Applications of the Lattice Boltzmann Method to Complex and Turbulent Flows

NASA Technical Reports Server (NTRS)

Luo, Li-Shi; Qi, Dewei; Wang, Lian-Ping; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

We briefly review the method of the lattice Boltzmann equation (LBE). We show the three-dimensional LBE simulation results for a non-spherical particle in Couette flow and 16 particles in sedimentation in fluid. We compare the LBE simulation of the three-dimensional homogeneous isotropic turbulence flow in a periodic cubic box of the size 1283 with the pseudo-spectral simulation, and find that the two results agree well with each other but the LBE method is more dissipative than the pseudo-spectral method in small scales, as expected.

Topics in spectral methods

NASA Technical Reports Server (NTRS)

Gottlieb, D.; Turkel, E.

1985-01-01

After detailing the construction of spectral approximations to time-dependent mixed initial boundary value problems, a study is conducted of differential equations of the form 'partial derivative of u/partial derivative of t = Lu + f', where for each t, u(t) belongs to a Hilbert space such that u satisfies homogeneous boundary conditions. For the sake of simplicity, it is assumed that L is an unbounded, time-independent linear operator. Attention is given to Fourier methods of both Galerkin and pseudospectral method types, the Galerkin method, the pseudospectral Chebyshev and Legendre methods, the error equation, hyperbolic partial differentiation equations, and time discretization and iterative methods.

A mixed pseudospectral/finite difference method for the axisymmetric flow in a heated, rotating spherical shell. [for experimental atmospheric simulation

NASA Technical Reports Server (NTRS)

Macaraeg, M. G.

1986-01-01

For a Spacelab flight, a model experiment of the earth's atmospheric circulation has been proposed. This experiment is known as the Atmospheric General Circulation Experiment (AGCE). In the experiment concentric spheres will rotate as a solid body, while a dielectric fluid is confined in a portion of the gap between the spheres. A zero gravity environment will be required in the context of the simulation of the gravitational body force on the atmosphere. The present study is concerned with the development of pseudospectral/finite difference (PS/FD) model and its subsequent application to physical cases relevant to the AGCE. The model is based on a hybrid scheme involving a pseudospectral latitudinal formulation, and finite difference radial and time discretization. The advantages of the use of the hybrid PS/FD method compared to a pure second-order accurate finite difference (FD) method are discussed, taking into account the higher accuracy and efficiency of the PS/FD method.

Time-splitting combined with exponential wave integrator fourier pseudospectral method for Schrödinger-Boussinesq system

NASA Astrophysics Data System (ADS)

Liao, Feng; Zhang, Luming; Wang, Shanshan

2018-02-01

In this article, we formulate an efficient and accurate numerical method for approximations of the coupled Schrödinger-Boussinesq (SBq) system. The main features of our method are based on: (i) the applications of a time-splitting Fourier spectral method for Schrödinger-like equation in SBq system, (ii) the utilizations of exponential wave integrator Fourier pseudospectral for spatial derivatives in the Boussinesq-like equation. The scheme is fully explicit and efficient due to fast Fourier transform. The numerical examples are presented to show the efficiency and accuracy of our method.

Multistage Spectral Relaxation Method for Solving the Hyperchaotic Complex Systems

PubMed Central

Saberi Nik, Hassan; Rebelo, Paulo

2014-01-01

We present a pseudospectral method application for solving the hyperchaotic complex systems. The proposed method, called the multistage spectral relaxation method (MSRM) is based on a technique of extending Gauss-Seidel type relaxation ideas to systems of nonlinear differential equations and using the Chebyshev pseudospectral methods to solve the resulting system on a sequence of multiple intervals. In this new application, the MSRM is used to solve famous hyperchaotic complex systems such as hyperchaotic complex Lorenz system and the complex permanent magnet synchronous motor. We compare this approach to the Runge-Kutta based ode45 solver to show that the MSRM gives accurate results. PMID:25386624

Pseudo-spectral methods applied to gravitational collapse.

NASA Astrophysics Data System (ADS)

Bonazzola, S.; Marck, J.-A.

The authors present codes for solving Newtonian gravitational collapse in spherical coordinates for the spherical, axial and true 3 D cases. The pseudo-spectral techniques are used. All quantities are expanded in Chebychev or Legendre polynomials or Fourier series for the periodic parts. The codes are able to handle in a rigorous way the pseudo-singularities τ = 0 and θ = 0, π. Illustrative results for each of the three cases are given.

A spectral multi-domain technique applied to high-speed chemically reacting flows

NASA Technical Reports Server (NTRS)

Macaraeg, Michele G.; Streett, Craig L.; Hussaini, M. Yousuff

1989-01-01

The first applications of a spectral multidomain method for viscous compressible flow is presented. The method imposes a global flux balance condition at the interface so that high-order continuity of the solution is preserved. The global flux balance is imposed in terms of a spectral integral of the discrete equations across adjoining domains. Since the discretized equations interior to each domain solved are uncoupled from each other, and since the interface relation has a block structure, the solution scheme can be adapted to the particular requirements of each subdomain. The spectral multidomain technique presented is well-suited for the multiple scales associated with the chemically reacting and transition flows in hypersonic research. A nonstaggered multidomain discretization is used for the chemically reacting flow calculation, and the first implementation of a staggered multidomain mesh is presented for accurately solving the stability equation for a viscous compressible fluid.

Simulation of confined magnetohydrodynamic flows with Dirichlet boundary conditions using a pseudo-spectral method with volume penalization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morales, Jorge A.; Leroy, Matthieu; Bos, Wouter J.T.

A volume penalization approach to simulate magnetohydrodynamic (MHD) flows in confined domains is presented. Here the incompressible visco-resistive MHD equations are solved using parallel pseudo-spectral solvers in Cartesian geometries. The volume penalization technique is an immersed boundary method which is characterized by a high flexibility for the geometry of the considered flow. In the present case, it allows to use other than periodic boundary conditions in a Fourier pseudo-spectral approach. The numerical method is validated and its convergence is assessed for two- and three-dimensional hydrodynamic (HD) and MHD flows, by comparing the numerical results with results from literature and analyticalmore » solutions. The test cases considered are two-dimensional Taylor–Couette flow, the z-pinch configuration, three dimensional Orszag–Tang flow, Ohmic-decay in a periodic cylinder, three-dimensional Taylor–Couette flow with and without axial magnetic field and three-dimensional Hartmann-instabilities in a cylinder with an imposed helical magnetic field. Finally, we present a magnetohydrodynamic flow simulation in toroidal geometry with non-symmetric cross section and imposing a helical magnetic field to illustrate the potential of the method.« less

A multi-domain trust management model for supporting RFID applications of IoT

PubMed Central

Li, Feng

2017-01-01

The use of RFID technology in complex and distributed environments often leads to a multi-domain RFID system, in which trust establishment among entities from heterogeneous domains without past interaction or prior agreed policy, is a challenge. The current trust management mechanisms in the literature do not meet the specific requirements in multi-domain RFID systems. Therefore, this paper analyzes the special challenges on trust management in multi-domain RFID systems, and identifies the implications and the requirements of the challenges on the solutions to the trust management of multi-domain RFID systems. A multi-domain trust management model is proposed, which provides a hierarchical trust management framework include a diversity of trust evaluation and establishment approaches. The simulation results and analysis show that the proposed method has excellent ability to deal with the trust relationships, better security, and higher accuracy rate. PMID:28708855

A multi-domain trust management model for supporting RFID applications of IoT.

PubMed

Wu, Xu; Li, Feng

2017-01-01

The use of RFID technology in complex and distributed environments often leads to a multi-domain RFID system, in which trust establishment among entities from heterogeneous domains without past interaction or prior agreed policy, is a challenge. The current trust management mechanisms in the literature do not meet the specific requirements in multi-domain RFID systems. Therefore, this paper analyzes the special challenges on trust management in multi-domain RFID systems, and identifies the implications and the requirements of the challenges on the solutions to the trust management of multi-domain RFID systems. A multi-domain trust management model is proposed, which provides a hierarchical trust management framework include a diversity of trust evaluation and establishment approaches. The simulation results and analysis show that the proposed method has excellent ability to deal with the trust relationships, better security, and higher accuracy rate.

Using SpF to Achieve Petascale for Legacy Pseudospectral Applications

NASA Technical Reports Server (NTRS)

Clune, Thomas L.; Jiang, Weiyuan

2014-01-01

Pseudospectral (PS) methods possess a number of characteristics (e.g., efficiency, accuracy, natural boundary conditions) that are extremely desirable for dynamo models. Unfortunately, dynamo models based upon PS methods face a number of daunting challenges, which include exposing additional parallelism, leveraging hardware accelerators, exploiting hybrid parallelism, and improving the scalability of global memory transposes. Although these issues are a concern for most models, solutions for PS methods tend to require far more pervasive changes to underlying data and control structures. Further, improvements in performance in one model are difficult to transfer to other models, resulting in significant duplication of effort across the research community. We have developed an extensible software framework for pseudospectral methods called SpF that is intended to enable extreme scalability and optimal performance. Highlevel abstractions provided by SpF unburden applications of the responsibility of managing domain decomposition and load balance while reducing the changes in code required to adapt to new computing architectures. The key design concept in SpF is that each phase of the numerical calculation is partitioned into disjoint numerical kernels that can be performed entirely inprocessor. The granularity of domain decomposition provided by SpF is only constrained by the datalocality requirements of these kernels. SpF builds on top of optimized vendor libraries for common numerical operations such as transforms, matrix solvers, etc., but can also be configured to use open source alternatives for portability. SpF includes several alternative schemes for global data redistribution and is expected to serve as an ideal testbed for further research into optimal approaches for different network architectures. In this presentation, we will describe our experience in porting legacy pseudospectral models, MoSST and DYNAMO, to use SpF as well as present preliminary performance results provided by the improved scalability.

Optimised collision avoidance for an ultra-close rendezvous with a failed satellite based on the Gauss pseudospectral method

NASA Astrophysics Data System (ADS)

Chu, Xiaoyu; Zhang, Jingrui; Lu, Shan; Zhang, Yao; Sun, Yue

2016-11-01

This paper presents a trajectory planning algorithm to optimise the collision avoidance of a chasing spacecraft operating in an ultra-close proximity to a failed satellite. The complex configuration and the tumbling motion of the failed satellite are considered. The two-spacecraft rendezvous dynamics are formulated based on the target body frame, and the collision avoidance constraints are detailed, particularly concerning the uncertainties. An optimisation solution of the approaching problem is generated using the Gauss pseudospectral method. A closed-loop control is used to track the optimised trajectory. Numerical results are provided to demonstrate the effectiveness of the proposed algorithms.

Modeling nonlinear ultrasound propagation in heterogeneous media with power law absorption using a k-space pseudospectral method.

PubMed

Treeby, Bradley E; Jaros, Jiri; Rendell, Alistair P; Cox, B T

2012-06-01

The simulation of nonlinear ultrasound propagation through tissue realistic media has a wide range of practical applications. However, this is a computationally difficult problem due to the large size of the computational domain compared to the acoustic wavelength. Here, the k-space pseudospectral method is used to reduce the number of grid points required per wavelength for accurate simulations. The model is based on coupled first-order acoustic equations valid for nonlinear wave propagation in heterogeneous media with power law absorption. These are derived from the equations of fluid mechanics and include a pressure-density relation that incorporates the effects of nonlinearity, power law absorption, and medium heterogeneities. The additional terms accounting for convective nonlinearity and power law absorption are expressed as spatial gradients making them efficient to numerically encode. The governing equations are then discretized using a k-space pseudospectral technique in which the spatial gradients are computed using the Fourier-collocation method. This increases the accuracy of the gradient calculation and thus relaxes the requirement for dense computational grids compared to conventional finite difference methods. The accuracy and utility of the developed model is demonstrated via several numerical experiments, including the 3D simulation of the beam pattern from a clinical ultrasound probe.

Highly efficient implementation of pseudospectral time-dependent density-functional theory for the calculation of excitation energies of large molecules.

PubMed

Cao, Yixiang; Hughes, Thomas; Giesen, Dave; Halls, Mathew D; Goldberg, Alexander; Vadicherla, Tati Reddy; Sastry, Madhavi; Patel, Bhargav; Sherman, Woody; Weisman, Andrew L; Friesner, Richard A

2016-06-15

We have developed and implemented pseudospectral time-dependent density-functional theory (TDDFT) in the quantum mechanics package Jaguar to calculate restricted singlet and restricted triplet, as well as unrestricted excitation energies with either full linear response (FLR) or the Tamm-Dancoff approximation (TDA) with the pseudospectral length scales, pseudospectral atomic corrections, and pseudospectral multigrid strategy included in the implementations to improve the chemical accuracy and to speed the pseudospectral calculations. The calculations based on pseudospectral time-dependent density-functional theory with full linear response (PS-FLR-TDDFT) and within the Tamm-Dancoff approximation (PS-TDA-TDDFT) for G2 set molecules using B3LYP/6-31G*(*) show mean and maximum absolute deviations of 0.0015 eV and 0.0081 eV, 0.0007 eV and 0.0064 eV, 0.0004 eV and 0.0022 eV for restricted singlet excitation energies, restricted triplet excitation energies, and unrestricted excitation energies, respectively; compared with the results calculated from the conventional spectral method. The application of PS-FLR-TDDFT to OLED molecules and organic dyes, as well as the comparisons for results calculated from PS-FLR-TDDFT and best estimations demonstrate that the accuracy of both PS-FLR-TDDFT and PS-TDA-TDDFT. Calculations for a set of medium-sized molecules, including Cn fullerenes and nanotubes, using the B3LYP functional and 6-31G(**) basis set show PS-TDA-TDDFT provides 19- to 34-fold speedups for Cn fullerenes with 450-1470 basis functions, 11- to 32-fold speedups for nanotubes with 660-3180 basis functions, and 9- to 16-fold speedups for organic molecules with 540-1340 basis functions compared to fully analytic calculations without sacrificing chemical accuracy. The calculations on a set of larger molecules, including the antibiotic drug Ramoplanin, the 46-residue crambin protein, fullerenes up to C540 and nanotubes up to 14×(6,6), using the B3LYP functional and 6-31G(**) basis set with up to 8100 basis functions show that PS-FLR-TDDFT CPU time scales as N(2.05) with the number of basis functions. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Fitted Fourier-pseudospectral methods for solving a delayed reaction-diffusion partial differential equation in biology

NASA Astrophysics Data System (ADS)

Adam, A. M. A.; Bashier, E. B. M.; Hashim, M. H. A.; Patidar, K. C.

2017-07-01

In this work, we design and analyze a fitted numerical method to solve a reaction-diffusion model with time delay, namely, a delayed version of a population model which is an extension of the logistic growth (LG) equation for a food-limited population proposed by Smith [F.E. Smith, Population dynamics in Daphnia magna and a new model for population growth, Ecology 44 (1963) 651-663]. Seeing that the analytical solution (in closed form) is hard to obtain, we seek for a robust numerical method. The method consists of a Fourier-pseudospectral semi-discretization in space and a fitted operator implicit-explicit scheme in temporal direction. The proposed method is analyzed for convergence and we found that it is unconditionally stable. Illustrative numerical results will be presented at the conference.

A mixed pseudospectral/finite difference method for a thermally driven fluid in a nonuniform gravitational field

NASA Technical Reports Server (NTRS)

Macaraeg, M. G.

1985-01-01

A numerical study of the steady, axisymmetric flow in a heated, rotating spherical shell is conducted to model the Atmospheric General Circulation Experiment (AGCE) proposed to run aboard a later shuttle mission. The AGCE will consist of concentric rotating spheres confining a dielectric fluid. By imposing a dielectric field across the fluid a radial body force will be created. The numerical solution technique is based on the incompressible Navier-Stokes equations. In the method a pseudospectral technique is based on the incompressible Navier-Stokes equations. In the method a pseudospectral technique is used in the latitudinal direction, and a second-order accurate finite difference scheme discretizes time and radial derivatives. This paper discusses the development and performance of this numerical scheme for the AGCE which has been modelled in the past only by pure FD formulations. In addition, previous models have not investigated the effect of using a dielectric force to simulate terrestrial gravity. The effect of this dielectric force on the flow field is investigated as well as a parameter study of varying rotation rates and boundary temperatures. Among the effects noted are the production of larger velocities and enhanced reversals of radial temperature gradients for a body force generated by the electric field.

Pseudospectral method for gravitational wave collapse

NASA Astrophysics Data System (ADS)

Hilditch, David; Weyhausen, Andreas; Brügmann, Bernd

2016-03-01

We present a new pseudospectral code, bamps, for numerical relativity written with the evolution of collapsing gravitational waves in mind. We employ the first-order generalized harmonic gauge formulation. The relevant theory is reviewed, and the numerical method is critically examined and specialized for the task at hand. In particular, we investigate formulation parameters—gauge- and constraint-preserving boundary conditions well suited to nonvanishing gauge source functions. Different types of axisymmetric twist-free moment-of-time-symmetry gravitational wave initial data are discussed. A treatment of the axisymmetric apparent horizon condition is presented with careful attention to regularity on axis. Our apparent horizon finder is then evaluated in a number of test cases. Moving on to evolutions, we investigate modifications to the generalized harmonic gauge constraint damping scheme to improve conservation in the strong-field regime. We demonstrate strong-scaling of our pseudospectral penalty code. We employ the Cartoon method to efficiently evolve axisymmetric data in our 3 +1 -dimensional code. We perform test evolutions of the Schwarzschild spacetime perturbed by gravitational waves and by gauge pulses, both to demonstrate the use of our black-hole excision scheme and for comparison with earlier results. Finally, numerical evolutions of supercritical Brill waves are presented to demonstrate durability of the excision scheme for the dynamical formation of a black hole.

SpF: Enabling Petascale Performance for Pseudospectral Dynamo Models

NASA Astrophysics Data System (ADS)

Jiang, W.; Clune, T.; Vriesema, J.; Gutmann, G.

2013-12-01

Pseudospectral (PS) methods possess a number of characteristics (e.g., efficiency, accuracy, natural boundary conditions) that are extremely desirable for dynamo models. Unfortunately, dynamo models based upon PS methods face a number of daunting challenges, which include exposing additional parallelism, leveraging hardware accelerators, exploiting hybrid parallelism, and improving the scalability of global memory transposes. Although these issues are a concern for most models, solutions for PS methods tend to require far more pervasive changes to underlying data and control structures. Further, improvements in performance in one model are difficult to transfer to other models, resulting in significant duplication of effort across the research community. We have developed an extensible software framework for pseudospectral methods called SpF that is intended to enable extreme scalability and optimal performance. High-level abstractions provided by SpF unburden applications of the responsibility of managing domain decomposition and load balance while reducing the changes in code required to adapt to new computing architectures. The key design concept in SpF is that each phase of the numerical calculation is partitioned into disjoint numerical 'kernels' that can be performed entirely in-processor. The granularity of domain-decomposition provided by SpF is only constrained by the data-locality requirements of these kernels. SpF builds on top of optimized vendor libraries for common numerical operations such as transforms, matrix solvers, etc., but can also be configured to use open source alternatives for portability. SpF includes several alternative schemes for global data redistribution and is expected to serve as an ideal testbed for further research into optimal approaches for different network architectures. In this presentation, we will describe the basic architecture of SpF as well as preliminary performance data and experience with adapting legacy dynamo codes. We will conclude with a discussion of planned extensions to SpF that will provide pseudospectral applications with additional flexibility with regard to time integration, linear solvers, and discretization in the radial direction.

Spectral simulations of an axisymmetric force-free pulsar magnetosphere

NASA Astrophysics Data System (ADS)

Cao, Gang; Zhang, Li; Sun, Sineng

2016-02-01

A pseudo-spectral method with an absorbing outer boundary is used to solve a set of time-dependent force-free equations. In this method, both electric and magnetic fields are expanded in terms of the vector spherical harmonic (VSH) functions in spherical geometry and the divergence-free state of the magnetic field is enforced analytically by a projection method. Our simulations show that the Deutsch vacuum solution and the Michel monopole solution can be reproduced well by our pseudo-spectral code. Further, the method is used to present a time-dependent simulation of the force-free pulsar magnetosphere for an aligned rotator. The simulations show that the current sheet in the equatorial plane can be resolved well and the spin-down luminosity obtained in the steady state is in good agreement with the value given by Spitkovsky.

High-order Discontinuous Element-based Schemes for the Inviscid Shallow Water Equations: Spectral Multidomain Penalty and Discontinuous Galerkin Methods

DTIC Science & Technology

2011-07-19

multidomain methods, Discontinuous Galerkin methods, interfacial treatment ∗ Jorge A. Escobar-Vargas, School of Civil and Environmental Engineering, Cornell...Click here to view linked References 1. Introduction Geophysical flows exhibit a complex structure and dynamics over a broad range of scales that...hyperbolic problems, where the interfacial patching was implemented with an upwind scheme based on a modified method of characteristics. This approach

Discrete conservation laws and the convergence of long time simulations of the mkdv equation

NASA Astrophysics Data System (ADS)

Gorria, C.; Alejo, M. A.; Vega, L.

2013-02-01

Pseudospectral collocation methods and finite difference methods have been used for approximating an important family of soliton like solutions of the mKdV equation. These solutions present a structural instability which make difficult to approximate their evolution in long time intervals with enough accuracy. The standard numerical methods do not guarantee the convergence to the proper solution of the initial value problem and often fail by approaching solutions associated to different initial conditions. In this frame the numerical schemes that preserve the discrete invariants related to some conservation laws of this equation produce better results than the methods which only take care of a high consistency order. Pseudospectral spatial discretization appear as the most robust of the numerical methods, but finite difference schemes are useful in order to analyze the rule played by the conservation of the invariants in the convergence.

An effective pseudospectral method for constraint dynamic optimisation problems with characteristic times

NASA Astrophysics Data System (ADS)

Xiao, Long; Liu, Xinggao; Ma, Liang; Zhang, Zeyin

2018-03-01

Dynamic optimisation problem with characteristic times, widely existing in many areas, is one of the frontiers and hotspots of dynamic optimisation researches. This paper considers a class of dynamic optimisation problems with constraints that depend on the interior points either fixed or variable, where a novel direct pseudospectral method using Legendre-Gauss (LG) collocation points for solving these problems is presented. The formula for the state at the terminal time of each subdomain is derived, which results in a linear combination of the state at the LG points in the subdomains so as to avoid the complex nonlinear integral. The sensitivities of the state at the collocation points with respect to the variable characteristic times are derived to improve the efficiency of the method. Three well-known characteristic time dynamic optimisation problems are solved and compared in detail among the reported literature methods. The research results show the effectiveness of the proposed method.

A multidomain spectral collocation method for the Stokes problem

NASA Technical Reports Server (NTRS)

Landriani, G. Sacchi; Vandeven, H.

1989-01-01

A multidomain spectral collocation scheme is proposed for the approximation of the two-dimensional Stokes problem. It is shown that the discrete velocity vector field is exactly divergence-free and we prove error estimates both for the velocity and the pressure.

Time domain simulation of harmonic ultrasound images and beam patterns in 3D using the k-space pseudospectral method.

PubMed

Treeby, Bradley E; Tumen, Mustafa; Cox, B T

2011-01-01

A k-space pseudospectral model is developed for the fast full-wave simulation of nonlinear ultrasound propagation through heterogeneous media. The model uses a novel equation of state to account for nonlinearity in addition to power law absorption. The spectral calculation of the spatial gradients enables a significant reduction in the number of required grid nodes compared to finite difference methods. The model is parallelized using a graphical processing unit (GPU) which allows the simulation of individual ultrasound scan lines using a 256 x 256 x 128 voxel grid in less than five minutes. Several numerical examples are given, including the simulation of harmonic ultrasound images and beam patterns using a linear phased array transducer.

Pseudospectral Model for Hybrid PIC Hall-effect Thruster Simulation

DTIC Science & Technology

2015-07-01

and Fernandez6 (hybrid- PIC ). This work follows the example of Lam and Fernandez but substitutes a spectral description in the azimuthal direction to...Paper 3. DATES COVERED (From - To) July 2015-July 2015 4. TITLE AND SUBTITLE Pseudospectral model for hybrid PIC Hall-effect thruster simulationect...of a pseudospectral azimuthal-axial hybrid- PIC HET code which is designed to explicitly resolve and filter azimuthal fluctuations in the

Stable multi-domain spectral penalty methods for fractional partial differential equations

NASA Astrophysics Data System (ADS)

Xu, Qinwu; Hesthaven, Jan S.

2014-01-01

We propose stable multi-domain spectral penalty methods suitable for solving fractional partial differential equations with fractional derivatives of any order. First, a high order discretization is proposed to approximate fractional derivatives of any order on any given grids based on orthogonal polynomials. The approximation order is analyzed and verified through numerical examples. Based on the discrete fractional derivative, we introduce stable multi-domain spectral penalty methods for solving fractional advection and diffusion equations. The equations are discretized in each sub-domain separately and the global schemes are obtained by weakly imposed boundary and interface conditions through a penalty term. Stability of the schemes are analyzed and numerical examples based on both uniform and nonuniform grids are considered to highlight the flexibility and high accuracy of the proposed schemes.

A conservative staggered-grid Chebyshev multidomain method for compressible flows

NASA Technical Reports Server (NTRS)

Kopriva, David A.; Kolias, John H.

1995-01-01

We present a new multidomain spectral collocation method that uses staggered grids for the solution of compressible flow problems. The solution unknowns are defined at the nodes of a Gauss quadrature rule. The fluxes are evaluated at the nodes of a Gauss-Lobatto rule. The method is conservative, free-stream preserving, and exponentially accurate. A significant advantage of the method is that subdomain corners are not included in the approximation, making solutions in complex geometries easier to compute.

A multi-domain spectral method for time-fractional differential equations

NASA Astrophysics Data System (ADS)

Chen, Feng; Xu, Qinwu; Hesthaven, Jan S.

2015-07-01

This paper proposes an approach for high-order time integration within a multi-domain setting for time-fractional differential equations. Since the kernel is singular or nearly singular, two main difficulties arise after the domain decomposition: how to properly account for the history/memory part and how to perform the integration accurately. To address these issues, we propose a novel hybrid approach for the numerical integration based on the combination of three-term-recurrence relations of Jacobi polynomials and high-order Gauss quadrature. The different approximations used in the hybrid approach are justified theoretically and through numerical examples. Based on this, we propose a new multi-domain spectral method for high-order accurate time integrations and study its stability properties by identifying the method as a generalized linear method. Numerical experiments confirm hp-convergence for both time-fractional differential equations and time-fractional partial differential equations.

An hp symplectic pseudospectral method for nonlinear optimal control

NASA Astrophysics Data System (ADS)

Peng, Haijun; Wang, Xinwei; Li, Mingwu; Chen, Biaosong

2017-01-01

An adaptive symplectic pseudospectral method based on the dual variational principle is proposed and is successfully applied to solving nonlinear optimal control problems in this paper. The proposed method satisfies the first order necessary conditions of continuous optimal control problems, also the symplectic property of the original continuous Hamiltonian system is preserved. The original optimal control problem is transferred into a set of nonlinear equations which can be solved easily by Newton-Raphson iterations, and the Jacobian matrix is found to be sparse and symmetric. The proposed method, on one hand, exhibits exponent convergence rates when the number of collocation points are increasing with the fixed number of sub-intervals; on the other hand, exhibits linear convergence rates when the number of sub-intervals is increasing with the fixed number of collocation points. Furthermore, combining with the hp method based on the residual error of dynamic constraints, the proposed method can achieve given precisions in a few iterations. Five examples highlight the high precision and high computational efficiency of the proposed method.

Spectral analysis of structure functions and their scaling exponents in forced isotropic turbulence

NASA Astrophysics Data System (ADS)

Linkmann, Moritz; McComb, W. David; Yoffe, Samuel; Berera, Arjun

2014-11-01

The pseudospectral method, in conjunction with a new technique for obtaining scaling exponents ζn from the structure functions Sn (r) , is presented as an alternative to the extended self-similarity (ESS) method and the use of generalized structure functions. We propose plotting the ratio | Sn (r) /S3 (r) | against the separation r in accordance with a standard technique for analysing experimental data. This method differs from the ESS technique, which plots the generalized structure functions Gn (r) against G3 (r) , where G3 (r) ~ r . Using our method for the particular case of S2 (r) we obtain the new result that the exponent ζ2 decreases as the Taylor-Reynolds number increases, with ζ2 --> 0 . 679 +/- 0 . 013 as Rλ --> ∞ . This supports the idea of finite-viscosity corrections to the K41 prediction for S2, and is the opposite of the result obtained by ESS. The pseudospectral method permits the forcing to be taken into account exactly through the calculation of the energy input in real space from the work spectrum of the stirring forces. The combination of the viscous and the forcing corrections as calculated by the pseudospectral method is shown to account for the deviation of S3 from Kolmogorov's ``four-fifths''-law at all scales. This work has made use of the resources provided by the UK supercomputing service HECToR, made available through the Edinburgh Compute and Data Facility (ECDF). A. B. is supported by STFC, S. R. Y. and M. F. L. are funded by EPSRC.

Computational aspects of pseudospectral Laguerre approximations

NASA Technical Reports Server (NTRS)

Funaro, Daniele

1989-01-01

Pseudospectral approximations in unbounded domains by Laguerre polynomials lead to ill-conditioned algorithms. Introduced are a scaling function and appropriate numerical procedures in order to limit these unpleasant phenomena.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jalas, S.; Dornmair, I.; Lehe, R.

Particle in Cell (PIC) simulations are a widely used tool for the investigation of both laser- and beam-driven plasma acceleration. It is a known issue that the beam quality can be artificially degraded by numerical Cherenkov radiation (NCR) resulting primarily from an incorrectly modeled dispersion relation. Pseudo-spectral solvers featuring infinite order stencils can strongly reduce NCR - or even suppress it - and are therefore well suited to correctly model the beam properties. For efficient parallelization of the PIC algorithm, however, localized solvers are inevitable. Arbitrary order pseudo-spectral methods provide this needed locality. Yet, these methods can again be pronemore » to NCR. Here in this paper, we show that acceptably low solver orders are sufficient to correctly model the physics of interest, while allowing for parallel computation by domain decomposition.« less

New Operational Matrices for Solving Fractional Differential Equations on the Half-Line

PubMed Central

2015-01-01

In this paper, the fractional-order generalized Laguerre operational matrices (FGLOM) of fractional derivatives and fractional integration are derived. These operational matrices are used together with spectral tau method for solving linear fractional differential equations (FDEs) of order ν (0 < ν < 1) on the half line. An upper bound of the absolute errors is obtained for the approximate and exact solutions. Fractional-order generalized Laguerre pseudo-spectral approximation is investigated for solving nonlinear initial value problem of fractional order ν. The extension of the fractional-order generalized Laguerre pseudo-spectral method is given to solve systems of FDEs. We present the advantages of using the spectral schemes based on fractional-order generalized Laguerre functions and compare them with other methods. Several numerical examples are implemented for FDEs and systems of FDEs including linear and nonlinear terms. We demonstrate the high accuracy and the efficiency of the proposed techniques. PMID:25996369

New operational matrices for solving fractional differential equations on the half-line.

PubMed

Bhrawy, Ali H; Taha, Taha M; Alzahrani, Ebraheem O; Alzahrani, Ebrahim O; Baleanu, Dumitru; Alzahrani, Abdulrahim A

2015-01-01

In this paper, the fractional-order generalized Laguerre operational matrices (FGLOM) of fractional derivatives and fractional integration are derived. These operational matrices are used together with spectral tau method for solving linear fractional differential equations (FDEs) of order ν (0 < ν < 1) on the half line. An upper bound of the absolute errors is obtained for the approximate and exact solutions. Fractional-order generalized Laguerre pseudo-spectral approximation is investigated for solving nonlinear initial value problem of fractional order ν. The extension of the fractional-order generalized Laguerre pseudo-spectral method is given to solve systems of FDEs. We present the advantages of using the spectral schemes based on fractional-order generalized Laguerre functions and compare them with other methods. Several numerical examples are implemented for FDEs and systems of FDEs including linear and nonlinear terms. We demonstrate the high accuracy and the efficiency of the proposed techniques.

A Multi-domain Spectral Method for Supersonic Reactive Flows

NASA Technical Reports Server (NTRS)

Don, Wai-Sun; Gottlieb, David; Jung, Jae-Hun; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

This paper has a dual purpose: it presents a multidomain Chebyshev method for the solution of the two-dimensional reactive compressible Navier-Stokes equations, and it reports the results of the application of this code to the numerical simulations of high Mach number reactive flows in recessed cavity. The computational method utilizes newly derived interface boundary conditions as well as an adaptive filtering technique to stabilize the computations. The results of the simulations are relevant to recessed cavity flameholders.

THE PSTD ALGORITHM: A TIME-DOMAIN METHOD REQUIRING ONLY TWO CELLS PER WAVELENGTH. (R825225)

EPA Science Inventory

A pseudospectral time-domain (PSTD) method is developed for solutions of Maxwell's equations. It uses the fast Fourier transform (FFT), instead of finite differences on conventional finite-difference-time-domain (FDTD) methods, to represent spatial derivatives. Because the Fourie...

Solution of the one-dimensional consolidation theory equation with a pseudospectral method

USGS Publications Warehouse

Sepulveda, N.; ,

1991-01-01

The one-dimensional consolidation theory equation is solved for an aquifer system using a pseudospectral method. The spatial derivatives are computed using Fast Fourier Transforms and the time derivative is solved using a fourth-order Runge-Kutta scheme. The computer model calculates compaction based on the void ratio changes accumulated during the simulated periods of time. Compactions and expansions resulting from groundwater withdrawals and recharges are simulated for two observation wells in Santa Clara Valley and two in San Joaquin Valley, California. Field data previously published are used to obtain mean values for the soil grain density and the compression index and to generate depth-dependent profiles for hydraulic conductivity and initial void ratio. The water-level plots for the wells studied were digitized and used to obtain the time dependent profiles of effective stress.

Pseudospectral calculation of helium wave functions, expectation values, and oscillator strength

NASA Astrophysics Data System (ADS)

Grabowski, Paul E.; Chernoff, David F.

2011-10-01

We show that the pseudospectral method is a powerful tool for finding precise solutions of Schrödinger’s equation for two-electron atoms with general angular momentum. Realizing the method’s full promise for atomic calculations requires special handling of singularities due to two-particle Coulomb interactions. We give a prescription for choosing coordinates and subdomains whose efficacy we illustrate by solving several challenging problems. One test centers on the determination of the nonrelativistic electric dipole oscillator strength for the helium 11S→21P transition. The result achieved, 0.27616499(27), is comparable to the best in the literature. The formally equivalent length, velocity, and acceleration expressions for the oscillator strength all yield roughly the same accuracy. We also calculate a diverse set of helium ground-state expectation values, reaching near state-of-the-art accuracy without the necessity of implementing any special-purpose numerics. These successes imply that general matrix elements are directly and reliably calculable with pseudospectral methods. A striking result is that all the relevant quantities tested in this paper—energy eigenvalues, S-state expectation values and a bound-bound dipole transition between the lowest energy S and P states—converge exponentially with increasing resolution and at roughly the same rate. Each individual calculation samples and weights the configuration space wave function uniquely but all behave in a qualitatively similar manner. These results suggest that the method has great promise for similarly accurate treatment of few-particle systems.

Enhancing magnetorheological effect using bimodal suspensions in the single-multidomain limit

NASA Astrophysics Data System (ADS)

Morillas, José R.; Bombard, Antonio J. F.; de Vicente, Juan

2018-07-01

We demonstrate a new route to enhance the magnetorheological effect using bimodal suspensions in the single-multidomain limit. Experimental results are satisfactorily compared to 3D finite element method simulations. The physical reason behind this enhancement is the coating of the larger particles by the smaller ones due to the remnant magnetization of the latter.

Particle-based solid for nonsmooth multidomain dynamics

NASA Astrophysics Data System (ADS)

Nordberg, John; Servin, Martin

2018-04-01

A method for simulation of elastoplastic solids in multibody systems with nonsmooth and multidomain dynamics is developed. The solid is discretised into pseudo-particles using the meshfree moving least squares method for computing the strain tensor. The particle's strain and stress tensor variables are mapped to a compliant deformation constraint. The discretised solid model thus fit a unified framework for nonsmooth multidomain dynamics simulations including rigid multibodies with complex kinematic constraints such as articulation joints, unilateral contacts with dry friction, drivelines, and hydraulics. The nonsmooth formulation allows for impact impulses to propagate instantly between the rigid multibody and the solid. Plasticity is introduced through an associative perfectly plastic modified Drucker-Prager model. The elastic and plastic dynamics are verified for simple test systems, and the capability of simulating tracked terrain vehicles driving on a deformable terrain is demonstrated.

A linear shock cell model for non-circular jets using conformal mapping with a pseudo-spectral hybrid scheme

NASA Technical Reports Server (NTRS)

Bhat, Thonse R. S.; Baty, Roy S.; Morris, Philip J.

1990-01-01

The shock structure in non-circular supersonic jets is predicted using a linear model. This model includes the effects of the finite thickness of the mixing layer and the turbulence in the jet shear layer. A numerical solution is obtained using a conformal mapping grid generation scheme with a hybrid pseudo-spectral discretization method. The uniform pressure perturbation at the jet exit is approximated by a Fourier-Mathieu series. The pressure at downstream locations is obtained from an eigenfunction expansion that is matched to the pressure perturbation at the jet exit. Results are presented for a circular jet and for an elliptic jet of aspect ratio 2.0. Comparisons are made with experimental data.

Model-free simulations of turbulent reactive flows

NASA Technical Reports Server (NTRS)

Givi, Peyman

1989-01-01

The current computational methods for solving transport equations of turbulent reacting single-phase flows are critically reviewed, with primary attention given to those methods that lead to model-free simulations. In particular, consideration is given to direct numerical simulations using spectral (Galerkin) and pseudospectral (collocation) methods, spectral element methods, and Lagrangian methods. The discussion also covers large eddy simulations and turbulence modeling.

The extended Fourier pseudospectral time-domain method for atmospheric sound propagation.

PubMed

Hornikx, Maarten; Waxler, Roger; Forssén, Jens

2010-10-01

An extended Fourier pseudospectral time-domain (PSTD) method is presented to model atmospheric sound propagation by solving the linearized Euler equations. In this method, evaluation of spatial derivatives is based on an eigenfunction expansion. Evaluation on a spatial grid requires only two spatial points per wavelength. Time iteration is done using a low-storage optimized six-stage Runge-Kutta method. This method is applied to two-dimensional non-moving media models, one with screens and one for an urban canyon, with generally high accuracy in both amplitude and phase. For a moving atmosphere, accurate results have been obtained in models with both a uniform and a logarithmic wind velocity profile over a rigid ground surface and in the presence of a screen. The method has also been validated for three-dimensional sound propagation over a screen. For that application, the developed method is in the order of 100 times faster than the second-order-accurate FDTD solution to the linearized Euler equations. The method is found to be well suited for atmospheric sound propagation simulations where effects of complex meteorology and straight rigid boundary surfaces are to be investigated.

A new method of imposing boundary conditions for hyperbolic equations

NASA Technical Reports Server (NTRS)

Funaro, D.; ative.

1987-01-01

A new method to impose boundary conditions for pseudospectral approximations to hyperbolic equations is suggested. This method involves the collocation of the equation at the boundary nodes as well as satisfying boundary conditions. Stability and convergence results are proven for the Chebyshev approximation of linear scalar hyperbolic equations. The eigenvalues of this method applied to parabolic equations are shown to be real and negative.

Arrhythmia Classification Based on Multi-Domain Feature Extraction for an ECG Recognition System.

PubMed

Li, Hongqiang; Yuan, Danyang; Wang, Youxi; Cui, Dianyin; Cao, Lu

2016-10-20

Automatic recognition of arrhythmias is particularly important in the diagnosis of heart diseases. This study presents an electrocardiogram (ECG) recognition system based on multi-domain feature extraction to classify ECG beats. An improved wavelet threshold method for ECG signal pre-processing is applied to remove noise interference. A novel multi-domain feature extraction method is proposed; this method employs kernel-independent component analysis in nonlinear feature extraction and uses discrete wavelet transform to extract frequency domain features. The proposed system utilises a support vector machine classifier optimized with a genetic algorithm to recognize different types of heartbeats. An ECG acquisition experimental platform, in which ECG beats are collected as ECG data for classification, is constructed to demonstrate the effectiveness of the system in ECG beat classification. The presented system, when applied to the MIT-BIH arrhythmia database, achieves a high classification accuracy of 98.8%. Experimental results based on the ECG acquisition experimental platform show that the system obtains a satisfactory classification accuracy of 97.3% and is able to classify ECG beats efficiently for the automatic identification of cardiac arrhythmias.

Arrhythmia Classification Based on Multi-Domain Feature Extraction for an ECG Recognition System

PubMed Central

Li, Hongqiang; Yuan, Danyang; Wang, Youxi; Cui, Dianyin; Cao, Lu

2016-01-01

Automatic recognition of arrhythmias is particularly important in the diagnosis of heart diseases. This study presents an electrocardiogram (ECG) recognition system based on multi-domain feature extraction to classify ECG beats. An improved wavelet threshold method for ECG signal pre-processing is applied to remove noise interference. A novel multi-domain feature extraction method is proposed; this method employs kernel-independent component analysis in nonlinear feature extraction and uses discrete wavelet transform to extract frequency domain features. The proposed system utilises a support vector machine classifier optimized with a genetic algorithm to recognize different types of heartbeats. An ECG acquisition experimental platform, in which ECG beats are collected as ECG data for classification, is constructed to demonstrate the effectiveness of the system in ECG beat classification. The presented system, when applied to the MIT-BIH arrhythmia database, achieves a high classification accuracy of 98.8%. Experimental results based on the ECG acquisition experimental platform show that the system obtains a satisfactory classification accuracy of 97.3% and is able to classify ECG beats efficiently for the automatic identification of cardiac arrhythmias. PMID:27775596

A Spectral Multi-Domain Penalty Method for Elliptic Problems Arising From a Time-Splitting Algorithm For the Incompressible Navier-Stokes Equations

NASA Astrophysics Data System (ADS)

Diamantopoulos, Theodore; Rowe, Kristopher; Diamessis, Peter

2017-11-01

The Collocation Penalty Method (CPM) solves a PDE on the interior of a domain, while weakly enforcing boundary conditions at domain edges via penalty terms, and naturally lends itself to high-order and multi-domain discretization. Such spectral multi-domain penalty methods (SMPM) have been used to solve the Navier-Stokes equations. Bounds for penalty coefficients are typically derived using the energy method to guarantee stability for time-dependent problems. The choice of collocation points and penalty parameter can greatly affect the conditioning and accuracy of a solution. Effort has been made in recent years to relate various high-order methods on multiple elements or domains under the umbrella of the Correction Procedure via Reconstruction (CPR). Most applications of CPR have focused on solving the compressible Navier-Stokes equations using explicit time-stepping procedures. A particularly important aspect which is still missing in the context of the SMPM is a study of the Helmholtz equation arising in many popular time-splitting schemes for the incompressible Navier-Stokes equations. Stability and convergence results for the SMPM for the Helmholtz equation will be presented. Emphasis will be placed on the efficiency and accuracy of high-order methods.

Order statistics inference for describing topological coupling and mechanical symmetry breaking in multidomain proteins

NASA Astrophysics Data System (ADS)

Kononova, Olga; Jones, Lee; Barsegov, V.

2013-09-01

Cooperativity is a hallmark of proteins, many of which show a modular architecture comprising discrete structural domains. Detecting and describing dynamic couplings between structural regions is difficult in view of the many-body nature of protein-protein interactions. By utilizing the GPU-based computational acceleration, we carried out simulations of the protein forced unfolding for the dimer WW - WW of the all-β-sheet WW domains used as a model multidomain protein. We found that while the physically non-interacting identical protein domains (WW) show nearly symmetric mechanical properties at low tension, reflected, e.g., in the similarity of their distributions of unfolding times, these properties become distinctly different when tension is increased. Moreover, the uncorrelated unfolding transitions at a low pulling force become increasingly more correlated (dependent) at higher forces. Hence, the applied force not only breaks "the mechanical symmetry" but also couples the physically non-interacting protein domains forming a multi-domain protein. We call this effect "the topological coupling." We developed a new theory, inspired by order statistics, to characterize protein-protein interactions in multi-domain proteins. The method utilizes the squared-Gaussian model, but it can also be used in conjunction with other parametric models for the distribution of unfolding times. The formalism can be taken to the single-molecule experimental lab to probe mechanical cooperativity and domain communication in multi-domain proteins.

A k-space method for large-scale models of wave propagation in tissue.

PubMed

Mast, T D; Souriau, L P; Liu, D L; Tabei, M; Nachman, A I; Waag, R C

2001-03-01

Large-scale simulation of ultrasonic pulse propagation in inhomogeneous tissue is important for the study of ultrasound-tissue interaction as well as for development of new imaging methods. Typical scales of interest span hundreds of wavelengths; most current two-dimensional methods, such as finite-difference and finite-element methods, are unable to compute propagation on this scale with the efficiency needed for imaging studies. Furthermore, for most available methods of simulating ultrasonic propagation, large-scale, three-dimensional computations of ultrasonic scattering are infeasible. Some of these difficulties have been overcome by previous pseudospectral and k-space methods, which allow substantial portions of the necessary computations to be executed using fast Fourier transforms. This paper presents a simplified derivation of the k-space method for a medium of variable sound speed and density; the derivation clearly shows the relationship of this k-space method to both past k-space methods and pseudospectral methods. In the present method, the spatial differential equations are solved by a simple Fourier transform method, and temporal iteration is performed using a k-t space propagator. The temporal iteration procedure is shown to be exact for homogeneous media, unconditionally stable for "slow" (c(x) < or = c0) media, and highly accurate for general weakly scattering media. The applicability of the k-space method to large-scale soft tissue modeling is shown by simulating two-dimensional propagation of an incident plane wave through several tissue-mimicking cylinders as well as a model chest wall cross section. A three-dimensional implementation of the k-space method is also employed for the example problem of propagation through a tissue-mimicking sphere. Numerical results indicate that the k-space method is accurate for large-scale soft tissue computations with much greater efficiency than that of an analogous leapfrog pseudospectral method or a 2-4 finite difference time-domain method. However, numerical results also indicate that the k-space method is less accurate than the finite-difference method for a high contrast scatterer with bone-like properties, although qualitative results can still be obtained by the k-space method with high efficiency. Possible extensions to the method, including representation of absorption effects, absorbing boundary conditions, elastic-wave propagation, and acoustic nonlinearity, are discussed.

Multidomain approach for calculating compressible flows

NASA Technical Reports Server (NTRS)

Cambier, L.; Chazzi, W.; Veuillot, J. P.; Viviand, H.

1982-01-01

A multidomain approach for calculating compressible flows by using unsteady or pseudo-unsteady methods is presented. This approach is based on a general technique of connecting together two domains in which hyperbolic systems (that may differ) are solved with the aid of compatibility relations associated with these systems. Some examples of this approach's application to calculating transonic flows in ideal fluids are shown, particularly the adjustment of shock waves. The approach is then applied to treating a shock/boundary layer interaction problem in a transonic channel.

Error analysis for spectral approximation of the Korteweg-De Vries equation

NASA Technical Reports Server (NTRS)

Maday, Y.; recent years.

1987-01-01

The conservation and convergence properties of spectral Fourier methods for the numerical approximation of the Korteweg-de Vries equation are analyzed. It is proved that the (aliased) collocation pseudospectral method enjoys the same convergence properties as the spectral Galerkin method, which is less effective from the computational point of view. This result provides a precise mathematical answer to a question raised by several authors in recent years.

Application of shifted Jacobi pseudospectral method for solving (in)finite-horizon min-max optimal control problems with uncertainty

NASA Astrophysics Data System (ADS)

Nikooeinejad, Z.; Delavarkhalafi, A.; Heydari, M.

2018-03-01

The difficulty of solving the min-max optimal control problems (M-MOCPs) with uncertainty using generalised Euler-Lagrange equations is caused by the combination of split boundary conditions, nonlinear differential equations and the manner in which the final time is treated. In this investigation, the shifted Jacobi pseudospectral method (SJPM) as a numerical technique for solving two-point boundary value problems (TPBVPs) in M-MOCPs for several boundary states is proposed. At first, a novel framework of approximate solutions which satisfied the split boundary conditions automatically for various boundary states is presented. Then, by applying the generalised Euler-Lagrange equations and expanding the required approximate solutions as elements of shifted Jacobi polynomials, finding a solution of TPBVPs in nonlinear M-MOCPs with uncertainty is reduced to the solution of a system of algebraic equations. Moreover, the Jacobi polynomials are particularly useful for boundary value problems in unbounded domain, which allow us to solve infinite- as well as finite and free final time problems by domain truncation method. Some numerical examples are given to demonstrate the accuracy and efficiency of the proposed method. A comparative study between the proposed method and other existing methods shows that the SJPM is simple and accurate.

Petascale turbulence simulation using a highly parallel fast multipole method on GPUs

NASA Astrophysics Data System (ADS)

Yokota, Rio; Barba, L. A.; Narumi, Tetsu; Yasuoka, Kenji

2013-03-01

This paper reports large-scale direct numerical simulations of homogeneous-isotropic fluid turbulence, achieving sustained performance of 1.08 petaflop/s on GPU hardware using single precision. The simulations use a vortex particle method to solve the Navier-Stokes equations, with a highly parallel fast multipole method (FMM) as numerical engine, and match the current record in mesh size for this application, a cube of 40963 computational points solved with a spectral method. The standard numerical approach used in this field is the pseudo-spectral method, relying on the FFT algorithm as the numerical engine. The particle-based simulations presented in this paper quantitatively match the kinetic energy spectrum obtained with a pseudo-spectral method, using a trusted code. In terms of parallel performance, weak scaling results show the FMM-based vortex method achieving 74% parallel efficiency on 4096 processes (one GPU per MPI process, 3 GPUs per node of the TSUBAME-2.0 system). The FFT-based spectral method is able to achieve just 14% parallel efficiency on the same number of MPI processes (using only CPU cores), due to the all-to-all communication pattern of the FFT algorithm. The calculation time for one time step was 108 s for the vortex method and 154 s for the spectral method, under these conditions. Computing with 69 billion particles, this work exceeds by an order of magnitude the largest vortex-method calculations to date.

An analysis of artificial viscosity effects on reacting flows using a spectral multi-domain technique

NASA Technical Reports Server (NTRS)

Macaraeg, M. G.; Streett, C. L.; Hussaini, M. Y.

1987-01-01

Standard techniques used to model chemically-reacting flows require an artificial viscosity for stability in the presence of strong shocks. The resulting shock is smeared over at least three computational cells, so that the thickness of the shock is dictated by the structure of the overall mesh and not the shock physics. A gas passing through a strong shock is thrown into a nonequilibrium state and subsequently relaxes down over some finite distance to an equilibrium end state. The artificial smearing of the shock envelops this relaxation zone which causes the chemical kinetics of the flow to be altered. A method is presented which can investigate these issues by following the chemical kinetics and flow kinetics of a gas passing through a fully resolved shock wave at hypersonic Mach numbers. A nonequilibrium chemistry model for air is incorporated into a spectral multidomain Navier-Stokes solution method. Since no artificial viscosity is needed for stability of the multidomain technique, the precise effect of this artifice on the chemical kinetics and relevant flow features can be determined.

Pseudospectral modeling and dispersion analysis of Rayleigh waves in viscoelastic media

USGS Publications Warehouse

Zhang, K.; Luo, Y.; Xia, J.; Chen, C.

2011-01-01

Multichannel Analysis of Surface Waves (MASW) is one of the most widely used techniques in environmental and engineering geophysics to determine shear-wave velocities and dynamic properties, which is based on the elastic layered system theory. Wave propagation in the Earth, however, has been recognized as viscoelastic and the propagation of Rayleigh waves presents substantial differences in viscoelastic media as compared with elastic media. Therefore, it is necessary to carry out numerical simulation and dispersion analysis of Rayleigh waves in viscoelastic media to better understand Rayleigh-wave behaviors in the real world. We apply a pseudospectral method to the calculation of the spatial derivatives using a Chebyshev difference operator in the vertical direction and a Fourier difference operator in the horizontal direction based on the velocity-stress elastodynamic equations and relations of linear viscoelastic solids. This approach stretches the spatial discrete grid to have a minimum grid size near the free surface so that high accuracy and resolution are achieved at the free surface, which allows an effective incorporation of the free surface boundary conditions since the Chebyshev method is nonperiodic. We first use an elastic homogeneous half-space model to demonstrate the accuracy of the pseudospectral method comparing with the analytical solution, and verify the correctness of the numerical modeling results for a viscoelastic half-space comparing the phase velocities of Rayleigh wave between the theoretical values and the dispersive image generated by high-resolution linear Radon transform. We then simulate three types of two-layer models to analyze dispersive-energy characteristics for near-surface applications. Results demonstrate that the phase velocity of Rayleigh waves in viscoelastic media is relatively higher than in elastic media and the fundamental mode increases by 10-16% when the frequency is above 10. Hz due to the velocity dispersion of P and S waves. ?? 2011 Elsevier Ltd.

Mapped Chebyshev Pseudo-Spectral Method for Dynamic Aero-Elastic Problem of Limit Cycle Oscillation

NASA Astrophysics Data System (ADS)

Im, Dong Kyun; Kim, Hyun Soon; Choi, Seongim

2018-05-01

A mapped Chebyshev pseudo-spectral method is developed as one of the Fourier-spectral approaches and solves nonlinear PDE systems for unsteady flows and dynamic aero-elastic problem in a given time interval, where the flows or elastic motions can be periodic, nonperiodic, or periodic with an unknown frequency. The method uses the Chebyshev polynomials of the first kind for the basis function and redistributes the standard Chebyshev-Gauss-Lobatto collocation points more evenly by a conformal mapping function for improved numerical stability. Contributions of the method are several. It can be an order of magnitude more efficient than the conventional finite difference-based, time-accurate computation, depending on the complexity of solutions and the number of collocation points. The method reformulates the dynamic aero-elastic problem in spectral form for coupled analysis of aerodynamics and structures, which can be effective for design optimization of unsteady and dynamic problems. A limit cycle oscillation (LCO) is chosen for the validation and a new method to determine the LCO frequency is introduced based on the minimization of a second derivative of the aero-elastic formulation. Two examples of the limit cycle oscillation are tested: nonlinear, one degree-of-freedom mass-spring-damper system and two degrees-of-freedom oscillating airfoil under pitch and plunge motions. Results show good agreements with those of the conventional time-accurate simulations and wind tunnel experiments.

An Access Control and Trust Management Framework for Loosely-Coupled Multidomain Environments

ERIC Educational Resources Information Center

Zhang, Yue

2010-01-01

Multidomain environments where multiple organizations interoperate with each other are becoming a reality as can be seen in emerging Internet-based enterprise applications. Access control to ensure secure interoperation in such an environment is a crucial challenge. A multidomain environment can be categorized as "tightly-coupled" and…

Revisiting and Extending Interface Penalties for Multi-Domain Summation-by-Parts Operators

NASA Technical Reports Server (NTRS)

Carpenter, Mark H.; Nordstrom, Jan; Gottlieb, David

2007-01-01

General interface coupling conditions are presented for multi-domain collocation methods, which satisfy the summation-by-parts (SBP) spatial discretization convention. The combined interior/interface operators are proven to be L2 stable, pointwise stable, and conservative, while maintaining the underlying accuracy of the interior SBP operator. The new interface conditions resemble (and were motivated by) those used in the discontinuous Galerkin finite element community, and maintain many of the same properties. Extensive validation studies are presented using two classes of high-order SBP operators: 1) central finite difference, and 2) Legendre spectral collocation.

On the boundary treatment in spectral methods for hyperbolic systems

NASA Technical Reports Server (NTRS)

Canuto, C.; Quarteroni, A.

1986-01-01

Spectral methods were successfully applied to the simulation of slow transients in gas transportation networks. Implicit time advancing techniques are naturally suggested by the nature of the problem. The correct treatment of the boundary conditions are clarified in order to avoid any stability restriction originated by the boundaries. The Beam and Warming and the Lerat schemes are unconditionally linearly stable when used with a Chebyshev pseudospectral method. Engineering accuracy for a gas transportation problem is achieved at Courant numbers up to 100.

On the boundary treatment in spectral methods for hyperbolic systems

NASA Technical Reports Server (NTRS)

Canuto, Claudio; Quarteroni, Alfio

1987-01-01

Spectral methods were successfully applied to the simulation of slow transients in gas transportation networks. Implicit time advancing techniques are naturally suggested by the nature of the problem. The correct treatment of the boundary conditions is clarified in order to avoid any stability restriction originated by the boundaries. The Beam and Warming and the Lerat schemes are unconditionally linearly stable when used with a Chebyshev pseudospectral method. Engineering accuracy for a gas transportation problem is achieved at Courant numbers up to 100.

Hybrid Solution of Stochastic Optimal Control Problems Using Gauss Pseudospectral Method and Generalized Polynomial Chaos Algorithms

DTIC Science & Technology

2012-03-01

0-486-41183-4. 15. Brown , Robert G. and Patrick Y. C. Hwang . Introduction to Random Signals and Applied Kalman Filtering. Wiley, New York, 1996. ISBN...stability and perfor- mance criteria. In the 1960’s, Kalman introduced the Linear Quadratic Regulator (LQR) method using an integral performance index...feedback of the state variables and was able to apply this method to time-varying and Multi-Input Multi-Output (MIMO) systems. Kalman further showed

openPSTD: The open source pseudospectral time-domain method for acoustic propagation

NASA Astrophysics Data System (ADS)

Hornikx, Maarten; Krijnen, Thomas; van Harten, Louis

2016-06-01

An open source implementation of the Fourier pseudospectral time-domain (PSTD) method for computing the propagation of sound is presented, which is geared towards applications in the built environment. Being a wave-based method, PSTD captures phenomena like diffraction, but maintains efficiency in processing time and memory usage as it allows to spatially sample close to the Nyquist criterion, thus keeping both the required spatial and temporal resolution coarse. In the implementation it has been opted to model the physical geometry as a composition of rectangular two-dimensional subdomains, hence initially restricting the implementation to orthogonal and two-dimensional situations. The strategy of using subdomains divides the problem domain into local subsets, which enables the simulation software to be built according to Object-Oriented Programming best practices and allows room for further computational parallelization. The software is built using the open source components, Blender, Numpy and Python, and has been published under an open source license itself as well. For accelerating the software, an option has been included to accelerate the calculations by a partial implementation of the code on the Graphical Processing Unit (GPU), which increases the throughput by up to fifteen times. The details of the implementation are reported, as well as the accuracy of the code.

Fuel-optimal low-thrust formation reconfiguration via Radau pseudospectral method

NASA Astrophysics Data System (ADS)

Li, Jing

2016-07-01

This paper investigates fuel-optimal low-thrust formation reconfiguration near circular orbit. Based on the Clohessy-Wiltshire equations, first-order necessary optimality conditions are derived from the Pontryagin's maximum principle. The fuel-optimal impulsive solution is utilized to divide the low-thrust trajectory into thrust and coast arcs. By introducing the switching times as optimization variables, the fuel-optimal low-thrust formation reconfiguration is posed as a nonlinear programming problem (NLP) via direct transcription using multiple-phase Radau pseudospectral method (RPM), which is then solved by a sparse nonlinear optimization software SNOPT. To facilitate optimality verification and, if necessary, further refinement of the optimized solution of the NLP, formulas for mass costate estimation and initial costates scaling are presented. Numerical examples are given to show the application of the proposed optimization method. To fix the problem, generic fuel-optimal low-thrust formation reconfiguration can be simplified as reconfiguration without any initial and terminal coast arcs, whose optimal solutions can be efficiently obtained from the multiple-phase RPM at the cost of a slight fuel increment. Finally, influence of the specific impulse and maximum thrust magnitude on the fuel-optimal low-thrust formation reconfiguration is analyzed. Numerical results shown the links and differences between the fuel-optimal impulsive and low-thrust solutions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schnack, D.D.; Lottati, I.; Mikic, Z.

The authors describe TRIM, a MHD code which uses finite volume discretization of the MHD equations on an unstructured adaptive grid of triangles in the poloidal plane. They apply it to problems related to modeling tokamak toroidal plasmas. The toroidal direction is treated by a pseudospectral method. Care was taken to center variables appropriately on the mesh and to construct a self adjoint diffusion operator for cell centered variables.

Translation and integration of numerical atomic orbitals in linear molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heinäsmäki, Sami, E-mail: sami.heinasmaki@gmail.com

2014-02-14

We present algorithms for translation and integration of atomic orbitals for LCAO calculations in linear molecules. The method applies to arbitrary radial functions given on a numerical mesh. The algorithms are based on pseudospectral differentiation matrices in two dimensions and the corresponding two-dimensional Gaussian quadratures. As a result, multicenter overlap and Coulomb integrals can be evaluated effectively.

A mixed pseudospectral/finite difference method for a thermally driven fluid in a nonuniform gravitational field

NASA Technical Reports Server (NTRS)

Macaraeg, M. G.

1985-01-01

A numerical study of the steady, axisymmetric flow in a heated, rotating spherical shell is conducted to model the Atmospheric General Circulation Experiment (AGCE) proposed to run aboard a later Shuttle mission. The AGCE will consist of concentric rotating spheres confining a dielectric fluid. By imposing a dielectric field across the fluid a radial body force will be created. The numerical solution technique is based on the incompressible Navier-Stokes equations. In the method a pseudospectral technique is used in the latitudinal direction, and a second-order accurate finite difference scheme discretizes time and radial derivatives. This paper discusses the development and performance of this numerical scheme for the AGCE which has been modeled in the past only by pure FD formulations. In addition, previous models have not investigated the effect of using a dielectric force to simulate terrestrial gravity. The effect of this dielectric force on the flow field is investigated as well as a parameter study of varying rotation rates and boundary temperatures. Among the effects noted are the production of larger velocities and enhanced reversals of radial temperature gradients for a body force generated by the electric field.

High precision computing with charge domain devices and a pseudo-spectral method therefor

NASA Technical Reports Server (NTRS)

Barhen, Jacob (Inventor); Toomarian, Nikzad (Inventor); Fijany, Amir (Inventor); Zak, Michail (Inventor)

1997-01-01

The present invention enhances the bit resolution of a CCD/CID MVM processor by storing each bit of each matrix element as a separate CCD charge packet. The bits of each input vector are separately multiplied by each bit of each matrix element in massive parallelism and the resulting products are combined appropriately to synthesize the correct product. In another aspect of the invention, such arrays are employed in a pseudo-spectral method of the invention, in which partial differential equations are solved by expressing each derivative analytically as matrices, and the state function is updated at each computation cycle by multiplying it by the matrices. The matrices are treated as synaptic arrays of a neural network and the state function vector elements are treated as neurons. In a further aspect of the invention, moving target detection is performed by driving the soliton equation with a vector of detector outputs. The neural architecture consists of two synaptic arrays corresponding to the two differential terms of the soliton-equation and an adder connected to the output thereof and to the output of the detector array to drive the soliton equation.

Matrix Pseudospectral Method for (Visco)Elastic Tides Modeling of Planetary Bodies

NASA Astrophysics Data System (ADS)

Zabranova, Eliska; Hanyk, Ladidslav; Matyska, Ctirad

2010-05-01

We deal with the equations and boundary conditions describing deformation and gravitational potential of prestressed spherically symmetric elastic bodies by decomposing governing equations into a series of boundary value problems (BVP) for ordinary differential equations (ODE) of the second order. In contrast to traditional Runge-Kutta integration techniques, highly accurate pseudospectral schemes are employed to directly discretize the BVP on Chebyshev grids and a set of linear algebraic equations with an almost block diagonal matrix is derived. As a consequence of keeping the governing ODEs of the second order instead of the usual first-order equations, the resulting algebraic system is half-sized but derivatives of the model parameters are required. Moreover, they can be easily evaluated for models, where structural parametres are piecewise polynomially dependent. Both accuracy and efficiency of the method are tested by evaluating the tidal Love numbers for the Earth's model PREM. Finally, we also derive complex Love numbers for models with the Maxwell viscoelastic rheology, where viscosity is a depth-dependent function. The method is applied to evaluation of the tidal Love numbers for models of Mars and Venus. The Love numbers of the two Martian models - the former optimized to cosmochemical data and the latter to the moment of inertia (Sohl and Spohn, 1997) - are h2=0.172 (0.212) and k2=0.093 (0.113). For Venus, the value of k2=0.295 (Konopliv and Yoder, 1996), obtained from the gravity-field analysis, is consistent with the results for our model with the liquid-core radius of 3110 km (Zábranová et al., 2009). Together with rapid evaluation of free oscillation periods by an analogous method, this combined matrix approach could by employed as an efficient numerical tool in structural studies of planetary bodies. REFERENCES Konopliv, A. S. and Yoder, C. F., 1996. Venusian k2 tidal Love number from Magellan and PVO tracking data, Geophys. Res. Lett., 23, 1857-1860. Sohl, F., and Spohn, T., 1997. The interior structure of Mars: Implications from SNC meteorites, J. Geophys. Res., 102, 1613-1635. Zabranova, E., Hanyk L. and Matyska, C.: Matrix Pseudospectral Method for Elastic Tides Modeling. In: Holota P. (Ed.): Mission and Passion: Science. A volume dedicated to Milan Bursa on the occasion of his 80th birthday. Published by the Czech National Committee of Geodesy and Geophysics. Prague, 2009, pp. 243-260.

Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains

PubMed Central

Vishwanath, Sneha

2018-01-01

The majority of the proteins encoded in the genomes of eukaryotes contain more than one domain. Reasons for high prevalence of multi-domain proteins in various organisms have been attributed to higher stability and functional and folding advantages over single-domain proteins. Despite these advantages, many proteins are composed of only one domain while their homologous domains are part of multi-domain proteins. In the study presented here, differences in the properties of protein domains in single-domain and multi-domain systems and their influence on functions are discussed. We studied 20 pairs of identical protein domains, which were crystallized in two forms (a) tethered to other proteins domains and (b) tethered to fewer protein domains than (a) or not tethered to any protein domain. Results suggest that tethering of domains in multi-domain proteins influences the structural, dynamic and energetic properties of the constituent protein domains. 50% of the protein domain pairs show significant structural deviations while 90% of the protein domain pairs show differences in dynamics and 12% of the residues show differences in the energetics. To gain further insights on the influence of tethering on the function of the domains, 4 pairs of homologous protein domains, where one of them is a full-length single-domain protein and the other protein domain is a part of a multi-domain protein, were studied. Analyses showed that identical and structurally equivalent functional residues show differential dynamics in homologous protein domains; though comparable dynamics between in-silico generated chimera protein and multi-domain proteins were observed. From these observations, the differences observed in the functions of homologous proteins could be attributed to the presence of tethered domain. Overall, we conclude that tethered domains in multi-domain proteins not only provide stability or folding advantages but also influence pathways resulting in differences in function or regulatory properties. PMID:29432415

Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains.

PubMed

Vishwanath, Sneha; de Brevern, Alexandre G; Srinivasan, Narayanaswamy

2018-02-01

The majority of the proteins encoded in the genomes of eukaryotes contain more than one domain. Reasons for high prevalence of multi-domain proteins in various organisms have been attributed to higher stability and functional and folding advantages over single-domain proteins. Despite these advantages, many proteins are composed of only one domain while their homologous domains are part of multi-domain proteins. In the study presented here, differences in the properties of protein domains in single-domain and multi-domain systems and their influence on functions are discussed. We studied 20 pairs of identical protein domains, which were crystallized in two forms (a) tethered to other proteins domains and (b) tethered to fewer protein domains than (a) or not tethered to any protein domain. Results suggest that tethering of domains in multi-domain proteins influences the structural, dynamic and energetic properties of the constituent protein domains. 50% of the protein domain pairs show significant structural deviations while 90% of the protein domain pairs show differences in dynamics and 12% of the residues show differences in the energetics. To gain further insights on the influence of tethering on the function of the domains, 4 pairs of homologous protein domains, where one of them is a full-length single-domain protein and the other protein domain is a part of a multi-domain protein, were studied. Analyses showed that identical and structurally equivalent functional residues show differential dynamics in homologous protein domains; though comparable dynamics between in-silico generated chimera protein and multi-domain proteins were observed. From these observations, the differences observed in the functions of homologous proteins could be attributed to the presence of tethered domain. Overall, we conclude that tethered domains in multi-domain proteins not only provide stability or folding advantages but also influence pathways resulting in differences in function or regulatory properties.

Analysis of crack propagation in roller bearings using the boundary integral equation method - A mixed-mode loading problem

NASA Technical Reports Server (NTRS)

Ghosn, L. J.

1988-01-01

Crack propagation in a rotating inner raceway of a high-speed roller bearing is analyzed using the boundary integral method. The model consists of an edge plate under plane strain condition upon which varying Hertzian stress fields are superimposed. A multidomain boundary integral equation using quadratic elements was written to determine the stress intensity factors KI and KII at the crack tip for various roller positions. The multidomain formulation allows the two faces of the crack to be modeled in two different subregions, making it possible to analyze crack closure when the roller is positioned on or close to the crack line. KI and KII stress intensity factors along any direction were computed. These calculations permit determination of crack growth direction along which the average KI times the alternating KI is maximum.

Intercomparison of general circulation models for hot extrasolar planets

NASA Astrophysics Data System (ADS)

Polichtchouk, I.; Cho, J. Y.-K.; Watkins, C.; Thrastarson, H. Th.; Umurhan, O. M.; de la Torre Juárez, M.

2014-02-01

We compare five general circulation models (GCMs) which have been recently used to study hot extrasolar planet atmospheres (BOB, CAM, IGCM, MITgcm, and PEQMOD), under three test cases useful for assessing model convergence and accuracy. Such a broad, detailed intercomparison has not been performed thus far for extrasolar planets study. The models considered all solve the traditional primitive equations, but employ different numerical algorithms or grids (e.g., pseudospectral and finite volume, with the latter separately in longitude-latitude and ‘cubed-sphere’ grids). The test cases are chosen to cleanly address specific aspects of the behaviors typically reported in hot extrasolar planet simulations: (1) steady-state, (2) nonlinearly evolving baroclinic wave, and (3) response to fast timescale thermal relaxation. When initialized with a steady jet, all models maintain the steadiness, as they should-except MITgcm in cubed-sphere grid. A very good agreement is obtained for a baroclinic wave evolving from an initial instability in pseudospectral models (only). However, exact numerical convergence is still not achieved across the pseudospectral models: amplitudes and phases are observably different. When subject to a typical ‘hot-Jupiter’-like forcing, all five models show quantitatively different behavior-although qualitatively similar, time-variable, quadrupole-dominated flows are produced. Hence, as have been advocated in several past studies, specific quantitative predictions (such as the location of large vortices and hot regions) by GCMs should be viewed with caution. Overall, in the tests considered here, pseudospectral models in pressure coordinate (PEBOB and PEQMOD) perform the best and MITgcm in cubed-sphere grid performs the worst.

Resilient Multi-Domain Command and Control: Enabling Solutions for 2025 with Virtual Reality

DTIC Science & Technology

2017-04-16

AIR WAR COLLEGE AIR UNIVERSITY RESILIENT MULTI-DOMAIN COMMAND AND CONTROL : ENABLING SOLUTIONS FOR 2025 WITH VIRTUAL REALITY by...monolithic, command and control (C2) sites, such as the theater Air Operation Centers (AOC), at risk. The Multi-Domain Command and Control (MDC2...Air Force respond to the these threats, considering the use of new and existing weapons and concepts, to ensure our ability to command, control and

Seismic wavefield propagation in 2D anisotropic media: Ray theory versus wave-equation simulation

NASA Astrophysics Data System (ADS)

Bai, Chao-ying; Hu, Guang-yi; Zhang, Yan-teng; Li, Zhong-sheng

2014-05-01

Despite the ray theory that is based on the high frequency assumption of the elastic wave-equation, the ray theory and the wave-equation simulation methods should be mutually proof of each other and hence jointly developed, but in fact parallel independent progressively. For this reason, in this paper we try an alternative way to mutually verify and test the computational accuracy and the solution correctness of both the ray theory (the multistage irregular shortest-path method) and the wave-equation simulation method (both the staggered finite difference method and the pseudo-spectral method) in anisotropic VTI and TTI media. Through the analysis and comparison of wavefield snapshot, common source gather profile and synthetic seismogram, it is able not only to verify the accuracy and correctness of each of the methods at least for kinematic features, but also to thoroughly understand the kinematic and dynamic features of the wave propagation in anisotropic media. The results show that both the staggered finite difference method and the pseudo-spectral method are able to yield the same results even for complex anisotropic media (such as a fault model); the multistage irregular shortest-path method is capable of predicting similar kinematic features as the wave-equation simulation method does, which can be used to mutually test each other for methodology accuracy and solution correctness. In addition, with the aid of the ray tracing results, it is easy to identify the multi-phases (or multiples) in the wavefield snapshot, common source point gather seismic section and synthetic seismogram predicted by the wave-equation simulation method, which is a key issue for later seismic application.

Wave scattering of complex local site in a layered half-space by using a multidomain IBEM: incident plane SH waves

NASA Astrophysics Data System (ADS)

Ba, Zhenning; Yin, Xiao

2016-06-01

A multidomain indirect boundary element method (IBEM) is proposed to study the wave scattering of plane SH waves by complex local site in a layered half-space. The new method, using both the full-space and layered half-space Green's functions as its fundamental solutions can also be regarded as a coupled method of the full-space IBEM and half-space IBEM. First, the whole model is decomposed into independent closed regions and an opened layered half-space region with all of the irregular interfaces; then, fictitious uniformly distributed loads are applied separately on the boundaries of each region, and scattered fields of the closed regions and the opened layered half-space region are constructed by calculating the full-space and layered half-space Green's functions, respectively; finally, all of the regions are assembled to establish the linear algebraic system that arises from discretization. The densities of the distributed loads are determined directly by solving the algebraic system. The accuracy and capability of the new approach are verified extensively by comparing its results with those of published approaches for a class of hills, valleys and embedded inclusions. And the capability of the new method is further displayed when it is used to investigate a hill-triple layered valley-hill coupled topography in a multilayered half-space. All of the numerical calculations presented in this paper demonstrate that the new method is very suitable for solving multidomain coupled multilayered wave scattering problems with the merits of high accuracy and representing the scattered fields in different kinds of regions more reasonably and flexibly.

Two-Stage Path Planning Approach for Designing Multiple Spacecraft Reconfiguration Maneuvers

NASA Technical Reports Server (NTRS)

Aoude, Georges S.; How, Jonathan P.; Garcia, Ian M.

2007-01-01

The paper presents a two-stage approach for designing optimal reconfiguration maneuvers for multiple spacecraft. These maneuvers involve well-coordinated and highly-coupled motions of the entire fleet of spacecraft while satisfying an arbitrary number of constraints. This problem is particularly difficult because of the nonlinearity of the attitude dynamics, the non-convexity of some of the constraints, and the coupling between the positions and attitudes of all spacecraft. As a result, the trajectory design must be solved as a single 6N DOF problem instead of N separate 6 DOF problems. The first stage of the solution approach quickly provides a feasible initial solution by solving a simplified version without differential constraints using a bi-directional Rapidly-exploring Random Tree (RRT) planner. A transition algorithm then augments this guess with feasible dynamics that are propagated from the beginning to the end of the trajectory. The resulting output is a feasible initial guess to the complete optimal control problem that is discretized in the second stage using a Gauss pseudospectral method (GPM) and solved using an off-the-shelf nonlinear solver. This paper also places emphasis on the importance of the initialization step in pseudospectral methods in order to decrease their computation times and enable the solution of a more complex class of problems. Several examples are presented and discussed.

Commentary on "A roadmap for the prevention of dementia II. Leon Thal Symposium 2008." The Multidomain Alzheimer Preventive Trial (MAPT): a new approach to the prevention of Alzheimer's disease.

PubMed

Gillette-Guyonnet, Sophie; Andrieu, Sandrine; Dantoine, Thierry; Dartigues, Jean-François; Touchon, Jacques; Vellas, B

2009-03-01

Because no effective curative approaches are available, preventive approaches in the field of Alzheimer's disease (AD) are needed. We present the design of the ongoing Multidomain Alzheimer Preventive Trial (MAPT) Study. Several previous studies suggested that many factors may be involved in the occurrence of AD at late ages. Because of the probable multifactorial nature of AD, it seems logical to initiate multidomain interventions to examine their potential synergistic effects. The MAPT Study aims to evaluate the efficacy of a multidomain intervention (nutritional, physical, and cognitive training) and omega 3 treatment in the prevention of cognitive decline in frail elderly persons aged 70 years or over. The study also collects imaging and biological data that could be used in future AD prevention and treatment trials. The MAPT Study is a 3-year, randomized, controlled trial conducted by university hospital practitioners specializing in memory disorders in four French cities (Bordeaux, Limoges, Montpellier, and Toulouse). The study plans to enroll 1200 frail elderly subjects on the basis of at least one of the following criteria: subjective memory complaint spontaneously expressed to a general practitioner, limitation in one instrumental activity of daily living (IADL), and slow walking speed. To demonstrate the protective effect of interventions, subjects are randomized into one of the following four groups: omega 3 alone, multidomain intervention alone, omega 3 plus multidomain intervention, or placebo (n = 300 each). The principal outcome measure is a change in cognitive function at 3 years, as determined by the Grober and Buschke Test. The MAPT Study is the first preventive trial involving multidomain interventions. Final results should be available in 2013.

Hybrid Fourier pseudospectral/discontinuous Galerkin time-domain method for wave propagation

NASA Astrophysics Data System (ADS)

Pagán Muñoz, Raúl; Hornikx, Maarten

2017-11-01

The Fourier Pseudospectral time-domain (Fourier PSTD) method was shown to be an efficient way of modelling acoustic propagation problems as described by the linearized Euler equations (LEE), but is limited to real-valued frequency independent boundary conditions and predominantly staircase-like boundary shapes. This paper presents a hybrid approach to solve the LEE, coupling Fourier PSTD with a nodal Discontinuous Galerkin (DG) method. DG exhibits almost no restrictions with respect to geometrical complexity or boundary conditions. The aim of this novel method is to allow the computation of complex geometries and to be a step towards the implementation of frequency dependent boundary conditions by using the benefits of DG at the boundaries, while keeping the efficient Fourier PSTD in the bulk of the domain. The hybridization approach is based on conformal meshes to avoid spatial interpolation of the DG solutions when transferring values from DG to Fourier PSTD, while the data transfer from Fourier PSTD to DG is done utilizing spectral interpolation of the Fourier PSTD solutions. The accuracy of the hybrid approach is presented for one- and two-dimensional acoustic problems and the main sources of error are investigated. It is concluded that the hybrid methodology does not introduce significant errors compared to the Fourier PSTD stand-alone solver. An example of a cylinder scattering problem is presented and accurate results have been obtained when using the proposed approach. Finally, no instabilities were found during long-time calculation using the current hybrid methodology on a two-dimensional domain.

Acquisition of a Multi-Domain Advanced Real-Time Simulator to Support DoD-focused Interdisciplinary Research at CSUB

DTIC Science & Technology

2017-10-17

Report: Acquisition of a Multi-Domain Advanced Real- Time Simulator to Support DoD-focused Interdisciplinary Research at CSUB The views, opinions and...reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions...University - Bakersfield Title: Acquisition of a Multi-Domain Advanced Real- Time Simulator to Support DoD-focused Interdisciplinary Research at CSUB Report

Sampling Approaches for Multi-Domain Internet Performance Measurement Infrastructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Calyam, Prasad

2014-09-15

The next-generation of high-performance networks being developed in DOE communities are critical for supporting current and emerging data-intensive science applications. The goal of this project is to investigate multi-domain network status sampling techniques and tools to measure/analyze performance, and thereby provide “network awareness” to end-users and network operators in DOE communities. We leverage the infrastructure and datasets available through perfSONAR, which is a multi-domain measurement framework that has been widely deployed in high-performance computing and networking communities; the DOE community is a core developer and the largest adopter of perfSONAR. Our investigations include development of semantic scheduling algorithms, measurement federationmore » policies, and tools to sample multi-domain and multi-layer network status within perfSONAR deployments. We validate our algorithms and policies with end-to-end measurement analysis tools for various monitoring objectives such as network weather forecasting, anomaly detection, and fault-diagnosis. In addition, we develop a multi-domain architecture for an enterprise-specific perfSONAR deployment that can implement monitoring-objective based sampling and that adheres to any domain-specific measurement policies.« less

Automatic coronary artery segmentation based on multi-domains remapping and quantile regression in angiographies.

PubMed

Li, Zhixun; Zhang, Yingtao; Gong, Huiling; Li, Weimin; Tang, Xianglong

2016-12-01

Coronary artery disease has become the most dangerous diseases to human life. And coronary artery segmentation is the basis of computer aided diagnosis and analysis. Existing segmentation methods are difficult to handle the complex vascular texture due to the projective nature in conventional coronary angiography. Due to large amount of data and complex vascular shapes, any manual annotation has become increasingly unrealistic. A fully automatic segmentation method is necessary in clinic practice. In this work, we study a method based on reliable boundaries via multi-domains remapping and robust discrepancy correction via distance balance and quantile regression for automatic coronary artery segmentation of angiography images. The proposed method can not only segment overlapping vascular structures robustly, but also achieve good performance in low contrast regions. The effectiveness of our approach is demonstrated on a variety of coronary blood vessels compared with the existing methods. The overall segmentation performances si, fnvf, fvpf and tpvf were 95.135%, 3.733%, 6.113%, 96.268%, respectively. Copyright © 2016 Elsevier Ltd. All rights reserved.

Analysis of the spectral vanishing viscosity method for periodic conservation laws

NASA Technical Reports Server (NTRS)

Maday, Yvon; Tadmor, Eitan

1988-01-01

The convergence of the spectral vanishing method for both the spectral and pseudospectral discretizations of the inviscid Burgers' equation is analyzed. It is proven that this kind of vanishing viscosity is responsible for a spectral decay of those Fourier coefficients located toward the end of the computed spectrum; consequently, the discretization error is shown to be spectrally small independent of whether the underlying solution is smooth or not. This in turn implies that the numerical solution remains uniformly bounded and convergence follows by compensated compactness arguments.

Multi-Domain SDN Survivability for Agricultural Wireless Sensor Networks.

PubMed

Huang, Tao; Yan, Siyu; Yang, Fan; Liu, Jiang

2016-11-06

Wireless sensor networks (WSNs) have been widely applied in agriculture field; meanwhile, the advent of multi-domain software-defined networks (SDNs) have improved the wireless resource utilization rate and strengthened network management. In recent times, multi-domain SDNs have been applied to agricultural sensor networks, namely multi-domain software-defined wireless sensor networks (SDWSNs). However, when the SDNs controlling agriculture networks suddenly become unavailable, whether intra-domain or inter-domain, sensor network communication is abnormal because of the loss of control. Moreover, there are controller and switch info-updating problems even if the controller becomes available again. To resolve these problems, this paper proposes a new approach based on an Open vSwitch extension for multi-domain SDWSNs, which can enhance agriculture network survivability and stability. We achieved this by designing a connection-state mechanism, a communication mechanism on both L2 and L3, and an info-updating mechanism based on Open vSwitch. The experimental results show that, whether it is agricultural inter-domain or intra-domain during the controller failure period, the sensor switches can enter failure recovery mode as soon as possible so that the sensor network keeps a stable throughput, a short failure recovery time below 300 ms, and low packet loss. Further, the domain can smoothly control the domain network again once the controller becomes available. This approach based on an Open vSwitch extension can enhance the survivability and stability of multi-domain SDWSNs in precision agriculture.

Multi-Domain SDN Survivability for Agricultural Wireless Sensor Networks

PubMed Central

Huang, Tao; Yan, Siyu; Yang, Fan; Liu, Jiang

2016-01-01

Wireless sensor networks (WSNs) have been widely applied in agriculture field; meanwhile, the advent of multi-domain software-defined networks (SDNs) have improved the wireless resource utilization rate and strengthened network management. In recent times, multi-domain SDNs have been applied to agricultural sensor networks, namely multi-domain software-defined wireless sensor networks (SDWSNs). However, when the SDNs controlling agriculture networks suddenly become unavailable, whether intra-domain or inter-domain, sensor network communication is abnormal because of the loss of control. Moreover, there are controller and switch info-updating problems even if the controller becomes available again. To resolve these problems, this paper proposes a new approach based on an Open vSwitch extension for multi-domain SDWSNs, which can enhance agriculture network survivability and stability. We achieved this by designing a connection-state mechanism, a communication mechanism on both L2 and L3, and an info-updating mechanism based on Open vSwitch. The experimental results show that, whether it is agricultural inter-domain or intra-domain during the controller failure period, the sensor switches can enter failure recovery mode as soon as possible so that the sensor network keeps a stable throughput, a short failure recovery time below 300 ms, and low packet loss. Further, the domain can smoothly control the domain network again once the controller becomes available. This approach based on an Open vSwitch extension can enhance the survivability and stability of multi-domain SDWSNs in precision agriculture. PMID:27827971

Robust iterative method for nonlinear Helmholtz equation

NASA Astrophysics Data System (ADS)

Yuan, Lijun; Lu, Ya Yan

2017-08-01

A new iterative method is developed for solving the two-dimensional nonlinear Helmholtz equation which governs polarized light in media with the optical Kerr nonlinearity. In the strongly nonlinear regime, the nonlinear Helmholtz equation could have multiple solutions related to phenomena such as optical bistability and symmetry breaking. The new method exhibits a much more robust convergence behavior than existing iterative methods, such as frozen-nonlinearity iteration, Newton's method and damped Newton's method, and it can be used to find solutions when good initial guesses are unavailable. Numerical results are presented for the scattering of light by a nonlinear circular cylinder based on the exact nonlocal boundary condition and a pseudospectral method in the polar coordinate system.

A cross-domain communication resource scheduling method for grid-enabled communication networks

NASA Astrophysics Data System (ADS)

Zheng, Xiangquan; Wen, Xiang; Zhang, Yongding

2011-10-01

To support a wide range of different grid applications in environments where various heterogeneous communication networks coexist, it is important to enable advanced capabilities in on-demand and dynamical integration and efficient co-share with cross-domain heterogeneous communication resource, thus providing communication services which are impossible for single communication resource to afford. Based on plug-and-play co-share and soft integration with communication resource, Grid-enabled communication network is flexibly built up to provide on-demand communication services for gird applications with various requirements on quality of service. Based on the analysis of joint job and communication resource scheduling in grid-enabled communication networks (GECN), this paper presents a cross multi-domain communication resource cooperatively scheduling method and describes the main processes such as traffic requirement resolution for communication services, cross multi-domain negotiation on communication resource, on-demand communication resource scheduling, and so on. The presented method is to afford communication service capability to cross-domain traffic delivery in GECNs. Further research work towards validation and implement of the presented method is pointed out at last.

Multi-domain boundary element method for axi-symmetric layered linear acoustic systems

NASA Astrophysics Data System (ADS)

Reiter, Paul; Ziegelwanger, Harald

2017-12-01

Homogeneous porous materials like rock wool or synthetic foam are the main tool for acoustic absorption. The conventional absorbing structure for sound-proofing consists of one or multiple absorbers placed in front of a rigid wall, with or without air-gaps in between. Various models exist to describe these so called multi-layered acoustic systems mathematically for incoming plane waves. However, there is no efficient method to calculate the sound field in a half space above a multi layered acoustic system for an incoming spherical wave. In this work, an axi-symmetric multi-domain boundary element method (BEM) for absorbing multi layered acoustic systems and incoming spherical waves is introduced. In the proposed BEM formulation, a complex wave number is used to model absorbing materials as a fluid and a coordinate transformation is introduced which simplifies singular integrals of the conventional BEM to non-singular radial and angular integrals. The radial and angular part are integrated analytically and numerically, respectively. The output of the method can be interpreted as a numerical half space Green's function for grounds consisting of layered materials.

Multiscale Multiphysics and Multidomain Models I: Basic Theory

PubMed Central

Wei, Guo-Wei

2013-01-01

This work extends our earlier two-domain formulation of a differential geometry based multiscale paradigm into a multidomain theory, which endows us the ability to simultaneously accommodate multiphysical descriptions of aqueous chemical, physical and biological systems, such as fuel cells, solar cells, nanofluidics, ion channels, viruses, RNA polymerases, molecular motors and large macromolecular complexes. The essential idea is to make use of the differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain of solvent from the microscopic domain of solute, and dynamically couple continuum and discrete descriptions. Our main strategy is to construct energy functionals to put on an equal footing of multiphysics, including polar (i.e., electrostatic) solvation, nonpolar solvation, chemical potential, quantum mechanics, fluid mechanics, molecular mechanics, coarse grained dynamics and elastic dynamics. The variational principle is applied to the energy functionals to derive desirable governing equations, such as multidomain Laplace-Beltrami (LB) equations for macromolecular morphologies, multidomain Poisson-Boltzmann (PB) equation or Poisson equation for electrostatic potential, generalized Nernst-Planck (NP) equations for the dynamics of charged solvent species, generalized Navier-Stokes (NS) equation for fluid dynamics, generalized Newton's equations for molecular dynamics (MD) or coarse-grained dynamics and equation of motion for elastic dynamics. Unlike the classical PB equation, our PB equation is an integral-differential equation due to solvent-solute interactions. To illustrate the proposed formalism, we have explicitly constructed three models, a multidomain solvation model, a multidomain charge transport model and a multidomain chemo-electro-fluid-MD-elastic model. Each solute domain is equipped with distinct surface tension, pressure, dielectric function, and charge density distribution. In addition to long-range Coulombic interactions, various non-electrostatic solvent-solute interactions are considered in the present modeling. We demonstrate the consistency between the non-equilibrium charge transport model and the equilibrium solvation model by showing the systematical reduction of the former to the latter at equilibrium. This paper also offers a brief review of the field. PMID:25382892

Multiscale Multiphysics and Multidomain Models I: Basic Theory.

PubMed

Wei, Guo-Wei

2013-12-01

This work extends our earlier two-domain formulation of a differential geometry based multiscale paradigm into a multidomain theory, which endows us the ability to simultaneously accommodate multiphysical descriptions of aqueous chemical, physical and biological systems, such as fuel cells, solar cells, nanofluidics, ion channels, viruses, RNA polymerases, molecular motors and large macromolecular complexes. The essential idea is to make use of the differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain of solvent from the microscopic domain of solute, and dynamically couple continuum and discrete descriptions. Our main strategy is to construct energy functionals to put on an equal footing of multiphysics, including polar (i.e., electrostatic) solvation, nonpolar solvation, chemical potential, quantum mechanics, fluid mechanics, molecular mechanics, coarse grained dynamics and elastic dynamics. The variational principle is applied to the energy functionals to derive desirable governing equations, such as multidomain Laplace-Beltrami (LB) equations for macromolecular morphologies, multidomain Poisson-Boltzmann (PB) equation or Poisson equation for electrostatic potential, generalized Nernst-Planck (NP) equations for the dynamics of charged solvent species, generalized Navier-Stokes (NS) equation for fluid dynamics, generalized Newton's equations for molecular dynamics (MD) or coarse-grained dynamics and equation of motion for elastic dynamics. Unlike the classical PB equation, our PB equation is an integral-differential equation due to solvent-solute interactions. To illustrate the proposed formalism, we have explicitly constructed three models, a multidomain solvation model, a multidomain charge transport model and a multidomain chemo-electro-fluid-MD-elastic model. Each solute domain is equipped with distinct surface tension, pressure, dielectric function, and charge density distribution. In addition to long-range Coulombic interactions, various non-electrostatic solvent-solute interactions are considered in the present modeling. We demonstrate the consistency between the non-equilibrium charge transport model and the equilibrium solvation model by showing the systematical reduction of the former to the latter at equilibrium. This paper also offers a brief review of the field.

A Logic for Inclusion of Administrative Domains and Administrators in Multi-domain Authorization

NASA Astrophysics Data System (ADS)

Iranmanesh, Zeinab; Amini, Morteza; Jalili, Rasool

Authorization policies for an administrative domain or a composition of multiple domains in multi-domain environments are determined by either one administrator or multiple administrators' cooperation. Several logic-based models for multi-domain environments' authorization have been proposed; however, they have not considered administrators and administrative domains in policies' representation. In this paper, we propose the syntax, proof theory, and semantics of a logic for multi-domain authorization policies including administrators and administrative domains. Considering administrators in policies provides the possibility of presenting composite administration having applicability in many collaborative applications. Indeed, administrators and administrative domains stated in policies can be used in authorization. The presented logic is based on modal logic and utilizes two calculi named the calculus of administrative domains and the calculus of administrators. It is also proved that the logic is sound. A case study is presented signifying the logic application in practical projects.

Analysis of Functional Dynamics of Modular Multidomain Proteins by SAXS and NMR.

PubMed

Thompson, Matthew K; Ehlinger, Aaron C; Chazin, Walter J

2017-01-01

Multiprotein machines drive virtually all primary cellular processes. Modular multidomain proteins are widely distributed within these dynamic complexes because they provide the flexibility needed to remodel structure as well as rapidly assemble and disassemble components of the machinery. Understanding the functional dynamics of modular multidomain proteins is a major challenge confronting structural biology today because their structure is not fixed in time. Small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy have proven particularly useful for the analysis of the structural dynamics of modular multidomain proteins because they provide highly complementary information for characterizing the architectural landscape accessible to these proteins. SAXS provides a global snapshot of all architectural space sampled by a molecule in solution. Furthermore, SAXS is sensitive to conformational changes, organization and oligomeric states of protein assemblies, and the existence of flexibility between globular domains in multiprotein complexes. The power of NMR to characterize dynamics provides uniquely complementary information to the global snapshot of the architectural ensemble provided by SAXS because it can directly measure domain motion. In particular, NMR parameters can be used to define the diffusion of domains within modular multidomain proteins, connecting the amplitude of interdomain motion to the architectural ensemble derived from SAXS. Our laboratory has been studying the roles of modular multidomain proteins involved in human DNA replication using SAXS and NMR. Here, we present the procedure for acquiring and analyzing SAXS and NMR data, using DNA primase and replication protein A as examples. © 2017 Elsevier Inc. All rights reserved.

An efficient hybrid pseudospectral/finite-difference scheme for solving the TTI pure P-wave equation

NASA Astrophysics Data System (ADS)

Zhan, Ge; Pestana, Reynam C.; Stoffa, Paul L.

2013-04-01

The pure P-wave equation for modelling and migration in tilted transversely isotropic (TTI) media has attracted more and more attention in imaging seismic data with anisotropy. The desirable feature is that it is absolutely free of shear-wave artefacts and the consequent alleviation of numerical instabilities generally suffered by some systems of coupled equations. However, due to several forward-backward Fourier transforms in wavefield updating at each time step, the computational cost is significant, and thereby hampers its prevalence. We propose to use a hybrid pseudospectral (PS) and finite-difference (FD) scheme to solve the pure P-wave equation. In the hybrid solution, most of the cost-consuming wavenumber terms in the equation are replaced by inexpensive FD operators, which in turn accelerates the computation and reduces the computational cost. To demonstrate the benefit in cost saving of the new scheme, 2D and 3D reverse-time migration (RTM) examples using the hybrid solution to the pure P-wave equation are carried out, and respective runtimes are listed and compared. Numerical results show that the hybrid strategy demands less computation time and is faster than using the PS method alone. Furthermore, this new TTI RTM algorithm with the hybrid method is computationally less expensive than that with the FD solution to conventional TTI coupled equations.

Effect of long-term omega 3 polyunsaturated fatty acid supplementation with or without multidomain intervention on cognitive function in elderly adults with memory complaints (MAPT): a randomised, placebo-controlled trial.

PubMed

Andrieu, Sandrine; Guyonnet, Sophie; Coley, Nicola; Cantet, Christelle; Bonnefoy, Marc; Bordes, Serge; Bories, Lawrence; Cufi, Marie-Noëlle; Dantoine, Thierry; Dartigues, Jean-François; Desclaux, Françoise; Gabelle, Audrey; Gasnier, Yannick; Pesce, Alain; Sudres, Kristel; Touchon, Jacques; Robert, Philippe; Rouaud, Olivier; Legrand, Philippe; Payoux, Pierre; Caubere, Jean-Paul; Weiner, Michael; Carrié, Isabelle; Ousset, Pierre-Jean; Vellas, Bruno

2017-05-01

No large trials have been done to investigate the efficacy of an intervention combining a specific compound and several lifestyle interventions compared with placebo for the prevention of cognitive decline. We tested the effect of omega 3 polyunsaturated fatty acid supplementation and a multidomain intervention (physical activity, cognitive training, and nutritional advice), alone or in combination, compared with placebo, on cognitive decline. The Multidomain Alzheimer Preventive Trial was a 3-year, multicentre, randomised, placebo-controlled superiority trial with four parallel groups at 13 memory centres in France and Monaco. Participants were non-demented, aged 70 years or older, and community-dwelling, and had either relayed a spontaneous memory complaint to their physician, limitations in one instrumental activity of daily living, or slow gait speed. They were randomly assigned (1:1:1:1) to either the multidomain intervention (43 group sessions integrating cognitive training, physical activity, and nutrition, and three preventive consultations) plus omega 3 polyunsaturated fatty acids (ie, two capsules a day providing a total daily dose of 800 mg docosahexaenoic acid and 225 mg eicosapentaenoic acid), the multidomain intervention plus placebo, omega 3 polyunsaturated fatty acids alone, or placebo alone. A computer-generated randomisation procedure was used to stratify patients by centre. All participants and study staff were blinded to polyunsaturated fatty acid or placebo assignment, but were unblinded to the multidomain intervention component. Assessment of cognitive outcomes was done by independent neuropsychologists blinded to group assignment. The primary outcome was change from baseline to 36 months on a composite Z score combining four cognitive tests (free and total recall of the Free and Cued Selective Reminding test, ten Mini-Mental State Examination orientation items, Digit Symbol Substitution Test, and Category Naming Test) in the modified intention-to-treat population. The trial was registered with ClinicalTrials.gov (NCT00672685). 1680 participants were enrolled and randomly allocated between May 30, 2008, and Feb 24, 2011. In the modified intention-to-treat population (n=1525), there were no significant differences in 3-year cognitive decline between any of the three intervention groups and the placebo group. Between-group differences compared with placebo were 0·093 (95% CI 0·001 to 0·184; adjusted p=0·142) for the combined intervention group, 0·079 (-0·012 to 0·170; 0·179) for the multidomain intervention plus placebo group, and 0·011 (-0·081 to 0·103; 0·812) for the omega 3 polyunsaturated fatty acids group. 146 (36%) participants in the multidomain plus polyunsaturated fatty acids group, 142 (34%) in the multidomain plus placebo group, 134 (33%) in the polyunsaturated fatty acids group, and 133 (32%) in the placebo group had at least one serious emerging adverse event. Four treatment-related deaths were recorded (two in the multidomain plus placebo group and two in the placebo group). The interventions did not raise any safety concerns and there were no differences between groups in serious or other adverse events. The multidomain intervention and polyunsaturated fatty acids, either alone or in combination, had no significant effects on cognitive decline over 3 years in elderly people with memory complaints. An effective multidomain intervention strategy to prevent or delay cognitive impairment and the target population remain to be determined, particularly in real-world settings. French Ministry of Health, Pierre Fabre Research Institute, Gerontopole, Exhonit Therapeutics, Avid Radiopharmaceuticals. Copyright © 2017 Elsevier Ltd. All rights reserved.

Space-dependent perfusion coefficient estimation in a 2D bioheat transfer problem

NASA Astrophysics Data System (ADS)

Bazán, Fermín S. V.; Bedin, Luciano; Borges, Leonardo S.

2017-05-01

In this work, a method for estimating the space-dependent perfusion coefficient parameter in a 2D bioheat transfer model is presented. In the method, the bioheat transfer model is transformed into a time-dependent semidiscrete system of ordinary differential equations involving perfusion coefficient values as parameters, and the estimation problem is solved through a nonlinear least squares technique. In particular, the bioheat problem is solved by the method of lines based on a highly accurate pseudospectral approach, and perfusion coefficient values are estimated by the regularized Gauss-Newton method coupled with a proper regularization parameter. The performance of the method on several test problems is illustrated numerically.

Balancing Power Absorption and Structural Loading for a Novel Fixed-Bottom Wave Energy Converter with Nonideal Power Take-Off in Regular Waves: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tom, Nathan M; Yu, Yi-Hsiang; Wright, Alan D

In this work, the net power delivered to the grid from a nonideal power take-off (PTO) is introduced followed by a review of the pseudo-spectral control theory. A power-to-load ratio, used to evaluate the pseudo-spectral controller performance, is discussed, and the results obtained from optimizing a multiterm objective function are compared against results obtained from maximizing the net output power to the grid. Simulation results are then presented for four different oscillating wave energy converter geometries to highlight the potential of combing both geometry and PTO control to maximize power while minimizing loads.

AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain–domain interaction prediction

PubMed Central

Xu, Dong; Jaroszewski, Lukasz; Li, Zhanwen; Godzik, Adam

2015-01-01

Motivation: Most proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new protein architectures. Template-based modeling methods can often detect homologous templates for individual domains, but templates that could be used to model the entire query protein are often not available. Results: We have developed a fast docking algorithm ab initio domain assembly (AIDA) for assembling multi-domain protein structures, guided by the ab initio folding potential. This approach can be extended to discontinuous domains (i.e. domains with ‘inserted’ domains). When tested on experimentally solved structures of multi-domain proteins, the relative domain positions were accurately found among top 5000 models in 86% of cases. AIDA server can use domain assignments provided by the user or predict them from the provided sequence. The latter approach is particularly useful for automated protein structure prediction servers. The blind test consisting of 95 CASP10 targets shows that domain boundaries could be successfully determined for 97% of targets. Availability and implementation: The AIDA package as well as the benchmark sets used here are available for download at http://ffas.burnham.org/AIDA/. Contact: adam@sanfordburnham.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25701568

Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: implications for three-dimensional modeling.

PubMed

Bhaskara, Ramachandra M; Padhi, Amrita; Srinivasan, Narayanaswamy

2014-07-01

With the preponderance of multidomain proteins in eukaryotic genomes, it is essential to recognize the constituent domains and their functions. Often function involves communications across the domain interfaces, and the knowledge of the interacting sites is essential to our understanding of the structure-function relationship. Using evolutionary information extracted from homologous domains in at least two diverse domain architectures (single and multidomain), we predict the interface residues corresponding to domains from the two-domain proteins. We also use information from the three-dimensional structures of individual domains of two-domain proteins to train naïve Bayes classifier model to predict the interfacial residues. Our predictions are highly accurate (∼85%) and specific (∼95%) to the domain-domain interfaces. This method is specific to multidomain proteins which contain domains in at least more than one protein architectural context. Using predicted residues to constrain domain-domain interaction, rigid-body docking was able to provide us with accurate full-length protein structures with correct orientation of domains. We believe that these results can be of considerable interest toward rational protein and interaction design, apart from providing us with valuable information on the nature of interactions. © 2013 Wiley Periodicals, Inc.

Numerical study of the small scale structures in Boussinesq convection

NASA Technical Reports Server (NTRS)

Weinan, E.; Shu, Chi-Wang

1992-01-01

Two-dimensional Boussinesq convection is studied numerically using two different methods: a filtered pseudospectral method and a high order accurate Essentially Nonoscillatory (ENO) scheme. The issue whether finite time singularity occurs for initially smooth flows is investigated. The numerical results suggest that the collapse of the bubble cap is unlikely to occur in resolved calculations. The strain rate corresponding to the intensification of the density gradient across the front saturates at the bubble cap. We also found that the cascade of energy to small scales is dominated by the formulation of thin and sharp fronts across which density jumps.

Challenges at Petascale for Pseudo-Spectral Methods on Spheres (A Last Hurrah?)

NASA Technical Reports Server (NTRS)

Clune, Thomas

2011-01-01

Conclusions: a) Proper software abstractions should enable rapid-exploration of platform-specific optimizations/ tradeoffs. b) Pseudo-spectra! methods are marginally viable for at least some classes of petascaie problems. i.e., GPU based machine with good bisection would be best. c) Scalability at exascale is possible, but the necessary resolution will make algorithm prohibitively expensive. Efficient implementations of realistic global transposes are mtricate and tedious in MPI. PS at petascaie requires exploration of a variety of strategies for spreading local and remote communic3tions. PGAS allows far simpler implementation and thus rapid exploration of variants.

Direct numerical simulations of a reacting turbulent mixing layer by a pseudospectral-spectral element method

NASA Technical Reports Server (NTRS)

Mcmurtry, Patrick A.; Givi, Peyman

1992-01-01

An account is given of the implementation of the spectral-element technique for simulating a chemically reacting, spatially developing turbulent mixing layer. Attention is given to experimental and numerical studies that have investigated the development, evolution, and mixing characteristics of shear flows. A mathematical formulation is presented of the physical configuration of the spatially developing reacting mixing layer, in conjunction with a detailed representation of the spectral-element method's application to the numerical simulation of mixing layers. Results from 2D and 3D calculations of chemically reacting mixing layers are given.

Simulation of charge transport in micro and nanoscale FETs with elements having different dielectric properties

NASA Astrophysics Data System (ADS)

Blokhin, A. M.; Kruglova, E. A.; Semisalov, B. V.

2018-03-01

The hydrodynamical model is used for description of the process of charge transport in semiconductors with a high rate of reliability. It is a set of nonlinear partial differential equations with small parameters and specific conditions at the boundaries of field effect transistors (FETs), which essentially complicates the process of finding its stationary solutions. To overcome these difficulties in the case of FETs with elements having different dielectric properties, a fast pseudospectral method has been developed. This method was used for advanced numerical simulation of charge transport in DG-MOSFET.

A web-based multidomain lifestyle intervention with connected devices for older adults: research protocol of the eMIND pilot randomized controlled trial.

PubMed

Pothier, Kristell; Soriano, G; Lussier, M; Naudin, A; Costa, N; Guyonnet, S; Piau, A; Ousset, P J; Nourhashemi, F; Vellas, B; de Souto Barreto, P

2018-01-24

Multidomain interventions composed of nutritional counseling, exercise and cognitive trainings have shown encouraging results as effective preventive strategies delaying age-related declines. However, these interventions are time- and resource-consuming. The use of Information and Communication Technologies (ICT) might facilitate the translation from research into real-world practice and reach a massive number of people. This article describes the protocol of the eMIND study, a randomized controlled trial (RCT) using a web-based multidomain intervention for older adults. One hundred and twenty older adults (≥ 65 years), with a spontaneous memory complaint, will be randomly assigned to a six-month web-based multidomain (nutritional counseling, physical and cognitive trainings) intervention group with a connected accelerometer (number of steps, energy expenditure), or to a control group with access to general information on healthy aging plus the accelerometer, but no access to the multidomain intervention. The main outcome is the feasibility/acceptability of the web-based intervention. Secondary clinical outcomes include: cognitive functions, physical performance, nutritional status and cost-effectiveness. We expect a high amount of adherers (ie, > 75% compliance to the protocol) to reflect the feasibility. Acceptability, assessed through interviews, should allow us to understand motivators and barriers to this ICT intervention. We also expect to provide data on its effects on various clinical outcomes and efficiency. The eMIND study will provide crucial information to help developing a future and larger web-based multidomain lifestyle RCT, which should facilitate the translation of this ICT intervention from the research world into real-life clinical practice for the healthcare of older adults.

Advances in Highly Constrained Multi-Phase Trajectory Generation using the General Pseudospectral Optimization Software (GPOPS)

DTIC Science & Technology

2013-08-01

release; distribution unlimited. PA Number 412-TW-PA-13395 f generic function g acceleration due to gravity h altitude L aerodynamic lift force L Lagrange...cost m vehicle mass M Mach number n number of coefficients in polynomial regression p highest order of polynomial regression Q dynamic pressure R...Method (RPM); the collocation points are defined by the roots of Legendre -Gauss- Radau (LGR) functions.9 GPOPS also automatically refines the “mesh” by

Statistical properties and correlation functions for drift waves

NASA Technical Reports Server (NTRS)

Horton, W.

1986-01-01

The dissipative one-field drift wave equation is solved using the pseudospectral method to generate steady-state fluctuations. The fluctuations are analyzed in terms of space-time correlation functions and modal probability distributions. Nearly Gaussian statistics and exponential decay of the two-time correlation functions occur in the presence of electron dissipation, while in the absence of electron dissipation long-lived vortical structures occur. Formulas from renormalized, Markovianized statistical turbulence theory are given in a local approximation to interpret the dissipative turbulence.

Investigation of Alien Wavelength Quality in Live Multi-Domain, Multi-Vendor Link Using Advanced Simulation Tool

NASA Astrophysics Data System (ADS)

Nordal Petersen, Martin; Nuijts, Roeland; Lange Bjørn, Lars

2014-05-01

This article presents an advanced optical model for simulation of alien wavelengths in multi-domain and multi-vendor dense wavelength-division multiplexing networks. The model aids optical network planners with a better understanding of the non-linear effects present in dense wavelength-division multiplexing systems and better utilization of alien wavelengths in future applications. The limiting physical effects for alien wavelengths are investigated in relation to power levels, channel spacing, and other factors. The simulation results are verified through experimental setup in live multi-domain dense wavelength-division multiplexing systems between two national research networks: SURFnet in Holland and NORDUnet in Denmark.

Self-assembling multidomain peptide fibers with aromatic cores

USDA-ARS?s Scientific Manuscript database

Self-assembling multidomain peptides have been shown to have desirable properties, such as the ability to form hydrogels that rapidly recover following shear-thinning and the potential to be tailored by amino acid selection to vary their elasticity and encapsulate and deliver proteins and cells. Her...

Optimal Lorentz-augmented spacecraft formation flying in elliptic orbits

NASA Astrophysics Data System (ADS)

Huang, Xu; Yan, Ye; Zhou, Yang

2015-06-01

An electrostatically charged spacecraft accelerates as it moves through the Earth's magnetic field due to the induced Lorentz force, providing a new means of propellantless electromagnetic propulsion for orbital maneuvers. The feasibility of Lorentz-augmented spacecraft formation flying in elliptic orbits is investigated in this paper. Assuming the Earth's magnetic field as a tilted dipole corotating with Earth, a nonlinear dynamical model that characterizes the orbital motion of Lorentz spacecraft in the vicinity of arbitrary elliptic orbits is developed. To establish a predetermined formation configuration at given terminal time, pseudospectral method is used to solve the optimal open-loop trajectories of hybrid control inputs consisted of Lorentz acceleration and thruster-generated control acceleration. A nontilted dipole model is also introduced to analyze the effect of dipole tilt angle via comparisons with the tilted one. Meanwhile, to guarantee finite-time convergence and system robustness against external perturbations, a continuous fast nonsingular terminal sliding mode controller is designed and the closed-loop system stability is proved by Lyapunov theory. Numerical simulations substantiate the validity of proposed open-loop and closed-loop control schemes, and the results indicate that an almost propellantless formation establishment can be achieved by choosing appropriate objective function in the pseudospectral method. Furthermore, compared to the nonsingular terminal sliding mode controller, the closed-loop controller presents superior convergence rate with only a bit more control effort. And the proposed controller can be applied in other Lorentz-augmented relative orbital control problems.

Nature of the protein universe

PubMed Central

Levitt, Michael

2009-01-01

The protein universe is the set of all proteins of all organisms. Here, all currently known sequences are analyzed in terms of families that have single-domain or multidomain architectures and whether they have a known three-dimensional structure. Growth of new single-domain families is very slow: Almost all growth comes from new multidomain architectures that are combinations of domains characterized by ≈15,000 sequence profiles. Single-domain families are mostly shared by the major groups of organisms, whereas multidomain architectures are specific and account for species diversity. There are known structures for a quarter of the single-domain families, and >70% of all sequences can be partially modeled thanks to their membership in these families. PMID:19541617

Distributed Grooming in Multi-Domain IP/MPLS-DWDM Networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Qing

2009-12-01

This paper studies distributed multi-domain, multilayer provisioning (grooming) in IP/MPLS-DWDM networks. Although many multi-domain studies have emerged over the years, these have primarily considered 'homogeneous' network layers. Meanwhile, most grooming studies have assumed idealized settings with 'global' link state across all layers. Hence there is a critical need to develop practical distributed grooming schemes for real-world networks consisting of multiple domains and technology layers. Along these lines, a detailed hierarchical framework is proposed to implement inter-layer routing, distributed grooming, and setup signaling. The performance of this solution is analyzed in detail using simulation studies and future work directions are alsomore » high-lighted.« less

Accurate, efficient, and (iso)geometrically flexible collocation methods for phase-field models

NASA Astrophysics Data System (ADS)

Gomez, Hector; Reali, Alessandro; Sangalli, Giancarlo

2014-04-01

We propose new collocation methods for phase-field models. Our algorithms are based on isogeometric analysis, a new technology that makes use of functions from computational geometry, such as, for example, Non-Uniform Rational B-Splines (NURBS). NURBS exhibit excellent approximability and controllable global smoothness, and can represent exactly most geometries encapsulated in Computer Aided Design (CAD) models. These attributes permitted us to derive accurate, efficient, and geometrically flexible collocation methods for phase-field models. The performance of our method is demonstrated by several numerical examples of phase separation modeled by the Cahn-Hilliard equation. We feel that our method successfully combines the geometrical flexibility of finite elements with the accuracy and simplicity of pseudo-spectral collocation methods, and is a viable alternative to classical collocation methods.

Black hole evolution by spectral methods

NASA Astrophysics Data System (ADS)

Kidder, Lawrence E.; Scheel, Mark A.; Teukolsky, Saul A.; Carlson, Eric D.; Cook, Gregory B.

2000-10-01

Current methods of evolving a spacetime containing one or more black holes are plagued by instabilities that prohibit long-term evolution. Some of these instabilities may be due to the numerical method used, traditionally finite differencing. In this paper, we explore the use of a pseudospectral collocation (PSC) method for the evolution of a spherically symmetric black hole spacetime in one dimension using a hyperbolic formulation of Einstein's equations. We demonstrate that our PSC method is able to evolve a spherically symmetric black hole spacetime forever without enforcing constraints, even if we add dynamics via a Klein-Gordon scalar field. We find that, in contrast with finite-differencing methods, black hole excision is a trivial operation using PSC applied to a hyperbolic formulation of Einstein's equations. We discuss the extension of this method to three spatial dimensions.

Balancing the Power-to-Load Ratio for a Novel Variable Geometry Wave Energy Converter with Nonideal Power Take-Off in Regular Waves: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tom, Nathan M; Yu, Yi-Hsiang; Wright, Alan D

This work attempts to balance power absorption against structural loading for a novel variable geometry wave energy converter. The variable geometry consists of four identical flaps that will be opened in ascending order starting with the flap closest to the seafloor and moving to the free surface. The influence of a pitch motion constraint on power absorption when utilizing a nonideal power take-off (PTO) is examined and found to reduce the losses associated with bidirectional energy flow. The power-to-load ratio is evaluated using pseudo-spectral control to determine the optimum PTO torque based on a multiterm objective function. The pseudo-spectral optimalmore » control problem is extended to include load metrics in the objective function, which may now consist of competing terms. Separate penalty weights are attached to the surge-foundation force and PTO control torque to tune the optimizer performance to emphasize either power absorption or load shedding. PTO efficiency is not included in the objective function, but the penalty weights are utilized to limit the force and torque amplitudes, thereby reducing losses associated with bidirectional energy flow. Results from pseudo-spectral control demonstrate that shedding a portion of the available wave energy can provide greater reductions in structural loads and reactive power.« less

Pseudo-spectral control of a novel oscillating surge wave energy converter in regular waves for power optimization including load reduction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tom, Nathan M.; Yu, Yi -Hsiang; Wright, Alan D.

The aim of this study is to describe a procedure to maximize the power-to-load ratio of a novel wave energy converter (WEC) that combines an oscillating surge wave energy converter with variable structural components. The control of the power-take-off torque will be on a wave-to-wave timescale, whereas the structure will be controlled statically such that the geometry remains the same throughout the wave period. Linear hydrodynamic theory is used to calculate the upper and lower bounds for the time-averaged absorbed power and surge foundation loads while assuming that the WEC motion remains sinusoidal. Previous work using pseudo-spectral techniques to solvemore » the optimal control problem focused solely on maximizing absorbed energy. This work extends the optimal control problem to include a measure of the surge foundation force in the optimization. The objective function includes two competing terms that force the optimizer to maximize power capture while minimizing structural loads. A penalty weight was included with the surge foundation force that allows control of the optimizer performance based on whether emphasis should be placed on power absorption or load shedding. Results from pseudo-spectral optimal control indicate that a unit reduction in time-averaged power can be accompanied by a greater reduction in surge-foundation force.« less

Pseudo-spectral control of a novel oscillating surge wave energy converter in regular waves for power optimization including load reduction

DOE PAGES

Tom, Nathan M.; Yu, Yi -Hsiang; Wright, Alan D.; ...

2017-04-18

The aim of this study is to describe a procedure to maximize the power-to-load ratio of a novel wave energy converter (WEC) that combines an oscillating surge wave energy converter with variable structural components. The control of the power-take-off torque will be on a wave-to-wave timescale, whereas the structure will be controlled statically such that the geometry remains the same throughout the wave period. Linear hydrodynamic theory is used to calculate the upper and lower bounds for the time-averaged absorbed power and surge foundation loads while assuming that the WEC motion remains sinusoidal. Previous work using pseudo-spectral techniques to solvemore » the optimal control problem focused solely on maximizing absorbed energy. This work extends the optimal control problem to include a measure of the surge foundation force in the optimization. The objective function includes two competing terms that force the optimizer to maximize power capture while minimizing structural loads. A penalty weight was included with the surge foundation force that allows control of the optimizer performance based on whether emphasis should be placed on power absorption or load shedding. Results from pseudo-spectral optimal control indicate that a unit reduction in time-averaged power can be accompanied by a greater reduction in surge-foundation force.« less

A feature dictionary supporting a multi-domain medical knowledge base.

PubMed

Naeymi-Rad, F

1989-01-01

Because different terminology is used by physicians of different specialties in different locations to refer to the same feature (signs, symptoms, test results), it is essential that our knowledge development tools provide a means to access a common pool of terms. This paper discusses the design of an online medical dictionary that provides a solution to this problem for developers of multi-domain knowledge bases for MEDAS (Medical Emergency Decision Assistance System). Our Feature Dictionary supports phrase equivalents for features, feature interactions, feature classifications, and translations to the binary features generated by the expert during knowledge creation. It is also used in the conversion of a domain knowledge to the database used by the MEDAS inference diagnostic sessions. The Feature Dictionary also provides capabilities for complex queries across multiple domains using the supported relations. The Feature Dictionary supports three methods for feature representation: (1) for binary features, (2) for continuous valued features, and (3) for derived features.

Polarization-resolved second-harmonic generation microscopy as a method to visualize protein-crystal domains

PubMed Central

DeWalt, Emma L.; Begue, Victoria J.; Ronau, Judith A.; Sullivan, Shane Z.; Das, Chittaranjan; Simpson, Garth J.

2013-01-01

Polarization-resolved second-harmonic generation (PR-SHG) microscopy is described and applied to identify the presence of multiple crystallographic domains within protein-crystal conglomerates, which was confirmed by synchrotron X-ray diffraction. Principal component analysis (PCA) of PR-SHG images resulted in principal component 2 (PC2) images with areas of contrasting negative and positive values for conglomerated crystals and PC2 images exhibiting uniformly positive or uniformly negative values for single crystals. Qualitative assessment of PC2 images allowed the identification of domains of different internal ordering within protein-crystal samples as well as differentiation between multi-domain conglomerated crystals and single crystals. PR-SHG assessments of crystalline domains were in good agreement with spatially resolved synchrotron X-ray diffraction measurements. These results have implications for improving the productive throughput of protein structure determination through early identification of multi-domain crystals. PMID:23275165

On the computation of steady Hopper flows. II: von Mises materials in various geometries

NASA Astrophysics Data System (ADS)

Gremaud, Pierre A.; Matthews, John V.; O'Malley, Meghan

2004-11-01

Similarity solutions are constructed for the flow of granular materials through hoppers. Unlike previous work, the present approach applies to nonaxisymmetric containers. The model involves ten unknowns (stresses, velocity, and plasticity function) determined by nine nonlinear first order partial differential equations together with a quadratic algebraic constraint (yield condition). A pseudospectral discretization is applied; the resulting problem is solved with a trust region method. The important role of the hopper geometry on the flow is illustrated by several numerical experiments of industrial relevance.

Pseudo-spectral methodology for a quantitative assessment of the cover of in-stream vegetation in small streams

NASA Astrophysics Data System (ADS)

Hershkovitz, Yaron; Anker, Yaakov; Ben-Dor, Eyal; Schwartz, Guy; Gasith, Avital

2010-05-01

In-stream vegetation is a key ecosystem component in many fluvial ecosystems, having cascading effects on stream conditions and biotic structure. Traditionally, ground-level surveys (e.g. grid and transect analyses) are commonly used for estimating cover of aquatic macrophytes. Nonetheless, this methodological approach is highly time consuming and usually yields information which is practically limited to habitat and sub-reach scales. In contrast, remote-sensing techniques (e.g. satellite imagery and airborne photography), enable collection of large datasets over section, stream and basin scales, in relatively short time and reasonable cost. However, the commonly used spatial high resolution (1m) is often inadequate for examining aquatic vegetation on habitat or sub-reach scales. We examined the utility of a pseudo-spectral methodology, using RGB digital photography for estimating the cover of in-stream vegetation in a small Mediterranean-climate stream. We compared this methodology with that obtained by traditional ground-level grid methodology and with an airborne hyper-spectral remote sensing survey (AISA-ES). The study was conducted along a 2 km section of an intermittent stream (Taninim stream, Israel). When studied, the stream was dominated by patches of watercress (Nasturtium officinale) and mats of filamentous algae (Cladophora glomerata). The extent of vegetation cover at the habitat and section scales (100 and 104 m, respectively) were estimated by the pseudo-spectral methodology, using an airborne Roli camera with a Phase-One P 45 (39 MP) CCD image acquisition unit. The swaths were taken in elevation of about 460 m having a spatial resolution of about 4 cm (NADIR). For measuring vegetation cover at the section scale (104 m) we also used a 'push-broom' AISA-ES hyper-spectral swath having a sensor configuration of 182 bands (350-2500 nm) at elevation of ca. 1,200 m (i.e. spatial resolution of ca. 1 m). Simultaneously, with every swath we used an Analytical Spectral Device (ASD) to measure hyper-spectral signatures (2150 bands configuration; 350-2500 nm) of selected ground-level targets (located by GPS) of soil, water; vegetation (common reed, watercress, filamentous algae) and standard EVA foam colored sheets (red, green, blue, black and white). Processing and analysis of the data were performed over an ITT ENVI platform. The hyper-spectral image underwent radiometric calibration according to the flight and sensor calibration parameters on CALIGEO platform and the raw DN scale was converted into radiance scale. Ground level visual survey of vegetation cover and height was applied at the habitat scale (100 m) by placing a 1m2 netted grids (10x10cm cells) along 'bank-to-bank' transect (in triplicates). Estimates of plant cover obtained by the pseudo-spectral methodology at the habitat scale were 35-61% for the watercress, 0.4-25% for the filamentous algae and 27-51% for plant-free patches. The respective estimates by ground level visual survey were 26-50, 14-43% and 36-50%. The pseudo-spectral methodology also yielded estimates for the section scale (104 m) of ca. 39% for the watercress, ca. 32% for the filamentous algae and 6% for plant-free patches. The respective estimates obtained by hyper-spectral swath were 38, 26 and 8%. Validation against ground-level measurements proved that pseudo-spectral methodology gives reasonably good estimates of in-stream plant cover. Therefore, this methodology can serve as a substitute for ground level estimates at small stream scales and for the low resolution hyper-spectral methodology at larger scales.

What’s After joint Multi Domain Operations as the Next Evolution in Warfare

DTIC Science & Technology

2017-03-15

132 Multi-domain operations is similarly a philosophy: descriptive in nature not prescriptive, a mindset rather than a method. Change Cannot Wait...this equates to ends, ways, and means respectively.191 The current service’s descriptions of why either focuses on the broad, winning the nations

LORENE: Spectral methods differential equations solver

NASA Astrophysics Data System (ADS)

Gourgoulhon, Eric; Grandclément, Philippe; Marck, Jean-Alain; Novak, Jérôme; Taniguchi, Keisuke

2016-08-01

LORENE (Langage Objet pour la RElativité NumériquE) solves various problems arising in numerical relativity, and more generally in computational astrophysics. It is a set of C++ classes and provides tools to solve partial differential equations by means of multi-domain spectral methods. LORENE classes implement basic structures such as arrays and matrices, but also abstract mathematical objects, such as tensors, and astrophysical objects, such as stars and black holes.

Modeling multidomain hydraulic properties of shrink-swell soils

NASA Astrophysics Data System (ADS)

Stewart, Ryan D.; Abou Najm, Majdi R.; Rupp, David E.; Selker, John S.

2016-10-01

Shrink-swell soils crack and become compacted as they dry, changing properties such as bulk density and hydraulic conductivity. Multidomain models divide soil into independent realms that allow soil cracks to be incorporated into classical flow and transport models. Incongruously, most applications of multidomain models assume that the porosity distributions, bulk density, and effective saturated hydraulic conductivity of the soil are constant. This study builds on a recently derived soil shrinkage model to develop a new multidomain, dual-permeability model that can accurately predict variations in soil hydraulic properties due to dynamic changes in crack size and connectivity. The model only requires estimates of soil gravimetric water content and a minimal set of parameters, all of which can be determined using laboratory and/or field measurements. We apply the model to eight clayey soils, and demonstrate its ability to quantify variations in volumetric water content (as can be determined during measurement of a soil water characteristic curve) and transient saturated hydraulic conductivity, Ks (as can be measured using infiltration tests). The proposed model is able to capture observed variations in Ks of one to more than two orders of magnitude. In contrast, other dual-permeability models assume that Ks is constant, resulting in the potential for large error when predicting water movement through shrink-swell soils. Overall, the multidomain model presented here successfully quantifies fluctuations in the hydraulic properties of shrink-swell soil matrices, and are suitable for use in physical flow and transport models based on Darcy's Law, the Richards Equation, and the advection-dispersion equation.

A Framework for Supporting Survivability, Network Planning and Cross-Layer Optimization in Future Multi-Domain Terabit Networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baldin, Ilya; Huang, Shu; Gopidi, Rajesh

This final project report describes the accomplishments, products and publications from the award. It includes the overview of the project goals to devise a framework for managing resources in multi-domain, multi-layer networks, as well the details of the mathematical problem formulation and the description of the prototype built to prove the concept.

Frailty Assessment in Heart Failure: an Overview of the Multi-domain Approach.

PubMed

McDonagh, Julee; Ferguson, Caleb; Newton, Phillip J

2018-02-01

The study aims (1) to provide a contemporary description of frailty assessment in heart failure and (2) to provide an overview of multi-domain frailty assessment in heart failure. Frailty assessment is an important predictive measure for mortality and hospitalisation in individuals with heart failure. To date, there are no frailty assessment instruments validated for use in heart failure. This has resulted in significant heterogeneity between studies regarding the assessment of frailty. The most common frailty assessment instrument used in heart failure is the Frailty Phenotype which focuses on five physical domains of frailty; the appropriateness a purely physical measure of frailty in individuals with heart failure who frequently experience decreased exercise tolerance and shortness of breath is yet to be determined. A limited number of studies have approached frailty assessment using a multi-domain view which may be more clinically relevant in heart failure. There remains a lack of consensus regarding frailty assessment and an absence of a validated instrument in heart failure. Despite this, frailty continues to be assessed frequently, primarily for research purposes, using predominantly physical frailty measures. A more multidimensional view of frailty assessment using a multi-domain approach will likely be more sensitive to identifying at risk patients.

Safe-trajectory optimization and tracking control in ultra-close proximity to a failed satellite

NASA Astrophysics Data System (ADS)

Zhang, Jingrui; Chu, Xiaoyu; Zhang, Yao; Hu, Quan; Zhai, Guang; Li, Yanyan

2018-03-01

This paper presents a trajectory-optimization method for a chaser spacecraft operating in ultra-close proximity to a failed satellite. Based on the combination of active and passive trajectory protection, the constraints in the optimization framework are formulated for collision avoidance and successful docking in the presence of any thruster failure. The constraints are then handled by an adaptive Gauss pseudospectral method, in which the dynamic residuals are used as the metric to determine the distribution of collocation points. A finite-time feedback control is further employed in tracking the optimized trajectory. In particular, the stability and convergence of the controller are proved. Numerical results are given to demonstrate the effectiveness of the proposed methods.

Multi-Domain, Multi-Method Measures of Metacognitive Activity: What Is All the Fuss about Metacognition ... Indeed?

ERIC Educational Resources Information Center

Meijer, Joost; Veenman, Marcel V. J.; van Hout-Wolters, Bernadette

2012-01-01

Studies about metacognition, intelligence and learning have rendered equivocal results. The mixed model assumes joint as well as independent influences of intelligence and metacognition on learning results. In this study, intelligence was measured by standard tests for reasoning, spatial ability and memory. Participants were 13-year-old school…

Fully coupled six-dimensional calculations of the water dimer vibration-rotation-tunneling states with split Wigner pseudospectral approach. II. Improvements and tests of additional potentials

NASA Astrophysics Data System (ADS)

Fellers, R. S.; Braly, L. B.; Saykally, R. J.; Leforestier, C.

1999-04-01

The SWPS method is improved by the addition of H.E.G. contractions for generating a more compact basis. An error in the definition of the internal fragment axis system used in our previous calculation is described and corrected. Fully coupled 6D (rigid monomers) VRT states are computed for several new water dimer potential surfaces and compared with experiment and our earlier SWPS results. This work sets the stage for refinement of such potential surfaces via regression analysis of VRT spectroscopic data.

Naturalistic Assessment of Everyday Activities and Prompting Technologies in Mild Cognitive Impairment

PubMed Central

Seelye, Adriana M.; Schmitter-Edgecombe, Maureen; Cook, Diane J.; Crandall, Aaron

2014-01-01

Older adults with mild cognitive impairment (MCI) often have difficulty performing complex instrumental activities of daily living (IADLs), which are critical to independent living. In this study, amnestic multi-domain MCI (N = 29), amnestic single-domain MCI (N = 18), and healthy older participants (N = 47) completed eight scripted IADLs (e.g., cook oatmeal on the stove) in a smart apartment testbed. We developed and experimented with a graded hierarchy of technology-based prompts to investigate both the amount of prompting and type of prompts required to assist individuals with MCI in completing the activities. When task errors occurred, progressive levels of assistance were provided, starting with the lowest level needed to adjust performance. Results showed that the multi-domain MCI group made more errors and required more prompts than the single-domain MCI and healthy older adult groups. Similar to the other two groups, the multi-domain MCI group responded well to the indirect prompts and did not need a higher level of prompting to get back on track successfully with the tasks. Need for prompting assistance was best predicted by verbal memory abilities in multi-domain amnestic MCI. Participants across groups indicated that they perceived the prompting technology to be very helpful. PMID:23351284

A Multiscale Software Tool for Field/Circuit Co-Simulation

DTIC Science & Technology

2011-12-15

technology fields: Number of graduating undergraduates who achieved a 3.5 GPA to 4.0 (4.0 max scale): Number of graduating undergraduates funded by a...times more efficient than FDTD for such a problem in 3D . The techniques in class (c) above include the discontinuous Galerkin method and multidomain...implements a finite-differential-time-domain method on single field propagation in a 3D space. We consider a cavity model which includes two electric

Defense Reform: Supporting the Whole-of-Government Approach in Tomorrow’s Crisis

DTIC Science & Technology

2017-03-29

government approach to trans-regional, multi-domain, and multi-functional threats. In addition to keeping military and political focus on broader...structure with more subordinate commands and less multi-domain and multi-functional integration, or in this case , vertical integration. Relying on ... APPROACH IN TOMORROW’S CRISIS 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Lt Col John B

The quaternary architecture of RARβ–RXRα heterodimer facilitates domain–domain signal transmission

DOE PAGES

Chandra, Vikas; Wu, Dalei; Li, Sheng; ...

2017-10-11

Assessing the physical connections and allosteric communications in multi-domain nuclear receptor (NR) polypeptides has remained challenging, with few crystal structures available to show their overall structural organizations. Here we report the quaternary architecture of multi-domain retinoic acid receptor beta-retinoic X receptor alpha (RAR beta-RXR alpha) heterodimer bound to DNA, ligands and coactivator peptides, examined through crystallographic, hydrogen-deuterium exchange mass spectrometry, mutagenesis and functional studies. The RAR beta ligand-binding domain (LBD) and DNA-binding domain (DBD) are physically connected to foster allosteric signal transmission between them. Direct comparisons among all the multi-domain NRs studied crystallographically to date show significant variations within theirmore » quaternary architectures, rather than a common architecture adhering to strict rules. RXR remains flexible and adaptive by maintaining loosely organized domains, while its hetero-dimerization partners use a surface patch on their LBDs to form domain-domain interactions with DBDs.« less

Experimental demonstration of bandwidth on demand (BoD) provisioning based on time scheduling in software-defined multi-domain optical networks

NASA Astrophysics Data System (ADS)

Zhao, Yongli; Li, Yajie; Wang, Xinbo; Chen, Bowen; Zhang, Jie

2016-09-01

A hierarchical software-defined networking (SDN) control architecture is designed for multi-domain optical networks with the Open Daylight (ODL) controller. The OpenFlow-based Control Virtual Network Interface (CVNI) protocol is deployed between the network orchestrator and the domain controllers. Then, a dynamic bandwidth on demand (BoD) provisioning solution is proposed based on time scheduling in software-defined multi-domain optical networks (SD-MDON). Shared Risk Link Groups (SRLG)-disjoint routing schemes are adopted to separate each tenant for reliability. The SD-MDON testbed is built based on the proposed hierarchical control architecture. Then the proposed time scheduling-based BoD (Ts-BoD) solution is experimentally demonstrated on the testbed. The performance of the Ts-BoD solution is evaluated with respect to blocking probability, resource utilization, and lightpath setup latency.

The quaternary architecture of RARβ–RXRα heterodimer facilitates domain–domain signal transmission

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chandra, Vikas; Wu, Dalei; Li, Sheng

Assessing the physical connections and allosteric communications in multi-domain nuclear receptor (NR) polypeptides has remained challenging, with few crystal structures available to show their overall structural organizations. Here we report the quaternary architecture of multi-domain retinoic acid receptor beta-retinoic X receptor alpha (RAR beta-RXR alpha) heterodimer bound to DNA, ligands and coactivator peptides, examined through crystallographic, hydrogen-deuterium exchange mass spectrometry, mutagenesis and functional studies. The RAR beta ligand-binding domain (LBD) and DNA-binding domain (DBD) are physically connected to foster allosteric signal transmission between them. Direct comparisons among all the multi-domain NRs studied crystallographically to date show significant variations within theirmore » quaternary architectures, rather than a common architecture adhering to strict rules. RXR remains flexible and adaptive by maintaining loosely organized domains, while its hetero-dimerization partners use a surface patch on their LBDs to form domain-domain interactions with DBDs.« less

Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand

NASA Astrophysics Data System (ADS)

Zhang, Xianjun; Zhao, Fei; Wu, Yiran; Yang, Jun; Han, Gye Won; Zhao, Suwen; Ishchenko, Andrii; Ye, Lintao; Lin, Xi; Ding, Kang; Dharmarajan, Venkatasubramanian; Griffin, Patrick R.; Gati, Cornelius; Nelson, Garrett; Hunter, Mark S.; Hanson, Michael A.; Cherezov, Vadim; Stevens, Raymond C.; Tan, Wenfu; Tao, Houchao; Xu, Fei

2017-05-01

The Smoothened receptor (SMO) belongs to the Class Frizzled of the G protein-coupled receptor (GPCR) superfamily, constituting a key component of the Hedgehog signalling pathway. Here we report the crystal structure of the multi-domain human SMO, bound and stabilized by a designed tool ligand TC114, using an X-ray free-electron laser source at 2.9 Å. The structure reveals a precise arrangement of three distinct domains: a seven-transmembrane helices domain (TMD), a hinge domain (HD) and an intact extracellular cysteine-rich domain (CRD). This architecture enables allosteric interactions between the domains that are important for ligand recognition and receptor activation. By combining the structural data, molecular dynamics simulation, and hydrogen-deuterium-exchange analysis, we demonstrate that transmembrane helix VI, extracellular loop 3 and the HD play a central role in transmitting the signal employing a unique GPCR activation mechanism, distinct from other multi-domain GPCRs.

Design of Control Plane Architecture Based on Cloud Platform and Experimental Network Demonstration for Multi-domain SDON

NASA Astrophysics Data System (ADS)

Li, Ming; Yin, Hongxi; Xing, Fangyuan; Wang, Jingchao; Wang, Honghuan

2016-02-01

With the features of network virtualization and resource programming, Software Defined Optical Network (SDON) is considered as the future development trend of optical network, provisioning a more flexible, efficient and open network function, supporting intraconnection and interconnection of data centers. Meanwhile cloud platform can provide powerful computing, storage and management capabilities. In this paper, with the coordination of SDON and cloud platform, a multi-domain SDON architecture based on cloud control plane has been proposed, which is composed of data centers with database (DB), path computation element (PCE), SDON controller and orchestrator. In addition, the structure of the multidomain SDON orchestrator and OpenFlow-enabled optical node are proposed to realize the combination of centralized and distributed effective management and control platform. Finally, the functional verification and demonstration are performed through our optical experiment network.

Nonlinear model predictive control of a wave energy converter based on differential flatness parameterisation

NASA Astrophysics Data System (ADS)

Li, Guang

2017-01-01

This paper presents a fast constrained optimization approach, which is tailored for nonlinear model predictive control of wave energy converters (WEC). The advantage of this approach relies on its exploitation of the differential flatness of the WEC model. This can reduce the dimension of the resulting nonlinear programming problem (NLP) derived from the continuous constrained optimal control of WEC using pseudospectral method. The alleviation of computational burden using this approach helps to promote an economic implementation of nonlinear model predictive control strategy for WEC control problems. The method is applicable to nonlinear WEC models, nonconvex objective functions and nonlinear constraints, which are commonly encountered in WEC control problems. Numerical simulations demonstrate the efficacy of this approach.

Numerical investigation of field enhancement by metal nano-particles using a hybrid FDTD-PSTD algorithm.

PubMed

Pernice, W H; Payne, F P; Gallagher, D F

2007-09-03

We present a novel numerical scheme for the simulation of the field enhancement by metal nano-particles in the time domain. The algorithm is based on a combination of the finite-difference time-domain method and the pseudo-spectral time-domain method for dispersive materials. The hybrid solver leads to an efficient subgridding algorithm that does not suffer from spurious field spikes as do FDTD schemes. Simulation of the field enhancement by gold particles shows the expected exponential field profile. The enhancement factors are computed for single particles and particle arrays. Due to the geometry conforming mesh the algorithm is stable for long integration times and thus suitable for the simulation of resonance phenomena in coupled nano-particle structures.

Properties of pTRM in Multidomain Grains and Their Implications for Palaeointensity Measurements

NASA Astrophysics Data System (ADS)

Biggin, A. J.; Michalk, D. M.

2009-05-01

As a consequence of their ubiquity in natural materials, much effort has been expended on trying to understand how 'multidomain' (sensu lato) grains behave in palaeointensity experiments. The known properties of multidomain thermoremanence (MD TRM) will be reviewed here and their implications for various types of palaeointensity experiments will be considered. The Dekkers-Boehnel and (quasi-) perpendicular palaeointensity methods tend to produce more accurate measurements from samples containing MD remanences than do Thellier-Thellier protocols. This is because they apply only a single type of thermal remagnetisation treatment and avoid the interleaving of demagnetisation and remagnetisation treatments which always produces non-ideal behaviour when MD grains are present in the sample. However, this benefit of using a single-heating technique does not apply if the TRM of the sample being measured carries a secondary (e.g. viscous) overprint. A kinematic model of MD TRM predicts that, if a substantial demagnetisation treatment is required to isolate the primary TRM of a sample, then even single-heating methods will produce non-ideal behaviour in the experiment. This effect probably explains why some recently made palaeointensity measurements performed using the Dekkers- Boehnel method on Mexican lavas appeared to produce over-high results. One way around this problem might be to perform the measurements of the remanence in the experiment at temperature instead of always cooling the sample to room temperature. This could enable the optimal experimental behaviour to be preserved in spite of a significant overprint but requires specialist equipment which is not available in all labs. In many palaeointensity experiments, it is simply not possible to avoid all the non-ideal effects associated with MD grains. Furthermore, there is the potential for sources of bias other than MD effects to impact on a palaeointensity experiment (thermochemical alteration being the most obvious) and the design of the experiment should take these into account also. Nonetheless, there are some steps that can be followed in any experiment in order to reduce the amount of bias that MD effects might have on the palaeointensity and these will be outlined.

The Impact of Cognitive Training on Cerebral White Matter in Community-Dwelling Elderly: One-Year Prospective Longitudinal Diffusion Tensor Imaging Study.

PubMed

Cao, Xinyi; Yao, Ye; Li, Ting; Cheng, Yan; Feng, Wei; Shen, Yuan; Li, Qingwei; Jiang, Lijuan; Wu, Wenyuan; Wang, Jijun; Sheng, Jianhua; Feng, Jianfeng; Li, Chunbo

2016-09-15

It has been shown that cognitive training (CogTr) is effective and recuperative for older adults, and can be used to fight against cognitive decline. In this study, we investigated whether behavioural gains from CogTr would extend to white matter (WM) microstructure, and whether training-induced changes in WM integrity would be associated with improvements in cognitive function, using diffusion tensor imaging (DTI). 48 healthy community elderly were either assigned to multi-domain or single-domain CogTr groups to receive 24 sessions over 12 weeks, or to a control group. DTI was performed at both baseline and 12-month follow-up. Positive effects of multi-domain CogTr on long-term changes in DTI indices were found in posterior parietal WM. Participants in the multi-domain group showed a trend of long-term decrease in axial diffusivity (AD) without significant change in fractional anisotropy (FA), mean diffusivity (MD) or radial diffusivity (RD), while those in the control group displayed a significant FA decrease, and an increase in MD and RD. In addition, significant relationships between an improvement in processing speed and changes in RD, MD and AD were found in the multi-domain group. These findings support the hypothesis that plasticity of WM can be modified by CogTr, even in late adulthood.

Searching Remote Homology with Spectral Clustering with Symmetry in Neighborhood Cluster Kernels

PubMed Central

Maulik, Ujjwal; Sarkar, Anasua

2013-01-01

Remote homology detection among proteins utilizing only the unlabelled sequences is a central problem in comparative genomics. The existing cluster kernel methods based on neighborhoods and profiles and the Markov clustering algorithms are currently the most popular methods for protein family recognition. The deviation from random walks with inflation or dependency on hard threshold in similarity measure in those methods requires an enhancement for homology detection among multi-domain proteins. We propose to combine spectral clustering with neighborhood kernels in Markov similarity for enhancing sensitivity in detecting homology independent of “recent” paralogs. The spectral clustering approach with new combined local alignment kernels more effectively exploits the unsupervised protein sequences globally reducing inter-cluster walks. When combined with the corrections based on modified symmetry based proximity norm deemphasizing outliers, the technique proposed in this article outperforms other state-of-the-art cluster kernels among all twelve implemented kernels. The comparison with the state-of-the-art string and mismatch kernels also show the superior performance scores provided by the proposed kernels. Similar performance improvement also is found over an existing large dataset. Therefore the proposed spectral clustering framework over combined local alignment kernels with modified symmetry based correction achieves superior performance for unsupervised remote homolog detection even in multi-domain and promiscuous domain proteins from Genolevures database families with better biological relevance. Source code available upon request. Contact: sarkar@labri.fr. PMID:23457439

Searching remote homology with spectral clustering with symmetry in neighborhood cluster kernels.

PubMed

Maulik, Ujjwal; Sarkar, Anasua

2013-01-01

Remote homology detection among proteins utilizing only the unlabelled sequences is a central problem in comparative genomics. The existing cluster kernel methods based on neighborhoods and profiles and the Markov clustering algorithms are currently the most popular methods for protein family recognition. The deviation from random walks with inflation or dependency on hard threshold in similarity measure in those methods requires an enhancement for homology detection among multi-domain proteins. We propose to combine spectral clustering with neighborhood kernels in Markov similarity for enhancing sensitivity in detecting homology independent of "recent" paralogs. The spectral clustering approach with new combined local alignment kernels more effectively exploits the unsupervised protein sequences globally reducing inter-cluster walks. When combined with the corrections based on modified symmetry based proximity norm deemphasizing outliers, the technique proposed in this article outperforms other state-of-the-art cluster kernels among all twelve implemented kernels. The comparison with the state-of-the-art string and mismatch kernels also show the superior performance scores provided by the proposed kernels. Similar performance improvement also is found over an existing large dataset. Therefore the proposed spectral clustering framework over combined local alignment kernels with modified symmetry based correction achieves superior performance for unsupervised remote homolog detection even in multi-domain and promiscuous domain proteins from Genolevures database families with better biological relevance. Source code available upon request. sarkar@labri.fr.

Mass transfer from a sphere in an oscillating flow with zero mean velocity

NASA Technical Reports Server (NTRS)

Drummond, Colin K.; Lyman, Frederic A.

1990-01-01

A pseudospectral numerical method is used for the solution of the Navier-Stokes and mass transport equations for a sphere in a sinusoidally oscillating flow with zero mean velocity. The flow is assumed laminar and axisymmetric about the sphere's polar axis. Oscillating flow results were obtained for Reynolds numbers (based on the free-stream oscillatory flow amplitude) between 1 and 150, and Strouhal numbers between 1 and 1000. Sherwood numbers were computed and their dependency on the flow frequency and amplitude discussed. An assessment of the validity of the quasi-steady assumption for mass transfer is based on these results.

Fully coupled six-dimensional calculations of the water dimer vibration-rotation-tunneling states with split Wigner pseudospectral approach. II. Improvements and tests of additional potentials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fellers, R.S.; Braly, L.B.; Saykally, R.J.

The SWPS method is improved by the addition of H.E.G. contractions for generating a more compact basis. An error in the definition of the internal fragment axis system used in our previous calculation is described and corrected. Fully coupled 6D (rigid monomers) VRT states are computed for several new water dimer potential surfaces and compared with experiment and our earlier SWPS results. This work sets the stage for refinement of such potential surfaces via regression analysis of VRT spectroscopic data. {copyright} {ital 1999 American Institute of Physics.}

Multipoint to multipoint routing and wavelength assignment in multi-domain optical networks

NASA Astrophysics Data System (ADS)

Qin, Panke; Wu, Jingru; Li, Xudong; Tang, Yongli

2018-01-01

In multi-point to multi-point (MP2MP) routing and wavelength assignment (RWA) problems, researchers usually assume the optical networks to be a single domain. However, the optical networks develop toward to multi-domain and larger scale in practice. In this context, multi-core shared tree (MST)-based MP2MP RWA are introduced problems including optimal multicast domain sequence selection, core nodes belonging in which domains and so on. In this letter, we focus on MST-based MP2MP RWA problems in multi-domain optical networks, mixed integer linear programming (MILP) formulations to optimally construct MP2MP multicast trees is presented. A heuristic algorithm base on network virtualization and weighted clustering algorithm (NV-WCA) is proposed. Simulation results show that, under different traffic patterns, the proposed algorithm achieves significant improvement on network resources occupation and multicast trees setup latency in contrast with the conventional algorithms which were proposed base on a single domain network environment.

Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand

DOE PAGES

Zhang, Xianjun; Zhao, Fei; Wu, Yiran; ...

2017-05-17

Here, the Smoothened receptor (SMO) belongs to the Class Frizzled of the G protein-coupled receptor (GPCR) superfamily, constituting a key component of the Hedgehog signalling pathway. Here we report the crystal structure of the multi-domain human SMO, bound and stabilized by a designed tool ligand TC114, using an X-ray free-electron laser source at 2.9 Å. The structure reveals a precise arrangement of three distinct domains: a seven-transmembrane helices domain (TMD), a hinge domain (HD) and an intact extracellular cysteine-rich domain (CRD). This architecture enables allosteric interactions between the domains that are important for ligand recognition and receptor activation. By combiningmore » the structural data, molecular dynamics simulation, and hydrogen-deuterium-exchange analysis, we demonstrate that transmembrane helix VI, extracellular loop 3 and the HD play a central role in transmitting the signal employing a unique GPCR activation mechanism, distinct from other multi-domain GPCRs.« less

Flow Cytometry Data Preparation Guidelines for Improved Automated Phenotypic Analysis.

PubMed

Jimenez-Carretero, Daniel; Ligos, José M; Martínez-López, María; Sancho, David; Montoya, María C

2018-05-15

Advances in flow cytometry (FCM) increasingly demand adoption of computational analysis tools to tackle the ever-growing data dimensionality. In this study, we tested different data input modes to evaluate how cytometry acquisition configuration and data compensation procedures affect the performance of unsupervised phenotyping tools. An analysis workflow was set up and tested for the detection of changes in reference bead subsets and in a rare subpopulation of murine lymph node CD103 + dendritic cells acquired by conventional or spectral cytometry. Raw spectral data or pseudospectral data acquired with the full set of available detectors by conventional cytometry consistently outperformed datasets acquired and compensated according to FCM standards. Our results thus challenge the paradigm of one-fluorochrome/one-parameter acquisition in FCM for unsupervised cluster-based analysis. Instead, we propose to configure instrument acquisition to use all available fluorescence detectors and to avoid integration and compensation procedures, thereby using raw spectral or pseudospectral data for improved automated phenotypic analysis. Copyright © 2018 by The American Association of Immunologists, Inc.

Navier-Stokes solution on the CYBER-203 by a pseudospectral technique

NASA Technical Reports Server (NTRS)

Lambiotte, J. J.; Hussaini, M. Y.; Bokhari, S.; Orszag, S. A.

1983-01-01

A three-level, time-split, mixed spectral/finite difference method for the numerical solution of the three-dimensional, compressible Navier-Stokes equations has been developed and implemented on the Control Data Corporation (CDC) CYBER-203. This method uses a spectral representation for the flow variables in the streamwise and spanwise coordinates, and central differences in the normal direction. The five dependent variables are interleaved one horizontal plane at a time and the array of their values at the grid points of each horizontal plane is a typical vector in the computation. The code is organized so as to require, per time step, a single forward-backward pass through the entire data base. The one-and two-dimensional Fast Fourier Transforms are performed using software especially developed for the CYBER-203.

Structural Assembly of Multidomain Proteins and Protein Complexes Guided by the Overall Rotational Diffusion Tensor

PubMed Central

Ryabov, Yaroslav; Fushman, David

2008-01-01

We present a simple and robust approach that uses the overall rotational diffusion tensor as a structural constraint for domain positioning in multidomain proteins and protein-protein complexes. This method offers the possibility to use NMR relaxation data for detailed structure characterization of such systems provided the structures of individual domains are available. The proposed approach extends the concept of using long-range information contained in the overall rotational diffusion tensor. In contrast to the existing approaches, we use both the principal axes and principal values of protein’s rotational diffusion tensor to determine not only the orientation but also the relative positioning of the individual domains in a protein. This is achieved by finding the domain arrangement in a molecule that provides the best possible agreement with all components of the overall rotational diffusion tensor derived from experimental data. The accuracy of the proposed approach is demonstrated for two protein systems with known domain arrangement and parameters of the overall tumbling: the HIV-1 protease homodimer and Maltose Binding Protein. The accuracy of the method and its sensitivity to domain positioning is also tested using computer-generated data for three protein complexes, for which the experimental diffusion tensors are not available. In addition, the proposed method is applied here to determine, for the first time, the structure of both open and closed conformations of Lys48-linked di-ubiquitin chain, where domain motions render impossible accurate structure determination by other methods. The proposed method opens new avenues for improving structure characterization of proteins in solution. PMID:17550252

Bowen-York trumpet data and black-hole simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hannam, Mark; Murchadha, Niall O; Husa, Sascha

2009-12-15

The most popular method to construct initial data for black-hole-binary simulations is the puncture method, in which compactified wormholes are given linear and angular momentum via the Bowen-York extrinsic curvature. When these data are evolved, they quickly approach a trumpet topology, suggesting that it would be preferable to use data that are in trumpet form from the outset. To achieve this, we extend the puncture method to allow the construction of Bowen-York trumpets, including an outline of an existence and uniqueness proof of the solutions. We construct boosted, spinning and binary Bowen-York puncture trumpets using a single-domain pseudospectral elliptic solver,more » and evolve the binary data and compare with standard wormhole-data results. We also show that for boosted trumpets the black-hole mass can be prescribed a priori, without recourse to the iterative procedure that is necessary for wormhole data.« less

Pseudospectra in non-Hermitian quantum mechanics

NASA Astrophysics Data System (ADS)

Krejčiřík, D.; Siegl, P.; Tater, M.; Viola, J.

2015-10-01

We propose giving the mathematical concept of the pseudospectrum a central role in quantum mechanics with non-Hermitian operators. We relate pseudospectral properties to quasi-Hermiticity, similarity to self-adjoint operators, and basis properties of eigenfunctions. The abstract results are illustrated by unexpected wild properties of operators familiar from PT -symmetric quantum mechanics.

Multiphoton ionization of many-electron atoms and highly-charged ions in intense laser fields: a relativistic time-dependent density functional theory approach

NASA Astrophysics Data System (ADS)

Tumakov, Dmitry A.; Telnov, Dmitry A.; Maltsev, Ilia A.; Plunien, Günter; Shabaev, Vladimir M.

2017-10-01

We develop an efficient numerical implementation of the relativistic time-dependent density functional theory (RTDDFT) to study multielectron highly-charged ions subject to intense linearly-polarized laser fields. The interaction with the electromagnetic field is described within the electric dipole approximation. The resulting time-dependent relativistic Kohn-Sham (RKS) equations possess an axial symmetry and are solved accurately and efficiently with the help of the time-dependent generalized pseudospectral method. As a case study, we calculate multiphoton ionization probabilities of the neutral argon atom and argon-like xenon ion. Relativistic effects are assessed by comparison of our present results with existing non-relativistic data.

Statistics for laminar flamelet modeling

NASA Technical Reports Server (NTRS)

Cant, R. S.; Rutland, C. J.; Trouve, A.

1990-01-01

Statistical information required to support modeling of turbulent premixed combustion by laminar flamelet methods is extracted from a database of the results of Direct Numerical Simulation of turbulent flames. The simulations were carried out previously by Rutland (1989) using a pseudo-spectral code on a three dimensional mesh of 128 points in each direction. One-step Arrhenius chemistry was employed together with small heat release. A framework for the interpretation of the data is provided by the Bray-Moss-Libby model for the mean turbulent reaction rate. Probability density functions are obtained over surfaces of the constant reaction progress variable for the tangential strain rate and the principal curvature. New insights are gained which will greatly aid the development of modeling approaches.

Multi-domain training in healthy old age: Hotel Plastisse as an iPad-based serious game to systematically compare multi-domain and single-domain training.

PubMed

Binder, Julia C; Zöllig, Jacqueline; Eschen, Anne; Mérillat, Susan; Röcke, Christina; Schoch, Sarah F; Jäncke, Lutz; Martin, Mike

2015-01-01

Finding effective training interventions for declining cognitive abilities in healthy aging is of great relevance, especially in view of the demographic development. Since it is assumed that transfer from the trained to untrained domains is more likely to occur when training conditions and transfer measures share a common underlying process, multi-domain training of several cognitive functions should increase the likelihood of such an overlap. In the first part, we give an overview of the literature showing that cognitive training using complex tasks, such as video games, leisure activities, or practicing a series of cognitive tasks, has shown promising results regarding transfer to a number of cognitive functions. These studies, however, do not allow direct inference about the underlying functions targeted by these training regimes. Custom-designed serious games allow to design training regimes according to specific cognitive functions and a target population's need. In the second part, we introduce the serious game Hotel Plastisse as an iPad-based training tool for older adults that allows the comparison of the simultaneous training of spatial navigation, visuomotor function, and inhibition to the training of each of these functions separately. Hotel Plastisse not only defines the cognitive functions of the multi-domain training clearly, but also implements training in an interesting learning environment including adaptive difficulty and feedback. We propose this novel training tool with the goal of furthering our understanding of how training regimes should be designed in order to affect cognitive functioning of older adults most broadly.

Effectiveness of a community-based multidomain cognitive intervention program in patients with Alzheimer's disease.

PubMed

Kim, Hee-Jin; Yang, YoungSoon; Oh, Jeong-Gun; Oh, Seongil; Choi, Hojin; Kim, Kyoung Hee; Kim, Seung Hyun

2016-02-01

The aim of the present study was to evaluate the efficacy of a multidomain program in patients with Alzheimer's disease (AD). A total of 53 patients with probable AD participated in the present study. The participants were classified to a cognitive programming group (n = 32) and control group (n = 21). Participants in the cognitive intervention program received multidomain cognitive stimulation including art, music, recollection and horticultural therapy, each period of intervention lasting 1 h. This program was repeated five times per week over a period of 6 months at the Seongdong-gu Center for Dementia. The Mini-Mental State Examination, the Korean version of Consortium to Establish a Registry for Alzheimer's Disease, Clinical dementia rating scales, and the Korean version of the Quality of Life-Alzheimer's Disease were used to evaluate cognitive ability at baseline and after intervention. After 6 months, cognitive abilities were compared between patients actively participating in cognitive intervention and the pharmacotherapy only group. Patients receiving cognitive intervention showed significant cognitive improvement in the word-list recognition and recall test scores versus the control. There was no change in the overall Clinical dementia rating score, but the domain of community affairs showed a significant improvement in the cognitive intervention group. Quality of Life-Alzheimer's Disease of caregivers was slightly improved in the cognitive intervention group after 6 months. Multidomain cognitive intervention by regional dementia centers has great potential in helping to maintain cognitive function in patients with dementia, increase their social activity and reduce depression, while enhancing the quality of life of caregivers. © 2015 Japan Geriatrics Society.

Memory, executive, and multidomain subtle cognitive impairment: clinical and biomarker findings.

PubMed

Toledo, Jon B; Bjerke, Maria; Chen, Kewei; Rozycki, Martin; Jack, Clifford R; Weiner, Michael W; Arnold, Steven E; Reiman, Eric M; Davatzikos, Christos; Shaw, Leslie M; Trojanowski, John Q

2015-07-14

We studied the biomarker signatures and prognoses of 3 different subtle cognitive impairment (SCI) groups (executive, memory, and multidomain) as well as the subjective memory complaints (SMC) group. We studied 522 healthy controls in the Alzheimer's Disease Neuroimaging Initiative (ADNI). Cutoffs for executive, memory, and multidomain SCI were defined using participants who remained cognitively normal (CN) for 7 years. CSF Alzheimer disease (AD) biomarkers, composite and region-of-interest (ROI) MRI, and fluorodeoxyglucose-PET measures were compared in these participants. Using a stringent cutoff (fifth percentile), 27.6% of the ADNI participants were classified as SCI. Most single ROI or global-based measures were not sensitive to detect differences between groups. Only MRI-SPARE-AD (Spatial Pattern of Abnormalities for Recognition of Early AD), a quantitative MRI pattern-based global index, showed differences between all groups, excluding the executive SCI group. Atrophy patterns differed in memory SCI and SMC. The CN and the SMC groups presented a similar distribution of preclinical dementia stages. Fifty percent of the participants with executive, memory, and multidomain SCI progressed to mild cognitive impairment or dementia at 7, 5, and 2 years, respectively. Our results indicate that (1) the different SCI categories have different clinical prognoses and biomarker signatures, (2) longitudinally followed CN subjects are needed to establish clinical cutoffs, (3) subjects with SMC show a frontal pattern of brain atrophy, and (4) pattern-based analyses outperform commonly used single ROI-based neuroimaging biomarkers and are needed to detect initial stages of cognitive impairment. © 2015 American Academy of Neurology.

Multi-domain training in healthy old age: Hotel Plastisse as an iPad-based serious game to systematically compare multi-domain and single-domain training

PubMed Central

Binder, Julia C.; Zöllig, Jacqueline; Eschen, Anne; Mérillat, Susan; Röcke, Christina; Schoch, Sarah F.; Jäncke, Lutz; Martin, Mike

2015-01-01

Finding effective training interventions for declining cognitive abilities in healthy aging is of great relevance, especially in view of the demographic development. Since it is assumed that transfer from the trained to untrained domains is more likely to occur when training conditions and transfer measures share a common underlying process, multi-domain training of several cognitive functions should increase the likelihood of such an overlap. In the first part, we give an overview of the literature showing that cognitive training using complex tasks, such as video games, leisure activities, or practicing a series of cognitive tasks, has shown promising results regarding transfer to a number of cognitive functions. These studies, however, do not allow direct inference about the underlying functions targeted by these training regimes. Custom-designed serious games allow to design training regimes according to specific cognitive functions and a target population's need. In the second part, we introduce the serious game Hotel Plastisse as an iPad-based training tool for older adults that allows the comparison of the simultaneous training of spatial navigation, visuomotor function, and inhibition to the training of each of these functions separately. Hotel Plastisse not only defines the cognitive functions of the multi-domain training clearly, but also implements training in an interesting learning environment including adaptive difficulty and feedback. We propose this novel training tool with the goal of furthering our understanding of how training regimes should be designed in order to affect cognitive functioning of older adults most broadly. PMID:26257643

Mechanical Unfolding Studies on Single-Domain SUMO and Multi-Domain Periplasmic Binding Proteins

NASA Astrophysics Data System (ADS)

Kotamarthi, Hema Chandra; Ainavarapu, Sri Rama Koti

Protein mechanics is a key component of many cellular and sub-cellular processes. The current review focuses on recent studies from our laboratory that probe the effect of sequence on the mechanical stability of structurally similar proteins and the unfolding mechanisms of multi-domain periplasmic binding proteins. Ubiquitin and small ubiquitin-related modifiers (SUMOs) are structurally similar and possess different mechanical stabilities, ubiquitin being stronger than SUMOs as revealed from their unfolding forces. These differences are plausibly due to the variation in number of inter-residue contacts. The unfolding potential widths determined from the pulling speed-dependent studies revealed that SUMOs are mechanically more flexible than ubiquitin. This flexibility of SUMOs plays a role in ligand binding and our single-molecule studies on SUMO interaction with SUMO binding motifs (SBMs) have shown that ligand binding decreases the SUMO flexibility and increases its mechanical stability. Studies on multi-domain periplasmic binding proteins have revealed that the unfolding energy landscape of these proteins is complex and they follow kinetic partitioning between two-state and multiple three-state pathways.

A Novel Approach with Time-Splitting Spectral Technique for the Coupled Schrödinger-Boussinesq Equations Involving Riesz Fractional Derivative

NASA Astrophysics Data System (ADS)

Saha Ray, S.

2017-09-01

In the present paper the Riesz fractional coupled Schrödinger-Boussinesq (S-B) equations have been solved by the time-splitting Fourier spectral (TSFS) method. This proposed technique is utilized for discretizing the Schrödinger like equation and further, a pseudospectral discretization has been employed for the Boussinesq-like equation. Apart from that an implicit finite difference approach has also been proposed to compare the results with the solutions obtained from the time-splitting technique. Furthermore, the time-splitting method is proved to be unconditionally stable. The error norms along with the graphical solutions have also been presented here. Supported by NBHM, Mumbai, under Department of Atomic Energy, Government of India vide Grant No. 2/48(7)/2015/NBHM (R.P.)/R&D II/11403

Ab initio quantum chemical calculation of electron transfer matrix elements for large molecules

NASA Astrophysics Data System (ADS)

Zhang, Linda Yu; Friesner, Richard A.; Murphy, Robert B.

1997-07-01

Using a diabatic state formalism and pseudospectral numerical methods, we have developed an efficient ab initio quantum chemical approach to the calculation of electron transfer matrix elements for large molecules. The theory is developed at the Hartree-Fock level and validated by comparison with results in the literature for small systems. As an example of the power of the method, we calculate the electronic coupling between two bacteriochlorophyll molecules in various intermolecular geometries. Only a single self-consistent field (SCF) calculation on each of the monomers is needed to generate coupling matrix elements for all of the molecular pairs. The largest calculations performed, utilizing 1778 basis functions, required ˜14 h on an IBM 390 workstation. This is considerably less cpu time than would be necessitated with a supermolecule adiabatic state calculation and a conventional electronic structure code.

Low-Thrust Transfers from Distant Retrograde Orbits to L2 Halo Orbits in the Earth-Moon System

NASA Technical Reports Server (NTRS)

Parrish, Nathan L.; Parker, Jeffrey S.; Hughes, Steven P.; Heiligers, Jeannette

2016-01-01

This paper presents a study of transfers between distant retrograde orbits (DROs) and L2 halo orbits in the Earth-Moon system that could be flown by a spacecraft with solar electric propulsion (SEP). Two collocation-based optimal control methods are used to optimize these highly-nonlinear transfers: Legendre pseudospectral and Hermite-Simpson. Transfers between DROs and halo orbits using low-thrust propulsion have not been studied previously. This paper offers a study of several families of trajectories, parameterized by the number of orbital revolutions in a synodic frame. Even with a poor initial guess, a method is described to reliably generate families of solutions. The circular restricted 3-body problem (CRTBP) is used throughout the paper so that the results are autonomous and simpler to understand.

A shifted Jacobi collocation algorithm for wave type equations with non-local conservation conditions

NASA Astrophysics Data System (ADS)

Doha, Eid H.; Bhrawy, Ali H.; Abdelkawy, Mohammed A.

2014-09-01

In this paper, we propose an efficient spectral collocation algorithm to solve numerically wave type equations subject to initial, boundary and non-local conservation conditions. The shifted Jacobi pseudospectral approximation is investigated for the discretization of the spatial variable of such equations. It possesses spectral accuracy in the spatial variable. The shifted Jacobi-Gauss-Lobatto (SJ-GL) quadrature rule is established for treating the non-local conservation conditions, and then the problem with its initial and non-local boundary conditions are reduced to a system of second-order ordinary differential equations in temporal variable. This system is solved by two-stage forth-order A-stable implicit RK scheme. Five numerical examples with comparisons are given. The computational results demonstrate that the proposed algorithm is more accurate than finite difference method, method of lines and spline collocation approach

Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution

PubMed Central

Wolf, Maxim Y; Wolf, Yuri I; Koonin, Eugene V

2008-01-01

Background Proteins show a broad range of evolutionary rates. Understanding the factors that are responsible for the characteristic rate of evolution of a given protein arguably is one of the major goals of evolutionary biology. A long-standing general assumption used to be that the evolution rate is, primarily, determined by the specific functional constraints that affect the given protein. These constrains were traditionally thought to depend both on the specific features of the protein's structure and its biological role. The advent of systems biology brought about new types of data, such as expression level and protein-protein interactions, and unexpectedly, a variety of correlations between protein evolution rate and these variables have been observed. The strongest connections by far were repeatedly seen between protein sequence evolution rate and the expression level of the respective gene. It has been hypothesized that this link is due to the selection for the robustness of the protein structure to mistranslation-induced misfolding that is particularly important for highly expressed proteins and is the dominant determinant of the sequence evolution rate. Results This work is an attempt to assess the relative contributions of protein domain structure and function, on the one hand, and expression level on the other hand, to the rate of sequence evolution. To this end, we performed a genome-wide analysis of the effect of the fusion of a pair of domains in multidomain proteins on the difference in the domain-specific evolutionary rates. The mistranslation-induced misfolding hypothesis would predict that, within multidomain proteins, fused domains, on average, should evolve at substantially closer rates than the same domains in different proteins because, within a mutlidomain protein, all domains are translated at the same rate. We performed a comprehensive comparison of the evolutionary rates of mammalian and plant protein domains that are either joined in multidomain proteins or contained in distinct proteins. Substantial homogenization of evolutionary rates in multidomain proteins was, indeed, observed in both animals and plants, although highly significant differences between domain-specific rates remained. The contributions of the translation rate, as determined by the effect of the fusion of a pair of domains within a multidomain protein, and intrinsic, domain-specific structural-functional constraints appear to be comparable in magnitude. Conclusion Fusion of domains in a multidomain protein results in substantial homogenization of the domain-specific evolutionary rates but significant differences between domain-specific evolution rates remain. Thus, the rate of translation and intrinsic structural-functional constraints both exert sizable and comparable effects on sequence evolution. Reviewers This article was reviewed by Sergei Maslov, Dennis Vitkup, Claus Wilke (nominated by Orly Alter), and Allan Drummond (nominated by Joel Bader). For the full reviews, please go to the Reviewers' Reports section. PMID:18840284

LARGE-SCALE SIMULATIONS OF ELECTROMAGNETIC AND ACOUSTIC MEASUREMENTS USING THE PSEUDOSPECTRAL TIME-DOMAIN (PSTD) ALGORITHM.(37) 2:917-926. (R825225)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

The magnetic structure and palaeomagnetic recording fidelity of sub-micron greigite (Fe3S4)

NASA Astrophysics Data System (ADS)

Valdez-Grijalva, Miguel A.; Nagy, Lesleis; Muxworthy, Adrian R.; Williams, Wyn; Fabian, Karl

2018-02-01

We present the results of a finite-element micromagnetic model of 30nm to 300nm greigite (Fe3S4) grains with a variety of equant morphologies. This grain size range covers the magnetic single-domain (SD) to pseudo single-domain (PSD) transition, and possibly also the PSD to multi-domain (MD) transition. The SD-PSD threshold d0 is determined to be 50nm ≤d0 ≤ 56nm depending on grain shape. The nudged elastic-band method was used to determine the room temperature energy barriers between stable states and thus the blocking volumes. It is found that, in the absence of interparticle magnetostatic interactions, the magnetisation of equant SD greigite is not stable on a geological scale and only PSD grains ≥ 70nm can be expected to carry a stable magnetisation over billion-year timescales, i.e., all non-interacting SD particles are essentially superparamagnetic. We further identify a mechanism for the PSD to multi-domain (MD) transition, which is of a continuous nature from PSD nucleation up to 300nm, when structures typical of MD behaviour like closure domains begin to form.

Cortical Thickness Changes Correlate with Cognition Changes after Cognitive Training: Evidence from a Chinese Community Study

PubMed Central

Jiang, Lijuan; Cao, Xinyi; Li, Ting; Tang, Yingying; Li, Wei; Wang, Jijun; Chan, Raymond C.; Li, Chunbo

2016-01-01

The aim of this study was to investigate whether changes in cortical thickness correlated with cognitive function changes in healthy older adults after receiving cognitive training interventions. Moreover, it also aimed to examine the differential impacts of a multi-domain and a single-domain cognitive training interventions. Longitudinal magnetic resonance imaging (MRI) scanning was performed on participants 65–75 years of age using the Siemens 3.0 T Trio Tim with the Magnetization Prepared Rapid Gradient Echo (MPRAGE) sequence. The cortical thickness was determined using FreeSurfer Software. Cognitive functioning was evaluated using the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS). There were significant group × time interaction effects on the left supramarginal, the left frontal pole cortical regions; and a marginal significant group × time interaction effects on visuospatial/constructional and delayed memory scores. In a multi-domain cognitive training group, a number of cortical region changes were significantly positively correlated with changes in attention, delayed memory, and the total score, but significantly negatively correlated with changes in immediate memory and language scores. In the single-domain cognitive training group, some cortical region changes were significantly positively associated with changes in immediate memory, delayed memory, and the total score, while they were significantly negatively associated with changes in visuospatial/constructional, language, and attention scores. Overall, multi-domain cognitive training offered more advantages in visuospatial/constructional, attention, and delayed memory abilities, while single-domain cognitive training benefited immediate memory ability more effectively. These findings suggest that healthy older adults benefit more from the multi-domain cognitive training than single-domain cognitive training. Cognitive training has impacted on cortical thickness changes in healthy elderly. PMID:27252649

Optimal reorientation of asymmetric underactuated spacecraft using differential flatness and receding horizon control

NASA Astrophysics Data System (ADS)

Cai, Wei-wei; Yang, Le-ping; Zhu, Yan-wei

2015-01-01

This paper presents a novel method integrating nominal trajectory optimization and tracking for the reorientation control of an underactuated spacecraft with only two available control torque inputs. By employing a pseudo input along the uncontrolled axis, the flatness property of a general underactuated spacecraft is extended explicitly, by which the reorientation trajectory optimization problem is formulated into the flat output space with all the differential constraints eliminated. Ultimately, the flat output optimization problem is transformed into a nonlinear programming problem via the Chebyshev pseudospectral method, which is improved by the conformal map and barycentric rational interpolation techniques to overcome the side effects of the differential matrix's ill-conditions on numerical accuracy. Treating the trajectory tracking control as a state regulation problem, we develop a robust closed-loop tracking control law using the receding-horizon control method, and compute the feedback control at each control cycle rapidly via the differential transformation method. Numerical simulation results show that the proposed control scheme is feasible and effective for the reorientation maneuver.

Investigating the Role of Large-Scale Domain Dynamics in Protein-Protein Interactions.

PubMed

Delaforge, Elise; Milles, Sigrid; Huang, Jie-Rong; Bouvier, Denis; Jensen, Malene Ringkjøbing; Sattler, Michael; Hart, Darren J; Blackledge, Martin

2016-01-01

Intrinsically disordered linkers provide multi-domain proteins with degrees of conformational freedom that are often essential for function. These highly dynamic assemblies represent a significant fraction of all proteomes, and deciphering the physical basis of their interactions represents a considerable challenge. Here we describe the difficulties associated with mapping the large-scale domain dynamics and describe two recent examples where solution state methods, in particular NMR spectroscopy, are used to investigate conformational exchange on very different timescales.

Investigating the Role of Large-Scale Domain Dynamics in Protein-Protein Interactions

PubMed Central

Delaforge, Elise; Milles, Sigrid; Huang, Jie-rong; Bouvier, Denis; Jensen, Malene Ringkjøbing; Sattler, Michael; Hart, Darren J.; Blackledge, Martin

2016-01-01

Intrinsically disordered linkers provide multi-domain proteins with degrees of conformational freedom that are often essential for function. These highly dynamic assemblies represent a significant fraction of all proteomes, and deciphering the physical basis of their interactions represents a considerable challenge. Here we describe the difficulties associated with mapping the large-scale domain dynamics and describe two recent examples where solution state methods, in particular NMR spectroscopy, are used to investigate conformational exchange on very different timescales. PMID:27679800

Composite annotations: requirements for mapping multiscale data and models to biomedical ontologies

PubMed Central

Cook, Daniel L.; Mejino, Jose L. V.; Neal, Maxwell L.; Gennari, John H.

2009-01-01

Current methods for annotating biomedical data resources rely on simple mappings between data elements and the contents of a variety of biomedical ontologies and controlled vocabularies. Here we point out that such simple mappings are inadequate for large-scale multiscale, multidomain integrative “virtual human” projects. For such integrative challenges, we describe a “composite annotation” schema that is simple yet sufficiently extensible for mapping the biomedical content of a variety of data sources and biosimulation models to available biomedical ontologies. PMID:19964601

Finite-temperature effects in helical quantum turbulence

NASA Astrophysics Data System (ADS)

Clark Di Leoni, Patricio; Mininni, Pablo D.; Brachet, Marc E.

2018-04-01

We perform a study of the evolution of helical quantum turbulence at different temperatures by solving numerically the Gross-Pitaevskii and the stochastic Ginzburg-Landau equations, using up to 40963 grid points with a pseudospectral method. We show that for temperatures close to the critical one, the fluid described by these equations can act as a classical viscous flow, with the decay of the incompressible kinetic energy and the helicity becoming exponential. The transition from this behavior to the one observed at zero temperature is smooth as a function of temperature. Moreover, the presence of strong thermal effects can inhibit the development of a proper turbulent cascade. We provide Ansätze for the effective viscosity and friction as a function of the temperature.

Fast Optimization for Aircraft Descent and Approach Trajectory

NASA Technical Reports Server (NTRS)

Luchinsky, Dmitry G.; Schuet, Stefan; Brenton, J.; Timucin, Dogan; Smith, David; Kaneshige, John

2017-01-01

We address problem of on-line scheduling of the aircraft descent and approach trajectory. We formulate a general multiphase optimal control problem for optimization of the descent trajectory and review available methods of its solution. We develop a fast algorithm for solution of this problem using two key components: (i) fast inference of the dynamical and control variables of the descending trajectory from the low dimensional flight profile data and (ii) efficient local search for the resulting reduced dimensionality non-linear optimization problem. We compare the performance of the proposed algorithm with numerical solution obtained using optimal control toolbox General Pseudospectral Optimal Control Software. We present results of the solution of the scheduling problem for aircraft descent using novel fast algorithm and discuss its future applications.

Effectiveness of Workplace Interventions in Return-to-Work for Musculoskeletal, Pain-Related and Mental Health Conditions: An Update of the Evidence and Messages for Practitioners.

PubMed

Cullen, K L; Irvin, E; Collie, A; Clay, F; Gensby, U; Jennings, P A; Hogg-Johnson, S; Kristman, V; Laberge, M; McKenzie, D; Newnam, S; Palagyi, A; Ruseckaite, R; Sheppard, D M; Shourie, S; Steenstra, I; Van Eerd, D; Amick, B C

2018-03-01

Purpose The objective of this systematic review was to synthesize evidence on the effectiveness of workplace-based return-to-work (RTW) interventions and work disability management (DM) interventions that assist workers with musculoskeletal (MSK) and pain-related conditions and mental health (MH) conditions with RTW. Methods We followed a systematic review process developed by the Institute for Work & Health and an adapted best evidence synthesis that ranked evidence as strong, moderate, limited, or insufficient. Results Seven electronic databases were searched from January 1990 until April 2015, yielding 8898 non-duplicate references. Evidence from 36 medium and high quality studies were synthesized on 12 different intervention categories across three broad domains: health-focused, service coordination, and work modification interventions. There was strong evidence that duration away from work from both MSK or pain-related conditions and MH conditions were significantly reduced by multi-domain interventions encompassing at least two of the three domains. There was moderate evidence that these multi-domain interventions had a positive impact on cost outcomes. There was strong evidence that cognitive behavioural therapy interventions that do not also include workplace modifications or service coordination components are not effective in helping workers with MH conditions in RTW. Evidence for the effectiveness of other single-domain interventions was mixed, with some studies reporting positive effects and others reporting no effects on lost time and work functioning. Conclusions While there is substantial research literature focused on RTW, there are only a small number of quality workplace-based RTW intervention studies that involve workers with MSK or pain-related conditions and MH conditions. We recommend implementing multi-domain interventions (i.e. with healthcare provision, service coordination, and work accommodation components) to help reduce lost time for MSK or pain-related conditions and MH conditions. Practitioners should also consider implementing these programs to help improve work functioning and reduce costs associated with work disability.

Broadening microwave absorption via a multi-domain structure

NASA Astrophysics Data System (ADS)

Liu, Zhengwang; Che, Renchao; Wei, Yong; Liu, Yupu; Elzatahry, Ahmed A.; Dahyan, Daifallah Al.; Zhao, Dongyuan

2017-04-01

Materials with a high saturation magnetization have gained increasing attention in the field of microwave absorption; therefore, the magnetization value depends on the magnetic configuration inside them. However, the broad-band absorption in the range of microwave frequency (2-18 GHz) is a great challenge. Herein, the three-dimensional (3D) Fe/C hollow microspheres are constructed by iron nanocrystals permeating inside carbon matrix with a saturation magnetization of 340 emu/g, which is 1.55 times as that of bulk Fe, unexpectedly. Electron tomography, electron holography, and Lorentz transmission electron microscopy imaging provide the powerful testimony about Fe/C interpenetration and multi-domain state constructed by vortex and stripe domains. Benefiting from the unique chemical and magnetic microstructures, the microwave minimum absorption is as strong as -55 dB and the bandwidth (<-10 dB) spans 12.5 GHz ranging from 5.5 to 18 GHz. Morphology and distribution of magnetic nano-domains can be facilely regulated by a controllable reduction sintering under H2/Ar gas and an optimized temperature over 450-850 °C. The findings might shed new light on the synthesis strategies of the materials with the broad-band frequency and understanding the association between multi-domain coupling and microwave absorption performance.

Crystallization and preliminary X-ray analysis of Na-ASP-1, a multi-domain pathogenesis-related-1 protein from the human hookworm parasite Necator americanus

PubMed Central

Asojo, Oluwatoyin A.; Loukas, Alex; Inan, Mehmet; Barent, Rick; Huang, Jicai; Plantz, Brad; Swanson, Amber; Gouthro, Mark; Meagher, Michael M.; Hotez, Peter J.

2005-01-01

Human hookworm infection is a major cause of anemia and malnutrition in the developing world. In an effort to control hookworm infection, the Human Hookworm Vaccine Initiative has identified candidate vaccine antigens from the infective larval stage (L3) of the parasite, including a family of pathogenesis-related-1 (PR-1) proteins known as the ancylostoma-secreted proteins (ASPs). The functions of the ASPs are unknown. In addition, it is unclear why some ASPs have one while others have multiple PR-1 domains. There are no known structures of a multi-domain ASP and in an effort to remedy this situation, recombinant Na-ASP-1 has been expressed, purified and crystallized. Na-ASP-1 is a 406-amino-acid multi-domain ASP from the prevalent human hookworm parasite Necator americanus. Useful X-ray data to 2.2 Å have been collected from a crystal that belongs to the monoclinic space group P21 with unit-cell parameters a = 67.7, b = 74.27, c = 84.60 Å, β = 112.12°. An initial molecular-replacement solution has been obtained with one monomer in the asymmetric unit. PMID:16511050

Multidomain lifestyle intervention benefits a large elderly population at risk for cognitive decline and dementia regardless of baseline characteristics: The FINGER trial.

PubMed

Rosenberg, Anna; Ngandu, Tiia; Rusanen, Minna; Antikainen, Riitta; Bäckman, Lars; Havulinna, Satu; Hänninen, Tuomo; Laatikainen, Tiina; Lehtisalo, Jenni; Levälahti, Esko; Lindström, Jaana; Paajanen, Teemu; Peltonen, Markku; Soininen, Hilkka; Stigsdotter-Neely, Anna; Strandberg, Timo; Tuomilehto, Jaakko; Solomon, Alina; Kivipelto, Miia

2018-03-01

The 2-year Finnish Geriatric Intervention Study to Prevent Cognitive Impairment and Disability (FINGER) multidomain lifestyle intervention trial (NCT01041989) demonstrated beneficial effects on cognition. We investigated whether sociodemographics, socioeconomic status, baseline cognition, or cardiovascular factors influenced intervention effects on cognition. The FINGER recruited 1260 people from the general Finnish population (60-77 years, at risk for dementia). Participants were randomized 1:1 to multidomain intervention (diet, exercise, cognition, and vascular risk management) and regular health advice. Primary outcome was change in cognition (Neuropsychological Test Battery z-score). Prespecified analyses to investigate whether participants' characteristics modified response to intervention were carried out using mixed-model repeated-measures analyses. Sociodemographics (sex, age, and education), socioeconomic status (income), cognition (Mini-Mental State Examination), cardiovascular factors (body mass index, blood pressure, cholesterol, fasting glucose, and overall cardiovascular risk), and cardiovascular comorbidity did not modify response to intervention (P-values for interaction > .05). The FINGER intervention was beneficial regardless of participants' characteristics and can thus be implemented in a large elderly population at increased risk for dementia. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Structural basis of detection and signaling of DNA single-strand breaks by human PARP-1

DOE PAGES

Eustermann, Sebastian; Wu, Wing -Fung; Langelier, Marie -France; ...

2015-11-25

Poly(ADP-ribose)polymerase 1 (PARP-1) is a key eukaryotic stress sensor that responds in seconds to DNA single-strand breaks (SSBs), the most frequent genomic damage. A burst of poly(ADP-ribose) synthesis initiates DNA damage response, whereas PARP-1 inhibition kills BRCA-deficient tumor cells selectively, providing the first anti-cancer therapy based on synthetic lethality. However, the mechanism underlying PARP-1’s function remained obscure; inherent dynamics of SSBs and PARP-1’s multi-domain architecture hindered structural studies. Here we reveal the structural basis of SSB detection and how multi-domain folding underlies the allosteric switch that determines PARP-1’s signaling response. Two flexibly linked N-terminal zinc fingers recognize the extreme deformabilitymore » of SSBs and drive co-operative, stepwise self-assembly of remaining PARP-1 domains to control the activity of the C-terminal catalytic domain. Automodifcation in cis explains the subsequent release of monomeric PARP-1 from DNA, allowing repair and replication to proceed. Finally, our results provide a molecular framework for understanding PARP inhibitor action and, more generally, allosteric control of dynamic, multi-domain proteins.« less

Domain Motion Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins.

PubMed

Kobayashi, Chigusa; Matsunaga, Yasuhiro; Koike, Ryotaro; Ota, Motonori; Sugita, Yuji

2015-11-19

Large conformational changes of multidomain proteins are difficult to simulate using all-atom molecular dynamics (MD) due to the slow time scale. We show that a simple modification of the structure-based coarse-grained (CG) model enables a stable and efficient MD simulation of those proteins. "Motion Tree", a tree diagram that describes conformational changes between two structures in a protein, provides information on rigid structural units (domains) and the magnitudes of domain motions. In our new CG model, which we call the DoME (domain motion enhanced) model, interdomain interactions are defined as being inversely proportional to the magnitude of the domain motions in the diagram, whereas intradomain interactions are kept constant. We applied the DoME model in combination with the Go model to simulations of adenylate kinase (AdK). The results of the DoME-Go simulation are consistent with an all-atom MD simulation for 10 μs as well as known experimental data. Unlike the conventional Go model, the DoME-Go model yields stable simulation trajectories against temperature changes and conformational transitions are easily sampled despite domain rigidity. Evidently, identification of domains and their interfaces is useful approach for CG modeling of multidomain proteins.

A computer-assisted study of pulse dynamics in anisotropic media

NASA Astrophysics Data System (ADS)

Krishnan, J.; Engelborghs, K.; Bär, M.; Lust, K.; Roose, D.; Kevrekidis, I. G.

2001-06-01

This study focuses on the computer-assisted stability analysis of travelling pulse-like structures in spatially periodic heterogeneous reaction-diffusion media. The physical motivation comes from pulse propagation in thin annular domains on a diffusionally anisotropic catalytic surface. The study was performed by computing the travelling pulse-like structures as limit cycles of the spatially discretized PDE, which in turn is performed in two ways: a Newton method based on a pseudospectral discretization of the PDE, and a Newton-Picard method based on a finite difference discretization. Details about the spectra of these modulated pulse-like structures are discussed, including how they may be compared with the spectra of pulses in homogeneous media. The effects of anisotropy on the dynamics of pulses and pulse pairs are studied. Beyond shifting the location of bifurcations present in homogeneous media, anisotropy can also introduce certain new instabilities.

Large eddy simulation of incompressible turbulent channel flow

NASA Technical Reports Server (NTRS)

Moin, P.; Reynolds, W. C.; Ferziger, J. H.

1978-01-01

The three-dimensional, time-dependent primitive equations of motion were numerically integrated for the case of turbulent channel flow. A partially implicit numerical method was developed. An important feature of this scheme is that the equation of continuity is solved directly. The residual field motions were simulated through an eddy viscosity model, while the large-scale field was obtained directly from the solution of the governing equations. An important portion of the initial velocity field was obtained from the solution of the linearized Navier-Stokes equations. The pseudospectral method was used for numerical differentiation in the horizontal directions, and second-order finite-difference schemes were used in the direction normal to the walls. The large eddy simulation technique is capable of reproducing some of the important features of wall-bounded turbulent flows. The resolvable portions of the root-mean square wall pressure fluctuations, pressure velocity-gradient correlations, and velocity pressure-gradient correlations are documented.

Point-particle method to compute diffusion-limited cellular uptake.

PubMed

Sozza, A; Piazza, F; Cencini, M; De Lillo, F; Boffetta, G

2018-02-01

We present an efficient point-particle approach to simulate reaction-diffusion processes of spherical absorbing particles in the diffusion-limited regime, as simple models of cellular uptake. The exact solution for a single absorber is used to calibrate the method, linking the numerical parameters to the physical particle radius and uptake rate. We study the configurations of multiple absorbers of increasing complexity to examine the performance of the method by comparing our simulations with available exact analytical or numerical results. We demonstrate the potential of the method to resolve the complex diffusive interactions, here quantified by the Sherwood number, measuring the uptake rate in terms of that of isolated absorbers. We implement the method in a pseudospectral solver that can be generalized to include fluid motion and fluid-particle interactions. As a test case of the presence of a flow, we consider the uptake rate by a particle in a linear shear flow. Overall, our method represents a powerful and flexible computational tool that can be employed to investigate many complex situations in biology, chemistry, and related sciences.

Reproduced multi-domain regions during demagnetization in Nd2Fe14B sintered magnets with different average grain sizes

NASA Astrophysics Data System (ADS)

Kobayashi, Kurima; Nimura, You-ta; Urushibata, Kimiko; Hayakawa, Kazuo

2018-04-01

We prepared five Nd2Fe14B sintered magnets with similar saturation polarizations (Js) of 1.38-1.43 T and anisotropy fields (Ha) of 6.76-8.52 T, but different grain sizes (DAV) of 3.1-8.4 μm in diameter and obviously different coercivities (μ0Hc) of 0.8-1.6 T. The observed difference in coercivity could not be explained by the Kronmüller equation, because of the similar Ha values and similar chemical compositions and microstructures resulting from similar preparation method except DAV. The Hc values themselves, however, are inversely proportional to DAV. During demagnetization after magnetization in a 5 T pulse field, domain wall motion (DWM) was observed except in the sample with μ0Hc = 1.6 T by using our step method. The DWM was also confirmed by susceptibility measurements using a custom-built vibrating sample magnetometer, and DWM was generated in the reproduced multi-domain regions (RMDR) during demagnetization. The magnitude of DWM as a polarization change in the RMDR was inversely proportional to the coercivities of the samples. Therefore, it should be considered that the propagation of the nucleated region through the grain boundary, which corresponds to the expansion process in previous studies, was different caused by, first, the difference in DAV, and, second, in grain boundary state which was varied by difference in final annealing temperature.

Advances in numerical and applied mathematics

NASA Technical Reports Server (NTRS)

South, J. C., Jr. (Editor); Hussaini, M. Y. (Editor)

1986-01-01

This collection of papers covers some recent developments in numerical analysis and computational fluid dynamics. Some of these studies are of a fundamental nature. They address basic issues such as intermediate boundary conditions for approximate factorization schemes, existence and uniqueness of steady states for time dependent problems, and pitfalls of implicit time stepping. The other studies deal with modern numerical methods such as total variation diminishing schemes, higher order variants of vortex and particle methods, spectral multidomain techniques, and front tracking techniques. There is also a paper on adaptive grids. The fluid dynamics papers treat the classical problems of imcompressible flows in helically coiled pipes, vortex breakdown, and transonic flows.

Quadrature imposition of compatibility conditions in Chebyshev methods

NASA Technical Reports Server (NTRS)

Gottlieb, D.; Streett, C. L.

1990-01-01

Often, in solving an elliptic equation with Neumann boundary conditions, a compatibility condition has to be imposed for well-posedness. This condition involves integrals of the forcing function. When pseudospectral Chebyshev methods are used to discretize the partial differential equation, these integrals have to be approximated by an appropriate quadrature formula. The Gauss-Chebyshev (or any variant of it, like the Gauss-Lobatto) formula can not be used here since the integrals under consideration do not include the weight function. A natural candidate to be used in approximating the integrals is the Clenshaw-Curtis formula, however it is shown that this is the wrong choice and it may lead to divergence if time dependent methods are used to march the solution to steady state. The correct quadrature formula is developed for these problems. This formula takes into account the degree of the polynomials involved. It is shown that this formula leads to a well conditioned Chebyshev approximation to the differential equations and that the compatibility condition is automatically satisfied.

Matrix eigenvalue method for free-oscillations modelling of spherical elastic bodies

NASA Astrophysics Data System (ADS)

Zábranová, E.; Hanyk, L.; Matyska, C.

2017-11-01

Deformations and changes of the gravitational potential of pre-stressed self-gravitating elastic bodies caused by free oscillations are described by means of the momentum and Poisson equations and the constitutive relation. For spherically symmetric bodies, the equations and boundary conditions are transformed into ordinary differential equations of the second order by the spherical harmonic decomposition and further discretized by highly accurate pseudospectral difference schemes on Chebyshev grids; we pay special attention to the conditions at the centre of the models. We thus obtain a series of matrix eigenvalue problems for eigenfrequencies and eigenfunctions of the free oscillations. Accuracy of the presented numerical approach is tested by means of the Rayleigh quotients calculated for the eigenfrequencies up to 500 mHz. Both the modal frequencies and eigenfunctions are benchmarked against the output from the Mineos software package based on shooting methods. The presented technique is a promising alternative to widely used methods because it is stable and with a good capability up to high frequencies.

Evolution of inviscid Kelvin-Helmholtz instability from a piecewise linear shear layer

NASA Astrophysics Data System (ADS)

Guha, Anirban; Rahmani, Mona; Lawrence, Gregory

2012-11-01

Here we study the evolution of 2D, inviscid Kelvin-Helmholtz instability (KH) ensuing from a piecewise linear shear layer. Although KH pertaining to smooth shear layers (eg. Hyperbolic tangent profile) has been thorough investigated in the past, very little is known about KH resulting from sharp shear layers. Pozrikidis and Higdon (1985) have shown that piecewise shear layer evolves into elliptical vortex patches. This non-linear state is dramatically different from the well known spiral-billow structure of KH. In fact, there is a little acknowledgement that elliptical vortex patches can represent non-linear KH. In this work, we show how such patches evolve through the interaction of vorticity waves. Our work is based on two types of computational methods (i) Contour Dynamics: a boundary-element method which tracks the evolution of the contour of a vortex patch using Lagrangian marker points, and (ii) Direct Numerical Simulation (DNS): an Eulerian pseudo-spectral method heavily used in studying hydrodynamic instability and turbulence.

The fifth-order partial differential equation for the description of the α + β Fermi-Pasta-Ulam model

NASA Astrophysics Data System (ADS)

Kudryashov, Nikolay A.; Volkov, Alexandr K.

2017-01-01

We study a new nonlinear partial differential equation of the fifth order for the description of perturbations in the Fermi-Pasta-Ulam mass chain. This fifth-order equation is an expansion of the Gardner equation for the description of the Fermi-Pasta-Ulam model. We use the potential of interaction between neighbouring masses with both quadratic and cubic terms. The equation is derived using the continuous limit. Unlike the previous works, we take into account higher order terms in the Taylor series expansions. We investigate the equation using the Painlevé approach. We show that the equation does not pass the Painlevé test and can not be integrated by the inverse scattering transform. We use the logistic function method and the Laurent expansion method to find travelling wave solutions of the fifth-order equation. We use the pseudospectral method for the numerical simulation of wave processes, described by the equation.

High-Order Methods for Incompressible Fluid Flow

NASA Astrophysics Data System (ADS)

Deville, M. O.; Fischer, P. F.; Mund, E. H.

2002-08-01

High-order numerical methods provide an efficient approach to simulating many physical problems. This book considers the range of mathematical, engineering, and computer science topics that form the foundation of high-order numerical methods for the simulation of incompressible fluid flows in complex domains. Introductory chapters present high-order spatial and temporal discretizations for one-dimensional problems. These are extended to multiple space dimensions with a detailed discussion of tensor-product forms, multi-domain methods, and preconditioners for iterative solution techniques. Numerous discretizations of the steady and unsteady Stokes and Navier-Stokes equations are presented, with particular sttention given to enforcement of imcompressibility. Advanced discretizations. implementation issues, and parallel and vector performance are considered in the closing sections. Numerous examples are provided throughout to illustrate the capabilities of high-order methods in actual applications.

Fast neural solution of a nonlinear wave equation

NASA Technical Reports Server (NTRS)

Toomarian, Nikzad; Barhen, Jacob

1992-01-01

A neural algorithm for rapidly simulating a certain class of nonlinear wave phenomena using analog VLSI neural hardware is presented and applied to the Korteweg-de Vries partial differential equation. The corresponding neural architecture is obtained from a pseudospectral representation of the spatial dependence, along with a leap-frog scheme for the temporal evolution. Numerical simulations demonstrated the robustness of the proposed approach.

C-terminal domains of bacterial proteases: structure, function and the biotechnological applications.

PubMed

Huang, J; Wu, C; Liu, D; Yang, X; Wu, R; Zhang, J; Ma, C; He, H

2017-01-01

C-terminal domains widely exist in the C-terminal region of multidomain proteases. As a β-sandwich domain in multidomain protease, the C-terminal domain plays an important role in proteolysis including regulation of the secretory process, anchoring and swelling the substrate molecule, presenting as an inhibitor for the preprotease and adapting the protein structural flexibility and stability. In this review, the diversity, structural characteristics and biological function of C-terminal protease domains are described. Furthermore, the application prospects of C-terminal domains, including polycystic kidney disease, prepeptidase C-terminal and collagen-binding domain, in the area of medicine and biological artificial materials are also discussed. © 2016 The Society for Applied Microbiology.

A Multi-Domain Self-Report Measure of Coparenting

PubMed Central

Feinberg, Mark E.; Brown, Louis D.; Kan, Marni L.

2012-01-01

SYNOPSIS Objective This study reports the psychometric properties of a multi-domain measure of the coparenting relationship in dual-parent families. Method 152 couples participating in a transition to parenthood study completed the Coparenting Relationship Scale and additional measures during home visits at child age 6 months, 1 year, and 3 years. Results Psychometric and construct validity assessments indicated the measure performed satisfactorily. The 35-item measure demonstrated good reliability and strong stability. Subscales measuring theoretically and empirically important aspects of coparenting (coparenting agreement, coparenting closeness, exposure of child to conflict, coparenting support, coparenting undermining, endorsement of partner’s parenting, and division of labor) demonstrated good reliability as well. A 14-item brief overall measure showed very strong associations with the overall measure. Relations of the full scale with a measure of social desirability were weak, and the full scale was positively associated with positive dimensions of the dyadic couple relationship (love, sex/romance, couple efficacy) and inversely associated with negative dimensions (conflict, ineffective arguing)—as expected. Conclusions This initial examination of the Coparenting Relationship Scale suggests that it possesses good psychometric properties (reliability, stability, construct validity, and inter-rater agreement), can be flexibly administered in short and long forms, and is positioned to promote further conceptual and methodological progress in the study of coparenting. PMID:23166477

Eliminating time dispersion from seismic wave modeling

NASA Astrophysics Data System (ADS)

Koene, Erik F. M.; Robertsson, Johan O. A.; Broggini, Filippo; Andersson, Fredrik

2018-04-01

We derive an expression for the error introduced by the second-order accurate temporal finite-difference (FD) operator, as present in the FD, pseudospectral and spectral element methods for seismic wave modeling applied to time-invariant media. The `time-dispersion' error speeds up the signal as a function of frequency and time step only. Time dispersion is thus independent of the propagation path, medium or spatial modeling error. We derive two transforms to either add or remove time dispersion from synthetic seismograms after a simulation. The transforms are compared to previous related work and demonstrated on wave modeling in acoustic as well as elastic media. In addition, an application to imaging is shown. The transforms enable accurate computation of synthetic seismograms at reduced cost, benefitting modeling applications in both exploration and global seismology.

Reynolds Stress Balance in Plane Wakes Subjected to Irrotational Strains

NASA Technical Reports Server (NTRS)

Rogers, Miichael M.; Merriam, Marshal (Technical Monitor)

1997-01-01

Direct numerical simulations of time-evolving turbulent plane wakes developing in the presence of various irrotational plane strains have been generated. A pseudospectral numerical method with up to 25 million modes is used to solve the equations in a reference frame moving with the irrotational strain. The initial condition for each simulation is taken from a previous turbulent self-similar plane wake direct numerical simulation at a velocity deficit Reynolds number, R(sub e), of about 2,000. All the terms in the equations governing the evolution of the Reynolds stresses have been calculated. The relative importance of the various terms is examined for the different strain geometries and the behavior of the individual terms is used to better assess whether the strained wakes are evolving self-similarly.

Effect of rotation rate on the forces of a rotating cylinder: Simulation and control

NASA Technical Reports Server (NTRS)

Burns, John A.; Ou, Yuh-Roung

1993-01-01

In this paper we present numerical solutions to several optimal control problems for an unsteady viscous flow. The main thrust of this work is devoted to simulation and control of an unsteady flow generated by a circular cylinder undergoing rotary motion. By treating the rotation rate as a control variable, we can formulate two optimal control problems and use a central difference/pseudospectral transform method to numerically compute the optimal control rates. Several types of rotations are considered as potential controls, and we show that a proper synchronization of forcing frequency with the natural vortex shedding frequency can greatly influence the flow. The results here indicate that using moving boundary controls for such systems may provide a feasible mechanism for flow control.

Unsteady three-dimensional marginal separation, including breakdown

NASA Technical Reports Server (NTRS)

Duck, Peter W.

1990-01-01

A situation involving a three-dimensional marginal separation is considered, where a (steady) boundary layer flow is on the verge of separating at a point (located along a line of symmetry/centerline). At this point, a triple-deck is included, thereby permitting a small amount of interaction to occur. Unsteadiness is included within this interaction region through some external means. It is shown that the problem reduces to the solution of a nonlinear, unsteady, partial-integro system, which is solved numerically by means of time-marching together with a pseudo-spectral method spatially. A number of solutions to this system are presented which strongly suggest a breakdown of this system may occur, at a finite spatial position, at a finite time. The structure and details of this breakdown are then described.

Quantitative Vectorial Magnetic Imaging of Multi Domain Rock Forming Minerals using Nitrogen-Vacancy Centers in Diamond

NASA Astrophysics Data System (ADS)

Shaar, R.; Farchi, E.; Farfurnik, D.; Ebert, Y.; Haim, G.; Bar-Gill, N.

2017-12-01

Magnetization in rock samples is crucial for paleomagnetometry research, as it harbors valuable geological information on long term processes, such as tectonic movements and the formation of oceans and continents. Nevertheless, current techniques are limited in their ability to measure high spatial resolution and high-sensitivity quantitative vectorial magnetic signatures from individual minerals and micrometer scale samples. As a result, our understanding of bulk rock magnetization is limited, specifically for the case of multi-domain minerals. In this work we use a newly developed nitrogen-vacancy magnetic microscope, capable of quantitative vectorial magnetic imaging with optical resolution. We demonstrate direct imaging of the vectorial magnetic field of a single, multi-domain dendritic magnetite, as well as the measurement and calculation of the weak magnetic moments of an individual grain on the micron scale. Our results were measured in a standoff distance of 3-10 μm, with 350 nm spatial resolution, magnetic sensitivity of 6 μT/√(Hz) and a field of view of 35 μm. The results presented here show the capabilities and the future potential of NV microscopy in measuring the magnetic signals of individual micrometer scale grains. These outcomes pave the way for future applications in paleomagnetometry, and for the fundamental understanding of magnetization in multi-domain samples.

An improved multi-domain convolution tracking algorithm

NASA Astrophysics Data System (ADS)

Sun, Xin; Wang, Haiying; Zeng, Yingsen

2018-04-01

Along with the wide application of the Deep Learning in the field of Computer vision, Deep learning has become a mainstream direction in the field of object tracking. The tracking algorithm in this paper is based on the improved multidomain convolution neural network, and the VOT video set is pre-trained on the network by multi-domain training strategy. In the process of online tracking, the network evaluates candidate targets sampled from vicinity of the prediction target in the previous with Gaussian distribution, and the candidate target with the highest score is recognized as the prediction target of this frame. The Bounding Box Regression model is introduced to make the prediction target closer to the ground-truths target box of the test set. Grouping-update strategy is involved to extract and select useful update samples in each frame, which can effectively prevent over fitting. And adapt to changes in both target and environment. To improve the speed of the algorithm while maintaining the performance, the number of candidate target succeed in adjusting dynamically with the help of Self-adaption parameter Strategy. Finally, the algorithm is tested by OTB set, compared with other high-performance tracking algorithms, and the plot of success rate and the accuracy are drawn. which illustrates outstanding performance of the tracking algorithm in this paper.

Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor.

PubMed

Levy, Yaakov

2017-09-26

Proteins, like other biomolecules, have a modular and hierarchical structure. Various building blocks are used to construct proteins of high structural complexity and diverse functionality. In multidomain proteins, for example, domains are fused to each other in different combinations to achieve different functions. Although the LEGO brick metaphor is justified as a means of simplifying the complexity of three-dimensional protein structures, several fundamental properties (such as allostery or the induced-fit mechanism) make deviation from it necessary to respect the plasticity, softness, and cross-talk that are essential to protein function. In this work, we illustrate recently reported protein behavior in multidomain proteins that deviates from the LEGO brick analogy. While earlier studies showed that a protein domain is often unaffected by being fused to another domain or becomes more stable following the formation of a new interface between the tethered domains, destabilization due to tethering has been reported for several systems. We illustrate that tethering may sometimes result in a multidomain protein behaving as "less than the sum of its parts". We survey these cases for which structure additivity does not guarantee thermodynamic additivity. Protein destabilization due to fusion to other domains may be linked in some cases to biological function and should be taken into account when designing large assemblies.

Nanomechanics of multidomain neuronal cell adhesion protein contactin revealed by single molecule AFM and SMD.

PubMed

Mikulska-Ruminska, Karolina; Kulik, Andrej J; Benadiba, Carine; Bahar, Ivet; Dietler, Giovanni; Nowak, Wieslaw

2017-08-18

Contactin-4 (CNTN4) is a complex cell adhesion molecule (CAM) localized at neuronal membranes, playing a key role in maintaining the mechanical integrity and signaling properties of the synapse. CNTN4 consists of six immunoglobulin C2 type (IgC2) domains and four fibronectin type III (FnIII) domains that are shared with many other CAMs. Mutations in CNTN4 gene have been linked to various psychiatric disorders. Toward elucidating the response of this modular protein to mechanical stress, we studied its force-induced unfolding using single molecule atomic force microscopy (smAFM) and steered molecular dynamics (SMD) simulations. Extensive smAFM and SMD data both indicate the distinctive mechanical behavior of the two types of modules distinguished by unique force-extension signatures. The data also reveal the heterogeneity of the response of the individual FNIII and IgC2 modules, which presumably plays a role in the adaptability of CNTN4 to maintaining cell-cell communication and adhesion properties under different conditions. Results show that extensive sampling of force spectra, facilitated by robot-enhanced AFM, can help reveal the existence of weak stabilizing interactions between the domains of multidomain proteins, and provide insights into the nanomechanics of such multidomain or heteromeric proteins.

SPLICEFINDER – A Fast and Easy Screening Method for Active Protein Trans-Splicing Positions

PubMed Central

Eppmann, Simone; Busche, Alena; Dikovskaya, Dina; Dötsch, Volker; Mootz, Henning D.

2013-01-01

Split intein enabled protein trans-splicing (PTS) is a powerful method for the ligation of two protein fragments, thereby paving the way for various protein modification or protein function control applications. PTS activity is strongly influenced by the amino acids directly flanking the splice junctions. However, to date no reliable prediction can be made whether or not a split intein is active in a particular foreign extein context. Here we describe SPLICEFINDER, a PCR-based method, allowing fast and easy screening for active split intein insertions in any target protein. Furthermore we demonstrate the applicability of SPLICEFINDER for segmental isotopic labeling as well as for the generation of multi-domain and enzymatically active proteins. PMID:24023792

Two-craft Coulomb formation study about circular orbits and libration points

NASA Astrophysics Data System (ADS)

Inampudi, Ravi Kishore

This dissertation investigates the dynamics and control of a two-craft Coulomb formation in circular orbits and at libration points; it addresses relative equilibria, stability and optimal reconfigurations of such formations. The relative equilibria of a two-craft tether formation connected by line-of-sight elastic forces moving in circular orbits and at libration points are investigated. In circular Earth orbits and Earth-Moon libration points, the radial, along-track, and orbit normal great circle equilibria conditions are found. An example of modeling the tether force using Coulomb force is discussed. Furthermore, the non-great-circle equilibria conditions for a two-spacecraft tether structure in circular Earth orbit and at collinear libration points are developed. Then the linearized dynamics and stability analysis of a 2-craft Coulomb formation at Earth-Moon libration points are studied. For orbit-radial equilibrium, Coulomb forces control the relative distance between the two satellites. The gravity gradient torques on the formation due to the two planets help stabilize the formation. Similar analysis is performed for along-track and orbit-normal relative equilibrium configurations. Where necessary, the craft use a hybrid thrusting-electrostatic actuation system. The two-craft dynamics at the libration points provide a general framework with circular Earth orbit dynamics forming a special case. In the presence of differential solar drag perturbations, a Lyapunov feedback controller is designed to stabilize a radial equilibrium, two-craft Coulomb formation at collinear libration points. The second part of the thesis investigates optimal reconfigurations of two-craft Coulomb formations in circular Earth orbits by applying nonlinear optimal control techniques. The objective of these reconfigurations is to maneuver the two-craft formation between two charged equilibria configurations. The reconfiguration of spacecraft is posed as an optimization problem using the calculus of variations approach. The optimality criteria are minimum time, minimum acceleration of the separation distance, minimum Coulomb and electric propulsion fuel usage, and minimum electrical power consumption. The continuous time problem is discretized using a pseudospectral method, and the resulting finite dimensional problem is solved using a sequential quadratic programming algorithm. The software package, DIDO, implements this approach. This second part illustrates how pseudospectral methods significantly simplify the solution-finding process.

Theoretical modeling of multiprotein complexes by iSPOT: Integration of small-angle X-ray scattering, hydroxyl radical footprinting, and computational docking.

PubMed

Huang, Wei; Ravikumar, Krishnakumar M; Parisien, Marc; Yang, Sichun

2016-12-01

Structural determination of protein-protein complexes such as multidomain nuclear receptors has been challenging for high-resolution structural techniques. Here, we present a combined use of multiple biophysical methods, termed iSPOT, an integration of shape information from small-angle X-ray scattering (SAXS), protection factors probed by hydroxyl radical footprinting, and a large series of computationally docked conformations from rigid-body or molecular dynamics (MD) simulations. Specifically tested on two model systems, the power of iSPOT is demonstrated to accurately predict the structures of a large protein-protein complex (TGFβ-FKBP12) and a multidomain nuclear receptor homodimer (HNF-4α), based on the structures of individual components of the complexes. Although neither SAXS nor footprinting alone can yield an unambiguous picture for each complex, the combination of both, seamlessly integrated in iSPOT, narrows down the best-fit structures that are about 3.2Å and 4.2Å in RMSD from their corresponding crystal structures, respectively. Furthermore, this proof-of-principle study based on the data synthetically derived from available crystal structures shows that the iSPOT-using either rigid-body or MD-based flexible docking-is capable of overcoming the shortcomings of standalone computational methods, especially for HNF-4α. By taking advantage of the integration of SAXS-based shape information and footprinting-based protection/accessibility as well as computational docking, this iSPOT platform is set to be a powerful approach towards accurate integrated modeling of many challenging multiprotein complexes. Copyright © 2016 Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Asojo, Oluwatoyin A., E-mail: oasojo@unmc.edu; Loukas, Alex; Division of Infectious Diseases and Immunology, Queensland Institute of Medical Research, Brisbane, QLD 4006

In order to clarify the structural basis of the pathogenesis-related-1 domain, Na-ASP-1, the first multi-domain ASP from the human hookworm parasite N. americanus, has been crystallized. 2.2 Å resolution data have been collected from a crystal belonging to the monoclinic space group P2{sub 1}. Human hookworm infection is a major cause of anemia and malnutrition in the developing world. In an effort to control hookworm infection, the Human Hookworm Vaccine Initiative has identified candidate vaccine antigens from the infective larval stage (L3) of the parasite, including a family of pathogenesis-related-1 (PR-1) proteins known as the ancylostoma-secreted proteins (ASPs). The functionsmore » of the ASPs are unknown. In addition, it is unclear why some ASPs have one while others have multiple PR-1 domains. There are no known structures of a multi-domain ASP and in an effort to remedy this situation, recombinant Na-ASP-1 has been expressed, purified and crystallized. Na-ASP-1 is a 406-amino-acid multi-domain ASP from the prevalent human hookworm parasite Necator americanus. Useful X-ray data to 2.2 Å have been collected from a crystal that belongs to the monoclinic space group P2{sub 1} with unit-cell parameters a = 67.7, b = 74.27, c = 84.60 Å, β = 112.12°. An initial molecular-replacement solution has been obtained with one monomer in the asymmetric unit.« less

Degradation of Granular Starch by the Bacterium Microbacterium aurum Strain B8.A Involves a Modular α-Amylase Enzyme System with FNIII and CBM25 Domains

PubMed Central

Eeuwema, Wieger; Sarian, Fean D.; van der Kaaij, Rachel M.

2015-01-01

The bacterium Microbacterium aurum strain B8.A, originally isolated from a potato plant wastewater facility, is able to degrade different types of starch granules. Here we report the characterization of an unusually large, multidomain M. aurum B8.A α-amylase enzyme (MaAmyA). MaAmyA is a 1,417-amino-acid (aa) protein with a predicted molecular mass of 148 kDa. Sequence analysis of MaAmyA showed that its catalytic core is a family GH13_32 α-amylase with the typical ABC domain structure, followed by a fibronectin (FNIII) domain, two carbohydrate binding modules (CBM25), and another three FNIII domains. Recombinant expression and purification yielded an enzyme with the ability to degrade wheat and potato starch granules by introducing pores. Characterization of various truncated mutants of MaAmyA revealed a direct relationship between the presence of CBM25 domains and the ability of MaAmyA to form pores in starch granules, while the FNIII domains most likely function as stable linkers. At the C terminus, MaAmyA carries a 300-aa domain which is uniquely associated with large multidomain amylases; its function remains to be elucidated. We concluded that M. aurum B8.A employs a multidomain enzyme system to initiate degradation of starch granules via pore formation. PMID:26187958

An Interpolation Approach to Optimal Trajectory Planning for Helicopter Unmanned Aerial Vehicles

DTIC Science & Technology

2012-06-01

Armament Data Line DOF Degree of Freedom PS Pseudospectral LGL Legendre -Gauss-Lobatto quadrature nodes ODE Ordinary Differential Equation xiv...low order polynomials patched together in such away so that the resulting trajectory has several continuous derivatives at all points. In [7], Murray...claims that splines are ideal for optimal control problems because each segment of the spline’s piecewise polynomials approximate the trajectory

Designing with non-linear viscoelastic fluids

NASA Astrophysics Data System (ADS)

Schuh, Jonathon; Lee, Yong Hoon; Allison, James; Ewoldt, Randy

2017-11-01

Material design is typically limited to hard materials or simple fluids; however, design with more complex materials can provide ways to enhance performance. Using the Criminale-Ericksen-Filbey (CEF) constitutive model in the thin film lubrication limit, we derive a modified Reynolds Equation (based on asymptotic analysis) that includes shear thinning, first normal stress, and terminal regime viscoelastic effects. This allows for designing non-linear viscoelastic fluids in thin-film creeping flow scenarios, i.e. optimizing the shape of rheological material properties to achieve different design objectives. We solve the modified Reynolds equation using the pseudo-spectral method, and describe a case study in full-film lubricated sliding where optimal fluid properties are identified. These material-agnostic property targets can then guide formulation of complex fluids which may use polymeric, colloidal, or other creative approaches to achieve the desired non-Newtonian properties.

Force-free electrodynamics in dynamical curved spacetimes

NASA Astrophysics Data System (ADS)

McWilliams, Sean

2015-04-01

We present results on our study of force-free electrodynamics in curved spacetimes. Specifically, we present several improvements to what has become the established set of evolution equations, and we apply these to study the nonlinear stability of analytically known force-free solutions for the first time. We implement our method in a new pseudo-spectral code built on top of the SpEC code for evolving dynamic spacetimes. Finally, we revisit these known solutions and attempt to clarify some interesting properties that render them analytically tractable. Finally, we preview some new work that similarly revisits the established approach to solving another problem in numerical relativity: the post-merger recoil from asymmetric gravitational-wave emission. These new results may have significant implications for the parameter dependence of recoils, and consequently on the statistical expectations for recoil velocities of merged systems.

Analysis of the low gravity tolerance of Bridgman-Stockbarger crystal growth. I - Steady and impulse accelerations

NASA Technical Reports Server (NTRS)

Alexander, J. Iwan D.; Ouazzani, Jalil; Rosenberger, Franz

1989-01-01

The effects of steady and impulse-type residual accelerations on dopant distributions during directional solidification in 2D and 3D 'generic' models of the Bridgman-Stockbarger technique are investigated using numerical methods. The calculations are based on the thermophysical properties of molten germanium doped with a low concentration of gallium. A Chebyshev collocation pseudospectral method is used for the solution of the governing momentum-, mass-, species-, and heat-transfer equations. Only convection caused by temperature gradients is considered. It is found that lateral nonuniformity in composition is very sensitive to the orientation of the steady component of the residual gravity vector and to the particular operating conditions under consideration. It is also found that laterally or radially averaged composition profiles are alone insufficient to describe the extent of residual convection in a spacecraft environment. The effects of impulse-type disturbances can be severe and can extend for times on the order of 1000 sec after the termination of the impulse.

A new multi-domain method based on an analytical control surface for linear and second-order mean drift wave loads on floating bodies

NASA Astrophysics Data System (ADS)

Liang, Hui; Chen, Xiaobo

2017-10-01

A novel multi-domain method based on an analytical control surface is proposed by combining the use of free-surface Green function and Rankine source function. A cylindrical control surface is introduced to subdivide the fluid domain into external and internal domains. Unlike the traditional domain decomposition strategy or multi-block method, the control surface here is not panelized, on which the velocity potential and normal velocity components are analytically expressed as a series of base functions composed of Laguerre function in vertical coordinate and Fourier series in the circumference. Free-surface Green function is applied in the external domain, and the boundary integral equation is constructed on the control surface in the sense of Galerkin collocation via integrating test functions orthogonal to base functions over the control surface. The external solution gives rise to the so-called Dirichlet-to-Neumann [DN2] and Neumann-to-Dirichlet [ND2] relations on the control surface. Irregular frequencies, which are only dependent on the radius of the control surface, are present in the external solution, and they are removed by extending the boundary integral equation to the interior free surface (circular disc) on which the null normal derivative of potential is imposed, and the dipole distribution is expressed as Fourier-Bessel expansion on the disc. In the internal domain, where the Rankine source function is adopted, new boundary integral equations are formulated. The point collocation is imposed over the body surface and free surface, while the collocation of the Galerkin type is applied on the control surface. The present method is valid in the computation of both linear and second-order mean drift wave loads. Furthermore, the second-order mean drift force based on the middle-field formulation can be calculated analytically by using the coefficients of the Fourier-Laguerre expansion.

From Structure to Function: A Comprehensive Compendium of Tools to Unveil Protein Domains and Understand Their Role in Cytokinesis.

PubMed

Rincon, Sergio A; Paoletti, Anne

2016-01-01

Unveiling the function of a novel protein is a challenging task that requires careful experimental design. Yeast cytokinesis is a conserved process that involves modular structural and regulatory proteins. For such proteins, an important step is to identify their domains and structural organization. Here we briefly discuss a collection of methods commonly used for sequence alignment and prediction of protein structure that represent powerful tools for the identification homologous domains and design of structure-function approaches to test experimentally the function of multi-domain proteins such as those implicated in yeast cytokinesis.

A Federated Digital Identity Management Approach for Business Processes

NASA Astrophysics Data System (ADS)

Bertino, Elisa; Ferrini, Rodolfo; Musci, Andrea; Paci, Federica; Steuer, Kevin J.

Business processes have gained a lot of attention because of the pressing need for integrating existing resources and services to better fulfill customer needs. A key feature of business processes is that they are built from composable services, referred to as component services, that may belong to different domains. In such a context, flexible multi-domain identity management solutions are crucial for increased security and user-convenience. In particular, it is important that during the execution of a business process the component services be able to verify the identity of the client to check that it has the required permissions for accessing the services. To address the problem of multi-domain identity management, we propose a multi-factor identity attribute verification protocol for business processes that assures clients privacy and handles naming heterogeneity.

A Randomized Controlled ERP Study on the Effects of Multi-Domain Cognitive Training and Task Difficulty on Task Switching Performance in Older Adults.

PubMed

Küper, Kristina; Gajewski, Patrick D; Frieg, Claudia; Falkenstein, Michael

2017-01-01

Executive functions are subject to a marked age-related decline, but have been shown to benefit from cognitive training interventions. As of yet, it is, however, still relatively unclear which neural mechanism can mediate training-related performance gains. In the present electrophysiological study, we examined the effects of multi-domain cognitive training on performance in an untrained cue-based task switch paradigm featuring Stroop color words: participants either had to indicate the word meaning of Stroop stimuli (word task) or perform the more difficult task of color naming (color task). One-hundred and three older adults (>65 years old) were randomly assigned to a training group receiving a 4-month multi-domain cognitive training, a passive no-contact control group or an active (social) control group receiving a 4-month relaxation training. For all groups, we recorded performance and EEG measures before and after the intervention. For the cognitive training group, but not for the two control groups, we observed an increase in response accuracy at posttest, irrespective of task and trial type. No training-related effects on reaction times were found. Cognitive training was also associated with an overall increase in N2 amplitude and a decrease of P2 latency on single trials. Training-related performance gains were thus likely mediated by an enhancement of response selection and improved access to relevant stimulus-response mappings. Additionally, cognitive training was associated with an amplitude decrease in the time window of the target-locked P3 at fronto-central electrodes. An increase in the switch positivity during advance task preparation emerged after both cognitive and relaxation training. Training-related behavioral and event-related potential (ERP) effects were not modulated by task difficulty. The data suggest that cognitive training increased slow negative potentials during target processing which enhanced the N2 and reduced a subsequent P3-like component on both switch and non-switch trials and irrespective of task difficulty. Our findings further corroborate the effectiveness of multi-domain cognitive training in older adults and indicate that ERPs can be instrumental in uncovering the neural processes underlying training-related performance gains.

Lateral resolution improvement in scanning nonlinear dielectric microscopy by measuring super-higher-order nonlinear dielectric constants

NASA Astrophysics Data System (ADS)

Chinone, N.; Yamasue, K.; Hiranaga, Y.; Honda, K.; Cho, Y.

2012-11-01

Scanning nonlinear dielectric microscopy (SNDM) can be used to visualize polarization distributions in ferroelectric materials and dopant profiles in semiconductor devices. Without using a special sharp tip, we achieved an improved lateral resolution in SNDM through the measurement of super-higher-order nonlinearity up to the fourth order. We observed a multidomain single crystal congruent LiTaO3 (CLT) sample, and a cross section of a metal-oxide-semiconductor (MOS) field-effect-transistor (FET). The imaged domain boundaries of the CLT were narrower in the super-higher-order images than in the conventional image. Compared to the conventional method, the super-higher-order method resolved the more detailed structure of the MOSFET.

Experimental and theoretical assessment of the multi-domain flow behaviour in a waste body during leachate infiltration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tinet, A-J., E-mail: tinet@ujf-grenoble.fr; Oxarango, L.; Centre for Research in Environmental, Coastal and Hydrological Engineering, School of Civil Engineering, Surveying and Construction, University of KwaZulu-Natal, Howard College Campus, Durban 4041

2011-08-15

The optimisation of landfill operation is a key challenge for the upcoming years. A promising solution to improve municipal solid waste (MSW) management is the bioreactor technology. A meso-scale (around 1 m{sup 3}) experimental set-up was performed to study the effect of moisture control in low density conditions with different leachate injection operations and bioreactor monitoring including the use of a neutron probe. The moisture content distribution evolution demonstrates a multi-domain flow behaviour. A classic van Genuchten-Mualem description of the connected porosity proved insufficient to correctly describe the observed phenomena. A bimodal description of the connected porosity is proposed asmore » solution and a connected/non-connected porosities numerical model was applied to the results. The model explains the experimental results reasonably well.« less

A unique GCN5-related glucosamine N-acetyltransferase region exist in the fungal multi-domain glycoside hydrolase family 3 β-N-acetylglucosaminidase

PubMed Central

Qin, Zhen; Xiao, Yibei; Yang, Xinbin; Mesters, Jeroen R.; Yang, Shaoqing; Jiang, Zhengqiang

2015-01-01

Glycoside hydrolase (GH) family 3 β-N-acetylglucosaminidases widely exist in the filamentous fungi, which may play a key role in chitin metabolism of fungi. A multi-domain GH family 3 β-N-acetylglucosaminidase from Rhizomucor miehei (RmNag), exhibiting a potential N-acetyltransferase region, has been recently reported to show great potential in industrial applications. In this study, the crystal structure of RmNag was determined at 2.80 Å resolution. The three-dimensional structure of RmNag showed four distinctive domains, which belong to two distinguishable functional regions — a GH family 3 β-N-acetylglucosaminidase region (N-terminal) and a N-acetyltransferase region (C-terminal). From structural and functional analysis, the C-terminal region of RmNag was identified as a unique tandem array linking general control non-derepressible 5 (GCN5)-related N-acetyltransferase (GNAT), which displayed glucosamine N-acetyltransferase activity. Structural analysis of this glucosamine N-acetyltransferase region revealed that a unique glucosamine binding pocket is located in the pantetheine arm binding terminal region of the conserved CoA binding pocket, which is different from all known GNAT members. This is the first structural report of a glucosamine N-acetyltransferase, which provides novel structural information about substrate specificity of GNATs. The structural and functional features of this multi-domain β-N-acetylglucosaminidase could be useful in studying the catalytic mechanism of GH family 3 proteins. PMID:26669854

A unique GCN5-related glucosamine N-acetyltransferase region exist in the fungal multi-domain glycoside hydrolase family 3 β-N-acetylglucosaminidase.

PubMed

Qin, Zhen; Xiao, Yibei; Yang, Xinbin; Mesters, Jeroen R; Yang, Shaoqing; Jiang, Zhengqiang

2015-12-16

Glycoside hydrolase (GH) family 3 β-N-acetylglucosaminidases widely exist in the filamentous fungi, which may play a key role in chitin metabolism of fungi. A multi-domain GH family 3 β-N-acetylglucosaminidase from Rhizomucor miehei (RmNag), exhibiting a potential N-acetyltransferase region, has been recently reported to show great potential in industrial applications. In this study, the crystal structure of RmNag was determined at 2.80 Å resolution. The three-dimensional structure of RmNag showed four distinctive domains, which belong to two distinguishable functional regions--a GH family 3 β-N-acetylglucosaminidase region (N-terminal) and a N-acetyltransferase region (C-terminal). From structural and functional analysis, the C-terminal region of RmNag was identified as a unique tandem array linking general control non-derepressible 5 (GCN5)-related N-acetyltransferase (GNAT), which displayed glucosamine N-acetyltransferase activity. Structural analysis of this glucosamine N-acetyltransferase region revealed that a unique glucosamine binding pocket is located in the pantetheine arm binding terminal region of the conserved CoA binding pocket, which is different from all known GNAT members. This is the first structural report of a glucosamine N-acetyltransferase, which provides novel structural information about substrate specificity of GNATs. The structural and functional features of this multi-domain β-N-acetylglucosaminidase could be useful in studying the catalytic mechanism of GH family 3 proteins.

Degradation of Granular Starch by the Bacterium Microbacterium aurum Strain B8.A Involves a Modular α-Amylase Enzyme System with FNIII and CBM25 Domains.

PubMed

Valk, Vincent; Eeuwema, Wieger; Sarian, Fean D; van der Kaaij, Rachel M; Dijkhuizen, Lubbert

2015-10-01

The bacterium Microbacterium aurum strain B8.A, originally isolated from a potato plant wastewater facility, is able to degrade different types of starch granules. Here we report the characterization of an unusually large, multidomain M. aurum B8.A α-amylase enzyme (MaAmyA). MaAmyA is a 1,417-amino-acid (aa) protein with a predicted molecular mass of 148 kDa. Sequence analysis of MaAmyA showed that its catalytic core is a family GH13_32 α-amylase with the typical ABC domain structure, followed by a fibronectin (FNIII) domain, two carbohydrate binding modules (CBM25), and another three FNIII domains. Recombinant expression and purification yielded an enzyme with the ability to degrade wheat and potato starch granules by introducing pores. Characterization of various truncated mutants of MaAmyA revealed a direct relationship between the presence of CBM25 domains and the ability of MaAmyA to form pores in starch granules, while the FNIII domains most likely function as stable linkers. At the C terminus, MaAmyA carries a 300-aa domain which is uniquely associated with large multidomain amylases; its function remains to be elucidated. We concluded that M. aurum B8.A employs a multidomain enzyme system to initiate degradation of starch granules via pore formation. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Folding of multidomain proteins: biophysical consequences of tethering even in apparently independent folding.

PubMed

Arviv, Oshrit; Levy, Yaakov

2012-12-01

Most eukaryotic and a substantial fraction of prokaryotic proteins are composed of more than one domain. The tethering of these evolutionary, structural, and functional units raises, among others, questions regarding the folding process of conjugated domains. Studying the folding of multidomain proteins in silico enables one to identify and isolate the tethering-induced biophysical determinants that govern crosstalks generated between neighboring domains. For this purpose, we carried out coarse-grained and atomistic molecular dynamics simulations of two two-domain constructs from the immunoglobulin-like β-sandwich fold. Each of these was experimentally shown to behave as the "sum of its parts," that is, the thermodynamic and kinetic folding behavior of the constituent domains of these constructs seems to occur independently, with the folding of each domain uncoupled from the folding of its partner in the two-domain construct. We show that the properties of the individual domains can be significantly affected by conjugation to another domain. The tethering may be accompanied by stabilizing as well as destabilizing factors whose magnitude depends on the size of the interface, the length, and the flexibility of the linker, and the relative stability of the domains. Accordingly, the folding of a multidomain protein should not be viewed as the sum of the folding patterns of each of its parts, but rather, it involves abrogating several effects that lead to this outcome. An imbalance between these effects may result in either stabilization or destabilization owing to the tethering. Copyright © 2012 Wiley Periodicals, Inc.

Investigation of electric charge on inertial particle dynamics in turbulence

NASA Astrophysics Data System (ADS)

Lu, Jiang; Shaw, Raymond

2014-11-01

The behavior of electrically charged, inertial particles in homogeneous, isotropic turbulence is investigated. Both like-charged and oppositely-charged particle interactions are considered. Direct numerical simulations (DNS) of turbulence in a periodic box using the pseudospectral numerical method are performed, with Lagrangian tracking of the particles. We study effects of mutual electrostatic repulsion and attraction on the particle dynamics, as quantified by the radial distribution function (RDF) and the radial relative velocity. For the like-charged particle case, the Coulomb force leads to a short range repulsion behavior and an RDF reminiscent of that for a dilute gas. For the oppositely-charged particle case, the Coulomb force increases the RDF beyond that already occurring for neutral inertial particles. For both cases, the relative velocities are calculated as a function of particle separation distance and show distinct deviations from the expected scaling within the dissipation range. This research was supported by NASA Grant NNX113AF90G.

A validated computational model for the design of surface textures in full-film lubricated sliding

NASA Astrophysics Data System (ADS)

Schuh, Jonathon; Lee, Yong Hoon; Allison, James; Ewoldt, Randy

2016-11-01

Our recent experimental work showed that asymmetry is needed for surface textures to decrease friction in full-film lubricated sliding (thrust bearings) with Newtonian fluids; textures reduce the shear load and produce a separating normal force. The sign of the separating normal force is not predicted by previous 1-D theories. Here we model the flow with the Reynolds equation in cylindrical coordinates, numerically implemented with a pseudo-spectral method. The model predictions match experiments, rationalize the sign of the normal force, and allow for design of surface texture geometry. To minimize sliding friction with angled cylindrical textures, an optimal angle of asymmetry β exists. The optimal angle depends on the film thickness but not the sliding velocity within the applicable range of the model. The model has also been used to optimize generalized surface texture topography while satisfying manufacturability constraints.

Experimental and numerical investigation of development of disturbances in the boundary layer on sharp and blunted cone

NASA Astrophysics Data System (ADS)

Borisov, S. P.; Bountin, D. A.; Gromyko, Yu. V.; Khotyanovsky, D. V.; Kudryavtsev, A. N.

2016-10-01

Development of disturbances in the supersonic boundary layer on sharp and blunted cones is studied both experimentally and theoretically. The experiments were conducted at the Transit-M hypersonic wind tunnel of the Institute of Theoretical and Applied Mechanics. Linear stability calculations use the basic flow profiles provided by the numerical simulations performed by solving the Navier-Stokes equations with the ANSYS Fluent and the in-house CFS3D code. Both the global pseudospectral Chebyshev method and the local iteration procedure are employed to solve the eigenvalue problem and determine linear stability characteristics. The calculated amplification factors for disturbances of various frequencies are compared with the experimentally measured pressure fluctuation spectra at different streamwise positions. It is shown that the linear stability calculations predict quite accurately the frequency of the most amplified disturbances and enable us to estimate reasonably well their relative amplitudes.

Impacts of Ocean Waves on the Atmospheric Surface Layer: Simulations and Observations

DTIC Science & Technology

2008-06-06

energy and pressure described in § 4 are solved using a mixed finite - difference pseudospectral scheme with a third-order Runge-Kutta time stepping with a...to that in our DNS code (Sullivan and McWilliams 2002; Sullivan et al. 2000). For our mixed finite - difference pseudospec- tral differencing scheme a...Poisson equation. The spatial discretization is pseu- dospectral along lines of constant or and second- order finite difference in the vertical

Stochastic Real-Time Optimal Control: A Pseudospectral Approach for Bearing-Only Trajectory Optimization

DTIC Science & Technology

2011-09-01

artificially creating enough baseline to enable triangulation. This motion comes at the expense of the primary mission, unless the entire purpose...control of a sUAS for surveillance and other mis-sions. Completely autonomous UAS control for surveillance missions is still an on-the-horizon...work, xapp, was correspondingly set to 2-m. Since the test platform for the algorithm was a helicopter vice a fixed-wing UAS , an aggressive flare segment

Iontophoretic transdermal drug delivery: a multi-layered approach.

PubMed

Pontrelli, Giuseppe; Lauricella, Marco; Ferreira, José A; Pena, Gonçalo

2017-12-11

We present a multi-layer mathematical model to describe the transdermal drug release from an iontophoretic system. The Nernst-Planck equation describes the basic convection-diffusion process, with the electric potential obtained by solving the Laplace's equation. These equations are complemented with suitable interface and boundary conditions in a multi-domain. The stability of the mathematical problem is discussed in different scenarios and a finite-difference method is used to solve the coupled system. Numerical experiments are included to illustrate the drug dynamics under different conditions. © The authors 2016. Published by Oxford University Press on behalf of the Institute of Mathematics and its Applications. All rights reserved.

Three-dimensional stress intensity factor analysis of a surface crack in a high-speed bearing

NASA Technical Reports Server (NTRS)

Ballarini, Roberto; Hsu, Yingchun

1990-01-01

The boundary element method is applied to calculate the stress intensity factors of a surface crack in the rotating inner raceway of a high-speed roller bearing. The three-dimensional model consists of an axially stressed surface cracked plate subjected to a moving Hertzian contact loading. A multidomain formulation and singular crack-tip elements were employed to calculate the stress intensity factors accurately and efficiently for a wide range of configuration parameters. The results can provide the basis for crack growth calculations and fatigue life predictions of high-performance rolling element bearings that are used in aircraft engines.

Reorientations, relaxations, metastabilities, and multidomains of skyrmion lattices

NASA Astrophysics Data System (ADS)

Bannenberg, L. J.; Qian, F.; Dalgliesh, R. M.; Martin, N.; Chaboussant, G.; Schmidt, M.; Schlagel, D. L.; Lograsso, T. A.; Wilhelm, H.; Pappas, C.

2017-11-01

Magnetic skyrmions are nanosized topologically protected spin textures with particlelike properties. They can form lattices perpendicular to the magnetic field, and the orientation of these skyrmion lattices with respect to the crystallographic lattice is governed by spin-orbit coupling. By performing small-angle neutron scattering measurements, we investigate the coupling between the crystallographic and skyrmion lattices in both Cu2OSeO3 and the archetype chiral magnet MnSi. The results reveal that the orientation of the skyrmion lattice is primarily determined by the magnetic field direction with respect to the crystallographic lattice. In addition, it is also influenced by the magnetic history of the sample, which can induce metastable lattices. Kinetic measurements show that these metastable skyrmion lattices may or may not relax to their equilibrium positions under macroscopic relaxation times. Furthermore, multidomain lattices may form when two or more equivalent crystallographic directions are favored by spin-orbit coupling and oriented perpendicular to the magnetic field.

Understanding pathogenic single-nucleotide polymorphisms in multidomain proteins – studies of isolated domains are not enough

PubMed Central

Randles, Lucy G; Dawes, Gwen J S; Wensley, Beth G; Steward, Annette; Nickson, Adrian A; Clarke, Jane

2013-01-01

Studying the effects of pathogenic mutations is more complex in multidomain proteins when compared with single domains: mutations occurring at domain boundaries may have a large effect on a neighbouring domain that will not be detected in a single-domain system. To demonstrate this, we present a study that utilizes well-characterized model protein domains from human spectrin to investigate the effect of disease-and non-disease-causing single point mutations occurring at the boundaries of human spectrin repeats. Our results show that mutations in the single domains have no clear correlation with stability and disease; however, when studied in a tandem model system, the disease-causing mutations are shown to disrupt stabilizing interactions that exist between domains. This results in a much larger decrease in stability than would otherwise have been predicted, and demonstrates the importance of studying such mutations in the correct protein context. PMID:23241237

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Xianjun; Zhao, Fei; Wu, Yiran

Here, the Smoothened receptor (SMO) belongs to the Class Frizzled of the G protein-coupled receptor (GPCR) superfamily, constituting a key component of the Hedgehog signalling pathway. Here we report the crystal structure of the multi-domain human SMO, bound and stabilized by a designed tool ligand TC114, using an X-ray free-electron laser source at 2.9 Å. The structure reveals a precise arrangement of three distinct domains: a seven-transmembrane helices domain (TMD), a hinge domain (HD) and an intact extracellular cysteine-rich domain (CRD). This architecture enables allosteric interactions between the domains that are important for ligand recognition and receptor activation. By combiningmore » the structural data, molecular dynamics simulation, and hydrogen-deuterium-exchange analysis, we demonstrate that transmembrane helix VI, extracellular loop 3 and the HD play a central role in transmitting the signal employing a unique GPCR activation mechanism, distinct from other multi-domain GPCRs.« less

Characterization of Protein Flexibility Using Small-Angle X-Ray Scattering and Amplified Collective Motion Simulations

PubMed Central

Wen, Bin; Peng, Junhui; Zuo, Xiaobing; Gong, Qingguo; Zhang, Zhiyong

2014-01-01

Large-scale flexibility within a multidomain protein often plays an important role in its biological function. Despite its inherent low resolution, small-angle x-ray scattering (SAXS) is well suited to investigate protein flexibility and determine, with the help of computational modeling, what kinds of protein conformations would coexist in solution. In this article, we develop a tool that combines SAXS data with a previously developed sampling technique called amplified collective motions (ACM) to elucidate structures of highly dynamic multidomain proteins in solution. We demonstrate the use of this tool in two proteins, bacteriophage T4 lysozyme and tandem WW domains of the formin-binding protein 21. The ACM simulations can sample the conformational space of proteins much more extensively than standard molecular dynamics (MD) simulations. Therefore, conformations generated by ACM are significantly better at reproducing the SAXS data than are those from MD simulations. PMID:25140431

Toward multidomain integrated network management for ATM and SDH networks

NASA Astrophysics Data System (ADS)

Galis, Alex; Gantenbein, Dieter; Covaci, Stefan; Bianza, Carlo; Karayannis, Fotis; Mykoniatis, George

1996-12-01

ACTS Project AC080 MISA has embarked upon the task of realizing and validating via European field trials integrated end-to-end management of hybrid SDH and ATM networks in the framework of open network provision. This paper reflects the initial work of the project and gives an overview of the proposed MISA system architecture and initial design. We describe our understanding of the underlying enterprise model in the network management context, including the concept of the MISA Global Broadband Connectivity Management service. It supports Integrated Broadband Communication by defining an end-to-end broadband connection service in a multi-domain business environment. Its implementation by the MISA consortium within trials across Europe aims for an efficient management of network resources of the SDH and ATM infrastructure, considering optimum end-to-end quality of service and the needs of a number of telecommunication actors: customers, value-added service providers, and network providers.

Baseline Telomere Length and Effects of a Multidomain Lifestyle Intervention on Cognition: The FINGER Randomized Controlled Trial

PubMed Central

Sindi, Shireen; Ngandu, Tiia; Hovatta, Iiris; Kåreholt, Ingemar; Antikainen, Riitta; Hänninen, Tuomo; Levälahti, Esko; Laatikainen, Tiina; Lindström, Jaana; Paajanen, Teemu; Peltonen, Markku; Khalsa, Dharma Singh; Wolozin, Benjamin; Strandberg, Timo; Tuomilehto, Jaakko; Soininen, Hilkka; Kivipelto, Miia; Solomon, Alina

2017-01-01

Leukocyte telomere length (LTL) is a biomarker of aging, and it is associated with lifestyle. It is currently unknown whether LTL is associated with the response to lifestyle interventions. The goal is to assess whether baseline LTL modified the cognitive benefits of a 2-year multidomain lifestyle intervention (exploratory analyses). The Finnish Geriatric Intervention Study to Prevent Cognitive Impairment and Disability (FINGER) was a 2-year randomized controlled trial including 1,260 people at risk of cognitive decline, aged 60–77 years identified from the general population. Participants were randomly assigned to the lifestyle intervention (diet, exercise, cognitive training, and vascular risk management) and control (general health advice) groups. Primary outcome was change in cognition (comprehensive neuropsychological test battery). Secondary outcomes were changes in cognitive domains: memory, executive functioning, and processing speed. 775 participants (392 control, 383 intervention) had baseline LTL (peripheral blood DNA). Mixed effects regression models with maximum likelihood estimation were used to analyze change in cognition as a function of randomization group, time, baseline LTL, and their interaction. Intervention and control groups did not significantly differ at baseline. Shorter LTL was related to less healthy baseline lifestyle. Intervention benefits on executive functioning were more pronounced among those with shorter baseline LTL (p-value for interaction was 0.010 adjusted for age and sex, and 0.007 additionally adjusted for baseline lifestyle factors). The FINGER intervention cognitive benefits were more pronounced with shorter baseline LTL, particularly for executive functioning, indicating that the multidomain lifestyle intervention was especially beneficial among higher-risk individuals. PMID:28777749

Hybrid protection algorithms based on game theory in multi-domain optical networks

NASA Astrophysics Data System (ADS)

Guo, Lei; Wu, Jingjing; Hou, Weigang; Liu, Yejun; Zhang, Lincong; Li, Hongming

2011-12-01

With the network size increasing, the optical backbone is divided into multiple domains and each domain has its own network operator and management policy. At the same time, the failures in optical network may lead to a huge data loss since each wavelength carries a lot of traffic. Therefore, the survivability in multi-domain optical network is very important. However, existing survivable algorithms can achieve only the unilateral optimization for profit of either users or network operators. Then, they cannot well find the double-win optimal solution with considering economic factors for both users and network operators. Thus, in this paper we develop the multi-domain network model with involving multiple Quality of Service (QoS) parameters. After presenting the link evaluation approach based on fuzzy mathematics, we propose the game model to find the optimal solution to maximize the user's utility, the network operator's utility, and the joint utility of user and network operator. Since the problem of finding double-win optimal solution is NP-complete, we propose two new hybrid protection algorithms, Intra-domain Sub-path Protection (ISP) algorithm and Inter-domain End-to-end Protection (IEP) algorithm. In ISP and IEP, the hybrid protection means that the intelligent algorithm based on Bacterial Colony Optimization (BCO) and the heuristic algorithm are used to solve the survivability in intra-domain routing and inter-domain routing, respectively. Simulation results show that ISP and IEP have the similar comprehensive utility. In addition, ISP has better resource utilization efficiency, lower blocking probability, and higher network operator's utility, while IEP has better user's utility.

Slush-like polar structures in single-crystal relaxors

NASA Astrophysics Data System (ADS)

Takenaka, Hiroyuki; Grinberg, Ilya; Liu, Shi; Rappe, Andrew M.

2017-06-01

Despite more than 50 years of investigation, it is still unclear how the underlying structure of relaxor ferroelectrics gives rise to their defining properties, such as ultrahigh piezoelectric coefficients, high permittivity over a broad temperature range, diffuse phase transitions, strong frequency dependence in dielectric response, and phonon anomalies. The model of polar nanoregions inside a non-polar matrix has been widely used to describe the structure of relaxor ferroelectrics. However, the lack of precise knowledge about the shapes, growth and dipole patterns of polar nanoregions has led to the characterization of relaxors as “hopeless messes”, and no predictive model for relaxor behaviour is currently available. Here we use molecular dynamics simulations of the prototypical Pb(Mg1/3,Nb2/3)O3-PbTiO3 relaxor material to examine its structure and the spatial and temporal polarization correlations. Our simulations show that the unusual properties of relaxors stem from the presence of a multi-domain state with extremely small domain sizes (2-10 nanometres), and no non-polar matrix, owing to the local dynamics. We find that polar structures in the multi-domain state in relaxors are analogous to those of the slush state of water. The multi-domain structure of relaxors that is revealed by our molecular dynamics simulations is consistent with recent experimental diffuse scattering results and indicates that relaxors have a high density of low-angle domain walls. This insight explains the recently discovered classes of relaxors that cannot be described by the polar nanoregion model, and provides guidance for the design and synthesis of new relaxor materials.

Baseline Telomere Length and Effects of a Multidomain Lifestyle Intervention on Cognition: The FINGER Randomized Controlled Trial.

PubMed

Sindi, Shireen; Ngandu, Tiia; Hovatta, Iiris; Kåreholt, Ingemar; Antikainen, Riitta; Hänninen, Tuomo; Levälahti, Esko; Laatikainen, Tiina; Lindström, Jaana; Paajanen, Teemu; Peltonen, Markku; Khalsa, Dharma Singh; Wolozin, Benjamin; Strandberg, Timo; Tuomilehto, Jaakko; Soininen, Hilkka; Kivipelto, Miia; Solomon, Alina

2017-01-01

Leukocyte telomere length (LTL) is a biomarker of aging, and it is associated with lifestyle. It is currently unknown whether LTL is associated with the response to lifestyle interventions. The goal is to assess whether baseline LTL modified the cognitive benefits of a 2-year multidomain lifestyle intervention (exploratory analyses). The Finnish Geriatric Intervention Study to Prevent Cognitive Impairment and Disability (FINGER) was a 2-year randomized controlled trial including 1,260 people at risk of cognitive decline, aged 60-77 years identified from the general population. Participants were randomly assigned to the lifestyle intervention (diet, exercise, cognitive training, and vascular risk management) and control (general health advice) groups. Primary outcome was change in cognition (comprehensive neuropsychological test battery). Secondary outcomes were changes in cognitive domains: memory, executive functioning, and processing speed. 775 participants (392 control, 383 intervention) had baseline LTL (peripheral blood DNA). Mixed effects regression models with maximum likelihood estimation were used to analyze change in cognition as a function of randomization group, time, baseline LTL, and their interaction. Intervention and control groups did not significantly differ at baseline. Shorter LTL was related to less healthy baseline lifestyle. Intervention benefits on executive functioning were more pronounced among those with shorter baseline LTL (p-value for interaction was 0.010 adjusted for age and sex, and 0.007 additionally adjusted for baseline lifestyle factors). The FINGER intervention cognitive benefits were more pronounced with shorter baseline LTL, particularly for executive functioning, indicating that the multidomain lifestyle intervention was especially beneficial among higher-risk individuals.

A 170kDa multi-domain cystatin of Fasciola gigantica is active in the male reproductive system.

PubMed

Geadkaew, Amornrat; Kosa, Nanthawat; Siricoon, Sinee; Grams, Suksiri Vichasri; Grams, Rudi

2014-09-01

Cystatins are functional as intra- and extracellular inhibitors of cysteine proteases and are expressed as single or multi-domain proteins. We have previously described two single domain type 1 cystatins in the trematode Fasciola gigantica that are released into the parasite's intestinal tract and exhibit inhibitory activity against endogenous and host cathepsin L and B proteases. In contrast, the here presented 170kDa multi-domain cystatin (FgMDC) comprises signal peptide and 12 tandem repeated cystatin-like domains with similarity to type 2 single domain cystatins. The domains show high sequence divergence with identity values often <20% and at only 26.8% between the highest matching domains 6 and 10. Several domains contain degenerated QVVAG core motifs and/or lack other important residues of active type 2 cystatins. Domain-specific antisera detected multiple forms of FgMDC ranging from <10 to >120kDa molecular mass in immunoblots of parasite crude extracts and ES product with different banding patterns for each antiserum demonstrating complex processing of the proprotein. The four domains with the highest conserved QVVAG motifs were expressed in Escherichia coli and the refolded recombinant proteins blocked cysteine protease activity in the parasite's ES product. Strikingly, immunohistochemical analysis using seven domain-specific antisera localized FgMDC in testis lobes and sperm. It is speculated that the processed cystatin-like domains have function analogous to the mammalian group of male reproductive tissue-specific type 2 cystatins and are functional in spermiogenesis and fertilization. Copyright © 2014 Elsevier B.V. All rights reserved.

Competing Pathways and Multiple Folding Nuclei in a Large Multidomain Protein, Luciferase.

PubMed

Scholl, Zackary N; Yang, Weitao; Marszalek, Piotr E

2017-05-09

Proteins obtain their final functional configuration through incremental folding with many intermediate steps in the folding pathway. If known, these intermediate steps could be valuable new targets for designing therapeutics and the sequence of events could elucidate the mechanism of refolding. However, determining these intermediate steps is hardly an easy feat, and has been elusive for most proteins, especially large, multidomain proteins. Here, we effectively map part of the folding pathway for the model large multidomain protein, Luciferase, by combining single-molecule force-spectroscopy experiments and coarse-grained simulation. Single-molecule refolding experiments reveal the initial nucleation of folding while simulations corroborate these stable core structures of Luciferase, and indicate the relative propensities for each to propagate to the final folded native state. Both experimental refolding and Monte Carlo simulations of Markov state models generated from simulation reveal that Luciferase most often folds along a pathway originating from the nucleation of the N-terminal domain, and that this pathway is the least likely to form nonnative structures. We then engineer truncated variants of Luciferase whose sequences corresponded to the putative structure from simulation and we use atomic force spectroscopy to determine their unfolding and stability. These experimental results corroborate the structures predicted from the folding simulation and strongly suggest that they are intermediates along the folding pathway. Taken together, our results suggest that initial Luciferase refolding occurs along a vectorial pathway and also suggest a mechanism that chaperones may exploit to prevent misfolding. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Simulation analysis of the transparency of cornea and sclera

NASA Astrophysics Data System (ADS)

Yang, Chih-Yao; Tseng, Snow H.

2017-02-01

Both consist of collagen fibrils, sclera is opaque whereas cornea is transparent for optical wavelengths. By employing the pseudospectral time-domain (PSTD) simulation technique, we model light impinging upon cornea and sclera, respectively. To analyze the scattering characteristics of light, the cornea and sclera are modeled by different sizes and arrangements of the non-absorbing collagen fibrils. Various factors are analyzed, including the wavelength of incident light, the thickness of the scattering media, position of the collagen fibrils, size distribution of the fibrils.

Three-dimensional marginal separation

NASA Technical Reports Server (NTRS)

Duck, Peter W.

1988-01-01

The three dimensional marginal separation of a boundary layer along a line of symmetry is considered. The key equation governing the displacement function is derived, and found to be a nonlinear integral equation in two space variables. This is solved iteratively using a pseudo-spectral approach, based partly in double Fourier space, and partly in physical space. Qualitatively, the results are similar to previously reported two dimensional results (which are also computed to test the accuracy of the numerical scheme); however quantitatively the three dimensional results are much different.

Trajectory optimization for lunar soft landing with complex constraints

NASA Astrophysics Data System (ADS)

Chu, Huiping; Ma, Lin; Wang, Kexin; Shao, Zhijiang; Song, Zhengyu

2017-11-01

A unified trajectory optimization framework with initialization strategies is proposed in this paper for lunar soft landing for various missions with specific requirements. Two main missions of interest are Apollo-like Landing from low lunar orbit and Vertical Takeoff Vertical Landing (a promising mobility method) on the lunar surface. The trajectory optimization is characterized by difficulties arising from discontinuous thrust, multi-phase connections, jump of attitude angle, and obstacles avoidance. Here R-function is applied to deal with the discontinuities of thrust, checkpoint constraints are introduced to connect multiple landing phases, attitude angular rate is designed to get rid of radical changes, and safeguards are imposed to avoid collision with obstacles. The resulting dynamic problems are generally with complex constraints. The unified framework based on Gauss Pseudospectral Method (GPM) and Nonlinear Programming (NLP) solver are designed to solve the problems efficiently. Advanced initialization strategies are developed to enhance both the convergence and computation efficiency. Numerical results demonstrate the adaptability of the framework for various landing missions, and the performance of successful solution of difficult dynamic problems.

A Randomized Controlled ERP Study on the Effects of Multi-Domain Cognitive Training and Task Difficulty on Task Switching Performance in Older Adults

PubMed Central

Küper, Kristina; Gajewski, Patrick D.; Frieg, Claudia; Falkenstein, Michael

2017-01-01

Executive functions are subject to a marked age-related decline, but have been shown to benefit from cognitive training interventions. As of yet, it is, however, still relatively unclear which neural mechanism can mediate training-related performance gains. In the present electrophysiological study, we examined the effects of multi-domain cognitive training on performance in an untrained cue-based task switch paradigm featuring Stroop color words: participants either had to indicate the word meaning of Stroop stimuli (word task) or perform the more difficult task of color naming (color task). One-hundred and three older adults (>65 years old) were randomly assigned to a training group receiving a 4-month multi-domain cognitive training, a passive no-contact control group or an active (social) control group receiving a 4-month relaxation training. For all groups, we recorded performance and EEG measures before and after the intervention. For the cognitive training group, but not for the two control groups, we observed an increase in response accuracy at posttest, irrespective of task and trial type. No training-related effects on reaction times were found. Cognitive training was also associated with an overall increase in N2 amplitude and a decrease of P2 latency on single trials. Training-related performance gains were thus likely mediated by an enhancement of response selection and improved access to relevant stimulus-response mappings. Additionally, cognitive training was associated with an amplitude decrease in the time window of the target-locked P3 at fronto-central electrodes. An increase in the switch positivity during advance task preparation emerged after both cognitive and relaxation training. Training-related behavioral and event-related potential (ERP) effects were not modulated by task difficulty. The data suggest that cognitive training increased slow negative potentials during target processing which enhanced the N2 and reduced a subsequent P3-like component on both switch and non-switch trials and irrespective of task difficulty. Our findings further corroborate the effectiveness of multi-domain cognitive training in older adults and indicate that ERPs can be instrumental in uncovering the neural processes underlying training-related performance gains. PMID:28446870

A New Computational Technique for the Generation of Optimised Aircraft Trajectories

NASA Astrophysics Data System (ADS)

Chircop, Kenneth; Gardi, Alessandro; Zammit-Mangion, David; Sabatini, Roberto

2017-12-01

A new computational technique based on Pseudospectral Discretisation (PSD) and adaptive bisection ɛ-constraint methods is proposed to solve multi-objective aircraft trajectory optimisation problems formulated as nonlinear optimal control problems. This technique is applicable to a variety of next-generation avionics and Air Traffic Management (ATM) Decision Support Systems (DSS) for strategic and tactical replanning operations. These include the future Flight Management Systems (FMS) and the 4-Dimensional Trajectory (4DT) planning and intent negotiation/validation tools envisaged by SESAR and NextGen for a global implementation. In particular, after describing the PSD method, the adaptive bisection ɛ-constraint method is presented to allow an efficient solution of problems in which two or multiple performance indices are to be minimized simultaneously. Initial simulation case studies were performed adopting suitable aircraft dynamics models and addressing a classical vertical trajectory optimisation problem with two objectives simultaneously. Subsequently, a more advanced 4DT simulation case study is presented with a focus on representative ATM optimisation objectives in the Terminal Manoeuvring Area (TMA). The simulation results are analysed in-depth and corroborated by flight performance analysis, supporting the validity of the proposed computational techniques.

A Comparison of Spectral Element and Finite Difference Methods Using Statically Refined Nonconforming Grids for the MHD Island Coalescence Instability Problem

NASA Astrophysics Data System (ADS)

Ng, C. S.; Rosenberg, D.; Pouquet, A.; Germaschewski, K.; Bhattacharjee, A.

2009-04-01

A recently developed spectral-element adaptive refinement incompressible magnetohydrodynamic (MHD) code [Rosenberg, Fournier, Fischer, Pouquet, J. Comp. Phys. 215, 59-80 (2006)] is applied to simulate the problem of MHD island coalescence instability (\\ci) in two dimensions. \\ci is a fundamental MHD process that can produce sharp current layers and subsequent reconnection and heating in a high-Lundquist number plasma such as the solar corona [Ng and Bhattacharjee, Phys. Plasmas, 5, 4028 (1998)]. Due to the formation of thin current layers, it is highly desirable to use adaptively or statically refined grids to resolve them, and to maintain accuracy at the same time. The output of the spectral-element static adaptive refinement simulations are compared with simulations using a finite difference method on the same refinement grids, and both methods are compared to pseudo-spectral simulations with uniform grids as baselines. It is shown that with the statically refined grids roughly scaling linearly with effective resolution, spectral element runs can maintain accuracy significantly higher than that of the finite difference runs, in some cases achieving close to full spectral accuracy.

Implicit LES using adaptive filtering

NASA Astrophysics Data System (ADS)

Sun, Guangrui; Domaradzki, Julian A.

2018-04-01

In implicit large eddy simulations (ILES) numerical dissipation prevents buildup of small scale energy in a manner similar to the explicit subgrid scale (SGS) models. If spectral methods are used the numerical dissipation is negligible but it can be introduced by applying a low-pass filter in the physical space, resulting in an effective ILES. In the present work we provide a comprehensive analysis of the numerical dissipation produced by different filtering operations in a turbulent channel flow simulated using a non-dissipative, pseudo-spectral Navier-Stokes solver. The amount of numerical dissipation imparted by filtering can be easily adjusted by changing how often a filter is applied. We show that when the additional numerical dissipation is close to the subgrid-scale (SGS) dissipation of an explicit LES the overall accuracy of ILES is also comparable, indicating that periodic filtering can replace explicit SGS models. A new method is proposed, which does not require any prior knowledge of a flow, to determine the filtering period adaptively. Once an optimal filtering period is found, the accuracy of ILES is significantly improved at low implementation complexity and computational cost. The method is general, performing well for different Reynolds numbers, grid resolutions, and filter shapes.

The Multigrid-Mask Numerical Method for Solution of Incompressible Navier-Stokes Equations

NASA Technical Reports Server (NTRS)

Ku, Hwar-Ching; Popel, Aleksander S.

1996-01-01

A multigrid-mask method for solution of incompressible Navier-Stokes equations in primitive variable form has been developed. The main objective is to apply this method in conjunction with the pseudospectral element method solving flow past multiple objects. There are two key steps involved in calculating flow past multiple objects. The first step utilizes only Cartesian grid points. This homogeneous or mask method step permits flow into the interior rectangular elements contained in objects, but with the restriction that the velocity for those Cartesian elements within and on the surface of an object should be small or zero. This step easily produces an approximate flow field on Cartesian grid points covering the entire flow field. The second or heterogeneous step corrects the approximate flow field to account for the actual shape of the objects by solving the flow field based on the local coordinates surrounding each object and adapted to it. The noise occurring in data communication between the global (low frequency) coordinates and the local (high frequency) coordinates is eliminated by the multigrid method when the Schwarz Alternating Procedure (SAP) is implemented. Two dimensional flow past circular and elliptic cylinders will be presented to demonstrate the versatility of the proposed method. An interesting phenomenon is found that when the second elliptic cylinder is placed in the wake of the first elliptic cylinder a traction force results in a negative drag coefficient.

Virtual network embedding in cross-domain network based on topology and resource attributes

NASA Astrophysics Data System (ADS)

Zhu, Lei; Zhang, Zhizhong; Feng, Linlin; Liu, Lilan

2018-03-01

Aiming at the network architecture ossification and the diversity of access technologies issues, this paper researches the cross-domain virtual network embedding algorithm. By analysing the topological attribute from the local and global perspective of nodes in the virtual network and the physical network, combined with the local network resource property, we rank the embedding priority of the nodes with PCA and TOPSIS methods. Besides, the link load distribution is considered. Above all, We proposed an cross-domain virtual network embedding algorithm based on topology and resource attributes. The simulation results depicts that our algorithm increases the acceptance rate of multi-domain virtual network requests, compared with the existing virtual network embedding algorithm.

Fully pseudospectral solution of the conformally invariant wave equation near the cylinder at spacelike infinity. III: nonspherical Schwarzschild waves and singularities at null infinity

NASA Astrophysics Data System (ADS)

Frauendiener, Jörg; Hennig, Jörg

2018-03-01

We extend earlier numerical and analytical considerations of the conformally invariant wave equation on a Schwarzschild background from the case of spherically symmetric solutions, discussed in Frauendiener and Hennig (2017 Class. Quantum Grav. 34 045005), to the case of general, nonsymmetric solutions. A key element of our approach is the modern standard representation of spacelike infinity as a cylinder. With a decomposition into spherical harmonics, we reduce the four-dimensional wave equation to a family of two-dimensional equations. These equations can be used to study the behaviour at the cylinder, where the solutions turn out to have, in general, logarithmic singularities at infinitely many orders. We derive regularity conditions that may be imposed on the initial data, in order to avoid the first singular terms. We then demonstrate that the fully pseudospectral time evolution scheme can be applied to this problem leading to a highly accurate numerical reconstruction of the nonsymmetric solutions. We are particularly interested in the behaviour of the solutions at future null infinity, and we numerically show that the singularities spread to null infinity from the critical set, where the cylinder approaches null infinity. The observed numerical behaviour is consistent with similar logarithmic singularities found analytically on the critical set. Finally, we demonstrate that even solutions with singularities at low orders can be obtained with high accuracy by virtue of a coordinate transformation that converts solutions with logarithmic singularities into smooth solutions.

seismo-live: Training in Computational Seismology using Jupyter Notebooks

NASA Astrophysics Data System (ADS)

Igel, H.; Krischer, L.; van Driel, M.; Tape, C.

2016-12-01

Practical training in computational methodologies is still underrepresented in Earth science curriculae despite the increasing use of sometimes highly sophisticated simulation technologies in research projects. At the same time well-engineered community codes make it easy to return simulation-based results yet with the danger that the inherent traps of numerical solutions are not well understood. It is our belief that training with highly simplified numerical solutions (here to the equations describing elastic wave propagation) with carefully chosen elementary ingredients of simulation technologies (e.g., finite-differencing, function interpolation, spectral derivatives, numerical integration) could substantially improve this situation. For this purpose we have initiated a community platform (www.seismo-live.org) where Python-based Jupyter notebooks can be accessed and run without and necessary downloads or local software installations. The increasingly popular Jupyter notebooks allow combining markup language, graphics, equations with interactive, executable python codes. We demonstrate the potential with training notebooks for the finite-difference method, pseudospectral methods, finite/spectral element methods, the finite-volume and the discontinuous Galerkin method. The platform already includes general Python training, introduction to the ObsPy library for seismology as well as seismic data processing and noise analysis. Submission of Jupyter notebooks for general seismology are encouraged. The platform can be used for complementary teaching in Earth Science courses on compute-intensive research areas.

Design and parametric study on energy harvesting from bridge vibration using tuned dual-mass damper systems

NASA Astrophysics Data System (ADS)

Takeya, Kouichi; Sasaki, Eiichi; Kobayashi, Yusuke

2016-01-01

A bridge vibration energy harvester has been proposed in this paper using a tuned dual-mass damper system, named hereafter Tuned Mass Generator (TMG). A linear electromagnetic transducer has been applied to harvest and make use of the unused reserve of energy the aforementioned damper system absorbs. The benefits of using dual-mass systems over single-mass systems for power generation have been clarified according to the theory of vibrations. TMG parameters have been determined considering multi-domain parameters, and TMG has been tuned using a newly proposed parameter design method. Theoretical analysis results have shown that for effective energy harvesting, it is essential that TMG has robustness against uncertainties in bridge vibrations and tuning errors, and the proposed parameter design method for TMG has demonstrated this feature.

On the suitability of the Thellier method of palaeointensity determinations on pseudo-single-domain and multidomain grains

NASA Astrophysics Data System (ADS)

Shcherbakov, V. P.; Shcherbakova, V. V.

2001-07-01

We report an experimental and theoretical study of non-linear Arai-Nagata diagrams for samples containing pseudo-single-domain (PSD) and multidomain (MD) magnetite. Our aim is to reveal the physical reasons for the deviation of these plots from ideal straight lines. Contrary to expectations, the concavity of the Arai-Nagata diagrams is not related to the two most noticeable violations of the Thellier laws documented for non-single-domain particles: the tail of partial thermoremanence and the dependence of the magnitude of pTRM on the thermal history of the sample. Indeed, the contributions from these two factors mutually cancel each other. Phenomenologically, the non-linear Arai-Nagata plots occur because samples during low-temperature stages of the Thellier procedure lose too much remanence and recover too little of it. The excessive loss of the previously imparted total TRM is due at least partly to some partial demagnetization of high-temperature TRM components and to progressive stabilization of domain structure during the repetitive heatings to moderate temperatures that form the basis of the Thellier procedure. For natural MD samples a linear fit to the low-temperature data points on the Arai-Nagata plots leads to a palaeointensity overestimated by as much as 60 per cent. The samples containing hydrothermally grown or crushed and sieved MD magnetite provide low-temperature apparent palaeointensities two to three times larger than the correct value. For small PSD samples the overestimate is less than 10-20 per cent and, in general, PSD samples can be used for the palaeointensity determinations.

Cooperativity and modularity in protein folding

PubMed Central

Sasai, Masaki; Chikenji, George; Terada, Tomoki P.

2016-01-01

A simple statistical mechanical model proposed by Wako and Saitô has explained the aspects of protein folding surprisingly well. This model was systematically applied to multiple proteins by Muñoz and Eaton and has since been referred to as the Wako-Saitô-Muñoz-Eaton (WSME) model. The success of the WSME model in explaining the folding of many proteins has verified the hypothesis that the folding is dominated by native interactions, which makes the energy landscape globally biased toward native conformation. Using the WSME and other related models, Saitô emphasized the importance of the hierarchical pathway in protein folding; folding starts with the creation of contiguous segments having a native-like configuration and proceeds as growth and coalescence of these segments. The Φ-values calculated for barnase with the WSME model suggested that segments contributing to the folding nucleus are similar to the structural modules defined by the pattern of native atomic contacts. The WSME model was extended to explain folding of multi-domain proteins having a complex topology, which opened the way to comprehensively understanding the folding process of multi-domain proteins. The WSME model was also extended to describe allosteric transitions, indicating that the allosteric structural movement does not occur as a deterministic sequential change between two conformations but as a stochastic diffusive motion over the dynamically changing energy landscape. Statistical mechanical viewpoint on folding, as highlighted by the WSME model, has been renovated in the context of modern methods and ideas, and will continue to provide insights on equilibrium and dynamical features of proteins. PMID:28409080

Conformational dynamics and ligand binding in the multi-domain protein PDC109.

PubMed

Kim, Hyun Jin; Choi, Moo Young; Kim, Hyung J; Llinás, Miguel

2010-02-18

PDC109 is a modular multi-domain protein with two fibronectin type II (Fn2) repeats joined by a linker. It plays a major role in bull sperm binding to the oviductal epithelium through its interactions with phosphorylcholines (PhCs), a head group of sperm cell membrane lipids. The crystal structure of the PDC109-PhC complex shows that each PhC binds to the corresponding Fn2 domain, while the two domains are on the same face of the protein. Long timescale explicit solvent molecular dynamics (MD) simulations of PDC109, in the presence and absence of PhC, suggest that PhC binding strongly correlates with the relative orientation of choline-phospholipid binding sites of the two Fn2 domains; unless the two domains tightly bind PhCs, they tend to change their relative orientation by deforming the flexible linker. The effective PDC109-PhC association constant of 28 M(-1), estimated from their potential of mean force is consistent with the experimental result. Principal component analysis of the long timescale MD simulations was compared to the significantly less expensive normal mode analysis of minimized structures. The comparison indicates that difference between relative domain motions of PDC109 with bound and unbound PhC is captured by the first principal component in the principal component analysis as well as the three lowest normal modes in the normal mode analysis. The present study illustrates the use of detailed MD simulations to clarify the energetics of specific ligand-domain interactions revealed by a static crystallographic model, as well as their influence on relative domain motions in a multi-domain protein.

Characterization of the starch-acting MaAmyB enzyme from Microbacterium aurum B8.A representing the novel subfamily GH13_42 with an unusual, multi-domain organization

PubMed Central

Valk, Vincent; van der Kaaij, Rachel M.; Dijkhuizen, Lubbert

2016-01-01

The bacterium Microbacterium aurum strain B8.A degrades granular starches, using the multi-domain MaAmyA α-amylase to initiate granule degradation through pore formation. This paper reports the characterization of the M. aurum B8.A MaAmyB enzyme, a second starch-acting enzyme with multiple FNIII and CBM25 domains. MaAmyB was characterized as an α-glucan 1,4-α-maltohexaosidase with the ability to subsequently hydrolyze maltohexaose to maltose through the release of glucose. MaAmyB also displays exo-activity with a double blocked PNPG7 substrate, releasing PNP. In M. aurum B8.A, MaAmyB may contribute to degradation of starch granules by rapidly hydrolyzing the helical and linear starch chains that become exposed after pore formation by MaAmyA. Bioinformatics analysis showed that MaAmyB represents a novel GH13 subfamily, designated GH13_42, currently with 165 members, all in Gram-positive soil dwelling bacteria, mostly Streptomyces. All members have an unusually large catalytic domain (AB-regions), due to three insertions compared to established α-amylases, and an aberrant C-region, which has only 30% identity to established GH13 C-regions. Most GH13_42 members have three N-terminal domains (2 CBM25 and 1 FNIII). This is unusual as starch binding domains are commonly found at the C-termini of α-amylases. The evolution of the multi-domain M. aurum B8.A MaAmyA and MaAmyB enzymes is discussed. PMID:27808246

A New Finite Difference Q-compensated RTM Algorithm in Tilted Transverse Isotropic (TTI) Media

NASA Astrophysics Data System (ADS)

Zhou, T.; Hu, W.; Ning, J.

2017-12-01

Attenuating anisotropic geological body is difficult to image with conventional migration methods. In such kind of scenarios, recorded seismic data suffer greatly from both amplitude decay and phase distortion, resulting in degraded resolution, poor illumination and incorrect migration depth in imaging results. To efficiently obtain high quality images, we propose a novel TTI QRTM algorithm based on Generalized Standard Linear Solid model combined with a unique multi-stage optimization technique to simultaneously correct the decayed amplitude and the distorted phase velocity. Numerical tests (shown in the figure) demonstrate that our TTI QRTM algorithm effectively corrects migration depth, significantly improves illumination, and enhances resolution within and below the low Q regions. The result of our new method is very close to the reference RTM image, while QRTM without TTI cannot get a correct image. Compared to the conventional QRTM method based on a pseudo-spectral operator for fractional Laplacian evaluation, our method is more computationally efficient for large scale applications and more suitable for GPU acceleration. With the current multi-stage dispersion optimization scheme, this TTI QRTM method best performs in the frequency range 10-70 Hz, and could be used in a wider frequency range. Furthermore, as this method can also handle frequency dependent Q, it has potential to be applied in imaging deep structures where low Q exists, such as subduction zones, volcanic zones or fault zones with passive source observations.

FERMI: A Flexible Expert Reasoner with Multi-Domain Inferencing.

DTIC Science & Technology

1985-07-29

for Life Sciences University of Leyden AFOSR Education Research Center Boiling AFB Boerhaavelaan 2 Washington. DC 20032-6448 2334 EN Leyden The... Kathleen McKeown Columbia University Dr. Michael Levine Department of Computer Science Educational Psychology New York, NY 10027 210 Education Bldg

The Multi-Domain Fibroblast/Myocyte Coupling in the Cardiac Tissue: A Theoretical Study.

PubMed

Greisas, Ariel; Zlochiver, Sharon

2016-09-01

Cardiac fibroblast proliferation and concomitant collagenous matrix accumulation (fibrosis) develop during multiple cardiac pathologies. Recent studies have demonstrated direct electrical coupling between myocytes and fibroblasts in vitro, and assessed the electrophysiological implications of such coupling. However, in the living tissues, such coupling has not been demonstrated, and only indirect coupling via the extracellular space is likely to exist. In this study we employed a multi-domain model to assess the modulation of the cardiac electrophysiological properties by neighboring fibroblasts assuming only indirect coupling. Numerical simulations in 1D and 2D human atrial models showed that extracellular coupling sustains a significant impact on conduction velocity (CV) and a less significant effect on the action potential duration. Both CV and the slope of the CV restitution increased with increasing fibroblast density. This effect was more substantial for lower extracellular conductance. In 2D, spiral waves exhibited reduced frequency with increasing fibroblast density, and the propensity of wavebreaks and complex dynamics at high pacing rates significantly increased.

A bacterial pioneer produces cellulase complexes that persist through community succession

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kolinko, Sebastian; Wu, Yu-Wei; Tachea, Firehiwot

Cultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, 'Candidatus Reconcilibacillus cellulovorans', possessed a gene cluster containing multidomain glycoside hydrolases (GHs). Purification of the soluble cellulase activity from a 300litre cultivation of this consortium revealed that ~70% of the activity arose from the 'Ca. Reconcilibacillus cellulovorans' multidomain GHs assembled into cellulase complexes through glycosylation. These remarkably stable complexes have supramolecular structures formore » enzymatic cellulose hydrolysis that are distinct from cellulosomes. The persistence of these complexes during cultivation indicates that they may be active through multiple cultivations of this consortium and act as public goods that sustain the community. Thus, the provision of extracellular GHs as public goods may influence microbial community dynamics in native biomass-deconstructing communities relevant to agriculture, human health and biotechnology.« less

A bacterial pioneer produces cellulase complexes that persist through community succession

DOE PAGES

Kolinko, Sebastian; Wu, Yu-Wei; Tachea, Firehiwot; ...

2017-11-06

Cultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, 'Candidatus Reconcilibacillus cellulovorans', possessed a gene cluster containing multidomain glycoside hydrolases (GHs). Purification of the soluble cellulase activity from a 300litre cultivation of this consortium revealed that ~70% of the activity arose from the 'Ca. Reconcilibacillus cellulovorans' multidomain GHs assembled into cellulase complexes through glycosylation. These remarkably stable complexes have supramolecular structures formore » enzymatic cellulose hydrolysis that are distinct from cellulosomes. The persistence of these complexes during cultivation indicates that they may be active through multiple cultivations of this consortium and act as public goods that sustain the community. Thus, the provision of extracellular GHs as public goods may influence microbial community dynamics in native biomass-deconstructing communities relevant to agriculture, human health and biotechnology.« less

A bacterial pioneer produces cellulase complexes that persist through community succession.

PubMed

Kolinko, Sebastian; Wu, Yu-Wei; Tachea, Firehiwot; Denzel, Evelyn; Hiras, Jennifer; Gabriel, Raphael; Bäcker, Nora; Chan, Leanne Jade G; Eichorst, Stephanie A; Frey, Dario; Chen, Qiushi; Azadi, Parastoo; Adams, Paul D; Pray, Todd R; Tanjore, Deepti; Petzold, Christopher J; Gladden, John M; Simmons, Blake A; Singer, Steven W

2018-01-01

Cultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, 'Candidatus Reconcilibacillus cellulovorans', possessed a gene cluster containing multidomain glycoside hydrolases (GHs). Purification of the soluble cellulase activity from a 300litre cultivation of this consortium revealed that ~70% of the activity arose from the 'Ca. Reconcilibacillus cellulovorans' multidomain GHs assembled into cellulase complexes through glycosylation. These remarkably stable complexes have supramolecular structures for enzymatic cellulose hydrolysis that are distinct from cellulosomes. The persistence of these complexes during cultivation indicates that they may be active through multiple cultivations of this consortium and act as public goods that sustain the community. The provision of extracellular GHs as public goods may influence microbial community dynamics in native biomass-deconstructing communities relevant to agriculture, human health and biotechnology.

Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism.

PubMed

Liberato, Marcelo V; Silveira, Rodrigo L; Prates, Érica T; de Araujo, Evandro A; Pellegrini, Vanessa O A; Camilo, Cesar M; Kadowaki, Marco A; Neto, Mario de O; Popov, Alexander; Skaf, Munir S; Polikarpov, Igor

2016-04-01

Glycoside hydrolases (GHs) play fundamental roles in the decomposition of lignocellulosic biomaterials. Here, we report the full-length structure of a cellulase from Bacillus licheniformis (BlCel5B), a member of the GH5 subfamily 4 that is entirely dependent on its two ancillary modules (Ig-like module and CBM46) for catalytic activity. Using X-ray crystallography, small-angle X-ray scattering and molecular dynamics simulations, we propose that the C-terminal CBM46 caps the distal N-terminal catalytic domain (CD) to establish a fully functional active site via a combination of large-scale multidomain conformational selection and induced-fit mechanisms. The Ig-like module is pivoting the packing and unpacking motions of CBM46 relative to CD in the assembly of the binding subsite. This is the first example of a multidomain GH relying on large amplitude motions of the CBM46 for assembly of the catalytically competent form of the enzyme.

Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism

NASA Astrophysics Data System (ADS)

Liberato, Marcelo V.; Silveira, Rodrigo L.; Prates, Érica T.; de Araujo, Evandro A.; Pellegrini, Vanessa O. A.; Camilo, Cesar M.; Kadowaki, Marco A.; Neto, Mario De O.; Popov, Alexander; Skaf, Munir S.; Polikarpov, Igor

2016-04-01

Glycoside hydrolases (GHs) play fundamental roles in the decomposition of lignocellulosic biomaterials. Here, we report the full-length structure of a cellulase from Bacillus licheniformis (BlCel5B), a member of the GH5 subfamily 4 that is entirely dependent on its two ancillary modules (Ig-like module and CBM46) for catalytic activity. Using X-ray crystallography, small-angle X-ray scattering and molecular dynamics simulations, we propose that the C-terminal CBM46 caps the distal N-terminal catalytic domain (CD) to establish a fully functional active site via a combination of large-scale multidomain conformational selection and induced-fit mechanisms. The Ig-like module is pivoting the packing and unpacking motions of CBM46 relative to CD in the assembly of the binding subsite. This is the first example of a multidomain GH relying on large amplitude motions of the CBM46 for assembly of the catalytically competent form of the enzyme.

Reorientations, relaxations, metastabilities, and multidomains of skyrmion lattices

DOE PAGES

Bannenberg, L. J.; Qian, F.; Dalgliesh, R. M.; ...

2017-11-13

Magnetic skyrmions are nanosized topologically protected spin textures with particlelike properties. They can form lattices perpendicular to the magnetic field, and the orientation of these skyrmion lattices with respect to the crystallographic lattice is governed by spin-orbit coupling. By performing small-angle neutron scattering measurements, we investigate the coupling between the crystallographic and skyrmion lattices in both Cu 2OSeO 3 and the archetype chiral magnet MnSi. The results reveal that the orientation of the skyrmion lattice is primarily determined by the magnetic field direction with respect to the crystallographic lattice. In addition, it is also influenced by the magnetic history ofmore » the sample, which can induce metastable lattices. Kinetic measurements show that these metastable skyrmion lattices may or may not relax to their equilibrium positions under macroscopic relaxation times. Moreover, multidomain lattices may form when two or more equivalent crystallographic directions are favored by spin-orbit coupling and oriented perpendicular to the magnetic field.« less

Consistent multiphase-field theory for interface driven multidomain dynamics

NASA Astrophysics Data System (ADS)

Tóth, Gyula I.; Pusztai, Tamás; Gránásy, László

2015-11-01

We present a multiphase-field theory for describing pattern formation in multidomain and/or multicomponent systems. The construction of the free energy functional and the dynamic equations is based on criteria that ensure mathematical and physical consistency. We first analyze previous multiphase-field theories and identify their advantageous and disadvantageous features. On the basis of this analysis, we introduce a way of constructing the free energy surface and derive a generalized multiphase description for arbitrary number of phases (or domains). The presented approach retains the variational formalism, reduces (or extends) naturally to lower (or higher) number of fields on the level of both the free energy functional and the dynamic equations, enables the use of arbitrary pairwise equilibrium interfacial properties, penalizes multiple junctions increasingly with the number of phases, ensures non-negative entropy production and the convergence of the dynamic solutions to the equilibrium solutions, and avoids the appearance of spurious phases on binary interfaces. The approach is tested for multicomponent phase separation and grain coarsening.

Magnetic vortex state and multi-domain pattern in electrodeposited hemispherical nanogranular nickel films

NASA Astrophysics Data System (ADS)

Samardak, Alexander; Sukovatitsina, Ekaterina; Ognev, Alexey; Stebliy, Maksim; Davydenko, Alexander; Chebotkevich, Ludmila; Keun Kim, Young; Nasirpouri, Forough; Janjan, Seyed-Mehdi; Nasirpouri, Farzad

2014-12-01

Magnetic states of nickel nanogranular films were studied in two distinct structures of individual and agglomerated granules electrodeposited on n-type Si(1 1 1) surface from a modified Watts bath at a low pH of 2. Magnetic force microscopy and micromagnetic simulations revealed three-dimensional out-of-plane magnetic vortex states in stand-alone hemispherical granules and their arrays, and multi-domain patterns in large agglomerates and integrated films. Once the granules coalesce into small chains or clusters, the coercivity values increased due to the reduction of inter-granular spacing and strengthening of the magnetostatic interaction. Further growth leads to the formation of a continuous granulated film which strongly affected the coercivity and remanence. This was characterized by the domain wall nucleation and propagation leading to a stripe domain pattern. Magnetoresistance measurements as a function of external magnetic field are indicative of anisotropic magnetoresistance (AMR) for the continuous films electrodeposited on Si substrate.

Nutritional Intervention as a Preventive Approach for Cognitive-Related Outcomes in Cognitively Healthy Older Adults: A Systematic Review.

PubMed

Solfrizzi, Vincenzo; Agosti, Pasquale; Lozupone, Madia; Custodero, Carlo; Schilardi, Andrea; Valiani, Vincenzo; Sardone, Rodolfo; Dibello, Vittorio; Di Lena, Luca; Lamanna, Angela; Stallone, Roberta; Bellomo, Antonello; Greco, Antonio; Daniele, Antonio; Seripa, Davide; Sabbà, Carlo; Logroscino, Giancarlo; Panza, Francesco

2018-05-26

The link diet-cognitive function/dementia has been largely investigated in observational studies; however, there was a lack of evidence from randomized clinical trials (RCTs) on the prevention of late-life cognitive disorders though dietary intervention in cognitively healthy older adults. In the present article, we systematically reviewed RCTs published in the last four years (2014-2017) exploring nutritional intervention efficacy in preventing the onset of late-life cognitive disorders and dementia in cognitively healthy subjects aged 60 years and older using different levels of investigation (i.e., dietary pattern changes/medical food/nutraceutical supplementation/multidomain approach and dietary macro- and micronutrient approaches) as well as possible underlying mechanisms of nutritional prevention. From the 35 included RCTs, there was moderate evidence that intervention through dietary pattern changes, medical food/nutraceutical supplementation, and multidomain approach improved specific cognitive domains or cognitive-related blood biomarkers. There was high evidence that protein supplementation improved specific cognitive domains or functional status in prefrail older adults without effect.

Alignment of crystal orientations of the multi-domain photonic crystals in Parides sesostris wing scales

PubMed Central

Yoshioka, S.; Fujita, H.; Kinoshita, S.; Matsuhana, B.

2014-01-01

It is known that the wing scales of the emerald-patched cattleheart butterfly, Parides sesostris, contain gyroid-type photonic crystals, which produce a green structural colour. However, the photonic crystal is not a single crystal that spreads over the entire scale, but it is separated into many small domains with different crystal orientations. As a photonic crystal generally has band gaps at different frequencies depending on the direction of light propagation, it seems mysterious that the scale is observed to be uniformly green under an optical microscope despite the multi-domain structure. In this study, we have carefully investigated the structure of the wing scale and discovered that the crystal orientations of different domains are not perfectly random, but there is a preferred crystal orientation that is aligned along the surface normal of the scale. This finding suggests that there is an additional factor during the developmental process of the microstructure that regulates the crystal orientation. PMID:24352678

Multidomain proteins under force

NASA Astrophysics Data System (ADS)

Valle-Orero, Jessica; Andrés Rivas-Pardo, Jaime; Popa, Ionel

2017-04-01

Advancements in single-molecule force spectroscopy techniques such as atomic force microscopy and magnetic tweezers allow investigation of how domain folding under force can play a physiological role. Combining these techniques with protein engineering and HaloTag covalent attachment, we investigate similarities and differences between four model proteins: I10 and I91—two immunoglobulin-like domains from the muscle protein titin, and two α + β fold proteins—ubiquitin and protein L. These proteins show a different mechanical response and have unique extensions under force. Remarkably, when normalized to their contour length, the size of the unfolding and refolding steps as a function of force reduces to a single master curve. This curve can be described using standard models of polymer elasticity, explaining the entropic nature of the measured steps. We further validate our measurements with a simple energy landscape model, which combines protein folding with polymer physics and accounts for the complex nature of tandem domains under force. This model can become a useful tool to help in deciphering the complexity of multidomain proteins operating under force.

Multidomain Skyrmion Lattice State in Cu2OSeO3.

PubMed

Zhang, S L; Bauer, A; Burn, D M; Milde, P; Neuber, E; Eng, L M; Berger, H; Pfleiderer, C; van der Laan, G; Hesjedal, T

2016-05-11

Magnetic skyrmions in chiral magnets are nanoscale, topologically protected magnetization swirls that are promising candidates for spintronics memory carriers. Therefore, observing and manipulating the skyrmion state on the surface level of the materials are of great importance for future applications. Here, we report a controlled way of creating a multidomain skyrmion state near the surface of a Cu2OSeO3 single crystal, observed by soft resonant elastic X-ray scattering. This technique is an ideal tool to probe the magnetic order at the L3 edge of 3d metal compounds giving an average depth sensitivity of ∼50 nm. The single-domain 6-fold-symmetric skyrmion lattice can be broken up into domains, overcoming the propagation directions imposed by the cubic anisotropy by applying the magnetic field in directions deviating from the major cubic axes. Our findings open the door to a new way to manipulate and engineer the skyrmion state locally on the surface or on the level of individual skyrmions, which will enable applications in the future.

Domain organizations of modular extracellular matrix proteins and their evolution.

PubMed

Engel, J

1996-11-01

Multidomain proteins which are composed of modular units are a rather recent invention of evolution. Domains are defined as autonomously folding regions of a protein, and many of them are similar in sequence and structure, indicating common ancestry. Their modular nature is emphasized by frequent repetitions in identical or in different proteins and by a large number of different combinations with other domains. The extracellular matrix is perhaps the largest biological system composed of modular mosaic proteins, and its astonishing complexity and diversity are based on them. A cluster of minireviews on modular proteins is being published in Matrix Biology. These deal with the evolution of modular proteins, the three-dimensional structure of domains and the ways in which these interact in a multidomain protein. They discuss structure-function relationships in calcium binding domains, collagen helices, alpha-helical coiled-coil domains and C-lectins. The present minireview is focused on some general aspects and serves as an introduction to the cluster.

New force replica exchange method and protein folding pathways probed by force-clamp technique.

PubMed

Kouza, Maksim; Hu, Chin-Kun; Li, Mai Suan

2008-01-28

We have developed a new extended replica exchange method to study thermodynamics of a system in the presence of external force. Our idea is based on the exchange between different force replicas to accelerate the equilibrium process. This new approach was applied to obtain the force-temperature phase diagram and other thermodynamical quantities of the three-domain ubiquitin. Using the C(alpha)-Go model and the Langevin dynamics, we have shown that the refolding pathways of single ubiquitin depend on which terminus is fixed. If the N end is fixed then the folding pathways are different compared to the case when both termini are free, but fixing the C terminal does not change them. Surprisingly, we have found that the anchoring terminal does not affect the pathways of individual secondary structures of three-domain ubiquitin, indicating the important role of the multidomain construction. Therefore, force-clamp experiments, in which one end of a protein is kept fixed, can probe the refolding pathways of a single free-end ubiquitin if one uses either the polyubiquitin or a single domain with the C terminus anchored. However, it is shown that anchoring one end does not affect refolding pathways of the titin domain I27, and the force-clamp spectroscopy is always capable to predict folding sequencing of this protein. We have obtained the reasonable estimate for unfolding barrier of ubiquitin, using the microscopic theory for the dependence of unfolding time on the external force. The linkage between residue Lys48 and the C terminal of ubiquitin is found to have the dramatic effect on the location of the transition state along the end-to-end distance reaction coordinate, but the multidomain construction leaves the transition state almost unchanged. We have found that the maximum force in the force-extension profile from constant velocity force pulling simulations depends on temperature nonlinearly. However, for some narrow temperature interval this dependence becomes linear, as have been observed in recent experiments.

Chaperonin-based biolayer interferometry to assess the kinetic stability of metastable, aggregation-prone proteins

PubMed Central

Lea, Wendy A.; Naik, Subhashchandra; Chaudhri, Tapan; Machen, Alexandra J.; O’Neil, Pierce T.; McGinn-Straub, Wesley; Tischer, Alexander; Auton, Matthew T.; Burns, Joshua R.; Baldwin, Michael R.; Khar, Karen R.; Karanicolas, John; Fisher, Mark T.

2017-01-01

Stabilizing the folded state of metastable and/or aggregation-prone proteins through exogenous ligand binding is an appealing strategy to decrease disease pathologies brought on by protein folding defects or deleterious kinetic transitions. Current methods of examining ligand binding to these marginally stable native states are limited, because protein aggregation typically interferes with analysis. Here, we describe a rapid method for assessing the kinetic stability of folded proteins and monitoring the effects of ligand stabilization for both intrinsically stable proteins (monomers, oligomers, multi-domain) and metastable proteins (e.g. low Tm) that uses a new GroEL chaperonin-based biolayer interferometry (BLI) denaturant-pulse platform. A kinetically controlled denaturation isotherm is generated by exposing a target protein immobilized on a BLI biosensor to increasing denaturant concentrations (urea or GnHCl) in a pulsatile manner to induce partial or complete unfolding of the attached protein population. Following the rapid removal of the denaturant, the extent of hydrophobic unfolded/partially folded species that remain is detected by increased GroEL binding. Since this kinetic denaturant pulse is brief, the amplitude of the GroEL binding to the immobilized protein depends on the duration of exposure to denaturant, the concentration of denaturant, wash times, and the underlying protein unfolding/refolding kinetics; fixing all other parameters and plotting GroEL binding amplitude versus denaturant pulse concentration results in a kinetically controlled denaturation isotherm. When folding osmolytes or stabilizing ligands are added to the immobilized target proteins before and during the denaturant pulse, the diminished population of unfolded/partially folded protein is manifested by a decreased GroEL binding and/or a marked shift in these kinetically controlled denaturation profiles to higher denaturant concentrations. This particular platform approach can be used to identify small molecules/solution conditions that can stabilize or destabilize thermally stable proteins, multi-domain proteins, oligomeric proteins, and most importantly, aggregation prone metastable proteins. PMID:27505032

An adjoint-based framework for maximizing mixing in binary fluids

NASA Astrophysics Data System (ADS)

Eggl, Maximilian; Schmid, Peter

2017-11-01

Mixing in the inertial, but laminar parameter regime is a common application in a wide range of industries. Enhancing the efficiency of mixing processes thus has a fundamental effect on product quality, material homogeneity and, last but not least, production costs. In this project, we address mixing efficiency in the above mentioned regime (Reynolds number Re = 1000 , Peclet number Pe = 1000) by developing and demonstrating an algorithm based on nonlinear adjoint looping that minimizes the variance of a passive scalar field which models our binary Newtonian fluids. The numerical method is based on the FLUSI code (Engels et al. 2016), a Fourier pseudo-spectral code, which we modified and augmented by scalar transport and adjoint equations. Mixing is accomplished by moving stirrers which are numerically modeled using a penalization approach. In our two-dimensional simulations we consider rotating circular and elliptic stirrers and extract optimal mixing strategies from the iterative scheme. The case of optimizing shape and rotational speed of the stirrers will be demonstrated.

INFFTM: Fast evaluation of 3d Fourier series in MATLAB with an application to quantum vortex reconnections

NASA Astrophysics Data System (ADS)

Caliari, Marco; Zuccher, Simone

2017-04-01

Although Fourier series approximation is ubiquitous in computational physics owing to the Fast Fourier Transform (FFT) algorithm, efficient techniques for the fast evaluation of a three-dimensional truncated Fourier series at a set of arbitrary points are quite rare, especially in MATLAB language. Here we employ the Nonequispaced Fast Fourier Transform (NFFT, by J. Keiner, S. Kunis, and D. Potts), a C library designed for this purpose, and provide a Matlab® and GNU Octave interface that makes NFFT easily available to the Numerical Analysis community. We test the effectiveness of our package in the framework of quantum vortex reconnections, where pseudospectral Fourier methods are commonly used and local high resolution is required in the post-processing stage. We show that the efficient evaluation of a truncated Fourier series at arbitrary points provides excellent results at a computational cost much smaller than carrying out a numerical simulation of the problem on a sufficiently fine regular grid that can reproduce comparable details of the reconnecting vortices.

Efficient solution of the Wigner-Liouville equation using a spectral decomposition of the force field

NASA Astrophysics Data System (ADS)

Van de Put, Maarten L.; Sorée, Bart; Magnus, Wim

2017-12-01

The Wigner-Liouville equation is reformulated using a spectral decomposition of the classical force field instead of the potential energy. The latter is shown to simplify the Wigner-Liouville kernel both conceptually and numerically as the spectral force Wigner-Liouville equation avoids the numerical evaluation of the highly oscillatory Wigner kernel which is nonlocal in both position and momentum. The quantum mechanical evolution is instead governed by a term local in space and non-local in momentum, where the non-locality in momentum has only a limited range. An interpretation of the time evolution in terms of two processes is presented; a classical evolution under the influence of the averaged driving field, and a probability-preserving quantum-mechanical generation and annihilation term. Using the inherent stability and reduced complexity, a direct deterministic numerical implementation using Chebyshev and Fourier pseudo-spectral methods is detailed. For the purpose of illustration, we present results for the time-evolution of a one-dimensional resonant tunneling diode driven out of equilibrium.

Hybrid parallelization of the XTOR-2F code for the simulation of two-fluid MHD instabilities in tokamaks

NASA Astrophysics Data System (ADS)

Marx, Alain; Lütjens, Hinrich

2017-03-01

A hybrid MPI/OpenMP parallel version of the XTOR-2F code [Lütjens and Luciani, J. Comput. Phys. 229 (2010) 8130] solving the two-fluid MHD equations in full tokamak geometry by means of an iterative Newton-Krylov matrix-free method has been developed. The present work shows that the code has been parallelized significantly despite the numerical profile of the problem solved by XTOR-2F, i.e. a discretization with pseudo-spectral representations in all angular directions, the stiffness of the two-fluid stability problem in tokamaks, and the use of a direct LU decomposition to invert the physical pre-conditioner at every Krylov iteration of the solver. The execution time of the parallelized version is an order of magnitude smaller than the sequential one for low resolution cases, with an increasing speedup when the discretization mesh is refined. Moreover, it allows to perform simulations with higher resolutions, previously forbidden because of memory limitations.

Rapid design and optimization of low-thrust rendezvous/interception trajectory for asteroid deflection missions

NASA Astrophysics Data System (ADS)

Li, Shuang; Zhu, Yongsheng; Wang, Yukai

2014-02-01

Asteroid deflection techniques are essential in order to protect the Earth from catastrophic impacts by hazardous asteroids. Rapid design and optimization of low-thrust rendezvous/interception trajectories is considered as one of the key technologies to successfully deflect potentially hazardous asteroids. In this paper, we address a general framework for the rapid design and optimization of low-thrust rendezvous/interception trajectories for future asteroid deflection missions. The design and optimization process includes three closely associated steps. Firstly, shape-based approaches and genetic algorithm (GA) are adopted to perform preliminary design, which provides a reasonable initial guess for subsequent accurate optimization. Secondly, Radau pseudospectral method is utilized to transcribe the low-thrust trajectory optimization problem into a discrete nonlinear programming (NLP) problem. Finally, sequential quadratic programming (SQP) is used to efficiently solve the nonlinear programming problem and obtain the optimal low-thrust rendezvous/interception trajectories. The rapid design and optimization algorithms developed in this paper are validated by three simulation cases with different performance indexes and boundary constraints.

A numerical and experimental study on the nonlinear evolution of long-crested irregular waves

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goullet, Arnaud; Choi, Wooyoung; Division of Ocean Systems Engineering, Korea Advanced Institute of Science and Technology, Daejeon 305-701

2011-01-15

The spatial evolution of nonlinear long-crested irregular waves characterized by the JONSWAP spectrum is studied numerically using a nonlinear wave model based on a pseudospectral (PS) method and the modified nonlinear Schroedinger (MNLS) equation. In addition, new laboratory experiments with two different spectral bandwidths are carried out and a number of wave probe measurements are made to validate these two wave models. Strongly nonlinear wave groups are observed experimentally and their propagation and interaction are studied in detail. For the comparison with experimental measurements, the two models need to be initialized with care and the initialization procedures are described. Themore » MNLS equation is found to approximate reasonably well for the wave fields with a relatively smaller Benjamin-Feir index, but the phase error increases as the propagation distance increases. The PS model with different orders of nonlinear approximation is solved numerically, and it is shown that the fifth-order model agrees well with our measurements prior to wave breaking for both spectral bandwidths.« less

Multidomain Operations: A Subtle but Significant Transition in Military Thought

DTIC Science & Technology

2016-01-01

power has given the joint force unrivaled dominance in the air. However, quantum advances in technology and the realities of fiscal constraints are...Additionally, he conducted research on design in Afghanistan during 2010, 2011, and 2012. The author of Operational Design: Distilling Clarity from

Semi-discrete approximations to nonlinear systems of conservation laws; consistency and L(infinity)-stability imply convergence

NASA Technical Reports Server (NTRS)

Tadmor, Eitan

1988-01-01

A convergence theory for semi-discrete approximations to nonlinear systems of conservation laws is developed. It is shown, by a series of scalar counter-examples, that consistency with the conservation law alone does not guarantee convergence. Instead, a notion of consistency which takes into account both the conservation law and its augmenting entropy condition is introduced. In this context it is concluded that consistency and L(infinity)-stability guarantee for a relevant class of admissible entropy functions, that their entropy production rate belongs to a compact subset of H(loc)sup -1 (x,t). One can now use compensated compactness arguments in order to turn this conclusion into a convergence proof. The current state of the art for these arguments includes the scalar and a wide class of 2 x 2 systems of conservation laws. The general framework of the vanishing viscosity method is studied as an effective way to meet the consistency and L(infinity)-stability requirements. How this method is utilized to enforce consistency and stability for scalar conservation laws is shown. In this context we prove, under the appropriate assumptions, the convergence of finite difference approximations (e.g., the high resolution TVD and UNO methods), finite element approximations (e.g., the Streamline-Diffusion methods) and spectral and pseudospectral approximations (e.g., the Spectral Viscosity methods).

Semi-discrete approximations to nonlinear systems of conservation laws; consistency and L(infinity)-stability imply convergence. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tadmor, E.

1988-07-01

A convergence theory for semi-discrete approximations to nonlinear systems of conservation laws is developed. It is shown, by a series of scalar counter-examples, that consistency with the conservation law alone does not guarantee convergence. Instead, a notion of consistency which takes into account both the conservation law and its augmenting entropy condition is introduced. In this context it is concluded that consistency and L(infinity)-stability guarantee for a relevant class of admissible entropy functions, that their entropy production rate belongs to a compact subset of H(loc)sup -1 (x,t). One can now use compensated compactness arguments in order to turn this conclusionmore » into a convergence proof. The current state of the art for these arguments includes the scalar and a wide class of 2 x 2 systems of conservation laws. The general framework of the vanishing viscosity method is studied as an effective way to meet the consistency and L(infinity)-stability requirements. How this method is utilized to enforce consistency and stability for scalar conservation laws is shown. In this context we prove, under the appropriate assumptions, the convergence of finite difference approximations (e.g., the high resolution TVD and UNO methods), finite element approximations (e.g., the Streamline-Diffusion methods) and spectral and pseudospectral approximations (e.g., the Spectral Viscosity methods).« less

Efficient relaxed-Jacobi smoothers for multigrid on parallel computers

NASA Astrophysics Data System (ADS)

Yang, Xiang; Mittal, Rajat

2017-03-01

In this Technical Note, we present a family of Jacobi-based multigrid smoothers suitable for the solution of discretized elliptic equations. These smoothers are based on the idea of scheduled-relaxation Jacobi proposed recently by Yang & Mittal (2014) [18] and employ two or three successive relaxed Jacobi iterations with relaxation factors derived so as to maximize the smoothing property of these iterations. The performance of these new smoothers measured in terms of convergence acceleration and computational workload, is assessed for multi-domain implementations typical of parallelized solvers, and compared to the lexicographic point Gauss-Seidel smoother. The tests include the geometric multigrid method on structured grids as well as the algebraic grid method on unstructured grids. The tests demonstrate that unlike Gauss-Seidel, the convergence of these Jacobi-based smoothers is unaffected by domain decomposition, and furthermore, they outperform the lexicographic Gauss-Seidel by factors that increase with domain partition count.

Generalized channeled polarimetry.

PubMed

Alenin, Andrey S; Tyo, J Scott

2014-05-01

Channeled polarimeters measure polarization by modulating the measured intensity in order to create polarization-dependent channels that can be demodulated to reveal the desired polarization information. A number of channeled systems have been described in the past, but their proposed designs often unintentionally sacrifice optimality for ease of algebraic reconstruction. To obtain more optimal systems, a generalized treatment of channeled polarimeters is required. This paper describes methods that enable handling of multi-domain modulations and reconstruction of polarization information using linear algebra. We make practical choices regarding use of either Fourier or direct channels to make these methods more immediately useful. Employing the introduced concepts to optimize existing systems often results in superficial system changes, like changing the order, orientation, thickness, or spacing of polarization elements. For the two examples we consider, we were able to reduce noise in the reconstruction to 34.1% and 57.9% of the original design values.

Carbene footprinting accurately maps binding sites in protein-ligand and protein-protein interactions

NASA Astrophysics Data System (ADS)

Manzi, Lucio; Barrow, Andrew S.; Scott, Daniel; Layfield, Robert; Wright, Timothy G.; Moses, John E.; Oldham, Neil J.

2016-11-01

Specific interactions between proteins and their binding partners are fundamental to life processes. The ability to detect protein complexes, and map their sites of binding, is crucial to understanding basic biology at the molecular level. Methods that employ sensitive analytical techniques such as mass spectrometry have the potential to provide valuable insights with very little material and on short time scales. Here we present a differential protein footprinting technique employing an efficient photo-activated probe for use with mass spectrometry. Using this methodology the location of a carbohydrate substrate was accurately mapped to the binding cleft of lysozyme, and in a more complex example, the interactions between a 100 kDa, multi-domain deubiquitinating enzyme, USP5 and a diubiquitin substrate were located to different functional domains. The much improved properties of this probe make carbene footprinting a viable method for rapid and accurate identification of protein binding sites utilizing benign, near-UV photoactivation.

Simulation of nonlinear propagation of biomedical ultrasound using pzflex and the Khokhlov-Zabolotskaya-Kuznetsov Texas code

PubMed Central

Qiao, Shan; Jackson, Edward; Coussios, Constantin C.; Cleveland, Robin O.

2016-01-01

Nonlinear acoustics plays an important role in both diagnostic and therapeutic applications of biomedical ultrasound and a number of research and commercial software packages are available. In this manuscript, predictions of two solvers available in a commercial software package, pzflex, one using the finite-element-method (FEM) and the other a pseudo-spectral method, spectralflex, are compared with measurements and the Khokhlov-Zabolotskaya-Kuznetsov (KZK) Texas code (a finite-difference time-domain algorithm). The pzflex methods solve the continuity equation, momentum equation and equation of state where they account for nonlinearity to second order whereas the KZK code solves a nonlinear wave equation with a paraxial approximation for diffraction. Measurements of the field from a single element 3.3 MHz focused transducer were compared with the simulations and there was good agreement for the fundamental frequency and the harmonics; however the FEM pzflex solver incurred a high computational cost to achieve equivalent accuracy. In addition, pzflex results exhibited non-physical oscillations in the spatial distribution of harmonics when the amplitudes were relatively low. It was found that spectralflex was able to accurately capture the nonlinear fields at reasonable computational cost. These results emphasize the need to benchmark nonlinear simulations before using codes as predictive tools. PMID:27914432

A pseudospectra-based approach to non-normal stability of embedded boundary methods

NASA Astrophysics Data System (ADS)

Rapaka, Narsimha; Samtaney, Ravi

2017-11-01

We present non-normal linear stability of embedded boundary (EB) methods employing pseudospectra and resolvent norms. Stability of the discrete linear wave equation is characterized in terms of the normalized distance of the EB to the nearest ghost node (α) in one and two dimensions. An important objective is that the CFL condition based on the Cartesian grid spacing remains unaffected by the EB. We consider various discretization methods including both central and upwind-biased schemes. Stability is guaranteed when α <=αmax ranges between 0.5 and 0.77 depending on the discretization scheme. Also, the stability characteristics remain the same in both one and two dimensions. Sharper limits on the sufficient conditions for stability are obtained based on the pseudospectral radius (the Kreiss constant) than the restrictive limits based on the usual singular value decomposition analysis. We present a simple and robust reclassification scheme for the ghost cells (``hybrid ghost cells'') to ensure Lax stability of the discrete systems. This has been tested successfully for both low and high order discretization schemes with transient growth of at most O (1). Moreover, we present a stable, fourth order EB reconstruction scheme. Supported by the KAUST Office of Competitive Research Funds under Award No. URF/1/1394-01.

Simulation of nonlinear propagation of biomedical ultrasound using pzflex and the Khokhlov-Zabolotskaya-Kuznetsov Texas code.

PubMed

Qiao, Shan; Jackson, Edward; Coussios, Constantin C; Cleveland, Robin O

2016-09-01

Nonlinear acoustics plays an important role in both diagnostic and therapeutic applications of biomedical ultrasound and a number of research and commercial software packages are available. In this manuscript, predictions of two solvers available in a commercial software package, pzflex, one using the finite-element-method (FEM) and the other a pseudo-spectral method, spectralflex, are compared with measurements and the Khokhlov-Zabolotskaya-Kuznetsov (KZK) Texas code (a finite-difference time-domain algorithm). The pzflex methods solve the continuity equation, momentum equation and equation of state where they account for nonlinearity to second order whereas the KZK code solves a nonlinear wave equation with a paraxial approximation for diffraction. Measurements of the field from a single element 3.3 MHz focused transducer were compared with the simulations and there was good agreement for the fundamental frequency and the harmonics; however the FEM pzflex solver incurred a high computational cost to achieve equivalent accuracy. In addition, pzflex results exhibited non-physical oscillations in the spatial distribution of harmonics when the amplitudes were relatively low. It was found that spectralflex was able to accurately capture the nonlinear fields at reasonable computational cost. These results emphasize the need to benchmark nonlinear simulations before using codes as predictive tools.

Multi-Scale Multi-Domain Model | Transportation Research | NREL

Science.gov Websites

framework for NREL's MSMD model. NREL's MSMD model quantifies the impacts of electrical/thermal pathway : NREL Macroscopic design factors and highly dynamic environmental conditions significantly influence the design of affordable, long-lasting, high-performing, and safe large battery systems. The MSMD framework

On-demand virtual optical network access using 100 Gb/s Ethernet.

PubMed

Ishida, Osamu; Takamichi, Toru; Arai, Sachine; Kawate, Ryusuke; Toyoda, Hidehiro; Morita, Itsuro; Araki, Soichiro; Ichikawa, Toshiyuki; Hoshida, Takeshi; Murai, Hitoshi

2011-12-12

Our Terabit LAN initiatives attempt to enhance the scalability and utilization of lambda resources. This paper describes bandwidth-on-demand virtualized 100GE access to WDM networks on a field fiber test-bed using multi-domain optical-path provisioning. © 2011 Optical Society of America

Biotechnology Conference: Protein Engineering Held in Oxford, United Kingdom on 5-8 April 1987.

DTIC Science & Technology

1987-07-27

engineered by protein engineering was reported by J. new variants which are now being checked. Brange (Novo Research Institute, Bags- Studies of a cassette...to Brange . Therefore, multidomain protein consisting of five Brange and his group applied protein en- putative domains: the fribonectin finger

Viriato: a Fourier-Hermite spectral code for strongly magnetised fluid-kinetic plasma dynamics

NASA Astrophysics Data System (ADS)

Loureiro, Nuno; Dorland, William; Fazendeiro, Luis; Kanekar, Anjor; Mallet, Alfred; Zocco, Alessandro

2015-11-01

We report on the algorithms and numerical methods used in Viriato, a novel fluid-kinetic code that solves two distinct sets of equations: (i) the Kinetic Reduced Electron Heating Model equations [Zocco & Schekochihin, 2011] and (ii) the kinetic reduced MHD (KRMHD) equations [Schekochihin et al., 2009]. Two main applications of these equations are magnetised (Alfvnénic) plasma turbulence and magnetic reconnection. Viriato uses operator splitting to separate the dynamics parallel and perpendicular to the ambient magnetic field (assumed strong). Along the magnetic field, Viriato allows for either a second-order accurate MacCormack method or, for higher accuracy, a spectral-like scheme. Perpendicular to the field Viriato is pseudo-spectral, and the time integration is performed by means of an iterative predictor-corrector scheme. In addition, a distinctive feature of Viriato is its spectral representation of the parallel velocity-space dependence, achieved by means of a Hermite representation of the perturbed distribution function. A series of linear and nonlinear benchmarks and tests are presented, with focus on 3D decaying kinetic turbulence. Work partially supported by Fundação para a Ciência e Tecnologia via Grants UID/FIS/50010/2013 and IF/00530/2013.

High-performance modeling of plasma-based acceleration and laser-plasma interactions

NASA Astrophysics Data System (ADS)

Vay, Jean-Luc; Blaclard, Guillaume; Godfrey, Brendan; Kirchen, Manuel; Lee, Patrick; Lehe, Remi; Lobet, Mathieu; Vincenti, Henri

2016-10-01

Large-scale numerical simulations are essential to the design of plasma-based accelerators and laser-plasma interations for ultra-high intensity (UHI) physics. The electromagnetic Particle-In-Cell (PIC) approach is the method of choice for self-consistent simulations, as it is based on first principles, and captures all kinetic effects, and also scale favorably to many cores on supercomputers. The standard PIC algorithm relies on second-order finite-difference discretization of the Maxwell and Newton-Lorentz equations. We present here novel formulations, based on very high-order pseudo-spectral Maxwell solvers, which enable near-total elimination of the numerical Cherenkov instability and increased accuracy over the standard PIC method for standard laboratory frame and Lorentz boosted frame simulations. We also present the latest implementations in the PIC modules Warp-PICSAR and FBPIC on the Intel Xeon Phi and GPU architectures. Examples of applications will be given on the simulation of laser-plasma accelerators and high-harmonic generation with plasma mirrors. Work supported by US-DOE Contracts DE-AC02-05CH11231 and by the European Commission through the Marie Slowdoska-Curie fellowship PICSSAR Grant Number 624543. Used resources of NERSC.

A phase-field method to analyze the dynamics of immiscible fluids in porous media

NASA Astrophysics Data System (ADS)

de Paoli, Marco; Roccon, Alessio; Zonta, Francesco; Soldati, Alfredo

2017-11-01

Liquid carbon dioxide (CO2) injected into geological formations (filled with brine) is not completely soluble in the surrounding fluid. For this reason, complex transport phenomena may occur across the interface that separates the two phases (CO2+brine and brine). Inspired by this geophysical instance, we used a Phase-Field Method (PFM) to describe the dynamics of two immiscible fluids in satured porous media. The basic idea of the PFM is to introduce an order parameter (ϕ) that varies continuously across the interfacial layer between the phases and is uniform in the bulk. The equation that describes the distribution of ϕ is the Cahn-Hilliard (CH) equation, which is coupled with the Darcy equation (to evaluate fluid velocity) through the buoyancy and Korteweg stress terms. The governing equations are solved through a pseudo-spectral technique (Fourier-Chebyshev). Our results show that the value of the surface tension between the two phases strongly influences the initial and the long term dynamics of the system. We believe that the proposed numerical approach, which grants an accurate evaluation of the interfacial fluxes of momentum/energy/species, is attractive to describe the transfer mechanism and the overall dynamics of immiscible and partially miscible phases.

Numerical simulation of wave-induced fluid flow seismic attenuation based on the Cole-Cole model.

PubMed

Picotti, Stefano; Carcione, José M

2017-07-01

The acoustic behavior of porous media can be simulated more realistically using a stress-strain relation based on the Cole-Cole model. In particular, seismic velocity dispersion and attenuation in porous rocks is well described by mesoscopic-loss models. Using the Zener model to simulate wave propagation is a rough approximation, while the Cole-Cole model provides an optimal description of the physics. Here, a time-domain algorithm is proposed based on the Grünwald-Letnikov numerical approximation of the fractional derivative involved in the time-domain representation of the Cole-Cole model, while the spatial derivatives are computed with the Fourier pseudospectral method. The numerical solution is successfully tested against an analytical solution. The methodology is applied to a model of saline aquifer, where carbon dioxide (CO 2 ) is injected. To follow the migration of the gas and detect possible leakages, seismic monitoring surveys should be carried out periodically. To this aim, the sensitivity of the seismic method must be carefully assessed for the specific case. The simulated test considers a possible leakage in the overburden, above the caprock, where the sandstone is partially saturated with gas and brine. The numerical examples illustrate the implementation of the theory.

New algorithms for field-theoretic block copolymer simulations: Progress on using adaptive-mesh refinement and sparse matrix solvers in SCFT calculations

NASA Astrophysics Data System (ADS)

Sides, Scott; Jamroz, Ben; Crockett, Robert; Pletzer, Alexander

2012-02-01

Self-consistent field theory (SCFT) for dense polymer melts has been highly successful in describing complex morphologies in block copolymers. Field-theoretic simulations such as these are able to access large length and time scales that are difficult or impossible for particle-based simulations such as molecular dynamics. The modified diffusion equations that arise as a consequence of the coarse-graining procedure in the SCF theory can be efficiently solved with a pseudo-spectral (PS) method that uses fast-Fourier transforms on uniform Cartesian grids. However, PS methods can be difficult to apply in many block copolymer SCFT simulations (eg. confinement, interface adsorption) in which small spatial regions might require finer resolution than most of the simulation grid. Progress on using new solver algorithms to address these problems will be presented. The Tech-X Chompst project aims at marrying the best of adaptive mesh refinement with linear matrix solver algorithms. The Tech-X code PolySwift++ is an SCFT simulation platform that leverages ongoing development in coupling Chombo, a package for solving PDEs via block-structured AMR calculations and embedded boundaries, with PETSc, a toolkit that includes a large assortment of sparse linear solvers.

Application of adaptive gridding to magnetohydrodynamic flows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schnack, D.D.; Lotatti, I.; Satyanarayana, P.

1996-12-31

The numerical simulation of the primitive, three-dimensional, time-dependent, resistive MHD equations on an unstructured, adaptive poloidal mesh using the TRIM code has been reported previously. The toroidal coordinate is approximated pseudo-spectrally with finite Fourier series and Fast-Fourier Transforms. The finite-volume algorithm preserves the magnetic field as solenoidal to round-off error, and also conserves mass, energy, and magnetic flux exactly. A semi-implicit method is used to allow for large time steps on the unstructured mesh. This is important for tokamak calculations where the relevant time scale is determined by the poloidal Alfven time. This also allows the viscosity to be treatedmore » implicitly. A conjugate-gradient method with pre-conditioning is used for matrix inversion. Applications to the growth and saturation of ideal instabilities in several toroidal fusion systems has been demonstrated. Recently we have concentrated on the details of the mesh adaption algorithm used in TRIM. We present several two-dimensional results relating to the use of grid adaptivity to track the evolution of hydrodynamic and MHD structures. Examples of plasma guns, opening switches, and supersonic flow over a magnetized sphere are presented. Issues relating to mesh adaption criteria are discussed.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tom, Nathan; Yu, Yi-Hsiang; Wright, Alan

The focus of this paper is to balance power absorption against structural loading for a novel fixed-bottom oscillating surge wave energy converter in both regular and irregular wave environments. The power-to-load ratio will be evaluated using pseudospectral control (PSC) to determine the optimum power-takeoff (PTO) torque based on a multiterm objective function. This paper extends the pseudospectral optimal control problem to not just maximize the time-averaged absorbed power but also include measures for the surge-foundation force and PTO torque in the optimization. The objective function may now potentially include three competing terms that the optimizer must balance. Separate weighting factorsmore » are attached to the surge-foundation force and PTO control torque that can be used to tune the optimizer performance to emphasize either power absorption or load shedding. To correct the pitch equation of motion, derived from linear hydrodynamic theory, a quadratic-viscous-drag torque has been included in the system dynamics; however, to continue the use of quadratic programming solvers, an iteratively obtained linearized drag coefficient was utilized that provided good accuracy in the predicted pitch motion. Furthermore, the analysis considers the use of a nonideal PTO unit to more accurately evaluate controller performance. The PTO efficiency is not directly included in the objective function but rather the weighting factors are utilized to limit the PTO torque amplitudes, thereby reducing the losses resulting from the bidirectional energy flow through a nonideal PTO. Results from PSC show that shedding a portion of the available wave energy can lead to greater reductions in structural loads, peak-to-average power ratio, and reactive power requirement.« less

Jupyter Notebooks for Earth Sciences: An Interactive Training Platform for Seismology

NASA Astrophysics Data System (ADS)

Igel, H.; Chow, B.; Donner, S.; Krischer, L.; van Driel, M.; Tape, C.

2017-12-01

We have initiated a community platform (http://www.seismo-live.org) where Python-based Jupyter notebooks (https://jupyter.org) can be accessed and run without necessary downloads or local software installations. The increasingly popular Jupyter notebooks allow the combination of markup language, graphics, and equations with interactive, executable Python code examples. Jupyter notebooks are a powerful and easy-to-grasp tool for students to develop entire projects, scientists to collaborate and efficiently interchange evolving workflows, and trainers to develop efficient practical material. Utilizing the tmpnb project (https://github.com/jupyter/tmpnb), we link the power of Jupyter notebooks with an underlying server, such that notebooks can be run from anywhere, even on smart phones. We demonstrate the potential with notebooks for 1) learning the programming language Python, 2) basic signal processing, 3) an introduction to the ObsPy library (https://obspy.org) for seismology, 4) seismic noise analysis, 5) an entire suite of notebooks for computational seismology (the finite-difference method, pseudospectral methods, finite/spectral element methods, the finite-volume and the discontinuous Galerkin methods, Instaseis), 6) rotational seismology, 7) making results in papers fully reproducible, 8) a rate-and-state friction toolkit, 9) glacial seismology. The platform is run as a community project using Github. Submission of complementary Jupyter notebooks is encouraged. Extension in the near future include linear(-ized) and nonlinear inverse problems.

GPELab, a Matlab toolbox to solve Gross-Pitaevskii equations II: Dynamics and stochastic simulations

NASA Astrophysics Data System (ADS)

Antoine, Xavier; Duboscq, Romain

2015-08-01

GPELab is a free Matlab toolbox for modeling and numerically solving large classes of systems of Gross-Pitaevskii equations that arise in the physics of Bose-Einstein condensates. The aim of this second paper, which follows (Antoine and Duboscq, 2014), is to first present the various pseudospectral schemes available in GPELab for computing the deterministic and stochastic nonlinear dynamics of Gross-Pitaevskii equations (Antoine, et al., 2013). Next, the corresponding GPELab functions are explained in detail. Finally, some numerical examples are provided to show how the code works for the complex dynamics of BEC problems.

Adult Education Attainment and Assessment Scores: A Cross-National Comparison. Stats in Brief. NCES 2018-007

ERIC Educational Resources Information Center

Mamedova, Saida; Sparks, Dinah; Hoyer, Kathleen Mulvaney

2017-01-01

The Organization for Economic Cooperation and Development (OECD) conducted the Program for the International Assessment of Adult Competencies (PIAAC), a multi-domain adult skills assessment with an extensive background questionnaire, in 2012. PIAAC is a global effort to understand how individuals' education, workplace experiences, and other…

Multi-Domain Risk and Protective Factor Predictors of Violent Behavior among At-Risk Youth

ERIC Educational Resources Information Center

Logan-Greene, Patricia; Nurius, Paula S.; Herting, Jerald R.; Hooven, Carole L.; Walsh, Elaine; Thompson, Elaine Adams

2011-01-01

This study extends prior examination of adolescent violence etiology, drawing on an ethnically diverse, community accessed, yet emotionally vulnerable sample (N = 849) of adolescents at-risk for school dropout. A balanced risk and protective factor framework captured theorized dimensions of strain, coping, and support resources. We tested the…

Exploring the evolution of protein function in Archaea.

PubMed

Goncearenco, Alexander; Berezovsky, Igor N

2012-05-30

Despite recent progress in studies of the evolution of protein function, the questions what were the first functional protein domains and what were their basic building blocks remain unresolved. Previously, we introduced the concept of elementary functional loops (EFLs), which are the functional units of enzymes that provide elementary reactions in biochemical transformations. They are presumably descendants of primordial catalytic peptides. We analyzed distant evolutionary connections between protein functions in Archaea based on the EFLs comprising them. We show examples of the involvement of EFLs in new functional domains, as well as reutilization of EFLs and functional domains in building multidomain structures and protein complexes. Our analysis of the archaeal superkingdom yields the dominating mechanisms in different periods of protein evolution, which resulted in several levels of the organization of biochemical function. First, functional domains emerged as combinations of prebiotic peptides with the very basic functions, such as nucleotide/phosphate and metal cofactor binding. Second, domain recombination brought to the evolutionary scene the multidomain proteins and complexes. Later, reutilization and de novo design of functional domains and elementary functional loops complemented evolution of protein function.

Weaker axially dipolar time-averaged paleomagnetic field based on multidomain-corrected paleointensities from Galapagos lavas.

PubMed

Wang, Huapei; Kent, Dennis V; Rochette, Pierre

2015-12-08

The geomagnetic field is predominantly dipolar today, and high-fidelity paleomagnetic mean directions from all over the globe strongly support the geocentric axial dipole (GAD) hypothesis for the past few million years. However, the bulk of paleointensity data fails to coincide with the axial dipole prediction of a factor-of-2 equator-to-pole increase in mean field strength, leaving the core dynamo process an enigma. Here, we obtain a multidomain-corrected Pliocene-Pleistocene average paleointensity of 21.6 ± 11.0 µT recorded by 27 lava flows from the Galapagos Archipelago near the Equator. Our new result in conjunction with a published comprehensive study of single-domain-behaved paleointensities from Antarctica (33.4 ± 13.9 µT) that also correspond to GAD directions suggests that the overall average paleomagnetic field over the past few million years has indeed been dominantly dipolar in intensity yet only ∼ 60% of the present-day field strength, with a long-term average virtual axial dipole magnetic moment of the Earth of only 4.9 ± 2.4 × 10(22) A ⋅ m(2).

The design and progress of a multidomain lifestyle intervention to improve brain health in middle-aged persons to reduce later Alzheimer's disease risk: The Gray Matters randomized trial.

PubMed

Norton, Maria C; Clark, Christine J; Tschanz, JoAnn T; Hartin, Phillip; Fauth, Elizabeth B; Gast, Julie A; Dorsch, Travis E; Wengreen, Heidi; Nugent, Chris; Robinson, W David; Lefevre, Michael; McClean, Sally; Cleland, Ian; Schaefer, Sydney Y; Aguilar, Sheryl

2015-06-01

Most Alzheimer's disease (AD) prevention studies focus on older adults or persons with existing cognitive impairment. This study describes the design and progress of a novel pilot intervention, the Gray Matters study. This proof-of-concept randomized controlled trial tests an evidence-based multidomain lifestyle intervention in 146 persons aged 40 to 64 years, in northern Utah. Data collectors were blinded to participants' randomization to treatment (n = 104) or control (n = 42). Intervention targeted physical activity, food choices, social engagement, cognitive simulation, sleep quality, and stress management, and uses a custom smartphone application, activity monitor, and educational materials. Secondary outcomes include biomarkers, body mass index, cognitive testing, and psychological surveys. Midway through the study, achievements include a 98.7% retention rate, a 96% rate of compliance with app data entry, and positive trends in behavioral change. Participants were empowered, learning that lifestyle might impact AD risk, exhibiting positive behavioral changes thus far.

Nano-structure of the laminin γ-1 short arm reveals an extended and curved multidomain assembly.

PubMed

Patel, Trushar R; Morris, Gordon A; Zwolanek, Daniela; Keene, Douglas R; Li, Jianhua; Harding, Stephen E; Koch, Manuel; Stetefeld, Jörg

2010-09-01

Laminins are multidomain glycoproteins that play important roles in development and maintenance of the extracellular matrix via their numerous interactions with other proteins. Several receptors for the laminin short arms revealed their importance in network formation and intercellular signaling. However, both the detailed structure of the laminin γ-1 short arm and its organization within the complexes is poorly understood due to the complexity of the molecule and the lack of a high-resolution structure. The presented data provide the first subatomic resolution structure for the laminin γ-1 short arm in solution. This was achieved using an integrated approach that combined a number of complementary biophysical techniques such as small angle X-ray scattering (SAXS), analytical ultracentrifugation, dynamic light scattering and electron microscopy. As a result of this study, we have obtained a significantly improved model for the laminin γ-1 short arm that represents a major step forward in molecular understanding of laminin-mediated complex formations. Crown Copyright © 2010. Published by Elsevier B.V. All rights reserved.

Ferromagnetic resonance studies of granular materials (abstract)

NASA Astrophysics Data System (ADS)

Rubinstein, Mark; Das, Badri; Chrisey, D. B.; Horwitz, J.; Koon, N. C.

1994-05-01

We have investigated the ferromagnetic resonance (FMR) spectra of several granular alloys displaying giant magnetoresistance (GMR). For this task, we have produced melt-spun ribbons of Fe5Co15Cu80 and Co20Cu80 by rapid quenching and thin films of Co80Cu20 by pulsed laser deposition. The salient feature of the FMR spectra is the increase of the resonance linewidth as a function of increasing annealing temperature. We have deconvoluted the FMR spectra to a single-domain powder pattern and a multidomain powder pattern. As a function of annealing temperature, the GMR of these samples attains a maximum value. Near the peak of the GMR curve, the FMR spectrum reveals that the ferromagnetic particles are half mono- and half multidomain. Since the maximum size of a single-domain particle is known, this enables us to estimate the spin diffusion length of the Cu conduction electrons. We have also demonstrated, theoretically and experimentally, that the appropriate demagnetizing field to apply to the ensemble of spherical magnetic particles that comprise our granular thin film is simply the field corresponding to the average magnetization.

Enhanced SH3/Linker Interaction Overcomes Abl Kinase Activation by Gatekeeper and Myristic Acid Binding Pocket Mutations and Increases Sensitivity to Small Molecule Inhibitors*

PubMed Central

Panjarian, Shoghag; Iacob, Roxana E.; Chen, Shugui; Wales, Thomas E.; Engen, John R.; Smithgall, Thomas E.

2013-01-01

Multidomain kinases such as c-Src and c-Abl are regulated by complex allosteric interactions involving their noncatalytic SH3 and SH2 domains. Here we show that enhancing natural allosteric control of kinase activity by SH3/linker engagement has long-range suppressive effects on the kinase activity of the c-Abl core. Surprisingly, enhanced SH3/linker interaction also dramatically sensitized the Bcr-Abl tyrosine kinase associated with chronic myelogenous leukemia to small molecule inhibitors that target either the active site or the myristic acid binding pocket in the kinase domain C-lobe. Dynamics analyses using hydrogen exchange mass spectrometry revealed a remarkable allosteric network linking the SH3 domain, the myristic acid binding pocket, and the active site of the c-Abl core, providing a structural basis for the biological observations. These results suggest a rational strategy for enhanced drug targeting of Bcr-Abl and other multidomain kinase systems that use multiple small molecules to exploit natural mechanisms of kinase control. PMID:23303187

Weaker axially dipolar time-averaged paleomagnetic field based on multidomain-corrected paleointensities from Galapagos lavas

PubMed Central

Wang, Huapei; Kent, Dennis V.; Rochette, Pierre

2015-01-01

The geomagnetic field is predominantly dipolar today, and high-fidelity paleomagnetic mean directions from all over the globe strongly support the geocentric axial dipole (GAD) hypothesis for the past few million years. However, the bulk of paleointensity data fails to coincide with the axial dipole prediction of a factor-of-2 equator-to-pole increase in mean field strength, leaving the core dynamo process an enigma. Here, we obtain a multidomain-corrected Pliocene–Pleistocene average paleointensity of 21.6 ± 11.0 µT recorded by 27 lava flows from the Galapagos Archipelago near the Equator. Our new result in conjunction with a published comprehensive study of single-domain–behaved paleointensities from Antarctica (33.4 ± 13.9 µT) that also correspond to GAD directions suggests that the overall average paleomagnetic field over the past few million years has indeed been dominantly dipolar in intensity yet only ∼60% of the present-day field strength, with a long-term average virtual axial dipole magnetic moment of the Earth of only 4.9 ± 2.4 × 1022 A⋅m2. PMID:26598664

Predicting the multi-domain progression of Parkinson's disease: a Bayesian multivariate generalized linear mixed-effect model.

PubMed

Wang, Ming; Li, Zheng; Lee, Eun Young; Lewis, Mechelle M; Zhang, Lijun; Sterling, Nicholas W; Wagner, Daymond; Eslinger, Paul; Du, Guangwei; Huang, Xuemei

2017-09-25

It is challenging for current statistical models to predict clinical progression of Parkinson's disease (PD) because of the involvement of multi-domains and longitudinal data. Past univariate longitudinal or multivariate analyses from cross-sectional trials have limited power to predict individual outcomes or a single moment. The multivariate generalized linear mixed-effect model (GLMM) under the Bayesian framework was proposed to study multi-domain longitudinal outcomes obtained at baseline, 18-, and 36-month. The outcomes included motor, non-motor, and postural instability scores from the MDS-UPDRS, and demographic and standardized clinical data were utilized as covariates. The dynamic prediction was performed for both internal and external subjects using the samples from the posterior distributions of the parameter estimates and random effects, and also the predictive accuracy was evaluated based on the root of mean square error (RMSE), absolute bias (AB) and the area under the receiver operating characteristic (ROC) curve. First, our prediction model identified clinical data that were differentially associated with motor, non-motor, and postural stability scores. Second, the predictive accuracy of our model for the training data was assessed, and improved prediction was gained in particularly for non-motor (RMSE and AB: 2.89 and 2.20) compared to univariate analysis (RMSE and AB: 3.04 and 2.35). Third, the individual-level predictions of longitudinal trajectories for the testing data were performed, with ~80% observed values falling within the 95% credible intervals. Multivariate general mixed models hold promise to predict clinical progression of individual outcomes in PD. The data was obtained from Dr. Xuemei Huang's NIH grant R01 NS060722 , part of NINDS PD Biomarker Program (PDBP). All data was entered within 24 h of collection to the Data Management Repository (DMR), which is publically available ( https://pdbp.ninds.nih.gov/data-management ).

Expression of recombinant glycoproteins in mammalian cells: towards an integrative approach to structural biology.

PubMed

Aricescu, A Radu; Owens, Raymond J

2013-06-01

Mammalian cells are rapidly becoming the system of choice for the production of recombinant glycoproteins for structural biology applications. Their use has enabled the structural investigation of a whole new set of targets including large, multi-domain and highly glycosylated eukaryotic cell surface receptors and their supra-molecular assemblies. We summarize the technical advances that have been made in mammalian expression technology and highlight some of the structural insights that have been obtained using these methods. Looking forward, it is clear that mammalian cell expression will provide exciting and unique opportunities for an integrative approach to the structural study of proteins, especially of human origin and medically relevant, by bridging the gap between the purified state and the cellular context. Copyright © 2013 Elsevier Ltd. All rights reserved.

Local dynamic subgrid-scale models in channel flow

NASA Technical Reports Server (NTRS)

Cabot, William H.

1994-01-01

The dynamic subgrid-scale (SGS) model has given good results in the large-eddy simulation (LES) of homogeneous isotropic or shear flow, and in the LES of channel flow, using averaging in two or three homogeneous directions (the DA model). In order to simulate flows in general, complex geometries (with few or no homogeneous directions), the dynamic SGS model needs to be applied at a local level in a numerically stable way. Channel flow, which is inhomogeneous and wall-bounded flow in only one direction, provides a good initial test for local SGS models. Tests of the dynamic localization model were performed previously in channel flow using a pseudospectral code and good results were obtained. Numerical instability due to persistently negative eddy viscosity was avoided by either constraining the eddy viscosity to be positive or by limiting the time that eddy viscosities could remain negative by co-evolving the SGS kinetic energy (the DLk model). The DLk model, however, was too expensive to run in the pseudospectral code due to a large near-wall term in the auxiliary SGS kinetic energy (k) equation. One objective was then to implement the DLk model in a second-order central finite difference channel code, in which the auxiliary k equation could be integrated implicitly in time at great reduction in cost, and to assess its performance in comparison with the plane-averaged dynamic model or with no model at all, and with direct numerical simulation (DNS) and/or experimental data. Other local dynamic SGS models have been proposed recently, e.g., constrained dynamic models with random backscatter, and with eddy viscosity terms that are averaged in time over material path lines rather than in space. Another objective was to incorporate and test these models in channel flow.

Balancing Power Absorption Against Structural Loads With Viscous Drag and Power-Takeoff Efficiency Considerations

DOE PAGES

Tom, Nathan; Yu, Yi-Hsiang; Wright, Alan; ...

2017-11-17

The focus of this paper is to balance power absorption against structural loading for a novel fixed-bottom oscillating surge wave energy converter in both regular and irregular wave environments. The power-to-load ratio will be evaluated using pseudospectral control (PSC) to determine the optimum power-takeoff (PTO) torque based on a multiterm objective function. This paper extends the pseudospectral optimal control problem to not just maximize the time-averaged absorbed power but also include measures for the surge-foundation force and PTO torque in the optimization. The objective function may now potentially include three competing terms that the optimizer must balance. Separate weighting factorsmore » are attached to the surge-foundation force and PTO control torque that can be used to tune the optimizer performance to emphasize either power absorption or load shedding. To correct the pitch equation of motion, derived from linear hydrodynamic theory, a quadratic-viscous-drag torque has been included in the system dynamics; however, to continue the use of quadratic programming solvers, an iteratively obtained linearized drag coefficient was utilized that provided good accuracy in the predicted pitch motion. Furthermore, the analysis considers the use of a nonideal PTO unit to more accurately evaluate controller performance. The PTO efficiency is not directly included in the objective function but rather the weighting factors are utilized to limit the PTO torque amplitudes, thereby reducing the losses resulting from the bidirectional energy flow through a nonideal PTO. Results from PSC show that shedding a portion of the available wave energy can lead to greater reductions in structural loads, peak-to-average power ratio, and reactive power requirement.« less

Enhanced Representation of Turbulent Flow Phenomena in Large-Eddy Simulations of the Atmospheric Boundary Layer using Grid Refinement with Pseudo-Spectral Numerics

NASA Astrophysics Data System (ADS)

Torkelson, G. Q.; Stoll, R., II

2017-12-01

Large Eddy Simulation (LES) is a tool commonly used to study the turbulent transport of momentum, heat, and moisture in the Atmospheric Boundary Layer (ABL). For a wide range of ABL LES applications, representing the full range of turbulent length scales in the flow field is a challenge. This is an acute problem in regions of the ABL with strong velocity or scalar gradients, which are typically poorly resolved by standard computational grids (e.g., near the ground surface, in the entrainment zone). Most efforts to address this problem have focused on advanced sub-grid scale (SGS) turbulence model development, or on the use of massive computational resources. While some work exists using embedded meshes, very little has been done on the use of grid refinement. Here, we explore the benefits of grid refinement in a pseudo-spectral LES numerical code. The code utilizes both uniform refinement of the grid in horizontal directions, and stretching of the grid in the vertical direction. Combining the two techniques allows us to refine areas of the flow while maintaining an acceptable grid aspect ratio. In tests that used only refinement of the vertical grid spacing, large grid aspect ratios were found to cause a significant unphysical spike in the stream-wise velocity variance near the ground surface. This was especially problematic in simulations of stably-stratified ABL flows. The use of advanced SGS models was not sufficient to alleviate this issue. The new refinement technique is evaluated using a series of idealized simulation test cases of neutrally and stably stratified ABLs. These test cases illustrate the ability of grid refinement to increase computational efficiency without loss in the representation of statistical features of the flow field.

Multidomain Trajectories of Psychological Functioning in Old Age: A Longitudinal Perspective on (Uneven) Successful Aging

ERIC Educational Resources Information Center

Morack, Jennifer; Ram, Nilam; Fauth, Elizabeth B.; Gerstorf, Denis

2013-01-01

Life-span developmentalists have long been interested in the nature of and the contributing factors to successful aging. Using variable-oriented approaches, research has revealed critical insights into the intricacies of human development and successful aging. In the present study, we opted instead for a more subgroup-oriented approach and…

Final Report - Cloud-Based Management Platform for Distributed, Multi-Domain Networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chowdhury, Pulak; Mukherjee, Biswanath

2017-11-03

In this Department of Energy (DOE) Small Business Innovation Research (SBIR) Phase II project final report, Ennetix presents the development of a solution for end-to-end monitoring, analysis, and visualization of network performance for distributed networks. This solution benefits enterprises of all sizes, operators of distributed and federated networks, and service providers.

Multidomain, multirecord-type Datatrieve-11 databases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Horning, R.R.

1983-01-01

Data bases consisting of multiple domains and multirecord-type domains present special problems in design, loading, maintenance, and report generation. The logical association of records is a fundamental concern in all these problem areas. This paper describes techniques for dealing with this and other specifics using Datatrieve-11, Sort-11, FORTRAN 77, and the RSX-11M Indirect Command File Processor.

Socioeconomic Status and the Health of Youth: A Multilevel, Multidomain Approach to Conceptualizing Pathways

ERIC Educational Resources Information Center

Schreier, Hannah M. C.; Chen, Edith

2013-01-01

Previous research has clearly established associations between low socioeconomic status (SES) and poor youth physical health outcomes. This article provides an overview of the main pathways through which low SES environments come to influence youth health. We focus on 2 prevalent chronic health problems in youth today, asthma and obesity. We…

A Multi-Domain Model of Risk Factors for ODD Symptoms in a Community Sample of 4-Year-Olds

ERIC Educational Resources Information Center

Lavigne, John V.; Gouze, Karen R.; Hopkins, Joyce; Bryant, Fred B.; LeBailly, Susan A.

2012-01-01

Few studies have been designed to assess the pathways by which risk factors are associated with symptoms of psychopathology across multiple domains, including contextual factors, parental depression, parenting, and child characteristics. The present study examines a cross-sectional model of risk factors for symptoms of Oppositional Defiant…

Simulations of inspiraling and merging double neutron stars using the Spectral Einstein Code

NASA Astrophysics Data System (ADS)

Haas, Roland; Ott, Christian D.; Szilagyi, Bela; Kaplan, Jeffrey D.; Lippuner, Jonas; Scheel, Mark A.; Barkett, Kevin; Muhlberger, Curran D.; Dietrich, Tim; Duez, Matthew D.; Foucart, Francois; Pfeiffer, Harald P.; Kidder, Lawrence E.; Teukolsky, Saul A.

2016-06-01

We present results on the inspiral, merger, and postmerger evolution of a neutron star-neutron star (NSNS) system. Our results are obtained using the hybrid pseudospectral-finite volume Spectral Einstein Code (SpEC). To test our numerical methods, we evolve an equal-mass system for ≈22 orbits before merger. This waveform is the longest waveform obtained from fully general-relativistic simulations for NSNSs to date. Such long (and accurate) numerical waveforms are required to further improve semianalytical models used in gravitational wave data analysis, for example, the effective one body models. We discuss in detail the improvements to SpEC's ability to simulate NSNS mergers, in particular mesh refined grids to better resolve the merger and postmerger phases. We provide a set of consistency checks and compare our results to NSNS merger simulations with the independent bam code. We find agreement between them, which increases confidence in results obtained with either code. This work paves the way for future studies using long waveforms and more complex microphysical descriptions of neutron star matter in SpEC.

Quantification of mixing in vesicle suspensions using numerical simulations in two dimensions.

PubMed

Kabacaoğlu, G; Quaife, B; Biros, G

2017-02-01

We study mixing in Stokesian vesicle suspensions in two dimensions on a cylindrical Couette apparatus using numerical simulations. The vesicle flow simulation is done using a boundary integral method, and the advection-diffusion equation for the mixing of the solute is solved using a pseudo-spectral scheme. We study the effect of the area fraction, the viscosity contrast between the inside (the vesicles) and the outside (the bulk) fluid, the initial condition of the solute, and the mixing metric. We compare mixing in the suspension with mixing in the Couette apparatus without vesicles. On the one hand, the presence of vesicles in most cases slightly suppresses mixing. This is because the solute can be only diffused across the vesicle interface and not advected. On the other hand, there exist spatial distributions of the solute for which the unperturbed Couette flow completely fails to mix whereas the presence of vesicles enables mixing. We derive a simple condition that relates the velocity and solute and can be used to characterize the cases in which the presence of vesicles promotes mixing.

Quantification of mixing in vesicle suspensions using numerical simulations in two dimensions

PubMed Central

Quaife, B.; Biros, G.

2017-01-01

We study mixing in Stokesian vesicle suspensions in two dimensions on a cylindrical Couette apparatus using numerical simulations. The vesicle flow simulation is done using a boundary integral method, and the advection-diffusion equation for the mixing of the solute is solved using a pseudo-spectral scheme. We study the effect of the area fraction, the viscosity contrast between the inside (the vesicles) and the outside (the bulk) fluid, the initial condition of the solute, and the mixing metric. We compare mixing in the suspension with mixing in the Couette apparatus without vesicles. On the one hand, the presence of vesicles in most cases slightly suppresses mixing. This is because the solute can be only diffused across the vesicle interface and not advected. On the other hand, there exist spatial distributions of the solute for which the unperturbed Couette flow completely fails to mix whereas the presence of vesicles enables mixing. We derive a simple condition that relates the velocity and solute and can be used to characterize the cases in which the presence of vesicles promotes mixing. PMID:28344432

Final Technical Report: Quantification of Uncertainty in Extreme Scale Computations (QUEST)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knio, Omar M.

QUEST is a SciDAC Institute comprising Sandia National Laboratories, Los Alamos National Laboratory, University of Southern California, Massachusetts Institute of Technology, University of Texas at Austin, and Duke University. The mission of QUEST is to: (1) develop a broad class of uncertainty quantification (UQ) methods/tools, and (2) provide UQ expertise and software to other SciDAC projects, thereby enabling/guiding their UQ activities. The Duke effort focused on the development of algorithms and utility software for non-intrusive sparse UQ representations, and on participation in the organization of annual workshops and tutorials to disseminate UQ tools to the community, and to gather inputmore » in order to adapt approaches to the needs of SciDAC customers. In particular, fundamental developments were made in (a) multiscale stochastic preconditioners, (b) gradient-based approaches to inverse problems, (c) adaptive pseudo-spectral approximations, (d) stochastic limit cycles, and (e) sensitivity analysis tools for noisy systems. In addition, large-scale demonstrations were performed, namely in the context of ocean general circulation models.« less

The CFL condition for spectral approximations to hyperbolic initial-boundary value problems

NASA Technical Reports Server (NTRS)

Gottlieb, David; Tadmor, Eitan

1991-01-01

The stability of spectral approximations to scalar hyperbolic initial-boundary value problems with variable coefficients are studied. Time is discretized by explicit multi-level or Runge-Kutta methods of order less than or equal to 3 (forward Euler time differencing is included), and spatial discretizations are studied by spectral and pseudospectral approximations associated with the general family of Jacobi polynomials. It is proved that these fully explicit spectral approximations are stable provided their time-step, delta t, is restricted by the CFL-like condition, delta t less than Const. N(exp-2), where N equals the spatial number of degrees of freedom. We give two independent proofs of this result, depending on two different choices of approximate L(exp 2)-weighted norms. In both approaches, the proofs hinge on a certain inverse inequality interesting for its own sake. The result confirms the commonly held belief that the above CFL stability restriction, which is extensively used in practical implementations, guarantees the stability (and hence the convergence) of fully-explicit spectral approximations in the nonperiodic case.

The CFL condition for spectral approximations to hyperbolic initial-boundary value problems

NASA Technical Reports Server (NTRS)

Gottlieb, David; Tadmor, Eitan

1990-01-01

The stability of spectral approximations to scalar hyperbolic initial-boundary value problems with variable coefficients are studied. Time is discretized by explicit multi-level or Runge-Kutta methods of order less than or equal to 3 (forward Euler time differencing is included), and spatial discretizations are studied by spectral and pseudospectral approximations associated with the general family of Jacobi polynomials. It is proved that these fully explicit spectral approximations are stable provided their time-step, delta t, is restricted by the CFL-like condition, delta t less than Const. N(exp-2), where N equals the spatial number of degrees of freedom. We give two independent proofs of this result, depending on two different choices of approximate L(exp 2)-weighted norms. In both approaches, the proofs hinge on a certain inverse inequality interesting for its own sake. The result confirms the commonly held belief that the above CFL stability restriction, which is extensively used in practical implementations, guarantees the stability (and hence the convergence) of fully-explicit spectral approximations in the nonperiodic case.

Multielectron effects in the photoelectron momentum distribution of noble-gas atoms driven by visible-to-infrared-frequency laser pulses: A time-dependent density-functional-theory approach

NASA Astrophysics Data System (ADS)

Murakami, Mitsuko; Zhang, G. P.; Chu, Shih-I.

2017-05-01

We present the photoelectron momentum distributions (PMDs) of helium, neon, and argon atoms driven by a linearly polarized, visible (527-nm) or near-infrared (800-nm) laser pulse (20 optical cycles in duration) based on the time-dependent density-functional theory (TDDFT) under the local-density approximation with a self-interaction correction. A set of time-dependent Kohn-Sham equations for all electrons in an atom is numerically solved using the generalized pseudospectral method. An effect of the electron-electron interaction driven by a visible laser field is not recognizable in the helium and neon PMDs except for a reduction of the overall photoelectron yield, but there is a clear difference between the PMDs of an argon atom calculated with the frozen-core approximation and TDDFT, indicating an interference of its M -shell wave functions during the ionization. Furthermore, we find that the PMDs of degenerate p states are well separated in intensity when driven by a near-infrared laser field, so that the single-active-electron approximation can be adopted safely.

Time-optimal trajectory planning for underactuated spacecraft using a hybrid particle swarm optimization algorithm

NASA Astrophysics Data System (ADS)

Zhuang, Yufei; Huang, Haibin

2014-02-01

A hybrid algorithm combining particle swarm optimization (PSO) algorithm with the Legendre pseudospectral method (LPM) is proposed for solving time-optimal trajectory planning problem of underactuated spacecrafts. At the beginning phase of the searching process, an initialization generator is constructed by the PSO algorithm due to its strong global searching ability and robustness to random initial values, however, PSO algorithm has a disadvantage that its convergence rate around the global optimum is slow. Then, when the change in fitness function is smaller than a predefined value, the searching algorithm is switched to the LPM to accelerate the searching process. Thus, with the obtained solutions by the PSO algorithm as a set of proper initial guesses, the hybrid algorithm can find a global optimum more quickly and accurately. 200 Monte Carlo simulations results demonstrate that the proposed hybrid PSO-LPM algorithm has greater advantages in terms of global searching capability and convergence rate than both single PSO algorithm and LPM algorithm. Moreover, the PSO-LPM algorithm is also robust to random initial values.

The Effect of Strain Rate on the Evolution of Plane Wakes Subjected to Irrotational Strains

NASA Technical Reports Server (NTRS)

Rogers, Michael M.; Merriam, Marshal (Technical Monitor)

1996-01-01

Direct numerical simulations of time-evolving turbulent plane wakes developing in the presence of irrotational plane strain applied at three different strain rates have been generated. The strain geometry is such that the flow is compressed in the streamwise direction and expanded in the cross-stream direction with the spanwise direction being unstrained. This geometry is the temporally evolving analogue of a spatially evolving wake in an adverse pressure gradient. A pseudospectral numerical method with up to 16 million modes is used to solve the equations in a reference frame moving with the irrotational strain. The initial condition for each simulation is taken from a previous turbulent self-similar plane wake direct numerical simulation at a velocity deficit Reynolds number, Re, of about 2,000. Although the evolutions of many statistics are nearly collapsed when plotted against total strain, there are some differences owing to the different strain rate histories. The impact of strain-rate on the wake spreading rate, the peak velocity deficit, the Reynolds stress profiles, and the flow structure is examined.

Numerical modelling of GPR electromagnetic fields for locating burial sites

NASA Astrophysics Data System (ADS)

Carcione, José M.; Karczewski, Jerzy; Mazurkiewicz, Ewelina; Tadeusiewicz, Ryszard; Tomecka-Suchoń, Sylwia

2017-11-01

Ground-penetrating radar (GPR) is commonly used for locating burial sites. In this article, we acquired radargrams at a site where a domestic pig cadaver was buried. The measurements were conducted with the ProEx System GPR manufactured by the Swedish company Mala Geoscience with an antenna of 500MHz. The event corresponding to the pig can be clearly seen in the measurements. In order to improve the interpretation, the electromagnetic field is compared to numerical simulations computed with the pseudo-spectral Fourier method. A geological model has been defined on the basis of assumed electromagnetic properties (permittivity, conductivity and magnetic permeability). The results, when compared with the GPR measurements, show a dissimilar amplitude behaviour, with a stronger reflection event from the bottom of the pit. We have therefore performed another simulation by decreasing the electrical conductivity of the body very close to that of air. The comparison improved, showing more reflections, which could be an indication that the body contains air or has been degraded to a certain extent that the electrical resistivity has greatly increased.

Investigation of cellular detonation structure formation via linear stability theory and 2D and 3D numerical simulations

NASA Astrophysics Data System (ADS)

Borisov, S. P.; Kudryavtsev, A. N.

2017-10-01

Linear and nonlinear stages of the instability of a plane detonation wave (DW) and the subsequent process of formation of cellular detonation structure are investigated. A simple model with one-step irreversible chemical reaction is used. The linear analysis is employed to predict the DW front structure at the early stages of its formation. An emerging eigenvalue problem is solved with a global method using a Chebyshev pseudospectral method and the LAPACK software library. A local iterative shooting procedure is used for eigenvalue refinement. Numerical simulations of a propagation of a DW in plane and rectangular channels are performed with a shock capturing WENO scheme of 5th order. A special method of a computational domain shift is implemented in order to maintain the DW in the domain. It is shown that the linear analysis gives certain predictions about the DW structure that are in agreement with the numerical simulations of early stages of DW propagation. However, at later stages, a merger of detonation cells occurs so that their number is approximately halved. Computations of DW propagation in a square channel reveal two different types of spatial structure of the DW front, "rectangular" and "diagonal" types. A spontaneous transition from the rectangular to diagonal type of structure is observed during propagation of the DW.

Strongly Coupled Fluid-Body Dynamics in the Immersed Boundary Projection Method

NASA Astrophysics Data System (ADS)

Wang, Chengjie; Eldredge, Jeff D.

2014-11-01

A computational algorithm is developed to simulate dynamically coupled interaction between fluid and rigid bodies. The basic computational framework is built upon a multi-domain immersed boundary method library, whirl, developed in previous work. In this library, the Navier-Stokes equations for incompressible flow are solved on a uniform Cartesian grid by the vorticity-based immersed boundary projection method of Colonius and Taira. A solver for the dynamics of rigid-body systems is also included. The fluid and rigid-body solvers are strongly coupled with an iterative approach based on the block Gauss-Seidel method. Interfacial force, with its intimate connection with the Lagrange multipliers used in the fluid solver, is used as the primary iteration variable. Relaxation, developed from a stability analysis of the iterative scheme, is used to achieve convergence in only 2-4 iterations per time step. Several two- and three-dimensional numerical tests are conducted to validate and demonstrate the method, including flapping of flexible wings, self-excited oscillations of a system of linked plates and three-dimensional propulsion of flexible fluked tail. This work has been supported by AFOSR, under Award FA9550-11-1-0098.

Multiscale multiphysics and multidomain models—Flexibility and rigidity

PubMed Central

Xia, Kelin; Opron, Kristopher; Wei, Guo-Wei

2013-01-01

The emerging complexity of large macromolecules has led to challenges in their full scale theoretical description and computer simulation. Multiscale multiphysics and multidomain models have been introduced to reduce the number of degrees of freedom while maintaining modeling accuracy and achieving computational efficiency. A total energy functional is constructed to put energies for polar and nonpolar solvation, chemical potential, fluid flow, molecular mechanics, and elastic dynamics on an equal footing. The variational principle is utilized to derive coupled governing equations for the above mentioned multiphysical descriptions. Among these governing equations is the Poisson-Boltzmann equation which describes continuum electrostatics with atomic charges. The present work introduces the theory of continuum elasticity with atomic rigidity (CEWAR). The essence of CEWAR is to formulate the shear modulus as a continuous function of atomic rigidity. As a result, the dynamics complexity of a macromolecular system is separated from its static complexity so that the more time-consuming dynamics is handled with continuum elasticity theory, while the less time-consuming static analysis is pursued with atomic approaches. We propose a simple method, flexibility-rigidity index (FRI), to analyze macromolecular flexibility and rigidity in atomic detail. The construction of FRI relies on the fundamental assumption that protein functions, such as flexibility, rigidity, and energy, are entirely determined by the structure of the protein and its environment, although the structure is in turn determined by all the interactions. As such, the FRI measures the topological connectivity of protein atoms or residues and characterizes the geometric compactness of the protein structure. As a consequence, the FRI does not resort to the interaction Hamiltonian and bypasses matrix diagonalization, which underpins most other flexibility analysis methods. FRI's computational complexity is of \\documentclass[12pt]{minimal}\\begin{document}${\\cal O}(N^2)$\\end{document}O(N2) at most, where N is the number of atoms or residues, in contrast to \\documentclass[12pt]{minimal}\\begin{document}${\\cal O}(N^3)$\\end{document}O(N3) for Hamiltonian based methods. We demonstrate that the proposed FRI gives rise to accurate prediction of protein B-Factor for a set of 263 proteins. We show that a parameter free FRI is able to achieve about 95% accuracy of the parameter optimized FRI. An interpolation algorithm is developed to construct continuous atomic flexibility functions for visualization and use with CEWAR. PMID:24320318

Multiscale multiphysics and multidomain models—Flexibility and rigidity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xia, Kelin; Opron, Kristopher; Wei, Guo-Wei, E-mail: wei@math.msu.edu

The emerging complexity of large macromolecules has led to challenges in their full scale theoretical description and computer simulation. Multiscale multiphysics and multidomain models have been introduced to reduce the number of degrees of freedom while maintaining modeling accuracy and achieving computational efficiency. A total energy functional is constructed to put energies for polar and nonpolar solvation, chemical potential, fluid flow, molecular mechanics, and elastic dynamics on an equal footing. The variational principle is utilized to derive coupled governing equations for the above mentioned multiphysical descriptions. Among these governing equations is the Poisson-Boltzmann equation which describes continuum electrostatics with atomicmore » charges. The present work introduces the theory of continuum elasticity with atomic rigidity (CEWAR). The essence of CEWAR is to formulate the shear modulus as a continuous function of atomic rigidity. As a result, the dynamics complexity of a macromolecular system is separated from its static complexity so that the more time-consuming dynamics is handled with continuum elasticity theory, while the less time-consuming static analysis is pursued with atomic approaches. We propose a simple method, flexibility-rigidity index (FRI), to analyze macromolecular flexibility and rigidity in atomic detail. The construction of FRI relies on the fundamental assumption that protein functions, such as flexibility, rigidity, and energy, are entirely determined by the structure of the protein and its environment, although the structure is in turn determined by all the interactions. As such, the FRI measures the topological connectivity of protein atoms or residues and characterizes the geometric compactness of the protein structure. As a consequence, the FRI does not resort to the interaction Hamiltonian and bypasses matrix diagonalization, which underpins most other flexibility analysis methods. FRI's computational complexity is of O(N{sup 2}) at most, where N is the number of atoms or residues, in contrast to O(N{sup 3}) for Hamiltonian based methods. We demonstrate that the proposed FRI gives rise to accurate prediction of protein B-Factor for a set of 263 proteins. We show that a parameter free FRI is able to achieve about 95% accuracy of the parameter optimized FRI. An interpolation algorithm is developed to construct continuous atomic flexibility functions for visualization and use with CEWAR.« less

A SEMI-LAGRANGIAN TWO-LEVEL PRECONDITIONED NEWTON-KRYLOV SOLVER FOR CONSTRAINED DIFFEOMORPHIC IMAGE REGISTRATION.

PubMed

Mang, Andreas; Biros, George

2017-01-01

We propose an efficient numerical algorithm for the solution of diffeomorphic image registration problems. We use a variational formulation constrained by a partial differential equation (PDE), where the constraints are a scalar transport equation. We use a pseudospectral discretization in space and second-order accurate semi-Lagrangian time stepping scheme for the transport equations. We solve for a stationary velocity field using a preconditioned, globalized, matrix-free Newton-Krylov scheme. We propose and test a two-level Hessian preconditioner. We consider two strategies for inverting the preconditioner on the coarse grid: a nested preconditioned conjugate gradient method (exact solve) and a nested Chebyshev iterative method (inexact solve) with a fixed number of iterations. We test the performance of our solver in different synthetic and real-world two-dimensional application scenarios. We study grid convergence and computational efficiency of our new scheme. We compare the performance of our solver against our initial implementation that uses the same spatial discretization but a standard, explicit, second-order Runge-Kutta scheme for the numerical time integration of the transport equations and a single-level preconditioner. Our improved scheme delivers significant speedups over our original implementation. As a highlight, we observe a 20 × speedup for a two dimensional, real world multi-subject medical image registration problem.

Effects of Density Stratification in Compressible Polytropic Convection

NASA Astrophysics Data System (ADS)

Manduca, Cathryn M.; Anders, Evan H.; Bordwell, Baylee; Brown, Benjamin P.; Burns, Keaton J.; Lecoanet, Daniel; Oishi, Jeffrey S.; Vasil, Geoffrey M.

2017-11-01

We study compressible convection in polytropically-stratified atmospheres, exploring the effect of varying the total density stratification. Using the Dedalus pseudospectral framework, we perform 2D and 3D simulations. In these experiments we vary the number of density scale heights, studying atmospheres with little stratification (1 density scale height) and significant stratification (5 density scale heights). We vary the level of convective driving (quantified by the Rayleigh number), and study flows at similar Mach numbers by fixing the initial superadiabaticity. We explore the differences between 2D and 3D simulations, and in particular study the equilibration between different reservoirs of energy (kinetic, potential and internal) in the evolved states.

Moist, Double-diffusive convection

NASA Astrophysics Data System (ADS)

Oishi, Jeffrey; Burns, Keaton; Brown, Ben; Lecoanet, Daniel; Vasil, Geoffrey

2017-11-01

Double-diffusive convection occurs when the competition between stabilizing and a destabilizing buoyancy source is mediated by a difference in the diffusivity of each source. Such convection is important in a wide variety of astrophysical and geophysical flows. However, in giant planets, double-diffusive convection occurs in regions where condensation of important components of the atmosphere occurs. Here, we present preliminary calculations of moist, double-diffusive convection using the Dedalus pseudospectral framework. Using a simple model for phase change, we verify growth rates for moist double diffusive convection from linear calculations and report on preliminary relationships between the ability to form liquid phase and the resulting Nusselt number in nonlinear simulations.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andrés, Nahuel, E-mail: nandres@iafe.uba.ar; Gómez, Daniel; Departamento de Física, Facultad de Ciencias Exactas y Naturales, Univrsidad de Buenos Aires, Pabellón I, 1428, Buenos Aires

We present a study of collisionless magnetic reconnection within the framework of full two-fluid MHD for a completely ionized hydrogen plasma, retaining the effects of the Hall current, electron pressure and electron inertia. We performed 2.5D simulations using a pseudo-spectral code with no dissipative effects. We check that the ideal invariants of the problem are conserved down to round-off errors. Our numerical results confirm that the change in the topology of the magnetic field lines is exclusively due to the presence of electron inertia. The computed reconnection rates remain a fair fraction of the Alfvén velocity, which therefore qualifies asmore » fast reconnection.« less

Preferentially oriented, High temperature superconductors by seeding and a method for their preparation

DOEpatents

Lee, Dominic F.; Kroeger, Donald M.; Goyal, Amit

2001-01-01

A multi-domained bulk REBa.sub.2 Cu.sub.3 O.sub.x with low-angle domain boundaries which resembles a quasi-single domained material and a method for producing the same comprising arranging multiple seeds, which can be small single crystals, single domained melt-textured REBa.sub.2 Cu.sub.3 O.sub.x pieces, textured substrates comprised of grains with low misorientation angles, or thick film REBa.sub.2 Cu.sub.3 O.sub.x deposited on such textured substrate, such seeds being tailored for various REBa.sub.2 Cu.sub.3 O.sub.x compounds, in specific pattern and relative seed orientations on a superconductor precursor material which may be placed in contact with a porous substrate so as to reduce the amount of liquid phase in the melt. Because seeds can be arranged in virtually any pattern, high quality REBa.sub.2 Cu.sub.3 O.sub.x elements of virtually unlimited size and complex geometry can be fabricated.

Method for preparing preferentially oriented, high temperature superconductors using solution reagents

DOEpatents

Lee, Dominic F.; Kroeger, Donald M.; Goyal, Amit

2002-01-01

A multi-domained bulk REBa.sub.2 CU.sub.3 O.sub.x with low-angle domain boundaries which resemble a quasi-single domained material and a method for producing the same comprising arranging multiple seeds, which can be small single crystals, single domained melt-textured REBa.sub.2 CU.sub.3 O.sub.x pieces, textured substrates comprises of grains with low misorientation angles, or thick film REBa.sub.2 CU.sub.3 O.sub.x deposited on such textured substrate, such seeds being tailored for various REBa.sub.2 CU.sub.3 O.sub.x compounds, in specific pattern and relative seed orientations on a superconductor precursor material which may be placed in contact with a porous substrate so as to reduce the amount of liquid phase in the melt. Because seeds can be arranged in virtually any pattern, high quality REBa.sub.2 CU.sub.3 O.sub.x elements of virtually unlimited size and complex geometry can be fabricated.

MOCASSIN-prot: a multi-objective clustering approach for protein similarity networks.

PubMed

Keel, Brittney N; Deng, Bo; Moriyama, Etsuko N

2018-04-15

Proteins often include multiple conserved domains. Various evolutionary events including duplication and loss of domains, domain shuffling, as well as sequence divergence contribute to generating complexities in protein structures, and consequently, in their functions. The evolutionary history of proteins is hence best modeled through networks that incorporate information both from the sequence divergence and the domain content. Here, a game-theoretic approach proposed for protein network construction is adapted into the framework of multi-objective optimization, and extended to incorporate clustering refinement procedure. The new method, MOCASSIN-prot, was applied to cluster multi-domain proteins from ten genomes. The performance of MOCASSIN-prot was compared against two protein clustering methods, Markov clustering (TRIBE-MCL) and spectral clustering (SCPS). We showed that compared to these two methods, MOCASSIN-prot, which uses both domain composition and quantitative sequence similarity information, generates fewer false positives. It achieves more functionally coherent protein clusters and better differentiates protein families. MOCASSIN-prot, implemented in Perl and Matlab, is freely available at http://bioinfolab.unl.edu/emlab/MOCASSINprot. emoriyama2@unl.edu. Supplementary data are available at Bioinformatics online.

Overview of the NASA Glenn Flux Reconstruction Based High-Order Unstructured Grid Code

NASA Technical Reports Server (NTRS)

Spiegel, Seth C.; DeBonis, James R.; Huynh, H. T.

2016-01-01

A computational fluid dynamics code based on the flux reconstruction (FR) method is currently being developed at NASA Glenn Research Center to ultimately provide a large- eddy simulation capability that is both accurate and efficient for complex aeropropulsion flows. The FR approach offers a simple and efficient method that is easy to implement and accurate to an arbitrary order on common grid cell geometries. The governing compressible Navier-Stokes equations are discretized in time using various explicit Runge-Kutta schemes, with the default being the 3-stage/3rd-order strong stability preserving scheme. The code is written in modern Fortran (i.e., Fortran 2008) and parallelization is attained through MPI for execution on distributed-memory high-performance computing systems. An h- refinement study of the isentropic Euler vortex problem is able to empirically demonstrate the capability of the FR method to achieve super-accuracy for inviscid flows. Additionally, the code is applied to the Taylor-Green vortex problem, performing numerous implicit large-eddy simulations across a range of grid resolutions and solution orders. The solution found by a pseudo-spectral code is commonly used as a reference solution to this problem, and the FR code is able to reproduce this solution using approximately the same grid resolution. Finally, an examination of the code's performance demonstrates good parallel scaling, as well as an implementation of the FR method with a computational cost/degree- of-freedom/time-step that is essentially independent of the solution order of accuracy for structured geometries.

Creating an Effective Multi-Domain Wide-Area Surveillance Platform to Enhance Border Security

DTIC Science & Technology

2008-03-01

SWOT ANALYSIS ........................................................................................43 I. ANALYSIS OF PROS AND CONS ...weaknesses and opportunities and SWOT analysis was also used to build pros and cons for the platform. All the interviewees liked unmanned platforms...because of the reduced night hour’s operations and SWOT analysis was also used to build pros and cons for the platform. All the interviewees really

BREAKING STOVEPIPES: BRIDGING GAPS IN AIR FORCE INDUSTRIAL CONTROL SYSTEMS MANAGEMENT TO ENABLE MULTI-DOMAIN MISSION ASSURANCE

DTIC Science & Technology

2016-02-16

sputter, and lights flicker and fail. An in-bound F-35, returning from its first strike mission for a quick-turn, has to divert as the runway is not ready...and mitigating risk of known vulnerabilities.” United States Scientific Advisory Board, Report on Defending and Operating in a Contested Cyber

NREL Kicks Off Next Phase of Advanced Computer-Aided Battery Engineering |

Science.gov Websites

lithium-ion (Li-ion) batteries, known as a multi-scale multi-domain (GH-MSMD) model framework, was News | NREL Kicks Off Next Phase of Advanced Computer-Aided Battery Engineering NREL Kicks Off Next Phase of Advanced Computer-Aided Battery Engineering March 16, 2016 NREL researcher looks across

Chemical probes and engineered constructs reveal a detailed unfolding mechanism for a solvent-free multi-domain protein

PubMed Central

Eschweiler, Joseph D.; Martini, Rachel M.; Ruotolo, Brandon T.

2017-01-01

Despite the growing application of gas-phase measurements in structural biology and drug discovery, the factors that govern protein stabilities and structures in a solvent-free environment are still poorly understood. Here, we examine the solvent-free unfolding pathway for a group of homologous serum albumins. Utilizing a combination of chemical probes and non-covalent reconstructions, we draw new specific conclusions regarding the unfolding of albumins in the gas-phase, as well as more-general inferences regarding the sensitivity of collision induced unfolding to changes in protein primary and tertiary structure. Our findings suggest that the general unfolding pathway of low charge state albumin ions is largely unaffected by changes in primary structure; however, the stabilities of intermediates along these pathways vary widely as sequences diverge. Additionally, we find that human albumin follows a domain associated unfolding pathway, and are able to assign each unfolded form observed in our gas-phase dataset to the disruption of specific domains within the protein. The totality of our data informs the first detailed mechanism for multi-domain protein unfolding in the gas phase, and highlights key similarities and differences from the known the solution-phase pathway. PMID:27959526

ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins

PubMed Central

Puntervoll, Pål; Linding, Rune; Gemünd, Christine; Chabanis-Davidson, Sophie; Mattingsdal, Morten; Cameron, Scott; Martin, David M. A.; Ausiello, Gabriele; Brannetti, Barbara; Costantini, Anna; Ferrè, Fabrizio; Maselli, Vincenza; Via, Allegra; Cesareni, Gianni; Diella, Francesca; Superti-Furga, Giulio; Wyrwicz, Lucjan; Ramu, Chenna; McGuigan, Caroline; Gudavalli, Rambabu; Letunic, Ivica; Bork, Peer; Rychlewski, Leszek; Küster, Bernhard; Helmer-Citterich, Manuela; Hunter, William N.; Aasland, Rein; Gibson, Toby J.

2003-01-01

Multidomain proteins predominate in eukaryotic proteomes. Individual functions assigned to different sequence segments combine to create a complex function for the whole protein. While on-line resources are available for revealing globular domains in sequences, there has hitherto been no comprehensive collection of small functional sites/motifs comparable to the globular domain resources, yet these are as important for the function of multidomain proteins. Short linear peptide motifs are used for cell compartment targeting, protein–protein interaction, regulation by phosphorylation, acetylation, glycosylation and a host of other post-translational modifications. ELM, the Eukaryotic Linear Motif server at http://elm.eu.org/, is a new bioinformatics resource for investigating candidate short non-globular functional motifs in eukaryotic proteins, aiming to fill the void in bioinformatics tools. Sequence comparisons with short motifs are difficult to evaluate because the usual significance assessments are inappropriate. Therefore the server is implemented with several logical filters to eliminate false positives. Current filters are for cell compartment, globular domain clash and taxonomic range. In favourable cases, the filters can reduce the number of retained matches by an order of magnitude or more. PMID:12824381

Structural Brain Changes after Traditional and Robot-Assisted Multi-Domain Cognitive Training in Community-Dwelling Healthy Elderly

PubMed Central

Kim, Geon Ha; Jeon, Seun; Im, Kiho; Kwon, Hunki; Lee, Byung Hwa; Kim, Ga Young; Jeong, Hana; Han, Noh Eul; Seo, Sang Won; Cho, Hanna; Noh, Young; Park, Sang Eon; Kim, Hojeong; Hwang, Jung Won; Yoon, Cindy W.; Kim, Hee Jin; Ye, Byoung Seok; Chin, Ju Hee; Kim, Jung-Hyun; Suh, Mee Kyung; Lee, Jong Min; Kim, Sung Tae; Choi, Mun-Taek; Kim, Mun Sang; Heilman, Kenneth M; Jeong, Jee Hyang; Na, Duk L.

2015-01-01

The purpose of this study was to investigate if multi-domain cognitive training, especially robot-assisted training, alters cortical thickness in the brains of elderly participants. A controlled trial was conducted with 85 volunteers without cognitive impairment who were 60 years old or older. Participants were first randomized into two groups. One group consisted of 48 participants who would receive cognitive training and 37 who would not receive training. The cognitive training group was randomly divided into two groups, 24 who received traditional cognitive training and 24 who received robot-assisted cognitive training. The training for both groups consisted of daily 90-min-session, five days a week for a total of 12 weeks. The primary outcome was the changes in cortical thickness. When compared to the control group, both groups who underwent cognitive training demonstrated attenuation of age related cortical thinning in the frontotemporal association cortices. When the robot and the traditional interventions were directly compared, the robot group showed less cortical thinning in the anterior cingulate cortices. Our results suggest that cognitive training can mitigate age-associated structural brain changes in the elderly. Trial Registration ClnicalTrials.gov NCT01596205 PMID:25898367

Folding pathway of a multidomain protein depends on its topology of domain connectivity

PubMed Central

Inanami, Takashi; Terada, Tomoki P.; Sasai, Masaki

2014-01-01

How do the folding mechanisms of multidomain proteins depend on protein topology? We addressed this question by developing an Ising-like structure-based model and applying it for the analysis of free-energy landscapes and folding kinetics of an example protein, Escherichia coli dihydrofolate reductase (DHFR). DHFR has two domains, one comprising discontinuous N- and C-terminal parts and the other comprising a continuous middle part of the chain. The simulated folding pathway of DHFR is a sequential process during which the continuous domain folds first, followed by the discontinuous domain, thereby avoiding the rapid decrease in conformation entropy caused by the association of the N- and C-terminal parts during the early phase of folding. Our simulated results consistently explain the observed experimental data on folding kinetics and predict an off-pathway structural fluctuation at equilibrium. For a circular permutant for which the topological complexity of wild-type DHFR is resolved, the balance between energy and entropy is modulated, resulting in the coexistence of the two folding pathways. This coexistence of pathways should account for the experimentally observed complex folding behavior of the circular permutant. PMID:25267632

Intercontinental Multi-Domain Monitoring for LHC with perfSONAR

NASA Astrophysics Data System (ADS)

Vicinanza, D.

2012-12-01

The Large Hadron Collider (LHC) is currently running at CERN in Geneva, Switzerland. Physicists are using LHC to recreate the conditions just after the Big Bang, by colliding two beams of particles and heavy ions head-on at very high energy. The project is generating more than 15 TB of raw data per year, plus 10 TB of “event summary data”. This data is sent out from CERN to eleven Tier 1 research centres in Europe, Asia, and North America using a multi-gigabits Optical Private Network (OPN), the LHCOPN. Tier 1 sites are then connected to 100+ academic and research institutions in the world (the Tier 2s) through a Multipoint to Multipoint network, the LHC Open Network Environment (LHCONE). Network monitoring on such complex network architecture to ensure robust and reliable operation is of crucial importance. The chosen approach for monitoring the OPN and ONE is based on the perfSONAR framework, which is designed for multi-domain monitoring environments. perfSONAR (www.perfsonar.net) is an infrastructure for performance monitoring data exchange between networks, making it easier to solve performance problems occurring between network measurement points interconnected through several network domains.

Systematic Domain Swaps of Iterative, Nonreducing Polyketide Synthases Provide a Mechanistic Understanding and Rationale For Catalytic Reprogramming

PubMed Central

2015-01-01

Iterative, nonreducing polyketide synthases (NR-PKSs) are multidomain enzymes responsible for the construction of the core architecture of aromatic polyketide natural products in fungi. Engineering these enzymes for the production of non-native metabolites has been a long-standing goal. We conducted a systematic survey of in vitro “domain swapped” NR-PKSs using an enzyme deconstruction approach. The NR-PKSs were dissected into mono- to multidomain fragments and recombined as noncognate pairs in vitro, reconstituting enzymatic activity. The enzymes used in this study produce aromatic polyketides that are representative of the four main chemical features set by the individual NR-PKS: starter unit selection, chain-length control, cyclization register control, and product release mechanism. We found that boundary conditions limit successful chemistry, which are dependent on a set of underlying enzymatic mechanisms. Crucial for successful redirection of catalysis, the rate of productive chemistry must outpace the rate of spontaneous derailment and thioesterase-mediated editing. Additionally, all of the domains in a noncognate system must interact efficiently if chemical redirection is to proceed. These observations refine and further substantiate current understanding of the mechanisms governing NR-PKS catalysis. PMID:24815013

Multi-domain utilization by TUT4 and TUT7 in control of let-7 biogenesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Faehnle, Christopher R.; Walleshauser, Jack; Joshua-Tor, Leemor

2017-07-03

The uridyl transferases TUT4 and TUT7 (collectively called TUT4(7)) switch between two modes of activity, either promoting expression of let-7 microRNA (monoU) or marking it for degradation (oligoU). Lin28 modulates the switch via recruitment of TUT4(7) to the precursor pre-let-7 in stem cells and human cancers. We found that TUT4(7) utilize two multidomain functional modules during the switch from monoU to oligoU. The catalytic module (CM) is essential for both activities, while the Lin28-interacting module (LIM) is indispensable for oligoU. A TUT7 CM structure trapped in the monoU activity staterevealed a duplex-RNA-binding pocket that orients group II pre-let-7 hairpins tomore » favor monoU addition. Conversely, the switch to oligoU requires the ZK domain of Lin28 to drive the formation of a stable ternary complex between pre-let-7 and the inactive LIM. Finally, ZK2 of TUT4(7) aids oligoU addition by engaging the growing oligoU tail through uracil-specific interactions.« less

Development of a Multi-Domain Assessment Tool for Quality Improvement Projects.

PubMed

Rosenbluth, Glenn; Burman, Natalie J; Ranji, Sumant R; Boscardin, Christy K

2017-08-01

Improving the quality of health care and education has become a mandate at all levels within the medical profession. While several published quality improvement (QI) assessment tools exist, all have limitations in addressing the range of QI projects undertaken by learners in undergraduate medical education, graduate medical education, and continuing medical education. We developed and validated a tool to assess QI projects with learner engagement across the educational continuum. After reviewing existing tools, we interviewed local faculty who taught QI to understand how learners were engaged and what these faculty wanted in an ideal assessment tool. We then developed a list of competencies associated with QI, established items linked to these competencies, revised the items using an iterative process, and collected validity evidence for the tool. The resulting Multi-Domain Assessment of Quality Improvement Projects (MAQIP) rating tool contains 9 items, with criteria that may be completely fulfilled, partially fulfilled, or not fulfilled. Interrater reliability was 0.77. Untrained local faculty were able to use the tool with minimal guidance. The MAQIP is a 9-item, user-friendly tool that can be used to assess QI projects at various stages and to provide formative and summative feedback to learners at all levels.

Exploring demands from the perspective of employees identified as being at risk of burnout

PubMed Central

Gauche, Cecile; de Beer, Leon T.; Brink, Lizelle

2017-01-01

ABSTRACT Purpose: Burnout has become an occupational health concern. However, little is known about the experiences of individuals identified as being at risk of burnout. This study aimed to address this gap by exploring employees’ experiences of well-being who were identified as burnout risks. Method: Interviews were conducted with 26 employees who agreed to participate in the study. A phenomenological approach was taken, with a case study design as the research strategy. Results: Three major themes were identified: job demands, life demands, and health concerns. It was evident that participants were experiencing demanding conditions in both their work and personal lives, indicating burnout to be a multi-domain phenomenon. Conclusions: Professionals and managers should take note of these results to assist and support employees who are identified as being at risk of burnout. PMID:28784048

Systematic methods for defining coarse-grained maps in large biomolecules.

PubMed

Zhang, Zhiyong

2015-01-01

Large biomolecules are involved in many important biological processes. It would be difficult to use large-scale atomistic molecular dynamics (MD) simulations to study the functional motions of these systems because of the computational expense. Therefore various coarse-grained (CG) approaches have attracted rapidly growing interest, which enable simulations of large biomolecules over longer effective timescales than all-atom MD simulations. The first issue in CG modeling is to construct CG maps from atomic structures. In this chapter, we review the recent development of a novel and systematic method for constructing CG representations of arbitrarily complex biomolecules, in order to preserve large-scale and functionally relevant essential dynamics (ED) at the CG level. In this ED-CG scheme, the essential dynamics can be characterized by principal component analysis (PCA) on a structural ensemble, or elastic network model (ENM) of a single atomic structure. Validation and applications of the method cover various biological systems, such as multi-domain proteins, protein complexes, and even biomolecular machines. The results demonstrate that the ED-CG method may serve as a very useful tool for identifying functional dynamics of large biomolecules at the CG level.

Light scattering by hexagonal ice crystals with distributed inclusions

NASA Astrophysics Data System (ADS)

Panetta, R. Lee; Zhang, Jia-Ning; Bi, Lei; Yang, Ping; Tang, Guanlin

2016-07-01

Inclusions of air bubbles or soot particles have significant effects on the single-scattering properties of ice crystals, effects that in turn have significant impacts on the radiation budget of an atmosphere containing the crystals. This study investigates some of the single-scattering effects in the case of hexagonal ice crystals, including effects on the backscattering depolarization ratio, a quantity of practical importance in the interpretation of lidar observations. One distinguishing feature of the study is an investigation of scattering properties at a visible wavelength for a crystal with size parameter (x) above 100, a size regime where one expects some agreement between exact methods and geometrical optics methods. This expectation is generally borne out in a test comparison of how the sensitivity of scattering properties to the distribution of a given volume fraction of included air is represented using (i) an approximate Monte Carlo Ray Tracing (MCRT) method and (ii) a numerically exact pseudo-spectral time-domain (PSTD) method. Another distinguishing feature of the study is a close examination, using the numerically exact Invariant-Imbedding T-Matrix (II-TM) method, of how some optical properties of importance to satellite remote sensing vary as the volume fraction of inclusions and size of crystal are varied. Although such an investigation of properties in the x>100 regime faces serious computational burdens that force a large number of idealizations and simplifications in the study, the results nevertheless provide an intriguing glimpse of what is evidently a quite complex sensitivity of optical scattering properties to inclusions of air or soot as volume fraction and size parameter are varied.

Explaining the Substantial Inter-Domain and Over-Time Correlations in Student Achievement: The Importance of Stable Student Attributes

ERIC Educational Resources Information Center

Marks, Gary N.

2016-01-01

Multi-domain and longitudinal studies of student achievement routinely find moderate to strong correlations across achievement domains and even stronger within-domain correlations over time. The purpose of this study is to examine the sources of these patterns analysing student achievement in 5 domains across Years 3, 5 and 7. The analysis is of…

Linking Semantic and Knowledge Representations in a Multi-Domain Dialogue System

DTIC Science & Technology

2007-06-01

accuracy evaluation presented in the next section shows that the generic version of the grammar performs similarly well on two evaluation domains...of extra insertions; for example, discourse adverbials such as now were inserted if present in the lattice. In addition, different tense and pronoun...automatic lexicon specialization technique improves parser speed and accuracy. 1 Introduction This paper presents an architecture of a language

IMPLICATIONS OF CROSS DOMAIN FIRES IN MULTI-DOMAIN BATTLE

DTIC Science & Technology

2017-04-06

States Air Force 6 April 2017 DISTRIBUTION A. Approved for public release: distribution unlimited. 1 DISCLAIMER The views expressed in this...their cyber capability that will ultimately reinforce their influence and power across the Middle East. In viewing North Korea threat capabilities...land-based assets operating in cross domain denial type operations. In viewing the historical warfare capabilities captured in 13 the case study

A Lattice-Boltzmann model to simulate diffractive nonlinear ultrasound beam propagation in a dissipative fluid medium

NASA Astrophysics Data System (ADS)

Abdi, Mohamad; Hajihasani, Mojtaba; Gharibzadeh, Shahriar; Tavakkoli, Jahan

2012-12-01

Ultrasound waves have been widely used in diagnostic and therapeutic medical applications. Accurate and effective simulation of ultrasound beam propagation and its interaction with tissue has been proved to be important. The nonlinear nature of the ultrasound beam propagation, especially in the therapeutic regime, plays an important role in the mechanisms of interaction with tissue. There are three main approaches in current computational fluid dynamics (CFD) methods to model and simulate nonlinear ultrasound beams: macroscopic, mesoscopic and microscopic approaches. In this work, a mesoscopic CFD method based on the Lattice-Boltzmann model (LBM) was investigated. In the developed method, the Boltzmann equation is evolved to simulate the flow of a Newtonian fluid with the collision model instead of solving the Navier-Stokes, continuity and state equations which are used in conventional CFD methods. The LBM has some prominent advantages over conventional CFD methods, including: (1) its parallel computational nature; (2) taking microscopic boundaries into account; and (3) capability of simulating in porous and inhomogeneous media. In our proposed method, the propagating medium is discretized with a square grid in 2 dimensions with 9 velocity vectors for each node. Using the developed model, the nonlinear distortion and shock front development of a finiteamplitude diffractive ultrasonic beam in a dissipative fluid medium was computed and validated against the published data. The results confirm that the LBM is an accurate and effective approach to model and simulate nonlinearity in finite-amplitude ultrasound beams with Mach numbers of up to 0.01 which, among others, falls within the range of therapeutic ultrasound regime such as high intensity focused ultrasound (HIFU) beams. A comparison between the HIFU nonlinear beam simulations using the proposed model and pseudospectral methods in a 2D geometry is presented.

Dynamic Modeling of the Madison Dynamo Experiment

NASA Astrophysics Data System (ADS)

Truitt, J. L.; Forest, C. B.; Wright, J. C.

1999-11-01

This work focuses on a computer simulation of the Magnetohydrodynamic equations applied in the geometry of the Madison Dynamo Experiemnt. An integration code is used to evolve both the magnetic field and the velocity field numerically in spherical coordinates using a pseudo-spectral algorithm. The focus is to realistically model an experiment to be undertaken by the Madison Dynamo Experiment Group. The first flows studied are the well documented ones of Dudley and James. The main goals of the simulation are to observe the dynamo effect with the back-reaction allowed, to observe the equipartition of magnetic and kinetic energy due to theoretically proposed turbulent effects, and to isolate and study the α and β effects.

A High-Order Finite Spectral Volume Method for Conservation Laws on Unstructured Grids

NASA Technical Reports Server (NTRS)

Wang, Z. J.; Liu, Yen; Kwak, Dochan (Technical Monitor)

2001-01-01

A time accurate, high-order, conservative, yet efficient method named Finite Spectral Volume (FSV) is developed for conservation laws on unstructured grids. The concept of a 'spectral volume' is introduced to achieve high-order accuracy in an efficient manner similar to spectral element and multi-domain spectral methods. In addition, each spectral volume is further sub-divided into control volumes (CVs), and cell-averaged data from these control volumes is used to reconstruct a high-order approximation in the spectral volume. Riemann solvers are used to compute the fluxes at spectral volume boundaries. Then cell-averaged state variables in the control volumes are updated independently. Furthermore, TVD (Total Variation Diminishing) and TVB (Total Variation Bounded) limiters are introduced in the FSV method to remove/reduce spurious oscillations near discontinuities. A very desirable feature of the FSV method is that the reconstruction is carried out only once, and analytically, and is the same for all cells of the same type, and that the reconstruction stencil is always non-singular, in contrast to the memory and CPU-intensive reconstruction in a high-order finite volume (FV) method. Discussions are made concerning why the FSV method is significantly more efficient than high-order finite volume and the Discontinuous Galerkin (DG) methods. Fundamental properties of the FSV method are studied and high-order accuracy is demonstrated for several model problems with and without discontinuities.

Sharing clinical information across care settings: the birth of an integrated assessment system

PubMed Central

Gray, Leonard C; Berg, Katherine; Fries, Brant E; Henrard, Jean-Claude; Hirdes, John P; Steel, Knight; Morris, John N

2009-01-01

Background Population ageing, the emergence of chronic illness, and the shift away from institutional care challenge conventional approaches to assessment systems which traditionally are problem and setting specific. Methods From 2002, the interRAI research collaborative undertook development of a suite of assessment tools to support assessment and care planning of persons with chronic illness, frailty, disability, or mental health problems across care settings. The suite constitutes an early example of a "third generation" assessment system. Results The rationale and development strategy for the suite is described, together with a description of potential applications. To date, ten instruments comprise the suite, each comprising "core" items shared among the majority of instruments and "optional" items that are specific to particular care settings or situations. Conclusion This comprehensive suite offers the opportunity for integrated multi-domain assessment, enabling electronic clinical records, data transfer, ease of interpretation and streamlined training. PMID:19402891

Multimodel methods for optimal control of aeroacoustics.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Guoquan; Collis, Samuel Scott

2005-01-01

A new multidomain/multiphysics computational framework for optimal control of aeroacoustic noise has been developed based on a near-field compressible Navier-Stokes solver coupled with a far-field linearized Euler solver both based on a discontinuous Galerkin formulation. In this approach, the coupling of near- and far-field domains is achieved by weakly enforcing continuity of normal fluxes across a coupling surface that encloses all nonlinearities and noise sources. For optimal control, gradient information is obtained by the solution of an appropriate adjoint problem that involves the propagation of adjoint information from the far-field to the near-field. This computational framework has been successfully appliedmore » to study optimal boundary-control of blade-vortex interaction, which is a significant noise source for helicopters on approach to landing. In the model-problem presented here, the noise propagated toward the ground is reduced by 12dB.« less

Modular assembly of proteins on nanoparticles.

PubMed

Ma, Wenwei; Saccardo, Angela; Roccatano, Danilo; Aboagye-Mensah, Dorothy; Alkaseem, Mohammad; Jewkes, Matthew; Di Nezza, Francesca; Baron, Mark; Soloviev, Mikhail; Ferrari, Enrico

2018-04-16

Generally, the high diversity of protein properties necessitates the development of unique nanoparticle bio-conjugation methods, optimized for each different protein. Here we describe a universal bio-conjugation approach which makes use of a new recombinant fusion protein combining two distinct domains. The N-terminal part is Glutathione S-Transferase (GST) from Schistosoma japonicum, for which we identify and characterize the remarkable ability to bind gold nanoparticles (GNPs) by forming gold-sulfur bonds (Au-S). The C-terminal part of this multi-domain construct is the SpyCatcher from Streptococcus pyogenes, which provides the ability to capture recombinant proteins encoding a SpyTag. Here we show that SpyCatcher can be immobilized covalently on GNPs through GST without the loss of its full functionality. We then show that GST-SpyCatcher activated particles are able to covalently bind a SpyTag modified protein by simple mixing, through the spontaneous formation of an unusual isopeptide bond.

Numerical investigation of heat transfer on film-cooled turbine blades.

PubMed

Ginibre, P; Lefebvre, M; Liamis, N

2001-05-01

The accurate heat transfer prediction of film-cooled blades is a key issue for the aerothermal turbine design. For this purpose, advanced numerical methods have been developed at Snecma Moteurs. The goal of this paper is the assessment of a three-dimensional Navier-Stokes solver, based on the ONERA CANARI-COMET code, devoted to the steady aerothermal computations of film-cooled blades. The code uses a multidomain approach to discretize the blade to blade channel with overlapping structured meshes for the injection holes. The turbulence closure is done by means of either Michel mixing length model or Spalart-Allmaras one transport equation model. Computations of thin 3D slices of three film-cooled nozzle guide vane blades with multiple injections are performed. Aerothermal predictions are compared to experiments carried out by the von Karman Institute. The behavior of the turbulence models is discussed, and velocity and temperature injection profiles are investigated.

A Summary Score for the Framingham Heart Study Neuropsychological Battery

PubMed Central

Downer, Brian; Fardo, David W.; Schmitt, Frederick A.

2015-01-01

Objective To calculate three summary scores of the Framingham Heart Study neuropsychological battery and determine which score best differentiates between subjects classified as having normal cognition, test-based impaired learning and memory, test-based multidomain impairment, and dementia. Method The final sample included 2,503 participants. Three summary scores were assessed: (a) composite score that provided equal weight to each subtest, (b) composite score that provided equal weight to each cognitive domain assessed by the neuropsychological battery, and (c) abbreviated score comprised of subtests for learning and memory. Receiver operating characteristic analysis was used to determine which summary score best differentiated between the four cognitive states. Results The summary score that provided equal weight to each subtest best differentiated between the four cognitive states. Discussion A summary score that provides equal weight to each subtest is an efficient way to utilize all of the cognitive data collected by a neuropsychological battery. PMID:25804903

Determination of the rotational diffusion tensor of macromolecules in solution from nmr relaxation data with a combination of exact and approximate methods--application to the determination of interdomain orientation in multidomain proteins.

PubMed

Ghose, R; Fushman, D; Cowburn, D

2001-04-01

In this paper we present a method for determining the rotational diffusion tensor from NMR relaxation data using a combination of approximate and exact methods. The approximate method, which is computationally less intensive, computes values of the principal components of the diffusion tensor and estimates the Euler angles, which relate the principal axis frame of the diffusion tensor to the molecular frame. The approximate values of the principal components are then used as starting points for an exact calculation by a downhill simplex search for the principal components of the tensor over a grid of the space of Euler angles relating the diffusion tensor frame to the molecular frame. The search space of Euler angles is restricted using the tensor orientations calculated using the approximate method. The utility of this approach is demonstrated using both simulated and experimental relaxation data. A quality factor that determines the extent of the agreement between the measured and predicted relaxation data is provided. This approach is then used to estimate the relative orientation of SH3 and SH2 domains in the SH(32) dual-domain construct of Abelson kinase complexed with a consolidated ligand. Copyright 2001 Academic Press.

The Combat Cloud: Enabling Multi-Domain Command and Control Across the Range of Military Operations

DTIC Science & Technology

2017-03-01

and joint by their very nature.3 The Combat Cloud architecture will enable MDC2 by increasing the interoperability of existing networks...order to provide operating platforms with a robust architecture that communicates with relevant players, operates at reduced levels of connectivity...responsibility or aircraft platform, and a Combat Cloud architecture helps focus thought toward achieving efficient MDC2 and effects rather than

Infusion of Autologous Lysed Plasma Into the Baboon: Assessment of Coagulation, Platelet, and Pulmonary Function

DTIC Science & Technology

1993-06-03

obtained from whole blood collected into a commercially available tube containing thrombin and epsilon aminocaproic acid (Wellcome 44 Diagnostics...first proposed by Hall & Slayter in 1959 as an extended, multidomained molecule. Electron microscopy, amino acid sequencing and proteolytic studies have...Plasminogen (Figure 7) is a single chain, 88 kilodalton glycoprotein. It contains 790 amino acids , 24 disulfide bridges and five homologous triple loop

Problems With Deployment of Multi-Domained, Multi-Homed Mobile Networks

NASA Technical Reports Server (NTRS)

Ivancic, William D.

2008-01-01

This document describes numerous problems associated with deployment of multi-homed mobile platforms consisting of multiple networks and traversing large geographical areas. The purpose of this document is to provide insight to real-world deployment issues and provide information to groups that are addressing many issues related to multi-homing, policy-base routing, route optimization and mobile security - particularly those groups within the Internet Engineering Task Force.

Numerical simulation using vorticity-vector potential formulation

NASA Technical Reports Server (NTRS)

Tokunaga, Hiroshi

1993-01-01

An accurate and efficient computational method is needed for three-dimensional incompressible viscous flows in engineering applications. On solving the turbulent shear flows directly or using the subgrid scale model, it is indispensable to resolve the small scale fluid motions as well as the large scale motions. From this point of view, the pseudo-spectral method is used so far as the computational method. However, the finite difference or the finite element methods are widely applied for computing the flow with practical importance since these methods are easily applied to the flows with complex geometric configurations. However, there exist several problems in applying the finite difference method to direct and large eddy simulations. Accuracy is one of most important problems. This point was already addressed by the present author on the direct simulations on the instability of the plane Poiseuille flow and also on the transition to turbulence. In order to obtain high efficiency, the multi-grid Poisson solver is combined with the higher-order, accurate finite difference method. The formulation method is also one of the most important problems in applying the finite difference method to the incompressible turbulent flows. The three-dimensional Navier-Stokes equations have been solved so far in the primitive variables formulation. One of the major difficulties of this method is the rigorous satisfaction of the equation of continuity. In general, the staggered grid is used for the satisfaction of the solenoidal condition for the velocity field at the wall boundary. However, the velocity field satisfies the equation of continuity automatically in the vorticity-vector potential formulation. From this point of view, the vorticity-vector potential method was extended to the generalized coordinate system. In the present article, we adopt the vorticity-vector potential formulation, the generalized coordinate system, and the 4th-order accurate difference method as the computational method. We present the computational method and apply the present method to computations of flows in a square cavity at large Reynolds number in order to investigate its effectiveness.

The development of efficient numerical time-domain modeling methods for geophysical wave propagation

NASA Astrophysics Data System (ADS)

Zhu, Lieyuan

This Ph.D. dissertation focuses on the numerical simulation of geophysical wave propagation in the time domain including elastic waves in solid media, the acoustic waves in fluid media, and the electromagnetic waves in dielectric media. This thesis shows that a linear system model can describe accurately the physical processes of those geophysical waves' propagation and can be used as a sound basis for modeling geophysical wave propagation phenomena. The generalized stability condition for numerical modeling of wave propagation is therefore discussed in the context of linear system theory. The efficiency of a series of different numerical algorithms in the time-domain for modeling geophysical wave propagation are discussed and compared. These algorithms include the finite-difference time-domain method, pseudospectral time domain method, alternating directional implicit (ADI) finite-difference time domain method. The advantages and disadvantages of these numerical methods are discussed and the specific stability condition for each modeling scheme is carefully derived in the context of the linear system theory. Based on the review and discussion of these existing approaches, the split step, ADI pseudospectral time domain (SS-ADI-PSTD) method is developed and tested for several cases. Moreover, the state-of-the-art stretched-coordinate perfect matched layer (SCPML) has also been implemented in SS-ADI-PSTD algorithm as the absorbing boundary condition for truncating the computational domain and absorbing the artificial reflection from the domain boundaries. After algorithmic development, a few case studies serve as the real-world examples to verify the capacities of the numerical algorithms and understand the capabilities and limitations of geophysical methods for detection of subsurface contamination. The first case is a study using ground penetrating radar (GPR) amplitude variation with offset (AVO) for subsurface non-aqueous-liquid (NAPL) contamination. The numerical AVO study reveals that the normalized residual polarization (NRP) variation with offset does not respond to subsurface NAPL existence when the offset is close to or larger than its critical value (which corresponds to critical incident angle) because the air and head waves dominate the recorded wave field and severely interfere with reflected waves in the TEz wave field. Thus it can be concluded that the NRP AVO/GPR method is invalid when source-receiver angle offset is close to or greater than its critical value due to incomplete and severely distorted reflection information. In other words, AVO is not a promising technique for detection of the subsurface NAPL, as claimed by some researchers. In addition, the robustness of the newly developed numerical algorithms is also verified by the AVO study for randomly-arranged layered media. Meanwhile, this case study also demonstrates again that the full-wave numerical modeling algorithms are superior to ray tracing method. The second case study focuses on the effect of the existence of a near-surface fault on the vertically incident P- and S- plane waves. The modeling results show that both P-wave vertical incidence and S-wave vertical incidence cases are qualified fault indicators. For the plane S-wave vertical incidence case, the horizontal location of the upper tip of the fault (the footwall side) can be identified without much effort, because all the recorded parameters on the surface including the maximum velocities and the maximum accelerations, and even their ratios H/V, have shown dramatic changes when crossing the upper tip of the fault. The centers of the transition zone of the all the curves of parameters are almost directly above the fault tip (roughly the horizontal center of the model). Compared with the case of the vertically incident P-wave source, it has been found that the S-wave vertical source is a better indicator for fault location, because the horizontal location of the tip of that fault cannot be clearly identified with the ratio of the horizontal to vertical velocity for the P-wave incident case.

A multidomain fusion protein in Listeria monocytogenes catalyzes the two primary activities for glutathione biosynthesis.

PubMed

Gopal, Shubha; Borovok, Ilya; Ofer, Amos; Yanku, Michaela; Cohen, Gerald; Goebel, Werner; Kreft, Jürgen; Aharonowitz, Yair

2005-06-01

Glutathione is the predominant low-molecular-weight peptide thiol present in living organisms and plays a key role in protecting cells against oxygen toxicity. Until now, glutathione synthesis was thought to occur solely through the consecutive action of two physically separate enzymes, gamma-glutamylcysteine ligase and glutathione synthetase. In this report we demonstrate that Listeria monocytogenes contains a novel multidomain protein (termed GshF) that carries out complete synthesis of glutathione. Evidence for this comes from experiments which showed that in vitro recombinant GshF directs the formation of glutathione from its constituent amino acids and the in vivo effect of a mutation in GshF that abolishes glutathione synthesis, results in accumulation of the intermediate gamma-glutamylcysteine, and causes hypersensitivity to oxidative agents. We identified GshF orthologs, consisting of a gamma-glutamylcysteine ligase (GshA) domain fused to an ATP-grasp domain, in 20 gram-positive and gram-negative bacteria. Remarkably, 95% of these bacteria are mammalian pathogens. A plausible origin for GshF-dependent glutathione biosynthesis in these bacteria was the recruitment by a GshA ancestor gene of an ATP-grasp gene and the subsequent spread of the fusion gene between mammalian hosts, most likely by horizontal gene transfer.

Comparative Study of Lectin Domains in Model Species: New Insights into Evolutionary Dynamics

PubMed Central

Van Holle, Sofie; De Schutter, Kristof; Eggermont, Lore; Tsaneva, Mariya; Dang, Liuyi; Van Damme, Els J. M.

2017-01-01

Lectins are present throughout the plant kingdom and are reported to be involved in diverse biological processes. In this study, we provide a comparative analysis of the lectin families from model species in a phylogenetic framework. The analysis focuses on the different plant lectin domains identified in five representative core angiosperm genomes (Arabidopsis thaliana, Glycine max, Cucumis sativus, Oryza sativa ssp. japonica and Oryza sativa ssp. indica). The genomes were screened for genes encoding lectin domains using a combination of Basic Local Alignment Search Tool (BLAST), hidden Markov models, and InterProScan analysis. Additionally, phylogenetic relationships were investigated by constructing maximum likelihood phylogenetic trees. The results demonstrate that the majority of the lectin families are present in each of the species under study. Domain organization analysis showed that most identified proteins are multi-domain proteins, owing to the modular rearrangement of protein domains during evolution. Most of these multi-domain proteins are widespread, while others display a lineage-specific distribution. Furthermore, the phylogenetic analyses reveal that some lectin families evolved to be similar to the phylogeny of the plant species, while others share a closer evolutionary history based on the corresponding protein domain architecture. Our results yield insights into the evolutionary relationships and functional divergence of plant lectins. PMID:28587095

Spin-Hall magnetoresistance in multidomain helical spiral systems

NASA Astrophysics Data System (ADS)

Aqeel, A.; Mostovoy, M.; van Wees, B. J.; Palstra, T. T. M.

2017-05-01

We study the spin-Hall magnetoresistance (SMR) in multidomain helical spiral magnet Cu2OSeO{{}3}| Pt heterostructures. We compare the SMR response of Cu2OSeO3 at 5 K, when the magnetic domains are almost frozen, to that at elevated temperatures, when domain walls move easily. At 5 K the SMR amplitude vanishes at low applied magnetic fields, while at 50 K it does not. This phenomenon can be explained by the effect of the magnetic field on the domain structure of Cu2OSeO3. At elevated temperatures the system can reach the thermodynamic equilibrium state, in which a single domain that has a minimal energy for a given field direction occupies the whole sample and gives rise to a nonzero SMR signal. In contrast at 5 K, the three types of domains with mutually orthogonal spiral wave vectors have equal volumes independent of the field direction, which leads to the cancellation of the SMR signal at low fields. In the single-domain conical spiral and collinear ferrimagnetic states, the angular and field dependence of the SMR is found to be same at all temperatures (T≤slant 50 K). This behavior can be understood within the framework of the SMR theory developed for collinear magnets.

Effects of Cognitive Training on Resting-State Functional Connectivity of Default Mode, Salience, and Central Executive Networks.

PubMed

Cao, Weifang; Cao, Xinyi; Hou, Changyue; Li, Ting; Cheng, Yan; Jiang, Lijuan; Luo, Cheng; Li, Chunbo; Yao, Dezhong

2016-01-01

Neuroimaging studies have documented that aging can disrupt certain higher cognitive systems such as the default mode network (DMN), the salience network and the central executive network (CEN). The effect of cognitive training on higher cognitive systems remains unclear. This study used a 1-year longitudinal design to explore the cognitive training effect on three higher cognitive networks in healthy older adults. The community-living healthy older adults were divided into two groups: the multi-domain cognitive training group (24 sessions of cognitive training over a 3-months period) and the wait-list control group. All subjects underwent cognitive measurements and resting-state functional magnetic resonance imaging scanning at baseline and at 1 year after the training ended. We examined training-related changes in functional connectivity (FC) within and between three networks. Compared with the baseline, we observed maintained or increased FC within all three networks after training. The scans after training also showed maintained anti-correlation of FC between the DMN and CEN compared to the baseline. These findings demonstrated that cognitive training maintained or improved the functional integration within networks and the coupling between the DMN and CEN in older adults. Our findings suggested that multi-domain cognitive training can mitigate the aging-related dysfunction of higher cognitive networks.

Complete stress-induced depolarization of relaxor ferroelectric crystals without transition through a non-polar phase

NASA Astrophysics Data System (ADS)

Shkuratov, Sergey I.; Baird, Jason; Antipov, Vladimir G.; Hackenberger, Wesley; Luo, Jun; Zhang, Shujun; Lynch, Christopher S.; Chase, Jay B.; Jo, Hwan R.; Roberts, Christopher C.

2018-03-01

The development of relaxor ferroelectric single crystal technology is driven by the ability to tailor ferroelectric properties through domain engineering not achievable in polycrystalline materials. In this study, three types of domain-engineered rhombohedral Pb(In1/2Nb1/2)O3-Pb(Mg1/3Nb2/3)O3-PbTiO3 crystals were subjected to transverse high strain rate loading. The experimental results indicate that the domain configuration has a significant effect on the stress-induced depolarization and the associated charge released. A complete depolarization of the single-domain crystals with 3m symmetry is observed, while multidomain crystals with 4mm and mm2 symmetries retain a fraction of their initial remanent polarization. The complete depolarization of single-domain crystals is unique without transition to a non-polar phase, with a stress-induced charge density of 0.48 C/m2. This is up to three times higher than that of the multidomain crystals and PbZrxTi1-xO3 ferroelectric ceramics that are critical for ultrahigh-power transducer applications. The main offering of this work is to propose a detailed mechanism for complete stress-induced depolarization in ferroelectric crystals which does not involve an intermediate transformation to a non-polar phase.

Structural Biology of Non-Ribosomal Peptide Synthetases

PubMed Central

Miller, Bradley R.; Gulick, Andrew M.

2016-01-01

Summary The non-ribosomal peptide synthetases are modular enzymes that catalyze synthesis of important peptide products from a variety of standard and non-proteinogenic amino acid substrates. Within a single module are multiple catalytic domains that are responsible for incorporation of a single residue. After the amino acid is activated and covalently attached to an integrated carrier protein domain, the substrates and intermediates are delivered to neighboring catalytic domains for peptide bond formation or, in some modules, chemical modification. In the final module, the peptide is delivered to a terminal thioesterase domain that catalyzes release of the peptide product. This multi-domain modular architecture raises questions about the structural features that enable this assembly line synthesis in an efficient manner. The structures of the core component domains have been determined and demonstrate insights into the catalytic activity. More recently, multi-domain structures have been determined and are providing clues to the features of these enzyme systems that govern the functional interaction between multiple domains. This chapter describes the structures of NRPS proteins and the strategies that are being used to assist structural studies of these dynamic proteins, including careful consideration of domain boundaries for generation of truncated proteins and the use of mechanism-based inhibitors that trap interactions between the catalytic and carrier protein domains. PMID:26831698

Selectivity of arsenite interaction with zinc finger proteins.

PubMed

Zhao, Linhong; Chen, Siming; Jia, Liangyuan; Shu, Shi; Zhu, Pingping; Liu, Yangzhong

2012-08-01

Arsenic is a carcinogenic element also used for the treatment of acute promyelocytic leukemia. The reactivity of proteins to arsenic must be associated with the various biological functions of As. Here, we investigated the selectivity of arsenite to zinc finger proteins (ZFPs) with different zinc binding motifs (C2H2, C3H, and C4). Single ZFP domain proteins were used for the direct comparison of the reactivity of different ZFPs. The binding constants and the reaction rates have been studied quantitatively. Results show that both the binding affinity and reaction rates of single-domain ZFPs follow the trend of C4 > C3H ≫ C2H2. Compared with the C2H2 motif ZFPs, the binding affinities of C3H and C4 motif ZFPs are nearly two orders of magnitude higher and the reaction rates are approximately two-fold higher. The formation of multi-domain ZFPs significantly enhances the reactivity of C2H2 type ZFPs, but has negligible effects on C3H and C4 ZFPs. Consequently, the reactivities of the three types of multi-domain ZFPs are rather similar. The 2D NMR spectra indicate that the As(III)-bound ZFPs are also unfolded, suggesting that arsenic binding interferes with the function of ZFPs.

The role of internal duplication in the evolution of multi-domain proteins.

PubMed

Nacher, J C; Hayashida, M; Akutsu, T

2010-08-01

Many proteins consist of several structural domains. These multi-domain proteins have likely been generated by selective genome growth dynamics during evolution to perform new functions as well as to create structures that fold on a biologically feasible time scale. Domain units frequently evolved through a variety of genetic shuffling mechanisms. Here we examine the protein domain statistics of more than 1000 organisms including eukaryotic, archaeal and bacterial species. The analysis extends earlier findings on asymmetric statistical laws for proteome to a wider variety of species. While proteins are composed of a wide range of domains, displaying a power-law decay, the computation of domain families for each protein reveals an exponential distribution, characterizing a protein universe composed of a thin number of unique families. Structural studies in proteomics have shown that domain repeats, or internal duplicated domains, represent a small but significant fraction of genome. In spite of its importance, this observation has been largely overlooked until recently. We model the evolutionary dynamics of proteome and demonstrate that these distinct distributions are in fact rooted in an internal duplication mechanism. This process generates the contemporary protein structural domain universe, determines its reduced thickness, and tames its growth. These findings have important implications, ranging from protein interaction network modeling to evolutionary studies based on fundamental mechanisms governing genome expansion.

Effects of Cognitive Training on Resting-State Functional Connectivity of Default Mode, Salience, and Central Executive Networks

PubMed Central

Cao, Weifang; Cao, Xinyi; Hou, Changyue; Li, Ting; Cheng, Yan; Jiang, Lijuan; Luo, Cheng; Li, Chunbo; Yao, Dezhong

2016-01-01

Neuroimaging studies have documented that aging can disrupt certain higher cognitive systems such as the default mode network (DMN), the salience network and the central executive network (CEN). The effect of cognitive training on higher cognitive systems remains unclear. This study used a 1-year longitudinal design to explore the cognitive training effect on three higher cognitive networks in healthy older adults. The community-living healthy older adults were divided into two groups: the multi-domain cognitive training group (24 sessions of cognitive training over a 3-months period) and the wait-list control group. All subjects underwent cognitive measurements and resting-state functional magnetic resonance imaging scanning at baseline and at 1 year after the training ended. We examined training-related changes in functional connectivity (FC) within and between three networks. Compared with the baseline, we observed maintained or increased FC within all three networks after training. The scans after training also showed maintained anti-correlation of FC between the DMN and CEN compared to the baseline. These findings demonstrated that cognitive training maintained or improved the functional integration within networks and the coupling between the DMN and CEN in older adults. Our findings suggested that multi-domain cognitive training can mitigate the aging-related dysfunction of higher cognitive networks. PMID:27148042

Expression of the Acidothermus cellulolyticus E1 endoglucanase in Caldicellulosiruptor bescii enhances its ability to deconstruct crystalline cellulose

DOE PAGES

Chung, Daehwan; Young, Jenna; Cha, Minseok; ...

2015-08-13

The Caldicellulosiruptor bescii genome encodes a potent set of carbohydrate-active enzymes (CAZymes), found primarily as multi-domain enzymes that exhibit high cellulolytic and hemicellulolytic activity on and allow utilization of a broad range of substrates, including plant biomass without conventional pretreatment. CelA, the most abundant cellulase in the C. bescii secretome, uniquely combines a GH9 endoglucanase and a GH48 exoglucanase in one protein. The most effective commercial enzyme cocktails used in vitro to pretreat biomass are derived from fungal cellulases (cellobiohydrolases, endoglucanases and a β-d-glucosidases) that act synergistically to release sugars for microbial conversion. The C. bescii genome contains six GH5more » domains in five different open reading frames. Four exist in multi-domain proteins and two as single catalytic domains. E1 is a GH5 endoglucanase reported to have high specific activity and simple architecture and is active at the growth temperature of C. bescii. E1 is an endo-1,4-β-glucanase linked to a family 2 carbohydrate-binding module shown to bind primarily to cellulosic substrates. As a result, we tested if the addition of this protein to the C. bescii secretome would improve its cellulolytic activity.« less

A multi-objective optimization approach accurately resolves protein domain architectures

PubMed Central

Bernardes, J.S.; Vieira, F.R.J.; Zaverucha, G.; Carbone, A.

2016-01-01

Motivation: Given a protein sequence and a number of potential domains matching it, what are the domain content and the most likely domain architecture for the sequence? This problem is of fundamental importance in protein annotation, constituting one of the main steps of all predictive annotation strategies. On the other hand, when potential domains are several and in conflict because of overlapping domain boundaries, finding a solution for the problem might become difficult. An accurate prediction of the domain architecture of a multi-domain protein provides important information for function prediction, comparative genomics and molecular evolution. Results: We developed DAMA (Domain Annotation by a Multi-objective Approach), a novel approach that identifies architectures through a multi-objective optimization algorithm combining scores of domain matches, previously observed multi-domain co-occurrence and domain overlapping. DAMA has been validated on a known benchmark dataset based on CATH structural domain assignments and on the set of Plasmodium falciparum proteins. When compared with existing tools on both datasets, it outperforms all of them. Availability and implementation: DAMA software is implemented in C++ and the source code can be found at http://www.lcqb.upmc.fr/DAMA. Contact: juliana.silva_bernardes@upmc.fr or alessandra.carbone@lip6.fr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26458889

Numerical Simulation of Strong Ground Motion at Mexico City:A Hybrid Approach for Efficient Evaluation of Site Amplification and Path Effects for Different Types of Earthquakes

NASA Astrophysics Data System (ADS)

Cruz, H.; Furumura, T.; Chavez-Garcia, F. J.

2002-12-01

The estimation of scenarios of the strong ground motions caused by future great earthquakes is an important problem in strong motion seismology. This was pointed out by the great 1985 Michoacan earthquake, which caused a great damage in Mexico City, 300 km away from the epicenter. Since the seismic wavefield is characterized by the source, path and site effects, the pattern of strong motion damage from different types of earthquakes should differ significantly. In this study, the scenarios for intermediate-depth normal-faulting, shallow-interplate thrust faulting, and crustal earthquakes have been estimated using a hybrid simulation technique. The character of the seismic wavefield propagating from the source to Mexico City for each earthquake was first calculated using the pseudospectral method for 2D SH waves. The site amplifications in the shallow structure of Mexico City are then calculated using the multiple SH wave reverberation theory. The scenarios of maximum ground motion for both inslab and interplate earthquakes obtained by the simulation show a good agreement with the observations. This indicates the effectiveness of the hybrid simulation approach to investigate the strong motion damage for future earthquakes.

A first-order k-space model for elastic wave propagation in heterogeneous media.

PubMed

Firouzi, K; Cox, B T; Treeby, B E; Saffari, N

2012-09-01

A pseudospectral model of linear elastic wave propagation is described based on the first order stress-velocity equations of elastodynamics. k-space adjustments to the spectral gradient calculations are derived from the dyadic Green's function solution to the second-order elastic wave equation and used to (a) ensure the solution is exact for homogeneous wave propagation for timesteps of arbitrarily large size, and (b) also allows larger time steps without loss of accuracy in heterogeneous media. The formulation in k-space allows the wavefield to be split easily into compressional and shear parts. A perfectly matched layer (PML) absorbing boundary condition was developed to effectively impose a radiation condition on the wavefield. The staggered grid, which is essential for accurate simulations, is described, along with other practical details of the implementation. The model is verified through comparison with exact solutions for canonical examples and further examples are given to show the efficiency of the method for practical problems. The efficiency of the model is by virtue of the reduced point-per-wavelength requirement, the use of the fast Fourier transform (FFT) to calculate the gradients in k space, and larger time steps made possible by the k-space adjustments.

Simulations of thermal Rayleigh-Marangoni convection in a three-layer liquid-metal-battery model

NASA Astrophysics Data System (ADS)

Köllner, Thomas; Boeck, Thomas; Schumacher, Jörg

2017-11-01

Operating a liquid-metal battery produces Ohmic losses in the electrolyte layer that separates both metal electrodes. As a consequence, temperature gradients establish which potentially cause thermal convection since density and interfacial tension depend on the local temperature. In our numerical investigations, we considered three plane, immiscible layers governed by the Navier-Stokes-Boussinesq equations held at a constant temperature of 500°C at the bottom and top. A homogeneous current is applied that leads to a preferential heating of the mid electrolyte layer. We chose a typical material combination of Li separated by LiCl-KCl (a molten salt) from Pb-Bi for which we analyzed the linear stability of pure thermal conduction and performed three-dimensional direct-numerical simulations by a pseudospectral method probing different: electrolyte layer heights, overall heights, and current densities. Four instability mechanisms are identified, which are partly coupled to each other: buoyant convection in the upper electrode, buoyant convection in the molten salt layer, and Marangoni convection at both interfaces between molten salt and electrode. The global turbulent heat transfer follows scaling predictions for internally heated buoyant convection. Financial support by the Deutsche Forschungsgemeinschaft under Grant No. KO 5515/1-1 is gratefully acknowledged.

Direct numerical simulation of incompressible acceleration-driven variable-density turbulence

NASA Astrophysics Data System (ADS)

Gat, Ilana; Matheou, Georgios; Chung, Daniel; Dimotakis, Paul

2015-11-01

Fully developed turbulence in variable-density flow driven by an externally imposed acceleration field, e.g., gravity, is fundamental in many applications, such as inertial confinement fusion, geophysics, and astrophysics. Aspects of this turbulence regime are poorly understood and are of interest to fluid modeling. We investigate incompressible acceleration-driven variable-density turbulence by a series of direct numerical simulations of high-density fluid in-between slabs of low-density fluid, in a triply-periodic domain. A pseudo-spectral numerical method with a Helmholtz-Hodge decomposition of the pressure field, which ensures mass conservation, is employed, as documented in Chung & Pullin (2010). A uniform dynamic viscosity and local Schmidt number of unity are assumed. This configuration encapsulates a combination of flow phenomena in a temporally evolving variable-density shear flow. Density ratios up to 10 and Reynolds numbers in the fully developed turbulent regime are investigated. The temporal evolution of the vertical velocity difference across the shear layer, shear-layer growth, mean density, and Reynolds number are discussed. Statistics of Lagrangian accelerations of fluid elements and of vorticity as a function of the density ratio are also presented. This material is based upon work supported by the AFOSR, the DOE, the NSF GRFP, and Caltech.

Semi-Numerical Studies of the Three-Meter Spherical Couette Experiment Utilizing Data Assimilation

NASA Astrophysics Data System (ADS)

Burnett, S. C.; Rojas, R.; Perevalov, A.; Lathrop, D. P.

2017-12-01

The model of the Earth's magnetic field has been investigated in recent years through experiments and numerical models. At the University of Maryland, experimental studies are implemented in a three-meter spherical Couette device filled with liquid sodium. The inner and outer spheres of this apparatus mimic the planet's inner core and core-mantle boundary, respectively. These experiments incorporate high velocity flows with Reynolds numbers 108. In spherical Couette geometry, the numerical scheme applied to this work features finite difference methods in the radial direction and pseudospectral spherical harmonic transforms elsewhere [Schaeffer, N. G3 (2013)]. Adding to the numerical model, data assimilation integrates the experimental outer-layer magnetic field measurements. This semi-numerical model can then be compared to the experimental results as well as forecasting magnetic field changes. Data assimilation makes it possible to get estimates of internal motions of the three-meter experiment that would otherwise be intrusive or impossible to obtain in experiments or too computationally expensive with a purely numerical code. If we can provide accurate models of the three-meter device, it is possible to attempt to model the geomagnetic field. We gratefully acknowledge the support of NSF Grant No. EAR1417148 & DGE1322106.

Semi-Numerical Studies of the Three-Meter Spherical Couette Experiment Utilizing Data Assimilation

NASA Astrophysics Data System (ADS)

Burnett, Sarah; Rojas, Ruben; Perevalov, Artur; Lathrop, Daniel; Ide, Kayo; Schaeffer, Nathanael

2017-11-01

The model of the Earth's magnetic field has been investigated in recent years through experiments and numerical models. At the University of Maryland, experimental studies are implemented in a three-meter spherical Couette device filled with liquid sodium. The inner and outer spheres of this apparatus mimic the planet's inner core and core-mantle boundary, respectively. These experiments incorporate high velocity flows with Reynolds numbers 108 . In spherical Couette geometry, the numerical scheme applied to this work features finite difference methods in the radial direction and pseudospectral spherical harmonic transforms elsewhere. Adding to the numerical model, data assimilation integrates the experimental outer-layer magnetic field measurements. This semi-numerical model can then be compared to the experimental results as well as forecasting magnetic field changes. Data assimilation makes it possible to get estimates of internal motions of the three-meter experiment that would otherwise be intrusive or impossible to obtain in experiments or too computationally expensive with a purely numerical code. If we can provide accurate models of the three-meter device, it is possible to attempt to model the geomagnetic field. We gratefully acknowledge the support of NSF Grant No. EAR1417148 & DGE1322106.

Onset of natural convection in a continuously perturbed system

NASA Astrophysics Data System (ADS)

Ghorbani, Zohreh; Riaz, Amir

2017-11-01

The convective mixing triggered by gravitational instability plays an important role in CO2 sequestration in saline aquifers. The linear stability analysis and the numerical simulation concerning convective mixing in porous media requires perturbations of small amplitude to be imposed on the concentration field in the form of an initial shape function. In aquifers, however, the instability is triggered by local porosity and permeability. In this work, we consider a canonical 2D homogeneous system where perturbations arise due to spatial variation of porosity in the system. The advantage of this approach is not only the elimination of the required initial shape function, but it also serves as a more realistic approach. Using a reduced nonlinear method, we first explore the effect of harmonic variations of porosity in the transverse and streamwise direction on the onset time of convection and late time behavior. We then obtain the optimal porosity structure that minimizes the convection onset. We further examine the effect of a random porosity distribution, that is independent of the spatial mode of porosity structure, on the convection onset. Using high-order pseudospectral DNS, we explore how the random distribution differs from the modal approach in predicting the onset time.

Coupling mesodomain positional ordering to intra-domain orientational ordering in block copolymer assembly

NASA Astrophysics Data System (ADS)

Burke, Christopher; Reddy, Abhiram; Prasad, Ishan; Grason, Gregory

Block copolymer (BCP) melts form a number of symmetric microphases, e.g. columnar or double gyroid phases. BCPs with a block composed of chiral monomers are observed to form bulk phases with broken chiral symmetry e.g. a phase of hexagonally ordered helical mesodomains. Other new structures may be possible, e.g. double gyroid with preferred chirality which has potential photonic applications. One approach to understanding chirality transfer from monomer to the bulk is to use self consistent field theory (SCFT) and incorporate an orientational order parameter with a preference for handed twist in chiral block segments, much like the texture of cholesteric liquid crystal. Polymer chains in achiral BCPs exhibit orientational ordering which couples to the microphase geometry; a spontaneous preference for ordering may have an effect on the geometry. The influence of a preference for chiral polar (vectorial) segment order has been studied to some extent, though the influence of coupling to chiral tensorial (nematic) order has not yet been developed. We present a computational approach using SCFT with vector and tensor order which employs well developed pseudo-spectral methods. Using this we explore how tensor order influences which structures form, and if it can promote chiral phases.

Geometrical effects on western intensification of wind-driven ocean currents: The rotated-channel Stommel model, coastal orientation, and curvature

NASA Astrophysics Data System (ADS)

Boyd, John P.; Sanjaya, Edwin

2014-03-01

We revisit early models of steady western boundary currents [Gulf Stream, Kuroshio, etc.] to explore the role of irregular coastlines on jets, both to advance the research frontier and to illuminate for education. In the framework of a steady-state, quasigeostrophic model with viscosity, bottom friction and nonlinearity, we prove that rotating a straight coastline, initially parallel to the meridians, significantly thickens the western boundary layer. We analyze an infinitely long, straight channel with arbitrary orientation and bottom friction using an exact solution and singular perturbation theory, and show that the model, though simpler than Stommel's, nevertheless captures both the western boundary jet (“Gulf Stream”) and the “orientation effect”. In the rest of the article, we restrict attention to the Stommel flow (that is, linear and inviscid except for bottom friction) and apply matched asymptotic expansions, radial basis function, Fourier-Chebyshev and Chebyshev-Chebyshev pseudospectral methods to explore the effects of coastal geometry in a variety of non-rectangular domains bounded by a circle, parabolas and squircles. Although our oceans are unabashedly idealized, the narrow spikes, broad jets and stationary points vividly illustrate the power and complexity of coastal control of western boundary layers.

Extreme multiplicity in cylindrical Rayleigh-Bénard convection. II. Bifurcation diagram and symmetry classification

NASA Astrophysics Data System (ADS)

Borońska, Katarzyna; Tuckerman, Laurette S.

2010-03-01

A large number of flows with distinctive patterns have been observed in experiments and simulations of Rayleigh-Bénard convection in a water-filled cylinder whose radius is twice the height. We have adapted a time-dependent pseudospectral code, first, to carry out Newton’s method and branch continuation and, second, to carry out the exponential power method and Arnoldi iteration to calculate leading eigenpairs and determine the stability of the steady states. The resulting bifurcation diagram represents a compromise between the tendency in the bulk toward parallel rolls and the requirement imposed by the boundary conditions that primary bifurcations be toward states whose azimuthal dependence is trigonometric. The diagram contains 17 branches of stable and unstable steady states. These can be classified geometrically as roll states containing two, three, and four rolls; axisymmetric patterns with one or two tori; threefold-symmetric patterns called Mercedes, Mitsubishi, marigold, and cloverleaf; trigonometric patterns called dipole and pizza; and less symmetric patterns called CO and asymmetric three rolls. The convective branches are connected to the conductive state and to each other by 16 primary and secondary pitchfork bifurcations and turning points. In order to better understand this complicated bifurcation diagram, we have partitioned it according to azimuthal symmetry. We have been able to determine the bifurcation-theoretic origin from the conductive state of all the branches observed at high Rayleigh number.

Safe landing area determination for a Moon lander by reachability analysis

NASA Astrophysics Data System (ADS)

Arslantaş, Yunus Emre; Oehlschlägel, Thimo; Sagliano, Marco

2016-11-01

In the last decades developments in space technology paved the way to more challenging missions like asteroid mining, space tourism and human expansion into the Solar System. These missions result in difficult tasks such as guidance schemes for re-entry, landing on celestial bodies and implementation of large angle maneuvers for spacecraft. There is a need for a safety system to increase the robustness and success of these missions. Reachability analysis meets this requirement by obtaining the set of all achievable states for a dynamical system starting from an initial condition with given admissible control inputs of the system. This paper proposes an algorithm for the approximation of nonconvex reachable sets (RS) by using optimal control. Therefore subset of the state space is discretized by equidistant points and for each grid point a distance function is defined. This distance function acts as an objective function for a related optimal control problem (OCP). Each infinite dimensional OCP is transcribed into a finite dimensional Nonlinear Programming Problem (NLP) by using Pseudospectral Methods (PSM). Finally, the NLPs are solved using available tools resulting in approximated reachable sets with information about the states of the dynamical system at these grid points. The algorithm is applied on a generic Moon landing mission. The proposed method computes approximated reachable sets and the attainable safe landing region with information about propellant consumption and time.

Assessment of topsoil contamination near the Stanisław Siedlecki Polish Polar Station in Hornsund, Svalbard, using magnetic methods

NASA Astrophysics Data System (ADS)

Gonet, T.; Górka-Kostrubiec, B.; Łuczak-Wilamowska, B.

2018-03-01

Topsoil contamination near the Stanisław Siedlecki Polish Polar Station (PPS), Hornsund, Svalbard, has been assessed using magnetic methods supplemented by chemical analyses and microscopic observations. Analysis of magnetic parameters has enabled to evaluate the concentration, magnetic mineralogy, and grain-size distribution of anthropogenic magnetic particles. Heavy-metal contamination near the PPS originates primarily from local sources. Anthropogenic spherical, magnetite-like particles were found near the station, whereas uncontaminated topsoil is devoid of such particles. Magnetic studies indicate that magnetite and goethite are the primary magnetic phases, with magnetite levels being higher in polluted area. Magnetic fraction of contaminated topsoil includes a mixture of single-domain and multi-domain grains, while uncontaminated topsoil contains smaller grains. Results show a clear correspondence between Pollution Load Index and magnetic susceptibility anomalies, and that the areal extent of PPS impact on the environment has not expanded significantly since 2004 (although a new contamination source, the scrap yard, is now present). A comparison of magnetic susceptibility measurements with metal analyses indicates that magnetic methods can be used as a rapid, inexpensive, non-invasive, and sensitive tool for the evaluation of topsoil contamination.

A 2 year multidomain intervention of diet, exercise, cognitive training, and vascular risk monitoring versus control to prevent cognitive decline in at-risk elderly people (FINGER): a randomised controlled trial.

PubMed

Ngandu, Tiia; Lehtisalo, Jenni; Solomon, Alina; Levälahti, Esko; Ahtiluoto, Satu; Antikainen, Riitta; Bäckman, Lars; Hänninen, Tuomo; Jula, Antti; Laatikainen, Tiina; Lindström, Jaana; Mangialasche, Francesca; Paajanen, Teemu; Pajala, Satu; Peltonen, Markku; Rauramaa, Rainer; Stigsdotter-Neely, Anna; Strandberg, Timo; Tuomilehto, Jaakko; Soininen, Hilkka; Kivipelto, Miia

2015-06-06

Modifiable vascular and lifestyle-related risk factors have been associated with dementia risk in observational studies. In the Finnish Geriatric Intervention Study to Prevent Cognitive Impairment and Disability (FINGER), a proof-of-concept randomised controlled trial, we aimed to assess a multidomain approach to prevent cognitive decline in at-risk elderly people from the general population. In a double-blind randomised controlled trial we enrolled individuals aged 60-77 years recruited from previous national surveys. Inclusion criteria were CAIDE (Cardiovascular Risk Factors, Aging and Dementia) Dementia Risk Score of at least 6 points and cognition at mean level or slightly lower than expected for age. We randomly assigned participants in a 1:1 ratio to a 2 year multidomain intervention (diet, exercise, cognitive training, vascular risk monitoring), or a control group (general health advice). Computer-generated allocation was done in blocks of four (two individuals randomly allocated to each group) at each site. Group allocation was not actively disclosed to participants and outcome assessors were masked to group allocation. The primary outcome was change in cognition as measured through comprehensive neuropsychological test battery (NTB) Z score. Analysis was by modified intention to treat (all participants with at least one post-baseline observation). This trial is registered at ClinicalTrials.gov, number NCT01041989. Between Sept 7, 2009, and Nov 24, 2011, we screened 2654 individuals and randomly assigned 1260 to the intervention group (n=631) or control group (n=629). 591 (94%) participants in the intervention group and 599 (95%) in the control group had at least one post-baseline assessment and were included in the modified intention-to-treat analysis. Estimated mean change in NTB total Z score at 2 years was 0·20 (SE 0·02, SD 0·51) in the intervention group and 0·16 (0·01, 0·51) in the control group. Between-group difference in the change of NTB total score per year was 0·022 (95% CI 0·002-0·042, p=0·030). 153 (12%) individuals dropped out overall. Adverse events occurred in 46 (7%) participants in the intervention group compared with six (1%) participants in the control group; the most common adverse event was musculoskeletal pain (32 [5%] individuals for intervention vs no individuals for control). Findings from this large, long-term, randomised controlled trial suggest that a multidomain intervention could improve or maintain cognitive functioning in at-risk elderly people from the general population. Academy of Finland, La Carita Foundation, Alzheimer Association, Alzheimer's Research and Prevention Foundation, Juho Vainio Foundation, Novo Nordisk Foundation, Finnish Social Insurance Institution, Ministry of Education and Culture, Salama bint Hamdan Al Nahyan Foundation, Axa Research Fund, EVO funding for University Hospitals of Kuopio, Oulu, and Turku and for Seinäjoki Central Hospital and Oulu City Hospital, Swedish Research Council, Swedish Research Council for Health, Working Life and Welfare, and af Jochnick Foundation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Controlled phase evolution and the occurrence of single domain CoFe2O4 nanoparticles synthesized by PVA assisted sol-gel method

NASA Astrophysics Data System (ADS)

Srinivasa Rao, K.; Ranga Nayakulu, S. V.; Chaitanya Varma, M.; Choudary, G. S. V. R. K.; Rao, K. H.

2018-04-01

The present investigation describes the development of cobalt ferrite nanoparticles having size less than 10 nm, by a sol-gel method using polyvinyl alcohol as chelating agent. X-ray results show all the samples, annealed above 700 °C have spinel structure. The information about phase evolution with reaction temperatures was obtained by subjecting the as-prepared powder for DSC/TGA study. High saturation magnetization of 84.63 emu/g has been observed for a particle size of 8.1 nm, a rare event reported till date. The dM/dH versus H curves suggest that the transition from single domain state to multi-domain state occurs with increasing annealing temperature and the critical size for the single domain nature of CoFe2O4 is around 6.5 nm. The estimated critical diameter for single domain particle (6.7 nm) is in good agreement with that (6.5 nm) obtained from Transmission Electron Micrographs. The highest coercivity (1645 Oe) has been found for a particle of size 6.5 nm.

Proof of Concept Integration of a Single-Level Service-Oriented Architecture into a Multi-Domain Secure Environment

DTIC Science & Technology

2008-03-01

Machine [29]. OC4J applications support Java Servlets , Web services, and the following J2EE specific standards: Extensible Markup Language (XML...IMAP Internet Message Access Protocol IP Internet Protocol IT Information Technology xviii J2EE Java Enterprise Environment JSR 168 Java ...LDAP), World Wide Web Distributed Authoring and Versioning (WebDav), Java Specification Request 168 (JSR 168), and Web Services for Remote

Landmine Warfare in Support of Multi-domain Battle: Balancing Discrimination and Military Effectiveness

DTIC Science & Technology

2017-05-25

Combat Team CCW Convention on Certain Conventional Weapons CTC Combat Training Center EMS Electro- Magnetic Spectrum FASCAM Family of...of a person or vehicle .”13 In the immediate aftermath of WWII, the economy of force, counter- mobility, and protection functions of landmines were...threat posed by the Soviet Union and the need for discrimination in the employment of persistent landmines by organizing them into well-marked fields

Toward Multi-Domain Battle: Combined Arms Precedents to Inform Today’s Joint Force

DTIC Science & Technology

2017-03-31

of war. Americans brought about several technical and operational innovations that supported the strategic bombing campaign. Combined-Systems...defense, strategic bombing , and amphibious warfare as examples of “combined-systems revolutions.”’8 Each of these innovations took decades to develop... bombing , and amphibious warfare, each of the interwar combined- system revolutions identified by Watts and Murray, are examples of the type of cross- domain

Determination of the Rotational Diffusion Tensor of Macromolecules in Solution from NMR Relaxation Data with a Combination of Exact and Approximate Methods—Application to the Determination of Interdomain Orientation in Multidomain Proteins

NASA Astrophysics Data System (ADS)

Ghose, Ranajeet; Fushman, David; Cowburn, David

2001-04-01

In this paper we present a method for determining the rotational diffusion tensor from NMR relaxation data using a combination of approximate and exact methods. The approximate method, which is computationally less intensive, computes values of the principal components of the diffusion tensor and estimates the Euler angles, which relate the principal axis frame of the diffusion tensor to the molecular frame. The approximate values of the principal components are then used as starting points for an exact calculation by a downhill simplex search for the principal components of the tensor over a grid of the space of Euler angles relating the diffusion tensor frame to the molecular frame. The search space of Euler angles is restricted using the tensor orientations calculated using the approximate method. The utility of this approach is demonstrated using both simulated and experimental relaxation data. A quality factor that determines the extent of the agreement between the measured and predicted relaxation data is provided. This approach is then used to estimate the relative orientation of SH3 and SH2 domains in the SH(32) dual-domain construct of Abelson kinase complexed with a consolidated ligand.

Noniterative accurate algorithm for the exact exchange potential of density-functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cinal, M.; Holas, A.

2007-10-15

An algorithm for determination of the exchange potential is constructed and tested. It represents a one-step procedure based on the equations derived by Krieger, Li, and Iafrate (KLI) [Phys. Rev. A 46, 5453 (1992)], implemented already as an iterative procedure by Kuemmel and Perdew [Phys. Rev. Lett. 90, 043004 (2003)]. Due to suitable transformation of the KLI equations, we can solve them avoiding iterations. Our algorithm is applied to the closed-shell atoms, from Be up to Kr, within the DFT exchange-only approximation. Using pseudospectral techniques for representing orbitals, we obtain extremely accurate values of total and orbital energies with errorsmore » at least four orders of magnitude smaller than known in the literature.« less

Route to chaos in porous-medium thermal convection

NASA Astrophysics Data System (ADS)

Kimura, S.; Schubert, G.; Straus, J. M.

1986-05-01

The transition to chaos in two-dimensional single-cell time-dependent convection in a square cross section of porous material saturated with fluid and heated from below is investigated theoretically by means of pseudospectral numerical simulations. The results are presented graphically and discussed in terms of the time-averaged Nusselt number, the oscillation mechanism, and similarities to Hele-Shaw convection. As the Rayleigh number (R) increases, the system is found to proceed from the steady state to a simply periodic state, a quasi-periodic state with two basic frequencies, a second simply periodic state, and finally to chaos. The transitions occur at R = 4 pi squared, 380-400, 500-520, 560-570, and 850-1000. The intermediate and chaotic regimes are characterized in detail.

AxiSEM3D: a new fast method for global wave propagation in 3-D Earth models with undulating discontinuities

NASA Astrophysics Data System (ADS)

Leng, K.; Nissen-Meyer, T.; van Driel, M.; Al-Attar, D.

2016-12-01

We present a new, computationally efficient numerical method to simulate global seismic wave propagation in realistic 3-D Earth models with laterally heterogeneous media and finite boundary perturbations. Our method is a hybrid of pseudo-spectral and spectral element methods (SEM). We characterize the azimuthal dependence of 3-D wavefields in terms of Fourier series, such that the 3-D equations of motion reduce to an algebraic system of coupled 2-D meridional equations, which can be solved by a 2-D spectral element method (based on www.axisem.info). Computational efficiency of our method stems from lateral smoothness of global Earth models (with respect to wavelength) as well as axial singularity of seismic point sources, which jointly confine the Fourier modes of wavefields to a few lower orders. All boundary perturbations that violate geometric spherical symmetry, including Earth's ellipticity, topography and bathymetry, undulations of internal discontinuities such as Moho and CMB, are uniformly considered by means of a Particle Relabeling Transformation.The MPI-based high performance C++ code AxiSEM3D, is now available for forward simulations upon 3-D Earth models with fluid outer core, ellipticity, and both mantle and crustal structures. We show novel benchmarks for global wave solutions in 3-D mantle structures between our method and an independent, fully discretized 3-D SEM with remarkable agreement. Performance comparisons are carried out on three state-of-the-art tomography models, with seismic period going down to 5s. It is shown that our method runs up to two orders of magnitude faster than the 3-D SEM for such settings, and such computational advantage scales favourably with seismic frequency. By examining wavefields passing through hypothetical Gaussian plumes of varying sharpness, we identify in model-wavelength space the limits where our method may lose its advantage.

Rational design of fiber forming supramolecular structures

PubMed Central

Wang, Benjamin K; Kanahara, Satoko M

2016-01-01

Recent strides in the development of multifunctional synthetic biomimetic materials through the self-assembly of multi-domain peptides and proteins over the past decade have been realized. Such engineered systems have wide-ranging application in bioengineering and medicine. This review focuses on fundamental fiber forming α-helical coiled-coil peptides, peptide amphiphiles, and amyloid-based self-assembling peptides; followed by higher order collagen- and elastin-mimetic peptides with an emphasis on chemical / biological characterization and biomimicry. PMID:27022140

Structure of PA1221, a nonribosomal peptide synthetase containing adenylation and peptidyl carrier protein domains.

PubMed

Mitchell, Carter A; Shi, Ce; Aldrich, Courtney C; Gulick, Andrew M

2012-04-17

Many bacteria use large modular enzymes for the synthesis of polyketide and peptide natural products. These multidomain enzymes contain integrated carrier domains that deliver bound substrates to multiple catalytic domains, requiring coordination of these chemical steps. Nonribosomal peptide synthetases (NRPSs) load amino acids onto carrier domains through the activity of an upstream adenylation domain. Our lab recently determined the structure of an engineered two-domain NRPS containing fused adenylation and carrier domains. This structure adopted a domain-swapped dimer that illustrated the interface between these two domains. To continue our investigation, we now examine PA1221, a natural two-domain protein from Pseudomonas aeruginosa. We have determined the amino acid specificity of this new enzyme and used domain specific mutations to demonstrate that loading the downstream carrier domain within a single protein molecule occurs more quickly than loading of a nonfused carrier domain intermolecularly. Finally, we have determined crystal structures of both apo- and holo-PA1221 proteins, the latter using a valine-adenosine vinylsulfonamide inhibitor that traps the adenylation domain-carrier domain interaction. The protein adopts an interface similar to that seen with the prior adenylation domain-carrier protein construct. A comparison of these structures with previous structures of multidomain NRPSs suggests that a large conformational change within the NRPS adenylation domains guides the carrier domain into the active site for thioester formation.

Toward a modular multi-material nanoparticle synthesis and assembly strategy via bionanocombinatorics: bifunctional peptides for linking Au and Ag nanomaterials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Briggs, Beverly D.; Palafox-Hernandez, J. Pablo; Li, Yue

Materials-binding peptides represent a unique avenue towards controlling the shape and size of nanoparticles (NPs) grown under aqueous conditions. Here, employing a bionanocombinatorics approach, two such materials-binding peptides were linked at either end of a photoswitchable spacer, forming a multi-domain materials-binding molecule to control the in situ synthesis and organization of Ag and Au NPs under ambient conditions. These multi-domain molecules retained the peptides’ ability to nucleate, grow, and stabilize Ag and Au NPs in aqueous media. Disordered co-assemblies of the two nanomaterials were observed by TEM imaging of dried samples after sequential growth of the two metals, and showedmore » a clustering behavior that was not observed without both metals and the linker molecules. While TEM evidence indicated the formation of AuNP/AgNP assemblies upon drying, SAXS analysis indicated that no extended assemblies existed in solution, suggesting that sample drying plays an important role in facilitating NP clustering. Molecular simulations and experimental data revealed tunable materials-binding based upon the isomerization state of the photoswitchable unit and metal employed. This work is a first step in generating externally actuated biomolecules with specific material-binding properties that could be used as the building blocks to achieve multi-material switchable NP assemblies.« less

Two-Step Self-Assembly of Liposome-Multidomain Peptide Nanofiber Hydrogel for Time-Controlled Release

PubMed Central

2015-01-01

Progress in self-assembly and supramolecular chemistry has been directed toward obtaining macromolecular assemblies with higher degrees of complexity, simulating the highly structured environment in natural systems. One approach to this type of complexity are multistep, multicomponent, self-assembling systems that allow approaches comparable to traditional multistep synthetic organic chemistry; however, only a few examples of this approach have appeared in the literature. Our previous work demonstrated nanofibrous mimics of the extracellular matrix. Here we demonstrate the ability to create a unique hydrogel, developed by stepwise self-assembly of multidomain peptide fibers and liposomes. The two-component system allows for controlled release of bioactive factors at multiple time points. The individual components of the self-assembled gel and the composite hydrogel were characterized by TEM, SEM, and rheometry, demonstrating that peptide nanofibers and lipid vesicles both retain their structural integrity in the composite gel. The rheological robustness of the hydrogel is shown to be largely unaffected by the presence of liposomes. Release studies from the composite gels loaded with different growth factors EGF, MCP-1, and PlGF-1 showed delay and prolongation of release by liposomes entrapped in the hydrogel compared to more rapid release from the hydrogel alone. This bimodal release system may have utility in systems where timed cascades of biological signals may be valuable, such as in tissue regeneration. PMID:25308335

Functional neuroanatomical associations of working memory in early-onset Alzheimer's disease.

PubMed

Kobylecki, Christopher; Haense, Cathleen; Harris, Jennifer M; Stopford, Cheryl L; Segobin, Shailendra H; Jones, Matthew; Richardson, Anna M T; Gerhard, Alexander; Anton-Rodriguez, José; Thompson, Jennifer C; Herholz, Karl; Snowden, Julie S

2018-01-01

To characterize metabolic correlates of working memory impairment in clinically defined subtypes of early-onset Alzheimer's disease. Established models of working memory suggest a key role for frontal lobe function, yet the association in Alzheimer's disease between working memory impairment and visuospatial and language symptoms suggests that temporoparietal neocortical dysfunction may be responsible. Twenty-four patients with predominantly early-onset Alzheimer's disease were clinically classified into groups with predominantly amnestic, multidomain or visual deficits. Patients underwent neuropsychological evaluation focused on the domains of episodic and working memory, T1-weighted magnetic resonance imaging and brain fluorodeoxyglucose positron emission tomography. Fluorodeoxyglucose positron emission tomography data were analysed by using a region-of-interest approach. Patients with multidomain and visual presentations performed more poorly on tests of working memory compared with amnestic Alzheimer's disease. Working memory performance correlated with glucose metabolism in left-sided temporoparietal, but not frontal neocortex. Carriers of the apolipoprotein E4 gene showed poorer episodic memory and better working memory performance compared with noncarriers. Our findings support the hypothesis that working memory changes in early-onset Alzheimer's disease are related to temporoparietal rather than frontal hypometabolism and show dissociation from episodic memory performance. They further support the concept of subtypes of Alzheimer's disease with distinct cognitive profiles due to prominent neocortical dysfunction early in the disease course. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

The role of surface electrostatics on the stability, function and regulation of human cystathionine β-synthase, a complex multidomain and oligomeric protein.

PubMed

Pey, Angel L; Majtan, Tomas; Kraus, Jan P

2014-09-01

Human cystathionine β-synthase (hCBS) is a key enzyme of sulfur amino acid metabolism, controlling the commitment of homocysteine to the transsulfuration pathway and antioxidant defense. Mutations in hCBS cause inherited homocystinuria (HCU), a rare inborn error of metabolism characterized by accumulation of toxic homocysteine in blood and urine. hCBS is a complex multidomain and oligomeric protein whose activity and stability are independently regulated by the binding of S-adenosyl-methionine (SAM) to two different types of sites at its C-terminal regulatory domain. Here we study the role of surface electrostatics on the complex regulation and stability of hCBS using biophysical and biochemical procedures. We show that the kinetic stability of the catalytic and regulatory domains is significantly affected by the modulation of surface electrostatics through noticeable structural and energetic changes along their denaturation pathways. We also show that surface electrostatics strongly affect SAM binding properties to those sites responsible for either enzyme activation or kinetic stabilization. Our results provide new insight into the regulation of hCBS activity and stability in vivo with implications for understanding HCU as a conformational disease. We also lend experimental support to the role of electrostatic interactions in the recently proposed binding modes of SAM leading to hCBS activation and kinetic stabilization. Copyright © 2014 Elsevier B.V. All rights reserved.

Determination of magnetic domain state of carbon coated iron nanoparticles via 57Fe zero-external-field NMR

NASA Astrophysics Data System (ADS)

Manjunatha, M.; Kumar, Rajeev; Sahoo, Balaram; Damle, Ramakrishna; Ramesh, K. P.

2018-05-01

The magnetic domain state of carbon coated iron nanopowder (Fe@C) was studied by the internal field nuclear magnetic resonance (IFNMR) at 77 K using the spin echo technique. The structure and magnetic properties of the sample were further characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), Mössbauer spectroscopy, vibrating sample magnetometry (VSM), thermogravimetric analysis (TGA) and Raman Spectroscopy. The obtained IFNMR results of Fe@C powder were compared with that of micron sized carbonyl iron (CI) and electrolytic iron (EI) powders. The calculated critical size of the single domain iron particles in Fe@C is ∼ 16 nm. A higher enhancement in echo amplitude was observed due to better response of the domain walls of multidomain particles in comparison to the single domain particles. The echo signal of CI and EI particles exhibit a single narrow intense peak corresponding to the domain walls, whereas Fe@C exhibits two low amplitude peaks at two different frequencies: a low frequency (46.6 MHz) peak corresponds to the response of the domain walls of the multidomain particles and the other high frequency (47.2 MHz) signal (a shoulder) corresponding to the response of the magnetic nuclei inside the domain. Our results help in determining the domain state of iron-based magnetic particles using 57Fe-IFNMR.

Cracking up (and down): Linking multi-domain hydraulic properties with multi-scale hydrological processes in shrink-swell soils

NASA Astrophysics Data System (ADS)

Stewart, R. D.; Rupp, D. E.; Abou Najm, M. R.; Selker, J. S.

2017-12-01

Shrink-swell soils, often classified as Vertisols or vertic intergrades, are found on every continent except Antarctica and within many agricultural and urban regions. These soils are characterized by cyclical shrinking and swelling, in which bulk density and porosity distributions vary as functions of time and soil moisture. Crack networks that form in these soils act as dominant environmental controls on the movement of water, contaminants, and gases, making it important to develop fundamental understanding and tractable models of their hydrologic characteristics and behaviors. In this study, which took place primarily in the Secano Interior region of South-Central Chile, we quantified soil-water interactions across scales using a diverse and innovative dataset. These measurements were then utilized to develop a set of parsimonious multi-domain models for describing hydraulic properties and hydrological processes in shrink-swell soils. In a series of examples, we show how this model can predict porosity distributions, crack widths, saturated hydraulic conductivities, and surface runoff (i.e., overland flow) thresholds, by capturing the dominant mechanisms by which water moves through and interacts with clayey soils. Altogether, these models successfully link small-scale shrinkage/swelling behaviors with large-scale thresholds, and can be applied to describe important processes such as infiltration, overland flow development, and the preferential flow and transport of fluids and gases.

Characterization of STIP, a multi-domain nuclear protein, highly conserved in metazoans, and essential for embryogenesis in Caenorhabditis elegans.

PubMed

Ji, Qiongmei; Huang, Cheng-Han; Peng, Jianbin; Hashmi, Sarwar; Ye, Tianzhang; Chen, Ying

2007-04-15

We report here the identification and characterization of STIP, a multi-domain nuclear protein that contains a G-patch, a coiled-coil, and several short tryptophan-tryptophan repeats highly conserved in metazoan species. To analyze their functional role in vivo, we cloned nematode stip-1 genes and determined the spatiotemporal pattern of Caenorhabditis elegans STIP-1 protein. RNA analyses and Western blots revealed that stip-1 mRNA was produced via trans-splicing and translated as a 95-kDa protein. Using reporter constructs, we found STIP-1 to be expressed at all developmental stages and in many tissue/cell types including worm oocyte nuclei. We found that STIP-1 is targeted to the nucleus and forms large polymers with a rod-like shape when expressed in mammalian cells. Using deletion mutants, we mapped the regions of STIP-1 involved in nuclear import and polymer assembly. We further showed that knockdown of C. elegans stip-1 by RNA interference arrested development and resulted in morphologic abnormalities around the 16-cell stage followed by 100% lethality, suggesting its essential role in worm embryogenesis. Importantly, the embryonic lethal phenotype could be faithfully rescued with Drosophila and human genes via transgenic expression. Our data provide the first direct evidence that STIP have a conserved essential nuclear function across metazoans from worms to humans.

Interplay of Dzyaloshinsky-Moriya and dipole-dipole interactions and their joint effects upon vortical structures on nanodisks

NASA Astrophysics Data System (ADS)

Liu, Zhaosen; Ciftja, Orion; Ian, Hou

2017-06-01

In transition metal oxides, magnetic dipole-dipole (DD) and chiral Dzyaloshinsky-Moriya (DM) interactions between nearest neighboring spins are comparable in magnitude. In particular, the effects of the DD interaction on the physical properties of magnetic nanosystems cannot be simply neglected due to its long-range character. For these reasons, we employed here a new quantum simulation approach in order to investigate the interplay of these two interactions and study their combined effects upon the magnetic vortical structures of monolayer nanodisks. Consequently, we found out from our computational results that, in the presence of Heisenberg exchange interaction, a sufficiently strong DD interaction is also able to induce a single magnetic vortex on a small nanodisk; a strong DM interaction usually gives rise to a multi-domain structure which evolves with changing temperature; In this circumstance, if a weak DD interaction is further considered, the multi-domains merge to form a single vortex in the whole magnetic phase. Moreover, if only the Heisenberg exchange and chiral DM interactions are considered in simulations, our results from calculations with different spin values show that the transition temperature TM is simply proportional to S (S + 1) ; if the temperature is scaled with TM, and the calculated magnetizations are divided by the spin value S, their curves exhibit very similar features in the whole temperature region below TM.

Structural model of the dimeric Parkinson’s protein LRRK2 reveals a compact architecture involving distant interdomain contacts

PubMed Central

Guaitoli, Giambattista; Raimondi, Francesco; Gilsbach, Bernd K.; Gómez-Llorente, Yacob; Deyaert, Egon; Renzi, Fabiana; Li, Xianting; Schaffner, Adam; Jagtap, Pravin Kumar Ankush; Boldt, Karsten; von Zweydorf, Felix; Gotthardt, Katja; Lorimer, Donald D.; Yue, Zhenyu; Burgin, Alex; Janjic, Nebojsa; Sattler, Michael; Versées, Wim; Ueffing, Marius; Ubarretxena-Belandia, Iban; Kortholt, Arjan; Gloeckner, Christian Johannes

2016-01-01

Leucine-rich repeat kinase 2 (LRRK2) is a large, multidomain protein containing two catalytic domains: a Ras of complex proteins (Roc) G-domain and a kinase domain. Mutations associated with familial and sporadic Parkinson’s disease (PD) have been identified in both catalytic domains, as well as in several of its multiple putative regulatory domains. Several of these mutations have been linked to increased kinase activity. Despite the role of LRRK2 in the pathogenesis of PD, little is known about its overall architecture and how PD-linked mutations alter its function and enzymatic activities. Here, we have modeled the 3D structure of dimeric, full-length LRRK2 by combining domain-based homology models with multiple experimental constraints provided by chemical cross-linking combined with mass spectrometry, negative-stain EM, and small-angle X-ray scattering. Our model reveals dimeric LRRK2 has a compact overall architecture with a tight, multidomain organization. Close contacts between the N-terminal ankyrin and C-terminal WD40 domains, and their proximity—together with the LRR domain—to the kinase domain suggest an intramolecular mechanism for LRRK2 kinase activity regulation. Overall, our studies provide, to our knowledge, the first structural framework for understanding the role of the different domains of full-length LRRK2 in the pathogenesis of PD. PMID:27357661

Modelization of highly nonlinear waves in coastal regions

NASA Astrophysics Data System (ADS)

Gouin, Maïté; Ducrozet, Guillaume; Ferrant, Pierre

2015-04-01

The proposed work deals with the development of a highly non-linear model for water wave propagation in coastal regions. The accurate modelization of surface gravity waves is of major interest in ocean engineering, especially in the field of marine renewable energy. These marine structures are intended to be settled in coastal regions where the effect of variable bathymetry may be significant on local wave conditions. This study presents a numerical model for the wave propagation with complex bathymetry. It is based on High-Order Spectral (HOS) method, initially limited to the propagation of non-linear wave fields over flat bottom. Such a model has been developed and validated at the LHEEA Lab. (Ecole Centrale Nantes) over the past few years and the current developments will enlarge its application range. This new numerical model will keep the interesting numerical properties of the original pseudo-spectral approach (convergence, efficiency with the use of FFTs, …) and enable the possibility to propagate highly non-linear wave fields over long time and large distance. Different validations will be provided in addition to the presentation of the method. At first, Bragg reflection will be studied with the proposed approach. If the Bragg condition is satisfied, the reflected wave generated by a sinusoidal bottom patch should be amplified as a result of resonant quadratic interactions between incident wave and bottom. Comparisons will be provided with experiments and reference solutions. Then, the method will be used to consider the transformation of a non-linear monochromatic wave as it propagates up and over a submerged bar. As the waves travel up the front slope of the bar, it steepens and high harmonics are generated due to non-linear interactions. Comparisons with experimental data will be provided. The different test cases will assess the accuracy and efficiency of the method proposed.

Trajectory Optimization: OTIS 4

NASA Technical Reports Server (NTRS)

Riehl, John P.; Sjauw, Waldy K.; Falck, Robert D.; Paris, Stephen W.

2010-01-01

The latest release of the Optimal Trajectories by Implicit Simulation (OTIS4) allows users to simulate and optimize aerospace vehicle trajectories. With OTIS4, one can seamlessly generate optimal trajectories and parametric vehicle designs simultaneously. New features also allow OTIS4 to solve non-aerospace continuous time optimal control problems. The inputs and outputs of OTIS4 have been updated extensively from previous versions. Inputs now make use of objectoriented constructs, including one called a metastring. Metastrings use a greatly improved calculator and common nomenclature to reduce the user s workload. They allow for more flexibility in specifying vehicle physical models, boundary conditions, and path constraints. The OTIS4 calculator supports common mathematical functions, Boolean operations, and conditional statements. This allows users to define their own variables for use as outputs, constraints, or objective functions. The user-defined outputs can directly interface with other programs, such as spreadsheets, plotting packages, and visualization programs. Internally, OTIS4 has more explicit and implicit integration procedures, including high-order collocation methods, the pseudo-spectral method, and several variations of multiple shooting. Users may switch easily between the various methods. Several unique numerical techniques such as automated variable scaling and implicit integration grid refinement, support the integration methods. OTIS4 is also significantly more user friendly than previous versions. The installation process is nearly identical on various platforms, including Microsoft Windows, Apple OS X, and Linux operating systems. Cross-platform scripts also help make the execution of OTIS and post-processing of data easier. OTIS4 is supplied free by NASA and is subject to ITAR (International Traffic in Arms Regulations) restrictions. Users must have a Fortran compiler, and a Python interpreter is highly recommended.

2.5-D poroelastic wave modelling in double porosity media

NASA Astrophysics Data System (ADS)

Liu, Xu; Greenhalgh, Stewart; Wang, Yanghua

2011-09-01

To approximate seismic wave propagation in double porosity media, the 2.5-D governing equations of poroelastic waves are developed and numerically solved. The equations are obtained by taking a Fourier transform in the strike or medium-invariant direction over all of the field quantities in the 3-D governing equations. The new memory variables from the Zener model are suggested as a way to represent the sum of the convolution integrals for both the solid particle velocity and the macroscopic fluid flux in the governing equations. By application of the memory equations, the field quantities at every time step need not be stored. However, this approximation allows just two Zener relaxation times to represent the very complex double porosity and dual permeability attenuation mechanism, and thus reduce the difficulty. The 2.5-D governing equations are numerically solved by a time-splitting method for the non-stiff parts and an explicit fourth-order Runge-Kutta method for the time integration and a Fourier pseudospectral staggered-grid for handling the spatial derivative terms. The 2.5-D solution has the advantage of producing a 3-D wavefield (point source) for a 2-D model but is much more computationally efficient than the full 3-D solution. As an illustrative example, we firstly show the computed 2.5-D wavefields in a homogeneous single porosity model for which we reformulated an analytic solution. Results for a two-layer, water-saturated double porosity model and a laterally heterogeneous double porosity structure are also presented.

Optimal spacecraft formation establishment and reconfiguration propelled by the geomagnetic Lorentz force

NASA Astrophysics Data System (ADS)

Huang, Xu; Yan, Ye; Zhou, Yang

2014-12-01

The Lorentz force acting on an electrostatically charged spacecraft as it moves through the planetary magnetic field could be utilized as propellantless electromagnetic propulsion for orbital maneuvering, such as spacecraft formation establishment and formation reconfiguration. By assuming that the Earth's magnetic field could be modeled as a tilted dipole located at the center of Earth that corotates with Earth, a dynamical model that describes the relative orbital motion of Lorentz spacecraft is developed. Based on the proposed dynamical model, the energy-optimal open-loop trajectories of control inputs, namely, the required specific charges of Lorentz spacecraft, for Lorentz-propelled spacecraft formation establishment or reconfiguration problems with both fixed and free final conditions constraints are derived via Gauss pseudospectral method. The effect of the magnetic dipole tilt angle on the optimal control inputs and the relative transfer trajectories for formation establishment or reconfiguration is also investigated by comparisons with the results derived from a nontilted dipole model. Furthermore, a closed-loop integral sliding mode controller is designed to guarantee the trajectory tracking in the presence of external disturbances and modeling errors. The stability of the closed-loop system is proved by a Lyapunov-based approach. Numerical simulations are presented to verify the validity of the proposed open-loop control methods and demonstrate the performance of the closed-loop controller. Also, the results indicate the dipole tilt angle should be considered when designing control strategies for Lorentz-propelled spacecraft formation establishment or reconfiguration.

Experimental demonstration of OSPF-TE extensions in muiti-domain OBS networks connected by GMPLS network

NASA Astrophysics Data System (ADS)

Tian, Chunlei; Yin, Yawei; Wu, Jian; Lin, Jintong

2008-11-01

The interworking network of Generalized Multi-Protocol Label Switching (GMPLS) and Optical Burst Switching (OBS) is attractive network architecture for the future IP/DWDM network nowadays. In this paper, OSPF-TE extensions for multi-domain Optical Burst Switching networks connected by GMPLS controlled WDM network are proposed, the corresponding experimental results such as the advertising latency are also presented by using an OBS network testbed. The experimental results show that it works effectively on the OBS/GMPLS networks.

The MYSTerious MOZ, a histone acetyltransferase with a key role in haematopoiesis

PubMed Central

Perez-Campo, Flor M; Costa, Guilherme; Lie-a-Ling, Michael; Kouskoff, Valerie; Lacaud, Georges

2013-01-01

The MOnocytic leukaemia Zing finger (MOZ; MYST3 or KAT6A1) gene is frequently found translocated in acute myeloid leukaemia. MOZ encodes a large multidomain protein that contains, besides others, a histone acetyl transferase catalytic domain. Several studies have now established the critical function of MOZ in haematopoiesis. In this review we summarize the recent findings that underscore the relevance of the different biological activities of MOZ in the regulation of haematopoiesis. PMID:23347099

Novel active principles from spider venom.

PubMed

Vassilevski, Alexander A; Grishin, Eugene V

2011-12-01

Spiders are one of the most intriguing groups of venomous animals. Substances found in their venom vary from simple inorganic compounds to large multi-domain proteins. In this article, we review some of the latest work presenting active principles that add to the known spider toxin universe. Two aspects of novelty are addressed in particular, structural (novel types of molecules in terms of structure) and functional (novel types of biological targets hit by substances from spider venom and novel mechanisms of action).

Mapping mechanical force propagation through biomolecular complexes

DOE PAGES

Schoeler, Constantin; Bernardi, Rafael C.; Malinowska, Klara H.; ...

2015-08-11

In this paper, we employ single-molecule force spectroscopy with an atomic force microscope (AFM) and steered molecular dynamics (SMD) simulations to reveal force propagation pathways through a mechanically ultrastable multidomain cellulosome protein complex. We demonstrate a new combination of network-based correlation analysis supported by AFM directional pulling experiments, which allowed us to visualize stiff paths through the protein complex along which force is transmitted. Finally, the results implicate specific force-propagation routes nonparallel to the pulling axis that are advantageous for achieving high dissociation forces.

Stabilization of Taylor-Couette flow due to time-periodic outer cylinder oscillation

NASA Technical Reports Server (NTRS)

Murray, B. T.; Mcfadden, G. B.; Coriell, S. R.

1990-01-01

The linear stability of circular Couette flow between concentric infinite cylinders is considered for the case when the inner cylinder is rotated at a constant angular velocity and the outer cylinder is driven sinusoidally in time with zero mean rotation. This configuration was studied experimentally by Walsh and Donnelly. The critical Reynolds numbers calculated from linear stability theory agree well with the experimental values, except at large modulation amplitudes and small frequencies. The theoretical values are obtained using Floquet theory implemented in two distinct approaches: a truncated Fourier series representation in time, and a fundamental solution matrix based on a Chebyshev pseudospectral representation in space. For large amplitude, low frequency modulation, the linear eigenfunctions are temporally complex, consisting of a quiescent region followed by rapid change in the perturbed flow velocities.

Quantum model of a hysteresis in a single-domain magnetically soft ferromagnetic

NASA Astrophysics Data System (ADS)

Ignatiev, V. K.; Lebedev, N. G.; Orlov, A. A.

2018-01-01

A quantum model of a single-domain magnetically soft ferromagnetic is proposed. The α-Fe crystal in a state of the saturation magnetization and a variable magnetic field is considered as a sample. The method of an effective Hamiltonian, including the operators of the Zeeman energy, the spin-orbit interaction and the interaction with the crystal field, is used in the model. An expansion of trial single-electron wave function in a series in small parameter of the spin-orbit interaction is suggested to account for the magnetic anisotropy. Within the framework of the Heisenberg representation, the nonlinear equations of motion for the magnetization and the orbital moment of single domain are obtained. Parameters of the modelling Hamiltonian are found from a comparison with experimental data on the magnetic anisotropy of iron. A phenomenological term of the magnetic friction is introduced into equation of the magnetization motion. Nonlinear equations are solved numerically by the Runge-Kutta method. A dependence of the single domain magnetization on magnetic field intensity has a characteristic form of a hysteresis loop which parameters are quantitatively coordinated with experimental data of researches of magnetic properties of nanoparticles of iron and iron oxide. The method is extended for modelling the magnetization dynamics of multi-domain ferromagnetic in the approximation of a strong crystal field.

A Non-Invasive NMR Method Based on Histidine Imidazoles to Analyze the pH-Modulation of Protein-Nucleic Acid Interfaces.

PubMed

Cruz-Gallardo, Isabel; Del Conte, Rebecca; Velázquez-Campoy, Adrián; García-Mauriño, Sofía M; Díaz-Moreno, Irene

2015-05-11

A useful (2) J(N-H) coupling-based NMR spectroscopic approach is proposed to unveil, at the molecular level, the contribution of the imidazole groups of histidines from RNA/DNA-binding proteins on the modulation of binding to nucleic acids by pH. Such protonation/deprotonation events have been monitored on the single His96 located at the second RNA/DNA recognition motif (RRM2) of T-cell intracellular antigen-1 (TIA-1) protein. The pKa values of the His96 ionizable groups were substantially higher in the complexes with short U-rich RNA and T-rich DNA oligonucleotides than those of the isolated TIA-1 RRM2. Herein, the methodology applied to determine changes in pKa of histidine side chains upon DNA/RNA binding, gives valuable information to understand the pH effect on multidomain DNA/RNA-binding proteins that shuttle among different cellular compartments. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Particle Deposition in Human Lungs due to Varying Cross-Sectional Ellipticity of Left and Right Main Bronchi

NASA Astrophysics Data System (ADS)

Roth, Steven; Oakes, Jessica; Shadden, Shawn

2015-11-01

Particle deposition in the human lungs can occur with every breathe. Airbourne particles can range from toxic constituents (e.g. tobacco smoke and air pollution) to aerosolized particles designed for drug treatment (e.g. insulin to treat diabetes). The effect of various realistic airway geometries on complex flow structures, and thus particle deposition sites, has yet to be extensively investigated using computational fluid dynamics (CFD). In this work, we created an image-based geometric airway model of the human lung and performed CFD simulations by employing multi-domain methods. Following the flow simulations, Lagrangian particle tracking was used to study the effect of cross-sectional shape on deposition sites in the conducting airways. From a single human lung model, the cross-sectional ellipticity (the ratio of major and minor diameters) of the left and right main bronchi was varied systematically from 2:1 to 1:1. The influence of the airway ellipticity on the surrounding flow field and particle deposition was determined.

Cumulative Disadvantage and Youth Well-Being: A Multi-Domain Examination with Life Course Implications

PubMed Central

Nurius, Paula S.; Prince, Dana M.; Rocha, Anita

2015-01-01

Purpose The accumulation of disadvantage has been shown to increase psychosocial stressors that impact life course well-being. This study tests for significant differences, based on disadvantage exposure, on youths’ emotional and physical health, as well as family supports, peer assets, and academic success, which hold potential for resilience and amelioration of negative health outcomes. Methods A 12 item cumulative disadvantage summed index derived from surveys of a racially and socioeconomically diverse sample of urban high school seniors (n=9,658) was used to distinguish youth at low, moderate, and high levels. Results Findings supported hypothesized stepped patterns such that as multiple disadvantages accumulate, a concomitant decline is evident across the assessed outcome variables (except positive academic identity). Post-hoc tests indicated a pattern of groups being significantly different from one another. Discussion Overall, results lend support for an additive stress load associated with stacked disadvantage, with implications for continuing trends into adulthood as well as preventive interventions PMID:26617431

Theory and simulation of time-fractional fluid diffusion in porous media

NASA Astrophysics Data System (ADS)

Carcione, José M.; Sanchez-Sesma, Francisco J.; Luzón, Francisco; Perez Gavilán, Juan J.

2013-08-01

We simulate a fluid flow in inhomogeneous anisotropic porous media using a time-fractional diffusion equation and the staggered Fourier pseudospectral method to compute the spatial derivatives. A fractional derivative of the order of 0 < ν < 2 replaces the first-order time derivative in the classical diffusion equation. It implies a time-dependent permeability tensor having a power-law time dependence, which describes memory effects and accounts for anomalous diffusion. We provide a complete analysis of the physics based on plane waves. The concepts of phase, group and energy velocities are analyzed to describe the location of the diffusion front, and the attenuation and quality factors are obtained to quantify the amplitude decay. We also obtain the frequency-domain Green function. The time derivative is computed with the Grünwald-Letnikov summation, which is a finite-difference generalization of the standard finite-difference operator to derivatives of fractional order. The results match the analytical solution obtained from the Green function. An example of the pressure field generated by a fluid injection in a heterogeneous sandstone illustrates the performance of the algorithm for different values of ν. The calculation requires storing the whole pressure field in the computer memory since anomalous diffusion ‘recalls the past’.

A flatfile of ground motion intensity measurements from induced earthquakes in Oklahoma and Kansas

USGS Publications Warehouse

Rennolet, Steven B.; Moschetti, Morgan P.; Thompson, Eric M.; Yeck, William

2018-01-01

We have produced a uniformly processed database of orientation-independent (RotD50, RotD100) ground motion intensity measurements containing peak horizontal ground motions (accelerations and velocities) and 5-percent-damped pseudospectral accelerations (0.1–10 s) from more than 3,800 M ≥ 3 earthquakes in Oklahoma and Kansas that occurred between January 2009 and December 2016. Ground motion time series were collected from regional, national, and temporary seismic arrays out to 500 km. We relocated the majority of the earthquake hypocenters using a multiple-event relocation algorithm to produce a set of near-uniformly processed hypocentral locations. Ground motion processing followed standard methods, with the primary objective of reducing the effects of noise on the measurements. Regional wave-propagation features and the high seismicity rate required careful selection of signal windows to ensure that we captured the entire ground motion record and that contaminating signals from extraneous earthquakes did not contribute to the database. Processing was carried out with an automated scheme and resulted in a database comprising more than 174,000 records (https://dx.doi.org/10.5066/F73B5X8N). We anticipate that these results will be useful for improved understanding of earthquake ground motions and for seismic hazard applications.

X-ray solution scattering combined with computation characterizing protein folds and multiple conformational states : computation and application.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, S.; Park, S.; Makowski, L.

Small angle X-ray scattering (SAXS) is an increasingly powerful technique to characterize the structure of biomolecules in solution. We present a computational method for accurately and efficiently computing the solution scattering curve from a protein with dynamical fluctuations. The method is built upon a coarse-grained (CG) representation of the protein. This CG approach takes advantage of the low-resolution character of solution scattering. It allows rapid determination of the scattering pattern from conformations extracted from CG simulations to obtain scattering characterization of the protein conformational landscapes. Important elements incorporated in the method include an effective residue-based structure factor for each aminomore » acid, an explicit treatment of the hydration layer at the surface of the protein, and an ensemble average of scattering from all accessible conformations to account for macromolecular flexibility. The CG model is calibrated and illustrated to accurately reproduce the experimental scattering curve of Hen egg white lysozyme. We then illustrate the computational method by calculating the solution scattering pattern of several representative protein folds and multiple conformational states. The results suggest that solution scattering data, when combined with a reliable computational method, have great potential for a better structural description of multi-domain complexes in different functional states, and for recognizing structural folds when sequence similarity to a protein of known structure is low. Possible applications of the method are discussed.« less

FVCOM one-way and two-way nesting using ESMF: Development and validation

NASA Astrophysics Data System (ADS)

Qi, Jianhua; Chen, Changsheng; Beardsley, Robert C.

2018-04-01

Built on the Earth System Modeling Framework (ESMF), the one-way and two-way nesting methods were implemented into the unstructured-grid Finite-Volume Community Ocean Model (FVCOM). These methods help utilize the unstructured-grid multi-domain nesting of FVCOM with an aim at resolving the multi-scale physical and ecosystem processes. A detail of procedures on implementing FVCOM into ESMF was described. The experiments were made to validate and evaluate the performance of the nested-grid FVCOM system. The first was made for a wave-current interaction case with a two-domain nesting with an emphasis on qualifying a critical need of nesting to resolve a high-resolution feature near the coast and harbor with little loss in computational efficiency. The second was conducted for the pseudo river plume cases to examine the differences in the model-simulated salinity between one-way and two-way nesting approaches and evaluate the performance of mass conservative two-way nesting method. The third was carried out for the river plume case in the realistic geometric domain in Mass Bay, supporting the importance for having the two-way nesting for coastal-estuarine integrated modeling. The nesting method described in this paper has been used in the Northeast Coastal Ocean Forecast System (NECOFS)-a global-regional-coastal nesting FVCOM system that has been placed into the end-to-end forecast and hindcast operations since 2007.

Investigating energy-based pool structure selection in the structure ensemble modeling with experimental distance constraints: The example from a multidomain protein Pub1.

PubMed

Zhu, Guanhua; Liu, Wei; Bao, Chenglong; Tong, Dudu; Ji, Hui; Shen, Zuowei; Yang, Daiwen; Lu, Lanyuan

2018-05-01

The structural variations of multidomain proteins with flexible parts mediate many biological processes, and a structure ensemble can be determined by selecting a weighted combination of representative structures from a simulated structure pool, producing the best fit to experimental constraints such as interatomic distance. In this study, a hybrid structure-based and physics-based atomistic force field with an efficient sampling strategy is adopted to simulate a model di-domain protein against experimental paramagnetic relaxation enhancement (PRE) data that correspond to distance constraints. The molecular dynamics simulations produce a wide range of conformations depicted on a protein energy landscape. Subsequently, a conformational ensemble recovered with low-energy structures and the minimum-size restraint is identified in good agreement with experimental PRE rates, and the result is also supported by chemical shift perturbations and small-angle X-ray scattering data. It is illustrated that the regularizations of energy and ensemble-size prevent an arbitrary interpretation of protein conformations. Moreover, energy is found to serve as a critical control to refine the structure pool and prevent data overfitting, because the absence of energy regularization exposes ensemble construction to the noise from high-energy structures and causes a more ambiguous representation of protein conformations. Finally, we perform structure-ensemble optimizations with a topology-based structure pool, to enhance the understanding on the ensemble results from different sources of pool candidates. © 2018 Wiley Periodicals, Inc.

Structure, dynamics and RNA binding of the multi-domain splicing factor TIA-1

PubMed Central

Wang, Iren; Hennig, Janosch; Jagtap, Pravin Kumar Ankush; Sonntag, Miriam; Valcárcel, Juan; Sattler, Michael

2014-01-01

Alternative pre-messenger ribonucleic acid (pre-mRNA) splicing is an essential process in eukaryotic gene regulation. The T-cell intracellular antigen-1 (TIA-1) is an apoptosis-promoting factor that modulates alternative splicing of transcripts, including the pre-mRNA encoding the membrane receptor Fas. TIA-1 is a multi-domain ribonucleic acid (RNA) binding protein that recognizes poly-uridine tract RNA sequences to facilitate 5′ splice site recognition by the U1 small nuclear ribonucleoprotein (snRNP). Here, we characterize the RNA interaction and conformational dynamics of TIA-1 by nuclear magnetic resonance (NMR), isothermal titration calorimetry (ITC) and small angle X-ray scattering (SAXS). Our NMR-derived solution structure of TIA-1 RRM2–RRM3 (RRM2,3) reveals that RRM2 adopts a canonical RNA recognition motif (RRM) fold, while RRM3 is preceded by an non-canonical helix α0. NMR and SAXS data show that all three RRMs are largely independent structural modules in the absence of RNA, while RNA binding induces a compact arrangement. RRM2,3 binds to pyrimidine-rich FAS pre-mRNA or poly-uridine (U9) RNA with nanomolar affinities. RRM1 has little intrinsic RNA binding affinity and does not strongly contribute to RNA binding in the context of RRM1,2,3. Our data unravel the role of binding avidity and the contributions of the TIA-1 RRMs for recognition of pyrimidine-rich RNAs. PMID:24682828

Negative capacitance in multidomain ferroelectric superlattices

NASA Astrophysics Data System (ADS)

Zubko, Pavlo; Wojdeł, Jacek C.; Hadjimichael, Marios; Fernandez-Pena, Stéphanie; Sené, Anaïs; Luk'Yanchuk, Igor; Triscone, Jean-Marc; Íñiguez, Jorge

2016-06-01

The stability of spontaneous electrical polarization in ferroelectrics is fundamental to many of their current applications, which range from the simple electric cigarette lighter to non-volatile random access memories. Research on nanoscale ferroelectrics reveals that their behaviour is profoundly different from that in bulk ferroelectrics, which could lead to new phenomena with potential for future devices. As ferroelectrics become thinner, maintaining a stable polarization becomes increasingly challenging. On the other hand, intentionally destabilizing this polarization can cause the effective electric permittivity of a ferroelectric to become negative, enabling it to behave as a negative capacitance when integrated in a heterostructure. Negative capacitance has been proposed as a way of overcoming fundamental limitations on the power consumption of field-effect transistors. However, experimental demonstrations of this phenomenon remain contentious. The prevalent interpretations based on homogeneous polarization models are difficult to reconcile with the expected strong tendency for domain formation, but the effect of domains on negative capacitance has received little attention. Here we report negative capacitance in a model system of multidomain ferroelectric-dielectric superlattices across a wide range of temperatures, in both the ferroelectric and paraelectric phases. Using a phenomenological model, we show that domain-wall motion not only gives rise to negative permittivity, but can also enhance, rather than limit, its temperature range. Our first-principles-based atomistic simulations provide detailed microscopic insight into the origin of this phenomenon, identifying the dominant contribution of near-interface layers and paving the way for its future exploitation.

The pretranslocation ribosome is targeted by GTP-bound EF-G in partially activated form

PubMed Central

Hauryliuk, Vasili; Mitkevich, Vladimir A.; Eliseeva, Natalia A.; Petrushanko, Irina Yu.; Ehrenberg, Måns; Makarov, Alexander A.

2008-01-01

Translocation of the tRNA·mRNA complex through the bacterial ribosome is driven by the multidomain guanosine triphosphatase elongation factor G (EF-G). We have used isothermal titration calorimetry to characterize the binding of GDP and GTP to free EF-G at 4°C, 20°C, and 37°C. The binding affinity of EF-G is higher to GDP than to GTP at 4°C, but lower at 37°C. The binding enthalpy and entropy change little with temperature in the case of GDP binding but change greatly in the case of GTP binding. These observations are compatible with a large decrease in the solvent-accessible hydrophobic surface area of EF-G on GTP, but not GDP, binding. The explanation we propose is the locking of the switch 1 and switch 2 peptide loops in the G domain of EF-G to the γ-phosphate of GTP. From these data, in conjunction with previously reported structural data on guanine nucleotide-bound EF-G, we suggest that EF-G enters the pretranslocation ribosome as an “activity chimera,” with the G domain activated by the presence of GTP but the overall factor conformation in the inactive form typical of a GDP-bound multidomain guanosine triphosphatase. We propose that the active overall conformation of EF-G is attained only in complex with the ribosome in its “ratcheted state,” with hybrid tRNA binding sites. PMID:18836081

Differential Evolution and Neofunctionalization of Snake Venom Metalloprotease Domains*

PubMed Central

Brust, Andreas; Sunagar, Kartik; Undheim, Eivind A.B.; Vetter, Irina; Yang, Daryl C.; Casewell, Nicholas R.; Jackson, Timothy N. W.; Koludarov, Ivan; Alewood, Paul F.; Hodgson, Wayne C.; Lewis, Richard J.; King, Glenn F.; Antunes, Agostinho; Hendrikx, Iwan; Fry, Bryan G.

2013-01-01

Snake venom metalloproteases (SVMP) are composed of five domains: signal peptide, propeptide, metalloprotease, disintegrin, and cysteine-rich. Secreted toxins are typically combinatorial variations of the latter three domains. The SVMP-encoding genes of Psammophis mossambicus venom are unique in containing only the signal and propeptide domains. We show that the Psammophis SVMP propeptide evolves rapidly and is subject to a high degree of positive selection. Unlike Psammophis, some species of Echis express both the typical multidomain and the unusual monodomain (propeptide only) SVMP, with the result that a lower level of variation is exerted upon the latter. We showed that most mutations in the multidomain Echis SVMP occurred in the protease domain responsible for proteolytic and hemorrhagic activities. The cysteine-rich and disintegrin-like domains, which are putatively responsible for making the P-III SVMPs more potent than the P-I and P-II forms, accumulate the remaining variation. Thus, the binding sites on the molecule's surface are evolving rapidly whereas the core remains relatively conserved. Bioassays conducted on two post-translationally cleaved novel proline-rich peptides from the P. mossambicus propeptide domain showed them to have been neofunctionalized for specific inhibition of mammalian a7 neuronal nicotinic acetylcholine receptors. We show that the proline rich postsynaptic specific neurotoxic peptides from Azemiops feae are the result of convergent evolution within the precursor region of the C-type natriuretic peptide instead of the SVMP. The results of this study reinforce the value of studying obscure venoms for biodiscovery of novel investigational ligands. PMID:23242553

An overlapping region between the two terminal folding units of the outer surface protein A (OspA) controls its folding behavior.

PubMed

Makabe, Koki; Nakamura, Takashi; Dhar, Debanjan; Ikura, Teikichi; Koide, Shohei; Kuwajima, Kunihiro

2018-04-27

Although many naturally occurring proteins consist of multiple domains, most studies on protein folding to date deal with single-domain proteins or isolated domains of multi-domain proteins. Studies of multi-domain protein folding are required for further advancing our understanding of protein folding mechanisms. Borrelia outer surface protein A (OspA) is a β-rich two-domain protein, in which two globular domains are connected by a rigid and stable single-layer β-sheet. Thus, OspA is particularly suited as a model system for studying the interplays of domains in protein folding. Here, we studied the equilibria and kinetics of the urea-induced folding-unfolding reactions of OspA probed with tryptophan fluorescence and ultraviolet circular dichroism. Global analysis of the experimental data revealed compelling lines of evidence for accumulation of an on-pathway intermediate during kinetic refolding and for the identity between the kinetic intermediate and a previously described equilibrium unfolding intermediate. The results suggest that the intermediate has the fully native structure in the N-terminal domain and the single layer β-sheet, with the C-terminal domain still unfolded. The observation of the productive on-pathway folding intermediate clearly indicates substantial interactions between the two domains mediated by the single-layer β-sheet. We propose that a rigid and stable intervening region between two domains creates an overlap between two folding units and can energetically couple their folding reactions. Copyright © 2018. Published by Elsevier Ltd.

Differential evolution and neofunctionalization of snake venom metalloprotease domains.

PubMed

Brust, Andreas; Sunagar, Kartik; Undheim, Eivind A B; Vetter, Irina; Yang, Daryl C; Yang, Dary C; Casewell, Nicholas R; Jackson, Timothy N W; Koludarov, Ivan; Alewood, Paul F; Hodgson, Wayne C; Lewis, Richard J; King, Glenn F; Antunes, Agostinho; Hendrikx, Iwan; Fry, Bryan G

2013-03-01

Snake venom metalloproteases (SVMP) are composed of five domains: signal peptide, propeptide, metalloprotease, disintegrin, and cysteine-rich. Secreted toxins are typically combinatorial variations of the latter three domains. The SVMP-encoding genes of Psammophis mossambicus venom are unique in containing only the signal and propeptide domains. We show that the Psammophis SVMP propeptide evolves rapidly and is subject to a high degree of positive selection. Unlike Psammophis, some species of Echis express both the typical multidomain and the unusual monodomain (propeptide only) SVMP, with the result that a lower level of variation is exerted upon the latter. We showed that most mutations in the multidomain Echis SVMP occurred in the protease domain responsible for proteolytic and hemorrhagic activities. The cysteine-rich and disintegrin-like domains, which are putatively responsible for making the P-III SVMPs more potent than the P-I and P-II forms, accumulate the remaining variation. Thus, the binding sites on the molecule's surface are evolving rapidly whereas the core remains relatively conserved. Bioassays conducted on two post-translationally cleaved novel proline-rich peptides from the P. mossambicus propeptide domain showed them to have been neofunctionalized for specific inhibition of mammalian a7 neuronal nicotinic acetylcholine receptors. We show that the proline rich postsynaptic specific neurotoxic peptides from Azemiops feae are the result of convergent evolution within the precursor region of the C-type natriuretic peptide instead of the SVMP. The results of this study reinforce the value of studying obscure venoms for biodiscovery of novel investigational ligands.

A paleointensity technique for multidomain igneous rocks

NASA Astrophysics Data System (ADS)

Wang, Huapei; Kent, Dennis V.

2013-10-01

We developed a paleointensity technique to account for concave-up Arai diagrams due to multidomain (MD) contributions to determine unbiased paleointensities for 24 trial samples from site GA-X in Pleistocene lavas from Floreana Island, Galapagos Archipelago. The main magnetization carrier is fine-grained low-titanium magnetite of variable grain size. We used a comprehensive back-zero-forth (BZF) heating technique by adding an additional zero-field heating between the Thellier two opposite in-field heating steps in order to estimate paleointensities in various standard protocols and provide internal self-consistency checks. After the first BZF experiment, we gave each sample a total thermal remanent magnetization (tTRM) by cooling from the Curie point in the presence of a low (15 µT) laboratory-applied field. Then we repeated the BZF protocol, with the laboratory-applied tTRM as a synthetic natural remanent magnetization (NRM), using the same laboratory-applied field and temperature steps to obtain the synthetic Arai signatures, which should only represent the domain-state dependent properties of the samples. We corrected the original Arai diagrams from the first BZF experiment by using the Arai signatures from the repeated BZF experiment, which neutralizes the typical MD concave-up effect. Eleven samples meet the Arai diagram post-selection criteria and provide qualified paleointensity estimates with a mean value for site GA-X of 4.23 ± 1.29 µT, consistent with an excursional geomagnetic field direction reported for this site.

Test Accuracy of Informant-Based Cognitive Screening Tests for Diagnosis of Dementia and Multidomain Cognitive Impairment in Stroke.

PubMed

McGovern, Aine; Pendlebury, Sarah T; Mishra, Nishant K; Fan, Yuhua; Quinn, Terence J

2016-02-01

Poststroke cognitive assessment can be performed using standardized questionnaires designed for family or care givers. We sought to describe the test accuracy of such informant-based assessments for diagnosis of dementia/multidomain cognitive impairment in stroke. We performed a systematic review using a sensitive search strategy across multidisciplinary electronic databases. We created summary test accuracy metrics and described reporting and quality using STARDdem and Quality Assessment of Diagnostic Accuracy Studies (QUADAS) tools, respectively. From 1432 titles, we included 11 studies. Ten papers used the Informant Questionnaire on Cognitive Decline in the Elderly (IQCODE). Four studies described IQCODE for diagnosis of poststroke dementia (n=1197); summary sensitivity: 0.81 (95% confidence interval, 0.60-0.93); summary specificty: 0.83 (95% confidence interval, 0.64-0.93). Five studies described IQCODE as tool for predicting future dementia (n=837); summary sensitivity: 0.60 (95% confidence interval, 0.32-0.83); summary specificity: 0.97 (95% confidence interval, 0.70-1.00). All papers had issues with at least 1 aspect of study reporting or quality. There is a limited literature on informant cognitive assessments in stroke. IQCODE as a diagnostic tool has test properties similar to other screening tools, IQCODE as a prognostic tool is specific but insensitive. We found no papers describing test accuracy of informant tests for diagnosis of prestroke cognitive decline, few papers on poststroke dementia and all included papers had issues with potential bias. © 2015 American Heart Association, Inc.

Free energy landscapes for initiation and branching of protein aggregation.

PubMed

Zheng, Weihua; Schafer, Nicholas P; Wolynes, Peter G

2013-12-17

Experiments on artificial multidomain protein constructs have probed the early stages of aggregation processes, but structural details of the species that initiate aggregation remain elusive. Using the associative-memory, water-mediated, structure and energy model known as AWSEM, a transferable coarse-grained protein model, we performed simulations of fused constructs composed of up to four copies of the Titin I27 domain or its mutant I27* (I59E). Free energy calculations enable us to quantify the conditions under which such multidomain constructs will spontaneously misfold. Consistent with experimental results, the dimer of I27 is found to be the smallest spontaneously misfolding construct. Our results show how structurally distinct misfolded states can be stabilized under different thermodynamic conditions, and this result provides a plausible link between the single-molecule misfolding experiments under native conditions and aggregation experiments under denaturing conditions. The conditions for spontaneous misfolding are determined by the interplay among temperature, effective local protein concentration, and the strength of the interdomain interactions. Above the folding temperature, fusing additional domains to the monomer destabilizes the native state, and the entropically stabilized amyloid-like state is favored. Because it is primarily energetically stabilized, the domain-swapped state is more likely to be important under native conditions. Both protofibril-like and branching structures are found in annealing simulations starting from extended structures, and these structures suggest a possible connection between the existence of multiple amyloidogenic segments in each domain and the formation of branched, amorphous aggregates as opposed to linear fibrillar structures.

Light Scattering by Ice Crystals Containing Air Bubbles

NASA Astrophysics Data System (ADS)

Zhang, J.; Panetta, R. L.; Yang, P.; Bi, L.

2014-12-01

The radiative effects of ice clouds are often difficult to estimate accurately, but are very important for interpretation of observations and for climate modeling. Our understanding of these effects is primarily based on scattering calculations, but due to the variability in ice habit it is computationally difficult to determine the required scattering and absorption properties, and the difficulties are only compounded by the need to include consideration of air and carbon inclusions of the sort frequently observed in collected samples. Much of the previous work on effects of inclusions in ice particles on scattering properties has been conducted with variants of geometric optics methods. We report on simulations of scattering by ice crystals with enclosed air bubbles using the pseudo-spectral time domain method (PSTD) and improved geometric optics method (IGOM). A Bouncing Ball Model (BBM) is proposed as a parametrization of air bubbles, and the results are compared with Monte Carlo radiative transfer calculations. Consistent with earlier studies, we find that air inclusions lead to a smoothing of variations in the phase function, weakening of halos, and a reduction of backscattering. We extend these studies by examining the effects of the particular arrangement of a fixed number of bubbles, as well as the effects of splitting a given number of bubbles into a greater number of smaller bubbles with the same total volume fraction. The result shows that the phase function will not change much for stochastic distributed air bubbles. It also shows that local maxima of phase functions are smoothed out for backward directions, when we break bubbles into small ones, single big bubble scatter favors more forward scattering than multi small internal scatters.

Ground motion simulation for the 23 August 2011, Mineral, Virginia earthquake using physics-based and stochastic broadband methods

USGS Publications Warehouse

Sun, Xiaodan; Hartzell, Stephen; Rezaeian, Sanaz

2015-01-01

Three broadband simulation methods are used to generate synthetic ground motions for the 2011 Mineral, Virginia, earthquake and compare with observed motions. The methods include a physics‐based model by Hartzell et al. (1999, 2005), a stochastic source‐based model by Boore (2009), and a stochastic site‐based model by Rezaeian and Der Kiureghian (2010, 2012). The ground‐motion dataset consists of 40 stations within 600 km of the epicenter. Several metrics are used to validate the simulations: (1) overall bias of response spectra and Fourier spectra (from 0.1 to 10 Hz); (2) spatial distribution of residuals for GMRotI50 peak ground acceleration (PGA), peak ground velocity, and pseudospectral acceleration (PSA) at various periods; (3) comparison with ground‐motion prediction equations (GMPEs) for the eastern United States. Our results show that (1) the physics‐based model provides satisfactory overall bias from 0.1 to 10 Hz and produces more realistic synthetic waveforms; (2) the stochastic site‐based model also yields more realistic synthetic waveforms and performs superiorly for frequencies greater than about 1 Hz; (3) the stochastic source‐based model has larger bias at lower frequencies (<0.5  Hz) and cannot reproduce the varying frequency content in the time domain. The spatial distribution of GMRotI50 residuals shows that there is no obvious pattern with distance in the simulation bias, but there is some azimuthal variability. The comparison between synthetics and GMPEs shows similar fall‐off with distance for all three models, comparable PGA and PSA amplitudes for the physics‐based and stochastic site‐based models, and systematic lower amplitudes for the stochastic source‐based model at lower frequencies (<0.5  Hz).

A New Method for Determining Structure Ensemble: Application to a RNA Binding Di-Domain Protein.

PubMed

Liu, Wei; Zhang, Jingfeng; Fan, Jing-Song; Tria, Giancarlo; Grüber, Gerhard; Yang, Daiwen

2016-05-10

Structure ensemble determination is the basis of understanding the structure-function relationship of a multidomain protein with weak domain-domain interactions. Paramagnetic relaxation enhancement has been proven a powerful tool in the study of structure ensembles, but there exist a number of challenges such as spin-label flexibility, domain dynamics, and overfitting. Here we propose a new (to our knowledge) method to describe structure ensembles using a minimal number of conformers. In this method, individual domains are considered rigid; the position of each spin-label conformer and the structure of each protein conformer are defined by three and six orthogonal parameters, respectively. First, the spin-label ensemble is determined by optimizing the positions and populations of spin-label conformers against intradomain paramagnetic relaxation enhancements with a genetic algorithm. Subsequently, the protein structure ensemble is optimized using a more efficient genetic algorithm-based approach and an overfitting indicator, both of which were established in this work. The method was validated using a reference ensemble with a set of conformers whose populations and structures are known. This method was also applied to study the structure ensemble of the tandem di-domain of a poly (U) binding protein. The determined ensemble was supported by small-angle x-ray scattering and nuclear magnetic resonance relaxation data. The ensemble obtained suggests an induced fit mechanism for recognition of target RNA by the protein. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Turbulent breakage of ductile aggregates.

PubMed

Marchioli, Cristian; Soldati, Alfredo

2015-05-01

In this paper we study breakage rate statistics of small colloidal aggregates in nonhomogeneous anisotropic turbulence. We use pseudospectral direct numerical simulation of turbulent channel flow and Lagrangian tracking to follow the motion of the aggregates, modeled as sub-Kolmogorov massless particles. We focus specifically on the effects produced by ductile rupture: This rupture is initially activated when fluctuating hydrodynamic stresses exceed a critical value, σ>σ(cr), and is brought to completion when the energy absorbed by the aggregate meets the critical breakage value. We show that ductile rupture breakage rates are significantly reduced with respect to the case of instantaneous brittle rupture (i.e., breakage occurs as soon as σ>σ(cr)). These discrepancies are due to the different energy values at play as well as to the statistical features of energy distribution in the anisotropic turbulence case examined.

An Initial Multi-Domain Modeling of an Actively Cooled Structure

NASA Technical Reports Server (NTRS)

Steinthorsson, Erlendur

1997-01-01

A methodology for the simulation of turbine cooling flows is being developed. The methodology seeks to combine numerical techniques that optimize both accuracy and computational efficiency. Key components of the methodology include the use of multiblock grid systems for modeling complex geometries, and multigrid convergence acceleration for enhancing computational efficiency in highly resolved fluid flow simulations. The use of the methodology has been demonstrated in several turbo machinery flow and heat transfer studies. Ongoing and future work involves implementing additional turbulence models, improving computational efficiency, adding AMR.

The MYSTerious MOZ, a histone acetyltransferase with a key role in haematopoiesis.

PubMed

Perez-Campo, Flor M; Costa, Guilherme; Lie-a-Ling, Michael; Kouskoff, Valerie; Lacaud, Georges

2013-06-01

The MOnocytic leukaemia Zing finger (MOZ; MYST3 or KAT6A(1)) gene is frequently found translocated in acute myeloid leukaemia. MOZ encodes a large multidomain protein that contains, besides others, a histone acetyl transferase catalytic domain. Several studies have now established the critical function of MOZ in haematopoiesis. In this review we summarize the recent findings that underscore the relevance of the different biological activities of MOZ in the regulation of haematopoiesis. © 2013 The Paterson Institute for Cancer Research Immunology © 2013 Blackwell Publishing Ltd.

Type II toxin: antitoxin systems. More than small selfish entities?

PubMed

Rocker, Andrea; Meinhart, Anton

2016-05-01

Toxin-antitoxin (TA) modules regulate metabolism and viability of bacteria and archaea. In type II TA systems these functions are generally thought to be performed by two small proteins. However, evidence is increasing that the toxins are much more diverse and can form multi-domain proteins. Recently, we published a novel type II TA system in which toxin and antitoxin are covalently linked into a single polypeptide chain. In this review we summarize the current knowledge on these elongated toxin homologs and provide perspectives for future study.

Multi-Domain Assembly of Nuclear Estrogen Receptors: Structural Insights into ER-Positive Breast Cancer Therapeutics

DTIC Science & Technology

2013-04-01

configurations in the top 25% and 30% of all unbiased simulations were also projected onto the energy globe [Fig. S3(B)]. These results show that each...Coarse-grained simulations of protein-protein association: An energy landscape perspective. Biophys J 103(4):837 – 845, 2012. 27. Yang, S., Onuchic, J. N...S1. The projected snapshots were taken only from free and released portions of PPR simulation cycles with a energy cutoff of ELBD−DBD < 0 kcal/mol and

Programmable DNA Hydrogels Assembled from Multidomain DNA Strands.

PubMed

Jiang, Huiling; Pan, Victor; Vivek, Skanda; Weeks, Eric R; Ke, Yonggang

2016-06-16

Hydrogels are important in biological and medical applications, such as drug delivery and tissue engineering. DNA hydrogels have attracted significant attention due to the programmability and biocompatibility of the material. We developed a series of low-cost one-strand DNA hydrogels self-assembled from single-stranded DNA monomers containing multiple palindromic domains. This new hydrogel design is simple and programmable. Thermal stability, mechanical properties, and loading capacity of these one-strand DNA hydrogels can be readily regulated by simply adjusting the DNA domains. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

1H, 15N and 13C assignments of domain 5 of Dictyostelium discoideum gelation factor (ABP-120) in its native and 8M urea-denatured states.

PubMed

Hsu, Shang-Te Danny; Cabrita, Lisa D; Christodoulou, John; Dobson, Christopher M

2009-06-01

The gelation factor from Dictyostelium discoideum (ABP-120) is an actin binding protein consisting of six immunoglobulin (Ig) domains in the C-terminal rod domain. We have recently used the pair of domains 5 and 6 of ABP-120 as a model system for studying multi-domain nascent chain folding on the ribosome. Here we present the NMR assignments of domain 5 in its native and 8M urea-denatured states.

AxiSEM3D: broadband seismic wavefields in 3-D aspherical Earth models

NASA Astrophysics Data System (ADS)

Leng, K.; Nissen-Meyer, T.; Zad, K. H.; van Driel, M.; Al-Attar, D.

2017-12-01

Seismology is the primary tool for data-informed inference of Earth structure and dynamics. Simulating seismic wave propagation at a global scale is fundamental to seismology, but remains as one of most challenging problems in scientific computing, because of both the multiscale nature of Earth's interior and the observable frequency band of seismic data. We present a novel numerical method to simulate global seismic wave propagation in realistic 3-D Earth models. Our method, named AxiSEM3D, is a hybrid of spectral element method and pseudospectral method. It reduces the azimuthal dimension of wavefields by means of a global Fourier series parameterization, of which the number of terms can be locally adapted to the inherent azimuthal smoothness of the wavefields. AxiSEM3D allows not only for material heterogeneities, such as velocity, density, anisotropy and attenuation, but also for finite undulations on radial discontinuities, both solid-solid and solid-fluid, and thereby a variety of aspherical Earth features such as ellipticity, topography, variable crustal thickness, and core-mantle boundary topography. Such interface undulations are equivalently interpreted as material perturbations of the contiguous media, based on the "particle relabelling transformation". Efficiency comparisons show that AxiSEM3D can be 1 to 3 orders of magnitude faster than conventional 3-D methods, with the speedup increasing with simulation frequency and decreasing with model complexity, but for all realistic structures the speedup remains at least one order of magnitude. The observable frequency range of global seismic data (up to 1 Hz) has been covered for wavefield modelling upon a 3-D Earth model with reasonable computing resources. We show an application of surface wave modelling within a state-of-the-art global crustal model (Crust1.0), with the synthetics compared to real data. The high-performance C++ code is released at github.com/AxiSEM3D/AxiSEM3D.

Acceleration of stable TTI P-wave reverse-time migration with GPUs

NASA Astrophysics Data System (ADS)

Kim, Youngseo; Cho, Yongchae; Jang, Ugeun; Shin, Changsoo

2013-03-01

When a pseudo-acoustic TTI (tilted transversely isotropic) coupled wave equation is used to implement reverse-time migration (RTM), shear wave energy is significantly included in the migration image. Because anisotropy has intrinsic elastic characteristics, coupling P-wave and S-wave modes in the pseudo-acoustic wave equation is inevitable. In RTM with only primary energy or the P-wave mode in seismic data, the S-wave energy is regarded as noise for the migration image. To solve this problem, we derive a pure P-wave equation for TTI media that excludes the S-wave energy. Additionally, we apply the rapid expansion method (REM) based on a Chebyshev expansion and a pseudo-spectral method (PSM) to calculate spatial derivatives in the wave equation. When REM is incorporated with the PSM for the spatial derivatives, wavefields with high numerical accuracy can be obtained without grid dispersion when performing numerical wave modeling. Another problem in the implementation of TTI RTM is that wavefields in an area with high gradients of dip or azimuth angles can be blown up in the progression of the forward and backward algorithms of the RTM. We stabilize the wavefields by applying a spatial-frequency domain high-cut filter when calculating the spatial derivatives using the PSM. In addition, to increase performance speed, the graphic processing unit (GPU) architecture is used instead of traditional CPU architecture. To confirm the degree of acceleration compared to the CPU version on our RTM, we then analyze the performance measurements according to the number of GPUs employed.

Direct Numerical Simulation of Turbulent Flow Over Complex Bathymetry

NASA Astrophysics Data System (ADS)

Yue, L.; Hsu, T. J.

2017-12-01

Direct numerical simulation (DNS) is regarded as a powerful tool in the investigation of turbulent flow featured with a wide range of time and spatial scales. With the application of coordinate transformation in a pseudo-spectral scheme, a parallelized numerical modeling system was created aiming at simulating flow over complex bathymetry with high numerical accuracy and efficiency. The transformed governing equations were integrated in time using a third-order low-storage Runge-Kutta method. For spatial discretization, the discrete Fourier expansion was adopted in the streamwise and spanwise direction, enforcing the periodic boundary condition in both directions. The Chebyshev expansion on Chebyshev-Gauss-Lobatto points was used in the wall-normal direction, assuming there is no-slip on top and bottom walls. The diffusion terms were discretized with a Crank-Nicolson scheme, while the advection terms dealiased with the 2/3 rule were discretized with an Adams-Bashforth scheme. In the prediction step, the velocity was calculated in physical domain by solving the resulting linear equation directly. However, the extra terms introduced by coordinate transformation impose a strict limitation to time step and an iteration method was applied to overcome this restriction in the correction step for pressure by solving the Helmholtz equation. The numerical solver is written in object-oriented C++ programing language utilizing Armadillo linear algebra library for matrix computation. Several benchmarking cases in laminar and turbulent flow were carried out to verify/validate the numerical model and very good agreements are achieved. Ongoing work focuses on implementing sediment transport capability for multiple sediment classes and parameterizations for flocculation processes.

Comparison of thermal and microwave paleointensity estimates in specimens that violate Thellier's laws

NASA Astrophysics Data System (ADS)

Grappone, J. M., Jr.; Biggin, A. J.; Barrett, T. J.; Hill, M. J.

2017-12-01

Deep in the Earth, thermodynamic behavior drives the geodynamo and creates the Earth's magnetic field. Determining how the strength of the field, its paleointensity (PI), varies with time, is vital to our understanding of Earth's evolution. Thellier-style paleointensity experiments assume the presence of non-interacting, single domain (SD) magnetic particles, which follow Thellier's laws. Most natural rocks however, contain larger, multi-domain (MD) or interacting single domain (ISD) particles that often violate these laws and cause experiments to fail. Even for samples that pass reliability criteria designed to minimize the impact of MD or ISD grains, different PI techniques can give systematically different estimates, implying violation of Thellier's laws. Our goal is to identify any disparities in PI results that may be explainable by protocol-specific MD and ISD behavior and determine optimum methods to maximize accuracy. Volcanic samples from the Hawai'ian SOH1 borehole previously produced method-dependent PI estimates. Previous studies showed consistently lower PI values when using a microwave (MW) system and the perpendicular method than using the original thermal Thellier-Thellier (OT) technique. However, the data were ambiguous regarding the cause of the discrepancy. The diverging estimates appeared to be either the result of using OT instead of the perpendicular method or the result of using MW protocols instead of thermal protocols. Comparison experiments were conducted using the thermal perpendicular method and microwave OT technique to bridge the gap. Preliminary data generally show that the perpendicular method gives lower estimates than OT for comparable Hlab values. MW estimates are also generally lower than thermal estimates using the same protocol.

Physical and Structural Studies on the Cryo-cooling of Insulin Crystals

NASA Technical Reports Server (NTRS)

Lovelace, J.; Bellamy, H.; Snell, E. H.; Borgstahl, G.

2003-01-01

Reflection profiles were analyzed from microgravity-(mg) and earth-grown insulin crystals to measure mosaicity (h) and to reveal mosaic domain structure and composition. The effects of cryocooling on single and multi-domain crystals were compared. The effects of cryocooling on insulin structure were also re-examined. Microgravity crystals were larger, more homogeneous, and more perfect than earth crystals. Several mg crystals contained primarily a single mosaic domain with havg of 0.005deg. The earth crystals varied in quality and all contained multiple domains with havg of 0.031deg. Cryocooling caused a 43-fold increase in h for mg crystals (havg=0.217deg) and an %fold increase for earth crystals (havg=0.246deg). These results indicate that very well-ordered crystals are not completely protected from the stresses associated with cryocooling, especially when structural perturbations occur. However, there were differences in the reflection profiles. For multi-mosaic domain crystals, each domain individually broadened and separated from the other domains upon cryo-cooling. Cryo-cooling did not cause an increase in the number of domains. A crystal composed of a single domain retained this domain structure and the reflection profiles simply broadened. Therefore, an improved signal-to-noise ratio for each reflection was measured from cryo-cooled single domain crystals relative to cryo-cooled multi-domain crystals. This improved signal, along with the increase in crystal size, facilitated the measurement of the weaker high- resolution reflections. The observed broadening of reflection profiles indicates increased variation in unit cell dimensions which may be linked to cryo-cooling-associated structural changes and disorder.

An exploration of subgroups of mild cognitive impairment based on cognitive, neuropsychiatric and functional features: analysis of data from the National Alzheimer's Coordinating Center.

PubMed

Hanfelt, John J; Wuu, Joanne; Sollinger, Ann B; Greenaway, Melanie C; Lah, James J; Levey, Allan I; Goldstein, Felicia C

2011-11-01

To empirically expand the existing subtypes of mild cognitive impairment (MCI) by incorporating information on neuropsychiatric and functional features, and to assess whether cerebrovascular disease (CVD) risk factors are associated with any of these subgroups. Latent class analysis using 1,655 patients with MCI. Participants in the Uniform Data Set (UDS) from 29 National Institutes of Health-supported Alzheimer's Disease Centers. Patients with a consensus diagnosis of MCI from each center and with a Mini-Mental State Examination score of 22 or greater. UDS cognitive battery, Neuropsychiatric Inventory Questionnaire, and Functional Assessment Questionnaire administered at initial visit. Seven empirically based subgroups of MCI were identified: 1) minimally impaired (relative frequency, 12%); 2) amnestic only (16%); 3) amnestic with functional and neuropsychiatric features (16%); 4) amnestic multidomain (12%); 5) amnestic multidomain with functional and neuropsychiatric features (12%); 6) functional and neuropsychiatric features (15%); and 7) executive function and language impairments (18%). Two of these subgroups with functional and neuropsychiatric features were at least 3.8 times more likely than the minimally impaired subgroup to have a Rosen-Hachinski score of 4 or greater, an indicator of probable CVD. Findings suggest that there are several distinct phenotypes of MCI characterized by prominent cognitive features, prominent functional features, and neuropsychiatric features or a combination of all three. Subgroups with functional and neuropsychiatric features are significantly more likely to have CVD, which suggests that there may be distinct differences in disease etiology from the other phenotypes.

The dynamic disulphide relay of quiescin sulphydryl oxidase.

PubMed

Alon, Assaf; Grossman, Iris; Gat, Yair; Kodali, Vamsi K; DiMaio, Frank; Mehlman, Tevie; Haran, Gilad; Baker, David; Thorpe, Colin; Fass, Deborah

2012-08-16

Protein stability, assembly, localization and regulation often depend on the formation of disulphide crosslinks between cysteine side chains. Enzymes known as sulphydryl oxidases catalyse de novo disulphide formation and initiate intra- and intermolecular dithiol/disulphide relays to deliver the disulphides to substrate proteins. Quiescin sulphydryl oxidase (QSOX) is a unique, multi-domain disulphide catalyst that is localized primarily to the Golgi apparatus and secreted fluids and has attracted attention owing to its overproduction in tumours. In addition to its physiological importance, QSOX is a mechanistically intriguing enzyme, encompassing functions typically carried out by a series of proteins in other disulphide-formation pathways. How disulphides are relayed through the multiple redox-active sites of QSOX and whether there is a functional benefit to concatenating these sites on a single polypeptide are open questions. Here we present the first crystal structure of an intact QSOX enzyme, derived from a trypanosome parasite. Notably, sequential sites in the disulphide relay were found more than 40 Å apart in this structure, too far for direct disulphide transfer. To resolve this puzzle, we trapped and crystallized an intermediate in the disulphide hand-off, which showed a 165° domain rotation relative to the original structure, bringing the two active sites within disulphide-bonding distance. The comparable structure of a mammalian QSOX enzyme, also presented here, shows further biochemical features that facilitate disulphide transfer in metazoan orthologues. Finally, we quantified the contribution of concatenation to QSOX activity, providing general lessons for the understanding of multi-domain enzymes and the design of new catalytic relays.

Magnetic effects of maghemitization of oceanic crust

USGS Publications Warehouse

Prevot, M.; Lecaille, A.; Mankinen, Edward A.

1981-01-01

Both theoretical considerations and available experimental results indicate that magnetic effects of maghemitization are strongly dependent on the grain size of the originally unoxidized titanomagnetite. Maghemitization of single‐domain titanomagnetite results in a decrease in coercivity, an increase in susceptibility, and a large decrease in Q ratio. Maghemitization of multidomain titanomagnetite results in an increase in coercivity, a decrease in susceptibility, and no large changes in Q ratio. Single‐domain titanomagnetite is probably resistant to the development of a chemical remanent magnetization (CRM), whereas multidomain titanomagnetite can acquire a CRM during maghemitization. The behavior of pseudo‐single‐domain titanomagnetite, which is the main carrier of remanence in submarine extrusive rocks, is investigated by comparing the magnetic properties of the French‐American Mid‐Ocean Undersea Study (FAMOUS) (less than 0.1 m.y. old) and the Leg 37 (3.5 m.y. old) pillow basalts recovered from the Mid‐Atlantic Ridge near 37°N. Combining electron microprobe analyses, Curie temperature measurements, and cell edge determinations, we find that the FAMOUS rocks are already oxidized (z = 0.38), possibly as a result of some high‐temperature maghemitization during cooling of the magma. Comparison with the more highly oxidized (z = 0.7) Leg 37 pillow basalts indicates that low‐temperature maghemitization of such rocks does not result in appreciable changes of coercivity and susceptibility, although the Q ratio does decrease and CRM seems to be acquired. Such a CRM could account for the anomalously low magnetic inclinations observed at most of the Leg 37 sites.

Magnetic signatures of Heinrich-like detrital layers in the Quaternary of the North Atlantic

NASA Astrophysics Data System (ADS)

Channell, J. E. T.; Hodell, D. A.

2013-05-01

Magnetic parameters are useful for distinguishing North Atlantic Heinrich-like detrital layers from background sediments. Here we compare magnetic properties with XRF scanning data back to 700 ka and 1.3 Ma at IODP Sites U1302-U1303 and U1308, respectively. Multi-domain magnetite, with grain sizes >20 µm, is characteristic of both Ca- and Si-rich detrital layers, as defined by XRF core scanning, confirming the contribution of ice rafting. Reflectance spectra and magnetic parameters distinguish Ca- and Si-rich IRD layers due the presence of high coercivity hematite in Si-rich layers. Heinrich layer 6 (H6) at Site U1302-U1303 is unlike other detrital layers, being marked by a 45-cm thick homogeneous cream-colored clay layer underlain by a thin (5-cm) graded coarse-sand. Comparison of Site U1302/03 and Site U1308 detrital layers implies a dominant Laurentide source for both Ca- and Si-rich detrital layers. At Site U1308, low benthic δ13C values during stadials are in-step with magnetic grain-size coarsening associated with Si-rich detrital layers back to 1.3 Ma, indicating a link between deep-sea ventilation and ice rafting. The surface-sediment tan-colored oxic layer (~2 m thick at Site U1308) yields magnetic hysteresis ratios that are offset from the single-domain to multi-domain (SD-MD) magnetite mixing-line in hysteresis-ratio diagrams. This offset is attributed to maghemite grain-coatings, that form on magnetite in surface sediment, and undergo dissolution as they pass through the oxic/anoxic boundary.

Crystal Structure of an Integron Gene Cassette-Associated Protein from Vibrio cholerae Identifies a Cationic Drug-Binding Module

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deshpande, Chandrika N.; Harrop, Stephen J.; Boucher, Yan

2012-02-15

The direct isolation of integron gene cassettes from cultivated and environmental microbial sources allows an assessment of the impact of the integron/gene cassette system on the emergence of new phenotypes, such as drug resistance or virulence. A structural approach is being exploited to investigate the modularity and function of novel integron gene cassettes. We report the 1.8 {angstrom} crystal structure of Cass2, an integron-associated protein derived from an environmental V. cholerae. The structure defines a monomeric beta-barrel protein with a fold related to the effector-binding portion of AraC/XylS transcription activators. The closest homologs of Cass2 are multi-drug binding proteins, suchmore » as BmrR. Consistent with this, a binding pocket made up of hydrophobic residues and a single glutamate side chain is evident in Cass2, occupied in the crystal form by polyethylene glycol. Fluorescence assays demonstrate that Cass2 is capable of binding cationic drug compounds with submicromolar affinity. The Cass2 module possesses a protein interaction surface proximal to its drug-binding cavity with features homologous to those seen in multi-domain transcriptional regulators. Genetic analysis identifies Cass2 to be representative of a larger family of independent effector-binding proteins associated with lateral gene transfer within Vibrio and closely-related species. We propose that the Cass2 family not only has capacity to form functional transcription regulator complexes, but represents possible evolutionary precursors to multi-domain regulators associated with cationic drug compounds.« less

Nutrient intake and dietary changes during a 2-year multi-domain lifestyle intervention among older adults: secondary analysis of the Finnish Geriatric Intervention Study to Prevent Cognitive Impairment and Disability (FINGER) randomised controlled trial.

PubMed

Lehtisalo, Jenni; Ngandu, Tiia; Valve, Päivi; Antikainen, Riitta; Laatikainen, Tiina; Strandberg, Timo; Soininen, Hilkka; Tuomilehto, Jaakko; Kivipelto, Miia; Lindström, Jaana

2017-08-01

Advancing age increases the risk for diseases and health concerns like cognitive decline, constituting a major public health challenge. Lifestyle, especially healthy diet, affects many risk factors related to chronic diseases, and thus lifestyle interventions among older adults may be beneficial in promoting successful ageing. We completed a randomised 2-year multi-domain lifestyle intervention trial aiming at prevention of cognitive decline among 631 participants in the intervention and 629 in the control group, aged 60-77 years at baseline. Dietary counselling was one of the intervention domains together with strength exercise, cognitive training and management of CVD risk factors. The aim of this paper was to describe success of the intervention - that is, how an intervention based on national dietary recommendations affected dietary habits as a part of multi-intervention. Composite dietary intervention adherence score comprising nine distinct goals (range 0-9 points from none to achieving all goals) was 5·0 at baseline, and increased in the intervention group after the 1st (P<0·001) and 2nd (P=0·005) year. The difference in change compared with the control group was significant at both years (P<0·001 and P=0·018). Intake of several vitamins and minerals decreased in the control group but remained unchanged or increased in the intervention group during the 2 years. Well-targeted dietary counselling may prevent age-related decline in diet quality and help in preventing cognitive decline.

Hematite Versus Magnetite as the Signature for Planetary Magnetic Anomalies?

NASA Technical Reports Server (NTRS)

Kletetshka, Gunther; Taylor, Patrick T.; Wasilewski, Peter J.

1999-01-01

Crustal magnetic anomalies are the result of adjacent geologic units having contrasting magnetization. This magnetization arises from induction and/or remanence. In a planetary context we now know that Mars has significant crustal magnetic anomalies due to remanent magnetization, while the Earth has some anomalies where remanence can be shown to be important. This picture, however, is less clear because of the nature and the magnitude of the geomagnetic field which is responsible for superimposed induced magnetization. Induced magnetization assumes a magnetite source, because of its much greater magnetic susceptibility when compared with other magnetic minerals. We investigated the TRM (thermoremanent magnetization) acquisition of hematite, in weak magnetic fields up to 1 mT, to determine if the remanent and induced magnetization of hematite could compete with magnetite. TRM acquisition curves of magnetite and hematite show that multi-domain hematite reaches TRM saturation (0.3 - 0.4 A sq m/kg) in fields as low as 100 microT. However, multi-domain magnetite reaches only a few percent of its TRM saturation in a field of 100 microT (0.02 - 0.06 A sq m/kg). These results suggest that a mineral such as hematite and, perhaps, other minerals with significant remanence and minor induced magnetization may play an important role in providing requisite magnetization contrast. Perhaps, and especially for the Mars case, we should reevaluate where hematite and other minerals, with efficient remanence acquisition, exist in significant concentration, allowing a more comprehensive explanation of Martian anomalies and better insight into the role of remanent magnetization in terrestrial crustal magnetic anomalies.

Differential Expression of Three Members of the Multidomain Adhesion CCp Family in Babesia bigemina, Babesia bovis and Theileria equi

PubMed Central

Bastos, Reginaldo G.; Suarez, Carlos E.; Laughery, Jacob M.; Johnson, Wendell C.; Ueti, Massaro W.; Knowles, Donald P.

2013-01-01

Members of the CCp protein family have been previously described to be expressed on gametocytes of apicomplexan Plasmodium parasites. Knocking out Plasmodium CCp genes blocks the development of the parasite in the mosquito vector, making the CCp proteins potential targets for the development of a transmission-blocking vaccine. Apicomplexans Babesia bovis and Babesia bigemina are the causative agents of bovine babesiosis, and apicomplexan Theileria equi causes equine piroplasmosis. Bovine babesiosis and equine piroplasmosis are the most economically important parasite diseases that affect worldwide cattle and equine industries, respectively. The recent sequencing of the B. bovis and T. equi genomes has provided the opportunity to identify novel genes involved in parasite biology. Here we characterize three members of the CCp family, named CCp1, CCp2 and CCp3, in B. bigemina, B. bovis and T. equi. Using B. bigemina as an in vitro model, expression of all three CCp genes and proteins was demonstrated in temperature-induced sexual stages. Transcripts for all three CCp genes were found in vivo in blood stages of T. equi, and transcripts for CCp3 were detected in vivo in blood stages of B. bovis. However, no protein expression was detected in T. equi blood stages or B. bovis blood stages or B. bovis tick stages. Collectively, the data demonstrated a differential pattern of expression of three orthologous genes of the multidomain adhesion CCp family by B. bigemina, B. bovis and T. equi. The novel CCp members represent potential targets for innovative approaches to control bovine babesiosis and equine piroplasmosis. PMID:23844089

Lowered performance in working memory and attentional sub-processes are most prominent in multi-domain amnestic mild cognitive impairment subtypes.

PubMed

Klekociuk, Shannon Z; Summers, Mathew J

2014-03-01

Research suggests that working memory and attention deficits may be present in mild cognitive impairment (MCI). However, the functional status of these domains within revised MCI subtypes remains unclear, particularly because previous studies have examined these cognitive domains with the same tests that were used to classify MCI subtypes. The aim of this study was to examine working memory and attention function in MCI subtypes on a battery of neuropsychological tests that were distinct from those used to classify MCI subtypes A total of 122 adults aged 60-90 years were classified at baseline as amnestic MCI, non-amnestic MCI, and multi-domain amnestic (a-MCI+). The attentional and working memory capacity of participants was examined using a battery of tests distinct from those used to classify MCI at screening. The a-MCI+ group demonstrated the poorest performance on all working memory tasks and specific sub-processes of attention. The non-amnestic MCI group had lowered performance on visual span and complex sustained attention only. There was no evidence of either attentional or working memory impairment in the amnestic MCI participants. When MCI cohorts are assessed on measures distinct from those used at classification, a-MCI+ subjects had the most compromised working memory and attention function. These results support previous findings that suggest a-MCI+ more closely resembles early stage Alzheimer's disease and those with a-MCI+ may be at increased rate of future cognitive decline compared to those with other MCI subtypes. © 2014 The Authors. Psychogeriatrics © 2014 Japanese Psychogeriatric Society.

Baseline Vascular Cognitive Impairment Predicts the Course of Apathetic Symptoms After Stroke: The CASPER Study.

PubMed

Douven, Elles; Köhler, Sebastian; Schievink, Syenna H J; van Oostenbrugge, Robert J; Staals, Julie; Verhey, Frans R J; Aalten, Pauline

2018-03-01

To examine the influence of vascular cognitive impairment (VCI) on the course of poststroke depression (PSD) and poststroke apathy (PSA). Included were 250 stroke patients who underwent neuropsychological and neuropsychiatric assessment 3 months after stroke (baseline) and at a 6- and 12-month follow-up after baseline. Linear mixed models tested the influence of VCI in at least one cognitive domain (any VCI) or multidomain VCI (VCI in multiple cognitive domains) at baseline and domain-specific VCI at baseline on levels of depression and apathy over time, with random effects for intercept and slope. Almost half of the patients showed any VCI at baseline, and any VCI was associated with increasing apathy levels from baseline to the 12-month follow-up. Patients with multidomain VCI had higher apathy scores at the 6- and 12-month follow-up compared with patients with VCI in a single cognitive domain. Domain-specific analyses showed that impaired executive function and slowed information processing speed went together with increasing apathy levels from baseline to 6- and 12-month follow-up. None of the cognitive variables predicted the course of depressive symptoms. Baseline VCI is associated with increasing apathy levels from baseline to the chronic stroke phase, whereas no association was found between baseline VCI and the course of depressive symptoms. Health professionals should be aware that apathy might be absent early after stroke but may evolve over time in patients with VCI. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sidler, Rolf, E-mail: rsidler@gmail.com; Carcione, José M.; Holliger, Klaus

We present a novel numerical approach for the comprehensive, flexible, and accurate simulation of poro-elastic wave propagation in 2D polar coordinates. An important application of this method and its extensions will be the modeling of complex seismic wave phenomena in fluid-filled boreholes, which represents a major, and as of yet largely unresolved, computational problem in exploration geophysics. In view of this, we consider a numerical mesh, which can be arbitrarily heterogeneous, consisting of two or more concentric rings representing the fluid in the center and the surrounding porous medium. The spatial discretization is based on a Chebyshev expansion in themore » radial direction and a Fourier expansion in the azimuthal direction and a Runge–Kutta integration scheme for the time evolution. A domain decomposition method is used to match the fluid–solid boundary conditions based on the method of characteristics. This multi-domain approach allows for significant reductions of the number of grid points in the azimuthal direction for the inner grid domain and thus for corresponding increases of the time step and enhancements of computational efficiency. The viability and accuracy of the proposed method has been rigorously tested and verified through comparisons with analytical solutions as well as with the results obtained with a corresponding, previously published, and independently benchmarked solution for 2D Cartesian coordinates. Finally, the proposed numerical solution also satisfies the reciprocity theorem, which indicates that the inherent singularity associated with the origin of the polar coordinate system is adequately handled.« less

Energy minimization on manifolds for docking flexible molecules

PubMed Central

Mirzaei, Hanieh; Zarbafian, Shahrooz; Villar, Elizabeth; Mottarella, Scott; Beglov, Dmitri; Vajda, Sandor; Paschalidis, Ioannis Ch.; Vakili, Pirooz; Kozakov, Dima

2015-01-01

In this paper we extend a recently introduced rigid body minimization algorithm, defined on manifolds, to the problem of minimizing the energy of interacting flexible molecules. The goal is to integrate moving the ligand in six dimensional rotational/translational space with internal rotations around rotatable bonds within the two molecules. We show that adding rotational degrees of freedom to the rigid moves of the ligand results in an overall optimization search space that is a manifold to which our manifold optimization approach can be extended. The effectiveness of the method is shown for three different docking problems of increasing complexity. First we minimize the energy of fragment-size ligands with a single rotatable bond as part of a protein mapping method developed for the identification of binding hot spots. Second, we consider energy minimization for docking a flexible ligand to a rigid protein receptor, an approach frequently used in existing methods. In the third problem we account for flexibility in both the ligand and the receptor. Results show that minimization using the manifold optimization algorithm is substantially more efficient than minimization using a traditional all-atom optimization algorithm while producing solutions of comparable quality. In addition to the specific problems considered, the method is general enough to be used in a large class of applications such as docking multidomain proteins with flexible hinges. The code is available under open source license (at http://cluspro.bu.edu/Code/Code_Rigtree.tar), and with minimal effort can be incorporated into any molecular modeling package. PMID:26478722

Tests of dynamic Lagrangian eddy viscosity models in Large Eddy Simulations of flow over three-dimensional bluff bodies

NASA Astrophysics Data System (ADS)

Tseng, Yu-Heng; Meneveau, Charles; Parlange, Marc B.

2004-11-01

Large Eddy Simulations (LES) of atmospheric boundary-layer air movement in urban environments are especially challenging due to complex ground topography. Typically in such applications, fairly coarse grids must be used where the subgrid-scale (SGS) model is expected to play a crucial role. A LES code using pseudo-spectral discretization in horizontal planes and second-order differencing in the vertical is implemented in conjunction with the immersed boundary method to incorporate complex ground topography, with the classic equilibrium log-law boundary condition in the new-wall region, and with several versions of the eddy-viscosity model: (1) the constant-coefficient Smagorinsky model, (2) the dynamic, scale-invariant Lagrangian model, and (3) the dynamic, scale-dependent Lagrangian model. Other planar-averaged type dynamic models are not suitable because spatial averaging is not possible without directions of statistical homogeneity. These SGS models are tested in LES of flow around a square cylinder and of flow over surface-mounted cubes. Effects on the mean flow are documented and found not to be major. Dynamic Lagrangian models give a physically more realistic SGS viscosity field, and in general, the scale-dependent Lagrangian model produces larger Smagorinsky coefficient than the scale-invariant one, leading to reduced distributions of resolved rms velocities especially in the boundary layers near the bluff bodies.

Reynolds Number Effect on Spatial Development of Viscous Flow Induced by Wave Propagation Over Bed Ripples

NASA Astrophysics Data System (ADS)

Dimas, Athanassios A.; Kolokythas, Gerasimos A.

Numerical simulations of the free-surface flow, developing by the propagation of nonlinear water waves over a rippled bottom, are performed assuming that the corresponding flow is two-dimensional, incompressible and viscous. The simulations are based on the numerical solution of the Navier-Stokes equations subject to the fully-nonlinear free-surface boundary conditions and appropriate bottom, inflow and outflow boundary conditions. The equations are properly transformed so that the computational domain becomes time-independent. For the spatial discretization, a hybrid scheme is used where central finite-differences, in the horizontal direction, and a pseudo-spectral approximation method with Chebyshev polynomials, in the vertical direction, are applied. A fractional time-step scheme is used for the temporal discretization. Over the rippled bed, the wave boundary layer thickness increases significantly, in comparison to the one over flat bed, due to flow separation at the ripple crests, which generates alternating circulation regions. The amplitude of the wall shear stress over the ripples increases with increasing ripple height or decreasing Reynolds number, while the corresponding friction force is insensitive to the ripple height change. The amplitude of the form drag forces due to dynamic and hydrostatic pressures increase with increasing ripple height but is insensitive to the Reynolds number change, therefore, the percentage of friction in the total drag force decreases with increasing ripple height or increasing Reynolds number.

The evolution of hyperboloidal data with the dual foliation formalism: mathematical analysis and wave equation tests

NASA Astrophysics Data System (ADS)

Hilditch, David; Harms, Enno; Bugner, Marcus; Rüter, Hannes; Brügmann, Bernd

2018-03-01

A long-standing problem in numerical relativity is the satisfactory treatment of future null-infinity. We propose an approach for the evolution of hyperboloidal initial data in which the outer boundary of the computational domain is placed at infinity. The main idea is to apply the ‘dual foliation’ formalism in combination with hyperboloidal coordinates and the generalized harmonic gauge formulation. The strength of the present approach is that, following the ideas of Zenginoğlu, a hyperboloidal layer can be naturally attached to a central region using standard coordinates of numerical relativity applications. Employing a generalization of the standard hyperboloidal slices, developed by Calabrese et al, we find that all formally singular terms take a trivial limit as we head to null-infinity. A byproduct is a numerical approach for hyperboloidal evolution of nonlinear wave equations violating the null-condition. The height-function method, used often for fixed background spacetimes, is generalized in such a way that the slices can be dynamically ‘waggled’ to maintain the desired outgoing coordinate lightspeed precisely. This is achieved by dynamically solving the eikonal equation. As a first numerical test of the new approach we solve the 3D flat space scalar wave equation. The simulations, performed with the pseudospectral bamps code, show that outgoing waves are cleanly absorbed at null-infinity and that errors converge away rapidly as resolution is increased.

Direct and Large Eddy Simulation of non-equilibrium wall-bounded turbulent flows

NASA Astrophysics Data System (ADS)

Park, Hee-Jun

2005-11-01

The performance of several existing SGS models in non-equilibrium wall-bounded turbulent flows is investigated through comparisons of LES and DNS. The test problem is a shear-driven three-dimensional turbulent channel flow at base Reτ˜210 established by impulsive motion of one of the channel walls in the spanwise direction with a spanwise velocity equal to 3/4 of the bulk mean velocity in the channel. The DNS and LES are performed using pseudo-spectral methods with resolutions of 128x128x129 and 32x64x65, respectively. The SGS models tested include the nonlinear Interactions Approximation model (NIA) [Haliloglu and Akhavan (2004)], the Dynamic Smagorinsky model (DSM) [Germano et al. (1991)], and the Dynamic Mixed Model (DMM) [Zang et al. (1993)]. The results show that NIA gives the best overall agreement with DNS. Both DMM and DSM over-predict the decay of the mean streamwise wall shear stress on the moving wall, while NIA gives results in close agreements with DNS. Similarly, NIA gives the best agreement with DNS in the prediction of the mean velocity, the higher-order turbulence statistics, and the lag angle between the mean shear and the turbulent shear stress. These results suggest that non-equilibrium wall-bounded turbulent flows can be accurately computed by LES with NIA as the SGS model.

Coupling extended magnetohydrodynamic fluid codes with radiofrequency ray tracing codes for fusion modeling

NASA Astrophysics Data System (ADS)

Jenkins, Thomas G.; Held, Eric D.

2015-09-01

Neoclassical tearing modes are macroscopic (L ∼ 1 m) instabilities in magnetic fusion experiments; if unchecked, these modes degrade plasma performance and may catastrophically destroy plasma confinement by inducing a disruption. Fortunately, the use of properly tuned and directed radiofrequency waves (λ ∼ 1 mm) can eliminate these modes. Numerical modeling of this difficult multiscale problem requires the integration of separate mathematical models for each length and time scale (Jenkins and Kruger, 2012 [21]); the extended MHD model captures macroscopic plasma evolution while the RF model tracks the flow and deposition of injected RF power through the evolving plasma profiles. The scale separation enables use of the eikonal (ray-tracing) approximation to model the RF wave propagation. In this work we demonstrate a technique, based on methods of computational geometry, for mapping the ensuing RF data (associated with discrete ray trajectories) onto the finite-element/pseudospectral grid that is used to model the extended MHD physics. In the new representation, the RF data can then be used to construct source terms in the equations of the extended MHD model, enabling quantitative modeling of RF-induced tearing mode stabilization. Though our specific implementation uses the NIMROD extended MHD (Sovinec et al., 2004 [22]) and GENRAY RF (Smirnov et al., 1994 [23]) codes, the approach presented can be applied more generally to any code coupling requiring the mapping of ray tracing data onto Eulerian grids.

The partial volume effect in the quantification of 1H magnetic resonance spectroscopy in Alzheimer's disease and aging.

PubMed

Mato Abad, Virginia; Quirós, Alicia; García-Álvarez, Roberto; Loureiro, Javier Pereira; Alvarez-Linera, Juan; Frank, Ana; Hernández-Tamames, Juan Antonio

2014-01-01

1H-MRS variability increases due to normal aging and also as a result of atrophy in grey and white matter caused by neurodegeneration. In this work, an automatic process was developed to integrate data from spectra and high-resolution anatomical images to quantify metabolites, taking into account tissue partial volumes within the voxel of interest avoiding additional spectra acquisitions required for partial volume correction. To evaluate this method, we use a cohort of 135 subjects (47 male and 88 female, aged between 57 and 99 years) classified into 4 groups: 38 healthy participants, 20 amnesic mild cognitive impairment patients, 22 multi-domain mild cognitive impairment patients, and 55 Alzheimer's disease patients. Our findings suggest that knowing the voxel composition of white and grey matter and cerebrospinal fluid is necessary to avoid partial volume variations in a single-voxel study and to decrease part of the variability found in metabolites quantification, particularly in those studies involving elder patients and neurodegenerative diseases. The proposed method facilitates the use of 1H-MRS techniques in statistical studies in Alzheimer's disease, because it provides more accurate quantitative measurements, reduces the inter-subject variability, and improves statistical results when performing group comparisons.

Magnetic fluid hyperthermia (MFH): Cancer treatment with AC magnetic field induced excitation of biocompatible superparamagnetic nanoparticles

NASA Astrophysics Data System (ADS)

Jordan, Andreas; Scholz, Regina; Wust, Peter; Fähling, Horst; Felix, Roland

1999-07-01

The story of hyperthermia with small particles in AC magnetic fields started in the late 1950s, but most of the studies were unfortunately conducted with inadequate animal systems, inexact thermometry and poor AC magnetic field parameters, so that any clinical implication was far behind the horizon. More than three decades later, it was found, that colloidal dispersions of superparamagnetic (subdomain) iron oxide nanoparticles exhibit an extraordinary specific absorption rate (SAR [ W/ g]), which is much higher at clinically tolerable H 0 f combinations in comparison to hysteresis heating of larger multidomain particles. This was the renaissance of a cancer treatment method, which has gained more and more attention in the last few years. Due to the increasing number of randomized clinical trials preferentially in Europe with conventional E-field hyperthermia systems, the general medical and physical experience in hyperthermia application is also rapidly growing. Taking this increasing clinical experience carefully into account together with the huge amount of new biological data on heat response of cells and tissues, the approach of magnetic fluid hyperthermia (MFH) is nowadays more promising than ever before. The present contribution reviews the current state of the art and some of the future perspectives supported by advanced methods of the so-called nanotechnology.

A 12-week multidomain intervention versus active control to reduce risk of Alzheimer’s disease: study protocol for a randomized controlled trial

PubMed Central

2013-01-01

Background Disappointing results from clinical trials of disease-modifying interventions for Alzheimer’s dementia (AD), along with reliable identification of modifiable risk factors in mid life from epidemiological studies, have contributed to calls to invest in risk-reduction interventions. It is also well known that AD-related pathological processes begin more than a decade before the development of clinical signs. These observations suggest that lifestyle interventions might be most effective when targeting non-symptomatic adults at risk of AD. To date, however, the few dementia risk-reduction programs available have targeted individual risk factors and/or were restricted to clinical settings. The current study describes the development of an evidence-based, theoretically-driven multidomain intervention to reduce AD risk in adults at risk. Method The design of Body Brain Life (BBL) is a randomized controlled trial (RCT) to evaluate a 12-week online AD risk-reduction intervention. Eligible participants with several modifiable risk factors on the Australian National University (ANU) AD Risk Index (ANU-ADRI) are randomly allocated to an online only group, an online and face-to-face group, or an active control group. We aim to recruit 180 participants, to undergo a comprehensive cognitive and physical assessment at baseline, post-intervention, and 6-month follow-up assessment. The intervention comprises seven online modules (dementia literacy, risk factor education, engagement in physical, social, and cognitive lifestyles, nutrition, and health monitoring) designed using contemporary models of health behavior change. Discussion The BBL program is a novel online intervention to reduce the risk of AD in middle-aged adults at risk. The trial is currently under way. It is hypothesized that participants in the intervention arms will make lifestyle changes in several domains, and that this will lead to a reduction in their AD risk profile. We also expect to show that health behavior change is underpinned by changes in psychological determinants of behavior. If successful, the findings will contribute to the development of further dementia risk reduction interventions, and thus contribute to the urgent need to lower dementia risk factors in the population to alter future projections of disease prevalence. Longer follow-up of BBL participants and replications using large samples are required to examine whether reduction in AD risk factors will be associated with reduced prevalence. Trial registration Reg. no. ACTRN12612000147886 PMID:23442574

The signaling helix: a common functional theme in diverse signaling proteins

PubMed Central

Anantharaman, Vivek; Balaji, S; Aravind, L

2006-01-01

Background The mechanism by which the signals are transmitted between receptor and effector domains in multi-domain signaling proteins is poorly understood. Results Using sensitive sequence analysis methods we identify a conserved helical segment of around 40 residues in a wide range of signaling proteins, including numerous sensor histidine kinases such as Sln1p, and receptor guanylyl cyclases such as the atrial natriuretic peptide receptor and nitric oxide receptors. We term this helical segment the signaling (S)-helix and present evidence that it forms a novel parallel coiled-coil element, distinct from previously known helical segments in signaling proteins, such as the Dimerization-Histidine phosphotransfer module of histidine kinases, the intra-cellular domains of the chemotaxis receptors, inter-GAF domain helical linkers and the α-helical HAMP module. Analysis of domain architectures allowed us to reconstruct the domain-neighborhood graph for the S-helix, which showed that the S-helix almost always occurs between two signaling domains. Several striking patterns in the domain neighborhood of the S-helix also became evident from the graph. It most often separates diverse N-terminal sensory domains from various C-terminal catalytic signaling domains such as histidine kinases, cNMP cyclase, PP2C phosphatases, NtrC-like AAA+ ATPases and diguanylate cyclases. It might also occur between two sensory domains such as PAS domains and occasionally between a DNA-binding HTH domain and a sensory domain. The sequence conservation pattern of the S-helix revealed the presence of a unique constellation of polar residues in the dimer-interface positions within the central heptad of the coiled-coil formed by the S-helix. Conclusion Combining these observations with previously reported mutagenesis studies on different S-helix-containing proteins we suggest that it functions as a switch that prevents constitutive activation of linked downstream signaling domains. However, upon occurrence of specific conformational changes due to binding of ligand or other sensory inputs in a linked upstream domain it transmits the signal to the downstream domain. Thus, the S-helix represents one of the most prevalent functional themes involved in the flow of signals between modules in diverse prokaryote-type multi-domain signaling proteins. Reviewers This article was reviewed by Frank Eisenhaber, Arcady Mushegian and Sandor Pongor. PMID:16953892

Optimizing Efficiency of Psychopathology Assessment through Quantitative Modeling: Development of a Brief Form of the Externalizing Spectrum Inventory

PubMed Central

Patrick, Christopher J.; Kramer, Mark D.; Krueger, Robert F.; Markon, Kristian E.

2014-01-01

The Externalizing Spectrum Inventory (ESI; Krueger, Markon, Patrick, Benning, & Kramer, 2007) provides for integrated, hierarchical assessment of a broad range of problem behaviors and traits in the domain of deficient impulse control. The ESI assesses traits and problems in this domain through 23 lower-order facet scales organized around three higher-order dimensions, reflecting general disinhibition, callous-aggression, and substance abuse. The full-form ESI contains 415 items, and a shorter form would be useful for questionnaire screening studies or multi-domain research protocols. The current work employed item response theory and structural modeling methods to create a 160-item brief form (ESI-bf) that provides for efficient measurement of the ESI’s lower-order facets and quantification of its higher-order dimensions either as scale-based factors or as item-based composites. The ESI-bf is recommended for use in research on psychological or neurobiological correlates of problems such as risk-taking, delinquency, aggression, and substance abuse, and studies of general and specific mechanisms that give rise to problems of these kinds. PMID:24320765

Preparation of hydroxyapatite/poly(lactic acid) hybrid microparticles for local drug delivery

NASA Astrophysics Data System (ADS)

Loca, D.; Locs, J.; Berzina-Cimdina, L.

2013-12-01

Calcium phosphate (CaP) bioceramic is well known as bioactive and biocompatible material in bone tissue regeneration applications. Apatitic CaP, especially nano sized hydroxyapatite (NHAp), is more similar to the natural apatite presented in the bone tissue than CaP bioceramics. In the current research NHAp was modified using biodegradable polymer - poly(lactic acid) (PLA) to develop composites providing bone regeneration and local drug delivery. NHAp/PLA microcapsules were prepared using solid-in-water-in-oil-in-water (s/w1/o/w2) encapsulation technology. The impact of primary and secondary emulsion stability on the emulsion droplet and microparticle properties was evaluated. The stability of final emulsion can be increased by varying the process parameters. Stable s/w1/o/w2 emulsion using 3ml of NHAp suspension, not less than 100ml of 4% PVA water solution and 10ml of 10% PLA solution in dichloromethane can be obtained. S/w1/o/w2 microencapuslation method can be effectively used for the preparation of multi-domain microcapsules achieving high NHAp encapsulation efficacy (93%).

A laplace transform-based technique for solving multiscale and multidomain problems: Application to a countercurrent hemodialyzer model.

PubMed

Simon, Laurent

2017-08-01

An integral-based method was employed to evaluate the behavior of a countercurrent hemodialyzer model. Solute transfer from the blood into the dialysate was described by writing mass balance equations over a section of the device. The approach provided Laplace transform concentration profiles on both sides of the membrane. Applications of the final value theorem led to the development of the effective time constants and steady-state concentrations in the exit streams. Transient responses were derived by a numerical inversion algorithm. Simulations show that the period elapsed, before reaching equilibrium in the effluents, decreased when the blood flow rate increased from 0.25 to 0.30 ml/s. The performance index decreased from 0.80 to 0.71 when the blood-to-dialysate flow ratio increased by 20% and increased from 0.80 to 0.85 when this fraction was reduced by 17%. The analytical solution predicted methadone removal in patients undergoing dialysis. Clinicians can use these findings to predict the time required to achieve a target extraction ratio. Copyright © 2017 Elsevier Ltd. All rights reserved.

A parallel multi-domain solution methodology applied to nonlinear thermal transport problems in nuclear fuel pins

DOE PAGES

Philip, Bobby; Berrill, Mark A.; Allu, Srikanth; ...

2015-01-26

We describe an efficient and nonlinearly consistent parallel solution methodology for solving coupled nonlinear thermal transport problems that occur in nuclear reactor applications over hundreds of individual 3D physical subdomains. Efficiency is obtained by leveraging knowledge of the physical domains, the physics on individual domains, and the couplings between them for preconditioning within a Jacobian Free Newton Krylov method. Details of the computational infrastructure that enabled this work, namely the open source Advanced Multi-Physics (AMP) package developed by the authors are described. The details of verification and validation experiments, and parallel performance analysis in weak and strong scaling studies demonstratingmore » the achieved efficiency of the algorithm are presented. Moreover, numerical experiments demonstrate that the preconditioner developed is independent of the number of fuel subdomains in a fuel rod, which is particularly important when simulating different types of fuel rods. Finally, we demonstrate the power of the coupling methodology by considering problems with couplings between surface and volume physics and coupling of nonlinear thermal transport in fuel rods to an external radiation transport code.« less

Magnetoabsorption and magnetic hysteresis in Ni ferrite nanoparticles

NASA Astrophysics Data System (ADS)

Hernández-Gómez, P.; Muñoz, J. M.; Valente, M. A.; Torres, C.; de Francisco, C.

2013-01-01

Nickel ferrite nanoparticles were prepared by a modified sol-gel technique employing coconut oil, and then annealed at different temperatures in 400-1200 °C range. This route of preparation has revealed to be one efficient and cheap technique to obtain high quality nickel ferrite nanosized powder. Sample particles sizes obtained with XRD data and Scherrer's formula lie in 13 nm to 138 nm, with increased size with annealing temperature. Hysteresis loops have been obtained at room temperature with an inductive method. Magnetic field induced microwave absorption in nanoscale ferrites is a recent an active area of research, in order to characterize and explore potential novel applications. In the present work microwave magnetoabsorption data of the annealed nickel ferrite nanoparticles are presented. These data have been obtained with a system based on a network analyzer that operates in the frequency range 0 - 8.5 GHz. At fields up to 400 mT we can observe a peak according to ferromagnetic resonance theory. Sample annealed at higher temperature exhibits different absorption, coercivity and saturation magnetization figures, revealing its multidomain character.

Turbulence statistics with quantified uncertainty in cold-wall supersonic channel flow

NASA Astrophysics Data System (ADS)

Ulerich, Rhys; Moser, Robert D.

2012-11-01

To investigate compressibility effects in wall-bounded turbulence, a series of direct numerical simulations of compressible channel flow with isothermal (cold) walls have been conducted. All combinations of Re = { 3000 , 5000 } and Ma = { 0 . 1 , 0 . 5 , 1 . 5 , 3 . 0 } have been simulated where the Reynolds and Mach numbers are based on bulk velocity and sound speed at the wall temperature. Turbulence statistics with precisely quantified uncertainties computed from these simulations will be presented and are being made available in a public data base at http://turbulence.ices.utexas.edu/. The simulations were performed using a new pseudo-spectral code called Suzerain, which was designed to efficiently produce high quality data on compressible, wall-bounded turbulent flows using a semi-implicit Fourier/B-spline numerical formulation. This work is supported by the Department of Energy [National Nuclear Security Administration] under Award Number [DE-FC52-08NA28615].

Numerical Simulation and Quantitative Uncertainty Assessment of Microchannel Flow

NASA Astrophysics Data System (ADS)

Debusschere, Bert; Najm, Habib; Knio, Omar; Matta, Alain; Ghanem, Roger; Le Maitre, Olivier

2002-11-01

This study investigates the effect of uncertainty in physical model parameters on computed electrokinetic flow of proteins in a microchannel with a potassium phosphate buffer. The coupled momentum, species transport, and electrostatic field equations give a detailed representation of electroosmotic and pressure-driven flow, including sample dispersion mechanisms. The chemistry model accounts for pH-dependent protein labeling reactions as well as detailed buffer electrochemistry in a mixed finite-rate/equilibrium formulation. To quantify uncertainty, the governing equations are reformulated using a pseudo-spectral stochastic methodology, which uses polynomial chaos expansions to describe uncertain/stochastic model parameters, boundary conditions, and flow quantities. Integration of the resulting equations for the spectral mode strengths gives the evolution of all stochastic modes for all variables. Results show the spatiotemporal evolution of uncertainties in predicted quantities and highlight the dominant parameters contributing to these uncertainties during various flow phases. This work is supported by DARPA.