Spectral Ewald Acceleration of Stokesian Dynamics for polydisperse suspensions
NASA Astrophysics Data System (ADS)
Wang, Mu; Brady, John F.
2016-02-01
In this work we develop the Spectral Ewald Accelerated Stokesian Dynamics (SEASD), a novel computational method for dynamic simulations of polydisperse colloidal suspensions with full hydrodynamic interactions. SEASD is based on the framework of Stokesian Dynamics (SD) with extension to compressible solvents, and uses the Spectral Ewald (SE) method [Lindbo and Tornberg (2010) [29
Active microrheology of Brownian suspensions via Accelerated Stokesian Dynamics simulations
NASA Astrophysics Data System (ADS)
Chu, Henry; Su, Yu; Gu, Kevin; Hoh, Nicholas; Zia, Roseanna
2015-11-01
The non-equilibrium rheological response of colloidal suspensions is studied via active microrheology utilizing Accelerated Stokesian Dynamics simulations. In our recent work, we derived the theory for micro-diffusivity and suspension stress in dilute suspensions of hydrodynamically interacting colloids. This work revealed that force-induced diffusion is anisotropic, with qualitative differences between diffusion along the line of the external force and that transverse to it, and connected these effects to the role of hydrodynamic, interparticle, and Brownian forces. This work also revealed that these forces play a similar qualitative role in the anisotropy of the stress and in the evolution of the non-equilibrium osmotic pressure. Here, we show that theoretical predictions hold for suspensions ranging from dilute to near maximum packing, and for a range of flow strengths from near-equilibrium to the pure-hydrodynamic limit.
Lattice Boltzmann Stokesian dynamics.
Ding, E J
2015-11-01
Lattice Boltzmann Stokesian dynamics (LBSD) is presented for simulation of particle suspension in Stokes flows. This method is developed from Stokesian dynamics (SD) with resistance and mobility matrices calculated using the time-independent lattice Boltzmann algorithm (TILBA). TILBA is distinguished from the traditional lattice Boltzmann method (LBM) in that a background matrix is generated prior to the calculation. The background matrix, once generated, can be reused for calculations for different scenarios, thus the computational cost for each such subsequent calculation is significantly reduced. The LBSD inherits the merits of the SD where both near- and far-field interactions are considered. It also inherits the merits of the LBM that the computational cost is almost independent of the particle shape. PMID:26651812
Lattice Boltzmann Stokesian dynamics
NASA Astrophysics Data System (ADS)
Ding, E. J.
2015-11-01
Lattice Boltzmann Stokesian dynamics (LBSD) is presented for simulation of particle suspension in Stokes flows. This method is developed from Stokesian dynamics (SD) with resistance and mobility matrices calculated using the time-independent lattice Boltzmann algorithm (TILBA). TILBA is distinguished from the traditional lattice Boltzmann method (LBM) in that a background matrix is generated prior to the calculation. The background matrix, once generated, can be reused for calculations for different scenarios, thus the computational cost for each such subsequent calculation is significantly reduced. The LBSD inherits the merits of the SD where both near- and far-field interactions are considered. It also inherits the merits of the LBM that the computational cost is almost independent of the particle shape.
Stokesian dynamics optimization of three linked spheres microswimmers
NASA Astrophysics Data System (ADS)
Marconi, V. I.; Berdakin, I.; Banchio, A. J.
2014-03-01
Self-propulsion of swimmers is only possible due to motility strategies able to overcome the absence of inertia. Only the swimming strategies that are time-irreversible are successful. One of the simplest swimmers fulfilling this requirement is the three-linked-spheres swimmer, TLS, a toy model swimmer built upon three spheres linked by two arms that contracts asynchronously. This TLS has received significant attention because it can be studied both, analytically and numerically. Using stokesian dynamics we investigate in detail the net displacement, velocities, forces and power consumption. We compare two swimming strategies: square and circular phase-space cycles. If the efficiency is defined as the ratio between power dissipation and the work needed to produce the same motion by an external force, we show that the most efficient swimmer is the one with almost maximum (maximum) arms contraction for square (circular) cycles. Interestingly, under these optimum conditions, the analytical predictions based on point force approximations of the hydrodynamic mobility tensor differ significantly from those found in our more accurate simulations. This fact highlights the importance of a proper treatment of the hydrodynamic interactions. Supported by CONICET and SeCyt-UNC, Cordoba, Argentina, and NSF(USA)-CONICET(Argentina).
Rigid body dynamics approach to Stokesian dynamics simulations of nonspherical particles
NASA Astrophysics Data System (ADS)
Kutteh, Ramzi
2010-05-01
We describe an algorithm for performing Stokesian dynamics (SD) simulations of suspensions of arbitrary shape rigid particles with hydrodynamic interactions, modeled as rigid groups of spheres, the hydrodynamic mobility matrix of which is accurately computable by several established schemes for spheres. The algorithm is based on Stokesian rigid body equations of translational and rotational motion, which we have derived by an approach formally analogous to that of Newtonian rigid body dynamics. Particle orientation is represented in terms of Euler parameters (quaternion of rotation). This rigid body SD algorithm (RBSDA) complements recently described constraint SD algorithms [R. Kutteh, J. Chem. Phys. 119, 9280 (2003); R. Kutteh, Phys. Rev. E 69, 011406 (2004)], over which it offers the same computational advantages in imposing total rigidity that the basic rigid body molecular dynamics (MD) algorithm offers over constraint MD algorithms. We show that SD simulation results generated with the RBSDA, in bounded and unbounded geometries, agree very well with those from experiment and other SD and non-SD methods, and are numerically identical to those from a constraint SD algorithm, HSHAKE. Finally, for completeness we also describe a third (additional to the constraint SD and rigid body SD approaches) more traditional approach for SD simulations of arbitrary shape rigid particles modeled as rigid groups of spheres.
Rigid body dynamics approach to Stokesian dynamics simulations of nonspherical particles.
Kutteh, Ramzi
2010-05-01
We describe an algorithm for performing Stokesian dynamics (SD) simulations of suspensions of arbitrary shape rigid particles with hydrodynamic interactions, modeled as rigid groups of spheres, the hydrodynamic mobility matrix of which is accurately computable by several established schemes for spheres. The algorithm is based on Stokesian rigid body equations of translational and rotational motion, which we have derived by an approach formally analogous to that of Newtonian rigid body dynamics. Particle orientation is represented in terms of Euler parameters (quaternion of rotation). This rigid body SD algorithm (RBSDA) complements recently described constraint SD algorithms [R. Kutteh, J. Chem. Phys. 119, 9280 (2003); R. Kutteh, Phys. Rev. E 69, 011406 (2004)], over which it offers the same computational advantages in imposing total rigidity that the basic rigid body molecular dynamics (MD) algorithm offers over constraint MD algorithms. We show that SD simulation results generated with the RBSDA, in bounded and unbounded geometries, agree very well with those from experiment and other SD and non-SD methods, and are numerically identical to those from a constraint SD algorithm, HSHAKE. Finally, for completeness we also describe a third (additional to the constraint SD and rigid body SD approaches) more traditional approach for SD simulations of arbitrary shape rigid particles modeled as rigid groups of spheres. PMID:20459156
A scalable parallel Stokesian Dynamics method for the simulation of colloidal suspensions
NASA Astrophysics Data System (ADS)
Bülow, F.; Hamberger, P.; Nirschl, H.; Dörfler, W.
2016-07-01
We have developed a new method for the efficient numerical simulation of colloidal suspensions. This method is designed and especially well-suited for parallel code execution, but it can also be applied to single-core programs. It combines the Stokesian Dynamics method with a variant of the widely used Barnes-Hut algorithm in order to reduce computational costs. This combination and the inherent parallelization of the method make simulations of large numbers of particles within days possible. The level of accuracy can be determined by the user and is limited by the truncation of the used multipole expansion. Compared to the original Stokesian Dynamics method the complexity can be reduced from O(N2) to linear complexity for dilute suspensions of strongly clustered particles, N being the number of particles. In case of non-clustered particles in a dense suspension, the complexity depends on the particle configuration and is between O(N) and O(Pnp,max2) , where P is the number of used processes and np,max = ⌈ N / P ⌉ , respectively.
NASA Astrophysics Data System (ADS)
Wang, Mu; Brady, John F.
2015-03-01
We present a comprehensive computational study of the short-time transport properties of bidisperse hard-sphere colloidal suspensions and the corresponding porous media. Our study covers bidisperse particle size ratios up to 4 and total volume fractions up to and beyond the monodisperse hard-sphere close packing limit. The many-body hydrodynamic interactions are computed using conventional Stokesian Dynamics (SD) via a Monte-Carlo approach. We address suspension properties including the short-time translational and rotational self-diffusivities, the instantaneous sedimentation velocity, the wavenumber-dependent partial hydrodynamic functions, and the high-frequency shear and bulk viscosities and porous media properties including the permeability and the translational and rotational hindered diffusivities. We carefully compare the SD computations with existing theoretical and numerical results. For suspensions, we also explore the range of validity of various approximation schemes, notably the pairwise additive approximations with the Percus-Yevick structural input. We critically assess the strengths and weaknesses of the SD algorithm for various transport properties. For very dense systems, we discuss in detail the interplay between the hydrodynamic interactions and the structures due to the presence of a second species of a different size.
Accelerated molecular dynamics methods
Perez, Danny
2011-01-04
The molecular dynamics method, although extremely powerful for materials simulations, is limited to times scales of roughly one microsecond or less. On longer time scales, dynamical evolution typically consists of infrequent events, which are usually activated processes. This course is focused on understanding infrequent-event dynamics, on methods for characterizing infrequent-event mechanisms and rate constants, and on methods for simulating long time scales in infrequent-event systems, emphasizing the recently developed accelerated molecular dynamics methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics). Some familiarity with basic statistical mechanics and molecular dynamics methods will be assumed.
GPU accelerated dislocation dynamics
NASA Astrophysics Data System (ADS)
Ferroni, Francesco; Tarleton, Edmund; Fitzgerald, Steven
2014-09-01
In this paper we analyze the computational bottlenecks in discrete dislocation dynamics modeling (associated with segment-segment interactions as well as the treatment of free surfaces), discuss the parallelization and optimization strategies, and demonstrate the effectiveness of Graphical Processing Unit (GPU) computation in accelerating dislocation dynamics simulations and expanding their scope. Individual algorithmic benchmark tests as well as an example large simulation of a thin film are presented.
Dynamics of pyroelectric accelerators
Ghaderi, R.; Davani, F. Abbasi
2015-01-26
Pyroelectric crystals are used to produce high energy electron beams. We have derived a method to model electric potential generation on LiTaO{sub 3} crystal during heating cycle. In this method, effect of heat transfer on the potential generation is investigated by some experiments. In addition, electron emission from the crystal surface is modeled by measurements and analysis. These spectral data are used to present a dynamic equation of electric potential with respect to thickness of the crystal and variation of its temperature. The dynamic equation's results for different thicknesses are compared with measured data. As a result, to attain more energetic electrons, best thickness of the crystals could be extracted from the equation. This allows for better understanding of pyroelectric crystals and help to study about current and energy of accelerated electrons.
Dynamics of Radiation Pressure Acceleration
Macchi, A.; Benedetti, C.; Pegoraro, F.; Veghini, S.
2010-02-02
We describe recent theoretical results on Radiation Pressure Acceleration of ions by ultraintense, circularly polarized laser pulses, giving an insight on the underlying dynamics and suggestions for the development of applications. In thick targets, we show how few-cycle pulses may generate single ion bunches in inhomogeneous density profiles. In thin targets, we present a refinement of the simple model of the accelerating mirror and a comparison of its predictions with simulation results, solving an apparent paradox.
Accelerated dynamics simulations of nanotubes.
Uberuaga, B. P.; Stuart, S. J.; Voter, A. F.
2002-01-01
We report on the application of accelerated dynamics techniques to the study of carbon nanotubes. We have used the parallel replica method and temperature accelerated dynamics simulations are currently in progress. In the parallel replica study, we have stretched tubes at a rate significantly lower than that used in previous studies. In these preliminary results, we find that there are qualitative differences in the rupture of the nanotubes at different temperatures. We plan on extending this investigation to include nanotubes of various chiralities. We also plan on exploring unique geometries of nanotubes.
Limit of stokesian settling concentration characterizes sludge settling velocity.
Mancell-Egala, William A S K; Kinnear, David J; Jones, Kimberly L; De Clippeleir, Haydée; Takács, Imre; Murthy, Sudhir N
2016-03-01
Flocculent settling (stokesian) is predominant within ideally operating clarifiers, and the shift to 'slower' hindered settling (non-stokesian) causes both failure and poor effluent quality. Therefore, a new metric for settling characteristics was developed and classified as Limit of Stokesian Settling (LOSS). The technique consisted of determining the total suspended solids (TSS) concentration at which mixed liquor settling characteristics transition from stokesian to non-stokesian settling. An image analytical technique was developed with the aid of MATLAB(®) to identify this transition. The MATLAB tool analyzed RGB images from video, and identified the presence of an interface by a dramatic shift in the Red indices. LOSS data for Secondary activated-sludge systems were analyzed for a period of 60 days at the Blue Plains Advanced Wastewater Treatment Plant. LOSS for secondary systems typically occurred between 600 and 700 mg TSS/L but reached 1000 mg TSS/L for a good settling secondary sludge and 500 mg TSS/L for a poor settling secondary sludge, settling quality was based on hindered settling rates. In addition, LOSS was collected for granular systems seeded with cyclone underflow from Strass Wastewater Treatment Plant, it was observed that LOSS was higher for granular systems ranging from 1600 to 5500 mg TSS/L for low and high levels of granulation, respectively. The monovalent to divalent cation ratio (M/D) was increased with the addition of sodium ions to deteriorate settling properties. Samples adjusted with higher M/D consistently had 100 mg TSS/L (15%) decrease in LOSS from the control. LOSS numbers collected experimentally were validated with the Takacs et al. (1991) settling model. When compared to flux curves with small changes in sludge matrix, LOSS was proven to be faster at characterizing hindered settling velocity and was less erratic. This is the first time a measurement method has been developed to characterize the transition from stokesian
Dynamically Reconfigurable Systolic Array Accelerator
NASA Technical Reports Server (NTRS)
Dasu, Aravind; Barnes, Robert
2012-01-01
A polymorphic systolic array framework has been developed that works in conjunction with an embedded microprocessor on a field-programmable gate array (FPGA), which allows for dynamic and complimentary scaling of acceleration levels of two algorithms active concurrently on the FPGA. Use is made of systolic arrays and a hardware-software co-design to obtain an efficient multi-application acceleration system. The flexible and simple framework allows hosting of a broader range of algorithms, and is extendable to more complex applications in the area of aerospace embedded systems. FPGA chips can be responsive to realtime demands for changing applications needs, but only if the electronic fabric can respond fast enough. This systolic array framework allows for rapid partial and dynamic reconfiguration of the chip in response to the real-time needs of scalability, and adaptability of executables.
The deadly swimming of Cercariae: an unusual Stokesian swimmer
NASA Astrophysics Data System (ADS)
Prakash, Manu; Krishnamurthy, Deepak
2014-11-01
Schistosomiasis, also known as Bilharzia, is a Neglected Tropical Disease (NTD) caused by a parasitic Trematode blood fluke worm. In terms of socio-economic and public health impact, Schistosomiasis is second only to Malaria as the most devastating parasitic disease in tropical countries; with roughly 200 million people infected at any time world-wide and up to 200,000 deaths every year. The infectious form of the parasite, known as Cercariae, emerge from snails into freshwater and infect humans by directly burrowing into the skin. Thus, anyone in contact with infected waters is at risk, which mostly includes children. By establishing a safe experimental means of studying the Cercariae in our lab, we report here their unusual swimming dynamics which include both head-first and tail-first swimming modes. These swimming modes are crucial for the chemotactic activity of Cercariae which allows them to seek out and burrow into human skin. By experimental and analytical means, we demonstrate that Cercariae break symmetry and achieve locomotion at small Reynolds number differently when compared to well-known methods involving traveling waves in the flagellum or chiral beating. Although they utilize the well-known drag anisotropy of a slender body in Stokes flow, the geometry and kinematics of their propulsion mechanism is novel. Based on these results, we propose a new kind of simple Stokesian swimmer (T-joint swimmer) in an attempt to explain the evolutionary advantages of this novel swimming mechanism. Using the above physical insights from a biological and global-health standpoint, we explore ways to hinder the chemotactic capabilities of this parasite.
Introduction to Accelerated Molecular Dynamics
Perez, Danny
2012-07-10
Molecular Dynamics is the numerical solution of the equations of motion of a set of atoms, given an interatomic potential V and some boundary and initial conditions. Molecular Dynamics is the largest scale model that gives unbiased dynamics [x(t),p(t)] in full atomistic detail. Molecular Dynamics: is simple; is 'exact' for classical dynamics (with respect to a given V); can be used to compute any (atomistic) thermodynamical or dynamical properties; naturally handles complexity -- the system does the right thing at the right time. The physics derives only from the interatomic potential.
Single particle dynamics in circular accelerators
Ruth, R.D.
1986-10-01
The purpose of this paper is to introduce the reader to the theory associated with the transverse dynamics of single particle, in circular accelerators. The discussion begins with a review of Hamiltonian dynamics and canonical transformations. The case of a single particle in a circular accelerator is considered with a discussion of non-linear terms and chromaticity. The canonical perturbation theory is presented and nonlinear resonances are considered. Finally, the concept of renormalization and residue criterion are examined. (FI)
Pulse Power Supply for Plasma Dynamic Accelerator
NASA Astrophysics Data System (ADS)
Yang, Xuanzong; Liu, Jian; Feng, Chunhua; Wang, Long
2008-06-01
A new concept of a coaxial plasma dynamic accelerator with a self-energized magnetic compressor coil to simulate the effects of space debris impact is demonstrated. A brief description is presented about the pulse power supply system including the charging circuit, start switch and current transfer system along with some of the key techniques for this kind of accelerator. Using this accelerator configuration, ceramic beads of 100 fim in diameter were accelerated to a speed as high as 18 km/sec. The facility can be used in a laboratory setting to study impact phenomena on solar array materials, potential structural materials for use in space.
Numerical homogenization on approach for stokesian suspensions.
Haines, B. M.; Berlyand, L. V.; Karpeev, D. A.
2012-01-20
swimming resulting from bacterial alignment can significantly alter other macroscopic properties of the suspension, such as the oxygen diffusivity and mixing rates. In order to understand the unique macroscopic properties of active suspensions the connection between microscopic swimming and alignment dynamics and the mesoscopic pattern formation must be clarified. This is difficult to do analytically in the fully general setting of moderately dense suspensions, because of the large number of bacteria involved (approx. 10{sup 10} cm{sup -3} in experiments) and the complex, time-dependent geometry of the system. Many reduced analytical models of bacterial have been proposed, but all of them require validation. While comparison with experiment is the ultimate test of a model's fidelity, it is difficult to conduct experiments matched to these models assumptions. Numerical simulation of the microscopic dynamics is an acceptable substitute, but it runs into the problem of having to discretize the fluid domain with a fine-grained boundary (the bacteria) and update the discretization as the domain evolves (bacteria move). This leads to a prohibitively high number of degrees of freedom and prohibitively high setup costs per timestep of simulation. In this technical report we propose numerical methods designed to alleviate these two difficulties. We indicate how to (1) construct an optimal discretization in terms of the number of degrees of freedom per digit of accuracy and (2) optimally update the discretization as the simulation evolves. The technical tool here is the derivation of rigorous error bounds on the error in the numerical solution when using our proposed discretization at the initial time as well as after a given elapsed simulation time. These error bounds should guide the construction of practical discretization schemes and update strategies. Our initial construction is carried out by using a theoretically convenient, but practically prohibitive spectral basis, which
Chaotic dynamics in accelerator physics. Progress report
Cary, J.R.
1992-11-30
Substantial progress was in several areas of accelerator dynamics. For developing understanding of longitudinal adiabatic dynamics, and for creating efficiency enhancements of recirculating free-electron lasers, was substantially completed. A computer code for analyzing the critical KAM tori that bound the dynamic aperture in circular machines was developed. Studies of modes that arise due to the interaction of coating beams with a narrow-spectrum impedance have begun. During this research educational and research ties with the accelerator community at large have been strengthened.
Tilt perception during dynamic linear acceleration.
Seidman, S H; Telford, L; Paige, G D
1998-04-01
Head tilt is a rotation of the head relative to gravity, as exemplified by head roll or pitch from the natural upright orientation. Tilt stimulates both the otolith organs, owing to shifts in gravitational orientation, and the semicircular canals in response to head rotation, which in turn drive a variety of behavioral and perceptual responses. Studies of tilt perception typically have not adequately isolated otolith and canal inputs or their dynamic contributions. True tilt cannot readily dissociate otolith from canal influences. Alternatively, centrifugation generates centripetal accelerations that simulate tilt, but still entails a rotatory (canal) stimulus during important periods of the stimulus profiles. We reevaluated the perception of head tilt in humans, but limited the stimulus to linear forces alone, thus isolating the influence of otolith inputs. This was accomplished by employing a centrifugation technique with a variable-radius spinning sled. This allowed us to accelerate the sled to a constant angular velocity (128 degrees/s), with the subject centered, and then apply dynamic centripetal accelerations after all rotatory perceptions were extinguished. These stimuli were presented in the subjects' naso-occipital axis by translating the subjects 50 cm eccentrically either forward or backward. Centripetal accelerations were thus induced (0.25 g), which combined with gravity to yield a dynamically shifting gravitoinertial force simulating pitch-tilt, but without actually rotating the head. A magnitude-estimation task was employed to characterize the dynamic perception of pitch-tilt. Tilt perception responded sluggishly to linear acceleration, typically reaching a peak after 10-30 s. Tilt perception also displayed an adaptation phenomenon. Adaptation was manifested as a per-stimulus decline in perceived tilt during prolonged stimulation and a reversal aftereffect upon return to zero acceleration (i.e., recentering the subject). We conclude that otolith
The Modern Temperature-Accelerated Dynamics Approach.
Zamora, Richard J; Uberuaga, Blas P; Perez, Danny; Voter, Arthur F
2016-06-01
Accelerated molecular dynamics (AMD) is a class of MD-based methods used to simulate atomistic systems in which the metastable state-to-state evolution is slow compared with thermal vibrations. Temperature-accelerated dynamics (TAD) is a particularly efficient AMD procedure in which the predicted evolution is hastened by elevating the temperature of the system and then recovering the correct state-to-state dynamics at the temperature of interest. TAD has been used to study various materials applications, often revealing surprising behavior beyond the reach of direct MD. This success has inspired several algorithmic performance enhancements, as well as the analysis of its mathematical framework. Recently, these enhancements have leveraged parallel programming techniques to enhance both the spatial and temporal scaling of the traditional approach. We review the ongoing evolution of the modern TAD method and introduce the latest development: speculatively parallel TAD. PMID:26979413
Accelerated transport and growth with symmetrized dynamics
NASA Astrophysics Data System (ADS)
Merikoski, Juha
2013-12-01
In this paper we consider a model of accelerated dynamics with the rules modified from those of the recently proposed [Dong et al., Phys. Rev. Lett. 109, 130602 (2012), 10.1103/PhysRevLett.109.130602] accelerated exclusion process (AEP) such that particle-vacancy symmetry is restored to facilitate a mapping to a solid-on-solid growth model in 1+1 dimensions. In addition to kicking a particle ahead of the moving particle, as in the AEP, in our model another particle from behind is drawn, provided it is within the "distance of interaction" denoted by ℓmax. We call our model the doubly accelerated exclusion process (DAEP). We observe accelerated transport and interface growth and widening of the cluster size distribution for cluster sizes above ℓmax, when compared with the ordinary totally asymmetric exclusion process (TASEP). We also characterize the difference between the TASEP, AEP, and DAEP by computing a "staggered" order parameter, which reveals the local order in the steady state. This order in part explains the behavior of the particle current as a function of density. The differences of the steady states are also reflected by the behavior of the temporal and spatial correlation functions in the interface picture.
Dynamic hierarchical algorithm for accelerated microfossil identification
NASA Astrophysics Data System (ADS)
Wong, Cindy M.; Joseph, Dileepan
2015-02-01
Marine microfossils provide a useful record of the Earth's resources and prehistory via biostratigraphy. To study Hydrocarbon reservoirs and prehistoric climate, geoscientists visually identify the species of microfossils found in core samples. Because microfossil identification is labour intensive, automation has been investigated since the 1980s. With the initial rule-based systems, users still had to examine each specimen under a microscope. While artificial neural network systems showed more promise for reducing expert labour, they also did not displace manual identification for a variety of reasons, which we aim to overcome. In our human-based computation approach, the most difficult step, namely taxon identification is outsourced via a frontend website to human volunteers. A backend algorithm, called dynamic hierarchical identification, uses unsupervised, supervised, and dynamic learning to accelerate microfossil identification. Unsupervised learning clusters specimens so that volunteers need not identify every specimen during supervised learning. Dynamic learning means interim computation outputs prioritize subsequent human inputs. Using a dataset of microfossils identified by an expert, we evaluated correct and incorrect genus and species rates versus simulated time, where each specimen identification defines a moment. The proposed algorithm accelerated microfossil identification effectively, especially compared to benchmark results obtained using a k-nearest neighbour method.
Accelerated Molecular Dynamics Simulations of Reactive Hydrocarbon Systems
Stuart, Steven J.
2014-02-25
The research activities in this project consisted of four different sub-projects. Three different accelerated dynamics techniques (parallel replica dynamics, hyperdynamics, and temperature-accelerated dynamics) were applied to the modeling of pyrolysis of hydrocarbons. In addition, parallel replica dynamics was applied to modeling of polymerization.
Stokesian swimming of a sphere at low Reynolds number by helical surface distortion
NASA Astrophysics Data System (ADS)
Felderhof, B. U.; Jones, R. B.
2016-07-01
Explicit expressions are derived for the matrices determining the mean translational and rotational swimming velocities and the mean rate of dissipation for Stokesian swimming at low Reynolds number of a distorting sphere in a viscous incompressible fluid. As an application, an efficient helical propeller-type stroke is found and its properties are calculated.
NASA Astrophysics Data System (ADS)
Kniaziev, R. R.; Sotnikov, G. V.
2016-09-01
We study theoretically transverse dynamics of the bunch of charged particles with the finite emittance in the plasma-dielectric wakefield accelerator. Parameters of bunches are chosen the same as available from the 15 MeV Argonne Wakefield Accelerator beamline. The goal of the paper is to study the behavior of bunches of charged particles with different emittances while accelerating these bunches by wakefields in plasma-dielectric structures. Obtained results allow us to determine the limits of the emittance of the bunch where dynamics of the accelerated particles remains stable.
Control of robot dynamics using acceleration control
NASA Technical Reports Server (NTRS)
Workman, G. L.; Prateru, S.; Li, W.; Hinman, Elaine
1992-01-01
Acceleration control of robotic devices can provide improvements to many space-based operations using flexible manipulators and to ground-based operations requiring better precision and efficiency than current industrial robots can provide. This paper reports on a preliminary study of acceleration measurement on robotic motion during parabolic flights on the NASA KC-135 and a parallel study of accelerations with and without gravity arising from computer simulated motions using TREETOPS software.
Accelerated Superposition State Molecular Dynamics for Condensed Phase Systems.
Ceotto, Michele; Ayton, Gary S; Voth, Gregory A
2008-04-01
An extension of superposition state molecular dynamics (SSMD) [Venkatnathan and Voth J. Chem. Theory Comput. 2005, 1, 36] is presented with the goal to accelerate timescales and enable the study of "long-time" phenomena for condensed phase systems. It does not require any a priori knowledge about final and transition state configurations, or specific topologies. The system is induced to explore new configurations by virtue of a fictitious (free-particle-like) accelerating potential. The acceleration method can be applied to all degrees of freedom in the system and can be applied to condensed phases and fluids. PMID:26620930
Calculation of structural dynamic forces and stresses using mode acceleration
NASA Technical Reports Server (NTRS)
Blelloch, Paul
1989-01-01
While the standard mode acceleration formulation in structural dynamics has often been interpreted to suggest that the reason for improved convergence obtainable is that the dynamic correction factor is divided by the modal frequencies-squared, an alternative formulation is presented which clearly indicates that the only difference between mode acceleration and mode displacement data recovery is the addition of a static correction term. Attention is given to the advantages in numerical implementation associated with this alternative, as well as to an illustrative example.
Beam Dynamics Design and Simulation in Ion Linear Accelerators (
Energy Science and Technology Software Center (ESTSC)
2006-08-01
Orginally, the ray tracing code TRACK has been developed to fulfill the many special requirements for the Rare Isotope Accelerator Facility known as RIA. Since no available beam-dynamics code met all the necessary requirements, modifications to the code TRACK were introduced to allow end-to-end (from the ion souce to the production target) simulations of the RIA machine, TRACK is a general beam-dynamics code and can be applied for the design, commissioning and operation of modernmore » ion linear accelerators and beam transport systems.« less
Beam Dynamics Design and Simulation in Ion Linear Accelerators (
Ostroumov, Peter N.; Asseev, Vladislav N.; Mustapha, and Brahim
2006-08-01
Orginally, the ray tracing code TRACK has been developed to fulfill the many special requirements for the Rare Isotope Accelerator Facility known as RIA. Since no available beam-dynamics code met all the necessary requirements, modifications to the code TRACK were introduced to allow end-to-end (from the ion souce to the production target) simulations of the RIA machine, TRACK is a general beam-dynamics code and can be applied for the design, commissioning and operation of modern ion linear accelerators and beam transport systems.
Acceleration of adiabatic quantum dynamics in electromagnetic fields
Masuda, Shumpei; Nakamura, Katsuhiro
2011-10-15
We show a method to accelerate quantum adiabatic dynamics of wave functions under electromagnetic field (EMF) by developing the preceding theory [Masuda and Nakamura, Proc. R. Soc. London Ser. A 466, 1135 (2010)]. Treating the orbital dynamics of a charged particle in EMF, we derive the driving field which accelerates quantum adiabatic dynamics in order to obtain the final adiabatic states in any desired short time. The scheme is consolidated by describing a way to overcome possible singularities in both the additional phase and driving potential due to nodes proper to wave functions under EMF. As explicit examples, we exhibit the fast forward of adiabatic squeezing and transport of excited Landau states with nonzero angular momentum, obtaining the result consistent with the transitionless quantum driving applied to the orbital dynamics in EMF.
Nonlinear dynamics of autonomous vehicles with limits on acceleration
NASA Astrophysics Data System (ADS)
Davis, L. C.
2014-07-01
The stability of autonomous vehicle platoons with limits on acceleration and deceleration is determined. If the leading-vehicle acceleration remains within the limits, all vehicles in the platoon remain within the limits when the relative-velocity feedback coefficient is equal to the headway time constant [k=1/h]. Furthermore, if the sensitivity α>1/h, no collisions occur. String stability for small perturbations is assumed and the initial condition is taken as the equilibrium state. Other values of k and α that give stability with no collisions are found from simulations. For vehicles with non-negligible mechanical response, simulations indicate that the acceleration-feedback-control gain might have to be dynamically adjusted to obtain optimal performance as the response time changes with engine speed. Stability is demonstrated for some perturbations that cause initial acceleration or deceleration greater than the limits, yet do not cause collisions.
Constant Acceleration: Experiments with a Fan-Driven Dynamics Cart.
ERIC Educational Resources Information Center
Morse, Robert A.
1993-01-01
Describes the rebuilding of a Project Physics fan cart on a PASCO dynamics cart chassis for achieving greatly reduced frictional forces. Suggests four experiments for the rebuilt cart: (1) acceleration on a level track, (2) initial negative velocity, (3) different masses and different forces, and (4) inclines. (MVL)
Accurate dynamics in an azimuthally-symmetric accelerating cavity
NASA Astrophysics Data System (ADS)
Appleby, R. B.; Abell, D. T.
2015-02-01
We consider beam dynamics in azimuthally-symmetric accelerating cavities, using the EMMA FFAG cavity as an example. By fitting a vector potential to the field map, we represent the linear and non-linear dynamics using truncated power series and mixed-variable generating functions. The analysis provides an accurate model for particle trajectories in the cavity, reveals potentially significant and measurable effects on the dynamics, and shows differences between cavity focusing models. The approach provides a unified treatment of transverse and longitudinal motion, and facilitates detailed map-based studies of motion in complex machines like FFAGs.
Deformation-induced accelerated dynamics in polymer glasses
Warren, Mya; Rottler, Joerg
2010-10-28
Molecular dynamics simulations are used to investigate the effects of deformation on the segmental dynamics in an aging polymer glass. Individual particle trajectories are decomposed into a series of discontinuous hops, from which we obtain the full distribution of relaxation times and displacements under three deformation protocols: step stress (creep), step strain, and constant strain rate deformation. As in experiments, the dynamics can be accelerated by several orders of magnitude during deformation, and the history dependence is entirely erased during yield (mechanical rejuvenation). Aging can be explained as a result of the long tails in the relaxation time distribution of the glass, and similarly, mechanical rejuvenation is understood through the observed narrowing of this distribution during yield. Although the relaxation time distributions under deformation are highly protocol specific, in each case they may be described by a universal acceleration factor that depends only on the strain.
Adiabatic invariants, diffusion and acceleration in rigid body dynamics
NASA Astrophysics Data System (ADS)
Borisov, Alexey V.; Mamaev, Ivan S.
2016-03-01
The onset of adiabatic chaos in rigid body dynamics is considered. A comparison of the analytically calculated diffusion coefficient describing probabilistic effects in the zone of chaos with a numerical experiment is made. An analysis of the splitting of asymptotic surfaces is performed and uncertainty curves are constructed in the Poincaré-Zhukovsky problem. The application of Hamiltonian methods to nonholonomic systems is discussed. New problem statements are given which are related to the destruction of an adiabatic invariant and to the acceleration of the system (Fermi's acceleration).
Temperature accelerated dynamics : introduction and application to crystal growth.
Montalenti, F.
2002-01-01
Temperature accelerated dynamics (TAD) simulations allow one to reach long time scales without needing any a priori information on the system dynamics. As a consequence, TAD is a powerful method for simulating complex phenomena where the dynamics is highly unpredictable and the time scale is longer than the one reachable by standard molecular dynamics (ns-ps) . In this paper, we shall focus our attention on crystal growth. We give an overview of the TAD method, and we demonstrate that at low temperatures a TAD simulation can be faster than a standard molecular dynamics simulation by several orders of magnitude, allowing one to match typical experimental time scales of seconds or longer. Moreover, we explicitely show how critical it is to match the experimental time scale, in order to predict the correct geometry of the growing surface.
Localization of Millisecond Dynamics: Dihedral Entropy from Accelerated MD.
Kamenik, Anna S; Kahler, Ursula; Fuchs, Julian E; Liedl, Klaus R
2016-08-01
Here, we demonstrate a method to capture local dynamics on a time scale 3 orders of magnitude beyond state-of-the-art simulation approaches. We apply accelerated molecular dynamics simulations for conformational sampling and extract reweighted backbone dihedral distributions. Local dynamics are characterized by torsional probabilities, resulting in residue-wise dihedral entropies. Our approach is successfully validated for three different protein systems of increasing size: alanine dipeptide, bovine pancreatic trypsin inhibitor (BPTI), and the major birch pollen allergen Bet v 1a. We demonstrate excellent agreement of flexibility profiles with both large-scale computer simulations and NMR experiments. Thus, our method provides efficient access to local protein dynamics on extended time scales of high biological relevance. PMID:27322931
Accelerated dynamics of supercooled glycerol in soft confinement
NASA Astrophysics Data System (ADS)
Blochowicz, T.; Gouirand, E.; Fricke, A.; Spehr, T.; Stühn, B.; Frick, B.
2009-06-01
We investigate the dynamics of supercooled glycerol in a soft confinement within microemulsion droplets. The structure of the system is characterized by small-angle neutron scattering. We show that temperature-stable droplets establish a confinement, which may be varied in size from about 1 to 10 nm. Subsequently we focus on the dynamics of glass-forming glycerol confined within nanodroplets of different sizes. By combining neutron backscattering and time-of-flight for a broad dynamic range we obtain the incoherent intermediate scattering function S(q,t), which reveals increasingly accelerated dynamics as glycerol is confined to smaller droplets and for the relaxation times a crossover from Vogel-Fulcher behavior in the bulk to an Arrhenius law in confinement.
Localization of Millisecond Dynamics: Dihedral Entropy from Accelerated MD
2016-01-01
Here, we demonstrate a method to capture local dynamics on a time scale 3 orders of magnitude beyond state-of-the-art simulation approaches. We apply accelerated molecular dynamics simulations for conformational sampling and extract reweighted backbone dihedral distributions. Local dynamics are characterized by torsional probabilities, resulting in residue-wise dihedral entropies. Our approach is successfully validated for three different protein systems of increasing size: alanine dipeptide, bovine pancreatic trypsin inhibitor (BPTI), and the major birch pollen allergen Bet v 1a. We demonstrate excellent agreement of flexibility profiles with both large-scale computer simulations and NMR experiments. Thus, our method provides efficient access to local protein dynamics on extended time scales of high biological relevance. PMID:27322931
Lagrangian observations of acceleration and bubble dynamics in plunging breakers
NASA Astrophysics Data System (ADS)
Canals, Miguel; Amador, Andre
2012-11-01
Understanding the three-dimensional structure of plunging waves is one of the most difficult problems in fundamental fluid dynamics. In this presentation we provide an analysis of field data collected in breaking waves using novel Lagrangian drifters with a diameter of 5-10 cm and equipped with miniature HD cameras and inertial measurement units. These drifters were deployed, using a personal watercraft, into the breaking region of waves ranging from 1-5 meters in height. We analyze in detail the time series of particle acceleration and rotation and how these quantities relate to the imagery captured by the camera aboard the drifters. This data represents the first dedicated study of the three-dimensional particle dynamics of plunging breakers. Going beyond the basic statistical analysis of the acceleration data, we make an attempt at characterizing the intensity of the wave breaking process using the bubble size and characteristics obtained from the HD video images. We also attempt to relate the spectral statistics of acceleration and particle rotation to existing Lagrangian turbulence models in the hopes of obtaining estimates of the kinetic energy dissipation in breaking waves, while taking into account the unsteady and heterogeneous nature of the turbulent flow.
GPU accelerated dynamic functional connectivity analysis for functional MRI data.
Akgün, Devrim; Sakoğlu, Ünal; Esquivel, Johnny; Adinoff, Bryon; Mete, Mutlu
2015-07-01
Recent advances in multi-core processors and graphics card based computational technologies have paved the way for an improved and dynamic utilization of parallel computing techniques. Numerous applications have been implemented for the acceleration of computationally-intensive problems in various computational science fields including bioinformatics, in which big data problems are prevalent. In neuroimaging, dynamic functional connectivity (DFC) analysis is a computationally demanding method used to investigate dynamic functional interactions among different brain regions or networks identified with functional magnetic resonance imaging (fMRI) data. In this study, we implemented and analyzed a parallel DFC algorithm based on thread-based and block-based approaches. The thread-based approach was designed to parallelize DFC computations and was implemented in both Open Multi-Processing (OpenMP) and Compute Unified Device Architecture (CUDA) programming platforms. Another approach developed in this study to better utilize CUDA architecture is the block-based approach, where parallelization involves smaller parts of fMRI time-courses obtained by sliding-windows. Experimental results showed that the proposed parallel design solutions enabled by the GPUs significantly reduce the computation time for DFC analysis. Multicore implementation using OpenMP on 8-core processor provides up to 7.7× speed-up. GPU implementation using CUDA yielded substantial accelerations ranging from 18.5× to 157× speed-up once thread-based and block-based approaches were combined in the analysis. Proposed parallel programming solutions showed that multi-core processor and CUDA-supported GPU implementations accelerated the DFC analyses significantly. Developed algorithms make the DFC analyses more practical for multi-subject studies with more dynamic analyses. PMID:25805449
Temperature accelerated dynamics in glass-forming materials.
Tsalikis, Dimitrios G; Lempesis, Nikolaos; Boulougouris, Georgios C; Theodorou, Doros N
2010-06-17
In this work we propose a methodology for improving dynamical sampling in molecular simulations via temperature acceleration. The proposed approach combines the novel methods of Voter for temperature-accelerated dynamics with the multiple histogram reweighting method of Ferrenberg and Swendsen, its dynamical extension by Nieto-Draghi et al., and with hazard plot analysis, allowing optimal sampling with small computational cost over time scales inaccessible to classical molecular dynamics simulations by utilizing the "inherent structure" idea. The time evolution of the system is viewed as a succession of transitions between "basins" in its potential energy landscape, each basin containing a local minimum of the energy (inherent structure). Applying the proposed algorithm to a glass-forming material consisting of a mixture of spherical atoms interacting via Lennard-Jones potentials, we show that it is possible to perform an exhaustive search and evaluate rate constants for basin-to-basin transitions that cover several orders of magnitude on the time scale, far beyond the abilities of any competitive dynamical study, revealing an extreme ruggedness of the potential energy landscape in the vicinity of the glass transition temperature. By analyzing the network of inherent structures, we find that there are characteristic distances and rate constants related to the dynamical entrapment of the system in a neighborhood of basins (a metabasin), whereas evidence to support a random energy model is provided. The multidimensional configurational space displays a self-similar character depicted by a fractal dimension around 2.7 (+/-0.5) for the set of sampled inherent structures. Only transitions with small Euclidean measure can be considered as localized. PMID:20491458
Radio Frequency Station - Beam Dynamics Interaction in Circular Accelerators
Mastoridis, Themistoklis
2010-08-01
The longitudinal beam dynamics in circular accelerators is mainly defined by the interaction of the beam current with the accelerating Radio Frequency (RF) stations. For stable operation, Low Level RF (LLRF) feedback systems are employed to reduce coherent instabilities and regulate the accelerating voltage. The LLRF system design has implications for the dynamics and stability of the closed-loop RF systems as well as for the particle beam, and is very sensitive to the operating range of accelerator currents and energies. Stability of the RF loop and the beam are necessary conditions for reliable machine operation. This dissertation describes theoretical formalisms and models that determine the longitudinal beam dynamics based on the LLRF implementation, time domain simulations that capture the dynamic behavior of the RF station-beam interaction, and measurements from the Positron-Electron Project (PEP-II) and the Large Hadron Collider (LHC) that validate the models and simulations. These models and simulations are structured to capture the technical characteristics of the system (noise contributions, non-linear elements, and more). As such, they provide useful results and insight for the development and design of future LLRF feedback systems. They also provide the opportunity to study diverse longitudinal beam dynamics effects such as coupled-bunch impedance driven instabilities and single bunch longitudinal emittance growth. Coupled-bunch instabilities and RF station power were the performance limiting effects for PEP-II. The sensitivity of the instabilities to individual LLRF parameters, the effectiveness of alternative operational algorithms, and the possible tradeoffs between RF loop and beam stability were studied. New algorithms were implemented, with significant performance improvement leading to a world record current during the last PEP-II run of 3212 mA for the Low Energy Ring. Longitudinal beam emittance growth due to RF noise is a major concern for LHC
Accelerated Testing of Polymeric Composites Using the Dynamic Mechanical Analyzer
NASA Technical Reports Server (NTRS)
Abdel-Magid, Becky M.; Gates, Thomas S.
2000-01-01
Creep properties of IM7/K3B composite material were obtained using three accelerated test methods at elevated temperatures. Results of flexural creep tests using the dynamic mechanical analyzer (DMA) were compared with results of conventional tensile and compression creep tests. The procedures of the three test methods are described and the results are presented. Despite minor differences in the time shift factor of the creep compliance curves, the DMA results compared favorably with the results from the tensile and compressive creep tests. Some insight is given into establishing correlations between creep compliance in flexure and creep compliance in tension and compression. It is shown that with careful consideration of the limitations of flexure creep, a viable and reliable accelerated test procedure can be developed using the DMA to obtain the viscoelastic properties of composites in extreme environments.
A gas-dynamical approach to radiation pressure acceleration
NASA Astrophysics Data System (ADS)
Schmidt, Peter; Boine-Frankenheim, Oliver
2016-06-01
The study of high intensity ion beams driven by high power pulsed lasers is an active field of research. Of particular interest is the radiation pressure acceleration, for which simulations predict narrow band ion energies up to GeV. We derive a laser-piston model by applying techniques for non-relativistic gas-dynamics. The model reveals a laser intensity limit, below which sufficient laser-piston acceleration is impossible. The relation between target thickness and piston velocity as a function of the laser pulse length yields an approximation for the permissible target thickness. We performed one-dimensional Particle-In-Cell simulations to confirm the predictions of the analytical model. These simulations also reveal the importance of electromagnetic energy transport. We find that this energy transport limits the achievable compression and rarefies the plasma.
Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo
White, Alexander J.; Gorshkov, Vyacheslav N.; Tretiak, Sergei; Mozyrsky, Dmitry
2015-07-07
Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficientmore » as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In many cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems.« less
The Acceleration Scale, Modified Newtonian Dynamics and Sterile Neutrinos
NASA Astrophysics Data System (ADS)
Diaferio, Antonaldo; Angus, Garry W.
General relativity is able to describe the dynamics of galaxies and larger cosmic structures only if most of the matter in the universe is dark, namely, it does not emit any electromagnetic radiation. Intriguingly, on the scale of galaxies, there is strong observational evidence that the presence of dark matter appears to be necessary only when the gravitational field inferred from the distribution of the luminous matter falls below an acceleration of the order of 10^{-10} m s^{-2}. In the standard model, which combines Newtonian gravity with dark matter, the origin of this acceleration scale is challenging and remains unsolved. On the contrary, the full set of observations can be neatly described, and were partly predicted, by a modification of Newtonian dynamics, dubbed MOND, that does not resort to the existence of dark matter. On the scale of galaxy clusters and beyond, however, MOND is not as successful as on the scale of galaxies, and the existence of some dark matter appears unavoidable. A model combining MOND with hot dark matter made of sterile neutrinos seems to be able to describe most of the astrophysical phenomenology, from the power spectrum of the cosmic microwave background anisotropies to the dynamics of dwarf galaxies. Whether there exists a yet unknown covariant theory that contains general relativity and Newtonian gravity in the weak field limit and MOND as the ultra-weak field limit is still an open question.
Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo
White, Alexander J.; Gorshkov, Vyacheslav N.; Tretiak, Sergei; Mozyrsky, Dmitry
2015-07-07
Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficient as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In many cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems.
Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo
White, Alexander J.; Gorshkov, Vyacheslav N.; Tretiak, Sergei; Mozyrsky, Dmitry
2015-07-07
Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficient as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In most cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems.
Characterization of micro- and mesoporous materials using accelerated dynamics adsorption.
Qajar, Ali; Peer, Maryam; Rajagopalan, Ramakrishnan; Foley, Henry C
2013-10-01
Porosimetry is a fundamental characterization technique used in development of new porous materials for catalysis, membrane separation, and adsorptive gas storage. Conventional methods like nitrogen and argon adsorption at cryogenic temperatures suffer from slow adsorption dynamics especially for microporous materials. In addition, CO2, the other common probe, is only useful for micropore characterization unless being compressed to exceedingly high pressures to cover all required adsorption pressures. Here, we investigated the effect of adsorption temperature, pressure, and type of probe molecule on the adsorption dynamics. Methyl chloride (MeCl) was used as the probe molecule, and measurements were conducted near room temperature under nonisothermal condition and subatmospheric pressure. A pressure control algorithm was proposed to accelerate adsorption dynamics by manipulating the chemical potential of the gas. Collected adsorption data are transformed into pore size distribution profiles using the Horvath-Kavazoe (HK), Saito-Foley (SF), and modified Kelvin methods revised for MeCl. Our study shows that the proposed algorithm significantly speeds up the rate of data collection without compromising the accuracy of the measurements. On average, the adsorption rates on carbonaceous and aluminosilicate samples were accelerated by at least a factor of 4-5. PMID:23919893
Front acceleration by dynamic selection in Fisher population waves
NASA Astrophysics Data System (ADS)
Bénichou, O.; Calvez, V.; Meunier, N.; Voituriez, R.
2012-10-01
We introduce a minimal model of population range expansion in which the phenotypes of individuals present no selective advantage and differ only in their diffusion rate. We show that such neutral phenotypic variability (i.e., that does not modify the growth rate) alone can yield phenotype segregation at the front edge, even in absence of genetic noise, and significantly impact the dynamical properties of the expansion wave. We present an exact asymptotic traveling wave solution and show analytically that phenotype segregation accelerates the front propagation. The results are compatible with field observations such as invasions of cane toads in Australia or bush crickets in Britain.
Ion dynamics in an E × B Hall plasma accelerator
NASA Astrophysics Data System (ADS)
Young, Christopher V.; Lucca Fabris, Andrea; Cappelli, Mark A.
2015-01-01
We show the time evolution of the ion velocity distribution function in a Hall plasma accelerator during a 20 kHz natural, quasi-periodic plasma oscillation. We apply a time-synchronized laser induced fluorescence technique at different locations along the channel midline, obtaining time- and spatially resolved ion velocity measurements. Strong velocity and density fluctuations and multiple ion populations are observed throughout the so-called "breathing mode" ionization instability, opening an experimental window into the detailed ion dynamics and physical processes at the heart of such devices.
High spatial resolution measurements of ram accelerator gas dynamic phenomena
NASA Technical Reports Server (NTRS)
Hinkey, J. B.; Burnham, E. A.; Bruckner, A. P.
1992-01-01
High spatial resolution experimental tube wall pressure measurements of ram accelerator gas dynamic phenomena are presented. The projectile resembles the centerbody of a ramjet and travels supersonically through a tube filled with a combustible gaseous mixture, with the tube acting as the outer cowling. Pressure data are recorded as the projectile passes by sensors mounted in the tube wall at various locations along the tube. Data obtained by using a special highly instrumented section of tube has allowed the recording of gas dynamic phenomena with a spatial resolution on the order of one tenth the projectile length. High spatial resolution tube wall pressure data from the three regimes of propulsion studied to date (subdetonative, transdetonative, and superdetonative) are presented and reveal the 3D character of the flowfield induced by projectile fins and the canting of the projectile body relative to the tube wall. Also presented for comparison to the experimental data are calculations made with an inviscid, 3D CFD code.
Numerical study of an inextensible, finite swimmer in Stokesian viscoelastic flow
NASA Astrophysics Data System (ADS)
Salazar, Daniel; Roma, Alexandre M.; Ceniceros, Hector D.
2016-06-01
A numerical investigation of an Immersed Boundary (IB) model of an effectively inextensible, finite swimmer in a Stokesian Oldroyd-B flow is presented. The swimmer model is a two-dimensional sheet of finite extent and its gait is generated by an elastic force which penalizes deviations from a target shape. A non-stiff IB method is employed to remove the impeding time step limitation induced by strong tangential forces on the swimmer. It is found that for a swimmer with a prescribed gait its mean propulsion speed decreases with increasing Deborah number De toward an apparent asymptotic minimal value. However, as the swimmer is allowed to deviate more from the target shape, the monotonic locomotion behavior with De is broken. For a sufficiently flexible swimmer, viscoelasticity can enhance locomotion but the swimmer in the viscoelastic fluid always remains slower than when it is propelling in a Newtonian fluid. Remarkably, the addition of viscoelastic stress diffusion dramatically alters the swimmer propulsion and can lead to a speed-up over the swimmer in the Newtonian fluid.
Accelerated molecular dynamics methods: introduction and recent developments
Uberuaga, Blas Pedro; Voter, Arthur F; Perez, Danny; Shim, Y; Amar, J G
2009-01-01
reaction pathways may be important, we return instead to a molecular dynamics treatment, in which the trajectory itself finds an appropriate way to escape from each state of the system. Since a direct integration of the trajectory would be limited to nanoseconds, while we are seeking to follow the system for much longer times, we modify the dynamics in some way to cause the first escape to happen much more quickly, thereby accelerating the dynamics. The key is to design the modified dynamics in a way that does as little damage as possible to the probability for escaping along a given pathway - i.e., we try to preserve the relative rate constants for the different possible escape paths out of the state. We can then use this modified dynamics to follow the system from state to state, reaching much longer times than we could reach with direct MD. The dynamics within any one state may no longer be meaningful, but the state-to-state dynamics, in the best case, as we discuss in the paper, can be exact. We have developed three methods in this accelerated molecular dynamics (AMD) class, in each case appealing to TST, either implicitly or explicitly, to design the modified dynamics. Each of these methods has its own advantages, and we and others have applied these methods to a wide range of problems. The purpose of this article is to give the reader a brief introduction to how these methods work, and discuss some of the recent developments that have been made to improve their power and applicability. Note that this brief review does not claim to be exhaustive: various other methods aiming at similar goals have been proposed in the literature. For the sake of brevity, our focus will exclusively be on the methods developed by the group.
Accelerating ring-polymer molecular dynamics with parallel-replica dynamics.
Lu, Chun-Yaung; Perez, Danny; Voter, Arthur F
2016-06-28
Nuclear quantum effects are important for systems containing light elements, and the effects are more prominent in the low temperature regime where the dynamics also becomes sluggish. We show that parallel replica (ParRep) dynamics, an accelerated molecular dynamics approach for infrequent-event systems, can be effectively combined with ring-polymer molecular dynamics, a semiclassical trajectory approach that gives a good approximation to zero-point and tunneling effects in activated escape processes. The resulting RP-ParRep method is a powerful tool for reaching long time scales in complex infrequent-event systems where quantum dynamics are important. Two illustrative examples, symmetric Eckart barrier crossing and interstitial helium diffusion in Fe and Fe-Cr alloy, are presented to demonstrate the accuracy and long-time scale capability of this approach. PMID:27369499
Accelerating ring-polymer molecular dynamics with parallel-replica dynamics
NASA Astrophysics Data System (ADS)
Lu, Chun-Yaung; Perez, Danny; Voter, Arthur F.
2016-06-01
Nuclear quantum effects are important for systems containing light elements, and the effects are more prominent in the low temperature regime where the dynamics also becomes sluggish. We show that parallel replica (ParRep) dynamics, an accelerated molecular dynamics approach for infrequent-event systems, can be effectively combined with ring-polymer molecular dynamics, a semiclassical trajectory approach that gives a good approximation to zero-point and tunneling effects in activated escape processes. The resulting RP-ParRep method is a powerful tool for reaching long time scales in complex infrequent-event systems where quantum dynamics are important. Two illustrative examples, symmetric Eckart barrier crossing and interstitial helium diffusion in Fe and Fe-Cr alloy, are presented to demonstrate the accuracy and long-time scale capability of this approach.
Improved scaling of temperature-accelerated dynamics using localization.
Shim, Yunsic; Amar, Jacques G
2016-07-01
While temperature-accelerated dynamics (TAD) is a powerful method for carrying out non-equilibrium simulations of systems over extended time scales, the computational cost of serial TAD increases approximately as N(3) where N is the number of atoms. In addition, although a parallel TAD method based on domain decomposition [Y. Shim et al., Phys. Rev. B 76, 205439 (2007)] has been shown to provide significantly improved scaling, the dynamics in such an approach is only approximate while the size of activated events is limited by the spatial decomposition size. Accordingly, it is of interest to develop methods to improve the scaling of serial TAD. As a first step in understanding the factors which determine the scaling behavior, we first present results for the overall scaling of serial TAD and its components, which were obtained from simulations of Ag/Ag(100) growth and Ag/Ag(100) annealing, and compare with theoretical predictions. We then discuss two methods based on localization which may be used to address two of the primary "bottlenecks" to the scaling of serial TAD with system size. By implementing both of these methods, we find that for intermediate system-sizes, the scaling is improved by almost a factor of N(1/2). Some additional possible methods to improve the scaling of TAD are also discussed. PMID:27394097
Improved scaling of temperature-accelerated dynamics using localization
NASA Astrophysics Data System (ADS)
Shim, Yunsic; Amar, Jacques G.
2016-07-01
While temperature-accelerated dynamics (TAD) is a powerful method for carrying out non-equilibrium simulations of systems over extended time scales, the computational cost of serial TAD increases approximately as N3 where N is the number of atoms. In addition, although a parallel TAD method based on domain decomposition [Y. Shim et al., Phys. Rev. B 76, 205439 (2007)] has been shown to provide significantly improved scaling, the dynamics in such an approach is only approximate while the size of activated events is limited by the spatial decomposition size. Accordingly, it is of interest to develop methods to improve the scaling of serial TAD. As a first step in understanding the factors which determine the scaling behavior, we first present results for the overall scaling of serial TAD and its components, which were obtained from simulations of Ag/Ag(100) growth and Ag/Ag(100) annealing, and compare with theoretical predictions. We then discuss two methods based on localization which may be used to address two of the primary "bottlenecks" to the scaling of serial TAD with system size. By implementing both of these methods, we find that for intermediate system-sizes, the scaling is improved by almost a factor of N1/2. Some additional possible methods to improve the scaling of TAD are also discussed.
Accelerated Molecular Dynamics studies of He Bubble Growth in Tungsten
NASA Astrophysics Data System (ADS)
Uberuaga, Blas; Sandoval, Luis; Perez, Danny; Voter, Arthur
2015-11-01
Understanding how materials respond to extreme environments is critical for predicting and improving performance. In materials such as tungsten exposed to plasmas for nuclear fusion applications, novel nanoscale fuzzes, comprised of tendrils of tungsten, form as a consequence of the implantation of He into the near surface. However, the detailed mechanisms that link He bubble formation to the ultimate development of fuzz are unclear. Molecular dynamics simulations provide insight into the He implantation process, but are necessarily performed at implantation rates that are orders of magnitudes faster than experiment. Here, using accelerated molecular dynamics methods, we examine the role of He implantation rates on the physical evolution of He bubbles in tungsten. We find that, as the He rate is reduced, new types of events involving the response of the tungsten matrix to the pressure in the bubble become competitive and change the overall evolution of the bubble as well as the subsequent morphology of the tungsten surface. We have also examined how bubble growth differs at various microstructural features. These results highlight the importance of performing simulations at experimentally relevant conditions in order to correctly capture the contributions of the various significant kinetic processes and predict the overall response of the material.
Electron dynamics and ion acceleration in expanding-plasma thrusters
NASA Astrophysics Data System (ADS)
Lafleur, T.; Cannat, F.; Jarrige, J.; Elias, P. Q.; Packan, D.
2015-12-01
In most expanding-plasma thrusters, ion acceleration occurs due to the formation of ambipolar-type electric fields; a process that depends strongly on the electron dynamics of the discharge. The electron properties also determine the heat flux leaving the thruster as well as the maximum ion energy, which are important parameters for the evaluation of thruster performance. Here we perform an experimental and theoretical investigation with both magnetized, and unmagnetized, low-pressure thrusters to explicitly determine the relationship between the ion energy, E i , and the electron temperature, T e0. With no magnetic field a relatively constant value of {{E}i}/{{T}e0}≈ 6 is found for xenon, while when a magnetic nozzle is present, {{E}i}/{{T}e0} is between about 4-5. These values are shown to be a function of both the magnetic field strength, as well as the electron energy distribution function, which changes significantly depending on the mass flow rate (and hence neutral gas pressure) used in the thruster. The relationship between the ion energy and electron temperature allows estimates to be made for polytropic indices of use in a number of fluid models, as well as estimates of the upper limits to the performance of these types of systems, which for xenon and argon result in maximum specific impulses of about 2500 s and 4500 s respectively.
Ridge-based bias potentials to accelerate molecular dynamics.
Xiao, Penghao; Duncan, Juliana; Zhang, Liang; Henkelman, Graeme
2015-12-28
An effective way to accelerate rare events in molecular dynamics simulations is to apply a bias potential which destabilizes minima without biasing the transitions between stable states. This approach, called hyperdynamics, is limited by our ability to construct general bias potentials without having to understand the reaction mechanisms available to the system, a priori. Current bias potentials are typically constructed in terms of a metric which quantifies the distance that a trajectory deviates from the reactant state minimum. Such metrics include detection of negative curvatures of the potential, an energy increase, or deviations in bond lengths from the minimum. When one of these properties exceeds a critical value, the bias potentials are constructed to approach zero. A problem common to each of these schemes is that their effectiveness decreases rapidly with system size. We attribute this problem to a diminishing volume defined by the metrics around a reactant minimum as compared to the total volume of the reactant state basin. In this work, we mitigate the dimensionality scaling problem by constructing bias potentials that are based upon the distance to the boundary of the reactant basin. This distance is quantified in two ways: (i) by following the minimum mode direction to the reactant boundary and (ii) by training a machine learning algorithm to give an analytic expression for the boundary to which the distance can be calculated. Both of these ridge-based bias potentials are demonstrated to scale qualitatively better with dimensionality than the existing methods. We attribute this improvement to a greater filling fraction of the reactant state using the ridge-based bias potentials as compared to the standard potentials. PMID:26723648
Dynamics of a current bridge in a coaxial plasma accelerator
NASA Astrophysics Data System (ADS)
Voronin, A. V.; Gusev, V. K.; Kobyakov, S. V.
2011-07-01
The pioneering investigation of the behavior of a current bridge in a coaxial accelerator with pulsed delivery of a working gas liberated from titanium hydride by an electrical discharge is reported. A new method to trace the motion of the current bridge using LEDs is suggested. The behavior of the current bridge in accelerators with axial and radial gas injection is studied. The parameters of an accelerator generating a pure plasma jet with a high kinetic energy (such as the size and polarity of electrodes, gas flow direction, and time delay between the delivery of the gas to the accelerator and its ionization) are optimized. The applicability of an electrodynamic model to this type of accelerator is discussed. Good agreement between experimental data and calculation results is obtained.
Chemical Accelerator Studies of Ion-Molecule Reaction Dynamics
NASA Astrophysics Data System (ADS)
Zhang, Jingfeng
1995-01-01
A chemical accelerator instrument has been used to study the dynamics of ion-molecule reaction processes in the gas phase. Specifically, the following reactions are investigated: eqalign{rm CO^+ + H_2&longrightarrowrm HCO ^+ + Hcrrm CO^+ + D_2& longrightarrowrm DCO^+ + Dcrrm CO^+ + HDlongrightarrow &rm HCO ^+ (DCO^+) + D (H)cr} . Both angular and velocity distributions of reactively scattered product ions are measured, as well as reaction cross sections as a function of reactant relative translational energy. Formation of HCO^+ ion from rm CO^+ + H_2 over the collision energy range from 0.35 to 3.02 eV (c.m.) follows closely the predictions of the spectator stripping model, and results in highly excited HCO^+ product ions. This reaction is found to proceed via a direct impulsive mechanism, without any long-lived intermediate complexes involved. The reaction cross section is proportional to E_{T} ^{-1/2}, where E_ {rm T} is the reactant ion relative translational energy. Deuterium atom transfer from D_2 to CO^+ over the collision energy range from 0.41 to 5.14 eV (c.m.) occurs also in a direct process. Reaction cross section is proportional to rm E_{T}^{ -1/2}. The results are very similar to those of the reaction rm CO^+ + H_2. The reaction CO^+ + HD has two product channels, leading to the formation of HCO ^+ and DCO^+, respectively. The reaction is studied over the energy range from 0.88 to 5.00 eV (c.m.). It is found that the production of HCO^+ is consistently the slightly favored reaction channel, which is attributed to the orientation isotope effect. The translational exoergicity for both reaction channels follows closely the prediction of spectator stripping model. Product DCO^+ ions are in higher excited states than HCO ^+ ions. Product velocity distribution contour maps indicate that, at the lowest energies, the DCO ^+ production channel has a longer reaction duration than the HCO^+ production channel, but both reaction channels are dominated by direct
Dynamics of plasma flow formation in a pulsed accelerator operating at a constant pressure
NASA Astrophysics Data System (ADS)
Baimbetov, F. B.; Zhukeshov, A. M.; Amrenova, A. U.
2007-01-01
Features in the dynamics of plasma flow formation at a constant pressure in a pulsed coaxial accelerator have been studied. The temperature and density of electrons in a plasma bunch have been determined using a probe technique.
Soil dynamics and accelerated erosion: a sensitivity analysis of the LPJ Dynamic vegetation model
NASA Astrophysics Data System (ADS)
Bouchoms, Samuel; Van Oost, Kristof; Vanacker, Veerle; Kaplan, Jed O.; Vanwalleghem, Tom
2013-04-01
It is widely accepted that humans have become a major geomorphic force by disturbing natural vegetation patterns. Land conversion for agriculture purposes removes the protection of soils by the natural vegetation and leads to increased soil erosion by one to two orders of magnitude, breaking the balance that exists between the loss of soils and its production. Accelerated erosion and deposition have a strong influence on evolution and heterogeneity of basic soil characteristics (soil thickness, hydrology, horizon development,…) as well as on organic matter storage and cycling. Yet, since they are operating at a long time scale, those processes are not represented in state-of-art Dynamic Global Vegetation Models, which is a clear lack when exploring vegetation dynamics over past centuries. The main objectives of this paper are (i) to test the sensitivity of a Dynamic Global Vegetation Model, in terms of NPP and organic matter turnover, variations in state variables in response to accelerated erosion and (ii) to assess the performance of the model under the impact of erosion for a case-study in Central Spain. We evaluated the Lund-Postdam-Jena Dynamic Vegetation Model (LPJ DVGM) (Sitch et al, 2003) which simulates vegetation growth and carbon pools at the surface and in the soil based on climatic, pedologic and topographic variables. We assessed its reactions to changes in key soil properties that are affected by erosion such as texture and soil depth. We present the results of where we manipulated soil texture and bulk density while keeping the environmental drivers of climate, slope and altitude constant. For parameters exhibiting a strong control on NPP or SOM, a factorial analysis was conducted to test for interaction effects. The simulations show an important dependence on the clay content, especially for the slow cycling carbon pools and the biomass production, though the underground litter seems to be mostly influenced by the silt content. The fast cycling C
NASA Astrophysics Data System (ADS)
Podbielska, Halina; Kasprzak, Henryk T.; Voloshin, Arkady S.; Pennig, Dietmar; von Bally, Gert
1992-08-01
The unilateral axially dynamic fixator (Orthofix) was mounted on a sheep tibial shaft. Three fixation modes: static, dynamic controlled, and dynamic free were examined by means of double exposure holographic interferometry. Simultaneously, the acceleration was measured by an accelerometer and displayed on the monitor together with loading characteristics. The first exposure was made before the acting force was applied to the tibia plateau. The second one after the moment when the acceleration wave started to propagate through the specimen. We stated that in the case of dynamization less torsion occurs at the fracture site. So far, we have not been able to determine any correlation between results of holographic and accelerometric measurements.
Beam dynamics in a long-pulse linear induction accelerator
Ekdahl, Carl; Abeyta, Epifanio O; Aragon, Paul; Archuleta, Rita; Cook, Gerald; Dalmas, Dale; Esquibel, Kevin; Gallegos, Robert A; Garnett, Robert; Harrison, James F; Johnson, Jeffrey B; Jacquez, Edward B; Mc Cuistian, Brian T; Montoya, Nicholas A; Nath, Subrato; Nielsen, Kurt; Oro, David; Prichard, Benjamin; Rose, Chris R; Sanchez, Manolito; Schauer, Martin M; Seitz, Gerald; Schulze, Martin; Bender, Howard A; Broste, William B; Carlson, Carl A; Frayer, Daniel K; Johnson, Douglas E; Tom, C Y; Trainham, C; Williams, John; Scarpetti, Raymond; Genoni, Thomas; Hughes, Thomas; Toma, Carsten
2010-01-01
The second axis of the Dual Axis Radiography of Hydrodynamic Testing (DARHT) facility produces up to four radiographs within an interval of 1.6 microseconds. It accomplishes this by slicing four micro-pulses out of a long 1.8-kA, 16.5-MeV electron beam pulse and focusing them onto a bremsstrahlung converter target. The long beam pulse is created by a dispenser cathode diode and accelerated by the unique DARHT Axis-II linear induction accelerator (LIA). Beam motion in the accelerator would be a problem for radiography. High frequency motion, such as from beam breakup instability, would blur the individual spots. Low frequency motion, such as produced by pulsed power variation, would produce spot to spot differences. In this article, we describe these sources of beam motion, and the measures we have taken to minimize it.
Dynamics of Mesoscale Magnetic Field in Diffusive Shock Acceleration
NASA Astrophysics Data System (ADS)
Diamond, P. H.; Malkov, M. A.
2007-01-01
We present a theory for the generation of mesoscale (krg<<1, where rg is the cosmic-ray gyroradius) magnetic fields during diffusive shock acceleration. The decay or modulational instability of resonantly excited Alfvén waves scattering off ambient density perturbations in the shock environment naturally generates larger scale fields. For a broad spectrum of perturbations, the physical mechanism of energy transfer is random refraction, represented by the diffusion of Alfvén wave packets in k-space. The scattering field can be produced directly by the decay instability or by the Drury instability, a hydrodynamic instability driven by the cosmic-ray pressure gradient. This process is of interest to acceleration since it generates waves of longer wavelength, and so enables the confinement and acceleration of higher energy particles. This process also limits the intensity of resonantly generated turbulent magnetic fields on rg scales.
NASA Astrophysics Data System (ADS)
Ryazhskikh, A. V.; Boger, A. A.; Slyusarev, M. I.; Ryazhskikh, V. I.
2016-01-01
The authors have developed a convective-diffusion model of sedimentation of solid Stokesian particles from a dispersed phase moving in an ideal-mixing regime in a plane channel as the initial boundary-value problem for the particle size function, whose solution was obtained in analytical form. The mixing coefficient has been found from the hydrodynamic analogy with turbulent viscosity, and the kinetic coefficients of settling on "wetted" surfaces have been determined on condition that the particles near the walls lose the convective velocity component but preserve the Brownian and Stokesian components. The obtained calculation results are consistent with the universally accepted ideas of separation of the solid phase of suspensions from flows on the settling surface.
Resonance, particle dynamics, and particle transmission in the micro-accelerator platform
McNeur, J.; Hazra, K. S.; Liu, G.; Sozer, E. B.; Travish, G.; Yoder, R. B.
2012-12-21
We describe particle dynamics in the Micro-Accelerator Platform (MAP), a slab-symmetric dielectric laser accelerator (DLA), and model the expected performance of recently fabricated MAP structures. The quality of the structure resonances has been characterized optically, and results are compared with simulation. 3D trajectory analysis is used to model acceleration in those same structures 'as built.' Results are applied to ongoing beam transmission and acceleration tests at NLCTA/E-163, in which transmission of 60 MeV injected electrons through the beam channel of the MAP was clearly observed, despite the overfilling of the structure by the beam.
Electron beam dynamics in the DARHT-II linear induction accelerator
Ekdahl, Carl A; Abeyta, Epifanio O; Aragon, Paul; Archuleta, Rita; Cook, Gerald; Dalmas, Dale; Esquibel, Kevin; Gallegos, Robert A; Garnett, Robert; Harrison, James F; Johnson, Jeffrey B; Jacquez, Edward B; Mccuistian, Brian T; Montoya, Nicholas A; Nath, Subrata; Nielsen, Kurt; Oro, David; Prichard, Benjamin; Rowton, Lawrence; Sanchez, Manolito; Scarpetti, Raymond; Schauer, Martin M; Seitz, Gerald; Schulze, Martin; Bender, Howard A; Broste, William B; Carlson, Carl A; Frayer, Daniel K; Johnson, Douglas E; Tom, C Y; Trainham, C; Genoni, Thomas; Hughes, Thomas; Toma, Carsten
2008-01-01
The DARHT-II linear induction accelerator (LIA) accelerates a 2-kA electron beam to more than 17 MeV. The beam pulse has a greater than 1.5-microsecond flattop region over which the electron kinetic energy is constant to within 1%. The beam dynamics are diagnosed with 21 beam-position monitors located throughout the injector, accelerator, and after the accelerator exit, where we also have beam imaging diagnostics. We discuss the tuning of the injector and accelerator, and present data for the resulting beam dynamics. We discuss the tuning procedures and other methods used to minimize beam motion, which is undesirable for its application as a bremsstrahlung source for multi-pulse radiography of exlosively driven hydrodynamic experiments. We also present beam stability measurements, which we relate to previous stability experiments at lower current and energy.
NASA Astrophysics Data System (ADS)
Tang, Li; Liu, Jing-Ning; Feng, Dan; Tong, Wei
2008-12-01
Existing security solutions in network storage environment perform poorly because cryptographic operations (encryption and decryption) implemented in software can dramatically reduce system performance. In this paper we propose a cryptographic hardware accelerator on dynamically reconfigurable platform for the security of high performance network storage system. We employ a dynamic reconfigurable platform based on a FPGA to implement a PowerPCbased embedded system, which executes cryptographic algorithms. To reduce the reconfiguration latency, we apply prefetch scheduling. Moreover, the processing elements could be dynamically configured to support different cryptographic algorithms according to the request received by the accelerator. In the experiment, we have implemented AES (Rijndael) and 3DES cryptographic algorithms in the reconfigurable accelerator. Our proposed reconfigurable cryptographic accelerator could dramatically increase the performance comparing with the traditional software-based network storage systems.
Lee, S. Y.
2014-04-07
We had carried out a design of an ultimate storage ring with beam emittance less than 10 picometer for the feasibility of coherent light source at X-ray wavelength. The accelerator has an inherent small dynamic aperture. We study method to improve the dynamic aperture and collective instability for an ultimate storage ring. Beam measurement and accelerator modeling are an integral part of accelerator physics. We develop the independent component analysis (ICA) and the orbit response matrix method for improving accelerator reliability and performance. In collaboration with scientists in National Laboratories, we also carry out experimental and theoretical studies on beam dynamics. Our proposed research topics are relevant to nuclear and particle physics using high brightness particle and photon beams.
Beam dynamics in resonant plasma wakefield acceleration at SPARC_LAB
NASA Astrophysics Data System (ADS)
Romeo, S.; Anania, M. P.; Chiadroni, E.; Croia, M.; Ferrario, M.; Marocchino, A.; Pompili, R.; Vaccarezza, C.
2016-09-01
Strategies to mitigate the increase of witness emittance and energy spread in beam driven plasma wakefield acceleration are investigated. Starting from the proposed resonant wakefield acceleration scheme in quasi-non-linear regime that is going to be carried out at SPARC_LAB, we performed systematic scans of the parameters to be used for drivers. The analysis will show that one of the main requirements to preserve witness quality during the acceleration is to have accelerating and focusing fields that are very stable during all the accelerating length. The difference between the dynamics of the leading bunch and the trailing bunch is pointed out. The classical condition on bunch length kpσz =√{ 2 } seems to be an ideal condition for the first driver within long accelerating lengths. The other drivers show to follow different longitudinal matching conditions. In the end a new method for the investigation of the matching for the first driver is introduced.
Wave and particle dynamics of the beat-wave accelerator
Gibbon, P. )
1989-10-15
We present two-dimensional wave-envelope studies of the interaction between a plasma beat-wave and the laser pumps which drive it. A new method of focusing is demonstrated which requires the plasma wave to be driven slightly below its resonant frequency. Test particles are employed to investigate possible means of extending the accelerator stage length. {copyright} 1989 American Institute of Physics
Cary, J.R.
1992-11-30
Substantial progress was in several areas of accelerator dynamics. For developing understanding of longitudinal adiabatic dynamics, and for creating efficiency enhancements of recirculating free-electron lasers, was substantially completed. A computer code for analyzing the critical KAM tori that bound the dynamic aperture in circular machines was developed. Studies of modes that arise due to the interaction of coating beams with a narrow-spectrum impedance have begun. During this research educational and research ties with the accelerator community at large have been strengthened.
Payne, A.N.
1993-05-17
We address the problem of developing system models that are suitable for studying the control of the longitudinal beam dynamics in induction accelerators for heavy ions. In particular, we present the preliminary results of our efforts to devise a general framework for building detailed, integrated models of accelerator systems consisting of pulsed power modular circuits, induction cells, beam dynamics, and control system elements. Such a framework will permit us to analyze and design the pulsed power modulators and the control systems required to effect precise control over the longitudinal beam dynamics.
Electron dynamics in a plasma focus. [electron acceleration
NASA Technical Reports Server (NTRS)
Hohl, F.; Gary, S. P.; Winters, P. A.
1977-01-01
Results are presented of a numerical integration of the three-dimensional relativistic equations of motion of electrons subject to given electric and magnetic fields deduced from experiments. Fields due to two different models are investigated. For the first model, the fields are those due to a circular distribution of axial current filaments. As the current filaments collapse toward the axis, large azimuthal magnetic and axial electric fields are induced. These fields effectively heat the electrons to a temperature of approximately 8 keV and accelerate electrons within the radius of the filaments to high axial velocities. Similar results are obtained for the current-reduction phase of focus formation. For the second model, the fields are those due to a uniform current distribution. Both the current-reduction and the compression phases were studied. These is little heating or acceleration of electrons during the compression phase because the electrons are tied to the magnetic field. However, during the current-reduction phase, electrons near the axis are accelerated toward the center electrode and reach energies of 100 keV. A criterion is obtained which limits the runaway electron current to about 400 A.
Particle acceleration by turbulent magnetohydro-dynamic reconnection
NASA Technical Reports Server (NTRS)
Matthaeus, W. H.; Ambrosiano, J. J.; Goldstein, M. L.
1984-01-01
Test particles in a two dimensional, turbulent MHD simulation are found to undergo significant acceleration. The magnetic field configuration is a periodic sheet pinch which undergoes reconnection. The test particles are trapped in the reconnection region for times of order an Alfven transit time in the large electric fields that characterize the turbulent reconnection process at the relatively large magnetic Reynolds number used in the simulation. The maximum speed attained by these particles is consistent with an analytic estimate which depends on the reconnection electric field, the Alfven speed, and the ratio of Larmor period to the Alfven transit time.
Beam dynamics simulations of post low energy beam transport section in RAON heavy ion accelerator
NASA Astrophysics Data System (ADS)
Jin, Hyunchang; Jang, Ji-Ho; Jang, Hyojae; Hong, In-Seok
2016-02-01
RAON (Rare isotope Accelerator Of Newness) heavy ion accelerator of the rare isotope science project in Daejeon, Korea, has been designed to accelerate multiple-charge-state beams to be used for various science programs. In the RAON accelerator, the rare isotope beams which are generated by an isotope separation on-line system with a wide range of nuclei and charges will be transported through the post Low Energy Beam Transport (LEBT) section to the Radio Frequency Quadrupole (RFQ). In order to transport many kinds of rare isotope beams stably to the RFQ, the post LEBT should be devised to satisfy the requirement of the RFQ at the end of post LEBT, simultaneously with the twiss parameters small. We will present the recent lattice design of the post LEBT in the RAON accelerator and the results of the beam dynamics simulations from it. In addition, the error analysis and correction in the post LEBT will be also described.
Ruth, R.D.; Chao, A.W.
1982-04-01
In this paper we present our studies on a plasma laser accelerator. First we look at the longitudinal dynamics and the trapping of particles in the potential well due to the longitudinal electric field in a plasma density wave. Next we study the plasma/laser interaction to obtain power requirements. Lastly, we qualitatively design a plasma/laser accelerator with parameters somewhat more modest than existing suggestions.
DTL cavity design and beam dynamics for a TAC linear proton accelerator
NASA Astrophysics Data System (ADS)
Caliskan, A.; Yılmaz, M.
2012-02-01
A 30 mA drift tube linac (DTL) accelerator has been designed using SUPERFISH code in the energy range of 3-55 MeV in the framework of the Turkish Accelerator Center (TAC) project. Optimization criteria in cavity design are effective shunt impedance (ZTT), transit-time factor and electrical breakdown limit. In geometrical optimization we have aimed to increase the energy gain in each RF gap of the DTL cells by maximizing the effective shunt impedance (ZTT) and the transit-time factor. Beam dynamics studies of the DTL accelerator have been performed using beam dynamics simulation codes of PATH and PARMILA. The results of both codes have been compared. In the beam dynamical studies, the rms values of beam emittance have been taken into account and a low emittance growth in both x and y directions has been attempted.
Soft matter dynamics: Accelerated fluid squeeze-out during slip
NASA Astrophysics Data System (ADS)
Hutt, W.; Persson, B. N. J.
2016-03-01
Using a Leonardo da Vinci experimental setup (constant driving force), we study the dependency of lubricated rubber friction on the time of stationary contact and on the sliding distance. We slide rectangular rubber blocks on smooth polymer surfaces lubricated by glycerol or by a grease. We observe a remarkable effect: during stationary contact the lubricant is only very slowly removed from the rubber-polymer interface, while during slip it is very rapidly removed resulting (for the grease lubricated surface) in complete stop of motion after a short time period, corresponding to a slip distance typically of order only a few times the length of the rubber block in the sliding direction. For an elastically stiff material, poly(methyl methacrylate), we observe the opposite effect: the sliding speed increases with time (acceleration), and the lubricant film thickness appears to increase. We propose an explanation for the observed effect based on transient elastohydrodynamics, which may be relevant also for other soft contacts.
Wavelet approach to accelerator problems. 1: Polynomial dynamics
Fedorova, A.; Zeitlin, M.; Parsa, Z.
1997-05-01
This is the first part of a series of talks in which the authors present applications of methods from wavelet analysis to polynomial approximations for a number of accelerator physics problems. In the general case they have the solution as a multiresolution expansion in the base of compactly supported wavelet basis. The solution is parameterized by solutions of two reduced algebraical problems, one is nonlinear and the second is some linear problem, which is obtained from one of the next wavelet constructions: Fast Wavelet Transform, Stationary Subdivision Schemes, the method of Connection Coefficients. In this paper the authors consider the problem of calculation of orbital motion in storage rings. The key point in the solution of this problem is the use of the methods of wavelet analysis, relatively novel set of mathematical methods, which gives one a possibility to work with well-localized bases in functional spaces and with the general type of operators (including pseudodifferential) in such bases.
Otazo, Ricardo; Candès, Emmanuel; Sodickson, Daniel K.
2014-01-01
Purpose To apply the low-rank plus sparse (L+S) matrix decomposition model to reconstruct undersampled dynamic MRI as a superposition of background and dynamic components in various problems of clinical interest. Theory and Methods The L+S model is natural to represent dynamic MRI data. Incoherence between k−t space (acquisition) and the singular vectors of L and the sparse domain of S is required to reconstruct undersampled data. Incoherence between L and S is required for robust separation of background and dynamic components. Multicoil L+S reconstruction is formulated using a convex optimization approach, where the nuclear-norm is used to enforce low-rank in L and the l1-norm to enforce sparsity in S. Feasibility of the L+S reconstruction was tested in several dynamic MRI experiments with true acceleration including cardiac perfusion, cardiac cine, time-resolved angiography, abdominal and breast perfusion using Cartesian and radial sampling. Results The L+S model increased compressibility of dynamic MRI data and thus enabled high acceleration factors. The inherent background separation improved background suppression performance compared to conventional data subtraction, which is sensitive to motion. Conclusion The high acceleration and background separation enabled by L+S promises to enhance spatial and temporal resolution and to enable background suppression without the need of subtraction or modeling. PMID:24760724
Ion and neutral dynamics in Hall plasma accelerator ionization instabilities
NASA Astrophysics Data System (ADS)
Lucca Fabris, Andrea; Young, Christopher; Cappelli, Mark
2015-09-01
Hall thrusters, the extensively studied E × B devices used for space propulsion applications, are rife with instabilities and fluctuations. Many are thought to be fundamentally linked to microscopic processes like electron transport across magnetic field lines and propellant ionization that in turn affect macroscopic properties like device performance and lifetime. One of the strongest oscillatory regimes is the ``breathing mode,'' characterized by a propagating ionization front, time-varying ion acceleration profiles, and quasi-periodic 10-50 kHz current oscillations. Determining the temporal and spatial evolution of plasma properties is critical to achieving a fundamental physical understanding of these processes. We present non-intrusive laser-induced fluorescence measurements of the local ion and neutral velocity distribution functions synchronized with the breathing mode oscillations. Measurements reveal strong ion velocity fluctuations, multiple ion populations arising in narrow time windows throughout the near-field plume, and the periodic population and depopulation of neutral excited states. Analyzing these detailed experimental results in the context of the existing literature clarifies the fundamental physical processes underlying the breathing mode. This work is sponsored by the U.S. Air Force Office of Scientific Research with Dr. M. Birkan as program manager. C.Y. acknowledges support from the DOE NSSA Stewardship Science Graduate Fellowship under contract DE-FC52-08NA28752.
Soft matter dynamics: Accelerated fluid squeeze-out during slip.
Hutt, W; Persson, B N J
2016-03-28
Using a Leonardo da Vinci experimental setup (constant driving force), we study the dependency of lubricated rubber friction on the time of stationary contact and on the sliding distance. We slide rectangular rubber blocks on smooth polymer surfaces lubricated by glycerol or by a grease. We observe a remarkable effect: during stationary contact the lubricant is only very slowly removed from the rubber-polymer interface, while during slip it is very rapidly removed resulting (for the grease lubricated surface) in complete stop of motion after a short time period, corresponding to a slip distance typically of order only a few times the length of the rubber block in the sliding direction. For an elastically stiff material, poly(methyl methacrylate), we observe the opposite effect: the sliding speed increases with time (acceleration), and the lubricant film thickness appears to increase. We propose an explanation for the observed effect based on transient elastohydrodynamics, which may be relevant also for other soft contacts. PMID:27036475
Embarrassingly Parallel Acceleration of Global Tractography via Dynamic Domain Partitioning
Wu, Haiyong; Chen, Geng; Jin, Yan; Shen, Dinggang; Yap, Pew-Thian
2016-01-01
Global tractography estimates brain connectivity by organizing signal-generating fiber segments in an optimal configuration that best describes the measured diffusion-weighted data, promising better stability than local greedy methods with respect to imaging noise. However, global tractography is computationally very demanding and requires computation times that are often prohibitive for clinical applications. We present here a reformulation of the global tractography algorithm for fast parallel implementation amendable to acceleration using multi-core CPUs and general-purpose GPUs. Our method is motivated by the key observation that each fiber segment is affected by a limited spatial neighborhood. In other words, a fiber segment is influenced only by the fiber segments that are (or can potentially be) connected to its two ends and also by the diffusion-weighted signal in its proximity. This observation makes it possible to parallelize the Markov chain Monte Carlo (MCMC) algorithm used in the global tractography algorithm so that concurrent updating of independent fiber segments can be carried out. Experiments show that the proposed algorithm can significantly speed up global tractography, while at the same time maintain or even improve tractography performance. PMID:27468263
Accelerating PS model-based dynamic cardiac MRI using compressed sensing.
Zhang, Xiaoyong; Xie, Guoxi; Shi, Caiyun; Su, Shi; Zhang, Yongqin; Liu, Xin; Qiu, Bensheng
2016-02-01
High spatiotemporal resolution MRI is a challenging topic in dynamic MRI field. Partial separability (PS) model has been successfully applied to dynamic cardiac MRI by exploiting data redundancy. However, the model requires substantial preprocessing data to accurately estimate the model parameters before image reconstruction. Since compressed sensing (CS) is a potential technique to accelerate MRI by reducing the number of acquired data, the combination of PS and CS, named as Stepped-SparsePS, was introduced to accelerate the preprocessing data acquisition of PS in this work. The proposed Stepped-SparsePS method sequentially reconstructs a set of aliased dynamic images in each channel based on PS model and then the final dynamic images from the aliased images using CS. The results from numerical simulations and in vivo experiments demonstrate that Stepped-SparsePS could significantly reduce data acquisition time while preserving high spatiotemporal resolution. PMID:26552006
Multi-GPU Accelerated Simulation of Dynamically Evolving Fluid Pathways
NASA Astrophysics Data System (ADS)
Räss, Ludovic; Omlin, Samuel; Moulas, Evangelos; Simon, Nina S. C.; Podladchikov, Yuri
2014-05-01
Fluid flow in porous rocks, both naturally occurring and caused by reservoir operations, mostly takes place along localized high permeability pathways. Pervasive flooding of the rock matrix is rarely observed, in particular for low permeability rocks. The pathways appear to form dynamically in response to the fluid flow itself; the amount of pathways, their location and their hydraulic conductivity may change in time. We propose a physically and thermodynamically consistent model that describes the formation and evolution of fluid pathways. The model consists of a system of equations describing poro-elasto-viscous deformation and flow. We have implemented the strongly coupled equations into a numerical model. Nonlinearity of the solid rheology is also taken into account. We have developed a fully three-dimensional numerical MATLAB application based on an iterative finite difference scheme. We have ported it to C-CUDA using MPI to run it on multi-GPU clusters. Numerical tuning of the application based on memory bandwidth throughput allows to approach hardware peak performance. Conducted high-resolution three-dimensional simulations predict the formation of dynamically evolving high porosity and permeability pathways as a natural outcome of porous flow coupled with rock deformation.
GPU-accelerated visualization of protein dynamics in ribbon mode
NASA Astrophysics Data System (ADS)
Wahle, Manuel; Birmanns, Stefan
2011-01-01
Proteins are biomolecules present in living organisms and essential for carrying out vital functions. Inherent to their functioning is folding into different spatial conformations, and to understand these processes, it is crucial to visually explore the structural changes. In recent years, significant advancements in experimental techniques and novel algorithms for post-processing of protein data have routinely revealed static and dynamic structures of increasing sizes. In turn, interactive visualization of the systems and their transitions became more challenging. Therefore, much research for the efficient display of protein dynamics has been done, with the focus being space filling models, but for the important class of abstract ribbon or cartoon representations, there exist only few methods for an efficient rendering. Yet, these models are of high interest to scientists, as they provide a compact and concise description of the structure elements along the protein main chain. In this work, a method was developed to speed up ribbon and cartoon visualizations. Separating two phases in the calculation of geometry allows to offload computational work from the CPU to the GPU. The first phase consists of computing a smooth curve along the protein's main chain on the CPU. In the second phase, conducted independently by the GPU, vertices along that curve are moved to set up the final geometrical representation of the molecule.
Education for Dynamic Economies: Action Plan To Accelerate Progress towards Education for All (EFA).
ERIC Educational Resources Information Center
World Bank, Washington, DC.
The World Bank's development committee met and reviewed the paper, "Education for Dynamic Economies." The paper assessed progress and identified key issues and challenges in meeting the goals of universal primary education. It concluded that these goals were unlikely to be attained without accelerated action at the country level and a scaling up…
Dynamics of the accelerator-driven system as a variable gain amplifier
Woosley, M.L. Jr.; Rydin, R.A.
1995-12-31
Historically, subcritical accelerator-driven systems have been called electronuclear devices. Interest in these devices has been revived for numerous nuclear applications, such as boron neutron capture therapy, accelerator transmutation of waste (ATW), and accelerator-based conversion (ABC). The latter systems are being investigated at Los Alamos National Laboratory for energy production and radioactive waste transmutation. The ATW and ABC in particular are accelerator-(source)-driven subcritical fluid-fueled systems. System dynamics are affected by movement of delayed neutron precursors and poisons into and out of the active multiplying region, giving both a reactivity effect and reduced {Beta} (called {Beta}{sub eff}). A salient dynamic characteristic of the system is that the neutron population (power) is very sensitive to the level of subcritical reactivity, which can depend on poisoning, depletion, and thermal feedback over short operational time scales. Ruby has pointed out that the dynamic behavior of systems containing sources is not fully appreciated. It is our purpose here to illustrate some of the more interesting dynamic characteristics of systems like ATW or ABC.
PARMTEQ: A beam-dynamics code fo the RFQ linear accelerator
Crandall, K.R.; Wangler, T.P.
1988-12-01
The PARMTEQ code is used for generating the complete cell design of a radio-frequency quadrupole linear accelerator and for multiparticle simulation of the beam dynamics. We present a review of the code, with an emphasis on the physics used to describe the particle motion and the cell generation.
Radiation Symmetry in Sandia Z Accelerator Dynamic Hohlraums
NASA Astrophysics Data System (ADS)
Bennett, G. R.; Bailey, J. E.; Chandler, G. A.; Cuneo, M. E.; Hebron, D. E.; Lash, J. S.; Porter, J. L.; Schroen-Carey, D. G.; Slutz, S. A.; Vesey, R. A.
2000-10-01
Although the dynamic hohlraum has achieved the highest radiation temperatures generated by any z-pinch configuration, a number of critical issues remain before the high-yield ICF concept of an internally-located capsule can be considered credible. Of particular importance to the imploding capsule, embedded in foam, is the thermal radiation asymmetry in the hohlraum r-z plane, arising from the Rayleigh-Taylor (RT) unstable z-pinch wire array forming the radiation cavity. Numerical simulation leads to an inadequate understanding of the RT instability growth and form, since, among other things, there is a discrepancy in the calculated and observed density variations between bubble and spikes. Likewise, by looking into the hohlraum open end for a direct observation, a wall emission uniformity measurement is precluded by the shallow viewing angle. However, to overcome this constraint, a semi-closed hohlraum configuration is described here, where a half W/half Al wire array permits a direct view through the low-opacity Al plasma and the optically thin foam. Sandia is a multiprogram laboratory operated by Sandia Corp., a Lockheed Martin Company, for the USDOE under Contract DE-AC04-94AL85000.
Kotter, John P
2012-11-01
The old ways of setting and implementing strategy are failing us, writes the author of Leading Change, in part because we can no longer keep up with the pace of change. Organizational leaders are torn between trying to stay ahead of increasingly fierce competition and needing to deliver this year's results. Although traditional hierarchies and managerial processes--the components of a company's "operating system"--can meet the daily demands of running an enterprise, they are rarely equipped to identify important hazards quickly, formulate creative strategic initiatives nimbly, and implement them speedily. The solution Kotter offers is a second system--an agile, networklike structure--that operates in concert with the first to create a dual operating system. In such a system the hierarchy can hand off the pursuit of big strategic initiatives to the strategy network, freeing itself to focus on incremental changes to improve efficiency. The network is populated by employees from all levels of the organization, giving it organizational knowledge, relationships, credibility, and influence. It can Liberate information from silos with ease. It has a dynamic structure free of bureaucratic layers, permitting a level of individualism, creativity, and innovation beyond the reach of any hierarchy. The network's core is a guiding coalition that represents each level and department in the hierarchy, with a broad range of skills. Its drivers are members of a "volunteer army" who are energized by and committed to the coalition's vividly formulated, high-stakes vision and strategy. Kotter has helped eight organizations, public and private, build dual operating systems over the past three years. He predicts that such systems will lead to long-term success in the 21st century--for shareholders, customers, employees, and companies themselves. PMID:23155997
Beam dynamics and wakefield simulations of the double grating accelerating structure
Najafabadi, B. Montazeri; Byer, R. L.; Ng, C. K.; England, R. J.; Peralta, E. A.; Soong, K.; Noble, R.; Wu, Z.
2012-12-21
Laser-driven acceleration in dielectric structures can provide gradients on the order of GeV/m. The small transverse dimension and tiny feature sizes introduce challenges in design, fabrication, and simulation studies of these structures. In this paper we present the results of beam dynamic simulation and short range longitudinal wakefield simulation of the double grating structure. We show the linear trend of acceleration in a dielectric accelerator design and calculate the maximum achievable gradient equal to 0.47E{sub 0} where E0 is maximum electric field of the laser excitation. On the other hand, using wakefield simulations, we show that the loss factor of the structure with 400nm gap size will be 0.12GV/m for a 10fC, 100as electron bunch which is an order of magnitude less than expected gradient near damage threshold of the device.
On Higher Ground: How Well Can Dynamic Body Acceleration Determine Speed in Variable Terrain?
Bidder, Owen R.; Qasem, Lama A.; Wilson, Rory P.
2012-01-01
Introduction Animal travel speed is an ecologically significant parameter, with implications for the study of energetics and animal behaviour. It is also necessary for the calculation of animal paths by dead-reckoning. Dead-reckoning uses heading and speed to calculate an animal’s path through its environment on a fine scale. It is often used in aquatic environments, where transmission telemetry is difficult. However, its adoption for tracking terrestrial animals is limited by our ability to measure speed accurately on a fine scale. Recently, tri-axial accelerometers have shown promise for estimating speed, but their accuracy appears affected by changes in substrate and surface gradients. The purpose of the present study was to evaluate four metrics of acceleration; Overall dynamic body acceleration (ODBA), vectorial dynamic body acceleration (VDBA), acceleration peak frequency and acceleration peak amplitude, as proxies for speed over hard, soft and inclined surfaces, using humans as a model species. Results A general linear model (GLM) showed a significant difference in the relationships between the metrics and speed depending on substrate or surface gradient. When the data from all surface types were considered together, VeDBA had the highest coefficient of determination. Conclusions All of the metrics showed some variation in their relationship with speed according to the surface type. This indicates that changes in the substrate or surface gradient during locomotion by animals would produce errors in speed estimates, and also in dead-reckoned tracks if they were calculated from speeds based entirely on a priori calibrations. However, we describe a method by which the relationship between acceleration metrics and speed can be corrected ad hoc, until tracks accord with periodic ground truthed positions, obtained via a secondary means (e.g. VHF or GPS telemetry). In this way, dead-reckoning provides a means to obtain fine scale movement data for terrestrial
Mohammad Hosseini Naveh, Zeynab; Malliavin, Therese E.; Maragliano, Luca; Cottone, Grazia; Ciccotti, Giovanni
2014-01-01
Despite the large number of studies available on nicotinic acetylcholine receptors, a complete account of the mechanistic aspects of their gating transition in response to ligand binding still remains elusive. As a first step toward dissecting the transition mechanism by accelerated sampling techniques, we study the ligand-induced conformational changes of the acetylcholine binding protein (AChBP), a widely accepted model for the full receptor extracellular domain. Using unbiased Molecular Dynamics (MD) and Temperature Accelerated Molecular Dynamics (TAMD) simulations we investigate the AChBP transition between the apo and the agonist-bound state. In long standard MD simulations, both conformations of the native protein are stable, while the agonist-bound structure evolves toward the apo one if the orientation of few key sidechains in the orthosteric cavity is modified. Conversely, TAMD simulations initiated from the native conformations are able to produce the spontaneous transition. With respect to the modified conformations, TAMD accelerates the transition by at least a factor 10. The analysis of some specific residue-residue interactions points out that the transition mechanism is based on the disruption/formation of few key hydrogen bonds. Finally, while early events of ligand dissociation are observed already in standard MD, TAMD accelerates the ligand detachment and, at the highest TAMD effective temperature, it is able to produce a complete dissociation path in one AChBP subunit. PMID:24551117
Object-Oriented Parallel Particle-in-Cell Code for Beam Dynamics Simulation in Linear Accelerators
Qiang, J.; Ryne, R.D.; Habib, S.; Decky, V.
1999-11-13
In this paper, we present an object-oriented three-dimensional parallel particle-in-cell code for beam dynamics simulation in linear accelerators. A two-dimensional parallel domain decomposition approach is employed within a message passing programming paradigm along with a dynamic load balancing. Implementing object-oriented software design provides the code with better maintainability, reusability, and extensibility compared with conventional structure based code. This also helps to encapsulate the details of communications syntax. Performance tests on SGI/Cray T3E-900 and SGI Origin 2000 machines show good scalability of the object-oriented code. Some important features of this code also include employing symplectic integration with linear maps of external focusing elements and using z as the independent variable, typical in accelerators. A successful application was done to simulate beam transport through three superconducting sections in the APT linac design.
Sasagawa, Shun; Shinya, Masahiro; Nakazawa, Kimitaka
2014-01-01
Recent studies have demonstrated that human quiet standing is a multijoint movement, whereby the central nervous system (CNS) is required to deal with dynamic interactions among the joints to achieve optimal motor performance. The purpose of this study was to investigate how the CNS deals with such interjoint interaction during quiet standing by examining the relationship between the kinetics (torque) and kinematics (angular acceleration) within the multi-degree of freedom system. We modeled quiet standing as a double-link inverted pendulum involving both ankle and hip joints and conducted an "induced acceleration analysis." We found that the net ankle and hip torques induced angular accelerations of comparable magnitudes to the ankle (3.8 ± 1.4°/s(2) and 3.3 ± 1.2°/s(2)) and hip (9.1 ± 3.2°/s(2) and 10.5 ± 3.5°/s(2)) joints, respectively. Angular accelerations induced by the net ankle and hip torques were modulated in a temporally antiphase pattern to one another in each of the two joints. These quantitative and temporal relationships allowed the angular accelerations induced by the two net torques to countercompensate one another, thereby substantially (∼70%) reducing the resultant angular accelerations of the individual joints. These results suggest that, by taking advantage of the interjoint interaction, the CNS prevents the net torques from producing large amplitudes of the resultant angular accelerations when combined with the kinematic effects of all other torques in the chain. PMID:24089399
Predictive Simulation and Design of Materials by Quasicontinuum and Accelerated Dynamics Methods
Luskin, Mitchell; James, Richard; Tadmor, Ellad
2014-03-30
This project developed the hyper-QC multiscale method to make possible the computation of previously inaccessible space and time scales for materials with thermally activated defects. The hyper-QC method combines the spatial coarse-graining feature of a finite temperature extension of the quasicontinuum (QC) method (aka “hot-QC”) with the accelerated dynamics feature of hyperdynamics. The hyper-QC method was developed, optimized, and tested from a rigorous mathematical foundation.
Accelerated electronic structure-based molecular dynamics simulations of shock-induced chemistry
NASA Astrophysics Data System (ADS)
Cawkwell, Marc
2015-06-01
The initiation and progression of shock-induced chemistry in organic materials at moderate temperatures and pressures are slow on the time scales available to regular molecular dynamics simulations. Accessing the requisite time scales is particularly challenging if the interatomic bonding is modeled using accurate yet expensive methods based explicitly on electronic structure. We have combined fast, energy conserving extended Lagrangian Born-Oppenheimer molecular dynamics with the parallel replica accelerated molecular dynamics formalism to study the relatively sluggish shock-induced chemistry of benzene around 13-20 GPa. We model interatomic bonding in hydrocarbons using self-consistent tight binding theory with an accurate and transferable parameterization. Shock compression and its associated transient, non-equilibrium effects are captured explicitly by combining the universal liquid Hugoniot with a simple shrinking-cell boundary condition. A number of novel methods for improving the performance of reactive electronic structure-based molecular dynamics by adapting the self-consistent field procedure on-the-fly will also be discussed. The use of accelerated molecular dynamics has enabled us to follow the initial stages of the nucleation and growth of carbon clusters in benzene under thermodynamic conditions pertinent to experiments.
NASA Technical Reports Server (NTRS)
Birn, Joachim; Hesse, Michael
1994-01-01
The acceleration of protons in a dynamically evolving magnetotail is investigated by tracing particles in the fields obtained from a three-dimensional resistive magnetohydrodynamic (MHD) simulation. The MHD simulation, representing plasmoid formation and ejection through a near-Earth reconnection process, leads to cross-tail electric fields of up to approximately 4 mV/m with integrated voltages across the tail of up to approximately 200 kV. Energization of particles takes place over a wide range along the tail, due to the large spatial extent of the increased electric field together with the finite cross-tail extent of the electric field region. Such accelerated particles appear earthward of the neutral line over a significant portion of the closed field line region inside of the separatrix, not just in the vicinity of the separatrix. Two different acceleration processes are identified: a 'quasi-potential' acceleration, due to particle motion in the direction of the cross-tail electric field, and a 'quasi-betatron' effect, which consists of multiple energy gains from repeated crossings of the acceleration region, mostly on Speiser-type orbits, in the spatially varying induced electric field. The major source region for accelerated particles in the hundreds of keV range is the central plasma sheet at the dawn flank outside the reconnection site. Since this source plasma is already hot and dense, its moderate energization by a factor of approximately 2 may be sufficient to explain the observed increases in the energetic particle fluxes. Particles from the tail are the source of beams at the plasma sheet/lobe boundary. The temporal increase in the energetic particle fluxes, estimated from the increase in energy gain, occurs on a fast timescale of a few minutes, coincident with a strong increase in B(sub z), despite the fact that the inner boundary ('injection boundary') of the distribution of energized particles is fairly smooth.
Stokesian peristaltic pumping in a three-dimensional tube with a phase-shifted asymmetry
NASA Astrophysics Data System (ADS)
Aranda, Vivian; Cortez, Ricardo; Fauci, Lisa
2011-08-01
Many physiological flows are driven by waves of muscular contractions passed along a tubular structure. This peristaltic pumping plays a role in ovum transport in the oviduct and in rapid sperm transport through the uterus. As such, flow due to peristalsis has been a central theme in classical biological fluid dynamics. Analytical approaches and numerical methods have been used to study flow in two-dimensional channels and three-dimensional tubes. In two dimensions, the effect of asymmetry due to a phase shift between the channel walls has been examined. However, in three dimensions, peristalsis in a non-axisymmetric tube has received little attention. Here, we present a computational model of peristaltic pumping of a viscous fluid in three dimensions based upon the method of regularized Stokeslets. In particular, we study the flow structure and mean flow in a three-dimensional tube whose asymmetry is governed by a single phase-shift parameter. We view this as a three-dimensional analog of the phase-shifted two-dimensional channel. We find that the maximum mean flow rate is achieved for the parameter that results in an axisymmetric tube. We also validate this approach by comparing our computational results with classical long-wavelength theory for the three-dimensional axisymmetric tube. This computational framework is easily implemented and may be adapted to more comprehensive physiological models where the kinematics of the tube walls are not specified a priori, but emerge due to the coupling of its passive elastic properties, force generating mechanisms, and the surrounding viscous fluid.
A model of Stokesian peristalsis and vesicle transport in a three-dimensional closed cavity.
Aranda, Vivian; Cortez, Ricardo; Fauci, Lisa
2015-06-25
The complexity of the mechanics involved in the mammalian reproductive process is evident. Neither an ovum nor an embryo is self-propelled, but move through the oviduct or uterus due to the peristaltic action of the tube walls, imposed pressure gradients, and perhaps ciliary motion. Here we use the method of regularized Stokeslets to model the transport of an ovum or an embryo within a peristaltic tube. We represent the ovum or the embryo as a spherical vesicle of finite volume - not a massless point particle. The outer membrane of the neutrally buoyant vesicle is discretized by nodes that are joined by a network of springs. The elastic moduli of these springs are chosen large enough so that a spherical shape is maintained. For simplicity, here we choose an axisymmetric tube where the geometry of the two-dimensional cross-section along the tube axis reflects that of the sagittal cross-section of the uterine cavity. Although the tube motion is axisymmetric, the presence of the vesicle within the tube requires a fully three-dimensional model. As was found in Yaniv et al. (2009, 2012) for a 2D closed channel, we find that the flow dynamics in a 3D peristaltic tube are strongly influenced by the closed end and the manner in which the peristaltic wave damps out towards the closure. In addition, we demonstrate that the trajectory of a vesicle of finite volume can greatly differ from the trajectory of a massless fluid particle initially placed at the vesicle׳s centroid. PMID:25817334
Heavy-ion beam dynamics in the RIA post-accelerator.
Ostroumov, P. N.; Kolomiets, A. A.; Aseev, V. N.; Physics
2005-01-01
The RIA post-accelerator (RIB) includes three main sections: a room temperature injector with design ion charge-to-mass ratio 1/240 and output energy of {approx} 93 keV/u, a superconducting (SC) linac for ions with charge-to-mass ratio 1/66 or higher up to an energy of {approx} 1 MeV/u and a higher energy SC linac including existing ATLAS to produce 10 MeV/u beams up to uranium. Two strippers are installed between the sections. Extensive accelerator design studies and end-to-end beam dynamics simulations have been performed to minimize the cost of the linac while providing high-quality and high-intensity radioactive beams. Specifically, we have found that cost-effective acceleration in the front end can be provided by several hybrid RFQs proposed and developed for acceleration of low-velocity heavy ions. For beam focusing in the second section it is appropriate to use electrostatic lenses and SC quadrupoles inside common cryostats with the resonators.
Dynamics of double layers, ion acceleration, and heat flux suppression during solar flares
Li, T. C.; Drake, J. F.; Swisdak, M.
2014-09-20
Observations of flare-heated electrons in the corona typically suggest confinement of electrons. The confinement mechanism, however, remains unclear. The transport of coronal hot electrons into ambient plasma was recently investigated by particle-in-cell (PIC) simulations. Electron transport was significantly suppressed by the formation of a highly localized, nonlinear electrostatic potential in the form of a double layer (DL). In this work large-scale PIC simulations are performed to explore the dynamics of DLs in larger systems where, instead of a single DL, multiple DLs are generated. The primary DL accelerates return current electrons, resulting in high velocity electron beams that interact with ambient ions. This forms a Buneman unstable system that spawns more DLs. Trapping of heated return current electrons between multiple DLs strongly suppresses electron transport. DLs also accelerate ambient ions and produce strong ion flows over an extended region. This clarifies the mechanism by which hot electrons in the corona couple to and accelerate ions to form the solar wind. These new dynamics in larger systems reveal a more likely picture of DL development and their impact on the ambient plasma in the solar corona. They are applicable to the preparation for in situ coronal space missions like the Solar Probe Plus.
Dynamic analysis of an accelerator-driven fluid-fueled subcritical radioactive waste burning system
Woosley, M.L. Jr.; Rydin, R.A.
1998-05-01
The recent revival of interest in accelerator-driven subcritical fluid-fueled systems is documented. Several important applications of these systems are mentioned, and this is used to motivate the need for dynamic analysis of the nuclear kinetics of such systems. A physical description of the Los alamos National Laboratory accelerator-based conversion (ABC) concept is provided. This system is used as the basis for the kinetics study in this research. The current approach to the dynamic simulation of an accelerator-driven subcritical fluid-fueled system includes four functional elements: a discrete ordinates model is used to calculate the flux distribution for the source-driven system; a nodal convection model is used to calculate time-dependent isotope and temperature distributions that impact reactivity; a nodal importance weighting model is used to calculate the reactivity impact of temperature and isotope distributions and to feed this information back to the time-dependent nodal convection model; and a transient driver is used to simulate transients, model the balance of plant, and record simulation data. Specific transients that have been analyzed with the current modeling system are discussed. These transients include loss-of-flow and loss-of-cooling accidents, xenon and samarium transients, and cold-plug and overfueling events. The results of various transients have uncovered unpredictable behavior, unresolved design issues, and the need for active control. The need for the development of a nodal-coupling spatial kinetics model is mentioned.
Evidence of source dominance in the dynamic behavior of accelerator-driven systems
Rydin, R.A.; Woosley, M.L. Jr.
1997-07-01
In a dynamic simulation method recently developed for accelerator-driven subcritical waste transmutation systems, power levels are renormalized dynamically based on the changing reactivity of the flowing system. For such systems, the power varies directly with the source strength, and inversely with the reactivity. The prompt-jump form of the point-kinetics equations has been used to provide the dynamic renormalization factor for the spatially dependent flowing-fuel system. A unique characteristic of the source-dominated system has been discovered. In the traditional reactor system, power changes are controlled by the half-life for decay of the longest-lived delayed neutron precursors. For the source-dominated system, the delayed neutron precursors do not appreciably slow the response of the system.
Electron-Beam Dynamics for an Advanced Flash-Radiography Accelerator
Ekdahl, Carl
2015-11-17
Beam dynamics issues were assessed for a new linear induction electron accelerator being designed for multipulse flash radiography of large explosively driven hydrodynamic experiments. Special attention was paid to equilibrium beam transport, possible emittance growth, and beam stability. Especially problematic would be high-frequency beam instabilities that could blur individual radiographic source spots, low-frequency beam motion that could cause pulse-to-pulse spot displacement, and emittance growth that could enlarge the source spots. Furthermore, beam physics issues were examined through theoretical analysis and computer simulations, including particle-in-cell codes. Beam instabilities investigated included beam breakup, image displacement, diocotron, parametric envelope, ion hose, and the resistive wall instability. The beam corkscrew motion and emittance growth from beam mismatch were also studied. It was concluded that a beam with radiographic quality equivalent to the present accelerators at Los Alamos National Laboratory will result if the same engineering standards and construction details are upheld.
Electron-Beam Dynamics for an Advanced Flash-Radiography Accelerator
Ekdahl, Carl
2015-12-01
Beam dynamics issues were assessed for a new linear induction electron accelerator being designed for multipulse flash radiography of large explosively driven hydrodynamic experiments. Special attention was paid to equilibrium beam transport, possible emittance growth, and beam stability. Especially problematic would be high-frequency beam instabilities that could blur individual radiographic source spots, low-frequency beam motion that could cause pulse-to-pulse spot displacement, and emittance growth that could enlarge the source spots. Furthermore, beam physics issues were examined through theoretical analysis and computer simulations, including particle-in-cell codes. Beam instabilities investigated included beam breakup, image displacement, diocotron, parametric envelope, ion hose, and the resistive wall instability. The beam corkscrew motion and emittance growth from beam mismatch were also studied. It was concluded that a beam with radiographic quality equivalent to the present accelerators at Los Alamos National Laboratory will result if the same engineering standards and construction details are upheld.
Electron-beam dynamics for an advanced flash-radiography accelerator
Ekdahl, Carl August Jr.
2015-06-22
Beam dynamics issues were assessed for a new linear induction electron accelerator. Special attention was paid to equilibrium beam transport, possible emittance growth, and beam stability. Especially problematic would be high-frequency beam instabilities that could blur individual radiographic source spots, low-frequency beam motion that could cause pulse-to-pulse spot displacement, and emittance growth that could enlarge the source spots. Beam physics issues were examined through theoretical analysis and computer simulations, including particle-in cell (PIC) codes. Beam instabilities investigated included beam breakup (BBU), image displacement, diocotron, parametric envelope, ion hose, and the resistive wall instability. Beam corkscrew motion and emittance growth from beam mismatch were also studied. It was concluded that a beam with radiographic quality equivalent to the present accelerators at Los Alamos will result if the same engineering standards and construction details are upheld.
Hybrid PIC Simulations of Particle Dynamics in Coaxial Plasma Jet Accelerators
NASA Astrophysics Data System (ADS)
Thoma, Carsten; Hughes, Thomas; Welch, Dale; Hakel, Peter
2007-11-01
We describe the results of 1D and 2D simulations of plasma jet accelerators using the particle-in-cell (PIC) code Lsp. Previous studies of 1D cartesian simulations have shown that ion particle dynamics at the plasma-vacuum interface depend critically on the local Hall parameter, which is strongly dependent on electron temperature. In a coaxial accelerator with finite transverse dimensions, large transverse ion motions, predicted at moderate Hall parameters in 1D, can lead to ion loss to the walls. The results of 2D r-z jet simulations are described and compared with the 1D cartesian results. The effects of particle loss and ablation at the wall are considered, as are electron heating mechanisms at the plasma-vacuum interface, including radiation losses. We will apply the results to the plasma jet experiments underway at HyperV Technologies Corp.
Radiative damping and electron beam dynamics in plasma-based accelerators.
Michel, P; Schroeder, C B; Shadwick, B A; Esarey, E; Leemans, W P
2006-08-01
The effects of radiation reaction on electron beam dynamics are studied in the context of plasma-based accelerators. Electrons accelerated in a plasma channel undergo transverse betatron oscillations due to strong focusing forces. These oscillations lead to emission by the electrons of synchrotron radiation, with a corresponding energy loss that affects the beam properties. An analytical model for the single particle orbits and beam moments including the classical radiation reaction force is derived and compared to the results of a particle transport code. Since the betatron amplitude depends on the initial transverse position of the electron, the resulting radiation can increase the relative energy spread of the beam to significant levels (e.g., several percent). This effect can be diminished by matching the beam into the channel, which could require micron sized beam radii for typical values of the beam emittance and plasma density. PMID:17025550
McGreevy, Ryan; Isralewitz, Barry
2014-01-01
Hybrid structure fitting methods combine data from cryo-electron microscopy and X-ray crystallography with molecular dynamics simulations for the determination of all-atom structures of large biomolecular complexes. Evaluating the quality-of-fit obtained from hybrid fitting is computationally demanding, particularly in the context of a multiplicity of structural conformations that must be evaluated. Existing tools for quality-of-fit analysis and visualization have previously targeted small structures and are too slow to be used interactively for large biomolecular complexes of particular interest today such as viruses or for long molecular dynamics trajectories as they arise in protein folding. We present new data-parallel and GPU-accelerated algorithms for rapid interactive computation of quality-of-fit metrics linking all-atom structures and molecular dynamics trajectories to experimentally determined density maps obtained from cryo-electron microscopy or X-ray crystallography. We evaluate the performance and accuracy of the new quality-of-fit analysis algorithms vis-a-vis existing tools, examine algorithm performance on GPU-accelerated desktop workstations and supercomputers, and describe new visualization techniques for results of hybrid structure fitting methods. PMID:25340325
Kitamura, Kei-ichiro; Takahira, Koh; Inari, Masato; Satoh, Yusuke; Hayakawa, Kazuichi; Tabuchi, Yoshiaki; Ogai, Kazuhiro; Nishiuchi, Takumi; Kondo, Takashi; Mikuni-Takagaki, Yuko; Chen, Wenxi; Hattori, Atsuhiko; Suzuki, Nobuo
2013-09-01
Zebrafish scales consist of bone-forming osteoblasts, bone-resorbing osteoclasts, and calcified bone matrix. To elucidate the underlying molecular mechanism of the effects induced by dynamic and static acceleration, we investigated the scale osteoblast- and osteoclast-specific marker gene expression involving osteoblast-osteoclast communication molecules. Osteoblasts express RANKL, which binds to the osteoclast surface receptor, RANK, and stimulates bone resorption. OPG, on the other hand, is secreted by osteoblast as a decoy receptor for RANKL, prevents RANKL from binding to RANK and thus prevents bone resorption. Therefore, the RANK-RANKL-OPG pathway contributes to the regulation of osteoclastogenesis by osteoblasts. Semaphorin 4D, in contrast, is expressed on osteoclasts, and binding to its receptor Plexin-B1 on osteoblasts results in suppression of bone formation. In the present study, we found that both dynamic and static acceleration at 3.0×g decreased RANKL/OPG ratio and increased osteoblast-specific functional mRNA such as alkaline phosphatase, while static acceleration increased and dynamic acceleration decreased osteoclast-specific mRNA such as cathepsin K. Static acceleration increased semaphorin 4D mRNA expression, while dynamic acceleration had no effect. The results of the present study indicated that osteoclasts have predominant control over bone metabolism via semaphorin 4D expression induced by static acceleration at 3.0×g. PMID:23632157
NASA Astrophysics Data System (ADS)
Otazo, Ricardo; Sodickson, Daniel K.; Candès, Emmanuel J.
2013-09-01
L+S matrix decomposition finds the low-rank (L) and sparse (S) components of a matrix M by solving the following convex optimization problem: min‖L‖*L+S matrix decomposition finds the low-rank (L) and sparse (S) components of a matrix M by solving the following convex optimization problem: ‖L ‖* + λ‖S‖1, subject to M=L+S, where ‖L‖* is the nuclear-norm or sum of singular values of L and ‖S‖1 is the 11-norm| or sum of absolute values of S. This work presents the application of the L+S decomposition to reconstruct incoherently undersampled dynamic MRI data as a superposition of a slowly or coherently changing background and sparse innovations. Feasibility of the method was tested in several accelerated dynamic MRI experiments including cardiac perfusion, time-resolved peripheral angiography and liver perfusion using Cartesian and radial sampling. The high acceleration and background separation enabled by L+S reconstruction promises to enhance spatial and temporal resolution and to enable background suppression without the need of subtraction or modeling.
Ion dynamics in an E × B Hall plasma accelerator
Young, Christopher V. Lucca Fabris, Andrea; Cappelli, Mark A.
2015-01-26
We show the time evolution of the ion velocity distribution function in a Hall plasma accelerator during a 20 kHz natural, quasi-periodic plasma oscillation. We apply a time-synchronized laser induced fluorescence technique at different locations along the channel midline, obtaining time- and spatially resolved ion velocity measurements. Strong velocity and density fluctuations and multiple ion populations are observed throughout the so-called “breathing mode” ionization instability, opening an experimental window into the detailed ion dynamics and physical processes at the heart of such devices.
A model for predicting aortic dynamic response to -G sub z impact acceleration.
NASA Technical Reports Server (NTRS)
Advani, S. H.; Tarnay, T. J.; Byars, E. F.; Love, J. S.
1972-01-01
A steady state dynamic response model for the radial motion of the aorta is developed from in vivo pressure-displacement and nerve stimulation experiments on canines. The model represented by a modified Van der Pol wave motion oscillator closely predicts steady state and perturbed response results. The applicability of the steady state canine aortic model to tailward acting impact forces is studied by means of the perturbed phase plane of the oscillator. The backflow through the aortic arch resulting from a specified acceleration-time profile is computed and an analysis for predicting the forced motion aortic response is presented.
NASA Astrophysics Data System (ADS)
Milgrom, M.
1994-02-01
We investigate particle dynamics that is governed by a nonstandard kinetic action of a special form. We are guided by a phenomenological scheme-the modified dynamics (MOND)-that imputes the mass discrepancy, observed in galactic systems, not to the presence of dark matter, but to a departure from Newtonian dynamics below a certain scale of accelerations, a0. The particle's equation of motion in a potential φ is derived from an action, S, of the form S ~ Sk[r(t), a0] - ∫ φ dt. The limit a0 --> 0 corresponds to Newtonian dynamics, and there the kinetic action Sk must take the standard form. In the opposite limit, a0 --> ∞ we require Sk --> 0-and more specifically, for circular orbits Sk ~ a-10-in order to attain the phenomenological success of MOND. Galilei-invariant such theories must be strongly nonlocal. This is a blessing, as such theories need not suffer from the illnesses that are endemic to higher-derivative theories. We comment on the possibility that such a modified law of motion is an effective theory resulting from the elimination of degrees of freedom pertaining to the universe at large (the near equality a0 ≍ cH0 being a trace of that connection). We derive a general virial relation for bounded trajectories. Exact solutions are obtained for circular orbits, which pertain to rotation curves of disk galaxies. We also explore, in passing, theories that depart from the conventional Newtonian dynamics for very low frequencies.
On-the-fly transition search and applications to temperature-accelerated dynamics
NASA Astrophysics Data System (ADS)
Shim, Yunsic; Amar, Jacques
2015-03-01
Temperature-accelerated dynamics (TAD) is a powerful method to study non-equilibrium processes and has been providing surprising insights for a variety of systems. While serial TAD simulations have been limited by the roughly N3 increase in the computational cost as a function of the number of atoms N in the system, recently we have shown that by carrying out parallel TAD simulations which combine spatial decomposition with our semi-rigorous synchronous sublattice algorithm, significantly improved scaling is possible. However, in this approach the size of activated events is limited by the processor size while the dynamics is not exact. Here we discuss progress in improving the scaling of serial TAD by combining the use of on-the-fly transition searching with our previously developed localized saddle-point method. We demonstrate improved performance for the cases of Ag/Ag(100) annealing and Cu/Cu(100) growth. Supported by NSF DMR-1410840.
Accelerated molecular dynamics and equation-free methods for simulating diffusion in solids.
Deng, Jie; Zimmerman, Jonathan A.; Thompson, Aidan Patrick; Brown, William Michael; Plimpton, Steven James; Zhou, Xiao Wang; Wagner, Gregory John; Erickson, Lindsay Crowl
2011-09-01
Many of the most important and hardest-to-solve problems related to the synthesis, performance, and aging of materials involve diffusion through the material or along surfaces and interfaces. These diffusion processes are driven by motions at the atomic scale, but traditional atomistic simulation methods such as molecular dynamics are limited to very short timescales on the order of the atomic vibration period (less than a picosecond), while macroscale diffusion takes place over timescales many orders of magnitude larger. We have completed an LDRD project with the goal of developing and implementing new simulation tools to overcome this timescale problem. In particular, we have focused on two main classes of methods: accelerated molecular dynamics methods that seek to extend the timescale attainable in atomistic simulations, and so-called 'equation-free' methods that combine a fine scale atomistic description of a system with a slower, coarse scale description in order to project the system forward over long times.
Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics
2012-01-01
In this work, we critically assess the ability of the all-atom enhanced sampling method accelerated molecular dynamics (aMD) to investigate conformational changes in proteins that typically occur on the millisecond time scale. We combine aMD with the inherent power of graphics processor units (GPUs) and apply the implementation to the bovine pancreatic trypsin inhibitor (BPTI). A 500 ns aMD simulation is compared to a previous millisecond unbiased brute force MD simulation carried out on BPTI, showing that the same conformational space is sampled by both approaches. To our knowledge, this represents the first implementation of aMD on GPUs and also the longest aMD simulation of a biomolecule run to date. Our implementation is available to the community in the latest release of the Amber software suite (v12), providing routine access to millisecond events sampled from dynamics simulations using off the shelf hardware. PMID:22984356
Abdoli-Arani, A.; Jazi, B.; Shokri, B.
2013-02-15
The dynamics and energy gain of an electron in the field of a transverse magnetic wave propagating inside an elliptical degenerate plasma waveguide is analytically investigated by finding the field components of the TM{sub mr} mode in this waveguide. Besides, by solving the relativistic momentum and energy equations the deflection angle and the acceleration gradient of the electron in the waveguide are obtained. Furthermore, the field components of the hybrid mode and the transferred power in the presence of the magnetic field in this waveguide are found. Also by applying the boundary conditions at the plasma-conductor interface, we calculate the dispersion relation. It is shown that the cutoff frequency of this mode is dependent on the plasma density but independent of the magnetic field. Then, a single-electron model for numerical calculations of the electron deflection angle and acceleration gradient inside the magnetized plasma-filled elliptical waveguide is generally presented to be used as a cascading process for the acceleration purposes.
Stothart, Mason R; Elliott, Kyle H; Wood, Thomas; Hatch, Scott A; Speakman, John R
2016-07-15
The integral of the dynamic component of acceleration over time has been proposed as a measure of energy expenditure in wild animals. We tested that idea by attaching accelerometers to the tails of free-ranging pelagic cormorants (Phalacrocorax pelagicus) and simultaneously estimating energy expenditure using doubly labelled water. Two different formulations of dynamic body acceleration, [vectorial and overall DBA (VeDBA and ODBA)], correlated with mass-specific energy expenditure (both R(2)=0.91). VeDBA models combining and separately parameterizing flying, diving, activity on land and surface swimming were consistently considered more parsimonious than time budget models and showed less variability in model fit. Additionally, we observed evidence for the presence of hypometabolic processes (i.e. reduced heart rate and body temperature; shunting of blood away from non-essential organs) that suppressed metabolism in cormorants while diving, which was the most metabolically important activity. We concluded that a combination of VeDBA and physiological processes accurately measured energy expenditure for cormorants. PMID:27207639
2013-01-01
The accelerated molecular dynamics (aMD) method has recently been shown to enhance the sampling of biomolecules in molecular dynamics (MD) simulations, often by several orders of magnitude. Here, we describe an implementation of the aMD method for the OpenMM application layer that takes full advantage of graphics processing units (GPUs) computing. The aMD method is shown to work in combination with the AMOEBA polarizable force field (AMOEBA-aMD), allowing the simulation of long time-scale events with a polarizable force field. Benchmarks are provided to show that the AMOEBA-aMD method is efficiently implemented and produces accurate results in its standard parametrization. For the BPTI protein, we demonstrate that the protein structure described with AMOEBA remains stable even on the extended time scales accessed at high levels of accelerations. For the DNA repair metalloenzyme endonuclease IV, we show that the use of the AMOEBA force field is a significant improvement over fixed charged models for describing the enzyme active-site. The new AMOEBA-aMD method is publicly available (http://wiki.simtk.org/openmm/VirtualRepository) and promises to be interesting for studying complex systems that can benefit from both the use of a polarizable force field and enhanced sampling. PMID:24634618
Role of radiation reaction forces in the dynamics of centrifugally accelerated particles
Dalakishvili, G. T.; Rogava, A. D.; Berezhiani, V. I.
2007-08-15
In this paper we study the influence of radiation reaction (RR) forces on the dynamics of centrifugally accelerated particles. It is assumed that the particles move along magnetic field lines anchored in the rotating central object. The common 'bead-on-the-wire' approximation is used. The solutions are found and analyzed for cases when the form of the prescribed trajectory (rigidly rotating field line) is approximated by: (a) straight line, and (b) Archimedes spiral. Dynamics of neutral and charged particles are compared with the emphasis on the role of RR forces in the latter case. It is shown that for charged particles there exist locations of stable equilibrium. It is demonstrated that for particular initial conditions RR forces cause centripetal motion of the particles: their 'falling' on the central rotating object. It is found that in the case of Archimedes spiral both neutral and charged particles can reach infinity where their motion has asymptotically force-free character. The possible importance of these processes for the acceleration of relativistic, charged particles by rotating magnetospheres in the context of the generation of nonthermal, high-energy emission of AGN and pulsars is discussed.
Role of radiation reaction forces in the dynamics of centrifugally accelerated particles
NASA Astrophysics Data System (ADS)
Dalakishvili, G. T.; Rogava, A. D.; Berezhiani, V. I.
2007-08-01
In this paper we study the influence of radiation reaction (RR) forces on the dynamics of centrifugally accelerated particles. It is assumed that the particles move along magnetic field lines anchored in the rotating central object. The common “bead-on-the-wire” approximation is used. The solutions are found and analyzed for cases when the form of the prescribed trajectory (rigidly rotating field line) is approximated by: (a) straight line, and (b) Archimedes spiral. Dynamics of neutral and charged particles are compared with the emphasis on the role of RR forces in the latter case. It is shown that for charged particles there exist locations of stable equilibrium. It is demonstrated that for particular initial conditions RR forces cause centripetal motion of the particles: their “falling” on the central rotating object. It is found that in the case of Archimedes spiral both neutral and charged particles can reach infinity where their motion has asymptotically force-free character. The possible importance of these processes for the acceleration of relativistic, charged particles by rotating magnetospheres in the context of the generation of nonthermal, high-energy emission of AGN and pulsars is discussed.
Nam, Kwangho
2013-08-13
The implementation and performance of the atom-centered density matrix propagation (ADMP) [J. Chem. Phys. 2001, 114, 9758] and the curvy-steps (CURV) methods [J. Chem. Phys. 2004, 121, 1152] are described. These methods solve the electronic Schrödinger equation approximately by propagating the electronic degrees of freedom using the extended Lagrangian molecular dynamics (ELMD) simulation approach. The ADMP and CURV methods are implemented and parallelized to accelerate semiempirical quantum mechanical (QM) methods (such as the MNDO, AM1, PM3, MNDO/d, and AM1/d methods). Test calculations show that both the ADMP and the CURV methods are 2∼4 times faster than the Born-Oppenheimer molecular dynamics (BOMD) method and conserve the total energy well. The accuracy of the ADMP and CURV simulations is comparable to the BOMD simulations. The parallel implementation accelerates the MD simulation by up to 28 fold for the ADMP method and 25 fold for the CURV method, respectively, relative to the speed of the single core BOMD. In addition, a multiple time scale (MTS) approach is introduced to further speed up the semiempirical QM and QM/MM ELMD simulations. Since a larger integration time step is used for the propagation of the nuclear coordinates than that for the electronic degrees of freedom, the MTS approach allows the ELMD simulation to be carried out with a time step that is larger than the time step accessible by the original ADMP and CURV methods. It renders MD simulation to be carried out about 20 times faster than the BOMD simulation, and yields results that are comparable to the single time scale simulation results. The use of the methods introduced in the present work provides an efficient way to extend the length of the QM and QM/MM molecular dynamics simulations beyond the length accessible by BOMD simulation. PMID:26584095
Electron beam dynamics in the long-pulse, high-current DARHT-II linear induction accelerator
Ekdahl, Carl A; Abeyta, Epifanio O; Aragon, Paul; Archuleta, Rita; Cook, Gerald; Dalmas, Dale; Esquibel, Kevin; Gallegos, Robert A; Garnett, Robert; Harrison, James F; Johnson, Jeffrey B; Jacquez, Edward B; Mccuistian, Brian T; Montoya, Nicholas A; Nath, Subrato; Nielsen, Kurt; Oro, David; Prichard, Benjamin; Rowton, Lawrence; Sanchez, Manolito; Scarpetti, Raymond; Schauer, Martin M; Seitz, Gerald; Schulze, Martin; Bender, Howard A; Broste, William B; Carlson, Carl A; Frayer, Daniel K; Johnson, Douglas E; Tom, C Y; Williams, John; Hughes, Thomas; Anaya, Richard; Caporaso, George; Chambers, Frank; Chen, Yu - Jiuan; Falabella, Steve; Guethlein, Gary; Raymond, Brett; Richardson, Roger; Trainham, C; Weir, John; Genoni, Thomas; Toma, Carsten
2009-01-01
The DARHT-II linear induction accelerator (LIA) now accelerates 2-kA electron beams to more than 17 MeV. This LIA is unique in that the accelerated current pulse width is greater than 2 microseconds. This pulse has a flat-top region where the final electron kinetic energy varies by less than 1% for more than 1.5 microseconds. The long risetime of the 6-cell injector current pulse is 0.5 {micro}s, which can be scraped off in a beam-head cleanup zone before entering the 68-cell main accelerator. We discuss our experience with tuning this novel accelerator; and present data for the resulting beam transport and dynamics. We also present beam stability data, and relate these to previous stability experiments at lower current and energy.
QM/QM' Direct Molecular Dynamics of Water-Accelerated Diels-Alder Reaction.
Liu, Fengjiao; Yang, Zhongyue; Mei, Ye; Houk, K N
2016-07-01
A QM/QM' direct molecular dynamics study of a water-accelerated Diels-Alder reaction in aqueous solution is reported. Cyclopentadiene and methyl vinyl ketone are known to react faster in water than in nonpolar solvents. We have explored how polarization of water molecules afforded by PM3 influences the nature of the transition state, and the reaction dynamics. We compare the results with previous studies on QM/MM and QM/MM+3QM water simulations from our laboratory. Transition state sampling in vacuum PM3 water boxes indicates that the asynchronicity is 0.54 Å in QM/QM', as compared to 0.48 Å in QM/MM, and 0.54 Å in QM/MM+3QM water. The mean time gap between the formation of two C-C bonds is 19 fs for QM/QM', compared to 20 fs for QM/MM, and 25 fs for QM/MM+3QM water. The samplings and time gaps are qualitatively consistent, indicating that water polarization is not significant in sampling and dynamics of bonding changes. The dynamics of hydrogen bonding between reacting molecules and water molecules was also analyzed. From reactants to transition states, H-bond shortening is 0.4 Å by QM/QM', while only 0.15 Å for QM/MM and QM/MM+3QM water. From reactants to transition states, the mean value of the H-bond angle increases by 19° in QM/QM', but only 4° in QM/MM, and 10° in QM/MM+3QM water. These suggest that water polarization is essential for the correct representation of dynamical formation of hydrogen bonds in the transition state by water reorientation. QM/QM' overestimates the hydrogen bonding enhancement because of its underestimation of neutral hydrogen bonding within the reactants, a general deficiency of PM3. PMID:27092967
Chatterjee, Abhijit; Voter, Arthur
2009-01-01
We develop a variation of the temperature accelerated dynamics (TAD) method, called the p-TAD method, that efficiently generates an on-the-fly kinetic Monte Carlo (KMC) process catalog with control over the accuracy of the catalog. It is assumed that transition state theory is valid. The p-TAD method guarantees that processes relevant at the timescales of interest to the simulation are present in the catalog with a chosen confidence. A confidence measure associated with the process catalog is derived. The dynamics is then studied using the process catalog with the KMC method. Effective accuracy of a p-TAD calculation is derived when a KMC catalog is reused for conditions different from those the catalog was originally generated for. Different KMC catalog generation strategies that exploit the features of the p-TAD method and ensure higher accuracy and/or computational efficiency are presented. The accuracy and the computational requirements of the p-TAD method are assessed. Comparisons to the original TAD method are made. As an example, we study dynamics in sub-monolayer Ag/Cu(110) at the time scale of seconds using the p-TAD method. It is demonstrated that the p-TAD method overcomes several challenges plaguing the conventional KMC method.
NASA Astrophysics Data System (ADS)
Tygier, S.; Appleby, R. B.; Garland, J. M.; Hock, K.; Owen, H.; Kelliher, D. J.; Sheehy, S. L.
2015-03-01
We present PyZgoubi, a framework that has been developed based on the tracking engine Zgoubi to model, optimise and visualise the dynamics in particle accelerators, especially fixed-field alternating-gradient (FFAG) accelerators. We show that PyZgoubi abstracts Zgoubi by wrapping it in an easy-to-use Python framework in order to allow simple construction, parameterisation, visualisation and optimisation of FFAG accelerator lattices. Its object oriented design gives it the flexibility and extensibility required for current novel FFAG design. We apply PyZgoubi to two example FFAGs; this includes determining the dynamic aperture of the PAMELA medical FFAG in the presence of magnet misalignments, and illustrating how PyZgoubi may be used to optimise FFAGs. We also discuss a robust definition of dynamic aperture in an FFAG and show its implementation in PyZgoubi.
Ultrananocrystalline Diamond Cantilever Wide Dynamic Range Acceleration/Vibration /Pressure Sensor
Krauss, Alan R.; Gruen, Dieter M.; Pellin, Michael J.; Auciello, Orlando
2003-09-02
An ultrananocrystalline diamond (UNCD) element formed in a cantilever configuration is used in a highly sensitive, ultra-small sensor for measuring acceleration, shock, vibration and static pressure over a wide dynamic range. The cantilever UNCD element may be used in combination with a single anode, with measurements made either optically or by capacitance. In another embodiment, the cantilever UNCD element is disposed between two anodes, with DC voltages applied to the two anodes. With a small AC modulated voltage applied to the UNCD cantilever element and because of the symmetry of the applied voltage and the anode-cathode gap distance in the Fowler-Nordheim equation, any change in the anode voltage ratio V1/V2 required to maintain a specified current ratio precisely matches any displacement of the UNCD cantilever element from equilibrium. By measuring changes in the anode voltage ratio required to maintain a specified current ratio, the deflection of the UNCD cantilever can be precisely determined. By appropriately modulating the voltages applied between the UNCD cantilever and the two anodes, or limit electrodes, precise independent measurements of pressure, uniaxial acceleration, vibration and shock can be made. This invention also contemplates a method for fabricating the cantilever UNCD structure for the sensor.
Ultrananocrystalline diamond cantilever wide dynamic range acceleration/vibration/pressure sensor
Krauss, Alan R.; Gruen, Dieter M.; Pellin, Michael J.; Auciello, Orlando
2002-07-23
An ultrananocrystalline diamond (UNCD) element formed in a cantilever configuration is used in a highly sensitive, ultra-small sensor for measuring acceleration, shock, vibration and static pressure over a wide dynamic range. The cantilever UNCD element may be used in combination with a single anode, with measurements made either optically or by capacitance. In another embodiment, the cantilever UNCD element is disposed between two anodes, with DC voltages applied to the two anodes. With a small AC modulated voltage applied to the UNCD cantilever element and because of the symmetry of the applied voltage and the anode-cathode gap distance in the Fowler-Nordheim equation, any change in the anode voltage ratio V1/N2 required to maintain a specified current ratio precisely matches any displacement of the UNCD cantilever element from equilibrium. By measuring changes in the anode voltage ratio required to maintain a specified current ratio, the deflection of the UNCD cantilever can be precisely determined. By appropriately modulating the voltages applied between the UNCD cantilever and the two anodes, or limit electrodes, precise independent measurements of pressure, uniaxial acceleration, vibration and shock can be made. This invention also contemplates a method for fabricating the cantilever UNCD structure for the sensor.
Electron-Beam Dynamics for an Advanced Flash-Radiography Accelerator
Ekdahl, Carl
2015-12-01
Beam dynamics issues were assessed for a new linear induction electron accelerator being designed for multipulse flash radiography of large explosively driven hydrodynamic experiments. Special attention was paid to equilibrium beam transport, possible emittance growth, and beam stability. Especially problematic would be high-frequency beam instabilities that could blur individual radiographic source spots, low-frequency beam motion that could cause pulse-to-pulse spot displacement, and emittance growth that could enlarge the source spots. Furthermore, beam physics issues were examined through theoretical analysis and computer simulations, including particle-in-cell codes. Beam instabilities investigated included beam breakup, image displacement, diocotron, parametric envelope, ion hose, and themore » resistive wall instability. The beam corkscrew motion and emittance growth from beam mismatch were also studied. It was concluded that a beam with radiographic quality equivalent to the present accelerators at Los Alamos National Laboratory will result if the same engineering standards and construction details are upheld.« less
E-beam dynamics calculations and comparison with measurements of a high duty accelerator at Boeing
Parazzoli, C.G.; Dowell, D.H.
1995-12-31
The electron dynamics in the photoinjector cavities and through the beamline for a high duty factor electron accelerator are computed. The particle in a cell code ARGUS, is first used in the low energy (< 2 MeV) region of the photoinjector, then the ARGUS-generated phase space at the photoinjector exit is used as input in the standard particle pusher code PARMELA, and the electron beam properties at the end of the beamline computed. Comparisons between the calculated and measured electron bea mradial profiles and emittances are presented for different values of the electron pulse charge. A discussion of the methodology used and on the accuracy of PARMELA in the low energy region of the photoinjector is given.
A comprehensive tool to analyse dynamic log files from an Elekta-Synergy accelerator
NASA Astrophysics Data System (ADS)
Arumugam, Sankar; Xing, Aitang; Pagulayan, Claire; Holloway, Lois
2014-03-01
This study presents the development of a software tool 'Treat Check' to analyse the dynamic log files from an Elekta - Synergy accelerator. The software generates formatted output in the form of a plot presenting errors in various treatment delivery parameters such as gantry angle, Multi Leaf Collimator (MLC) leaf position, jaw position and Monitor Units (MU) for each of the control-points (CP) of the treatment beam. The plots are automatically saved in Portable Document Format (pdf). The software also has the functionality to introduce these treatment delivery errors into the original plan in the Pinnacle (Philips) treatment planning system (TPS) in order to assess the clinical impact of treatment delivery errors on delivered dose.
Evaluation of Dynamic Mechanical Loading as an Accelerated Test Method for Ribbon Fatigue
Bosco, Nick; Silverman, Timothy J.; Wohlgemuth, John; Kurtz, Sarah; Inoue, Masanao; Sakurai, Keiichiro; Shioda, Tsuyoshi; Zenkoh, Hirofumi; Hirota, Kusato; Miyashita, Masanori; Tadanori, Tanahashi; Suzuki, Soh; Chen, Yifeng; Verlinden, Pierre J.
2014-12-31
Dynamic Mechanical Loading (DML) of photovoltaic modules is explored as a route to quickly fatigue copper interconnect ribbons. Results indicate that most of the interconnect ribbons may be strained through module mechanical loading to a level that will result in failure in a few hundred to thousands of cycles. Considering the speed at which DML may be applied, this translates into a few hours of testing. To evaluate the equivalence of DML to thermal cycling, parallel tests were conducted with thermal cycling. Preliminary analysis suggests that one +/-1 kPa DML cycle is roughly equivalent to one standard accelerated thermal cycle and approximately 175 of these cycles are equivalent to a 25-year exposure in Golden Colorado for the mechanism of module ribbon fatigue.
2012-01-01
In the present work, we employ excited state accelerated ab initio molecular dynamics (A-AIMD) to efficiently study the excited state energy landscape and photophysical topology of a variety of molecular systems. In particular, we focus on two important challenges for the modeling of excited electronic states: (i) the identification and characterization of conical intersections and crossing seams, in order to predict different and often competing radiationless decay mechanisms, and (ii) the description of the solvent effect on the absorption and emission spectra of chemical species in solution. In particular, using as examples the Schiff bases formaldimine and salicylidenaniline, we show that A-AIMD can be readily employed to explore the conformational space around crossing seams in molecular systems with very different photochemistry. Using acetone in water as an example, we demonstrate that the enhanced configurational space sampling may be used to accurately and efficiently describe both the prominent features and line-shapes of absorption and emission spectra. PMID:22904696
Dynamic stability in parametric resonance of axially accelerating viscoelastic Timoshenko beams
NASA Astrophysics Data System (ADS)
Chen, Li-Qun; Tang, You-Qi; Lim, C. W.
2010-03-01
This paper investigates dynamic stability of an axially accelerating viscoelastic beam undergoing parametric resonance. The effects of shear deformation and rotary inertia are taken into account by the Timoshenko thick beam theory. The beam material obeys the Kelvin model in which the material time derivative is used. The axial speed is characterized as a simple harmonic variation about the constant mean speed. The governing partial-differential equations are derived from Newton's second law, Euler's angular momentum principle, and the constitutive relation. The method of multiple scales is applied to the equations to establish the solvability conditions in summation and principal parametric resonances. The sufficient and necessary condition of the stability is derived from the Routh-Hurvitz criterion. Some numerical examples are presented to demonstrate the effects of related parameters on the stability boundaries.
Evaluation of Dynamic Mechanical Loading as an Accelerated Test Method for Ribbon Fatigue: Preprint
Bosco, N.; Silverman, T. J.; Wohlgemuth, J.; Kurtz, S.; Inoue, M.; Sakurai, K.; Shinoda, T.; Zenkoh, H.; Hirota, K.; Miyashita, M.; Tadanori, T.; Suzuki, S.
2015-04-07
Dynamic Mechanical Loading (DML) of photovoltaic modules is explored as a route to quickly fatigue copper interconnect ribbons. Results indicate that most of the interconnect ribbons may be strained through module mechanical loading to a level that will result in failure in a few hundred to thousands of cycles. Considering the speed at which DML may be applied, this translates into a few hours o testing. To evaluate the equivalence of DML to thermal cycling, parallel tests were conducted with thermal cycling. Preliminary analysis suggests that one +/-1 kPa DML cycle is roughly equivalent to one standard accelerated thermal cycle and approximately 175 of these cycles are equivalent to a 25-year exposure in Golden Colorado for the mechanism of module ribbon fatigue.
NASA Technical Reports Server (NTRS)
Hung, R. J.; Pan, H. L.
1995-01-01
The dynamical behavior of spacecraft propellant affected by the asymmetric combined gravity gradient and jitter accelerations, in particular the effect of surface tension on partially-filled rotating fluids applicable to a full-scale Gravity Probe-B Spacecraft dewar tank has been investigated. Three different cases of orbital accelerations: (1) gravity gradient-dominated, (2) equally weighted between gravity gradient and jitter, and (3) gravity jitter-dominated accelerations are studied. The results of slosh wave excitation along the liquid-vapor interface induced by gravity gradient-dominated accelerations provide a torsional moment with tidal motion of bubble oscillations in the rotating dewar. The results are clearly seen from the twisting shape of the bubble oscillations driven by gravity gradient-dominated acceleration. The results of slosh wave excitation along the liquid-vapor interface induced by gravity jitter-dominated acceleration indicate the results of bubble motion in a manner of down-and-up and leftward-and-rightward movement of oscillation when the bubble is rotating with respect to rotating dewar axis. Fluctuations of angular momentum, fluid moment and bubble mass center caused by slosh wave excitations driven by gravity gradient acceleration or gravity jitter acceleration are also investigated.
2015-01-01
Many problems studied via molecular dynamics require accurate estimates of various thermodynamic properties, such as the free energies of different states of a system, which in turn requires well-converged sampling of the ensemble of possible structures. Enhanced sampling techniques are often applied to provide faster convergence than is possible with traditional molecular dynamics simulations. Hamiltonian replica exchange molecular dynamics (H-REMD) is a particularly attractive method, as it allows the incorporation of a variety of enhanced sampling techniques through modifications to the various Hamiltonians. In this work, we study the enhanced sampling of the RNA tetranucleotide r(GACC) provided by H-REMD combined with accelerated molecular dynamics (aMD), where a boosting potential is applied to torsions, and compare this to the enhanced sampling provided by H-REMD in which torsion potential barrier heights are scaled down to lower force constants. We show that H-REMD and multidimensional REMD (M-REMD) combined with aMD does indeed enhance sampling for r(GACC), and that the addition of the temperature dimension in the M-REMD simulations is necessary to efficiently sample rare conformations. Interestingly, we find that the rate of convergence can be improved in a single H-REMD dimension by simply increasing the number of replicas from 8 to 24 without increasing the maximum level of bias. The results also indicate that factors beyond replica spacing, such as round trip times and time spent at each replica, must be considered in order to achieve optimal sampling efficiency. PMID:24625009
Ruth, R.D.; Chen, P.
1986-03-01
In this paper we discuss plasma accelerators which might provide high gradient accelerating fields suitable for TeV linear colliders. In particular we discuss two types of plasma accelerators which have been proposed, the Plasma Beat Wave Accelerator and the Plasma Wake Field Accelerator. We show that the electric fields in the plasma for both schemes are very similar, and thus the dynamics of the driven beams are very similar. The differences appear in the parameters associated with the driving beams. In particular to obtain a given accelerating gradient, the Plasma Wake Field Accelerator has a higher efficiency and a lower total energy for the driving beam. Finally, we show for the Plasma Wake Field Accelerator that one can accelerate high quality low emittance beams and, in principle, obtain efficiencies and energy spreads comparable to those obtained with conventional techniques.
Liu, Ya; Tu, GuoGang; Lai, XiaoPing; Kuang, BinHai; Li, ShaoHua
2016-10-01
Aminopeptidase N (APN) is a zinc-dependent ectopeptidase involved in cell proliferation, secretion, invasion, and angiogenesis, and is widely recognized as an important cancer target. However, the mechanisms whereby ligands leave the active site of APN remain unknown. Investigating ligand dissociation processes is quite difficult, both in classical simulation methods and in experimental approaches. In this study, random acceleration molecular dynamics (RAMD) simulation was used to investigate the potential dissociation pathways of ligand from APN. The results revealed three pathways (channels A, B and C) for ligand release. Channel A, which matches the hypothetical channel region, was the most preferred region for bestatin to dissociate from the enzyme, and is probably the major channel for the inner bound ligand. In addition, two alternative channels (channels B and C) were shown to be possible pathways for ligand egression. Meanwhile, we identified key residues controlling the dynamic features of APN channels. Identification of the dissociation routes will provide further mechanistic insights into APN, which will benefit the development of more promising APN inhibitors. Graphical Abstract The release pathways of bestatin inside active site of aminopeptidase N were simulated using RAMD simulation. PMID:27624165
k-t Group sparse: a method for accelerating dynamic MRI.
Usman, M; Prieto, C; Schaeffter, T; Batchelor, P G
2011-10-01
Compressed sensing (CS) is a data-reduction technique that has been applied to speed up the acquisition in MRI. However, the use of this technique in dynamic MR applications has been limited in terms of the maximum achievable reduction factor. In general, noise-like artefacts and bad temporal fidelity are visible in standard CS MRI reconstructions when high reduction factors are used. To increase the maximum achievable reduction factor, additional or prior information can be incorporated in the CS reconstruction. Here, a novel CS reconstruction method is proposed that exploits the structure within the sparse representation of a signal by enforcing the support components to be in the form of groups. These groups act like a constraint in the reconstruction. The information about the support region can be easily obtained from training data in dynamic MRI acquisitions. The proposed approach was tested in two-dimensional cardiac cine MRI with both downsampled and undersampled data. Results show that higher acceleration factors (up to 9-fold), with improved spatial and temporal quality, can be obtained with the proposed approach in comparison to the standard CS reconstructions. PMID:21394781
Accelerated dynamic MRI exploiting sparsity and low-rank structure: k-t SLR.
Lingala, Sajan Goud; Hu, Yue; DiBella, Edward; Jacob, Mathews
2011-05-01
We introduce a novel algorithm to reconstruct dynamic magnetic resonance imaging (MRI) data from under-sampled k-t space data. In contrast to classical model based cine MRI schemes that rely on the sparsity or banded structure in Fourier space, we use the compact representation of the data in the Karhunen Louve transform (KLT) domain to exploit the correlations in the dataset. The use of the data-dependent KL transform makes our approach ideally suited to a range of dynamic imaging problems, even when the motion is not periodic. In comparison to current KLT-based methods that rely on a two-step approach to first estimate the basis functions and then use it for reconstruction, we pose the problem as a spectrally regularized matrix recovery problem. By simultaneously determining the temporal basis functions and its spatial weights from the entire measured data, the proposed scheme is capable of providing high quality reconstructions at a range of accelerations. In addition to using the compact representation in the KLT domain, we also exploit the sparsity of the data to further improve the recovery rate. Validations using numerical phantoms and in vivo cardiac perfusion MRI data demonstrate the significant improvement in performance offered by the proposed scheme over existing methods. PMID:21292593
NASA Astrophysics Data System (ADS)
Jacobitz, Frank G.; Schneider, Kai; Bos, Wouter J. T.; Farge, Marie
2016-01-01
The acceleration statistics of sheared and rotating homogeneous turbulence are studied using direct numerical simulation results. The statistical properties of Lagrangian and Eulerian accelerations are considered together with the influence of the rotation to shear ratio, as well as the scale dependence of their statistics. The probability density functions (pdfs) of both Lagrangian and Eulerian accelerations show a strong and similar dependence on the rotation to shear ratio. The variance and flatness of both accelerations are analyzed and the extreme values of the Eulerian acceleration are observed to be above those of the Lagrangian acceleration. For strong rotation it is observed that flatness yields values close to three, corresponding to Gaussian-like behavior, and for moderate and vanishing rotation the flatness increases. Furthermore, the Lagrangian and Eulerian accelerations are shown to be strongly correlated for strong rotation due to a reduced nonlinear term in this case. A wavelet-based scale-dependent analysis shows that the flatness of both Eulerian and Lagrangian accelerations increases as scale decreases, which provides evidence for intermittent behavior. For strong rotation the Eulerian acceleration is even more intermittent than the Lagrangian acceleration, while the opposite result is obtained for moderate rotation. Moreover, the dynamics of a passive scalar with gradient production in the direction of the mean velocity gradient is analyzed and the influence of the rotation to shear ratio is studied. Concerning the concentration of a passive scalar spread by the flow, the pdf of its Eulerian time rate of change presents higher extreme values than those of its Lagrangian time rate of change. This suggests that the Eulerian time rate of change of scalar concentration is mainly due to advection, while its Lagrangian counterpart is only due to gradient production and viscous dissipation.
Jacobitz, Frank G; Schneider, Kai; Bos, Wouter J T; Farge, Marie
2016-01-01
The acceleration statistics of sheared and rotating homogeneous turbulence are studied using direct numerical simulation results. The statistical properties of Lagrangian and Eulerian accelerations are considered together with the influence of the rotation to shear ratio, as well as the scale dependence of their statistics. The probability density functions (pdfs) of both Lagrangian and Eulerian accelerations show a strong and similar dependence on the rotation to shear ratio. The variance and flatness of both accelerations are analyzed and the extreme values of the Eulerian acceleration are observed to be above those of the Lagrangian acceleration. For strong rotation it is observed that flatness yields values close to three, corresponding to Gaussian-like behavior, and for moderate and vanishing rotation the flatness increases. Furthermore, the Lagrangian and Eulerian accelerations are shown to be strongly correlated for strong rotation due to a reduced nonlinear term in this case. A wavelet-based scale-dependent analysis shows that the flatness of both Eulerian and Lagrangian accelerations increases as scale decreases, which provides evidence for intermittent behavior. For strong rotation the Eulerian acceleration is even more intermittent than the Lagrangian acceleration, while the opposite result is obtained for moderate rotation. Moreover, the dynamics of a passive scalar with gradient production in the direction of the mean velocity gradient is analyzed and the influence of the rotation to shear ratio is studied. Concerning the concentration of a passive scalar spread by the flow, the pdf of its Eulerian time rate of change presents higher extreme values than those of its Lagrangian time rate of change. This suggests that the Eulerian time rate of change of scalar concentration is mainly due to advection, while its Lagrangian counterpart is only due to gradient production and viscous dissipation. PMID:26871161
Glowacki, David R; O'Connor, Michael; Calabró, Gaetano; Price, James; Tew, Philip; Mitchell, Thomas; Hyde, Joseph; Tew, David P; Coughtrie, David J; McIntosh-Smith, Simon
2014-01-01
With advances in computational power, the rapidly growing role of computational/simulation methodologies in the physical sciences, and the development of new human-computer interaction technologies, the field of interactive molecular dynamics seems destined to expand. In this paper, we describe and benchmark the software algorithms and hardware setup for carrying out interactive molecular dynamics utilizing an array of consumer depth sensors. The system works by interpreting the human form as an energy landscape, and superimposing this landscape on a molecular dynamics simulation to chaperone the motion of the simulated atoms, affecting both graphics and sonified simulation data. GPU acceleration has been key to achieving our target of 60 frames per second (FPS), giving an extremely fluid interactive experience. GPU acceleration has also allowed us to scale the system for use in immersive 360° spaces with an array of up to ten depth sensors, allowing several users to simultaneously chaperone the dynamics. The flexibility of our platform for carrying out molecular dynamics simulations has been considerably enhanced by wrappers that facilitate fast communication with a portable selection of GPU-accelerated molecular force evaluation routines. In this paper, we describe a 360° atmospheric molecular dynamics simulation we have run in a chemistry/physics education context. We also describe initial tests in which users have been able to chaperone the dynamics of 10-alanine peptide embedded in an explicit water solvent. Using this system, both expert and novice users have been able to accelerate peptide rare event dynamics by 3-4 orders of magnitude. PMID:25340458
Monti, R; Savino, R; Paterna, D
2005-07-01
The different acceleration components on the ISS that are responsible for the generation of convective motions in a fluid cell either in the presence of density gradients or in quasi-isodense processes, are analyzed. The NASA measurements of the quasi-steady and periodic acceleration on the ISS are considered and their effects on fluid-dynamic experiments are computed and discussed under different assumptions. In particular, numerical simulations are carried out to identify the relative importance of linear and pendular accelerations, due to possible rotations of the P/L around its center of mass. The effects caused by variable accelerations created by an isolation mount that exhibits an attenuation factor not constant within the payload volume, caused by the reaction forces of the umbilicals, are computed and analyzed. PMID:15900644
Gedeon, Patrick C.; Thomas, James R.; Madura, Jeffry D.
2015-01-01
Molecular dynamics simulation provides a powerful and accurate method to model protein conformational change, yet timescale limitations often prevent direct assessment of the kinetic properties of interest. A large number of molecular dynamic steps are necessary for rare events to occur, which allow a system to overcome energy barriers and conformationally transition from one potential energy minimum to another. For many proteins, the energy landscape is further complicated by a multitude of potential energy wells, each separated by high free-energy barriers and each potentially representative of a functionally important protein conformation. To overcome these obstacles, accelerated molecular dynamics utilizes a robust bias potential function to simulate the transition between different potential energy minima. This straightforward approach more efficiently samples conformational space in comparison to classical molecular dynamics simulation, does not require advanced knowledge of the potential energy landscape and converges to the proper canonical distribution. Here, we review the theory behind accelerated molecular dynamics and discuss the approach in the context of modeling protein conformational change. As a practical example, we provide a detailed, step-by-step explanation of how to perform an accelerated molecular dynamics simulation using a model neurotransmitter transporter embedded in a lipid cell membrane. Changes in protein conformation of relevance to the substrate transport cycle are then examined using principle component analysis. PMID:25330967
Interaction dynamics of high Reynolds number magnetized plasma flow on the CTIX plasma accelerator
NASA Astrophysics Data System (ADS)
Howard, Stephen James
The Compact Toroid Injection eXperiment, (CTIX), is a coaxial railgun that forms and accelerates magnetized plasma rings called compact toroids (CT's). CTIX consists of a pair of cylindrical coaxial electrodes with the region between them kept at high vacuum (2 m long, 15 cm outer diameter). Hydrogen is typically the dominant constituent of the CT plasma, however helium can also be used. The railgun effect that accelerates the CT can be accounted for by the Lorentz j x B force density created by the power input from a capacitor bank of roughly a Giga-Watt peak. The final velocity of the CT can be as high as 300 km/s, with an acceleration of about 3 billion times Earth's gravity. The compact toroid is able to withstand these forces because of a large internal magnetic field of about 1 Tesla. Understanding the nature of high speed flow of a magnetized plasma has been the primary challenge of this work. In this dissertation we will explore a sequence of fundamental questions regarding the plasma physics of CTIX. First we will go over some new results about the structure and dynamics of the compact toroid's magnetic field, and its electrical resistivity. Then we will present the results from a sequence of key experiments involving reconnection/compression and thermalization of the plasma during interaction of the CT with target magnetic fields of various geometries. Next, we look at the Doppler shift of a spectral line of the He II ion as a measurement of plasma velocity, and to gain insight into the ionization physics of helium in our plasma. These preliminary experiments provide the background for our primary experimental tool for investigating turbulence, a technique called Gas Puff Imaging (GPI) in which a cloud of helium can be used to enhance plasma brightness, allowing plasma density fluctuations to be imaged. We will conclude with an analysis of the images that show coherent density waves, as well as the transition to turbulence during the interaction with a
Rouboa, Abel; Silva, António; Leal, Luís; Rocha, Jorge; Alves, Francisco
2006-01-01
Propulsive forces generated by swimmers hand/forearm, have been studied through experimental tests. However, there are serious doubts as to whether forces quantified in this way are accurate enough to be meaningful. In order to solve some experimental problems, some numerical techniques have been proposed using Computational Fluid Dynamics (CFD). The main purpose of the present work was threefold. First, disseminate the use of CFD as a new tool in swimming research. Second, apply the CFD method in the calculation of drag and lift coefficients resulting from the numerical resolution equations of the flow around the swimmers hand/forearm using the steady flow conditions. Third, evaluate the effect of hand/forearm acceleration on drag and lift coefficients. For these purposes three, two-dimensional (2D), models of a right male hand/forearm were studied. A frontal model (theta = 90 degrees, Phi = 90 degrees) and two lateral models, one with the thumb as leading edge (theta = 0 degrees, = 90 degrees), and the other with the small finger as the leading edge (theta = 0 degrees, Phi = 180 degrees). The governing system of equations considered was the incompressible Reynolds averaged Navier-Stokes equations with the standard k-epsilon model. The main results reported that, under the steady-state flow condition, the drag coefficient was the one that contributes more for propulsion, and was almost constant for the whole range of velocities, with a maximum value of 1.16 (Cd = 1.16). This is valid when the orientation of the hand/forearm is plane and the model is perpendicular to the direction of the flow. Under the hand /forearm acceleration condition, the measured values for propulsive forces calculation were approximately 22.5% (54.440 N) higher than the forces produced under the steady flow condition (44.428 N). By the results, pointed out, we can conclude that: (i) CFD can be considered an interesting new approach for hydrodynamic forces calculation on swimming, (ii) the
Studies of beam dynamics in relativistic klystron two-beam accelerators
Lidia, Steven M.
1999-11-01
Two-beam accelerators (TBAs) based upon free-electron lasers (FELs) or relativistic klystrons (RK-TBAs) have been proposed as efficient power sources for next generation high-energy linear colliders. Studies have demonstrated the possibility of building TBAs from X-band ({approximately}8-12 GHz) through Ka band ({approximately} 30-35 GHz) frequency regions. Provided that further prototyping shows stable beam propagation with minimal current loss and production of good quality, high-power rf fields, this technology is compatible with current schemes for electron-positron colliders in the multi-TeV center-of-mass scale. A new method of simulating the beam dynamics in accelerators of this type has been developed in this dissertation. There are three main components to this simulation. The first is a tracking algorithm to generate nonlinear transfer maps for pushing noninteracting particles through the external fields. The second component is a 3D Particle-In-Cell (PIC) algorithm that solves a set of Helmholtz equations for the self-fields, including the conducting boundary condition, and generates impulses that are interleaved with the nonlinear maps by means of a split-operation algorithm. The Helmholtz equations are solved by a multi-grid algorithm. The third component is an equivalent circuit equation solver that advances the modal rf cavity fields in time due to excitation by the modulated beam. The RTA project is described, and the simulation code is used to design the latter portions of the experiment. Detailed calculations of the beam dynamics and of the rf cavity output are presented and discussed. A beamline design is presented that will generate nearly 1.2 GW of power from 40 input, gain, and output rv cavities over a 10 m distance. The simulations show that beam current losses are acceptable, and that longitudinal and transverse focusing techniques are sufficient capable of maintaining a high degree of beam quality along the entire beamline. Additional
Kalyaanamoorthy, Subha; Chen, Yi-Ping Phoebe
2012-02-27
Molecular channel exploration perseveres to be the prominent solution for eliciting structure and accessibility of active site and other internal spaces of macromolecules. The volume and silhouette characterization of these channels provides answers for the issues of substrate access and ligand swapping between the obscured active site and the exterior of the protein. Histone deacetylases (HDACs) are metal-dependent enzymes that are involved in the cell growth, cell cycle regulation, and progression, and their deregulations have been linked with different types of cancers. Hence HDACs, especially the class I family, are widely recognized as the important cancer targets, and the characterizations of their structures and functions have been of special interest in cancer drug discovery. The class I HDACs are known to possess two different protein channels, an 11 Å and a 14 Å (named channels A and B1, respectively), of which the former is a ligand or substrate occupying tunnel that leads to the buried active site zinc ion and the latter is speculated to be involved in product release. In this work, we have carried out random acceleration molecular dynamics (RAMD) simulations coupled with the classical molecular dynamics to explore the release of the ligand, N-(2-aminophenyl) benzamide (LLX) from the active sites of the recently solved X-ray crystal structure of HDAC2 and the computationally modeled HDAC1 proteins. The RAMD simulations identified significant structural and dynamic features of the HDAC channels, especially the key 'gate-keeping' amino acid residues that control these channels and the ligand release events. Further, this study identified a novel and unique channel B2, a subchannel from channel B1, in the HDAC1 protein structure. The roles of water molecules in the LLX release from the HDAC1 and HDAC2 enzymes are also discussed. Such structural and dynamic properties of the HDAC protein channels that govern the ligand escape reactions will provide
Bochenkov, Vladimir; Suetin, Nikolay; Shankar, Sadasivan
2014-09-07
A new method, the Extended Temperature-Accelerated Dynamics (XTAD), is introduced for modeling long-timescale evolution of large rare-event systems. The method is based on the Temperature-Accelerated Dynamics approach [M. Sørensen and A. Voter, J. Chem. Phys. 112, 9599 (2000)], but uses full-scale parallel molecular dynamics simulations to probe a potential energy surface of an entire system, combined with the adaptive on-the-fly system decomposition for analyzing the energetics of rare events. The method removes limitations on a feasible system size and enables to handle simultaneous diffusion events, including both large-scale concerted and local transitions. Due to the intrinsically parallel algorithm, XTAD not only allows studies of various diffusion mechanisms in solid state physics, but also opens the avenue for atomistic simulations of a range of technologically relevant processes in material science, such as thin film growth on nano- and microstructured surfaces.
TEXES OBSERVATIONS OF M SUPERGIANTS: DYNAMICS AND THERMODYNAMICS OF WIND ACCELERATION
Harper, Graham M.; Richter, Matthew J.; Ryde, Nils; Brown, Alexander; Brown, Joanna; Greathouse, Thomas K.; Strong, Shadrian
2009-08-20
We have detected [Fe II] 17.94 {mu}m and 24.52 {mu}m emission from a sample of M supergiants ({mu} Cep, {alpha} Sco, {alpha} Ori, CE Tau, AD Per, and {alpha} Her) using the Texas Echelon Cross Echelle Spectrograph on NASA's Infrared Telescope Facility. These low opacity emission lines are resolved at R {approx_equal} 50, 000 and provide new diagnostics of the dynamics and thermodynamics of the stellar wind acceleration zone. The [Fe II] lines, from the first excited term (a {sup 4} F), are sensitive to the warm plasma where energy is deposited into the extended atmosphere to form the chromosphere and wind outflow. These diagnostics complement previous Kuiper Airborne Observatory and Infrared Space Observatory observations which were sensitive to the cooler and more extended circumstellar envelopes. The turbulent velocities of V{sub turb} {approx_equal} 12-13 km s{sup -1} observed in the [Fe II] a {sup 4} F forbidden lines are found to be a common property of our sample, and are less than that derived from the hotter chromospheric C II] 2325 A lines observed in {alpha} Ori, where V{sub turb} {approx_equal} 17-19 km s{sup -1}. For the first time, we have dynamically resolved the motions of the dominant cool atmospheric component discovered in {alpha} Ori from multiwavelength radio interferometry by Lim et al. Surprisingly, the emission centroids are quite Gaussian and at rest with respect to the M supergiants. These constraints combined with model calculations of the infrared emission line fluxes for {alpha} Ori imply that the warm material has a low outflow velocity and is located close to the star. We have also detected narrow [Fe I] 24.04 {mu}m emission that confirms Fe II is the dominant ionization state in {alpha} Ori's extended atmosphere.
NASA Astrophysics Data System (ADS)
Geng, Hua Y.
2015-02-01
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model-the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of rs = 0.912.
A nonlinear particle dynamics map of wakefield acceleration in a linear collider
Tajima, T.; Cheshkov, S.; Horton, W.; Yokoya, K.
1998-08-01
The performance of a wakefield accelerator in a high energy collider application is analyzed. In order to carry out this task, it is necessary to construct a strawman design system (no matter how preliminary) and build a code of the systems approach. A nonlinear dynamics map built on a simple theoretical model of the wakefield generated by the laser pulse (or whatever other method) is obtained and they employ this as a base for building a system with multi-stages (and components) as a high energy collider. The crucial figures of merit for such a system other than the final energy include the emittance (that determines the luminosity). The more complex the system is, the more opportunities the system has to degrade the emittance (or entropy of the beam). Thus the map gu ides one to identify where the crucial elements lie that affect the emittance. They find that a strong focusing force of the wakefield coupled with a possible jitter of the axis (or laser aiming) of each stage and a spread in the betatron frequencies arising from different phase space positions for individual particles leads to a phase space mixing. This sensitively controls the emittance degradation. They show that in the case of a uniform plasma the effect of emittance growth is large and may cause serious problems. They discuss possibilities to avoid it and control the situation.
Geng, Hua Y.
2015-02-15
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model—the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of r{sub s}=0.912.
Static and dynamic parasitic magnetizations and their control in superconducting accelerator dipoles
NASA Astrophysics Data System (ADS)
Collings, E. W.; Sumption, M. D.
2001-05-01
Long dipole magnets guide the particle beams in synchrotron-type high energy accelerators. In principal Cu-wound DC-excited dipoles could be designed to deliver a very uniform transverse bore field, i.e. with small or negligible harmonic (multipolar) distortion. But if the Cu is replaced by (a) superconducting strand that is (b) wound into a Rutherford cable carrying a time-varying transport current, extra magnetizations present within the windings cause distortions of the otherwise uniform field. The static (persistent-current) strand magnetization can be reduced by reducing the filament diameter, and the residue compensated or corrected by strategically placed active or passive components. The cable’s interstrand coupling currents can be controlled by increasing the interstrand contact resistance by: adjusting the level of native oxidation of the strand, coating it, or by inserting a ribbon-like core into the cable itself. Methods of locally compensating the magnetization of NbTi and Nb 3Sn strand and cable are discussed, progress in coupling-current suppression through the use of coatings and cores is reviewed, and a method of simultaneously reducing both the static and dynamic magnetizations of a NbTi cable by means of a thin Ni core is suggested.
Impedance Dynamics in the Self-Magnetic Pinch (SMP) Diode on the RITS-6 Accelerator
NASA Astrophysics Data System (ADS)
Renk, Timothy; Johnston, Mark; Leckbee, Joshua; Webb, Timothy; Mazarakis, Michael; Kiefer, Mark; Bennett, Nichelle
2014-10-01
The RITS-6 inductive voltage adder (IVA) accelerator (3.5-8.5 MeV) at Sandia National Laboratories produces high-power (TW) focused electron beams (<3 mm diameter) for flash x-ray radiography applications. The Self-Magnetic Pinch (SMP) diode utilizes a hollowed metal cathode to produce a pinched focus onto a high Z metal converter. The electron flow from the IVA driver into the load region complicates understanding of diode evolution. There is growing evidence that reducing cathode size below some ``optimum'' value in order to achieve desired spot size reduction results in pinch instabilities leading to either reduced dose-rate, early radiation power termination, or both. We are studying evolving pinch dynamics with current and x-ray monitors, optical diagnostics, and spectroscopy, as well as with LSP [1] code simulations. We are also planning changes to anode-cathode materials as well as changes to the diode aspect ratio in an attempt to mitigate the above trends and improve pinch stability while achieving simultaneous spot size reduction. Experiments are ongoing, and latest results will be reported [1]. LSP is a software product of ATK Mission Research, Albuquerque, NM. Sandia National Laboratories is a multiprogram laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Adminis-tration under Contract DE-AC04-94AL85000.
Stewart, Benjamin J; Navid, Ali; Turteltaub, Kenneth W; Bench, Graham
2010-12-01
Metabolic flux, the flow of metabolites through networks of enzymes, represents the dynamic productive output of cells. Improved understanding of intracellular metabolic fluxes will enable targeted manipulation of metabolic pathways of medical and industrial importance to a greater degree than is currently possible. Flux balance analysis (FBA) is a constraint-based approach to modeling metabolic fluxes, but its utility is limited by a lack of experimental measurements. Incorporation of experimentally measured fluxes as system constraints will significantly improve the overall accuracy of FBA. We applied a novel, two-tiered approach in the yeast Saccharomyces cerevisiae to measure nutrient consumption rates (extracellular fluxes) and a targeted intracellular flux using a (14)C-labeled precursor with HPLC separation and flux quantitation by accelerator mass spectrometry (AMS). The use of AMS to trace the intracellular fate of (14)C-glutamine allowed the calculation of intracellular metabolic flux through this pathway, with glutathione as the metabolic end point. Measured flux values provided global constraints for the yeast FBA model which reduced model uncertainty by more than 20%, proving the importance of additional constraints in improving the accuracy of model predictions and demonstrating the use of AMS to measure intracellular metabolic fluxes. Our results highlight the need to use intracellular fluxes to constrain the models. We show that inclusion of just one such measurement alone can reduce the average variability of model predicted fluxes by 10%. PMID:21062031
Desforges, F. G.; Paradkar, B. S. Ju, J.; Audet, T. L.; Maynard, G.; Cros, B.; Hansson, M.; Senje, L.; Persson, A.; Lundh, O.; Wahlström, C.-G.; Dobosz-Dufrénoy, S.; Monot, P.; Vay, J.-L.
2014-12-15
The dynamics of ionization-induced electron injection in high density (∼1.2 × 10{sup 19} cm{sup −3}) regime of laser wakefield acceleration is investigated by analyzing the betatron X-ray emission. In such high density operation, the laser normalized vector potential exceeds the injection-thresholds of both ionization-injection and self-injection due to self-focusing. In this regime, direct experimental evidence of early on-set of ionization-induced injection into the plasma wave is given by mapping the X-ray emission zone inside the plasma. Particle-In-Cell simulations show that this early on-set of ionization-induced injection, due to its lower trapping threshold, suppresses the trapping of self-injected electrons. A comparative study of the electron and X-ray properties is performed for both self-injection and ionization-induced injection. An increase of X-ray fluence by at least a factor of two is observed in the case of ionization-induced injection due to increased trapped charge compared to self-injection mechanism.
Yin, L; Albright, B J; Bowers, K J; Jung, D; Fernández, J C; Hegelich, B M
2011-07-22
Breakout afterburner (BOA) laser-ion acceleration has been demonstrated for the first time in the laboratory. In the BOA, an initially solid-density target undergoes relativistically induced transparency, initiating a period of enhanced ion acceleration. First-ever kinetic simulations of the BOA in three dimensions show that the ion beam forms lobes in the direction orthogonal to laser polarization and propagation. Analytic theory presented for the electron dynamics in the laser ponderomotive field explains how azimuthal symmetry breaks even for a symmetric laser intensity profile; these results are consistent with recent experiments at the Trident laser facility. PMID:21867015
NASA Astrophysics Data System (ADS)
Yin, L.; Albright, B. J.; Bowers, K. J.; Jung, D.; Fernández, J. C.; Hegelich, B. M.
2011-07-01
Breakout afterburner (BOA) laser-ion acceleration has been demonstrated for the first time in the laboratory. In the BOA, an initially solid-density target undergoes relativistically induced transparency, initiating a period of enhanced ion acceleration. First-ever kinetic simulations of the BOA in three dimensions show that the ion beam forms lobes in the direction orthogonal to laser polarization and propagation. Analytic theory presented for the electron dynamics in the laser ponderomotive field explains how azimuthal symmetry breaks even for a symmetric laser intensity profile; these results are consistent with recent experiments at the Trident laser facility.
NASA Astrophysics Data System (ADS)
Shi, Yu; Liang, Long; Ge, Hai-Wen; Reitz, Rolf D.
2010-03-01
Acceleration of the chemistry solver for engine combustion is of much interest due to the fact that in practical engine simulations extensive computational time is spent solving the fuel oxidation and emission formation chemistry. A dynamic adaptive chemistry (DAC) scheme based on a directed relation graph error propagation (DRGEP) method has been applied to study homogeneous charge compression ignition (HCCI) engine combustion with detailed chemistry (over 500 species) previously using an R-value-based breadth-first search (RBFS) algorithm, which significantly reduced computational times (by as much as 30-fold). The present paper extends the use of this on-the-fly kinetic mechanism reduction scheme to model combustion in direct-injection (DI) engines. It was found that the DAC scheme becomes less efficient when applied to DI engine simulations using a kinetic mechanism of relatively small size and the accuracy of the original DAC scheme decreases for conventional non-premixed combustion engine. The present study also focuses on determination of search-initiating species, involvement of the NOx chemistry, selection of a proper error tolerance, as well as treatment of the interaction of chemical heat release and the fuel spray. Both the DAC schemes were integrated into the ERC KIVA-3v2 code, and simulations were conducted to compare the two schemes. In general, the present DAC scheme has better efficiency and similar accuracy compared to the previous DAC scheme. The efficiency depends on the size of the chemical kinetics mechanism used and the engine operating conditions. For cases using a small n-heptane kinetic mechanism of 34 species, 30% of the computational time is saved, and 50% for a larger n-heptane kinetic mechanism of 61 species. The paper also demonstrates that by combining the present DAC scheme with an adaptive multi-grid chemistry (AMC) solver, it is feasible to simulate a direct-injection engine using a detailed n-heptane mechanism with 543 species
Laser ion acceleration by using the dynamic motion of a target
Morita, Toshimasa
2013-09-15
Proton acceleration by using a 620 TW, 18 J laser pulse of peak intensity of 5×10{sup 21} W/cm{sup 2} irradiating a disk target is examined using three-dimensional particle-in-cell simulations. It is shown that protons are accelerated efficiently to high energy for a “light” material in the first layer of a double-layer target, because a strongly inhomogeneous expansion of the first layer occurs by a Coulomb explosion within such a material. Moreover, a large movement of the first layer for the accelerated protons is produced by radiation-pressure-dominant acceleration. A time-varying electric potential produced by this expanding and moving ion cloud accelerates protons effectively. In addition, using the best material for the target, one can generate a proton beam with an energy of 200 MeV and an energy spread of 2%.
Suzuki, Yasuyuki; Morimoto, Hiroki; Kiyono, Ken; Morasso, Pietro; Nomura, Taishin
2015-08-01
Multiple joint movements during human quiet standing exhibit characteristic inter-joint coordination, shortly referred to as reciprocal relationship, in which angular acceleration of the hip joint is linearly and negatively correlated with that of the ankle joint (antiphase coordination) and, moreover, acceleration of the center of mass (CoM) of the double-inverted-pendulum (DIP) model of the human body is close to zero constantly. A question considered in this study is whether the reciprocal relationship is established by active neural control of the posture, or rather it is a biomechanical consequence of non-actively controlled body dynamics. To answer this question, we consider a DIP model of quiet standing, and show that the reciprocal relationship always holds by Newton's second law applied to the DIP model with human anthropometric dimensions, regardless of passive and active joint torque patterns acting on the ankle and hip joints. We then show that characteristic frequencies included in experimental sway trajectories with the reciprocal relationship match with harmonics of the eigenfrequency of the stable antiphase eigenmode of the non-actively controlled DIP-like unstable body dynamics. The results suggest that non-actively controlled DIP-like mechanical dynamics is a major cause of the minimization of the CoM acceleration during quiet standing, which is consistent with a type of control strategy that allows switching off active neural control intermittently for suitable periods of time during quiet standing. PMID:26736538
Investigations of Beam Dynamics Issues at Current and Future Hadron Accelerators
Ellison, James; Lau, Stephen; Heinemann, Klaus; Bizzozero, David
2015-03-12
Final Report Abstract for DE-FG02-99ER4110, May 15, 2011- October 15, 2014 There is a synergy between the fields of Beam Dynamics (BD) in modern particle accelerators and Applied Mathematics (AMa). We have formulated significant problems in BD and have developed and applied tools within the contexts of dynamical systems, topological methods, numerical analysis and scientific computing, probability and stochastic processes, and mathematical statistics. We summarize the three main areas of our AMa work since 2011. First, we continued our study of Vlasov-Maxwell systems. Previously, we developed a state of the art algorithm and code (VM3@A) to calculate coherent synchrotron radiation in single pass systems. In this cycle we carefully analyzed the major expense, namely the integral-over-history (IOH), and developed two approaches to speed up integration. The first strategy uses a representation of the Bessel function J0 in terms of exponentials. The second relies on “local sequences” developed recently for radiation boundary conditions, which are used to reduce computational domains. Although motivated by practicality, both strategies involve interesting and rather deep analysis and approximation theory. As an alternative to VM3@A, we are integrating Maxwell’s equations by a time-stepping method, bypass- ing the IOH, using a Discontinuous Galerkin (DG) method. DG is a generalization of Finite Element and Finite Volume methods. It is spectrally convergent, unlike the commonly used Finite Difference methods, and can handle complicated vacuum chamber geometries. We have applied this in several contexts and have obtained very nice results including an explanation of an experiment at the Canadian Light Source, where the geometry is quite complex. Second, we continued our study of spin dynamics in storage rings. There is much current and proposed activity where spin polarized beams are being used in testing the Standard Model and its modifications. Our work has focused
Generation of mesoscale magnetic fields and the dynamics of Cosmic Ray acceleration
NASA Astrophysics Data System (ADS)
Diamond, P. H.; Malkov, M. A.
The problem of the cosmic ray origin is discussed in connection with their acceleration in supernova remnant shocks. The diffusive shock acceleration mechanism is reviewed and its potential to accelerate particles to the maximum energy of (presumably) galactic cosmic rays (1018eV ) is considered. It is argued that to reach such energies, a strong magnetic field at scales larger than the particle gyroradius must be created as a result of the acceleration process, itself. One specific mechanism suggested here is based on the generation of Alfven wave at the gyroradius scale with a subsequent transfer to longer scales via interaction with strong acoustic turbulence in the shock precursor. The acoustic turbulence in turn, may be generated by Drury instability or by parametric instability of the Alfven waves. The generation mechanism is modulational instability of CR generated Alfven wave packets induced, in turn, by scattering off acoustic fluctuations in the shock precursor which are generated by Drury instability.
Yerkes, K.L.; Hallinan, K.P.
1995-12-31
The dynamic response of a heated meniscus within a capillary tube subjected to single and multiple cycle transient acceleration induced forces was studied experimentally and analytically. A capillary tube was partially filled with ethyl alcohol and mounted on a centrifuge for visual observation of the dynamic response of the meniscus subject to an acceleration transient. A one-dimensional mathematical model was formulated to predict the dynamic response of the meniscus and compared with experimental results. For the case in which the meniscus was heated, thermocapillary stresses in the near contact line region were accounted for in the model by an effective change in contact angle to account for adverse thermocapillary stresses present at the contact line. Experimental results and analytical calculations were compared for a Bond number of 1.47 and a capillary number of 3.00 {times} 10{sup {minus}6}. Experimental data of the meniscus recession and advance agreed well with a one-dimensional equation of motion accounting for the ``dynamic`` contact angle.
NASA Astrophysics Data System (ADS)
Giboudot, Y.; Wolski, A.
2012-04-01
Transfer maps for magnetic components are fundamental to studies of beam dynamics in accelerators. In the work presented here, transfer maps are computed in Taylor form for a particle moving through any specified magnetostatic field by applying an explicit symplectic integrator in a differential algebra code. The techniques developed are illustrated by their application to study the beam dynamics in the electron model for many applications (EMMA), the first nonscaling fixed-field alternating-gradient accelerator ever built. The EMMA lattice has 4 degrees of freedom (strength and transverse position of each of the two quadrupoles in each periodic cell). Transfer maps may be used to predict efficiently the dynamics in any lattice configuration. The transfer map is represented by a mixed variable generating function, obtained by interpolation between the maps for a set of reference configurations: use of mixed variable generating functions ensures the symplecticity of the map. An optimization routine uses the interpolation technique to look for a lattice defined by four constraints on the time of flight at different beam energies. This provides a way to determine the lattice configuration required to produce the desired dynamical characteristics. These tools are benchmarked against data from the recent EMMA commissioning.
NASA Astrophysics Data System (ADS)
Langbein, J. O.; Evans, J. R.; Blume, F.; Johanson, I. A.
2012-12-01
Global Navigational Satellite Systems (GNSS) are being employed to augment seismic instrumentation to record large, dynamic displacements and accelerations from large earthquakes. To date, however, there have been only a few tests that independently characterize the GNSS at frequencies and displacements that occur during large earthquakes (a number of error sources might influence such GPS result, including loss of lock or bias in signal tracking loops). Many of these tests consist of replaying the observed accelerations for select earthquakes recorded by seismic instruments through a shake-table on which a GNSS antenna is attached. Then the derived displacement from the accelerometer is compared with the displacement estimated from the GNSS system, or the GNSS derived acceleration is compared with the acceleration of the shake table. Neither comparison is optimal since derived quantities are used, and in particular, displacements derived from acceleration data have many sources of error at long periods. Another approach is to test the response of the GNSS receiver using a GNSS-simulator where synthetic GNSS signals are generated that mimic the signals that are actually received. Ebinuma and Kato (Earth Planet Space, 2012) describe a series of controlled tests using this approach with three different GNSS receivers. As a "real world" test, we performed similar experiments using a shake table, in open air with normal views of GNSS satellites, with controlled displacement inputs but, importantly, measured the displacement and acceleration of this table independently. We used a single-axis shake-table having up to 40 cm horizontal displacement and independently measured the position of the stage to better than 0.1 mm (from table servo loop optical reference; accelerations measured by accelerometers attached to moving part of stage). We tested five different GNSS receivers recording both GPS and GLONASS at 50 samples per second (sps), with the exception of the Trimble
Stancari, G.; Carlson, K.; McGee, M. W.; Nobrega, L. E.; Romanov, A. L.; Ruan, J.; Valishev, A.; Noll, D.
2015-06-01
Recent developments in the study of integrable Hamiltonian systems have led to nonlinear accelerator lattice designs with two transverse invariants. These lattices may drastically improve the performance of high-power machines, providing wide tune spreads and Landau damping to protect the beam from instabilities, while preserving dynamic aperture. To test the feasibility of these concepts, the Integrable Optics Test Accelerator (IOTA) is being designed and built at Fermilab. One way to obtain a nonlinear integrable lattice is by using the fields generated by a magnetically confined electron beam (electron lens) overlapping with the circulating beam. The parameters of the required device are similar to the ones of existing electron lenses. We present theory, numerical simulations, and first design studies of electron lenses for nonlinear integrable optics.
Laser Wakefield Acceleration: Structural and Dynamic Studies. Final Technical Report ER40954
Downer, Michael C.
2014-12-19
Particle accelerators enable scientists to study the fundamental structure of the universe, but have become the largest and most expensive of scientific instruments. In this project, we advanced the science and technology of laser-plasma accelerators, which are thousands of times smaller and less expensive than their conventional counterparts. In a laser-plasma accelerator, a powerful laser pulse exerts light pressure on an ionized gas, or plasma, thereby driving an electron density wave, which resembles the wake behind a boat. Electrostatic fields within this plasma wake reach tens of billions of volts per meter, fields far stronger than ordinary non-plasma matter (such as the matter that a conventional accelerator is made of) can withstand. Under the right conditions, stray electrons from the surrounding plasma become trapped within these “wake-fields”, surf them, and acquire energy much faster than is possible in a conventional accelerator. Laser-plasma accelerators thus might herald a new generation of compact, low-cost accelerators for future particle physics, x-ray and medical research. In this project, we made two major advances in the science of laser-plasma accelerators. The first of these was to accelerate electrons beyond 1 gigaelectronvolt (1 GeV) for the first time. In experimental results reported in Nature Communications in 2013, about 1 billion electrons were captured from a tenuous plasma (about 1/100 of atmosphere density) and accelerated to 2 GeV within about one inch, while maintaining less than 5% energy spread, and spreading out less than ½ milliradian (i.e. ½ millimeter per meter of travel). Low energy spread and high beam collimation are important for applications of accelerators as coherent x-ray sources or particle colliders. This advance was made possible by exploiting unique properties of the Texas Petawatt Laser, a powerful laser at the University of Texas at Austin that produces pulses of 150 femtoseconds (1 femtosecond is 10
Beam dynamics study of a 30 MeV electron linear accelerator to drive a neutron source
Kumar, Sandeep; Yang, Haeryong; Kang, Heung-Sik
2014-02-14
An experimental neutron facility based on 32 MeV/18.47 kW electron linac has been studied by means of PARMELA simulation code. Beam dynamics study for a traveling wave constant gradient electron accelerator is carried out to reach the preferential operation parameters (E = 30 MeV, P = 18 kW, dE/E < 12.47% for 99% particles). The whole linac comprises mainly E-gun, pre-buncher, buncher, and 2 accelerating columns. A disk-loaded, on-axis-coupled, 2π/3-mode type accelerating rf cavity is considered for this linac. After numerous optimizations of linac parameters, 32 MeV beam energy is obtained at the end of the linac. As high electron energy is required to produce acceptable neutron flux. The final neutron flux is estimated to be 5 × 10{sup 11} n/cm{sup 2}/s/mA. Future development will be the real design of a 30 MeV electron linac based on S band traveling wave.
NASA Astrophysics Data System (ADS)
Stygar, W. A.; Reisman, D. B.; Stoltzfus, B. S.; Austin, K. N.; Ao, T.; Benage, J. F.; Breden, E. W.; Cooper, R. A.; Cuneo, M. E.; Davis, J.-P.; Ennis, J. B.; Gard, P. D.; Greiser, G. W.; Gruner, F. R.; Haill, T. A.; Hutsel, B. T.; Jones, P. A.; LeChien, K. R.; Leckbee, J. J.; Lewis, S. A.; Lucero, D. J.; McKee, G. R.; Moore, J. K.; Mulville, T. D.; Muron, D. J.; Root, S.; Savage, M. E.; Sceiford, M. E.; Spielman, R. B.; Waisman, E. M.; Wisher, M. L.
2016-07-01
We have developed a conceptual design of a next-generation pulsed-power accelerator that is optimized for megajoule-class dynamic-material-physics experiments. Sufficient electrical energy is delivered by the accelerator to a physics load to achieve—within centimeter-scale samples—material pressures as high as 1 TPa. The accelerator design is based on an architecture that is founded on three concepts: single-stage electrical-pulse compression, impedance matching, and transit-time-isolated drive circuits. The prime power source of the accelerator consists of 600 independent impedance-matched Marx generators. Each Marx comprises eight 5.8-GW bricks connected electrically in series, and generates a 100-ns 46-GW electrical-power pulse. A 450-ns-long water-insulated coaxial-transmission-line impedance transformer transports the power generated by each Marx to a system of twelve 2.5-m-radius water-insulated conical transmission lines. The conical lines are connected electrically in parallel at a 66-cm radius by a water-insulated 45-post sextuple-post-hole convolute. The convolute sums the electrical currents at the outputs of the conical lines, and delivers the combined current to a single solid-dielectric-insulated radial transmission line. The radial line in turn transmits the combined current to the load. Since much of the accelerator is water insulated, we refer to it as Neptune. Neptune is 40 m in diameter, stores 4.8 MJ of electrical energy in its Marx capacitors, and generates 28 TW of peak electrical power. Since the Marxes are transit-time isolated from each other for 900 ns, they can be triggered at different times to construct-over an interval as long as 1 μ s -the specific load-current time history required for a given experiment. Neptune delivers 1 MJ and 20 MA in a 380-ns current pulse to an 18 -m Ω load; hence Neptune is a megajoule-class 20-MA arbitrary waveform generator. Neptune will allow the international scientific community to conduct dynamic
Progress In Plasma Accelerator Development for Dynamic Formation of Plasma Liners
NASA Technical Reports Server (NTRS)
Thio, Y. C. Francis; Eskridge, Richard; Martin, Adam; Smith, James; Lee, Michael; Cassibry, Jason T.; Griffin, Steven; Rodgers, Stephen L. (Technical Monitor)
2002-01-01
An experimental plasma accelerator for magnetic target fusion (MTF) applications under development at the NASA Marshall Space Flight Center is described. The accelerator is a coaxial pulsed plasma thruster (Figure 1). It has been tested experimentally and plasma jet velocities of approx.50 km/sec have been obtained. The plasma jet has been photographed with 10-ns exposure times to reveal a stable and repeatable plasma structure (Figure 2). Data for velocity profile information has been obtained using light pipes and magnetic probes embedded in the gun walls to record the plasma and current transit respectively at various barrel locations. Preliminary spatially resolved spectral data and magnetic field probe data are also presented. A high speed triggering system has been developed and tested as a means of reducing the gun "jitter". This jitter is being characterized and future work for second generation "ultra-low jitter" gun development is being identified.
Guo, Fan; Liu, Yi -Hsin; Daughton, William; Li, Hui
2015-06-17
Magnetic reconnection is thought to be the driver for many explosive phenomena in the universe. The energy release and particle acceleration during reconnection have been proposed as a mechanism for producing high-energy emissions and cosmic rays. We carry out two- and three-dimensional (3D) kinetic simulations to investigate relativistic magnetic reconnection and the associated particle acceleration. The simulations focus on electron–positron plasmas starting with a magnetically dominated, force-free current sheet (σ ≡ B2 / (4πnemec2) >> 1). For this limit, we demonstrate that relativistic reconnection is highly efficient at accelerating particles through a first-order Fermi process accomplished by the curvature driftmore » of particles along the electric field induced by the relativistic flows. This mechanism gives rise to the formation of hard power-law spectra f α (γ - 1)-p and approaches p = 1 for sufficiently large σ and system size. Eventually most of the available magnetic free energy is converted into nonthermal particle kinetic energy. An analytic model is presented to explain the key results and predict a general condition for the formation of power-law distributions. The development of reconnection in these regimes leads to relativistic inflow and outflow speeds and enhanced reconnection rates relative to nonrelativistic regimes. In the 3D simulation, the interplay between secondary kink and tearing instabilities leads to strong magnetic turbulence, but does not significantly change the energy conversion, reconnection rate, or particle acceleration. This paper suggests that relativistic reconnection sites are strong sources of nonthermal particles, which may have important implications for a variety of high-energy astrophysical problems.« less
Guo, Fan; Liu, Yi -Hsin; Daughton, William; Li, Hui
2015-06-17
Magnetic reconnection is thought to be the driver for many explosive phenomena in the universe. The energy release and particle acceleration during reconnection have been proposed as a mechanism for producing high-energy emissions and cosmic rays. We carry out two- and three-dimensional (3D) kinetic simulations to investigate relativistic magnetic reconnection and the associated particle acceleration. The simulations focus on electron–positron plasmas starting with a magnetically dominated, force-free current sheet (σ ≡ B^{2} / (4πn_{e}m_{e}c^{2}) >> 1). For this limit, we demonstrate that relativistic reconnection is highly efficient at accelerating particles through a first-order Fermi process accomplished by the curvature drift of particles along the electric field induced by the relativistic flows. This mechanism gives rise to the formation of hard power-law spectra f α (γ - 1)^{-p} and approaches p = 1 for sufficiently large σ and system size. Eventually most of the available magnetic free energy is converted into nonthermal particle kinetic energy. An analytic model is presented to explain the key results and predict a general condition for the formation of power-law distributions. The development of reconnection in these regimes leads to relativistic inflow and outflow speeds and enhanced reconnection rates relative to nonrelativistic regimes. In the 3D simulation, the interplay between secondary kink and tearing instabilities leads to strong magnetic turbulence, but does not significantly change the energy conversion, reconnection rate, or particle acceleration. This paper suggests that relativistic reconnection sites are strong sources of nonthermal particles, which may have important implications for a variety of high-energy astrophysical problems.
NASA Astrophysics Data System (ADS)
Guo, Fan; Liu, Yi-Hsin; Daughton, William; Li, Hui
2015-06-01
Magnetic reconnection is thought to be the driver for many explosive phenomena in the universe. The energy release and particle acceleration during reconnection have been proposed as a mechanism for producing high-energy emissions and cosmic rays. We carry out two- and three-dimensional (3D) kinetic simulations to investigate relativistic magnetic reconnection and the associated particle acceleration. The simulations focus on electron-positron plasmas starting with a magnetically dominated, force-free current sheet (σ \\equiv {B}2/(4π {n}e{m}e{c}2)\\gg 1). For this limit, we demonstrate that relativistic reconnection is highly efficient at accelerating particles through a first-order Fermi process accomplished by the curvature drift of particles along the electric field induced by the relativistic flows. This mechanism gives rise to the formation of hard power-law spectra f\\propto {(γ -1)}-p and approaches p = 1 for sufficiently large σ and system size. Eventually most of the available magnetic free energy is converted into nonthermal particle kinetic energy. An analytic model is presented to explain the key results and predict a general condition for the formation of power-law distributions. The development of reconnection in these regimes leads to relativistic inflow and outflow speeds and enhanced reconnection rates relative to nonrelativistic regimes. In the 3D simulation, the interplay between secondary kink and tearing instabilities leads to strong magnetic turbulence, but does not significantly change the energy conversion, reconnection rate, or particle acceleration. This study suggests that relativistic reconnection sites are strong sources of nonthermal particles, which may have important implications for a variety of high-energy astrophysical problems.
NASA Astrophysics Data System (ADS)
Kueny, C. S.; Wang, L.-F.; Chen, Y.-J.; Hewett, D. W.
1999-11-01
The 2-D axisymmetric PIC code GYMNOS has been used to model electron beam dynamics in the ETA-II accelerator at LLNL. Experiments on ETA-II seek to produce a high-brightness, low-emittance electron beam and deliver it to an X-ray converter target. These experiments are relevant to the DARHT II (Dual Axis Radiography Hydrodynamic Test) and AHF (Advanced Hydrotest Facility) projects, which will provide X-ray radiography diagnostics as part of the US Science-Based Stockpile Stewardship Program. We present simulations of both the ETA-II injector which produces the initial beam, and of the target region where X-ray generation occurs. GYMNOS employs the Embedded Curved Boundary (ECB) model to provide accurate beam modeling near the injector cathode and the target surfaces, and was recently upgraded with a non-uniform mesh to efficiently model the beam over a range of spatial scales. Modeling of the ETA-II injector has provided guidance on experimental parameters necessary for producing a high-quality beam for transport through the accelerator. Simulations of the target region have modeled the effects of backstreaming ions and backscattered electrons on beam dynamics, and investigated possible measures to minimize degradation in beam quality and final spot size.
Ceotto, Michele; Zhuang, Yu; Hase, William L
2013-02-01
This paper shows how a compact finite difference Hessian approximation scheme can be proficiently implemented into semiclassical initial value representation molecular dynamics. Effects of the approximation on the monodromy matrix calculation are tested by propagating initial sampling distributions to determine power spectra for analytic potential energy surfaces and for "on the fly" carbon dioxide direct dynamics. With the approximation scheme the computational cost is significantly reduced, making ab initio direct semiclassical dynamics computationally more feasible and, at the same time, properly reproducing important quantum effects inherent in the monodromy matrix and the pre-exponential factor of the semiclassical propagator. PMID:23406107
Dynamics of ponderomotive ion acceleration in a laser-plasma channel
Kovalev, V. F.; Bychenkov, V. Yu.
2015-04-15
Analytical solution to the Cauchy problem for the kinetic equation describing the radial acceleration of ions under the action of the ponderomotive force of a laser beam undergoing guided propagation in transparent plasma is constructed. Spatial and temporal dependences of the ion distribution function and the integral ion characteristics, such as the density, average velocity, and energy spectrum, are obtained for an axisymmetric laser-plasma channel. The formation of a density peak near the channel boundary and the effect of ion flow breaking for a quasi-stationary laser beam are described analytically.
Phase-space dynamics of ionization injection in plasma-based accelerators.
Xu, X L; Hua, J F; Li, F; Zhang, C J; Yan, L X; Du, Y C; Huang, W H; Chen, H B; Tang, C X; Lu, W; Yu, P; An, W; Joshi, C; Mori, W B
2014-01-24
The evolution of beam phase space in ionization injection into plasma wakefields is studied using theory and particle-in-cell simulations. The injection process involves both longitudinal and transverse phase mixing, leading initially to a rapid emittance growth followed by oscillation, decay, and a slow growth to saturation. An analytic theory for this evolution is presented and verified through particle-in-cell simulations. This theory includes the effects of injection distance (time), acceleration distance, wakefield structure, and nonlinear space charge forces, and it also shows how ultralow emittance beams can be produced using ionization injection methods. PMID:24484147
Dynamics of Electric Fields Driving the Laser Acceleration of Multi-MeV Protons
Romagnani, L.; Borghesi, M.; Kar, S.; Fuchs, J.; Antici, P.; Audebert, P.; Ceccherini, F.; Macchi, A.; Cowan, T.; Grismayer, T.; Mora, P.; Pretzler, G.; Toncian, T.; Willi, O.; Schiavi, A.
2005-11-04
The acceleration of multi-MeV protons from the rear surface of thin solid foils irradiated by an intense ({approx}10{sup 18} W/cm{sup 2}) and short ({approx}1.5 ps) laser pulse has been investigated using transverse proton probing. The structure of the electric field driving the expansion of the proton beam has been resolved with high spatial and temporal resolution. The main features of the experimental observations, namely, an initial intense sheath field and a late time field peaking at the beam front, are consistent with the results from particle-in-cell and fluid simulations of thin plasma expansion into a vacuum.
Sävert, A; Mangles, S P D; Schnell, M; Siminos, E; Cole, J M; Leier, M; Reuter, M; Schwab, M B; Möller, M; Poder, K; Jäckel, O; Paulus, G G; Spielmann, C; Skupin, S; Najmudin, Z; Kaluza, M C
2015-07-31
We present few-femtosecond shadowgraphic snapshots taken during the nonlinear evolution of the plasma wave in a laser wakefield accelerator with transverse synchronized few-cycle probe pulses. These snapshots can be directly associated with the electron density distribution within the plasma wave and give quantitative information about its size and shape. Our results show that self-injection of electrons into the first plasma-wave period is induced by a lengthening of the first plasma period. Three-dimensional particle-in-cell simulations support our observations. PMID:26274425
Ganesan, Narayan; Bauer, Brad A; Lucas, Timothy R; Patel, Sandeep; Taufer, Michela
2011-11-15
We present results of molecular dynamics simulations of fully hydrated DMPC bilayers performed on graphics processing units (GPUs) using current state-of-the-art non-polarizable force fields and a local GPU-enabled molecular dynamics code named FEN ZI. We treat the conditionally convergent electrostatic interaction energy exactly using the particle mesh Ewald method (PME) for solution of Poisson's Equation for the electrostatic potential under periodic boundary conditions. We discuss elements of our implementation of the PME algorithm on GPUs as well as pertinent performance issues. We proceed to show results of simulations of extended lipid bilayer systems using our program, FEN ZI. We performed simulations of DMPC bilayer systems consisting of 17,004, 68,484, and 273,936 atoms in explicit solvent. We present bilayer structural properties (atomic number densities, electron density profiles), deuterium order parameters (S(CD)), electrostatic properties (dipole potential, water dipole moments), and orientational properties of water. Predicted properties demonstrate excellent agreement with experiment and previous all-atom molecular dynamics simulations. We observe no statistically significant differences in calculated structural or electrostatic properties for different system sizes, suggesting the small bilayer simulations (less than 100 lipid molecules) provide equivalent representation of structural and electrostatic properties associated with significantly larger systems (over 1000 lipid molecules). We stress that the three system size representations will have differences in other properties such as surface capillary wave dynamics or surface tension related effects that are not probed in the current study. The latter properties are inherently dependent on system size. This contribution suggests the suitability of applying emerging GPU technologies to studies of an important class of biological environments, that of lipid bilayers and their associated integral
NASA Astrophysics Data System (ADS)
Heesemann, M.; Davis, E. E.
2015-12-01
We describe a new tool developed to facilitate the study of inter-related geodetic, geodynamic, seismic, and oceanographic phenomena. It incorporates a novel tri-axial accelerometer developed by Quartz Seismic Sensors, Inc, a pressure sensor developed by Paroscientific Inc., and a low-power, high-precision frequency counter and data logger built by RBR, Ltd. The sensors, counters, and loggers are housed in a 7 cm o.d., 70 cm long pressure case designed for use in up to 12 km of water. Sampling intervals are programmable from 0.1 s to 1 hr; standard memory can store up to 30 million samples; total power consumption is roughly 115 mW when operating continuously (1 s.p.s. or higher) and proportionately lower when operating intermittently (e.g., 2 mW at 1 sample per min.). Serial and USB communications protocols allow a variety of download and cable-connection options. Measurement precision of the order of 10-8 of full scale (e.g., 4000 m water depth, 1 g) allows observations of pressure and acceleration variations of 0.4 Pa and 0.1 μm s-2. Long-term variations in vertical acceleration are sensitive to displacement through the gravity gradient at a level of roughly 2 cm; long-term variations in horizontal acceleration are sensitive to tilt at a level of 0.01 μRad. With these sensitivities and the broad bandwidth (5 Hz to DC), ground motion associated with microseisms and seismic waves, tidal loading, and slow and rapid geodynamic deformation normally studied by disparate instruments can be observed with a single tool. The first c. 1-year deployment with the instrument connected to the Ocean Networks Canada NEPTUNE observatory cable is underway to study interseismic deformation of the Cascadia subduction zone. It will then be deployed at the Hikurangi subduction zone to study episodic slow slip. Deployment of the tool for the initial test was accomplished by pushing the tool vertically below the seafloor with the remotely operated vehicle Jason, with no profile
Acceleration of the KINETICS Integrated Dynamical/Chemical Computational Model Using MPI
NASA Technical Reports Server (NTRS)
Grossman, Max; Willacy, Karen; Allen, Mark
2011-01-01
Understanding the evolution of a planet's atmosphere not only provides a better theoretical understanding of planetary physics and the formation of planets, but also grants useful insight into Earth's own atmosphere. One of the tools used at JPL for the modeling of planetary atmospheres and protostellar disks is KINETICS. KINETICS can simulate years of complex dynamics and chemistry.
Cetinbaş, Murat; Shakhnovich, Eugene I
2013-01-01
Although molecular chaperones are essential components of protein homeostatic machinery, their mechanism of action and impact on adaptation and evolutionary dynamics remain controversial. Here we developed a physics-based ab initio multi-scale model of a living cell for population dynamics simulations to elucidate the effect of chaperones on adaptive evolution. The 6-loci genomes of model cells encode model proteins, whose folding and interactions in cellular milieu can be evaluated exactly from their genome sequences. A genotype-phenotype relationship that is based on a simple yet non-trivially postulated protein-protein interaction (PPI) network determines the cell division rate. Model proteins can exist in native and molten globule states and participate in functional and all possible promiscuous non-functional PPIs. We find that an active chaperone mechanism, whereby chaperones directly catalyze protein folding, has a significant impact on the cellular fitness and the rate of evolutionary dynamics, while passive chaperones, which just maintain misfolded proteins in soluble complexes have a negligible effect on the fitness. We find that by partially releasing the constraint on protein stability, active chaperones promote a deeper exploration of sequence space to strengthen functional PPIs, and diminish the non-functional PPIs. A key experimentally testable prediction emerging from our analysis is that down-regulation of chaperones that catalyze protein folding significantly slows down the adaptation dynamics. PMID:24244114
GPU accelerated Monte Carlo simulation of Brownian motors dynamics with CUDA
NASA Astrophysics Data System (ADS)
Spiechowicz, J.; Kostur, M.; Machura, L.
2015-06-01
This work presents an updated and extended guide on methods of a proper acceleration of the Monte Carlo integration of stochastic differential equations with the commonly available NVIDIA Graphics Processing Units using the CUDA programming environment. We outline the general aspects of the scientific computing on graphics cards and demonstrate them with two models of a well known phenomenon of the noise induced transport of Brownian motors in periodic structures. As a source of fluctuations in the considered systems we selected the three most commonly occurring noises: the Gaussian white noise, the white Poissonian noise and the dichotomous process also known as a random telegraph signal. The detailed discussion on various aspects of the applied numerical schemes is also presented. The measured speedup can be of the astonishing order of about 3000 when compared to a typical CPU. This number significantly expands the range of problems solvable by use of stochastic simulations, allowing even an interactive research in some cases.
Morozov, A. A.; Evtushenko, A. B.; Bulgakov, A. V.
2015-02-02
The expansion of a plume produced by low-fluence laser ablation of graphite in vacuum is investigated experimentally and by direct Monte Carlo simulations in an attempt to explain hyperthermal particle energies for thermally vaporized materials. We demonstrate that the translation energy of neutral particles, ∼2 times higher than classical expectations, is due to two effects, hydrodynamic plume acceleration into the forward direction and kinetic selection of fast particles in the on-axis region. Both effects depend on the collision number within the plume and on the particles internal degrees of freedom. The simulations allow ablation properties to be evaluated, such as ablation rate and surface temperature, based on time-of-flight measurements. Available experimental data on kinetic energies of various laser-produced particles are well described by the presented model.
NASA Astrophysics Data System (ADS)
Morozov, A. A.; Evtushenko, A. B.; Bulgakov, A. V.
2015-02-01
The expansion of a plume produced by low-fluence laser ablation of graphite in vacuum is investigated experimentally and by direct Monte Carlo simulations in an attempt to explain hyperthermal particle energies for thermally vaporized materials. We demonstrate that the translation energy of neutral particles, ˜2 times higher than classical expectations, is due to two effects, hydrodynamic plume acceleration into the forward direction and kinetic selection of fast particles in the on-axis region. Both effects depend on the collision number within the plume and on the particles internal degrees of freedom. The simulations allow ablation properties to be evaluated, such as ablation rate and surface temperature, based on time-of-flight measurements. Available experimental data on kinetic energies of various laser-produced particles are well described by the presented model.
Forest stand growth dynamics in Central Europe have accelerated since 1870
Pretzsch, Hans; Biber, Peter; Schütze, Gerhard; Uhl, Enno; Rötzer, Thomas
2014-01-01
Forest ecosystems have been exposed to climate change for more than 100 years, whereas the consequences on forest growth remain elusive. Based on the oldest existing experimental forest plots in Central Europe, we show that, currently, the dominant tree species Norway spruce and European beech exhibit significantly faster tree growth (+32 to 77%), stand volume growth (+10 to 30%) and standing stock accumulation (+6 to 7%) than in 1960. Stands still follow similar general allometric rules, but proceed more rapidly through usual trajectories. As forest stands develop faster, tree numbers are currently 17–20% lower than in past same-aged stands. Self-thinning lines remain constant, while growth rates increase indicating the stock of resources have not changed, while growth velocity and turnover have altered. Statistical analyses of the experimental plots, and application of an ecophysiological model, suggest that mainly the rise in temperature and extended growing seasons contribute to increased growth acceleration, particularly on fertile sites. PMID:25216297
Li, H.; Yu, S.S.; Sessler, A.M.
1994-10-01
In this paper the authors present a design study on the longitudinal dynamics of a relativistic klystron two-beam accelerator (RK-TBA) scheme which has been proposed as a power source candidate for a 1 TeV next linear collider (NLC). They address the issue of maintaining stable power output at desired level for a 300-m long TBA with 150 extraction cavities and present their simulation results to demonstrate that it can be achieved by inductively detuning the extraction cavities to counter the space charge debunching effect on the drive beam. They then carry out simulation study to show that the beam bunches desired by the RK-TBA can be efficiently obtained by first chopping an initially uniform beam of low energy into a train of beam bunches with modest longitudinal dimension and then using the {open_quotes}adiabatic capture{close_quotes} scheme to bunch and accelerate these beam bunches into tight bunches at the operating energy of the drive beam. The authors have also examined the {open_quotes}after burner{close_quotes} scheme which is implemented in their RK-TBA design for efficiency enhancement.
NASA Astrophysics Data System (ADS)
Yan, Dahai; He, Jianjian; Liao, Jinyuan; Zhang, Li; Zhang, Shuang-Nan
2016-02-01
We study the dynamic changes of electron energy distribution (EED) through systematically analysing the quasi-simultaneous spectral energy distributions (SEDs) of the flat spectrum radio quasar 3C 279 in different states. With Markov chain Monte Carlo technique we model fourteen SEDs of 3C 279 using a leptonic model with a three-parameter log-parabola EED. The 14 SEDs can be satisfactorily fitted with the one-zone leptonic model. The observed γ rays in 13 states are attributed to Compton scattering of external infrared photons from a surrounding dusty torus. The curved γ ray spectrum observed during 2014 2-8 April is well explained by the external Compton of dust radiation. It is found that there is a clear positive correlation between the curvature parameter b of the EED and the electron peak energy γ ^' }_pk. No significant correlation between b and the synchrotron peak frequency νs is found, due to the varied product of Doppler factor and fluid magnetic field from state to state. We interpret the correlation of b-γ ^' }_pk in a stochastic acceleration scenario. This positive correlation is in agreement with the prediction in the stage when the balance between acceleration and radiative cooling of the electrons is nearly established in the case of the turbulence spectral index q = 2.
Dell, G.F.
1983-01-01
The PATRICIA particle tracking program has been used to study chromatic effects in the Brookhaven CBA (Colliding Beam Accelerator). The short term behavior of particles in the CBA has been followed for particle histories of 300 turns. Contributions from magnet multipoles characteristic of superconducting magnets and closed orbit errors have been included in determining the dynamic aperture of the CBA for on and off momentum particles. The width of the third integer stopband produced by the temperature dependence of magnetization induced sextupoles in the CBA cable dipoles is evaluated for helium distribution systems having periodicity of one and six. The stopband width at a tune of 68/3 is naturally zero for the system having a periodicity of six and is approx. 10/sup -4/ for the system having a periodicity of one. Results from theory are compared with results obtained with PATRICIA; the results agree within a factor of slightly more than two.
Ravi Samtaney
2009-02-10
We present a numerical method to solve the linear stability of impulsively accelerated density interfaces in two dimensions such as those arising in the Richtmyer-Meshkov instability. The method uses an Eulerian approach, and is based on an unwind method to compute the temporally evolving base state and a flux vector splitting method for the perturbations. The method is applicable to either gas dynamics or magnetohydrodynamics. Numerical examples are presented for cases in which a hydrodynamic shock interacts with a single or double density interface, and a doubly shocked single density interface. Convergence tests show that the method is spatially second order accurate for smooth flows, and between first and second order accurate for flows with shocks.
Cahalan, J. E.; Ama, T.; Palmiotti, G.; Taiwo, T. A.; Yang, W. S.
2000-03-09
The VARIANT-K and DIF3D-K nodal spatial kinetics computer codes have been coupled to the SAS4A and SASSYS-1 liquid metal reactor accident and systems analysis codes. SAS4A and SASSYS-1 have been extended with the addition of heavy liquid metal (Pb and Pb-Bi) thermophysical properties, heat transfer correlations, and fluid dynamics correlations. The coupling methodology and heavy liquid metal modeling additions are described. The new computer code suite has been applied to analysis of neutron source and thermal-hydraulics transients in a model of an accelerator-driven minor actinide burner design proposed in an OECD/NEA/NSC benchmark specification. Modeling assumptions and input data generation procedures are described. Results of transient analyses are reported, with emphasis on comparison of P1 and P3 variational nodal transport theory results with nodal diffusion theory results, and on significance of spatial kinetics effects.
Raval, Alpan; Piana, Stefano; Eastwood, Michael P; Shaw, David E
2016-01-01
Molecular dynamics (MD) simulation is a well-established tool for the computational study of protein structure and dynamics, but its application to the important problem of protein structure prediction remains challenging, in part because extremely long timescales can be required to reach the native structure. Here, we examine the extent to which the use of low-resolution information in the form of residue-residue contacts, which can often be inferred from bioinformatics or experimental studies, can accelerate the determination of protein structure in simulation. We incorporated sets of 62, 31, or 15 contact-based restraints in MD simulations of ubiquitin, a benchmark system known to fold to the native state on the millisecond timescale in unrestrained simulations. One-third of the restrained simulations folded to the native state within a few tens of microseconds-a speedup of over an order of magnitude compared with unrestrained simulations and a demonstration of the potential for limited amounts of structural information to accelerate structure determination. Almost all of the remaining ubiquitin simulations reached near-native conformations within a few tens of microseconds, but remained trapped there, apparently due to the restraints. We discuss potential methodological improvements that would facilitate escape from these near-native traps and allow more simulations to quickly reach the native state. Finally, using a target from the Critical Assessment of protein Structure Prediction (CASP) experiment, we show that distance restraints can improve simulation accuracy: In our simulations, restraints stabilized the native state of the protein, enabling a reasonable structural model to be inferred. PMID:26266489
Varatharaj, C; Ravikumar, M; Sathiyan, S; Supe, S S
2011-01-01
Peripheral dose (PD) or the dose outside the geometrical boundaries of the radiation field is of clinical importance when anatomical structures with low dose tolerances might be involved(1). It is the aim of this study is to estimate the PD on linear accelerators on different wedge systems without multileaf collimator (MLC). Measurements were performed on a dual energy linear accelerator equipped with tertiary MLC and enhanced dynamic wedge (EDW). Measurements were made using an ionization chamber embedded in a Radiation Field Analyser (RFA-300) with the secondary collimator and MLC setting of 5x5, 10x10, 15x15, and 20x20 cm2, and with the MLC fully retracted. The effects of SSD on PD were measured at three SSDs of 90, 100, and 110 cm for the irradiation fields of 5x5, 10x10, 15x15, and 20x20 cm2 and the effects of the three different wedges (Upper wedge, Lower Wedge and Enhanced Dynamic Wedge) on PD were measured for 45° wedges with field size of 15x15 cm2. Data were taken from 3 cm to 24 cm away from the field edge. Results show that due to tertiary MLC, PD can be reduced by means of a factor of two to three at certain distance from the edge of the field compared with TG-36 data. In between the wedges, the PD was less for the EDW when compared with the upper and lower physical wedges. We conclude that the reduction in PD is significant in reducing or eliminating the need for external peripheral shielding to reduce the dose on affected critical organs. PMID:21177206
Implosion dynamics of wire-array z-pinches on the COBRA accelerator
NASA Astrophysics Data System (ADS)
McBride, R. D.; Bell, K. S.; Blesener, I. C.; Chalenski, D. A.; Douglass, J. D.; Greenly, J. B.; Knapp, P. F.; Pikuz, S. A.; Shelkovenko, T. A.; Blanchard, T.; Wilhelm, H.; Hammer, D. A.; Kusse, B. R.
2007-11-01
Experimental results characterizing wire-array z-pinch implosion dynamics on the 1-MA, 100-ns rise time COBRA pulsed power generator are presented. Diagnostics fielded include an optical streak camera, a time-gated XUV framing camera, a laser shadowgraph system, filtered time-integrated pinhole cameras, a focusing x-ray spectrometer with spatial resolution (FSSR), a load voltage monitor, a faraday cup, a bolometer, silicon diodes and diamond photoconducting detectors (PCDs). The load geometries investigated in this set of experiments include cylindrical arrays ranging from 6 to 16 mm in diameter, and consisting of 8, 16, or 32 wires of either aluminum (Al) or tungsten (W). The data produced by the entire suite of diagnostics are analyzed and presented to provide an overall picture of implosion dynamics and timing on COBRA. In particular, data fitting to various implosion trajectory models, as well as x-ray pulse shape dependencies on various loads and implosion characteristics are presented and discussed.
Dynamic real-time 4D cardiac MDCT image display using GPU-accelerated volume rendering.
Zhang, Qi; Eagleson, Roy; Peters, Terry M
2009-09-01
Intraoperative cardiac monitoring, accurate preoperative diagnosis, and surgical planning are important components of minimally-invasive cardiac therapy. Retrospective, electrocardiographically (ECG) gated, multidetector computed tomographical (MDCT), four-dimensional (3D + time), real-time, cardiac image visualization is an important tool for the surgeon in such procedure, particularly if the dynamic volumetric image can be registered to, and fused with the actual patient anatomy. The addition of stereoscopic imaging provides a more intuitive environment by adding binocular vision and depth cues to structures within the beating heart. In this paper, we describe the design and implementation of a comprehensive stereoscopic 4D cardiac image visualization and manipulation platform, based on the opacity density radiation model, which exploits the power of modern graphics processing units (GPUs) in the rendering pipeline. In addition, we present a new algorithm to synchronize the phases of the dynamic heart to clinical ECG signals, and to calculate and compensate for latencies in the visualization pipeline. A dynamic multiresolution display is implemented to enable the interactive selection and emphasis of volume of interest (VOI) within the entire contextual cardiac volume and to enhance performance, and a novel color and opacity adjustment algorithm is designed to increase the uniformity of the rendered multiresolution image of heart. Our system provides a visualization environment superior to noninteractive software-based implementations, but with a rendering speed that is comparable to traditional, but inferior quality, volume rendering approaches based on texture mapping. This retrospective ECG-gated dynamic cardiac display system can provide real-time feedback regarding the suspected pathology, function, and structural defects, as well as anatomical information such as chamber volume and morphology. PMID:19467840
Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
Kürten, Charlotte; Syrén, Per-Olof
2016-01-01
Enzyme catalysis evolved in an aqueous environment. The influence of solvent dynamics on catalysis is, however, currently poorly understood and usually neglected. The study of water dynamics in enzymes and the associated thermodynamical consequences is highly complex and has involved computer simulations, nuclear magnetic resonance (NMR) experiments, and calorimetry. Water tunnels that connect the active site with the surrounding solvent are key to solvent displacement and dynamics. The protocol herein allows for the engineering of these motifs for water transport, which affects specificity, activity and thermodynamics. By providing a biophysical framework founded on theory and experiments, the method presented herein can be used by researchers without previous expertise in computer modeling or biophysical chemistry. The method will advance our understanding of enzyme catalysis on the molecular level by measuring the enthalpic and entropic changes associated with catalysis by enzyme variants with obstructed water tunnels. The protocol can be used for the study of membrane-bound enzymes and other complex systems. This will enhance our understanding of the importance of solvent reorganization in catalysis as well as provide new catalytic strategies in protein design and engineering. PMID:26862836
Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes.
Kürten, Charlotte; Syrén, Per-Olof
2016-01-01
Enzyme catalysis evolved in an aqueous environment. The influence of solvent dynamics on catalysis is, however, currently poorly understood and usually neglected. The study of water dynamics in enzymes and the associated thermodynamical consequences is highly complex and has involved computer simulations, nuclear magnetic resonance (NMR) experiments, and calorimetry. Water tunnels that connect the active site with the surrounding solvent are key to solvent displacement and dynamics. The protocol herein allows for the engineering of these motifs for water transport, which affects specificity, activity and thermodynamics. By providing a biophysical framework founded on theory and experiments, the method presented herein can be used by researchers without previous expertise in computer modeling or biophysical chemistry. The method will advance our understanding of enzyme catalysis on the molecular level by measuring the enthalpic and entropic changes associated with catalysis by enzyme variants with obstructed water tunnels. The protocol can be used for the study of membrane-bound enzymes and other complex systems. This will enhance our understanding of the importance of solvent reorganization in catalysis as well as provide new catalytic strategies in protein design and engineering. PMID:26862836
Accelerating Molecular Dynamics Simulations to Investigate Shock Response at the Mesoscales
NASA Astrophysics Data System (ADS)
Dongare, Avinash; Agarwal, Garvit; Valisetty, Ramakrishna; Namburu, Raju; Rajendran, Arunachalam
The capability of large-scale molecular dynamics (MD) simulations to model dynamic response of materials is limited to system sizes at the nanoscales and the nanosecond timescales. A new method called quasi-coarse-grained dynamics (QCGD) is developed to expand the capabilities of MD simulations to the mesoscales. The QCGD method is based on solving the equations of motion for a chosen set of representative atoms from an atomistic microstructure and retaining the energetics of these atoms as would be predicted in MD simulations. The QCGD method allows the modeling of larger size systems and larger time-steps for simulations and thus is able to extend the capabilities of MD simulations to model materials behavior at mesoscales. The success of the QCGD method is demonstrated by reproducing the shock propagation and failure behavior of single crystal and nanocrystalline Al microstructures as predicted using MD simulations and also modeling the shock response and failure behavior of Al microstructures at the micron length scales. The scaling relationships, the hugoniot behavior, and the predicted spall strengths using the MD and the QCGD simulations will be presented. This work is sponsored by the US Army Research Office under Contract# W911NF-14-1-0257.
NASA Astrophysics Data System (ADS)
Grzemba, B.; Popov, V. L.; Starcevic, J.; Popov, M.
2012-04-01
Shallow earthquakes can be considered as a result of tribological instabilities, so called stick-slip behaviour [1,2], meaning that sudden slip occurs at already existing rupture zones. From a contact mechanics point of view it is clear, that no motion can arise completely sudden, the material will always creep in an existing contact in the load direction before breaking loose. If there is a measureable creep before the instability, this could serve as a precursor. To examine this theory in detail, we built up an elementary laboratory model with pronounced stick-slip behaviour. Different material pairings, such as steel-steel, steel-glass and marble-granite, were analysed at different driving force rates. The displacement was measured with a resolution of 8 nm. We were able to show that a measureable accelerated creep precedes the instability. Near the instability, this creep is sufficiently regular to serve as a basis for a highly accurate prediction of the onset of macroscopic slip [3]. In our model a prediction is possible within the last few percents of the preceding stick time. We are hopeful to extend this period. Furthermore, we showed that the slow creep as well as the fast slip can be described very well by the Dieterich-Ruina-friction law, if we include the contribution of local contact rigidity. The simulation meets the experimental curves over five orders of magnitude. This friction law was originally formulated for rocks [4,5] and takes into account the dependency of the coefficient of friction on the sliding velocity and on the contact history. The simulations using the Dieterich-Ruina-friction law back up the observation of a universal behaviour of the creep's acceleration. We are working on several extensions of our model to more dimensions in order to move closer towards representing a full three-dimensional continuum. The first step will be an extension to two degrees of freedom to analyse the interdependencies of the instabilities. We also plan
Reed, B W; LaGrange, T; Shuttlesworth, R M; Gibson, D J; Campbell, G H; Browning, N D
2009-12-29
We describe a modification to a transmission electron microscope (TEM) that allows it to briefly (using a pulsed-laser-driven photocathode) operate at currents in excess of 10 mA while keeping the effects of condenser lens aberrations to a minimum. This modification allows real-space imaging of material microstructure with a resolution of order 10 nm over regions several {micro}m across with an exposure time of 15 ns. This is more than 6 orders of magnitude faster than typical video-rate TEM imaging. The key is the addition of a weak magnetic lens to couple the large-diameter high-current beam exiting the accelerator into the acceptance aperture of a conventional TEM condenser lens system. We show that the performance of the system is essentially consistent with models derived from ray tracing and finite element simulations. The instrument can also be operated as a conventional TEM by using the electron gun in a thermionic mode. The modification enables very high electron current densities in {micro}m-sized areas and could also be used in a non-pulsed system for high-throughput imaging and analytical TEM.
Reed, B W; LaGrange, T; Shuttlesworth, R M; Gibson, D J; Campbell, G H; Browning, N D
2010-05-01
We describe a modification to a transmission electron microscope (TEM) that allows it to briefly (using a pulsed-laser-driven photocathode) operate at currents in excess of 10 mA while keeping the effects of condenser lens aberrations to a minimum. This modification allows real-space imaging of material microstructure with a resolution of order 10 nm over regions several microm across with an exposure time of 15 ns. This is more than six orders of magnitude faster than typical video-rate TEM imaging. The key is the addition of a weak magnetic lens to couple the large-diameter high-current beam exiting the accelerator into the acceptance aperture of a conventional TEM condenser lens system. We show that the performance of the system is essentially consistent with models derived from ray tracing and finite element simulations. The instrument can also be operated as a conventional TEM by using the electron gun in a thermionic mode. The modification enables very high electron current densities in microm-sized areas and could also be used in a nonpulsed system for high-throughput imaging and analytical TEM. PMID:20515144
NASA Astrophysics Data System (ADS)
Gourgouliatos, Konstantinos N.; Lyutikov, Maxim
2012-02-01
We study the expansion of low-density cavities produced by active galactic nucleus jets in clusters of galaxies. The long-term stability of these cavities requires the presence of linked magnetic fields. We find solutions describing the self-similar expansion of structures containing large-scale electromagnetic fields. Unlike the force-free spheromak-like configurations, these solutions have no surface currents and, thus, are less susceptible to resistive decay. The cavities are internally confined by external pressure, with zero gradient at the surface. If the adiabatic index of the plasma within the cavity is Γ > 4/3, the expansion ultimately leads to the formation of large-scale current sheets. The resulting dissipation of the magnetic field can only partially offset the adiabatic and radiative losses of radio-emitting electrons. We demonstrate that if the formation of large-scale current sheets is accompanied by explosive reconnection of the magnetic field, the resulting reconnection layer can accelerate cosmic rays to ultrahigh energies. We speculate that the enhanced flux of ultrahigh energy cosmic rays towards Centaurus A originates at the cavities due to magnetic reconnection.
Dynamical Effects Due to Fringe Field of the Magnets in Circular Accelerators
Cai, Y.; Nosochkov, Yu.; /SLAC
2005-05-16
The leading Lie generators, including the chromatic effects, due to hard-edge fringe field of single multipole and solenoid are derived from the vector potentials within a Hamiltonian system. These nonlinear generators are applied to the interaction region of PEP-II to analyze the linear errors due to the feed-down from the off-centered quadrupoles and solenoid. The nonlinear effects of tune shifts at large amplitude, the synchro-betatron sidebands near half integer and their impacts on the dynamic aperture are studied in the paper.
Interpretation of atomic motion in flexible molecules: Accelerating molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Omelyan, Igor; Kovalenko, Andriy
2012-02-01
We propose a new approach to split up the velocities of atoms of flexible molecules into translational, rotational, and vibrational components. As a result, the kinetic energy of the system can easily be expressed in terms of only three parts related to the above components. This is distinct from the standard Eckart method, where the cumbersome Coriolis contribution to the kinetic energy appears additionally. The absence of such a contribution within the proposed approach allows us to readily extend the microcanonical multiple-time-step dynamics of flexible molecules to the canonical-isokinetic Nosé-Hoover chain ensemble by explicitly integrating the translational, orientational, and vibrational motion. The previous extensions dealt exclusively with translational degrees of freedom of separate atoms, leading to a limitation on the size of the outer time step of 100 femtoseconds. We show on molecular dynamics simulations of the flexible TIP3P water model that the new canonical-isokinetic formulation gives a possibility to significantly overcome this limitation. In particular, huge outer time steps of order from a few hundred femtoseconds up to several picoseconds can now be employed to study conformational properties without loss of accuracy.
AWE-WQ: Fast-Forwarding Molecular Dynamics Using the Accelerated Weighted Ensemble
2015-01-01
A limitation of traditional molecular dynamics (MD) is that reaction rates are difficult to compute. This is due to the rarity of observing transitions between metastable states since high energy barriers trap the system in these states. Recently the weighted ensemble (WE) family of methods have emerged which can flexibly and efficiently sample conformational space without being trapped and allow calculation of unbiased rates. However, while WE can sample correctly and efficiently, a scalable implementation applicable to interesting biomolecular systems is not available. We provide here a GPLv2 implementation called AWE-WQ of a WE algorithm using the master/worker distributed computing WorkQueue (WQ) framework. AWE-WQ is scalable to thousands of nodes and supports dynamic allocation of computer resources, heterogeneous resource usage (such as central processing units (CPU) and graphical processing units (GPUs) concurrently), seamless heterogeneous cluster usage (i.e., campus grids and cloud providers), and support for arbitrary MD codes such as GROMACS, while ensuring that all statistics are unbiased. We applied AWE-WQ to a 34 residue protein which simulated 1.5 ms over 8 months with peak aggregate performance of 1000 ns/h. Comparison was done with a 200 μs simulation collected on a GPU over a similar timespan. The folding and unfolded rates were of comparable accuracy. PMID:25207854
Deformation corrected compressed sensing (DC-CS): a novel framework for accelerated dynamic MRI
Lingala, Sajan Goud; DiBella, Edward; Jacob, Mathews
2015-01-01
We propose a novel deformation corrected compressed sensing (DC-CS) framework to recover contrast enhanced dynamic magnetic resonance images from undersampled measurements. We introduce a formulation that is capable of handling a wide class of sparsity/compactness priors on the deformation corrected dynamic signal. In this work, we consider example compactness priors such as sparsity in temporal Fourier domain, sparsity in temporal finite difference domain, and nuclear norm penalty to exploit low rank structure. Using variable splitting, we decouple the complex optimization problem to simpler and well understood sub problems; the resulting algorithm alternates between simple steps of shrinkage based denoising, deformable registration, and a quadratic optimization step. Additionally, we employ efficient continuation strategies to reduce the risk of convergence to local minima. The decoupling enabled by the proposed scheme enables us to apply this scheme to contrast enhanced MRI applications. Through experiments on numerical phantom and in vivo myocardial perfusion MRI datasets, we observe superior image quality of the proposed DC-CS scheme in comparison to the classical k-t FOCUSS with motion estimation/correction scheme, and demonstrate reduced motion artifacts over classical compressed sensing schemes that utilize the compact priors on the original deformation uncorrected signal. PMID:25095251
NASA Astrophysics Data System (ADS)
Chen, Heng-Hui
2004-06-01
An analysis of stability and chaotic dynamics is presented by a single-axis rate gyro subjected to linear feedback control loops. This rate gyro is supposed to be mounted on a space vehicle which undergoes an uncertain angular velocity ωZ( t) around its spin axis. And simultaneously acceleration ω˙X(t) occurs with respect to the output axis. The necessary and sufficient conditions of stability for the autonomous case, whose vehicle undergoes a steady rotation, were provided by Routh-Hurwitz theory. Also, the degeneracy conditions of the non-hyperbolic point were derived and the dynamics of the resulting system on the center manifold near the double-zero degenerate point by using center manifold and normal form methods were examined. The stability of the non-linear non-autonomous system was investigated by Liapunov stability and instability theorems. As the electrical time constant is much smaller than the mechanical time constant, the singularly perturbed system can be obtained by the singular perturbation theory. The Liapunov stability of this system by studying the reduced and boundary-layer systems was also analyzed. Numerical simulations were performed to verify the analytical results. The stable regions of the autonomous system were obtained in parametric diagrams. For the non-autonomous case in which ωZ( t) oscillates near boundary of stability, periodic, quasiperiodic and chaotic motions were demonstrated by using time history, phase plane and Poincaré maps.
A coupled ordinates method for solution acceleration of rarefied gas dynamics simulations
Das, Shankhadeep; Mathur, Sanjay R.; Alexeenko, Alina; Murthy, Jayathi Y.
2015-05-15
Non-equilibrium rarefied flows are frequently encountered in a wide range of applications, including atmospheric re-entry vehicles, vacuum technology, and microscale devices. Rarefied flows at the microscale can be effectively modeled using the ellipsoidal statistical Bhatnagar–Gross–Krook (ESBGK) form of the Boltzmann kinetic equation. Numerical solutions of these equations are often based on the finite volume method (FVM) in physical space and the discrete ordinates method in velocity space. However, existing solvers use a sequential solution procedure wherein the velocity distribution functions are implicitly coupled in physical space, but are solved sequentially in velocity space. This leads to explicit coupling of the distribution function values in velocity space and slows down convergence in systems with low Knudsen numbers. Furthermore, this also makes it difficult to solve multiscale problems or problems in which there is a large range of Knudsen numbers. In this paper, we extend the coupled ordinates method (COMET), previously developed to study participating radiative heat transfer, to solve the ESBGK equations. In this method, at each cell in the physical domain, distribution function values for all velocity ordinates are solved simultaneously. This coupled solution is used as a relaxation sweep in a geometric multigrid method in the spatial domain. Enhancements to COMET to account for the non-linearity of the ESBGK equations, as well as the coupled implementation of boundary conditions, are presented. The methodology works well with arbitrary convex polyhedral meshes, and is shown to give significantly faster solutions than the conventional sequential solution procedure. Acceleration factors of 5–9 are obtained for low to moderate Knudsen numbers on single processor platforms.
Tunneling dynamics of superfluid Fermi gases in an accelerating optical lattice
Tie Lu; Xue Jukui
2010-11-15
The nonlinear Landau-Zener tunneling and the nonlinear Rabi oscillations of superfluid Fermi gases between Bloch bands in an accelerating optical lattice are discussed. Within the hydrodynamic theory and a two-level model, the tunneling probability of superfluid Fermi gases between Bloch bands is obtained. We find that, as the system crosses from the Bose-Einstein condensation (BEC) side to the BCS side, the tunneling rate is closely related to the particle density: when the density is smaller (larger) than a critical value, the tunneling rate at unitarity is larger (smaller) than that in the BEC limit. This is well explained in terms of an effective interaction and an effective potential. Furthermore, the nonlinear Rabi oscillations of superfluid Fermi gases between the bands are discussed by imposing a periodic modulation on the level bias and the strength of the lattice. Analytical expressions of the critical density for suppressing or enhancing the Rabi oscillations are obtained. It is shown that, as the system crosses from the BEC side to the BCS side, the critical density strongly depends on the modulation parameters (i.e., the modulation amplitude and the modulation frequency). For a fixed density, a high-frequency or low-frequency modulation can suppress or enhance the Rabi oscillations both at unitarity and in the BEC limit. For an intermediate modulation frequency, the Rabi oscillations are chaotic along the entire BEC-BCS crossover, especially, on the BCS side. Interestingly, we find that the modulation of the lattice strength only with an intermediate modulation frequency has significant effect on the Rabi oscillations both in the BEC limit and at unitarity; that is, an intermediate-frequency modulation can enhance the Rabi oscillations, especially on the BCS side.
NASA Astrophysics Data System (ADS)
Krause, Alexander Grey
Light has long been used for the precise measurement of moving bodies, but the burgeoning field of optomechanics is concerned with the interaction of light and matter in a regime where the typically weak radiation pressure force of light is able to push back on the moving object. This field began with the realization in the late 1960's that the momentum imparted by a recoiling photon on a mirror would place fundamental limits on the smallest measurable displacement of that mirror. This coupling between the frequency of light and the motion of a mechanical object does much more than simply add noise, however. It has been used to cool objects to their quantum ground state, demonstrate electromagnetically-induced-transparency, and modify the damping and spring constant of the resonator. Amazingly, these radiation pressure effects have now been demonstrated in systems ranging 18 orders of magnitude in mass (kg to fg). In this work we will focus on three diverse experiments in three different optomechanical devices which span the fields of inertial sensors, closed-loop feedback, and nonlinear dynamics. The mechanical elements presented cover 6 orders of magnitude in mass (ng to fg), but they all employ nano-scale photonic crystals to trap light and resonantly enhance the light-matter interaction. In the first experiment we take advantage of the sub-femtometer displacement resolution of our photonic crystals to demonstrate a sensitive chip-scale optical accelerometer with a kHz-frequency mechanical resonator. This sensor has a noise density of approximately 10 micro-g/rt-Hz over a useable bandwidth of approximately 20 kHz and we demonstrate at least 50 dB of linear dynamic sensor range. We also discuss methods to further improve performance of this device by a factor of 10. In the second experiment, we used a closed-loop measurement and feedback system to damp and cool a room-temperature MHz-frequency mechanical oscillator from a phonon occupation of 6.5 million down to
Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks
NASA Astrophysics Data System (ADS)
Zhao, Hui; Sen, Soumyo; Udayabhaskararao, T.; Sawczyk, Michał; Kučanda, Kristina; Manna, Debasish; Kundu, Pintu K.; Lee, Ji-Woong; Král, Petr; Klajn, Rafal
2016-01-01
The chemical behaviour of molecules can be significantly modified by confinement to volumes comparable to the dimensions of the molecules. Although such confined spaces can be found in various nanostructured materials, such as zeolites, nanoporous organic frameworks and colloidal nanocrystal assemblies, the slow diffusion of molecules in and out of these materials has greatly hampered studying the effect of confinement on their physicochemical properties. Here, we show that this diffusion limitation can be overcome by reversibly creating and destroying confined environments by means of ultraviolet and visible light irradiation. We use colloidal nanocrystals functionalized with light-responsive ligands that readily self-assemble and trap various molecules from the surrounding bulk solution. Once trapped, these molecules can undergo chemical reactions with increased rates and with stereoselectivities significantly different from those in bulk solution. Illumination with visible light disassembles these nanoflasks, releasing the product in solution and thereby establishes a catalytic cycle. These dynamic nanoflasks can be useful for studying chemical reactivities in confined environments and for synthesizing molecules that are otherwise hard to achieve in bulk solution.
Lee, Jun-Tae; Sudheendra, L.; Kennedy, Ian M.
2012-01-01
A rapid and simple magnetic particle-based immunoassay has been demonstrated in a capillary mixing system. Antibody-coated micrometer size super-paramagnetic polystyrene (SPP) particles were used in an assay for rabbit IgG in a sandwich (non-competitive) format. The kinetics of the assay was compared between a plate – based system and a single capillary tube. The interaction between the antigen (R-IgG) and the antibody (anti-R-IgG) that was carried by the SPP particles in a rotating capillary was tested under a stationary magnetic field. Competing magnetic and viscous drag forces helped to enhance the interaction between the analyte and the capture antibodies on the particles. The dimensionless Mason number (Mn) was employed to characterize the magnetic particle dynamics – a previously determined critical Mason number (Mnc) was employed as a guide to the appropriate experimental conditions of magnetic field strength and rotational speed of the capillary. The advantage of the rotating capillary system included a short assay time and a reduced reactive volume (20μl). The results show that the immunoassay kinetics were improved by the formation of chains of the SPP particles for the conditions that corresponded to the critical Mason number. PMID:22931580
NASA Astrophysics Data System (ADS)
Wang, Sibo; Xu, Junbo; Wen, Hao
2014-12-01
The heavy crude oil consists of thousands of compounds and much of them have large molecular weights and complex structures. Studying the aggregation and diffusion behavior of asphaltenes can facilitate the understanding of the heavy crude oil. In previous studies, the fused aromatic rings were treated as rigid bodies so that dissipative particle dynamics (DPD) integrated with the quaternion method can be used to study asphaltene systems. In this work, DPD integrated with the quaternion method is implemented on graphics processing units (GPUs). Compared with the serial program, tens of times speedup can be achieved when simulations performed on a single GPU. Using multiple GPUs can provide faster computation speed and more storage space for simulations of significant large systems. By using large systems, simulations of the asphaltene-toluene system at extremely dilute concentrations can be performed. The determined diffusion coefficients of asphaltenes are similar to that in experimental studies. At last, the aggregation behavior of asphaltenes in heptane was investigated, and the simulation results agreed with the modified Yen model. Monomers, nanoaggregates and clusters were observed from the simulations at different concentrations.
NASA Astrophysics Data System (ADS)
Normand, A. E.; Smith, A. N.; Long, J. R.; Reddy, K. R.
2014-12-01
13C magic angle spinning (MAS) solid state Nuclear Magnetic Resonance (ssNMR) has become an essential tool for discerning the chemical composition of soil organic matter (SOM). However, the technique is limited due to the inherent insensitivity of NMR resulting in long acquisition times, especially for low carbon (C) soil. The pursuits of higher magnetic fields or concentrating C with hydrofluoric acid are limited solutions for signal improvement. Recent advances in dynamic nuclear polarization (DNP) have addressed the insensitivity of NMR. DNP utilizes the greater polarization of an unpaired electron in a given magnetic field and transfers that polarization to an NMR active nucleus of interest via microwave irradiation. Signal enhancements of up to a few orders of magnitude have been achieved for various DNP experiments. In this novel study, we conduct DNP 13C cross-polarization (CP) MAS ssNMR experiments of SOM varying in soil C content and chemical composition. DNP signal enhancements reduce the experiment run time allowing samples with low C to be analyzed in hours rather than days. We compare 13C CP MAS ssNMR of SOM with multiple magnetic field strengths, hydrofluoric acid treatment, and novel DNP approaches. We also explore DNP surface enhanced NMR Spectroscopy (SENP) to determine the surface chemistry of SOM. The presented results and future DNP MAS ssNMR advances will lead to further understanding of the nature and processes of SOM.
Hoffman, D.M.; Caley, L.E.
1981-01-01
The dynamic mechanical properties and molecular weight distribution of two polymer bonded explosives, LX-10-1 and PBX-9502, maintained at 23, 60, and 74/sup 0/C for 3 years were studied. LX-10-1 is 94.5% 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane explosive bonded together with 5.5% Viton A fluoropolymer. PBX-9502 is 95% triaminotrinitrobenzene explosive bonded with 5% Kel-F-800 fluoropolymer. There are two mechanical relaxations in the LX-10-1 in the military temperature range. The relaxation at -10/sup 0/C is associated with the glass transition temperature of the Viton A binder. A second weak relaxation occurs at about 30/sup 0/C in all LX-10-1 samples tested. This relaxation is probably associated with small amounts of crystallinity in the binder although this has not been demonstrated. There is a slight increase in modulus of the LX-10-1 with accelerated aging temperature. Changes in the dynamic mechanical properties of PBX-9502 are ascribed to crystallization of the chlorotrifluoroethylene component of the Kel-F-800 binder. The molecular weight of the Viton A binder decreased slight with increasing aging temperature. Using the kinetics of random scission the activation energy for polymer degradation in the presence of the explosive was 1.19 kcal/mole. The Arrhenius preexponential term and activation energy predict an expected use-life in excess of 60 years for LX-10-1. The Kel-F-800 in PBX-9502 is also extremely stable.
FINAL REPORT DE-FG02-04ER41317 Advanced Computation and Chaotic Dynamics for Beams and Accelerators
Cary, John R
2014-09-08
During the year ending in August 2013, we continued to investigate the potential of photonic crystal (PhC) materials for acceleration purposes. We worked to characterize acceleration ability of simple PhC accelerator structures, as well as to characterize PhC materials to determine whether current fabrication techniques can meet the needs of future accelerating structures. We have also continued to design and optimize PhC accelerator structures, with the ultimate goal of finding a new kind of accelerator structure that could offer significant advantages over current RF acceleration technology. This design and optimization of these requires high performance computation, and we continue to work on methods to make such computation faster and more efficient.
None
2011-10-06
1a) Introduction and motivation 1b) History and accelerator types 2) Transverse beam dynamics 3a) Longitudinal beam dynamics 3b) Figure of merit of a synchrotron/collider 3c) Beam control 4) Main limiting factors 5) Technical challenges Prerequisite knowledge: Previous knowledge of accelerators is not required.
None
2011-10-06
1a) Introduction and motivation 1b) History and accelerator types 2) Transverse beam dynamics 3a) Longitudinal beam dynamics 3b) Figure of merit of a synchrotron/collider 3c) Beam control 4) Main limiting factors 5) Technical challenges Prerequisite knowledge: Previous knowledge of accelerators is not required.
None
2011-10-06
1a) Introduction and motivation 1b) History and accelerator types 2) Transverse beam dynamics 3a) Longitudinal beam dynamics 3b) Figure of merit of a synchrotron/collider 3c) Beam control 4) Main limiting factors 5) Technical challenges Prerequisite knowledge: Previous knowledge of accelerators is not required.
Miwa, Masafumi; Oishi, Kazato; Nakagawa, Yasuhiro; Maeno, Hiromichi; Anzai, Hiroki; Kumagai, Hajime; Okano, Kanji; Tobioka, Hisaya; Hirooka, Hiroyuki
2015-01-01
Estimating the energy expenditure of farm animals at pasture is important for efficient animal management. In recent years, an alternative technique for estimating energy expenditure by measuring body acceleration has been widely performed in wildlife and human studies, but the availability of the technique in farm animals has not yet been examined. In the present study, we tested the potential use of an acceleration index, overall dynamic body acceleration (ODBA), as a new proxy for estimating the energy expenditure of grazing farm animals (cattle, goats and sheep) at pasture with the simultaneous evaluation of a conventional proxy, heart rate. Body accelerations in three axes and heart rate for cows (n = 8, two breeds), goats (n = 6) and sheep (n = 5) were recorded, and the effect of ODBA calculated from the body accelerations on heart rate was analyzed. In addition, the effects of the two other activity indices, the number of steps and vectorial dynamic body acceleration (VeDBA), on heart rate were also investigated. The results of the comparison among three activity indices indicated that ODBA was the best predictor for heart rate. Although the relationship between ODBA and heart rate was different between the groups of species and breeds and between individuals (P<0.01), the difference could be explained by different body weights; a common equation could be established by correcting the body weights (M: kg): heart rate (beats/min) = 147.263∙M-0.141 + 889.640∙M-0.179∙ODBA (g). Combining this equation with the previously reported energy expenditure per heartbeat, we estimated the energy expenditure of the tested animals, and the results indicated that ODBA is a good proxy for estimating the energy expenditure of grazing farm animals across species and breeds. The utility and simplicity of the procedure with acceleration loggers could make the accelerometry technique a worthwhile option in field research and commercial farm use. PMID:26030931
NASA Astrophysics Data System (ADS)
Tang, Yu-Hang; Karniadakis, George Em
2014-11-01
We present a scalable dissipative particle dynamics simulation code, fully implemented on the Graphics Processing Units (GPUs) using a hybrid CUDA/MPI programming model, which achieves 10-30 times speedup on a single GPU over 16 CPU cores and almost linear weak scaling across a thousand nodes. A unified framework is developed within which the efficient generation of the neighbor list and maintaining particle data locality are addressed. Our algorithm generates strictly ordered neighbor lists in parallel, while the construction is deterministic and makes no use of atomic operations or sorting. Such neighbor list leads to optimal data loading efficiency when combined with a two-level particle reordering scheme. A faster in situ generation scheme for Gaussian random numbers is proposed using precomputed binary signatures. We designed custom transcendental functions that are fast and accurate for evaluating the pairwise interaction. The correctness and accuracy of the code is verified through a set of test cases simulating Poiseuille flow and spontaneous vesicle formation. Computer benchmarks demonstrate the speedup of our implementation over the CPU implementation as well as strong and weak scalability. A large-scale simulation of spontaneous vesicle formation consisting of 128 million particles was conducted to further illustrate the practicality of our code in real-world applications. Catalogue identifier: AETN_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AETN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 1 602 716 No. of bytes in distributed program, including test data, etc.: 26 489 166 Distribution format: tar.gz Programming language: C/C++, CUDA C/C++, MPI. Computer: Any computers having nVidia GPGPUs with compute capability 3.0. Operating system: Linux. Has the code been
Friedman, A.; Barnard, J.J.; Cohen, R.H.; Grote, D.P.; Lund, S.M.; Sharp, W.M.; Faltens, A.; Henestroza, E.; Jung, J.-Y.; Kwan, J.W.; Lee, E.P.; Leitner, M.A.; Logan, B.G.; Vay, J.-L.; Waldron, W.L.; Davidson, R.C.; Dorf, M.; Gilson, E.P.; Kaganovich, I.D.
2009-12-19
Intense beams of heavy ions are well suited for heating matter to regimes of emerging interest. A new facility, NDCX-II, will enable studies of warm dense matter at {approx}1 eV and near-solid density, and of heavy-ion inertial fusion target physics relevant to electric power production. For these applications the beam must deposit its energy rapidly, before the target can expand significantly. To form such pulses, ion beams are temporally compressed in neutralizing plasma; current amplification factors of {approx}50-100 are routinely obtained on the Neutralized Drift Compression Experiment (NDCX) at LBNL. In the NDCX-II physics design, an initial non-neutralized compression renders the pulse short enough that existing high-voltage pulsed power can be employed. This compression is first halted and then reversed by the beam's longitudinal space-charge field. Downstream induction cells provide acceleration and impose the head-to-tail velocity gradient that leads to the final neutralized compression onto the target. This paper describes the discrete-particle simulation models (1-D, 2-D, and 3-D) employed and the space-charge-dominated beam dynamics being realized.
Friedman, A; Barnard, J J; Cohen, R H; Grote, D P; Lund, S M; Sharp, W M; Faltens, A; Henestroza, E; Jung, J; Kwan, J W; Lee, E P; Leitner, M A; Logan, B G; Vay, J; Waldron, W L; Davidson, R C; Dorf, M; Gilson, E P; Kaganovich, I
2009-11-19
Intense beams of heavy ions are well suited for heating matter to regimes of emerging interest. A new facility, NDCX-II, will enable studies of warm dense matter at {approx}1 eV and near-solid density, and of heavy-ion inertial fusion target physics relevant to electric power production. For these applications the beam must deposit its energy rapidly, before the target can expand significantly. To form such pulses, ion beams are temporally compressed in neutralizing plasma; current amplification factors of {approx}50-100 are routinely obtained on the Neutralized Drift Compression Experiment (NDCX) at LBNL. In the NDCX-II physics design, an initial non-neutralized compression renders the pulse short enough that existing high-voltage pulsed power can be employed. This compression is first halted and then reversed by the beam's longitudinal space-charge field. Downstream induction cells provide acceleration and impose the head-to-tail velocity gradient that leads to the final neutralized compression onto the target. This paper describes the discrete-particle simulation models (1-D, 2-D, and 3-D) employed and the space-charge-dominated beam dynamics being realized.
NASA Astrophysics Data System (ADS)
Alexander, C.; Haill, T.; Dalton, D.; Rovang, D.; Lamppa, D.
2013-06-01
The recently developed magnetically applied pressure-shear (MAPS) technique used to measure dynamic material strength at high pressures on magneto-hydrodynamic (MHD) drive pulsed power platforms has been implemented on the Sandia Z accelerator. MAPS relies on an external magnetic field normal to the plane of the MHD drive current to directly induce a shear stress wave in addition to the usual longitudinal stress wave. This shear wave is used to directly probe the strength of a sample. By implementing this technique on Z, far greater pressures can be attained than were previously available using other MHD facilities. In addition, the use of isentropic compression will limit sample heating allowing the measurement to be made at a much lower temperature than under shock compression. Details of the experimental approach, including design considerations and analysis of the results, will be presented along with the results of Z experiments measuring the strength of tantalum at pressures up to 50 GPa, a five-fold increase in pressure over previous results using this technique. Sandia National Labs is a multi-program laboratory managed and operated by Sandia Corp., a wholly owned subsidiary of Lockheed Martin Corp., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.
Rihaoui, M.; Gai, W.; Kim, K.J.; Piot, Philippe; Power, John Gorham; Sun, Y.E.; /Fermilab
2009-01-01
Transverse-to-longitudinal emittance exchange has promising applications in various advanced acceleration and light source concepts. A proof-of-principle experiment to demonstrate this phase space manipulation method is currently being planned at the Argonne Wakefield Accelerator. The experiment focuses on exchanging a low longitudinal emittance with a high transverse horizontal emittance and also incorporates room for possible parametric studies e.g. using an incoming flat beam with tunable horizontal emittance. In this paper, we present realistic start-to-end beam dynamics simulation of the scheme, explore the limitations of this phase space exchange.
Gao, F.; Gai, W.; Power, J. G.; Kim, K. J.; Sun, Y. E.; Piot, P.; Rihaoui, M.; High Energy Physics; Northern Illinois Univ.; FNAL
2009-01-01
Transverse-to-longitudinal emittance exchange has promising applications in various advanced acceleration and light source concepts. A proof-of-principle experiment to demonstrate this phase space manipulation method is currently being planned at the Argonne Wakefield Accelerator. The experiment focuses on exchanging a low longitudinal emittance with a high transverse horizontal emittance and also incorporates room for possible parametric studies e.g. using an incoming flat beam with tunable horizontal emittance. In this paper, we present realistic start-to-end beam dynamics simulation of the scheme, explore the limitations of this phase space exchange.
Rihaoui, M.; Gai, W.; Kim, K.-J.; Power, J. G.; Piot, P.; Sun, Y.-E.
2009-01-22
Transverse-to-longitudinal emittance exchange has promising applications in various advanced acceleration and light source concepts. A proof-of-principle experiment to demonstrate this phase space manipulation method is currently being planned at the Argonne Wakefield Accelerator. The experiment focuses on exchanging a low longitudinal emittance with a high transverse horizontal emittance and also incorporates room for possible parametric studies e.g. using an incoming flat beam with tunable horizontal emittance. In this paper, we present realistic start-to-end beam dynamics simulation of the scheme, explore the limitations of this phase space exchange.
MV image-based dynamic MLC tracking of a NiTi stent in pig lungs on a linear accelerator
Poulsen, Per R; Carl, Jesper; Nielsen, Jane; Nielsen, Martin S; Thomsen, Jakob B; Jensen, Henrik K; Kjærgaard, Benedict; Zepernick, Peter R; Worm, Esben; Fledelius, Walther; Cho, Byungchul; Sawant, Amit; Ruan, Dan; Keall, Paul J
2011-01-01
Purpose: To investigate the accuracy and potential limitations of MV image-based dynamic MLC tracking in a porcine model on a linear accelerator. Methods and Materials: A thermo-expandable NiTi stent designed for kV x-ray visualization of lung lesions was inserted into the bronchia of three anaesthetized Göttingen minipigs. A 4DCT scan was used for planning a 5-field conformal treatment with circular MLC apertures. A 22.5Gy single fraction treatment was delivered to the pigs. The peak-to-peak stent motion was 3-8mm with breathing periods of 1.2-4 seconds. Prior to treatment, x-ray images were used for image-guided setup based on the stent. During treatment delivery, continuous portal images were acquired at 7.5Hz. The stent was segmented in the images and used for continuous adaptation of the MLC aperture. Offline, the tracking error in beam’s eye view of the MV beam was calculated for each image as the difference between the MLC aperture center and the segmented stent position. The standard deviations of the systematic error Σ and the random error σ were determined and compared with the would-be errors for a non-tracking treatment with pre-treatment image-guided setup. Results: Reliable stent segmentation was obtained for 11 out of 15 fields. Segmentation failures occurred when image contrast was dominated by overlapping anatomical structures (ribs, diaphragm) rather than by the stent, which was designed for kV rather than MV x-ray visibility. For the 11 fields with reliable segmentation, Σ was 0.5mm/0.4mm in the two imager directions, while σ was 0.5mm/1.1mm. Without tracking, Σ and σ would have been 1.7mm/1.4mm and 0.8mm/1.4mm, respectively. Conclusion: For the first time, in vivo DMLC tracking has been demonstrated on a linear accelerator showing the potential for improved targeting accuracy. The study mimicked the envisioned patient workflow of future patient treatments. Clinical implementation of MV image-based tracking would require markers designed
NASA Astrophysics Data System (ADS)
Michailidou, V. N.; Swan, J. W.; Brady, J. F.; Petekidis, G.
2013-10-01
Evanescent wave dynamic light scattering and Stokesian dynamics simulations were employed to study the dynamics of hard-sphere colloidal particles near a hard wall in concentrated suspensions. The evanescent wave averaged short-time diffusion coefficients were determined from experimental correlation functions over a range of scattering wave vectors and penetration depths. Stokesian dynamics simulations performed for similar conditions allow a direct comparison of both the short-time self- and collective diffusivity. As seen earlier [V. N. Michailidou, G. Petekidis, J. W. Swan, and J. F. Brady, Phys. Rev. Lett. 102, 068302 (2009)] while the near wall dynamics in the dilute regime slow down compared to the free bulk diffusion, the reduction is negligible at higher volume fractions due to an interplay between the particle-wall and particle-particle hydrodynamic interactions. Here, we provide a comprehensive comparison between experiments and simulations and discuss the interplay of particle-wall and particle-particle hydrodynamics in the self- and cooperative dynamics determined at different scattering wave vectors and penetration depths.
Beam dynamics studies on the 100 MeV/100 kW electron linear accelerator for NSC KIPT neutron source
NASA Astrophysics Data System (ADS)
Pei, Shi-Lun; Chi, Yun-Long; Wang, Shu-Hong; Pei, Guo-Xi; Zhou, Zu-Sheng; Hou, Mi; Mykola, Ayzatskiy; Ivan, Karnaukhov; Volodymyr, Kushnir; Viktor, Mytrochenko; Andrey, Zelinsky
2012-07-01
We designed a 100 MeV/100 kW electron linear accelerator for NSC KIPT, which will be used to drive a neutron source on the basis of subcritical assembly. Beam dynamics studies have been conducted to reach the design requirements (E = 100 MeV, P = 100 kW, dE/E < 1% for 99% particles). In this paper, we will present the progress of the design and the dynamic simulation results. For high intensity and long beam pulse linear accelerators, the BBU effect is one big issue; special care has been taken in the accelerating structure design. To satisfy the energy spread requirement at the linac exit, the particles with large energy difference from the synchronous particle should be eliminated at a low energy stage to ease the design of the collimation system and radiation shielding. A dispersion free chicane with 4 bending magnets is introduced downstream of the 1st accelerating section; the unwanted particles will be collimated there.
Cortes-Ciriano, Isidro; Bouvier, Guillaume; Nilges, Michael; Maragliano, Luca; Malliavin, Thérèse E
2015-07-14
Many proteins exhibit an equilibrium between multiple conformations, some of them being characterized only by low-resolution information. Visiting all conformations is a demanding task for computational techniques performing enhanced but unfocused exploration of collective variable (CV) space. Otherwise, pulling a structure toward a target condition biases the exploration in a way difficult to assess. To address this problem, we introduce here the soft-ratcheting temperature-accelerated molecular dynamics (sr-TAMD), where the exploration of CV space by TAMD is coupled to a soft-ratcheting algorithm that filters the evolving CV values according to a predefined criterion. Any low resolution or even qualitative information can be used to orient the exploration. We validate this technique by exploring the conformational space of the inactive state of the catalytic domain of the adenyl cyclase AC from Bordetella pertussis. The domain AC gets activated by association with calmodulin (CaM), and the available crystal structure shows that in the complex the protein has an elongated shape. High-resolution data are not available for the inactive, CaM-free protein state, but hydrodynamic measurements have shown that the inactive AC displays a more globular conformation. Here, using as CVs several geometric centers, we use sr-TAMD to enhance CV space sampling while filtering for CV values that correspond to centers moving close to each other, and we thus rapidly visit regions of conformational space that correspond to globular structures. The set of conformations sampled using sr-TAMD provides the most extensive description of the inactive state of AC up to now, consistent with available experimental information. PMID:26575778