alignment of mirror based pentaprisms for scanning deflectometric devices

    Energy Technology Data Exchange (ETDEWEB)

    Barber, Samuel K.; Geckeler, Ralf D.; Yashchuk, Valeriy V.; Gubarev, Mikhail V.; Buchheim, Jana; Siewert, Frank; Zeschke, Thomas

    2011-03-04

    In the recent work [Proc. of SPIE 7801, 7801-2/1-12 (2010), Opt. Eng. 50(5) (2011), in press], we have reported on improvement of the Developmental Long Trace Profiler (DLTP), a slope measuring profiler available at the Advanced Light Source Optical Metrology Laboratory, achieved by replacing the bulk pentaprism with a mirror based pentaprism (MBPP). An original experimental procedure for optimal mutual alignment of the MBPP mirrors has been suggested and verified with numerical ray tracing simulations. It has been experimentally shown that the optimally aligned MBPP allows the elimination of systematic errors introduced by inhomogeneity of the optical material and fabrication imperfections of the bulk pentaprism. In the present article, we provide the analytical derivation and verification of easily executed optimal alignment algorithms for two different designs of mirror based pentaprisms. We also provide an analytical description for the mechanism for reduction of the systematic errors introduced by a typical high quality bulk pentaprism. It is also shown that residual misalignments of an MBPP introduce entirely negligible systematic errors in surface slope measurements with scanning deflectometric devices.

  1. Orthodontic tooth movement with clear aligners.

    Science.gov (United States)

    Drake, Carl T; McGorray, Susan P; Dolce, Calogero; Nair, Madhu; Wheeler, Timothy T

    2012-01-01

    Clear aligners provide a convenient model to measure orthodontic tooth movement (OTM). We examined the role of in vivo aligner material fatigue and subject-specific factors in tooth movement. Fifteen subjects seeking orthodontic treatment at the University of Florida were enrolled. Results were compared with data previously collected from 37 subjects enrolled in a similar protocol. Subjects were followed prospectively for eight weeks. An upper central incisor was programmed to move 0.5 mm. every two weeks using clear aligners. A duplicate aligner was provided for the second week of each cycle. Weekly polyvinyl siloxane (PVS) impressions were taken, and digital models were fabricated to measure OTM. Initial and final cone beam computed tomography (CBCT) images were obtained to characterize OTM. Results were compared to data from a similar protocol, where subjects received a new aligner biweekly. No significant difference was found in the amount of OTM between the two groups, with mean total OTM of 1.11 mm. (standard deviation (SD) 0.30) and 1.07 mm. (SD 0.33) for the weekly aligner and biweekly control groups, respectively (P = 0.72). Over eight weeks, in two-week intervals, material fatigue does not play a significant role in the rate or amount of tooth movement.

  2. Studies in the reaction dynamics of beam-gas chemiluminescent reactions

    International Nuclear Information System (INIS)

    Prisant, M.G.

    1984-01-01

    This thesis develops techniques for the analysis and interpretation of data obtained from beam-gas chemiluminescence experiments. These techniques are applied to experimental studies of atom transfer reactions of the type A + BC → AB + C. A procedure is developed for determining the product rotational alignment in the center-of-mass frame from polarization measurements of chemiluminescent atom-diatom exchange reactions under beam-gas conditions. Knowledge of a vector property of a reaction, such as product alignment, provides information on the disposition of angular momentum by a chemical reaction. Fluorescence polarization and hence product alignment are measured for two prototype reactions. The reaction of metastable calcium atoms with hydrogen-chloride gas yields highly aligned calcium-chloride product which exhibits little variation of alignment with vibrational state. The reaction of ground-state calcium with fluorine gas yields moderately aligned product which shows strong variation of alignment with vibration. A multi-surface direct-interaction model is developed to interpret product alignment and population data. The predictions of this model for the reaction of calcium with fluorine show reasonable agreement with experiment

  3. Remote sensing of local structure of the quasi-perpendicular Earth's bow shock by using field-aligned beams

    Directory of Open Access Journals (Sweden)

    B. Miao

    2009-03-01

    Full Text Available Field-aligned ion beams (FABs originate at the quasi-perpendicular Earth's bow shock and constitute an important ion population in the foreshock region. The bulk velocity of these FABs depends significantly on the shock normal angle, which is the angle between shock normal and upstream interplanetary magnetic field (IMF. This dependency may therefore be taken as an indicator of the local structure of the shock. Applying the direct reflection model to Cluster measurements, we have developed a method that uses proton FABs in the foreshock region for remote sensing of the local shock structure. The comparison of the model results with the multi-spacecraft observations of FAB events shows very good agreement in terms of wave amplitude and frequency of surface waves at the shock front.

  4. Commissioning the CMS Alignment and Calibration Framework

    CERN Document Server

    Futyan, David

    2009-01-01

    The CMS experiment has developed a powerful framework to ensure the precise and prompt alignment and calibration of its components, which is a major prerequisite to achieve the optimal performance for physics analysis. The prompt alignment and calibration strategy harnesses computing resources both at the Tier-0 site and the CERN Analysis Facility (CAF) to ensure fast turnaround for updating the corresponding database payloads. An essential element is the creation of dedicated data streams concentrating the specific event information required by the various alignment and calibration workflows. The resulting low latency is required for feeding the resulting constants into the prompt reconstruction process, which is essential for achieving swift physics analysis of the LHC data. This report discusses the implementation and the computational aspects of the alignment and calibration framework. Recent commissioning campaigns with cosmic muons, beam halo and simulated data have been used to gain detailed experience...

  5. Seeking the perfect alignment

    CERN Multimedia

    2002-01-01

    The first full-scale tests of the ATLAS Muon Spectrometer are about to begin in Prévessin. The set-up includes several layers of Monitored Drift Tubes Chambers (MDTs) and will allow tests of the performance of the detectors and of their highly accurate alignment system.   Monitored Drift Chambers in Building 887 in Prévessin, where they are just about to be tested. Muon chambers are keeping the ATLAS Muon Spectrometer team quite busy this summer. Now that most people go on holiday, the beam and alignment tests for these chambers are just starting. These chambers will measure with high accuracy the momentum of high-energy muons, and this implies very demanding requirements for their alignment. The MDT chambers consist of drift tubes, which are gas-filled metal tubes, 3 cm in diameter, with wires running down their axes. With high voltage between the wire and the tube wall, the ionisation due to traversing muons is detected as electrical pulses. With careful timing of the pulses, the position of the muon t...

  6. Alignment and position visualization methods for the biomedical imaging and therapy (BMIT) MRT lift

    International Nuclear Information System (INIS)

    Bree, Michael; Miller, Denise; Kerr, Graham; Belev, George; Wysokinski, Tomasz W.; Dolton, Wade

    2016-01-01

    The Microbeam Radiation Therapy (MRT) Lift is an eight stage positioning and scanning system at the Canadian Light Source’s BMIT Facility. Alignment of the sample with the beam using the MRT Lift is a time consuming and challenging task. The BMIT Group has developed a Python-based MRT Lift positioning and control program that uses a combination of computational and iterative methods to independently adjust the sample’s X, Y, Z, pitch and roll positions. The program offers “1-Click” alignment of the sample to the beam. Use of a wireframe visualization technique enables even minute movements to be illustrated. Proposed movements and the resulting MRT Lift position can be manually verified before being applied. Optional integration with the SolidWorks modelling platform allows high quality renderings of the MRT Lift in its current or proposed position to be displayed in real time. Human factors principles are incorporated into the program with the objective of delivering easy to use controls for this complex device.

  7. Alignment and position visualization methods for the biomedical imaging and therapy (BMIT) MRT lift

    Energy Technology Data Exchange (ETDEWEB)

    Bree, Michael, E-mail: michael.bree@lightsource.ca; Miller, Denise; Kerr, Graham; Belev, George; Wysokinski, Tomasz W.; Dolton, Wade [Canadian Light Source Inc., 44 Innovation Blvd, Saskatoon, SK S7N 2V3 Canada (Canada)

    2016-07-27

    The Microbeam Radiation Therapy (MRT) Lift is an eight stage positioning and scanning system at the Canadian Light Source’s BMIT Facility. Alignment of the sample with the beam using the MRT Lift is a time consuming and challenging task. The BMIT Group has developed a Python-based MRT Lift positioning and control program that uses a combination of computational and iterative methods to independently adjust the sample’s X, Y, Z, pitch and roll positions. The program offers “1-Click” alignment of the sample to the beam. Use of a wireframe visualization technique enables even minute movements to be illustrated. Proposed movements and the resulting MRT Lift position can be manually verified before being applied. Optional integration with the SolidWorks modelling platform allows high quality renderings of the MRT Lift in its current or proposed position to be displayed in real time. Human factors principles are incorporated into the program with the objective of delivering easy to use controls for this complex device.

  8. Prediction of molecular alignment of nucleic acids in aligned media

    International Nuclear Information System (INIS)

    Wu Bin; Petersen, Michael; Girard, Frederic; Tessari, Marco; Wijmenga, Sybren S.

    2006-01-01

    We demonstrate - using the data base of all deposited DNA and RNA structures aligned in Pf1-medium and RDC refined - that for nucleic acids in a Pf1-medium the electrostatic alignment tensor can be predicted reliably and accurately via a simple and fast calculation based on the gyration tensor spanned out by the phosphodiester atoms. The rhombicity is well predicted over its full range from 0 to 0.66, while the alignment tensor orientation is predicted correctly for rhombicities up to ca. 0.4, for larger rhombicities it appears to deviate somewhat more than expected based on structural noise and measurement error. This simple analytical approach is based on the Debye-Huckel approximation for the electrostatic interaction potential, valid at distances sufficiently far away from a poly-ionic charged surface, a condition naturally enforced when the charge of alignment medium and solute are of equal sign, as for nucleic acids in a Pf1-phage medium. For the usual salt strengths and nucleic acid sizes, the Debye-Huckel screening length is smaller than the nucleic acid size, but large enough for the collective of Debye-Huckel spheres to encompass the whole molecule. The molecular alignment is then purely electrostatic, but it's functional form is under these conditions similar to that for steric alignment. The proposed analytical expression allows for very fast calculation of the alignment tensor and hence RDCs from the conformation of the nucleic acid molecule. This information provides opportunities for improved structure determination of nucleic acids, including better assessment of dynamics in (multi-domain) nucleic acids and the possibility to incorporate alignment tensor prediction from shape directly into the structure calculation process. The procedures are incorporated into MATLAB scripts, which are available on request

  9. Molecular bond formation in Na* + N2 energy transfer: Crossed beam study of atomic alignment and orientation

    International Nuclear Information System (INIS)

    Reiland, W.; Jamieson, G.; Tittes, U.; Hertel, I.V.

    1982-01-01

    We report the first full analysis of collisionally induced atomic alignment and orientation for a molecular collision process. In an experiment with crossed supersonic beams of N 2 and laser excited Na(3 2 Psub(3/2)) we have studied the dependence of angular and energy resolved differential quenching cross sections as a function of the linear and circular polarization of the exciting laser light. The ansisotropies observed in the linear polarization data range up to 2:1 when corrected for electron and nuclear spin relaxation. The maximum effect is found at small scattering angles and intermediate energy transfer where the cross section is also largest. The atomic alignment angle most favourable for quenching relates to the scattering angle and can be understood in a model picture in such a way that the (NaN 2 )* molecular system is formed at internuclear distances as low as R = 10a 0 . The circular asymmetry is small but with significant structure and is attributed to interaction on different potential surfaces at R > 10a 0 . Full analysis of the four measurable parameter is given in terms of the density matrix in a frame with z-axis perpendicular to collision plane which allows a clear understanding of the properties of atomic reflection symmetry and coherence of the scattering process. (orig.)

  10. Design and fabrication of a eccentric wheels based motorised alignment mechanism for cylindrical accelerator components

    International Nuclear Information System (INIS)

    Mundra, G.; Jain, V.; Karmarkar, Mangesh; Kotaiah, S.

    2006-01-01

    Precision alignment mechanisms with long term stability are required for accelerator components. For some of the components motorised and remotely operable alignment mechanism are required. An eccentric wheel mechanism based alignment system is very much suitable for such application. One such alignment system is designed, a prototype is machined/fabricated for SFDTL type accelerating structure and preliminary trial experiments have been done. (author)

  11. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    2011-01-01

    A new set of muon alignment constants was approved in August. The relative position between muon chambers is essentially unchanged, indicating good detector stability. The main changes concern the global positioning of the barrel and of the endcap rings to match the new Tracker geometry. Detailed studies of the differences between track-based and optical alignment of DTs have proven to be a valuable tool for constraining Tracker alignment weak modes, and this information is now being used as part of the alignment procedure. In addition to the “split-cosmic” analysis used to investigate the muon momentum resolution at high momentum, a new procedure based on reconstructing the invariant mass of di-muons from boosted Zs is under development. Both procedures show an improvement in the momentum precision of Global Muons with respect to Tracker-only Muons. Recent developments in track-based alignment include a better treatment of the tails of residual distributions and accounting for correla...

  12. A method to align a bent crystal for channeling experiments by using quasichanneling oscillations

    Science.gov (United States)

    Sytov, A. I.; Guidi, V.; Tikhomirov, V. V.; Bandiera, L.; Bagli, E.; Germogli, G.; Mazzolari, A.; Romagnoni, M.

    2018-04-01

    A method to calculate both the bent crystal angle of alignment and radius of curvature by using only one distribution of deflection angles has been developed. The method is based on measuring of the angular position of recently predicted and observed quasichanneling oscillations in the deflection angle distribution and consequent fitting of both the radius and angular alignment by analytic formulae. In this paper this method is applied on the example of simulated angular distributions over a wide range of values of both radius and alignment for electrons. It is carried out through the example of (111) nonequidistant planes though this technique is general and could be applied to any kind of planes. In addition, the method application constraints are also discussed. It is shown by simulations that this method, being in fact a sort of beam diagnostics, allows one in a certain case to increase the crystal alignment accuracy as well as to control precisely the radius of curvature inside an accelerator tube without vacuum breaking. In addition, it speeds up the procedure of crystal alignment in channeling experiments, reducing beamtime consuming.

  13. Calibration and alignment of the CMS silicon tracking detector

    International Nuclear Information System (INIS)

    Stoye, M.

    2007-07-01

    The Large Hadron Collider (LHC) will dominate the high energy physics program in the coming decade. The discovery of the standard model Higgs boson and the discovery of super-symmetric particles are within the reach at the energy scale explored by the LHC. However, the high luminosity and the high energy of the colliding protons lead to challenging demands on the detectors. The hostile radiation environment requires irradiation hard detectors, where the innermost subdetectors, consisting of silicon modules, are most affected. This thesis is devoted to the calibration and alignment of the silicon tracking detector. Electron test beam data, taken at DESY, have been used to investigate the performance of detector modules which previously were irradiated with protons up to a dose expected after 10 years of operation. The irradiated sensors turned out to be still better than required. The performance of the inner tracking systems will be dominated by the degree to which the positions of the sensors can be determined. Only a track based alignment procedure can reach the required precision. Such an alignment procedure is a major challenge given that about 50000 geometry constants need to be measured. Making use of the novel χ 2 minimization program Millepede II an alignment strategy has been developed in which all detector components are aligned simultaneously, as many sources of information as possible are used, and all correlations between the position parameters of the detectors are taken into account. Utilizing simulated data, a proof of concept of the alignment strategy is shown. (orig.)

  14. Calibration and alignment of the CMS silicon tracking detector

    Energy Technology Data Exchange (ETDEWEB)

    Stoye, M.

    2007-07-15

    The Large Hadron Collider (LHC) will dominate the high energy physics program in the coming decade. The discovery of the standard model Higgs boson and the discovery of super-symmetric particles are within the reach at the energy scale explored by the LHC. However, the high luminosity and the high energy of the colliding protons lead to challenging demands on the detectors. The hostile radiation environment requires irradiation hard detectors, where the innermost subdetectors, consisting of silicon modules, are most affected. This thesis is devoted to the calibration and alignment of the silicon tracking detector. Electron test beam data, taken at DESY, have been used to investigate the performance of detector modules which previously were irradiated with protons up to a dose expected after 10 years of operation. The irradiated sensors turned out to be still better than required. The performance of the inner tracking systems will be dominated by the degree to which the positions of the sensors can be determined. Only a track based alignment procedure can reach the required precision. Such an alignment procedure is a major challenge given that about 50000 geometry constants need to be measured. Making use of the novel {chi}{sup 2} minimization program Millepede II an alignment strategy has been developed in which all detector components are aligned simultaneously, as many sources of information as possible are used, and all correlations between the position parameters of the detectors are taken into account. Utilizing simulated data, a proof of concept of the alignment strategy is shown. (orig.)

  15. Computer codes for automatic tuning of the beam transport at the UNILAC

    International Nuclear Information System (INIS)

    Dahl, L.; Ehrich, A.

    1984-01-01

    For application in routine operation fully automatic computer controlled algorithms are developed for tuning of beam transport elements at the Unilac. Computations, based on emittance measurements, simulate the beam behaviour and evaluate quadrupole settings, in order to produce defined beam properties at specified positions along the accelerator. The interactive program is controlled using a graphic display on which the beam emittances and envelopes are plotted. To align the beam onto the ion-optical axis of the accelerator two automatic computer controlled procedures have been developed. The misalignment of the beam is determined by variation of quadrupole or steering magnet settings with simultaneous measurement of the beam distribution on profile grids. According to the result a pair of steering magnet settings are adjusted to bend the beam on the axis. The effects of computer controlled tuning on beam quality and operation are reported

  16. Latest polarization and beam characterization results of the Orsay polarized electron source

    International Nuclear Information System (INIS)

    Arianer, J.; Cohen, S.; Essabaa, S.; Frascaria, R.; Zerhouni, O.

    1995-01-01

    The Orsay polarized electron source based on the chemi-ionization of aligned He(2 3 S 1 ) atoms and CO 2 molecules is briefly described. The latest results concerning electron polarization and beam emittance are presented. The present development status is also discussed. (K.A.)

  17. Coordination Analysis Using Global Structural Constraints and Alignment-based Local Features

    Science.gov (United States)

    Hara, Kazuo; Shimbo, Masashi; Matsumoto, Yuji

    We propose a hybrid approach to coordinate structure analysis that combines a simple grammar to ensure consistent global structure of coordinations in a sentence, and features based on sequence alignment to capture local symmetry of conjuncts. The weight of the alignment-based features, which in turn determines the score of coordinate structures, is optimized by perceptron training on a given corpus. A bottom-up chart parsing algorithm efficiently finds the best scoring structure, taking both nested or non-overlapping flat coordinations into account. We demonstrate that our approach outperforms existing parsers in coordination scope detection on the Genia corpus.

  18. Alignment and orientation effects in beam-foil experiments

    International Nuclear Information System (INIS)

    Band, Y.B.

    1975-01-01

    A theory of the orientation and alignment of atoms observed upon emergence from tilted foils is presented. The interaction with the foil surface is taken into account in the production process of particular states. Once they are produced, the evolution of these states, under the influence of the residual field near the surface, is calculated in the fashion introduced by Eck. The most general effect of this evolution is presented

  19. Oriented Edge-Based Feature Descriptor for Multi-Sensor Image Alignment and Enhancement

    Directory of Open Access Journals (Sweden)

    Myung-Ho Ju

    2013-10-01

    Full Text Available In this paper, we present an efficient image alignment and enhancement method for multi-sensor images. The shape of the object captured in a multi-sensor images can be determined by comparing variability of contrast using corresponding edges across multi-sensor image. Using this cue, we construct a robust feature descriptor based on the magnitudes of the oriented edges. Our proposed method enables fast image alignment by identifying matching features in multi-sensor images. We enhance the aligned multi-sensor images through the fusion of the salient regions from each image. The results of stitching the multi-sensor images and their enhancement demonstrate that our proposed method can align and enhance multi-sensor images more efficiently than previous methods.

  20. The SPL-based Neutrino Super Beam

    CERN Document Server

    Baussan, E; Bobeth, C; Bouquerel, E; Caretta, O; Cupial, P; Davenne, T; Densham, C; Dracos, M; Fitton, M; Gaudiot, G; Kozien, M; Lacny, L; Lepers, B; Longhin, A; Loveridge, P; Osswald, F; Poussot, P; Rooney, M; Skoczen, B; Szybinski, B; Ustrzycka, A; Vassilopoulos, N; Wilcox, D; Wroblewski, A; Wurtz, J; Zeter, V; Zito, M

    2012-01-01

    The EUROnu Super Beam work package has studied a neutrino beam based on SPL at CERN and aimed at MEMPHYS, a large water Cherenkov detector, proposed for the Laboratoire Souterrain de Modane (Fr\\'ejus tunnel, France), with a baseline of 130 km. The aim of this proposed experiment is to study the CP violation in the neutrino sector. In the study reported here, we have developed the conceptual design of the neutrino beam, especially the target and the magnetic focusing device. Indeed, this beam present several unprecedented challenges, like the high primary proton beam power (4 MW), the high repetition rate (50 Hz) and the low energy of the protons (4.5 GeV). The design is completed by a study of all the main component of the system, starting from the transport system to guide the beam to the target up to the beam dump.

  1. Alignment modification for pencil eye shields

    International Nuclear Information System (INIS)

    Evans, M.D.; Pla, M.; Podgorsak, E.B.

    1989-01-01

    Accurate alignment of pencil beam eye shields to protect the lens of the eye may be made easier by means of a simple modification of existing apparatus. This involves drilling a small hole through the center of the shield to isolate the rayline directed to the lens and fabricating a suitable plug for this hole

  2. Squid based beam current meter

    International Nuclear Information System (INIS)

    Kuchnir, M.

    1983-01-01

    A SQUID based beam current meter has the capability of measuring the current of a beam with as little as 30 x 155 antiprotons (with a signal to noise ratio of 2). If low noise dc current is used to cancel most of the beam or an up-down counter is used to count auto-resets this sensitivity will be available at any time in the acumulation process. This current meter will therefore be a unique diagnostic tool for optimizing the performance of several Tev I components. Besides requiring liquid helium it seems that its only drawback is not to follow with the above sensitivity a sudden beam change larger than 16 μA, something that could be done using a second one in a less sensitive configuration

  3. Status and experiece with the alignment of Linac4

    CERN Document Server

    Fuchs, Jean-Frederic

    2016-01-01

    LINAC4 (L4) is an H- linear accelerator that will deliver, for the High Luminosity LHC (HL-LHC) project requirements, a beam of protons at 160 MeV energy to the PS complex and then to the LHC. Its connection to the PS booster will take place during the Long Shutdown 2 (LS2) in 2019-2020 or earlier if any major failure of the LINAC2. The Linac4 project requires the precise alignment with a tolerance of about +/- 0.2 mm in both the horizontal and vertical planes, of elements along approximately 150 m beam line. This paper will give a status, an overview of the challenges of the alignment, the issues solved by the survey section, the techniques and methodology used to realise the survey activities over the last five years.

  4. GraphAlignment: Bayesian pairwise alignment of biological networks

    Directory of Open Access Journals (Sweden)

    Kolář Michal

    2012-11-01

    Full Text Available Abstract Background With increased experimental availability and accuracy of bio-molecular networks, tools for their comparative and evolutionary analysis are needed. A key component for such studies is the alignment of networks. Results We introduce the Bioconductor package GraphAlignment for pairwise alignment of bio-molecular networks. The alignment incorporates information both from network vertices and network edges and is based on an explicit evolutionary model, allowing inference of all scoring parameters directly from empirical data. We compare the performance of our algorithm to an alternative algorithm, Græmlin 2.0. On simulated data, GraphAlignment outperforms Græmlin 2.0 in several benchmarks except for computational complexity. When there is little or no noise in the data, GraphAlignment is slower than Græmlin 2.0. It is faster than Græmlin 2.0 when processing noisy data containing spurious vertex associations. Its typical case complexity grows approximately as O(N2.6. On empirical bacterial protein-protein interaction networks (PIN and gene co-expression networks, GraphAlignment outperforms Græmlin 2.0 with respect to coverage and specificity, albeit by a small margin. On large eukaryotic PIN, Græmlin 2.0 outperforms GraphAlignment. Conclusions The GraphAlignment algorithm is robust to spurious vertex associations, correctly resolves paralogs, and shows very good performance in identification of homologous vertices defined by high vertex and/or interaction similarity. The simplicity and generality of GraphAlignment edge scoring makes the algorithm an appropriate choice for global alignment of networks.

  5. Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity

    Directory of Open Access Journals (Sweden)

    Lyngsø Rune

    2010-04-01

    Full Text Available Abstract Background The dynamic motions of many proteins are central to their function. It therefore follows that the dynamic requirements of a protein are evolutionary constrained. In order to assess and quantify this, one needs to compare the dynamic motions of different proteins. Comparing the dynamics of distinct proteins may also provide insight into how protein motions are modified by variations in sequence and, consequently, by structure. The optimal way of comparing complex molecular motions is, however, far from trivial. The majority of comparative molecular dynamics studies performed to date relied upon prior sequence or structural alignment to define which residues were equivalent in 3-dimensional space. Results Here we discuss an alternative methodology for comparative molecular dynamics that does not require any prior alignment information. We show it is possible to align proteins based solely on their dynamics and that we can use these dynamics-based alignments to quantify the dynamic similarity of proteins. Our method was tested on 10 representative members of the PDZ domain family. Conclusions As a result of creating pair-wise dynamics-based alignments of PDZ domains, we have found evolutionarily conserved patterns in their backbone dynamics. The dynamic similarity of PDZ domains is highly correlated with their structural similarity as calculated with Dali. However, significant differences in their dynamics can be detected indicating that sequence has a more refined role to play in protein dynamics than just dictating the overall fold. We suggest that the method should be generally applicable.

  6. Commissioning the CMS alignment and calibration framework

    International Nuclear Information System (INIS)

    Futyan, David

    2010-01-01

    The CMS experiment has developed a powerful framework to ensure the precise and prompt alignment and calibration of its components, which is a major prerequisite to achieve the optimal performance for physics analysis. The prompt alignment and calibration strategy harnesses computing resources both at the Tier-0 site and the CERN Analysis Facility (CAF) to ensure fast turnaround for updating the corresponding database payloads. An essential element is the creation of dedicated data streams concentrating the specific event information required by the various alignment and calibration workflows. The resulting low latency is required for feeding the resulting constants into the prompt reconstruction process, which is essential for achieving swift physics analysis of the LHC data. This report discusses the implementation and the computational aspects of the alignment and calibration framework. Recent commissioning campaigns with cosmic muons, beam halo and simulated data have been used to gain detailed experience with this framework, and results of this validation are reported.

  7. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    Z. Szillasi and G. Gomez.

    2013-01-01

    When CMS is opened up, major components of the Link and Barrel Alignment systems will be removed. This operation, besides allowing for maintenance of the detector underneath, is needed for making interventions that will reinforce the alignment measurements and make the operation of the alignment system more reliable. For that purpose and also for their general maintenance and recalibration, the alignment components will be transferred to the Alignment Lab situated in the ISR area. For the track-based alignment, attention is focused on the determination of systematic uncertainties, which have become dominant, since now there is a large statistics of muon tracks. This will allow for an improved Monte Carlo misalignment scenario and updated alignment position errors, crucial for high-momentum muon analysis such as Z′ searches.

  8. Beam Based RF Voltage Measurements and Longitudinal Beam Tomography at the Fermilab Booster

    Energy Technology Data Exchange (ETDEWEB)

    Bhat, C. M. [Fermilab; Bhat, S. [Fermilab

    2017-10-19

    Increasing proton beam power on neutrino production targets is one of the major goals of the Fermilab long term accelerator programs. In this effort, the Fermilab 8 GeV Booster synchrotron plays a critical role for at least the next two decades. Therefore, understanding the Booster in great detail is important as we continue to improve its performance. For example, it is important to know accurately the available RF power in the Booster by carrying out beam-based measurements in order to specify the needed upgrades to the Booster RF system. Since the Booster magnetic field is changing continuously measuring/calibrating the RF voltage is not a trivial task. Here, we present a beam based method for the RF voltage measurements. Data analysis is carried out using computer programs developed in Python and MATLAB. The method presented here is applicable to any RCS which do not have flat-bottom and flat-top in the acceleration magnetic ramps. We have also carried out longitudinal beam tomography at injection and extraction energies with the data used for RF voltage measurements. Beam based RF voltage measurements and beam tomography were never done before for the Fermilab Booster. The results from these investigations will be very useful in future intensity upgrades.

  9. pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment.

    Science.gov (United States)

    Warris, Sven; Timal, N Roshan N; Kempenaar, Marcel; Poortinga, Arne M; van de Geest, Henri; Varbanescu, Ana L; Nap, Jan-Peter

    2018-01-01

    Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of hardware platforms. Moreover, there is a need to promote the adoption of parallel computing in bioinformatics by making its use and extension more simple through more and better application of high-level languages commonly used in bioinformatics, such as Python. The novel application pyPaSWAS presents the parallel SW sequence alignment code fully packed in Python. It is a generic SW implementation running on several hardware platforms with multi-core systems and/or GPUs that provides accurate sequence alignments that also can be inspected for alignment details. Additionally, pyPaSWAS support the affine gap penalty. Python libraries are used for automated system configuration, I/O and logging. This way, the Python environment will stimulate further extension and use of pyPaSWAS. pyPaSWAS presents an easy Python-based environment for accurate and retrievable parallel SW sequence alignments on GPUs and multi-core systems. The strategy of integrating Python with high-performance parallel compute languages to create a developer- and user-friendly environment should be considered for other computationally intensive bioinformatics algorithms.

  10. Gas dynamics considerations in a non-invasive profile monitor for charged particle beams

    CERN Document Server

    Tzoganis, Vasilis; Welsch, Carsten P

    2014-01-01

    A non-invasive, gas jet-based, beam profile monitor has been developed in the QUASAR Group at the Cockcroft Institute, UK. This allows on-line measurement of the 2-dimensional transverse profile of particle beams with negligible disturbance to either primary beam or accelerator vacuum. The monitor is suitable for use with beams across a wide range of energies and intensities. In this setup a nozzle-skimmer system shapes a thin supersonic gas jet into a curtain. However, the small dimensions of the gas inlet nozzle and subsequent skimmers were shown to be the cause of many operational problems. In this paper, the dynamics of gas jet formation transport and shaping is discussed before an image-processing based alignment technique is introduced. Furthermore, experimental results obtained with a 5 keV electron beam are discussed and the effects of gas stagnation pressure on the acquired beam are presented.

  11. Formation of biaxial texture in metal films by selective ion beam etching

    Energy Technology Data Exchange (ETDEWEB)

    Park, S.J. [Department of Materials Science and Engineering, University of Florida, 106 Rhines Hall, P.O. Box 116400, Gainesville, FL 32611 (United States); Norton, D.P. [Department of Materials Science and Engineering, University of Florida, 106 Rhines Hall, P.O. Box 116400, Gainesville, FL 32611 (United States)]. E-mail: dnort@mse.ufl.edu; Selvamanickam, Venkat [IGC-SuperPower, LLC, 450 Duane Avenue, Schenectady, NY 12304 (United States)

    2006-05-15

    The formation of in-plane texture via ion bombardment of uniaxially textured metal films was investigated. In particular, selective grain Ar ion beam etching of uniaxially textured (0 0 1) Ni was used to achieve in-plane aligned Ni grains. Unlike conventional ion beam assisted deposition, the ion beam irradiates the uniaxially textured film surface with no impinging deposition flux. The initial uniaxial texture is established via surface energy minimization with no ion irradiation. Within this sequential texturing method, in-plane grain alignment is driven by selective etching and grain overgrowth. Biaxial texture was achieved for ion beam irradiation at elevated temperature.

  12. Formation of biaxial texture in metal films by selective ion beam etching

    International Nuclear Information System (INIS)

    Park, S.J.; Norton, D.P.; Selvamanickam, Venkat

    2006-01-01

    The formation of in-plane texture via ion bombardment of uniaxially textured metal films was investigated. In particular, selective grain Ar ion beam etching of uniaxially textured (0 0 1) Ni was used to achieve in-plane aligned Ni grains. Unlike conventional ion beam assisted deposition, the ion beam irradiates the uniaxially textured film surface with no impinging deposition flux. The initial uniaxial texture is established via surface energy minimization with no ion irradiation. Within this sequential texturing method, in-plane grain alignment is driven by selective etching and grain overgrowth. Biaxial texture was achieved for ion beam irradiation at elevated temperature

  13. Application for surveying technology for the alignment of large optical systems

    International Nuclear Information System (INIS)

    Bauke, W.

    1984-01-01

    Precise alignment of optical elements in large optical systems is difficult if many elements are positioned such that direct alignment or boresighting becomes impossible. A practical approach is to identify discrete optical path segments and align these using standard surveying or optical-tooling instrumentation. One simply has to develop an alignment theory in which the alignment optical path duplicates or closely approximates the optical path of the operational device. The surveying instruments can then be used to simulate the optical input beams to the system segments to be aligned. Auxiliary targets and reflectors may be added, and the alignment procedure may be augmented by standard optical test instrumentation and techniques. Examples are given using theodolites, transits, and levels with autocollimating capability and micrometer adaptors to perform boresighting and autocollimation techniques on segments of the optical train of the Antares Laser Fusion System at Los Alamos National Laboratory

  14. Use of webcams as tools for alignment and supervision of a Thomson scattering system in the near infrared

    Energy Technology Data Exchange (ETDEWEB)

    Andrebe, Y., E-mail: yanis.andrebe@epfl.ch [Ecole Polytechnique Federale de Lausanne (EPFL), Centre de Recherches en Physique des Plasmas, Association Euratom-Confederation Suisse, Station 13, 1015 Lausanne (Switzerland); Behn, R.; Duval, B.P.; Etienne, P.; Pitzschke, A. [Ecole Polytechnique Federale de Lausanne (EPFL), Centre de Recherches en Physique des Plasmas, Association Euratom-Confederation Suisse, Station 13, 1015 Lausanne (Switzerland)

    2011-10-15

    The alignment stability is a major concern for Thomson scattering systems. Even small angular deviations of the laser beams crossing the plasma lead to a loss of the calibration resulting in unreliable measurements of the electron density profile. For the TCV (Tokamak a Configuration Variable) installation, the beam paths from the laser output to the vacuum chamber are {approx}25 m long and include several optical components. In order to monitor the alignment on a regular basis, a set of 9 cameras has been installed at several locations along the beam path. They view the actual laser beam pattern by recording the scattered light from an intercepting optical surface (mirror or window) together with the position of markers used for reference. Small 'webcams' are used for this purpose; they feature adequate intensity response at the laser wavelength of 1.06 {mu}m, are compact, cheap and several units may be connected to a server PC simultaneously. The real-time images from all the cameras are accessible from a Web browser. This installation has proven to be extremely useful in the early detection of alignment problems and to assist the alignment procedure .

  15. First Experiences of Beam Presence Detection Based on Dedicated Beam Position Monitors

    CERN Document Server

    Jalal, A; Gasior, M; Todd, B

    2011-01-01

    High intensity particle beam injection into the LHC is only permitted when a low intensity pilot beam is already circulating in the LHC. This requirement addresses some of the risks associated with high intensity injection, and is enforced by a so-called Beam Presence Flag (BPF) system which is part of the interlock chain between the LHC and its injector complex. For the 2010 LHC run, the detection of the presence of this pilot beam was implemented using the LHC Fast Beam Current Transformer (FBCT) system. However, the primary function of the FBCTs, that is reliable measurement of beam currents, did not allow the BPF system to satisfy all quality requirements of the LHC Machine Protection System (MPS). Safety requirements associated with high intensity injections triggered the development of a dedicated system, based on Beam Position Monitors (BPM). This system was meant to work first in parallel with the FBCT BPF system and eventually replace it. At the end of 2010 and in 2011, this new BP...

  16. Measuring coalignment of retroreflectors with large lateral incoming-outgoing beam offset

    Energy Technology Data Exchange (ETDEWEB)

    Schütze, Daniel, E-mail: Daniel.Schuetze@aei.mpg.de; Sheard, Benjamin S.; Heinzel, Gerhard; Danzmann, Karsten [Max Planck Institute for Gravitational Physics (Albert Einstein Institute) and Institute for Gravitational Physics, Leibniz Universität Hannover, Callinstr. 38, 30167 Hanover (Germany); Farrant, David [Commonwealth Scientific and Industrial Research Organisation, Bradfield Road, Lindfield, NSW 2070 (Australia); Shaddock, Daniel A. [Centre for Gravitational Physics, Australian National University, Acton, ACT 0200 (Australia)

    2014-03-15

    A method based on phase-shifting Fizeau interferometry is presented with which retroreflectors with large incoming-outgoing beam separations can be tested. The method relies on a flat Reference Bar that is used to align two auxiliary mirrors parallel to each other to extend the aperture of the interferometer. The method is applied to measure the beam coalignment of a prototype Triple Mirror Assembly of the GRACE Follow-On Laser Ranging Interferometer, a future satellite-to-satellite tracking device for Earth gravimetry. The Triple Mirror Assembly features a lateral beam offset of incoming and outgoing beam of 600 mm, whereas the acceptance angle for the incoming beam is only about ±2 mrad. With the developed method, the beam coalignment of the prototype Triple Mirror Assembly was measured to be 9 μrad with a repeatability of below 1 μrad.

  17. Measuring coalignment of retroreflectors with large lateral incoming-outgoing beam offset

    International Nuclear Information System (INIS)

    Schütze, Daniel; Sheard, Benjamin S.; Heinzel, Gerhard; Danzmann, Karsten; Farrant, David; Shaddock, Daniel A.

    2014-01-01

    A method based on phase-shifting Fizeau interferometry is presented with which retroreflectors with large incoming-outgoing beam separations can be tested. The method relies on a flat Reference Bar that is used to align two auxiliary mirrors parallel to each other to extend the aperture of the interferometer. The method is applied to measure the beam coalignment of a prototype Triple Mirror Assembly of the GRACE Follow-On Laser Ranging Interferometer, a future satellite-to-satellite tracking device for Earth gravimetry. The Triple Mirror Assembly features a lateral beam offset of incoming and outgoing beam of 600 mm, whereas the acceptance angle for the incoming beam is only about ±2 mrad. With the developed method, the beam coalignment of the prototype Triple Mirror Assembly was measured to be 9 μrad with a repeatability of below 1 μrad

  18. RevTrans: multiple alignment of coding DNA from aligned amino acid sequences

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Pedersen, Anders Gorm

    2003-01-01

    The simple fact that proteins are built from 20 amino acids while DNA only contains four different bases, means that the 'signal-to-noise ratio' in protein sequence alignments is much better than in alignments of DNA. Besides this information-theoretical advantage, protein alignments also benefit...... proteins. It is therefore preferable to align coding DNA at the amino acid level and it is for this purpose we have constructed the program RevTrans. RevTrans constructs a multiple DNA alignment by: (i) translating the DNA; (ii) aligning the resulting peptide sequences; and (iii) building a multiple DNA...

  19. Ion Dynamics at Shocks: Ion Reflection and Beam Formation at Quasi-perpendicular Shocks

    International Nuclear Information System (INIS)

    Kucharek, Harald; Moebius, Eberhard

    2005-01-01

    The physics of collisionless shocks is controlled by the ion dynamics. The generation of gyrating ions by reflection as well as the formation of field-aligned ion beams are essential parts of this dynamic. On the one hand reflection is most likely the first interaction of ions with the shock before they undergo the downstream thermalization process. On the other hand field-aligned ion beams, predominately found at the quasi-perpendicular bow shock, propagate into the distant foreshock region and may create wave activity. We revisit ion reflection, the source and basic production mechanism of field-aligned ion beams, by using multi-spacecraft measurements and contrast these observations with existing theories. Finally, we propose an alternative production mechanism

  20. Final focus test beam

    International Nuclear Information System (INIS)

    1991-03-01

    This report discusses the following: the Final Focus Test Beam Project; optical design; magnets; instrumentation; magnetic measurement and BPM calibration; mechanical alignment and stabilization; vacuum system; power supplies; control system; radiation shielding and personnel protection; infrastructure; and administration

  1. Dosimetric performance evaluation regarding proton beam incident angles of a lithium-based AB-BNCT design

    International Nuclear Information System (INIS)

    Lee, Pei-Yi; Jiang, Shiang-Huei; Liu, Yuan-Hao

    2014-01-01

    The 7 Li(p,xn) 7 Be nuclear reaction, based on the low-energy protons, could produce soft neutrons for accelerator-based boron neutron capture therapy (AB-BNCT). Based on the fact that the induced neutron field is relatively divergent, the relationship between the incident angle of proton beam and the neutron beam quality was evaluated in this study. To provide an intense epithermal neutron beam, a beam-shaping assembly (BSA) was designed. And a modified Snyder head phantom was used in the calculations for evaluating the dosimetric performance. From the calculated results, the intensity of epithermal neutrons increased with the increase in proton incident angle. Hence, either the irradiation time or the required proton current can be reduced. When the incident angle of 2.5-MeV proton beam is 120 deg., the required proton current is ∼13.3 mA for an irradiation time of half an hour. The results of this study show that the BSA designs can generate neutron beams with good intensity and penetrability. Using a 20-mA, 2.5-MeV proton beam as the source, the required irradiation time, to induce 60 RBE-Gy of maximum tumour dose, is less than half an hour in any proton beam alignments. On the premise that the dosimetric performances are similar, the intensity of epithermal neutrons can be increased by using non-collinear (e.g. 90 deg., 120 deg.) incident protons. Thus, either the irradiation time or the required proton current can be reduced. The use of 120 deg. BSA model shows the possibility to reduce the required proton current to ∼13.3 mA when the goal of irradiation time is 30 min. The decrease of required proton beam current certainly will make the use of lithium target much easier. In June 2013, a 5-MeV, 30-mA radio frequency quadruple (RFQ) accelerator for BNCT was built at INFN-LNL (Legnaro National Laboratories, Italy), which shows a possibility to build a suitable RFQ accelerator for the authors' design. In addition, a 2.5-MeV, 30-mA Tandem accelerator was

  2. A spatial mechanism for pilot laser alignment with four independently controlled degrees of freedom

    NARCIS (Netherlands)

    Kreutz, Ernst-Wolfgang; Meijer, J.; Quenzer, A.; Schuöcker, Dieter

    1987-01-01

    Alignment mechanism for optical components, such as mirrors for manipulating laser beams, frequently require four degrees of freedom: two translations and two rotations, i.e. a four axis system. When the adjustment of one axis influences the others, as often will be the case, alignment procedures

  3. Alignment of mapping system for magnet cyclotron DECY-13

    International Nuclear Information System (INIS)

    Idrus Abdul Kudus; Taufik; Kurnia Wibowo

    2016-01-01

    A cyclotron is composed of some main and specific components, such as magnet system, ion source, RF system and extractor. A magnet is one of important component in a cyclotron that serves as ion beam bending so the ion beam trajectory is circular. Magnet design should with the requirement of cyclotron that proton energy is 13 MeV. In the construction of the cyclotron magnet, a mapping tool of the magnetic field is required for analysis in shimming process in order to optimize the magnetic field. The magnetic field mapping process is carried out in the median plane of the magnet poles. The magnetic field mapping is carried out repeatedly during the shimming process. During this process, the mapping tool is possible to experience a shift or change in position, for that it is necessary to alignment in order to make sure that the probe is in the median plane of magnet poles and to ensure their positions are always the same on each repetition mapping. During this process, it is possible to experience a shift mapping tool or change the position, for this it is needed to process alignment to ensure the position of the probe is in the median plane magnetic poles and ensure their positions are always the same on each repetition mapping. Alignment on the mapping tool are the height position, zeroing tesla meter and two hall probe mapping. The parameters form the basis for magnetic field measurements based on the three elements: an alignment system on the engine mapping, mapping tool reference point and stage movement of x-y coordinates. Shifts occur due to change in elevation mapping tool table and center coordinates x and y in the mapping process. Changes made to shift mapping coordinates can be shifted as far as 1 to 2 mm for each hall probe in the x and y coordinates with altitude changes 0.05° mapping table and measurement of tesla meter changes in 0.002 T. (author)

  4. Agent Based Model in SAS Environment for Rail Transit System Alignment Determination

    Directory of Open Access Journals (Sweden)

    I Made Indradjaja Brunner

    2018-04-01

    Full Text Available Transit system had been proposed for the urban area of Honolulu. One consideration to be determined is the alignment of the transit system. Decision to set the transit alignment will have influences on which areas will be served, who will be benefiting, as well as who will be impacted. Inputs for the decision usually conducted through public meetings, where community members are shown numbers of maps with pre-set routes. That approach could lead to a rather subjective decision by the community members. This paper attempts to discuss the utilization of grid map in determining the best alignment for rail transit system in Honolulu, Hawaii. It tries to use a more objective approach using various data derived from thematic maps. Overlaid maps are aggregated into a uniform 0.1-square mile vector based grid map system in GIS environment. The large dataset in the GIS environment is analyzed and manipulated using SAS software. The SAS procedure is applied to select the location of the alignment using a rational and deterministic approach. Grid cells that are superior compared to the others are selected based on several predefined criteria. Location of the dominant cells indicates possible transit alignment. The SAS procedure is designed to allow a transient vector called the GUIDE (Grid Unit with Intelligent Directional Expertise agent to analyze several cells at its vicinity and to move towards a cell with the highest value. Each time the agent landed on a cell, it left a mark. The chain of those marks shows location for the transit alignment. This study shows that the combination of ArcGIS and SAS allows a robust analysis of spatial data and manipulation of its datasets, which can be used to run a simulation mimicking the Agent-Based Modelling. This study also opens up further study possibilities by increasing number of factors analyzed by the agent, as well as creating a composite value of multi-factors.

  5. Nonlinearities in the response of beam position monitors

    International Nuclear Information System (INIS)

    Assmann, R.; Dehning, B.; Matheson, J.; Prochnow, J.

    2000-01-01

    At the LEP e + /e - collider at CERN, Geneva, a Spectrometer is used to determine the beam energy with a relative accuracy of 10 -4 .The Spectrometer measures the change in bending angle in a dipole magnet, the beam trajectory being obtained using beam position monitors (BPMs), which must have an accuracy close to 1 μm in order to achieve the desired precision. The BPMs used feature an aluminum block with an elliptical aperture and capacitive pickup electrodes. The response depends on the electrode geometry and also on the shape of the monitor aperture. In addition, the size of the beam itself contributes if the beam is off-center. The beam size varies according to the beta and dispersion functions at the Spectrometer, so that each BPM may exhibit a systematic shift of the measured beam position. We have investigated the implications of such shifts on the performance of the Spectrometer. We present analytical results, a computer model of the BPM response, and comparison with measurements. The model suggests strategies such as beam-based alignment to minimize the systematic effects arising from the BPMs

  6. LHC Collimators with Embedded Beam Position Monitors: a New Adbanced Mechanical Design

    CERN Document Server

    Dallocchio, A; Boccard, C; Carra, F; Gasior, M; Gentini, L; Timmins, M

    2011-01-01

    The LHC collimation system, ensuring both functions of beam cleaning and machine protection, is potentially submitted to high-energy beam impacts. Currently the collimators setup is performed by monitoring beam losses generated by the collimator jaws when approaching the particle beam. This procedure is applied to all LHC collimators (almost one hundred), taking several hours, and needs to be repeated if beam settings change significantly. Furthermore, during the beam-based alignment, the LHC tertiary collimators are potentially exposed to abnormal losses entailing possible damage to their tungsten jaws. To improve the efficiency of the machine operation and better control the particle beam a new advanced design embedding Beam Position Monitors (BPM) into the movable collimator jaws has been developed. This paper describes the mechanical design of various types of future collimators with embedded BPMs. Experimental measurements performed on a simplified functional prototype installed in the CERN SPS showed th...

  7. LHC Collimators with Embedded Beam Position Monitors: A New Advanced Mechanical Design

    CERN Document Server

    Dallocchio, A; Boccard, C; Carra, F; Gasior, M; Gentini, L; Timmins, M A

    2011-01-01

    The LHC collimation system, ensuring both functions of beam cleaning and machine protection, is potentially submitted to high-energy beam impacts. Currently the collimators setup is performed by monitoring beam losses generated by the collimator jaws when approaching the particle beam. This procedure is applied to all LHC collimators (almost one hundred), taking several hours, and needs to be repeated if beam settings change significantly. Furthermore, during the beam-based alignment, the LHC tertiary collimators are potentially exposed to abnormal losses entailing possible damage to their tungsten jaws. To improve the efficiency of the machine operation and better control the particle beam a new advanced design embedding Beam Position Monitors (BPM) into the movable collimator jaws has been developed. This paper describes the mechanical design of various types of future collimators with embedded BPMs. Experimental measurements performed on a simplified functional prototype installed in the CERN SPS showed th...

  8. Toward a view-oriented approach for aligning RDF-based biomedical repositories.

    Science.gov (United States)

    Anguita, A; García-Remesal, M; de la Iglesia, D; Graf, N; Maojo, V

    2015-01-01

    This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems". The need for complementary access to multiple RDF databases has fostered new lines of research, but also entailed new challenges due to data representation disparities. While several approaches for RDF-based database integration have been proposed, those focused on schema alignment have become the most widely adopted. All state-of-the-art solutions for aligning RDF-based sources resort to a simple technique inherited from legacy relational database integration methods. This technique - known as element-to-element (e2e) mappings - is based on establishing 1:1 mappings between single primitive elements - e.g. concepts, attributes, relationships, etc. - belonging to the source and target schemas. However, due to the intrinsic nature of RDF - a representation language based on defining tuples -, one may find RDF elements whose semantics vary dramatically when combined into a view involving other RDF elements - i.e. they depend on their context. The latter cannot be adequately represented in the target schema by resorting to the traditional e2e approach. These approaches fail to properly address this issue without explicitly modifying the target ontology, thus lacking the required expressiveness for properly reflecting the intended semantics in the alignment information. To enhance existing RDF schema alignment techniques by providing a mechanism to properly represent elements with context-dependent semantics, thus enabling users to perform more expressive alignments, including scenarios that cannot be adequately addressed by the existing approaches. Instead of establishing 1:1 correspondences between single primitive elements of the schemas, we propose adopting a view-based approach. The latter is targeted at establishing mapping relationships between RDF subgraphs - that can be regarded as the equivalent of views in traditional

  9. Beam based measurement of beam position monitor electrode gains

    Directory of Open Access Journals (Sweden)

    D. L. Rubin

    2010-09-01

    Full Text Available Low emittance tuning at the Cornell Electron Storage Ring (CESR test accelerator depends on precision measurement of vertical dispersion and transverse coupling. The CESR beam position monitors (BPMs consist of four button electrodes, instrumented with electronics that allow acquisition of turn-by-turn data. The response to the beam will vary among the four electrodes due to differences in electronic gain and/or misalignment. This variation in the response of the BPM electrodes will couple real horizontal offset to apparent vertical position, and introduce spurious measurements of coupling and vertical dispersion. To alleviate this systematic effect, a beam based technique to measure the relative response of the four electrodes has been developed. With typical CESR parameters, simulations show that turn-by-turn BPM data can be used to determine electrode gains to within ∼0.1%.

  10. Beam based measurement of beam position monitor electrode gains

    Science.gov (United States)

    Rubin, D. L.; Billing, M.; Meller, R.; Palmer, M.; Rendina, M.; Rider, N.; Sagan, D.; Shanks, J.; Strohman, C.

    2010-09-01

    Low emittance tuning at the Cornell Electron Storage Ring (CESR) test accelerator depends on precision measurement of vertical dispersion and transverse coupling. The CESR beam position monitors (BPMs) consist of four button electrodes, instrumented with electronics that allow acquisition of turn-by-turn data. The response to the beam will vary among the four electrodes due to differences in electronic gain and/or misalignment. This variation in the response of the BPM electrodes will couple real horizontal offset to apparent vertical position, and introduce spurious measurements of coupling and vertical dispersion. To alleviate this systematic effect, a beam based technique to measure the relative response of the four electrodes has been developed. With typical CESR parameters, simulations show that turn-by-turn BPM data can be used to determine electrode gains to within ˜0.1%.

  11. SU-E-J-181: Effect of Prostate Motion On Combined Brachytherapy and External Beam Dose Based On Daily Motion of the Prostate

    Energy Technology Data Exchange (ETDEWEB)

    Narayana, V; McLaughlin, P [Providence Cancer Center, Southfield, MI (United States); University of Michigan, Ann Arbor, MI (United States); Ealbaj, J [University of Michigan, Ann Arbor, MI (United States)

    2015-06-15

    Purpose: In this study, the adequacy of target expansions on the combined external beam and implant dose was examined based on the measured daily motion of the prostate. Methods: Thirty patients received an I–125 prostate implant prescribed to dose of 90Gy. This was followed by external beam to deliver a dose of 90Gyeq (external beam equivalent) to the prostate over 25 to 30 fractions. An ideal IMRT plan was developed by optimizing the external beam dose based on the delivered implant dose. The implant dose was converted to an equivalent external beam dose using the linear quadratic model. Patients were set up on the treatment table by daily orthogonal imaging and aligning the marker seeds in the prostate. Orthogonal images were obtained at the end of treatment to assess prostate intrafraction motion. Based on the observed motion of the markers between the initial and final images, 5 individual plans showing the actual dose delivered to the patient were calculated. A final true dose distribution was established based on summing the implant dose and the 5 external beam plans. Dose to the prostate, seminal vesicles, lymphnodes and normal tissues, rectal wall, urethra and lower sphincter were calculated and compared to ideal. On 18 patients who were sexually active, dose to the corpus cavernosum and internal pudendal artery was also calculated. Results: The average prostate motion in 3 orthogonal directions was less than 1 mm with a standard deviation of less than +2 mm. Dose and volume parameters showed that there was no decrease in dose to the targets and a marginal decrease in dose to in normal tissues. Conclusion: Dose delivered by seed implant moves with the prostate, decreasing the impact of intrafractions dose movement on actual dose delivered. Combined brachytherapy and external beam dose delivered to the prostate was not sensitive to prostate motion.

  12. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    M. Dallavalle

    2013-01-01

    A new Muon misalignment scenario for 2011 (7 TeV) Monte Carlo re-processing was re-leased. The scenario is based on running of standard track-based reference-target algorithm (exactly as in data) using single-muon simulated sample (with the transverse-momentum spectrum matching data). It used statistics similar to what was used for alignment with 2011 data, starting from an initially misaligned Muon geometry from uncertainties of hardware measurements and using the latest Tracker misalignment geometry. Validation of the scenario (with muons from Z decay and high-pT simulated muons) shows that it describes data well. The study of systematic uncertainties (dominant by now due to huge amount of data collected by CMS and used for muon alignment) is finalised. Realistic alignment position errors are being obtained from the estimated uncertainties and are expected to improve the muon reconstruction performance. Concerning the Hardware Alignment System, the upgrade of the Barrel Alignment is in progress. By now, d...

  13. Feasibility study into the use of silicon photo-diodes for the alignment of collimated X-rays on the SRS

    CERN Document Server

    Buffey, S G

    1999-01-01

    Dynamic alignment of beam on the crystal during data collection was studied. Development of silicon photo-diode detectors for the vacuum ultraviolet and soft X-ray spectral regions has led to the use of such devices as beam alignment tools for Protein Crystallography beamlines on the Synchrotron Radiation Source at Daresbury. Quadrant photo-diodes are used to provide signals proportional to the number of photons hitting each photo-diode, these are amplified, digitised and then summed to give the x-y position of the beam centre. (author)

  14. Investigation of Accelerated Partial Breast Patient Alignment and Treatment With Helical Tomotherapy Unit

    International Nuclear Information System (INIS)

    Langen, Katja M.; Buchholz, Daniel J.; Burch, Doug R. C.; Burkavage, Rob C.; Limaye, Arti U.; Meeks, Sanford L.; Kupelian, Patrick A.; Ruchala, Kenneth J.; Haimerl, Jason; Henderson, Doug; Olivera, Gustavo H.

    2008-01-01

    Purpose: To determine the precision of megavoltage computed tomography (MVCT)-based alignment of the seroma cavity for patients undergoing partial breast irradiation; and to determine whether accelerated partial breast irradiation (APBI) plans can be generated for TomoTherapy deliveries that meet the National Surgical Adjuvant Breast and Bowel Project (NSABP) B-39/Radiation Therapy Oncology Group (RTOG) 0413 protocol guidelines for target coverage and normal tissue dose limitations. Methods and Materials: We obtained 50 MVCT images from 10 patients. An interuser study was designed to assess the alignment precision. Using a standard helical and a fixed beam prototype ('topotherapy') optimizer, two APBI plans for each patient were developed. Results: The precision of the MVCT-based seroma cavity alignment was better than 2 mm if averaged over the patient population. Both treatment techniques could be used to generate acceptable APBI plans for patients that fulfilled the recommended NSABP B-39/RTOG-0413 selection criteria. For plans of comparable treatment time, the conformation of the prescription dose to the target was greater for helical deliveries, while the ipsilateral lung dose was significantly reduced for the topotherapy plans. Conclusions: The inherent volumetric imaging capabilities of a TomoTherapy Hi-Art unit allow for alignment of patients undergoing partial breast irradiation that is determined from the visibility of the seroma cavity on the MVCT image. The precision of the MVCT-based alignment was better than 2 mm (± standard deviation) when averaged over the patient population. Using the NSABP B-39/RTOG-0413 guidelines, acceptable APBI treatment plans can be generated using helical- or topotherapy-based delivery techniques

  15. The beam-beam limit in asymmetric colliders: Optimization of the B-factory parameter base

    International Nuclear Information System (INIS)

    Tennyson, J.L.

    1990-01-01

    This paper presents a general theory of the beam-beam limit in symmetric and asymmetric lepton ring colliders. It shows how the beam-beam limit in these accelerators affects the maximum attainable luminosity and presents a specific algorithm for parameter base optimization. It is shown that the special problems inherent in asymmetric colliders derive not from the asymmetry, but from the fact that the two beams must be in different rings. Computer simulation experiments are used to demonstrate the various phenomena discussed in the theory

  16. Track-Based Alignment of the Inner Detector of ATLAS

    Directory of Open Access Journals (Sweden)

    Ovcharova Ana

    2012-06-01

    Full Text Available ATLAS is a multipurpose experiment at the LHC. The tracking system of ATLAS, embedded in a 2 T solenoidal field, is composed of different technologies: silicon planar sensors (pixel and microstrips and drift-tubes. The procedure used to align the ATLAS tracker and the results of the alignment using data recorded during 2010 and 2011 using LHC proton-proton collision runs at 7 TeV are presented. Validation of the alignment is performed by measuring the alignment observables as well as many other physics observables, notably resonance invariant masses in a wide mass range (KS, J/Ψ and Z. The E/p distributions for electrons from Z → ee and W → ev are also extensively used. The results indicate that, after the alignment with real data, the attained precision of the alignment constants is approximately 5 μm. The systematic errors due to the alignment that may affect physics results are under study.

  17. High yield growth of patterned vertically aligned carbon nanotubes using inkjet-printed catalyst.

    Science.gov (United States)

    Beard, James D; Stringer, Jonathan; Ghita, Oana R; Smith, Patrick J

    2013-10-09

    This study reports on the fabrication of vertically aligned carbon nanotubes localized at specific sites on a growth substrate by deposition of a nanoparticle suspension using inkjet printing. Carbon nanotubes were grown with high yield as vertically aligned forests to a length of approximately 400 μm. The use of inkjet printing for catalyst fabrication considerably improves the production rate of vertically aligned patterned nanotube forests compared with conventional patterning techniques, for example, electron beam lithography or photolithography.

  18. Study of device mass production capability of the character projection based electron beam direct writing process technology toward 14 nm node and beyond

    Science.gov (United States)

    Kojima, Yoshinori; Takahashi, Yasushi; Takakuwa, Masaki; Ohshio, Shuzo; Sugatani, Shinji; Tujimura, Ryo; Takita, Hiroshi; Ogino, Kozo; Hoshino, Hiromi; Ito, Yoshio; Miyajima, Masaaki; Kon, Jun-ichi

    2012-03-01

    Techniques to appropriately control the key factors for a character projection (CP) based electron beam direct writing (EBDW) technology for mass production are shown and discussed. In order to achieve accurate CD control, the CP technique using the master CP is adopted. Another CP technique, the Packed CP, is used to obtain suitable shot count. For the alignment on the some critical layers which have the normally an even surface, the alignment methodology differ from photolithography is required. The process that etches the SiO2 material in the shallow trench isolation is added and then the alignment marks can be detected using electron beam even at the gate layer, which is normally on an even surface. The proximity effect correction using the simplified electron energy flux model and the hybrid exposure are used to obtain enough process margins. As a result, the sufficient CD accuracy, overlay accuracy, and yield are obtained on the 65 nm node device. The condition in our system is checked using self-diagnosis on a regular basis, and scheduled maintenances have been properly performed. Due to the proper system control, more than 10,000 production wafers have been successfully exposed so far without any major system downtime. It is shown that those techniques can be adapted to the 32 nm node production with slight modifications. For the 14 nm node and beyond, however, the drastic increment of the shot count becomes more of a concern. The Multi column cell (MCC) exposure method, the key concept of which is the parallelization of the electron beam columns with a CP, can overcome this concern. It is expected that by using the MCC exposure system, those techniques will be applicable to the rapid establishment for the 14 nm node technology.

  19. Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

    Directory of Open Access Journals (Sweden)

    Emanuel Santos

    Full Text Available Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system.

  20. Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

    Science.gov (United States)

    Santos, Emanuel; Faria, Daniel; Pesquita, Catia; Couto, Francisco M

    2015-01-01

    Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system.

  1. Accurate and robust brain image alignment using boundary-based registration.

    Science.gov (United States)

    Greve, Douglas N; Fischl, Bruce

    2009-10-15

    The fine spatial scales of the structures in the human brain represent an enormous challenge to the successful integration of information from different images for both within- and between-subject analysis. While many algorithms to register image pairs from the same subject exist, visual inspection shows that their accuracy and robustness to be suspect, particularly when there are strong intensity gradients and/or only part of the brain is imaged. This paper introduces a new algorithm called Boundary-Based Registration, or BBR. The novelty of BBR is that it treats the two images very differently. The reference image must be of sufficient resolution and quality to extract surfaces that separate tissue types. The input image is then aligned to the reference by maximizing the intensity gradient across tissue boundaries. Several lower quality images can be aligned through their alignment with the reference. Visual inspection and fMRI results show that BBR is more accurate than correlation ratio or normalized mutual information and is considerably more robust to even strong intensity inhomogeneities. BBR also excels at aligning partial-brain images to whole-brain images, a domain in which existing registration algorithms frequently fail. Even in the limit of registering a single slice, we show the BBR results to be robust and accurate.

  2. Transient, Small-Scale Field-Aligned Currents in the Plasma Sheet Boundary Layer During Storm Time Substorms

    Science.gov (United States)

    Nakamura, R.; Sergeev, V. A.; Baumjohann, W.; Plaschke, F.; Magnes, W.; Fischer, D.; Varsani, A.; Schmid, D.; Nakamura, T. K. M.; Russell, C. T.; hide

    2016-01-01

    We report on field-aligned current observations by the four Magnetospheric Multiscale (MMS) spacecraft near the plasma sheet boundary layer (PSBL) during two major substorms on 23 June 2015. Small-scale field-aligned currents were found embedded in fluctuating PSBL flux tubes near the Separatrix region. We resolve, for the first time, short-lived earthward (downward) intense field-aligned current sheets with thicknesses of a few tens of kilometers, which are well below the ion scale, on flux tubes moving equatorward earth ward during outward plasma sheet expansion. They coincide with upward field-aligned electron beams with energies of a few hundred eV. These electrons are most likely due to acceleration associated with a reconnection jet or high-energy ion beam-produced disturbances. The observations highlight coupling of multiscale processes in PSBL as a consequence of magnetotail reconnection.

  3. Self-alignment of a compact large-area atomic Sagnac interferometer

    International Nuclear Information System (INIS)

    Tackmann, G; Berg, P; Schubert, C; Abend, S; Gilowski, M; Ertmer, W; Rasel, E M

    2012-01-01

    We report on the realization of a compact atomic Mach-Zehnder-type Sagnac interferometer of 13.7 cm length, which covers an area of 19 mm 2 previously reported only for large thermal beam interferometers. According to Sagnac's formula, which holds for both light and atoms, the sensitivity for rotation rates increases linearly with the area enclosed by the interferometer. The use of cold atoms instead of thermal atoms enables miniaturization of Sagnac interferometers without sacrificing large areas. In comparison with thermal beams, slow atoms offer better matching of the initial beam velocity and the velocity with which the matter waves separate. In our case, the area is spanned by a cold atomic beam of 2.79 m s -1 , which is split, deflected and combined by driving a Raman transition between the two hyperfine ground states of 87 Rb in three spatially separated light zones. The use of cold atoms requires a precise angular alignment and high wave front quality of the three independent light zones over the cloud envelope. We present a procedure for mutually aligning the beam splitters at the microradian level by making use of the atom interferometer itself in different configurations. With this method, we currently achieve a sensitivity of 6.1×10 -7 rad s -1 Hz -1/2 . (paper)

  4. Three-dimensional hindfoot alignment measurements based on biplanar radiographs: comparison with standard radiographic measurements

    International Nuclear Information System (INIS)

    Sutter, Reto; Pfirrmann, Christian W.A.; Buck, Florian M.; Espinosa, Norman

    2013-01-01

    To establish a hindfoot alignment measurement technique based on low-dose biplanar radiographs and compare with hindfoot alignment measurements on long axial view radiographs, which is the current reference standard. Long axial view radiographs and low-dose biplanar radiographs of a phantom consisting of a human foot skeleton embedded in acrylic glass (phantom A) and a plastic model of a human foot in three different hindfoot positions (phantoms B1-B3) were imaged in different foot positions (20 internal to 20 external rotation). Two independent readers measured hindfoot alignment on long axial view radiographs and performed 3D hindfoot alignment measurements based on biplanar radiographs on two different occasions. Time for three-dimensional (3D) measurements was determined. Intraclass correlation coefficients (ICC) were calculated. Hindfoot alignment measurements on long axial view radiographs were characterized by a large positional variation, with a range of 14 /13 valgus to 22 /27 varus (reader 1/2 for phantom A), whereas the range of 3D hindfoot alignment measurements was 7.3 /6.0 to 9.0 /10.5 varus (reader 1/2 for phantom A), with a mean and standard deviation of 8.1 ± 0.6/8.7 ± 1.4 respectively. Interobserver agreement was high (ICC = 0.926 for phantom A, and ICC = 0.886 for phantoms B1-B3), and agreement between different readouts was high (ICC = 0.895-0.995 for reader 1, and ICC = 0.987-0.994 for reader 2) for 3D measurements. Mean duration of 3D measurements was 84 ± 15/113 ± 15 s for reader 1/2. Three-dimensional hindfoot alignment measurements based on biplanar radiographs were independent of foot positioning during image acquisition and reader independent. In this phantom study, the 3D measurements were substantially more precise than the standard radiographic measurements. (orig.)

  5. Enhanced optical alignment of a digital micro mirror device through Bayesian adaptive exploration

    Science.gov (United States)

    Wynne, Kevin B.; Knuth, Kevin H.; Petruccelli, Jonathan

    2017-12-01

    As the use of Digital Micro Mirror Devices (DMDs) becomes more prevalent in optics research, the ability to precisely locate the Fourier "footprint" of an image beam at the Fourier plane becomes a pressing need. In this approach, Bayesian adaptive exploration techniques were employed to characterize the size and position of the beam on a DMD located at the Fourier plane. It couples a Bayesian inference engine with an inquiry engine to implement the search. The inquiry engine explores the DMD by engaging mirrors and recording light intensity values based on the maximization of the expected information gain. Using the data collected from this exploration, the Bayesian inference engine updates the posterior probability describing the beam's characteristics. The process is iterated until the beam is located to within the desired precision. This methodology not only locates the center and radius of the beam with remarkable precision but accomplishes the task in far less time than a brute force search. The employed approach has applications to system alignment for both Fourier processing and coded aperture design.

  6. A unified model for transfer alignment at random misalignment angles based on second-order EKF

    International Nuclear Information System (INIS)

    Cui, Xiao; Qin, Yongyuan; Yan, Gongmin; Liu, Zhenbo; Mei, Chunbo

    2017-01-01

    In the transfer alignment process of inertial navigation systems (INSs), the conventional linear error model based on the small misalignment angle assumption cannot be applied to large misalignment situations. Furthermore, the nonlinear model based on the large misalignment angle suffers from redundant computation with nonlinear filters. This paper presents a unified model for transfer alignment suitable for arbitrary misalignment angles. The alignment problem is transformed into an estimation of the relative attitude between the master INS (MINS) and the slave INS (SINS), by decomposing the attitude matrix of the latter. Based on the Rodriguez parameters, a unified alignment model in the inertial frame with the linear state-space equation and a second order nonlinear measurement equation are established, without making any assumptions about the misalignment angles. Furthermore, we employ the Taylor series expansions on the second-order nonlinear measurement equation to implement the second-order extended Kalman filter (EKF2). Monte-Carlo simulations demonstrate that the initial alignment can be fulfilled within 10 s, with higher accuracy and much smaller computational cost compared with the traditional unscented Kalman filter (UKF) at large misalignment angles. (paper)

  7. A unified model for transfer alignment at random misalignment angles based on second-order EKF

    Science.gov (United States)

    Cui, Xiao; Mei, Chunbo; Qin, Yongyuan; Yan, Gongmin; Liu, Zhenbo

    2017-04-01

    In the transfer alignment process of inertial navigation systems (INSs), the conventional linear error model based on the small misalignment angle assumption cannot be applied to large misalignment situations. Furthermore, the nonlinear model based on the large misalignment angle suffers from redundant computation with nonlinear filters. This paper presents a unified model for transfer alignment suitable for arbitrary misalignment angles. The alignment problem is transformed into an estimation of the relative attitude between the master INS (MINS) and the slave INS (SINS), by decomposing the attitude matrix of the latter. Based on the Rodriguez parameters, a unified alignment model in the inertial frame with the linear state-space equation and a second order nonlinear measurement equation are established, without making any assumptions about the misalignment angles. Furthermore, we employ the Taylor series expansions on the second-order nonlinear measurement equation to implement the second-order extended Kalman filter (EKF2). Monte-Carlo simulations demonstrate that the initial alignment can be fulfilled within 10 s, with higher accuracy and much smaller computational cost compared with the traditional unscented Kalman filter (UKF) at large misalignment angles.

  8. Ion-beam texturing of uniaxially textured Ni films

    International Nuclear Information System (INIS)

    Park, S.J.; Norton, D.P.; Selvamanickam, Venkat

    2005-01-01

    The formation of biaxial texture in uniaxially textured Ni thin films via Ar-ion irradiation is reported. The ion-beam irradiation was not simultaneous with deposition. Instead, the ion beam irradiates the uniaxially textured film surface with no impinging deposition flux, which differs from conventional ion-beam-assisted deposition. The uniaxial texture is established via a nonion beam process, with the in-plane texture imposed on the uniaxial film via ion beam bombardment. Within this sequential ion beam texturing method, grain alignment is driven by selective etching and grain overgrowth

  9. Alignment and geodesy for the ESRF project

    International Nuclear Information System (INIS)

    Roux, D.

    1990-01-01

    New generation accelerators and storage rings for synchrotron radiation require ever increasing precision of alignment, precision which moreover must be preserved over a maximum length of time. The use of ever smaller beam dimensions, and ever narrower vacuum chambers leads the magnet positioning tolerances to be reduced to a minimum. Thus, unlike in the past, annual realignment due to progressive deterioration of the ground stability can no longer be envisaged. Permanent monitoring of the ground stability must be guaranteed and its effects compensated, as soon as significant deterioration is recorded. It is this viewpoint that has dictated the choices made by ESRF in the field of alignment and monitoring

  10. Alignment of CT-PPS detectors in 2016, before TS2

    CERN Document Server

    Kaspar, J

    2017-01-01

    This note presents the first alignment of the CMS-TOTEM Precision Proton Spectrometer (CT-PPS) using the data from before Technical Stop 2 (TS2), 2016. This new procedure involves two stages. In the first one, data from a special calibration fill are used. In this fill, both horizontal and vertical Roman Pots (RPs) were inserted very close to the beam. In the second stage, hit distributions from physics fills (with only horizontal RPs inserted) are matched to the previously aligned reference from the calibration fill. The alignment and optics calibration is verified by reconstructing consistent $\\xi$ spectra from different RPs and LHC fills.

  11. Constructive Alignment for Teaching Model-Based Design for Concurrency

    DEFF Research Database (Denmark)

    Brabrand, Claus

    2007-01-01

    "How can we make sure our students learn what we want them to?" is the number one question in teaching. This paper is intended to provide the reader with: i) a general answer to this question based on the theory of constructive alignment by John Biggs; ii) relevant insights for bringing this answer...

  12. Integrated three-dimensional digital assessment of accuracy of anterior tooth movement using clear aligners

    OpenAIRE

    Zhang, Xiao-Juan; He, Li; Guo, Hong-Ming; Tian, Jie; Bai, Yu-Xing; Li, Song

    2015-01-01

    Objective To assess the accuracy of anterior tooth movement using clear aligners in integrated three-dimensional digital models. Methods Cone-beam computed tomography was performed before and after treatment with clear aligners in 32 patients. Plaster casts were laser-scanned for virtual setup and aligner fabrication. Differences in predicted and achieved root and crown positions of anterior teeth were compared on superimposed maxillofacial digital images and virtual models and analyzed by St...

  13. High-damage-threshold static laser beam shaping using optically patterned liquid-crystal devices.

    Science.gov (United States)

    Dorrer, C; Wei, S K-H; Leung, P; Vargas, M; Wegman, K; Boulé, J; Zhao, Z; Marshall, K L; Chen, S H

    2011-10-15

    Beam shaping of coherent laser beams is demonstrated using liquid crystal (LC) cells with optically patterned pixels. The twist angle of a nematic LC is locally set to either 0 or 90° by an alignment layer prepared via exposure to polarized UV light. The two distinct pixel types induce either no polarization rotation or a 90° polarization rotation, respectively, on a linearly polarized optical field. An LC device placed between polarizers functions as a binary transmission beam shaper with a highly improved damage threshold compared to metal beam shapers. Using a coumarin-based photoalignment layer, various devices have been fabricated and tested, with a measured single-shot nanosecond damage threshold higher than 30 J/cm2.

  14. Structure based alignment and clustering of proteins (STRALCP)

    Science.gov (United States)

    Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

    2013-06-18

    Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

  15. Optical beam classification using deep learning: a comparison with rule- and feature-based classification

    Science.gov (United States)

    Alom, Md. Zahangir; Awwal, Abdul A. S.; Lowe-Webb, Roger; Taha, Tarek M.

    2017-08-01

    Deep-learning methods are gaining popularity because of their state-of-the-art performance in image classification tasks. In this paper, we explore classification of laser-beam images from the National Ignition Facility (NIF) using a novel deeplearning approach. NIF is the world's largest, most energetic laser. It has nearly 40,000 optics that precisely guide, reflect, amplify, and focus 192 laser beams onto a fusion target. NIF utilizes four petawatt lasers called the Advanced Radiographic Capability (ARC) to produce backlighting X-ray illumination to capture implosion dynamics of NIF experiments with picosecond temporal resolution. In the current operational configuration, four independent short-pulse ARC beams are created and combined in a split-beam configuration in each of two NIF apertures at the entry of the pre-amplifier. The subaperture beams then propagate through the NIF beampath up to the ARC compressor. Each ARC beamlet is separately compressed with a dedicated set of four gratings and recombined as sub-apertures for transport to the parabola vessel, where the beams are focused using parabolic mirrors and pointed to the target. Small angular errors in the compressor gratings can cause the sub-aperture beams to diverge from one another and prevent accurate alignment through the transport section between the compressor and parabolic mirrors. This is an off-normal condition that must be detected and corrected. The goal of the off-normal check is to determine whether the ARC beamlets are sufficiently overlapped into a merged single spot or diverged into two distinct spots. Thus, the objective of the current work is three-fold: developing a simple algorithm to perform off-normal classification, exploring the use of Convolutional Neural Network (CNN) for the same task, and understanding the inter-relationship of the two approaches. The CNN recognition results are compared with other machine-learning approaches, such as Deep Neural Network (DNN) and Support

  16. Alignment of the TFTR bumper limiter

    International Nuclear Information System (INIS)

    Barnes, G.W.; Owens, D.K.; Loesser, G.D.; Ulrickson, M.

    1989-01-01

    The TFTR Bumper Limiter (BL) is an axisymmetric toroidal limiter mounted on the inner wall of the vacuum vessel. It subtends 120 degree poloidally and has a surface area of 22 m 2 . The plasma facing surface consists of 1,000 kg of graphite tiles mounted on watercooled Inconel backing plates. During the initial installation in the Spring of 1985, the limiter surface was aligned to the toroidal magnetic field by mechanical and magnetic measurements to an estimated accuracy of ±2 mm. During subsequent operation, especially in the 1988 run period in which 30 MW of Neutral Beam Injection routinely occurred, several tiles at points on the limiter which protruded slightly into the plasma were severely damaged. The damage, cracked and spalled tiles, is believed to be initiated by high energy disruptions and aggravated by normal high power operation. The damage pattern and temperature rise during normal operation are consistent with this interpretation. A vacuum vessel opening to replace the damaged tiles and realign the limiter was required. The bumper limiter was reshaped to be circular to ±0.5 mm at the midplane by means of mechanical measurements in order to better distribute the heat loads and eliminate hot spots. The ±0.5 mm accuracy is determined by the variation in individual tile thickness which is ±0.5 mm. This paper describes the methods used to mechanically align the limiter and presents evidence based on machine operation with plasma that the limiter is reasonably well aligned with the toroidal field. Future work dealing with the alignment of the total limiter to the toroidal field using mechanical and magnetic measurements and the replacement of a subset of the carbon tiles with carbon-carbon composite material is also discussed. 7 refs., 4 figs

  17. Stability study of the higher order mode beam position monitors at the Accelerating cavities at FLASH

    CERN Document Server

    Shi, L; Jones., R M

    2014-01-01

    erating cavities at FLASH linac, DESY, are equipped with electronics for beam position monitoring, which are based on HOM signals from special couplers. These monitors provide the beam position without additional vacuum components and at low cost. Moreover, they can be used to align the beam in the cavities to reduce the HOM effects on the beam. However, the HOMBPM (Higher Order Mode based Beam Position Monitor) shows an instability problem over time. In this paper, we will present the status of studies on this issue. Several methods are utilized to calibrate the HOMBPMs. These methods include DLR (Direct Linear Regression), and SVD (Singular Value Decomposition). We found that SVD generally is more suitable for HOMBPM calibration. We focus on the HOMBPMs at 1.3 GHz cavities. Techniques developed here are applicable to 3.9 ...

  18. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    Since December, the muon alignment community has focused on analyzing the data recorded so far in order to produce new DT and CSC Alignment Records for the second reprocessing of CRAFT data. Two independent algorithms were developed which align the DT chambers using global tracks, thus providing, for the first time, a relative alignment of the barrel with respect to the tracker. These results are an important ingredient for the second CRAFT reprocessing and allow, for example, a more detailed study of any possible mis-modelling of the magnetic field in the muon spectrometer. Both algorithms are constructed in such a way that the resulting alignment constants are not affected, to first order, by any such mis-modelling. The CSC chambers have not yet been included in this global track-based alignment due to a lack of statistics, since only a few cosmics go through the tracker and the CSCs. A strategy exists to align the CSCs using the barrel as a reference until collision tracks become available. Aligning the ...

  19. High-Energy Beam Transport system

    International Nuclear Information System (INIS)

    Melson, K.E.; Farrell, J.A.; Liska, D.J.

    1979-01-01

    The High-Energy Beam Transport (HEBT) system for the Fusion Materials Irradiation Test (FMIT) Facility is to be installed at the Hanford Engineering Development Laboratory (HEDL) at Richland, Washington. The linear accelerator must transport a large emittance, high-current, high-power, continuous-duty deuteron beam with a large energy spread either to a lithium target or a beam stop. A periodic quadrupole and bending-magnet system provides the beam transport and focusing on target with small beam aberrations. A special rf cavity distributes the energy in the beam so that the Bragg Peak is distributed within the lithium target. Operation of the rf control system, the Energy Dispersion Cavity (EDC), and the beam transport magnets is tested on the beam stop during accelerator turn-on. Characterizing the beam will require extensions of beam diagnostic techniques and noninterceptive sensors. Provisions are being made in the facility for suspending the transport system from overhead supports using a cluster system to simplify maintenance and alignment techniques

  20. HIE-ISOLDE HEBT beam optics studies with MADX

    CERN Document Server

    Parfenova, A; Fraser, M A; Goddard, B; Martino, M; Voulot, D; CERN. Geneva. ATS Department

    2014-01-01

    Beam design and beam optics studies for the HIE-ISOLDE transfer lines [1, 2] have been carried out in MADX [3], and benchmarked against TRACE 3-D results [4, 5, 6]. Magnet field errors and alignment imperfections leading to deviations from design parameters have been treated explicitly, and the sensitivity of the machine lattice to different individual error sources was studied. Errors of different types have been considered and their effects on the machine have been corrected [7]. As a result, the tolerances for the various error contributions have been specified for the different equipment systems. The design choices for the expected magnet field and power supply quality, alignment tolerances, instrument resolution and physical apertures were validated. The baseline layout contains three identical branch lines as presented in Fig. 1. The detailed beam optics study with MADX was carried out for the beam line XT01. The large energy range from 0.3 to 10 MeV/u requested for the experiments sets a number of chal...

  1. Phantom and Clinical Study of Differences in Cone Beam Computed Tomographic Registration When Aligned to Maximum and Average Intensity Projection

    Energy Technology Data Exchange (ETDEWEB)

    Shirai, Kiyonori [Department of Radiation Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka (Japan); Nishiyama, Kinji, E-mail: sirai-ki@mc.pref.osaka.jp [Department of Radiation Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka (Japan); Katsuda, Toshizo [Department of Radiology, National Cerebral and Cardiovascular Center, Osaka (Japan); Teshima, Teruki; Ueda, Yoshihiro; Miyazaki, Masayoshi; Tsujii, Katsutomo [Department of Radiation Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka (Japan)

    2014-01-01

    Purpose: To determine whether maximum or average intensity projection (MIP or AIP, respectively) reconstructed from 4-dimensional computed tomography (4DCT) is preferred for alignment to cone beam CT (CBCT) images in lung stereotactic body radiation therapy. Methods and Materials: Stationary CT and 4DCT images were acquired with a target phantom at the center of motion and moving along the superior–inferior (SI) direction, respectively. Motion profiles were asymmetrical waveforms with amplitudes of 10, 15, and 20 mm and a 4-second cycle. Stationary CBCT and dynamic CBCT images were acquired in the same manner as stationary CT and 4DCT images. Stationary CBCT was aligned to stationary CT, and the couch position was used as the baseline. Dynamic CBCT was aligned to the MIP and AIP of corresponding amplitudes. Registration error was defined as the SI deviation of the couch position from the baseline. In 16 patients with isolated lung lesions, free-breathing CBCT (FBCBCT) was registered to AIP and MIP (64 sessions in total), and the difference in couch shifts was calculated. Results: In the phantom study, registration errors were within 0.1 mm for AIP and 1.5 to 1.8 mm toward the inferior direction for MIP. In the patient study, the difference in the couch shifts (mean, range) was insignificant in the right-left (0.0 mm, ≤1.0 mm) and anterior–posterior (0.0 mm, ≤2.1 mm) directions. In the SI direction, however, the couch position significantly shifted in the inferior direction after MIP registration compared with after AIP registration (mean, −0.6 mm; ranging 1.7 mm to the superior side and 3.5 mm to the inferior side, P=.02). Conclusions: AIP is recommended as the reference image for registration to FBCBCT when target alignment is performed in the presence of asymmetrical respiratory motion, whereas MIP causes systematic target positioning error.

  2. Phantom and Clinical Study of Differences in Cone Beam Computed Tomographic Registration When Aligned to Maximum and Average Intensity Projection

    International Nuclear Information System (INIS)

    Shirai, Kiyonori; Nishiyama, Kinji; Katsuda, Toshizo; Teshima, Teruki; Ueda, Yoshihiro; Miyazaki, Masayoshi; Tsujii, Katsutomo

    2014-01-01

    Purpose: To determine whether maximum or average intensity projection (MIP or AIP, respectively) reconstructed from 4-dimensional computed tomography (4DCT) is preferred for alignment to cone beam CT (CBCT) images in lung stereotactic body radiation therapy. Methods and Materials: Stationary CT and 4DCT images were acquired with a target phantom at the center of motion and moving along the superior–inferior (SI) direction, respectively. Motion profiles were asymmetrical waveforms with amplitudes of 10, 15, and 20 mm and a 4-second cycle. Stationary CBCT and dynamic CBCT images were acquired in the same manner as stationary CT and 4DCT images. Stationary CBCT was aligned to stationary CT, and the couch position was used as the baseline. Dynamic CBCT was aligned to the MIP and AIP of corresponding amplitudes. Registration error was defined as the SI deviation of the couch position from the baseline. In 16 patients with isolated lung lesions, free-breathing CBCT (FBCBCT) was registered to AIP and MIP (64 sessions in total), and the difference in couch shifts was calculated. Results: In the phantom study, registration errors were within 0.1 mm for AIP and 1.5 to 1.8 mm toward the inferior direction for MIP. In the patient study, the difference in the couch shifts (mean, range) was insignificant in the right-left (0.0 mm, ≤1.0 mm) and anterior–posterior (0.0 mm, ≤2.1 mm) directions. In the SI direction, however, the couch position significantly shifted in the inferior direction after MIP registration compared with after AIP registration (mean, −0.6 mm; ranging 1.7 mm to the superior side and 3.5 mm to the inferior side, P=.02). Conclusions: AIP is recommended as the reference image for registration to FBCBCT when target alignment is performed in the presence of asymmetrical respiratory motion, whereas MIP causes systematic target positioning error

  3. First experiences of beam presence detection based on dedicated beam position monitors

    International Nuclear Information System (INIS)

    Jalal, A.; Gabourin, S.; Gasior, M.; Todd, B.

    2012-01-01

    High intensity particle beam injection into the LHC is only permitted when a low intensity pilot beam is already circulating in the LHC. This requirement addresses some of the risks associated with high intensity injection, and is enforced by a so-called Beam Presence Flag (BPF) system which is part of the interlock chain between the LHC and its injector complex. For the 2010 LHC run, the detection of the presence of this pilot beam was implemented using the LHC Fast Beam Current Transformer (FBCT) system. However, the primary function of the FBCTs, that is reliable measurement of beam currents, did not allow the BPF system to satisfy all quality requirements of the LHC Machine Protection System (MPS). Safety requirements associated with high intensity injections triggered the development of a dedicated system, based on Beam Position Monitors (BPM). This system was meant to work first in parallel with the FBCT BPF system and eventually replace it. At the end of 2010 and in 2011, this new BPF implementation based on BPMs was designed, built, tested and deployed. This paper reviews both the FBCT and BPM implementation of the BPF system, outlining the changes during the transition period. The paper briefly describes the testing methods, focuses on the results obtained from the tests performed during the end of 2010 LHC run and shows the changes made for the BPM BPF system deployment in LHC in 2011. Whilst the system has been proved to work with a threshold of 6*10 8 charges, it has been implemented with a threshold of 2*10 9 charges to protect the LHC. (authors)

  4. Can a semi-automated surface matching and principal axis-based algorithm accurately quantify femoral shaft fracture alignment in six degrees of freedom?

    Science.gov (United States)

    Crookshank, Meghan C; Beek, Maarten; Singh, Devin; Schemitsch, Emil H; Whyne, Cari M

    2013-07-01

    Accurate alignment of femoral shaft fractures treated with intramedullary nailing remains a challenge for orthopaedic surgeons. The aim of this study is to develop and validate a cone-beam CT-based, semi-automated algorithm to quantify the malalignment in six degrees of freedom (6DOF) using a surface matching and principal axes-based approach. Complex comminuted diaphyseal fractures were created in nine cadaveric femora and cone-beam CT images were acquired (27 cases total). Scans were cropped and segmented using intensity-based thresholding, producing superior, inferior and comminution volumes. Cylinders were fit to estimate the long axes of the superior and inferior fragments. The angle and distance between the two cylindrical axes were calculated to determine flexion/extension and varus/valgus angulation and medial/lateral and anterior/posterior translations, respectively. Both surfaces were unwrapped about the cylindrical axes. Three methods of matching the unwrapped surface for determination of periaxial rotation were compared based on minimizing the distance between features. The calculated corrections were compared to the input malalignment conditions. All 6DOF were calculated to within current clinical tolerances for all but two cases. This algorithm yielded accurate quantification of malalignment of femoral shaft fractures for fracture gaps up to 60 mm, based on a single CBCT image of the fractured limb. Copyright © 2012 IPEM. Published by Elsevier Ltd. All rights reserved.

  5. Remote sensing of local structure of the quasi-perpendicular Earth's bow shock by using field-aligned beams

    Directory of Open Access Journals (Sweden)

    B. Miao

    2009-03-01

    Full Text Available Field-aligned ion beams (FABs originate at the quasi-perpendicular Earth's bow shock and constitute an important ion population in the foreshock region. The bulk velocity of these FABs depends significantly on the shock normal angle, which is the angle between shock normal and upstream interplanetary magnetic field (IMF. This dependency may therefore be taken as an indicator of the local structure of the shock. Applying the direct reflection model to Cluster measurements, we have developed a method that uses proton FABs in the foreshock region for remote sensing of the local shock structure. The comparison of the model results with the multi-spacecraft observations of FAB events shows very good agreement in terms of wave amplitude and frequency of surface waves at the shock front.

  6. Graphene as transmissive electrodes and aligning layers for liquid-crystal-based electro-optic devices.

    Science.gov (United States)

    Basu, Rajratan; Shalov, Samuel A

    2017-07-01

    In a conventional liquid crystal (LC) cell, polyimide layers are used to align the LC homogeneously in the cell, and transmissive indium tin oxide (ITO) electrodes are used to apply the electric field to reorient the LC along the field. It is experimentally presented here that monolayer graphene films on the two glass substrates can function concurrently as the LC aligning layers and the transparent electrodes to fabricate an LC cell, without using the conventional polyimide and ITO substrates. This replacement can effectively decrease the thickness of all the alignment layers and electrodes from about 100 nm to less than 1 nm. The interaction between LC and graphene through π-π electron stacking imposes a planar alignment on the LC in the graphene-based cell-which is verified using a crossed polarized microscope. The graphene-based LC cell exhibits an excellent nematic director reorientation process from planar to homeotropic configuration through the application of an electric field-which is probed by dielectric and electro-optic measurements. Finally, it is shown that the electro-optic switching is significantly faster in the graphene-based LC cell than in a conventional ITO-polyimide LC cell.

  7. Arc-based smoothing of ion beam intensity on targets

    International Nuclear Information System (INIS)

    Friedman, Alex

    2012-01-01

    By manipulating a set of ion beams upstream of a target, it is possible to arrange for a smoother deposition pattern, so as to achieve more uniform illumination of the target. A uniform energy deposition pattern is important for applications including ion-beam-driven high energy density physics and heavy-ion beam-driven inertial fusion energy (“heavy-ion fusion”). Here, we consider an approach to such smoothing that is based on rapidly “wobbling” each of the beams back and forth along a short arc-shaped path, via oscillating fields applied upstream of the final pulse compression. In this technique, uniformity is achieved in the time-averaged sense; this is sufficient provided the beam oscillation timescale is short relative to the hydrodynamic timescale of the target implosion. This work builds on two earlier concepts: elliptical beams applied to a distributed-radiator target [D. A. Callahan and M. Tabak, Phys. Plasmas 7, 2083 (2000)] and beams that are wobbled so as to trace a number of full rotations around a circular or elliptical path [R. C. Arnold et al., Nucl. Instrum. Methods 199, 557 (1982)]. Here, we describe the arc-based smoothing approach and compare it to results obtainable using an elliptical-beam prescription. In particular, we assess the potential of these approaches for minimization of azimuthal asymmetry, for the case of a ring of beams arranged on a cone. It is found that, for small numbers of beams on the ring, the arc-based smoothing approach offers superior uniformity. In contrast with the full-rotation approach, arc-based smoothing remains usable when the geometry precludes wobbling the beams around a full circle, e.g., for the X-target [E. Henestroza, B. G. Logan, and L. J. Perkins, Phys. Plasmas 18, 032702 (2011)] and some classes of distributed-radiator targets.

  8. Slit disk for modified faraday cup diagnostic for determining power density of electron and ion beams

    Science.gov (United States)

    Teruya, Alan T [Livermore, CA; Elmer,; John, W [Danville, CA; Palmer, Todd A [State College, PA

    2011-03-08

    A diagnostic system for characterization of an electron beam or an ion beam includes an electrical conducting disk of refractory material having a circumference, a center, and a Faraday cup assembly positioned to receive the electron beam or ion beam. At least one slit in the disk provides diagnostic characterization of the electron beam or ion beam. The at least one slit is located between the circumference and the center of the disk and includes a radial portion that is in radial alignment with the center and a portion that deviates from radial alignment with the center. The electron beam or ion beam is directed onto the disk and translated to the at least one slit wherein the electron beam or ion beam enters the at least one slit for providing diagnostic characterization of the electron beam or ion beam.

  9. Automatic laser beam position control on the Isolde-Rilis experiment

    CERN Document Server

    Grancharova, D; Fedosseev, V; Suberlucq, Guy; CERN. Geneva. AB Department

    2003-01-01

    The On-Line Isotope Mass Separator ISOLDE at CERN is a facility for production of radioactive ion beams by the interaction of proton beams with a thick target. One of the most widely used types of ion source at ISOLDE is a chemically selective laser ion source based on the method of laser ionization of atoms in a hot cavity - RILIS (Resonance Ionization Laser Ion Source). The optical set-up of RILIS includes three copper vapour lasers, a set of dye lasers and frequency multiplication crystals giving up to three different beams of tuneable wavelengths. This paper will focus on the transport of the laser beams to the targets at distances of 18 m and 23 m, the development of the acquisition of their position and finally the automatic control of optics for an accurate alignment.

  10. Plasma Channel Diagnostic Based on Laser Centroid Oscillations

    International Nuclear Information System (INIS)

    Gonsalves, Anthony; Nakamura, Kei; Lin, Chen; Osterhoff, Jens; Shiraishi, Satomi; Schroeder, Carl; Geddes, Cameron; Toth, Csaba; Esarey, Eric; Leemans, Wim

    2010-01-01

    A technique has been developed for measuring the properties of discharge-based plasma channels by monitoring the centroid location of a laser beam exiting the channel as a function of input alignment offset between the laser and the channel. The centroid position of low-intensity ( 14 Wcm -2 ) laser pulses focused at the input of a hydrogen-filled capillary discharge waveguide was scanned and the exit positions recorded to determine the channel shape and depth with an accuracy of a few %. In addition, accurate alignment of the laser beam through the plasma channel can be provided by minimizing laser centroid motion at the channel exit as the channel depth is scanned either by scanning the plasma density or the discharge timing. The improvement in alignment accuracy provided by this technique will be crucial for minimizing electron beam pointing errors in laser plasma accelerators.

  11. A prototype distributed object-oriented architecture for image-based automatic laser alignment

    International Nuclear Information System (INIS)

    Stout, E.A.; Kamm, V.J.M.; Spann, J.M.; Van Arsdall, P.J.

    1996-01-01

    Designing a computer control system for the National Ignition Facility (NIF) is a complex undertaking because of the system's large size and its distributed nature. The controls team is addressing that complexity by adopting the object-oriented programming paradigm, designing reusable software frameworks, and using the Common Object Request Broker Architecture (CORBA) for distribution. A prototype system for image-based automatic laser alignment has been developed to evaluate and gain experience with CORBA and OOP in a small distributed system. The prototype is also important in evaluating alignment concepts, image processing techniques, speed and accuracy of automatic alignment objectives for the NIF, and control hardware for aligment devices. The prototype system has met its inital objectives and provides a basis for continued development

  12. Design development of bellows for the DNB beam source

    International Nuclear Information System (INIS)

    Singh, Dhananjay Kumar; Venkata Nagaraju, M.; Joshi, Jaydeep; Patel, Hitesh; Yadav, Ashish; Pillai, Suraj; Singh, Mahendrajit; Bandyopadhyay, Mainak; Chakraborty, A.K.; Sharma, Dheeraj

    2017-01-01

    Establishing a procedure and mechanism for alignment of Ion beams in Neutral Beam (NB) sources for ITER like systems are complex due to large traversal distances (∼21 m) and restricted use of flexible elements into the system. For the beam source of DNB, movement requirements for beam alignment are the combination of tilting (±9mrad), rotation (±9mrad) and translation (±25mm). The present work describes the design development of a system composed of three single ply ‘Gimbal’ type bellow system, placed in series, in L-shaped hydraulic lines (size DN50, DN20 and DN15). The paper shall detail out the generation of initial requirements, transformation of movements at bellow locations, selection of bellows/combination of bellows, minimizing the induced movements by optimization of bellows location, estimation of movements through CEASAR II and the design compliance with respect to EJMA code

  13. Performance analysis for W-band antenna alignment using accurate mechanical beam steering

    DEFF Research Database (Denmark)

    Morales Vicente, Alvaro; Rodríguez Páez, Juan Sebastián; Gallardo, Omar

    2017-01-01

    This article presents a study of antenna alignment impact on bit error rate for a wireless link between two directive W-band horn antennas where one of them is mechanically steered by a Stewart platform. Such a technique is applied to find the optimal alignment between transmitter and receiver...... with an accuracy of 18 both in azimuth and elevation angles. The maximum degree of misalignment which can be tolerated is also reported for different values of optical power in the generation of W-band signals by photonic up-conversion. (C) 2017 Wiley Periodicals, Inc....

  14. Principles of alignment of multi-beam lasers for thermonuclear purposes

    International Nuclear Information System (INIS)

    Basov, N.G.; Belyan, B.F.; Zhilkin, G.P.

    1978-01-01

    The problems of methods and equipment for power pulse laser adjustment, as well as the problem of adjustment automatization are considered. The adjustment of a power 12-channel ''Dolphin'' laser installation on the neodymium glass is taken as a concrete object. The adjustment objects are optical track of laser installation, guidance and laser radiation focusing system on the target, the system of target delivery to the focal volume, control system of element optical quality of laser installation and laser beams, as well as target radiation conditions in vacuum chamber. List of requirements of adjustment beams, possible sources of adjustment beams, equipment complex and laser installation adjustment methods are considered. The principles and scheme solutions of automatic adjustment of optical elements are discussed and the description of working samples of automatic joints is given. The problem of working laser beams imitation by adjusting and the possibilities of automatization of laser radiation space-angle characteristics control are considered. The control scheme of adjustment processes with computer as well as the switching on of adjustment automatic subsystem in the general automatization scheme of the ''Dolphin'' installation are discussed

  15. A multi-satellite study of accelerated ionospheric ion beams above the polar cap

    Directory of Open Access Journals (Sweden)

    R. Maggiolo

    2006-07-01

    Full Text Available This paper presents a study of nearly field-aligned outflowing ion beams observed on the Cluster satellites over the polar cap. Data are taken at geocentric radial distances of the order of 5–9 RE. The distinction is made between ion beams originating from the polar cusp/cleft and beams accelerated almost along the magnetic field line passing by the spacecraft. Polar cusp beams are characterized by nearly field-aligned proton and oxygen ions with an energy ratio EO+ / EH+, of the order of 3 to 4, due to the ion energy repartition inside the source and to the latitudinal extension of the source. Rapid variations in the outflowing ion energy are linked with pulses/modifications of the convection electric field. Cluster data allow one to show that these perturbations of the convection velocity and the associated ion structures propagate at the convection velocity. In contrast, polar cap local ion beams are characterized by field-aligned proton and oxygen ions with similar energies. These beams show the typical inverted V structures usually observed in the auroral zone and are associated with a quasi-static converging electric field indicative of a field-aligned electric field. The field-aligned potential drop fits well the ion energy profile. The simultaneous observation of precipitating electrons and upflowing ions of similar energies at the Cluster orbit indicates that the spacecraft are crossing the mid-altitude part of the acceleration region. In the polar cap, the parallel electric field can thus extend to altitudes higher than 5 Earth radii. A detailed analysis of the distribution functions shows that the ions are heated during their parallel acceleration and that energy is exchanged between H+ and O+. Furthermore, intense electrostatic waves are observed simultaneously. These observations could be due to an ion-ion two-stream instability.

  16. Investigation of beam effect on porous silicon

    Energy Technology Data Exchange (ETDEWEB)

    Kotai, E. E-mail: kotai@rmki.kfki.hu; Paszti, F.; Szilagyi, E

    2000-03-01

    When performing Rutherford Backscattering Spectroscopy (RBS) measurements combined with channeling on 'columnar' porous silicon (PS) samples with beam aligned to the direction of the pores, a strong beam effect was observed. The minimum yield as a function of the beam dose for different porous samples was compared with the yield measured on single crystal silicon. It was demonstrated that the beam effect strongly depends on the porosity of the sample. Bombardment in the random direction caused about 10% higher change in the minimum yield than in the channel direction.

  17. Investigation of beam effect on porous silicon

    International Nuclear Information System (INIS)

    Kotai, E.; Paszti, F.; Szilagyi, E.

    2000-01-01

    When performing Rutherford Backscattering Spectroscopy (RBS) measurements combined with channeling on 'columnar' porous silicon (PS) samples with beam aligned to the direction of the pores, a strong beam effect was observed. The minimum yield as a function of the beam dose for different porous samples was compared with the yield measured on single crystal silicon. It was demonstrated that the beam effect strongly depends on the porosity of the sample. Bombardment in the random direction caused about 10% higher change in the minimum yield than in the channel direction

  18. Single-particle beam dynamics in Boomerang

    International Nuclear Information System (INIS)

    Jackson, Alan; Nishimura, Hiroshi

    2003-01-01

    We describe simulations of the beam dynamics in the storage ring (Boomerang), a 3-GeV third-generation light source being designed for the Australian Synchrotron Project[1]. The simulations were performed with the code Goemon[2]. They form the basis for design specifications for storage ring components (apertures, alignment tolerances, magnet quality, etc.), and for determining performance characteristics such as coupling and beam lifetime

  19. The CMS Silicon Tracker Alignment

    CERN Document Server

    Castello, R

    2008-01-01

    The alignment of the Strip and Pixel Tracker of the Compact Muon Solenoid experiment, with its large number of independent silicon sensors and its excellent spatial resolution, is a complex and challenging task. Besides high precision mounting, survey measurements and the Laser Alignment System, track-based alignment is needed to reach the envisaged precision.\\\\ Three different algorithms for track-based alignment were successfully tested on a sample of cosmic-ray data collected at the Tracker Integration Facility, where 15\\% of the Tracker was tested. These results, together with those coming from the CMS global run, will provide the basis for the full-scale alignment of the Tracker, which will be carried out with the first \\emph{p-p} collisions.

  20. Synergistic Instance-Level Subspace Alignment for Fine-Grained Sketch-Based Image Retrieval.

    Science.gov (United States)

    Li, Ke; Pang, Kaiyue; Song, Yi-Zhe; Hospedales, Timothy M; Xiang, Tao; Zhang, Honggang

    2017-08-25

    We study the problem of fine-grained sketch-based image retrieval. By performing instance-level (rather than category-level) retrieval, it embodies a timely and practical application, particularly with the ubiquitous availability of touchscreens. Three factors contribute to the challenging nature of the problem: (i) free-hand sketches are inherently abstract and iconic, making visual comparisons with photos difficult, (ii) sketches and photos are in two different visual domains, i.e. black and white lines vs. color pixels, and (iii) fine-grained distinctions are especially challenging when executed across domain and abstraction-level. To address these challenges, we propose to bridge the image-sketch gap both at the high-level via parts and attributes, as well as at the low-level, via introducing a new domain alignment method. More specifically, (i) we contribute a dataset with 304 photos and 912 sketches, where each sketch and image is annotated with its semantic parts and associated part-level attributes. With the help of this dataset, we investigate (ii) how strongly-supervised deformable part-based models can be learned that subsequently enable automatic detection of part-level attributes, and provide pose-aligned sketch-image comparisons. To reduce the sketch-image gap when comparing low-level features, we also (iii) propose a novel method for instance-level domain-alignment, that exploits both subspace and instance-level cues to better align the domains. Finally (iv) these are combined in a matching framework integrating aligned low-level features, mid-level geometric structure and high-level semantic attributes. Extensive experiments conducted on our new dataset demonstrate effectiveness of the proposed method.

  1. Pairwise Sequence Alignment Library

    Energy Technology Data Exchange (ETDEWEB)

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  2. Performance based design of reinforced concrete beams under impact

    Directory of Open Access Journals (Sweden)

    S. Tachibana

    2010-06-01

    Full Text Available The purpose of this research is to collect fundamental data and to establish a performance-based design method for reinforced concrete beams under perpendicular impact load.

    Series of low speed impact experiments using reinforced concrete beams were performed varying span length, cross section and main reinforcement.

    The experimental results are evaluated focusing on the impact load characteristics and the impact behaviours of reinforced concrete beams. Various characteristic values and their relationships are investigated such as the collision energy, the impact force duration, the energy absorbed by the beams and the beam response values. Also the bending performance of the reinforced concrete beams against perpendicular impact is evaluated.

    An equation is proposed to estimate the maximum displacement of the beam based on the collision energy and the static ultimate bending strength. The validity of the proposed equation is confirmed by comparison with experimental results obtained by other researchers as well as numerical results obtained by FEM simulations. The proposed equation allows for a performance based design of the structure accounting for the actual deformation due to the expected impact action.

  3. Developmental long trace profiler using optimally aligned mirror based pentaprism

    International Nuclear Information System (INIS)

    Barber, Samuel K.; Morrison, Gregory Y.; Yashchuk, Valeriy V.; Gubarev, Mikhail V.; Geckeler, Ralf D.; Buchheim, Jana; Siewert, Frank; Zeschke, Thomas

    2010-01-01

    A low-budget surface slope measuring instrument, the Developmental Long Trace Profiler (DLTP), was recently brought into operation at the Advanced Light Source Optical Metrology Laboratory (Nucl. Instr. and Meth. A 616, 212-223 (2010)). The instrument is based on a precisely calibrated autocollimator and a movable pentaprism. The capability of the DLTP to achieve sub-microradian surface slope metrology has been verified via cross-comparison measurements with other high-performance slope measuring instruments when measuring the same high-quality test optics. In the present work, a further improvement of the DLTP is achieved by replacing the existing bulk pentaprism with a specially designed mirror based pentaprism. A mirror based pentaprism offers the possibility to eliminate systematic errors introduced by inhomogeneity of the optical material and fabrication imperfections of a bulk pentaprism. We provide the details of the mirror based pentaprism design and describe an original experimental procedure for precision mutual alignment of the mirrors. The algorithm of the alignment procedure and its efficiency are verified with rigorous ray tracing simulations. Results of measurements of a spherically curved test mirror and a flat test mirror using the original bulk pentaprism are compared with measurements using the new mirror based pentaprism, demonstrating the improved performance.

  4. Self-optimizing approach for automated laser resonator alignment

    Science.gov (United States)

    Brecher, C.; Schmitt, R.; Loosen, P.; Guerrero, V.; Pyschny, N.; Pavim, A.; Gatej, A.

    2012-02-01

    Nowadays, the assembly of laser systems is dominated by manual operations, involving elaborate alignment by means of adjustable mountings. From a competition perspective, the most challenging problem in laser source manufacturing is price pressure, a result of cost competition exerted mainly from Asia. From an economical point of view, an automated assembly of laser systems defines a better approach to produce more reliable units at lower cost. However, the step from today's manual solutions towards an automated assembly requires parallel developments regarding product design, automation equipment and assembly processes. This paper introduces briefly the idea of self-optimizing technical systems as a new approach towards highly flexible automation. Technically, the work focuses on the precision assembly of laser resonators, which is one of the final and most crucial assembly steps in terms of beam quality and laser power. The paper presents a new design approach for miniaturized laser systems and new automation concepts for a robot-based precision assembly, as well as passive and active alignment methods, which are based on a self-optimizing approach. Very promising results have already been achieved, considerably reducing the duration and complexity of the laser resonator assembly. These results as well as future development perspectives are discussed.

  5. TotalReCaller: improved accuracy and performance via integrated alignment and base-calling.

    Science.gov (United States)

    Menges, Fabian; Narzisi, Giuseppe; Mishra, Bud

    2011-09-01

    Currently, re-sequencing approaches use multiple modules serially to interpret raw sequencing data from next-generation sequencing platforms, while remaining oblivious to the genomic information until the final alignment step. Such approaches fail to exploit the full information from both raw sequencing data and the reference genome that can yield better quality sequence reads, SNP-calls, variant detection, as well as an alignment at the best possible location in the reference genome. Thus, there is a need for novel reference-guided bioinformatics algorithms for interpreting analog signals representing sequences of the bases ({A, C, G, T}), while simultaneously aligning possible sequence reads to a source reference genome whenever available. Here, we propose a new base-calling algorithm, TotalReCaller, to achieve improved performance. A linear error model for the raw intensity data and Burrows-Wheeler transform (BWT) based alignment are combined utilizing a Bayesian score function, which is then globally optimized over all possible genomic locations using an efficient branch-and-bound approach. The algorithm has been implemented in soft- and hardware [field-programmable gate array (FPGA)] to achieve real-time performance. Empirical results on real high-throughput Illumina data were used to evaluate TotalReCaller's performance relative to its peers-Bustard, BayesCall, Ibis and Rolexa-based on several criteria, particularly those important in clinical and scientific applications. Namely, it was evaluated for (i) its base-calling speed and throughput, (ii) its read accuracy and (iii) its specificity and sensitivity in variant calling. A software implementation of TotalReCaller as well as additional information, is available at: http://bioinformatics.nyu.edu/wordpress/projects/totalrecaller/ fabian.menges@nyu.edu.

  6. Simulation of beamline alignment operations

    International Nuclear Information System (INIS)

    Annese, C; Miller, M G.

    1999-01-01

    The CORBA-based Simulator was a Laboratory Directed Research and Development (LDRD) project that applied simulation techniques to explore critical questions about distributed control systems. The simulator project used a three-prong approach that studied object-oriented distribution tools, computer network modeling, and simulation of key control system scenarios. The National Ignition Facility's (NIF) optical alignment system was modeled to study control system operations. The alignment of NIF's 192 beamlines is a large complex operation involving more than 100 computer systems and 8000 mechanized devices. The alignment process is defined by a detailed set of procedures; however, many of the steps are deterministic. The alignment steps for a poorly aligned component are similar to that of a nearly aligned component; however, additional operations/iterations are required to complete the process. Thus, the same alignment operations will require variable amounts of time to perform depending on the current alignment condition as well as other factors. Simulation of the alignment process is necessary to understand beamline alignment time requirements and how shared resources such as the Output Sensor and Target Alignment Sensor effect alignment efficiency. The simulation has provided alignment time estimates and other results based on documented alignment procedures and alignment experience gained in the laboratory. Computer communication time, mechanical hardware actuation times, image processing algorithm execution times, etc. have been experimentally determined and incorporated into the model. Previous analysis of alignment operations utilized average implementation times for all alignment operations. Resource sharing becomes rather simple to model when only average values are used. The time required to actually implement the many individual alignment operations will be quite dynamic. The simulation model estimates the time to complete an operation using

  7. Alignment Condition-Based Robust Adaptive Iterative Learning Control of Uncertain Robot System

    Directory of Open Access Journals (Sweden)

    Guofeng Tong

    2014-04-01

    Full Text Available This paper proposes an adaptive iterative learning control strategy integrated with saturation-based robust control for uncertain robot system in presence of modelling uncertainties, unknown parameter, and external disturbance under alignment condition. An important merit is that it achieves adaptive switching of gain matrix both in conventional PD-type feedforward control and robust adaptive control in the iteration domain simultaneously. The analysis of convergence of proposed control law is based on Lyapunov's direct method under alignment initial condition. Simulation results demonstrate the faster learning rate and better robust performance with proposed algorithm by comparing with other existing robust controllers. The actual experiment on three-DOF robot manipulator shows its better practical effectiveness.

  8. Performance of the KTeV high-energy neutral kaon beam at Fermilab

    International Nuclear Information System (INIS)

    Bocean, V.

    1998-01-01

    The performance of the primary and secondary beams for the KTeV experiments E832 and E799-II is reviewed. The beam was commissioned in the summer of 1996 and initially operated for approximately one year. The report includes results on the primary beam, target station including primary beam dump and muon sweeping system, neutral beam collimation system, and alignment

  9. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    S. Szillasi

    2013-01-01

    The CMS detector has been gradually opened and whenever a wheel became exposed the first operation was the removal of the MABs, the sensor structures of the Hardware Barrel Alignment System. By the last days of June all 36 MABs have arrived at the Alignment Lab at the ISR where, as part of the Alignment Upgrade Project, they are refurbished with new Survey target holders. Their electronic checkout is on the way and finally they will be recalibrated. During LS1 the alignment system will be upgraded in order to allow more precise reconstruction of the MB4 chambers in Sector 10 and Sector 4. This requires new sensor components, so called MiniMABs (pictured below), that have already been assembled and calibrated. Image 6: Calibrated MiniMABs are ready for installation For the track-based alignment, the systematic uncertainties of the algorithm are under scrutiny: this study will enable the production of an improved Monte Carlo misalignment scenario and to update alignment position errors eventually, crucial...

  10. Extended particle-based simulation for magnetic-aligned compaction of hard magnetic particles

    Energy Technology Data Exchange (ETDEWEB)

    Soda, Rikio; Takagi, Kenta; Ozaki, Kimihiro, E-mail: r-soda@aist.go.jp

    2015-12-15

    In order to understand the magnetic-aligned compaction process, we develop a three-dimensional (3D) discrete element method for simulating the motion of hard magnetic particles subjected to strong compression and magnetic fields. The proposed simulation model also considers the exact magnetic force involved via the calculation of the magnetic moment. First, to validate the simulation model, single-action compaction in the absence of a magnetic field was calculated. The calculated compaction curves are in good quantitative agreement with experimental ones. Based on this simulation model, the alignment behavior of Nd–Fe–B particles during compression under the application of a static magnetic field. The developed simulation model enables the visualization of particle behavior including the misorientation of the magnetization easy axis, which provided the quantitative relationships between applied pressure and particle misorientation. - Highlights: • A practical 3D DEM simulation technique for magnetic-aligned compaction was developed. • An extended simulation model was introduced for hard magnetic particles. • Magnetic-aligned compaction was simulated using the developed simulation model.

  11. Real-time control and data-acquisition system for high-energy neutral-beam injectors

    International Nuclear Information System (INIS)

    Glad, A.S.; Jacobson, V.

    1981-12-01

    The need for a real-time control system and a data acquisition, processing and archiving system operating in parallel on the same computer became a requirement on General Atomic's Doublet III fusion energy project with the addition of high energy neutral beam injectors. The data acquisition processing and archiving system is driven from external events and is sequenced through each experimental shot utilizing ModComp's intertask message service. This system processes, archives and displays on operator console CRTs all physics diagnostic data related to the neutral beam injectores such as temperature, beam alignment, etc. The real-time control system is data base driven and provides periodic monitoring and control of the numerous dynamic subsystems of the neutral beam injectors such as power supplies, timing, water cooling, etc

  12. Beam delivery system with a non-digitized diffractive beam splitter for laser-drilling of silicon

    Science.gov (United States)

    Amako, J.; Fujii, E.

    2016-02-01

    We report a beam-delivery system consisting of a non-digitized diffractive beam splitter and a Fourier transform lens. The system is applied to the deep-drilling of silicon using a nanosecond pulse laser in the manufacture of inkjet printer heads. In this process, a circularly polarized pulse beam is divided into an array of uniform beams, which are then delivered precisely to the process points. To meet these requirements, the splitter was designed to be polarization-independent with an efficiency>95%. The optical elements were assembled so as to allow the fine tuning of the effective overall focal length by adjusting the wavefront curvature of the beam. Using the system, a beam alignment accuracy ofbeam array and the throughput was substantially improved (10,000 points on a silicon wafer drilled in ~1 min). This beam-delivery scheme works for a variety of laser applications that require parallel processing.

  13. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez and Y. Pakhotin

    2012-01-01

      A new track-based alignment for the DT chambers is ready for deployment: an offline tag has already been produced which will become part of the 52X Global Tag. This alignment was validated within the muon alignment group both at low and high momentum using a W/Z skim sample. It shows an improved mass resolution for pairs of stand-alone muons, improved curvature resolution at high momentum, and improved DT segment extrapolation residuals. The validation workflow for high-momentum muons used to depend solely on the “split cosmics” method, looking at the curvature difference between muon tracks reconstructed in the upper or lower half of CMS. The validation has now been extended to include energetic muons decaying from heavily boosted Zs: the di-muon invariant mass for global and stand-alone muons is reconstructed, and the invariant mass resolution is compared for different alignments. The main areas of development over the next few months will be preparing a new track-based C...

  14. Alignment-Annotator web server: rendering and annotating sequence alignments.

    Science.gov (United States)

    Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

    2014-07-01

    Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Electron Signal Detection for the Beam-Finder Wire of the Linac Coherent Light Source Undulator

    International Nuclear Information System (INIS)

    Wu, Juhao; Emma, P.; Field, R.C.; SLAC

    2006-01-01

    The Linac Coherent Light Source (LCLS) is a SASE x-ray Free-Electron Laser (FEL) based on the final kilometer of the Stanford Linear Accelerator. The tight tolerances for positioning the electron beam close to the undulator axis calls for the introduction of Beam Finder Wire (BFW) device. A BFW device close to the upstream end of the undulator segment and a quadrupole close to the down stream end of the undulator segment will allow a beam-based undulator segment alignment. Based on the scattering of the electrons on the BFW, we can detect the electron signal in the main dump bends after the undulator to find the beam position. We propose to use a threshold Cherenkov counter for this purpose. According to the signal strength at such a Cherenkov counter, we then suggest choice of material and size for such a BFW device in the undulator

  16. NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction

    Directory of Open Access Journals (Sweden)

    Lund Ole

    2009-09-01

    Full Text Available Abstract Background The major histocompatibility complex (MHC molecule plays a central role in controlling the adaptive immune response to infections. MHC class I molecules present peptides derived from intracellular proteins to cytotoxic T cells, whereas MHC class II molecules stimulate cellular and humoral immunity through presentation of extracellularly derived peptides to helper T cells. Identification of which peptides will bind a given MHC molecule is thus of great importance for the understanding of host-pathogen interactions, and large efforts have been placed in developing algorithms capable of predicting this binding event. Results Here, we present a novel artificial neural network-based method, NN-align that allows for simultaneous identification of the MHC class II binding core and binding affinity. NN-align is trained using a novel training algorithm that allows for correction of bias in the training data due to redundant binding core representation. Incorporation of information about the residues flanking the peptide-binding core is shown to significantly improve the prediction accuracy. The method is evaluated on a large-scale benchmark consisting of six independent data sets covering 14 human MHC class II alleles, and is demonstrated to outperform other state-of-the-art MHC class II prediction methods. Conclusion The NN-align method is competitive with the state-of-the-art MHC class II peptide binding prediction algorithms. The method is publicly available at http://www.cbs.dtu.dk/services/NetMHCII-2.0.

  17. Sparse alignment for robust tensor learning.

    Science.gov (United States)

    Lai, Zhihui; Wong, Wai Keung; Xu, Yong; Zhao, Cairong; Sun, Mingming

    2014-10-01

    Multilinear/tensor extensions of manifold learning based algorithms have been widely used in computer vision and pattern recognition. This paper first provides a systematic analysis of the multilinear extensions for the most popular methods by using alignment techniques, thereby obtaining a general tensor alignment framework. From this framework, it is easy to show that the manifold learning based tensor learning methods are intrinsically different from the alignment techniques. Based on the alignment framework, a robust tensor learning method called sparse tensor alignment (STA) is then proposed for unsupervised tensor feature extraction. Different from the existing tensor learning methods, L1- and L2-norms are introduced to enhance the robustness in the alignment step of the STA. The advantage of the proposed technique is that the difficulty in selecting the size of the local neighborhood can be avoided in the manifold learning based tensor feature extraction algorithms. Although STA is an unsupervised learning method, the sparsity encodes the discriminative information in the alignment step and provides the robustness of STA. Extensive experiments on the well-known image databases as well as action and hand gesture databases by encoding object images as tensors demonstrate that the proposed STA algorithm gives the most competitive performance when compared with the tensor-based unsupervised learning methods.

  18. Automatic learning-based beam angle selection for thoracic IMRT

    International Nuclear Information System (INIS)

    Amit, Guy; Marshall, Andrea; Purdie, Thomas G.; Jaffray, David A.; Levinshtein, Alex; Hope, Andrew J.; Lindsay, Patricia; Pekar, Vladimir

    2015-01-01

    Purpose: The treatment of thoracic cancer using external beam radiation requires an optimal selection of the radiation beam directions to ensure effective coverage of the target volume and to avoid unnecessary treatment of normal healthy tissues. Intensity modulated radiation therapy (IMRT) planning is a lengthy process, which requires the planner to iterate between choosing beam angles, specifying dose–volume objectives and executing IMRT optimization. In thorax treatment planning, where there are no class solutions for beam placement, beam angle selection is performed manually, based on the planner’s clinical experience. The purpose of this work is to propose and study a computationally efficient framework that utilizes machine learning to automatically select treatment beam angles. Such a framework may be helpful for reducing the overall planning workload. Methods: The authors introduce an automated beam selection method, based on learning the relationships between beam angles and anatomical features. Using a large set of clinically approved IMRT plans, a random forest regression algorithm is trained to map a multitude of anatomical features into an individual beam score. An optimization scheme is then built to select and adjust the beam angles, considering the learned interbeam dependencies. The validity and quality of the automatically selected beams evaluated using the manually selected beams from the corresponding clinical plans as the ground truth. Results: The analysis included 149 clinically approved thoracic IMRT plans. For a randomly selected test subset of 27 plans, IMRT plans were generated using automatically selected beams and compared to the clinical plans. The comparison of the predicted and the clinical beam angles demonstrated a good average correspondence between the two (angular distance 16.8° ± 10°, correlation 0.75 ± 0.2). The dose distributions of the semiautomatic and clinical plans were equivalent in terms of primary target volume

  19. CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping

    Directory of Open Access Journals (Sweden)

    Shi Weisong

    2011-06-01

    Full Text Available Abstract Background Research in genetics has developed rapidly recently due to the aid of next generation sequencing (NGS. However, massively-parallel NGS produces enormous amounts of data, which leads to storage, compatibility, scalability, and performance issues. The Cloud Computing and MapReduce framework, which utilizes hundreds or thousands of shared computers to map sequencing reads quickly and efficiently to reference genome sequences, appears to be a very promising solution for these issues. Consequently, it has been adopted by many organizations recently, and the initial results are very promising. However, since these are only initial steps toward this trend, the developed software does not provide adequate primary functions like bisulfite, pair-end mapping, etc., in on-site software such as RMAP or BS Seeker. In addition, existing MapReduce-based applications were not designed to process the long reads produced by the most recent second-generation and third-generation NGS instruments and, therefore, are inefficient. Last, it is difficult for a majority of biologists untrained in programming skills to use these tools because most were developed on Linux with a command line interface. Results To urge the trend of using Cloud technologies in genomics and prepare for advances in second- and third-generation DNA sequencing, we have built a Hadoop MapReduce-based application, CloudAligner, which achieves higher performance, covers most primary features, is more accurate, and has a user-friendly interface. It was also designed to be able to deal with long sequences. The performance gain of CloudAligner over Cloud-based counterparts (35 to 80% mainly comes from the omission of the reduce phase. In comparison to local-based approaches, the performance gain of CloudAligner is from the partition and parallel processing of the huge reference genome as well as the reads. The source code of CloudAligner is available at http

  20. CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping.

    Science.gov (United States)

    Nguyen, Tung; Shi, Weisong; Ruden, Douglas

    2011-06-06

    Research in genetics has developed rapidly recently due to the aid of next generation sequencing (NGS). However, massively-parallel NGS produces enormous amounts of data, which leads to storage, compatibility, scalability, and performance issues. The Cloud Computing and MapReduce framework, which utilizes hundreds or thousands of shared computers to map sequencing reads quickly and efficiently to reference genome sequences, appears to be a very promising solution for these issues. Consequently, it has been adopted by many organizations recently, and the initial results are very promising. However, since these are only initial steps toward this trend, the developed software does not provide adequate primary functions like bisulfite, pair-end mapping, etc., in on-site software such as RMAP or BS Seeker. In addition, existing MapReduce-based applications were not designed to process the long reads produced by the most recent second-generation and third-generation NGS instruments and, therefore, are inefficient. Last, it is difficult for a majority of biologists untrained in programming skills to use these tools because most were developed on Linux with a command line interface. To urge the trend of using Cloud technologies in genomics and prepare for advances in second- and third-generation DNA sequencing, we have built a Hadoop MapReduce-based application, CloudAligner, which achieves higher performance, covers most primary features, is more accurate, and has a user-friendly interface. It was also designed to be able to deal with long sequences. The performance gain of CloudAligner over Cloud-based counterparts (35 to 80%) mainly comes from the omission of the reduce phase. In comparison to local-based approaches, the performance gain of CloudAligner is from the partition and parallel processing of the huge reference genome as well as the reads. The source code of CloudAligner is available at http://cloudaligner.sourceforge.net/ and its web version is at http

  1. Enhanced optical alignment of a digital micro mirror device through Bayesian adaptive exploration

    Directory of Open Access Journals (Sweden)

    Kevin B. Wynne

    2017-12-01

    Full Text Available As the use of Digital Micro Mirror Devices (DMDs becomes more prevalent in optics research, the ability to precisely locate the Fourier “footprint” of an image beam at the Fourier plane becomes a pressing need. In this approach, Bayesian adaptive exploration techniques were employed to characterize the size and position of the beam on a DMD located at the Fourier plane. It couples a Bayesian inference engine with an inquiry engine to implement the search. The inquiry engine explores the DMD by engaging mirrors and recording light intensity values based on the maximization of the expected information gain. Using the data collected from this exploration, the Bayesian inference engine updates the posterior probability describing the beam’s characteristics. The process is iterated until the beam is located to within the desired precision. This methodology not only locates the center and radius of the beam with remarkable precision but accomplishes the task in far less time than a brute force search. The employed approach has applications to system alignment for both Fourier processing and coded aperture design.

  2. Implementation of EPICS based Control System for Radioisotope Beam line

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jae-Ha; Ahn, Tae-Sung; Song, Young-Gi; Kwon, Hyeok-Jung; Cho, Yong-Sub [Korea Atomic Energy Research Institute, Gyeongju (Korea, Republic of)

    2015-10-15

    Korea Mult-purpose Accelerator Complex (KOMAC) has been operating 100 MeV proton linear accelerator . For operating 100 MeV linac, various control system has been implemented such as vacuum, power supply, RCCS and etc. KOMAC is operating two beam lines so that clients can use 100 MeV proton beam for their experiment. KOMAC sends beam to beam line and target room using two dipole magnets and several quadrupole magnets. As demand for experiments and Radius Isotope using beam is increased, another beam line is under construction and RI beam line control system is need. To synchronize with KOMAC control system, RI beam line control system is based on Experimental Physics and Industrial control System (EPICS) software. The beam is transported to RI beam line to control magnet power supply and vacuum. Implementation of RI beam line control system is presented and some preliminary results are reported. The base RI beam line control system is implemented. It can control beam direction and vacuum. Comparing archived data and current data, RI beam line and control system will be improved. In the future, scroll pump and gate control system will be implemented using programmable logic controller PLC. RI beam interlock sequence will be added to KOMAC interlock system to protect linac.

  3. K2 and K2*: efficient alignment-free sequence similarity measurement based on Kendall statistics.

    Science.gov (United States)

    Lin, Jie; Adjeroh, Donald A; Jiang, Bing-Hua; Jiang, Yue

    2018-05-15

    Alignment-free sequence comparison methods can compute the pairwise similarity between a huge number of sequences much faster than sequence-alignment based methods. We propose a new non-parametric alignment-free sequence comparison method, called K2, based on the Kendall statistics. Comparing to the other state-of-the-art alignment-free comparison methods, K2 demonstrates competitive performance in generating the phylogenetic tree, in evaluating functionally related regulatory sequences, and in computing the edit distance (similarity/dissimilarity) between sequences. Furthermore, the K2 approach is much faster than the other methods. An improved method, K2*, is also proposed, which is able to determine the appropriate algorithmic parameter (length) automatically, without first considering different values. Comparative analysis with the state-of-the-art alignment-free sequence similarity methods demonstrates the superiority of the proposed approaches, especially with increasing sequence length, or increasing dataset sizes. The K2 and K2* approaches are implemented in the R language as a package and is freely available for open access (http://community.wvu.edu/daadjeroh/projects/K2/K2_1.0.tar.gz). yueljiang@163.com. Supplementary data are available at Bioinformatics online.

  4. Measurement of the attosecond emission from aligned molecules

    International Nuclear Information System (INIS)

    Boutu, W.; Merdji, H.; Fitour, R.; Monchicourt, P.; Breger, P.; Carre, B.; Salieres, P.

    2006-01-01

    Complete test of publication follows. Recently, a number of papers have demonstrated the interest of high-order harmonic generation (HHG) from molecules aligned with respect to the laser polarization. Itatani et al. (Nature 432, 867 (2004)) have shown that a precise characterization of the harmonic emission allows performing a tomographic reconstruction of the molecular orbitals that radiate. Kanai et al. (Nature 435, 470 (2005)) have evidenced quantum interferences in the recombination process of HHG that are directly related to the molecular structure. In all of these papers, only the HHG intensity was measured. The relative harmonic phase, though more difficult to measure, contains important information on the interference process, and is needed for an ab initio tomographic reconstruction. Finally, while the attosecond emission from atoms has been thoroughly studied, in particular by our group (Mairesse et al., Science (302, 1540 (2003)), it has not been investigated in molecules. In a first experiment (Wabnitz et al., EPJD (2006)), we measured the amplitude and relative phase of harmonics radiated by un-aligned nitrogen molecules. Small but reproducible deviations from the phase of harmonics generated in argon (same ionization potential as nitrogen) were measured for low orders. In a recent experiment, we have measured, up to high order, the harmonic amplitude and relative phase for aligned molecules (N 2 and CO 2 ). In order to align the molecules, we used the so-called nonadiabatic technique: a rotational wavepacket is created by a strong enough and short aligning pulse, so that a field-free alignment is obtained at the revival (a few ps after the aligning pulse). The measurement of phase locking between neighboring harmonics was performed through the photoionization of a target gas by the harmonic beam in presence of a sufficiently intense 'dressing' laser beam (RABITT technique). The harmonic phase measured when the CO 2 molecules are aligned parallel to

  5. Pareto optimal pairwise sequence alignment.

    Science.gov (United States)

    DeRonne, Kevin W; Karypis, George

    2013-01-01

    Sequence alignment using evolutionary profiles is a commonly employed tool when investigating a protein. Many profile-profile scoring functions have been developed for use in such alignments, but there has not yet been a comprehensive study of Pareto optimal pairwise alignments for combining multiple such functions. We show that the problem of generating Pareto optimal pairwise alignments has an optimal substructure property, and develop an efficient algorithm for generating Pareto optimal frontiers of pairwise alignments. All possible sets of two, three, and four profile scoring functions are used from a pool of 11 functions and applied to 588 pairs of proteins in the ce_ref data set. The performance of the best objective combinations on ce_ref is also evaluated on an independent set of 913 protein pairs extracted from the BAliBASE RV11 data set. Our dynamic-programming-based heuristic approach produces approximated Pareto optimal frontiers of pairwise alignments that contain comparable alignments to those on the exact frontier, but on average in less than 1/58th the time in the case of four objectives. Our results show that the Pareto frontiers contain alignments whose quality is better than the alignments obtained by single objectives. However, the task of identifying a single high-quality alignment among those in the Pareto frontier remains challenging.

  6. Physician-Hospital Alignment in Orthopedic Surgery.

    Science.gov (United States)

    Bushnell, Brandon D

    2015-09-01

    The concept of "alignment" between physicians and hospitals is a popular buzzword in the age of health care reform. Despite their often tumultuous histories, physicians and hospitals find themselves under increasing pressures to work together toward common goals. However, effective alignment is more than just simple cooperation between parties. The process of achieving alignment does not have simple, universal steps. Alignment will differ based on individual situational factors and the type of specialty involved. Ultimately, however, there are principles that underlie the concept of alignment and should be a part of any physician-hospital alignment efforts. In orthopedic surgery, alignment involves the clinical, administrative, financial, and even personal aspects of a surgeon's practice. It must be based on the principles of financial interest, clinical authority, administrative participation, transparency, focus on the patient, and mutual necessity. Alignment can take on various forms as well, with popular models consisting of shared governance and comanagement, gainsharing, bundled payments, accountable care organizations, and other methods. As regulatory and financial pressures continue to motivate physicians and hospitals to develop alignment relationships, new and innovative methods of alignment will also appear. Existing models will mature and evolve, with individual variability based on local factors. However, certain trends seem to be appearing as time progresses and alignment relationships deepen, including regional and national collaboration, population management, and changes in the legal system. This article explores the history, principles, and specific methods of physician-hospital alignment and its critical importance for the future of health care delivery. Copyright 2015, SLACK Incorporated.

  7. RNA Structural Alignments, Part I

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Gorodkin, Jan

    2014-01-01

    Simultaneous alignment and secondary structure prediction of RNA sequences is often referred to as "RNA structural alignment." A class of the methods for structural alignment is based on the principles proposed by Sankoff more than 25 years ago. The Sankoff algorithm simultaneously folds and aligns...... is so high that it took more than a decade before the first implementation of a Sankoff style algorithm was published. However, with the faster computers available today and the improved heuristics used in the implementations the Sankoff-based methods have become practical. This chapter describes...... the methods based on the Sankoff algorithm. All the practical implementations of the algorithm use heuristics to make them run in reasonable time and memory. These heuristics are also described in this chapter....

  8. High resolution Fresnel zone plate laser alignment system

    International Nuclear Information System (INIS)

    Bressler, V.E.; Fischer, G.E.; Ruland, R.E.; Wang, T.

    1992-03-01

    The existing Fresnel zone plate laser alignment system is currently being extended and upgraded for the Final Focus Test Beam (FFTB). Previously, the resolution of this system has been several tens of micrometers. After the upgrade, the resolution will be a few micrometers. Details of the upgrade as well as simulation and experimental results will be presented

  9. Micro computer aided beam transport for the SF cyclotron

    International Nuclear Information System (INIS)

    Honma, Toshihiro; Yamazaki, Tsutomu.

    1984-01-01

    An improvement of the beam transport system for the SF cyclotron is described. The system was designed to handle on-line alignment of the beam extracted from the SF cyclotron onto the optical axis of the transport line. It also enables to measure the beam emittance. The measurement of the emittance parameters is in particular necessary to calculate the beam optics. The calculation has been modified to become easy to handle. With the help of the computer-aided on-line beam profile measurement system, the operation of the beam transport system is very subservient to shorten the beam-tuning time and to improve the beam-transmission efficiency and the quality. (author)

  10. Closed-orbit correction using the new beam position monitor electronic of Elsa Bonn

    CERN Document Server

    Dietrich, J; Keil, J

    2000-01-01

    RF and digital electronics, developed at the Forschungszentrum Jülich/IKP were integrated to form the new beam position monitor (BPM) system at the Electron Stretcher Accelerator (ELSA) of the University of Bonn. With this system the preservation of the polarization level during acceleration was currently improved by a good correction of the closed-orbit. All BPM offsets relative to the magnetic quadrupole centers were determined by the method of beam-based alignment. The optics functions measured by the BPM system are in good agreement with theoretical predictions.

  11. Alignment of the VISA Undulator

    International Nuclear Information System (INIS)

    Ruland, Robert E.

    2000-01-01

    As part of the R and D program towards a fourth generation light source, a Self-Amplified Spontaneous Emission (SASE) demonstration is being prepared. The Visible-Infrared SASE Amplifier (VISA) undulator is being installed at Brookhaven National Laboratory. The VISA undulator is an in-vacuum, 4-meter long, 1.8 cm period, pure-permanent magnet device, with a novel, strong focusing, permanent magnet FODO array included within the fixed, 6 mm undulator gap. The undulator is constructed of 99 cm long segments. To attain maximum SASE gain requires establishing overlap of electron and photon beams to within 50 pm rms. This imposes challenging tolerances on mechanical fabrication and magnetic field quality, and necessitates use of laser straightness interferometry for calibration and alignment of the magnetic axes of the undulator segments. This paper describes the magnetic centerline determination, and the fiducialization and alignment processes, which were performed to meet the tolerance goal

  12. Polarization-dependent spectra in the photoassociative ionization of cold atoms in a bright sodium beam

    International Nuclear Information System (INIS)

    Ramirez-Serrano, Jaime; DeGraffenreid, William; Weiner, John

    2002-01-01

    We report measurements of cold photoassociative ionization (PAI) spectra obtained from collisions within a slow, bright Na atomic beam. A high-brightness atom flux, obtained by optical cooling and focusing of the atom beam, permits a high degree of alignment and orientation of binary collisions with respect to the laboratory atom-beam axis. The results reveal features of PAI spectra not accessible in conventional magneto-optical trap studies. We take advantage of this high degree of alignment to selectively excite autoionizing doubly excited states of specific symmetry

  13. Introduction of hind foot coronal alignment view

    International Nuclear Information System (INIS)

    Moon, Il Bong; Jeon, Ju Seob; Yoon, Kang Cheol; Choi, Nam Kil; Kim, Seung Kook

    2006-01-01

    Accurate clinical evaluation of the alignment of the calcaneus relative to the tibia in the coronal plane is essential in the evaluation and treatment of hind foot pathologic condition. Previously described standard anteroposterior, lateral, and oblique radiographic methods of the foot or ankle do not demonstrate alignment of the tibia relation to the calcaneus in the coronal plane. The purpose of this study was to introduce hind foot coronal alignment view. Both feet were imaged simultaneously on an elevated, radiolucent foot stand equipment. Both feet stood on a radiolucent platform with equal weight on both feet. Both feet are located foot axis longitudinal perpendicular to the platform. Silhouette tracing around both feet are made, and line is then drawn to bisect the silhouette of the second toe and the outline of the heel. The x-ray beam is angled down approximately 15 .deg. to 20 .deg. This image described tibial axis and medial, lateral tuberosity of calcaneus. Calcaneus do not rotated. The view is showed by talotibial joint space. Although computed tomographic and magnetic resonance imaging techniques are capable of demonstrating coronal hind foot alignment, they lack usefulness in most clinical situations because the foot is imaged in a non-weight bearing position. But hind foot coronal alignment view is obtained for evaluating position changing of inversion, eversion of the hind foot and varus, valgus deformity of calcaneus

  14. Neural network approximation of nonlinearity in laser nano-metrology system based on TLMI

    Energy Technology Data Exchange (ETDEWEB)

    Olyaee, Saeed; Hamedi, Samaneh, E-mail: s_olyaee@srttu.edu [Nano-photonics and Optoelectronics Research Laboratory (NORLab), Faculty of Electrical and Computer Engineering, Shahid Rajaee Teacher Training University (SRTTU), Lavizan, 16788, Tehran (Iran, Islamic Republic of)

    2011-02-01

    In this paper, an approach based on neural network (NN) for nonlinearity modeling in a nano-metrology system using three-longitudinal-mode laser heterodyne interferometer (TLMI) for length and displacement measurements is presented. We model nonlinearity errors that arise from elliptically and non-orthogonally polarized laser beams, rotational error in the alignment of laser head with respect to the polarizing beam splitter, rotational error in the alignment of the mixing polarizer, and unequal transmission coefficients in the polarizing beam splitter. Here we use a neural network algorithm based on the multi-layer perceptron (MLP) network. The simulation results show that multi-layer feed forward perceptron network is successfully applicable to real noisy interferometer signals.

  15. Neural network approximation of nonlinearity in laser nano-metrology system based on TLMI

    International Nuclear Information System (INIS)

    Olyaee, Saeed; Hamedi, Samaneh

    2011-01-01

    In this paper, an approach based on neural network (NN) for nonlinearity modeling in a nano-metrology system using three-longitudinal-mode laser heterodyne interferometer (TLMI) for length and displacement measurements is presented. We model nonlinearity errors that arise from elliptically and non-orthogonally polarized laser beams, rotational error in the alignment of laser head with respect to the polarizing beam splitter, rotational error in the alignment of the mixing polarizer, and unequal transmission coefficients in the polarizing beam splitter. Here we use a neural network algorithm based on the multi-layer perceptron (MLP) network. The simulation results show that multi-layer feed forward perceptron network is successfully applicable to real noisy interferometer signals.

  16. A new beamstop for microfocus X-ray capillary beams

    Energy Technology Data Exchange (ETDEWEB)

    Englich, Ulrich, E-mail: ue22@cornell.edu [Cornell University, Macromolecular Diffraction at CHESS (MacCHESS), Cornell High Energy Synchrotron Source, 200L Wilson Laboratory, Ithaca, NY 14853 (United States); Revesz, Peter [Cornell University, Cornell High Energy Synchrotron Source, Ithaca, NY 14853 (United States); Miller, William [Cornell University, Macromolecular Diffraction at CHESS (MacCHESS), Cornell High Energy Synchrotron Source, 200L Wilson Laboratory, Ithaca, NY 14853 (United States)

    2011-09-01

    In order to accurately measure the photon flux and to assist in aligning the beam, we have designed a modified beamstop device based on a photo diode integrated with the beamstop. The beamstop contains a small CdWO{sub 4} crystal that completely stops the X-rays and at the same time produces photoluminescence proportional to the X-ray flux. The light is then guided to a photosensitive diode using a flexible light pipe to monitor the flux. With this device we achieve the goal of stopping the primary X-ray beam and simultaneously monitoring the X-ray intensity, thus eliminating the need for integrating ion-chambers into the capillary or collimator mount.

  17. Optical and x-ray alignment approaches for off-plane reflection gratings

    Science.gov (United States)

    Allured, Ryan; Donovan, Benjamin D.; DeRoo, Casey T.; Marlowe, Hannah R.; McEntaffer, Randall L.; Tutt, James H.; Cheimets, Peter N.; Hertz, Edward; Smith, Randall K.; Burwitz, Vadim; Hartner, Gisela; Menz, Benedikt

    2015-09-01

    Off-plane reflection gratings offer the potential for high-resolution, high-throughput X-ray spectroscopy on future missions. Typically, the gratings are placed in the path of a converging beam from an X-ray telescope. In the off-plane reflection grating case, these gratings must be co-aligned such that their diffracted spectra overlap at the focal plane. Misalignments degrade spectral resolution and effective area. In-situ X-ray alignment of a pair of off-plane reflection gratings in the path of a silicon pore optics module has been performed at the MPE PANTER beamline in Germany. However, in-situ X-ray alignment may not be feasible when assembling all of the gratings required for a satellite mission. In that event, optical methods must be developed to achieve spectral alignment. We have developed an alignment approach utilizing a Shack-Hartmann wavefront sensor and diffraction of an ultraviolet laser. We are fabricating the necessary hardware, and will be taking a prototype grating module to an X-ray beamline for performance testing following assembly and alignment.

  18. Electron beam based transversal profile measurements of intense ion beams

    International Nuclear Information System (INIS)

    El Moussati, Said

    2014-01-01

    A non-invasive diagnostic method for the experimental determination of the transverse profile of an intense ion beam has been developed and investigated theoretically as well as experimentally within the framework of the present work. The method is based on the deflection of electrons when passing the electromagnetic field of an ion beam. To achieve this an electron beam is employed with a specifically prepared transversal profile. This distinguish this method from similar ones which use thin electron beams for scanning the electromagnetic field [Roy et al. 2005; Blockland10]. The diagnostic method presented in this work will be subsequently called ''Electron-Beam-Imaging'' (EBI). First of all the influence of the electromagnetic field of the ion beam on the electrons has been theoretically analyzed. It was found that the magnetic field causes only a shift of the electrons along the ion beam axis, while the electric field only causes a shift in a plane transverse to the ion beam. Moreover, in the non-relativistic case the magnetic force is significantly smaller than the Coulomb one and the electrons suffer due to the magnetic field just a shift and continue to move parallel to their initial trajectory. Under the influence of the electric field, the electrons move away from the ion beam axis, their resulting trajectory shows a specific angle compared to the original direction. This deflection angle practically depends just on the electric field of the ion beam. Thus the magnetic field has been neglected when analysing the experimental data. The theoretical model provides a relationship between the deflection angle of the electrons and the charge distribution in the cross section of the ion beam. The model however only can be applied for small deflection angles. This implies a relationship between the line-charge density of the ion beam and the initial kinetic energy of the electrons. Numerical investigations have been carried out to clarify the

  19. Hohlraum Target Alignment from X-ray Detector Images using Starburst Design Patterns

    International Nuclear Information System (INIS)

    Leach, R.R.; Conder, A.; Edwards, O.; Kroll, J.; Kozioziemski, B.; Mapoles, E.; McGuigan, D.; Wilhelmsen, K.

    2010-01-01

    National Ignition Facility (NIF) is a high-energy laser facility comprised of 192 laser beams focused with enough power and precision on a hydrogen-filled spherical, cryogenic target to initiate a fusion reaction. The target container, or hohlraum, must be accurately aligned to an x-ray imaging system to allow careful monitoring of the frozen fuel layer in the target. To achieve alignment, x-ray images are acquired through starburst-shaped windows cut into opposite sides of the hohlraum. When the hohlraum is in alignment, the starburst pattern pairs match nearly exactly and allow a clear view of the ice layer formation on the edge of the target capsule. During the alignment process, x-ray image analysis is applied to determine the direction and magnitude of adjustment required. X-ray detector and source are moved in concert during the alignment process. The automated pointing alignment system described here is both accurate and efficient. In this paper, we describe the control and associated image processing that enables automation of the starburst pointing alignment.

  20. An Electron Beam Profile Instrument Based on FBGs

    Directory of Open Access Journals (Sweden)

    Dan Sporea

    2014-08-01

    Full Text Available Along with the dose rate and the total irradiation dose measurements, the knowledge of the beam localization and the beam profile/energy distribution in the beam are parameters of interest for charged particle accelerator installations when they are used in scientific investigations, industrial applications or medical treatments. The transverse profile of the beam, its position, its centroid location, and its focus or flatness depend on the instrument operating conditions or on the beam exit setup. Proof-of-concept of a new type of charged particle beam diagnostics based on fiber Bragg gratings (FBGs was demonstrated. Its operating principle relies on the measurement of the peak wavelength changes for an array of FBG sensors as function of the temperature following the exposure to an electron beam. Periodically, the sensor irradiation is stopped and the FBG are force cooled to a reference temperature with which the temperature influencing each sensor during beam exposure is compared. Commercially available FBGs, and FBGs written in radiation resistant optical fibers, were tested under electron beam irradiation in order to study their possible use in this application.

  1. Beam finding algorithms at the interaction point of B factories

    International Nuclear Information System (INIS)

    Kozanecki, W.

    1992-10-01

    We review existing methods to bring beams in collision in circular machines, and examine collision alignment strategies proposed for e + e - B-factories. The two-ring feature of such machines, while imposing more stringent demands on beam control, also opens up new diagnostic possibilities

  2. libgapmis: extending short-read alignments.

    Science.gov (United States)

    Alachiotis, Nikolaos; Berger, Simon; Flouri, Tomáš; Pissis, Solon P; Stamatakis, Alexandros

    2013-01-01

    A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure such as time and memory efficiency, sensitivity, and accuracy. These tools allow for a small number of mismatches in the alignment; however, their ability to allow for gaps varies greatly, with many performing poorly or not allowing them at all. The seed-and-extend strategy is applied in most short-read alignment programmes. After aligning a substring of the reference sequence against the high-quality prefix of a short read--the seed--an important problem is to find the best possible alignment between a substring of the reference sequence succeeding and the remaining suffix of low quality of the read--extend. The fact that the reads are rather short and that the gap occurrence frequency observed in various studies is rather low suggest that aligning (parts of) those reads with a single gap is in fact desirable. In this article, we present libgapmis, a library for extending pairwise short-read alignments. Apart from the standard CPU version, it includes ultrafast SSE- and GPU-based implementations. libgapmis is based on an algorithm computing a modified version of the traditional dynamic-programming matrix for sequence alignment. Extensive experimental results demonstrate that the functions of the CPU version provided in this library accelerate the computations by a factor of 20 compared to other programmes. The analogous SSE- and GPU-based implementations accelerate the computations by a factor of 6 and 11, respectively, compared to the CPU version. The library also provides the user the flexibility to split the read into fragments, based on the observed gap occurrence frequency and the length of the read, thereby allowing for a variable, but bounded, number of gaps in the alignment. We present libgapmis, a library for extending pairwise short-read alignments. We

  3. Image-based quantification of fiber alignment within electrospun tissue engineering scaffolds is related to mechanical anisotropy.

    Science.gov (United States)

    Fee, Timothy; Downs, Crawford; Eberhardt, Alan; Zhou, Yong; Berry, Joel

    2016-07-01

    It is well documented that electrospun tissue engineering scaffolds can be fabricated with variable degrees of fiber alignment to produce scaffolds with anisotropic mechanical properties. Several attempts have been made to quantify the degree of fiber alignment within an electrospun scaffold using image-based methods. However, these methods are limited by the inability to produce a quantitative measure of alignment that can be used to make comparisons across publications. Therefore, we have developed a new approach to quantifying the alignment present within a scaffold from scanning electron microscopic (SEM) images. The alignment is determined by using the Sobel approximation of the image gradient to determine the distribution of gradient angles with an image. This data was fit to a Von Mises distribution to find the dispersion parameter κ, which was used as a quantitative measure of fiber alignment. We fabricated four groups of electrospun polycaprolactone (PCL) + Gelatin scaffolds with alignments ranging from κ = 1.9 (aligned) to κ = 0.25 (random) and tested our alignment quantification method on these scaffolds. It was found that our alignment quantification method could distinguish between scaffolds of different alignments more accurately than two other published methods. Additionally, the alignment parameter κ was found to be a good predictor the mechanical anisotropy of our electrospun scaffolds. The ability to quantify fiber alignment within and make direct comparisons of scaffold fiber alignment across publications can reduce ambiguity between published results where cells are cultured on "highly aligned" fibrous scaffolds. This could have important implications for characterizing mechanics and cellular behavior on aligned tissue engineering scaffolds. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1680-1686, 2016. © 2016 Wiley Periodicals, Inc.

  4. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    2012-01-01

      A new muon alignment has been produced for 2012 A+B data reconstruction. It uses the latest Tracker alignment and single-muon data samples to align both DTs and CSCs. Physics validation has been performed and shows a modest improvement in stand-alone muon momentum resolution in the barrel, where the alignment is essentially unchanged from the previous version. The reference-target track-based algorithm using only collision muons is employed for the first time to align the CSCs, and a substantial improvement in resolution is observed in the endcap and overlap regions for stand-alone muons. This new alignment is undergoing the approval process and is expected to be deployed as part of a new global tag in the beginning of December. The pT dependence of the φ-bias in curvature observed in Monte Carlo was traced to a relative vertical misalignment between the Tracker and barrel muon systems. Moving the barrel as a whole to match the Tracker cures this pT dependence, leaving only the &phi...

  5. Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner

    DEFF Research Database (Denmark)

    Lu, David V; Brown, Randall H; Arumugam, Manimozhiyan

    2009-01-01

    MOTIVATION: The most accurate way to determine the intron-exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary...... determinant of alignment accuracy, while heuristics that prevent consideration of certain alignments are a primary determinant of runtime and memory usage. Both accuracy and speed are important considerations in choosing an alignment algorithm, but scoring systems have received much less attention than...

  6. Review of tolerances at the Final Focus Test Beam

    International Nuclear Information System (INIS)

    Bulos, F.; Burke, D.; Helm, R.; Irwin, J.; Roy, G.; Yamamoto, N.

    1991-01-01

    The authors review the tolerances associated with the Final Focus Test Beam (FFTB). The authors have computed the acceptability window of the input beam for orbit jitter, emittance beta functions mismatch, incoming dispersion and coupling; tolerances on magnet alignment, strength and multipole content; and the initial tuneability capture of the line

  7. Polarization Studies in Fast-Ion Beam Spectroscopy

    International Nuclear Information System (INIS)

    Trabert, E

    2001-01-01

    In a historical review, the observations and the insight gained from polarization studies of fast ions interacting with solid targets are presented. These began with J. Macek's recognition of zero-field quantum beats in beam-foil spectroscopy as indicating alignment, and D.G. Ellis' density operator analysis that suggested the observability of orientation when using tilted foils. Lastly H. Winter's studies of the ion-beam surface interaction at grazing incidence yielded the means to produce a high degree of nuclear orientation in ion beams

  8. Impedance computations and beam-based measurements: A problem of discrepancy

    Science.gov (United States)

    Smaluk, Victor

    2018-04-01

    High intensity of particle beams is crucial for high-performance operation of modern electron-positron storage rings, both colliders and light sources. The beam intensity is limited by the interaction of the beam with self-induced electromagnetic fields (wake fields) proportional to the vacuum chamber impedance. For a new accelerator project, the total broadband impedance is computed by element-wise wake-field simulations using computer codes. For a machine in operation, the impedance can be measured experimentally using beam-based techniques. In this article, a comparative analysis of impedance computations and beam-based measurements is presented for 15 electron-positron storage rings. The measured data and the predictions based on the computed impedance budgets show a significant discrepancy. Three possible reasons for the discrepancy are discussed: interference of the wake fields excited by a beam in adjacent components of the vacuum chamber, effect of computation mesh size, and effect of insufficient bandwidth of the computed impedance.

  9. Simple methods of aligning four-circle diffractometers with crystal reflections

    Energy Technology Data Exchange (ETDEWEB)

    Mitsui, Y [Tokyo Univ. (Japan). Faculty of Pharmaceutical Sciences

    1979-08-01

    Simple methods of aligning four-circle diffractometers with crystal reflections are devised. They provide the methods to check (1) perpendicularity of chi plane to the incident beam, (2) zero point of 2theta and linearity of focus-chi center-receiving aperture and (3) zero point of chi.

  10. Linear to Circular Polarisation Conversion using Birefringent Properties of Aligned Crystals for Multi-GeV Photons

    CERN Document Server

    Apyan, A.; Badelek, B.; Ballestrero, S.; Biino, C.; Birol, I.; Cenci, P.; Connell, S.H.; Eichblatt, S.; Fonseca, T.; Freund, A.; Gorini, B.; Groess, R.; Ispirian, K.; Ketel, T.J.; Kononets, Yu.V.; Lopez, A.; Mangiarotti, A.; van Rens, B.; Sellschop, J.P.F.; Shieh, M.; Sona, P.; Strakhovenko, V.; Uggerhoj, E.; Uggerhj, Ulrik Ingerslev; Unel, G.; Velasco, M.; Vilakazi, Z.Z.; Wessely, O.; Kononets, Yu.V.

    2003-01-01

    We present the first experimental results on the use of a thick aligned Si crystal acting as a quarter wave plate to induce a degree of circular polarisation in a high energy linearly polarised photon beam. The linearly polarised photon beam is produced from coherent bremsstrahlung radiation by 178 GeV unpolarised electrons incident on an aligned Si crystal, acting as a radiator. The linear polarisation of the photon beam is characterised by measuring the asymmetry in electron-positron pair production in a Ge crystal, for different crystal orientations. The Ge crystal therefore acts as an analyser. The birefringence phenomenon, which converts the linear polarisation to circular polarisation, is observed by letting the linearly polarised photons beam pass through a thick Si quarter wave plate crystal, and then measuring the asymmetry in electron-positron pair production again for a selection of relative angles between the crystallographic planes of the radiator, analyser and quarter wave plate. The systematics...

  11. Negative ion based neutral beams for plasma heating

    International Nuclear Information System (INIS)

    Prelec, K.

    1978-01-01

    Neutral beam systems based on negative ions have been considered because of a high expected power efficiency. Methods for the production, acceleration and neutralization of negative ions will be reviewed and possibilities for an application in neutral beam lines explored

  12. A Wire Position Monitor System for the ISAC-II Cryomodule Components Alignment

    CERN Document Server

    Rawnsley, B; Dutto, G; Fong, K; Laxdal, R E; Ries, T

    2004-01-01

    TRIUMF is developing ISAC-II, a superconducting (SC) linac. It will comprise 9 cryomodules with a total of 48 niobium cavities and 12 SC solenoids. They must remain aligned at liquid He temperatures: cavities to ±400 μm and solenoids to ±200 μm after a vertical contraction of ~4 mm. A wire position monitor (WPM) system based on a TESLA design has been developed, built, and tested with a prototype cryomodule. The system is based on the measurement of signals induced in pickups by a 215 MHz signal carried by a wire through the WPMs. The wire is stretched between the warm tank walls parallel to the beam axis providing a position reference. The sensors, one per cavity and two per solenoid, are attached to the cold elements to monitor their motion during pre-alignment, pumping and cool down. A WPM consists of four 50 Ω striplines spaced 90° apart. A GaAs multiplexer scans the WPMs and a Bergoz card converts the RF signals to DC X and Y voltages. National Ins...

  13. The AAG's ALIGNED Toolkit: A Place-based Approach to Fostering Diversity in the Geosciences

    Science.gov (United States)

    Rodrigue, C. M.

    2012-12-01

    Where do we look to attract a more diverse group of students to academic programs in geography and the geosciences? What do we do once we find them? This presentation introduces the ALIGNED Toolkit developed by the Association of American Geographers, with funding from the NSF's Opportunities to Enhance Diversity in the Geosciences (OEDG) Program. ALIGNED (Addressing Locally-tailored Information Infrastructure and Geoscience Needs for Enhancing Diversity) seeks to align the needs of university departments and underrepresented students by drawing upon the intellectual wealth of geography and spatial science to provide better informed, knowledge-based action to enhance diversity in higher education and the geoscience workforce. The project seeks to inform and transform the ways in which departments and programs envision and realize their own goals to enhance diversity, promote inclusion, and broaden participation. We also seek to provide the data, information, knowledge, and best practices needed in order to enhance the recruitment and retention of underrepresented students. The ALIGNED Toolkit is currently in a beta release, available to 13 pilot departments and 50 testing departments of geography/geosciences. It consolidates a variety of data from departments, the U.S. Census Bureau, and the U.S. Department of Education's National Center for Education Statistics to provide interactive, GIS-based visualizations across multiple scales. It also incorporates a place-based, geographic perspective to support departments in their efforts to enhance diversity. A member of ALIGNED's senior personnel, who is also a representative of one of the pilot departments, will provide an overview and preview of the tool while sharing her department's experiences in progressing toward its diversity goals. A brief discussion on how geoscience departments might benefit from the ALIGNED approach and resources will follow. Undergraduate advisors, graduate program directors, department

  14. Optical encoder based on a nondiffractive beam

    International Nuclear Information System (INIS)

    Lutenberg, Ariel; Perez-Quintian, Fernando; Rebollo, Maria A.

    2008-01-01

    Optical encoders are used in industrial and laboratory motion equipment to measure rotations and linear displacements. We introduce a design of an optical encoder based on a nondiffractive beam. We expect that the invariant profile and radial symmetry of the nondiffractive beam provide the design with remarkable tolerance to mechanical perturbations. We experimentally demonstrate that the proposed design generates a suitable output sinusoidal signal with low harmonic distortion. Moreover, we present a numerical model of the system based on the angular spectrum approximation whose predictions are in excellent agreement with the experimental results

  15. Confocal Microscope Alignment of Nanocrystals for Coherent Diffraction Imaging

    International Nuclear Information System (INIS)

    Beitra, Loren; Watari, Moyu; Matsuura, Takashi; Shimamoto, Naonobu; Harder, Ross; Robinson, Ian

    2010-01-01

    We have installed and tested an Olympus LEXT confocal microscope at the 34-ID-C beamline of the Advanced Photon Source (APS). The beamline is for Coherent X-ray Diffraction (CXD) experiments in which a nanometre-sized crystal is aligned inside a focussed X-ray beam. The microscope was required for three-dimensional (3D) sample alignment to get around sphere-of-confusion issues when locating Bragg peaks in reciprocal space. In this way, and by use of strategic sample preparations, we have succeeded in measuring six Bragg peaks from a single 200 nm gold crystal and obtained six projections of its internal displacement field. This enables the clear identification of stacking-fault bands within the crystal. The confocal alignment method will allow a full determination of the strain tensor provided three or more Bragg reflections from the same crystal are found.

  16. Review of tolerances at the Final Focus Test Beam

    International Nuclear Information System (INIS)

    Bulos, F.; Burke, D.; Helm, R.; Irwin, J.; Roy, G.; Yamamoto, N.

    1991-05-01

    We review the tolerances associated with the Final Focus Test Beam (FFTB). We have computed the acceptability window of the input beam for orbit jitter, emittance beta functions mismatch, incoming dispersion and coupling; tolerances on magnet alignment, strength and multipole content; and the initial tuneability capture of the line. 2 refs., 1 fig

  17. A multi-satellite study of accelerated ionospheric ion beams above the polar cap

    Directory of Open Access Journals (Sweden)

    R. Maggiolo

    2006-07-01

    Full Text Available This paper presents a study of nearly field-aligned outflowing ion beams observed on the Cluster satellites over the polar cap. Data are taken at geocentric radial distances of the order of 5–9 RE. The distinction is made between ion beams originating from the polar cusp/cleft and beams accelerated almost along the magnetic field line passing by the spacecraft. Polar cusp beams are characterized by nearly field-aligned proton and oxygen ions with an energy ratio EO+ / EH+, of the order of 3 to 4, due to the ion energy repartition inside the source and to the latitudinal extension of the source. Rapid variations in the outflowing ion energy are linked with pulses/modifications of the convection electric field. Cluster data allow one to show that these perturbations of the convection velocity and the associated ion structures propagate at the convection velocity.

    In contrast, polar cap local ion beams are characterized by field-aligned proton and oxygen ions with similar energies. These beams show the typical inverted V structures usually observed in the auroral zone and are associated with a quasi-static converging electric field indicative of a field-aligned electric field. The field-aligned potential drop fits well the ion energy profile. The simultaneous observation of precipitating electrons and upflowing ions of similar energies at the Cluster orbit indicates that the spacecraft are crossing the mid-altitude part of the acceleration region. In the polar cap, the parallel electric field can thus extend to altitudes higher than 5 Earth radii. A detailed analysis of the distribution functions shows that the ions are heated during their parallel acceleration and that energy is exchanged between H+ and O+. Furthermore, intense electrostatic waves are observed simultaneously. These observations could be due to an ion-ion two-stream instability.

  18. Alignment for new Subaru ring

    International Nuclear Information System (INIS)

    Zhang, Ch.; Matsui, S.; Hashimoto, S.

    1999-01-01

    The New SUBARU is a synchrotron light source being constructed at the SPring-8 site. The main facility is a 1.5 GeV electron storage ring that provides light beam in the region from VUV to soft X-ray using SPring-8's 1 GeV linac as an injector. The ring, with a circumference of about 119 meters, is composed of six bending cells. Each bending cell has two normal dipoles of 34 degree and one inverse dipole of -8 degree. The ring has six straight sections: two very long straight sections for a 11-m long undulator and an optical klystron, four short straight sections for a 2.3-m undulator, a super-conducting wiggler, rf cavity and injection, etc. The magnets of the storage ring are composed of 12 dipoles (BMs), 6 invert dipoles (BIs), 56 quadrupoles and 44 sextupoles, etc. For the magnet alignment, positions of the dipoles (the BMs and BIs) are determined by network survey method. The multipoles, which are mounted on girders between the dipoles, are aligned with a laser-CCD camera system. This article presents the methodology used to position the different components and particularly to assure the precise alignment of the multipoles. (authors)

  19. Photon beam position monitor

    Science.gov (United States)

    Kuzay, Tuncer M.; Shu, Deming

    1995-01-01

    A photon beam position monitor for use in the front end of a beamline of a high heat flux and high energy photon source such as a synchrotron radiation storage ring detects and measures the position and, when a pair of such monitors are used in tandem, the slope of a photon beam emanating from an insertion device such as a wiggler or an undulator inserted in the straight sections of the ring. The photon beam position monitor includes a plurality of spaced blades for precisely locating the photon beam, with each blade comprised of chemical vapor deposition (CVD) diamond with an outer metal coating of a photon sensitive metal such as tungsten, molybdenum, etc., which combination emits electrons when a high energy photon beam is incident upon the blade. Two such monitors are contemplated for use in the front end of the beamline, with the two monitors having vertically and horizontally offset detector blades to avoid blade "shadowing". Provision is made for aligning the detector blades with the photon beam and limiting detector blade temperature during operation.

  20. Semiautomated improvement of RNA alignments

    DEFF Research Database (Denmark)

    Andersen, Ebbe Sloth; Lind-Thomsen, Allan; Knudsen, Bjarne

    2007-01-01

    connects to external tools to provide a flexible semiautomatic editing environment. A new method, Pcluster, is introduced for dividing the sequences of an RNA alignment into subgroups with secondary structure differences. Pcluster was used to evaluate 574 seed alignments obtained from the Rfam database...... and we identified 71 alignments with significant prediction of inconsistent base pairs and 102 alignments with significant prediction of novel base pairs. Four RNA families were used to illustrate how SARSE can be used to manually or automatically correct the inconsistent base pairs detected by Pcluster......: the mir-399 RNA, vertebrate telomase RNA (vert-TR), bacterial transfer-messenger RNA (tmRNA), and the signal recognition particle (SRP) RNA. The general use of the method is illustrated by the ability to accommodate pseudoknots and handle even large and divergent RNA families. The open architecture...

  1. Analysis of computational complexity for HT-based fingerprint alignment algorithms on java card environment

    CSIR Research Space (South Africa)

    Mlambo, CS

    2015-01-01

    Full Text Available In this paper, implementations of three Hough Transform based fingerprint alignment algorithms are analyzed with respect to time complexity on Java Card environment. Three algorithms are: Local Match Based Approach (LMBA), Discretized Rotation Based...

  2. Numerical simulation on beam breakup unstability of linear induction accelerator

    International Nuclear Information System (INIS)

    Zhang Kaizhi; Wang Huacen; Lin Yuzheng

    2003-01-01

    A code is written to simulate BBU in induction linac according to theoretical analysis. The general form of evolution of BBU in induction linac is investigated at first, then the effect of related parameters on BBU is analyzed, for example, the alignment error, oscillation frequency of beam centroid, beam pulse shape and acceleration gradient. At last measures are put forward to damp beam breakup unstability (BBU)

  3. A test beam upgrade based on the BEPC-LINAC

    International Nuclear Information System (INIS)

    Li Jiacai; Wu Yuanming; Cui Xiangzong; Zhang Liangsheng; Zhou Baoqing; Liu Zhengquan; Zhang Shaoping; Sun Changchun; Zhang Zhuxiang; Zhang Caidi; Zheng Linsheng; Liu Shixing; Shen Ji; Yin Zejie; Zhang Yongming; Chen Ziyu

    2004-01-01

    A total of three beam lines, E1, E2 and E3 have based on the LINAC of BEPC. The E1 beam is to be used for intense slow-positron facility. The E2 is a primary positron or electron beam with an energy of 1.3-1.5 GeV. The E3 is a secondary electron or pion test beam with a momentum can be adjustable continuously. The position accuracy of a detected particle is 0.2-0.4 mm with an event rate of 3 - 4 Hz. This beam has been successfully used for some detectors beam test. (author)

  4. A unified analysis of FBP-based algorithms in helical cone-beam and circular cone- and fan-beam scans

    International Nuclear Information System (INIS)

    Pan Xiaochuan; Xia Dan; Zou Yu; Yu Lifeng

    2004-01-01

    A circular scanning trajectory is and will likely remain a popular choice of trajectory in computed tomography (CT) imaging because it is easy to implement and control. Filtered-backprojection (FBP)-based algorithms have been developed previously for approximate and exact reconstruction of the entire image or a region of interest within the image in circular cone-beam and fan-beam cases. Recently, we have developed a 3D FBP-based algorithm for image reconstruction on PI-line segments in a helical cone-beam scan. In this work, we demonstrated that the 3D FBP-based algorithm indeed provided a rather general formulation for image reconstruction from divergent projections (such as cone-beam and fan-beam projections). On the basis of this formulation we derived new approximate or exact algorithms for image reconstruction in circular cone-beam or fan-beam scans, which can be interpreted as special cases of the helical scan. Existing algorithms corresponding to the derived algorithms were identified. We also performed a preliminary numerical study to verify our theoretical results in each of the cases. The results in the work can readily be generalized to other non-circular trajectories

  5. Study of CMOS Image Sensors for the Alignment System of the CMS Experiment

    Energy Technology Data Exchange (ETDEWEB)

    Virto, A. L.; Vila, I.; Rodrigo, T.; Matorras, F.; Figueroa, C. F.; Calvo, E.; Calderon, A.; Arce, P.; Oller, J. C.; Molinero, A.; Josa, M. I.; Fuentes, J.; Ferrando, A.; Fernandez, M. G.; Barcala, J. M.

    2002-07-01

    We report on an in-depth study made on commercial CMOS image sensors in order to determine their feasibility for beam light position detection in the CMS multipoint alignment scheme. (Author) 21 refs.

  6. Alignment of the MSGC barrel support structure

    International Nuclear Information System (INIS)

    Kari, Tammi; Miikka, Kotamaki; Tommi, Vanhala; Antti, Onnela

    1999-01-01

    The MSGC barrel is a sub-part of the tracking system of the CMS experiment at the LHC. The mechanical support structure of the MSGC barrel consists of ladder-like support beams carrying the detector modules and of four disks supporting the ladders. The required alignment precision of the modules, a few tens of micrometers, is designed to be obtained by precise part manufacture and by careful measurement of the alignment during the assembly of the structure. In the paper the use of digital photogrammetry for the measurement of the alignment of the disks and for the structural verification is presented. Digital photogrammetry was chosen from a number of potential methods after a careful evaluation. The use of photogrammetry for the structural verification of a prototype is presented. The displacements were measured both of unloaded and loaded disk by using photogrammetry and linear displacement transducers for verification. The displacements obtained from the two measurement methods corresponded well, not only to each other, but also to the results given by finite element analysis. The structural verification will be done and the alignment procedure will be tested with a full-sized prototype of a half of the MSGC barrel. Preparations for the photogrammetry measurements are presented and the design of the required supplementary equipment is shown. (authors)

  7. Alignment of the MSGC barrel support structure

    Energy Technology Data Exchange (ETDEWEB)

    Kari, Tammi; Miikka, Kotamaki; Tommi, Vanhala [HIP, Helsinki Institute of Physics, CERN/EP, Geneva (Switzerland); Antti, Onnela [CERN, Conseil Europeen pour la recherche nucleaire, Laboratoire europeen pour la physique des particules, Geneve (Switzerland)

    1999-07-01

    The MSGC barrel is a sub-part of the tracking system of the CMS experiment at the LHC. The mechanical support structure of the MSGC barrel consists of ladder-like support beams carrying the detector modules and of four disks supporting the ladders. The required alignment precision of the modules, a few tens of micrometers, is designed to be obtained by precise part manufacture and by careful measurement of the alignment during the assembly of the structure. In the paper the use of digital photogrammetry for the measurement of the alignment of the disks and for the structural verification is presented. Digital photogrammetry was chosen from a number of potential methods after a careful evaluation. The use of photogrammetry for the structural verification of a prototype is presented. The displacements were measured both of unloaded and loaded disk by using photogrammetry and linear displacement transducers for verification. The displacements obtained from the two measurement methods corresponded well, not only to each other, but also to the results given by finite element analysis. The structural verification will be done and the alignment procedure will be tested with a full-sized prototype of a half of the MSGC barrel. Preparations for the photogrammetry measurements are presented and the design of the required supplementary equipment is shown. (authors)

  8. In-plane aligned YBCO film on textured YSZ buffer layer deposited on NiCr alloy tape by laser ablation with only O+ ion beam assistance

    International Nuclear Information System (INIS)

    Xin Tang Huang

    2000-01-01

    High critical current density and in-plane aligned YBa 2 Cu 3 O 7-x (YBCO) film on a textured yttria-stabilized zirconia (YSZ) buffer layer deposited on NiCr alloy (Hastelloy c-275) tape by laser ablation with only O + ion beam assistance was fabricated. The values of the x-ray phi-scan full width at half-maximum (FWHM) for YSZ(202) and YBCO(103) are 18 deg. and 11 deg., respectively. The critical current density of YBCO film is 7.9 x 105 A cm -2 at liquid nitrogen temperature and zero field, and its critical temperature is 90 K. (author)

  9. A Novel Marker Based Method to Teeth Alignment in MRI

    Science.gov (United States)

    Luukinen, Jean-Marc; Aalto, Daniel; Malinen, Jarmo; Niikuni, Naoko; Saunavaara, Jani; Jääsaari, Päivi; Ojalammi, Antti; Parkkola, Riitta; Soukka, Tero; Happonen, Risto-Pekka

    2018-04-01

    Magnetic resonance imaging (MRI) can precisely capture the anatomy of the vocal tract. However, the crowns of teeth are not visible in standard MRI scans. In this study, a marker-based teeth alignment method is presented and evaluated. Ten patients undergoing orthognathic surgery were enrolled. Supraglottal airways were imaged preoperatively using structural MRI. MRI visible markers were developed, and they were attached to maxillary teeth and corresponding locations on the dental casts. Repeated measurements of intermarker distances in MRI and in a replica model was compared using linear regression analysis. Dental cast MRI and corresponding caliper measurements did not differ significantly. In contrast, the marker locations in vivo differed somewhat from the dental cast measurements likely due to marker placement inaccuracies. The markers were clearly visible in MRI and allowed for dental models to be aligned to head and neck MRI scans.

  10. Beam position diagnostics with higher order modes in third harmonic superconducting accelerating cavities

    International Nuclear Information System (INIS)

    Zhang, Pei

    2013-02-01

    Higher order modes (HOM) are electromagnetic resonant fields. They can be excited by an electron beam entering an accelerating cavity, and constitute a component of the wakefield. This wakefield has the potential to dilute the beam quality and, in the worst case, result in a beam-break-up instability. It is therefore important to ensure that these fields are well suppressed by extracting energy through special couplers. In addition, the effect of the transverse wakefield can be reduced by aligning the beam on the cavity axis. This is due to their strength depending on the transverse offset of the excitation beam. For suitably small offsets the dominant components of the transverse wakefield are dipole modes, with a linear dependence on the transverse offset of the excitation bunch. This fact enables the transverse beam position inside the cavity to be determined by measuring the dipole modes extracted from the couplers, similar to a cavity beam position monitor (BPM), but requires no additional vacuum instrumentation. At the FLASH facility in DESY, 1.3 GHz (known as TESLA) and 3.9 GHz (third harmonic) cavities are installed. Wakefields in 3.9 GHz cavities are significantly larger than in the 1.3 GHz cavities. It is therefore important to mitigate the adverse effects of HOMs to the beam by aligning the beam on the electric axis of the cavities. This alignment requires an accurate beam position diagnostics inside the 3.9 GHz cavities. It is this aspect that is focused on in this thesis. Although the principle of beam diagnostics with HOM has been demonstrated on 1.3 GHz cavities, the realization in 3.9 GHz cavities is considerably more challenging. This is due to the dense HOM spectrum and the relatively strong coupling of most HOMs amongst the four cavities in the third harmonic cryo-module. A comprehensive series of simulations and HOM spectra measurements have been performed in order to study the modal band structure of the 3.9 GHz cavities. The dependencies of

  11. Beam position diagnostics with higher order modes in third harmonic superconducting accelerating cavities

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Pei

    2013-02-15

    Higher order modes (HOM) are electromagnetic resonant fields. They can be excited by an electron beam entering an accelerating cavity, and constitute a component of the wakefield. This wakefield has the potential to dilute the beam quality and, in the worst case, result in a beam-break-up instability. It is therefore important to ensure that these fields are well suppressed by extracting energy through special couplers. In addition, the effect of the transverse wakefield can be reduced by aligning the beam on the cavity axis. This is due to their strength depending on the transverse offset of the excitation beam. For suitably small offsets the dominant components of the transverse wakefield are dipole modes, with a linear dependence on the transverse offset of the excitation bunch. This fact enables the transverse beam position inside the cavity to be determined by measuring the dipole modes extracted from the couplers, similar to a cavity beam position monitor (BPM), but requires no additional vacuum instrumentation. At the FLASH facility in DESY, 1.3 GHz (known as TESLA) and 3.9 GHz (third harmonic) cavities are installed. Wakefields in 3.9 GHz cavities are significantly larger than in the 1.3 GHz cavities. It is therefore important to mitigate the adverse effects of HOMs to the beam by aligning the beam on the electric axis of the cavities. This alignment requires an accurate beam position diagnostics inside the 3.9 GHz cavities. It is this aspect that is focused on in this thesis. Although the principle of beam diagnostics with HOM has been demonstrated on 1.3 GHz cavities, the realization in 3.9 GHz cavities is considerably more challenging. This is due to the dense HOM spectrum and the relatively strong coupling of most HOMs amongst the four cavities in the third harmonic cryo-module. A comprehensive series of simulations and HOM spectra measurements have been performed in order to study the modal band structure of the 3.9 GHz cavities. The dependencies of

  12. Optical design of the National Ignition Facility main laser and switchyard/target area beam transport systems

    Science.gov (United States)

    Miller, John L.; English, R. Edward, Jr.; Korniski, Ronald J.; Rodgers, J. Michael

    1999-07-01

    The optical design of the main laser and transport mirror sections of the National Ignition Facility are described. For the main laser the configuration, layout constraints, multiple beam arrangement, pinhole layout and beam paths, clear aperture budget, ray trace models, alignment constraints, lens designs, wavefront performance, and pupil aberrations are discussed. For the transport mirror system the layout, alignment controls and clear aperture budget are described.

  13. Automatic alignment device for focal spot measurements in the center of the field for mammography; Sistema automatico de alinhamento para avaliacao do ponto focal no centro do campo de equipamentos mamograficos

    Energy Technology Data Exchange (ETDEWEB)

    Vieira, Marcelo A.C.; Watanabe, Alex O.; Oliveira Junior, Paulo D.; Schiabel, Homero [Universidade de Sao Paulo (USP), Sao Carlos, SP (Brazil). Escola de Engenharia. Dept. de Engenharia Eletrica], e-mail: mvieira@sc.usp.br

    2010-03-15

    Some quality control procedures used for mammography, such as focal spot evaluation, requires previous alignment of the measurement equipment with the X-ray central beam. However, alignment procedures are, in general, the most difficult task and the one that needs more time to be performed. Moreover, the operator sometimes is exposed to radiation during this procedure. This work presents an automatic alignment system for mammographic equipment that allows locating the central ray of the radiation beam and, immediately, aligns with it by dislocating itself automatically along the field. The system consists on a bidirectional moving device, connected to a CCD sensor for digital radiographic image acquisition. A computational analysis of a radiographic image, acquired at any position on the field, is performed in order to determine its positioning under the X-ray beam. Finally, a mechanical system for two moving directions, electronically controlled by a microcontroller under USB communication, makes the system to align automatically with the radiation beam central ray. The alignment process is fully automatic, fast and accurate, with no operator exposure to radiation, which allows a considerable time saving for quality control procedures achievement for mammography. (author)

  14. Applications of power beaming from space-based nuclear power stations. [Laser beaming to airplanes; microwave beaming to ground

    Energy Technology Data Exchange (ETDEWEB)

    Powell, J.R.; Botts, T.E.; Hertzberg, A.

    1981-01-01

    Power beaming from space-based reactor systems is examined using an advanced compact, lightweight Rotating Bed Reactor (RBR). Closed Brayton power conversion efficiencies in the range of 30 to 40% can be achieved with turbines, with reactor exit temperatures on the order of 2000/sup 0/K and a liquid drop radiator to reject heat at temperatures of approx. 500/sup 0/K. Higher RBR coolant temperatures (up to approx. 3000/sup 0/K) are possible, but gains in power conversion efficiency are minimal, due to lower expander efficiency (e.g., a MHD generator). Two power beaming applications are examined - laser beaming to airplanes and microwave beaming to fixed ground receivers. Use of the RBR greatly reduces system weight and cost, as compared to solar power sources. Payback times are a few years at present prices for power and airplane fuel.

  15. Rapid Transfer Alignment of MEMS SINS Based on Adaptive Incremental Kalman Filter.

    Science.gov (United States)

    Chu, Hairong; Sun, Tingting; Zhang, Baiqiang; Zhang, Hongwei; Chen, Yang

    2017-01-14

    In airborne MEMS SINS transfer alignment, the error of MEMS IMU is highly environment-dependent and the parameters of the system model are also uncertain, which may lead to large error and bad convergence of the Kalman filter. In order to solve this problem, an improved adaptive incremental Kalman filter (AIKF) algorithm is proposed. First, the model of SINS transfer alignment is defined based on the "Velocity and Attitude" matching method. Then the detailed algorithm progress of AIKF and its recurrence formulas are presented. The performance and calculation amount of AKF and AIKF are also compared. Finally, a simulation test is designed to verify the accuracy and the rapidity of the AIKF algorithm by comparing it with KF and AKF. The results show that the AIKF algorithm has better estimation accuracy and shorter convergence time, especially for the bias of the gyroscope and the accelerometer, which can meet the accuracy and rapidity requirement of transfer alignment.

  16. Rapid Transfer Alignment of MEMS SINS Based on Adaptive Incremental Kalman Filter

    Directory of Open Access Journals (Sweden)

    Hairong Chu

    2017-01-01

    Full Text Available In airborne MEMS SINS transfer alignment, the error of MEMS IMU is highly environment-dependent and the parameters of the system model are also uncertain, which may lead to large error and bad convergence of the Kalman filter. In order to solve this problem, an improved adaptive incremental Kalman filter (AIKF algorithm is proposed. First, the model of SINS transfer alignment is defined based on the “Velocity and Attitude” matching method. Then the detailed algorithm progress of AIKF and its recurrence formulas are presented. The performance and calculation amount of AKF and AIKF are also compared. Finally, a simulation test is designed to verify the accuracy and the rapidity of the AIKF algorithm by comparing it with KF and AKF. The results show that the AIKF algorithm has better estimation accuracy and shorter convergence time, especially for the bias of the gyroscope and the accelerometer, which can meet the accuracy and rapidity requirement of transfer alignment.

  17. A scintillating fibre-based profiler for low intensity ion beams

    Energy Technology Data Exchange (ETDEWEB)

    Finocchiaro, P. [Istituto Nazionale di Fisica Nucleare, Catania (Italy); Amato, A. [Istituto Nazionale di Fisica Nucleare, Catania (Italy); Ciavola, G. [Istituto Nazionale di Fisica Nucleare, Catania (Italy); Cuttone, G. [Istituto Nazionale di Fisica Nucleare, Catania (Italy); Gu, M. [Istituto Nazionale di Fisica Nucleare, Catania (Italy); Raia, G. [Istituto Nazionale di Fisica Nucleare, Catania (Italy); Rovelli, A. [Istituto Nazionale di Fisica Nucleare, Catania (Italy)

    1997-01-11

    In the framework of the EXCYT radioactive ion beam facility, now under development at LNS Catania, we have developed a new beam profile monitor based on a scintillating fibre and a photodetector. Its sensitivity allows the detection of single beam particles in pulse mode, thus representing a useful tool for diagnostics of low and very low intensity beams. (orig.).

  18. A scintillating fibre-based profiler for low intensity ion beams

    International Nuclear Information System (INIS)

    Finocchiaro, P.; Amato, A.; Ciavola, G.; Cuttone, G.; Gu, M.; Raia, G.; Rovelli, A.

    1997-01-01

    In the framework of the EXCYT radioactive ion beam facility, now under development at LNS Catania, we have developed a new beam profile monitor based on a scintillating fibre and a photodetector. Its sensitivity allows the detection of single beam particles in pulse mode, thus representing a useful tool for diagnostics of low and very low intensity beams. (orig.)

  19. Band Alignment at GaN/Single-Layer WSe2 Interface

    KAUST Repository

    Tangi, Malleswararao

    2017-02-21

    We study the band discontinuity at the GaN/single-layer (SL) WSe2 heterointerface. The GaN thin layer is epitaxially grown by molecular beam epitaxy on chemically vapor deposited SL-WSe2/c-sapphire. We confirm that the WSe2 was formed as an SL from structural and optical analyses using atomic force microscopy, scanning transmission electron microscopy, micro-Raman, absorbance, and microphotoluminescence spectra. The determination of band offset parameters at the GaN/SL-WSe2 heterojunction is obtained by high-resolution X-ray photoelectron spectroscopy, electron affinities, and the electronic bandgap values of SL-WSe2 and GaN. The valence band and conduction band offset values are determined to be 2.25 ± 0.15 and 0.80 ± 0.15 eV, respectively, with type II band alignment. The band alignment parameters determined here provide a route toward the integration of group III nitride semiconducting materials with transition metal dichalcogenides (TMDs) for designing and modeling of their heterojunction-based electronic and optoelectronic devices.

  20. Band Alignment at GaN/Single-Layer WSe2 Interface

    KAUST Repository

    Tangi, Malleswararao; Mishra, Pawan; Tseng, Chien-Chih; Ng, Tien Khee; Hedhili, Mohamed N.; Anjum, Dalaver H.; Alias, Mohd Sharizal; Wei, Nini; Li, Lain-Jong; Ooi, Boon S.

    2017-01-01

    We study the band discontinuity at the GaN/single-layer (SL) WSe2 heterointerface. The GaN thin layer is epitaxially grown by molecular beam epitaxy on chemically vapor deposited SL-WSe2/c-sapphire. We confirm that the WSe2 was formed as an SL from structural and optical analyses using atomic force microscopy, scanning transmission electron microscopy, micro-Raman, absorbance, and microphotoluminescence spectra. The determination of band offset parameters at the GaN/SL-WSe2 heterojunction is obtained by high-resolution X-ray photoelectron spectroscopy, electron affinities, and the electronic bandgap values of SL-WSe2 and GaN. The valence band and conduction band offset values are determined to be 2.25 ± 0.15 and 0.80 ± 0.15 eV, respectively, with type II band alignment. The band alignment parameters determined here provide a route toward the integration of group III nitride semiconducting materials with transition metal dichalcogenides (TMDs) for designing and modeling of their heterojunction-based electronic and optoelectronic devices.

  1. Development and preliminary evaluation of a new anatomically based prosthetic alignment method for below-knee prosthesis.

    Science.gov (United States)

    Tafti, Nahid; Karimlou, Masoud; Mardani, Mohammad Ali; Jafarpisheh, Amir Salar; Aminian, Gholam Reza; Safari, Reza

    2018-04-20

    The objectives of current study were to a) assess similarities and relationships between anatomical landmark-based angles and distances of lower limbs in unilateral transtibial amputees and b) develop and evaluate a new anatomically based static prosthetic alignment method. First sub-study assessed the anthropometrical differences and relationships between the lower limbs in the photographs taken from amputees. Data were analysed via paired t-test and regression analysis. Results show no significant differences in frontal and transverse planes. In the sagittal plane, the anthropometric parameters of the amputated limb were significantly correlated to the corresponding variables of the sound limb. The results served as bases for the development of a new prosthetic alignment method. The method was evaluated on a single subject study. Prosthetic alignment carried out by an experienced prosthetist was compared with such alignment adjusted by an inexperienced prosthetist but with the use of the developed method. In sagittal and frontal planes, the socket angle was tuned with respect to the shin angle, and the position of the prosthetic foot was tuned in relation to the pelvic landmarks. Further study is needed to assess the proposed method on a larger sample of amputees and prosthetists.

  2. Value-based insurance design: aligning incentives and evidence in pulmonary medicine.

    Science.gov (United States)

    Fendrick, A Mark; Zank, Daniel C

    2013-11-01

    When consumers are required to pay the same out-of-pocket amount for pulmonary services for which clinical benefits depend on patient characteristics, clinical indication, and provider choice, there is an enormous potential for both underutilization and overutilization. Unlike most current one-size-fits-all health plan designs, value-based insurance design (V-BID) explicitly acknowledges clinical heterogeneity across the continuum of care. By adding clinical nuance to benefit design, V-BID seeks to align consumer and provider incentives with value, encouraging the use of high-value services and discouraging the use of low-value interventions. This article describes the concept of V-BID; creates a framework for its development in pulmonary medicine; and outlines how this concept aligns with research, care delivery, and payment reform initiatives.

  3. AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework.

    Directory of Open Access Journals (Sweden)

    Qi Zheng

    2016-10-01

    Full Text Available Accurate mapping of next-generation sequencing (NGS reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost's algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost.

  4. AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework.

    Science.gov (United States)

    Zheng, Qi; Grice, Elizabeth A

    2016-10-01

    Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost's algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost.

  5. Electron beam writing on semiconductors

    International Nuclear Information System (INIS)

    Bierhenke, H.; Kutzer, E.; Pascher, A.; Plitzner, H.; Rummel, P.; Siemens A.G., Muenchen; Siemens A.G., Muenchen

    1979-08-01

    Reported are the results of the 3 1/2 year research project 'Electron beam Writing on Semiconductors'. Work has been done in the field of direct wafer exposure techniques, and of mask making. Described are resist technology, setting up of a research device, exploration of alignment procedures, manufacturing of devices and their radiation influence. Furthermore, investigations and measurements of an electron beam machine bought for mask making purposes, the development of LSI-circuits with this machine, the software necessary and important developments of digital subsystems are reported. (orig.) [de

  6. High-speed all-optical DNA local sequence alignment based on a three-dimensional artificial neural network.

    Science.gov (United States)

    Maleki, Ehsan; Babashah, Hossein; Koohi, Somayyeh; Kavehvash, Zahra

    2017-07-01

    This paper presents an optical processing approach for exploring a large number of genome sequences. Specifically, we propose an optical correlator for global alignment and an extended moiré matching technique for local analysis of spatially coded DNA, whose output is fed to a novel three-dimensional artificial neural network for local DNA alignment. All-optical implementation of the proposed 3D artificial neural network is developed and its accuracy is verified in Zemax. Thanks to its parallel processing capability, the proposed structure performs local alignment of 4 million sequences of 150 base pairs in a few seconds, which is much faster than its electrical counterparts, such as the basic local alignment search tool.

  7. Laser beam propagation in nematic liquid crystals at the temperature close to the nematicisotropic critical point.

    Science.gov (United States)

    Chen, Yu-Jen; Lin, Yu-Sung; Jiang, I-Min; Tsai, Ming-Shan

    2008-03-17

    This study investigates the optical nonlinearity of beam propagation in homogeneously aligned nematic liquid crystal (NLC) cells at a temperature close to the nematic-isotropic temperature (TNI). The undulate propagation mode with convergent and divergent loops appearing alternately is reported and the thermally enhanced optical reorientation nonlinearity at the focus is described. The optically induced phase transition exists along the pump beam direction. With the application of the conscopic technique, the arrangements of LC at the focus are proposed in this study. Results of this study demonstrate that the evolution of the LC configuration was affected by the pump beam based on the analysis of conoscopic patterns.

  8. Review of alignment activities for indus-1 and 2 at CAT

    International Nuclear Information System (INIS)

    Nema, P.K.; Sahu, R.K.; Prasad, V.

    1999-01-01

    Survey and alignment activities at CAT (Centre for Advanced Technology - India) are related to two accelerator projects called INDUS-1 and INDUS -2. Former is a 450 MeV SRS and latter is a 2.5 GeV SRS. Both the machines use a 450/700 MeV booster synchrotron and 20 MeV pre-injector microtron for injection. Indus-1 was commissioned with 100 mA stored beam current in May 1999. Indus-2 is under construction and expected to be commissioned within next 4 years. Survey and alignment work of booster synchrotron and Indus-1 (storage ring) was accomplished using optical surveying techniques with software ECDS-2 of Kern. That was possible due to small size of machines of Indus-1. For Indus-2 with circumference of 172.47 m, the network surveying and alignment scheme has been planned. Indus-2 is a high brilliance machine and this puts more stringent requirements on alignment. This paper describes methodology and performance results of Indus-1 alignment and strategy for Indus-2. (authors)

  9. Alignment analysis of urban railways based on passenger travel demand

    DEFF Research Database (Denmark)

    Andersen, Jonas Lohmann Elkjær; Landex, Alex

    2010-01-01

    Planning of urban railways like Metro and especially Light Rail Transit often result in multiple alignment alternatives from where it can be difficult to select the best one. Travel demand is a good foundation for evaluating a railway alignment for its ability to attract passengers. Therefore...... and can be applied as decision support in different stages of the urban railway alignment planning....

  10. Quality measures for HRR alignment based ISAR imaging algorithms

    CSIR Research Space (South Africa)

    Janse van Rensburg, V

    2013-05-01

    Full Text Available Some Inverse Synthetic Aperture Radar (ISAR) algorithms form the image in a two-step process of range alignment and phase conjugation. This paper discusses a comprehensive set of measures used to quantify the quality of range alignment, with the aim...

  11. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    Gervasio Gomez

    2012-01-01

      The new alignment for the DT chambers has been successfully used in physics analysis starting with the 52X Global Tag. The remaining main areas of development over the next few months will be preparing a new track-based CSC alignment and producing realistic APEs (alignment position errors) and MC misalignment scenarios to match the latest muon alignment constants. Work on these items has been delayed from the intended timeline, mostly due to a large involvement of the muon alignment man-power in physics analyses over the first half of this year. As CMS keeps probing higher and higher energies, special attention must be paid to the reconstruction of very-high-energy muons. Recent muon POG reports from mid-June show a φ-dependence in curvature bias in Monte Carlo samples. This bias is observed already at the tracker level, where it is constant with muon pT, while it grows with pT as muon chamber information is added to the tracks. Similar studies show a much smaller effect in data, at le...

  12. Design process for NIF laser alignment and beam diagnostics

    Energy Technology Data Exchange (ETDEWEB)

    Grey, A., LLNL

    1998-06-09

    In a controller for an adaptive optic system designed to correct phase aberrations in a high power laser, the wavefront sensor is a discrete Hartmann-Shack design. It uses an army of lenslets (like a fly` s eye) to focus the laser into 77 spots on a CCD camera. Average local tilt of the wavefront across each lenslet changes the position of its focal spot. The system requires 0.1 pixel accuracy in determining the focal spot location. We determine a small area around each spot` s previous location. Within this area, we calculate the centroid of the light intensity in x and y. This calculation fails if the spot regions overlap. Especially during initial acquisition of a highly distorted beam, distinguishing overlapping spots is difficult. However, low resolution analysis of the overlapping spots allows the system to estimate their positions. With this estimate, it can use the deformable mirror to correct the beam enough so we can detect the spots using conventional image processing.

  13. Concept and design of an alignment monitoring system for the CBM RICH mirrors

    Energy Technology Data Exchange (ETDEWEB)

    Bendarouach, Jordan [Justus Liebig University (Germany); Collaboration: CBM-Collaboration

    2016-07-01

    The Compressed Baryonic Matter (CBM) experiment at the future FAIR (Facility for Antiproton and Ion Research) complex will investigate the phase diagram of strongly interacting matter at high baryon density and moderate temperatures in A+A collisions from 2-11 AGeV (SIS100) beam energy. One of the key detector components required for this CBM physics program is the RICH (Ring Imaging CHerenkov) detector, developed for efficient and clean electron identification and pion suppression. The detector consists of about 80 spherical glass mirror tiles, distributed over two sphere parts. An important aspect to guarantee a stable operation of the RICH detector is the alignment of the mirrors. A method originally developed and inspired by the HERA-B experiment uses recorded data to assess mirror alignment of the RICH mirror system. Measurements of Cherenkov distances and angles on the PMT plane may reveal potential misalignments of the considered tile. If mirror misalignment is revealed, it can be subsequently included and rectified by correction routines, which should mostly increase ring reconstruction as well as ring-track matching efficiencies. Results of this alignment method based on simulated events, reproducing potential mirror misalignments, its limits and first correction routines are presented.

  14. Acceleration of laser-injected electron beams in an electron-beam driven plasma wakefield accelerator

    International Nuclear Information System (INIS)

    Knetsch, Alexander

    2018-03-01

    Plasma wakefields deliver accelerating fields that are approximately a 100 times higher than those in conventional radiofrequency or even superconducting radiofrequency cavities. This opens a transformative path towards novel, compact and potentially ubiquitous accelerators. These prospects, and the increasing demand for electron accelerator beamtime for various applications in natural, material and life sciences, motivate the research and development on novel plasma-based accelerator concepts. However, these electron beam sources need to be understood and controlled. The focus of this thesis is on electron beam-driven plasma wakefield acceleration (PWFA) and the controlled injection and acceleration of secondary electron bunches in the accelerating wake fields by means of a short-pulse near-infrared laser. Two laser-triggered injection methods are explored. The first one is the Trojan Horse Injection, which relies on very good alignment and timing control between electron beam and laser pulse and then promises electron bunches with hitherto unprecedented quality as regards emittance and brightness. The physics of electron injection in the Trojan Horse case is explored with a focus on the final longitudinal bunch length. Then a theoretical and numerical study is presented that examines the physics of Trojan Horse injection when performed in an expanding wake generated by a smooth density down-ramp. The benefits are radically decreased drive-electron bunch requirements and a unique bunch-length control that enables longitudinal electron-bunch shaping. The second laser-triggered injection method is the Plasma Torch Injection, which is a versatile, all-optical laser-plasma-based method capable to realize tunable density downramp injection. At the SLAC National Laboratory, the first proof-of-principle was achieved both for Trojan Horse and Plasma Torch injection. Setup details and results are reported in the experimental part of the thesis along with the commissioning

  15. Band Alignment Determination of Two-Dimensional Heterojunctions and Their Electronic Applications

    KAUST Repository

    Chiu, Ming-Hui

    2018-05-09

    Two-dimensional (2D) layered materials such as MoS2 have been recognized as high on-off ratio semiconductors which are promising candidates for electronic and optoelectronic devices. In addition to the use of individual 2D materials, the accelerated field of 2D heterostructures enables even greater functionalities. Device designs differ, and they are strongly controlled by the electronic band alignment. For example, photovoltaic cells require type II heterostructures for light harvesting, and light-emitting diodes benefit from multiple quantum wells with the type I band alignment for high emission efficiency. The vertical tunneling field-effect transistor for next-generation electronics depends on nearly broken-gap band alignment for boosting its performance. To tailor these 2D layered materials toward possible future applications, the understanding of 2D heterostructure band alignment becomes critically important. In the first part of this thesis, we discuss the band alignment of 2D heterostructures. To do so, we firstly study the interlayer coupling between two dissimilar 2D materials. We conclude that a post-anneal process could enhance the interlayer coupling of as-transferred 2D heterostructures, and heterostructural stacking imposes similar symmetry changes as homostructural stacking. Later, we precisely determine the quasi particle bandgap and band alignment of the MoS2/WSe2 heterostructure by using scan tunneling microscopy/spectroscopy (STM/S) and micron-beam X-ray photoelectron spectroscopy (μ-XPS) techniques. Lastly, we prove that the band alignment of 2D heterojunctions can be accurately predicted by Anderson’s model, which has previously failed to predict conventional bulk heterostructures. In the second part of this thesis, we develop a new Chemical Vapor Deposition (CVD) method capable of precisely controlling the growth area of p- and n-type transition metal dichalcogenides (TMDCs) and further form lateral or vertical 2D heterostructures. This

  16. Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

    Directory of Open Access Journals (Sweden)

    Xin He

    2009-03-01

    Full Text Available Cross-species comparison has emerged as a powerful paradigm for predicting cis-regulatory modules (CRMs and understanding their evolution. The comparison requires reliable sequence alignment, which remains a challenging task for less conserved noncoding sequences. Furthermore, the existing models of DNA sequence evolution generally do not explicitly treat the special properties of CRM sequences. To address these limitations, we propose a model of CRM evolution that captures different modes of evolution of functional transcription factor binding sites (TFBSs and the background sequences. A particularly novel aspect of our work is a probabilistic model of gains and losses of TFBSs, a process being recognized as an important part of regulatory sequence evolution. We present a computational framework that uses this model to solve the problems of CRM alignment and prediction. Our alignment method is similar to existing methods of statistical alignment but uses the conserved binding sites to improve alignment. Our CRM prediction method deals with the inherent uncertainties of binding site annotations and sequence alignment in a probabilistic framework. In simulated as well as real data, we demonstrate that our program is able to improve both alignment and prediction of CRM sequences over several state-of-the-art methods. Finally, we used alignments produced by our program to study binding site conservation in genome-wide binding data of key transcription factors in the Drosophila blastoderm, with two intriguing results: (i the factor-bound sequences are under strong evolutionary constraints even if their neighboring genes are not expressed in the blastoderm and (ii binding sites in distal bound sequences (relative to transcription start sites tend to be more conserved than those in proximal regions. Our approach is implemented as software, EMMA (Evolutionary Model-based cis-regulatory Module Analysis, ready to be applied in a broad biological context.

  17. Beam-Based Diagnostics of RF-Breakdown in the Two-Beam Test-Stand in CTF3

    CERN Document Server

    Johnson, M

    2007-01-01

    The general outline of a beam-based diagnostic method of RF-breakdown, using BPMs, at the two-beam test-stand in CTF3 is discussed. The basic components of the set-up and their functions in the diagnostic are described. Estimations of the expected error in the measured parameters are performed.

  18. Development of distributed ion pumps for g-2 beam vacuum system

    Energy Technology Data Exchange (ETDEWEB)

    Hseuh, H.C.; Mapes, M.; Snydstrup, L.

    1993-06-01

    Distributed ion pumps (DIPs) will be used for the beam vacuum system of the g-2 muon storage ring. The magnetic field intensity and alignment angle at the DIP locations are not uniform. The pumping behavior of several different ion pump elements under this non-uniform magnetic field has been studied. The results are compared with the theoretical predictions. Based on these results, the optimum design of the g-2 DIPs has been developed.

  19. Development of distributed ion pumps for g-2 beam vacuum system

    Energy Technology Data Exchange (ETDEWEB)

    Hseuh, H.C.; Mapes, M.; Snydstrup, L.

    1993-01-01

    Distributed ion pumps (DIPs) will be used for the beam vacuum system of the g-2 muon storage ring. The magnetic field intensity and alignment angle at the DIP locations are not uniform. The pumping behavior of several different ion pump elements under this non-uniform magnetic field has been studied. The results are compared with the theoretical predictions. Based on these results, the optimum design of the g-2 DIPs has been developed.

  20. Markov random field based automatic image alignment for electron tomography.

    Science.gov (United States)

    Amat, Fernando; Moussavi, Farshid; Comolli, Luis R; Elidan, Gal; Downing, Kenneth H; Horowitz, Mark

    2008-03-01

    We present a method for automatic full-precision alignment of the images in a tomographic tilt series. Full-precision automatic alignment of cryo electron microscopy images has remained a difficult challenge to date, due to the limited electron dose and low image contrast. These facts lead to poor signal to noise ratio (SNR) in the images, which causes automatic feature trackers to generate errors, even with high contrast gold particles as fiducial features. To enable fully automatic alignment for full-precision reconstructions, we frame the problem probabilistically as finding the most likely particle tracks given a set of noisy images, using contextual information to make the solution more robust to the noise in each image. To solve this maximum likelihood problem, we use Markov Random Fields (MRF) to establish the correspondence of features in alignment and robust optimization for projection model estimation. The resulting algorithm, called Robust Alignment and Projection Estimation for Tomographic Reconstruction, or RAPTOR, has not needed any manual intervention for the difficult datasets we have tried, and has provided sub-pixel alignment that is as good as the manual approach by an expert user. We are able to automatically map complete and partial marker trajectories and thus obtain highly accurate image alignment. Our method has been applied to challenging cryo electron tomographic datasets with low SNR from intact bacterial cells, as well as several plastic section and X-ray datasets.

  1. QUASAR--scoring and ranking of sequence-structure alignments.

    Science.gov (United States)

    Birzele, Fabian; Gewehr, Jan E; Zimmer, Ralf

    2005-12-15

    Sequence-structure alignments are a common means for protein structure prediction in the fields of fold recognition and homology modeling, and there is a broad variety of programs that provide such alignments based on sequence similarity, secondary structure or contact potentials. Nevertheless, finding the best sequence-structure alignment in a pool of alignments remains a difficult problem. QUASAR (quality of sequence-structure alignments ranking) provides a unifying framework for scoring sequence-structure alignments that aids finding well-performing combinations of well-known and custom-made scoring schemes. Those scoring functions can be benchmarked against widely accepted quality scores like MaxSub, TMScore, Touch and APDB, thus enabling users to test their own alignment scores against 'standard-of-truth' structure-based scores. Furthermore, individual score combinations can be optimized with respect to benchmark sets based on known structural relationships using QUASAR's in-built optimization routines.

  2. Experimental Results from a Microwave Cavity Beam Position Monitor

    International Nuclear Information System (INIS)

    Balakin, V.; Bazhan, A.; Lunev, P.; Solyak, N.; Vogel, V.; Zhogolev, P.; Lisitsyn, A.; Yakimenko, V.

    1999-01-01

    Future Linear Colliders have hard requirements for the beam transverse position stability in the accelerator. A beam Position Monitor (BPM) with the resolution better than 0.1 micron in the single bunch regime is needed to control the stability of the beam position along the linac. Proposed BPM is based on the measurement of the asymmetrical mode excited by single bunch in the cavity. Four stages of signal processing (space-, time-, frequency- and phase-filtering providing the required signal-to-noise ratio) are used to obtain extremely high resolution. The measurement set-up was designed by BINP and installed at ATF/BNL to test experimentally this concept. The set-up includes three two-coordinates BPM's at the frequency of 13.566 GHz, and reference intensity/phase cavity. BPM's were mounted on support table. The two-coordinates movers allow to move and align BPM's along the straight line, using the signals from the beam. The position of each monitor is controlled by the sensors with the accuracy 0.03 micron. The information from three monitors allows to exclude angle and position jitter of the beam and measure BPM resolution. In the experiments the resolution of about 0.15 micron for 0.25 nC beam intensity was obtained, that is close to the value required

  3. Alignment methods: strategies, challenges, benchmarking, and comparative overview.

    Science.gov (United States)

    Löytynoja, Ari

    2012-01-01

    Comparative evolutionary analyses of molecular sequences are solely based on the identities and differences detected between homologous characters. Errors in this homology statement, that is errors in the alignment of the sequences, are likely to lead to errors in the downstream analyses. Sequence alignment and phylogenetic inference are tightly connected and many popular alignment programs use the phylogeny to divide the alignment problem into smaller tasks. They then neglect the phylogenetic tree, however, and produce alignments that are not evolutionarily meaningful. The use of phylogeny-aware methods reduces the error but the resulting alignments, with evolutionarily correct representation of homology, can challenge the existing practices and methods for viewing and visualising the sequences. The inter-dependency of alignment and phylogeny can be resolved by joint estimation of the two; methods based on statistical models allow for inferring the alignment parameters from the data and correctly take into account the uncertainty of the solution but remain computationally challenging. Widely used alignment methods are based on heuristic algorithms and unlikely to find globally optimal solutions. The whole concept of one correct alignment for the sequences is questionable, however, as there typically exist vast numbers of alternative, roughly equally good alignments that should also be considered. This uncertainty is hidden by many popular alignment programs and is rarely correctly taken into account in the downstream analyses. The quest for finding and improving the alignment solution is complicated by the lack of suitable measures of alignment goodness. The difficulty of comparing alternative solutions also affects benchmarks of alignment methods and the results strongly depend on the measure used. As the effects of alignment error cannot be predicted, comparing the alignments' performance in downstream analyses is recommended.

  4. A Method for SINS Alignment with Large Initial Misalignment Angles Based on Kalman Filter with Parameters Resetting

    Directory of Open Access Journals (Sweden)

    Xixiang Liu

    2014-01-01

    Full Text Available In the initial alignment process of strapdown inertial navigation system (SINS, large initial misalignment angles always bring nonlinear problem, which causes alignment failure when the classical linear error model and standard Kalman filter are used. In this paper, the problem of large misalignment angles in SINS initial alignment is investigated, and the key reason for alignment failure is given as the state covariance from Kalman filter cannot represent the true one during the steady filtering process. According to the analysis, an alignment method for SINS based on multiresetting the state covariance matrix of Kalman filter is designed to deal with large initial misalignment angles, in which classical linear error model and standard Kalman filter are used, but the state covariance matrix should be multireset before the steady process until large misalignment angles are decreased to small ones. The performance of the proposed method is evaluated by simulation and car test, and the results indicate that the proposed method can fulfill initial alignment with large misalignment angles effectively and the alignment accuracy of the proposed method is as precise as that of alignment with small misalignment angles.

  5. The New Digital-Receiver-Based System for Antiproton Beam Diagnostics

    CERN Document Server

    Angoletta, Maria Elena; Ludwig, M; Marqversen, O; Pedersen, F

    2001-01-01

    An innovative system to measure antiproton beam intensity, momentum spread and mean momentum in CERN's Antiproton Decelerator (AD) is described. This system is based on a state-of-the-art Digital Receiver (DRX) board, consisting of 8 Digital Down-Converter (DDC) chips and one Digital Signal Processor (DSP). An ultra-low-noise, wide-band AC beam transformer (0.2 MHz - 30 MHz) is used to measure AC beam current modulation. For bunched beams, the intensity is obtained by measuring the amplitude of the fundamental and second RF Fourier components. On the magnetic plateaus the beam is debunched for stochastic or electron cooling and longitudinal beam properties (intensity, momentum spread and mean momentum) are measured by FFT-based spectral analysis of Schottky signals. The system thus provides real time information characterising the machine performance; it has been used for troubleshooting and to fine-tune the AD, thus achieving further improved performances. This system has been operating since May 2000 and ty...

  6. Observations of the spatial and temporal structure of field-aligned beam and gyrating ring distributions at the quasi-perpendicular bow shock with Cluster CIS

    Directory of Open Access Journals (Sweden)

    E. Möbius

    2001-09-01

    Full Text Available During the early orbit phase, the Cluster spacecraft have repeatedly crossed the perpendicular Earth’s bow shock and provided the first multi-spacecraft measurements. We have analyzed data from the Cluster Ion Spectrometry experiment (CIS, which observes the 3D-ion distribution function of the major species in the energy range of 5 eV to 40 keV with a 4 s resolution. Beams of reflected ions were observed simultaneously at all spacecraft locations and could be tracked from upstream to the shock itself. They were found to originate from the same distribution of ions that constitutes the reflected gyrating ions, which form a ring distribution in the velocity space immediately upstream and downstream of the shock. This observation suggests a common origin of ring and beam populations at quasi-perpendicular shocks in the form of specular reflection and immediate pitch angle scattering. Generally, the spatial evolution across the shock is very similar on all spacecraft, but phased in time according to their relative location. However, a distinct temporal structure of the ion fluxes in the field-aligned beam is observed that varies simultaneously on all spacecraft. This is likely to reflect the variations in the reflection and scattering efficiencies.Key words. Interplanetary physics (planetary bow shocks; energetic particles; instruments and techniques

  7. The PIAFE project: instrumentation and beam studies

    International Nuclear Information System (INIS)

    Laamyem, M.

    1996-01-01

    The beam transport of low energy radioactive ions over long distances was a key problem for the PIAFE project. The construction of a 18 m long portion validated the technical choices. Problems dealing with the alignment of the beam transport line supports and the quadrupoles have been solved. The beam/residual gas interaction model was confirmed through the measurement of both the charge exchange cross section and the growth of the emittance due to coulomb scattering. This work shows that low energy exotic ions can be transported over long distances with a vacuum around 10 -8 mbar

  8. Effect of field-aligned-beam in parallel diffusion of energetic particles in the Earth's foreshock

    Science.gov (United States)

    Matsukiyo, S.; Nakanishi, K.; Otsuka, F.; Kis, A.; Lemperger, I.; Hada, T.

    2016-12-01

    Diffusive shock acceleration (DSA) is one of the plausible acceleration mechanisms of cosmic rays. In the standard DSA model the partial density of the accelerated particles, diffused into upstream, exponentially decreases as the distance to the shock increases. Kis et al. (GRL, 31, L20801, 2004) examined the density gradients of energetic ions upstream of the bow shock with high accuracy by using Cluster data. They estimated the diffusion coefficients of energetic ions for the event in February 18, 2003 and showed that the obtained diffusion coefficients are significantly smaller than those estimated in the past statistical study. This implies that particle acceleration at the bow shock can be more efficient than considered before. Here, we focus on the effect of the field-aligned-beam (FAB) which is often observed in the foreshock, and examine how the FAB affects the efficiency of diffusion of the energetic ions by performing test particle simulations. The upstream turbulence is given by the superposition of parallel Alfven waves with power-law energy spectrum with random phase approximation. In the spectrum we further add a peak corresponding to the waves resonantly generated by the FAB. The dependence of the diffusion coefficient on the presence of the FAB as well as total energy of the turbulence, power-law index of the turbulence, and intensity of FAB oriented waves are discussed.

  9. Landmark matching based retinal image alignment by enforcing sparsity in correspondence matrix.

    Science.gov (United States)

    Zheng, Yuanjie; Daniel, Ebenezer; Hunter, Allan A; Xiao, Rui; Gao, Jianbin; Li, Hongsheng; Maguire, Maureen G; Brainard, David H; Gee, James C

    2014-08-01

    Retinal image alignment is fundamental to many applications in diagnosis of eye diseases. In this paper, we address the problem of landmark matching based retinal image alignment. We propose a novel landmark matching formulation by enforcing sparsity in the correspondence matrix and offer its solutions based on linear programming. The proposed formulation not only enables a joint estimation of the landmark correspondences and a predefined transformation model but also combines the benefits of the softassign strategy (Chui and Rangarajan, 2003) and the combinatorial optimization of linear programming. We also introduced a set of reinforced self-similarities descriptors which can better characterize local photometric and geometric properties of the retinal image. Theoretical analysis and experimental results with both fundus color images and angiogram images show the superior performances of our algorithms to several state-of-the-art techniques. Copyright © 2013 Elsevier B.V. All rights reserved.

  10. BinAligner: a heuristic method to align biological networks.

    Science.gov (United States)

    Yang, Jialiang; Li, Jun; Grünewald, Stefan; Wan, Xiu-Feng

    2013-01-01

    The advances in high throughput omics technologies have made it possible to characterize molecular interactions within and across various species. Alignments and comparison of molecular networks across species will help detect orthologs and conserved functional modules and provide insights on the evolutionary relationships of the compared species. However, such analyses are not trivial due to the complexity of network and high computational cost. Here we develop a mixture of global and local algorithm, BinAligner, for network alignments. Based on the hypotheses that the similarity between two vertices across networks would be context dependent and that the information from the edges and the structures of subnetworks can be more informative than vertices alone, two scoring schema, 1-neighborhood subnetwork and graphlet, were introduced to derive the scoring matrices between networks, besides the commonly used scoring scheme from vertices. Then the alignment problem is formulated as an assignment problem, which is solved by the combinatorial optimization algorithm, such as the Hungarian method. The proposed algorithm was applied and validated in aligning the protein-protein interaction network of Kaposi's sarcoma associated herpesvirus (KSHV) and that of varicella zoster virus (VZV). Interestingly, we identified several putative functional orthologous proteins with similar functions but very low sequence similarity between the two viruses. For example, KSHV open reading frame 56 (ORF56) and VZV ORF55 are helicase-primase subunits with sequence identity 14.6%, and KSHV ORF75 and VZV ORF44 are tegument proteins with sequence identity 15.3%. These functional pairs can not be identified if one restricts the alignment into orthologous protein pairs. In addition, BinAligner identified a conserved pathway between two viruses, which consists of 7 orthologous protein pairs and these proteins are connected by conserved links. This pathway might be crucial for virus packing and

  11. Modematic: a fast laser beam analyzing system for high power CO2-laser beams

    Science.gov (United States)

    Olsen, Flemming O.; Ulrich, Dan

    2003-03-01

    The performance of an industrial laser is very much depending upon the characteristics of the laser beam. The ISO standards 11146 and 11154 describing test methods for laser beam parameters have been approved. To implement these methods in industry is difficult and especially for the infrared laser sources, such as the CO2-laser, the availabl analyzing systems are slow, difficult to apply and having limited reliability due to the nature of the detection methods. In an EUREKA-project the goal was defined to develop a laser beam analyzing system dedicated to high power CO2-lasers, which could fulfill the demands for an entire analyzing system, automating the time consuming pre-alignment and beam conditioning work required before a beam mode analyses, automating the analyzing sequences and data analysis required to determine the laser beam caustics and last but not least to deliver reliable close to real time data to the operator. The results of this project work will be described in this paper. The research project has led to the development of the Modematic laser beam analyzer, which is ready for the market.

  12. Electron Beam Diagnostics in Plasmas Based on Electron Beam Ionization

    Science.gov (United States)

    Leonhardt, Darrin; Leal-Quiros, Edbertho; Blackwell, David; Walton, Scott; Murphy, Donald; Fernsler, Richard; Meger, Robert

    2001-10-01

    Over the last few years, electron beam ionization has been shown to be a viable generator of high density plasmas with numerous applications in materials modification. To better understand these plasmas, we have fielded electron beam diagnostics to more clearly understand the propagation of the beam as it travels through the background gas and creates the plasma. These diagnostics vary greatly in sophistication, ranging from differentially pumped systems with energy selective elements to metal 'hockey pucks' covered with thin layers of insulation to electrically isolate the detector from the plasma but pass high energy beam electrons. Most importantly, absolute measurements of spatially resolved beam current densities are measured in a variety of pulsed and continuous beam sources. The energy distribution of the beam current(s) will be further discussed, through experiments incorporating various energy resolving elements such as simple grids and more sophisticated cylindrical lens geometries. The results are compared with other experiments of high energy electron beams through gases and appropriate disparities and caveats will be discussed. Finally, plasma parameters are correlated to the measured beam parameters for a more global picture of electron beam produced plasmas.

  13. Beam-based calibration system of BPM offset on BEPC

    International Nuclear Information System (INIS)

    Hu Chunliang

    2004-01-01

    The ever-increasing demand for better performance from circular accelerators requires improved methods to calibrate beam position monitors (BPM). A beam based calibration system has been established to locate the centers of the BPM with respect to the magnetic center of quadrupole magnets. Additional windings are applied to the quadrupole magnets to make the quadrupole magnetic strength individually adjustable and the number of the power supply of all 32 additional windings is only one. Software system has been finished to automatically measure the offsets of BPMs. The effect of the beam-based calibration system shows that the calibration of BPM has been more quickly and accurately

  14. Aligning the unalignable: bacteriophage whole genome alignments.

    Science.gov (United States)

    Bérard, Sèverine; Chateau, Annie; Pompidor, Nicolas; Guertin, Paul; Bergeron, Anne; Swenson, Krister M

    2016-01-13

    In recent years, many studies focused on the description and comparison of large sets of related bacteriophage genomes. Due to the peculiar mosaic structure of these genomes, few informative approaches for comparing whole genomes exist: dot plots diagrams give a mostly qualitative assessment of the similarity/dissimilarity between two or more genomes, and clustering techniques are used to classify genomes. Multiple alignments are conspicuously absent from this scene. Indeed, whole genome aligners interpret lack of similarity between sequences as an indication of rearrangements, insertions, or losses. This behavior makes them ill-prepared to align bacteriophage genomes, where even closely related strains can accomplish the same biological function with highly dissimilar sequences. In this paper, we propose a multiple alignment strategy that exploits functional collinearity shared by related strains of bacteriophages, and uses partial orders to capture mosaicism of sets of genomes. As classical alignments do, the computed alignments can be used to predict that genes have the same biological function, even in the absence of detectable similarity. The Alpha aligner implements these ideas in visual interactive displays, and is used to compute several examples of alignments of Staphylococcus aureus and Mycobacterium bacteriophages, involving up to 29 genomes. Using these datasets, we prove that Alpha alignments are at least as good as those computed by standard aligners. Comparison with the progressive Mauve aligner - which implements a partial order strategy, but whose alignments are linearized - shows a greatly improved interactive graphic display, while avoiding misalignments. Multiple alignments of whole bacteriophage genomes work, and will become an important conceptual and visual tool in comparative genomics of sets of related strains. A python implementation of Alpha, along with installation instructions for Ubuntu and OSX, is available on bitbucket (https://bitbucket.org/thekswenson/alpha).

  15. Application of ion beams for polymeric carbon based biomaterials

    International Nuclear Information System (INIS)

    Evelyn, A.L.

    2001-01-01

    Ion beams have been shown to be quite suitable for the modification and analysis of carbon based biomaterials. Glassy polymeric carbon (GPC), made from cured phenolic resins, has a high chemical inertness that makes it useful as a biomaterial in medicine for drug delivery systems and for the manufacture of heart valves and other prosthetic devices. Low and high-energy ion beams have been used, with both partially and fully cured phenolic resins, to enhance biological cell/tissue growth on, and to increase tissue adhesion to GPC surfaces. Samples bombarded with energetic ion beams in the keV to MeV range exhibited increased surface roughness, measured using optical microscopy and atomic force microscopy. Ion beams were also used to perform nuclear reaction analyses of GPC encapsulated drugs for use in internal drug delivery systems. The results from the high energy bombardment were more dramatic and are shown in this paper. The interaction of energetic ions has demonstrated the useful application of ion beams to enhance the properties of carbon-based biomaterials

  16. SU-E-J-33: Comparison Between Soft Tissue Alignment and Bony Alignment for Pancreatic Cancer Radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Suh, Y; Crane, C; Krishnan, S; Das, P; Koay, E; Beddar, S [UT MD Anderson Cancer Center, Houston, TX (United States)

    2015-06-15

    Purpose An IGRT modality for pancreatic cancer treatment with dose escalation at our institution is in-room daily CT imaging. The purpose of this study is to assess the difference between soft tissue alignment and bony alignment for pancreatic tumor localization. Methods Eighteen patients with pancreatic tumors who underwent IMRT treatment with an inspiration breath-hold technique between July 2012 and February 2015 are included in this study. Prior to each treatment, a CT scan was acquired. The CT image guidance started with auto-alignment to either the bony anatomy (vertebral bodies) or fiducials (for the six patients with the stent in/near the tumor) and then, when necessary, manual adjustments were made based on soft tissue alignment using clinical software (CT-Assisted Targeting system). The difference between soft tissue alignment and bony/fiducial alignment was evaluated. Results Of all 380 treatments, manual adjustment was made in 225 treatments, ranging from 11% (3 treatments out of 28) to 96% (27 treatments out of 28) per patient. The mean of the difference between soft tissue alignment and bony/fiducial alignment per patient ranged from −3.6 to 0.3 mm, −1.5 to 2.8 mm, and −3.3 to 3.4 mm in the AP, SI, and RL directions, respectively. The maximum difference over all treatments was −9.5, −14.6, and −14.6 mm in the AP, SI, and RL directions, respectively. Conclusion About 60% of the time, manual adjustment based on soft tissue alignment was required. The extent of manual adjustment was usually small but varied significantly from patient to patient. The ultimate goal of the IGRT modality using daily CT imaging is not to fully cover the target but to spare organs-at-risk as much as possible to avoid them moving into higher dose gradients than accepted in the treatment plan. To this end, manual adjustment based on soft tissue alignment is critically important.

  17. Tidal alignment of galaxies

    Energy Technology Data Exchange (ETDEWEB)

    Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš

    2015-08-01

    We develop an analytic model for galaxy intrinsic alignments (IA) based on the theory of tidal alignment. We calculate all relevant nonlinear corrections at one-loop order, including effects from nonlinear density evolution, galaxy biasing, and source density weighting. Contributions from density weighting are found to be particularly important and lead to bias dependence of the IA amplitude, even on large scales. This effect may be responsible for much of the luminosity dependence in IA observations. The increase in IA amplitude for more highly biased galaxies reflects their locations in regions with large tidal fields. We also consider the impact of smoothing the tidal field on halo scales. We compare the performance of this consistent nonlinear model in describing the observed alignment of luminous red galaxies with the linear model as well as the frequently used "nonlinear alignment model," finding a significant improvement on small and intermediate scales. We also show that the cross-correlation between density and IA (the "GI" term) can be effectively separated into source alignment and source clustering, and we accurately model the observed alignment down to the one-halo regime using the tidal field from the fully nonlinear halo-matter cross correlation. Inside the one-halo regime, the average alignment of galaxies with density tracers no longer follows the tidal alignment prediction, likely reflecting nonlinear processes that must be considered when modeling IA on these scales. Finally, we discuss tidal alignment in the context of cosmic shear measurements.

  18. Reliability of lower limb alignment measures using an established landmark-based method with a customized computer software program

    Science.gov (United States)

    Sled, Elizabeth A.; Sheehy, Lisa M.; Felson, David T.; Costigan, Patrick A.; Lam, Miu; Cooke, T. Derek V.

    2010-01-01

    The objective of the study was to evaluate the reliability of frontal plane lower limb alignment measures using a landmark-based method by (1) comparing inter- and intra-reader reliability between measurements of alignment obtained manually with those using a computer program, and (2) determining inter- and intra-reader reliability of computer-assisted alignment measures from full-limb radiographs. An established method for measuring alignment was used, involving selection of 10 femoral and tibial bone landmarks. 1) To compare manual and computer methods, we used digital images and matching paper copies of five alignment patterns simulating healthy and malaligned limbs drawn using AutoCAD. Seven readers were trained in each system. Paper copies were measured manually and repeat measurements were performed daily for 3 days, followed by a similar routine with the digital images using the computer. 2) To examine the reliability of computer-assisted measures from full-limb radiographs, 100 images (200 limbs) were selected as a random sample from 1,500 full-limb digital radiographs which were part of the Multicenter Osteoarthritis (MOST) Study. Three trained readers used the software program to measure alignment twice from the batch of 100 images, with two or more weeks between batch handling. Manual and computer measures of alignment showed excellent agreement (intraclass correlations [ICCs] 0.977 – 0.999 for computer analysis; 0.820 – 0.995 for manual measures). The computer program applied to full-limb radiographs produced alignment measurements with high inter- and intra-reader reliability (ICCs 0.839 – 0.998). In conclusion, alignment measures using a bone landmark-based approach and a computer program were highly reliable between multiple readers. PMID:19882339

  19. Strategy and validation of fiducialisation for the pre-alignment of CLIC components

    CERN Document Server

    Griffet, S; Kemppinen, J; Mainaud Durand, H; Rude, V; Sterbini, G

    2012-01-01

    The feasibility of the high energy e+ e- linear collider CLIC (Compact Linear Collider) is very dependent on the ability to accurately pre-align its components. There are two 20 km long Main Linacs which meet in an interaction point (IP). The Main Linacs are composed of thousands of 2 m long modules. One of the challenges is to meet very tight alignment tolerances at the level of CLIC module: for example, the magnetic centre of a Drive Beam Quad needs to be aligned within 20 µm rms with respect to a straight line. Such accuracies cannot be achieved using usual measurement devices. Thus it is necessary to work in close collaboration with the metrology lab. To test and improve many critical points, including alignment, a CLIC mock-up is being assembled at CERN. This paper describes the application of the strategy of fiducialisation for the pre-alignment of CLIC mock-up components. It also deals with the first results obtained by performing measurements using a CMM (Coordinate Measuring Machine) to ensure the f...

  20. A value-based maturity model for IT alignment in networked businesses

    NARCIS (Netherlands)

    Santana Tapia, R.G.

    Business-IT alignment can be achieved at various levels of maturity. Supposing that an organization has tried to achieve business-IT alignment, a question to face is: how is that organization going to know the level of maturity of its alignment situation in order to plan future ways of action? That

  1. Optical derotator alignment using image-processing algorithm for tracking laser vibrometer measurements of rotating objects.

    Science.gov (United States)

    Khalil, Hossam; Kim, Dongkyu; Jo, Youngjoon; Park, Kyihwan

    2017-06-01

    An optical component called a Dove prism is used to rotate the laser beam of a laser-scanning vibrometer (LSV). This is called a derotator and is used for measuring the vibration of rotating objects. The main advantage of a derotator is that it works independently from an LSV. However, this device requires very specific alignment, in which the axis of the Dove prism must coincide with the rotational axis of the object. If the derotator is misaligned with the rotating object, the results of the vibration measurement are imprecise, owing to the alteration of the laser beam on the surface of the rotating object. In this study, a method is proposed for aligning a derotator with a rotating object through an image-processing algorithm that obtains the trajectory of a landmark attached to the object. After the trajectory of the landmark is mathematically modeled, the amount of derotator misalignment with respect to the object is calculated. The accuracy of the proposed method for aligning the derotator with the rotating object is experimentally tested.

  2. Enhanced Alignment Techniques for the Thomson Scattering Diagnostic on the Lithium Tokamak eXperiment (LTX)

    Science.gov (United States)

    Merino, Enrique; Kozub, Tom; Boyle, Dennis; Lucia, Matthew; Majeski, Richard; Kaita, Robert; Schmitt, John C.; Leblanc, Benoit; Diallo, Ahmed; Jacobson, C. M.

    2014-10-01

    The Thomson Scattering (TS) System in LTX is used to measure electron temperature and density profiles of core and edge plasmas. In view of TS measurements showing low signal-to-noise and high stray light, numerous improvements were performed in recent months. These will allow for better measurements. Due to the nature of LTX's lithium coated walls, a particular challenge was presented by alignment procedures which required insertion and precise positioning of equipment in the vacuum vessel without breaking vacuum. To overcome these difficulties, the laser flight tubes were removed and an alignment probe setup placed along the beam line on a differentially pumped assembly. The probe was then driven into the vacuum vessel and back-illumination of the viewing optics on it allowed for alignment and spatial calibration. Other upgrades included better bracing of flight tubes and viewing optics as well as a redesigned beam dump. An overview of these improvements will be presented. Supported by US DOE Contracts DE-AC02-09CH11466 and DE-AC52-07NA27344.

  3. Alignment and girder position of MSE septa in the new LSS4 extraction channel of the SPS

    CERN Document Server

    Balhan, B; Rizzo, A; Weterings, W; CERN. Geneva. SPS and LHC Division

    2002-01-01

    For the extraction of the beam from the Super Proton Synchrotron (SPS) to ring 2 of the Large Hadron Collider (LHC) and the CERN Neutrino to Gran Sasso (CNGS)facility, a new fast-extraction system is being constructed in the long straight section LSS4 of the SPS. Besides extraction bumpers, enlarged aperture quadrupoles and extraction kicker magnets (MKE), six conventional DC septum magnets (MSE) are used. These magnets are mounted on a single rigid support girder, pre-aligned so as to follow the trajectory of the extracted beam and optimise the available aperture. The girder has been motorised in order to optimise the local SPS aperture during setting up, so as to avoid the risk of circulating beam impact on the septum coils. In this note, we briefly present the trajectory and apertures of the beam, we describe the calculations and methods that have been used to determine the magnet position on the girder, and finally we report on the details of the girder movement and alignment.

  4. Experimental demonstration of dielectric structure based two beam acceleration

    International Nuclear Information System (INIS)

    Gai, W.; Conde, M. E.; Konecny, R.; Power, J. G.; Schoessow, P.; Sun, X.; Zou, P.

    2000-01-01

    We report on the experimental results of the dielectric based two beam accelerator (step-up transformer). By using a single high charge beam, we have generated and extracted a high power RF pulse from a 7.8 GHz primary dielectric structure and then subsequently transferred to a second accelerating structure with higher dielectric constant and smaller transverse dimensions. We have measured the energy change of a second (witness) beam passing through the acceleration stage. The measured gradient is >4 times the deceleration gradient. The detailed experiment of set-up and results of the measurements are dimmed. Future plans for the development of a 100 MeV demonstration accelerator based on this technique is presented

  5. Experimental demonstration of dielectric structure based two beam acceleration.

    Energy Technology Data Exchange (ETDEWEB)

    Gai, W.; Conde, M. E.; Konecny, R.; Power, J. G.; Schoessow, P.; Sun, X.; Zou, P.

    2000-11-28

    We report on the experimental results of the dielectric based two beam accelerator (step-up transformer). By using a single high charge beam, we have generated and extracted a high power RF pulse from a 7.8 GHz primary dielectric structure and then subsequently transferred to a second accelerating structure with higher dielectric constant and smaller transverse dimensions. We have measured the energy change of a second (witness) beam passing through the acceleration stage. The measured gradient is >4 times the deceleration gradient. The detailed experiment of set-up and results of the measurements are dimmed. Future plans for the development of a 100 MeV demonstration accelerator based on this technique is presented.

  6. Multipoint alignment monitoring with amorphous silicon position detectors in a complex light path

    Energy Technology Data Exchange (ETDEWEB)

    Alberdi, J.; Arce, P.; Barcala, J.M.; Calvo, E. [CIEMAT, Madrid (Spain); Ferrando, A., E-mail: antonio.ferrando@ciemat.e [CIEMAT, Madrid (Spain); Josa, M.I.; Molinero, A.; Navarrete, J.; Oller, J.C.; Yuste, C. [CIEMAT, Madrid (Spain); Calderon, A.; Gomez, G.; Gonzalez-Sanchez, F.J.; Martinez-Rivero, C.; Matorras, F.; Rodrigo, T.; Ruiz-Arbol, P.; Sobron, M.; Vila, I.; Virto, A.L. [Instituto de Fisica de Cantabria. CSIC-University of Cantabria, Santander (Spain)

    2010-12-01

    This document presents an application of the new generation of amorphous silicon position detecting (ASPD) sensors to multipoint alignment. Twelve units are monitored along a 20 m long laser beam, where the light path is deflected by 90{sup o} using a pentaprism.

  7. Multipoint alignment monitoring with amorphous silicon position detectors in a complex light path

    International Nuclear Information System (INIS)

    Alberdi, J.; Arce, P.; Barcala, J.M.; Calvo, E.; Ferrando, A.; Josa, M.I.; Molinero, A.; Navarrete, J.; Oller, J.C.; Yuste, C.; Calderon, A.; Gomez, G.; Gonzalez-Sanchez, F.J.; Martinez-Rivero, C.; Matorras, F.; Rodrigo, T.; Ruiz-Arbol, P.; Sobron, M.; Vila, I.; Virto, A.L.

    2010-01-01

    This document presents an application of the new generation of amorphous silicon position detecting (ASPD) sensors to multipoint alignment. Twelve units are monitored along a 20 m long laser beam, where the light path is deflected by 90 o using a pentaprism.

  8. pyPaSWAS : Python-based multi-core CPU and GPU sequence alignment

    NARCIS (Netherlands)

    Warris, Sven; Timal, N Roshan N; Kempenaar, Marcel; Poortinga, Arne M; van de Geest, Henri; Varbanescu, Ana L; Nap, Jan-Peter

    2018-01-01

    BACKGROUND: Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of

  9. Laser-assisted simultaneous transfer and patterning of vertically aligned carbon nanotube arrays on polymer substrates for flexible devices.

    Science.gov (United States)

    In, Jung Bin; Lee, Daeho; Fornasiero, Francesco; Noy, Aleksandr; Grigoropoulos, Costas P

    2012-09-25

    We demonstrate a laser-assisted dry transfer technique for assembling patterns of vertically aligned carbon nanotube arrays on a flexible polymeric substrate. A laser beam is applied to the interface of a nanotube array and a polycarbonate sheet in contact with one another. The absorbed laser heat promotes nanotube adhesion to the polymer in the irradiated regions and enables selective pattern transfer. A combination of the thermal transfer mechanism with rapid direct writing capability of focused laser beam irradiation allows us to achieve simultaneous material transfer and direct micropatterning in a single processing step. Furthermore, we demonstrate that malleability of the nanotube arrays transferred onto a flexible substrate enables post-transfer tailoring of electric conductance by collapsing the aligned nanotubes in different directions. This work suggests that the laser-assisted transfer technique provides an efficient route to using vertically aligned nanotubes as conductive elements in flexible device applications.

  10. Study and application of micrometric alignment on the prototype girders of the CLIC Two-Beam Module

    CERN Document Server

    Gazis, Nikolaos; Mainaud-Durand, Hélène; Samochkine, Alexandre; Anastasopoulos, Michail

    2011-01-01

    The Compact LInear Collider (CLIC), currently under study at CERN, aims at the development of a Multi-TeV e+ e- collider. The micro-precision CLIC RF-structures will have an accelerating gradient of 100 MV/m and will be mounted and aligned on specially developed supporting girders. The girder fabrication constraints are dictated by stringent physics requirements. The micrometric pre-alignment over several kilometers of girders, allow for the CLIC structures to fulfill their acceleration and collision functionality. Study of such girders and their sophisticated alignment method, is a challenging case involving dedicated mechanical design as well as prototype production and experimental testing.

  11. Assembly process of the ITER neutral beam injectors

    Energy Technology Data Exchange (ETDEWEB)

    Graceffa, J., E-mail: joseph.graceffa@iter.org [ITER Organization, Route de Vinon sur Verdon, 13115 Saint Paul lez Durance (France); Boilson, D.; Hemsworth, R.; Petrov, V.; Schunke, B.; Urbani, M. [ITER Organization, Route de Vinon sur Verdon, 13115 Saint Paul lez Durance (France); Pilard, V. [Fusion for Energy, C/ Josep Pla, n°2, Torres Diagonal Litoral, Edificio B3, 08019 Barcelona (Spain)

    2013-10-15

    The ITER neutral beam (NB) injectors are used for heating and diagnostics operations. There are 4 injectors in total, 3 heating neutral beam injectors (HNBs) and one diagnostic neutral beam injector (DNB). Two HNBs and the DNB will start injection into ITER during the hydrogen/helium phase of ITER operations. A third HNB is considered as an upgrade to the ITER heating systems, and the impact of the later installation and use of that injector have to be taken into account when considering the installation and assembly of the whole NB system. It is assumed that if a third HNB is to be installed, it will be installed before the nuclear phase of the ITER project. The total weight of one injector is around 1200 t and it is composed of 18 main components and 36 sets of shielding plates. The overall dimensions are length 20 m, height 10 m and width 5 m. Assembly of the first two HNBs and the DNB will start before the first plasma is produced in ITER, but as the time required to assemble one injector is estimated at around 1.5 year, the assembly will be divided into 2 steps, one prior to first plasma, and the second during the machine second assembly phase. To comply with this challenging schedule the assembly sequence has been defined to allow assembly of three first injectors in parallel. Due to the similar design between the DNB and HNBs it has been decided to use the same tools, which will be designed to accommodate the differences between the two sets of components. This reduces the global cost of the assembly and the overall assembly time for the injector system. The alignment and positioning of the injectors is a major consideration for the injector assembly as the alignment of the beamline components and the beam source are critical if good injector performance is to be achieved. The theoretical axes of the beams are defined relative to the duct liners which are installed in the NB ports. The concept adopted to achieve the required alignment accuracy is to use the

  12. MISTICA: Minimum Spanning Tree-Based Coarse Image Alignment for Microscopy Image Sequences.

    Science.gov (United States)

    Ray, Nilanjan; McArdle, Sara; Ley, Klaus; Acton, Scott T

    2016-11-01

    Registration of an in vivo microscopy image sequence is necessary in many significant studies, including studies of atherosclerosis in large arteries and the heart. Significant cardiac and respiratory motion of the living subject, occasional spells of focal plane changes, drift in the field of view, and long image sequences are the principal roadblocks. The first step in such a registration process is the removal of translational and rotational motion. Next, a deformable registration can be performed. The focus of our study here is to remove the translation and/or rigid body motion that we refer to here as coarse alignment. The existing techniques for coarse alignment are unable to accommodate long sequences often consisting of periods of poor quality images (as quantified by a suitable perceptual measure). Many existing methods require the user to select an anchor image to which other images are registered. We propose a novel method for coarse image sequence alignment based on minimum weighted spanning trees (MISTICA) that overcomes these difficulties. The principal idea behind MISTICA is to reorder the images in shorter sequences, to demote nonconforming or poor quality images in the registration process, and to mitigate the error propagation. The anchor image is selected automatically making MISTICA completely automated. MISTICA is computationally efficient. It has a single tuning parameter that determines graph width, which can also be eliminated by the way of additional computation. MISTICA outperforms existing alignment methods when applied to microscopy image sequences of mouse arteries.

  13. Characteristics of possible beam losses in superconducting cyclotron

    International Nuclear Information System (INIS)

    Pradhan, J.; Paul, Santanu; Debnath, Jayanta; Dutta, Atanu; Bhunia, Uttam; Naser, Md. Zamal Abdul; Singh, Vinay; Agrawal, Ankur; Dey, Malay Kanti

    2015-01-01

    In a compact superconducting cyclotron large coherent oscillation and off-centering of the beam may cause large amount of beam loss. The off-centered beam may hit the beam chamber wall prohibiting extraction of the beam. Or it may hit the RF liner surfaces due to vertical blow-up across various resonances during acceleration. The vertical shift of beam caused by the mis-alignment gradually moves the beam out of geometrical median plane eventually leading to internal beam losses. The loss of isochronisms results the reduction of beam intensity depending on the particle phase history. Small field perturbations generated by trim coils have been used to identify the beam loss mechanisms in the superconducting cyclotron at out centre. Besides, the beam loss due to interaction of accelerating ions with residual gases is also discussed. The beam profile obtained from differential and three finger probes gives a clear insight of the loss-mechanism. The paper describes different beam losses observed in the cyclotron with corresponding beam profiles under different field perturbations, Special emphasis is given on characteristics features of beam-current profile to identify the cause of beam loss. (author)

  14. SU-E-T-403: Evaluation of the Beam Performance of a Varian TrueBeam Linear Accelerator Under External Device-Based Gated Delivery Conditions

    International Nuclear Information System (INIS)

    Kobulnicky, K; Pawlak, D; Purwar, A

    2015-01-01

    Purpose: To examine the beam performance of a Varian TrueBeam linear accelerator under external device-based gated delivery conditions. Methods: Six gating cycles were used to evaluate the gating performance of a standard production TrueBeam system that was not specially tuned in any way. The system was equipped with a factory installed external gating interface (EXGI). An in-house EXGI tester box was used to simulate the input gating signals. The gating cycles were selected based on long beam-on and short beam-off times, short beam-on and long beam-off times, or equal beam on and off times to check linac performance. The beam latencies were measured as the time difference between the logic high gating signal and the first or last target pulses with an oscilloscope. Tissue-Phantom Ratio, beam flatness, and dose distributions from 5 different plans were measured using the 6 different gating durations and the un-gated irradiation. A PTW 729 2-D array was used to compare 5 plans versus the un-gated delivery with a 1%/1mm gamma index passing criteria. Results: The beam latencies of the linac were based off of 20 samples for beam-on and beam-off, for each gating cycle. The average beam-on delays were measured to be between 57 and 66msec, with a maximum of 88 msec. The beam off latencies averaged between 19 and 26msec, with a maximum of 48 msec. TPR20,10 measurements showed beam energy stability within 0.5% of the un-gated delivery. Beam flatness was better than 2.5% for all gated cycles. All but two deliveries, the open field with 4 seconds on, 1 second off, and a five field IMRT plan with 0.5 seconds on, 2.5 seconds off, had >90% passing rate. Conclusion: TrueBeam demonstrates excellent beam stability with minimal beam latencies under external device-based gated operations. Dosimetric measurements show minimal variation in beam energy, flatness, and plan delivery. Authors are employees of Varian Medical Systems, Inc

  15. SU-E-T-403: Evaluation of the Beam Performance of a Varian TrueBeam Linear Accelerator Under External Device-Based Gated Delivery Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Kobulnicky, K; Pawlak, D; Purwar, A [Varian Medical Systems, Inc., Palo Alto, CA (United States)

    2015-06-15

    Purpose: To examine the beam performance of a Varian TrueBeam linear accelerator under external device-based gated delivery conditions. Methods: Six gating cycles were used to evaluate the gating performance of a standard production TrueBeam system that was not specially tuned in any way. The system was equipped with a factory installed external gating interface (EXGI). An in-house EXGI tester box was used to simulate the input gating signals. The gating cycles were selected based on long beam-on and short beam-off times, short beam-on and long beam-off times, or equal beam on and off times to check linac performance. The beam latencies were measured as the time difference between the logic high gating signal and the first or last target pulses with an oscilloscope. Tissue-Phantom Ratio, beam flatness, and dose distributions from 5 different plans were measured using the 6 different gating durations and the un-gated irradiation. A PTW 729 2-D array was used to compare 5 plans versus the un-gated delivery with a 1%/1mm gamma index passing criteria. Results: The beam latencies of the linac were based off of 20 samples for beam-on and beam-off, for each gating cycle. The average beam-on delays were measured to be between 57 and 66msec, with a maximum of 88 msec. The beam off latencies averaged between 19 and 26msec, with a maximum of 48 msec. TPR20,10 measurements showed beam energy stability within 0.5% of the un-gated delivery. Beam flatness was better than 2.5% for all gated cycles. All but two deliveries, the open field with 4 seconds on, 1 second off, and a five field IMRT plan with 0.5 seconds on, 2.5 seconds off, had >90% passing rate. Conclusion: TrueBeam demonstrates excellent beam stability with minimal beam latencies under external device-based gated operations. Dosimetric measurements show minimal variation in beam energy, flatness, and plan delivery. Authors are employees of Varian Medical Systems, Inc.

  16. Ion beam alignment in the MSX-4 mass spectrometer

    International Nuclear Information System (INIS)

    Busygin, A.I.; Nevzorov, A.A.; Ul'masbaev, B.Sh.

    1977-01-01

    A method for electrically adjusting an ion beam in an MSKh-4 mass-spectrometer has been developed. The adjusting system consists of two deflecting plates fastened to the frame of the ion source. By adjusting the potential difference at the plates in the range 0-150 v, one can increase the intensity of the mass-spectrum by a factor of 3 to 5

  17. Accelerator Based Neutron Beams for Neutron Capture Therapy

    International Nuclear Information System (INIS)

    Yanch, Jacquelyn C.

    2003-01-01

    The DOE-funded accelerator BNCT program at the Massachusetts Institute of Technology has resulted in the only operating accelerator-based epithermal neutron beam facility capable of generating significant dose rates in the world. With five separate beamlines and two different epithermal neutron beam assemblies installed, we are currently capable of treating patients with rheumatoid arthritis in less than 15 minutes (knee joints) or 4 minutes (finger joints) or irradiating patients with shallow brain tumors to a healthy tissue dose of 12.6 Gy in 3.6 hours. The accelerator, designed by Newton scientific Incorporated, is located in dedicated laboratory space that MIT renovated specifically for this project. The Laboratory for Accelerator Beam Applications consists of an accelerator room, a control room, a shielded radiation vault, and additional laboratory space nearby. In addition to the design, construction and characterization of the tandem electrostatic accelerator, this program also resulted in other significant accomplishments. Assemblies for generating epithermal neutron beams were designed, constructed and experimentally evaluated using mixed-field dosimetry techniques. Strategies for target construction and target cooling were implemented and tested. We demonstrated that the method of submerged jet impingement using water as the coolant is capable of handling power densities of up to 6 x 10(sup 7) W/m(sup 2) with heat transfer coefficients of 10(sup 6)W/m(sup 2)-K. Experiments with the liquid metal gallium demonstrated its superiority compared with water with little effect on the neutronic properties of the epithermal beam. Monoenergetic proton beams generated using the accelerator were used to evaluate proton RBE as a function of LET and demonstrated a maximum RBE at approximately 30-40 keV/um, a finding consistent with results published by other researchers. We also developed an experimental approach to biological intercomparison of epithermal beams and

  18. Improving alignment in Tract-based spatial statistics: evaluation and optimization of image registration

    NARCIS (Netherlands)

    de Groot, Marius; Vernooij, Meike W.; Klein, Stefan; Ikram, M. Arfan; Vos, Frans M.; Smith, Stephen M.; Niessen, Wiro J.; Andersson, Jesper L. R.

    2013-01-01

    Anatomical alignment in neuroimaging studies is of such importance that considerable effort is put into improving the registration used to establish spatial correspondence. Tract-based spatial statistics (TBSS) is a popular method for comparing diffusion characteristics across subjects. TBSS

  19. Improving alignment in Tract-based spatial statistics : Evaluation and optimization of image registration

    NARCIS (Netherlands)

    De Groot, M.; Vernooij, M.W.; Klein, S.; Arfan Ikram, M.; Vos, F.M.; Smith, S.M.; Niessen, W.J.; Andersson, J.L.R.

    2013-01-01

    Anatomical alignment in neuroimaging studies is of such importance that considerable effort is put into improving the registration used to establish spatial correspondence. Tract-based spatial statistics (TBSS) is a popular method for comparing diffusion characteristics across subjects. TBSS

  20. High-accuracy alignment based on atmospherical dispersion - technological approaches and solutions for the dual-wavelength transmitter

    International Nuclear Information System (INIS)

    Burkhard, Boeckem

    1999-01-01

    In the course of the progressive developments of sophisticated geodetic systems utilizing electromagnetic waves in the visible or near IR-range a more detailed knowledge of the propagation medium and coevally solutions of atmospherically induced limitations will become important. An alignment system based on atmospherical dispersion, called a dispersometer, is a metrological solution to the atmospherically induced limitations, in optical alignment and direction observations of high accuracy. In the dispersometer we are using the dual-wavelength method for dispersive air to obtain refraction compensated angle measurements, the detrimental impact of atmospheric turbulence notwithstanding. The principle of the dual-wavelength method utilizes atmospherical dispersion, i.e. the wavelength dependence of the refractive index. The difference angle between two light beams of different wavelengths, which is called the dispersion angle Δβ, is to first approximation proportional to the refraction angle: β IR ν(β blue - β IR ) = ν Δβ, this equation implies that the dispersion angle has to be measured at least 42 times more accurate than the desired accuracy of the refraction angle for the wavelengths used in the present dispersometer. This required accuracy constitutes one major difficulty for the instrumental performance in applying the dispersion effect. However, the dual-wavelength method can only be successfully used in an optimized transmitter-receiver combination. Beyond the above mentioned resolution requirement for the detector, major difficulties in instrumental realization arise in the availability of a suitable dual-wavelength laser light source, laser light modulation with a very high extinction ratio and coaxial emittance of mono-mode radiation at both wavelengths. Therefore, this paper focuses on the solutions of the dual-wavelength transmitter introducing a new hardware approach and a complete re-design of the in [1] proposed conception of the dual

  1. Beam-centric algorithm for pretreatment patient position correction in external beam radiation therapy

    International Nuclear Information System (INIS)

    Bose, Supratik; Shukla, Himanshu; Maltz, Jonathan

    2010-01-01

    Purpose: In current image guided pretreatment patient position adjustment methods, image registration is used to determine alignment parameters. Since most positioning hardware lacks the full six degrees of freedom (DOF), accuracy is compromised. The authors show that such compromises are often unnecessary when one models the planned treatment beams as part of the adjustment calculation process. The authors present a flexible algorithm for determining optimal realizable adjustments for both step-and-shoot and arc delivery methods. Methods: The beam shape model is based on the polygonal intersection of each beam segment with the plane in pretreatment image volume that passes through machine isocenter perpendicular to the central axis of the beam. Under a virtual six-DOF correction, ideal positions of these polygon vertices are computed. The proposed method determines the couch, gantry, and collimator adjustments that minimize the total mismatch of all vertices over all segments with respect to their ideal positions. Using this geometric error metric as a function of the number of available DOF, the user may select the most desirable correction regime. Results: For a simulated treatment plan consisting of three equally weighted coplanar fixed beams, the authors achieve a 7% residual geometric error (with respect to the ideal correction, considered 0% error) by applying gantry rotation as well as translation and isocentric rotation of the couch. For a clinical head-and-neck intensity modulated radiotherapy plan with seven beams and five segments per beam, the corresponding error is 6%. Correction involving only couch translation (typical clinical practice) leads to a much larger 18% mismatch. Clinically significant consequences of more accurate adjustment are apparent in the dose volume histograms of target and critical structures. Conclusions: The algorithm achieves improvements in delivery accuracy using standard delivery hardware without significantly increasing

  2. Neutral-beam aiming and calorimetry for MFTF-B

    International Nuclear Information System (INIS)

    Goldner, A.I.; Margolies, D.

    1981-01-01

    The vessel for the Tandem Mirror Fusion Test Facility (MFTF-B) will have up to eleven 0.5-s-duration neutral-beam injectors for the initial heating of the MFTF-B plasma. Knowing the exact alignment of the beams and their total power is critical to the performance of the experiment. Using prototype aiming and calorimetry systems on the High Voltage Test Stand (HVTS) at Lawrence Livermore National Laboratory (LLNL), we hope to prove our ability to obtain an aiming accuracy of +-1 cm at the plasma and a calorimetric accuracy of +-5% of the actual total beam energy

  3. Antiproton source beam position system

    International Nuclear Information System (INIS)

    Bagwell, T.; Holmes, S.; McCarthy, J.; Webber, R.

    1984-05-01

    The TeV I Beam Position Monitor (BPM) system is designed to provide a useful diagnostic tool during the commissioning and operational phases of the antiproton source. Simply stated the design goal is to provide single turn position information for intensities of > 1x10 9 particles, and multi-turn (clocked orbit) information for beam intensities of > 1x10 7 particles, both with sub-millimeter resolution. It is anticipated that the system will be used during commissioning for establishing the first turn through the Debuncher and Accumulator, for aligning injection orbits, for providing information necessary to correct closed orbits, and for measuring various machine parameters (e.g. tunes, dispersion, aperture, chromaticity). During normal antiproton operation the system will be used to monitor the beam position throughout the accumulation process

  4. Deformation effect in the fast neutron total cross section of aligned /sup 59/Co

    Energy Technology Data Exchange (ETDEWEB)

    Fasoli, U.; Pavan, P.; Toniolo, D.; Zago, G.; Zannoni, R.; Galeazzi, G.

    1982-07-19

    The variation of the total neutron cross section, ..delta.. sigma/sub align/, on /sup 59/Co due to nuclear alignment of the target in the beam direction, has been measured over the energy range from 0.8 to 20 MeV, employing a cobalt single-crystal with a 34% nuclear alignment degree. The results show that ..delta.. sigma/sub align/ oscillates from a minimum of -5% at about 2.5 MeV to a maximum of +1% at about 10 MeV. The data were successfully fitted by optical model coupled-channel calculations. The coupling terms were deduced from a model representing the /sup 59/Co nucleus as a virbrational /sup 60/Ni core coupled to a proton-hole in a (lf 7/2) shell, without free parameters. The optical model parameters were determined by fitting the total cross-section independently measured. The theoretical calculations show that, at lower energies, ..delta.. sigma/sub align/ depends appreciably on the coupling with the low-lying levels.

  5. Unraveling the growth of vertically aligned multi-walled carbon nanotubes by chemical vapor deposition

    International Nuclear Information System (INIS)

    Ramirez, A; Royo, C; Latorre, N; Mallada, R; Monzón, A; Tiggelaar, R M

    2014-01-01

    The interaction between the main operational variables during the growth of vertically aligned multiwalled carbon nanotubes (VA-MWCNTs) by catalytic chemical vapor deposition is studied. In this contribution, we report the influence of the carbon source (i.e. acetylene, ethylene and propylene), the reaction/activation temperature, the rate of heating, the reaction time, the metal loading, and the metallic nanoparticle size and distribution on the growth and alignment of carbon nanotubes. Fe/Al thin films deposited onto silicon samples by electron-beam evaporation are used as catalyst. A phenomenological growth mechanism is proposed to explain the interaction between these multiple factors. Three different outcomes of the synthesis process are found: i) formation of forests of non-aligned, randomly oriented multi-walled carbon nanotubes, ii) growth of vertically aligned tubes with a thin and homogeneous carbonaceous layer on the top, and iii) formation of vertically aligned carbon nanotubes. This carbonaceous layer (ii) has not been reported before. The main requirements to promote vertically aligned carbon nanotube growth are determined. (paper)

  6. Experimental image alignment system

    Science.gov (United States)

    Moyer, A. L.; Kowel, S. T.; Kornreich, P. G.

    1980-01-01

    A microcomputer-based instrument for image alignment with respect to a reference image is described which uses the DEFT sensor (Direct Electronic Fourier Transform) for image sensing and preprocessing. The instrument alignment algorithm which uses the two-dimensional Fourier transform as input is also described. It generates signals used to steer the stage carrying the test image into the correct orientation. This algorithm has computational advantages over algorithms which use image intensity data as input and is suitable for a microcomputer-based instrument since the two-dimensional Fourier transform is provided by the DEFT sensor.

  7. Beam transport calculations for BARC-TIFR 14UD pelletron

    International Nuclear Information System (INIS)

    Prasad, K.G.

    1993-01-01

    The 14UD pelletron tandem accelerator installed at Tata Institute of Fundamental Research (TIFR) as a joint BARC-TIFR project, is supplied by National Electrostatic Corporation (NEC), U.S.A. To optimise the parameters of various elements along the beam path, it is essential to work out the beam optics of the entire system. There are various computer codes in use for such calculations. All these codes, except the detailed ray tracing programs, use matrix formulation. Thus each ion optical element is characterised in terms of a transport matrix, whose elements are assumed to be independent of particle trajectory. We have performed only the first order calculations, meaning thereby that no aberrations are included. Further, all calculations are carried out assuming ideal conditions like axial beam injection, perfectly aligned beam line elements, etc. The main code that has been employed in our calculations is based on the one at the Australian National University, Canberra, suitably modified for use with CYBER 170/730 computer at TIFR. However, codes at NEC and Stony Brook were also used for the checking the results. The results of calculations are given and discussed. (author). 2 figs

  8. Stochastic sampling of the RNA structural alignment space.

    Science.gov (United States)

    Harmanci, Arif Ozgun; Sharma, Gaurav; Mathews, David H

    2009-07-01

    A novel method is presented for predicting the common secondary structures and alignment of two homologous RNA sequences by sampling the 'structural alignment' space, i.e. the joint space of their alignments and common secondary structures. The structural alignment space is sampled according to a pseudo-Boltzmann distribution based on a pseudo-free energy change that combines base pairing probabilities from a thermodynamic model and alignment probabilities from a hidden Markov model. By virtue of the implicit comparative analysis between the two sequences, the method offers an improvement over single sequence sampling of the Boltzmann ensemble. A cluster analysis shows that the samples obtained from joint sampling of the structural alignment space cluster more closely than samples generated by the single sequence method. On average, the representative (centroid) structure and alignment of the most populated cluster in the sample of structures and alignments generated by joint sampling are more accurate than single sequence sampling and alignment based on sequence alone, respectively. The 'best' centroid structure that is closest to the known structure among all the centroids is, on average, more accurate than structure predictions of other methods. Additionally, cluster analysis identifies, on average, a few clusters, whose centroids can be presented as alternative candidates. The source code for the proposed method can be downloaded at http://rna.urmc.rochester.edu.

  9. Progressive multiple sequence alignments from triplets

    Directory of Open Access Journals (Sweden)

    Stadler Peter F

    2007-07-01

    Full Text Available Abstract Background The quality of progressive sequence alignments strongly depends on the accuracy of the individual pairwise alignment steps since gaps that are introduced at one step cannot be removed at later aggregation steps. Adjacent insertions and deletions necessarily appear in arbitrary order in pairwise alignments and hence form an unavoidable source of errors. Research Here we present a modified variant of progressive sequence alignments that addresses both issues. Instead of pairwise alignments we use exact dynamic programming to align sequence or profile triples. This avoids a large fractions of the ambiguities arising in pairwise alignments. In the subsequent aggregation steps we follow the logic of the Neighbor-Net algorithm, which constructs a phylogenetic network by step-wisely replacing triples by pairs instead of combining pairs to singletons. To this end the three-way alignments are subdivided into two partial alignments, at which stage all-gap columns are naturally removed. This alleviates the "once a gap, always a gap" problem of progressive alignment procedures. Conclusion The three-way Neighbor-Net based alignment program aln3nn is shown to compare favorably on both protein sequences and nucleic acids sequences to other progressive alignment tools. In the latter case one easily can include scoring terms that consider secondary structure features. Overall, the quality of resulting alignments in general exceeds that of clustalw or other multiple alignments tools even though our software does not included heuristics for context dependent (mismatch scores.

  10. Self-aligned periodic Ni nano dots embedded in nano-oxide layer

    International Nuclear Information System (INIS)

    Doi, M.; Izumi, M.; Kawasaki, S.; Miyake, K.; Sahashi, M.

    2007-01-01

    The Ni nano constriction dots embedded in the Ta-nano-oxide layer (NOL) was prepared by the ion beam sputtering (IBS) method. After the various conditions of the oxidations, the structural analyses of the NOL were performed by RHEED, AES and in situ STM/AFM observations. From the current image of the conductive AFM for NOL, the periodically aligned metallic dots with the size around 5-10 nm were successfully observed. The mechanism of the formation of the self-organized aligned Ni nano constriction dots is discussed from the standpoint of the grain size, the crystal orientation, the preferred oxidation of Ta at the diffused interface

  11. Plasma based Ar+ beam assisted poly(dimethylsiloxane) surface modification

    International Nuclear Information System (INIS)

    Vladkova, T.G.; Keranov, I.L.; Dineff, P.D.; Youroukov, S.Y.; Avramova, I.A.; Krasteva, N.; Altankov, G.P.

    2005-01-01

    Plasma based Ar + beam performed in RF (13.56 MHz) low-pressure (200 mTorr) glow discharge (at 100 W, 1200 W and 2500 W) with a serial capacitance was employed for surface modification of poly(dimethylsiloxane) (PDMS) aimed at improvement of its interactions with living cells. The presence of a serial capacitance ensures arise of an ion-flow inside the plasma volume directed toward the treated sample and the vary of the discharge power ensures varied density of the ion-flow. XPS analysis was performed to study the changes in the surface chemical composition of the modified samples and the corresponding changes in the surface energy were monitored by contact angle measurements. We found that plasma based Ar + beam transforms the initially hydrophobic PDMS surface into a hydrophilic one mainly due to a raising of the polar component of the surface tension, this effect being most probably due to an enrichment of the modified surface layer with permanent dipoles of a [SiO x ]-based network and elimination of the original methyl groups. The initial adhesion of human fibroblast cells was studied on the described above plasma based Ar + beam modified and acrylic acid (AA) grafted or not fibronectin (FN) pre-coated or bare surfaces. The cell response seems to be related with the peculiar structure and wettability of the modified PDMS surface layer after plasma based Ar + beam treatment followed or not by AA grafting

  12. Generating millimeter-wave Bessel beam with orbital angular momentum using reflective-type metasurface inherently integrated with source

    Science.gov (United States)

    Shen, Yizhu; Yang, Jiawei; Meng, Hongfu; Dou, Wenbin; Hu, Sanming

    2018-04-01

    Metasurfaces, orbital angular momenta (OAM), and non-diffractive Bessel beams have been attracting worldwide research. Combining the benefits of these three promising techniques, this paper proposes a metasurface-based reflective-type approach to generate a first-order Bessel beam carrying OAM. To validate this approach, a millimeter-wave metasurface is analyzed, designed, fabricated, and measured. Experimental results agree well with simulation. Moreover, this reflective-type metasurface, generating a Bessel beam with OAM, is inherently integrated with a planar feeding source in the same single-layer printed circuit board. Therefore, the proposed design features low profile, low cost, easy integration with front-end active circuits, and no alignment error between the feeding source and the metasurface.

  13. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.; Bonny, Talal; Salama, Khaled N.

    2012-01-01

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  14. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  15. Track based alignment of the CMS silicon tracker and its implication on physics performance

    International Nuclear Information System (INIS)

    Draeger, Jula

    2011-08-01

    In order to fully exploit the discovery potential of the CMS detector for new physics beyond the Standard Model at the high luminosity and centre-of-mass energy provided by the Large Hadron Collider, a careful calibration of the detector and profound understanding of its impact on physics performance are necessary to provide realistic uncertainties for the measurements of physics processes. This thesis describes the track-based alignment of the inner tracking system of CMS with the Millepede II algorithm. Using the combined information of tracks from cosmic rays and collisions taken in 2010, a remarkable local alignment precision has been reached that meets the design specification for most regions of the detector and takes into account instabilities of the detector geometry over time. In addition, the impact of the alignment of b tagging or the Z boson resonance are investigated. The latter is studied to investigate the impact of correlated detector distortions which hardly influence the overall solution of the minimisation problem but introduce biases in the track parameters and thus the derived physics quantities. The determination and constraint of these weak modes present the future challenge of the alignment task at CMS. (orig.)

  16. Track based alignment of the CMS silicon tracker and its implication on physics performance

    Energy Technology Data Exchange (ETDEWEB)

    Draeger, Jula

    2011-08-15

    In order to fully exploit the discovery potential of the CMS detector for new physics beyond the Standard Model at the high luminosity and centre-of-mass energy provided by the Large Hadron Collider, a careful calibration of the detector and profound understanding of its impact on physics performance are necessary to provide realistic uncertainties for the measurements of physics processes. This thesis describes the track-based alignment of the inner tracking system of CMS with the Millepede II algorithm. Using the combined information of tracks from cosmic rays and collisions taken in 2010, a remarkable local alignment precision has been reached that meets the design specification for most regions of the detector and takes into account instabilities of the detector geometry over time. In addition, the impact of the alignment of b tagging or the Z boson resonance are investigated. The latter is studied to investigate the impact of correlated detector distortions which hardly influence the overall solution of the minimisation problem but introduce biases in the track parameters and thus the derived physics quantities. The determination and constraint of these weak modes present the future challenge of the alignment task at CMS. (orig.)

  17. Physics design of heavy-ion irradiation beam line on HI-13 tandem accelerator

    International Nuclear Information System (INIS)

    Zhu Fei; Peng Zhaohua; Hu Yueming; Jiao Xuesheng; Chen Dongfeng; Cao Yali

    2014-01-01

    Background: Heavy-ion microporous membrane is a new kind of filter material, which has prosperous application in the fields of medical and biological agents, electronic, food, environmental science, materials science, etc. Purpose: Polyester membranes were irradiated with 32 S produced by HI-13 tandem accelerator to develop a microporous membrane at CIAE, and the irradiation uniformity is determined by the beam distribution, also the microporous uniformity is required higher than 90%. Methods: An octupole magnet was used to correct the beam distribution from Gauss to uniform. Meanwhile, main parameters of beam line were given, and the alignment tolerances for optical elements were also analyzed. Results: Alignment tolerance of the optical elements could cause great influence on the beam center deviation in the process of correction, which would destroy the irradiation uniformity. Steering magnet was applied to meet with the design requirements. Conclusion: This study provides a practical and feasible way for industrial production of heavy-ion microporous membrane. (authors)

  18. AlignMe—a membrane protein sequence alignment web server

    Science.gov (United States)

    Stamm, Marcus; Staritzbichler, René; Khafizov, Kamil; Forrest, Lucy R.

    2014-01-01

    We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe. The server makes available two operational modes of AlignMe: (i) sequence to sequence alignment, taking two sequences in fasta format as input, combining information about each sequence from multiple sources and producing a pair-wise alignment (PW mode); and (ii) alignment of two multiple sequence alignments to create family-averaged hydropathy profile alignments (HP mode). For the PW sequence alignment mode, four different optimized parameter sets are provided, each suited to pairs of sequences with a specific similarity level. These settings utilize different types of inputs: (position-specific) substitution matrices, secondary structure predictions and transmembrane propensities from transmembrane predictions or hydrophobicity scales. In the second (HP) mode, each input multiple sequence alignment is converted into a hydrophobicity profile averaged over the provided set of sequence homologs; the two profiles are then aligned. The HP mode enables qualitative comparison of transmembrane topologies (and therefore potentially of 3D folds) of two membrane proteins, which can be useful if the proteins have low sequence similarity. In summary, the AlignMe web server provides user-friendly access to a set of tools for analysis and comparison of membrane protein sequences. Access is available at http://www.bioinfo.mpg.de/AlignMe PMID:24753425

  19. Spreadsheet-based program for alignment of overlapping DNA sequences.

    Science.gov (United States)

    Anbazhagan, R; Gabrielson, E

    1999-06-01

    Molecular biology laboratories frequently face the challenge of aligning small overlapping DNA sequences derived from a long DNA segment. Here, we present a short program that can be used to adapt Excel spreadsheets as a tool for aligning DNA sequences, regardless of their orientation. The program runs on any Windows or Macintosh operating system computer with Excel 97 or Excel 98. The program is available for use as an Excel file, which can be downloaded from the BioTechniques Web site. Upon execution, the program opens a specially designed customized workbook and is capable of identifying overlapping regions between two sequence fragments and displaying the sequence alignment. It also performs a number of specialized functions such as recognition of restriction enzyme cutting sites and CpG island mapping without costly specialized software.

  20. Beam propagation considerations in the Aurora laser system

    International Nuclear Information System (INIS)

    Rosoche, L.A.; Mc Leod, J.; Hanlon, J.A.

    1987-01-01

    Aurora is a high-power KrF laser system now being constructed for inertial confinement fusion (ICF) studies. It will use optical angular multiplexing and serial amplification by electron-beam-driven KrF amplifiers to deliver a stacked, multikilojoule 5-ns-duration laser pulse to ICF targets. The requirements of angular multiplexing KrF lasers at the multikilojoule level dictate path lengths on the order of 1 km. The inherent complicated path crossings produced by angular multiplexing and pulse stacking do not allow isolation of individual beam lines, so the optical quality of the long beam paths must be controlled. Propagation of the 248-nm light beams over long paths in air is affected by scattering, absorption thermal gradients and turbulence, beam alignment, and control and optical component figure errors