2d PDE Linear Symmetric Matrix Solver
1983-10-01
ICCG2 (Incomplete Cholesky factorized Conjugate Gradient algorithm for 2d symmetric problems) was developed to solve a linear symmetric matrix system arising from a 9-point discretization of two-dimensional elliptic and parabolic partial differential equations found in plasma physics applications, such as resistive MHD, spatial diffusive transport, and phase space transport (Fokker-Planck equation) problems. These problems share the common feature of being stiff and requiring implicit solution techniques. When these parabolic or elliptic PDE''s are discretized withmore » finite-difference or finite-element methods,the resulting matrix system is frequently of block-tridiagonal form. To use ICCG2, the discretization of the two-dimensional partial differential equation and its boundary conditions must result in a block-tridiagonal supermatrix composed of elementary tridiagonal matrices. The incomplete Cholesky conjugate gradient algorithm is used to solve the linear symmetric matrix equation. Loops are arranged to vectorize on the Cray1 with the CFT compiler, wherever possible. Recursive loops, which cannot be vectorized, are written for optimum scalar speed. For matrices lacking symmetry, ILUCG2 should be used. Similar methods in three dimensions are available in ICCG3 and ILUCG3. A general source containing extensions and macros, which must be processed by a pre-compiler to obtain the standard FORTRAN source, is provided along with the standard FORTRAN source because it is believed to be more readable. The pre-compiler is not included, but pre-compilation may be performed by a text editor as described in the UCRL-88746 Preprint.« less
2d PDE Linear Asymmetric Matrix Solver
1983-10-01
ILUCG2 (Incomplete LU factorized Conjugate Gradient algorithm for 2d problems) was developed to solve a linear asymmetric matrix system arising from a 9-point discretization of two-dimensional elliptic and parabolic partial differential equations found in plasma physics applications, such as plasma diffusion, equilibria, and phase space transport (Fokker-Planck equation) problems. These equations share the common feature of being stiff and requiring implicit solution techniques. When these parabolic or elliptic PDE''s are discretized with finite-difference or finite-elementmore » methods, the resulting matrix system is frequently of block-tridiagonal form. To use ILUCG2, the discretization of the two-dimensional partial differential equation and its boundary conditions must result in a block-tridiagonal supermatrix composed of elementary tridiagonal matrices. A generalization of the incomplete Cholesky conjugate gradient algorithm is used to solve the matrix equation. Loops are arranged to vectorize on the Cray1 with the CFT compiler, wherever possible. Recursive loops, which cannot be vectorized, are written for optimum scalar speed. For problems having a symmetric matrix ICCG2 should be used since it runs up to four times faster and uses approximately 30% less storage. Similar methods in three dimensions are available in ICCG3 and ILUCG3. A general source, containing extensions and macros, which must be processed by a pre-compiler to obtain the standard FORTRAN source, is provided along with the standard FORTRAN source because it is believed to be more readable. The pre-compiler is not included, but pre-compilation may be performed by a text editor as described in the UCRL-88746 Preprint.« less
Multiscale Universal Interface: A concurrent framework for coupling heterogeneous solvers
NASA Astrophysics Data System (ADS)
Tang, Yu-Hang; Kudo, Shuhei; Bian, Xin; Li, Zhen; Karniadakis, George Em
2015-09-01
Concurrently coupled numerical simulations using heterogeneous solvers are powerful tools for modeling multiscale phenomena. However, major modifications to existing codes are often required to enable such simulations, posing significant difficulties in practice. In this paper we present a C++ library, i.e. the Multiscale Universal Interface (MUI), which is capable of facilitating the coupling effort for a wide range of multiscale simulations. The library adopts a header-only form with minimal external dependency and hence can be easily dropped into existing codes. A data sampler concept is introduced, combined with a hybrid dynamic/static typing mechanism, to create an easily customizable framework for solver-independent data interpretation. The library integrates MPI MPMD support and an asynchronous communication protocol to handle inter-solver information exchange irrespective of the solvers' own MPI awareness. Template metaprogramming is heavily employed to simultaneously improve runtime performance and code flexibility. We validated the library by solving three different multiscale problems, which also serve to demonstrate the flexibility of the framework in handling heterogeneous models and solvers. In the first example, a Couette flow was simulated using two concurrently coupled Smoothed Particle Hydrodynamics (SPH) simulations of different spatial resolutions. In the second example, we coupled the deterministic SPH method with the stochastic Dissipative Particle Dynamics (DPD) method to study the effect of surface grafting on the hydrodynamics properties on the surface. In the third example, we consider conjugate heat transfer between a solid domain and a fluid domain by coupling the particle-based energy-conserving DPD (eDPD) method with the Finite Element Method (FEM).
Multiscale Universal Interface: A concurrent framework for coupling heterogeneous solvers
Tang, Yu-Hang; Kudo, Shuhei; Bian, Xin; Li, Zhen; Karniadakis, George Em
2015-09-15
Graphical abstract: - Abstract: Concurrently coupled numerical simulations using heterogeneous solvers are powerful tools for modeling multiscale phenomena. However, major modifications to existing codes are often required to enable such simulations, posing significant difficulties in practice. In this paper we present a C++ library, i.e. the Multiscale Universal Interface (MUI), which is capable of facilitating the coupling effort for a wide range of multiscale simulations. The library adopts a header-only form with minimal external dependency and hence can be easily dropped into existing codes. A data sampler concept is introduced, combined with a hybrid dynamic/static typing mechanism, to create an easily customizable framework for solver-independent data interpretation. The library integrates MPI MPMD support and an asynchronous communication protocol to handle inter-solver information exchange irrespective of the solvers' own MPI awareness. Template metaprogramming is heavily employed to simultaneously improve runtime performance and code flexibility. We validated the library by solving three different multiscale problems, which also serve to demonstrate the flexibility of the framework in handling heterogeneous models and solvers. In the first example, a Couette flow was simulated using two concurrently coupled Smoothed Particle Hydrodynamics (SPH) simulations of different spatial resolutions. In the second example, we coupled the deterministic SPH method with the stochastic Dissipative Particle Dynamics (DPD) method to study the effect of surface grafting on the hydrodynamics properties on the surface. In the third example, we consider conjugate heat transfer between a solid domain and a fluid domain by coupling the particle-based energy-conserving DPD (eDPD) method with the Finite Element Method (FEM)
A Multiscale Wavelet Solver with O( n) Complexity
NASA Astrophysics Data System (ADS)
Williams, John R.; Amaratunga, Kevin
1995-11-01
In this paper, we use the biorthogonal wavelets recently constructed by Dahlke and Weinreich to implement a highly efficient procedure for solving a certain class of one-dimensional problems, (∂21/∂x21)u = f,I ɛ Z, I > 0. For these problems, the discrete biorthogonal wavelet transform allows us to set up a system of wavelet-Galerkin equations in which the scales are uncoupled, so that a true multiscale solution procedure may be formulated. We prove that the resulting stiffness matrix is in fact an almost perfectly diagonal matrix (the original aim of the construction was to achieve a block diagonal structure) and we show that this leads to an algorithm whose cost is O(n). We also present numerical results which demonstrate that the multiscale biorthogonal wavelet algorithm is superior to the more conventional single scale orthogonal wavelet approach both in terms of speed and in terms of convergence.
Bakhos, Tania; Saibaba, Arvind K.; Kitanidis, Peter K.
2015-10-15
We consider the problem of estimating parameters in large-scale weakly nonlinear inverse problems for which the underlying governing equations is a linear, time-dependent, parabolic partial differential equation. A major challenge in solving these inverse problems using Newton-type methods is the computational cost associated with solving the forward problem and with repeated construction of the Jacobian, which represents the sensitivity of the measurements to the unknown parameters. Forming the Jacobian can be prohibitively expensive because it requires repeated solutions of the forward and adjoint time-dependent parabolic partial differential equations corresponding to multiple sources and receivers. We propose an efficient method based on a Laplace transform-based exponential time integrator combined with a flexible Krylov subspace approach to solve the resulting shifted systems of equations efficiently. Our proposed solver speeds up the computation of the forward and adjoint problems, thus yielding significant speedup in total inversion time. We consider an application from Transient Hydraulic Tomography (THT), which is an imaging technique to estimate hydraulic parameters related to the subsurface from pressure measurements obtained by a series of pumping tests. The algorithms discussed are applied to a synthetic example taken from THT to demonstrate the resulting computational gains of this proposed method.
Terascale Optimal PDE Simulations
David Keyes
2009-07-28
The Terascale Optimal PDE Solvers (TOPS) Integrated Software Infrastructure Center (ISIC) was created to develop and implement algorithms and support scientific investigations performed by DOE-sponsored researchers. These simulations often involve the solution of partial differential equations (PDEs) on terascale computers. The TOPS Center researched, developed and deployed an integrated toolkit of open-source, optimal complexity solvers for the nonlinear partial differential equations that arise in many DOE application areas, including fusion, accelerator design, global climate change and reactive chemistry. The algorithms created as part of this project were also designed to reduce current computational bottlenecks by orders of magnitude on terascale computers, enabling scientific simulation on a scale heretofore impossible.
Min Yun, B; Aidun, Cyrus K; Yoganathan, Ajit P
2014-10-01
Bileaflet mechanical heart valves (BMHVs) are among the most popular prostheses to replace defective native valves. However, complex flow phenomena caused by the prosthesis are thought to induce serious thromboembolic complications. This study aims at employing a novel multiscale numerical method that models realistic sized suspended platelets for assessing blood damage potential in flow through BMHVs. A previously validated lattice-Boltzmann method (LBM) is used to simulate pulsatile flow through a 23 mm St. Jude Medical (SJM) Regent™ valve in the aortic position at very high spatiotemporal resolution with the presence of thousands of suspended platelets. Platelet damage is modeled for both the systolic and diastolic phases of the cardiac cycle. No platelets exceed activation thresholds for any of the simulations. Platelet damage is determined to be particularly high for suspended elements trapped in recirculation zones, which suggests a shift of focus in blood damage studies away from instantaneous flow fields and toward high flow mixing regions. In the diastolic phase, leakage flow through the b-datum gap is shown to cause highest damage to platelets. This multiscale numerical method may be used as a generic solver for evaluating blood damage in other cardiovascular flows and devices. PMID:25070372
NASA Astrophysics Data System (ADS)
Cerroni, D.; Manservisi, S.; Pozzetti, G.
2015-11-01
In this work we investigate the potentialities of multi-scale engineering techniques to approach complex problems related to biomedical and biological fields. In particular we study the interaction between blood and blood vessel focusing on the presence of an aneurysm. The study of each component of the cardiovascular system is very difficult due to the fact that the movement of the fluid and solid is determined by the rest of system through dynamical boundary conditions. The use of multi-scale techniques allows us to investigate the effect of the whole loop on the aneurysm dynamic. A three-dimensional fluid-structure interaction model for the aneurysm is developed and coupled to a mono-dimensional one for the remaining part of the cardiovascular system, where a point zero-dimensional model for the heart is provided. In this manner it is possible to achieve rigorous and quantitative investigations of the cardiovascular disease without loosing the system dynamic. In order to study this biomedical problem we use a monolithic fluid-structure interaction (FSI) model where the fluid and solid equations are solved together. The use of a monolithic solver allows us to handle the convergence issues caused by large deformations. By using this monolithic approach different solid and fluid regions are treated as a single continuum and the interface conditions are automatically taken into account. In this way the iterative process characteristic of the commonly used segregated approach, it is not needed any more.
NASA Astrophysics Data System (ADS)
Vencels, Juris; Delzanno, Gian Luca; Manzini, Gianmarco; Markidis, Stefano; Peng, Ivy Bo; Roytershteyn, Vadim
2016-05-01
We present the design and implementation of a spectral code, called SpectralPlasmaSolver (SPS), for the solution of the multi-dimensional Vlasov-Maxwell equations. The method is based on a Hermite-Fourier decomposition of the particle distribution function. The code is written in Fortran and uses the PETSc library for solving the non-linear equations and preconditioning and the FFTW library for the convolutions. SPS is parallelized for shared- memory machines using OpenMP. As a verification example, we discuss simulations of the two-dimensional Orszag-Tang vortex problem and successfully compare them against a fully kinetic Particle-In-Cell simulation. An assessment of the performance of the code is presented, showing a significant improvement in the code running-time achieved by preconditioning, while strong scaling tests show a factor of 10 speed-up using 16 threads.
Multithreaded Model for Dynamic Load Balancing Parallel Adaptive PDE Computations
NASA Technical Reports Server (NTRS)
Chrisochoides, Nikos
1995-01-01
We present a multithreaded model for the dynamic load-balancing of numerical, adaptive computations required for the solution of Partial Differential Equations (PDE's) on multiprocessors. Multithreading is used as a means of exploring concurrency in the processor level in order to tolerate synchronization costs inherent to traditional (non-threaded) parallel adaptive PDE solvers. Our preliminary analysis for parallel, adaptive PDE solvers indicates that multithreading can be used an a mechanism to mask overheads required for the dynamic balancing of processor workloads with computations required for the actual numerical solution of the PDE's. Also, multithreading can simplify the implementation of dynamic load-balancing algorithms, a task that is very difficult for traditional data parallel adaptive PDE computations. Unfortunately, multithreading does not always simplify program complexity, often makes code re-usability not an easy task, and increases software complexity.
Heroux, Michael A.
2007-03-01
HPCCG is a simple PDE application and preconditioned conjugate gradient solver that solves a linear system on a beam-shaped domain. Although it does not address many performance issues present in real engineering applications, such as load imbalance and preconditioner scalability, it can serve as a first "sanity test" of new processor design choices, inter-connect network design choices and the scalability of a new computer system. Because it is self-contained, easy to compile and easily scaled to 100s or 1000s of porcessors, it can be an attractive study code for computer system designers.
2007-03-01
HPCCG is a simple PDE application and preconditioned conjugate gradient solver that solves a linear system on a beam-shaped domain. Although it does not address many performance issues present in real engineering applications, such as load imbalance and preconditioner scalability, it can serve as a first "sanity test" of new processor design choices, inter-connect network design choices and the scalability of a new computer system. Because it is self-contained, easy to compile and easily scaledmore » to 100s or 1000s of porcessors, it can be an attractive study code for computer system designers.« less
NASA Astrophysics Data System (ADS)
Prástaro, Agostino
2008-02-01
Following our previous results on this subject [R.P. Agarwal, A. Prástaro, Geometry of PDE's. III(I): Webs on PDE's and integral bordism groups. The general theory, Adv. Math. Sci. Appl. 17 (2007) 239-266; R.P. Agarwal, A. Prástaro, Geometry of PDE's. III(II): Webs on PDE's and integral bordism groups. Applications to Riemannian geometry PDE's, Adv. Math. Sci. Appl. 17 (2007) 267-285; A. Prástaro, Geometry of PDE's and Mechanics, World Scientific, Singapore, 1996; A. Prástaro, Quantum and integral (co)bordism in partial differential equations, Acta Appl. Math. (5) (3) (1998) 243-302; A. Prástaro, (Co)bordism groups in PDE's, Acta Appl. Math. 59 (2) (1999) 111-201; A. Prástaro, Quantized Partial Differential Equations, World Scientific Publishing Co, Singapore, 2004, 500 pp.; A. Prástaro, Geometry of PDE's. I: Integral bordism groups in PDE's, J. Math. Anal. Appl. 319 (2006) 547-566; A. Prástaro, Geometry of PDE's. II: Variational PDE's and integral bordism groups, J. Math. Anal. Appl. 321 (2006) 930-948; A. Prástaro, Th.M. Rassias, Ulam stability in geometry of PDE's, Nonlinear Funct. Anal. Appl. 8 (2) (2003) 259-278; I. Stakgold, Boundary Value Problems of Mathematical Physics, I, The MacMillan Company, New York, 1967; I. Stakgold, Boundary Value Problems of Mathematical Physics, II, Collier-MacMillan, Canada, Ltd, Toronto, Ontario, 1968], integral bordism groups of the Navier-Stokes equation are calculated for smooth, singular and weak solutions, respectively. Then a characterization of global solutions is made on this ground. Enough conditions to assure existence of global smooth solutions are given and related to nullity of integral characteristic numbers of the boundaries. Stability of global solutions are related to some characteristic numbers of the space-like Cauchy dataE Global solutions of variational problems constrained by (NS) are classified by means of suitable integral bordism groups too.
Efficient Implementation of Multigrid Solvers on Message-Passing Parrallel Systems
NASA Technical Reports Server (NTRS)
Lou, John
1994-01-01
We discuss our implementation strategies for finite difference multigrid partial differential equation (PDE) solvers on message-passing systems. Our target parallel architecture is Intel parallel computers: the Delta and Paragon system.
Large Scale Non-Linear Programming for PDE Constrained Optimization
VAN BLOEMEN WAANDERS, BART G.; BARTLETT, ROSCOE A.; LONG, KEVIN R.; BOGGS, PAUL T.; SALINGER, ANDREW G.
2002-10-01
Three years of large-scale PDE-constrained optimization research and development are summarized in this report. We have developed an optimization framework for 3 levels of SAND optimization and developed a powerful PDE prototyping tool. The optimization algorithms have been interfaced and tested on CVD problems using a chemically reacting fluid flow simulator resulting in an order of magnitude reduction in compute time over a black box method. Sandia's simulation environment is reviewed by characterizing each discipline and identifying a possible target level of optimization. Because SAND algorithms are difficult to test on actual production codes, a symbolic simulator (Sundance) was developed and interfaced with a reduced-space sequential quadratic programming framework (rSQP++) to provide a PDE prototyping environment. The power of Sundance/rSQP++ is demonstrated by applying optimization to a series of different PDE-based problems. In addition, we show the merits of SAND methods by comparing seven levels of optimization for a source-inversion problem using Sundance and rSQP++. Algorithmic results are discussed for hierarchical control methods. The design of an interior point quadratic programming solver is presented.
Stanley, Vendall S.; Heroux, Michael A.; Hoekstra, Robert J.; Sala, Marzio
2004-03-01
Amesos is the Direct Sparse Solver Package in Trilinos. The goal of Amesos is to make AX=S as easy as it sounds, at least for direct methods. Amesos provides interfaces to a number of third party sparse direct solvers, including SuperLU, SuperLU MPI, DSCPACK, UMFPACK and KLU. Amesos provides a common object oriented interface to the best sparse direct solvers in the world. A sparse direct solver solves for x in Ax = b. where A is a matrix and x and b are vectors (or multi-vectors). A sparse direct solver flrst factors A into trinagular matrices L and U such that A = LU via gaussian elimination and then solves LU x = b. Switching amongst solvers in Amesos roquires a change to a single parameter. Yet, no solver needs to be linked it, unless it is used. All conversions between the matrices provided by the user and the format required by the underlying solver is performed by Amesos. As new sparse direct solvers are created, they will be incorporated into Amesos, allowing the user to simpty link with the new solver, change a single parameter in the calling sequence, and use the new solver. Amesos allows users to specify whether the matrix has changed. Amesos can be used anywhere that any sparse direct solver is needed.
2004-03-01
Amesos is the Direct Sparse Solver Package in Trilinos. The goal of Amesos is to make AX=S as easy as it sounds, at least for direct methods. Amesos provides interfaces to a number of third party sparse direct solvers, including SuperLU, SuperLU MPI, DSCPACK, UMFPACK and KLU. Amesos provides a common object oriented interface to the best sparse direct solvers in the world. A sparse direct solver solves for x in Ax = b. wheremore » A is a matrix and x and b are vectors (or multi-vectors). A sparse direct solver flrst factors A into trinagular matrices L and U such that A = LU via gaussian elimination and then solves LU x = b. Switching amongst solvers in Amesos roquires a change to a single parameter. Yet, no solver needs to be linked it, unless it is used. All conversions between the matrices provided by the user and the format required by the underlying solver is performed by Amesos. As new sparse direct solvers are created, they will be incorporated into Amesos, allowing the user to simpty link with the new solver, change a single parameter in the calling sequence, and use the new solver. Amesos allows users to specify whether the matrix has changed. Amesos can be used anywhere that any sparse direct solver is needed.« less
A framework for the construction of preconditioners for systems of PDE
Holmgren, S.; Otto, K.
1994-12-31
The authors consider the solution of systems of partial differential equations (PDE) in 2D or 3D using preconditioned CG-like iterative methods. The PDE is discretized using a finite difference scheme with arbitrary order of accuracy. The arising sparse and highly structured system of equations is preconditioned using a discretization of a modified PDE, possibly exploiting a different discretization stencil. The preconditioner corresponds to a separable problem, and the discretization in one space direction is constructed so that the corresponding matrix is diagonalized by a unitary transformation. If this transformation is computable using a fast O(n log{sub 2} n) algorithm, the resulting preconditioner solve is of the same complexity. Also, since the preconditioner solves are based on a dimensional splitting, the intrinsic parallelism is good. Different choices of the unitary transformation are considered, e.g., the discrete Fourier transform, sine transform, and modified sine transform. The preconditioners fully exploit the structure of the original problem, and it is shown how to compute the parameters describing them subject to different optimality constraints. Some of these results recover results derived by e.g. R. Chan, T. Chan, and E. Tyrtyshnikov, but here they are stated in a {open_quotes}PDE context{close_quotes}. Numerical experiments where different preconditioners are exploited are presented. Primarily, high-order accurate discretizations for first-order PDE problems are studied, but also second-order derivatives are considered. The results indicate that utilizing preconditioners based on fast solvers for modified PDE problems yields good solution algorithms. These results extend previously derived theoretical and numerical results for second-order approximations for first-order PDE, exploiting preconditioners based on fast Fourier transforms.
On PDE solution in transient optimization of gas networks
NASA Astrophysics Data System (ADS)
Steinbach, Marc C.
2007-06-01
Operative planning in gas distribution networks leads to large-scale mixed-integer optimization problems involving a hyperbolic PDE defined on a graph. We consider the NLP obtained under prescribed combinatorial decisions--or as relaxation in a branch-and-bound framework, addressing in particular the KKT systems arising in primal-dual interior methods. We propose a custom solution algorithm using sparse projections locally in time, based on the KKT systems' structural properties in space as induced by the discretized gas flow equations in combination with the underlying network topology. The numerical efficiency and accuracy of the algorithm are investigated, and detailed computational comparisons with a previously developed control space method and with the multifrontal solver MA27 are provided.
Bordner, J.; Saied, F.
1996-12-31
GLab3D is an enhancement of an interactive environment (MGLab) for experimenting with iterative solvers and multigrid algorithms. It is implemented in MATLAB. The new version has built-in 3D elliptic pde`s and several iterative methods and preconditioners that were not available in the original version. A sparse direct solver option has also been included. The multigrid solvers have also been extended to 3D. The discretization and pde domains are restricted to standard finite differences on the unit square/cube. The power of this software studies in the fact that no programming is needed to solve, for example, the convection-diffusion equation in 3D with TFQMR and a customized V-cycle preconditioner, for a variety of problem sizes and mesh Reynolds, numbers. In addition to the graphical user interface, some sample drivers are included to show how experiments can be composed using the underlying suite of problems and solvers.
Demirbas, Didem; Wyman, Arlene R.; Shimizu-Albergine, Masami; Cakici, Ozgur; Beavo, Joseph A.; Hoffman, Charles S.
2013-01-01
A cell-based high-throughput screen (HTS) was developed to detect phosphodiesterase 8 (PDE8) and PDE4/8 combination inhibitors. By replacing the Schizosaccharomyces pombe PDE gene with the murine PDE8A1 gene in strains lacking adenylyl cyclase, we generated strains whose protein kinase A (PKA)-stimulated growth in 5-fluoro orotic acid (5FOA) medium reflects PDE8 activity. From our previously-identified PDE4 and PDE7 inhibitors, we identified a PDE4/8 inhibitor that allowed us to optimize screening conditions. Of 222,711 compounds screened, ∼0.2% displayed composite Z scores of >20. Additional yeast-based assays using the most effective 367 compounds identified 30 candidates for further characterization. Among these, compound BC8-15 displayed the lowest IC50 value for both PDE4 and PDE8 inhibition in in vitro enzyme assays. This compound also displays significant activity against PDE10A and PDE11A. BC8-15 elevates steroidogenesis in mouse Leydig cells as a single pharmacological agent. Assays using BC8-15 and two structural derivatives support a model in which PDE8 is a primary regulator of testosterone production by Leydig cells, with an additional role for PDE4 in this process. BC8-15, BC8-15A, and BC8-15C, which are commercially available compounds, display distinct patterns of activity against PDE4, PDE8, PDE10A, and PDE11A, representing a chemical toolkit that could be used to examine the biological roles of these enzymes in cell culture systems. PMID:23967182
Biomolecular surface construction by PDE transform
Zheng, Qiong; Yang, Siyang; Wei, Guo-Wei
2011-01-01
This work proposes a new framework for the surface generation based on the partial differential equation (PDE) transform. The PDE transform has recently been introduced as a general approach for the mode decomposition of images, signals, and data. It relies on the use of arbitrarily high order PDEs to achieve the time-frequency localization, control the spectral distribution, and regulate the spatial resolution. The present work provides a new variational derivation of high order PDE transforms. The fast Fourier transform is utilized to accomplish the PDE transform so as to avoid stringent stability constraints in solving high order PDEs. As a consequence, the time integration of high order PDEs can be done efficiently with the fast Fourier transform. The present approach is validated with a variety of test examples in two and three-dimensional settings. We explore the impact of the PDE transform parameters, such as the PDE order and propagation time, on the quality of resulting surfaces. Additionally, we utilize a set of 10 proteins to compare the computational efficiency of the present surface generation method and the MSMS approach in Cartesian meshes. Moreover, we analyze the present method by examining some benchmark indicators of biomolecular surface, i.e., surface area, surface enclosed volume, solvation free energy and surface electrostatic potential. A test set of 13 protein molecules is used in the present investigation. The electrostatic analysis is carried out via the Poisson-Boltzmann equation model. To further demonstrate the utility of the present PDE transform based surface method, we solve the Poisson-Nernst-Planck (PNP) equations with a PDE transform surface of a protein. Second order convergence is observed for the electrostatic potential and concentrations. Finally, to test the capability and efficiency of the present PDE transform based surface generation method, we apply it to the construction of an excessively large biomolecule, a virus
Wilson, Lindsay S; Brandon, Nicholas J
2015-01-01
Cyclic AMP and cyclic GMP are essential second messengers that regulate multiple signaling pathways in virtually all cell types. Their accumulation in cells is finely regulated by cyclic nucleotide phosphodiesterases (PDEs), the only enzymes that can degrade these signaling molecules and thus provide exquisite control over intracellular signaling processes. One PDE family, PDE10A, is highly enriched in the brain and its unique expression profile in specific brain regions of interest, in particular to antipsychotic treatment, has made it an attractive therapeutic target for the treatment of schizophrenia. However, after a Phase II trial failure of a selective PDE10A inhibitor for the treatment of schizophrenia, it has encouraged the field to reexamine the role of this enzyme in the brain, and the possible CNS disorders in which PDE10A inhibition could be therapeutic. We will review the localization of PDE10A, both within the brain and the neuron and discuss how its role in regulating cAMP and cGMP accumulation modulates intracellular signaling pathways. Since this cellular signaling has best been documented in the striatum, we will focus our discussion of PDE10A in the context of disorders that affect the basal ganglia, including psychiatric disorders such as bipolar disorder and autism spectrum disorders and the movement disorders, including Parkinson's disease and Huntington's disease.
Galindo-Tovar, Alejandro; Vargas, María Luisa; Kaumann, Alberto J
2016-02-01
Phosphodiesterases PDE2, PDE3, and PDE4 are expressed in murine sinoatrial cells. PDE3 and/or PDE4 reduce heart rate but apparently do not influence the tachycardia mediated through sinoatrial β1- and β2-adrenoceptors despite the high content of sinoatrial cAMP. The function of PDE2 is, however, uncertain. Prostaglandin PGE1 elicits sinoatrial tachycardia through EP receptors, but the control by phosphodiesterases is unknown. We investigated on spontaneously beating right atria of mice the effects of the PDE2 inhibitors Bay 60-7550 and EHNA on basal beating and the tachycardia produced by noradrenaline (3 nM) and PGE1 (1 μM). Bay 60-7550 (1 μM), but not EHNA (10 μM), increased basal sinoatrial beating. EHNA also failed to produce tachycardia in the presence of the adenosine deaminase inhibitor 2'-deoxycoformycin (10 μM), remaining inconclusive whether PDE2 reduces basal sinoatrial beating. Rolipram (10 μM) and cilostamide (300 nM) caused moderate tachycardia. The tachycardia evoked by Bay 60-7550 was similar in the absence and presence of rolipram. Noradrenaline elicited stable tachycardia that was not increased by Bay 60-7550. A stable tachycardia caused by PGE1 was not increased by the inhibitors of PDE2, PDE3, and PDE4. Unlike PDE3 and PDE4 which reduce murine basal sinoatrial beating, a possible effect of PDE2 needs further research. The stable tachycardia produced by noradrenaline and PGE1, together with the lack potentiation by the inhibitors of PDE2, PDE3, and PDE4, suggests that cAMP generated at the receptor compartments is hardly hydrolyzed by these phophodiesterases. Evidence from human volunteers is consistent with this proposal.
Wunder, Frank; Quednau, Ramona; Geerts, Andreas; Barg, Martina; Tersteegen, Adrian
2013-10-01
We report here the generation and pharmacological characterization of two novel PDE 4B1 and PDE 4D3 reporter cell lines. Intracellular cAMP levels are monitored in these cells by a cAMP-sensitive biosensor. We used the recombinant PDE 4B1 and PDE 4D3 reporter cell lines to characterize the cellular effects of various competitive and allosteric PDE 4 inhibitors. In addition, we compared the cellular activity of these PDE 4 inhibitors with the in vitro inhibition of full-length PDE 4D3 and a truncated enzyme comprising the PDE 4D3 catalytic domain. Two different groups of PDE 4 inhibitors could be identified. The first group, including competitive inhibitors like roflumilast, cilomilast and piclamilast, shows similar in vitro activity on full-length and truncated PDE 4D3 and comparably low cellular activity. The second group, including the allosteric inhibitors PMNPQ, D159153, and D159404, shows much better inhibition of full-length versus truncated PDE 4D3. In addition, these compounds show high cellular activity. Our data obtained with the prototype PDE 4 inhibitor rolipram show that rolipram has properties intermediate between the two groups. The results imply that these novel PDE 4 reporter cell lines are well-suited for the characterization of the cellular activity of PDE 4 inhibitors and may also support a better understanding of the complex PDE 4 pharmacology.
Multiscale Simulation Framework for Coupled Fluid Flow and Mechanical Deformation
Tchelepi, Hamdi
2014-11-14
A multiscale linear-solver framework for the pressure equation associated with flow in highly heterogeneous porous formations was developed. The multiscale based approach is cast in a general algebraic form, which facilitates integration of the new scalable linear solver in existing flow simulators. The Algebraic Multiscale Solver (AMS) is employed as a preconditioner within a multi-stage strategy. The formulations investigated include the standard MultiScale Finite-Element (MSFE) andMultiScale Finite-Volume (MSFV) methods. The local-stage solvers include incomplete factorization and the so-called Correction Functions (CF) associated with the MSFV approach. Extensive testing of AMS, as an iterative linear solver, indicate excellent convergence rates and computational scalability. AMS compares favorably with advanced Algebraic MultiGrid (AMG) solvers for highly detailed three-dimensional heterogeneous models. Moreover, AMS is expected to be especially beneficial in solving time-dependent problems of coupled multiphase flow and transport in large-scale subsurface formations.
A survey of deterministic solvers for rarefied flows (Invited)
NASA Astrophysics Data System (ADS)
Mieussens, Luc
2014-12-01
Numerical simulations of rarefied gas flows are generally made with DSMC methods. Up to a recent period, deterministic numerical methods based on a discretization of the Boltzmann equation were restricted to simple problems (1D, linearized flows, or simple geometries, for instance). In the last decade, several deterministic solvers have been developed in different teams to tackle more complex problems like 2D and 3D flows. Some of them are based on the full Boltzmann equation. Solving this equation numerically is still very challenging, and 3D solvers are still restricted to monoatomic gases, even if recent works have proved it was possible to simulate simple flows for polyatomic gases. Other solvers are based on simpler BGK like models: they allow for much more intensive simulations on 3D flows for realistic geometries, but treating complex gases requires extended BGK models that are still under development. In this paper, we discuss the main features of these existing solvers, and we focus on their strengths and inefficiencies. We will also review some recent results that show how these solvers can be improved: - higher accuracy (higher order finite volume methods, discontinuous Galerkin approaches) - lower memory and CPU costs with special velocity discretization (adaptive grids, spectral methods) - multi-scale simulations by using hybrid and asymptotic preserving schemes - efficient implementation on high performance computers (parallel computing, hybrid parallelization) Finally, we propose some perspectives to make these solvers more efficient and more popular.
Implementing Multiscale Fluid Simulations using Multiscale Universal Interface
NASA Astrophysics Data System (ADS)
Tang, Yu-Hang; Kudo, Shuhei; Bian, Xin; Li, Zhen; Karniadakis, George; Crunch Team
2015-11-01
The power of multiscale fluid simulations lies in its ability to recover a hierarchical levels of details by choreographing multiple solvers, thus extending the length and time scale accessible given a fixed amount of computing power. However, practical difficulties frequently arise when stitching together solvers which were not designed to be coupled, and would often result in tedious and unsustainable coding effort. The Multiscale Universal Interface (MUI) aims to solve this problem by exposing a small set of generalized programming interfaces that can be dropped into existing solvers with minimal intrusion. Three deployment cases will be given for demonstrating real-world applications of MUI. In the first case we used MUI to implement simulations of polymer-grafted surface in flow using Smoothed Particle Hydrodynamics/Dissipative Particle Dynamics (SPH/DPD) and state variable coupling. In the second case we constructed coupled DPD/Finite Element Method (FEM) simulation of conjugate heat transfer in heterogeneous coolant. In the third case we built hybrid DPD/molecular dynamics (MD) simulations by blending the forces on atoms at interface regions. Supported by the DOE Collaboratory on Mathematics for Mesoscopic Modeling of Materials (CM4) and AFOSR FA9550-12-1-0463. Computer hours at ORNL allocated through INCITE BIP118 and DD102.
PDE-10A inhibitors as insulin secretagogues.
Cantin, Louis-David; Magnuson, Steven; Gunn, David; Barucci, Nicole; Breuhaus, Marina; Bullock, William H; Burke, Jennifer; Claus, Thomas H; Daly, Michelle; Decarr, Lynn; Gore-Willse, Ann; Hoover-Litty, Helana; Kumarasinghe, Ellalahewage S; Li, Yaxin; Liang, Sidney X; Livingston, James N; Lowinger, Timothy; Macdougall, Margit; Ogutu, Herbert O; Olague, Alan; Ott-Morgan, Ronda; Schoenleber, Robert W; Tersteegen, Adrian; Wickens, Philip; Zhang, Zhonghua; Zhu, Jian; Zhu, Lei; Sweet, Laurel J
2007-05-15
Modulation of cAMP levels has been linked to insulin secretion in preclinical animal models and in humans. The high expression of PDE-10A in pancreatic islets suggested that inhibition of this enzyme may provide the necessary modulation to elicit increased insulin secretion. Using an HTS approach, we have identified quinoline-based PDE-10A inhibitors as insulin secretagogues in vitro. Optimized compounds were evaluated in vivo where improvements in glucose tolerance and increases in insulin secretion were measured. PMID:17400452
Parallel Multigrid Equation Solver
2001-09-07
Prometheus is a fully parallel multigrid equation solver for matrices that arise in unstructured grid finite element applications. It includes a geometric and an algebraic multigrid method and has solved problems of up to 76 mullion degrees of feedom, problems in linear elasticity on the ASCI blue pacific and ASCI red machines.
ODE/PDE analysis of corneal curvature.
Płociniczak, Lukasz; Griffiths, Graham W; Schiesser, William E
2014-10-01
The starting point for this paper is a nonlinear, two-point boundary value ordinary differential equation (BVODE) that defines corneal curvature according to a static force balance. A numerical solution to the BVODE is computed by first converting the BVODE to a parabolic partial differential equation (PDE) by adding an initial value (t, pseudo-time) derivative to the BVODE. A numerical solution to the PDE is then computed by the method of lines (MOL) with the calculation proceeding to a sufficiently large value of t such that the derivative in t reduces to essentially zero. The PDE solution at this point is also the solution for the BVODE. This procedure is implemented in R (an open source scientific programming system) and the programming is discussed in some detail. A series approximation to the solution is derived from which an estimate for the rate of convergence is obtained. This is compared to a fitted exponential model. Also, two linear approximations are derived, one of which leads to a closed form solution. Both provide solutions very close to that obtained from the full nonlinear model. An estimate for the cornea radius of curvature is also derived. The paper concludes with a discussion of the features of the solution to the ODE/PDE system.
2004-03-01
PLIRIS is an object-oriented solver built on top of a previous matrix solver used in a number of application codes. Puns solves a linear system directly via LU factorization with partial pivoting. The user provides the linear system in terms of Epetra Objects including a matrix and right-hand-sides. The user can then factor the matrix and perform the forward and back solve at a later time or solve for multiple right-hand-sides at once. This packagemore » is used when dense matrices are obtained in the problem formulation. These dense matrices occur whenever boundary element techniques are chosen for the solution procedure. This has been used in electromagnetics for both static and frequency domain problems.« less
Adaptive kinetic-fluid solvers for heterogeneous computing architectures
NASA Astrophysics Data System (ADS)
Zabelok, Sergey; Arslanbekov, Robert; Kolobov, Vladimir
2015-12-01
We show feasibility and benefits of porting an adaptive multi-scale kinetic-fluid code to CPU-GPU systems. Challenges are due to the irregular data access for adaptive Cartesian mesh, vast difference of computational cost between kinetic and fluid cells, and desire to evenly load all CPUs and GPUs during grid adaptation and algorithm refinement. Our Unified Flow Solver (UFS) combines Adaptive Mesh Refinement (AMR) with automatic cell-by-cell selection of kinetic or fluid solvers based on continuum breakdown criteria. Using GPUs enables hybrid simulations of mixed rarefied-continuum flows with a million of Boltzmann cells each having a 24 × 24 × 24 velocity mesh. We describe the implementation of CUDA kernels for three modules in UFS: the direct Boltzmann solver using the discrete velocity method (DVM), the Direct Simulation Monte Carlo (DSMC) solver, and a mesoscopic solver based on the Lattice Boltzmann Method (LBM), all using adaptive Cartesian mesh. Double digit speedups on single GPU and good scaling for multi-GPUs have been demonstrated.
Erdogan, S; Houslay, M D
1997-01-01
The cAMP phosphodiesterase (PDE) 3 and PDE4 isoforms provide the major cAMP-hydrolysing PDE activities in Jurkat T-cells, with additional contributions from the PDE1 and PDE2 isoforms. Challenge of cells with the adenylate cyclase activator forskolin led to a rapid, albeit transient, increase in PDE3 activity occurring over the first 45 min, followed by a sustained increase in PDE3 activity which began after approximately 3 h and continued for at least 24 h. Only this second phase of increase in PDE3 activity was blocked by the transcriptional inhibitor actinomycin D. After approximately 3 h of exposure to forskolin, PDE4 activity had increased, via a process that could be inhibited by actinomycin D, and it remained elevated for at least a 24 h period. Such actions of forskolin were mimicked by cholera toxin and 8-bromo-cAMP. Forskolin increased intracellular cAMP concentrations in a time-dependent fashion and its action was enhanced when PDE induction was blocked with actinomycin D. Reverse transcription (RT)-PCR analysis, using generic primers designed to detect transcripts representing enzymically active products of the four PDE4 genes, identified transcripts for PDE4A and PDE4D but not for PDE4B or PDE4C in untreated Jurkat T-cells. Forskolin treatment did not induce transcripts for either PDE4B or PDE4C; however, it reduced the RT-PCR signal for PDE4A transcripts and markedly enhanced that for PDE4D transcripts. Using RT-PCR primers for PDE4 splice variants, a weak signal for PDE4D1 was evident in control cells whereas, in forskolin-treated cells, clear signals for both PDE4D1 and PDE4D2 were detected. RT-PCR analysis of the PDE4A species indicated that it was not the PDE4A isoform PDE-46 (PDE4A4B). Immunoblotting of control cells for PDE4 forms identified a single PDE4A species of approximately 118 kDa, which migrated distinctly from the PDE4A4B isoform PDE-46, with immunoprecipitation analyses showing that it provided all of the PDE4 activity in control
On the structure of parallelism in a highly concurrent PDE solver
NASA Technical Reports Server (NTRS)
Gannon, D.; Van Rosendale, J.
1986-01-01
A parallel multigrid algorithm for solving elliptic partial differential equations is developed and evaluated. A V-cycle multigrid method is altered to increase the degree of parallelism. A numerical analysis of the resulting concurrent-iteration multigrid algorithm is performed; its architectural implications are considered; highly parallel systems without shared memory are examined (including mesh-connected arrays, mesh-shuffle-connected systems, permutation networks, and direct VLSI embeddings); and the results of numerical experiments are presented in tables and graphs.
Scalable solvers and applications
Ribbens, C J
2000-10-27
The purpose of this report is to summarize research activities carried out under Lawrence Livermore National Laboratory (LLNL) research subcontract B501073. This contract supported the principal investigator (P1), Dr. Calvin Ribbens, during his sabbatical visit to LLNL from August 1999 through June 2000. Results and conclusions from the work are summarized below in two major sections. The first section covers contributions to the Scalable Linear Solvers and hypre projects in the Center for Applied Scientific Computing (CASC). The second section describes results from collaboration with Patrice Turchi of LLNL's Chemistry and Materials Science Directorate (CMS). A list of publications supported by this subcontract appears at the end of the report.
A PDE Sensitivity Equation Method for Optimal Aerodynamic Design
NASA Technical Reports Server (NTRS)
Borggaard, Jeff; Burns, John
1996-01-01
The use of gradient based optimization algorithms in inverse design is well established as a practical approach to aerodynamic design. A typical procedure uses a simulation scheme to evaluate the objective function (from the approximate states) and its gradient, then passes this information to an optimization algorithm. Once the simulation scheme (CFD flow solver) has been selected and used to provide approximate function evaluations, there are several possible approaches to the problem of computing gradients. One popular method is to differentiate the simulation scheme and compute design sensitivities that are then used to obtain gradients. Although this black-box approach has many advantages in shape optimization problems, one must compute mesh sensitivities in order to compute the design sensitivity. In this paper, we present an alternative approach using the PDE sensitivity equation to develop algorithms for computing gradients. This approach has the advantage that mesh sensitivities need not be computed. Moreover, when it is possible to use the CFD scheme for both the forward problem and the sensitivity equation, then there are computational advantages. An apparent disadvantage of this approach is that it does not always produce consistent derivatives. However, for a proper combination of discretization schemes, one can show asymptotic consistency under mesh refinement, which is often sufficient to guarantee convergence of the optimal design algorithm. In particular, we show that when asymptotically consistent schemes are combined with a trust-region optimization algorithm, the resulting optimal design method converges. We denote this approach as the sensitivity equation method. The sensitivity equation method is presented, convergence results are given and the approach is illustrated on two optimal design problems involving shocks.
Vang, Amanda G.; Basole, Chaitali; Dong, Hongli; Nguyen, Rebecca K.; Housley, William; Guernsey, Linda; Adami, Alexander J.; Thrall, Roger S.; Clark, Robert B.; Epstein, Paul M.; Brocke, Stefan
2016-01-01
Abolishing the inhibitory signal of intracellular cAMP is a prerequisite for effector T (Teff) cell function. The regulation of cAMP within leukocytes critically depends on its degradation by cyclic nucleotide phosphodiesterases (PDEs). We have previously shown that PDE8A, a PDE isoform with 40–100-fold greater affinity for cAMP than PDE4, is selectively expressed in Teff vs. regulatory T (Treg) cells and controls CD4+ Teff cell adhesion and chemotaxis. Here, we determined PDE8A expression and function in CD4+ Teff cell populations in vivo. Using magnetic bead separation to purify leukocyte populations from the lung draining hilar lymph node (HLN) in a mouse model of ovalbumin-induced allergic airway disease (AAD), we found by Western immunoblot and quantitative (q)RT-PCR that PDE8A protein and gene expression are enhanced in the CD4+ T cell fraction over the course of the acute inflammatory disease and recede at the late tolerant non-inflammatory stage. To evaluate PDE8A as a potential drug target, we compared the selective and combined effects of the recently characterized highly potent PDE8-selective inhibitor PF-04957325 with the PDE4-selective inhibitor piclamilast (PICL). As previously shown, PF-04957325 suppresses T cell adhesion to endothelial cells. In contrast, we found that PICL alone increased firm T cell adhesion to endothelial cells by ~20% and significantly abrogated the inhibitory effect of PF-04957325 on T cell adhesion by over 50% when cells were co-exposed to PICL and PF-04957325. Despite its robust effect on T cell adhesion, PF-04957325 was over two orders of magnitude less efficient than PICL in suppressing polyclonal Teff cell proliferation, and showed no effect on cytokine gene expression in these cells. More importantly, PDE8 inhibition did not suppress proliferation and cytokine production of myelin-antigen reactive proinflammatory Teff cells in vivo and in vitro. Thus, targeting PDE8 through PF-04957325 selectively regulates Teff cell
Vang, Amanda G; Basole, Chaitali; Dong, Hongli; Nguyen, Rebecca K; Housley, William; Guernsey, Linda; Adami, Alexander J; Thrall, Roger S; Clark, Robert B; Epstein, Paul M; Brocke, Stefan
2016-01-01
Abolishing the inhibitory signal of intracellular cAMP is a prerequisite for effector T (Teff) cell function. The regulation of cAMP within leukocytes critically depends on its degradation by cyclic nucleotide phosphodiesterases (PDEs). We have previously shown that PDE8A, a PDE isoform with 40-100-fold greater affinity for cAMP than PDE4, is selectively expressed in Teff vs. regulatory T (Treg) cells and controls CD4(+) Teff cell adhesion and chemotaxis. Here, we determined PDE8A expression and function in CD4(+) Teff cell populations in vivo. Using magnetic bead separation to purify leukocyte populations from the lung draining hilar lymph node (HLN) in a mouse model of ovalbumin-induced allergic airway disease (AAD), we found by Western immunoblot and quantitative (q)RT-PCR that PDE8A protein and gene expression are enhanced in the CD4(+) T cell fraction over the course of the acute inflammatory disease and recede at the late tolerant non-inflammatory stage. To evaluate PDE8A as a potential drug target, we compared the selective and combined effects of the recently characterized highly potent PDE8-selective inhibitor PF-04957325 with the PDE4-selective inhibitor piclamilast (PICL). As previously shown, PF-04957325 suppresses T cell adhesion to endothelial cells. In contrast, we found that PICL alone increased firm T cell adhesion to endothelial cells by ~20% and significantly abrogated the inhibitory effect of PF-04957325 on T cell adhesion by over 50% when cells were co-exposed to PICL and PF-04957325. Despite its robust effect on T cell adhesion, PF-04957325 was over two orders of magnitude less efficient than PICL in suppressing polyclonal Teff cell proliferation, and showed no effect on cytokine gene expression in these cells. More importantly, PDE8 inhibition did not suppress proliferation and cytokine production of myelin-antigen reactive proinflammatory Teff cells in vivo and in vitro. Thus, targeting PDE8 through PF-04957325 selectively regulates Teff
Vang, Amanda G; Basole, Chaitali; Dong, Hongli; Nguyen, Rebecca K; Housley, William; Guernsey, Linda; Adami, Alexander J; Thrall, Roger S; Clark, Robert B; Epstein, Paul M; Brocke, Stefan
2016-01-01
Abolishing the inhibitory signal of intracellular cAMP is a prerequisite for effector T (Teff) cell function. The regulation of cAMP within leukocytes critically depends on its degradation by cyclic nucleotide phosphodiesterases (PDEs). We have previously shown that PDE8A, a PDE isoform with 40-100-fold greater affinity for cAMP than PDE4, is selectively expressed in Teff vs. regulatory T (Treg) cells and controls CD4(+) Teff cell adhesion and chemotaxis. Here, we determined PDE8A expression and function in CD4(+) Teff cell populations in vivo. Using magnetic bead separation to purify leukocyte populations from the lung draining hilar lymph node (HLN) in a mouse model of ovalbumin-induced allergic airway disease (AAD), we found by Western immunoblot and quantitative (q)RT-PCR that PDE8A protein and gene expression are enhanced in the CD4(+) T cell fraction over the course of the acute inflammatory disease and recede at the late tolerant non-inflammatory stage. To evaluate PDE8A as a potential drug target, we compared the selective and combined effects of the recently characterized highly potent PDE8-selective inhibitor PF-04957325 with the PDE4-selective inhibitor piclamilast (PICL). As previously shown, PF-04957325 suppresses T cell adhesion to endothelial cells. In contrast, we found that PICL alone increased firm T cell adhesion to endothelial cells by ~20% and significantly abrogated the inhibitory effect of PF-04957325 on T cell adhesion by over 50% when cells were co-exposed to PICL and PF-04957325. Despite its robust effect on T cell adhesion, PF-04957325 was over two orders of magnitude less efficient than PICL in suppressing polyclonal Teff cell proliferation, and showed no effect on cytokine gene expression in these cells. More importantly, PDE8 inhibition did not suppress proliferation and cytokine production of myelin-antigen reactive proinflammatory Teff cells in vivo and in vitro. Thus, targeting PDE8 through PF-04957325 selectively regulates Teff
Vang, Amanda G.; Basole, Chaitali; Dong, Hongli; Nguyen, Rebecca K.; Housley, William; Guernsey, Linda; Adami, Alexander J.; Thrall, Roger S.; Clark, Robert B.; Epstein, Paul M.; Brocke, Stefan
2016-01-01
Abolishing the inhibitory signal of intracellular cAMP is a prerequisite for effector T (Teff) cell function. The regulation of cAMP within leukocytes critically depends on its degradation by cyclic nucleotide phosphodiesterases (PDEs). We have previously shown that PDE8A, a PDE isoform with 40–100-fold greater affinity for cAMP than PDE4, is selectively expressed in Teff vs. regulatory T (Treg) cells and controls CD4+ Teff cell adhesion and chemotaxis. Here, we determined PDE8A expression and function in CD4+ Teff cell populations in vivo. Using magnetic bead separation to purify leukocyte populations from the lung draining hilar lymph node (HLN) in a mouse model of ovalbumin-induced allergic airway disease (AAD), we found by Western immunoblot and quantitative (q)RT-PCR that PDE8A protein and gene expression are enhanced in the CD4+ T cell fraction over the course of the acute inflammatory disease and recede at the late tolerant non-inflammatory stage. To evaluate PDE8A as a potential drug target, we compared the selective and combined effects of the recently characterized highly potent PDE8-selective inhibitor PF-04957325 with the PDE4-selective inhibitor piclamilast (PICL). As previously shown, PF-04957325 suppresses T cell adhesion to endothelial cells. In contrast, we found that PICL alone increased firm T cell adhesion to endothelial cells by ~20% and significantly abrogated the inhibitory effect of PF-04957325 on T cell adhesion by over 50% when cells were co-exposed to PICL and PF-04957325. Despite its robust effect on T cell adhesion, PF-04957325 was over two orders of magnitude less efficient than PICL in suppressing polyclonal Teff cell proliferation, and showed no effect on cytokine gene expression in these cells. More importantly, PDE8 inhibition did not suppress proliferation and cytokine production of myelin-antigen reactive proinflammatory Teff cells in vivo and in vitro. Thus, targeting PDE8 through PF-04957325 selectively regulates Teff cell
Parallel tridiagonal equation solvers
NASA Technical Reports Server (NTRS)
Stone, H. S.
1974-01-01
Three parallel algorithms were compared for the direct solution of tridiagonal linear systems of equations. The algorithms are suitable for computers such as ILLIAC 4 and CDC STAR. For array computers similar to ILLIAC 4, cyclic odd-even reduction has the least operation count for highly structured sets of equations, and recursive doubling has the least count for relatively unstructured sets of equations. Since the difference in operation counts for these two algorithms is not substantial, their relative running times may be more related to overhead operations, which are not measured in this paper. The third algorithm, based on Buneman's Poisson solver, has more arithmetic operations than the others, and appears to be the least favorable. For pipeline computers similar to CDC STAR, cyclic odd-even reduction appears to be the most preferable algorithm for all cases.
Amesos2 Templated Direct Sparse Solver Package
2011-05-24
Amesos2 is a templated direct sparse solver package. Amesos2 provides interfaces to direct sparse solvers, rather than providing native solver capabilities. Amesos2 is a derivative work of the Trilinos package Amesos.
A novel high-order, entropy stable, 3D AMR MHD solver with guaranteed positive pressure
NASA Astrophysics Data System (ADS)
Derigs, Dominik; Winters, Andrew R.; Gassner, Gregor J.; Walch, Stefanie
2016-07-01
We describe a high-order numerical magnetohydrodynamics (MHD) solver built upon a novel non-linear entropy stable numerical flux function that supports eight travelling wave solutions. By construction the solver conserves mass, momentum, and energy and is entropy stable. The method is designed to treat the divergence-free constraint on the magnetic field in a similar fashion to a hyperbolic divergence cleaning technique. The solver described herein is especially well-suited for flows involving strong discontinuities. Furthermore, we present a new formulation to guarantee positivity of the pressure. We present the underlying theory and implementation of the new solver into the multi-physics, multi-scale adaptive mesh refinement (AMR) simulation code FLASH (http://flash.uchicago.edu)
Workload Characterization of CFD Applications Using Partial Differential Equation Solvers
NASA Technical Reports Server (NTRS)
Waheed, Abdul; Yan, Jerry; Saini, Subhash (Technical Monitor)
1998-01-01
Workload characterization is used for modeling and evaluating of computing systems at different levels of detail. We present workload characterization for a class of Computational Fluid Dynamics (CFD) applications that solve Partial Differential Equations (PDEs). This workload characterization focuses on three high performance computing platforms: SGI Origin2000, EBM SP-2, a cluster of Intel Pentium Pro bases PCs. We execute extensive measurement-based experiments on these platforms to gather statistics of system resource usage, which results in workload characterization. Our workload characterization approach yields a coarse-grain resource utilization behavior that is being applied for performance modeling and evaluation of distributed high performance metacomputing systems. In addition, this study enhances our understanding of interactions between PDE solver workloads and high performance computing platforms and is useful for tuning these applications.
PDE4B as a microglia target to reduce neuroinflammation.
Pearse, Damien D; Hughes, Zoë A
2016-10-01
The importance of microglia in immune homeostasis within the brain is undisputed. Their role in a diversity of neurological and psychiatric diseases as well as CNS injury is the subject of much investigation. Cyclic adenosine monophosphate (AMP) is a critical regulator of microglia homeostasis; as the predominant negative modulator of cyclic AMP signaling within microglia, phosphodiesterase 4 (PDE4) represents a promising target for modulating immune function. PDE4 expression is regulated by inflammation, and in turn, PDE4 inhibition can alter microglia reactivity. As the prototypic PDE4 inhibitor, rolipram, was tested clinically in the 1980s, drug discovery and clinical development of PDE4 inhibitors have been severely hampered by tolerability issues involving nausea and emesis. The two PDE4 inhibitors approved for peripheral inflammatory disorders (roflumilast and apremilast) lack brain penetration and are dose-limited by side effects making them unsuitable for modulating microglial function. Subtype selective inhibitors targeting PDE4B are of high interest given the critical role PDE4B plays in immune function versus the association of PDE4D with nausea and emesis. The challenges and requirements for successful development of a novel brain-penetrant PDE4B inhibitor are discussed in the context of early clinical development strategies. Furthermore, the challenges of monitoring the state of microglia in vivo are highlighted, including a description of the currently available tools and their limitations. Continued drug discovery efforts to identify safe and well-tolerated, brain-penetrant PDE4 inhibitors are a reflection of the confidence in the rationale for modulation of this target to produce meaningful therapeutic benefit in a wide range of neurological conditions and injury. GLIA 2016;64:1698-1709. PMID:27038323
A Comparison of PETSC Library and HPF Implementations of an Archetypal PDE Computation
NASA Technical Reports Server (NTRS)
Hayder, M. Ehtesham; Keyes, David E.; Mehrotra, Piyush
1997-01-01
Two paradigms for distributed-memory parallel computation that free the application programmer from the details of message passing are compared for an archetypal structured scientific computation a nonlinear, structured-grid partial differential equation boundary value problem using the same algorithm on the same hardware. Both paradigms, parallel libraries represented by Argonne's PETSC, and parallel languages represented by the Portland Group's HPF, are found to be easy to use for this problem class, and both are reasonably effective in exploiting concurrency after a short learning curve. The level of involvement required by the application programmer under either paradigm includes specification of the data partitioning (corresponding to a geometrically simple decomposition of the domain of the PDE). Programming in SPAM style for the PETSC library requires writing the routines that discretize the PDE and its Jacobian, managing subdomain-to-processor mappings (affine global- to-local index mappings), and interfacing to library solver routines. Programming for HPF requires a complete sequential implementation of the same algorithm, introducing concurrency through subdomain blocking (an effort similar to the index mapping), and modest experimentation with rewriting loops to elucidate to the compiler the latent concurrency. Correctness and scalability are cross-validated on up to 32 nodes of an IBM SP2.
PDE regularization for Bayesian reconstruction of emission tomography
NASA Astrophysics Data System (ADS)
Wang, Zhentian; Zhang, Li; Xing, Yuxiang; Zhao, Ziran
2008-03-01
The aim of the present study is to investigate a type of Bayesian reconstruction which utilizes partial differential equations (PDE) image models as regularization. PDE image models are widely used in image restoration and segmentation. In a PDE model, the image can be viewed as the solution of an evolutionary differential equation. The variation of the image can be regard as a descent of an energy function, which entitles us to use PDE models in Bayesian reconstruction. In this paper, two PDE models called anisotropic diffusion are studied. Both of them have the characteristics of edge-preserving and denoising like the popular median root prior (MRP). We use PDE regularization with an Ordered Subsets accelerated Bayesian one step late (OSL) reconstruction algorithm for emission tomography. The OS accelerated OSL algorithm is more practical than a non-accelerated one. The proposed algorithm is called OSEM-PDE. We validated the OSEM-PDE using a Zubal phantom in numerical experiments with attenuation correction and quantum noise considered, and the results are compared with OSEM and an OS version of MRP (OSEM-MRP) reconstruction. OSEM-PDE shows better results both in bias and variance. The reconstruction images are smoother and have sharper edges, thus are more applicable for post processing such as segmentation. We validate this using a k-means segmentation algorithm. The classic OSEM is not convergent especially in noisy condition. However, in our experiment, OSEM-PDE can benefit from OS acceleration and keep stable and convergent while OSEM-MRP failed to converge.
NASA Technical Reports Server (NTRS)
Ilin, Andrew V.
2006-01-01
The Magnetic Field Solver computer program calculates the magnetic field generated by a group of collinear, cylindrical axisymmetric electromagnet coils. Given the current flowing in, and the number of turns, axial position, and axial and radial dimensions of each coil, the program calculates matrix coefficients for a finite-difference system of equations that approximates a two-dimensional partial differential equation for the magnetic potential contributed by the coil. The program iteratively solves these finite-difference equations by use of the modified incomplete Cholesky preconditioned-conjugate-gradient method. The total magnetic potential as a function of axial (z) and radial (r) position is then calculated as a sum of the magnetic potentials of the individual coils, using a high-accuracy interpolation scheme. Then the r and z components of the magnetic field as functions of r and z are calculated from the total magnetic potential by use of a high-accuracy finite-difference scheme. Notably, for the finite-difference calculations, the program generates nonuniform two-dimensional computational meshes from nonuniform one-dimensional meshes. Each mesh is generated in such a way as to minimize the numerical error for a benchmark one-dimensional magnetostatic problem.
Sherlock Holmes, Master Problem Solver.
ERIC Educational Resources Information Center
Ballew, Hunter
1994-01-01
Shows the connections between Sherlock Holmes's investigative methods and mathematical problem solving, including observations, characteristics of the problem solver, importance of data, questioning the obvious, learning from experience, learning from errors, and indirect proof. (MKR)
X. Frank Xu
2010-03-30
Multiscale modeling of stochastic systems, or uncertainty quantization of multiscale modeling is becoming an emerging research frontier, with rapidly growing engineering applications in nanotechnology, biotechnology, advanced materials, and geo-systems, etc. While tremendous efforts have been devoted to either stochastic methods or multiscale methods, little combined work had been done on integration of multiscale and stochastic methods, and there was no method formally available to tackle multiscale problems involving uncertainties. By developing an innovative Multiscale Stochastic Finite Element Method (MSFEM), this research has made a ground-breaking contribution to the emerging field of Multiscale Stochastic Modeling (MSM) (Fig 1). The theory of MSFEM basically decomposes a boundary value problem of random microstructure into a slow scale deterministic problem and a fast scale stochastic one. The slow scale problem corresponds to common engineering modeling practices where fine-scale microstructure is approximated by certain effective constitutive constants, which can be solved by using standard numerical solvers. The fast scale problem evaluates fluctuations of local quantities due to random microstructure, which is important for scale-coupling systems and particularly those involving failure mechanisms. The Green-function-based fast-scale solver developed in this research overcomes the curse-of-dimensionality commonly met in conventional approaches, by proposing a random field-based orthogonal expansion approach. The MSFEM formulated in this project paves the way to deliver the first computational tool/software on uncertainty quantification of multiscale systems. The applications of MSFEM on engineering problems will directly enhance our modeling capability on materials science (composite materials, nanostructures), geophysics (porous media, earthquake), biological systems (biological tissues, bones, protein folding). Continuous development of MSFEM will
PDE Nozzle Optimization Using a Genetic Algorithm
NASA Technical Reports Server (NTRS)
Billings, Dana; Turner, James E. (Technical Monitor)
2000-01-01
Genetic algorithms, which simulate evolution in natural systems, have been used to find solutions to optimization problems that seem intractable to standard approaches. In this study, the feasibility of using a GA to find an optimum, fixed profile nozzle for a pulse detonation engine (PDE) is demonstrated. The objective was to maximize impulse during the detonation wave passage and blow-down phases of operation. Impulse of each profile variant was obtained by using the CFD code Mozart/2.0 to simulate the transient flow. After 7 generations, the method has identified a nozzle profile that certainly is a candidate for optimum solution. The constraints on the generality of this possible solution remain to be clarified.
Sponziello, Marialuisa; Verrienti, Antonella; Rosignolo, Francesca; De Rose, Roberta Francesca; Pecce, Valeria; Maggisano, Valentina; Durante, Cosimo; Bulotta, Stefania; Damante, Giuseppe; Giacomelli, Laura; Di Gioia, Cira Rosaria Tiziana; Filetti, Sebastiano; Russo, Diego; Celano, Marilena
2015-11-01
Recent studies have revealed in normal thyroid tissue the presence of the transcript of several phosphodiesterases (PDEs), enzymes responsible for the hydrolysis of cyclic nucleotides. In this work, we analyzed the expression of PDE5 in a series of human papillary thyroid carcinomas (PTCs) presenting or not BRAF V600E mutation and classified according to ATA risk criteria. Furthermore, we tested the effects of two PDE5 inhibitors (sildenafil, tadalafil) against human thyroid cancer cells. PDE5 gene and protein expression were analyzed in two different cohorts of PTCs by real-time PCR using a TaqMan micro-fluid card system and Western blot. MTT and migration assay were used to evaluate the effects of PDE5 inhibitors on proliferation and migration of TPC-1, BCPAP, and 8505C cells. In a first series of 36 PTCs, we found higher expression levels of PDE5A in tumors versus non-tumor (normal) tissues. PTCs with BRAF mutation showed higher levels of mRNA compared with those without mutation. No significant differences were detected between subgroups with low and intermediate ATA risk. Upregulation of PDE5 was also detected in tumor tissue proteins. Similar results were obtained analyzing the second cohort of 50 PTCs. Moreover, all tumor tissues with high PDE5 levels showed reduction of Thyroglobulin, TSH receptor, Thyroperoxidase, and NIS transcripts. In thyroid cancer cells in vitro, sildenafil and tadalafil determined a reduction of proliferation and cellular migration. Our findings demonstrate for the first time an overexpression of PDE5 in PTCs, and the ability of PDE5 inhibitors to block the proliferation of thyroid cancer cells in culture, therefore, suggesting that specific inhibition of PDE5 may be proposed for the treatment of these tumors. PMID:25837309
Nonlinear Control of Delay and PDE Systems
NASA Astrophysics Data System (ADS)
Bekiaris-Liberis, Nikolaos
In this dissertation we develop systematic procedures for the control and analysis of general nonlinear systems with delays and of nonlinear PDE systems. We design predictor feedback laws (i.e., feedback laws that use the future, rather than the current state of the system) for the compensation of delays (i.e., after the control signal reaches the system for the first time, the system behaves as there were no delay at all) that can be time-varying or state-dependent, on the input and on the state of nonlinear systems. We also provide designs of predic- tor feedback laws for linear systems with constant distributed delays and known or unknown plant parameters, and for linear systems with simultaneous known or unknown constant delays on the input and the state. Moreover, we intro- duce infinite-dimensional backstepping transformations for each particular prob-lem, which enables us to construct Lyapunov-Krasovskii functionals. With the available Lyapunov-Krasovskii functionals we study stability, as well as, robust- ness of our control laws to plant uncertainties. We deal with coupled PDE-ODE systems. We consider nonlinear systems with wave actuator dynamics, for which we design a predictor inspired feedback law. We study stability of the closed-loop system either by constructing Lyapunov functionals, or using arguments of explicit solutions. We also consider linear sys- tems with distributed actuator and sensor dynamics governed by diffusion or wave PDEs, for which we design stabilizing feedback laws. We study stability of the closed-loop systems using Lyapunov functionals that we construct with the intro- duction of infinite-dimensional transformations of forwarding type. Finally, we develop a control design methodology for coupled nonlinear first-order hyperbolic PDEs through an application to automotive catalysts.
PDE and cognitive processing: beyond the memory domain.
Heckman, P R A; Blokland, A; Ramaekers, J; Prickaerts, J
2015-03-01
Phosphodiesterase inhibitors (PDE-Is) enhance cAMP and/or cGMP signaling via reducing the degradation of these cyclic nucleotides. Both cAMP and cGMP signaling are essential for a variety of cellular functions and exert their effects both pre- and post-synaptically. Either of these second messengers relays and amplifies incoming signals at receptors on the cell surface making them important elements in signal transduction cascades and essential in cellular signaling in a variety of cell functions including neurotransmitter release and neuroprotection. Consequently, these processes can be influenced by PDE-Is as they increase cAMP and/or cGMP concentrations. PDE-Is have been considered as possible therapeutic agents to treat impaired memory function linked to several brain disorders, including depression, schizophrenia and Alzheimer's disease (AD). This review will, however, focus on the possible role of phosphodiesterases (PDEs) in cognitive decline beyond the memory domain. Here we will discuss the involvement of PDEs on three related domains: attention, information filtering (sensory- and sensorimotor gating) and response inhibition (drug-induced hyperlocomotion). Currently, these are emerging cognitive domains in the field of PDE research. Here we discuss experimental studies and the potential beneficial effects of PDE-I drugs on these cognitive domains, as effects of PDE-Is on these domains could potentially influence effects on memory performance. Overall, PDE4 seems to be the most promising target for all domains discussed in this review.
Novel mutations in PDE6B causing human retinitis pigmentosa
Cheng, Lu-Lu; Han, Ru-Yi; Yang, Fa-Yu; Yu, Xin-Ping; Xu, Jin-Ling; Min, Qing-Jie; Tian, Jie; Ge, Xiang-Lian; Zheng, Si-Si; Lin, Ye-Wen; Zheng, Yi-Han; Qu, Jia; Gu, Feng
2016-01-01
AIM To identify the genetic defects of a Chinese patient with sporadic retinitis pigmentosa (RP). METHODS Ophthalmologic examinations were performed on the sporadic RP patient, 144 genes associated with retinal diseases were scanned with capture next generation sequencing (CNGS) approach. Two heterozygous mutations in PDE6B were confirmed in the pedigree by Sanger sequencing subsequently. The carrier frequency of PDE6B mutations of reported PDE6B mutations based on the available two public exome databases (1000 Genomes Project and ESP6500 Genomes Project) and one in-house exome database was investigated. RESULTS We identified compound heterozygosity of two novel nonsense mutations c.1133G>A (p.W378X) and c.2395C>T (p.R799X) in PDE6B, one reported causative gene for RP. Neither of the two mutations in our study was presented in three exome databases. Two mutations (p.R74C and p.T604I) in PDE6B have relatively high frequencies in the ESP6500 and in-house databases, respectively, while no common dominant mutation in each of the database or across all databases. CONCLUSION We demonstrates that compound heterozygosity of two novel nonsense mutations in PDE6B could lead to RP. These results collectively point to enormous potential of next-generation sequencing in determining the genetic etiology of RP and how various mutations in PDE6B contribute to the genetic heterogeneity of RP. PMID:27588261
Fortin, Marylène; D'Anjou, Hélène; Higgins, Marie-Ève; Gougeon, Jasmine; Aubé, Paméla; Moktefi, Kamel; Mouissi, Sonia; Séguin, Serge; Séguin, Rosanne; Renzi, Paolo M; Paquet, Luc; Ferrari, Nicolay
2009-01-01
Background Recent development in the field of COPD has focused on strategies aimed at reducing the underlying inflammation through selective inhibition of the phosphodiesterase type IV (PDE4) isoform. Although the anti-inflammatory and bronchodilator activity of selective PDE4 inhibitors has been well documented, their low therapeutic ratio and dose-dependent systemic side effects have limited their clinical utility. This study examined the effect of 2'-deoxy-2'-Fluoro-β-D-Arabinonucleic Acid (FANA)-containing antisense oligonucleotides (AON) targeting the mRNA for the PDE4B/4D and 7A subtypes on lung inflammatory markers, both in vitro and in vivo. Methods Normal human bronchial epithelial (NHBE) cells were transfected with FANA AON against PDE4B/4D and 7A alone or in combination. mRNA levels for target PDE subtypes, as well as secretion of pro-inflammatory chemokines were then measured following cell stimulation. Mice were treated with combined PDE4B/4D and 7A AON via endo-tracheal delivery, or with roflumilast via oral delivery, and exposed to cigarette smoke for one week. Target mRNA inhibition, as well as influx of inflammatory cells and mediators were measured in lung lavages. A two-week smoke exposure protocol was also used to test the longer term potency of PDE4B/4D and 7A AONs. Results In NHBE cells, PDE4B/4D and 7A AONs dose-dependently and specifically inhibited expression of their respective target mRNA. When used in combination, PDE4B/4D and 7A AONs significantly abrogated the cytokine-induced secretion of IL-8 and MCP-1 to near baseline levels. In mice treated with combined PDE4B/4D and 7A AONs and exposed to cigarette smoke, significant protection against the smoke-induced recruitment of neutrophils and production of KC and pro-MMP-9 was obtained, which was correlated with inhibition of target mRNA in cells from lung lavages. In this model, PDE AONs exerted more potent and broader anti-inflammatory effects against smoke-induced lung inflammation
Selective Extraction of Entangled Textures via Adaptive PDE Transform.
Wang, Yang; Wei, Guo-Wei; Yang, Siyang
2012-01-01
Texture and feature extraction is an important research area with a wide range of applications in science and technology. Selective extraction of entangled textures is a challenging task due to spatial entanglement, orientation mixing, and high-frequency overlapping. The partial differential equation (PDE) transform is an efficient method for functional mode decomposition. The present work introduces adaptive PDE transform algorithm to appropriately threshold the statistical variance of the local variation of functional modes. The proposed adaptive PDE transform is applied to the selective extraction of entangled textures. Successful separations of human face, clothes, background, natural landscape, text, forest, camouflaged sniper and neuron skeletons have validated the proposed method.
Optimal control of coupled PDE networks with automated code generation
NASA Astrophysics Data System (ADS)
Papadopoulos, D.
2012-09-01
The purpose of this work is to present a framework for the optimal control of coupled PDE networks. A coupled PDE network is a system of partial differential equations coupled together. Such systems can be represented as a directed graph. A domain specific language (DSL)—an extension of the DOT language—is used for the description of such a coupled PDE network. The adjoint equations and the gradient, required for its optimal control, are computed with the help of a computer algebra system (CAS). Automated code generation techniques have been used for the generation of the PDE systems of both the direct and the adjoint equations. Both the direct and adjoint equations are solved with the standard finite element method. Finally, for the numerical optimization of the system standard optimization techniques are used such as BFGS and Newton conjugate gradient.
Novel Roflumilast analogs as soft PDE4 inhibitors.
Boland, Sandro; Alen, Jo; Bourin, Arnaud; Castermans, Karolien; Boumans, Nicki; Panitti, Laura; Vanormelingen, Jessica; Leysen, Dirk; Defert, Olivier
2014-09-15
PDE4 inhibitors are of high interest for treatment of a wide range of inflammatory or autoimmune diseases. Their potential however has not yet been realized due to target-associated side effects, resulting in a low therapeutic window. We herein report the design, synthesis and evaluation of novel PDE4 inhibitors containing a γ-lactone structure. Such molecules are designed to undergo metabolic inactivation when entering circulation, thereby limiting systemic exposure and reducing the risk for side effects. The resulting inhibitors were highly active on both PDE4B1 and PDE4D2 and underwent rapid degradation in human plasma by paraoxonase 1. In contrast, their metabolites displayed markedly reduced permeability and/or on-target activity.
Scalable Parallel Algebraic Multigrid Solvers
Bank, R; Lu, S; Tong, C; Vassilevski, P
2005-03-23
The authors propose a parallel algebraic multilevel algorithm (AMG), which has the novel feature that the subproblem residing in each processor is defined over the entire partition domain, although the vast majority of unknowns for each subproblem are associated with the partition owned by the corresponding processor. This feature ensures that a global coarse description of the problem is contained within each of the subproblems. The advantages of this approach are that interprocessor communication is minimized in the solution process while an optimal order of convergence rate is preserved; and the speed of local subproblem solvers can be maximized using the best existing sequential algebraic solvers.
Multiscale integration schemes for jump-diffusion systems
Givon, D.; Kevrekidis, I.G.
2008-12-09
We study a two-time-scale system of jump-diffusion stochastic differential equations. We analyze a class of multiscale integration methods for these systems, which, in the spirit of [1], consist of a hybridization between a standard solver for the slow components and short runs for the fast dynamics, which are used to estimate the effect that the fast components have on the slow ones. We obtain explicit bounds for the discrepancy between the results of the multiscale integration method and the slow components of the original system.
NASA Astrophysics Data System (ADS)
Schaa, R.; Gross, L.; du Plessis, J.
2016-04-01
We present a general finite-element solver, escript, tailored to solve geophysical forward and inverse modeling problems in terms of partial differential equations (PDEs) with suitable boundary conditions. Escript’s abstract interface allows geoscientists to focus on solving the actual problem without being experts in numerical modeling. General-purpose finite element solvers have found wide use especially in engineering fields and find increasing application in the geophysical disciplines as these offer a single interface to tackle different geophysical problems. These solvers are useful for data interpretation and for research, but can also be a useful tool in educational settings. This paper serves as an introduction into PDE-based modeling with escript where we demonstrate in detail how escript is used to solve two different forward modeling problems from applied geophysics (3D DC resistivity and 2D magnetotellurics). Based on these two different cases, other geophysical modeling work can easily be realized. The escript package is implemented as a Python library and allows the solution of coupled, linear or non-linear, time-dependent PDEs. Parallel execution for both shared and distributed memory architectures is supported and can be used without modifications to the scripts.
Banjac, Ana; Zimmermann, Markus O; Boeckler, Frank M; Kurz, Ursula; Schultz, Anita; Schultz, Joachim E
2012-03-01
The dimeric mammalian phosphodiesterases (PDEs) are regulated by N-terminal domains. In PDE5, the GAF-A subdomain of a GAF-tandem (GAF-A and -B) binds the activator cGMP and in PDE10 GAF-B binds cAMP. GAF-tandem chimeras of PDE5 and 10 in which the 36 aa linker helix between GAF-A and -B was swapped lost allosteric regulation of a reporter adenylyl cyclase. In 16 consecutive constructs we substituted the PDE10 linker with that from PDE5. An initial stretch of 10 amino acids coded for isoform specificity. A C240Y substitution uncoupled cyclase activity from regulation, whereas C240F, L or G did not. The C240Y substitution increased basal activity to stimulated levels. Notably, over the next 12 substitutions basal cyclase activity decreased linearly. Further targeted substitutions were based on homology modeling using the PDE2 structure. No combination of substitutions within the initial 10 linker residues caused loss of regulation. The full 10 aa stretch was required. Modeling indicated a potential interaction of the linker with a loop from GAF-A. To interrupt H-bonding a glycine substitution of the loop segment was generated. Despite reduction of basal activity, loss of regulation was maintained. Possibly, the orientation of the linker helix is determined by formation of the dimer at the initial linker segment. Downstream deflections of the linker helix may have caused loss of regulation.
MULTISCALE MATHEMATICS FOR BIOMASS CONVERSION TO RENEWABLE HYDROGEN
Vlachos, Dionisios; Plechac, Petr; Katsoulakis, Markos
2013-09-05
The overall objective of this project is to develop multiscale models for understanding and eventually designing complex processes for renewables. To the best of our knowledge, our work is the first attempt at modeling complex reacting systems, whose performance relies on underlying multiscale mathematics. Our specific application lies at the heart of biofuels initiatives of DOE and entails modeling of catalytic systems, to enable economic, environmentally benign, and efficient conversion of biomass into either hydrogen or valuable chemicals. Specific goals include: (i) Development of rigorous spatio-temporal coarse-grained kinetic Monte Carlo (KMC) mathematics and simulation for microscopic processes encountered in biomass transformation. (ii) Development of hybrid multiscale simulation that links stochastic simulation to a deterministic partial differential equation (PDE) model for an entire reactor. (iii) Development of hybrid multiscale simulation that links KMC simulation with quantum density functional theory (DFT) calculations. (iv) Development of parallelization of models of (i)-(iii) to take advantage of Petaflop computing and enable real world applications of complex, multiscale models. In this NCE period, we continued addressing these objectives and completed the proposed work. Main initiatives, key results, and activities are outlined.
PDE5 Exists in Human Neurons and is a Viable Therapeutic Target for Neurologic Disease
Teich, Andrew F.; Sakurai, Mikako; Patel, Mitesh; Holman, Cameron; Saeed, Faisal; Fiorito, Jole; Arancio, Ottavio
2016-01-01
Phosphodiesterase 5 (PDE5) is a critical component of the cGMP-PKG axis of cellular signaling in neurons, and inhibition of PDE5 has been shown to be therapeutic in a wide range of neurologic conditions in animal models. However, enthusiasm for PDE5 inhibitors in humans is limited by data suggesting that PDE5 may not exist in human neurons. Here, we first show that past attempts to quantify PDE5 mRNA were flawed due to the use of incorrect primers, and that when correct primers are used, PDE5 mRNA is detectable in human brain tissue. We then show that PDE5 protein exists in human brain by western blot and ELISA. Most importantly, we performed immunohistochemistry and demonstrate that PDE5 is present in human neurons. We hope that this work will trigger a renewed interest in the development of PDE5 inhibitors for neurologic disease. PMID:26967220
Multiscale modeling of mucosal immune responses
2015-01-01
Computational modeling techniques are playing increasingly important roles in advancing a systems-level mechanistic understanding of biological processes. Computer simulations guide and underpin experimental and clinical efforts. This study presents ENteric Immune Simulator (ENISI), a multiscale modeling tool for modeling the mucosal immune responses. ENISI's modeling environment can simulate in silico experiments from molecular signaling pathways to tissue level events such as tissue lesion formation. ENISI's architecture integrates multiple modeling technologies including ABM (agent-based modeling), ODE (ordinary differential equations), SDE (stochastic modeling equations), and PDE (partial differential equations). This paper focuses on the implementation and developmental challenges of ENISI. A multiscale model of mucosal immune responses during colonic inflammation, including CD4+ T cell differentiation and tissue level cell-cell interactions was developed to illustrate the capabilities, power and scope of ENISI MSM. Background Computational techniques are becoming increasingly powerful and modeling tools for biological systems are of greater needs. Biological systems are inherently multiscale, from molecules to tissues and from nano-seconds to a lifespan of several years or decades. ENISI MSM integrates multiple modeling technologies to understand immunological processes from signaling pathways within cells to lesion formation at the tissue level. This paper examines and summarizes the technical details of ENISI, from its initial version to its latest cutting-edge implementation. Implementation Object-oriented programming approach is adopted to develop a suite of tools based on ENISI. Multiple modeling technologies are integrated to visualize tissues, cells as well as proteins; furthermore, performance matching between the scales is addressed. Conclusion We used ENISI MSM for developing predictive multiscale models of the mucosal immune system during gut
A high-accuracy Eulerian gyrokinetic solver for collisional plasmas
NASA Astrophysics Data System (ADS)
Candy, J.; Belli, E. A.; Bravenec, R. V.
2016-11-01
We describe a new approach to solve the electromagnetic gyrokinetic equations which is optimized for accurate treatment of multispecies Fokker-Planck collisions including both pitch-angle and energy diffusion. The new algorithm is spectral/pseudospectral in four of the five phase space dimensions, and in the fieldline direction a novel 5th-order conservative upwind scheme is used to permit high-accuracy electromagnetic simulation even in the limit of very high plasma β and vanishingly small perpendicular wavenumber, k⊥ → 0. To our knowledge, this is the first pseudospectral implementation of the collision operator in a gyrokinetic code. We show that the new solver agrees closely with GYRO in the limit of weak Lorentz collisions, but gives a significantly more realistic description of collisions at high collision frequency. The numerical methods are also designed to be efficient and scalable for multiscale simulations that treat ion-scale and electron-scale turbulence simultaneously.
Time-domain Raman analytical forward solvers.
Martelli, Fabrizio; Binzoni, Tiziano; Sekar, Sanathana Konugolu Venkata; Farina, Andrea; Cavalieri, Stefano; Pifferi, Antonio
2016-09-01
A set of time-domain analytical forward solvers for Raman signals detected from homogeneous diffusive media is presented. The time-domain solvers have been developed for two geometries: the parallelepiped and the finite cylinder. The potential presence of a background fluorescence emission, contaminating the Raman signal, has also been taken into account. All the solvers have been obtained as solutions of the time dependent diffusion equation. The validation of the solvers has been performed by means of comparisons with the results of "gold standard" Monte Carlo simulations. These forward solvers provide an accurate tool to explore the information content encoded in the time-resolved Raman measurements. PMID:27607645
Multiscale Methods for Nuclear Reactor Analysis
NASA Astrophysics Data System (ADS)
Collins, Benjamin S.
The ability to accurately predict local pin powers in nuclear reactors is necessary to understand the mechanisms that cause fuel pin failure during steady state and transient operation. In the research presented here, methods are developed to improve the local solution using high order methods with boundary conditions from a low order global solution. Several different core configurations were tested to determine the improvement in the local pin powers compared to the standard techniques, that use diffusion theory and pin power reconstruction (PPR). Two different multiscale methods were developed and analyzed; the post-refinement multiscale method and the embedded multiscale method. The post-refinement multiscale methods use the global solution to determine boundary conditions for the local solution. The local solution is solved using either a fixed boundary source or an albedo boundary condition; this solution is "post-refinement" and thus has no impact on the global solution. The embedded multiscale method allows the local solver to change the global solution to provide an improved global and local solution. The post-refinement multiscale method is assessed using three core designs. When the local solution has more energy groups, the fixed source method has some difficulties near the interface: however the albedo method works well for all cases. In order to remedy the issue with boundary condition errors for the fixed source method, a buffer region is used to act as a filter, which decreases the sensitivity of the solution to the boundary condition. Both the albedo and fixed source methods benefit from the use of a buffer region. Unlike the post-refinement method, the embedded multiscale method alters the global solution. The ability to change the global solution allows for refinement in areas where the errors in the few group nodal diffusion are typically large. The embedded method is shown to improve the global solution when it is applied to a MOX/LEU assembly
PDE-5 Inhibitors for BPH-Associated LUTS.
Brousil, Philip; Shabbir, Majid; Zacharakis, E; Sahai, Arun
2015-01-01
Lower urinary tract symptoms associated with benign prostatic hyperplasia (BPH-LUTS) are a highly prevalent problem, and with considerable burden to quality of life. Evidence has emerged that a strong correlation exists in men suffering both BPH-LUTS and erectile dysfunction (ED). Phosphodiesterase type 5 inhibitors (PDE5i) have been shown to be highly effective in treating ED and more recently there is evidence that men with LUTS also benefit. In this review article we discuss the common pathogenic pathways of ED and LUTS, the scientific basis of PDE5i use, the efficacy of PDE5i in LUTS either as monotherapy or in combination with other established medications used in LUTS. PMID:26470799
Novel PDE4 Inhibitors Derived from Chinese Medicine Forsythia
Coon, Tiffany A.; McKelvey, Alison C.; Weathington, Nate M.; Birru, Rahel L.; Lear, Travis; Leikauf, George D.; Chen, Bill B.
2014-01-01
Cyclic adenosine monophosphate (cAMP) is a crucial intracellular second messenger molecule that converts extracellular molecules to intracellular signal transduction pathways generating cell- and stimulus-specific effects. Importantly, specific phosphodiesterase (PDE) subtypes control the amplitude and duration of cAMP-induced physiological processes and are therefore a prominent pharmacological target currently used in a variety of fields. Here we tested the extracts from traditional Chinese medicine, Forsythia suspense seeds, which have been used for more than 2000 years to relieve respiratory symptoms. Using structural-functional analysis we found its major lignin, Forsynthin, acted as an immunosuppressant by inhibiting PDE4 in inflammatory and immune cell. Moreover, several novel, selective small molecule derivatives of Forsythin were tested in vitro and in murine models of viral and bacterial pneumonia, sepsis and cytokine-driven systemic inflammation. Thus, pharmacological targeting of PDE4 may be a promising strategy for immune-related disorders characterized by amplified host inflammatory response. PMID:25549252
On unstructured grids and solvers
NASA Technical Reports Server (NTRS)
Barth, T. J.
1990-01-01
The fundamentals and the state-of-the-art technology for unstructured grids and solvers are highlighted. Algorithms and techniques pertinent to mesh generation are discussed. It is shown that grid generation and grid manipulation schemes rely on fast multidimensional searching. Flow solution techniques for the Euler equations, which can be derived from the integral form of the equations are discussed. Sample calculations are also provided.
Parallel multiscale simulations of a brain aneurysm
NASA Astrophysics Data System (ADS)
Grinberg, Leopold; Fedosov, Dmitry A.; Karniadakis, George Em
2013-07-01
Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier-Stokes solver NɛκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NɛκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future
Parallel multiscale simulations of a brain aneurysm
Grinberg, Leopold; Fedosov, Dmitry A.; Karniadakis, George Em
2013-07-01
Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier–Stokes solver NεκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NεκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in
Pseudo-time methods for constrained optimization problems governed by PDE
NASA Technical Reports Server (NTRS)
Taasan, Shlomo
1995-01-01
In this paper we present a novel method for solving optimization problems governed by partial differential equations. Existing methods are gradient information in marching toward the minimum, where the constrained PDE is solved once (sometimes only approximately) per each optimization step. Such methods can be viewed as a marching techniques on the intersection of the state and costate hypersurfaces while improving the residuals of the design equations per each iteration. In contrast, the method presented here march on the design hypersurface and at each iteration improve the residuals of the state and costate equations. The new method is usually much less expensive per iteration step since, in most problems of practical interest, the design equation involves much less unknowns that that of either the state or costate equations. Convergence is shown using energy estimates for the evolution equations governing the iterative process. Numerical tests show that the new method allows the solution of the optimization problem in a cost of solving the analysis problems just a few times, independent of the number of design parameters. The method can be applied using single grid iterations as well as with multigrid solvers.
Alexander, M S; Gasperini, M J; Tsai, P T; Gibbs, D E; Spinazzola, J M; Marshall, J L; Feyder, M J; Pletcher, M T; Chekler, E L P; Morris, C A; Sahin, M; Harms, J F; Schmidt, C J; Kleiman, R J; Kunkel, L M
2016-01-01
Duchenne muscular dystrophy is caused by mutations in the DYSTROPHIN gene. Although primarily associated with muscle wasting, a significant portion of patients (approximately 25%) are also diagnosed with autism spectrum disorder. We describe social behavioral deficits in dystrophin-deficient mice and present evidence of cerebellar deficits in cGMP production. We demonstrate therapeutic potential for selective inhibitors of the cGMP-specific PDE5A and PDE9A enzymes to restore social behaviors in dystrophin-deficient mice. PMID:27676442
Terascale Optimal PDE Simulations (TOPS) Center
Professor Olof B. Widlund
2007-07-09
Our work has focused on the development and analysis of domain decomposition algorithms for a variety of problems arising in continuum mechanics modeling. In particular, we have extended and analyzed FETI-DP and BDDC algorithms; these iterative solvers were first introduced and studied by Charbel Farhat and his collaborators, see [11, 45, 12], and by Clark Dohrmann of SANDIA, Albuquerque, see [43, 2, 1], respectively. These two closely related families of methods are of particular interest since they are used more extensively than other iterative substructuring methods to solve very large and difficult problems. Thus, the FETI algorithms are part of the SALINAS system developed by the SANDIA National Laboratories for very large scale computations, and as already noted, BDDC was first developed by a SANDIA scientist, Dr. Clark Dohrmann. The FETI algorithms are also making inroads in commercial engineering software systems. We also note that the analysis of these algorithms poses very real mathematical challenges. The success in developing this theory has, in several instances, led to significant improvements in the performance of these algorithms. A very desirable feature of these iterative substructuring and other domain decomposition algorithms is that they respect the memory hierarchy of modern parallel and distributed computing systems, which is essential for approaching peak floating point performance. The development of improved methods, together with more powerful computer systems, is making it possible to carry out simulations in three dimensions, with quite high resolution, relatively easily. This work is supported by high quality software systems, such as Argonne's PETSc library, which facilitates code development as well as the access to a variety of parallel and distributed computer systems. The success in finding scalable and robust domain decomposition algorithms for very large number of processors and very large finite element problems is, e
Spatial adaptive sampling in multiscale simulation
NASA Astrophysics Data System (ADS)
Rouet-Leduc, Bertrand; Barros, Kipton; Cieren, Emmanuel; Elango, Venmugil; Junghans, Christoph; Lookman, Turab; Mohd-Yusof, Jamaludin; Pavel, Robert S.; Rivera, Axel Y.; Roehm, Dominic; McPherson, Allen L.; Germann, Timothy C.
2014-07-01
In a common approach to multiscale simulation, an incomplete set of macroscale equations must be supplemented with constitutive data provided by fine-scale simulation. Collecting statistics from these fine-scale simulations is typically the overwhelming computational cost. We reduce this cost by interpolating the results of fine-scale simulation over the spatial domain of the macro-solver. Unlike previous adaptive sampling strategies, we do not interpolate on the potentially very high dimensional space of inputs to the fine-scale simulation. Our approach is local in space and time, avoids the need for a central database, and is designed to parallelize well on large computer clusters. To demonstrate our method, we simulate one-dimensional elastodynamic shock propagation using the Heterogeneous Multiscale Method (HMM); we find that spatial adaptive sampling requires only ≈50×N0.14 fine-scale simulations to reconstruct the stress field at all N grid points. Related multiscale approaches, such as Equation Free methods, may also benefit from spatial adaptive sampling.
Student's Lab Assignments in PDE Course with MAPLE.
ERIC Educational Resources Information Center
Ponidi, B. Alhadi
Computer-aided software has been used intensively in many mathematics courses, especially in computational subjects, to solve initial value and boundary value problems in Partial Differential Equations (PDE). Many software packages were used in student lab assignments such as FORTRAN, PASCAL, MATLAB, MATHEMATICA, and MAPLE in order to accelerate…
PDE5 inhibitors enhance celecoxib killing in multiple tumor types.
Booth, Laurence; Roberts, Jane L; Cruickshanks, Nichola; Tavallai, Seyedmehrad; Webb, Timothy; Samuel, Peter; Conley, Adam; Binion, Brittany; Young, Harold F; Poklepovic, Andrew; Spiegel, Sarah; Dent, Paul
2015-05-01
The present studies determined whether clinically relevant phosphodiesterase 5 (PDE5) inhibitors interacted with a clinically relevant NSAID, celecoxib, to kill tumor cells. Celecoxib and PDE5 inhibitors interacted in a greater than additive fashion to kill multiple tumor cell types. Celecoxib and sildenafil killed ex vivo primary human glioma cells as well as their associated activated microglia. Knock down of PDE5 recapitulated the effects of PDE5 inhibitor treatment; the nitric oxide synthase inhibitor L-NAME suppressed drug combination toxicity. The effects of celecoxib were COX2 independent. Over-expression of c-FLIP-s or knock down of CD95/FADD significantly reduced killing by the drug combination. CD95 activation was dependent on nitric oxide and ceramide signaling. CD95 signaling activated the JNK pathway and inhibition of JNK suppressed cell killing. The drug combination inactivated mTOR and increased the levels of autophagy and knock down of Beclin1 or ATG5 strongly suppressed killing by the drug combination. The drug combination caused an ER stress response; knock down of IRE1α/XBP1 enhanced killing whereas knock down of eIF2α/ATF4/CHOP suppressed killing. Sildenafil and celecoxib treatment suppressed the growth of mammary tumors in vivo. Collectively our data demonstrate that clinically achievable concentrations of celecoxib and sildenafil have the potential to be a new therapeutic approach for cancer. PMID:25303541
PDE5 Inhibitors Enhance Celecoxib Killing in Multiple Tumor Types
BOOTH, LAURENCE; ROBERTS, JANE L.; CRUICKSHANKS, NICHOLA; TAVALLAI, SEYEDMEHRAD; WEBB, TIMOTHY; SAMUEL, PETER; CONLEY, ADAM; BINION, BRITTANY; YOUNG, HAROLD F.; POKLEPOVIC, ANDREW; SPIEGEL, SARAH; DENT, PAUL
2015-01-01
The present studies determined whether clinically relevant phosphodiesterase 5 (PDE5) inhibitors interacted with a clinically relevant NSAID, celecoxib, to kill tumor cells. Celecoxib and PDE5 inhibitors interacted in a greater than additive fashion to kill multiple tumor cell types. Celecoxib and sildenafil killed ex vivo primary human glioma cells as well as their associated activated microglia. Knock down of PDE5 recapitulated the effects of PDE5 inhibitor treatment; the nitric oxide synthase inhibitor L-NAME suppressed drug combination toxicity. The effects of celecoxib were COX2 independent. Over-expression of c-FLIP-s or knock down of CD95/FADD significantly reduced killing by the drug combination. CD95 activation was dependent on nitric oxide and ceramide signaling. CD95 signaling activated the JNK pathway and inhibition of JNK suppressed cell killing. The drug combination inactivated mTOR and increased the levels of autophagy and knock down of Beclin1 or ATG5 strongly suppressed killing by the drug combination. The drug combination caused an ER stress response; knock down of IRE1α/XBP1 enhanced killing whereas knock down of eIF2α/ATF4/CHOP suppressed killing. Sildenafil and celecoxib treatment suppressed the growth of mammary tumors in vivo. Collectively our data demonstrate that clinically achievable concentrations of celecoxib and sildenafil have the potential to be a new therapeutic approach for cancer. PMID:25303541
Finite Element Interface to Linear Solvers
Williams, Alan
2005-03-18
Sparse systems of linear equations arise in many engineering applications, including finite elements, finite volumes, and others. The solution of linear systems is often the most computationally intensive portion of the application. Depending on the complexity of problems addressed by the application, there may be no single solver capable of solving all of the linear systems that arise. This motivates the desire to switch an application from one solver librwy to another, depending on the problem being solved. The interfaces provided by solver libraries differ greatly, making it difficult to switch an application code from one library to another. The amount of library-specific code in an application Can be greatly reduced by having an abstraction layer between solver libraries and the application, putting a common "face" on various solver libraries. One such abstraction layer is the Finite Element Interface to Linear Solvers (EEl), which has seen significant use by finite element applications at Sandia National Laboratories and Lawrence Livermore National Laboratory.
Analysis Tools for CFD Multigrid Solvers
NASA Technical Reports Server (NTRS)
Mineck, Raymond E.; Thomas, James L.; Diskin, Boris
2004-01-01
Analysis tools are needed to guide the development and evaluate the performance of multigrid solvers for the fluid flow equations. Classical analysis tools, such as local mode analysis, often fail to accurately predict performance. Two-grid analysis tools, herein referred to as Idealized Coarse Grid and Idealized Relaxation iterations, have been developed and evaluated within a pilot multigrid solver. These new tools are applicable to general systems of equations and/or discretizations and point to problem areas within an existing multigrid solver. Idealized Relaxation and Idealized Coarse Grid are applied in developing textbook-efficient multigrid solvers for incompressible stagnation flow problems.
Redrobe, John P; Rasmussen, Lars K; Christoffersen, Claus T; Bundgaard, Christoffer; Jørgensen, Morten
2015-08-15
Here, we present a preliminary pharmacological characterisation of Lu AF33241, a novel, brain penetrant phosphodiesterase inhibitor of (PDE) 2A and 10A tool compound, in in vitro/in vivo assays indicative of PDE2A and/or PDE10A inhibition, and in vivo models/assays relevant to cognitive processing and antipsychotic-like activity. An assay was also included to investigate potential effects on motor activity. The in vitro selectivity of Lu AF33241 was determined against a panel of PDE enzymes. Lu AF33241 potently inhibited both full-length recombinant hPDE2A (Ki=4.2nM) and hPDE10A (Ki=42nM). The compound moderately inhibited both hPDE1C (Ki=1200nM), hPDE7B (Ki=890nM), and hPDE11A (Ki=1800nM). Lu AF33241 displayed a Ki above 5000nM against all other tested members of the PDE family. Albeit within a narrow dose range, Lu AF33241 attenuated sub-chronic phencyclidine-induced deficits in novel object recognition (3 and 10mg/kg), displayed antipsychotic-like activity in the conditioned avoidance response paradigm (10mg/kg), and did not induce catalepsy within a dose-range of 2-6mg/kg. Further catalepsy studies are needed to investigate a predictive safety window. Lu AF33241 represents a novel PDE2A/PDE10A inhibitor tool compound that may serve to further the understanding of the roles played by these enzymes in various CNS disorders.
Magnetospheric Multiscale (MMS) Orbit
This animation shows the orbits of Magnetospheric Multiscale (MMS) mission, a Solar-Terrestrial Probe mission comprising of four identically instrumented spacecraft that will study the Earth's magn...
Phosphodiesterase4D (PDE4D)--A risk factor for atrial fibrillation and stroke?
Jørgensen, Carina; Yasmeen, Saiqa; Iversen, Helle K; Kruuse, Christina
2015-12-15
Mutations in the gene encoding phosphodiesterase 4D (PDE4D) enzyme are associated with ischemic stroke; however the functional implications of such mutations are not well understood. PDE4D is part of a complex protein family modulating intracellular signalling by cyclic nucleotides. The PDE4 family includes subtypes A-D, all of which show unique intracellular, cellular and tissue distribution. PDE4D is the major subtype expressed in human atrial myocytes and involved in the pathophysiology of arrhythmias, such as atrial fibrillation. The PDE4D enzyme hydrolyses cyclic adenosine monophosphate (cAMP). Though diverging results are reported, several population based studies describe association of various PDE4D single nucleotide polymorphisms (SNP) with cardio-embolic stroke in particular. Functionally, a down regulation of PDE4D variants has been reported in stroke patients. The anti-inflammatory and vasodilator properties of PDE4 inhibitors make them suitable for treatment of stroke and cardiovascular disease. PDE4D has recently been suggested as factor in atrial fibrillation. This review summarizes the possible function of PDE4D in the brain, heart, and vasculature. Further, association of the described SNPs, in particular, with cardioembolic stroke, is reviewed. Current findings on the PDE4D mutations suggest functionality involves an increased cardiac risk factor as well as augmented risk of atrial fibrillation. PMID:26671126
Brullo, Chiara; Massa, Matteo; Villa, Carla; Ricciarelli, Roberta; Rivera, Daniela; Pronzato, Maria Adelaide; Fedele, Ernesto; Barocelli, Elisabetta; Bertoni, Simona; Flammini, Lisa; Bruno, Olga
2015-07-01
A new series of selective PDE4D inhibitors has been designed and synthesized by replacing 3-methoxy group with 3-difluoromethoxy isoster moiety in our previously reported cathecolic structures. All compounds showed a good PDE4D3 inhibitory activity, most of them being inactive toward other PDE4 isoforms (PDE4A4, PDE4B2 and PDE4C2). Compound 3b, chosen among the synthesized compounds as the most promising in terms of inhibitory activity, selectivity and safety, showed an improved pharmacokinetic profile compared to its non fluorinated analogue. Spontaneous locomotor activity, assessed in an open field apparatus, showed that, differently from rolipram and diazepam, selective PDE4D inhibitors, such as compounds 3b, 5b and 7b, did not affect locomotion, whereas compound 1b showed a tendency to reduce the distance traveled and to prolong the immobility period, possibly due to a poor selectivity.
Estimating the magnitude of near-membrane PDE4 activity in living cells.
Xin, Wenkuan; Feinstein, Wei P; Britain, Andrea L; Ochoa, Cristhiaan D; Zhu, Bing; Richter, Wito; Leavesley, Silas J; Rich, Thomas C
2015-09-15
Recent studies have demonstrated that functionally discrete pools of phosphodiesterase (PDE) activity regulate distinct cellular functions. While the importance of localized pools of enzyme activity has become apparent, few studies have estimated enzyme activity within discrete subcellular compartments. Here we present an approach to estimate near-membrane PDE activity. First, total PDE activity is measured using traditional PDE activity assays. Second, known cAMP concentrations are dialyzed into single cells and the spatial spread of cAMP is monitored using cyclic nucleotide-gated channels. Third, mathematical models are used to estimate the spatial distribution of PDE activity within cells. Using this three-tiered approach, we observed two pharmacologically distinct pools of PDE activity, a rolipram-sensitive pool and an 8-methoxymethyl IBMX (8MM-IBMX)-sensitive pool. We observed that the rolipram-sensitive PDE (PDE4) was primarily responsible for cAMP hydrolysis near the plasma membrane. Finally, we observed that PDE4 was capable of blunting cAMP levels near the plasma membrane even when 100 μM cAMP were introduced into the cell via a patch pipette. Two compartment models predict that PDE activity near the plasma membrane, near cyclic nucleotide-gated channels, was significantly lower than total cellular PDE activity and that a slow spatial spread of cAMP allowed PDE activity to effectively hydrolyze near-membrane cAMP. These results imply that cAMP levels near the plasma membrane are distinct from those in other subcellular compartments; PDE activity is not uniform within cells; and localized pools of AC and PDE activities are responsible for controlling cAMP levels within distinct subcellular compartments.
KLU2 Direct Linear Solver Package
2012-01-04
KLU2 is a direct sparse solver for solving unsymmetric linear systems. It is related to the existing KLU solver, (in Amesos package and also as a stand-alone package from University of Florida) but provides template support for scalar and ordinal types. It uses a left looking LU factorization method.
Improving Resource-Unaware SAT Solvers
NASA Astrophysics Data System (ADS)
Hölldobler, Steffen; Manthey, Norbert; Saptawijaya, Ari
The paper discusses cache utilization in state-of-the-art SAT solvers. The aim of the study is to show how a resource-unaware SAT solver can be improved by utilizing the cache sensibly. The analysis is performed on a CDCL-based SAT solver using a subset of the industrial SAT Competition 2009 benchmark. For the analysis, the total cycles, the resource stall cycles, the L2 cache hits and the L2 cache misses are traced using sample based profiling. Based on the analysis, several techniques - some of which have not been used in SAT solvers so far - are proposed resulting in a combined speedup up to 83% without affecting the search path of the solver. The average speedup on the benchmark is 60%. The new techniques are also applied to MiniSAT2.0 improving its runtime by 20% on average.
Belos Block Linear Solvers Package
2004-03-01
Belos is an extensible and interoperable framework for large-scale, iterative methods for solving systems of linear equations with multiple right-hand sides. The motivation for this framework is to provide a generic interface to a collection of algorithms for solving large-scale linear systems. Belos is interoperable because both the matrix and vectors are considered to be opaque objects--only knowledge of the matrix and vectors via elementary operations is necessary. An implementation of Balos is accomplished viamore » the use of interfaces. One of the goals of Belos is to allow the user flexibility in specifying the data representation for the matrix and vectors and so leverage any existing software investment. The algorithms that will be included in package are Krylov-based linear solvers, like Block GMRES (Generalized Minimal RESidual) and Block CG (Conjugate-Gradient).« less
A local PDE model of aggregation formation in bacterial colonies
NASA Astrophysics Data System (ADS)
Chavy-Waddy, Paul-Christopher; Kolokolnikov, Theodore
2016-10-01
We study pattern formation in a model of cyanobacteria motion recently proposed by Galante, Wisen, Bhaya and Levy. By taking a continuum limit of their model, we derive a novel fourth-order nonlinear parabolic PDE equation that governs the behaviour of the model. This PDE is {{u}t}=-{{u}xx}-{{u}xxxx}+α {{≤ft(\\frac{{{u}x}{{u}xx}}{u}\\right)}x} . We then derive the instability thresholds for the onset of pattern formation. We also compute analytically the spatial profiles of the steady state aggregation density. These profiles are shown to be of the form \\text{sec}{{\\text{h}}p} where the exponent p is related to the parameters of the model. Full numerical simulations give a favorable comparison between the continuum and the underlying discrete system, and show that the aggregation profiles are stable above the critical threshold.
Interactive Medical Image Segmentation using PDE Control of Active Contours
Karasev, Peter; Kolesov, Ivan; Fritscher, Karl; Vela, Patricio; Mitchell, Phillip; Tannenbaum, Allen
2014-01-01
Segmentation of injured or unusual anatomic structures in medical imagery is a problem that has continued to elude fully automated solutions. In this paper, the goal of easy-to-use and consistent interactive segmentation is transformed into a control synthesis problem. A nominal level set PDE is assumed to be given; this open-loop system achieves correct segmentation under ideal conditions, but does not agree with a human expert's ideal boundary for real image data. Perturbing the state and dynamics of a level set PDE via the accumulated user input and an observer-like system leads to desirable closed-loop behavior. The input structure is designed such that a user can stabilize the boundary in some desired state without needing to understand any mathematical parameters. Effectiveness of the technique is illustrated with applications to the challenging segmentations of a patellar tendon in MR and a shattered femur in CT. PMID:23893712
β1-adrenergic receptor antagonists signal via PDE4 translocation.
Richter, Wito; Mika, Delphine; Blanchard, Elise; Day, Peter; Conti, Marco
2013-03-01
It is generally assumed that antagonists of Gs-coupled receptors do not activate cAMP signalling, because they do not stimulate cAMP production via Gs-protein/adenylyl cyclase activation. Here, we report a new signalling pathway whereby antagonists of β1-adrenergic receptors (β1ARs) increase cAMP levels locally without stimulating cAMP production directly. Binding of antagonists causes dissociation of a preformed complex between β1ARs and Type-4 cyclic nucleotide phosphodiesterases (PDE4s). This reduces the local concentration of cAMP-hydrolytic activity, thereby increasing submembrane cAMP and PKA activity. Our study identifies receptor/PDE4 complex dissociation as a novel mechanism of antagonist action that contributes to the pharmacological properties of β1AR antagonists and might be shared by other receptor subtypes.
NASA Astrophysics Data System (ADS)
Boscheri, Walter; Balsara, Dinshaw S.; Dumbser, Michael
2014-06-01
In this paper we use the genuinely multidimensional HLL Riemann solvers recently developed by Balsara et al. in [13] to construct a new class of computationally efficient high order Lagrangian ADER-WENO one-step ALE finite volume schemes on unstructured triangular meshes. A nonlinear WENO reconstruction operator allows the algorithm to achieve high order of accuracy in space, while high order of accuracy in time is obtained by the use of an ADER time-stepping technique based on a local space-time Galerkin predictor. The multidimensional HLL and HLLC Riemann solvers operate at each vertex of the grid, considering the entire Voronoi neighborhood of each node and allow for larger time steps than conventional one-dimensional Riemann solvers. The results produced by the multidimensional Riemann solver are then used twice in our one-step ALE algorithm: first, as a node solver that assigns a unique velocity vector to each vertex, in order to preserve the continuity of the computational mesh; second, as a building block for genuinely multidimensional numerical flux evaluation that allows the scheme to run with larger time steps compared to conventional finite volume schemes that use classical one-dimensional Riemann solvers in normal direction. The space-time flux integral computation is carried out at the boundaries of each triangular space-time control volume using the Simpson quadrature rule in space and Gauss-Legendre quadrature in time. A rezoning step may be necessary in order to overcome element overlapping or crossing-over. Since our one-step ALE finite volume scheme is based directly on a space-time conservation formulation of the governing PDE system, the remapping stage is not needed, making our algorithm a so-called direct ALE method.
NASA Astrophysics Data System (ADS)
Balsara, Dinshaw S.; Vides, Jeaniffer; Gurski, Katharine; Nkonga, Boniface; Dumbser, Michael; Garain, Sudip; Audit, Edouard
2016-01-01
Just as the quality of a one-dimensional approximate Riemann solver is improved by the inclusion of internal sub-structure, the quality of a multidimensional Riemann solver is also similarly improved. Such multidimensional Riemann problems arise when multiple states come together at the vertex of a mesh. The interaction of the resulting one-dimensional Riemann problems gives rise to a strongly-interacting state. We wish to endow this strongly-interacting state with physically-motivated sub-structure. The self-similar formulation of Balsara [16] proves especially useful for this purpose. While that work is based on a Galerkin projection, in this paper we present an analogous self-similar formulation that is based on a different interpretation. In the present formulation, we interpret the shock jumps at the boundary of the strongly-interacting state quite literally. The enforcement of the shock jump conditions is done with a least squares projection (Vides, Nkonga and Audit [67]). With that interpretation, we again show that the multidimensional Riemann solver can be endowed with sub-structure. However, we find that the most efficient implementation arises when we use a flux vector splitting and a least squares projection. An alternative formulation that is based on the full characteristic matrices is also presented. The multidimensional Riemann solvers that are demonstrated here use one-dimensional HLLC Riemann solvers as building blocks. Several stringent test problems drawn from hydrodynamics and MHD are presented to show that the method works. Results from structured and unstructured meshes demonstrate the versatility of our method. The reader is also invited to watch a video introduction to multidimensional Riemann solvers on http://www.nd.edu/~dbalsara/Numerical-PDE-Course.
Universal structure and universal equations (PDE) for unitary ensembles
NASA Astrophysics Data System (ADS)
Rumanov, Igor
2010-08-01
Random matrix ensembles with unitary invariance of measure (UE) are described in a unified way using a combination of Tracy-Widom (TW) and Adler-Shiota-van Moerbeke approaches to the derivation of partial differential equations (PDEs) for spectral gap probabilities. First, general three-term recurrence relations for UE restricted to subsets of real line, or, in other words, for functions in the resolvent kernel, are obtained. Using them, simple universal relations between all TW dependent variables and one-dimensional Toda lattice τ-functions are found. A universal system of PDE for UE is derived from previous relations, which leads also to a single independent PDE for spectral gap probability of various UE. Thus, orthogonal function bases and Toda lattice are seen at the core of correspondence of different approaches. Moreover, Toda-AKNS system provides a common structure of PDE for unitary ensembles. Interestingly, this structure can be seen in two very different forms: one arises from orthogonal function-Toda lattice considerations, while the other comes from Schlesinger equations for isomonodromic deformations and their relation to TW equations. The simple example of Gaussian matrices most neatly exposes this structure.
Diggle, Christine P; Sukoff Rizzo, Stacey J; Popiolek, Michael; Hinttala, Reetta; Schülke, Jan-Philip; Kurian, Manju A; Carr, Ian M; Markham, Alexander F; Bonthron, David T; Watson, Christopher; Sharif, Saghira Malik; Reinhart, Veronica; James, Larry C; Vanase-Frawley, Michelle A; Charych, Erik; Allen, Melanie; Harms, John; Schmidt, Christopher J; Ng, Joanne; Pysden, Karen; Strick, Christine; Vieira, Päivi; Mankinen, Katariina; Kokkonen, Hannaleena; Kallioinen, Matti; Sormunen, Raija; Rinne, Juha O; Johansson, Jarkko; Alakurtti, Kati; Huilaja, Laura; Hurskainen, Tiina; Tasanen, Kaisa; Anttila, Eija; Marques, Tiago Reis; Howes, Oliver; Politis, Marius; Fahiminiya, Somayyeh; Nguyen, Khanh Q; Majewski, Jacek; Uusimaa, Johanna; Sheridan, Eamonn; Brandon, Nicholas J
2016-04-01
Deficits in the basal ganglia pathways modulating cortical motor activity underlie both Parkinson disease (PD) and Huntington disease (HD). Phosphodiesterase 10A (PDE10A) is enriched in the striatum, and animal data suggest that it is a key regulator of this circuitry. Here, we report on germline PDE10A mutations in eight individuals from two families affected by a hyperkinetic movement disorder due to homozygous mutations c.320A>G (p.Tyr107Cys) and c.346G>C (p.Ala116Pro). Both mutations lead to a reduction in PDE10A levels in recombinant cellular systems, and critically, positron-emission-tomography (PET) studies with a specific PDE10A ligand confirmed that the p.Tyr107Cys variant also reduced striatal PDE10A levels in one of the affected individuals. A knock-in mouse model carrying the homologous p.Tyr97Cys variant had decreased striatal PDE10A and also displayed motor abnormalities. Striatal preparations from this animal had an impaired capacity to degrade cyclic adenosine monophosphate (cAMP) and a blunted pharmacological response to PDE10A inhibitors. These observations highlight the critical role of PDE10A in motor control across species. PMID:27058446
Diggle, Christine P.; Sukoff Rizzo, Stacey J.; Popiolek, Michael; Hinttala, Reetta; Schülke, Jan-Philip; Kurian, Manju A.; Carr, Ian M.; Markham, Alexander F.; Bonthron, David T.; Watson, Christopher; Sharif, Saghira Malik; Reinhart, Veronica; James, Larry C.; Vanase-Frawley, Michelle A.; Charych, Erik; Allen, Melanie; Harms, John; Schmidt, Christopher J.; Ng, Joanne; Pysden, Karen; Strick, Christine; Vieira, Päivi; Mankinen, Katariina; Kokkonen, Hannaleena; Kallioinen, Matti; Sormunen, Raija; Rinne, Juha O.; Johansson, Jarkko; Alakurtti, Kati; Huilaja, Laura; Hurskainen, Tiina; Tasanen, Kaisa; Anttila, Eija; Marques, Tiago Reis; Howes, Oliver; Politis, Marius; Fahiminiya, Somayyeh; Nguyen, Khanh Q.; Majewski, Jacek; Uusimaa, Johanna; Sheridan, Eamonn; Brandon, Nicholas J.
2016-01-01
Deficits in the basal ganglia pathways modulating cortical motor activity underlie both Parkinson disease (PD) and Huntington disease (HD). Phosphodiesterase 10A (PDE10A) is enriched in the striatum, and animal data suggest that it is a key regulator of this circuitry. Here, we report on germline PDE10A mutations in eight individuals from two families affected by a hyperkinetic movement disorder due to homozygous mutations c.320A>G (p.Tyr107Cys) and c.346G>C (p.Ala116Pro). Both mutations lead to a reduction in PDE10A levels in recombinant cellular systems, and critically, positron-emission-tomography (PET) studies with a specific PDE10A ligand confirmed that the p.Tyr107Cys variant also reduced striatal PDE10A levels in one of the affected individuals. A knock-in mouse model carrying the homologous p.Tyr97Cys variant had decreased striatal PDE10A and also displayed motor abnormalities. Striatal preparations from this animal had an impaired capacity to degrade cyclic adenosine monophosphate (cAMP) and a blunted pharmacological response to PDE10A inhibitors. These observations highlight the critical role of PDE10A in motor control across species. PMID:27058446
PDE4D phosphorylation: A coincidence detector integrating multiple signaling pathways.
Mika, Delphine; Conti, Marco
2016-07-01
In Eukaryotes, more than 100 different phosphodiesterase (PDE) proteins serve to fine-tune cyclic nucleotide (cAMP and cGMP) signals and contribute to specificity of signaling. In mammals, PDEs are divided into 11 families, of which PDE4 represents the largest family. Four genes (pde4a, pde4b, pde4c and pde4d) encode for this class of enzymes in mammals and give rise to more than 20 variants. Within this family of genes, PDE4D was discovered on the basis of its regulatory properties and its induction by hormones and cAMP. PDE4D has often been used as the prototype PDE4 and large body of work has been generated on the biochemical, pharmacological, and physiological properties of this enzyme. This review covers the regulation of PDE4D by phosphorylation, the impact of this regulation in the context of the structure of this protein, and the functional consequences of this complex pattern of posttranslational modifications. PMID:26562185
Domain Organization and Conformational Plasticity of the G Protein Effector, PDE6*
Zhang, Zhixian; He, Feng; Constantine, Ryan; Baker, Matthew L.; Baehr, Wolfgang; Schmid, Michael F.; Wensel, Theodore G.; Agosto, Melina A.
2015-01-01
The cGMP phosphodiesterase of rod photoreceptor cells, PDE6, is the key effector enzyme in phototransduction. Two large catalytic subunits, PDE6α and -β, each contain one catalytic domain and two non-catalytic GAF domains, whereas two small inhibitory PDE6γ subunits allow tight regulation by the G protein transducin. The structure of holo-PDE6 in complex with the ROS-1 antibody Fab fragment was determined by cryo-electron microscopy. The ∼11 Å map revealed previously unseen features of PDE6, and each domain was readily fit with high resolution structures. A structure of PDE6 in complex with prenyl-binding protein (PrBP/δ) indicated the location of the PDE6 C-terminal prenylations. Reconstructions of complexes with Fab fragments bound to N or C termini of PDE6γ revealed that PDE6γ stretches from the catalytic domain at one end of the holoenzyme to the GAF-A domain at the other. Removal of PDE6γ caused dramatic structural rearrangements, which were reversed upon its restoration. PMID:25809480
Does phosphodiesterase 11A (PDE11A) hold promise as a future therapeutic target?
Kelly, Michy P
2015-01-01
Phosphodiesterase 11A (PDE11A) is the most recently discovered 3', 5'-cyclic nucleotide phosphodiesterase. By breaking down both cAMP and cGMP, PDE11A is a critical regulator of intracellular signaling. To date, PDE11A has been implicated to play a role in tumorigenesis, brain function, and inflammation. Here, we consolidate and, where necessary, reconcile the PDE11A literature to evaluate this enzyme as a potential therapeutic target. We compare the results and methodologies of numerous studies that report conflicting tissue expression profiles for PDE11A. We conclude that PDE11A expression is relatively restricted in the body, with reliable expression reported in tissues such as the brain (particularly the hippocampus), the prostate, and the adrenal gland. Each of the four PDE11A splice variants (PDE11A1-4) appears to exhibit a distinct tissue expression profile and has a unique N-terminal regulatory region, suggesting that each isoform could be individually targeted with a small molecule or biologic. Progress has been made in identifying a tool PDE11A inhibitor as well as an activator; however, the functional effects of these pharmacological tools remain to be determined. Importantly, PDE11A knockout mice do exist and appear healthy into late age, suggesting a potential safety window for targeting this enzyme. Considering the implication of PDE11A in disease-relevant biology, the potential to selectively target specific PDE11A variants, and the possibility of either activating or inhibiting the enzyme, we believe PDE11A holds promise as a potential future therapeutic target.
Kuwayama, H; Snippe, H; Derks, M; Roelofs, J; Van Haastert, P J
2001-01-01
In Dictyostelium cAMP and cGMP have important functions as first and second messengers in chemotaxis and development. Two cyclic-nucleotide phosphodiesterases (DdPDE 1 and 2) have been identified previously, an extracellular dual-specificity enzyme and an intracellular cAMP-specific enzyme (encoded by the psdA and regA genes respectively). Biochemical data suggest the presence of at least one cGMP-specific phosphodiesterase (PDE) that is activated by cGMP. Using bioinformatics we identified a partial sequence in the Dictyostelium expressed sequence tag database that shows a high degree of amino acid sequence identity with mammalian PDE catalytic domains (DdPDE3). The deduced amino acid sequence of a full-length DdPDE3 cDNA isolated in this study predicts a 60 kDa protein with a 300-residue C-terminal PDE catalytic domain, which is preceded by approx. 200 residues rich in asparagine and glutamine residues. Expression of the DdPDE3 catalytic domain in Escherichia coli shows that the enzyme has Michaelis-Menten kinetics and a higher affinity for cGMP (K(m)=0.22 microM) than for cAMP (K(m)=145 microM); cGMP does not stimulate enzyme activity. The enzyme requires bivalent cations for activity; Mn(2+) is preferred to Mg(2+), whereas Ca(2+) yields no activity. DdPDE3 is inhibited by 3-isobutyl-1-methylxanthine with an IC(50) of approx. 60 microM. Overexpression of the DdPDE3 catalytic domain in Dictyostelium confirms these kinetic properties without indications of its activation by cGMP. The properties of DdPDE3 resemble those of mammalian PDE9, which also shows the highest sequence similarity within the catalytic domains. DdPDE3 is the first cGMP-selective PDE identified in lower eukaryotes. PMID:11171061
Identification and tissue-specific expression of PDE7 phosphodiesterase splice variants
Bloom, Timothy J.; Beavo, Joseph A.
1996-01-01
Type 7 cyclic nucleotide phosphodiesterases (PDE7s) are a newly described family of enzymes having high affinity and specificity for cAMP. However, little is known about their structure, function, or regulation. We have isolated a mouse skeletal muscle cDNA representing a new alternative splice variant (PDE7A2) of the PDE7 gene. The ORF encodes a 456-amino acid protein having a predicted molecular weight of 52.4 kDa. The 5′ end of the mouse PDE7A2 is divergent from the 5′ end of the human PDE7A1 sequence and is more hydrophobic. A comparison of the 5′ ends of the two cDNA clones with human genomic sequence indicates that they represent alternate splice products rather than species variation. RNase protection analysis of several mouse tissues indicates that PDE7 is expressed widely with highest levels in skeletal muscle. HPLC fractionation and Western blot analysis of two human lymphocyte T-cell lines shows that an unknown PDE activity described by Ichimura and Kase [Ichimura, M. & Kase, H. (1993) Biochem. Biophys. Res. Commun. 193, 985–990] is most likely to be PDE7A1. A single immunoreactive band of ≈55 kDa, which comigrates with PDE7A1, is seen in fractions of the HPLC profile containing this activity suggesting that the original human PDE7A1 clone contains a full-length ORF, and is not truncated at the 5′ end as was originally postulated. In a human lymphocyte B-cell line and also in mouse skeletal muscle, a large amount of PDE7 mRNA but little PDE7 protein or activity is expressed suggesting that the translation or stability of PDE7 protein may be highly regulated in these tissues. PMID:8943082
MUSIC: MUlti-Scale Initial Conditions
NASA Astrophysics Data System (ADS)
Hahn, Oliver; Abel, Tom
2013-11-01
MUSIC generates multi-scale initial conditions with multiple levels of refinements for cosmological ‘zoom-in’ simulations. The code uses an adaptive convolution of Gaussian white noise with a real-space transfer function kernel together with an adaptive multi-grid Poisson solver to generate displacements and velocities following first- (1LPT) or second-order Lagrangian perturbation theory (2LPT). MUSIC achieves rms relative errors of the order of 10-4 for displacements and velocities in the refinement region and thus improves in terms of errors by about two orders of magnitude over previous approaches. In addition, errors are localized at coarse-fine boundaries and do not suffer from Fourier space-induced interference ringing.
Sahu, Maitrayee; Sahu, Abhiram
2015-11-01
Leptin signaling in the hypothalamus is critical for normal food intake and body weight regulation. Cumulative evidence suggests that besides the signal transducer and activator of transcription-3 (STAT3) pathway, several non-STAT3 pathways including the phosphodiesterase-3B (PDE3B) pathway mediate leptin signaling in the hypothalamus. We have shown that PDE3B is localized in various hypothalamic sites implicated in the regulation of energy homeostasis and that the anorectic and body weight reducing effects of leptin are mediated by the activation of PDE3B. It is still unknown if PDE3B is expressed in the long form of the leptin-receptor (ObRb)-expressing neurons in the hypothalamus and whether leptin induces STAT3 activation in PDE3B-expressing neurons. In this study, we examined co-localization of PDE3B with ObRb neurons in various hypothalamic nuclei in ObRb-GFP mice that were treated with leptin (5mg/kg, ip) for 2h. Results showed that most of the ObRb neurons in the arcuate nucleus (ARC, 93%), ventromedial nucleus (VMN, 94%), dorsomedial nucleus (DMN, 95%), ventral premammillary nucleus (PMv, 97%) and lateral hypothalamus (LH, 97%) co-expressed PDE3B. We next examined co-localization of p-STAT3 and PDE3B in the hypothalamus in C57BL6 mice that were treated with leptin (5mg/kg, ip) for 1h. The results showed that almost all p-STAT3 positive neurons in different hypothalamic nuclei including ARC, VMN, DMN, LH and PMv areas expressed PDE3B. These results suggest the possibility for a direct role for the PDE3B pathway in mediating leptin action in the hypothalamus.
ALPS - A LINEAR PROGRAM SOLVER
NASA Technical Reports Server (NTRS)
Viterna, L. A.
1994-01-01
Linear programming is a widely-used engineering and management tool. Scheduling, resource allocation, and production planning are all well-known applications of linear programs (LP's). Most LP's are too large to be solved by hand, so over the decades many computer codes for solving LP's have been developed. ALPS, A Linear Program Solver, is a full-featured LP analysis program. ALPS can solve plain linear programs as well as more complicated mixed integer and pure integer programs. ALPS also contains an efficient solution technique for pure binary (0-1 integer) programs. One of the many weaknesses of LP solvers is the lack of interaction with the user. ALPS is a menu-driven program with no special commands or keywords to learn. In addition, ALPS contains a full-screen editor to enter and maintain the LP formulation. These formulations can be written to and read from plain ASCII files for portability. For those less experienced in LP formulation, ALPS contains a problem "parser" which checks the formulation for errors. ALPS creates fully formatted, readable reports that can be sent to a printer or output file. ALPS is written entirely in IBM's APL2/PC product, Version 1.01. The APL2 workspace containing all the ALPS code can be run on any APL2/PC system (AT or 386). On a 32-bit system, this configuration can take advantage of all extended memory. The user can also examine and modify the ALPS code. The APL2 workspace has also been "packed" to be run on any DOS system (without APL2) as a stand-alone "EXE" file, but has limited memory capacity on a 640K system. A numeric coprocessor (80X87) is optional but recommended. The standard distribution medium for ALPS is a 5.25 inch 360K MS-DOS format diskette. IBM, IBM PC and IBM APL2 are registered trademarks of International Business Machines Corporation. MS-DOS is a registered trademark of Microsoft Corporation.
GARDNER, P.R.
2006-04-01
Sudoku, also known as Number Place, is a logic-based placement puzzle. The aim of the puzzle is to enter a numerical digit from 1 through 9 in each cell of a 9 x 9 grid made up of 3 x 3 subgrids (called ''regions''), starting with various digits given in some cells (the ''givens''). Each row, column, and region must contain only one instance of each numeral. Completing the puzzle requires patience and logical ability. Although first published in a U.S. puzzle magazine in 1979, Sudoku initially caught on in Japan in 1986 and attained international popularity in 2005. Last fall, after noticing Sudoku puzzles in some newspapers and magazines, I attempted a few just to see how hard they were. Of course, the difficulties varied considerably. ''Obviously'' one could use Trial and Error but all the advice was to ''Use Logic''. Thinking to flex, and strengthen, those powers, I began to tackle the puzzles systematically. That is, when I discovered a new tactical rule, I would write it down, eventually generating a list of ten or so, with some having overlap. They served pretty well except for the more difficult puzzles, but even then I managed to develop an additional three rules that covered all of them until I hit the Oregonian puzzle shown. With all of my rules, I could not seem to solve that puzzle. Initially putting my failure down to rapid mental fatigue (being unable to hold a sufficient quantity of information in my mind at one time), I decided to write a program to implement my rules and see what I had failed to notice earlier. The solver, too, failed. That is, my rules were insufficient to solve that particular puzzle. I happened across a book written by a fellow who constructs such puzzles and who claimed that, sometimes, the only tactic left was trial and error. With a trial and error routine implemented, my solver successfully completed the Oregonian puzzle, and has successfully solved every puzzle submitted to it since.
SIERRA framework version 4 : solver services.
Williams, Alan B.
2005-02-01
Several SIERRA applications make use of third-party libraries to solve systems of linear and nonlinear equations, and to solve eigenproblems. The classes and interfaces in the SIERRA framework that provide linear system assembly services and access to solver libraries are collectively referred to as solver services. This paper provides an overview of SIERRA's solver services including the design goals that drove the development, and relationships and interactions among the various classes. The process of assembling and manipulating linear systems will be described, as well as access to solution methods and other operations.
Michie, A M; Lobban, M; Müller, T; Harnett, M M; Houslay, M D
1996-02-01
The PDE2, cyclic GMP-stimulated, and the PDE4, cyclic AMP-specific enzymes provide the major, detectable cyclic AMP phosphodiesterase activities in murine thymocytes. In the absence of the cyclic GMP, PDE4 activity predominated (approximately 80% total) but in the presence of low (10 microM) cyclic GMP concentrations, PDE2 activity constituted the major PDE activity in thymocytes (approximately 80% total). The PDE4 selective inhibitor rolipram dose-dependently inhibited thymocyte PDE4 activity (IC50 approximately 65 nM). PDE2 was dose-dependently activated (EC50 approximately 1 microM) by cyclic GMP and inhibited by erythro-9-(2-hydroxy-3-nonyl)-adenine (EHNA) (IC50 approximately 4 microM). EHNA was shown to serve as a selective inhibitor of PDE-2 activity as assessed from studies using separated PDE1, PDE2, PDE3 and PDE4 species from hepatocytes as well as human PDE2 and PDE4 enzymes. EHNA completely ablated the ability of cyclic GMP to activate PDE2 activity, whilst having a much smaller inhibitory effect on the unstimulated PDE2 activity. EHNA exhibited normal Michaelian kinetics of inhibition for the cyclic GMP-stimulated PDE2 activity with Hill plots near unity. Apparent negative co-operative effect were seen in the absence of cyclic GMP with Hill coefficients of approximately 0.3 for inhibition of PDE2 activity. Within 5 min of challenge of thymocytes with the lectin phytohaemagglutinin (PHA) there was a transient decrease (approximately 83%) in PDE-4 activity and in PDE2 activity (approximately 40%). Both anti-TCR antibodies also caused an initial reduction in the PDE4 activity which was followed by a sustained and profound increase in activity. In contrast to that observed with PHA, anti-TCR/CD3 antisera had little effect on PDE2 activity. It is suggested that, dependent upon the intracellular concentrations of cyclic GMP, thymocyte cyclic AMP metabolism can be expected to switch from being under the predominant control of PDE4 activity to that determined
NASA Technical Reports Server (NTRS)
Ferencz, Donald C.; Viterna, Larry A.
1991-01-01
ALPS is a computer program which can be used to solve general linear program (optimization) problems. ALPS was designed for those who have minimal linear programming (LP) knowledge and features a menu-driven scheme to guide the user through the process of creating and solving LP formulations. Once created, the problems can be edited and stored in standard DOS ASCII files to provide portability to various word processors or even other linear programming packages. Unlike many math-oriented LP solvers, ALPS contains an LP parser that reads through the LP formulation and reports several types of errors to the user. ALPS provides a large amount of solution data which is often useful in problem solving. In addition to pure linear programs, ALPS can solve for integer, mixed integer, and binary type problems. Pure linear programs are solved with the revised simplex method. Integer or mixed integer programs are solved initially with the revised simplex, and the completed using the branch-and-bound technique. Binary programs are solved with the method of implicit enumeration. This manual describes how to use ALPS to create, edit, and solve linear programming problems. Instructions for installing ALPS on a PC compatible computer are included in the appendices along with a general introduction to linear programming. A programmers guide is also included for assistance in modifying and maintaining the program.
Euler solvers for transonic applications
NASA Technical Reports Server (NTRS)
Vanleer, Bram
1989-01-01
The 1980s may well be called the Euler era of applied aerodynamics. Computer codes based on discrete approximations of the Euler equations are now routinely used to obtain solutions of transonic flow problems in which the effects of entropy and vorticity production are significant. Such codes can even predict separation from a sharp edge, owing to the inclusion of artificial dissipation, intended to lend numerical stability to the calculation but at the same time enforcing the Kutta condition. One effect not correctly predictable by Euler codes is the separation from a smooth surface, and neither is viscous drag; for these some form of the Navier-Stokes equation is needed. It, therefore, comes as no surprise to observe that the Navier-Stokes has already begun before Euler solutions were fully exploited. Moreover, most numerical developments for the Euler equations are now constrained by the requirement that the techniques introduced, notably artificial dissipation, must not interfere with the new physics added when going from an Euler to a full Navier-Stokes approximation. In order to appreciate the contributions of Euler solvers to the understanding of transonic aerodynamics, it is useful to review the components of these computational tools. Space discretization, time- or pseudo-time marching and boundary procedures, the essential constituents are discussed. The subject of grid generation and grid adaptation to the solution are touched upon only where relevant. A list of unanswered questions and an outlook for the future are covered.
A Linear PDE Approach to the Bellman Equation of Ergodic Control with Periodic Structure
Fujita, Y.
2003-03-12
In this paper we give a new proof of the existence result of Bensoussan [1, Theorem II-6.1] for the Bellman equation of ergodic control with periodic structure. This Bellman equation is a nonlinear PDE, and he constructed its solution by using the solution of a nonlinear PDE. On the contrary, our key idea is to solve two linear PDEs. Hence, we propose a linear PDE approach to this Bellman equation.
Parallelizing alternating direction implicit solver on GPUs
Technology Transfer Automated Retrieval System (TEKTRAN)
We present a parallel Alternating Direction Implicit (ADI) solver on GPUs. Our implementation significantly improves existing implementations in two aspects. First, we address the scalability issue of existing Parallel Cyclic Reduction (PCR) implementations by eliminating their hardware resource con...
Multiscale Design of Advanced Materials based on Hybrid Ab Initio and Quasicontinuum Methods
Luskin, Mitchell
2014-03-12
This project united researchers from mathematics, chemistry, computer science, and engineering for the development of new multiscale methods for the design of materials. Our approach was highly interdisciplinary, but it had two unifying themes: first, we utilized modern mathematical ideas about change-of-scale and state-of-the-art numerical analysis to develop computational methods and codes to solve real multiscale problems of DOE interest; and, second, we took very seriously the need for quantum mechanics-based atomistic forces, and based our methods on fast solvers of chemically accurate methods.
Macklin, Paul; Cristini, Vittorio
2013-01-01
Simulating cancer behavior across multiple biological scales in space and time, i.e., multiscale cancer modeling, is increasingly being recognized as a powerful tool to refine hypotheses, focus experiments, and enable more accurate predictions. A growing number of examples illustrate the value of this approach in providing quantitative insight on the initiation, progression, and treatment of cancer. In this review, we introduce the most recent and important multiscale cancer modeling works that have successfully established a mechanistic link between different biological scales. Biophysical, biochemical, and biomechanical factors are considered in these models. We also discuss innovative, cutting-edge modeling methods that are moving predictive multiscale cancer modeling toward clinical application. Furthermore, because the development of multiscale cancer models requires a new level of collaboration among scientists from a variety of fields such as biology, medicine, physics, mathematics, engineering, and computer science, an innovative Web-based infrastructure is needed to support this growing community. PMID:21529163
O'Donnell
2000-03-01
Presentations at the William Harvey Research Conference on PDE Inhibitors described the molecular biology, biochemical regulation. pharmacology, and therapeutic utility of inhibitors of cyclic nucleotide phosphodiesterases (PDEs). Most of the talks focused on PDE4 and PDE5. two members of the 11-member PDE family that have attracted much interest over the last several years. These enzymes have been shown to be targets for drugs with wide-ranging clinical utility, including treatment of inflammation, depression, and male erectile dysfunction. The continued investigation of PDEs and the development of potent and selective inhibitors should provide even more therapeutic agents in years to come.
Finite Element Interface to Linear Solvers
2005-03-18
Sparse systems of linear equations arise in many engineering applications, including finite elements, finite volumes, and others. The solution of linear systems is often the most computationally intensive portion of the application. Depending on the complexity of problems addressed by the application, there may be no single solver capable of solving all of the linear systems that arise. This motivates the desire to switch an application from one solver librwy to another, depending on themore » problem being solved. The interfaces provided by solver libraries differ greatly, making it difficult to switch an application code from one library to another. The amount of library-specific code in an application Can be greatly reduced by having an abstraction layer between solver libraries and the application, putting a common "face" on various solver libraries. One such abstraction layer is the Finite Element Interface to Linear Solvers (EEl), which has seen significant use by finite element applications at Sandia National Laboratories and Lawrence Livermore National Laboratory.« less
A parallel PCG solver for MODFLOW.
Dong, Yanhui; Li, Guomin
2009-01-01
In order to simulate large-scale ground water flow problems more efficiently with MODFLOW, the OpenMP programming paradigm was used to parallelize the preconditioned conjugate-gradient (PCG) solver with in this study. Incremental parallelization, the significant advantage supported by OpenMP on a shared-memory computer, made the solver transit to a parallel program smoothly one block of code at a time. The parallel PCG solver, suitable for both MODFLOW-2000 and MODFLOW-2005, is verified using an 8-processor computer. Both the impact of compilers and different model domain sizes were considered in the numerical experiments. Based on the timing results, execution times using the parallel PCG solver are typically about 1.40 to 5.31 times faster than those using the serial one. In addition, the simulation results are the exact same as the original PCG solver, because the majority of serial codes were not changed. It is worth noting that this parallelizing approach reduces cost in terms of software maintenance because only a single source PCG solver code needs to be maintained in the MODFLOW source tree. PMID:19563427
A multiscale two-point flux-approximation method
Møyner, Olav Lie, Knut-Andreas
2014-10-15
A large number of multiscale finite-volume methods have been developed over the past decade to compute conservative approximations to multiphase flow problems in heterogeneous porous media. In particular, several iterative and algebraic multiscale frameworks that seek to reduce the fine-scale residual towards machine precision have been presented. Common for all such methods is that they rely on a compatible primal–dual coarse partition, which makes it challenging to extend them to stratigraphic and unstructured grids. Herein, we propose a general idea for how one can formulate multiscale finite-volume methods using only a primal coarse partition. To this end, we use two key ingredients that are computed numerically: (i) elementary functions that correspond to flow solutions used in transmissibility upscaling, and (ii) partition-of-unity functions used to combine elementary functions into basis functions. We exemplify the idea by deriving a multiscale two-point flux-approximation (MsTPFA) method, which is robust with regards to strong heterogeneities in the permeability field and can easily handle general grids with unstructured fine- and coarse-scale connections. The method can easily be adapted to arbitrary levels of coarsening, and can be used both as a standalone solver and as a preconditioner. Several numerical experiments are presented to demonstrate that the MsTPFA method can be used to solve elliptic pressure problems on a wide variety of geological models in a robust and efficient manner.
Multiscale modeling and simulation of brain blood flow
NASA Astrophysics Data System (ADS)
Perdikaris, Paris; Grinberg, Leopold; Karniadakis, George Em
2016-02-01
The aim of this work is to present an overview of recent advances in multi-scale modeling of brain blood flow. In particular, we present some approaches that enable the in silico study of multi-scale and multi-physics phenomena in the cerebral vasculature. We discuss the formulation of continuum and atomistic modeling approaches, present a consistent framework for their concurrent coupling, and list some of the challenges that one needs to overcome in achieving a seamless and scalable integration of heterogeneous numerical solvers. The effectiveness of the proposed framework is demonstrated in a realistic case involving modeling the thrombus formation process taking place on the wall of a patient-specific cerebral aneurysm. This highlights the ability of multi-scale algorithms to resolve important biophysical processes that span several spatial and temporal scales, potentially yielding new insight into the key aspects of brain blood flow in health and disease. Finally, we discuss open questions in multi-scale modeling and emerging topics of future research.
Domain decomposition in time for PDE-constrained optimization
Barker, Andrew T.; Stoll, Martin
2015-08-28
Here, PDE-constrained optimization problems have a wide range of applications, but they lead to very large and ill-conditioned linear systems, especially if the problems are time dependent. In this paper we outline an approach for dealing with such problems by decomposing them in time and applying an additive Schwarz preconditioner in time, so that we can take advantage of parallel computers to deal with the very large linear systems. We then illustrate the performance of our method on a variety of problems.
Simulation of Stochastic Processes by Coupled ODE-PDE
NASA Technical Reports Server (NTRS)
Zak, Michail
2008-01-01
A document discusses the emergence of randomness in solutions of coupled, fully deterministic ODE-PDE (ordinary differential equations-partial differential equations) due to failure of the Lipschitz condition as a new phenomenon. It is possible to exploit the special properties of ordinary differential equations (represented by an arbitrarily chosen, dynamical system) coupled with the corresponding Liouville equations (used to describe the evolution of initial uncertainties in terms of joint probability distribution) in order to simulate stochastic processes with the proscribed probability distributions. The important advantage of the proposed approach is that the simulation does not require a random-number generator.
Tau approximation techniques for identification of coefficients in parabolic PDE
NASA Technical Reports Server (NTRS)
Banks, H. T.; Wade, J. G.
1989-01-01
A variant of the Tau method, called the weak Tau method, is developed on the basis of the weak form of the PDE for use in least-squares parameter estimation; also presented is a suitable abstract convergence framework. The emphasis is on the theoretical framework that allows treatment of the weak Tau method when it is applied to a wide class of inverse problems, including those for diffusion-advection equations, the Fokker-Planck model for population dynamics, and damped beam equations. Extensive numerical testing of the weak Tau method has demonstrated that it compares quite favorably with existing methods.
Pyrazolopyridines as potent PDE4B inhibitors: 5-Heterocycle SAR
Mitchell, Charlotte J.; Ballantine, Stuart P.; Coe, Diane M.; Cook, Caroline M.; Delves, Christopher J.; Dowle, Mike D.; Edlin, Chris D.; Hamblin, J. Nicole; Holman, Stuart; Johnson, Martin R.; Jones, Paul S.; Keeling, Sue E.; Kranz, Michael; Lindvall, Mika; Lucas, Fiona S.; Neu, Margarete; Solanke, Yemisi E.; Somers, Don O.; Trivedi, Naimisha A.; Wiseman, Joanne O.
2012-05-03
Following the discovery of 4-(substituted amino)-1-alkyl-pyrazolo[3,4-b]pyridine-5-carboxamides as potent and selective phosphodiesterase 4B inhibitors, [Hamblin, J. N.; Angell, T.; Ballentine, S., et al. Bioorg. Med. Chem. Lett.2008, 18, 4237] the SAR of the 5-position was investigated further. A range of substituted heterocycles showed good potencies against PDE4. Optimisation using X-ray crystallography and computational modelling led to the discovery of 16, with sub-nM inhibition of LPS-induced TNF-{alpha} production from isolated human peripheral blood mononuclear cells.
Matte, Suzanne L.; Laue, Thomas M.; Cote, Rick H.
2012-01-01
As the central effector of visual transduction, the regulation of photoreceptor phosphodiesterase (PDE6) is controlled by both allosteric mechanisms and extrinsic binding partners. However, the conformational changes and interactions of PDE6 with known interacting proteins are poorly understood. Using a fluorescence detection system for the analytical ultracentrifuge, we examined allosteric changes in PDE6 structure and protein-protein interactions with its inhibitory γ-subunit, the prenyl-binding protein (PrBP/δ), and activated transducin. In solution, the PDE6 catalytic dimer (Pαβ) exhibits a more asymmetric shape (axial ratio of 6.6) than reported previously. The inhibitory Pγ subunit behaves as an intrinsically disordered protein in solution but binds with high affinity to the catalytic dimer to reconstitute the holoenzyme without a detectable change in shape. Whereas the closely related PDE5 homodimer undergoes a significant change in its sedimentation properties upon cGMP binding to its regulatory cGMP binding site, no such change was detected upon ligand binding to the PDE6 catalytic dimer. However, when Pαβ was reconstituted with Pγ truncation mutants lacking the C-terminal inhibitory region, cGMP-dependent allosteric changes were observed. PrBP/δ bound to the PDE6 holoenzyme with high affinity (KD = 6.2 nm) and induced elongation of the protein complex. Binding of activated transducin to PDE6 holoenzyme resulted in a concentration-dependent increase in the sedimentation coefficient, reflecting a dynamic equilibrium between transducin and PDE6. We conclude that allosteric regulation of PDE6 is more complex than for PDE5 and is dependent on interactions of regions of Pγ with the catalytic dimer. PMID:22514270
Shepherd, Malcolm; McSorley, Theresa; Olsen, Aileen E; Johnston, Lee Ann; Thomson, Neil C; Baillie, George S; Houslay, Miles D; Bolger, Graeme B
2003-01-01
We have isolated cDNAs encoding PDE4B4, a new cAMP-specific phosphodiesterase (PDE4) isoform with novel properties. The amino acid sequence of PDE4B4 demonstrates that it is encoded by the PDE4B gene, but that it differs from the previously isolated PDE4B1, PDE4B2 and PDE4B3 isoforms by the presence of a novel N-terminal region of 17 amino acids. PDE4B4 contains both of the upstream conserved region 1 (UCR1) and UCR2 regulatory units that are characteristic of 'long' PDE4 isoforms. RNase protection demonstrated that PDE4B4 mRNA is expressed preferentially in liver, skeletal muscle and various regions of the brain, which differs from the pattern of tissue distribution of the other known PDE4B long forms, PDE4B1 and PDE4B3. Expression of PDE4B4 cDNA in COS7 cells produced a protein of 85 kDa under denaturing conditions. Subcellular fractionation of recombinant, COS7-cell expressed PDE4B4 showed that the protein was localized within the cytosol, which was confirmed by confocal microscopic analysis of living COS7 cells transfected with a green fluorescent protein-PDE4B4 chimaera. PDE4B4 exhibited a K(m) for cAMP of 5.4 microM and a V(max), relative to that of the long PDE4B1 isoform, of 2.1. PDE4B4 was inhibited by the prototypical PDE4 inhibitor rolipram [4-[3-(cyclopentoxyl)-4-methoxyphenyl]-2-pyrrolidinone] with an IC(50) of 83 nM. Treatment of COS7 cells with forskolin, to elevate cAMP levels, produced activation of PDE4B4, which was associated with the phosphorylation of PDE4B4 on Ser-56 within UCR1. The unique tissue distribution and intracellular targeting of PDE4B4 suggests that this isoform may have a distinct functional role in regulating cAMP levels in specific cell types. PMID:12441002
NASA Astrophysics Data System (ADS)
Mena, Andres; Ferrero, Jose M.; Rodriguez Matas, Jose F.
2015-11-01
Solving the electric activity of the heart possess a big challenge, not only because of the structural complexities inherent to the heart tissue, but also because of the complex electric behaviour of the cardiac cells. The multi-scale nature of the electrophysiology problem makes difficult its numerical solution, requiring temporal and spatial resolutions of 0.1 ms and 0.2 mm respectively for accurate simulations, leading to models with millions degrees of freedom that need to be solved for thousand time steps. Solution of this problem requires the use of algorithms with higher level of parallelism in multi-core platforms. In this regard the newer programmable graphic processing units (GPU) has become a valid alternative due to their tremendous computational horsepower. This paper presents results obtained with a novel electrophysiology simulation software entirely developed in Compute Unified Device Architecture (CUDA). The software implements fully explicit and semi-implicit solvers for the monodomain model, using operator splitting. Performance is compared with classical multi-core MPI based solvers operating on dedicated high-performance computer clusters. Results obtained with the GPU based solver show enormous potential for this technology with accelerations over 50 × for three-dimensional problems.
NASA Astrophysics Data System (ADS)
Mena, Andres; Ferrero, Jose M.; Rodriguez Matas, Jose F.
2015-11-01
Solving the electric activity of the heart possess a big challenge, not only because of the structural complexities inherent to the heart tissue, but also because of the complex electric behaviour of the cardiac cells. The multi-scale nature of the electrophysiology problem makes difficult its numerical solution, requiring temporal and spatial resolutions of 0.1 ms and 0.2 mm respectively for accurate simulations, leading to models with millions degrees of freedom that need to be solved for thousand time steps. Solution of this problem requires the use of algorithms with higher level of parallelism in multi-core platforms. In this regard the newer programmable graphic processing units (GPU) has become a valid alternative due to their tremendous computational horsepower. This paper presents results obtained with a novel electrophysiology simulation software entirely developed in Compute Unified Device Architecture (CUDA). The software implements fully explicit and semi-implicit solvers for the monodomain model, using operator splitting. Performance is compared with classical multi-core MPI based solvers operating on dedicated high-performance computer clusters. Results obtained with the GPU based solver show enormous potential for this technology with accelerations over 50 × for three-dimensional problems.
Parallel PDE-Based Simulations Using the Common Component Architecture
McInnes, Lois C.; Allan, Benjamin A.; Armstrong, Robert; Benson, Steven J.; Bernholdt, David E.; Dahlgren, Tamara L.; Diachin, Lori; Krishnan, Manoj Kumar; Kohl, James A.; Larson, J. Walter; Lefantzi, Sophia; Nieplocha, Jarek; Norris, Boyana; Parker, Steven G.; Ray, Jaideep; Zhou, Shujia
2006-03-05
Summary. The complexity of parallel PDE-based simulations continues to increase as multimodel, multiphysics, and multi-institutional projects become widespread. A goal of componentbased software engineering in such large-scale simulations is to help manage this complexity by enabling better interoperability among various codes that have been independently developed by different groups. The Common Component Architecture (CCA) Forum is defining a component architecture specification to address the challenges of high-performance scientific computing. In addition, several execution frameworks, supporting infrastructure, and generalpurpose components are being developed. Furthermore, this group is collaborating with others in the high-performance computing community to design suites of domain-specific component interface specifications and underlying implementations. This chapter discusses recent work on leveraging these CCA efforts in parallel PDE-based simulations involving accelerator design, climate modeling, combustion, and accidental fires and explosions. We explain how component technology helps to address the different challenges posed by each of these applications, and we highlight how component interfaces built on existing parallel toolkits facilitate the reuse of software for parallel mesh manipulation, discretization, linear algebra, integration, optimization, and parallel data redistribution. We also present performance data to demonstrate the suitability of this approach, and we discuss strategies for applying component technologies to both new and existing applications.
Mesh Algorithms for PDE with Sieve I: Mesh Distribution
Knepley, Matthew G.; Karpeev, Dmitry A.
2009-01-01
We have developed a new programming framework, called Sieve, to support parallel numerical partial differential equation(s) (PDE) algorithms operating over distributed meshes. We have also developed a reference implementation of Sieve in C++ as a library of generic algorithms operating on distributed containers conforming to the Sieve interface. Sieve makes instances of the incidence relation, or arrows, the conceptual first-class objects represented in the containers. Further, generic algorithms acting on this arrow container are systematically used to provide natural geometric operations on the topology and also, through duality, on the data. Finally, coverings and duality are used to encode notmore » only individual meshes, but all types of hierarchies underlying PDE data structures, including multigrid and mesh partitions. In order to demonstrate the usefulness of the framework, we show how the mesh partition data can be represented and manipulated using the same fundamental mechanisms used to represent meshes. We present the complete description of an algorithm to encode a mesh partition and then distribute a mesh, which is independent of the mesh dimension, element shape, or embedding. Moreover, data associated with the mesh can be similarly distributed with exactly the same algorithm. The use of a high level of abstraction within the Sieve leads to several benefits in terms of code reuse, simplicity, and extensibility. We discuss these benefits and compare our approach to other existing mesh libraries.« less
PDE5 inhibitors protect against post-infarction heart failure.
Li, Na; Yuan, Yuan; Li, Shuang; Zeng, Cao; Yu, Wenjun; Shen, Mingzhi; Zhang, Rongqing; Li, Congye; Zhang, Yingmei; Wang, Haichang
2016-01-01
Heart failure (HF) is one of the main causes for cardiovascular morbidity and mortality. This study was designed to examine the effect of PDE-5 inhibition on cardiac geometry, function and apoptosis in post-infarct HF. Our data revealed that treatment of the PDE-5 inhibitor sildenafil, beginning 3 days after left anterior descending coronary artery ligation, attenuated LV remodeling, cardiac dysfunction, cardiomyocyte apoptosis and mitochondrial anomalies including ATP production, mitochondrial respiratory defects, decline of mitochondrial membrane potential (MMP) and compromised mitochondrial ultrastructure. Sildenafil partially ameliorated the downregulation of Sirt3 protein and acetylation of PGC-1alpha in peri-infarct myocardial regions. In cultured neonatal mouse ventricular myocytes subjected to hypoxia for 24 hrs, sildenafil suppressed apoptosis, promoted ATP production and elevated MMP, along with the increased Sirt3 protein expression and decreased PGC-1alpha acetylation. Interestingly, knock down of Sirt3 attenuated or nullified sildenafil-offered beneficial effects. Our findings demonstrated that sildenafil exerts its cardioprotective effect against post-infarction injury by improving mitochondrial ultrastructure and function via the Sirt3/PGC-1alpha pathway. This observation should shed some lights towards application of sildenafil in energy-related cardiovascular diseases. PMID:27100500
A novel thermoregulatory role for PDE10A in mouse and human adipocytes.
Hankir, Mohammed K; Kranz, Mathias; Gnad, Thorsten; Weiner, Juliane; Wagner, Sally; Deuther-Conrad, Winnie; Bronisch, Felix; Steinhoff, Karen; Luthardt, Julia; Klöting, Nora; Hesse, Swen; Seibyl, John P; Sabri, Osama; Heiker, John T; Blüher, Matthias; Pfeifer, Alexander; Brust, Peter; Fenske, Wiebke K
2016-01-01
Phosphodiesterase type 10A (PDE10A) is highly enriched in striatum and is under evaluation as a drug target for several psychiatric/neurodegenerative diseases. Preclinical studies implicate PDE10A in the regulation of energy homeostasis, but the mechanisms remain unclear. By utilizing small-animal PET/MRI and the novel radioligand [(18)F]-AQ28A, we found marked levels of PDE10A in interscapular brown adipose tissue (BAT) of mice. Pharmacological inactivation of PDE10A with the highly selective inhibitor MP-10 recruited BAT and potentiated thermogenesis in vivo In diet-induced obese mice, chronic administration of MP-10 caused weight loss associated with increased energy expenditure, browning of white adipose tissue, and improved insulin sensitivity. Analysis of human PET data further revealed marked levels of PDE10A in the supraclavicular region where brown/beige adipocytes are clustered in adults. Finally, the inhibition of PDE10A with MP-10 stimulated thermogenic gene expression in human brown adipocytes and induced browning of human white adipocytes. Collectively, our findings highlight a novel thermoregulatory role for PDE10A in mouse and human adipocytes and promote PDE10A inhibitors as promising candidates for the treatment of obesity and diabetes. PMID:27247380
Design and Microwave Assisted Synthesis of Coumarin Derivatives as PDE Inhibitors.
Kumbar, Mahadev N; Kamble, Ravindra R; Kamble, Atulkumar A; Salian, Sujith Raj; Kumari, Sandhya; Nair, Ramya; Kalthur, Guruprasad; Adiga, Satish Kumar; Prasad, D Jagadeesh
2016-01-01
Coumarins appended to benzimidazole through pyrazole are designed and synthesized using microwave irradiation. These compounds were analyzed for phosphodiesterase (PDE) inhibition indirectly by motility pattern in human spermatozoa. Some of the synthesized compounds, namely, 5d, 5e, 5f, 5g, 5h, and 5k, have exhibited potent inhibitory activity on PDE.
PDE5 inhibitors enhance the lethality of standard of care chemotherapy in pediatric CNS tumor cells.
Roberts, Jane L; Booth, Laurence; Conley, Adam; Cruickshanks, Nichola; Malkin, Mark; Kukreja, Rakesh C; Grant, Steven; Poklepovic, Andrew; Dent, Paul
2014-06-01
We determined whether clinically relevant phosphodiesterase 5 (PDE5) inhibitors interacted with clinically relevant chemotherapies to kill medulloblastoma cells. In medulloblastoma cells PDE5 inhibitors interacted in a greater than additive fashion with vincristine/etoposide/cisplatin to cause cell death. Knockdown of PDE5 expression recapitulated the combination effects of PDE5 inhibitor drugs with chemotherapy drugs. Expression of dominant negative caspase 9 did not significantly inhibit chemotherapy lethality but did significantly reduce enhanced killing in combination with the PDE5 inhibitor sildenafil. Overexpression of BCL-XL and c-FLIP-s suppressed individual and combination drug toxicities. Knockdown of CD95 or FADD suppressed drug combination toxicity. Treatment with PDE5 inhibitors and chemotherapy drugs promoted autophagy which was maximal at ~12 h post-treatment, and in a cell type-dependent manner knockdown of Beclin1 or ATG5 either suppressed or enhanced drug combination lethality. PDE5 inhibitors enhanced the induction of chemotherapy-induced DNA damage in a nitric oxide synthase-dependent fashion. In conclusion, our data demonstrate that the combination of PDE5 inhibitors with standard of care chemotherapy agents for medulloblastoma represents a possible novel modality for future treatment of this disease. PMID:24651037
Design and Microwave Assisted Synthesis of Coumarin Derivatives as PDE Inhibitors
Kumbar, Mahadev N.; Kamble, Ravindra R.; Kamble, Atulkumar A.; Salian, Sujith Raj; Kumari, Sandhya; Nair, Ramya; Kalthur, Guruprasad; Adiga, Satish Kumar; Prasad, D. Jagadeesh
2016-01-01
Coumarins appended to benzimidazole through pyrazole are designed and synthesized using microwave irradiation. These compounds were analyzed for phosphodiesterase (PDE) inhibition indirectly by motility pattern in human spermatozoa. Some of the synthesized compounds, namely, 5d, 5e, 5f, 5g, 5h, and 5k, have exhibited potent inhibitory activity on PDE. PMID:26998358
How Schools and Students Respond to School Improvement Programs: The Case of Brazil's PDE
ERIC Educational Resources Information Center
Carnoy, Martin; Gove, Amber K.; Loeb, Susanna; Marshall, Jeffrey H.; Socias, Miguel
2008-01-01
This study uses rich empirical data from Brazil to assess how a government program (PDE) that decentralizes school management decisions changes what goes on in schools and how these changes affect student outcomes. It appears that the PDE resulted in some improvements in management and learning materials, but little change in other areas including…
Adaptive multiscale model reduction with Generalized Multiscale Finite Element Methods
NASA Astrophysics Data System (ADS)
Chung, Eric; Efendiev, Yalchin; Hou, Thomas Y.
2016-09-01
In this paper, we discuss a general multiscale model reduction framework based on multiscale finite element methods. We give a brief overview of related multiscale methods. Due to page limitations, the overview focuses on a few related methods and is not intended to be comprehensive. We present a general adaptive multiscale model reduction framework, the Generalized Multiscale Finite Element Method. Besides the method's basic outline, we discuss some important ingredients needed for the method's success. We also discuss several applications. The proposed method allows performing local model reduction in the presence of high contrast and no scale separation.
NASA Astrophysics Data System (ADS)
Haven, Emmanuel
2005-11-01
Analytical solutions to the backward Kolmogorov PDE are very dependent on the functional form of b(y,t) and a(y,t). We suggest one solution technique for obtaining analytical solutions via the use of an adiabatic approximation to the Schrödinger PDE. This approximation takes the specific form of a so-called WKB (W D Wentzel [G. Wentzel, Eine Verallgemeinerung der Quantenbedingungen für die Zwecke der Wellenmechanik, Z. Phys. 38 (1926) 518-529], K D Kramers [H. Kramers, Wellenmechanik und halbzahlige Quantisierung, Z. Phys. 39 (1926) 828-840], B D Brillouin [L. Brillouin, La mécanique ondulatoire de Schrödinger: une méthode générale de résolution par approximations successives, C. R. Acad. Sci. 183 (1926) 24-26]) approximation. We provide for two examples, in financial option pricing, where we show how the proposed approximation could be of use.
PHLPP2 Downregulation Contributes to Lung Carcinogenesis Following B[a]P/B[a]PDE Exposure
Huang, Haishan; Pan, Xiaofu; Jin, Honglei; Li, Yang; Zhang, Lin; Yang, Caili; Liu, Pei; Liu, Ya; Chen, Lili; Li, Jingxia; Zhu, Junlan; Zeng, Xingruo; Fu, Kai; Chen, Guorong; Gao, Jimin; Huang, Chuanshu
2015-01-01
Purpose The carcinogenic capacity of B[a]P/B[a]PDE is supported by epidemiologic studies. However, the molecular mechanisms responsible for B[a]P/B[a]PDE-caused lung cancer have not been well investigated. We evaluated here the role of novel target PHLPP2 in lung inflammation and carcinogenesis upon B[a]P/B[a]PDE exposure. Experimental Design We used the Western blotting, RT-PCR, [35S]methionine pulse and immunohistochemistry staining to determine PHLPP2 downregulation following B[a]P/B[a]PDE exposure. Both B[a]PDE-induced Beas-2B cell transformation model and B[a]P-caused mouse lung cancer model were used to elucidate the mechanisms leading to PHLPP2 downregulation and lung carcinogenesis. The important findings were also extended to in vivo human studies. Results We found that B[a]P/B[a]PDE exposure downregulated PHLPP2 expression in human lung epithelial cells in vitro and in mouse lung tissues in vivo. The ectopic expression of PHLPP2 dramatically inhibited cell transformation upon B[a]PDE exposure. Mechanistic studies showed that miR-205 induction was crucial for inhibition of PHLPP2 protein translation by targeting PHLPP2-3′-UTR. Interestingly, PHLPP2 expression was inversely associated with tumor necrosis factor alpha (TNFα) expression, with low PHLPP2 and high TNFα expression in lung cancer tissues compared with the paired adjacent normal lung tissues. Additional studies revealed that PHLPP2 exhibited its antitumorigenic effect of B[a]P/B[a]PDE through the repression of inflammatory TNFα transcription. Conclusions Our studies not only first time identify PHLPP2 downregulation by lung carcinogen B[a]P/B[a]PDE, but also elucidate a novel molecular mechanisms underlying lung inflammation and carcinogenesis upon B[a]P/B[a]PDE exposure. PMID:25977341
Using SPARK as a Solver for Modelica
Wetter, Michael; Wetter, Michael; Haves, Philip; Moshier, Michael A.; Sowell, Edward F.
2008-06-30
Modelica is an object-oriented acausal modeling language that is well positioned to become a de-facto standard for expressing models of complex physical systems. To simulate a model expressed in Modelica, it needs to be translated into executable code. For generating run-time efficient code, such a translation needs to employ algebraic formula manipulations. As the SPARK solver has been shown to be competitive for generating such code but currently cannot be used with the Modelica language, we report in this paper how SPARK's symbolic and numerical algorithms can be implemented in OpenModelica, an open-source implementation of a Modelica modeling and simulation environment. We also report benchmark results that show that for our air flow network simulation benchmark, the SPARK solver is competitive with Dymola, which is believed to provide the best solver for Modelica.
New iterative solvers for the NAG Libraries
Salvini, S.; Shaw, G.
1996-12-31
The purpose of this paper is to introduce the work which has been carried out at NAG Ltd to update the iterative solvers for sparse systems of linear equations, both symmetric and unsymmetric, in the NAG Fortran 77 Library. Our current plans to extend this work and include it in our other numerical libraries in our range are also briefly mentioned. We have added to the Library the new Chapter F11, entirely dedicated to sparse linear algebra. At Mark 17, the F11 Chapter includes sparse iterative solvers, preconditioners, utilities and black-box routines for sparse symmetric (both positive-definite and indefinite) linear systems. Mark 18 will add solvers, preconditioners, utilities and black-boxes for sparse unsymmetric systems: the development of these has already been completed.
Xie, Moses; Blackman, Brigitte; Scheitrum, Colleen; Mika, Delphine; Blanchard, Elise; Lei, Tao; Conti, Marco; Richter, Wito
2014-05-01
PDE4s (type 4 cyclic nucleotide phosphodiesterases) are divided into long and short forms by the presence or absence of conserved N-terminal domains termed UCRs (upstream conserved regions). We have shown previously that PDE4D2, a short variant, is a monomer, whereas PDE4D3, a long variant, is a dimer. In the present study, we have determined the apparent molecular masses of various long and short PDE4 variants by size-exclusion chromatography and sucrose density-gradient centrifugation. Our results indicate that dimerization is a conserved property of all long PDE4 forms, whereas short forms are monomers. Dimerization is mediated by the UCR domains. Given their high sequence conservation, the UCR domains mediate not only homo-oligomerization, but also hetero-oligomerization of distinct PDE4 long forms as detected by co-immunoprecipitation assays and FRET microscopy. Endogenous PDE4 hetero-oligomers are, however, low in abundance compared with homo-dimers, revealing the presence of mechanisms that predispose PDE4s towards homo-oligomerization. Oligomerization is a prerequisite for the regulatory properties of the PDE4 long forms, such as their PKA (protein kinase A)-dependent activation, but is not necessary for PDE4 protein-protein interactions. As a result, individual PDE4 protomers may independently mediate protein-protein interactions, providing a mechanism whereby PDE4s contribute to the assembly of macromolecular signalling complexes.
ODE System Solver W. Krylov Iteration & Rootfinding
1991-09-09
LSODKR is a new initial value ODE solver for stiff and nonstiff systems. It is a variant of the LSODPK and LSODE solvers, intended mainly for large stiff systems. The main differences between LSODKR and LSODE are the following: (a) for stiff systems, LSODKR uses a corrector iteration composed of Newton iteration and one of four preconditioned Krylov subspace iteration methods. The user must supply routines for the preconditioning operations, (b) Within the corrector iteration,more » LSODKR does automatic switching between functional (fixpoint) iteration and modified Newton iteration, (c) LSODKR includes the ability to find roots of given functions of the solution during the integration.« less
Compartmentalized PDE4A5 Signaling Impairs Hippocampal Synaptic Plasticity and Long-Term Memory
Park, Alan J.; Tolentino, Rosa E.; Bruinenberg, Vibeke M.; Tudor, Jennifer C.; Lee, Yool; Hansen, Rolf T.; Guercio, Leonardo A.; Linton, Edward; Neves-Zaph, Susana R.; Meerlo, Peter; Baillie, George S.; Houslay, Miles D.
2016-01-01
Alterations in cAMP signaling are thought to contribute to neurocognitive and neuropsychiatric disorders. Members of the cAMP-specific phosphodiesterase 4 (PDE4) family, which contains >25 different isoforms, play a key role in determining spatial cAMP degradation so as to orchestrate compartmentalized cAMP signaling in cells. Each isoform binds to a different set of protein complexes through its unique N-terminal domain, thereby leading to targeted degradation of cAMP in specific intracellular compartments. However, the functional role of specific compartmentalized PDE4 isoforms has not been examined in vivo. Here, we show that increasing protein levels of the PDE4A5 isoform in mouse hippocampal excitatory neurons impairs a long-lasting form of hippocampal synaptic plasticity and attenuates hippocampus-dependent long-term memories without affecting anxiety. In contrast, viral expression of a truncated version of PDE4A5, which lacks the unique N-terminal targeting domain, does not affect long-term memory. Further, overexpression of the PDE4A1 isoform, which targets a different subset of signalosomes, leaves memory undisturbed. Fluorescence resonance energy transfer sensor-based cAMP measurements reveal that the full-length PDE4A5, in contrast to the truncated form, hampers forskolin-mediated increases in neuronal cAMP levels. Our study indicates that the unique N-terminal localization domain of PDE4A5 is essential for the targeting of specific cAMP-dependent signaling underlying synaptic plasticity and memory. The development of compounds to disrupt the compartmentalization of individual PDE4 isoforms by targeting their unique N-terminal domains may provide a fruitful approach to prevent cognitive deficits in neuropsychiatric and neurocognitive disorders that are associated with alterations in cAMP signaling. SIGNIFICANCE STATEMENT Neurons exhibit localized signaling processes that enable biochemical cascades to be activated selectively in specific subcellular
Machné, Rainer; Finney, Andrew; Müller, Stefan; Lu, James; Widder, Stefanie; Flamm, Christoph
2006-06-01
The SBML ODE Solver Library (SOSlib) is a programming library for symbolic and numerical analysis of chemical reaction network models encoded in the Systems Biology Markup Language (SBML). It is written in ISO C and distributed under the open source LGPL license. The package employs libSBML structures for formula representation and associated functions to construct a system of ordinary differential equations, their Jacobian matrix and other derivatives. SUNDIALS' CVODES is incorporated for numerical integration and sensitivity analysis. Preliminary benchmarking results give a rough overview on the behavior of different tools and are discussed in the Supplementary Material. The native application program interface provides fine-grained interfaces to all internal data structures, symbolic operations and numerical routines, enabling the construction of very efficient analytic applications and hybrid or multi-scale solvers with interfaces to SBML and non SBML data sources. Optional modules based on XMGrace and Graphviz allow quick inspection of structure and dynamics. PMID:16527832
Exome sequencing identifies PDE4D mutations in acrodysostosis.
Lee, Hane; Graham, John M; Rimoin, David L; Lachman, Ralph S; Krejci, Pavel; Tompson, Stuart W; Nelson, Stanley F; Krakow, Deborah; Cohn, Daniel H
2012-04-01
Acrodysostosis is a dominantly-inherited, multisystem disorder characterized by skeletal, endocrine, and neurological abnormalities. To identify the molecular basis of acrodysostosis, we performed exome sequencing on five genetically independent cases. Three different missense mutations in PDE4D, which encodes cyclic AMP (cAMP)-specific phosphodiesterase 4D, were found to be heterozygous in three of the cases. Two of the mutations were demonstrated to have occurred de novo, providing strong genetic evidence of causation. Two additional cases were heterozygous for de novo missense mutations in PRKAR1A, which encodes the cAMP-dependent regulatory subunit of protein kinase A and which has been recently reported to be the cause of a form of acrodysostosis resistant to multiple hormones. These findings demonstrate that acrodysostosis is genetically heterogeneous and underscore the exquisite sensitivity of many tissues to alterations in cAMP homeostasis. PMID:22464252
NASA Astrophysics Data System (ADS)
Bhattacharjee, Satyaki; Matouš, Karel
2016-05-01
A new manifold-based reduced order model for nonlinear problems in multiscale modeling of heterogeneous hyperelastic materials is presented. The model relies on a global geometric framework for nonlinear dimensionality reduction (Isomap), and the macroscopic loading parameters are linked to the reduced space using a Neural Network. The proposed model provides both homogenization and localization of the multiscale solution in the context of computational homogenization. To construct the manifold, we perform a number of large three-dimensional simulations of a statistically representative unit cell using a parallel finite strain finite element solver. The manifold-based reduced order model is verified using common principles from the machine-learning community. Both homogenization and localization of the multiscale solution are demonstrated on a large three-dimensional example and the local microscopic fields as well as the homogenized macroscopic potential are obtained with acceptable engineering accuracy.
DISC1, PDE4B, and NDE1 at the centrosome and synapse
Bradshaw, Nicholas J.; Ogawa, Fumiaki; Antolin-Fontes, Beatriz; Chubb, Jennifer E.; Carlyle, Becky C.; Christie, Sheila; Claessens, Antoine; Porteous, David J.; Millar, J. Kirsty
2008-12-26
Disrupted-In-Schizophrenia 1 (DISC1) is a risk factor for schizophrenia and other major mental illnesses. Its protein binding partners include the Nuclear Distribution Factor E Homologs (NDE1 and NDEL1), LIS1, and phosphodiesterases 4B and 4D (PDE4B and PDE4D). We demonstrate that NDE1, NDEL1 and LIS1, together with their binding partner dynein, associate with DISC1, PDE4B and PDE4D within the cell, and provide evidence that this complex is present at the centrosome. LIS1 and NDEL1 have been previously suggested to be synaptic, and we now demonstrate localisation of DISC1, NDE1, and PDE4B at synapses in cultured neurons. NDE1 is phosphorylated by cAMP-dependant Protein Kinase A (PKA), whose activity is, in turn, regulated by the cAMP hydrolysis activity of phosphodiesterases, including PDE4. We propose that DISC1 acts as an assembly scaffold for all of these proteins and that the NDE1/NDEL1/LIS1/dynein complex is modulated by cAMP levels via PKA and PDE4.
New classes of PDE7 inhibitors identified by a fission yeast-based HTS
Alaamery, Manal A.; Wyman, Arlene R.; Ivey, F. Douglas; Allain, Christina; Demirbas, Didem; Wang, Lili; Ceyhan, Ozge; Hoffman, Charles S.
2010-01-01
Studies of the phosphodiesterase PDE7 family are impeded by there being only one commercially-available PDE7 inhibitor, BRL50481. We have employed a high throughput screen of commercial chemical libraries, using a fission yeast-based assay, to identify PDE7 inhibitors that include steroids, podocarpanes, and an unusual heterocyclic compound, BC30. In vitro enzyme assays measuring the potency of BC30 and two podocarpanes, in comparison with BRL50481, produce data consistent with those from yeast-based assays. In other enzyme assays, BC30 stimulates the PDE4D catalytic domain, but not full-length PDE4D2, suggesting an allosteric site of action. BC30 significantly enhances the anti-inflammatory effect of the PDE4 inhibitor rolipram as measured by release of TNFα from activated monocytes. These studies introduce several new PDE7 inhibitors that may be excellent candidates for medicinal chemistry due to the requirements for drug-like characteristics placed on them by the nature of the yeast-based screen. PMID:20228279
Identification of cancer cytotoxic modulators of PDE3A by predictive chemogenomics
de Waal, Luc; Lewis, Timothy A.; Rees, Matthew G.; Tsherniak, Aviad; Wu, Xiaoyun; Choi, Peter S.; Gechijian, Lara; Hartigan, Christina; Faloon, Patrick W.; Hickey, Mark J.; Tolliday, Nicola; Carr, Steven A.; Clemons, Paul A.; Munoz, Benito; Wagner, Bridget K.; Shamji, Alykhan F.; Koehler, Angela N.; Schenone, Monica; Burgin, Alex B.; Schreiber, Stuart L.; Greulich, Heidi; Meyerson, Matthew
2015-01-01
High cancer death rates indicate the need for new anti-cancer therapeutic agents. Approaches to discover new cancer drugs include target-based drug discovery and phenotypic screening. Here, we identified phosphodiesterase 3A modulators as cell-selective cancer cytotoxic compounds by phenotypic compound library screening and target deconvolution by predictive chemogenomics. We found that sensitivity to 6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-one, or DNMDP, across 766 cancer cell lines correlates with expression of the phosphodiesterase 3A gene, PDE3A. Like DNMDP, a subset of known PDE3A inhibitors kill selected cancer cells while others do not. Furthermore, PDE3A depletion leads to DNMDP resistance. We demonstrated that DNMDP binding to PDE3A promotes an interaction between PDE3A and Schlafen 12 (SLFN12), suggesting a neomorphic activity. Co-expression of SLFN12 with PDE3A correlates with DNMDP sensitivity, while depletion of SLFN12 results in decreased DNMDP sensitivity. Our results implicate PDE3A modulators as candidate cancer therapeutic agents and demonstrate the power of predictive chemogenomics in small-molecule discovery. PMID:26656089
Equation solvers for distributed-memory computers
NASA Technical Reports Server (NTRS)
Storaasli, Olaf O.
1994-01-01
A large number of scientific and engineering problems require the rapid solution of large systems of simultaneous equations. The performance of parallel computers in this area now dwarfs traditional vector computers by nearly an order of magnitude. This talk describes the major issues involved in parallel equation solvers with particular emphasis on the Intel Paragon, IBM SP-1 and SP-2 processors.
Parallel solvers for reservoir simulation on MIMD computers
Piault, E.; Willien, F.; Roux, F.X.
1995-12-01
We have investigated parallel solvers for reservoir simulation. We compare different solvers and preconditioners using T3D and SP1 parallel computers. We use block diagonal domain decomposition preconditioner with non-overlapping sub-domains.
Rare inactivating PDE11A variants associated with testicular germ cell tumors.
Pathak, Anand; Stewart, Douglas R; Faucz, Fabio R; Xekouki, Paraskevi; Bass, Sara; Vogt, Aurelie; Zhang, Xijun; Boland, Joseph; Yeager, Meredith; Loud, Jennifer T; Nathanson, Katherine L; McGlynn, Katherine A; Stratakis, Constantine A; Greene, Mark H; Mirabello, Lisa
2015-12-01
Germline inactivating mutations of isoform 4 of phosphodiesterase (PDE) 11A (coded by the PDE11A gene) have been associated with familial adrenocortical tumors and familial testicular cancer. Testicular tissue is unique in expressing all four isoforms of PDE11A. In a prior candidate gene study of 94 familial testicular germ cell tumor (TGCT) subjects, we identified a significant association between the presence of functionally abnormal variants in PDE11A and familial TGCT risk. To validate this novel observation, we sequenced the PDE11A coding region in 259 additional TGCT patients (both familial and sporadic) and 363 controls. We identified 55 PDE11A variants: 20 missense, four splice-site, two nonsense, seven synonymous, and 22 intronic. Ten missense variants were novel; nine occurred in transcript variant 4 and one in transcript variant 3. Five rare mutations (p.F258Y, p.G291R, p.V820M, p.R545X, and p.K568R) were present only in cases and were significantly more common in cases vs controls (P=0.0037). The latter two novel variants were functionally characterized and shown to be functionally inactivating, resulting in reduced PDE activity and increased cAMP levels. In further analysis of this cohort, we focused on white participants only to minimize confounding due to population stratification. This study builds upon our prior reports implicating PDE11A variants in familial TGCT, provides the first independent validation of those findings, extends that work to sporadic testicular cancer, demonstrates that these variants are uncommonly but reproducibly associated with TGCT, and refines our understanding regarding which specific inactivating PDE11A variants are most likely to be associated with TGCT risk. PMID:26459559
NASA Astrophysics Data System (ADS)
Cusini, Matteo; Lukyanov, Alexander A.; Natvig, Jostein; Hajibeygi, Hadi
2015-10-01
We develop the first multiscale method for fully implicit (FIM) simulations of multiphase flow in porous media, namely CPR-MS method. Built on the FIM Jacobian matrix, the pressure system is obtained by employing a Constrained Pressure Residual (CPR) operator. Multiscale Finite Element (MSFE) and Finite Volume (MSFV) methods are then formulated algebraically to obtain efficient and accurate solutions of this pressure equation. The multiscale prediction stage (first-stage) is coupled with a corrector stage (second-stage) employed on the full system residual. The converged solution is enhanced through outer GMRES iterations preconditioned by these first and second stage operators. While the second-stage FIM stage is solved using a classical iterative solver, the multiscale stage is investigated in full detail. Several choices for fine-scale pre- and post-smoothing along with different choices of coarse-scale solvers are considered for a range of heterogeneous three-dimensional cases with capillarity and three-phase systems. The CPR-MS method is the first of its kind, and extends the applicability of the so-far developed multiscale methods (both MSFE and MSFV) to displacements with strong coupling terms.
Egbert, Jeremy R; Uliasz, Tracy F; Shuhaibar, Leia C; Geerts, Andreas; Wunder, Frank; Kleiman, Robin J; Humphrey, John M; Lampe, Paul D; Artemyev, Nikolai O; Rybalkin, Sergei D; Beavo, Joseph A; Movsesian, Matthew A; Jaffe, Laurinda A
2016-05-01
The meiotic cell cycle of mammalian oocytes in preovulatory follicles is held in prophase arrest by diffusion of cGMP from the surrounding granulosa cells into the oocyte. Luteinizing hormone (LH) then releases meiotic arrest by lowering cGMP in the granulosa cells. The LH-induced reduction of cGMP is caused in part by a decrease in guanylyl cyclase activity, but the observation that the cGMP phosphodiesterase PDE5 is phosphorylated during LH signaling suggests that an increase in PDE5 activity could also contribute. To investigate this idea, we measured cGMP-hydrolytic activity in rat ovarian follicles. Basal activity was due primarily to PDE1A and PDE5, and LH increased PDE5 activity. The increase in PDE5 activity was accompanied by phosphorylation of PDE5 at serine 92, a protein kinase A/G consensus site. Both the phosphorylation and the increase in activity were promoted by elevating cAMP and opposed by inhibiting protein kinase A, supporting the hypothesis that LH activates PDE5 by stimulating its phosphorylation by protein kinase A. Inhibition of PDE5 activity partially suppressed LH-induced meiotic resumption as indicated by nuclear envelope breakdown, but inhibition of both PDE5 and PDE1 activities was needed to completely inhibit this response. These results show that activities of both PDE5 and PDE1 contribute to the LH-induced resumption of meiosis in rat oocytes, and that phosphorylation and activation of PDE5 is a regulatory mechanism.
Gutierrez, Juan B; Lai, Ming-Jun; Slavov, George
2015-12-01
We study a time dependent partial differential equation (PDE) which arises from classic models in ecology involving logistic growth with Allee effect by introducing a discrete weak solution. Existence, uniqueness and stability of the discrete weak solutions are discussed. We use bivariate splines to approximate the discrete weak solution of the nonlinear PDE. A computational algorithm is designed to solve this PDE. A convergence analysis of the algorithm is presented. We present some simulations of population development over some irregular domains. Finally, we discuss applications in epidemiology and other ecological problems.
Convergence acceleration for time-independent first-order PDE using optimal PNB-approximations
Holmgren, S.; Branden, H.
1996-12-31
We consider solving time-independent (steady-state) flow problems in 2D or 3D governed by hyperbolic or {open_quotes}almost hyperbolic{close_quotes} systems of partial differential equations (PDE). Examples of such PDE are the Euler and the Navier-Stokes equations. The PDE is discretized using a finite difference or finite volume scheme with arbitrary order of accuracy. If the matrix B describes the discretized differential operator and u denotes the approximate solution, the discrete problem is given by a large system of equations.
Multiscale geometric modeling of macromolecules I: Cartesian representation
Xia, Kelin; Feng, Xin; Chen, Zhan; Tong, Yiying; Wei, Guo Wei
2013-01-01
This paper focuses on the geometric modeling and computational algorithm development of biomolecular structures from two data sources: Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in the Eulerian (or Cartesian) representation. Molecular surface (MS) contains non-smooth geometric singularities, such as cusps, tips and self-intersecting facets, which often lead to computational instabilities in molecular simulations, and violate the physical principle of surface free energy minimization. Variational multiscale surface definitions are proposed based on geometric flows and solvation analysis of biomolecular systems. Our approach leads to geometric and potential driven Laplace-Beltrami flows for biomolecular surface evolution and formation. The resulting surfaces are free of geometric singularities and minimize the total free energy of the biomolecular system. High order partial differential equation (PDE)-based nonlinear filters are employed for EMDB data processing. We show the efficacy of this approach in feature-preserving noise reduction. After the construction of protein multiresolution surfaces, we explore the analysis and characterization of surface morphology by using a variety of curvature definitions. Apart from the classical Gaussian curvature and mean curvature, maximum curvature, minimum curvature, shape index, and curvedness are also applied to macromolecular surface analysis for the first time. Our curvature analysis is uniquely coupled to the analysis of electrostatic surface potential, which is a by-product of our variational multiscale solvation models. As an expository investigation, we particularly emphasize the numerical algorithms and computational protocols for practical applications of the above multiscale geometric models. Such information may otherwise be scattered over the vast literature on this topic. Based on the curvature and electrostatic analysis from our multiresolution surfaces, we introduce a new concept, the
Multiscale geometric modeling of macromolecules I: Cartesian representation
Xia, Kelin; Feng, Xin; Chen, Zhan; Tong, Yiying; Wei, Guo-Wei
2014-01-15
This paper focuses on the geometric modeling and computational algorithm development of biomolecular structures from two data sources: Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in the Eulerian (or Cartesian) representation. Molecular surface (MS) contains non-smooth geometric singularities, such as cusps, tips and self-intersecting facets, which often lead to computational instabilities in molecular simulations, and violate the physical principle of surface free energy minimization. Variational multiscale surface definitions are proposed based on geometric flows and solvation analysis of biomolecular systems. Our approach leads to geometric and potential driven Laplace–Beltrami flows for biomolecular surface evolution and formation. The resulting surfaces are free of geometric singularities and minimize the total free energy of the biomolecular system. High order partial differential equation (PDE)-based nonlinear filters are employed for EMDB data processing. We show the efficacy of this approach in feature-preserving noise reduction. After the construction of protein multiresolution surfaces, we explore the analysis and characterization of surface morphology by using a variety of curvature definitions. Apart from the classical Gaussian curvature and mean curvature, maximum curvature, minimum curvature, shape index, and curvedness are also applied to macromolecular surface analysis for the first time. Our curvature analysis is uniquely coupled to the analysis of electrostatic surface potential, which is a by-product of our variational multiscale solvation models. As an expository investigation, we particularly emphasize the numerical algorithms and computational protocols for practical applications of the above multiscale geometric models. Such information may otherwise be scattered over the vast literature on this topic. Based on the curvature and electrostatic analysis from our multiresolution surfaces, we introduce a new concept, the
Multiscale geometric modeling of macromolecules I: Cartesian representation
NASA Astrophysics Data System (ADS)
Xia, Kelin; Feng, Xin; Chen, Zhan; Tong, Yiying; Wei, Guo-Wei
2014-01-01
This paper focuses on the geometric modeling and computational algorithm development of biomolecular structures from two data sources: Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in the Eulerian (or Cartesian) representation. Molecular surface (MS) contains non-smooth geometric singularities, such as cusps, tips and self-intersecting facets, which often lead to computational instabilities in molecular simulations, and violate the physical principle of surface free energy minimization. Variational multiscale surface definitions are proposed based on geometric flows and solvation analysis of biomolecular systems. Our approach leads to geometric and potential driven Laplace-Beltrami flows for biomolecular surface evolution and formation. The resulting surfaces are free of geometric singularities and minimize the total free energy of the biomolecular system. High order partial differential equation (PDE)-based nonlinear filters are employed for EMDB data processing. We show the efficacy of this approach in feature-preserving noise reduction. After the construction of protein multiresolution surfaces, we explore the analysis and characterization of surface morphology by using a variety of curvature definitions. Apart from the classical Gaussian curvature and mean curvature, maximum curvature, minimum curvature, shape index, and curvedness are also applied to macromolecular surface analysis for the first time. Our curvature analysis is uniquely coupled to the analysis of electrostatic surface potential, which is a by-product of our variational multiscale solvation models. As an expository investigation, we particularly emphasize the numerical algorithms and computational protocols for practical applications of the above multiscale geometric models. Such information may otherwise be scattered over the vast literature on this topic. Based on the curvature and electrostatic analysis from our multiresolution surfaces, we introduce a new concept, the
Johnston, Lee Ann; Erdogan, Suat; Cheung, York Fong; Sullivan, Michael; Barber, Rachael; Lynch, Martin J; Baillie, George S; Van Heeke, Gino; Adams, David R; Huston, Elaine; Houslay, Miles D
2004-01-01
PDE4A7 is an isoform encoded by the human PDE4A cAMP-specific phosphodiesterase gene that fails to hydrolyse cAMP and whose transcripts are widely expressed. Removal of either the N- or C-terminal unique portions of PDE4A7 did not reconstitute catalytic activity, showing that they did not exert a chronic inhibitory effect. A chimera (Hyb2), formed by swapping the unique N-terminal portion of PDE4A7 with that of the active PDE4A4C form, was not catalytically active. However, one formed (Hyb1) by swapping the unique C-terminal portion of PDE4A7 with that common to all active PDE4 isoforms was catalytically active. Compared with the active PDE4A4B isoform, Hyb1 exhibited a similar K(m) value for cAMP and IC50 value for rolipram inhibition, but was less sensitive to inhibition by Ro-20-1724 and denbufylline, and considerably more sensitive to thermal denaturation. The unique C-terminal region of PDE4A7 was unable to support an active catalytic unit, whereas its unique N-terminal region can. The N-terminal portion of the PDE4 catalytic unit is essential for catalytic activity and can be supplied by either highly conserved sequence found in active PDE4 isoforms from all four PDE4 subfamilies or the unique N-terminal portion of PDE4A7. A discrete portion of the conserved C-terminal region in active PDE4A isoforms underpins their aberrant migration on SDS/PAGE. Unlike active PDE4A isoforms, PDE4A7 is exclusively localized to the P1 particulate fraction in cells. A region located within the C-terminal portion of active PDE4 isoforms prevents such exclusive targeting. Three functional regions in PDE4A isoforms are identified, which influence catalytic activity, subcellular targeting and conformational status. PMID:15025561
NASA Astrophysics Data System (ADS)
Moura, Scott; Bendtsen, Jan; Ruiz, Victor
2014-07-01
This paper develops methods for model identification of aggregated thermostatically controlled loads (TCLs) in smart grids, via partial differential equation (PDE) techniques. Control of aggregated TCLs provides a promising opportunity to mitigate the mismatch between power generation and demand, thus enhancing grid reliability and enabling renewable energy penetration. To this end, this paper focuses on developing parameter identification algorithms for a PDE-based model of aggregated TCLs. First, a two-state boundary-coupled hyperbolic PDE model for homogenous TCL populations is derived. This model is extended to heterogeneous populations by including a diffusive term, which provides an elegant control-oriented model. Next, a passive parameter identification scheme and a swapping-based identification scheme are derived for the PDE model structure. Simulation results demonstrate the efficacy of each method under various autonomous and non-autonomous scenarios. The proposed models can subsequently be employed to provide system critical information for power system monitoring and control.
Lobban, M; Shakur, Y; Beattie, J; Houslay, M D
1994-12-01
In order to detect the two splice variant forms of type-IVB cyclic AMP phosphodiesterase (PDE) activity, DPD (type-IVB1) and PDE-4 (type-IVB2), anti-peptide antisera were generated. One set ('DPD/PDE-4-common'), generated against a peptide sequence found at the common C-terminus of these two PDEs, detected both PDEs. A second set was PDE-4 specific, being directed against a peptide sequence found within the unique N-terminal region of PDE-4. In brain, DPD was found exclusively in the cytosol and PDE-4 exclusively associated with membranes. Both brain DPD and PDE-4 activities, isolated by immunoprecipitation, were cyclic AMP-specific (KmcyclicAMP: approximately 5 microM for DPD; approximately 4 microM for PDE-4) and were inhibited by low rolipram concentrations (K1rolipram approximately 1 microM for both). Transient expression of DPD in COS-1 cells allowed identification of an approx. 64 kDa species which co-migrated on SDS/PAGE with the immunoreactive species identified in both brain cytosol and membrane fractions using the DPD/PDE-4-common antisera. The subunit size observed for PDE-4 (approx. 64 kDa) in brain membranes was similar to that predicted from the cDNA sequence, but that observed for DPD was approx. 4 kDa greater. Type-IV, rolipram-inhibited PDE activity was found in all brain regions except the pituitary, where it formed between 30 and 70% of the PDE activity in membrane and cytosolic fractions when assayed with 1 microM cyclic AMP, PDE-4 formed 40-50% of the membrane type-IV activity in all brain regions save the midbrain (approx. 20%). DPD distribution was highly restricted to certain regions, providing approx. 35% of the type-IV cytosolic activity in hippocampus and 13-21% in cortex, hypothalamus and striatum with no presence in brain stem, cerebellum, midbrain and pituitary. The combined type-IVB PDE activities of DPD and PDE-4 contributed approx. 10% of the total PDE activity in most brain regions except for the pituitary (zero) and the mid
Phosphodiesterase 3B (PDE3B) regulates NLRP3 inflammasome in adipose tissue
Ahmad, Faiyaz; Chung, Youn Wook; Tang, Yan; Hockman, Steven C.; Liu, Shiwei; Khan, Yusuf; Huo, Kevin; Billings, Eric; Amar, Marcelo J.; Remaley, Alan T.; Manganiello, Vincent C.
2016-01-01
Activation of inflammation in white adipose tissue (WAT), includes infiltration/expansion of WAT macrophages, contributes pathogenesis of obesity, insulin resistance, and metabolic syndrome. The inflammasome comprises an intracellular sensor (NLR), caspase-1 and the adaptor ASC. Inflammasome activation leads to maturation of caspase-1 and processing of IL1β, contributing to many metabolic disorders and directing adipocytes to a more insulin-resistant phenotype. Ablation of PDE3B in WAT prevents inflammasome activation by reducing expression of NLRP3, caspase-1, ASC, AIM2, TNFα, IL1β and proinflammatory genes. Following IP injection of lipopolysaccharide (LPS), serum levels of IL1β and TNFα were reduced in PDE3B−/−mice compared to WT. Activation of signaling cascades, which mediate inflammasome responses, were modulated in PDE3B−/−mice WAT, including smad, NFAT, NFkB, and MAP kinases. Moreover, expression of chemokine CCL2, MCP-1 and its receptor CCR2, which play an important role in macrophage chemotaxis, were reduced in WAT of PDE3B−/−mice. In addition, atherosclerotic plaque formation was significantly reduced in the aorta of apoE−/−/PDE3B−/−and LDL-R−/−/PDE3B−/−mice compared to apoE−/−and LDL-R−/−mice, respectively. Obesity-induced changes in serum-cholesterol were blocked in PDE3B−/−mice. Collectively, these data establish a role for PDE3B in modulating inflammatory response, which may contribute to a reduced inflammatory state in adipose tissue. PMID:27321128
Retinitis pigmentosa: impact of different Pde6a point mutations on the disease phenotype.
Sothilingam, Vithiyanjali; Garcia Garrido, Marina; Jiao, Kangwei; Buena-Atienza, Elena; Sahaboglu, Ayse; Trifunović, Dragana; Balendran, Sukirthini; Koepfli, Tanja; Mühlfriedel, Regine; Schön, Christian; Biel, Martin; Heckmann, Angelique; Beck, Susanne C; Michalakis, Stylianos; Wissinger, Bernd; Seeliger, Mathias W; Paquet-Durand, François
2015-10-01
Mutations in the PDE6A gene can cause rod photoreceptors degeneration and the blinding disease retinitis pigmentosa (RP). While a number of pathogenic PDE6A mutations have been described, little is known about their impact on compound heterozygous situations and potential interactions of different disease-causing alleles. Here, we used a novel mouse model for the Pde6a R562W mutation in combination with an existing line carrying the V685M mutation to generate compound heterozygous Pde6a V685M/R562W animals, exactly homologous to a case of human RP. We compared the progression of photoreceptor degeneration in these compound heterozygous mice with the homozygous V685M and R562W mutants, and additionally with the D670G line that is known for a relatively mild phenotype. We investigated PDE6A expression, cyclic guanosine mono-phosphate accumulation, calpain and caspase activity, in vivo retinal function and morphology, as well as photoreceptor cell death and survival. This analysis confirms the severity of different Pde6a mutations and indicates that compound heterozygous mutants behave like intermediates of the respective homozygous situations. Specifically, the severity of the four different Pde6a situations may be categorized by the pace of photoreceptor degeneration: V685M (fastest) > V685M/R562W > R562W > D670G (slowest). While calpain activity was strongly increased in all four mutants, caspase activity was not. This points to the execution of non-apoptotic cell death and may lead to the identification of new targets for therapeutic interventions. For individual RP patients, our study may help to predict time-courses for Pde6a-related retinal degeneration and thereby facilitate the definition of a window-of-opportunity for clinical interventions. PMID:26188004
Aleph Field Solver Challenge Problem Results Summary.
Hooper, Russell; Moore, Stan Gerald
2015-01-01
Aleph models continuum electrostatic and steady and transient thermal fields using a finite-element method. Much work has gone into expanding the core solver capability to support enriched mod- eling consisting of multiple interacting fields, special boundary conditions and two-way interfacial coupling with particles modeled using Aleph's complementary particle-in-cell capability. This report provides quantitative evidence for correct implementation of Aleph's field solver via order- of-convergence assessments on a collection of problems of increasing complexity. It is intended to provide Aleph with a pedigree and to establish a basis for confidence in results for more challeng- ing problems important to Sandia's mission that Aleph was specifically designed to address.
Domain decomposition for the SPN solver MINOS
Jamelot, Erell; Baudron, Anne-Marie; Lautard, Jean-Jacques
2012-07-01
In this article we present a domain decomposition method for the mixed SPN equations, discretized with Raviart-Thomas-Nedelec finite elements. This domain decomposition is based on the iterative Schwarz algorithm with Robin interface conditions to handle communications. After having described this method, we give details on how to optimize the convergence. Finally, we give some numerical results computed in a realistic 3D domain. The computations are done with the MINOS solver of the APOLLO3 (R) code. (authors)
A perspective on unstructured grid flow solvers
NASA Technical Reports Server (NTRS)
Venkatakrishnan, V.
1995-01-01
This survey paper assesses the status of compressible Euler and Navier-Stokes solvers on unstructured grids. Different spatial and temporal discretization options for steady and unsteady flows are discussed. The integration of these components into an overall framework to solve practical problems is addressed. Issues such as grid adaptation, higher order methods, hybrid discretizations and parallel computing are briefly discussed. Finally, some outstanding issues and future research directions are presented.
Zaprinast impairs spatial memory by increasing PDE5 expression in the rat hippocampus.
Giorgi, Mauro; Pompili, Assunta; Cardarelli, Silvia; Castelli, Valentina; Biagioni, Stefano; Sancesario, Giuseppe; Gasbarri, Antonella
2015-02-01
In this work, we report the effect of post-training intraperitoneal administration of zaprinast on rat memory retention in the Morris water maze task that revealed a significant memory impairment at the intermediate dose of 10mg/kg. Zaprinast is capable of inhibiting both striatal and hippocampal PDE activity but to a different extent which is probably due to the different PDE isoforms expressed in these areas. To assess the possible involvement of cyclic nucleotides in rat memory impairment, we compared the effects obtained 30 min after the zaprinast injection with respect to 24h after injection by measuring both cyclic nucleotide levels and PDE activity. As expected, 30 min after the zaprinast administration, we observed an increase of cyclic nucleotides, which returned to a basal level within 24h, with the exception of the hippocampal cGMP which was significantly decreased at the dose of 10mg/kg of zaprinast. This increase in the hippocampal region is the result of a cGMP-specific PDE5 induction, confirmed by sildenafil inhibition, in agreement with literature data that demonstrate transcriptional regulation of PDE5 by cAMP/cGMP intracellular levels. Our results highlight the possible rebound effect of PDE inhibitors. PMID:25281278
Zaprinast impairs spatial memory by increasing PDE5 expression in the rat hippocampus.
Giorgi, Mauro; Pompili, Assunta; Cardarelli, Silvia; Castelli, Valentina; Biagioni, Stefano; Sancesario, Giuseppe; Gasbarri, Antonella
2015-02-01
In this work, we report the effect of post-training intraperitoneal administration of zaprinast on rat memory retention in the Morris water maze task that revealed a significant memory impairment at the intermediate dose of 10mg/kg. Zaprinast is capable of inhibiting both striatal and hippocampal PDE activity but to a different extent which is probably due to the different PDE isoforms expressed in these areas. To assess the possible involvement of cyclic nucleotides in rat memory impairment, we compared the effects obtained 30 min after the zaprinast injection with respect to 24h after injection by measuring both cyclic nucleotide levels and PDE activity. As expected, 30 min after the zaprinast administration, we observed an increase of cyclic nucleotides, which returned to a basal level within 24h, with the exception of the hippocampal cGMP which was significantly decreased at the dose of 10mg/kg of zaprinast. This increase in the hippocampal region is the result of a cGMP-specific PDE5 induction, confirmed by sildenafil inhibition, in agreement with literature data that demonstrate transcriptional regulation of PDE5 by cAMP/cGMP intracellular levels. Our results highlight the possible rebound effect of PDE inhibitors.
Srinath Vadlamani; Scott Kruger; Travis Austin
2008-06-19
Extended magnetohydrodynamic (MHD) codes are used to model the large, slow-growing instabilities that are projected to limit the performance of International Thermonuclear Experimental Reactor (ITER). The multiscale nature of the extended MHD equations requires an implicit approach. The current linear solvers needed for the implicit algorithm scale poorly because the resultant matrices are so ill-conditioned. A new solver is needed, especially one that scales to the petascale. The most successful scalable parallel processor solvers to date are multigrid solvers. Applying multigrid techniques to a set of equations whose fundamental modes are dispersive waves is a promising solution to CEMM problems. For the Phase 1, we implemented multigrid preconditioners from the HYPRE project of the Center for Applied Scientific Computing at LLNL via PETSc of the DOE SciDAC TOPS for the real matrix systems of the extended MHD code NIMROD which is a one of the primary modeling codes of the OFES-funded Center for Extended Magnetohydrodynamic Modeling (CEMM) SciDAC. We implemented the multigrid solvers on the fusion test problem that allows for real matrix systems with success, and in the process learned about the details of NIMROD data structures and the difficulties of inverting NIMROD operators. The further success of this project will allow for efficient usage of future petascale computers at the National Leadership Facilities: Oak Ridge National Laboratory, Argonne National Laboratory, and National Energy Research Scientific Computing Center. The project will be a collaborative effort between computational plasma physicists and applied mathematicians at Tech-X Corporation, applied mathematicians Front Range Scientific Computations, Inc. (who are collaborators on the HYPRE project), and other computational plasma physicists involved with the CEMM project.
A multigrid solver for the semiconductor equations
NASA Technical Reports Server (NTRS)
Bachmann, Bernhard
1993-01-01
We present a multigrid solver for the exponential fitting method. The solver is applied to the current continuity equations of semiconductor device simulation in two dimensions. The exponential fitting method is based on a mixed finite element discretization using the lowest-order Raviart-Thomas triangular element. This discretization method yields a good approximation of front layers and guarantees current conservation. The corresponding stiffness matrix is an M-matrix. 'Standard' multigrid solvers, however, cannot be applied to the resulting system, as this is dominated by an unsymmetric part, which is due to the presence of strong convection in part of the domain. To overcome this difficulty, we explore the connection between Raviart-Thomas mixed methods and the nonconforming Crouzeix-Raviart finite element discretization. In this way we can construct nonstandard prolongation and restriction operators using easily computable weighted L(exp 2)-projections based on suitable quadrature rules and the upwind effects of the discretization. The resulting multigrid algorithm shows very good results, even for real-world problems and for locally refined grids.
Data on the utilization of treatment modalities for ED in Taiwan in the era of PDE5 inhibitors.
Tsai, W-K; Jiann, B-P
2014-01-01
Oral PDE5 inhibitors, intracavernosal injection and penile implants are mainstay treatments for ED. Data on their utilization reflect economic aspects of ED, but are underreported. We report utilization data and user characteristics for these modalities in Taiwan between 1999 and 2011. Sales data on PDE5 inhibitors-sildenafil citrate, tadalafil and vardenafil and on alprostadil were retrieved from International Market Services Health, and on penile implants from the local importing company for them. Users' clinical characteristics were derived from one institution. Between 1999 and 2011, sales of PDE5 inhibitors increased 5.9-fold, whereas those of alprostadil and penile implants remained stable. Over 90% of PDE5 inhibitors were purchased in pharmacies without a prescription. Between 1999 and 2011, the number of patients who received PDE5 inhibitors (n=4715) exceeded those who underwent penile injection (n=333) and penile implantation (n=108). The mean age of patients with ED who first received PDE5 inhibitors tended to decrease over consecutive years. Discontinuation of treatment with PDE5 inhibitors or intracavernosal injection reached 90% within 3 years of treatment initiation. Our data on the increasing market for PDE5 inhibitors and the trend for first use of PDE5 inhibitors at younger ages highlight the growing burden of ED and the acceptance of PDE5 inhibitors as the primary treatment for ED. PMID:24451166
Kwak, Hyun Jeong; Nam, Ji Yeon; Song, Jin Sook; No, Zaesung; Yang, Sung Don; Cheon, Hyae Gyeong
2012-06-15
Phosphodiesterase-4 (PDE-4) is responsible for metabolizing adenosine 3',5'-cyclic monophosphate that reduces the activation of a wide range of inflammatory cells including eosinophils. PDE-4 inhibitors are under development for the treatment of respiratory diseases such as asthma and chronic obstructive pulmonary disease. Herein, we report a novel PDE-4 inhibitor, PDE-423 (3-[1-(3-cyclopropylmethoxy-4-difluoromethoxybenzyl)-1H-pyrazol-3-yl]-benzoic acid), which shows good in vitro and in vivo oral activities. PDE-423 exhibited in vitro IC(50)s of 140 nM and 550 nM in enzyme assay and cell-based assay, respectively. In vivo study using ovalbumin-induced asthmatic mice revealed that PDE-423 reduced methacholine-stimulated airway hyperreactivity in a dose-dependent manner by once daily oral administration (ED(50)=18.3 mg/kg), in parallel with decreased eosinophil peroxidase activity and improved lung histology. In addition, PDE-423 was effective in diminishing lipopolysaccharide-induced neutrophilia in vivo as well as in vitro. Oral administration of PDE-423 (100 mg/kg) had no effect on the duration of xylazine/ketamine-induced anesthesia and did not induce vomiting incidence in ferrets up to the dose of 1000 mg/kg. The present study indicates that a novel PDE-4 inhibitor, PDE-423, has good pharmacological profiles implicating this as a potential candidate for the development of a new anti-asthmatic drug. PMID:22554769
Hegde, Shweta; Ji, Hao; Oliver, David; Patel, Neema S; Poupore, Nicolas; Shtutman, Michael; Kelly, Michy P
2016-10-29
Despite the fact that appropriate social behaviors are vital to thriving in one's environment, little is understood of the molecular mechanisms controlling social behaviors or how social experience sculpts these signaling pathways. Here, we determine if Phosphodiesterase 11A (PDE11A), an enzyme that is enriched in the ventral hippocampal formation (VHIPP) and that breaks down cAMP and cGMP, regulates social behaviors. PDE11 wild-type (WT), heterozygous (HT), and knockout (KO) mice were tested in various social approach assays and gene expression differences were measured by RNA sequencing. The effect of social isolation on PDE11A4 compartmentalization and subsequent social interactions and social memory was also assessed. Deletion of PDE11A triggered age- and sex-dependent deficits in social approach in specific social contexts but not others. Mice appear to detect altered social behaviors of PDE11A KO mice, because C57BL/6J mice prefer to spend time with a sex-matched PDE11A WT vs. its KO littermate; whereas, a PDE11A KO prefers to spend time with a novel PDE11A KO vs. its WT littermate. Not only is PDE11A required for intact social interactions, we found that 1month of social isolation vs. group housing decreased PDE11A4 protein expression specifically within the membrane fraction of VHIPP. This isolation-induced decrease in PDE11A4 expression appears functional because social isolation impairs subsequent social approach behavior and social memory in a PDE11A genotype-dependent manner. Pathway analyses following RNA sequencing suggests PDE11A is a key regulator of the oxytocin pathway and membrane signaling, consistent with its pivotal role in regulating social behavior. PMID:27544407
Hegde, Shweta; Ji, Hao; Oliver, David; Patel, Neema S; Poupore, Nicolas; Shtutman, Michael; Kelly, Michy P
2016-10-29
Despite the fact that appropriate social behaviors are vital to thriving in one's environment, little is understood of the molecular mechanisms controlling social behaviors or how social experience sculpts these signaling pathways. Here, we determine if Phosphodiesterase 11A (PDE11A), an enzyme that is enriched in the ventral hippocampal formation (VHIPP) and that breaks down cAMP and cGMP, regulates social behaviors. PDE11 wild-type (WT), heterozygous (HT), and knockout (KO) mice were tested in various social approach assays and gene expression differences were measured by RNA sequencing. The effect of social isolation on PDE11A4 compartmentalization and subsequent social interactions and social memory was also assessed. Deletion of PDE11A triggered age- and sex-dependent deficits in social approach in specific social contexts but not others. Mice appear to detect altered social behaviors of PDE11A KO mice, because C57BL/6J mice prefer to spend time with a sex-matched PDE11A WT vs. its KO littermate; whereas, a PDE11A KO prefers to spend time with a novel PDE11A KO vs. its WT littermate. Not only is PDE11A required for intact social interactions, we found that 1month of social isolation vs. group housing decreased PDE11A4 protein expression specifically within the membrane fraction of VHIPP. This isolation-induced decrease in PDE11A4 expression appears functional because social isolation impairs subsequent social approach behavior and social memory in a PDE11A genotype-dependent manner. Pathway analyses following RNA sequencing suggests PDE11A is a key regulator of the oxytocin pathway and membrane signaling, consistent with its pivotal role in regulating social behavior.
MILAMIN 2 - Fast MATLAB FEM solver
NASA Astrophysics Data System (ADS)
Dabrowski, Marcin; Krotkiewski, Marcin; Schmid, Daniel W.
2013-04-01
MILAMIN is a free and efficient MATLAB-based two-dimensional FEM solver utilizing unstructured meshes [Dabrowski et al., G-cubed (2008)]. The code consists of steady-state thermal diffusion and incompressible Stokes flow solvers implemented in approximately 200 lines of native MATLAB code. The brevity makes the code easily customizable. An important quality of MILAMIN is speed - it can handle millions of nodes within minutes on one CPU core of a standard desktop computer, and is faster than many commercial solutions. The new MILAMIN 2 allows three-dimensional modeling. It is designed as a set of functional modules that can be used as building blocks for efficient FEM simulations using MATLAB. The utilities are largely implemented as native MATLAB functions. For performance critical parts we use MUTILS - a suite of compiled MEX functions optimized for shared memory multi-core computers. The most important features of MILAMIN 2 are: 1. Modular approach to defining, tracking, and discretizing the geometry of the model 2. Interfaces to external mesh generators (e.g., Triangle, Fade2d, T3D) and mesh utilities (e.g., element type conversion, fast point location, boundary extraction) 3. Efficient computation of the stiffness matrix for a wide range of element types, anisotropic materials and three-dimensional problems 4. Fast global matrix assembly using a dedicated MEX function 5. Automatic integration rules 6. Flexible prescription (spatial, temporal, and field functions) and efficient application of Dirichlet, Neuman, and periodic boundary conditions 7. Treatment of transient and non-linear problems 8. Various iterative and multi-level solution strategies 9. Post-processing tools (e.g., numerical integration) 10. Visualization primitives using MATLAB, and VTK export functions We provide a large number of examples that show how to implement a custom FEM solver using the MILAMIN 2 framework. The examples are MATLAB scripts of increasing complexity that address a given
Multiscale Modeling of Cavitating Bubbly Flows
NASA Astrophysics Data System (ADS)
Ma, J.; Hsiao, C.-T.; Chahine, G. L.
2013-03-01
Modeling of cavitating bubbly flows is challenging due to the wide range of characteristic lengths of the physics at play: from micrometers (e.g., bubble nuclei radius) to meters (e.g., propeller diameter or sheet cavity length). To address this, we present here a multiscale approach which integrates a Discrete Bubble Model for dispersed microbubbles and a level set N-S solver for macro cavities, along with a mesoscale transition model to bridge the two. This approach was implemented in 3DYNAFScopyright and used to simulate sheet-to-cloud cavitation over a hydrofoil. The hybrid model captures well the full cavitation process starting from free field nuclei and nucleation from solid surfaces. In low pressure region of the foil small nuclei are seen to grow large and eventually merge to form a large scale sheet cavity. A reentrant jet forms under the cavity, travels upstream, and breaks it, resulting in a bubble cloud of a large amount of microbubbles as the broken pockets shrink and travel downstream. This is in good agreement with experimental observations based of sheet lengths and frequency of lift force oscillation. DOE-SBIR, ONR (monitored by Dr. Ki-Han Kim)
Vencels, Juris; Delzanno, Gian Luca; Johnson, Alec; Peng, Ivy Bo; Laure, Erwin; Markidis, Stefano
2015-06-01
A spectral method for kinetic plasma simulations based on the expansion of the velocity distribution function in a variable number of Hermite polynomials is presented. The method is based on a set of non-linear equations that is solved to determine the coefficients of the Hermite expansion satisfying the Vlasov and Poisson equations. In this paper, we first show that this technique combines the fluid and kinetic approaches into one framework. Second, we present an adaptive strategy to increase and decrease the number of Hermite functions dynamically during the simulation. The technique is applied to the Landau damping and two-stream instabilitymore » test problems. Performance results show 21% and 47% saving of total simulation time in the Landau and two-stream instability test cases, respectively.« less
Vencels, Juris; Delzanno, Gian Luca; Johnson, Alec; Peng, Ivy Bo; Laure, Erwin; Markidis, Stefano
2015-06-01
A spectral method for kinetic plasma simulations based on the expansion of the velocity distribution function in a variable number of Hermite polynomials is presented. The method is based on a set of non-linear equations that is solved to determine the coefficients of the Hermite expansion satisfying the Vlasov and Poisson equations. In this paper, we first show that this technique combines the fluid and kinetic approaches into one framework. Second, we present an adaptive strategy to increase and decrease the number of Hermite functions dynamically during the simulation. The technique is applied to the Landau damping and two-stream instability test problems. Performance results show 21% and 47% saving of total simulation time in the Landau and two-stream instability test cases, respectively.
PDE5 inhibitors as therapeutics for heart disease, diabetes and cancer.
Das, Anindita; Durrant, David; Salloum, Fadi N; Xi, Lei; Kukreja, Rakesh C
2015-03-01
The phosphodiesterase 5 (PDE5) inhibitors, including sildenafil (Viagra™), vardenafil (Levitra™), and tadalafil (Cialis™) have been developed for treatment of erectile dysfunction. Moreover, sildenafil and tadalafil are used for the management of pulmonary arterial hypertension in patients. Since our first report showing the cardioprotective effect of sildenafil in 2002, there has been tremendous growth of preclinical and clinical studies on the use of PDE5 inhibitors for cardiovascular diseases and cancer. Numerous animal studies have demonstrated that PDE5 inhibitors have powerful protective effect against myocardial ischemia/reperfusion (I/R) injury, doxorubicin cardiotoxicity, ischemic and diabetic cardiomyopathy, cardiac hypertrophy, Duchenne muscular dystrophy and the improvement of stem cell efficacy for myocardial repair. Mechanistically, PDE5 inhibitors protect the heart against I/R injury through increased expression of nitric oxide synthases, activation of protein kinase G (PKG), PKG-dependent hydrogen sulfide generation, and phosphorylation of glycogen synthase kinase-3β - a master switch immediately proximal to mitochondrial permeability transition pore and the end effector of cardioprotection. In addition, PDE5 inhibitors enhance the sensitivity of certain types of cancer to standard chemotherapeutic drugs, including doxorubicin. Many clinical trials with PDE5 inhibitors have focused on the potential cardiovascular and anti-cancer benefits. Despite mixed results of these clinical trials, there is a continuing strong interest by basic scientists and clinical investigators in exploring their new clinical uses. It is our hope that future new mechanistic investigations and carefully designed clinical trials would help in reaping additional benefits of PDE5 inhibitors for cardiovascular disease and cancer in patients. PMID:25444755
Development of a series of novel carbon-11 labeled PDE10A inhibitors.
Stepanov, Vladimir; Miura, Shotaro; Takano, Akihiro; Amini, Nahid; Nakao, Ryuji; Hasui, Tomoaki; Nakashima, Kosuke; Taniguchi, Takahiko; Kimura, Haruhide; Kuroita, Takanobu; Halldin, Christer
2015-05-15
Phosphodiesterase 10A (PDE10A) is a member of the PDE family of enzymes that degrades cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP). Our aim was to label a series of structurally related PDE10A inhibitors with carbon-11 and evaluate them as potential positron emission tomography (PET) radioligands for PDE10A using nonhuman primates. The series consisted of seven compounds based on the 3-(1H-pyrazol-5-yl)pyridazin-4(1H)-one backbone. These compounds were selected from the initial larger library based on a number of parameters such as affinity, selectivity for hPDE10A in in vitro tests, lipophilicity, and on the results of multidrug resistance protein 1 (MDR1)-LLCPK1 and the parallel artificial membrane permeability assays. Seven radioligands (KIT-1, 3, 5, 6, 7, 9, and 12) were radiolabeled with carbon-11 employing O-methylation on the hydroxyl moiety using [(11)C]methyl triflate. In vivo examination of each radioligand was performed using PET in rhesus monkeys; analysis of radiometabolites in plasma also was conducted using HPLC. All seven radioligands were labeled with high (>90%) incorporation of [(11)C]methyl triflate into their appropriate precursors and with high specific radioactivity. Carbon-11 labeled KIT-5 and KIT-6 showed high accumulation in the striatum, consistent with the known anatomical distribution of PDE10A in brain, accompanied by fast washout and high specific binding ratio. In particular [(11)C]KIT-6, named [(11)C]T-773, is a promising PET tool for further examination of PDE10A in human brain. PMID:25891816
PDE5 inhibitors as therapeutics for heart disease, diabetes and cancer
Das, Anindita; Durrant, David; Salloum, Fadi N; Xi, Lei; Kukreja, Rakesh C
2015-01-01
The phosphodiesterase 5 (PDE5) inhibitors, including sildenafil (Viagra™), vardenafil (Levitra™), and tadalafil (Cialis™) have been developed for treatment of erectile dysfunction. Moreover, sildenafil and tadalafil are used for the management of pulmonary arterial hypertension in patients. Since our first report showing the cardioprotective effect of sildenafil in 2002, there has been tremendous growth of preclinical and clinical studies on the use of PDE5 inhibitors for cardiovascular diseases and cancer. Numerous animal studies have demonstrated that PDE5 inhibitors have powerful protective effect against myocardial ischemia/reperfusion (I/R) injury, doxorubicin cardiotoxicity, ischemic and diabetic cardiomyopathy, cardiac hypertrophy, Duchenne muscular dystrophy and the improvement stem cell efficacy for myocardial repair. Mechanistically, PDE5 inhibitors protect the heart against I/R injury through increased expression of nitric oxide synthases, activation of protein kinase G (PKG), PKG-dependent hydrogen sulfide generation, and phosphorylation of glycogen synthase kinase-3β - a master switch immediately proximal to mitochondrial permeability transition pore and the end effector of cardioprotection. In addition, PDE5 inhibitors enhance the sensitivity of certain types of cancer to standard chemotherapeutic drugs, including doxorubicin. Many clinical trials with PDE5 inhibitors have focused on the potential cardiovascular and cancer benefits. Despite mixed results of these clinical trials, there is continuing strong interest by basic scientists and clinical investigators in exploring their new clinical uses. It is our hope that future new mechanistic investigations and carefully designed clinical trials would help in reaping additional benefits of PDE5 inhibitors for cardiovascular disease and cancer in patients. PMID:25444755
PDE 7 Inhibitors: New Potential Drugs for the Therapy of Spinal Cord Injury
Paterniti, Irene; Mazzon, Emanuela; Gil, Carmen; Impellizzeri, Daniela; Palomo, Valle; Redondo, Myriam; Perez, Daniel I.; Esposito, Emanuela; Martinez, Ana; Cuzzocrea, Salvatore
2011-01-01
Background Primary traumatic mechanical injury to the spinal cord (SCI) causes the death of a number of neurons that to date can neither be recovered nor regenerated. During the last years our group has been involved in the design, synthesis and evaluation of PDE7 inhibitors as new innovative drugs for several neurological disorders. Our working hypothesis is based on two different facts. Firstly, neuroinflammation is modulated by cAMP levels, thus the key role for phosphodiesterases (PDEs), which hydrolyze cAMP, is undoubtedly demonstrated. On the other hand, PDE7 is expressed simultaneously on leukocytes and on the brain, highlighting the potential crucial role of PDE7 as drug target for neuroinflammation. Methodology/Principal Findings Here we present two chemically diverse families of PDE7 inhibitors, designed using computational techniques such as virtual screening and neuronal networks. We report their biological profile and their efficacy in an experimental SCI model induced by the application of vascular clips (force of 24 g) to the dura via a four-level T5–T8 laminectomy. We have selected two candidates, namely S14 and VP1.15, as PDE7 inhibitors. These compounds increase cAMP production both in macrophage and neuronal cell lines. Regarding drug-like properties, compounds were able to cross the blood brain barrier using parallel artificial membranes (PAMPA) methodology. SCI in mice resulted in severe trauma characterized by edema, neutrophil infiltration, and production of a range of inflammatory mediators, tissue damage, and apoptosis. Treatment of the mice with S14 and VP1.15, two PDE7 inhibitors, significantly reduced the degree of spinal cord inflammation, tissue injury (histological score), and TNF-α, IL-6, COX-2 and iNOS expression. Conclusions/Significance All these data together led us to propose PDE7 inhibitors, and specifically S14 and VP1.15, as potential drug candidates to be further studied for the treatment of SCI. PMID:21297958
NASA Astrophysics Data System (ADS)
Ford, C.; Wiesendanger, C.
1997-02-01
The standard MS renormalization prescription is inadequate for dealing with multi-scale problems. To illustrate this we consider the computation of the effective potential in the Higgs-Yukawa model. It is argued that it is natural to employ a two-scale renormalization group. We give a modified version of a two-scale scheme introduced by Einhorn and Jones. In such schemes the beta functions necessarily contain potentially large logarithms of the RG scale ratios. For credible perturbation theory one must implement a large logarithms resummation on the beta functions themselves. We show how the integrability condition for the two RG equations allows one to perform this resummation.
Approximate Riemann solvers for the Godunov SPH (GSPH)
NASA Astrophysics Data System (ADS)
Puri, Kunal; Ramachandran, Prabhu
2014-08-01
The Godunov Smoothed Particle Hydrodynamics (GSPH) method is coupled with non-iterative, approximate Riemann solvers for solutions to the compressible Euler equations. The use of approximate solvers avoids the expensive solution of the non-linear Riemann problem for every interacting particle pair, as required by GSPH. In addition, we establish an equivalence between the dissipative terms of GSPH and the signal based SPH artificial viscosity, under the restriction of a class of approximate Riemann solvers. This equivalence is used to explain the anomalous “wall heating” experienced by GSPH and we provide some suggestions to overcome it. Numerical tests in one and two dimensions are used to validate the proposed Riemann solvers. A general SPH pairing instability is observed for two-dimensional problems when using unequal mass particles. In general, Ducowicz Roe's and HLLC approximate Riemann solvers are found to be suitable replacements for the iterative Riemann solver in the original GSPH scheme.
Robust parallel iterative solvers for linear and least-squares problems, Final Technical Report
Saad, Yousef
2014-01-16
The primary goal of this project is to study and develop robust iterative methods for solving linear systems of equations and least squares systems. The focus of the Minnesota team is on algorithms development, robustness issues, and on tests and validation of the methods on realistic problems. 1. The project begun with an investigation on how to practically update a preconditioner obtained from an ILU-type factorization, when the coefficient matrix changes. 2. We investigated strategies to improve robustness in parallel preconditioners in a specific case of a PDE with discontinuous coefficients. 3. We explored ways to adapt standard preconditioners for solving linear systems arising from the Helmholtz equation. These are often difficult linear systems to solve by iterative methods. 4. We have also worked on purely theoretical issues related to the analysis of Krylov subspace methods for linear systems. 5. We developed an effective strategy for performing ILU factorizations for the case when the matrix is highly indefinite. The strategy uses shifting in some optimal way. The method was extended to the solution of Helmholtz equations by using complex shifts, yielding very good results in many cases. 6. We addressed the difficult problem of preconditioning sparse systems of equations on GPUs. 7. A by-product of the above work is a software package consisting of an iterative solver library for GPUs based on CUDA. This was made publicly available. It was the first such library that offers complete iterative solvers for GPUs. 8. We considered another form of ILU which blends coarsening techniques from Multigrid with algebraic multilevel methods. 9. We have released a new version on our parallel solver - called pARMS [new version is version 3]. As part of this we have tested the code in complex settings - including the solution of Maxwell and Helmholtz equations and for a problem of crystal growth.10. As an application of polynomial preconditioning we considered the
Updates to the NEQAIR Radiation Solver
NASA Technical Reports Server (NTRS)
Cruden, Brett A.; Brandis, Aaron M.
2014-01-01
The NEQAIR code is one of the original heritage solvers for radiative heating prediction in aerothermal environments, and is still used today for mission design purposes. This paper discusses the implementation of the first major revision to the NEQAIR code in the last five years, NEQAIR v14.0. The most notable features of NEQAIR v14.0 are the parallelization of the radiation computation, reducing runtimes by about 30×, and the inclusion of mid-wave CO2 infrared radiation.
DPS--a computerised diagnostic problem solver.
Bartos, P; Gyárfas, F; Popper, M
1982-01-01
The paper contains a short description of the DPS system which is a computerized diagnostic problem solver. The system is under development of the Research Institute of Medical Bionics in Bratislava, Czechoslovakia. Its underlying philosophy yields from viewing the diagnostic process as process of cognitive problem solving. The implementation of the system is based on the methods of Artificial Intelligence and utilisation of production systems and frame theory should be noted in this context. Finally a list of program modules and their characterisation is presented.
Input-output-controlled nonlinear equation solvers
NASA Technical Reports Server (NTRS)
Padovan, Joseph
1988-01-01
To upgrade the efficiency and stability of the successive substitution (SS) and Newton-Raphson (NR) schemes, the concept of input-output-controlled solvers (IOCS) is introduced. By employing the formal properties of the constrained version of the SS and NR schemes, the IOCS algorithm can handle indefiniteness of the system Jacobian, can maintain iterate monotonicity, and provide for separate control of load incrementation and iterate excursions, as well as having other features. To illustrate the algorithmic properties, the results for several benchmark examples are presented. These define the associated numerical efficiency and stability of the IOCS.
Multiscale simulation of ideal mixtures using smoothed dissipative particle dynamics.
Petsev, Nikolai D; Leal, L Gary; Shell, M Scott
2016-02-28
Smoothed dissipative particle dynamics (SDPD) [P. Español and M. Revenga, Phys. Rev. E 67, 026705 (2003)] is a thermodynamically consistent particle-based continuum hydrodynamics solver that features scale-dependent thermal fluctuations. We obtain a new formulation of this stochastic method for ideal two-component mixtures through a discretization of the advection-diffusion equation with thermal noise in the concentration field. The resulting multicomponent approach is consistent with the interpretation of the SDPD particles as moving volumes of fluid and reproduces the correct fluctuations and diffusion dynamics. Subsequently, we provide a general multiscale multicomponent SDPD framework for simulations of molecularly miscible systems spanning length scales from nanometers to the non-fluctuating continuum limit. This approach reproduces appropriate equilibrium properties and is validated with simulation of simple one-dimensional diffusion across multiple length scales. PMID:26931689
Multiscale simulation of ideal mixtures using smoothed dissipative particle dynamics
NASA Astrophysics Data System (ADS)
Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott
2016-02-01
Smoothed dissipative particle dynamics (SDPD) [P. Español and M. Revenga, Phys. Rev. E 67, 026705 (2003)] is a thermodynamically consistent particle-based continuum hydrodynamics solver that features scale-dependent thermal fluctuations. We obtain a new formulation of this stochastic method for ideal two-component mixtures through a discretization of the advection-diffusion equation with thermal noise in the concentration field. The resulting multicomponent approach is consistent with the interpretation of the SDPD particles as moving volumes of fluid and reproduces the correct fluctuations and diffusion dynamics. Subsequently, we provide a general multiscale multicomponent SDPD framework for simulations of molecularly miscible systems spanning length scales from nanometers to the non-fluctuating continuum limit. This approach reproduces appropriate equilibrium properties and is validated with simulation of simple one-dimensional diffusion across multiple length scales.
On the relationship between ODE solvers and iterative solvers for linear equations
Lorber, A.; Joubert, W.; Carey, G.F.
1994-12-31
The connection between the solution of linear systems of equations by both iterative methods and explicit time stepping techniques is investigated. Based on the similarities, a suite of Runge-Kutta time integration schemes with extended stability domains are developed using Chebyshev iteration polynomials. These Runge-Kutta schemes are applied to linear and non-linear systems arising from the numerical solution of PDE`s containing either physical or artificial transient terms. Specifically, the solutions of model linear convection and convection-diffusion equations are presented, as well as the solution of a representative non-linear Navier-Stokes fluid flow problem. Included are results of parallel computations.
Identification of novel mutations confirms PDE4D as a major gene causing acrodysostosis.
Lynch, Danielle C; Dyment, David A; Huang, Lijia; Nikkel, Sarah M; Lacombe, Didier; Campeau, Philippe M; Lee, Brendan; Bacino, Carlos A; Michaud, Jacques L; Bernier, Francois P; Parboosingh, Jillian S; Innes, A Micheil
2013-01-01
Acrodysostosis is characterized by nasal hypoplasia, peripheral dysostosis, variable short stature, and intellectual impairment. Recently, mutations in PRKAR1A were reported in patients with acrodysostosis and hormone resistance. Subsequently, mutations in a phosphodiesterase gene (PDE4D) were identified in seven sporadic cases. We sequenced PDE4D in seven acrodysostosis patients from five families. Missense mutations were identified in all cases. Families showed de novo inheritance except one family with three affected children whose father was subsequently found to have subtle features of acrodysostosis. There were no recurrent mutations. Short stature and endocrine resistance are rare in this series; however, cognitive involvement and obesity were frequent. This last finding is relevant given PDE4D is insulin responsive and potentially involved in lipolysis. PDE4D encodes a cyclic AMP regulator and places PDE4D-related acrodysostosis within the same family of diseases as pseudohypoparathyroidism, pseudopseudohypoparathyroidism, PRKAR1A-related acrodysostosis and brachydactyly-mental retardation syndrome; all characterized by cognitive impairment and short distal extremities. PMID:23033274
Rutin inhibits B[a]PDE-induced cyclooxygenase-2 expression by targeting EGFR kinase activity.
Choi, Seunghwan; Lim, Tae-Gyu; Hwang, Mun Kyung; Kim, Yoon-A; Kim, Jiyoung; Kang, Nam Joo; Jang, Tae Su; Park, Jun-Seong; Yeom, Myeong Hun; Lee, Ki Won
2013-11-15
Rutin is a well-known flavonoid that exists in various natural sources. Accumulative studies have represented the biological effects of rutin, such as anti-oxidative and anti-inflammatory effects. However, the underlying mechanisms of rutin and its direct targets are not understood. We investigated whether rutin reduced B[a]PDE-induced-COX-2 expression. The transactivation of AP-1 and NF-κB were inhibited by rutin. Rutin also attenuated B[a]PDE-induced Raf/MEK/ERK and Akt activation, but had no effect on the phosphorylation of EGFR. An in vitro kinase assay revealed rutin suppressed EGFR kinase activity. We also confirmed direct binding between rutin and EGFR, and found that the binding was regressed by ATP. The EGFR inhibitor also inhibited the B[a]PDE-induced MEK/ERK and Akt signaling pathways and subsequently, suppressed COX-2 expression and promoter activity, in addition to suppressing the transactivation of AP-1 and NF-κB. In EGFR(-/-)mouse embryonic fibroblast cells, B[a]PDE-induced COX-2 expression was also diminished. Collectively, rutin inhibits B[a]PDE-induced COX-2 expression by suppressing the Raf/MEK/ERK and Akt signaling pathways. EGFR appeared to be the direct target of rutin.
Wang, Jun-Wei; Wu, Huai-Ning; Li, Han-Xiong
2012-06-01
In this paper, a distributed fuzzy control design based on Proportional-spatial Derivative (P-sD) is proposed for the exponential stabilization of a class of nonlinear spatially distributed systems described by parabolic partial differential equations (PDEs). Initially, a Takagi-Sugeno (T-S) fuzzy parabolic PDE model is proposed to accurately represent the nonlinear parabolic PDE system. Then, based on the T-S fuzzy PDE model, a novel distributed fuzzy P-sD state feedback controller is developed by combining the PDE theory and the Lyapunov technique, such that the closed-loop PDE system is exponentially stable with a given decay rate. The sufficient condition on the existence of an exponentially stabilizing fuzzy controller is given in terms of a set of spatial differential linear matrix inequalities (SDLMIs). A recursive algorithm based on the finite-difference approximation and the linear matrix inequality (LMI) techniques is also provided to solve these SDLMIs. Finally, the developed design methodology is successfully applied to the feedback control of the Fitz-Hugh-Nagumo equation.
Identification of novel mutations confirms PDE4D as a major gene causing acrodysostosis.
Lynch, Danielle C; Dyment, David A; Huang, Lijia; Nikkel, Sarah M; Lacombe, Didier; Campeau, Philippe M; Lee, Brendan; Bacino, Carlos A; Michaud, Jacques L; Bernier, Francois P; Parboosingh, Jillian S; Innes, A Micheil
2013-01-01
Acrodysostosis is characterized by nasal hypoplasia, peripheral dysostosis, variable short stature, and intellectual impairment. Recently, mutations in PRKAR1A were reported in patients with acrodysostosis and hormone resistance. Subsequently, mutations in a phosphodiesterase gene (PDE4D) were identified in seven sporadic cases. We sequenced PDE4D in seven acrodysostosis patients from five families. Missense mutations were identified in all cases. Families showed de novo inheritance except one family with three affected children whose father was subsequently found to have subtle features of acrodysostosis. There were no recurrent mutations. Short stature and endocrine resistance are rare in this series; however, cognitive involvement and obesity were frequent. This last finding is relevant given PDE4D is insulin responsive and potentially involved in lipolysis. PDE4D encodes a cyclic AMP regulator and places PDE4D-related acrodysostosis within the same family of diseases as pseudohypoparathyroidism, pseudopseudohypoparathyroidism, PRKAR1A-related acrodysostosis and brachydactyly-mental retardation syndrome; all characterized by cognitive impairment and short distal extremities.
MULTISCALE PHENOMENA IN MATERIALS
A. BISHOP
2000-09-01
This project developed and supported a technology base in nonequilibrium phenomena underpinning fundamental issues in condensed matter and materials science, and applied this technology to selected problems. In this way the increasingly sophisticated synthesis and characterization available for classes of complex electronic and structural materials provided a testbed for nonlinear science, while nonlinear and nonequilibrium techniques helped advance our understanding of the scientific principles underlying the control of material microstructure, their evolution, fundamental to macroscopic functionalities. The project focused on overlapping areas of emerging thrusts and programs in the Los Alamos materials community for which nonlinear and nonequilibrium approaches will have decisive roles and where productive teamwork among elements of modeling, simulations, synthesis, characterization and applications could be anticipated--particularly multiscale and nonequilibrium phenomena, and complex matter in and between fields of soft, hard and biomimetic materials. Principal topics were: (i) Complex organic and inorganic electronic materials, including hard, soft and biomimetic materials, self-assembly processes and photophysics; (ii) Microstructure and evolution in multiscale and hierarchical materials, including dynamic fracture and friction, dislocation and large-scale deformation, metastability, and inhomogeneity; and (iii) Equilibrium and nonequilibrium phases and phase transformations, emphasizing competing interactions, frustration, landscapes, glassy and stochastic dynamics, and energy focusing.
Multiscale reactive molecular dynamics
Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.
2012-01-01
Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system. PMID:23249062
Using the scalable nonlinear equations solvers package
Gropp, W.D.; McInnes, L.C.; Smith, B.F.
1995-02-01
SNES (Scalable Nonlinear Equations Solvers) is a software package for the numerical solution of large-scale systems of nonlinear equations on both uniprocessors and parallel architectures. SNES also contains a component for the solution of unconstrained minimization problems, called SUMS (Scalable Unconstrained Minimization Solvers). Newton-like methods, which are known for their efficiency and robustness, constitute the core of the package. As part of the multilevel PETSc library, SNES incorporates many features and options from other parts of PETSc. In keeping with the spirit of the PETSc library, the nonlinear solution routines are data-structure-neutral, making them flexible and easily extensible. This users guide contains a detailed description of uniprocessor usage of SNES, with some added comments regarding multiprocessor usage. At this time the parallel version is undergoing refinement and extension, as we work toward a common interface for the uniprocessor and parallel cases. Thus, forthcoming versions of the software will contain additional features, and changes to parallel interface may result at any time. The new parallel version will employ the MPI (Message Passing Interface) standard for interprocessor communication. Since most of these details will be hidden, users will need to perform only minimal message-passing programming.
On code verification of RANS solvers
NASA Astrophysics Data System (ADS)
Eça, L.; Klaij, C. M.; Vaz, G.; Hoekstra, M.; Pereira, F. S.
2016-04-01
This article discusses Code Verification of Reynolds-Averaged Navier Stokes (RANS) solvers that rely on face based finite volume discretizations for volumes of arbitrary shape. The study includes test cases with known analytical solutions (generated with the method of manufactured solutions) corresponding to laminar and turbulent flow, with the latter using eddy-viscosity turbulence models. The procedure to perform Code Verification based on grid refinement studies is discussed and the requirements for its correct application are illustrated in a simple one-dimensional problem. It is shown that geometrically similar grids are recommended for proper Code Verification and so the data should not have scatter making the use of least square fits unnecessary. Results show that it may be advantageous to determine the extrapolated error to cell size/time step zero instead of assuming that it is zero, especially when it is hard to determine the asymptotic order of grid convergence. In the RANS examples, several of the features of the ReFRESCO solver are checked including the effects of the available turbulence models in the convergence properties of the code. It is shown that it is required to account for non-orthogonality effects in the discretization of the diffusion terms and that the turbulence quantities transport equations can deteriorate the order of grid convergence of mean flow quantities.
A PDE Pricing Framework for Cross-Currency Interest Rate Derivatives with Target Redemption Features
NASA Astrophysics Data System (ADS)
Christara, Christina C.; Minh Dang, Duy; Jackson, Kenneth R.; Lakhany, Asif
2010-09-01
We propose a general framework for efficient pricing via a partial differential equation (PDE) approach for exotic cross-currency interest rate (IR) derivatives, with strong emphasis on long-dated foreign exchange (FX) IR hybrids, namely Power Reverse Dual Currency (PRDC) swaps with a FX Target Redemption (FX-TARN) provision. The FX-TARN provision provides a cap on the FX-linked PRDC coupon amounts, and once the accumulated coupon amount reaches this cap, the underlying PRDC swap terminates. Our PDE pricing framework is based on an auxiliary state variable to keep track of the total accumulated PRDC coupon amount. Finite differences on uniform grids and the Alternating Direction Implicit (ADI) method are used for the spatial and time discretizations, respectively, of the model-dependent PDE corresponding to each discretized value of the auxiliary variable. Numerical examples illustrating the convergence properties of the numerical methods are provided.
Efficient Integration of Coupled Electrical-Chemical Systems in Multiscale Neuronal Simulations.
Brocke, Ekaterina; Bhalla, Upinder S; Djurfeldt, Mikael; Hellgren Kotaleski, Jeanette; Hanke, Michael
2016-01-01
Multiscale modeling and simulations in neuroscience is gaining scientific attention due to its growing importance and unexplored capabilities. For instance, it can help to acquire better understanding of biological phenomena that have important features at multiple scales of time and space. This includes synaptic plasticity, memory formation and modulation, homeostasis. There are several ways to organize multiscale simulations depending on the scientific problem and the system to be modeled. One of the possibilities is to simulate different components of a multiscale system simultaneously and exchange data when required. The latter may become a challenging task for several reasons. First, the components of a multiscale system usually span different spatial and temporal scales, such that rigorous analysis of possible coupling solutions is required. Then, the components can be defined by different mathematical formalisms. For certain classes of problems a number of coupling mechanisms have been proposed and successfully used. However, a strict mathematical theory is missing in many cases. Recent work in the field has not so far investigated artifacts that may arise during coupled integration of different approximation methods. Moreover, in neuroscience, the coupling of widely used numerical fixed step size solvers may lead to unexpected inefficiency. In this paper we address the question of possible numerical artifacts that can arise during the integration of a coupled system. We develop an efficient strategy to couple the components comprising a multiscale test problem in neuroscience. We introduce an efficient coupling method based on the second-order backward differentiation formula (BDF2) numerical approximation. The method uses an adaptive step size integration with an error estimation proposed by Skelboe (2000). The method shows a significant advantage over conventional fixed step size solvers used in neuroscience for similar problems. We explore different
Efficient Integration of Coupled Electrical-Chemical Systems in Multiscale Neuronal Simulations
Brocke, Ekaterina; Bhalla, Upinder S.; Djurfeldt, Mikael; Hellgren Kotaleski, Jeanette; Hanke, Michael
2016-01-01
Multiscale modeling and simulations in neuroscience is gaining scientific attention due to its growing importance and unexplored capabilities. For instance, it can help to acquire better understanding of biological phenomena that have important features at multiple scales of time and space. This includes synaptic plasticity, memory formation and modulation, homeostasis. There are several ways to organize multiscale simulations depending on the scientific problem and the system to be modeled. One of the possibilities is to simulate different components of a multiscale system simultaneously and exchange data when required. The latter may become a challenging task for several reasons. First, the components of a multiscale system usually span different spatial and temporal scales, such that rigorous analysis of possible coupling solutions is required. Then, the components can be defined by different mathematical formalisms. For certain classes of problems a number of coupling mechanisms have been proposed and successfully used. However, a strict mathematical theory is missing in many cases. Recent work in the field has not so far investigated artifacts that may arise during coupled integration of different approximation methods. Moreover, in neuroscience, the coupling of widely used numerical fixed step size solvers may lead to unexpected inefficiency. In this paper we address the question of possible numerical artifacts that can arise during the integration of a coupled system. We develop an efficient strategy to couple the components comprising a multiscale test problem in neuroscience. We introduce an efficient coupling method based on the second-order backward differentiation formula (BDF2) numerical approximation. The method uses an adaptive step size integration with an error estimation proposed by Skelboe (2000). The method shows a significant advantage over conventional fixed step size solvers used in neuroscience for similar problems. We explore different
Efficient Integration of Coupled Electrical-Chemical Systems in Multiscale Neuronal Simulations.
Brocke, Ekaterina; Bhalla, Upinder S; Djurfeldt, Mikael; Hellgren Kotaleski, Jeanette; Hanke, Michael
2016-01-01
Multiscale modeling and simulations in neuroscience is gaining scientific attention due to its growing importance and unexplored capabilities. For instance, it can help to acquire better understanding of biological phenomena that have important features at multiple scales of time and space. This includes synaptic plasticity, memory formation and modulation, homeostasis. There are several ways to organize multiscale simulations depending on the scientific problem and the system to be modeled. One of the possibilities is to simulate different components of a multiscale system simultaneously and exchange data when required. The latter may become a challenging task for several reasons. First, the components of a multiscale system usually span different spatial and temporal scales, such that rigorous analysis of possible coupling solutions is required. Then, the components can be defined by different mathematical formalisms. For certain classes of problems a number of coupling mechanisms have been proposed and successfully used. However, a strict mathematical theory is missing in many cases. Recent work in the field has not so far investigated artifacts that may arise during coupled integration of different approximation methods. Moreover, in neuroscience, the coupling of widely used numerical fixed step size solvers may lead to unexpected inefficiency. In this paper we address the question of possible numerical artifacts that can arise during the integration of a coupled system. We develop an efficient strategy to couple the components comprising a multiscale test problem in neuroscience. We introduce an efficient coupling method based on the second-order backward differentiation formula (BDF2) numerical approximation. The method uses an adaptive step size integration with an error estimation proposed by Skelboe (2000). The method shows a significant advantage over conventional fixed step size solvers used in neuroscience for similar problems. We explore different
Efficient Integration of Coupled Electrical-Chemical Systems in Multiscale Neuronal Simulations
Brocke, Ekaterina; Bhalla, Upinder S.; Djurfeldt, Mikael; Hellgren Kotaleski, Jeanette; Hanke, Michael
2016-01-01
Multiscale modeling and simulations in neuroscience is gaining scientific attention due to its growing importance and unexplored capabilities. For instance, it can help to acquire better understanding of biological phenomena that have important features at multiple scales of time and space. This includes synaptic plasticity, memory formation and modulation, homeostasis. There are several ways to organize multiscale simulations depending on the scientific problem and the system to be modeled. One of the possibilities is to simulate different components of a multiscale system simultaneously and exchange data when required. The latter may become a challenging task for several reasons. First, the components of a multiscale system usually span different spatial and temporal scales, such that rigorous analysis of possible coupling solutions is required. Then, the components can be defined by different mathematical formalisms. For certain classes of problems a number of coupling mechanisms have been proposed and successfully used. However, a strict mathematical theory is missing in many cases. Recent work in the field has not so far investigated artifacts that may arise during coupled integration of different approximation methods. Moreover, in neuroscience, the coupling of widely used numerical fixed step size solvers may lead to unexpected inefficiency. In this paper we address the question of possible numerical artifacts that can arise during the integration of a coupled system. We develop an efficient strategy to couple the components comprising a multiscale test problem in neuroscience. We introduce an efficient coupling method based on the second-order backward differentiation formula (BDF2) numerical approximation. The method uses an adaptive step size integration with an error estimation proposed by Skelboe (2000). The method shows a significant advantage over conventional fixed step size solvers used in neuroscience for similar problems. We explore different
Richter, Wito; Hermsdorf, Thomas; Kronbach, Thomas; Dettmer, Dietrich
2002-06-01
We have investigated the refolding and purification of the catalytic domain of human 3',5'-cyclic nucleotide phosphodiesterase 7A1 (PDE7A1) expressed in Escherichia coli. A cDNA encoding an N-terminal-truncated PDE7A1(147-482-His) was amplified by RT-PCR from human peripheral blood cells and inserted into the vector pET21-C for bacterial expression of the enzyme fused to a C-terminal His-tag. The PDE was found to be expressed in the form of inclusion bodies which could be refolded to an active enzyme in buffer containing high concentrations of arginine hydrochloride, ethylene glycol, and magnesium chloride at pH 8.5. The PDE7A1(147-482-His) construct could be purified after dialysis and concentration steps by either Zn2+-IDA-Sepharose chromatography or ResourceQ ion-exchange chromatography to homogeneity. In comparison to the metal-chelate column, the ResourceQ purification resulted in a distinctly better yield and enrichment of the protein. Both the Vmax (0.46 micromol. min(-1). mg(-1) ) and the K(m) (0.1 microM) of the purified enzyme were found to be comparable with published data for native or recombinant catalytically active expressed PDE7A1. Using SDS/PAGE, a molecular mass of 39 kDa was determined (theoretical value 38.783 kDa). As known from several other mammalian PDEs, size-exclusion chromatography using refolded PDE7A1(147-482-His) indicated the formation of dimers. The purified enzyme was soluble at concentrations up to 100 microg/ml. A further increase of protein concentration resulted, however, in precipitation of the enzyme.
Functional Analysis of a c-di-AMP-specific Phosphodiesterase MsPDE from Mycobacterium smegmatis
Tang, Qing; Luo, Yunchao; Zheng, Cao; Yin, Kang; Ali, Maria Kanwal; Li, Xinfeng; He, Jin
2015-01-01
Cyclic di‑AMP (c-di-AMP) is a second signaling molecule involved in the regulation of bacterial physiological processes and interaction between pathogen and host. However, the regulatory network mediated by c-di-AMP in Mycobacterium remains obscure. In M. smegmatis, a diadenylate cyclase (DAC) was reported recently, but there is still no investigation on c-di-AMP phosphodiesterase (PDE). Here, we provide a systematic study on signaling mechanism of c-di-AMP PDE in M. smegmatis. Based on our enzymatic analysis, MsPDE (MSMEG_2630), which contained a DHH-DHHA1 domain, displayed a 200-fold higher hydrolytic efficiency (kcat/Km) to c-di-AMP than to c-di-GMP. MsPDE was capable of converting c-di-AMP to pApA and AMP, and hydrolyzing pApA to AMP. Site-directed mutations in DHH and DHHA1 revealed that DHH domain was critical for the phosphodiesterase activity. To explore the regulatory role of c-di-AMP in vivo, we constructed the mspde mutant (Δmspde) and found that deficiency of MsPDE significantly enhanced intracellular C12-C20 fatty acid accumulation. Deficiency of DAC in many bacteria results in cell death. However, we acquired the M. smegmatis strain with DAC gene disrupted (ΔmsdisA) by homologous recombination approach. Deletion of msdisA reduced bacterial C12-C20 fatty acids production but scarcely affected bacterial survival. We also provided evidences that superfluous c-di-AMP in M. smegmatis could lead to abnormal colonial morphology. Collectively, our results indicate that MsPDE is a functional c-di-AMP-specific phosphodiesterase both in vitro and in vivo. Our study also expands the regulatory network mediated by c-di-AMP in M. smegmatis. PMID:26078723
Performance of distributed multiscale simulations
Borgdorff, J.; Ben Belgacem, M.; Bona-Casas, C.; Fazendeiro, L.; Groen, D.; Hoenen, O.; Mizeranschi, A.; Suter, J. L.; Coster, D.; Coveney, P. V.; Dubitzky, W.; Hoekstra, A. G.; Strand, P.; Chopard, B.
2014-01-01
Multiscale simulations model phenomena across natural scales using monolithic or component-based code, running on local or distributed resources. In this work, we investigate the performance of distributed multiscale computing of component-based models, guided by six multiscale applications with different characteristics and from several disciplines. Three modes of distributed multiscale computing are identified: supplementing local dependencies with large-scale resources, load distribution over multiple resources, and load balancing of small- and large-scale resources. We find that the first mode has the apparent benefit of increasing simulation speed, and the second mode can increase simulation speed if local resources are limited. Depending on resource reservation and model coupling topology, the third mode may result in a reduction of resource consumption. PMID:24982258
Sen, Oishik; Davis, Sean; Jacobs, Gustaaf; Udaykumar, H.S.
2015-08-01
The effectiveness of several metamodeling techniques, viz. the Polynomial Stochastic Collocation method, Adaptive Stochastic Collocation method, a Radial Basis Function Neural Network, a Kriging Method and a Dynamic Kriging Method is evaluated. This is done with the express purpose of using metamodels to bridge scales between micro- and macro-scale models in a multi-scale multimaterial simulation. The rate of convergence of the error when used to reconstruct hypersurfaces of known functions is studied. For sufficiently large number of training points, Stochastic Collocation methods generally converge faster than the other metamodeling techniques, while the DKG method converges faster when the number of input points is less than 100 in a two-dimensional parameter space. Because the input points correspond to computationally expensive micro/meso-scale computations, the DKG is favored for bridging scales in a multi-scale solver.
Frequency-domain elastic full-waveform multiscale inversion method based on dual-level parallelism
NASA Astrophysics Data System (ADS)
Li, Yuan-Yuan; Li, Zhen-Chun; Zhang, Kai; Zhang, Xuan
2015-12-01
The complexity of an elastic wavefield increases the nonlinearity of inversion. To some extent, multiscale inversion decreases the nonlinearity of inversion and prevents it from falling into local extremes. A multiscale strategy based on the simultaneous use of frequency groups and layer stripping method based on damped wave field improves the stability of inversion. A dual-level parallel algorithm is then used to decrease the computational cost and improve practicability. The seismic wave modeling of a single frequency and inversion in a frequency group are computed in parallel by multiple nodes based on multifrontal massively parallel sparse direct solver and MPI. Numerical tests using an overthrust model show that the proposed inversion algorithm can effectively improve the stability and accuracy of inversion by selecting the appropriate inversion frequency and damping factor in lowfrequency seismic data.
A multiscale overlapped coupling formulation for large-deformation strain localization
NASA Astrophysics Data System (ADS)
Sun, WaiChing; Mota, Alejandro
2014-09-01
We generalize the multiscale overlapped domain framework to couple multiple rate-independent standard dissipative material models in the finite deformation regime across different length scales. We show that a fully coupled multiscale incremental boundary-value problem can be recast as the stationary point that optimizes the partitioned incremental work of a three-field energy functional. We also establish inf-sup tests to examine the numerical stability issues that arise from enforcing weak compatibility in the three-field formulation. We also devise a new block solver for the domain coupling problem and demonstrate the performance of the formulation with one-dimensional numerical examples. These simulations indicate that it is sufficient to introduce a localization limiter in a confined region of interest to regularize the partial differential equation if loss of ellipticity occurs.
Coupling vs decoupling approaches for PDE/ODE systems modeling intercellular signaling
NASA Astrophysics Data System (ADS)
Carraro, Thomas; Friedmann, Elfriede; Gerecht, Daniel
2016-06-01
We consider PDE/ODE systems for the simulation of intercellular signaling in multicellular environments. The intracellular processes for each cell described here by ODEs determine the long-time dynamics, but the PDE part dominates the solving effort. Thus, it is not clear if commonly used decoupling methods can outperform a coupling approach. Based on a sensitivity analysis, we present a systematic comparison between coupling and decoupling approaches for this class of problems and show numerical results. For biologically relevant configurations of the model, our quantitative study shows that a coupling approach performs much better than a decoupling one.
FRS 1000, an extract of red onion peel, strongly inhibits phosphodiesterase 5A (PDE 5A).
Lines, T C; Ono, M
2006-03-01
As part of our ongoing search for flavonoids that are bioactive in humans, it was determined that FRS 1000, a beverage containing flavonoids extracted from onion peel, showed unexpected improvement of male sexual function. An in vitro enzyme assay clearly showed that FRS 1000 has a strong phosphodiesterase 5A (PDE 5A) inhibitory activity, which is considered to be important for treatment of erectile dysfunction. Detailed assays of each major ingredient indicated that the antioxidative flavonoid quercetin was responsible for the activity. Results also suggested that PDE 5A inhibition is not directly related to the free radical scavenging activity of flavonoids. PMID:16492525
Multiscale modeling for materials design: Molecular square catalysts
NASA Astrophysics Data System (ADS)
Majumder, Debarshi
descriptions of the fluid phase with kinetic Monte Carlo (kMC) simulations of the catalyst domain. A number of catalytic domains, solved using kMC, were placed as patches along the length of the reactor and communicated with the continuum solver using patch dynamics concepts such as lifting, restriction and interpolation. This allowed the resolution of the species' profiles in both axial and radial directions of membrane reactors and monoliths, which is a novel strategy in the multiscale modeling of heterogeneous systems.
Atomistic hybrid DSMC/NEMD method for nonequilibrium multiscale simulations
Gu Kai; Watkins, Charles B. Koplik, Joel
2010-03-01
A multiscale hybrid method for coupling the direct simulation Monte Carlo (DSMC) method to the nonequilibrium molecular dynamics (NEMD) method is introduced. The method addresses Knudsen layer type gas flows within a few mean free paths of an interface or about an object with dimensions of the order of a few mean free paths. It employs the NEMD method to resolve nanoscale phenomena closest to the interface along with coupled DSMC simulation of the remainder of the Knudsen layer. The hybrid DSMC/NEMD method is a particle based algorithm without a buffer zone. It incorporates a new, modified generalized soft sphere (MGSS) molecular collision model to improve the poor computational efficiency of the traditional generalized soft sphere GSS model and to achieve DSMC compatibility with Lennard-Jones NEMD molecular interactions. An equilibrium gas, a Fourier thermal flow, and an oscillatory Couette flow, are simulated to validate the method. The method shows good agreement with Maxwell-Boltzmann theory for the equilibrium system, Chapman-Enskog theory for Fourier flow, and pure DSMC simulations for oscillatory Couette flow. Speedup in CPU time of the hybrid solver is benchmarked against a pure NEMD solver baseline for different system sizes and solver domain partitions. Finally, the hybrid method is applied to investigate interaction of argon gas with solid surface molecules in a parametric study of the influence of wetting effects and solid molecular mass on energy transfer and thermal accommodation coefficients. It is determined that wetting effect strength and solid molecular mass have a significant impact on the energy transfer between gas and solid phases and thermal accommodation coefficient.
The Magnetospheric Multiscale Constellation
NASA Astrophysics Data System (ADS)
Tooley, C. R.; Black, R. K.; Robertson, B. P.; Stone, J. M.; Pope, S. E.; Davis, G. T.
2016-03-01
The Magnetospheric Multiscale (MMS) mission is the fourth mission of the Solar Terrestrial Probe (STP) program of the National Aeronautics and Space Administration (NASA). The MMS mission was launched on March 12, 2015. The MMS mission consists of four identically instrumented spin-stabilized observatories which are flown in formation to perform the first definitive study of magnetic reconnection in space. The MMS mission was presented with numerous technical challenges, including the simultaneous construction and launch of four identical large spacecraft with 100 instruments total, stringent electromagnetic cleanliness requirements, closed-loop precision maneuvering and pointing of spinning flexible spacecraft, on-board GPS based orbit determination far above the GPS constellation, and a flight dynamics design that enables formation flying with separation distances as small as 10 km. This paper describes the overall mission design and presents an overview of the design, testing, and early on-orbit operation of the spacecraft systems and instrument suite.
jShyLU Scalable Hybrid Preconditioner and Solver
2012-09-11
ShyLU is numerical software to solve sparse linear systems of equations. ShyLU uses a hybrid direct-iterative Schur complement method, and may be used either as a preconditioner or as a solver. ShyLU is parallel and optimized for a single compute Solver node. ShyLU will be a package in the Trilinos software framework.
Experiences with linear solvers for oil reservoir simulation problems
Joubert, W.; Janardhan, R.; Biswas, D.; Carey, G.
1996-12-31
This talk will focus on practical experiences with iterative linear solver algorithms used in conjunction with Amoco Production Company`s Falcon oil reservoir simulation code. The goal of this study is to determine the best linear solver algorithms for these types of problems. The results of numerical experiments will be presented.
ERIC Educational Resources Information Center
Jang, Deok-Jin; Park, Soo-Won; Lee, Jin-A; Lee, Changhoon; Chae, Yeon-Su; Park, Hyungju; Kim, Min-Jeong; Choi, Sun-Lim; Lee, Nuribalhae; Kim, Hyoung; Kaang, Bong-Kiun
2010-01-01
Phosphodiesterases (PDEs) are known to play a key role in the compartmentalization of cAMP signaling; however, the molecular mechanisms underlying intracellular localization of different PDE isoforms are not understood. In this study, we have found that each of the supershort, short, and long forms of apPDE4 showed distinct localization in the…
MULTISCALE THERMOHYDROLOGIC MODEL
T.A. Buscheck
2001-12-21
The purpose of the Multiscale Thermohydrologic Model (MSTHM) is to describe the thermohydrologic evolution of the near-field environment (NFE) and engineered barrier system (EBS) throughout the potential high-level nuclear waste repository at Yucca Mountain for a particular engineering design (CRWMS M&O 2000c). The process-level model will provide thermohydrologic (TH) information and data (such as in-drift temperature, relative humidity, liquid saturation, etc.) for use in other technical products. This data is provided throughout the entire repository area as a function of time. The MSTHM couples the Smeared-heat-source Drift-scale Thermal-conduction (SDT), Line-average-heat-source Drift-scale Thermohydrologic (LDTH), Discrete-heat-source Drift-scale Thermal-conduction (DDT), and Smeared-heat-source Mountain-scale Thermal-conduction (SMT) submodels such that the flow of water and water vapor through partially-saturated fractured rock is considered. The MSTHM accounts for 3-D drift-scale and mountain-scale heat flow, repository-scale variability of stratigraphy and infiltration flux, and waste package (WP)-to-WP variability in heat output from WPs. All submodels use the nonisothermal unsaturated-saturated flow and transport (NUFT) simulation code. The MSTHM is implemented in several data-processing steps. The four major steps are: (1) submodel input-file preparation, (2) execution of the four submodel families with the use of the NUFT code, (3) execution of the multiscale thermohydrologic abstraction code (MSTHAC), and (4) binning and post-processing (i.e., graphics preparation) of the output from MSTHAC. Section 6 describes the MSTHM in detail. The objectives of this Analyses and Model Report (AMR) are to investigate near field (NF) and EBS thermohydrologic environments throughout the repository area at various evolution periods, and to provide TH data that may be used in other process model reports.
Shape reanalysis and sensitivities utilizing preconditioned iterative boundary solvers
NASA Technical Reports Server (NTRS)
Guru Prasad, K.; Kane, J. H.
1992-01-01
The computational advantages associated with the utilization of preconditined iterative equation solvers are quantified for the reanalysis of perturbed shapes using continuum structural boundary element analysis (BEA). Both single- and multi-zone three-dimensional problems are examined. Significant reductions in computer time are obtained by making use of previously computed solution vectors and preconditioners in subsequent analyses. The effectiveness of this technique is demonstrated for the computation of shape response sensitivities required in shape optimization. Computer times and accuracies achieved using the preconditioned iterative solvers are compared with those obtained via direct solvers and implicit differentiation of the boundary integral equations. It is concluded that this approach employing preconditioned iterative equation solvers in reanalysis and sensitivity analysis can be competitive with if not superior to those involving direct solvers.
A real-time impurity solver for DMFT
NASA Astrophysics Data System (ADS)
Kim, Hyungwon; Aron, Camille; Han, Jong E.; Kotliar, Gabriel
Dynamical mean-field theory (DMFT) offers a non-perturbative approach to problems with strongly correlated electrons. The method heavily relies on the ability to numerically solve an auxiliary Anderson-type impurity problem. While powerful Matsubara-frequency solvers have been developed over the past two decades to tackle equilibrium situations, the status of real-time impurity solvers that could compete with Matsubara-frequency solvers and be readily generalizable to non-equilibrium situations is still premature. We present a real-time solver which is based on a quantum Master equation description of the dissipative dynamics of the impurity and its exact diagonalization. As a benchmark, we illustrate the strengths of our solver in the context of the equilibrium Mott-insulator transition of the one-band Hubbard model and compare it with iterative perturbation theory (IPT) method. Finally, we discuss its direct application to a nonequilibrium situation.
Parallel solver for trajectory optimization search directions
NASA Technical Reports Server (NTRS)
Psiaki, M. L.; Park, K. H.
1992-01-01
A key algorithmic element of a real-time trajectory optimization hardware/software implementation is presented, the search step solver. This is one piece of an algorithm whose overall goal is to make nonlinear trajectory optimization fast enough to provide real-time commands during guidance of a vehicle such as an aeromaneuvering orbiter or the National Aerospace Plane. Many methods of nonlinear programming require the solution of a quadratic program (QP) at each iteration to determine the search step. In the trajectory optimization case, the QP has a special dynamic programming structure. The algorithm exploits this special structure with a divide- and conquer type of parallel implementation. The algorithm solves a (p.N)-stage problem on N processors in O(p + log2 N) operations. The algorithm yields a factor of 8 speed-up over the fastest known serial algorithm when solving a 1024-stage test problem on 32 processors.
Scalable Adaptive Multilevel Solvers for Multiphysics Problems
Xu, Jinchao
2014-12-01
In this project, we investigated adaptive, parallel, and multilevel methods for numerical modeling of various real-world applications, including Magnetohydrodynamics (MHD), complex fluids, Electromagnetism, Navier-Stokes equations, and reservoir simulation. First, we have designed improved mathematical models and numerical discretizaitons for viscoelastic fluids and MHD. Second, we have derived new a posteriori error estimators and extended the applicability of adaptivity to various problems. Third, we have developed multilevel solvers for solving scalar partial differential equations (PDEs) as well as coupled systems of PDEs, especially on unstructured grids. Moreover, we have integrated the study between adaptive method and multilevel methods, and made significant efforts and advances in adaptive multilevel methods of the multi-physics problems.
Optimising a parallel conjugate gradient solver
Field, M.R.
1996-12-31
This work arises from the introduction of a parallel iterative solver to a large structural analysis finite element code. The code is called FEX and it was developed at Hitachi`s Mechanical Engineering Laboratory. The FEX package can deal with a large range of structural analysis problems using a large number of finite element techniques. FEX can solve either stress or thermal analysis problems of a range of different types from plane stress to a full three-dimensional model. These problems can consist of a number of different materials which can be modelled by a range of material models. The structure being modelled can have the load applied at either a point or a surface, or by a pressure, a centrifugal force or just gravity. Alternatively a thermal load can be applied with a given initial temperature. The displacement of the structure can be constrained by having a fixed boundary or by prescribing the displacement at a boundary.
General purpose nonlinear system solver based on Newton-Krylov method.
2013-12-01
KINSOL is part of a software family called SUNDIALS: SUite of Nonlinear and Differential/Algebraic equation Solvers [1]. KINSOL is a general-purpose nonlinear system solver based on Newton-Krylov and fixed-point solver technologies [2].
Brennenstuhl, Christina; Tanimoto, Naoyuki; Burkard, Markus; Wagner, Rebecca; Bolz, Sylvia; Trifunovic, Dragana; Kabagema-Bilan, Clement; Paquet-Durand, Francois; Beck, Susanne C.; Huber, Gesine; Seeliger, Mathias W.; Ruth, Peter; Wissinger, Bernd; Lukowski, Robert
2015-01-01
Phosphodiesterase-6 (PDE6) is a multisubunit enzyme that plays a key role in the visual transduction cascade in rod and cone photoreceptors. Each type of photoreceptor utilizes discrete catalytic and inhibitory PDE6 subunits to fulfill its physiological tasks, i.e. the degradation of cyclic guanosine-3′,5′-monophosphate at specifically tuned rates and kinetics. Recently, the human PDE6H gene was identified as a novel locus for autosomal recessive (incomplete) color blindness. However, the three different classes of cones were not affected to the same extent. Short wave cone function was more preserved than middle and long wave cone function indicating that some basic regulation of the PDE6 multisubunit enzyme was maintained albeit by a unknown mechanism. To study normal and disease-related functions of cone Pde6h in vivo, we generated Pde6h knock-out (Pde6h−/−) mice. Expression of PDE6H in murine eyes was restricted to both outer segments and synaptic terminals of short and long/middle cone photoreceptors, whereas Pde6h−/− retinae remained PDE6H-negative. Combined in vivo assessment of retinal morphology with histomorphological analyses revealed a normal overall integrity of the retinal organization and an unaltered distribution of the different cone photoreceptor subtypes upon Pde6h ablation. In contrast to human patients, our electroretinographic examinations of Pde6h−/− mice suggest no defects in cone/rod-driven retinal signaling and therefore preserved visual functions. To this end, we were able to demonstrate the presence of rod PDE6G in cones indicating functional substitution of PDE6. The disparities between human and murine phenotypes caused by mutant Pde6h/PDE6H suggest species-to-species differences in the vulnerability of biochemical and neurosensory pathways of the visual signal transduction system. PMID:25739440
Brennenstuhl, Christina; Tanimoto, Naoyuki; Burkard, Markus; Wagner, Rebecca; Bolz, Sylvia; Trifunovic, Dragana; Kabagema-Bilan, Clement; Paquet-Durand, Francois; Beck, Susanne C; Huber, Gesine; Seeliger, Mathias W; Ruth, Peter; Wissinger, Bernd; Lukowski, Robert
2015-04-17
Phosphodiesterase-6 (PDE6) is a multisubunit enzyme that plays a key role in the visual transduction cascade in rod and cone photoreceptors. Each type of photoreceptor utilizes discrete catalytic and inhibitory PDE6 subunits to fulfill its physiological tasks, i.e. the degradation of cyclic guanosine-3',5'-monophosphate at specifically tuned rates and kinetics. Recently, the human PDE6H gene was identified as a novel locus for autosomal recessive (incomplete) color blindness. However, the three different classes of cones were not affected to the same extent. Short wave cone function was more preserved than middle and long wave cone function indicating that some basic regulation of the PDE6 multisubunit enzyme was maintained albeit by a unknown mechanism. To study normal and disease-related functions of cone Pde6h in vivo, we generated Pde6h knock-out (Pde6h(-/-)) mice. Expression of PDE6H in murine eyes was restricted to both outer segments and synaptic terminals of short and long/middle cone photoreceptors, whereas Pde6h(-/-) retinae remained PDE6H-negative. Combined in vivo assessment of retinal morphology with histomorphological analyses revealed a normal overall integrity of the retinal organization and an unaltered distribution of the different cone photoreceptor subtypes upon Pde6h ablation. In contrast to human patients, our electroretinographic examinations of Pde6h(-/-) mice suggest no defects in cone/rod-driven retinal signaling and therefore preserved visual functions. To this end, we were able to demonstrate the presence of rod PDE6G in cones indicating functional substitution of PDE6. The disparities between human and murine phenotypes caused by mutant Pde6h/PDE6H suggest species-to-species differences in the vulnerability of biochemical and neurosensory pathways of the visual signal transduction system. PMID:25739440
NASA Astrophysics Data System (ADS)
Liu, Yan; Shen, Weidong; Tian, Baolin; Mao, De-kang
2015-03-01
We develop a new and more general formula for the construction of two dimensional nodal Riemann solver for a cell-centered Lagrangian scheme developed by Maire and his co-workers which allows us to use general one dimensional Riemann solvers that have intermediate velocity and pressure in the construction. The old formula for the scheme used in the papers of Maire et al. is only a special case of our new formula. We present an entropy discussion, which indicates that the schemes with nodal solvers constructed following the old formula, which can only use the 1D Riemann solvers satisfying our strong entropy condition, are usually numerically very dissipative. To develop numerically less dissipative schemes we introduce a so-called weak entropy condition, and present a one dimensional Riemann solver that satisfies the weak entropy condition but not the strong entropy condition. Analysis shows that the scheme using this 1D solver is numerically less dissipative than the schemes using solvers satisfying the strong condition. Finally, several numerical examples are presented to show that our new formula works well and the scheme using the one dimensional solver satisfying the weak entropy condition improves the accuracy in smooth region, resolution around rarefaction waves and two dimensional symmetry; however it sometimes produces small velocity oscillations and mesh distortions.
Yan, Luchun; Liu, Jiemin; Qu, Chen; Gu, Xingye; Zhao, Xia
2015-01-28
In order to explore the odor interaction of binary odor mixtures, a series of odor intensity evaluation tests were performed using both individual components and binary mixtures of aldehydes. Based on the linear relation between the logarithm of odor activity value and odor intensity of individual substances, the relationship between concentrations of individual constituents and their joint odor intensity was investigated by employing a partial differential equation (PDE) model. The obtained results showed that the binary odor interaction was mainly influenced by the mixing ratio of two constituents, but not the concentration level of an odor sample. Besides, an extended PDE model was also proposed on the basis of the above experiments. Through a series of odor intensity matching tests for several different binary odor mixtures, the extended PDE model was proved effective at odor intensity prediction. Furthermore, odorants of the same chemical group and similar odor type exhibited similar characteristics in the binary odor interaction. The overall results suggested that the PDE model is a more interpretable way of demonstrating the odor interactions of binary odor mixtures.
Choi, Catherine H; Schoenfeld, Brian P; Weisz, Eliana D; Bell, Aaron J; Chambers, Daniel B; Hinchey, Joseph; Choi, Richard J; Hinchey, Paul; Kollaros, Maria; Gertner, Michael J; Ferrick, Neal J; Terlizzi, Allison M; Yohn, Nicole; Koenigsberg, Eric; Liebelt, David A; Zukin, R Suzanne; Woo, Newton H; Tranfaglia, Michael R; Louneva, Natalia; Arnold, Steven E; Siegel, Steven J; Bolduc, Francois V; McDonald, Thomas V; Jongens, Thomas A; McBride, Sean M J
2015-01-01
Fragile X syndrome (FXS) is the leading cause of both intellectual disability and autism resulting from a single gene mutation. Previously, we characterized cognitive impairments and brain structural defects in a Drosophila model of FXS and demonstrated that these impairments were rescued by treatment with metabotropic glutamate receptor (mGluR) antagonists or lithium. A well-documented biochemical defect observed in fly and mouse FXS models and FXS patients is low cAMP levels. cAMP levels can be regulated by mGluR signaling. Herein, we demonstrate PDE-4 inhibition as a therapeutic strategy to ameliorate memory impairments and brain structural defects in the Drosophila model of fragile X. Furthermore, we examine the effects of PDE-4 inhibition by pharmacologic treatment in the fragile X mouse model. We demonstrate that acute inhibition of PDE-4 by pharmacologic treatment in hippocampal slices rescues the enhanced mGluR-dependent LTD phenotype observed in FXS mice. Additionally, we find that chronic treatment of FXS model mice, in adulthood, also restores the level of mGluR-dependent LTD to that observed in wild-type animals. Translating the findings of successful pharmacologic intervention from the Drosophila model into the mouse model of FXS is an important advance, in that this identifies and validates PDE-4 inhibition as potential therapeutic intervention for the treatment of individuals afflicted with FXS.
Discovery of novel potent imidazo[1,2-b]pyridazine PDE10a inhibitors.
Meegalla, Sanath K; Huang, Hui; Illig, Carl R; Parks, Daniel J; Chen, Jinsheng; Lee, Yu-Kai; Wilson, Kenneth J; Patel, Sharmila K; Cheung, Wing S; Lu, Tianbao; Kirchner, Thomas; Askari, Hossein B; Geisler, John; Patch, Raymond J; Gibbs, Alan C; Rady, Brian; Connelly, Margery; Player, Mark R
2016-09-01
Design and optimization of a novel series of imidazo[1,2-b]pyridazine PDE10a inhibitors are described. Compound 31 displays excellent pharmacokinetic properties and was also evaluated as an insulin secretagogue in vitro and in vivo. PMID:27491708
A nonsense mutation in PDE6H causes autosomal-recessive incomplete achromatopsia.
Kohl, Susanne; Coppieters, Frauke; Meire, Françoise; Schaich, Simone; Roosing, Susanne; Brennenstuhl, Christina; Bolz, Sylvia; van Genderen, Maria M; Riemslag, Frans C C; Lukowski, Robert; den Hollander, Anneke I; Cremers, Frans P M; De Baere, Elfride; Hoyng, Carel B; Wissinger, Bernd
2012-09-01
Achromatopsia (ACHM) is an autosomal-recessive retinal dystrophy characterized by color blindness, photophobia, nystagmus, and severely reduced visual acuity. Its prevalence has been estimated to about 1 in 30,000 individuals. Four genes, GNAT2, PDE6C, CNGA3, and CNGB3, have been implicated in ACHM, and all encode functional components of the phototransduction cascade in cone photoreceptors. Applying a functional-candidate-gene approach that focused on screening additional genes involved in this process in a cohort of 611 index cases with ACHM or other cone photoreceptor disorders, we detected a homozygous single base change (c.35C>G) resulting in a nonsense mutation (p.Ser12(∗)) in PDE6H, encoding the inhibitory γ subunit of the cone photoreceptor cyclic guanosine monophosphate phosphodiesterase. The c.35C>G mutation was present in three individuals from two independent families with a clinical diagnosis of incomplete ACHM and preserved short-wavelength-sensitive cone function. Moreover, we show through immunohistochemical colocalization studies in mouse retina that Pde6h is evenly present in all retinal cone photoreceptors, a fact that had been under debate in the past. These findings add PDE6H to the set of genes involved in autosomal-recessive cone disorders and demonstrate the importance of the inhibitory γ subunit in cone phototransduction. PMID:22901948
Discovery of Phosphodiesterase 10A (PDE10A) PET Tracer AMG 580 to Support Clinical Studies.
Hu, Essa; Chen, Ning; Kunz, Roxanne K; Hwang, Dah-Ren; Michelsen, Klaus; Davis, Carl; Ma, Ji; Shi, Jianxia; Lester-Zeiner, Dianna; Hungate, Randall; Treanor, James; Chen, Hang; Allen, Jennifer R
2016-07-14
We report the discovery of PDE10A PET tracer AMG 580 developed to support proof of concept studies with PDE10A inhibitors in the clinic. To find a tracer with higher binding potential (BPND) in NHP than our previously reported tracer 1, we implemented a surface plasmon resonance assay to measure the binding off-rate to identify candidates with slower washout rate in vivo. Five candidates (2-6) from two structurally distinct scaffolds were identified that possessed both the in vitro characteristics that would favor central penetration and the structural features necessary for PET isotope radiolabeling. Two cinnolines (2, 3) and one keto-benzimidazole (5) exhibited PDE10A target specificity and brain uptake comparable to or better than 1 in the in vivo LC-MS/MS kinetics distribution study in SD rats. In NHP PET imaging study, [(18)F]-5 produced a significantly improved BPND of 3.1 and was nominated as PDE10A PET tracer clinical candidate for further studies. PMID:27437084
Ginting, Victor
2014-03-15
it was demonstrated that a posteriori analyses in general and in particular one that uses adjoint methods can accurately and efficiently compute numerical error estimates and sensitivity for critical Quantities of Interest (QoIs) that depend on a large number of parameters. Activities include: analysis and implementation of several time integration techniques for solving system of ODEs as typically obtained from spatial discretization of PDE systems; multirate integration methods for ordinary differential equations; formulation and analysis of an iterative multi-discretization Galerkin finite element method for multi-scale reaction-diffusion equations; investigation of an inexpensive postprocessing technique to estimate the error of finite element solution of the second-order quasi-linear elliptic problems measured in some global metrics; investigation of an application of the residual-based a posteriori error estimates to symmetric interior penalty discontinuous Galerkin method for solving a class of second order quasi-linear elliptic problems; a posteriori analysis of explicit time integrations for system of linear ordinary differential equations; derivation of accurate a posteriori goal oriented error estimates for a user-defined quantity of interest for two classes of first and second order IMEX schemes for advection-diffusion-reaction problems; Postprocessing finite element solution; and A Bayesian Framework for Uncertain Quantification of Porous Media Flows.
Comparison of open-source linear programming solvers.
Gearhart, Jared Lee; Adair, Kristin Lynn; Durfee, Justin David.; Jones, Katherine A.; Martin, Nathaniel; Detry, Richard Joseph
2013-10-01
When developing linear programming models, issues such as budget limitations, customer requirements, or licensing may preclude the use of commercial linear programming solvers. In such cases, one option is to use an open-source linear programming solver. A survey of linear programming tools was conducted to identify potential open-source solvers. From this survey, four open-source solvers were tested using a collection of linear programming test problems and the results were compared to IBM ILOG CPLEX Optimizer (CPLEX) [1], an industry standard. The solvers considered were: COIN-OR Linear Programming (CLP) [2], [3], GNU Linear Programming Kit (GLPK) [4], lp_solve [5] and Modular In-core Nonlinear Optimization System (MINOS) [6]. As no open-source solver outperforms CPLEX, this study demonstrates the power of commercial linear programming software. CLP was found to be the top performing open-source solver considered in terms of capability and speed. GLPK also performed well but cannot match the speed of CLP or CPLEX. lp_solve and MINOS were considerably slower and encountered issues when solving several test problems.
De Novo Mutations in PDE10A Cause Childhood-Onset Chorea with Bilateral Striatal Lesions.
Mencacci, Niccolò E; Kamsteeg, Erik-Jan; Nakashima, Kosuke; R'Bibo, Lea; Lynch, David S; Balint, Bettina; Willemsen, Michèl A A P; Adams, Matthew E; Wiethoff, Sarah; Suzuki, Kazunori; Davies, Ceri H; Ng, Joanne; Meyer, Esther; Veneziano, Liana; Giunti, Paola; Hughes, Deborah; Raymond, F Lucy; Carecchio, Miryam; Zorzi, Giovanna; Nardocci, Nardo; Barzaghi, Chiara; Garavaglia, Barbara; Salpietro, Vincenzo; Hardy, John; Pittman, Alan M; Houlden, Henry; Kurian, Manju A; Kimura, Haruhide; Vissers, Lisenka E L M; Wood, Nicholas W; Bhatia, Kailash P
2016-04-01
Chorea is a hyperkinetic movement disorder resulting from dysfunction of striatal medium spiny neurons (MSNs), which form the main output projections from the basal ganglia. Here, we used whole-exome sequencing to unravel the underlying genetic cause in three unrelated individuals with a very similar and unique clinical presentation of childhood-onset chorea and characteristic brain MRI showing symmetrical bilateral striatal lesions. All individuals were identified to carry a de novo heterozygous mutation in PDE10A (c.898T>C [p.Phe300Leu] in two individuals and c.1000T>C [p.Phe334Leu] in one individual), encoding a phosphodiesterase highly and selectively present in MSNs. PDE10A contributes to the regulation of the intracellular levels of cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP). Both substitutions affect highly conserved amino acids located in the regulatory GAF-B domain, which, by binding to cAMP, stimulates the activity of the PDE10A catalytic domain. In silico modeling showed that the altered residues are located deep in the binding pocket, where they are likely to alter cAMP binding properties. In vitro functional studies showed that neither substitution affects the basal PDE10A activity, but they severely disrupt the stimulatory effect mediated by cAMP binding to the GAF-B domain. The identification of PDE10A mutations as a cause of chorea further motivates the study of cAMP signaling in MSNs and highlights the crucial role of striatal cAMP signaling in the regulation of basal ganglia circuitry. Pharmacological modulation of this pathway could offer promising etiologically targeted treatments for chorea and other hyperkinetic movement disorders. PMID:27058447
Exome sequencing identifies PDE4D mutations as another cause of acrodysostosis.
Michot, Caroline; Le Goff, Carine; Goldenberg, Alice; Abhyankar, Avinash; Klein, Céline; Kinning, Esther; Guerrot, Anne-Marie; Flahaut, Philippe; Duncombe, Alice; Baujat, Genevieve; Lyonnet, Stanislas; Thalassinos, Caroline; Nitschke, Patrick; Casanova, Jean-Laurent; Le Merrer, Martine; Munnich, Arnold; Cormier-Daire, Valérie
2012-04-01
Acrodysostosis is a rare autosomal-dominant condition characterized by facial dysostosis, severe brachydactyly with cone-shaped epiphyses, and short stature. Moderate intellectual disability and resistance to multiple hormones might also be present. Recently, a recurrent mutation (c.1102C>T [p.Arg368*]) in PRKAR1A has been identified in three individuals with acrodysostosis and resistance to multiple hormones. After studying ten unrelated acrodysostosis cases, we report here de novo PRKAR1A mutations in five out of the ten individuals (we found c.1102C>T [p.Arg368(∗)] in four of the ten and c.1117T>C [p.Tyr373His] in one of the ten). We performed exome sequencing in two of the five remaining individuals and selected phosphodiesterase 4D (PDE4D) as a candidate gene. PDE4D encodes a class IV cyclic AMP (cAMP)-specific phosphodiesterase that regulates cAMP concentration. Exome analysis detected heterozygous PDE4D mutations (c.673C>A [p.Pro225Thr] and c.677T>C [p.Phe226Ser]) in these two individuals. Screening of PDE4D identified heterozygous mutations (c.568T>G [p.Ser190Ala] and c.1759A>C [p.Thr587Pro]) in two additional acrodysostosis cases. These mutations occurred de novo in all four cases. The four individuals with PDE4D mutations shared common clinical features, namely characteristic midface and nasal hypoplasia and moderate intellectual disability. Metabolic screening was normal in three of these four individuals. However, resistance to parathyroid hormone and thyrotropin was consistently observed in the five cases with PRKAR1A mutations. Finally, our study further supports the key role of the cAMP signaling pathway in skeletogenesis. PMID:22464250
The PDE4 inhibitor roflumilast improves memory in rodents at non-emetic doses.
Vanmierlo, Tim; Creemers, Pim; Akkerman, Sven; van Duinen, Marlies; Sambeth, Anke; De Vry, Jochen; Uz, Tolga; Blokland, Arjan; Prickaerts, Jos
2016-04-15
Enhancement of central availability of the second messenger cAMP is a promising approach to improve cognitive function. Pharmacological inhibition of phosphodiesterase type 4 (PDE4), a group of cAMP hydrolyzing enzymes in the brain, has been shown to improve cognitive performances in rodents and monkeys. However, inhibition of PDE4 is generally associated with severe emetic side-effects. Roflumilast, an FDA-approved PDE4 inhibitor for treatment of chronic obstructive pulmonary disease (COPD), is yielding only mild emetic side effects. In the present study we investigate the potential of roflumilast as a cognition enhancer and to determine the potential coinciding emetic response in comparison to rolipram, a classic PDE4 inhibitor with pronounced emetic effects. Cognition enhancement was evaluated in mice and it was found that both roflumilast and rolipram enhanced memory in an object location task (0.03mg/kg), whereas only roflumilast was effective in a spatial Y-maze (0.1mg/kg). Emetic potential was measured using competition of PDE4 inhibition for α2-adrenergic receptor antagonism in which recovery from xylazine/ketamine-mediated anesthesia is used as a surrogate marker. While rolipram displayed emetic properties at a dose 10 times the memory-enhancing dose, roflumilast only showed increased emetic-like properties at a dose 100 times the memory-enhancing dose. Moreover, combining sub-efficacious doses of the approved cognition-enhancer donepezil and roflumilast, which did not improve memory when given alone, fully restored object recognition memory deficit in rats induced by the muscarinic receptor antagonist scopolamine. These findings suggest that roflumilast offers a more favorable window for treatment of cognitive deficits compared to rolipram.
A non-conforming 3D spherical harmonic transport solver
Van Criekingen, S.
2006-07-01
A new 3D transport solver for the time-independent Boltzmann transport equation has been developed. This solver is based on the second-order even-parity form of the transport equation. The angular discretization is performed through the expansion of the angular neutron flux in spherical harmonics (PN method). The novelty of this solver is the use of non-conforming finite elements for the spatial discretization. Such elements lead to a discontinuous flux approximation. This interface continuity requirement relaxation property is shared with mixed-dual formulations such as the ones based on Raviart-Thomas finite elements. Encouraging numerical results are presented. (authors)
Multi-GPU kinetic solvers using MPI and CUDA
NASA Astrophysics Data System (ADS)
Zabelok, Sergey; Arslanbekov, Robert; Kolobov, Vladimir
2014-12-01
This paper describes recent progress towards porting a Unified Flow Solver (UFS) to heterogeneous parallel computing. The main challenge of porting UFS to graphics processing units (GPUs) comes from the dynamically adapted mesh, which causes irregular data access. We describe the implementation of CUDA kernels for three modules in UFS: the direct Boltzmann solver using discrete velocity method (DVM), the DSMC module, and the Lattice Boltzmann Method (LBM) solver, all using octree Cartesian mesh with adaptive Mesh Refinement (AMR). Double digit speedup on single GPU and good scaling for multi-GPU has been demonstrated.
The Magnetospheric Multiscale Magnetometers
NASA Astrophysics Data System (ADS)
Russell, C. T.; Anderson, B. J.; Baumjohann, W.; Bromund, K. R.; Dearborn, D.; Fischer, D.; Le, G.; Leinweber, H. K.; Leneman, D.; Magnes, W.; Means, J. D.; Moldwin, M. B.; Nakamura, R.; Pierce, D.; Plaschke, F.; Rowe, K. M.; Slavin, J. A.; Strangeway, R. J.; Torbert, R.; Hagen, C.; Jernej, I.; Valavanoglou, A.; Richter, I.
2016-03-01
The success of the Magnetospheric Multiscale mission depends on the accurate measurement of the magnetic field on all four spacecraft. To ensure this success, two independently designed and built fluxgate magnetometers were developed, avoiding single-point failures. The magnetometers were dubbed the digital fluxgate (DFG), which uses an ASIC implementation and was supplied by the Space Research Institute of the Austrian Academy of Sciences and the analogue magnetometer (AFG) with a more traditional circuit board design supplied by the University of California, Los Angeles. A stringent magnetic cleanliness program was executed under the supervision of the Johns Hopkins University's Applied Physics Laboratory. To achieve mission objectives, the calibration determined on the ground will be refined in space to ensure all eight magnetometers are precisely inter-calibrated. Near real-time data plays a key role in the transmission of high-resolution observations stored on board so rapid processing of the low-resolution data is required. This article describes these instruments, the magnetic cleanliness program, and the instrument pre-launch calibrations, the planned in-flight calibration program, and the information flow that provides the data on the rapid time scale needed for mission success.
Reeuwijk, N M; Venhuis, B J; de Kaste, D; Hoogenboom, L A P; Rietjens, I M C M; Martena, M J
2013-01-01
Herbal food supplements, claiming to enhance sexual potency, may contain deliberately added active pharmacological ingredients (APIs) that can be used for the treatment of erectile dysfunction (ED). The aim of this study was to determine whether herbal food supplements on the Dutch market indeed contain APIs that inhibit phosphodiesterase type 5 (PDE-5) inhibitors, such as sildenafil and analogous PDE-5 inhibitors. Herbal food supplements intended to enhance sexual potency (n = 71), and two soft drinks, were sampled from 2003 up to and including 2012. In 23 herbal supplements, nine different PDE-5 inhibitors were identified; in a few cases (n = 3), more than one inhibitor was indentified. The presence of these APIs was however not stated on the label. The concentrations of PDE-5 inhibitors per dose unit were analysed. Furthermore, the potential pharmacologically active properties of the detected PDE-5 inhibitors were estimated by using data from the scientific and patent literature regarding (1) in vitro PDE-5 activity, (2) reported effective doses of registered drugs with PDE-5 inhibitor activity and (3) similarity to other structural analogues. It was concluded that 18 of the 23 herbal food supplements, when used as recommended, would have significant pharmacological effects due to added APIs. Adequate use of existing regulation and control measures seems necessary to protect consumers against the adverse effects of these products.
Kim, S-C; Lee, Y-S; Seo, K-K; Jung, G-W; Kim, T-H
2014-01-01
This study was aimed to identify characteristics of ED patients who discontinued PDE5i despite successful intercourse. Data were collected using a questionnaire from 34 urologic clinics regardless of the effect (success or failure) of PDE5i treatment by visiting the clinics (717), e-mail (64) or post (101) for 882 ED patients who had previously taken any kind of PDE5i on demand four or more times. Discontinuation of PDE5i was defined if the patient had never taken PDE5i for the previous 1 year despite successful intercourse. Of the 882 patients, 485 were included in the final analysis. Difference in the socio-demographic, ED- and partner-related data between the continuation and discontinuation group and factors influencing discontinuation of the PDE5i were analyzed. Among 485 respondents (mean age, 53.6), 116 (23.9%) had discontinued PDE5i use despite successful intercourse. Most common reasons for the discontinuation were ‘reluctant medication-dependent intercourse' (31.0%), ‘spontaneous recovery of erectile function without further treatment' (30.2%), and ‘high cost' (26.7%). In multiple logistic regression analysis, independent factors influencing discontinuation of the drug were cause of ED (psychogenic), short duration of ED, low education (⩽ middle school), and religion (Catholic). In partner-related compliance, only partner's religion (Catholic) was a significant factor. PMID:24305610
Reeuwijk, N M; Venhuis, B J; de Kaste, D; Hoogenboom, L A P; Rietjens, I M C M; Martena, M J
2013-01-01
Herbal food supplements, claiming to enhance sexual potency, may contain deliberately added active pharmacological ingredients (APIs) that can be used for the treatment of erectile dysfunction (ED). The aim of this study was to determine whether herbal food supplements on the Dutch market indeed contain APIs that inhibit phosphodiesterase type 5 (PDE-5) inhibitors, such as sildenafil and analogous PDE-5 inhibitors. Herbal food supplements intended to enhance sexual potency (n = 71), and two soft drinks, were sampled from 2003 up to and including 2012. In 23 herbal supplements, nine different PDE-5 inhibitors were identified; in a few cases (n = 3), more than one inhibitor was indentified. The presence of these APIs was however not stated on the label. The concentrations of PDE-5 inhibitors per dose unit were analysed. Furthermore, the potential pharmacologically active properties of the detected PDE-5 inhibitors were estimated by using data from the scientific and patent literature regarding (1) in vitro PDE-5 activity, (2) reported effective doses of registered drugs with PDE-5 inhibitor activity and (3) similarity to other structural analogues. It was concluded that 18 of the 23 herbal food supplements, when used as recommended, would have significant pharmacological effects due to added APIs. Adequate use of existing regulation and control measures seems necessary to protect consumers against the adverse effects of these products. PMID:24261938
Kim, S-C; Lee, Y-S; Seo, K-K; Jung, G-W; Kim, T-H
2014-01-01
This study was aimed to identify characteristics of ED patients who discontinued PDE5i despite successful intercourse. Data were collected using a questionnaire from 34 urologic clinics regardless of the effect (success or failure) of PDE5i treatment by visiting the clinics (717), e-mail (64) or post (101) for 882 ED patients who had previously taken any kind of PDE5i on demand four or more times. Discontinuation of PDE5i was defined if the patient had never taken PDE5i for the previous 1 year despite successful intercourse. Of the 882 patients, 485 were included in the final analysis. Difference in the socio-demographic, ED- and partner-related data between the continuation and discontinuation group and factors influencing discontinuation of the PDE5i were analyzed. Among 485 respondents (mean age, 53.6), 116 (23.9%) had discontinued PDE5i use despite successful intercourse. Most common reasons for the discontinuation were 'reluctant medication-dependent intercourse' (31.0%), 'spontaneous recovery of erectile function without further treatment' (30.2%), and 'high cost' (26.7%). In multiple logistic regression analysis, independent factors influencing discontinuation of the drug were cause of ED (psychogenic), short duration of ED, low education (⩽ middle school), and religion (Catholic). In partner-related compliance, only partner's religion (Catholic) was a significant factor. PMID:24305610
Gobejishvili, Leila; Barve, Shirish; Breitkopf-Heinlein, Katja; Li, Yan; Zhang, JingWen; Avila, Diana V; Dooley, Steven; McClain, Craig J
2013-10-01
Anti-inflammatory and antifibrotic effects of the broad spectrum phosphodiesterase (PDE) inhibitor pentoxifylline have suggested an important role for cyclic nucleotides in the pathogenesis of hepatic fibrosis; however, studies examining the role of specific PDEs are lacking. Endotoxemia and Toll-like receptor 4 (TLR4)-mediated inflammatory and profibrotic signaling play a major role in the development of hepatic fibrosis. Because cAMP-specific PDE4 critically regulates lipopolysaccharide (LPS)-TLR4-induced inflammatory cytokine expression, its pathogenic role in bile duct ligation-induced hepatic injury and fibrogenesis in Sprague-Dawley rats was examined. Initiation of cholestatic liver injury and fibrosis was accompanied by a significant induction of PDE4A, B, and D expression and activity. Treatment with the PDE4-specific inhibitor rolipram significantly decreased liver PDE4 activity, hepatic inflammatory and profibrotic cytokine expression, injury, and fibrosis. At the cellular level, in relevance to endotoxemia and inflammatory cytokine production, PDE4B was observed to play a major regulatory role in the LPS-inducible tumor necrosis factor (TNF) production by isolated Kupffer cells. Moreover, PDE4 expression was also involved in the in vitro activation and transdifferentiation of isolated hepatic stellate cells (HSCs). Particularly, PDE4A, B, and D upregulation preceded induction of the HSC activation marker α-smooth muscle actin (α-SMA). In vitro treatment of HSCs with rolipram effectively attenuated α-SMA, collagen expression, and accompanying morphologic changes. Overall, these data strongly suggest that upregulation of PDE4 expression during cholestatic liver injury plays a potential pathogenic role in the development of inflammation, injury, and fibrosis. PMID:23887098
Soler, Fernando; Fernández-Belda, Francisco; Pérez-Schindler, Joaquín; Handschin, Christoph; Fuente, Teodomiro
2015-01-01
The important regulator of cardiac function, cAMP, is hydrolyzed by different cyclic nucleotide phosphodiesterases (PDEs), whose expression and activity are not uniform throughout the heart. Of these enzymes, PDE2 shapes β1 adrenoceptor-dependent cardiac cAMP signaling, both in the right and left ventricular myocardium, but its role in regulating β2 adrenoceptor-mediated responses is less well known. Our aim was to investigate possible differences in PDE2 transcription and activity between right (RV) and left (LV) rat ventricular myocardium, as well as its role in regulating β2 adrenoceptor effects. The free walls of the RV and the LV were obtained from Sprague–Dawley rat hearts. Relative mRNA for PDE2 (quantified by qPCR) and PDE2 activity (evaluated by a colorimetric procedure and using the PDE2 inhibitor EHNA) were determined in RV and LV. Also, β2 adrenoceptor-mediated effects (β2-adrenoceptor agonist salbutamol + β1 adrenoceptor antagonist CGP-20712A) on contractility and cAMP concentrations, in the absence or presence of EHNA, were studied in the RV and LV. PDE2 transcript levels were less abundant in RV than in LV and the contribution of PDE2 to the total PDE activity was around 25% lower in the microsomal fraction of the RV compared with the LV. β2 adrenoceptor activation increased inotropy and cAMP levels in the LV when measured in the presence of EHNA, but no such effects were observed in the RV, either in the presence or absence of EHNA. These results indicate interventricular differences in PDE2 transcript and activity levels, which may distinctly regulate β2 adrenoceptor-mediated contractility and cAMP concentrations in the RV and in the LV of the rat heart. PMID:25432985
Hunter, Roger W; Mackintosh, Carol; Hers, Ingeborg
2009-05-01
The elevation of [cAMP](i) is an important mechanism of platelet inhibition and is regulated by the opposing activity of adenylyl cyclase and phosphodiesterase (PDE). In this study, we demonstrate that a variety of platelet agonists, including thrombin, significantly enhance the activity of PDE3A in a phosphorylation-dependent manner. Stimulation of platelets with the PAR-1 agonist SFLLRN resulted in rapid and transient phosphorylation of PDE3A on Ser(312), Ser(428), Ser(438), Ser(465), and Ser(492), in parallel with the PKC (protein kinase C) substrate, pleckstrin. Furthermore, phosphorylation and activation of PDE3A required the activation of PKC, but not of PI3K/PKB, mTOR/p70S6K, or ERK/RSK. Activation of PKC by phorbol esters also resulted in phosphorylation of the same PDE3A sites in a PKC-dependent, PKB-independent manner. This was further supported by the finding that IGF-1, which strongly activates PI3K/PKB, but not PKC, did not regulate PDE3A. Platelet activation also led to a PKC-dependent association between PDE3A and 14-3-3 proteins. In contrast, cAMP-elevating agents such as PGE(1) and forskolin-induced phosphorylation of Ser(312) and increased PDE3A activity, but did not stimulate 14-3-3 binding. Finally, complete antagonism of PGE(1)-evoked cAMP accumulation by thrombin required both G(i) and PKC activation. Together, these results demonstrate that platelet activation stimulates PKC-dependent phosphorylation of PDE3A on Ser(312), Ser(428), Ser(438), Ser(465), and Ser(492) leading to a subsequent increase in cAMP hydrolysis and 14-3-3 binding. PMID:19261611
Houslay, Miles D; Adams, David R
2003-01-01
cAMP is a second messenger that controls many key cellular functions. The only way to inactivate cAMP is to degrade it through the action of cAMP phosphodiesterases (PDEs). PDEs are thus poised to play a key regulatory role. PDE4 cAMP-specific phosphodiesterases appear to have specific functions with selective inhibitors serving as potent anti-inflammatory agents. The recent elucidation of the structure of the PDE4 catalytic unit allows for molecular insight into the mode of catalysis as well as substrate and inhibitor selectivity. The four PDE4 genes encode over 16 isoforms, each of which is characterized by a unique N-terminal region. PDE4 isoforms play a pivotal role in controlling functionally and spatially distinct pools of cAMP by virtue of their unique intracellular targeting. Targeting occurs by association with proteins, such as arrestins, SRC family tyrosyl kinases, A-kinase anchoring proteins ('AKAPs') and receptor for activated C kinase 1 ('RACK1'), and, in the case of isoform PDE4A1, by a specific interaction (TAPAS-1) with phosphatidic acid. PDE4 isoforms are 'designed' to be regulated by extracellular-signal-related protein kinase (ERK), which binds to anchor sites on the PDE4 catalytic domain that it phosphorylates. The upstream conserved region 1 (UCR1) and 2 (UCR2) modules that abut the PDE4 catalytic unit confer regulatory functions by orchestrating the functional outcome of phosphorylation by cAMP-dependent protein kinase ('PKA') and ERK. PDE4 enzymes stand at a crossroads that allows them to integrate various signalling pathways with that of cAMP in spatially distinct compartments. PMID:12444918
Generic task problem solvers in Soar
NASA Technical Reports Server (NTRS)
Johnson, Todd R.; Smith, Jack W., Jr.; Chandrasekaran, B.
1989-01-01
Two trends can be discerned in research in problem solving architectures in the last few years. On one hand, interest in task-specific architectures has grown, wherein types of problems of general utility are identified, and special architectures that support the development of problem solving systems for those types of problems are proposed. These architectures help in the acquisition and specification of knowledge by providing inference methods that are appropriate for the type of problem. However, knowledge based systems which use only one type of problem solving method are very brittle, and adding more types of methods requires a principled approach to integrating them in a flexible way. Contrasting with this trend is the proposal for a flexible, general architecture contained in the work on Soar. Soar has features which make it attractive for flexible use of all potentially relevant knowledge or methods. But as the theory Soar does not make commitments to specific types of problem solvers or provide guidance for their construction. It was investigated how task-specific architectures can be constructed in Soar to retain as many of the advantages as possible of both approaches. Examples were used from the Generic Task approach for building knowledge based systems. Though this approach was developed and applied for a number of problems, the ideas are applicable to other task-specific approaches as well.
Elliptic Solvers for Adaptive Mesh Refinement Grids
Quinlan, D.J.; Dendy, J.E., Jr.; Shapira, Y.
1999-06-03
We are developing multigrid methods that will efficiently solve elliptic problems with anisotropic and discontinuous coefficients on adaptive grids. The final product will be a library that provides for the simplified solution of such problems. This library will directly benefit the efforts of other Laboratory groups. The focus of this work is research on serial and parallel elliptic algorithms and the inclusion of our black-box multigrid techniques into this new setting. The approach applies the Los Alamos object-oriented class libraries that greatly simplify the development of serial and parallel adaptive mesh refinement applications. In the final year of this LDRD, we focused on putting the software together; in particular we completed the final AMR++ library, we wrote tutorials and manuals, and we built example applications. We implemented the Fast Adaptive Composite Grid method as the principal elliptic solver. We presented results at the Overset Grid Conference and other more AMR specific conferences. We worked on optimization of serial and parallel performance and published several papers on the details of this work. Performance remains an important issue and is the subject of continuing research work.
NASA Technical Reports Server (NTRS)
Raju, Manthena S.
1998-01-01
Sprays occur in a wide variety of industrial and power applications and in the processing of materials. A liquid spray is a phase flow with a gas as the continuous phase and a liquid as the dispersed phase (in the form of droplets or ligaments). Interactions between the two phases, which are coupled through exchanges of mass, momentum, and energy, can occur in different ways at different times and locations involving various thermal, mass, and fluid dynamic factors. An understanding of the flow, combustion, and thermal properties of a rapidly vaporizing spray requires careful modeling of the rate-controlling processes associated with the spray's turbulent transport, mixing, chemical kinetics, evaporation, and spreading rates, as well as other phenomena. In an attempt to advance the state-of-the-art in multidimensional numerical methods, we at the NASA Lewis Research Center extended our previous work on sprays to unstructured grids and parallel computing. LSPRAY, which was developed by M.S. Raju of Nyma, Inc., is designed to be massively parallel and could easily be coupled with any existing gas-phase flow and/or Monte Carlo probability density function (PDF) solver. The LSPRAY solver accommodates the use of an unstructured mesh with mixed triangular, quadrilateral, and/or tetrahedral elements in the gas-phase solvers. It is used specifically for fuel sprays within gas turbine combustors, but it has many other uses. The spray model used in LSPRAY provided favorable results when applied to stratified-charge rotary combustion (Wankel) engines and several other confined and unconfined spray flames. The source code will be available with the National Combustion Code (NCC) as a complete package.
Sugiyama, Takuji; Narukawa, Yuji; Shibata, Shunsuke; Masui, Ryo; Kiuchia, Fumiyuki
2016-06-01
The MeOH extract of agarwood showed inhibitory activity against phosphodiesterase (PDE) 3A. Fractionation of the extract led to the isolation of two new 2-(2-phenylethyl)chromones, 6,8-dihydroxy-2-[2-(4'-methoxyphenyl)ethyl]chromone (6), and 6,7-dihydroxy-2-(2-phenylethyl)chromone (8), together with six known compounds. All isolated compounds were tested for their PDE 3A inhibitory activity using fluorescence polarization method. Compound 7 showed PDE 3A inhibitory activity with IC50 of 4.83 μM.
Sopko, Nikolai A.; Matsui, Hotaka; Hannan, Johanna L.; Berkowitz, Dan; Champion, Hunter C.; Hsu, Lewis L.; Musicki, Biljana; Burnett, Arthur L.; Bivalacqua, Trinity J.
2015-01-01
Introduction Recent research suggests that priapism in Sickle Cell Disease (SCD) is due to dysregulation of penile erection homeostasis including alteration of nitric oxide synthase (NOS) and phosphodiesterase 5 (PDE5) activities by excessive levels of reactive oxygen species (ROS) released during hemolysis. It is unknown if sub-acute exposure to hemolysis is sufficient or if chronic reconditioning of erectile tissues is required for perturbation of homeostatic pathways and whether PDE5 inhibitor (PDE5I) treatment can restore erectile homeostasis in the sub-acute setting. Aims To investigate the effects of sub-acute hemolysis (3 month exposure) on priapism and NO pathway regulation. Methods Mice underwent bone marrow transplantation with either SCD (BM-SS) or wild type (WT) bone marrow. BM-SS mice were treated with sildenafil 100mg/kg/day. We measured intracavernous pressure (ICP) measurements with or without cavernosal nerve stimulation (CNS) following bone marrow transplantation to assess for priapism. Main Outcome Measures ICP and frequency of erections were assessed. Penile tissues were analyzed for NOS, PKG, PDE5, and ROS activities. Results BM-SS mice demonstrated a priapism phenotype. PDE5I treatment reduced the frequency of erections in BM-SS mice (1.7 ± 1.1 vs. 5.5 ± 2.8 erections/hour, p<0.05). Penile tissues from BM-SS mice demonstrated decreased NOS, PKG, PDE5 and elevated ROS activities compared to that of control mice. PDE5I treatment increased NOS (11.6 ± 1.3% vs. 7.8 ± 2.3%, p<0.05) and PDE5 (76.3 ± 9.8% vs. 52.3 ± 11.1%, p<0.05) activities and decreased ROS activity (137.8 ± 12.1% vs. 199.1 ± 11.3%, p<0.05) compared to non-PDE5I treated BM-SS mice. PKG activity was increased beyond control levels with PDE5I treatment (158.4 ± 10.3%, p<0.05). Conclusion Short-term hemolysis is sufficient to establish a priapism phenotype and results in loss of erectile function. PDE5I treatment ameliorates priapism, in part, due to restored NO balance with
Performance of NASA Equation Solvers on Computational Mechanics Applications
NASA Technical Reports Server (NTRS)
Storaasli, Olaf O.
1996-01-01
This paper describes the performance of a new family of NASA-developed equation solvers used for large-scale (i.e. 551,705 equations) structural analysis. To minimize computer time and memory, the solvers are divided by application and matrix characteristics (sparse/dense, real/complex, symmetric/nonsymmetric, size: in-core/out of core) and exploit the hardware features of current and future computers. In this paper, the equation solvers, which are written in FORTRAN, and are therefore easily transportable, are shown to be faster than specialized computer library routines utilizing assembly code. Twenty NASA structural benchmark models with NASA solver timings reside on World Wide Web with a challenge to beat them.
Two-dimensional time dependent Riemann solvers for neutron transport
Brunner, Thomas A. . E-mail: tabrunn@sandia.gov; Holloway, James Paul
2005-11-20
A two-dimensional Riemann solver is developed for the spherical harmonics approximation to the time dependent neutron transport equation. The eigenstructure of the resulting equations is explored, giving insight into both the spherical harmonics approximation and the Riemann solver. The classic Roe-type Riemann solver used here was developed for one-dimensional problems, but can be used in multidimensional problems by treating each face of a two-dimensional computation cell in a locally one-dimensional way. Several test problems are used to explore the capabilities of both the Riemann solver and the spherical harmonics approximation. The numerical solution for a simple line source problem is compared to the analytic solution to both the P{sub 1} equation and the full transport solution. A lattice problem is used to test the method on a more challenging problem.
Parallel iterative solvers and preconditioners using approximate hierarchical methods
Grama, A.; Kumar, V.; Sameh, A.
1996-12-31
In this paper, we report results of the performance, convergence, and accuracy of a parallel GMRES solver for Boundary Element Methods. The solver uses a hierarchical approximate matrix-vector product based on a hybrid Barnes-Hut / Fast Multipole Method. We study the impact of various accuracy parameters on the convergence and show that with minimal loss in accuracy, our solver yields significant speedups. We demonstrate the excellent parallel efficiency and scalability of our solver. The combined speedups from approximation and parallelism represent an improvement of several orders in solution time. We also develop fast and paralellizable preconditioners for this problem. We report on the performance of an inner-outer scheme and a preconditioner based on truncated Green`s function. Experimental results on a 256 processor Cray T3D are presented.
Multiscale Thermohydrologic Model
T. Buscheck
2004-10-12
The purpose of the multiscale thermohydrologic model (MSTHM) is to predict the possible range of thermal-hydrologic conditions, resulting from uncertainty and variability, in the repository emplacement drifts, including the invert, and in the adjoining host rock for the repository at Yucca Mountain. Thus, the goal is to predict the range of possible thermal-hydrologic conditions across the repository; this is quite different from predicting a single expected thermal-hydrologic response. The MSTHM calculates the following thermal-hydrologic parameters: temperature, relative humidity, liquid-phase saturation, evaporation rate, air-mass fraction, gas-phase pressure, capillary pressure, and liquid- and gas-phase fluxes (Table 1-1). These thermal-hydrologic parameters are required to support ''Total System Performance Assessment (TSPA) Model/Analysis for the License Application'' (BSC 2004 [DIRS 168504]). The thermal-hydrologic parameters are determined as a function of position along each of the emplacement drifts and as a function of waste package type. These parameters are determined at various reference locations within the emplacement drifts, including the waste package and drip-shield surfaces and in the invert. The parameters are also determined at various defined locations in the adjoining host rock. The MSTHM uses data obtained from the data tracking numbers (DTNs) listed in Table 4.1-1. The majority of those DTNs were generated from the following analyses and model reports: (1) ''UZ Flow Model and Submodels'' (BSC 2004 [DIRS 169861]); (2) ''Development of Numerical Grids for UZ Flow and Transport Modeling'' (BSC 2004); (3) ''Calibrated Properties Model'' (BSC 2004 [DIRS 169857]); (4) ''Thermal Conductivity of the Potential Repository Horizon'' (BSC 2004 [DIRS 169854]); (5) ''Thermal Conductivity of the Non-Repository Lithostratigraphic Layers'' (BSC 2004 [DIRS 170033]); (6) ''Ventilation Model and Analysis Report'' (BSC 2004 [DIRS 169862]); (7) ''Heat Capacity
AB020. Penile rehabilitation with PDE5 inhibitors in men following radical prostatectomy
Jiann, Bang-Ping
2015-01-01
Post-radical prostatectomy (RP) erectile dysfunction (ED) remains a challenge for the urologist. Despite the improvements in surgical technique, ED occurs between 20% and 90% in patients treated with bilateral nerve-sparing RP. Patient factors, cancer selection, type of surgery, surgical techniques, and surgeon factors represent the key significant contributors to erectile function recovery. The aim of a penile rehabilitation program is to preserve the functional smooth-muscle content of the corpus cavernosum during the neuropraxia period. Phosphodiesterase type 5 (PDE5) inhibitors are commonly used in rehabilitation programs. In animal models, such an approach could promote erectile function recovery, improve smooth muscle-to-collagen penile ration, reduce penile apoptotic index, preserve penile endothelial function and promote neuroprotection during nerve damage. Despite the strong basic science support from animal studies, discordant results have been reached in humans. The previous randomized trials comparing chronic versus on-demand PDE-5 inhibitors use after RP may be affected by improper patient selection in that only men at low risk of postoperative ED were included. These patients would recover erectile function regardless of the type of PDE5 inhibitor administration because of their excellent baseline profile. Prospective, randomized trials have shown a significant benefit of daily PDE5-I administration as compared with placebo in terms of postoperative EF recovery. Patients with intermediate risk of ED after surgery are the best candidates for daily treatment with PDE5 inhibitor after bilateral nerve-sparing RP. The maximal effect of penile rehabilitation may be found in those men with a certain (but not high) degree of systemic and erectile impairment preoperatively. In conclusion, penile rehabilitation could achieve faster and better natural erectile function after RP and should be started as early as possible. Chronic use of PDE5-I may confer the
Hegde, Shweta; Capell, Will R; Ibrahim, Baher A; Klett, Jennifer; Patel, Neema S; Sougiannis, Alexander T; Kelly, Michy P
2016-01-01
The capacity to form long-lasting social memories is critical to our health and survival. cAMP signaling in the ventral hippocampal formation (VHIPP) appears to be required for social memory formation, but the phosphodiesterase (PDE) involved remains unknown. Previously, we showed that PDE11A, which degrades cAMP and cGMP, is preferentially expressed in CA1 and subiculum of the VHIPP. Here, we determine whether PDE11A is expressed in neurons where it could directly influence synaptic plasticity and whether expression is required for the consolidation and/or retrieval of social memories. In CA1, and possibly CA2, PDE11A4 is expressed throughout neuronal cell bodies, dendrites (stratum radiatum), and axons (fimbria), but not astrocytes. Unlike PDE2A, PDE9A, or PDE10A, PDE11A4 expression begins very low at postnatal day 7 (P7) and dramatically increases until P28, at which time it stabilizes to young adult levels. This expression pattern is consistent with the fact that PDE11A is required for social long-term memory (LTM) formation during adolescence and adulthood. Male and female PDE11 knockout (KO) mice show normal short-term memory (STM) for social odor recognition (SOR) and social transmission of food preference (STFP), but no LTM 24 h post training. Importantly, PDE11A KO mice show normal LTM for nonsocial odor recognition. Deletion of PDE11A may impair memory consolidation by impairing requisite protein translation in the VHIPP. Relative to WT littermates, PDE11A KO mice show reduced expression of RSK2 and lowered phosphorylation of S6 (pS6–235/236). Together, these data suggest PDE11A is selectively required for the proper consolidation of recognition and associative social memories. PMID:27339393
Temkitthawon, Prapapan; Hinds, Thomas R.; Beavo, Joseph A.; Viyoch, Jarupa; Suwanborirux, Khanit; Pongamornkul, Wittaya; Sawasdee, Pattara; Ingkaninan, Kornkanok
2014-01-01
Aim of the study A number of medicinal plants are used in traditional medicine to treat erectile dysfunction. Since cyclic nucleotide PDEs inhibitors underlie several current treatments for this condition, we sought to show whether these plants might contain substantial amounts of PDE5 inhibitors. Materials and methods Forty one plant extracts and eight 7-methoxyflavones from Kaempferia parviflora Wall. ex Baker were screened for PDE5 and PDE6 inhibitory activities using the two-step radioactive assay. The PDE5 and PDE6 were prepared from mice lung and chicken retinas, respectively. All plant extracts were tested at 50 μg/ml whereas the pure compounds were tested at 10 μM. Results From forty one plant extracts tested, four showed the PDE5 inhibitory effect. The chemical constituents isolated from rhizomes of Kaempferia parviflora were further investigated on inhibitory activity against PDE5 and PDE6. The results showed that 7-methoxyflavones from this plant showed inhibition toward both enzymes. The most potent PDE5 inhibitor was 5,7-dimethoxyflavone (IC50 = 10.64 ± 2.09 μM, selectivity on PDE5 over PDE6 = 3.71). Structure activity relationship showed that the methoxyl group at C-5 position of 7-methoxyflavones was necessary for PDE5 inhibition. Conclusions Kaempferia parviflora rhizome extract and its 7-methoxyflavone constituents had moderate inhibitory activity against PDE5. This finding provides an explanation for enhancing sexual performance in the traditional use of Kaempferia parviflora. Moreover, 5,7-dimethoxyflavones should make a useful lead compound to further develop clinically efficacious PDE5 inhibitors. PMID:21884777
NASA Astrophysics Data System (ADS)
Angelidis, Dionysios; Sotiropoulos, Fotis
2015-11-01
The geometrical details of wind turbines determine the structure of the turbulence in the near and far wake and should be taken in account when performing high fidelity calculations. Multi-resolution simulations coupled with an immersed boundary method constitutes a powerful framework for high-fidelity calculations past wind farms located over complex terrains. We develop a 3D Immersed-Boundary Adaptive Mesh Refinement flow solver (IB-AMR) which enables turbine-resolving LES of wind turbines. The idea of using a hybrid staggered/non-staggered grid layout adopted in the Curvilinear Immersed Boundary Method (CURVIB) has been successfully incorporated on unstructured meshes and the fractional step method has been employed. The overall performance and robustness of the second order accurate, parallel, unstructured solver is evaluated by comparing the numerical simulations against conforming grid calculations and experimental measurements of laminar and turbulent flows over complex geometries. We also present turbine-resolving multi-scale LES considering all the details affecting the induced flow field; including the geometry of the tower, the nacelle and especially the rotor blades of a wind tunnel scale turbine. This material is based upon work supported by the Department of Energy under Award Number DE-EE0005482 and the Sandia National Laboratories.
A robust multilevel simultaneous eigenvalue solver
NASA Technical Reports Server (NTRS)
Costiner, Sorin; Taasan, Shlomo
1993-01-01
Multilevel (ML) algorithms for eigenvalue problems are often faced with several types of difficulties such as: the mixing of approximated eigenvectors by the solution process, the approximation of incomplete clusters of eigenvectors, the poor representation of solution on coarse levels, and the existence of close or equal eigenvalues. Algorithms that do not treat appropriately these difficulties usually fail, or their performance degrades when facing them. These issues motivated the development of a robust adaptive ML algorithm which treats these difficulties, for the calculation of a few eigenvectors and their corresponding eigenvalues. The main techniques used in the new algorithm include: the adaptive completion and separation of the relevant clusters on different levels, the simultaneous treatment of solutions within each cluster, and the robustness tests which monitor the algorithm's efficiency and convergence. The eigenvectors' separation efficiency is based on a new ML projection technique generalizing the Rayleigh Ritz projection, combined with a technique, the backrotations. These separation techniques, when combined with an FMG formulation, in many cases lead to algorithms of O(qN) complexity, for q eigenvectors of size N on the finest level. Previously developed ML algorithms are less focused on the mentioned difficulties. Moreover, algorithms which employ fine level separation techniques are of O(q(sub 2)N) complexity and usually do not overcome all these difficulties. Computational examples are presented where Schrodinger type eigenvalue problems in 2-D and 3-D, having equal and closely clustered eigenvalues, are solved with the efficiency of the Poisson multigrid solver. A second order approximation is obtained in O(qN) work, where the total computational work is equivalent to only a few fine level relaxations per eigenvector.
A Comparative Study of Randomized Constraint Solvers for Random-Symbolic Testing
NASA Technical Reports Server (NTRS)
Takaki, Mitsuo; Cavalcanti, Diego; Gheyi, Rohit; Iyoda, Juliano; dAmorim, Marcelo; Prudencio, Ricardo
2009-01-01
The complexity of constraints is a major obstacle for constraint-based software verification. Automatic constraint solvers are fundamentally incomplete: input constraints often build on some undecidable theory or some theory the solver does not support. This paper proposes and evaluates several randomized solvers to address this issue. We compare the effectiveness of a symbolic solver (CVC3), a random solver, three hybrid solvers (i.e., mix of random and symbolic), and two heuristic search solvers. We evaluate the solvers on two benchmarks: one consisting of manually generated constraints and another generated with a concolic execution of 8 subjects. In addition to fully decidable constraints, the benchmarks include constraints with non-linear integer arithmetic, integer modulo and division, bitwise arithmetic, and floating-point arithmetic. As expected symbolic solving (in particular, CVC3) subsumes the other solvers for the concolic execution of subjects that only generate decidable constraints. For the remaining subjects the solvers are complementary.
Yoshikawa, Masato; Hitaka, Takenori; Hasui, Tomoaki; Fushimi, Makoto; Kunitomo, Jun; Kokubo, Hironori; Oki, Hideyuki; Nakashima, Kosuke; Taniguchi, Takahiko
2016-08-15
Utilizing structure-based drug design techniques, we designed and synthesized phosphodiesterase 10A (PDE10A) inhibitors based on pyridazin-4(1H)-one. These compounds can interact with Tyr683 in the PDE10A selectivity pocket. Pyridazin-4(1H)-one derivative 1 was linked with a benzimidazole group through an alkyl spacer to interact with the OH of Tyr683 and fill the PDE10A selectivity pocket. After optimizing the linker length, we identified 1-(cyclopropylmethyl)-5-[3-(1-methyl-1H-benzimidazol-2-yl)propoxy]-3-(1-phenyl-1H-pyrazol-5-yl)pyridazin-4(1H)-one (16f) as having highly potent PDE10A inhibitory activity (IC50=0.76nM) and perfect selectivity against other PDEs (>13,000-fold, IC50=>10,000nM). The crystal structure of 16f bound to PDE10A revealed that the benzimidazole moiety was located deep within the PDE10A selectivity pocket and interacted with Tyr683. Additionally, a bidentate interaction existed between the 5-alkoxypyridazin-4(1H)-one moiety and the conserved Gln716 present in all PDEs. PMID:27301679
Multi-Scale Infrastructure Assessment
The U.S. Environmental Protection Agency’s (EPA) multi-scale infrastructure assessment project supports both water resource adaptation to climate change and the rehabilitation of the nation’s aging water infrastructure by providing tools, scientific data and information to progra...
PDE-constrained multispectral imaging of tissue chromophores with the equation of radiative transfer
Kim, Hyun Keol; Flexman, Molly; Yamashiro, Darrell J.; Kandel, Jessica J.; Hielscher, Andreas H.
2010-01-01
We introduce a transport-theory-based PDE-constrained multispectral model for direct imaging of the spatial distributions of chromophores concentrations in biological tissue. The method solves the forward problem (boundary radiance at each wavelength) and the inverse problem (spatial distribution of chromophores concentrations), in an all-at-once manner in the framework of a reduced Hessian sequential quadratic programming method. To illustrate the code’s performance, we present numerical and experimental studies involving tumor bearing mice. It is shown that the PDE-constrained multispectral method accelerates the reconstruction process by up to 15 times compared to unconstrained reconstruction algorithms and provides more accurate results as compared to the so-called two-step approach to multi-wavelength imaging. PMID:21258511
Microvascular dysfunction and efficacy of PDE5 inhibitors in BPH-LUTS.
Cellek, Selim; Cameron, Norman E; Cotter, Mary A; Fry, Christopher H; Ilo, Dapo
2014-04-01
Benign prostatic hyperplasia (BPH)-related lower urinary tract symptoms (LUTS) and erectile dysfunction commonly coexist, and both respond to phosphodiesterase (PDE) 5 inhibitors, suggesting a shared pathophysiological mechanism. We propose that both BPH-LUTS and erectile dysfunction are caused by microvascular dysfunction within the pelvic organs, and we present an overview of preclinical and clinical studies supporting the hypothesis that, within both the penis and the lower urinary tract, a combination of endothelial and neural dysfunction leads to a vicious cycle of hypoxia, vasoconstriction, altered smooth muscle contractility, and degeneration of autonomic neurons and ganglia. This hypothesis explains much of the preclinical and clinical research relating to these two conditions, and provides a rationale for further investigation into the effects of PDE5 inhibitors on the pathophysiology and symptoms of BPH-LUTS.
Investigation of Thrust Augmentation and Acoustic Performance by Ejectors on PDE
NASA Astrophysics Data System (ADS)
Xu, Gui-yang; Weng, Chun-sheng; Li, Ning; Huang, Xiao-long
2016-04-01
Thrust augmentation and acoustic performance of a Pulse Detonation Engine (PDE) with ejector system is experimentally investigated. For these tests the LEjector/DEjector is varied from 1.18 to 4 and the axial placement of the ejector relative to the PDE exhaust is varied from an x/DPDE of -3 to 3. Results from the tests show that the optimum LEjector/DEjector based on thrust augmentation and Overall Sound Pressure Level (OASPL) is found to be 2.61. The divergent ejector performed the best based on thrust augmentation, while the reduction effect for OASPL and Peak Sound Pressure Level (PSPL) at 60° is most prominent for the convergent ejector. The optimum axial position based on thrust augmentation is determined to be x/DPDE = 2, while, x/DPDE = 0 based on OASPL and PSPL.
Toward Interoperable Mesh, Geometry and Field Components for PDE Simulation Development
Chand, K K; Diachin, L F; Li, X; Ollivier-Gooch, C; Seol, E S; Shephard, M; Tautges, T; Trease, H
2005-07-11
Mesh-based PDE simulation codes are becoming increasingly sophisticated and rely on advanced meshing and discretization tools. Unfortunately, it is still difficult to interchange or interoperate tools developed by different communities to experiment with various technologies or to develop new capabilities. To address these difficulties, we have developed component interfaces designed to support the information flow of mesh-based PDE simulations. We describe this information flow and discuss typical roles and services provided by the geometry, mesh, and field components of the simulation. Based on this delineation for the roles of each component, we give a high-level description of the abstract data model and set of interfaces developed by the Department of Energy's Interoperable Tools for Advanced Petascale Simulation (ITAPS) center. These common interfaces are critical to our interoperability goal, and we give examples of several services based upon these interfaces including mesh adaptation and mesh improvement.
Microvascular dysfunction and efficacy of PDE5 inhibitors in BPH-LUTS.
Cellek, Selim; Cameron, Norman E; Cotter, Mary A; Fry, Christopher H; Ilo, Dapo
2014-04-01
Benign prostatic hyperplasia (BPH)-related lower urinary tract symptoms (LUTS) and erectile dysfunction commonly coexist, and both respond to phosphodiesterase (PDE) 5 inhibitors, suggesting a shared pathophysiological mechanism. We propose that both BPH-LUTS and erectile dysfunction are caused by microvascular dysfunction within the pelvic organs, and we present an overview of preclinical and clinical studies supporting the hypothesis that, within both the penis and the lower urinary tract, a combination of endothelial and neural dysfunction leads to a vicious cycle of hypoxia, vasoconstriction, altered smooth muscle contractility, and degeneration of autonomic neurons and ganglia. This hypothesis explains much of the preclinical and clinical research relating to these two conditions, and provides a rationale for further investigation into the effects of PDE5 inhibitors on the pathophysiology and symptoms of BPH-LUTS. PMID:24619381
A Riccati type PDE for light-front higher helicity vertices
NASA Astrophysics Data System (ADS)
Bengtsson, Anders K. H.
2014-09-01
This paper is based on a curious observation about an equation related to the tracelessness constraints of higher spin gauge fields. A similar equation also occurs in the theory of continuous spin representations of the Poincaré group. Expressed in an oscillator basis for the higher spin fields, the equation becomes a non-linear partial differential operator of the Riccati type acting on the vertex functions. The consequences of the equation for the cubic vertex is investigated in the light-front formulation of higher spin theory. The vertex is fixed by the PDE up to a set of terms that can be considered as boundary data for the PDE. These terms can serve as off-shell quantum corrections.
The estimation of material and patch parameters in a PDE-based circular plate model
NASA Technical Reports Server (NTRS)
Banks, H. T.; Smith, Ralph C.; Brown, D. E.; Metcalf, Vern L.; Silcox, R. J.
1995-01-01
The estimation of material and patch parameters for a system involving a circular plate, to which piezoceramic patches are bonded, is considered. A partial differential equation (PDE) model for the thin circular plate is used with the passive and active contributions form the patches included in the internal and external bending moments. This model contains piecewise constant parameters describing the density, flexural rigidity, Poisson ratio, and Kelvin-Voigt damping for the system as well as patch constants and a coefficient for viscous air damping. Examples demonstrating the estimation of these parameters with experimental acceleration data and a variety of inputs to the experimental plate are presented. By using a physically-derived PDE model to describe the system, parameter sets consistent across experiments are obtained, even when phenomena such as damping due to electric circuits affect the system dynamics.
Quantitative analysis of numerical solvers for oscillatory biomolecular system models
Quo, Chang F; Wang, May D
2008-01-01
Background This article provides guidelines for selecting optimal numerical solvers for biomolecular system models. Because various parameters of the same system could have drastically different ranges from 10-15 to 1010, the ODEs can be stiff and ill-conditioned, resulting in non-unique, non-existing, or non-reproducible modeling solutions. Previous studies have not examined in depth how to best select numerical solvers for biomolecular system models, which makes it difficult to experimentally validate the modeling results. To address this problem, we have chosen one of the well-known stiff initial value problems with limit cycle behavior as a test-bed system model. Solving this model, we have illustrated that different answers may result from different numerical solvers. We use MATLAB numerical solvers because they are optimized and widely used by the modeling community. We have also conducted a systematic study of numerical solver performances by using qualitative and quantitative measures such as convergence, accuracy, and computational cost (i.e. in terms of function evaluation, partial derivative, LU decomposition, and "take-off" points). The results show that the modeling solutions can be drastically different using different numerical solvers. Thus, it is important to intelligently select numerical solvers when solving biomolecular system models. Results The classic Belousov-Zhabotinskii (BZ) reaction is described by the Oregonator model and is used as a case study. We report two guidelines in selecting optimal numerical solver(s) for stiff, complex oscillatory systems: (i) for problems with unknown parameters, ode45 is the optimal choice regardless of the relative error tolerance; (ii) for known stiff problems, both ode113 and ode15s are good choices under strict relative tolerance conditions. Conclusions For any given biomolecular model, by building a library of numerical solvers with quantitative performance assessment metric, we show that it is possible
Portegies, J. M.; Fick, R. H. J.; Sanguinetti, G. R.; Meesters, S. P. L.; Girard, G.; Duits, R.
2015-01-01
We propose two strategies to improve the quality of tractography results computed from diffusion weighted magnetic resonance imaging (DW-MRI) data. Both methods are based on the same PDE framework, defined in the coupled space of positions and orientations, associated with a stochastic process describing the enhancement of elongated structures while preserving crossing structures. In the first method we use the enhancement PDE for contextual regularization of a fiber orientation distribution (FOD) that is obtained on individual voxels from high angular resolution diffusion imaging (HARDI) data via constrained spherical deconvolution (CSD). Thereby we improve the FOD as input for subsequent tractography. Secondly, we introduce the fiber to bundle coherence (FBC), a measure for quantification of fiber alignment. The FBC is computed from a tractography result using the same PDE framework and provides a criterion for removing the spurious fibers. We validate the proposed combination of CSD and enhancement on phantom data and on human data, acquired with different scanning protocols. On the phantom data we find that PDE enhancements improve both local metrics and global metrics of tractography results, compared to CSD without enhancements. On the human data we show that the enhancements allow for a better reconstruction of crossing fiber bundles and they reduce the variability of the tractography output with respect to the acquisition parameters. Finally, we show that both the enhancement of the FODs and the use of the FBC measure on the tractography improve the stability with respect to different stochastic realizations of probabilistic tractography. This is shown in a clinical application: the reconstruction of the optic radiation for epilepsy surgery planning. PMID:26465600
Optimality conditions for the numerical solution of optimization problems with PDE constraints :
Aguilo Valentin, Miguel Alejandro; Ridzal, Denis
2014-03-01
A theoretical framework for the numerical solution of partial di erential equation (PDE) constrained optimization problems is presented in this report. This theoretical framework embodies the fundamental infrastructure required to e ciently implement and solve this class of problems. Detail derivations of the optimality conditions required to accurately solve several parameter identi cation and optimal control problems are also provided in this report. This will allow the reader to further understand how the theoretical abstraction presented in this report translates to the application.
Portegies, J M; Fick, R H J; Sanguinetti, G R; Meesters, S P L; Girard, G; Duits, R
2015-01-01
We propose two strategies to improve the quality of tractography results computed from diffusion weighted magnetic resonance imaging (DW-MRI) data. Both methods are based on the same PDE framework, defined in the coupled space of positions and orientations, associated with a stochastic process describing the enhancement of elongated structures while preserving crossing structures. In the first method we use the enhancement PDE for contextual regularization of a fiber orientation distribution (FOD) that is obtained on individual voxels from high angular resolution diffusion imaging (HARDI) data via constrained spherical deconvolution (CSD). Thereby we improve the FOD as input for subsequent tractography. Secondly, we introduce the fiber to bundle coherence (FBC), a measure for quantification of fiber alignment. The FBC is computed from a tractography result using the same PDE framework and provides a criterion for removing the spurious fibers. We validate the proposed combination of CSD and enhancement on phantom data and on human data, acquired with different scanning protocols. On the phantom data we find that PDE enhancements improve both local metrics and global metrics of tractography results, compared to CSD without enhancements. On the human data we show that the enhancements allow for a better reconstruction of crossing fiber bundles and they reduce the variability of the tractography output with respect to the acquisition parameters. Finally, we show that both the enhancement of the FODs and the use of the FBC measure on the tractography improve the stability with respect to different stochastic realizations of probabilistic tractography. This is shown in a clinical application: the reconstruction of the optic radiation for epilepsy surgery planning.
Portegies, J M; Fick, R H J; Sanguinetti, G R; Meesters, S P L; Girard, G; Duits, R
2015-01-01
We propose two strategies to improve the quality of tractography results computed from diffusion weighted magnetic resonance imaging (DW-MRI) data. Both methods are based on the same PDE framework, defined in the coupled space of positions and orientations, associated with a stochastic process describing the enhancement of elongated structures while preserving crossing structures. In the first method we use the enhancement PDE for contextual regularization of a fiber orientation distribution (FOD) that is obtained on individual voxels from high angular resolution diffusion imaging (HARDI) data via constrained spherical deconvolution (CSD). Thereby we improve the FOD as input for subsequent tractography. Secondly, we introduce the fiber to bundle coherence (FBC), a measure for quantification of fiber alignment. The FBC is computed from a tractography result using the same PDE framework and provides a criterion for removing the spurious fibers. We validate the proposed combination of CSD and enhancement on phantom data and on human data, acquired with different scanning protocols. On the phantom data we find that PDE enhancements improve both local metrics and global metrics of tractography results, compared to CSD without enhancements. On the human data we show that the enhancements allow for a better reconstruction of crossing fiber bundles and they reduce the variability of the tractography output with respect to the acquisition parameters. Finally, we show that both the enhancement of the FODs and the use of the FBC measure on the tractography improve the stability with respect to different stochastic realizations of probabilistic tractography. This is shown in a clinical application: the reconstruction of the optic radiation for epilepsy surgery planning. PMID:26465600
Low-complexity PDE-based approach for automatic microarray image processing.
Belean, Bogdan; Terebes, Romulus; Bot, Adrian
2015-02-01
Microarray image processing is known as a valuable tool for gene expression estimation, a crucial step in understanding biological processes within living organisms. Automation and reliability are open subjects in microarray image processing, where grid alignment and spot segmentation are essential processes that can influence the quality of gene expression information. The paper proposes a novel partial differential equation (PDE)-based approach for fully automatic grid alignment in case of microarray images. Our approach can handle image distortions and performs grid alignment using the vertical and horizontal luminance function profiles. These profiles are evolved using a hyperbolic shock filter PDE and then refined using the autocorrelation function. The results are compared with the ones delivered by state-of-the-art approaches for grid alignment in terms of accuracy and computational complexity. Using the same PDE formalism and curve fitting, automatic spot segmentation is achieved and visual results are presented. Considering microarray images with different spots layouts, reliable results in terms of accuracy and reduced computational complexity are achieved, compared with existing software platforms and state-of-the-art methods for microarray image processing.
Mutations in the PDE6B gene in autosomal recessive retinitis pigmentosa
Danciger, M.; Blaney, J.; Gao, Y.Q.; Zhao, D.Y.
1995-11-01
We have studied 24 small families with presumed autosomal recessive inheritance of retinitis pigmentosa by a combination of haplotype analysis and exon screening. Initial analysis of the families was made with a dinucleotide repeat polymorphism adjacent to the gene for rod cGMP-phosphodiesterase (PDE6B). This was followed by denaturing gradient gel electrophoresis (DGGE) and single-strand conformation polymorphism electrophoresis (SSCPE) of the 22 exons and a portion of the 5{prime} untranslated region of the PDE6B gene in the probands of each family in which the PDE6B locus could not be ruled out from segregating with disease. Two probands were found with compound heterozygous mutations: Gly576Asp and His620(1-bp del) mutations were present in one proband, and a Lys706X null mutation and an AG to AT splice acceptor site mutation in intron 2 were present in the other. Only the affecteds of each of the two families carried both corresponding mutations. 29 refs., 3 figs., 1 tab.
Wang, Li; Burmeister, Brian T.; Johnson, Keven R.; Baillie, George S.; Karginov, Andrei V.; Skidgel, Randal A.; O’Bryan, John P.; Carnegie, Graeme K.
2015-01-01
Hypertrophy increases the risk of heart failure and arrhythmia. Prevention or reversal of the maladaptive hypertrophic phenotype has thus been proposed to treat heart failure. Chronic β-adrenergic receptor (β-AR) stimulation induces cardiomyocyte hypertrophy by elevating 3′, 5′-cyclic adenosine monophosphate (cAMP) levels and activating downstream effectors such protein kinase A (PKA). Conversely, hydrolysis of cAMP by phosphodiesterases (PDEs) spatiotemporally restricts cAMP signaling. Here, we demonstrate that PDE4, but not PDE3, is critical in regulating cardiomyocyte hypertrophy, and may represent a potential target for preventing maladaptive hypertrophy. We identify a sequence within the upstream conserved region 1 of PDE4D, termed UCR1C, as a novel activator of PDE4 long isoforms. UCR1C activates PDE4 in complex with A-Kinase anchoring protein (AKAP)-Lbc resulting in decreased PKA signaling facilitated by AKAP-Lbc. Expression of UCR1C in cardiomyocytes inhibits hypertrophy in response to chronic β-AR stimulation. This effect is partially due to inhibition of nuclear PKA activity, which decreases phosphorylation of the transcription factor cAMP response element-binding protein (CREB). In conclusion, PDE4 activation by UCR1C attenuates cardiomyocyte hypertrophy by specifically inhibiting nuclear PKA activity. PMID:25683917
Dutta, Nirmal
2016-01-01
ABSTRACT RPGR (retinitis pigmentosa GTPase regulator) is a ciliary protein associated with several forms of inherited retinal degenerative diseases. PDE6D is a ubiquitously expressed prenyl-binding protein and involved in ciliary targeting of prenylated proteins. The current working model for the RPGR function depicts that RPGR acts as a scaffold protein to recruit cargo-loaded PDE6D to primary cilia. Here, we present evidence demonstrating an alternative relationship between RPGR and PDE6D, in which RPGR is a cargo of PDE6D for ciliary targeting. We found that the constitutive isoform of RPGR, which is prenylated, requires prenylation for its ciliary localization. We also found that there are at least two independent ciliary targeting signals in RPGR: one within the N-terminal region that contains the RCC1-like domain and the other near the prenylation site at the C-terminus. Ablation of PDE6D blocked ciliary targeting of RPGR. Our study indicates that prenylated RPGR is one of the cargos of PDE6D for ciliary trafficking and provides insight into the mechanisms by which RPGR is targeted to cilia. PMID:27493202
Dutta, Nirmal; Seo, Seongjin
2016-09-15
RPGR (retinitis pigmentosa GTPase regulator) is a ciliary protein associated with several forms of inherited retinal degenerative diseases. PDE6D is a ubiquitously expressed prenyl-binding protein and involved in ciliary targeting of prenylated proteins. The current working model for the RPGR function depicts that RPGR acts as a scaffold protein to recruit cargo-loaded PDE6D to primary cilia. Here, we present evidence demonstrating an alternative relationship between RPGR and PDE6D, in which RPGR is a cargo of PDE6D for ciliary targeting. We found that the constitutive isoform of RPGR, which is prenylated, requires prenylation for its ciliary localization. We also found that there are at least two independent ciliary targeting signals in RPGR: one within the N-terminal region that contains the RCC1-like domain and the other near the prenylation site at the C-terminus. Ablation of PDE6D blocked ciliary targeting of RPGR. Our study indicates that prenylated RPGR is one of the cargos of PDE6D for ciliary trafficking and provides insight into the mechanisms by which RPGR is targeted to cilia.
Dutta, Nirmal; Seo, Seongjin
2016-01-01
RPGR (retinitis pigmentosa GTPase regulator) is a ciliary protein associated with several forms of inherited retinal degenerative diseases. PDE6D is a ubiquitously expressed prenyl-binding protein and involved in ciliary targeting of prenylated proteins. The current working model for the RPGR function depicts that RPGR acts as a scaffold protein to recruit cargo-loaded PDE6D to primary cilia. Here, we present evidence demonstrating an alternative relationship between RPGR and PDE6D, in which RPGR is a cargo of PDE6D for ciliary targeting. We found that the constitutive isoform of RPGR, which is prenylated, requires prenylation for its ciliary localization. We also found that there are at least two independent ciliary targeting signals in RPGR: one within the N-terminal region that contains the RCC1-like domain and the other near the prenylation site at the C-terminus. Ablation of PDE6D blocked ciliary targeting of RPGR. Our study indicates that prenylated RPGR is one of the cargos of PDE6D for ciliary trafficking and provides insight into the mechanisms by which RPGR is targeted to cilia. PMID:27493202
Richter, Wito; Day, Peter; Agrawal, Rani; Bruss, Matthew D; Granier, Sébastien; Wang, Yvonne L; Rasmussen, Søren G F; Horner, Kathleen; Wang, Ping; Lei, Tao; Patterson, Andrew J; Kobilka, Brian; Conti, Marco
2008-01-23
Beta1- and beta2-adrenergic receptors (betaARs) are highly homologous, yet they play clearly distinct roles in cardiac physiology and pathology. Myocyte contraction, for instance, is readily stimulated by beta1AR but not beta2AR signaling, and chronic stimulation of the two receptors has opposing effects on myocyte apoptosis and cell survival. Differences in the assembly of macromolecular signaling complexes may explain the distinct biological outcomes. Here, we demonstrate that beta1AR forms a signaling complex with a cAMP-specific phosphodiesterase (PDE) in a manner inherently different from a beta2AR/beta-arrestin/PDE complex reported previously. The beta1AR binds a PDE variant, PDE4D8, in a direct manner, and occupancy of the receptor by an agonist causes dissociation of this complex. Conversely, agonist binding to the beta2AR is a prerequisite for the recruitment of a complex consisting of beta-arrestin and the PDE4D variant, PDE4D5, to the receptor. We propose that the distinct modes of interaction with PDEs result in divergent cAMP signals in the vicinity of the two receptors, thus, providing an additional layer of complexity to enforce the specificity of beta1- and beta2-adrenoceptor signaling.
Thomae, David; Morley, Thomas J; Lee, Hsiaoju S; Barret, Olivier; Constantinescu, Cristian; Papin, Caroline; Baldwin, Ronald M; Tamagnan, Gilles D; Alagille, David
2016-05-15
Phosphodiesterase (PDE) 4 is the most prevalent PDE in the central nervous system (CNS) and catalyzes hydrolysis of intracellular cAMP, a secondary messenger. By therapeutic inhibition of PDE4, intracellular cAMP levels can be stabilized, and the symptoms of psychiatric and neurodegenerative disorders including depression, memory loss and Parkinson's disease can be ameliorated. Radiotracers targeting PDE4 can be used to study PDE4 density and function, and evaluate new PDE4 therapeutics, in vivo in a non-invasive way, as has been shown using the carbon-11 labeled PDE4 inhibitor R-(-)-rolipram. Herein we describe a small series of rolipram analogs that contain fluoro- or iodo-substituents that could be used as fluorine-18 PET or iodine-123 SPECT PDE4 radiotracers. This series was evaluated with an in vitro binding assay and a 4-(fluoromethyl) derivative of rolipram, MNI-617, was identified, with a five-fold increase in affinity for PDE4 (Kd = 0.26 nM) over R-(-)-rolipram (Kd = 1.6 nM). A deutero-analogue d2 -[(18) F]MNI-617 was radiolabeled and produced in 23% yield with high (>5 Ci/µmol) specific activity and evaluated in non-human primate, where it rapidly entered the brain, with SUVs between 4 and 5, and with a distribution pattern consistent with that of PDE4. PMID:27006107
Janisch, Kerstin M; Kasanuki, J. Mie; Naumann, Matthew C; Davis, Richard J; Lin, Chyuan-Sheng; Semple-Rowland, Susan; Tsang, Stephen H
2009-01-01
The γ subunit of rod-specific cGMP phosphodiesterase 6 (PDE6γ), an effector of the G-protein GNAT1, is a key regulator of phototransduction. The results of several in vitro biochemical reconstitution experiments conducted to examine the effects of phosphorylation of PDE6γ on its ability to regulate the PDE6 catalytic core have been inconsistent, showing that phosphorylation of PDE6γ may increase or decrease the ability of PDE6γ to deactivate phototransduction. To resolve role of phosphorylation of PDE6γ in living photoreceptors, we generated transgenic mice in which either one or both Threonine (T) sites in PDE6γ (T22 and T35), which are candidates for putative regulatory phosphorylation, were substituted with alanine (A). Phosphorylation of these sites was examined as a function of light exposure. We found that phosphorylation of T22 increases with light exposure in intact mouse rods while constitutive phosphorylation of T35 is unaffected by light in intact mouse rods and cones. Phosphorylation of the cone isoform of PDE6γ, PDE6H, is constitutively phosphorylated at the T20 residue. Light-induced T22 phosphorylation was lost in T35A transgenic rods, and T35 phosphorylation was extinguished in T22A transgenic rods. The interdependency of phosphorylation of T22 and T35 suggests that light-induced, post-translational modification of PDE6γ is essential for the regulation of G-protein signaling. PMID:19878658
NASA Astrophysics Data System (ADS)
Balsara, Dinshaw S.; Kim, Jinho
2016-05-01
The relativistic magnetohydrodynamics (RMHD) set of equations has recently seen an increased use in astrophysical computations. Even so, RMHD codes remain fragile. The reconstruction can sometimes yield superluminal velocities in certain parts of the mesh. The current generation of RMHD codes does not have any particularly good strategy for avoiding such an unphysical situation. In this paper we present a reconstruction strategy that overcomes this problem by making a single conservative to primitive transformation per cell followed by higher order WENO reconstruction on a carefully chosen set of primitives that guarantee subluminal reconstruction of the flow variables. For temporal evolution via a predictor step we also present second, third and fourth order accurate ADER methods that keep the velocity subluminal during the predictor step. The methods presented here are very general and should apply to other PDE systems where physical realizability is most easily asserted in the primitive variables. The RMHD system also requires the magnetic field to be evolved in a divergence-free fashion. In the treatment of classical numerical MHD the analogous issue has seen much recent progress with the advent of multidimensional Riemann solvers. By developing multidimensional Riemann solvers for RMHD, we show that similar advances extend to RMHD. As a result, the face-centered magnetic fields can be evolved much more accurately using the edge-centered electric fields in the corrector step. Those edge-centered electric fields come from a multidimensional Riemann solver for RMHD which we present in this paper. The overall update results in a one-step, fully conservative scheme that is suited for AMR. In this paper we also develop several new test problems for RMHD. We show that RMHD vortices can be designed that propagate on the computational mesh as self-preserving structures. These RMHD vortex test problems provide a means to do truly multidimensional accuracy testing for
NASA Astrophysics Data System (ADS)
Iacobellis, Vincent
Composite and nanocomposite materials exhibit behaviour which is inherently multiscale, extending from the atomistic to continuum levels. In composites, damage growth tends to occur at the nano and microstructural scale by means of crack growth and fibre-matrix debonding. Concurrent multiscale modeling provides a means of efficiently solving such localized phenomena, however its use in this application has been limited due to a number of existing issues in the multiscale field. These include the seamless transfer of information between continuum and atomistic domains, the small timesteps required for dynamic simulation, and limited research into concurrent multiscale modeling of amorphous polymeric materials. The objective of this thesis is thus twofold: to formulate a generalized approach to solving a coupled atomistic-to-continuum system that addresses these issues and to extend the application space of concurrent multiscale modeling to damage modeling in composite microstructures. To achieve these objectives, a finite element based multiscale technique termed the Bridging Cell Method (BCM), has been formulated with a focus on crystalline material systems. Case studies are then presented that show the effectiveness of the developed technique with respect to full atomistic simulations. The BCM is also demonstrated for applications of stress around a nanovoid, nanoindentation, and crack growth due to monotonic and cyclic loading. Next, the BCM is extended to modeling amorphous polymeric material systems where an adaptive solver and a two-step iterative solution algorithm are introduced. Finally, the amorphous and crystalline BCM is applied to modeling a polymer-graphite interface. This interface model is used to obtain cohesive zone parameters which are used in a cohesive zone model of fibre-matrix interfacial cracking in a composite microstructure. This allows for an investigation of the temperature dependent damage mechanics from the nano to microscale within
Performance Models for the Spike Banded Linear System Solver
Manguoglu, Murat; Saied, Faisal; Sameh, Ahmed; Grama, Ananth
2011-01-01
With availability of large-scale parallel platforms comprised of tens-of-thousands of processors and beyond, there is significant impetus for the development of scalable parallel sparse linear system solvers and preconditioners. An integral part of this design process is the development of performance models capable of predicting performance and providing accurate cost models for the solvers and preconditioners. There has been some work in the past on characterizing performance of the iterative solvers themselves. In this paper, we investigate the problem of characterizing performance and scalability of banded preconditioners. Recent work has demonstrated the superior convergence properties and robustness of banded preconditioners,more » compared to state-of-the-art ILU family of preconditioners as well as algebraic multigrid preconditioners. Furthermore, when used in conjunction with efficient banded solvers, banded preconditioners are capable of significantly faster time-to-solution. Our banded solver, the Truncated Spike algorithm is specifically designed for parallel performance and tolerance to deep memory hierarchies. Its regular structure is also highly amenable to accurate performance characterization. Using these characteristics, we derive the following results in this paper: (i) we develop parallel formulations of the Truncated Spike solver, (ii) we develop a highly accurate pseudo-analytical parallel performance model for our solver, (iii) we show excellent predication capabilities of our model – based on which we argue the high scalability of our solver. Our pseudo-analytical performance model is based on analytical performance characterization of each phase of our solver. These analytical models are then parameterized using actual runtime information on target platforms. An important consequence of our performance models is that they reveal underlying performance bottlenecks in both serial and parallel formulations. All of our results are validated
Foundations for a multiscale collaborative Earth model
NASA Astrophysics Data System (ADS)
Afanasiev, Michael; Peter, Daniel; Sager, Korbinian; Simutė, Saulė; Ermert, Laura; Krischer, Lion; Fichtner, Andreas
2016-01-01
We present a computational framework for the assimilation of local to global seismic data into a consistent model describing Earth structure on all seismically accessible scales. This Collaborative Seismic Earth Model (CSEM) is designed to meet the following requirements: (i) Flexible geometric parametrization, capable of capturing topography and bathymetry, as well as all aspects of potentially resolvable structure, including small-scale heterogeneities and deformations of internal discontinuities. (ii) Independence of any particular wave equation solver, in order to enable the combination of inversion techniques suitable for different types of seismic data. (iii) Physical parametrization that allows for full anisotropy and for variations in attenuation and density. While not all of these parameters are always resolvable, the assimilation of data that constrain any parameter subset should be possible. (iv) Ability to accommodate successive refinements through the incorporation of updates on any scale as new data or inversion techniques become available. (v) Enable collaborative Earth model construction. The structure of the initial CSEM is represented on a variable-resolution tetrahedral mesh. It is assembled from a long-wavelength 3-D global model into which several regional-scale tomographies are embedded. We illustrate the CSEM workflow of successive updating with two examples from Japan and the Western Mediterranean, where we constrain smaller scale structure using full-waveform inversion. Furthermore, we demonstrate the ability of the CSEM to act as a vehicle for the combination of different tomographic techniques with a joint full-waveform and traveltime ray tomography of Europe. This combination broadens the exploitable frequency range of the individual techniques, thereby improving resolution. We perform two iterations of a whole-Earth full-waveform inversion using a long-period reference data set from 225 globally recorded earthquakes. At this early stage
The novel high-performance 3-D MT inverse solver
NASA Astrophysics Data System (ADS)
Kruglyakov, Mikhail; Geraskin, Alexey; Kuvshinov, Alexey
2016-04-01
We present novel, robust, scalable, and fast 3-D magnetotelluric (MT) inverse solver. The solver is written in multi-language paradigm to make it as efficient, readable and maintainable as possible. Separation of concerns and single responsibility concepts go through implementation of the solver. As a forward modelling engine a modern scalable solver extrEMe, based on contracting integral equation approach, is used. Iterative gradient-type (quasi-Newton) optimization scheme is invoked to search for (regularized) inverse problem solution, and adjoint source approach is used to calculate efficiently the gradient of the misfit. The inverse solver is able to deal with highly detailed and contrasting models, allows for working (separately or jointly) with any type of MT responses, and supports massive parallelization. Moreover, different parallelization strategies implemented in the code allow optimal usage of available computational resources for a given problem statement. To parameterize an inverse domain the so-called mask parameterization is implemented, which means that one can merge any subset of forward modelling cells in order to account for (usually) irregular distribution of observation sites. We report results of 3-D numerical experiments aimed at analysing the robustness, performance and scalability of the code. In particular, our computational experiments carried out at different platforms ranging from modern laptops to HPC Piz Daint (6th supercomputer in the world) demonstrate practically linear scalability of the code up to thousands of nodes.
MULTISCALE THERMOHYDROLOGIC MODEL
T. Buscheck
2005-07-07
The intended purpose of the multiscale thermohydrologic model (MSTHM) is to predict the possible range of thermal-hydrologic conditions, resulting from uncertainty and variability, in the repository emplacement drifts, including the invert, and in the adjoining host rock for the repository at Yucca Mountain. The goal of the MSTHM is to predict a reasonable range of possible thermal-hydrologic conditions within the emplacement drift. To be reasonable, this range includes the influence of waste-package-to-waste-package heat output variability relevant to the license application design, as well as the influence of uncertainty and variability in the geologic and hydrologic conditions relevant to predicting the thermal-hydrologic response in emplacement drifts. This goal is quite different from the goal of a model to predict a single expected thermal-hydrologic response. As a result, the development and validation of the MSTHM and the associated analyses using this model are focused on the goal of predicting a reasonable range of thermal-hydrologic conditions resulting from parametric uncertainty and waste-package-to-waste-package heat-output variability. Thermal-hydrologic conditions within emplacement drifts depend primarily on thermal-hydrologic conditions in the host rock at the drift wall and on the temperature difference between the drift wall and the drip-shield and waste-package surfaces. Thus, the ability to predict a reasonable range of relevant in-drift MSTHM output parameters (e.g., temperature and relative humidity) is based on valid predictions of thermal-hydrologic processes in the host rock, as well as valid predictions of heat-transfer processes between the drift wall and the drip-shield and waste-package surfaces. Because the invert contains crushed gravel derived from the host rock, the invert is, in effect, an extension of the host rock, with thermal and hydrologic properties that have been modified by virtue of the crushing (and the resulting
The Magnetospheric Multiscale Mission
NASA Astrophysics Data System (ADS)
Burch, James
Magnetospheric Multiscale (MMS), a NASA four-spacecraft mission scheduled for launch in November 2014, will investigate magnetic reconnection in the boundary regions of the Earth’s magnetosphere, particularly along its dayside boundary with the solar wind and the neutral sheet in the magnetic tail. Among the important questions about reconnection that will be addressed are the following: Under what conditions can magnetic-field energy be converted to plasma energy by the annihilation of magnetic field through reconnection? How does reconnection vary with time, and what factors influence its temporal behavior? What microscale processes are responsible for reconnection? What determines the rate of reconnection? In order to accomplish its goals the MMS spacecraft must probe both those regions in which the magnetic fields are very nearly antiparallel and regions where a significant guide field exists. From previous missions we know the approximate speeds with which reconnection layers move through space to be from tens to hundreds of km/s. For electron skin depths of 5 to 10 km, the full 3D electron population (10 eV to above 20 keV) has to be sampled at rates greater than 10/s. The MMS Fast-Plasma Instrument (FPI) will sample electrons at greater than 30/s. Because the ion skin depth is larger, FPI will make full ion measurements at rates of greater than 6/s. 3D E-field measurements will be made by MMS once every ms. MMS will use an Active Spacecraft Potential Control device (ASPOC), which emits indium ions to neutralize the photoelectron current and keep the spacecraft from charging to more than +4 V. Because ion dynamics in Hall reconnection depend sensitively on ion mass, MMS includes a new-generation Hot Plasma Composition Analyzer (HPCA) that corrects problems with high proton fluxes that have prevented accurate ion-composition measurements near the dayside magnetospheric boundary. Finally, Energetic Particle Detector (EPD) measurements of electrons and
A multiple right hand side iterative solver for history matching
Killough, J.E.; Sharma, Y.; Dupuy, A.; Bissell, R.; Wallis, J.
1995-12-31
History matching of oil and gas reservoirs can be accelerated by directly calculating the gradients of observed quantities (e.g., well pressure) with respect to the adjustable reserve parameters (e.g., permeability). This leads to a set of linear equations which add a significant overhead to the full simulation run without gradients. Direct Gauss elimination solvers can be used to address this problem by performing the factorization of the matrix only once and then reusing the factor matrix for the solution of the multiple right hand sides. This is a limited technique, however. Experience has shown that problems with greater than few thousand cells may not be practical for direct solvers because of computation time and memory limitations. This paper discusses the implementation of a multiple right hand side iterative linear equation solver (MRHS) for a system of adjoint equations to significantly enhance the performance of a gradient simulator.
Gpu Implementation of a Viscous Flow Solver on Unstructured Grids
NASA Astrophysics Data System (ADS)
Xu, Tianhao; Chen, Long
2016-06-01
Graphics processing units have gained popularities in scientific computing over past several years due to their outstanding parallel computing capability. Computational fluid dynamics applications involve large amounts of calculations, therefore a latest GPU card is preferable of which the peak computing performance and memory bandwidth are much better than a contemporary high-end CPU. We herein focus on the detailed implementation of our GPU targeting Reynolds-averaged Navier-Stokes equations solver based on finite-volume method. The solver employs a vertex-centered scheme on unstructured grids for the sake of being capable of handling complex topologies. Multiple optimizations are carried out to improve the memory accessing performance and kernel utilization. Both steady and unsteady flow simulation cases are carried out using explicit Runge-Kutta scheme. The solver with GPU acceleration in this paper is demonstrated to have competitive advantages over the CPU targeting one.
Two Solvers for Tractable Temporal Constraints with Preferences
NASA Technical Reports Server (NTRS)
Rossi, F.; Khatib,L.; Morris, P.; Morris, R.; Clancy, Daniel (Technical Monitor)
2002-01-01
A number of reasoning problems involving the manipulation of temporal information can naturally be viewed as implicitly inducing an ordering of potential local decisions involving time on the basis of preferences. Soft temporal constraints problems allow to describe in a natural way scenarios where events happen over time and preferences are associated to event distances and durations. In general, solving soft temporal problems require exponential time in the worst case, but there are interesting subclasses of problems which are polynomially solvable. We describe two solvers based on two different approaches for solving the same tractable subclass. For each solver we present the theoretical results it stands on, a description of the algorithm and some experimental results. The random generator used to build the problems on which tests are performed is also described. Finally, we compare the two solvers highlighting the tradeoff between performance and representational power.
Multiscale vulnerability of complex networks.
Boccaletti, Stefano; Buldú, Javier; Criado, Regino; Flores, Julio; Latora, Vito; Pello, Javier; Romance, Miguel
2007-12-01
We present a novel approach to quantify the vulnerability of a complex network, i.e., the capacity of a graph to maintain its functional performance under random damages or malicious attacks. The proposed measure represents a multiscale evaluation of vulnerability, and makes use of combined powers of the links' betweenness. We show that the proposed approach is able to properly describe some cases for which earlier measures of vulnerability fail. The relevant applications of our method for technological network design are outlined.
Effects of PDE5 Inhibitors and sGC Stimulators in a Rat Model of Artificial Ureteral Calculosis
Sandner, Peter; Tinel, Hanna; Affaitati, Giannapia; Costantini, Raffaele; Giamberardino, Maria Adele
2015-01-01
Urinary colics from calculosis are frequent and intense forms of pain whose current pharmacological treatment remains unsatisfactory. New and more effective drugs are needed to control symptoms and improve stone expulsion. Recent evidence suggested that the Nitric Oxide (NO) / cyclic guanosine monophosphate (cGMP) / phosphodiesterase type 5 (PDE5) system may contribute to ureteral motility influencing stone expulsion. We investigated if PDE5 inhibitors and sGC stimulators influence ureteral contractility, pain behaviour and stone expulsion in a rat model of ureteral calculosis. We investigated: a)the sex-specific PDE5 distribution in the rat ureter; b)the functional in vitro effects of vardenafil and sildenafil (PDE5 inhibitors) and BAY41-2272 (sGC stimulator) on induced ureteral contractility in rats and c)the in vivo effectiveness of vardenafil and BAY41-2272, alone and combined with ketoprofen, vs hyoscine-N-butylbromide alone or combined with ketoprofen, on behavioural pain indicators and stone expulsion in rats with artificial calculosis in one ureter. PDE5 was abundantly expressed in male and female rats’ ureter. In vitro, both vardenafil and BAY41-2272 significantly relaxed pre-contracted ureteral strips. In vivo, all compounds significantly reduced number and global duration of “ureteral crises” and post-stone lumbar muscle hyperalgesia in calculosis rats. The highest level of reduction of the pain behaviour was observed with BAY41-2272 among all spasmolytics administered alone, and with the combination of ketoprofen with BAY41-2272. The percentage of stone expulsion was maximal in the ketoprofen+BAY41-2272 group. The NO/cGMP/PDE5 pathway is involved in the regulation of ureteral contractility and pain behaviour in urinary calculosis. PDE5 inhibitors and sGC stimulators could become a potent new option for treatment of urinary colic pain. PMID:26509272
Effects of PDE5 Inhibitors and sGC Stimulators in a Rat Model of Artificial Ureteral Calculosis.
Sandner, Peter; Tinel, Hanna; Affaitati, Giannapia; Costantini, Raffaele; Giamberardino, Maria Adele
2015-01-01
Urinary colics from calculosis are frequent and intense forms of pain whose current pharmacological treatment remains unsatisfactory. New and more effective drugs are needed to control symptoms and improve stone expulsion. Recent evidence suggested that the Nitric Oxide (NO) / cyclic guanosine monophosphate (cGMP)/phosphodiesterase type 5 (PDE5) system may contribute to ureteral motility influencing stone expulsion. We investigated if PDE5 inhibitors and sGC stimulators influence ureteral contractility, pain behaviour and stone expulsion in a rat model of ureteral calculosis. We investigated: a) the sex-specific PDE5 distribution in the rat ureter; b) the functional in vitro effects of vardenafil and sildenafil (PDE5 inhibitors) and BAY41-2272 (sGC stimulator) on induced ureteral contractility in rats and c) the in vivo effectiveness of vardenafil and BAY41-2272, alone and combined with ketoprofen, vs hyoscine-N-butylbromide alone or combined with ketoprofen, on behavioural pain indicators and stone expulsion in rats with artificial calculosis in one ureter. PDE5 was abundantly expressed in male and female rats' ureter. In vitro, both vardenafil and BAY41-2272 significantly relaxed pre-contracted ureteral strips. In vivo, all compounds significantly reduced number and global duration of "ureteral crises" and post-stone lumbar muscle hyperalgesia in calculosis rats. The highest level of reduction of the pain behaviour was observed with BAY41-2272 among all spasmolytics administered alone, and with the combination of ketoprofen with BAY41-2272. The percentage of stone expulsion was maximal in the ketoprofen+BAY41-2272 group. The NO/cGMP/PDE5 pathway is involved in the regulation of ureteral contractility and pain behaviour in urinary calculosis. PDE5 inhibitors and sGC stimulators could become a potent new option for treatment of urinary colic pain.
LAPACKrc: Fast linear algebra kernels/solvers for FPGA accelerators
NASA Astrophysics Data System (ADS)
Gonzalez, Juan; Núñez, Rafael C.
2009-07-01
We present LAPACKrc, a family of FPGA-based linear algebra solvers able to achieve more than 100x speedup per commodity processor on certain problems. LAPACKrc subsumes some of the LAPACK and ScaLAPACK functionalities, and it also incorporates sparse direct and iterative matrix solvers. Current LAPACKrc prototypes demonstrate between 40x-150x speedup compared against top-of-the-line hardware/software systems. A technology roadmap is in place to validate current performance of LAPACKrc in HPC applications, and to increase the computational throughput by factors of hundreds within the next few years.
Numerical System Solver Developed for the National Cycle Program
NASA Technical Reports Server (NTRS)
Binder, Michael P.
1999-01-01
As part of the National Cycle Program (NCP), a powerful new numerical solver has been developed to support the simulation of aeropropulsion systems. This software uses a hierarchical object-oriented design. It can provide steady-state and time-dependent solutions to nonlinear and even discontinuous problems typically encountered when aircraft and spacecraft propulsion systems are simulated. It also can handle constrained solutions, in which one or more factors may limit the behavior of the engine system. Timedependent simulation capabilities include adaptive time-stepping and synchronization with digital control elements. The NCP solver is playing an important role in making the NCP a flexible, powerful, and reliable simulation package.
Profile solver in C for finite element equations
NASA Astrophysics Data System (ADS)
Hededal, O.; Krenk, S.
1994-08-01
This paper presents an efficient, pointer based profile solver with standard matrix indexing. Constrained equations Ax = b where x contains known and unknown values are solved and the full vectors x and b are obtained. Pseudo-code algorithms are formulated for a row oriented form of the LDL(sup T) factorization and implemented directly as a C code. The solver is implemented in C because of the close relation between two-dimensional arrays and pointers which makes it possible to write a clear and efficient code.
Li, Junfeng; Zhang, Xiang; Jin, Hongjun; Fan, Jinda; Flores, Hubert; Perlmutter, Joel S.; Tu, Zhude
2015-01-01
A series of fluorine-containing PDE10A inhibitors were designed and synthesized to improve the metabolic stability of [11C]MP-10. Twenty of the 22 new analogues had high potency and selectivity for PDE10A: 18a–j, 19d–j, 20a–b, and 21b had IC50 values <5 nM for PDE10A. Seven F-18 labeled compounds [18F]18a–e, [18F]18g, and [18F]20a were radiosynthesized by 18F-introduction onto the quinoline rather than the pyrazole moiety of the MP-10 pharmacophore and performed in vivo evaluation. Biodistribution studies in rats showed ~2-fold higher activity in the PDE10A-enriched striatum than nontarget brain regions; this ratio increased from 5 to 30 min postinjection, particularly for [18F]18a–d and [18F]20a. Micro-PET studies of [18F]18d and [18F]20a in nonhuman primates provided clear visualization of striatum with suitable equilibrium kinetics and favorable metabolic stability. These results suggest this strategy may identify a 18F-labeled PET tracer for quantifying the levels of PDE10A in patients with CNS disorders including Huntington’s disease and schizophrenia. PMID:26430878
Differential Geometry Based Multiscale Models
Wei, Guo-Wei
2010-01-01
Large chemical and biological systems such as fuel cells, ion channels, molecular motors, and viruses are of great importance to the scientific community and public health. Typically, these complex systems in conjunction with their aquatic environment pose a fabulous challenge to theoretical description, simulation, and prediction. In this work, we propose a differential geometry based multiscale paradigm to model complex macromolecular systems, and to put macroscopic and microscopic descriptions on an equal footing. In our approach, the differential geometry theory of surfaces and geometric measure theory are employed as a natural means to couple the macroscopic continuum mechanical description of the aquatic environment with the microscopic discrete atom-istic description of the macromolecule. Multiscale free energy functionals, or multiscale action functionals are constructed as a unified framework to derive the governing equations for the dynamics of different scales and different descriptions. Two types of aqueous macromolecular complexes, ones that are near equilibrium and others that are far from equilibrium, are considered in our formulations. We show that generalized Navier–Stokes equations for the fluid dynamics, generalized Poisson equations or generalized Poisson–Boltzmann equations for electrostatic interactions, and Newton's equation for the molecular dynamics can be derived by the least action principle. These equations are coupled through the continuum-discrete interface whose dynamics is governed by potential driven geometric flows. Comparison is given to classical descriptions of the fluid and electrostatic interactions without geometric flow based micro-macro interfaces. The detailed balance of forces is emphasized in the present work. We further extend the proposed multiscale paradigm to micro-macro analysis of electrohydrodynamics, electrophoresis, fuel cells, and ion channels. We derive generalized Poisson–Nernst–Planck equations that
Differential geometry based multiscale models.
Wei, Guo-Wei
2010-08-01
Large chemical and biological systems such as fuel cells, ion channels, molecular motors, and viruses are of great importance to the scientific community and public health. Typically, these complex systems in conjunction with their aquatic environment pose a fabulous challenge to theoretical description, simulation, and prediction. In this work, we propose a differential geometry based multiscale paradigm to model complex macromolecular systems, and to put macroscopic and microscopic descriptions on an equal footing. In our approach, the differential geometry theory of surfaces and geometric measure theory are employed as a natural means to couple the macroscopic continuum mechanical description of the aquatic environment with the microscopic discrete atomistic description of the macromolecule. Multiscale free energy functionals, or multiscale action functionals are constructed as a unified framework to derive the governing equations for the dynamics of different scales and different descriptions. Two types of aqueous macromolecular complexes, ones that are near equilibrium and others that are far from equilibrium, are considered in our formulations. We show that generalized Navier-Stokes equations for the fluid dynamics, generalized Poisson equations or generalized Poisson-Boltzmann equations for electrostatic interactions, and Newton's equation for the molecular dynamics can be derived by the least action principle. These equations are coupled through the continuum-discrete interface whose dynamics is governed by potential driven geometric flows. Comparison is given to classical descriptions of the fluid and electrostatic interactions without geometric flow based micro-macro interfaces. The detailed balance of forces is emphasized in the present work. We further extend the proposed multiscale paradigm to micro-macro analysis of electrohydrodynamics, electrophoresis, fuel cells, and ion channels. We derive generalized Poisson-Nernst-Planck equations that are
Differential geometry based multiscale models.
Wei, Guo-Wei
2010-08-01
Large chemical and biological systems such as fuel cells, ion channels, molecular motors, and viruses are of great importance to the scientific community and public health. Typically, these complex systems in conjunction with their aquatic environment pose a fabulous challenge to theoretical description, simulation, and prediction. In this work, we propose a differential geometry based multiscale paradigm to model complex macromolecular systems, and to put macroscopic and microscopic descriptions on an equal footing. In our approach, the differential geometry theory of surfaces and geometric measure theory are employed as a natural means to couple the macroscopic continuum mechanical description of the aquatic environment with the microscopic discrete atomistic description of the macromolecule. Multiscale free energy functionals, or multiscale action functionals are constructed as a unified framework to derive the governing equations for the dynamics of different scales and different descriptions. Two types of aqueous macromolecular complexes, ones that are near equilibrium and others that are far from equilibrium, are considered in our formulations. We show that generalized Navier-Stokes equations for the fluid dynamics, generalized Poisson equations or generalized Poisson-Boltzmann equations for electrostatic interactions, and Newton's equation for the molecular dynamics can be derived by the least action principle. These equations are coupled through the continuum-discrete interface whose dynamics is governed by potential driven geometric flows. Comparison is given to classical descriptions of the fluid and electrostatic interactions without geometric flow based micro-macro interfaces. The detailed balance of forces is emphasized in the present work. We further extend the proposed multiscale paradigm to micro-macro analysis of electrohydrodynamics, electrophoresis, fuel cells, and ion channels. We derive generalized Poisson-Nernst-Planck equations that are
NASA Technical Reports Server (NTRS)
Ricks, Trenton M.; Lacy, Thomas E., Jr.; Bednarcyk, Brett A.; Arnold, Steven M.; Hutchins, John W.
2014-01-01
A multiscale modeling methodology was developed for continuous fiber composites that incorporates a statistical distribution of fiber strengths into coupled multiscale micromechanics/finite element (FE) analyses. A modified two-parameter Weibull cumulative distribution function, which accounts for the effect of fiber length on the probability of failure, was used to characterize the statistical distribution of fiber strengths. A parametric study using the NASA Micromechanics Analysis Code with the Generalized Method of Cells (MAC/GMC) was performed to assess the effect of variable fiber strengths on local composite failure within a repeating unit cell (RUC) and subsequent global failure. The NASA code FEAMAC and the ABAQUS finite element solver were used to analyze the progressive failure of a unidirectional SCS-6/TIMETAL 21S metal matrix composite tensile dogbone specimen at 650 degC. Multiscale progressive failure analyses were performed to quantify the effect of spatially varying fiber strengths on the RUC-averaged and global stress-strain responses and failure. The ultimate composite strengths and distribution of failure locations (predominately within the gage section) reasonably matched the experimentally observed failure behavior. The predicted composite failure behavior suggests that use of macroscale models that exploit global geometric symmetries are inappropriate for cases where the actual distribution of local fiber strengths displays no such symmetries. This issue has not received much attention in the literature. Moreover, the model discretization at a specific length scale can have a profound effect on the computational costs associated with multiscale simulations.models that yield accurate yet tractable results.
Data Assimilation and Propagation of Uncertainty in Multiscale Cardiovascular Simulation
NASA Astrophysics Data System (ADS)
Schiavazzi, Daniele; Marsden, Alison
2015-11-01
Cardiovascular modeling is the application of computational tools to predict hemodynamics. State-of-the-art techniques couple a 3D incompressible Navier-Stokes solver with a boundary circulation model and can predict local and peripheral hemodynamics, analyze the post-operative performance of surgical designs and complement clinical data collection minimizing invasive and risky measurement practices. The ability of these tools to make useful predictions is directly related to their accuracy in representing measured physiologies. Tuning of model parameters is therefore a topic of paramount importance and should include clinical data uncertainty, revealing how this uncertainty will affect the predictions. We propose a fully Bayesian, multi-level approach to data assimilation of uncertain clinical data in multiscale circulation models. To reduce the computational cost, we use a stable, condensed approximation of the 3D model build by linear sparse regression of the pressure/flow rate relationship at the outlets. Finally, we consider the problem of non-invasively propagating the uncertainty in model parameters to the resulting hemodynamics and compare Monte Carlo simulation with Stochastic Collocation approaches based on Polynomial or Multi-resolution Chaos expansions.
Multiscale molecular dynamics using the matched interface and boundary method
Geng Weihua; Wei, G.W.
2011-01-20
The Poisson-Boltzmann (PB) equation is an established multiscale model for electrostatic analysis of biomolecules and other dielectric systems. PB based molecular dynamics (MD) approach has a potential to tackle large biological systems. Obstacles that hinder the current development of PB based MD methods are concerns in accuracy, stability, efficiency and reliability. The presence of complex solvent-solute interface, geometric singularities and charge singularities leads to challenges in the numerical solution of the PB equation and electrostatic force evaluation in PB based MD methods. Recently, the matched interface and boundary (MIB) method has been utilized to develop the first second order accurate PB solver that is numerically stable in dealing with discontinuous dielectric coefficients, complex geometric singularities and singular source charges. The present work develops the PB based MD approach using the MIB method. New formulation of electrostatic forces is derived to allow the use of sharp molecular surfaces. Accurate reaction field forces are obtained by directly differentiating the electrostatic potential. Dielectric boundary forces are evaluated at the solvent-solute interface using an accurate Cartesian-grid surface integration method. The electrostatic forces located at reentrant surfaces are appropriately assigned to related atoms. Extensive numerical tests are carried out to validate the accuracy and stability of the present electrostatic force calculation. The new PB based MD method is implemented in conjunction with the AMBER package. MIB based MD simulations of biomolecules are demonstrated via a few example systems.
A CaMKII/PDE4D negative feedback regulates cAMP signaling
Mika, Delphine; Richter, Wito; Conti, Marco
2015-01-01
cAMP production and protein kinase A (PKA) are the most widely studied steps in β-adrenergic receptor (βAR) signaling in the heart; however, the multifunctional Ca2+/calmodulin-dependent protein kinase II (CaMKII) is also activated in response to βAR stimulation and is involved in the regulation of cardiac excitation-contraction coupling. Its activity and expression are increased during cardiac hypertrophy, in heart failure, and under conditions that promote arrhythmias both in animal models and in the human heart, underscoring the clinical relevance of CaMKII in cardiac pathophysiology. Both CaMKII and PKA phosphorylate a number of protein targets critical for Ca2+ handling and contraction with similar, but not always identical, functional consequences. How these two pathways communicate with each other remains incompletely understood, however. To maintain homeostasis, cyclic nucleotide levels are regulated by phosphodiesterases (PDEs), with PDE4s predominantly responsible for cAMP degradation in the rodent heart. Here we have reassessed the interaction between cAMP/PKA and Ca2+/CaMKII signaling. We demonstrate that CaMKII activity constrains basal and βAR-activated cAMP levels. Moreover, we show that these effects are mediated, at least in part, by CaMKII regulation of PDE4D. This regulation establishes a negative feedback loop necessary to maintain cAMP/CaMKII homeostasis, revealing a previously unidentified function for PDE4D as a critical integrator of cAMP/PKA and Ca2+/CaMKII signaling. PMID:25646485
Patel, Dhavalkumar Narendrabhai; Li, Lin; Kee, Chee-Leong; Ge, Xiaowei; Low, Min-Yong; Koh, Hwee-Ling
2014-01-01
The popularity of phosphodiesterase type 5 (PDE-5) enzyme inhibitors for the treatment of erectile dysfunction has led to the increase in prevalence of illicit sexual performance enhancement products. PDE-5 inhibitors, namely sildenafil, tadalafil and vardenafil, and their unapproved designer analogues are being increasingly used as adulterants in the herbal products and health supplements marketed for sexual performance enhancement. To date, more than 50 unapproved analogues of prescription PDE-5 inhibitors were found as adulterants in the literature. To avoid detection of such adulteration by standard screening protocols, the perpetrators of such illegal products are investing time and resources to synthesize exotic analogues and devise novel means for adulteration. A comprehensive review of conventional and advance analytical techniques to detect and characterize the adulterants is presented. The rapid identification and structural elucidation of unknown analogues as adulterants is greatly enhanced by the wide myriad of analytical techniques employed, including high performance liquid chromatography (HPLC), gas chromatography-mass spectrometry (GC-MS), liquid chromatography mass-spectrometry (LC-MS), nuclear magnetic resonance (NMR) spectroscopy, vibrational spectroscopy, liquid chromatography-Fourier transform ion cyclotron resonance-mass spectrometry (LC-FT-ICR-MS), liquid chromatograph-hybrid triple quadrupole linear ion trap mass spectrometer with information dependent acquisition, ultra high performance liquid chromatography-time of flight-mass spectrometry (UHPLC-TOF-MS), ion mobility spectroscopy (IMS) and immunoassay methods. The many challenges in detecting and characterizing such adulterants, and the need for concerted effort to curb adulteration in order to safe guard public safety and interest are discussed.
Punzalan, Florencio Rusty; Kunieda, Yoshitoshi; Amano, Akira
2015-01-01
Clinical and experimental studies involving human hearts can have certain limitations. Methods such as computer simulations can be an important alternative or supplemental tool. Physiological simulation at the tissue or organ level typically involves the handling of partial differential equations (PDEs). Boundary conditions and distributed parameters, such as those used in pharmacokinetics simulation, add to the complexity of the PDE solution. These factors can tailor PDE solutions and their corresponding program code to specific problems. Boundary condition and parameter changes in the customized code are usually prone to errors and time-consuming. We propose a general approach for handling PDEs and boundary conditions in computational models using a replacement scheme for discretization. This study is an extension of a program generator that we introduced in a previous publication. The program generator can generate code for multi-cell simulations of cardiac electrophysiology. Improvements to the system allow it to handle simultaneous equations in the biological function model as well as implicit PDE numerical schemes. The replacement scheme involves substituting all partial differential terms with numerical solution equations. Once the model and boundary equations are discretized with the numerical solution scheme, instances of the equations are generated to undergo dependency analysis. The result of the dependency analysis is then used to generate the program code. The resulting program code are in Java or C programming language. To validate the automatic handling of boundary conditions in the program code generator, we generated simulation code using the FHN, Luo-Rudy 1, and Hund-Rudy cell models and run cell-to-cell coupling and action potential propagation simulations. One of the simulations is based on a published experiment and simulation results are compared with the experimental data. We conclude that the proposed program code generator can be used to
A perception- and PDE-based nonlinear transformation for processing spoken words
NASA Astrophysics Data System (ADS)
Qi, Yingyong; Xin, Jack
2001-02-01
Speech signals are often produced or received in the presence of noise, which is known to degrade the performance of a speech recognition system. In this paper, a perception- and PDE-based nonlinear transformation was developed to process spoken words in noisy environment. Our goal is to distinguish essential speech features and suppress noise so that the processed words are better recognized by a computer software. The nonlinear transformation was made on the spectrogram (short-term Fourier spectra) of speech signals, which reveals the signal energy distribution in time and frequency. The transformation reduces noise through time adaptation (reducing temporally slowly varying portions of spectra) and enhances spectral peaks (formants) by evolving a focusing quadratic fourth-order PDE. Short-term spectra of speech signals were initially divided into three (low, mid and high) frequency bands based on the critical bandwidth of human audition. An algorithm was developed to trace the upper and lower intensity envelopes of signal in each band. The difference between the upper and lower envelopes reflects the signal-to-noise (SNR) ratio of each band. Constant, low SNR signals in each band were adaptively decreased to reduce noise. Then evolution of the focusing PDE was used to enhance the spectral peaks, and further reduce noise interference. Numerical results on noisy spoken words indicated that the transformed spectral pattern of the spoken words was insensitive to noise for SNR ranging from 0 to 20 dB (decibel). The spectral distances between noisy words and original words decreased after the transformation. A numerical experiment was performed on 11 spoken words at SNR=5 dB. A noisy word is recognized numerically by computing the closest L2 spectral distance from the clean template. The experiment reached a recognition rate as high as 100%. Analyses on the properties of the transformation are provided.
Patel, Dhavalkumar Narendrabhai; Li, Lin; Kee, Chee-Leong; Ge, Xiaowei; Low, Min-Yong; Koh, Hwee-Ling
2014-01-01
The popularity of phosphodiesterase type 5 (PDE-5) enzyme inhibitors for the treatment of erectile dysfunction has led to the increase in prevalence of illicit sexual performance enhancement products. PDE-5 inhibitors, namely sildenafil, tadalafil and vardenafil, and their unapproved designer analogues are being increasingly used as adulterants in the herbal products and health supplements marketed for sexual performance enhancement. To date, more than 50 unapproved analogues of prescription PDE-5 inhibitors were found as adulterants in the literature. To avoid detection of such adulteration by standard screening protocols, the perpetrators of such illegal products are investing time and resources to synthesize exotic analogues and devise novel means for adulteration. A comprehensive review of conventional and advance analytical techniques to detect and characterize the adulterants is presented. The rapid identification and structural elucidation of unknown analogues as adulterants is greatly enhanced by the wide myriad of analytical techniques employed, including high performance liquid chromatography (HPLC), gas chromatography-mass spectrometry (GC-MS), liquid chromatography mass-spectrometry (LC-MS), nuclear magnetic resonance (NMR) spectroscopy, vibrational spectroscopy, liquid chromatography-Fourier transform ion cyclotron resonance-mass spectrometry (LC-FT-ICR-MS), liquid chromatograph-hybrid triple quadrupole linear ion trap mass spectrometer with information dependent acquisition, ultra high performance liquid chromatography-time of flight-mass spectrometry (UHPLC-TOF-MS), ion mobility spectroscopy (IMS) and immunoassay methods. The many challenges in detecting and characterizing such adulterants, and the need for concerted effort to curb adulteration in order to safe guard public safety and interest are discussed. PMID:23721687
Punzalan, Florencio Rusty; Kunieda, Yoshitoshi; Amano, Akira
2015-01-01
Clinical and experimental studies involving human hearts can have certain limitations. Methods such as computer simulations can be an important alternative or supplemental tool. Physiological simulation at the tissue or organ level typically involves the handling of partial differential equations (PDEs). Boundary conditions and distributed parameters, such as those used in pharmacokinetics simulation, add to the complexity of the PDE solution. These factors can tailor PDE solutions and their corresponding program code to specific problems. Boundary condition and parameter changes in the customized code are usually prone to errors and time-consuming. We propose a general approach for handling PDEs and boundary conditions in computational models using a replacement scheme for discretization. This study is an extension of a program generator that we introduced in a previous publication. The program generator can generate code for multi-cell simulations of cardiac electrophysiology. Improvements to the system allow it to handle simultaneous equations in the biological function model as well as implicit PDE numerical schemes. The replacement scheme involves substituting all partial differential terms with numerical solution equations. Once the model and boundary equations are discretized with the numerical solution scheme, instances of the equations are generated to undergo dependency analysis. The result of the dependency analysis is then used to generate the program code. The resulting program code are in Java or C programming language. To validate the automatic handling of boundary conditions in the program code generator, we generated simulation code using the FHN, Luo-Rudy 1, and Hund-Rudy cell models and run cell-to-cell coupling and action potential propagation simulations. One of the simulations is based on a published experiment and simulation results are compared with the experimental data. We conclude that the proposed program code generator can be used to
Yang, Shao-Hua; Bi, Xiao-Jun; Xie, Yan; Li, Cong; Zhang, Sheng-Li; Zhang, Qin; Sun, Dong-Xiao
2015-01-01
Phosphodiesterase9A (PDE9A) is a cyclic guanosine monophosphate (cGMP)-specific enzyme widely expressed among the tissues, which is important in activating cGMP-dependent signaling pathways. In our previous genome-wide association study, a single nucleotide polymorphism (SNP) (BTA-55340-no-rsb) located in the intron 14 of PDE9A, was found to be significantly associated with protein yield. In addition, we found that PDE9A was highly expressed in mammary gland by analyzing its mRNA expression in different tissues. The objectives of this study were to identify genetic polymorphisms of PDE9A and to determine the effects of these variants on milk production traits in dairy cattle. DNA sequencing identified 11 single nucleotide polymorphisms (SNPs) and six SNPs in 5′ regulatory region were genotyped to test for the subsequent association analyses. After Bonferroni correction for multiple testing, all these identified SNPs were statistically significant for one or more milk production traits (p < 0.0001~0.0077). Interestingly, haplotype-based association analysis revealed similar effects on milk production traits (p < 0.01). In follow-up RNA expression analyses, two SNPs (c.-1376 G>A, c.-724 A>G) were involved in the regulation of gene expression. Consequently, our findings provide confirmatory evidences for associations of PDE9A variants with milk production traits and these identified SNPs may serve as genetic markers to accelerate Chinese Holstein breeding program. PMID:26556348
Liu, Jianrong; Wenzel, Barbara; Dukic-Stefanovic, Sladjana; Teodoro, Rodrigo; Ludwig, Friedrich-Alexander; Deuther-Conrad, Winnie; Schröder, Susann; Chezal, Jean-Michel; Moreau, Emmanuel; Brust, Peter; Maisonial-Besset, Aurélie
2016-01-01
Phosphodiesterases (PDEs) are enzymes that play a major role in cell signalling by hydrolysing the secondary messengers cyclic adenosine monophosphate (cAMP) and/or cyclic guanosine monophosphate (cGMP) throughout the body and brain. Altered cyclic nucleotide-mediated signalling has been associated with a wide array of disorders, including neurodegenerative disorders. Recently, PDE5 has been shown to be involved in neurodegenerative disorders such as Alzheimer’s disease, but its precise role has not been elucidated yet. To visualize and quantify the expression of this enzyme in brain, we developed a radiotracer for specific PET imaging of PDE5. A quinoline-based lead compound has been structurally modified resulting in the fluoroethoxymethyl derivative ICF24027 with high inhibitory activity towards PDE5 (IC50 = 1.86 nM). Radiolabelling with fluorine-18 was performed by a one-step nucleophilic substitution reaction using a tosylate precursor (RCY(EOB) = 12.9% ± 1.8%; RCP > 99%; SA(EOS) = 70–126 GBq/μmol). In vitro autoradiographic studies of [18F]ICF24027 on different mouse tissue as well as on porcine brain slices demonstrated a moderate specific binding to PDE5. In vivo studies in mice revealed that [18F]ICF24027 was metabolized under formation of brain penetrable radiometabolites making the radiotracer unsuitable for PET imaging of PDE5 in brain. PMID:27110797
Piccart, Elisabeth; De Backer, Jean-François; Gall, David; Lambot, Laurie; Raes, Adam; Vanhoof, Greet; Schiffmann, Serge; D'Hooge, Rudi
2014-07-15
The striatum is the main input structure to the basal ganglia and consists mainly out of medium spiny neurons. The numerous spines on their dendrites render them capable of integrating cortical glutamatergic inputs with a motivational dopaminergic signal that originates in the midbrain. This integrative function is thought to underly attribution of incentive salience, a process that is severely disrupted in schizophrenic patients. Phosphodiesterase 10A (PDE10A) is located mainly to the striatal medium spiny neurons and hydrolyses cAMP and cGMP, key determinants of MSN signaling. We show here that genetic depletion of PDE10A critically mediates attribution of salience to reward-predicting cues, evident in impaired performance in PDE10A knockout mice in an instrumentally conditioned reinforcement task. We furthermore report modest impairment of latent inhibition in PDE10A knockout mice, and unaltered prepulse inhibition. We suggest that the lack of effect on PPI is due to the pre-attentional nature of this task. Finally, we performed whole-cell patch clamp recordings and confirm suggested changes in intrinsic membrane excitability. A decrease in spontaneous firing in striatal medium spiny neurons was found. These data show that PDE10A plays a pivotal role in striatal signaling and striatum-mediated salience attribution.
Prediction of meteor shower associated with Comet 122P/de Vico
NASA Astrophysics Data System (ADS)
Tomko, Dusan; Neslusan, Lubos
2013-01-01
We model, for a far past, a theoretical stream associated with Comet 122P/de Vico and follow its dynamical evolution until present. Selecting the modeled particles approaching the Earth's orbit at the present, we predict the characteristics of a potential meteor shower and try to identify these particles with the meteors in three databases (photo, radar, and video). Our overall prediction is, however, negative because only the particles released from the comet nucleus before approximately 37 000 years ago are found to evolve into a collision course with the Earth and, therefore, form a possible shower. Meteoroids are known to survive a much shorter time in interplanetary space, unfortunately.
Carnosic acid slows photoreceptor degeneration in the Pde6brd10 mouse model of retinitis pigmentosa
Kang, Kai; Tarchick, Matthew J.; Yu, Xiaoshan; Beight, Craig; Bu, Ping; Yu, Minzhong
2016-01-01
The photoreceptor cell death associated with the various genetic forms of retinitis pigmentosa (RP) is currently untreatable and leads to partial or complete vision loss. Carnosic acid (CA) upregulates endogenous antioxidant enzymes and has proven neuroprotective in studies of neurodegenerative models affecting the brain. In this study, we examined the potential effect of CA on photoreceptor death in the Pde6brd10 mouse model of RP. Our data shows that CA provided morphological and functional preservation of photoreceptors. CA appears to exert its neuroprotective effects through inhibition of oxidative stress and endoplasmic reticulum stress. PMID:26961159
A discontinuous Galerkin method for two-dimensional PDE models of Asian options
NASA Astrophysics Data System (ADS)
Hozman, J.; Tichý, T.; Cvejnová, D.
2016-06-01
In our previous research we have focused on the problem of plain vanilla option valuation using discontinuous Galerkin method for numerical PDE solution. Here we extend a simple one-dimensional problem into two-dimensional one and design a scheme for valuation of Asian options, i.e. options with payoff depending on the average of prices collected over prespecified horizon. The algorithm is based on the approach combining the advantages of the finite element methods together with the piecewise polynomial generally discontinuous approximations. Finally, an illustrative example using DAX option market data is provided.
Apremilast is a selective PDE4 inhibitor with regulatory effects on innate immunity.
Schafer, P H; Parton, A; Capone, L; Cedzik, D; Brady, H; Evans, J F; Man, H-W; Muller, G W; Stirling, D I; Chopra, R
2014-09-01
Apremilast, an oral small molecule inhibitor of phosphodiesterase 4 (PDE4), is in development for chronic inflammatory disorders, and has shown efficacy in psoriasis, psoriatic arthropathies, and Behçet's syndrome. In March 2014, the US Food and Drug Administration approved apremilast for the treatment of adult patients with active psoriatic arthritis. The properties of apremilast were evaluated to determine its specificity, effects on intracellular signaling, gene and protein expression, and in vivo pharmacology using models of innate and adaptive immunity. Apremilast inhibited PDE4 isoforms from all four sub-families (A1A, B1, B2, C1, and D2), with IC50 values in the range of 10 to 100 nM. Apremilast did not significantly inhibit other PDEs, kinases, enzymes, or receptors. While both apremilast and thalidomide share a phthalimide ring structure, apremilast lacks the glutarimide ring and thus fails to bind to cereblon, the target of thalidomide action. In monocytes and T cells, apremilast elevated intracellular cAMP and induced phosphorylation of the protein kinase A substrates CREB and activating transcription factor-1 while inhibiting NF-κB transcriptional activity, resulting in both up- and down-regulation of several genes induced via TLR4. Apremilast reduced interferon-α production by plasmacytoid dendritic cells and inhibited T-cell cytokine production, but had little effect on B-cell immunoglobulin secretion. In a transgenic T-cell and B-cell transfer murine model, apremilast (5mg/kg/day p.o.) did not affect clonal expansion of either T or B cells and had little or no effect on their expression of activation markers. The effect of apremilast on innate immunity was tested in the ferret lung neutrophilia model, which allows monitoring of the known PDE4 inhibitor gastrointestinal side effects (nausea and vomiting). Apremilast significantly inhibited lung neutrophilia at 1mg/kg, but did not induce significant emetic reflexes at doses <30 mg/kg. Overall, the
Navier-Stokes Solvers and Generalizations for Reacting Flow Problems
Elman, Howard C
2013-01-27
This is an overview of our accomplishments during the final term of this grant (1 September 2008 -- 30 June 2012). These fall mainly into three categories: fast algorithms for linear eigenvalue problems; solution algorithms and modeling methods for partial differential equations with uncertain coefficients; and preconditioning methods and solvers for models of computational fluid dynamics (CFD).
Intellectual Abilities That Discriminate Good and Poor Problem Solvers.
ERIC Educational Resources Information Center
Meyer, Ruth Ann
1981-01-01
This study compared good and poor fourth-grade problem solvers on a battery of 19 "reference" tests for verbal, induction, numerical, word fluency, memory, perceptual speed, and simple visualization abilities. Results suggest verbal, numerical, and especially induction abilities are important to successful mathematical problem solving. (MP)
Coordinate Projection-based Solver for ODE with Invariants
2008-04-08
CPODES is a general purpose (serial and parallel) solver for systems of ordinary differential equation (ODE) with invariants. It implements a coordinate projection approach using different types of projection (orthogonal or oblique) and one of several methods for the decompositon of the Jacobian of the invariant equations.
The Adaptive Multi-scale Simulation Infrastructure
Tobin, William R.
2015-09-01
The Adaptive Multi-scale Simulation Infrastructure (AMSI) is a set of libraries and tools developed to support the development, implementation, and execution of general multimodel simulations. Using a minimal set of simulation meta-data AMSI allows for minimally intrusive work to adapt existent single-scale simulations for use in multi-scale simulations. Support for dynamic runtime operations such as single- and multi-scale adaptive properties is a key focus of AMSI. Particular focus has been spent on the development on scale-sensitive load balancing operations to allow single-scale simulations incorporated into a multi-scale simulation using AMSI to use standard load-balancing operations without affecting the integrity of the overall multi-scale simulation.
Fluid simulations with atomistic resolution: a hybrid multiscale method with field-wise coupling
Borg, Matthew K.; Lockerby, Duncan A.; Reese, Jason M.
2013-12-15
We present a new hybrid method for simulating dense fluid systems that exhibit multiscale behaviour, in particular, systems in which a Navier–Stokes model may not be valid in parts of the computational domain. We apply molecular dynamics as a local microscopic refinement for correcting the Navier–Stokes constitutive approximation in the bulk of the domain, as well as providing a direct measurement of velocity slip at bounding surfaces. Our hybrid approach differs from existing techniques, such as the heterogeneous multiscale method (HMM), in some fundamental respects. In our method, the individual molecular solvers, which provide information to the macro model, are not coupled with the continuum grid at nodes (i.e. point-wise coupling), instead coupling occurs over distributed heterogeneous fields (here referred to as field-wise coupling). This affords two major advantages. Whereas point-wise coupled HMM is limited to regions of flow that are highly scale-separated in all spatial directions (i.e. where the state of non-equilibrium in the fluid can be adequately described by a single strain tensor and temperature gradient vector), our field-wise coupled HMM has no such limitations and so can be applied to flows with arbitrarily-varying degrees of scale separation (e.g. flow from a large reservoir into a nano-channel). The second major advantage is that the position of molecular elements does not need to be collocated with nodes of the continuum grid, which means that the resolution of the microscopic correction can be adjusted independently of the resolution of the continuum model. This in turn means the computational cost and accuracy of the molecular correction can be independently controlled and optimised. The macroscopic constraints on the individual molecular solvers are artificial body-force distributions, used in conjunction with standard periodicity. We test our hybrid method on the Poiseuille flow problem for both Newtonian (Lennard-Jones) and non
Avila, Diana V; Barker, David F; Zhang, JingWen; McClain, Craig J; Barve, Shirish; Gobejishvili, Leila
2016-09-01
Alcohol-induced hepatic steatosis is a significant risk factor for progressive liver disease. Cyclic adenosine monophosphate (cAMP) signalling has been shown to significantly regulate lipid metabolism; however, the role of altered cAMP homeostasis in alcohol-mediated hepatic steatosis has never been studied. Our previous work demonstrated that increased expression of hepatic phosphodiesterase 4 (Pde4), which specifically hydrolyses and decreases cAMP levels, plays a pathogenic role in the development of liver inflammation/injury. The aim of this study was to examine the role of PDE4 in alcohol-induced hepatic steatosis. C57BL/6 wild-type and Pde4b knockout (Pde4b(-/-) ) mice were pair-fed control or ethanol liquid diets. One group of wild-type mice received rolipram, a PDE4-specific inhibitor, during alcohol feeding. We demonstrate for the first time that an early increase in PDE4 enzyme expression and a resultant decrease in hepatic cAMP levels are associated with the significant reduction in carnitine palmitoyltransferase 1A (Cpt1a) expression. Notably, alcohol-fed (AF) Pde4b(-/-) mice and AF wild-type mice treated with rolipram had significantly lower hepatic free fatty acid content compared with AF wild-type mice. Importantly, PDE4 inhibition in alcohol-fed mice prevented the decrease in hepatic Cpt1a expression via the Pparα/Sirt1/Pgc1α pathway. These results demonstrate that the alcohol- induced increase in hepatic Pde4, specifically Pde4b expression, and compromised cAMP signalling predispose the liver to impaired fatty acid oxidation and the development of steatosis. Moreover, these data also suggest that hepatic PDE4 may be a clinically relevant therapeutic target for the treatment of alcohol-induced hepatic steatosis. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. PMID:27287961
Migration of vectorized iterative solvers to distributed memory architectures
Pommerell, C.; Ruehl, R.
1994-12-31
Both necessity and opportunity motivate the use of high-performance computers for iterative linear solvers. Necessity results from the size of the problems being solved-smaller problems are often better handled by direct methods. Opportunity arises from the formulation of the iterative methods in terms of simple linear algebra operations, even if this {open_quote}natural{close_quotes} parallelism is not easy to exploit in irregularly structured sparse matrices and with good preconditioners. As a result, high-performance implementations of iterative solvers have attracted a lot of interest in recent years. Most efforts are geared to vectorize or parallelize the dominating operation-structured or unstructured sparse matrix-vector multiplication, or to increase locality and parallelism by reformulating the algorithm-reducing global synchronization in inner products or local data exchange in preconditioners. Target architectures for iterative solvers currently include mostly vector supercomputers and architectures with one or few optimized (e.g., super-scalar and/or super-pipelined RISC) processors and hierarchical memory systems. More recently, parallel computers with physically distributed memory and a better price/performance ratio have been offered by vendors as a very interesting alternative to vector supercomputers. However, programming comfort on such distributed memory parallel processors (DMPPs) still lags behind. Here the authors are concerned with iterative solvers and their changing computing environment. In particular, they are considering migration from traditional vector supercomputers to DMPPs. Application requirements force one to use flexible and portable libraries. They want to extend the portability of iterative solvers rather than reimplementing everything for each new machine, or even for each new architecture.
Decision Engines for Software Analysis Using Satisfiability Modulo Theories Solvers
NASA Technical Reports Server (NTRS)
Bjorner, Nikolaj
2010-01-01
The area of software analysis, testing and verification is now undergoing a revolution thanks to the use of automated and scalable support for logical methods. A well-recognized premise is that at the core of software analysis engines is invariably a component using logical formulas for describing states and transformations between system states. The process of using this information for discovering and checking program properties (including such important properties as safety and security) amounts to automatic theorem proving. In particular, theorem provers that directly support common software constructs offer a compelling basis. Such provers are commonly called satisfiability modulo theories (SMT) solvers. Z3 is a state-of-the-art SMT solver. It is developed at Microsoft Research. It can be used to check the satisfiability of logical formulas over one or more theories such as arithmetic, bit-vectors, lists, records and arrays. The talk describes some of the technology behind modern SMT solvers, including the solver Z3. Z3 is currently mainly targeted at solving problems that arise in software analysis and verification. It has been applied to various contexts, such as systems for dynamic symbolic simulation (Pex, SAGE, Vigilante), for program verification and extended static checking (Spec#/Boggie, VCC, HAVOC), for software model checking (Yogi, SLAM), model-based design (FORMULA), security protocol code (F7), program run-time analysis and invariant generation (VS3). We will describe how it integrates support for a variety of theories that arise naturally in the context of the applications. There are several new promising avenues and the talk will touch on some of these and the challenges related to SMT solvers. Proceedings
Peridynamic Multiscale Finite Element Methods
Costa, Timothy; Bond, Stephen D.; Littlewood, David John; Moore, Stan Gerald
2015-12-01
The problem of computing quantum-accurate design-scale solutions to mechanics problems is rich with applications and serves as the background to modern multiscale science research. The prob- lem can be broken into component problems comprised of communicating across adjacent scales, which when strung together create a pipeline for information to travel from quantum scales to design scales. Traditionally, this involves connections between a) quantum electronic structure calculations and molecular dynamics and between b) molecular dynamics and local partial differ- ential equation models at the design scale. The second step, b), is particularly challenging since the appropriate scales of molecular dynamic and local partial differential equation models do not overlap. The peridynamic model for continuum mechanics provides an advantage in this endeavor, as the basic equations of peridynamics are valid at a wide range of scales limiting from the classical partial differential equation models valid at the design scale to the scale of molecular dynamics. In this work we focus on the development of multiscale finite element methods for the peridynamic model, in an effort to create a mathematically consistent channel for microscale information to travel from the upper limits of the molecular dynamics scale to the design scale. In particular, we first develop a Nonlocal Multiscale Finite Element Method which solves the peridynamic model at multiple scales to include microscale information at the coarse-scale. We then consider a method that solves a fine-scale peridynamic model to build element-support basis functions for a coarse- scale local partial differential equation model, called the Mixed Locality Multiscale Finite Element Method. Given decades of research and development into finite element codes for the local partial differential equation models of continuum mechanics there is a strong desire to couple local and nonlocal models to leverage the speed and state of the
Efficient three-dimensional Poisson solvers in open rectangular conducting pipe
NASA Astrophysics Data System (ADS)
Qiang, Ji
2016-06-01
Three-dimensional (3D) Poisson solver plays an important role in the study of space-charge effects on charged particle beam dynamics in particle accelerators. In this paper, we propose three new 3D Poisson solvers for a charged particle beam in an open rectangular conducting pipe. These three solvers include a spectral integrated Green function (IGF) solver, a 3D spectral solver, and a 3D integrated Green function solver. These solvers effectively handle the longitudinal open boundary condition using a finite computational domain that contains the beam itself. This saves the computational cost of using an extra larger longitudinal domain in order to set up an appropriate finite boundary condition. Using an integrated Green function also avoids the need to resolve rapid variation of the Green function inside the beam. The numerical operational cost of the spectral IGF solver and the 3D IGF solver scales as O(N log(N)) , where N is the number of grid points. The cost of the 3D spectral solver scales as O(Nn N) , where Nn is the maximum longitudinal mode number. We compare these three solvers using several numerical examples and discuss the advantageous regime of each solver in the physical application.
Faria, Ana Paula Cabral de; Modolo, Rodrigo; Moreno, Beatriz Vaz Domingues; Moreno, Heitor
2015-01-01
Resistant hypertension (RHTN) is a multifactorial disease characterized by blood pressure (BP) levels above goal (140/90 mmHg) in spite of the concurrent use of three or more antihypertensive drugs of different classes. Moreover, it is well known that RHTN subjects have high prevalence of left ventricular diastolic dysfunction (LVDD), which leads to increased risk of heart failure progression. This review gathers data from studies evaluating the effects of phosphodiesterase-5 (PDE-5) inhibitors (administration of acute sildenafil and short-term tadalafil) on diastolic function, biochemical and hemodynamic parameters in patients with RHTN. Acute study with sildenafil treatment found that inhibition of PDE-5 improved hemodynamic parameters and diastolic relaxation. In addition, short-term study with the use of tadalafil demonstrated improvement of LVDD, cGMP and BNP-32 levels, regardless of BP reduction. No endothelial function changes were observed in the studies. The findings of acute and short-term studies revealed potential therapeutic effects of IPDE-5 drugs on LVDD in RHTN patients.
Effective viscosity of bacterial suspensions: a three-dimensional PDE model with stochastic torque.
Haines, B. M.; Aranson, I. S.; Berlyand, L.; Karpeev, D. A.
2012-01-01
We present a PDE model for dilute suspensions of swimming bacteria in a three-dimensional Stokesian fluid. This model is used to calculate the statistically-stationary bulk deviatoric stress and effective viscosity of the suspension from the microscopic details of the interaction of an elongated body with the background flow. A bacterium is modeled as an impenetrable prolate spheroid with self-propulsion provided by a point force, which appears in the model as an inhomogeneous delta function in the PDE. The bacterium is also subject to a stochastic torque in order to model tumbling (random reorientation). Due to a bacterium's asymmetric shape, interactions with prescribed generic planar background flows, such as a pure straining or planar shear flow, cause the bacterium to preferentially align in certain directions. Due to the stochastic torque, the steady-state distribution of orientations is unique for a given background flow. Under this distribution of orientations, self-propulsion produces a reduction in the effective viscosity. For sufficiently weak background flows, the effect of self-propulsion on the effective viscosity dominates all other contributions, leading to an effective viscosity of the suspension that is lower than the viscosity of the ambient fluid. This is in qualitative agreement with recent experiments on suspensions of Bacillus subtilis.
PDE5 inhibitors enhance tumor permeability and efficacy of chemotherapy in a rat brain tumor model.
Black, Keith L; Yin, Dali; Ong, John M; Hu, Jinwei; Konda, Bindu M; Wang, Xiao; Ko, MinHee K; Bayan, Jennifer-Ann; Sacapano, Manuel R; Espinoza, Andreas; Irvin, Dwain K; Shu, Yan
2008-09-16
The blood-brain tumor barrier (BTB) significantly limits delivery of therapeutic concentrations of chemotherapy to brain tumors. A novel approach to selectively increase drug delivery is pharmacologic modulation of signaling molecules that regulate BTB permeability, such as those in cGMP signaling. Here we show that oral administration of sildenafil (Viagra) and vardenafil (Levitra), inhibitors of cGMP-specific PDE5, selectively increased tumor capillary permeability in 9L gliosarcoma-bearing rats with no significant increase in normal brain capillaries. Tumor-bearing rats treated with the chemotherapy agent, adriamycin, in combination with vardenafil survived significantly longer than rats treated with adriamycin alone. The selective increase in tumor capillary permeability appears to be mediated by a selective increase in tumor cGMP levels and increased vesicular transport through tumor capillaries, and could be attenuated by iberiotoxin, a selective inhibitor for calcium-dependent potassium (K(Ca)) channels, that are effectors in cGMP signaling. The effect by sildenafil could be further increased by simultaneously using another BTB "opener", bradykinin. Collectively, this data demonstrates that oral administration of PDE5 inhibitors selectively increases BTB permeability and enhances anti-tumor efficacy for a chemotherapeutic agent. These findings have significant implications for improving delivery of anti-tumor agents to brain tumors. PMID:18674521
A Cell-based PDE4 Assay in 1536-well Plate format for High Throughput Screening
Titus, Steven A.; Li, Xiao; Southall, Noel; Lu, Jianming; Inglese, James; Brasch, Michael; Austin, Christopher P.; Zheng, Wei
2009-01-01
The cyclic nucleotide phosphodiesterases (PDEs) are intracellular enzymes that catalyze the hydrolysis of 3', 5'-cyclic nucleotides, such as cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP), to their corresponding 5'-nucleotide monophosphates. These enzymes play an important role in controlling cellular concentrations of cyclic nucleotides and thus regulate a variety of cellular signaling events. PDEs are emerging as drug targets for several diseases including asthma, cardiovascular disease, ADHD, Parkinson’s disease, and Alzheimer’s disease. Though biochemical assays with purified recombinant PDE enzymes and cAMP or cGMP substrate are commonly used for compound screening, cell-based assays would provide a better assessment of compound activity in a more physiological context. Here we report the development and validation of a new cell-based PDE4 assay using a constitutively active GPCR as a driving force for cAMP production and a cyclic nucleotide gated (CNG) cation channel as a biosensor in 1536-well plates. PMID:18591513
Inhibition of PDE5 Restores Depressed Baroreflex Sensitivity in Renovascular Hypertensive Rats
Cavalcanti, Clênia de Oliveira; Alves, Rafael R.; de Oliveira, Alessandro L.; Cruz, Josiane de Campos; de França-Silva, Maria do Socorro; Braga, Valdir de Andrade; Balarini, Camille de Moura
2016-01-01
Renal artery stenosis is frequently associated with resistant hypertension, which is defined as failure to normalize blood pressure (BP) even when combined drugs are used. Inhibition of PDE5 by sildenafil has been shown to increase endothelial function and decrease blood pressure in experimental models. However, no available study evaluated the baroreflex sensitivity nor autonomic balance in renovascular hypertensive rats treated with sildenafil. In a translational medicine perspective, our hypothesis is that sildenafil could improve autonomic imbalance and baroreflex sensitivity, contributing to lower blood pressure. Renovascular hypertensive 2-kidney-1-clip (2K1C) and sham rats were treated with sildenafil (45 mg/Kg/day) during 7 days. At the end of treatment, BP and heart rate (HR) were recorded in conscious rats after a 24-h-recovery period. Spontaneous and drug-induced baroreflex sensitivity and autonomic tone were evaluated; in addition, lipid peroxidation was measured in plasma samples. Treatment was efficient in increasing both spontaneous and induced baroreflex sensitivity in treated hypertensive animals. Inhibition of PDE5 was also capable of ameliorating autonomic imbalance in 2K1C rats and decreasing systemic oxidative stress. Taken together, these beneficial effects resulted in significant reductions in BP without affecting HR. We suggest that sildenafil could be considered as a promising alternative to treat resistant hypertension. PMID:26858657
Faria, Ana Paula Cabral de; Modolo, Rodrigo; Moreno, Beatriz Vaz Domingues; Moreno, Heitor
2015-01-01
Resistant hypertension (RHTN) is a multifactorial disease characterized by blood pressure (BP) levels above goal (140/90 mmHg) in spite of the concurrent use of three or more antihypertensive drugs of different classes. Moreover, it is well known that RHTN subjects have high prevalence of left ventricular diastolic dysfunction (LVDD), which leads to increased risk of heart failure progression. This review gathers data from studies evaluating the effects of phosphodiesterase-5 (PDE-5) inhibitors (administration of acute sildenafil and short-term tadalafil) on diastolic function, biochemical and hemodynamic parameters in patients with RHTN. Acute study with sildenafil treatment found that inhibition of PDE-5 improved hemodynamic parameters and diastolic relaxation. In addition, short-term study with the use of tadalafil demonstrated improvement of LVDD, cGMP and BNP-32 levels, regardless of BP reduction. No endothelial function changes were observed in the studies. The findings of acute and short-term studies revealed potential therapeutic effects of IPDE-5 drugs on LVDD in RHTN patients. PMID:25352458
Rodríguez-Izquierdo, Marta; Martínez-Salamanca, Juan I; Moncada, Ignacio; Linares Espinós, Estefanía; del Portillo, Luis; Areche, Jennifer; Carballido, Joaquín
2013-09-01
Androgens play an essential role in the corporo-venous occlusive mechanism that provokes erection. Accordingly to various studies based on animal models,testosterone deficit syndrome causes an endothelial disorder in the corpora cavernosa with diminished secretion of NO, alteration of penile smooth muscle and tunica albuginea structure, and increase of the number of adipocytes within the erectile tissue, which favors fibrosis and impairs erection. All these alterations are reversible with the exogenous administration of androgens. There are not enough studies to get definitive conclusions about androgen supply improving erectile dysfunction in patients with hypogonadism. Studies have been published in which seems that exogenous testosterone could be useful in the treatment of this type of patients. Nevertheless,in most published randomized double blind studies comparing with placebo, testosterone supply does not provide greater benefit on erectile dysfunction than PDE-5 Inhibitors exclusively. All studies coincide in the need to optimize the treatment with PDE-5 Inhibitors since they do have proven to be effective for the treatment of erectile dysfunction in patients with testosterone deficit syndrome. PMID:24047632
2009-08-01
The code to be released is a new addition to the LAMMPS molecular dynamics code. LAMMPS is developed and maintained by Sandia, is publicly available, and is used widely by both natioanl laboratories and academics. The new addition to be released enables LAMMPS to perform molecular dynamics simulations of shock waves using the Multi-scale Shock Simulation Technique (MSST) which we have developed and has been previously published. This technique enables molecular dynamics simulations of shockmore » waves in materials for orders of magnitude longer timescales than the direct, commonly employed approach.« less
Mika, Delphine; Richter, Wito; Westenbroek, Ruth E; Catterall, William A; Conti, Marco
2014-03-01
Multiple cAMP phosphodiesterase (PDE) isoforms play divergent roles in cardiac homeostasis but the molecular basis for their non-redundant function remains poorly understood. Here, we report a novel role for the PDE4B isoform in β-adrenergic (βAR) signaling in the heart. Genetic ablation of PDE4B disrupted βAR-induced cAMP transients, as measured by FRET sensors, at the sarcolemma but not in the bulk cytosol of cardiomyocytes. This effect was further restricted to a subsarcolemmal compartment because PDE4B regulates β1AR-, but not β2AR- or PGE2-induced responses. The spatially restricted function of PDE4B was confirmed by its selective effects on PKA-mediated phosphorylation patterns. PDE4B limited the PKA-mediated phosphorylation of key players in excitation-contraction coupling that reside in the sarcolemmal compartment, including L-type Ca(2+) channels and ryanodine receptors, but not phosphorylation of distal cytosolic proteins. β1AR- but not β2AR-ligation induced PKA-dependent activation of PDE4B and interruption of this negative feedback with PKA inhibitors increased sarcolemmal cAMP. Thus, PDE4B mediates a crucial PKA-dependent feedback that controls β1AR-dependent cAMP signals in a restricted subsarcolemmal domain. Disruption of this feedback augments local cAMP/PKA signals, leading to an increased intracellular Ca(2+) level and contraction rate.
Griebel, M. E-mail: ruettgers@ins.uni-bonn.de; Rüttgers, A. E-mail: ruettgers@ins.uni-bonn.de
2014-05-15
The multiscale FENE model is applied to a 3D square-square contraction flow problem. For this purpose, the stochastic Brownian configuration field method (BCF) has been coupled with our fully parallelized three-dimensional Navier-Stokes solver NaSt3DGPF. The robustness of the BCF method enables the numerical simulation of high Deborah number flows for which most macroscopic methods suffer from stability issues. The results of our simulations are compared with that of experimental measurements from literature and show a very good agreement. In particular, flow phenomena such as a strong vortex enhancement, streamline divergence and a flow inversion for highly elastic flows are reproduced. Due to their computational complexity, our simulations require massively parallel computations. Using a domain decomposition approach with MPI, the implementation achieves excellent scale-up results for up to 128 processors.
Modeling Complex Biological Flows in Multi-Scale Systems using the APDEC Framework
Trebotich, D
2006-06-24
We have developed advanced numerical algorithms to model biological fluids in multiscale flow environments using the software framework developed under the SciDAC APDEC ISIC. The foundation of our computational effort is an approach for modeling DNA-laden fluids as ''bead-rod'' polymers whose dynamics are fully coupled to an incompressible viscous solvent. The method is capable of modeling short range forces and interactions between particles using soft potentials and rigid constraints. Our methods are based on higher-order finite difference methods in complex geometry with adaptivity, leveraging algorithms and solvers in the APDEC Framework. Our Cartesian grid embedded boundary approach to incompressible viscous flow in irregular geometries has also been interfaced to a fast and accurate level-sets method within the APDEC Framework for extracting surfaces from volume renderings of medical image data and used to simulate cardio-vascular and pulmonary flows in critical anatomies.
NASA Technical Reports Server (NTRS)
Ricks, Trenton M.; Lacy, Thomas E., Jr.; Pineda, Evan J.; Bednarcyk, Brett A.; Arnold, Steven M.
2013-01-01
A multiscale modeling methodology, which incorporates a statistical distribution of fiber strengths into coupled micromechanics/ finite element analyses, is applied to unidirectional polymer matrix composites (PMCs) to analyze the effect of mesh discretization both at the micro- and macroscales on the predicted ultimate tensile (UTS) strength and failure behavior. The NASA code FEAMAC and the ABAQUS finite element solver were used to analyze the progressive failure of a PMC tensile specimen that initiates at the repeating unit cell (RUC) level. Three different finite element mesh densities were employed and each coupled with an appropriate RUC. Multiple simulations were performed in order to assess the effect of a statistical distribution of fiber strengths on the bulk composite failure and predicted strength. The coupled effects of both the micro- and macroscale discretizations were found to have a noticeable effect on the predicted UTS and computational efficiency of the simulations.
Towards a Multiscale Approach to Cybersecurity Modeling
Hogan, Emilie A.; Hui, Peter SY; Choudhury, Sutanay; Halappanavar, Mahantesh; Oler, Kiri J.; Joslyn, Cliff A.
2013-11-12
We propose a multiscale approach to modeling cyber networks, with the goal of capturing a view of the network and overall situational awareness with respect to a few key properties--- connectivity, distance, and centrality--- for a system under an active attack. We focus on theoretical and algorithmic foundations of multiscale graphs, coming from an algorithmic perspective, with the goal of modeling cyber system defense as a specific use case scenario. We first define a notion of \\emph{multiscale} graphs, in contrast with their well-studied single-scale counterparts. We develop multiscale analogs of paths and distance metrics. As a simple, motivating example of a common metric, we present a multiscale analog of the all-pairs shortest-path problem, along with a multiscale analog of a well-known algorithm which solves it. From a cyber defense perspective, this metric might be used to model the distance from an attacker's position in the network to a sensitive machine. In addition, we investigate probabilistic models of connectivity. These models exploit the hierarchy to quantify the likelihood that sensitive targets might be reachable from compromised nodes. We believe that our novel multiscale approach to modeling cyber-physical systems will advance several aspects of cyber defense, specifically allowing for a more efficient and agile approach to defending these systems.
Multiscale optimization in neural nets.
Mjolsness, E; Garrett, C D; Miranker, W L
1991-01-01
One way to speed up convergence in a large optimization problem is to introduce a smaller, approximate version of the problem at a coarser scale and to alternate between relaxation steps for the fine-scale and coarse-scale problems. Such an optimization method for neural networks governed by quite general objective functions is presented. At the coarse scale, there is a smaller approximating neural net which, like the original net, is nonlinear and has a nonquadratic objective function. The transitions and information flow from fine to coarse scale and back do not disrupt the optimization, and the user need only specify a partition of the original fine-scale variables. Thus, the method can be applied easily to many problems and networks. There is generally about a fivefold improvement in estimated cost under the multiscale method. In the networks to which it was applied, a nontrivial speedup by a constant factor of between two and five was observed, independent of problem size. Further improvements in computational cost are very likely to be available, especially for problem-specific multiscale neural net methods.
A parallel-vector equation solver for unsymmetric matrices on supercomputers
NASA Technical Reports Server (NTRS)
Qin, J.; Mei, C.; Nguyen, D. T.; Gray, C. E., Jr.
1991-01-01
A parallel-vector unsymmetric equation solver is presented. The solver exploits both vector and parallel capabilities provided by modern, high-performance supercomputers. A special storage scheme and loop-unrolling technique are used to optimize the vector performance. A parallel FORTRAN language is used to develop the solver on the CRAY 2 and CRAY Y-MP multiple processing computer environment. Three numerical examples are presented which demonstrate the efficiency and accuracy of this equation solver. The first two examples demonstrate the improved performance, and the third example utilizes the proposed solver to solve a highly nonlinear, unsymmetric finite element formulation for panel flutter.
Rethinking Electrostatic Solvers in Particle Simulations for the Exascale Era
NASA Astrophysics Data System (ADS)
Deca, Jan; Markidis, Stefano; Lapenta, Giovanni; Járleberg, Erik; Apostolov, Rossen; Laure, Erwin
2012-10-01
In preparation to the exascale era, an alternative approach to calculate the electrostatic forces in Particle Mesh (PM) methods is proposed. While the traditional techniques are based on the calculation of the electrostatic potential by solving the Poisson equation, in the new approach the electric field is calculated by solving Ampère's law. When the Ampere's law is discretized explicitly in time, the electric field values on the mesh are simply updated from the previous values. In this way, the electrostatic solver becomes an embarrassingly parallel problem, making the algorithm extremely scalable and suitable for exascale computing platforms. An implementation PM code with the new electrostatic solver is presented to show that the proposed method produces correct results. It is a very promising algorithm for exascale PM simulations.
LDRD report : parallel repartitioning for optimal solver performance.
Heaphy, Robert; Devine, Karen Dragon; Preis, Robert; Hendrickson, Bruce Alan; Heroux, Michael Allen; Boman, Erik Gunnar
2004-02-01
We have developed infrastructure, utilities and partitioning methods to improve data partitioning in linear solvers and preconditioners. Our efforts included incorporation of data repartitioning capabilities from the Zoltan toolkit into the Trilinos solver framework, (allowing dynamic repartitioning of Trilinos matrices); implementation of efficient distributed data directories and unstructured communication utilities in Zoltan and Trilinos; development of a new multi-constraint geometric partitioning algorithm (which can generate one decomposition that is good with respect to multiple criteria); and research into hypergraph partitioning algorithms (which provide up to 56% reduction of communication volume compared to graph partitioning for a number of emerging applications). This report includes descriptions of the infrastructure and algorithms developed, along with results demonstrating the effectiveness of our approaches.
Benchmarking ICRF Full-wave Solvers for ITER
R. V. Budny, L. Berry, R. Bilato, P. Bonoli, M. Brambilla, R. J. Dumont, A. Fukuyama, R. Harvey, E. F. Jaeger, K. Indireshkumar, E. Lerche, D. McCune, C. K. Phillips, V. Vdovin, J. Wright, and members of the ITPA-IOS
2011-01-06
Abstract Benchmarking of full-wave solvers for ICRF simulations is performed using plasma profiles and equilibria obtained from integrated self-consistent modeling predictions of four ITER plasmas. One is for a high performance baseline (5.3 T, 15 MA) DT H-mode. The others are for half-field, half-current plasmas of interest for the pre-activation phase with bulk plasma ion species being either hydrogen or He4. The predicted profiles are used by six full-wave solver groups to simulate the ICRF electromagnetic fields and heating, and by three of these groups to simulate the current-drive. Approximate agreement is achieved for the predicted heating power for the DT and He4 cases. Factor of two disagreements are found for the cases with second harmonic He3 heating in bulk H cases. Approximate agreement is achieved simulating the ICRF current drive.
An exact solver for the DCJ median problem.
Zhang, Meng; Arndt, William; Tang, Jijun
2009-01-01
The "double-cut-and-join" (DCJ) model of genome rearrangement proposed by Yancopoulos et al. uses the single DCJ operation to account for all genome rearrangement events. Given three signed permutations, the DCJ median problem is to find a fourth permutation that minimizes the sum of the pairwise DCJ distances between it and the three others. In this paper, we present a branch-and-bound method that provides accurate solution to the multichromosomal DCJ median problems. We conduct extensive simulations and the results show that the DCJ median solver performs better than other median solvers for most of the test cases. These experiments also suggest that DCJ model is more suitable for real datasets where both reversals and transpositions occur.
Elliptic Solvers with Adaptive Mesh Refinement on Complex Geometries
Phillip, B.
2000-07-24
Adaptive Mesh Refinement (AMR) is a numerical technique for locally tailoring the resolution computational grids. Multilevel algorithms for solving elliptic problems on adaptive grids include the Fast Adaptive Composite grid method (FAC) and its parallel variants (AFAC and AFACx). Theory that confirms the independence of the convergence rates of FAC and AFAC on the number of refinement levels exists under certain ellipticity and approximation property conditions. Similar theory needs to be developed for AFACx. The effectiveness of multigrid-based elliptic solvers such as FAC, AFAC, and AFACx on adaptively refined overlapping grids is not clearly understood. Finally, a non-trivial eye model problem will be solved by combining the power of using overlapping grids for complex moving geometries, AMR, and multilevel elliptic solvers.
Scalable Out-of-Core Solvers on Xeon Phi Cluster
D'Azevedo, Ed F; Chan, Ki Shing; Su, Shiquan; Wong, Kwai
2015-01-01
This paper documents the implementation of a distributive out-of-core (OOC) solver for performing LU and Cholesky factorizations of a large dense matrix on clusters of many-core programmable co-processors. The out-of- core algorithm combines both the left-looking and right-looking schemes aimed to minimize the movement of data between the CPU host and the co-processor, optimizing data locality as well as computing throughput. The OOC solver is built to align with the format of the ScaLAPACK software library, making it readily portable to any existing codes using ScaLAPACK. A runtime analysis conducted on Beacon (an Intel Xeon plus Intel Xeon Phi cluster which composed of 48 nodes of multi-core CPU and MIC) at the Na- tional Institute for Computational Sciences is presented. Comparison of the performance on the Intel Xeon Phi and GPU clusters are also provided.
A functional implementation of the Jacobi eigen-solver
Boehm, A.P.W. . Dept. of Computer Science); Hiromoto, R.E. )
1993-01-01
In this paper, we describe the systematic development of two implementations of the Jacobi eigen-solver and give performance results for the MIT/Motorola Monsoon dataflow machine. Our study is carried out using MINT, the MIT Monsoon simulator. The design of these implementations follows from the mathematics of the Jacobi method, and not from a translation of an existing sequential code. The functional semantics with respect to array updates, which cause excessive array copying, has lead us to a new implementation of a parallel group-rotations'' algorithm first described by Sameh. Our version of this algorithm requires 0(n[sup 3]) operations, whereas Sameh's original version requires 0(n[sup 4]) operations. The implementations are programmed in the language Id, and although Id has non-functional features, we have restricted the development of our eigen-solvers to the functional sub-set of the language.
A functional implementation of the Jacobi eigen-solver
Boehm, A.P.W.; Hiromoto, R.E.
1993-02-01
In this paper, we describe the systematic development of two implementations of the Jacobi eigen-solver and give performance results for the MIT/Motorola Monsoon dataflow machine. Our study is carried out using MINT, the MIT Monsoon simulator. The design of these implementations follows from the mathematics of the Jacobi method, and not from a translation of an existing sequential code. The functional semantics with respect to array updates, which cause excessive array copying, has lead us to a new implementation of a parallel ``group-rotations`` algorithm first described by Sameh. Our version of this algorithm requires 0(n{sup 3}) operations, whereas Sameh`s original version requires 0(n{sup 4}) operations. The implementations are programmed in the language Id, and although Id has non-functional features, we have restricted the development of our eigen-solvers to the functional sub-set of the language.
A spectral Poisson solver for kinetic plasma simulation
NASA Astrophysics Data System (ADS)
Szeremley, Daniel; Obberath, Jens; Brinkmann, Ralf
2011-10-01
Plasma resonance spectroscopy is a well established plasma diagnostic method, realized in several designs. One of these designs is the multipole resonance probe (MRP). In its idealized - geometrically simplified - version it consists of two dielectrically shielded, hemispherical electrodes to which an RF signal is applied. A numerical tool is under development which is capable of simulating the dynamics of the plasma surrounding the MRP in electrostatic approximation. In this contribution we concentrate on the specialized Poisson solver for that tool. The plasma is represented by an ensemble of point charges. By expanding both the charge density and the potential into spherical harmonics, a largely analytical solution of the Poisson problem can be employed. For a practical implementation, the expansion must be appropriately truncated. With this spectral solver we are able to efficiently solve the Poisson equation in a kinetic plasma simulation without the need of introducing a spatial discretization.
A Nonlinear Modal Aeroelastic Solver for FUN3D
NASA Technical Reports Server (NTRS)
Goldman, Benjamin D.; Bartels, Robert E.; Biedron, Robert T.; Scott, Robert C.
2016-01-01
A nonlinear structural solver has been implemented internally within the NASA FUN3D computational fluid dynamics code, allowing for some new aeroelastic capabilities. Using a modal representation of the structure, a set of differential or differential-algebraic equations are derived for general thin structures with geometric nonlinearities. ODEPACK and LAPACK routines are linked with FUN3D, and the nonlinear equations are solved at each CFD time step. The existing predictor-corrector method is retained, whereby the structural solution is updated after mesh deformation. The nonlinear solver is validated using a test case for a flexible aeroshell at transonic, supersonic, and hypersonic flow conditions. Agreement with linear theory is seen for the static aeroelastic solutions at relatively low dynamic pressures, but structural nonlinearities limit deformation amplitudes at high dynamic pressures. No flutter was found at any of the tested trajectory points, though LCO may be possible in the transonic regime.
On improving linear solver performance: a block variant of GMRES
Baker, A H; Dennis, J M; Jessup, E R
2004-05-10
The increasing gap between processor performance and memory access time warrants the re-examination of data movement in iterative linear solver algorithms. For this reason, we explore and establish the feasibility of modifying a standard iterative linear solver algorithm in a manner that reduces the movement of data through memory. In particular, we present an alternative to the restarted GMRES algorithm for solving a single right-hand side linear system Ax = b based on solving the block linear system AX = B. Algorithm performance, i.e. time to solution, is improved by using the matrix A in operations on groups of vectors. Experimental results demonstrate the importance of implementation choices on data movement as well as the effectiveness of the new method on a variety of problems from different application areas.
Verification and Validation Studies for the LAVA CFD Solver
NASA Technical Reports Server (NTRS)
Moini-Yekta, Shayan; Barad, Michael F; Sozer, Emre; Brehm, Christoph; Housman, Jeffrey A.; Kiris, Cetin C.
2013-01-01
The verification and validation of the Launch Ascent and Vehicle Aerodynamics (LAVA) computational fluid dynamics (CFD) solver is presented. A modern strategy for verification and validation is described incorporating verification tests, validation benchmarks, continuous integration and version control methods for automated testing in a collaborative development environment. The purpose of the approach is to integrate the verification and validation process into the development of the solver and improve productivity. This paper uses the Method of Manufactured Solutions (MMS) for the verification of 2D Euler equations, 3D Navier-Stokes equations as well as turbulence models. A method for systematic refinement of unstructured grids is also presented. Verification using inviscid vortex propagation and flow over a flat plate is highlighted. Simulation results using laminar and turbulent flow past a NACA 0012 airfoil and ONERA M6 wing are validated against experimental and numerical data.
An Upwind Solver for the National Combustion Code
NASA Technical Reports Server (NTRS)
Sockol, Peter M.
2011-01-01
An upwind solver is presented for the unstructured grid National Combustion Code (NCC). The compressible Navier-Stokes equations with time-derivative preconditioning and preconditioned flux-difference splitting of the inviscid terms are used. First order derivatives are computed on cell faces and used to evaluate the shear stresses and heat fluxes. A new flux limiter uses these same first order derivatives in the evaluation of left and right states used in the flux-difference splitting. The k-epsilon turbulence equations are solved with the same second-order method. The new solver has been installed in a recent version of NCC and the resulting code has been tested successfully in 2D on two laminar cases with known solutions and one turbulent case with experimental data.
Parallel Auxiliary Space AMG Solver for $H(div)$ Problems
Kolev, Tzanio V.; Vassilevski, Panayot S.
2012-12-18
We present a family of scalable preconditioners for matrices arising in the discretization of $H(div)$ problems using the lowest order Raviart--Thomas finite elements. Our approach belongs to the class of “auxiliary space''--based methods and requires only the finite element stiffness matrix plus some minimal additional discretization information about the topology and orientation of mesh entities. Also, we provide a detailed algebraic description of the theory, parallel implementation, and different variants of this parallel auxiliary space divergence solver (ADS) and discuss its relations to the Hiptmair--Xu (HX) auxiliary space decomposition of $H(div)$ [SIAM J. Numer. Anal., 45 (2007), pp. 2483--2509] and to the auxiliary space Maxwell solver AMS [J. Comput. Math., 27 (2009), pp. 604--623]. Finally, an extensive set of numerical experiments demonstrates the robustness and scalability of our implementation on large-scale $H(div)$ problems with large jumps in the material coefficients.
CASTRO: A NEW COMPRESSIBLE ASTROPHYSICAL SOLVER. II. GRAY RADIATION HYDRODYNAMICS
Zhang, W.; Almgren, A.; Bell, J.; Howell, L.; Burrows, A.
2011-10-01
We describe the development of a flux-limited gray radiation solver for the compressible astrophysics code, CASTRO. CASTRO uses an Eulerian grid with block-structured adaptive mesh refinement based on a nested hierarchy of logically rectangular variable-sized grids with simultaneous refinement in both space and time. The gray radiation solver is based on a mixed-frame formulation of radiation hydrodynamics. In our approach, the system is split into two parts, one part that couples the radiation and fluid in a hyperbolic subsystem, and another parabolic part that evolves radiation diffusion and source-sink terms. The hyperbolic subsystem is solved explicitly with a high-order Godunov scheme, whereas the parabolic part is solved implicitly with a first-order backward Euler method.
Brittle Solvers: Lessons and insights into effective solvers for visco-plasticity in geodynamics
NASA Astrophysics Data System (ADS)
Spiegelman, M. W.; May, D.; Wilson, C. R.
2014-12-01
Plasticity/Fracture and rock failure are essential ingredients in geodynamic models as terrestrial rocks do not possess an infinite yield strength. Numerous physical mechanisms have been proposed to limit the strength of rocks, including low temperature plasticity and brittle fracture. While ductile and creep behavior of rocks at depth is largely accepted, the constitutive relations associated with brittle failure, or shear localisation, are more controversial. Nevertheless, there are really only a few macroscopic constitutive laws for visco-plasticity that are regularly used in geodynamics models. Independent of derivation, all of these can be cast as simple effective viscosities which act as stress limiters with different choices for yield surfaces; the most common being a von Mises (constant yield stress) or Drucker-Prager (pressure dependent yield-stress) criterion. The choice of plasticity model, however, can have significant consequences for the degree of non-linearity in a problem and the choice and efficiency of non-linear solvers. Here we describe a series of simplified 2 and 3-D model problems to elucidate several issues associated with obtaining accurate description and solution of visco-plastic problems. We demonstrate that1) Picard/Successive substitution schemes for solution of the non-linear problems can often stall at large values of the non-linear residual, thus producing spurious solutions2) Combined Picard/Newton schemes can be effective for a range of plasticity models, however, they can produce serious convergence problems for strongly pressure dependent plasticity models such as Drucker-Prager.3) Nevertheless, full Drucker-Prager may not be the plasticity model of choice for strong materials as the dynamic pressures produced in these layers can develop pathological behavior with Drucker-Prager, leading to stress strengthening rather than stress weakening behavior.4) In general, for any incompressible Stoke's problem, it is highly advisable to
NASA Astrophysics Data System (ADS)
Bui-Thanh, T.; Girolami, M.
2014-11-01
We consider the Riemann manifold Hamiltonian Monte Carlo (RMHMC) method for solving statistical inverse problems governed by partial differential equations (PDEs). The Bayesian framework is employed to cast the inverse problem into the task of statistical inference whose solution is the posterior distribution in infinite dimensional parameter space conditional upon observation data and Gaussian prior measure. We discretize both the likelihood and the prior using the H1-conforming finite element method together with a matrix transfer technique. The power of the RMHMC method is that it exploits the geometric structure induced by the PDE constraints of the underlying inverse problem. Consequently, each RMHMC posterior sample is almost uncorrelated/independent from the others providing statistically efficient Markov chain simulation. However this statistical efficiency comes at a computational cost. This motivates us to consider computationally more efficient strategies for RMHMC. At the heart of our construction is the fact that for Gaussian error structures the Fisher information matrix coincides with the Gauss-Newton Hessian. We exploit this fact in considering a computationally simplified RMHMC method combining state-of-the-art adjoint techniques and the superiority of the RMHMC method. Specifically, we first form the Gauss-Newton Hessian at the maximum a posteriori point and then use it as a fixed constant metric tensor throughout RMHMC simulation. This eliminates the need for the computationally costly differential geometric Christoffel symbols, which in turn greatly reduces computational effort at a corresponding loss of sampling efficiency. We further reduce the cost of forming the Fisher information matrix by using a low rank approximation via a randomized singular value decomposition technique. This is efficient since a small number of Hessian-vector products are required. The Hessian-vector product in turn requires only two extra PDE solves using the adjoint
Scaling Algebraic Multigrid Solvers: On the Road to Exascale
Baker, A H; Falgout, R D; Gamblin, T; Kolev, T; Schulz, M; Yang, U M
2010-12-12
Algebraic Multigrid (AMG) solvers are an essential component of many large-scale scientific simulation codes. Their continued numerical scalability and efficient implementation is critical for preparing these codes for exascale. Our experiences on modern multi-core machines show that significant challenges must be addressed for AMG to perform well on such machines. We discuss our experiences and describe the techniques we have used to overcome scalability challenges for AMG on hybrid architectures in preparation for exascale.
A chemical reaction network solver for the astrophysics code NIRVANA
NASA Astrophysics Data System (ADS)
Ziegler, U.
2016-02-01
Context. Chemistry often plays an important role in astrophysical gases. It regulates thermal properties by changing species abundances and via ionization processes. This way, time-dependent cooling mechanisms and other chemistry-related energy sources can have a profound influence on the dynamical evolution of an astrophysical system. Modeling those effects with the underlying chemical kinetics in realistic magneto-gasdynamical simulations provide the basis for a better link to observations. Aims: The present work describes the implementation of a chemical reaction network solver into the magneto-gasdynamical code NIRVANA. For this purpose a multispecies structure is installed, and a new module for evolving the rate equations of chemical kinetics is developed and coupled to the dynamical part of the code. A small chemical network for a hydrogen-helium plasma was constructed including associated thermal processes which is used in test problems. Methods: Evolving a chemical network within time-dependent simulations requires the additional solution of a set of coupled advection-reaction equations for species and gas temperature. Second-order Strang-splitting is used to separate the advection part from the reaction part. The ordinary differential equation (ODE) system representing the reaction part is solved with a fourth-order generalized Runge-Kutta method applicable for stiff systems inherent to astrochemistry. Results: A series of tests was performed in order to check the correctness of numerical and technical implementation. Tests include well-known stiff ODE problems from the mathematical literature in order to confirm accuracy properties of the solver used as well as problems combining gasdynamics and chemistry. Overall, very satisfactory results are achieved. Conclusions: The NIRVANA code is now ready to handle astrochemical processes in time-dependent simulations. An easy-to-use interface allows implementation of complex networks including thermal processes
An automatic ordering method for incomplete factorization iterative solvers
Forsyth, P.A.; Tang, W.P. . Dept. of Computer Science); D'Azevedo, E.F.D. )
1991-01-01
The minimum discarded fill (MDF) ordering strategy for incomplete factorization iterative solvers is developed. MDF ordering is demonstrated for several model son-symmetric problems, as well as a water-flooding simulation which uses an unstructured grid. The model problems show a three to five fold decrease in the number of iterations compared to natural orderings. Greater than twofold improvement was observed for the waterflooding simulation. 26 refs., 7 figs., 3 tabs.
A contribution to the great Riemann solver debate
NASA Technical Reports Server (NTRS)
Quirk, James J.
1992-01-01
The aims of this paper are threefold: to increase the level of awareness within the shock capturing community to the fact that many Godunov-type methods contain subtle flaws that can cause spurious solutions to be computed; to identify one mechanism that might thwart attempts to produce very high resolution simulations; and to proffer a simple strategy for overcoming the specific failings of individual Riemann solvers.
Boltzmann Solver with Adaptive Mesh in Velocity Space
Kolobov, Vladimir I.; Arslanbekov, Robert R.; Frolova, Anna A.
2011-05-20
We describe the implementation of direct Boltzmann solver with Adaptive Mesh in Velocity Space (AMVS) using quad/octree data structure. The benefits of the AMVS technique are demonstrated for the charged particle transport in weakly ionized plasmas where the collision integral is linear. We also describe the implementation of AMVS for the nonlinear Boltzmann collision integral. Test computations demonstrate both advantages and deficiencies of the current method for calculations of narrow-kernel distributions.
Direct linear programming solver in C for structural applications
NASA Astrophysics Data System (ADS)
Damkilde, L.; Hoyer, O.; Krenk, S.
1994-08-01
An optimization problem can be characterized by an object-function, which is maximized, and restrictions, which limit the variation of the variables. A subclass of optimization is Linear Programming (LP), where both the object-function and the restrictions are linear functions of the variables. The traditional solution methods for LP problems are based on the simplex method, and it is customary to allow only non-negative variables. Compared to other optimization routines the LP solvers are more robust and the optimum is reached in a finite number of steps and is not sensitive to the starting point. For structural applications many optimization problems can be linearized and solved by LP routines. However, the structural variables are not always non-negative, and this requires a reformation, where a variable x is substituted by the difference of two non-negative variables, x(sup + ) and x(sup - ). The transformation causes a doubling of the number of variables, and in a computer implementation the memory allocation doubles and for a typical problem the execution time at least doubles. This paper describes a LP solver written in C, which can handle a combination of non-negative variables and unlimited variables. The LP solver also allows restart, and this may reduce the computational costs if the solution to a similar LP problem is known a priori. The algorithm is based on the simplex method, and differs only in the logical choices. Application of the new LP solver will at the same time give both a more direct problem formulation and a more efficient program.
NASA Astrophysics Data System (ADS)
Ulz, Manfred H.
2015-01-01
Multiscale models are designed to handle problems with different length scales and time scales in a suitable and efficient manner. Such problems include inelastic deformation or failure of materials. In particular, hierarchical multiscale methods are computationally powerful as no direct coupling between the scales is given. This paper proposes a hierarchical two-scale setting appropriate for isothermal quasi-static problems: a macroscale treated by continuum mechanics and the finite element method and a microscale modelled by a canonical ensemble of statistical mechanics solved with molecular dynamics. This model will be implemented into the framework of the heterogeneous multiscale method. The focus is laid on an efficient coupling of the macro- and micro-solvers. An iterative solution algorithm presents the macroscopic solver, which invokes for each iteration an atomistic computation. As the microscopic computation is considered to be very time consuming, two optimisation strategies are proposed. Firstly, the macroscopic solver is chosen to reduce the number of required iterations to a minimum. Secondly, the number of time steps used for the time average on the microscale will be increased with each iteration. As a result, the molecular dynamics cell will be allowed to reach its state of thermodynamic equilibrium only in the last macroscopic iteration step. In the preceding iteration steps, the molecular dynamics cell will reach a state close to equilibrium by using considerably fewer microscopic time steps. This adapted number of microsteps will result in an accelerated algorithm (aFE-MD-HMM) obtaining the same accuracy of results at significantly reduced computational cost. Numerical examples demonstrate the performance of the proposed scheme.
Transonic Drag Prediction Using an Unstructured Multigrid Solver
NASA Technical Reports Server (NTRS)
Mavriplis, D. J.; Levy, David W.
2001-01-01
This paper summarizes the results obtained with the NSU-3D unstructured multigrid solver for the AIAA Drag Prediction Workshop held in Anaheim, CA, June 2001. The test case for the workshop consists of a wing-body configuration at transonic flow conditions. Flow analyses for a complete test matrix of lift coefficient values and Mach numbers at a constant Reynolds number are performed, thus producing a set of drag polars and drag rise curves which are compared with experimental data. Results were obtained independently by both authors using an identical baseline grid and different refined grids. Most cases were run in parallel on commodity cluster-type machines while the largest cases were run on an SGI Origin machine using 128 processors. The objective of this paper is to study the accuracy of the subject unstructured grid solver for predicting drag in the transonic cruise regime, to assess the efficiency of the method in terms of convergence, cpu time, and memory, and to determine the effects of grid resolution on this predictive ability and its computational efficiency. A good predictive ability is demonstrated over a wide range of conditions, although accuracy was found to degrade for cases at higher Mach numbers and lift values where increasing amounts of flow separation occur. The ability to rapidly compute large numbers of cases at varying flow conditions using an unstructured solver on inexpensive clusters of commodity computers is also demonstrated.
Fast linear solvers for variable density turbulent flows
NASA Astrophysics Data System (ADS)
Pouransari, Hadi; Mani, Ali; Darve, Eric
2015-11-01
Variable density flows are ubiquitous in variety of natural and industrial systems. Two-phase and multi-phase flows in natural and industrial processes, astrophysical flows, and flows involved in combustion processes are such examples. For an ideal gas subject to low-Mach approximation, variations in temperature can lead to a non-uniform density field. In this work, we consider radiatively heated particle-laden turbulent flows as an example application in which density variability is resulted from inhomogeneities in the heat absorption by an inhomogeneous particle field. Under such conditions, the divergence constraint of the fluid is enforced through a variable coefficient Poisson equation. Inversion of the discretized variable coefficient Poisson operator is difficult using the conventional linear solvers as the size of the problem grows. We apply a novel hierarchical linear solve algorithm based on low-rank approximations. The proposed linear solver could be applied to variety of linear systems arising from discretized partial differential equations. It can be used as a standalone direct-solver with tunable accuracy and linear complexity, or as a high-accuracy pre-conditioner in conjunction with other iterative methods.
A Survey of Solver-Related Geometry and Meshing Issues
NASA Technical Reports Server (NTRS)
Masters, James; Daniel, Derick; Gudenkauf, Jared; Hine, David; Sideroff, Chris
2016-01-01
There is a concern in the computational fluid dynamics community that mesh generation is a significant bottleneck in the CFD workflow. This is one of several papers that will help set the stage for a moderated panel discussion addressing this issue. Although certain general "rules of thumb" and a priori mesh metrics can be used to ensure that some base level of mesh quality is achieved, inadequate consideration is often given to the type of solver or particular flow regime on which the mesh will be utilized. This paper explores how an analyst may want to think differently about a mesh based on considerations such as if a flow is compressible vs. incompressible or hypersonic vs. subsonic or if the solver is node-centered vs. cell-centered. This paper is a high-level investigation intended to provide general insight into how considering the nature of the solver or flow when performing mesh generation has the potential to increase the accuracy and/or robustness of the solution and drive the mesh generation process to a state where it is no longer a hindrance to the analysis process.
QED multi-dimensional vacuum polarization finite-difference solver
NASA Astrophysics Data System (ADS)
Carneiro, Pedro; Grismayer, Thomas; Silva, Luís; Fonseca, Ricardo
2015-11-01
The Extreme Light Infrastructure (ELI) is expected to deliver peak intensities of 1023 - 1024 W/cm2 allowing to probe nonlinear Quantum Electrodynamics (QED) phenomena in an unprecedented regime. Within the framework of QED, the second order process of photon-photon scattering leads to a set of extended Maxwell's equations [W. Heisenberg and H. Euler, Z. Physik 98, 714] effectively creating nonlinear polarization and magnetization terms that account for the nonlinear response of the vacuum. To model this in a self-consistent way, we present a multi dimensional generalized Maxwell equation finite difference solver with significantly enhanced dispersive properties, which was implemented in the OSIRIS particle-in-cell code [R.A. Fonseca et al. LNCS 2331, pp. 342-351, 2002]. We present a detailed numerical analysis of this electromagnetic solver. As an illustration of the properties of the solver, we explore several examples in extreme conditions. We confirm the theoretical prediction of vacuum birefringence of a pulse propagating in the presence of an intense static background field [arXiv:1301.4918 [quant-ph
NITSOL: A Newton iterative solver for nonlinear systems
Pernice, M.; Walker, H.F.
1996-12-31
Newton iterative methods, also known as truncated Newton methods, are implementations of Newton`s method in which the linear systems that characterize Newton steps are solved approximately using iterative linear algebra methods. Here, we outline a well-developed Newton iterative algorithm together with a Fortran implementation called NITSOL. The basic algorithm is an inexact Newton method globalized by backtracking, in which each initial trial step is determined by applying an iterative linear solver until an inexact Newton criterion is satisfied. In the implementation, the user can specify inexact Newton criteria in several ways and select an iterative linear solver from among several popular {open_quotes}transpose-free{close_quotes} Krylov subspace methods. Jacobian-vector products used by the Krylov solver can be either evaluated analytically with a user-supplied routine or approximated using finite differences of function values. A flexible interface permits a wide variety of preconditioning strategies and allows the user to define a preconditioner and optionally update it periodically. We give details of these and other features and demonstrate the performance of the implementation on a representative set of test problems.
PDE6δ-mediated sorting of INPP5E into the cilium is determined by cargo-carrier affinity.
Fansa, Eyad Kalawy; Kösling, Stefanie Kristine; Zent, Eldar; Wittinghofer, Alfred; Ismail, Shehab
2016-01-01
The phosphodiesterase 6 delta subunit (PDE6δ) shuttles several farnesylated cargos between membranes. The cargo sorting mechanism between cilia and other compartments is not understood. Here we show using the inositol polyphosphate 5'-phosphatase E (INPP5E) and the GTP-binding protein (Rheb) that cargo sorting depends on the affinity towards PDE6δ and the specificity of cargo release. High-affinity cargo is exclusively released by the ciliary transport regulator Arl3, while low-affinity cargo is released by Arl3 and its non-ciliary homologue Arl2. Structures of PDE6δ/cargo complexes reveal the molecular basis of the sorting signal which depends on the residues at the -1 and -3 positions relative to farnesylated cysteine. Structure-guided mutation allows the generation of a low-affinity INPP5E mutant which loses exclusive ciliary localization. We postulate that the affinity to PDE6δ and the release by Arl2/3 in addition to a retention signal are the determinants for cargo sorting and enrichment at its destination. PMID:27063844
Luo, Biao; Wu, Huai-Ning
2012-12-01
This paper addresses the approximate optimal control problem for a class of parabolic partial differential equation (PDE) systems with nonlinear spatial differential operators. An approximate optimal control design method is proposed on the basis of the empirical eigenfunctions (EEFs) and neural network (NN). First, based on the data collected from the PDE system, the Karhunen-Loève decomposition is used to compute the EEFs. With those EEFs, the PDE system is formulated as a high-order ordinary differential equation (ODE) system. To further reduce its dimension, the singular perturbation (SP) technique is employed to derive a reduced-order model (ROM), which can accurately describe the dominant dynamics of the PDE system. Second, the Hamilton-Jacobi-Bellman (HJB) method is applied to synthesize an optimal controller based on the ROM, where the closed-loop asymptotic stability of the high-order ODE system can be guaranteed by the SP theory. By dividing the optimal control law into two parts, the linear part is obtained by solving an algebraic Riccati equation, and a new type of HJB-like equation is derived for designing the nonlinear part. Third, a control update strategy based on successive approximation is proposed to solve the HJB-like equation, and its convergence is proved. Furthermore, an NN approach is used to approximate the cost function. Finally, we apply the developed approximate optimal control method to a diffusion-reaction process with a nonlinear spatial operator, and the simulation results illustrate its effectiveness. PMID:22588610
Multiscale modelling in immunology: a review.
Cappuccio, Antonio; Tieri, Paolo; Castiglione, Filippo
2016-05-01
One of the greatest challenges in biomedicine is to get a unified view of observations made from the molecular up to the organism scale. Towards this goal, multiscale models have been highly instrumental in contexts such as the cardiovascular field, angiogenesis, neurosciences and tumour biology. More recently, such models are becoming an increasingly important resource to address immunological questions as well. Systematic mining of the literature in multiscale modelling led us to identify three main fields of immunological applications: host-virus interactions, inflammatory diseases and their treatment and development of multiscale simulation platforms for immunological research and for educational purposes. Here, we review the current developments in these directions, which illustrate that multiscale models can consistently integrate immunological data generated at several scales, and can be used to describe and optimize therapeutic treatments of complex immune diseases.
Collaborating for Multi-Scale Chemical Science
William H. Green
2006-07-14
Advanced model reduction methods were developed and integrated into the CMCS multiscale chemical science simulation software. The new technologies were used to simulate HCCI engines and burner flames with exceptional fidelity.
On multiscale entropy analysis for physiological data
NASA Astrophysics Data System (ADS)
Thuraisingham, Ranjit A.; Gottwald, Georg A.
2006-07-01
We perform an analysis of cardiac data using multiscale entropy as proposed in Costa et al. [Multiscale entropy analysis of complex physiological time series, Phys. Rev. Lett. 89 (2002) 068102]. We reproduce the signatures of the multiscale entropy for the three cases of young healthy hearts, atrial fibrillation and congestive heart failure. We show that one has to be cautious how to interpret these signatures in terms of the underlying dynamics. In particular, we show that different dynamical systems can exhibit the same signatures depending on the sampling time, and that similar systems may have different signatures depending on the time scales involved. Besides the total amount of data we identify the sampling time, the correlation time and the period of possible nonlinear oscillations as important time scales which have to be involved in a detailed analysis of the signatures of multiscale entropies. We illustrate our ideas with the Lorenz equation as a simple deterministic chaotic system.
Ramanujam, Ravikrishna; Naqvi, Naweed I.
2010-01-01
Cyclic AMP-dependent pathways mediate the communication between external stimuli and the intracellular signaling machinery, thereby influencing important aspects of cellular growth, morphogenesis and differentiation. Crucial to proper function and robustness of these signaling cascades is the strict regulation and maintenance of intracellular levels of cAMP through a fine balance between biosynthesis (by adenylate cyclases) and hydrolysis (by cAMP phosphodiesterases). We functionally characterized gene-deletion mutants of a high-affinity (PdeH) and a low-affinity (PdeL) cAMP phosphodiesterase in order to gain insights into the spatial and temporal regulation of cAMP signaling in the rice-blast fungus Magnaporthe oryzae. In contrast to the expendable PdeL function, the PdeH activity was found to be a key regulator of asexual and pathogenic development in M. oryzae. Loss of PdeH led to increased accumulation of intracellular cAMP during vegetative and infectious growth. Furthermore, the pdeHΔ showed enhanced conidiation (2–3 fold), precocious appressorial development, loss of surface dependency during pathogenesis, and highly reduced in planta growth and host colonization. A pdeHΔ pdeLΔ mutant showed reduced conidiation, exhibited dramatically increased (∼10 fold) cAMP levels relative to the wild type, and was completely defective in virulence. Exogenous addition of 8-Br-cAMP to the wild type simulated the pdeHΔ defects in conidiation as well as in planta growth and development. While a fully functional GFP-PdeH was cytosolic but associated dynamically with the plasma membrane and vesicular compartments, the GFP-PdeL localized predominantly to the nucleus. Based on data from cAMP measurements and Real-Time RTPCR, we uncover a PdeH-dependent biphasic regulation of cAMP levels during early and late stages of appressorial development in M. oryzae. We propose that PdeH-mediated sustenance and dynamic regulation of cAMP signaling during M. oryzae development is
Prediction of evolution of meteor shower associated with comet 122P/de Vico
NASA Astrophysics Data System (ADS)
Tomko, D.
2014-04-01
We deal with a theoretical meteoroid stream of the comet 122P/de Vico. For five perihelion passages in the distant past, we model a theoretical stream and follow its dynamical evolution until the present. We predict the characteristics of potential a meteor shower approaching the Earth's orbit and we make also the identification of the particles of the predicted shower with the real meteors in three databases (photo, radar, and video). Our overall prediction is, however, negative because only the particles released from the comet nucleus before approximately 37 000 years are found to evolve into a collision course with the Earth and, therefore, form a possible shower. Many meteoroids do not survive such a long time in interplanetary space.
NASA Technical Reports Server (NTRS)
Smith, Ralph C.
1994-01-01
A Galerkin method for systems of PDE's in circular geometries is presented with motivating problems being drawn from structural, acoustic, and structural acoustic applications. Depending upon the application under consideration, piecewise splines or Legendre polynomials are used when approximating the system dynamics with modifications included to incorporate the analytic solution decay near the coordinate singularity. This provides an efficient method which retains its accuracy throughout the circular domain without degradation at singularity. Because the problems under consideration are linear or weakly nonlinear with constant or piecewise constant coefficients, transform methods for the problems are not investigated. While the specific method is developed for the two dimensional wave equations on a circular domain and the equation of transverse motion for a thin circular plate, examples demonstrating the extension of the techniques to a fully coupled structural acoustic system are used to illustrate the flexibility of the method when approximating the dynamics of more complex systems.
Solid state of a new PDE-5 inhibitor DA-8159: characterization, dissolution, transformation.
Ryu, Ji Yoon; Sohn, Young-Taek
2012-05-01
The polymorphic forms of a new PDE-5 inhibitor DA-8159 were prepared and characterized by differential scanning calorimetry (DSC), powder X-ray diffractometry (PXRD) and thermogravimetric analysis (TG). Two crystal forms and one amorphous form of DA-8159 have been isolated by recrystallization and characterized by DSC, TG and PXRD. From the TG data it was confirmed that two crystal forms are neither solvates nor hydrates. The PXRD patterns of the two crystal forms were different. In the dissolution studies in simulated intestinal fluid at 37 ± 0.5°C, the solubility decreased in the order of amorphous form > Form 1 > Form 2. After storage of 60 days, Form 1 was transformed to Form 2. Form 2 was not transformed. The amorphous form was transformed to Form 2 at 52% R.H. and 95% R.H., but it did not transform at 0% R.H. PMID:22644853
NASA Technical Reports Server (NTRS)
Hunt, L. R.; Villarreal, Ramiro
1987-01-01
System theorists understand that the same mathematical objects which determine controllability for nonlinear control systems of ordinary differential equations (ODEs) also determine hypoellipticity for linear partial differentail equations (PDEs). Moreover, almost any study of ODE systems begins with linear systems. It is remarkable that Hormander's paper on hypoellipticity of second order linear p.d.e.'s starts with equations due to Kolmogorov, which are shown to be analogous to the linear PDEs. Eigenvalue placement by state feedback for a controllable linear system can be paralleled for a Kolmogorov equation if an appropriate type of feedback is introduced. Results concerning transformations of nonlinear systems to linear systems are similar to results for transforming a linear PDE to a Kolmogorov equation.
NASA Astrophysics Data System (ADS)
Tang, Chen; Zhang, Junjiang; Sun, Chen; Su, Yonggang; Su, Kai Leung
2015-05-01
Nuclear graphite has been widely used as moderating and reflecting materials. However, due to severe neutron irradiation under high temperature, nuclear graphite is prone to deteriorate, resulting in massive microscopic flaws and even cracks under large stress in the later period of its service life. It is indispensable, therefore, to understand the fracture behavior of nuclear graphite to provide reference to structural integrity and safety analysis of nuclear graphite members in reactors. In this paper, we investigated the fracture expansion in nuclear graphite based on PDE image processing methods. We used the second-order oriented partial differential equations filtering model (SOOPDE) to denoise speckle noise, then used the oriented gradient vector fields for to obtain skeletons. The full-field displacement of fractured nuclear graphite and the location of the crack tip were lastly measured under various loading conditions.
Experimental confirmation of a PDE-based approach to design of feedback controls
NASA Technical Reports Server (NTRS)
Banks, H. T.; Smith, Ralph C.; Brown, D. E.; Silcox, R. J.; Metcalf, Vern L.
1995-01-01
Issues regarding the experimental implementation of partial differential equation based controllers are discussed in this work. While the motivating application involves the reduction of vibration levels for a circular plate through excitation of surface-mounted piezoceramic patches, the general techniques described here will extend to a variety of applications. The initial step is the development of a PDE model which accurately captures the physics of the underlying process. This model is then discretized to yield a vector-valued initial value problem. Optimal control theory is used to determine continuous-time voltages to the patches, and the approximations needed to facilitate discrete time implementation are addressed. Finally, experimental results demonstrating the control of both transient and steady state vibrations through these techniques are presented.
Fisher, A. C.; Bailey, D. S.; Kaiser, T. B.; Eder, D. C.; Gunney, B. T. N.; Masters, N. D.; Koniges, A. E.; Anderson, R. W.
2015-02-01
Here, we present a novel method for the solution of the diffusion equation on a composite AMR mesh. This approach is suitable for including diffusion based physics modules to hydrocodes that support ALE and AMR capabilities. To illustrate, we proffer our implementations of diffusion based radiation transport and heat conduction in a hydrocode called ALE-AMR. Numerical experiments conducted with the diffusion solver and associated physics packages yield 2nd order convergence in the L_{2} norm.
Muscle MRS detects elevated PDE/ATP ratios prior to fatty infiltration in Becker muscular dystrophy.
Wokke, B H; Hooijmans, M T; van den Bergen, J C; Webb, A G; Verschuuren, J J; Kan, H E
2014-11-01
Becker muscular dystrophy (BMD) is characterized by progressive muscle weakness. Muscles show structural changes (fatty infiltration, fibrosis) and metabolic changes, both of which can be assessed using MRI and MRS. It is unknown at what stage of the disease process metabolic changes arise and how this might vary for different metabolites. In this study we assessed metabolic changes in skeletal muscles of Becker patients, both with and without fatty infiltration, quantified via Dixon MRI and (31) P MRS. MRI and (31) P MRS scans were obtained from 25 Becker patients and 14 healthy controls using a 7 T MR scanner. Five lower-leg muscles were individually assessed for fat and muscle metabolite levels. In the peroneus, soleus and anterior tibialis muscles with non-increased fat levels, PDE/ATP ratios were higher (P < 0.02) compared with controls, whereas in all muscles with increased fat levels PDE/ATP ratios were higher compared with healthy controls (P ≤ 0.05). The Pi /ATP ratio in the peroneus muscles was higher in muscles with increased fat fractions (P = 0.005), and the PCr/ATP ratio was lower in the anterior tibialis muscles with increased fat fractions (P = 0.005). There were no other significant changes in metabolites, but an increase in tissue pH was found in all muscles of the total group of BMD patients in comparison with healthy controls (P < 0.05). These findings suggest that (31) P MRS can be used to detect early changes in individual muscles of BMD patients, which are present before the onset of fatty infiltration.
Fast solvers for optimal control problems from pattern formation
NASA Astrophysics Data System (ADS)
Stoll, Martin; Pearson, John W.; Maini, Philip K.
2016-01-01
The modeling of pattern formation in biological systems using various models of reaction-diffusion type has been an active research topic for many years. We here look at a parameter identification (or PDE-constrained optimization) problem where the Schnakenberg and Gierer-Meinhardt equations, two well-known pattern formation models, form the constraints to an objective function. Our main focus is on the efficient solution of the associated nonlinear programming problems via a Lagrange-Newton scheme. In particular we focus on the fast and robust solution of the resulting large linear systems, which are of saddle point form. We illustrate this by considering several two- and three-dimensional setups for both models. Additionally, we discuss an image-driven formulation that allows us to identify parameters of the model to match an observed quantity obtained from an image.
Multiscale simulation of DC corona discharge and ozone generation from nanostructures
NASA Astrophysics Data System (ADS)
Wang, Pengxiang
simulation of corona discharges from nanostructures, a one-dimensional (1-D) multiscale model is used due to the prohibitive computational expense associated with two-dimensional (2-D) modeling. Near the nanoscale discharge electrode surface, a kinetic model based on PIC-MCC is used due to a relatively large Knudsen number in this region. Far away from the nanoscale discharge electrode, a continuum model is used since the Knudsen number is very small there. The multiscale modeling results are compared with experimental data. The quantitative agreement in positive discharges and qualitative agreement in negative discharges validate the modeling approach. The mechanism of sustaining the discharge process from nanostructures is revealed and is found to be different from that of discharge from micro- or macro-sized electrodes. Finally, the corona plasma model is combined with a plasma chemistry model and a transport model to predict the ozone production from the nanoscale corona. The dependence of ozone production on the applied potential and air velocity is studied. The electric field distribution in a 2-D multiscale domain (from nanoscale to microscale) is predicted by solving the Poisson's equation using a finite difference scheme. The discretized linear equations are solved using a multigrid method under the framework of PETSc on a paralleled supercomputer. Although the Poisson solver is able to resolve the multiscale field, the prohibitively long computation time limits the use of a 2-D solver in the current PIC-MCC scheme.
Multiscale modelling of DNA mechanics
NASA Astrophysics Data System (ADS)
Dršata, Tomáš; Lankaš, Filip
2015-08-01
Mechanical properties of DNA are important not only in a wide range of biological processes but also in the emerging field of DNA nanotechnology. We review some of the recent developments in modeling these properties, emphasizing the multiscale nature of the problem. Modern atomic resolution, explicit solvent molecular dynamics simulations have contributed to our understanding of DNA fine structure and conformational polymorphism. These simulations may serve as data sources to parameterize rigid base models which themselves have undergone major development. A consistent buildup of larger entities involving multiple rigid bases enables us to describe DNA at more global scales. Free energy methods to impose large strains on DNA, as well as bead models and other approaches, are also briefly discussed.
Multiscale dynamics in relaxor ferroelectrics
Toulouse, J.; Cai, L; Pattnaik, R. K.; Boatner, Lynn A
2014-01-01
The multiscale dynamics of complex oxides is illustrated by pairs of mechanical resonances that are excited in the relaxor ferroelectric K1 xLixTaO3 (KLT). These macroscopic resonances are shown to originate in the collective dynamics of piezoelectric polar nanodomains (PND) interacting with the surrounding lattice. Their characteristic Fano lineshapes and rapid evolution with temperature reveal the coherent interplay between the piezoelectric oscillations and orientational relaxations of the PNDs at higher temperature and the contribution of heterophase oscillations near the phase transition. A theoretical model is presented, that describes the evolution of the resonances over the entire temperature range. Similar resonances are observed in other relaxors and must therefore be a common characteristics of these systems.
MULTISCALE MODELING OF POLYMER NANOCOMPOSITES
Maiti, A
2007-07-16
Polymer Nanocomposites are an important class of nanomaterials with potential applications including but not limited to structural and cushion materials, electromagnetic and heat shields, conducting plastics, sensors, and catalysts for various chemical and bio processes. Success in most such applications hinges on molecular-level control of structure and assembly, and a deep understanding of how the overall morphology of various components and the interfaces between them affect the composite properties at the macroscale. The length and time-scales associated with such assemblies are prohibitively large for a full atomistic modeling. Instead we adopt a multiscale methodology in which atomic-level interactions between different components of a composite are incorporated into a coarse-grained simulation of the mesoscale morphology, which is then represented on a numerical grid and the macroscopic properties computed using a finite-elements method.
Ribaudo, Giovanni; Pagano, Mario Angelo; Pavan, Valeria; Redaelli, Marco; Zorzan, Maira; Pezzani, Raffaele; Mucignat-Caretta, Carla; Vendrame, Tiziano; Bova, Sergio; Zagotto, Giuseppe
2015-09-01
Natural (iso)flavonoids have been recently reported to inhibit cyclic nucleotide phosphodiesterases (PDEs) and induce vasorelaxation, albeit the results described in the literature are discordant. The cGMP-selective isoform PDE-5A, in particular, represents the target of sildenafil and its analogues in the treatment of erectile dysfunction (ED) and pulmonary hypertension by promoting relaxation in vascular smooth muscle through the activation of the NO/cGMP pathway. We undertook this study to verify if osajin and pomiferin, two natural prenylated isoflavones and major constituents of Maclura pomifera extracts previously investigated for their anticancer, antibacterial and antidiabetic properties, show inhibitory activity on PDE-5A. These two isoflavones were isolated from the plant extracts and then synthetically modified to obtain a set of semi-synthetic derivatives with slight and focused modifications on the natural scaffold. The compounds were at first screened against PDE-5A in vitro and, based on the encouraging results, further tested for their relaxant effect on isolated rat artery rings. Computational docking studies were also carried out to explore the mode of interaction with the target protein. The obtained data were compared to the behaviour of the well-known PDE-5A inhibitor sildenafil. Our results demonstrate that semi-synthetic derivatives of osajin and pomiferin show an inhibitory effect on the isolated enzyme that, for some of the compounds, is accompanied by a vasorelaxant activity. Based on our findings, we propose the here described isoflavones as potential lead compounds for the development, starting from natural scaffolds, of a new class of PDE-5A inhibitors with vasorelaxant properties.
A concurrent multiscale micromorphic molecular dynamics
Li, Shaofan Tong, Qi
2015-04-21
In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation.
Multiscale coupling of molecular dynamics and peridynamics
NASA Astrophysics Data System (ADS)
Tong, Qi; Li, Shaofan
2016-10-01
We propose a multiscale computational model to couple molecular dynamics and peridynamics. The multiscale coupling model is based on a previously developed multiscale micromorphic molecular dynamics (MMMD) theory, which has three dynamics equations at three different scales, namely, microscale, mesoscale, and macroscale. In the proposed multiscale coupling approach, we divide the simulation domain into atomistic region and macroscale region. Molecular dynamics is used to simulate atom motions in atomistic region, and peridynamics is used to simulate macroscale material point motions in macroscale region, and both methods are nonlocal particle methods. A transition zone is introduced as a messenger to pass the information between the two regions or scales. We employ the "supercell" developed in the MMMD theory as the transition element, which is named as the adaptive multiscale element due to its ability of passing information from different scales, because the adaptive multiscale element can realize both top-down and bottom-up communications. We introduce the Cauchy-Born rule based stress evaluation into state-based peridynamics formulation to formulate atomistic-enriched constitutive relations. To mitigate the issue of wave reflection on the interface, a filter is constructed by switching on and off the MMMD dynamic equations at different scales. Benchmark tests of one-dimensional (1-D) and two-dimensional (2-D) wave propagations from atomistic region to macro region are presented. The mechanical wave can transit through the interface smoothly without spurious wave deflections, and the filtering process is proven to be efficient.
Li, Nan; Chen, Xi; Zhu, Bing; Ramírez-Alcántara, Verónica; Canzoneri, Joshua C.; Lee, Kevin; Sigler, Sara; Gary, Bernard; Li, Yonghe; Zhang, Wei; Moyer, Mary P.; Salter, E. Alan; Wierzbicki, Andrzej; Keeton, Adam B.; Piazza, Gary A.
2015-01-01
Previous studies suggest the anti-inflammatory drug, sulindac inhibits tumorigenesis by a COX independent mechanism involving cGMP PDE inhibition. Here we report that the cGMP PDE isozymes, PDE5 and 10, are elevated in colon tumor cells compared with normal colonocytes, and that inhibitors and siRNAs can selectively suppress colon tumor cell growth. Combined treatment with inhibitors or dual knockdown suppresses tumor cell growth to a greater extent than inhibition from either isozyme alone. A novel sulindac derivative, ADT-094 was designed to lack COX-1/-2 inhibitory activity but have improved potency to inhibit PDE5 and 10. ADT-094 displayed >500 fold higher potency to inhibit colon tumor cell growth compared with sulindac by activating cGMP/PKG signaling to suppress proliferation and induce apoptosis. Combined inhibition of PDE5 and 10 by treatment with ADT-094, PDE isozyme-selective inhibitors, or by siRNA knockdown also suppresses β-catenin, TCF transcriptional activity, and the levels of downstream targets, cyclin D1 and survivin. These results suggest that dual inhibition of PDE5 and 10 represents novel strategy for developing potent and selective anticancer drugs. PMID:26299804
Ning, Chen; Wen, Jiaming; Zhang, Yujin; Dai, Yingbo; Wang, Wei; Zhang, Weiru; Qi, Lin; Grenz, Almut; Eltzschig, Holger K.; Blackburn, Michael R.; Kellems, Rodney E.; Xia, Yang
2014-01-01
Priapism is featured with prolonged and painful penile erection and is prevalent among males with sickle cell disease (SCD). The disorder is a dangerous urological and hematological emergency since it is associated with ischemic tissue damage and erectile disability. Here we report that phosphodiesterase-5 (PDE5) gene expression and PDE activity is significantly reduced in penile tissues of two independent priapic models: SCD mice and adenosine deaminase (ADA)-deficient mice. Moreover, using ADA enzyme therapy to reduce adenosine or a specific antagonist to block A2B adenosine receptor (ADORA2B) signaling, we successfully attenuated priapism in both ADA−/− and SCD mice by restoring penile PDE5 gene expression to normal levels. This finding led us to further discover that excess adenosine signaling via ADORA2B activation directly reduces PDE5 gene expression in a hypoxia-inducible factor-1α (HIF-1α)-dependent manner. Overall, we reveal that excess adenosine-mediated ADORA2B signaling underlies reduced penile PDE activity by decreasing PDE5 gene expression in a HIF-1α-dependent manner and provide new insight for the pathogenesis of priapism and novel therapies for the disease.—Ning, C., Wen, J., Zhang, Y., Dai, Y., Wang, W., Zhang, W., Qi, L., Grenz, A., Eltzschig, H. K., Blackburn, M. R., Kellems, R. E., Xia, Y. Excess adenosine A2B receptor signaling contributes to priapism through HIF-1α mediated reduction of PDE5 gene expression. PMID:24614760
Hanna, Carol B.; Yao, Shan; Wu, Xuemei; Jensen, Jeffrey T.
2012-01-01
Objective To identify a cGMP-specific phosphodiesterase (PDE) in non-human primate germinal vesicle (GV) oocytes and establish a proposed effect on oocyte maturation through preliminary experiments in mouse GV oocytes. Design Controlled non-human primate and rodent experiments. Setting Academic research institution. Animals Rhesus macaques and B6/129F1 mice. Interventions Rhesus macaques were stimulated with FSH to collect GV oocytes and cumulus for gene expression analysis. Female mice were stimulated with PMSG to collect GV oocytes. Main Outcome Measures PDE transcript expression in primate GV oocytes and cumulus cells. Fluorescence polarization (FP) measurements of PDE3A activity. Spontaneous resumption of meiosis in mouse GV oocytes. Results Five PDE transcripts were detected in Rhesus GV oocytes, only PDE9A was cGMP-specific. FP assays indicated cGMP has an inhibitory effect on PDE3A while the PDE9 inhibitor, BAY73-6691, did not. Similarly, BAY73-6691, had little effect on preventing spontaneous maturation in oocytes, but did augment the inhibitory effects of cGMP. Inclusion of 0µM (control), 10µM, 100µM, and 1 mM BAY73-6691 significantly increased the proportion of mouse oocytes maintaining GV arrest in the presence of the cGMP analog 8-Br-cGMP at: 100µM (8.8%, 11.4%, 18.8%, and 28%), 500µM (21.1%, 38.1%, 74.5%,and 66.5%), and 1 mM (57.8%, 74.5%, 93.9%, and 94.0%) respectively, when P<0.05. Conclusions PDE9 is a cGMP-specific hydrolyzing enzyme present in primate oocytes, and PDE9 antagonists augment the inhibitory effect of cGMP during spontaneous in vitro maturation of GV mouse oocytes. PMID:22704629
Torphy, T J
2000-02-01
This meeting underscored advances in the exploitation of cyclic nucleotide phosphodiesterases (PDEs) as drug targets. One highlight of the meeting was the disclosure of a new PDE isozyme, bringing to 11 the total number of genetically distinct isozyme families thus far identified. Also reported was the phenotypic characterization of a PDE4D murine genetic knockout. With respect to drug discovery and development, the most encouraging information presented centered on advances in targeting PDE4 with therapeutically useful inhibitors. Historically, the therapeutic utility of isozyme-selective PDE4 inhibitors has been limited by class-associated side effects, namely nausea and dyspepsia. New PDE4 inhibitors are being designed with the specific intent of improving upon the therapeutic ratio of first-generation agents. The profiles of two second-generation PDE4 inhibitors, SB-207499 (Ariflo; Smithkline Beecham plc) and PD-189659, were presented. SB-207499 demonstrated marked efficacy in phase II clinical trials in patients with moderate-to-severe chronic obstructive pulmonary disease (COPD), a disease of very high unmet medical need. PD-189659 has yet to enter clinical trials, but its preclinical profile indicates that this agent can produce substantial anti-inflammatory effects without producing class-associated side effects in animal models. A number of presentations were also given on the utility of PDE5 inhibitors in the treatment of male erectile dysfunction (MED). The widespread use of Viagra (sildenafil; Pfizer Inc) over the last year has reinforced the perception that PDE5 inhibitors are safe and effective agents for the treatment of MED. The overall tenor of the meeting was distinctly upbeat, with most participants believing that PDE isozymes are becoming ever more accessible as targets for drug discovery in a variety of therapeutic areas.
Wagner, Gregory John; Collis, Samuel Scott; Templeton, Jeremy Alan; Lehoucq, Richard B.; Parks, Michael L.; Jones, Reese E.; Silling, Stewart Andrew; Scovazzi, Guglielmo; Bochev, Pavel B.
2007-10-01
This report is a collection of documents written as part of the Laboratory Directed Research and Development (LDRD) project A Mathematical Framework for Multiscale Science and Engineering: The Variational Multiscale Method and Interscale Transfer Operators. We present developments in two categories of multiscale mathematics and analysis. The first, continuum-to-continuum (CtC) multiscale, includes problems that allow application of the same continuum model at all scales with the primary barrier to simulation being computing resources. The second, atomistic-to-continuum (AtC) multiscale, represents applications where detailed physics at the atomistic or molecular level must be simulated to resolve the small scales, but the effect on and coupling to the continuum level is frequently unclear.
Multi-Scale Initial Conditions For Cosmological Simulations
Hahn, Oliver; Abel, Tom; /KIPAC, Menlo Park /ZAH, Heidelberg /HITS, Heidelberg
2011-11-04
We discuss a new algorithm to generate multi-scale initial conditions with multiple levels of refinements for cosmological 'zoom-in' simulations. The method uses an adaptive convolution of Gaussian white noise with a real-space transfer function kernel together with an adaptive multi-grid Poisson solver to generate displacements and velocities following first- (1LPT) or second-order Lagrangian perturbation theory (2LPT). The new algorithm achieves rms relative errors of the order of 10{sup -4} for displacements and velocities in the refinement region and thus improves in terms of errors by about two orders of magnitude over previous approaches. In addition, errors are localized at coarse-fine boundaries and do not suffer from Fourier-space-induced interference ringing. An optional hybrid multi-grid and Fast Fourier Transform (FFT) based scheme is introduced which has identical Fourier-space behaviour as traditional approaches. Using a suite of re-simulations of a galaxy cluster halo our real-space-based approach is found to reproduce correlation functions, density profiles, key halo properties and subhalo abundances with per cent level accuracy. Finally, we generalize our approach for two-component baryon and dark-matter simulations and demonstrate that the power spectrum evolution is in excellent agreement with linear perturbation theory. For initial baryon density fields, it is suggested to use the local Lagrangian approximation in order to generate a density field for mesh-based codes that is consistent with the Lagrangian perturbation theory instead of the current practice of using the Eulerian linearly scaled densities.
Kaname, Tadashi; Ki, Chang-Seok; Niikawa, Norio; Baillie, George S; Day, Jonathan P; Yamamura, Ken-Ichi; Ohta, Tohru; Nishimura, Gen; Mastuura, Nobuo; Kim, Ok-Hwa; Sohn, Young Bae; Kim, Hyun Woo; Cho, Sung Yoon; Ko, Ah-Ra; Lee, Jin Young; Kim, Hyun Wook; Ryu, Sung Ho; Rhee, Hwanseok; Yang, Kap-Seok; Joo, Keehyoung; Lee, Jooyoung; Kim, Chi Hwa; Cho, Kwang-Hyun; Kim, Dongsan; Yanagi, Kumiko; Naritomi, Kenji; Yoshiura, Ko-Ichiro; Kondoh, Tatsuro; Nii, Eiji; Tonoki, Hidefumi; Houslay, Miles D; Jin, Dong-Kyu
2014-11-01
Acrodysostosis without hormone resistance is a rare skeletal disorder characterized by brachydactyly, nasal hypoplasia, mental retardation and occasionally developmental delay. Recently, loss-of-function mutations in the gene encoding cAMP-hydrolyzing phosphodiesterase-4D (PDE4D) have been reported to cause this rare condition but the pathomechanism has not been fully elucidated. To understand the pathogenetic mechanism of PDE4D mutations, we conducted 3D modeling studies to predict changes in the binding efficacy of cAMP to the catalytic pocket in PDE4D mutants. Our results indicated diminished enzyme activity in the two mutants we analyzed (Gly673Asp and Ile678Thr; based on PDE4D4 residue numbering). Ectopic expression of PDE4D mutants in HEK293 cells demonstrated this reduction in activity, which was identified by increased cAMP levels. However, the cells from an acrodysostosis patient showed low cAMP accumulation, which resulted in a decrease in the phosphorylated cAMP Response Element-Binding Protein (pCREB)/CREB ratio. The reason for this discrepancy was due to a compensatory increase in expression levels of PDE4A and PDE4B isoforms, which accounted for the paradoxical decrease in cAMP levels in the patient cells expressing mutant isoforms with a lowered PDE4D activity. Skeletal radiographs of 10-week-old knockout (KO) rats showed that the distal part of the forelimb was shorter than in wild-type (WT) rats and that all the metacarpals and phalanges were also shorter in KO, as the name acrodysostosis implies. Like the G-protein α-stimulatory subunit and PRKAR1A, PDE4D critically regulates the cAMP signal transduction pathway and influences bone formation in a way that activity-compromising PDE4D mutations can result in skeletal dysplasia. We propose that specific inhibitory PDE4D mutations can lead to the molecular pathology of acrodysostosis without hormone resistance but that the pathological phenotype may well be dependent on an over-compensatory induction
2015-01-01
A novel series of pyrido[4,3-e][1,2,4]triazolo[4,3-a]pyrazines is reported as potent PDE2/PDE10 inhibitors with drug-like properties. Selectivity for PDE2 was obtained by introducing a linear, lipophilic moiety on the meta-position of the phenyl ring pending from the triazole. The SAR and protein flexibility were explored with free energy perturbation calculations. Rat pharmacokinetic data and in vivo receptor occupancy data are given for two representative compounds 6 and 12. PMID:25815146
NASA Astrophysics Data System (ADS)
Guo, Xiaocheng
2015-06-01
By revisiting the derivation of the previously developed HLLC Riemann solver for magneto-hydrodynamics (MHD), the paper presents an extended HLLC Riemann solver specifically designed for the MHD system in which the magnetic field can be decomposed into a strong internal magnetic field and an external component. The derived HLLC Riemann solver satisfies the conservation laws. The numerical tests show that the extended solver deals with the global MHD simulation of the Earth's magnetosphere well, and maintains high numerical resolution. It recovers the previously developed HLLC Riemann solver for the MHD as long as the internal field is set to zero. Thus, it is backward compatible with the previous HLLC solver, and suitable for the MHD simulations no matter whether a strong internal magnetic field is included or not.
Application of Aeroelastic Solvers Based on Navier Stokes Equations
NASA Technical Reports Server (NTRS)
Keith, Theo G., Jr.; Srivastava, Rakesh
2001-01-01
The propulsion element of the NASA Advanced Subsonic Technology (AST) initiative is directed towards increasing the overall efficiency of current aircraft engines. This effort requires an increase in the efficiency of various components, such as fans, compressors, turbines etc. Improvement in engine efficiency can be accomplished through the use of lighter materials, larger diameter fans and/or higher-pressure ratio compressors. However, each of these has the potential to result in aeroelastic problems such as flutter or forced response. To address the aeroelastic problems, the Structural Dynamics Branch of NASA Glenn has been involved in the development of numerical capabilities for analyzing the aeroelastic stability characteristics and forced response of wide chord fans, multi-stage compressors and turbines. In order to design an engine to safely perform a set of desired tasks, accurate information of the stresses on the blade during the entire cycle of blade motion is required. This requirement in turn demands that accurate knowledge of steady and unsteady blade loading is available. To obtain the steady and unsteady aerodynamic forces for the complex flows around the engine components, for the flow regimes encountered by the rotor, an advanced compressible Navier-Stokes solver is required. A finite volume based Navier-Stokes solver has been developed at Mississippi State University (MSU) for solving the flow field around multistage rotors. The focus of the current research effort, under NASA Cooperative Agreement NCC3- 596 was on developing an aeroelastic analysis code (entitled TURBO-AE) based on the Navier-Stokes solver developed by MSU. The TURBO-AE code has been developed for flutter analysis of turbomachine components and delivered to NASA and its industry partners. The code has been verified. validated and is being applied by NASA Glenn and by aircraft engine manufacturers to analyze the aeroelastic stability characteristics of modem fans, compressors
A New Robust Solver for Saturated-Unsaturated Richards' Equation
NASA Astrophysics Data System (ADS)
Barajas-Solano, D. A.; Tartakovsky, D. M.
2012-12-01
We present a novel approach for the numerical integration of the saturated-unsaturated Richards' equation, a degenerate parabolic partial differential equation that models flow in porous media. The method is based on the mixed (pore pressure-water content) form of RE, written as a set of differential algebraic equations (DAEs) of index-1 for the fully saturated case and index-2 for the partially saturated case. A DAE-based approach allows us to overcome the numerical challenges posed by the degenerate nature of the Richards' equation. The resulting set of DAEs is solved using the stiffly-accurate, single-step, 3-stage implicit Runge-Kutta method Radau IIA, chosen for its favorable accuracy and stability properties, and its ease of implementation. For each time step a nonlinear system of equations on the intermediate Runge-Kutta states of the pore pressure is solved, written so to ensure that the next step pore pressure and water content correspond to one another correctly. The implementation of our approach compares favorably to state-of-the-art DAE-based solvers in both one- and two-dimensional simulations. These solvers use multi-step backward difference formulas together with a pressure-based form of Richards' equation. To the best of our knowledge, our method is the first instance of a successful DAE-based solver that uses the mixed form of Richards' equation. We consider this a promising line of research, with future work to be done on the use of globally convergent methods for the solution of the occurring nonlinear systems of equations.
A computationally efficient Multicomponent Equilibrium Solver for Aerosols (MESA)
NASA Astrophysics Data System (ADS)
Zaveri, Rahul A.; Easter, Richard C.; Peters, Leonard K.
2005-12-01
Development and application of a new Multicomponent Equilibrium Solver for Aerosols (MESA) is described for systems containing H+, NH4+, Na+, Ca2+, SO42-, HSO4-, NO3-, and Cl- ions. The equilibrium solution is obtained by integrating a set of pseudo-transient ordinary differential equations describing the precipitation and dissolution reactions for all the possible salts to steady state. A comprehensive temperature dependent mutual deliquescence relative humidity (MDRH) parameterization is developed for all the possible salt mixtures, thereby eliminating the need for a rigorous numerical solution when ambient RH is less than MDRH(T). The solver is unconditionally stable, mass conserving, and shows robust convergence. Performance of MESA was evaluated against the Web-based AIM Model III, which served as a benchmark for accuracy, and the EQUISOLV II solver for speed. Important differences in the convergence and thermodynamic errors in MESA and EQUISOLV II are discussed. The average ratios of speeds of MESA over EQUISOLV II ranged between 1.4 and 5.8, with minimum and maximum ratios of 0.6 and 17, respectively. Because MESA directly diagnoses MDRH, it is significantly more efficient when RH < MDRH. MESA's superior performance is partially due to its "hard-wired" code for the present system as opposed to EQUISOLV II, which has a more generalized structure for solving any number and type of reactions at temperatures down to 190 K. These considerations suggest that MESA is highly attractive for use in 3-D aerosol/air-quality models for lower tropospheric applications (T > 240 K) in which both accuracy and computational efficiency are critical.
Code Verification of the HIGRAD Computational Fluid Dynamics Solver
Van Buren, Kendra L.; Canfield, Jesse M.; Hemez, Francois M.; Sauer, Jeremy A.
2012-05-04
The purpose of this report is to outline code and solution verification activities applied to HIGRAD, a Computational Fluid Dynamics (CFD) solver of the compressible Navier-Stokes equations developed at the Los Alamos National Laboratory, and used to simulate various phenomena such as the propagation of wildfires and atmospheric hydrodynamics. Code verification efforts, as described in this report, are an important first step to establish the credibility of numerical simulations. They provide evidence that the mathematical formulation is properly implemented without significant mistakes that would adversely impact the application of interest. Highly accurate analytical solutions are derived for four code verification test problems that exercise different aspects of the code. These test problems are referred to as: (i) the quiet start, (ii) the passive advection, (iii) the passive diffusion, and (iv) the piston-like problem. These problems are simulated using HIGRAD with different levels of mesh discretization and the numerical solutions are compared to their analytical counterparts. In addition, the rates of convergence are estimated to verify the numerical performance of the solver. The first three test problems produce numerical approximations as expected. The fourth test problem (piston-like) indicates the extent to which the code is able to simulate a 'mild' discontinuity, which is a condition that would typically be better handled by a Lagrangian formulation. The current investigation concludes that the numerical implementation of the solver performs as expected. The quality of solutions is sufficient to provide credible simulations of fluid flows around wind turbines. The main caveat associated to these findings is the low coverage provided by these four problems, and somewhat limited verification activities. A more comprehensive evaluation of HIGRAD may be beneficial for future studies.
Schaal, Sandra Marie; Garg, Maneesh Sen; Ghosh, Mousumi; Lovera, Lilie; Lopez, Michael; Patel, Monal; Louro, Jack; Patel, Samik; Tuesta, Luis; Chan, Wai-Man; Pearse, Damien Daniel
2012-01-01
The extent of damage following spinal cord injury (SCI) can be reduced by various neuroprotective regimens that include maintaining levels of cyclic adenosine monophosphate (cyclic AMP), via administration of the phosphodiesterase 4 (PDE4) inhibitor Rolipram. The current study sought to determine the optimal neuroprotective dose, route and therapeutic window for Rolipram following contusive SCI in rat as well as its prominent PDE target and putative mechanism of protection. Rolipram or vehicle control (10% ethanol) was given subcutaneously (s.c.) daily for 2 wk post-injury (PI) after which the preservation of oligodendrocytes, neurons and central myelinated axons was stereologically assessed. Doses of 0.1 mg/kg to 1.0 mg/kg (given at 1 h PI) increased neuronal survival; 0.5 mg to 1.0 mg/kg protected oligodendrocytes and 1.0 mg/kg produced optimal preservation of central myelinated axons. Ethanol also demonstrated significant neuronal and oligo-protection; though the preservation provided was significantly less than Rolipram. Subsequent use of this optimal Rolipram dose, 1.0 mg/kg, via different routes (i.v., s.c. or oral, 1 h PI), demonstrated that i.v. administration produced the most significant and consistent cyto- and axo- protection, although all routes were effective. Examination of the therapeutic window for i.v. Rolipram (1.0 mg/kg), when initiated between 1 and 48 h after SCI, revealed maximal neuroprotection at 2 h post-SCI, although the protective efficacy of Rolipram could still be observed when administration was delayed for up to 48 h PI. Importantly, use of the optimal Rolipram regimen significantly improved locomotor function after SCI as measured by the BBB score. Lastly we show SCI-induced changes in PDE4A, B and D expression and phosphorylation as well as cytokine expression and immune cell infiltration. We demonstrate that Rolipram abrogates SCI-induced PDE4B1 and PDE4A5 production, PDE4A5 phosphorylation, MCP-1 expression and immune cell
Reformulation of the Fourier-Bessel steady state mode solver
NASA Astrophysics Data System (ADS)
Gauthier, Robert C.
2016-09-01
The Fourier-Bessel resonator state mode solver is reformulated using Maxwell's field coupled curl equations. The matrix generating expressions are greatly simplified as well as a reduction in the number of pre-computed tables making the technique simpler to implement on a desktop computer. The reformulation maintains the theoretical equivalence of the permittivity and permeability and as such structures containing both electric and magnetic properties can be examined. Computation examples are presented for a surface nanoscale axial photonic resonator and hybrid { ε , μ } quasi-crystal resonator.
Some fast elliptic solvers on parallel architectures and their complexities
NASA Technical Reports Server (NTRS)
Gallopoulos, E.; Saad, Y.
1989-01-01
The discretization of separable elliptic partial differential equations leads to linear systems with special block tridiagonal matrices. Several methods are known to solve these systems, the most general of which is the Block Cyclic Reduction (BCR) algorithm which handles equations with nonconstant coefficients. A method was recently proposed to parallelize and vectorize BCR. In this paper, the mapping of BCR on distributed memory architectures is discussed, and its complexity is compared with that of other approaches including the Alternating-Direction method. A fast parallel solver is also described, based on an explicit formula for the solution, which has parallel computational compelxity lower than that of parallel BCR.
Some fast elliptic solvers on parallel architectures and their complexities
NASA Technical Reports Server (NTRS)
Gallopoulos, E.; Saad, Youcef
1989-01-01
The discretization of separable elliptic partial differential equations leads to linear systems with special block triangular matrices. Several methods are known to solve these systems, the most general of which is the Block Cyclic Reduction (BCR) algorithm which handles equations with nonconsistant coefficients. A method was recently proposed to parallelize and vectorize BCR. Here, the mapping of BCR on distributed memory architectures is discussed, and its complexity is compared with that of other approaches, including the Alternating-Direction method. A fast parallel solver is also described, based on an explicit formula for the solution, which has parallel computational complexity lower than that of parallel BCR.
Algorithms for parallel flow solvers on message passing architectures
NASA Astrophysics Data System (ADS)
Vanderwijngaart, Rob F.
1995-01-01
The purpose of this project has been to identify and test suitable technologies for implementation of fluid flow solvers -- possibly coupled with structures and heat equation solvers -- on MIMD parallel computers. In the course of this investigation much attention has been paid to efficient domain decomposition strategies for ADI-type algorithms. Multi-partitioning derives its efficiency from the assignment of several blocks of grid points to each processor in the parallel computer. A coarse-grain parallelism is obtained, and a near-perfect load balance results. In uni-partitioning every processor receives responsibility for exactly one block of grid points instead of several. This necessitates fine-grain pipelined program execution in order to obtain a reasonable load balance. Although fine-grain parallelism is less desirable on many systems, especially high-latency networks of workstations, uni-partition methods are still in wide use in production codes for flow problems. Consequently, it remains important to achieve good efficiency with this technique that has essentially been superseded by multi-partitioning for parallel ADI-type algorithms. Another reason for the concentration on improving the performance of pipeline methods is their applicability in other types of flow solver kernels with stronger implied data dependence. Analytical expressions can be derived for the size of the dynamic load imbalance incurred in traditional pipelines. From these it can be determined what is the optimal first-processor retardation that leads to the shortest total completion time for the pipeline process. Theoretical predictions of pipeline performance with and without optimization match experimental observations on the iPSC/860 very well. Analysis of pipeline performance also highlights the effect of uncareful grid partitioning in flow solvers that employ pipeline algorithms. If grid blocks at boundaries are not at least as large in the wall-normal direction as those
Hierarchically parallelized constrained nonlinear solvers with automated substructuring
NASA Technical Reports Server (NTRS)
Padovan, J.; Kwang, A.
1991-01-01
This paper develops a parallelizable multilevel constrained nonlinear equation solver. The substructuring process is automated to yield appropriately balanced partitioning of each succeeding level. Due to the generality of the procedure, both sequential, partially and fully parallel environments can be handled. This includes both single and multiprocessor assignment per individual partition. Several benchmark examples are presented. These illustrate the robustness of the procedure as well as its capacity to yield significant reductions in memory utilization and calculational effort due both to updating and inversion.
Hierarchically Parallelized Constrained Nonlinear Solvers with Automated Substructuring
NASA Technical Reports Server (NTRS)
Padovan, Joe; Kwang, Abel
1994-01-01
This paper develops a parallelizable multilevel multiple constrained nonlinear equation solver. The substructuring process is automated to yield appropriately balanced partitioning of each succeeding level. Due to the generality of the procedure,_sequential, as well as partially and fully parallel environments can be handled. This includes both single and multiprocessor assignment per individual partition. Several benchmark examples are presented. These illustrate the robustness of the procedure as well as its capability to yield significant reductions in memory utilization and calculational effort due both to updating and inversion.
Advances in the hydrodynamics solver of CO5BOLD
NASA Astrophysics Data System (ADS)
Freytag, Bernd
Many features of the Roe solver used in the hydrodynamics module of CO5BOLD have recently been added or overhauled, including the reconstruction methods (by adding the new second-order ``Frankenstein's method''), the treatment of transversal velocities, energy-flux averaging and entropy-wave treatment at small Mach numbers, the CTU scheme to combine the one-dimensional fluxes, and additional safety measures. All this results in a significantly better behavior at low Mach number flows, and an improved stability at larger Mach numbers requiring less (or no) additional tensor viscosity, which then leads to a noticeable increase in effective resolution.
FDIPS: Finite Difference Iterative Potential-field Solver
NASA Astrophysics Data System (ADS)
Toth, Gabor; van der Holst, Bartholomeus; Huang, Zhenguang
2016-06-01
FDIPS is a finite difference iterative potential-field solver that can generate the 3D potential magnetic field solution based on a magnetogram. It is offered as an alternative to the spherical harmonics approach, as when the number of spherical harmonics is increased, using the raw magnetogram data given on a grid that is uniform in the sine of the latitude coordinate can result in inaccurate and unreliable results, especially in the polar regions close to the Sun. FDIPS is written in Fortran 90 and uses the MPI library for parallel execution.
Object-Oriented Design for Sparse Direct Solvers
NASA Technical Reports Server (NTRS)
Dobrian, Florin; Kumfert, Gary; Pothen, Alex
1999-01-01
We discuss the object-oriented design of a software package for solving sparse, symmetric systems of equations (positive definite and indefinite) by direct methods. At the highest layers, we decouple data structure classes from algorithmic classes for flexibility. We describe the important structural and algorithmic classes in our design, and discuss the trade-offs we made for high performance. The kernels at the lower layers were optimized by hand. Our results show no performance loss from our object-oriented design, while providing flexibility, case of use, and extensibility over solvers using procedural design.
Performance issues for iterative solvers in device simulation
NASA Technical Reports Server (NTRS)
Fan, Qing; Forsyth, P. A.; Mcmacken, J. R. F.; Tang, Wei-Pai
1994-01-01
Due to memory limitations, iterative methods have become the method of choice for large scale semiconductor device simulation. However, it is well known that these methods still suffer from reliability problems. The linear systems which appear in numerical simulation of semiconductor devices are notoriously ill-conditioned. In order to produce robust algorithms for practical problems, careful attention must be given to many implementation issues. This paper concentrates on strategies for developing robust preconditioners. In addition, effective data structures and convergence check issues are also discussed. These algorithms are compared with a standard direct sparse matrix solver on a variety of problems.
Preconditioned CG-solvers and finite element grids
Bauer, R.; Selberherr, S.
1994-12-31
To extract parasitic capacitances in wiring structures of integrated circuits the authors developed the two- and three-dimensional finite element program SCAP (Smart Capacitance Analysis Program). The program computes the task of the electrostatic field from a solution of Poisson`s equation via finite elements and calculates the energies from which the capacitance matrix is extracted. The unknown potential vector, which has for three-dimensional applications 5000-50000 unknowns, is computed by a ICCG solver. Currently three- and six-node triangular, four- and ten-node tetrahedronal elements are supported.
Novel accurate and scalable 3-D MT forward solver based on a contracting integral equation method
NASA Astrophysics Data System (ADS)
Kruglyakov, M.; Geraskin, A.; Kuvshinov, A.
2016-11-01
We present a novel, open source 3-D MT forward solver based on a method of integral equations (IE) with contracting kernel. Special attention in the solver is paid to accurate calculations of Green's functions and their integrals which are cornerstones of any IE solution. The solver supports massive parallelization and is able to deal with highly detailed and contrasting models. We report results of a 3-D numerical experiment aimed at analyzing the accuracy and scalability of the code.
Multiscale study of metal nanoparticles
NASA Astrophysics Data System (ADS)
Lee, Byeongchan
Extremely small structures with reduced dimensionality have emerged as a scientific motif for their interesting properties. In particular, metal nanoparticles have been identified as a fundamental material in many catalytic activities; as a consequence, a better understanding of structure-function relationship of nanoparticles has become crucial. The functional analysis of nanoparticles, reactivity for example, requires an accurate method at the electronic structure level, whereas the structural analysis to find energetically stable local minima is beyond the scope of quantum mechanical methods as the computational cost becomes prohibitingly high. The challenge is that the inherent length scale and accuracy associated with any single method hardly covers the broad scale range spanned by both structural and functional analyses. In order to address this, and effectively explore the energetics and reactivity of metal nanoparticles, a hierarchical multiscale modeling is developed, where methodologies of different length scales, i.e. first principles density functional theory, atomistic calculations, and continuum modeling, are utilized in a sequential fashion. This work has focused on identifying the essential information that bridges two different methods so that a successive use of different methods is seamless. The bond characteristics of low coordination systems have been obtained with first principles calculations, and incorporated into the atomistic simulation. This also rectifies the deficiency of conventional interatomic potentials fitted to bulk properties, and improves the accuracy of atomistic calculations for nanoparticles. For the systematic shape selection of nanoparticles, we have improved the Wulff-type construction using a semi-continuum approach, in which atomistic surface energetics and crystallinity of materials are added on to the continuum framework. The developed multiscale modeling scheme is applied to the rational design of platinum
Multiply scaled constrained nonlinear equation solvers. [for nonlinear heat conduction problems
NASA Technical Reports Server (NTRS)
Padovan, Joe; Krishna, Lala
1986-01-01
To improve the numerical stability of nonlinear equation solvers, a partitioned multiply scaled constraint scheme is developed. This scheme enables hierarchical levels of control for nonlinear equation solvers. To complement the procedure, partitioned convergence checks are established along with self-adaptive partitioning schemes. Overall, such procedures greatly enhance the numerical stability of the original solvers. To demonstrate and motivate the development of the scheme, the problem of nonlinear heat conduction is considered. In this context the main emphasis is given to successive substitution-type schemes. To verify the improved numerical characteristics associated with partitioned multiply scaled solvers, results are presented for several benchmark examples.
A GPU-accelerated flow solver for incompressible two-phase fluid flows
NASA Astrophysics Data System (ADS)
Codyer, Stephen; Raessi, Mehdi; Khanna, Gaurav
2011-11-01
We present a numerical solver for incompressible, immiscible, two-phase fluid flows that is accelerated by using Graphics Processing Units (GPUs). The Navier-Stokes equations are solved by the projection method, which involves solving a pressure Poisson problem at each time step. A second-order discretization of the Poisson problem leads to a sparse matrix with five and seven diagonals for two- and three-dimensional simulations, respectively. Running a serial linear algebra solver on a single CPU can take 50-99.9% of the total simulation time to solve the above system for pressure. To remove this bottleneck, we utilized the large parallelization capabilities of GPUs; we developed a linear algebra solver based on the conjugate gradient iterative method (CGIM) by using CUDA 4.0 libraries and compared its performance with CUSP, an open-source, GPU library for linear algebra. Compared to running the CGIM solver on a single CPU core, for a 2D case, our GPU solver yields speedups of up to 88x in solver time and 81x overall time on a single GPU card. In 3D cases, the speedups are up to 81x (solver) and 15x (overall). Speedup is faster at higher grid resolutions and our GPU solver outperforms CUSP. Current work examines the acceleration versus a parallel CGIM CPU solver.
Zhang, Xiu-Jun; Gao, Xiong-Zhuo; Yao, Wei; Cote, Rick H
2012-07-27
The cGMP phosphodiesterase (PDE6) involved in visual transduction in photoreceptor cells contains two inhibitory γ-subunits (Pγ) which bind to the catalytic core (Pαβ) to inhibit catalysis and stimulate cGMP binding to the GAF domains of Pαβ. During visual excitation, interaction of activated transducin with Pγ relieves inhibition. Pγ also participates in a complex with RGS9-1 and other proteins to accelerate the GTPase activity of activated transducin. We studied the structural determinants for these important functions of Pγ. First, we identified two important sites in the middle region of Pγ (amino acids 27-38 and 52-54) that significantly stabilize the overall binding affinity of Pγ with Pαβ. The ability of Pγ to stimulate noncatalytic cGMP binding to the GAF domains of PDE6 has been localized to amino acids 27-30 of Pγ. Transducin activation of PDE6 catalysis critically depends on the presence of Ile54 in the glycine-rich region of Pγ in order to relieve inhibition of catalysis. The central glycine-rich region of Pγ is also required for transducin to increase cGMP exchange at the GAF domains. Finally, Thr-65 and/or Val-66 of Pγ are critical residues for Pγ to stimulate GTPase activity of transducin in a complex with RGS9-1. We propose that the glycine-rich region of Pγ is a primary docking site for PDE6-interacting proteins involved in the activation/inactivation pathways of visual transduction. This functional mapping of Pγ with its binding partners demonstrates the remarkable versatility of this multifunctional protein and its central role in regulating the activation and lifetime of visual transduction.
A regularizing iterative ensemble Kalman method for PDE-constrained inverse problems
NASA Astrophysics Data System (ADS)
Iglesias, Marco A.
2016-02-01
We introduce a derivative-free computational framework for approximating solutions to nonlinear PDE-constrained inverse problems. The general aim is to merge ideas from iterative regularization with ensemble Kalman methods from Bayesian inference to develop a derivative-free stable method easy to implement in applications where the PDE (forward) model is only accessible as a black box (e.g. with commercial software). The proposed regularizing ensemble Kalman method can be derived as an approximation of the regularizing Levenberg-Marquardt (LM) scheme (Hanke 1997 Inverse Problems 13 79-95) in which the derivative of the forward operator and its adjoint are replaced with empirical covariances from an ensemble of elements from the admissible space of solutions. The resulting ensemble method consists of an update formula that is applied to each ensemble member and that has a regularization parameter selected in a similar fashion to the one in the LM scheme. Moreover, an early termination of the scheme is proposed according to a discrepancy principle-type of criterion. The proposed method can be also viewed as a regularizing version of standard Kalman approaches which are often unstable unless ad hoc fixes, such as covariance localization, are implemented. The aim of this paper is to provide a detailed numerical investigation of the regularizing and convergence properties of the proposed regularizing ensemble Kalman scheme; the proof of these properties is an open problem. By means of numerical experiments, we investigate the conditions under which the proposed method inherits the regularizing properties of the LM scheme of (Hanke 1997 Inverse Problems 13 79-95) and is thus stable and suitable for its application in problems where the computation of the Fréchet derivative is not computationally feasible. More concretely, we study the effect of ensemble size, number of measurements, selection of initial ensemble and tunable parameters on the performance of the method
A Multiscale Bidirectional Coupling Framework
Kabilan, Senthil; Kuprat, Andrew P.; Hlastala, Michael P.; Corley, Richard A.; Einstein, Daniel R.
2011-12-01
The lung is geometrically articulated across multiple scales from the trachea to the alveoli. A major computational challenge is to tightly link ODEs that describe lower scales to 3D finite element or finite volume models of airway mechanics using iterative communication between scales. In this study, we developed a novel multiscale computational framework for bidirectionally coupling 3D CFD models and systems of lower order ODEs. To validate the coupling framework, a four and eight generation Weibel lung model was constructed. For the coupled CFD-ODE simulations, the lung models were truncated at different generations and a RL circuit represented the truncated portion. The flow characteristics from the coupled models were compared to untruncated full 3D CFD models at peak inhalation and peak exhalation. Results showed that at no time or simulation was the difference in mass flux and/or pressure at a given location between uncoupled and coupled models was greater than 2.43%. The flow characteristics at prime locations for the coupled models showed good agreement to uncoupled models. Remarkably, due to reuse of the Krylov subspace, the cost of the ODE coupling is not much greater than uncoupled full 3D-CFD computations with simple prescribed pressure values at the outlets.
Multiscale modelling of saliva secretion.
Sneyd, James; Crampin, Edmund; Yule, David
2014-11-01
We review a multiscale model of saliva secretion, describing in brief how the model is constructed and what we have so far learned from it. The model begins at the level of inositol trisphosphate receptors (IPR), and proceeds through the cellular level (with a model of acinar cell calcium dynamics) to the multicellular level (with a model of the acinus), finally to a model of a saliva production unit that includes an acinus and associated duct. The model at the level of the entire salivary gland is not yet completed. Particular results from the model so far include (i) the importance of modal behaviour of IPR, (ii) the relative unimportance of Ca(2+) oscillation frequency as a controller of saliva secretion, (iii) the need for the periodic Ca(2+) waves to be as fast as possible in order to maximise water transport, (iv) the presence of functional K(+) channels in the apical membrane increases saliva secretion, (v) the relative unimportance of acinar spatial structure for isotonic water transport, (vi) the prediction that duct cells are highly depolarised, (vii) the prediction that the secondary saliva takes at least 1mm (from the acinus) to reach ionic equilibrium. We end with a brief discussion of future directions for the model, both in construction and in the study of scientific questions.
MULTISCALE DISCRETIZATION OF SHAPE CONTOURS
Prasad, L.; Rao, R.
2000-09-01
We present an efficient multi-scale scheme to adaptively approximate the continuous (or densely sampled) contour of a planar shape at varying resolutions. The notion of shape is intimately related to the notion of contour, and the efficient representation of the contour of a shape is vital to a computational understanding of the shape. Any polygonal approximation of a planar smooth curve is equivalent to a piecewise constant approximation of the parameterized X and Y coordinate functions of a discrete point set obtained by densely sampling the curve. Using the Haar wavelet transform for the piecewise approximation yields a hierarchical scheme in which the size of the approximating point set is traded off against the morphological accuracy of the approximation. Our algorithm compresses the representation of the initial shape contour to a sparse sequence of points in the plane defining the vertices of the shape's polygonal approximation. Furthermore, it is possible to control the overall resolution of the approximation by a single, scale-independent parameter.
Multi-scale Material Appearance
NASA Astrophysics Data System (ADS)
Wu, Hongzhi
Modeling and rendering the appearance of materials is important for a diverse range of applications of computer graphics - from automobile design to movies and cultural heritage. The appearance of materials varies considerably at different scales, posing significant challenges due to the sheer complexity of the data, as well the need to maintain inter-scale consistency constraints. This thesis presents a series of studies around the modeling, rendering and editing of multi-scale material appearance. To efficiently render material appearance at multiple scales, we develop an object-space precomputed adaptive sampling method, which precomputes a hierarchy of view-independent points that preserve multi-level appearance. To support bi-scale material appearance design, we propose a novel reflectance filtering algorithm, which rapidly computes the large-scale appearance from small-scale details, by exploiting the low-rank structures of Bidirectional Visible Normal Distribution Functions and pre-rotated Bidirectional Reflectance Distribution Functions in the matrix formulation of the rendering algorithm. This approach can guide the physical realization of appearance, as well as the modeling of real-world materials using very sparse measurements. Finally, we present a bi-scale-inspired high-quality general representation for material appearance described by Bidirectional Texture Functions. Our representation is at once compact, easily editable, and amenable to efficient rendering.
Multiscale Modeling of Hematologic Disorders
Fedosov, Dmitry A.; Pivkin, Igor; Pan, Wenxiao; Dao, Ming; Caswell, Bruce; Karniadakis, George E.
2012-01-28
Parasitic infectious diseases and other hereditary hematologic disorders are often associated with major changes in the shape and viscoelastic properties of red blood cells (RBCs). Such changes can disrupt blood flow and even brain perfusion, as in the case of cerebral malaria. Modeling of these hematologic disorders requires a seamless multiscale approach, where blood cells and blood flow in the entire arterial tree are represented accurately using physiologically consistent parameters. In this chapter, we present a computational methodology based on dissipative particle dynamics (DPD) which models RBCs as well as whole blood in health and disease. DPD is a Lagrangian method that can be derived from systematic coarse-graining of molecular dynamics but can scale efficiently up to small arteries and can also be used to model RBCs down to spectrin level. To this end, we present two complementary mathematical models for RBCs and describe a systematic procedure on extracting the relevant input parameters from optical tweezers and microfluidic experiments for single RBCs. We then use these validated RBC models to predict the behavior of whole healthy blood and compare with experimental results. The same procedure is applied to modeling malaria, and results for infected single RBCs and whole blood are presented.
Multiscale modelling of evolving foams
NASA Astrophysics Data System (ADS)
Saye, R. I.; Sethian, J. A.
2016-06-01
We present a set of multi-scale interlinked algorithms to model the dynamics of evolving foams. These algorithms couple the key effects of macroscopic bubble rearrangement, thin film drainage, and membrane rupture. For each of the mechanisms, we construct consistent and accurate algorithms, and couple them together to work across the wide range of space and time scales that occur in foam dynamics. These algorithms include second order finite difference projection methods for computing incompressible fluid flow on the macroscale, second order finite element methods to solve thin film drainage equations in the lamellae and Plateau borders, multiphase Voronoi Implicit Interface Methods to track interconnected membrane boundaries and capture topological changes, and Lagrangian particle methods for conservative liquid redistribution during rearrangement and rupture. We derive a full set of numerical approximations that are coupled via interface jump conditions and flux boundary conditions, and show convergence for the individual mechanisms. We demonstrate our approach by computing a variety of foam dynamics, including coupled evolution of three-dimensional bubble clusters attached to an anchored membrane and collapse of a foam cluster.
Riemann solvers and Alfven waves in black hole magnetospheres
NASA Astrophysics Data System (ADS)
Punsly, Brian; Balsara, Dinshaw; Kim, Jinho; Garain, Sudip
2016-09-01
In the magnetosphere of a rotating black hole, an inner Alfven critical surface (IACS) must be crossed by inflowing plasma. Inside the IACS, Alfven waves are inward directed toward the black hole. The majority of the proper volume of the active region of spacetime (the ergosphere) is inside of the IACS. The charge and the totally transverse momentum flux (the momentum flux transverse to both the wave normal and the unperturbed magnetic field) are both determined exclusively by the Alfven polarization. Thus, it is important for numerical simulations of black hole magnetospheres to minimize the dissipation of Alfven waves. Elements of the dissipated wave emerge in adjacent cells regardless of the IACS, there is no mechanism to prevent Alfvenic information from crossing outward. Thus, numerical dissipation can affect how simulated magnetospheres attain the substantial Goldreich-Julian charge density associated with the rotating magnetic field. In order to help minimize dissipation of Alfven waves in relativistic numerical simulations we have formulated a one-dimensional Riemann solver, called HLLI, which incorporates the Alfven discontinuity and the contact discontinuity. We have also formulated a multidimensional Riemann solver, called MuSIC, that enables low dissipation propagation of Alfven waves in multiple dimensions. The importance of higher order schemes in lowering the numerical dissipation of Alfven waves is also catalogued.
A massively parallel fractional step solver for incompressible flows
Houzeaux, G. Vazquez, M. Aubry, R. Cela, J.M.
2009-09-20
This paper presents a parallel implementation of fractional solvers for the incompressible Navier-Stokes equations using an algebraic approach. Under this framework, predictor-corrector and incremental projection schemes are seen as sub-classes of the same class, making apparent its differences and similarities. An additional advantage of this approach is to set a common basis for a parallelization strategy, which can be extended to other split techniques or to compressible flows. The predictor-corrector scheme consists in solving the momentum equation and a modified 'continuity' equation (namely a simple iteration for the pressure Schur complement) consecutively in order to converge to the monolithic solution, thus avoiding fractional errors. On the other hand, the incremental projection scheme solves only one iteration of the predictor-corrector per time step and adds a correction equation to fulfill the mass conservation. As shown in the paper, these two schemes are very well suited for massively parallel implementation. In fact, when compared with monolithic schemes, simpler solvers and preconditioners can be used to solve the non-symmetric momentum equations (GMRES, Bi-CGSTAB) and to solve the symmetric continuity equation (CG, Deflated CG). This gives good speedup properties of the algorithm. The implementation of the mesh partitioning technique is presented, as well as the parallel performances and speedups for thousands of processors.
Using computer algebra and SMT solvers in algebraic biology
NASA Astrophysics Data System (ADS)
Pineda Osorio, Mateo
2014-05-01
Biologic processes are represented as Boolean networks, in a discrete time. The dynamics within these networks are approached with the help of SMT Solvers and the use of computer algebra. Software such as Maple and Z3 was used in this case. The number of stationary states for each network was calculated. The network studied here corresponds to the immune system under the effects of drastic mood changes. Mood is considered as a Boolean variable that affects the entire dynamics of the immune system, changing the Boolean satisfiability and the number of stationary states of the immune network. Results obtained show Z3's great potential as a SMT Solver. Some of these results were verified in Maple, even though it showed not to be as suitable for the problem approach. The solving code was constructed using Z3-Python and Z3-SMT-LiB. Results obtained are important in biology systems and are expected to help in the design of immune therapies. As a future line of research, more complex Boolean network representations of the immune system as well as the whole psychological apparatus are suggested.
Matrix decomposition graphics processing unit solver for Poisson image editing
NASA Astrophysics Data System (ADS)
Lei, Zhao; Wei, Li
2012-10-01
In recent years, gradient-domain methods have been widely discussed in the image processing field, including seamless cloning and image stitching. These algorithms are commonly carried out by solving a large sparse linear system: the Poisson equation. However, solving the Poisson equation is a computational and memory intensive task which makes it not suitable for real-time image editing. A new matrix decomposition graphics processing unit (GPU) solver (MDGS) is proposed to settle the problem. A matrix decomposition method is used to distribute the work among GPU threads, so that MDGS will take full advantage of the computing power of current GPUs. Additionally, MDGS is a hybrid solver (combines both the direct and iterative techniques) and has two-level architecture. These enable MDGS to generate identical solutions with those of the common Poisson methods and achieve high convergence rate in most cases. This approach is advantageous in terms of parallelizability, enabling real-time image processing, low memory-taken and extensive applications.
Agglomeration Multigrid for an Unstructured-Grid Flow Solver
NASA Technical Reports Server (NTRS)
Frink, Neal; Pandya, Mohagna J.
2004-01-01
An agglomeration multigrid scheme has been implemented into the sequential version of the NASA code USM3Dns, tetrahedral cell-centered finite volume Euler/Navier-Stokes flow solver. Efficiency and robustness of the multigrid-enhanced flow solver have been assessed for three configurations assuming an inviscid flow and one configuration assuming a viscous fully turbulent flow. The inviscid studies include a transonic flow over the ONERA M6 wing and a generic business jet with flow-through nacelles and a low subsonic flow over a high-lift trapezoidal wing. The viscous case includes a fully turbulent flow over the RAE 2822 rectangular wing. The multigrid solutions converged with 12%-33% of the Central Processing Unit (CPU) time required by the solutions obtained without multigrid. For all of the inviscid cases, multigrid in conjunction with an explicit time-stepping scheme performed the best with regard to the run time memory and CPU time requirements. However, for the viscous case multigrid had to be used with an implicit backward Euler time-stepping scheme that increased the run time memory requirement by 22% as compared to the run made without multigrid.
An efficient chemical kinetics solver using high dimensional model representation
Shorter, J.A.; Ip, P.C.; Rabitz, H.A.
1999-09-09
A high dimensional model representation (HDMR) technique is introduced to capture the input-output behavior of chemical kinetic models. The HDMR expresses the output chemical species concentrations as a rapidly convergent hierarchical correlated function expansion in the input variables. In this paper, the input variables are taken as the species concentrations at time t{sub i} and the output is the concentrations at time t{sub i} + {delta}, where {delta} can be much larger than conventional integration time steps. A specially designed set of model runs is performed to determine the correlated functions making up the HDMR. The resultant HDMR can be used to (1) identify the key input variables acting independently or cooperatively on the output, and (2) create a high speed fully equivalent operational model (FEOM) serving to replace the original kinetic model and its differential equation solver. A demonstration of the HDMR technique is presented for stratospheric chemical kinetics. The FEOM proved to give accurate and stable chemical concentrations out to long times of many years. In addition, the FEOM was found to be orders of magnitude faster than a conventional stiff equation solver. This computational acceleration should have significance in many chemical kinetic applications.
CASTRO: A NEW COMPRESSIBLE ASTROPHYSICAL SOLVER. III. MULTIGROUP RADIATION HYDRODYNAMICS
Zhang, W.; Almgren, A.; Bell, J.; Howell, L.; Burrows, A.; Dolence, J.
2013-01-15
We present a formulation for multigroup radiation hydrodynamics that is correct to order O(v/c) using the comoving-frame approach and the flux-limited diffusion approximation. We describe a numerical algorithm for solving the system, implemented in the compressible astrophysics code, CASTRO. CASTRO uses a Eulerian grid with block-structured adaptive mesh refinement based on a nested hierarchy of logically rectangular variable-sized grids with simultaneous refinement in both space and time. In our multigroup radiation solver, the system is split into three parts: one part that couples the radiation and fluid in a hyperbolic subsystem, another part that advects the radiation in frequency space, and a parabolic part that evolves radiation diffusion and source-sink terms. The hyperbolic subsystem and the frequency space advection are solved explicitly with high-order Godunov schemes, whereas the parabolic part is solved implicitly with a first-order backward Euler method. Our multigroup radiation solver works for both neutrino and photon radiation.
CASTRO: A New Compressible Astrophysical Solver. III. Multigroup Radiation Hydrodynamics
NASA Astrophysics Data System (ADS)
Zhang, W.; Howell, L.; Almgren, A.; Burrows, A.; Dolence, J.; Bell, J.
2013-01-01
We present a formulation for multigroup radiation hydrodynamics that is correct to order O(v/c) using the comoving-frame approach and the flux-limited diffusion approximation. We describe a numerical algorithm for solving the system, implemented in the compressible astrophysics code, CASTRO. CASTRO uses a Eulerian grid with block-structured adaptive mesh refinement based on a nested hierarchy of logically rectangular variable-sized grids with simultaneous refinement in both space and time. In our multigroup radiation solver, the system is split into three parts: one part that couples the radiation and fluid in a hyperbolic subsystem, another part that advects the radiation in frequency space, and a parabolic part that evolves radiation diffusion and source-sink terms. The hyperbolic subsystem and the frequency space advection are solved explicitly with high-order Godunov schemes, whereas the parabolic part is solved implicitly with a first-order backward Euler method. Our multigroup radiation solver works for both neutrino and photon radiation.
Lythgoe, Casey; McVary, Kevin T
2013-12-01
The relationship between lower urinary tract symptoms secondary to BPH and ED has recently been the subject of significant research due to the prevalence of both conditions concomitantly existing in older men. Many large-scale studies have demonstrated an association between erectile dysfunction and lower urinary tract symptoms. Although the mechanisms underlying the relationship between LUTS and ED are not fully elucidated, several theories are currently proposed in literature: the nitric oxide/cGMP pathway, RhoA/Rho-kinase signaling, pelvic atherosclerosis associated with chronic hypoxia, and autonomic adrenergic hyperactivity. The mechanisms by which these pathways affect the bladder, prostate, pelvic vasculature and spinal cord are also the subject of current research. In this chapter, we examine the randomized, placebo-controlled trials that have evaluated the use of PDE-5Is in LUTS, as well as randomized, controlled trials (RCTs) researching combination PDE-5Is and alpha blockers. PMID:24136683
User documentation for PVODE, an ODE solver for parallel computers
Hindmarsh, A.C., LLNL
1998-05-01
PVODE is a general purpose ordinary differential equation (ODE) solver for stiff and nonstiff ODES It is based on CVODE [5] [6], which is written in ANSI- standard C PVODE uses MPI (Message-Passing Interface) [8] and a revised version of the vector module in CVODE to achieve parallelism and portability PVODE is intended for the SPMD (Single Program Multiple Data) environment with distributed memory, in which all vectors are identically distributed across processors In particular, the vector module is designed to help the user assign a contiguous segment of a given vector to each of the processors for parallel computation The idea is for each processor to solve a certain fixed subset of the ODES To better understand PVODE, we first need to understand CVODE and its historical background The ODE solver CVODE, which was written by Cohen and Hindmarsh, combines features of two earlier Fortran codes, VODE [l] and VODPK [3] Those two codes were written by Brown, Byrne, and Hindmarsh. Both use variable-coefficient multi-step integration methods, and address both stiff and nonstiff systems (Stiffness is defined as the presence of one or more very small damping time constants ) VODE uses direct linear algebraic techniques to solve the underlying banded or dense linear systems of equations in conjunction with a modified Newton method in the stiff ODE case On the other hand, VODPK uses a preconditioned Krylov iterative method [2] to solve the underlying linear system User-supplied preconditioners directly address the dominant source of stiffness Consequently, CVODE implements both the direct and iterative methods Currently, with regard to the nonlinear and linear system solution, PVODE has three method options available. functional iteration, Newton iteration with a diagonal approximate Jacobian, and Newton iteration with the iterative method SPGMR (Scaled Preconditioned Generalized Minimal Residual method) Both CVODE and PVODE are written in such a way that other linear
Franklin, Kelle M.; Hauser, Sheketha R.; Lasek, Amy W.; McClintick, Jeanette; Ding, Zheng-Ming; McBride, William J.; Bell, Richard L.
2015-01-01
Rationale Phosphodiesterase-4 (PDE4) and neuroimmune signaling have been posited to regulate alcohol drinking. Objectives This study evaluated the involvement of PDE4 and Il22ra2 on ethanol (EtOH) intake by alcohol-preferring (P) and high-alcohol drinking (HAD1) rats. Methods Exp 1 determined the dose-response effects of PDE4 inhibitors, rolipram and Ro 20-1724, on 2h/day free-choice EtOH intake by adult P and HAD1 rats. Exps 2–3 examined the effects of repeated administration with the PDE4 inhibitors on EtOH or sucrose intake, and locomotor behavior. Exp 4 determined Pde4-associated gene expression differences in subregions of the extended amygdala, between high- and low-alcohol-consuming rat lines. Exp 5 evaluated the effects of infusing short hairpin RNA to knock down Il22ra2 in the nucleus accumbens (NAc) shell on 24h free-choice EtOH drinking by P rats. Results Administration of rolipram or Ro 20-1724 reduced EtOH intake by P rats; Ro 20-1724 reduced EtOH intake by HAD1 rats. Repeated rolipram or Ro 20-1724 exposure reduced EtOH intake by P and HAD1 rats. PDE4 inhibition induced motor impairment during the first hour of EtOH intake by P rats. Higher gene expression levels for PDE4A were found in the NAc shell of P vs. NP rats. ShRNAs targeting Il22ra2 in the NAc shell significantly reduced chronic EtOH intake. Conclusions PDE4 and neuroinflammatory/immune signaling pathways could represent molecular targets for the treatment of alcohol use disorders, in genetically predisposed subjects. This study underscores the importance of testing compounds over multiple days and rat lines when determining efficacy to disrupt excessive alcohol intake. PMID:25585681
Redrobe, John P; Jørgensen, Morten; Christoffersen, Claus T; Montezinho, Liliana P; Bastlund, Jesper F; Carnerup, Martin; Bundgaard, Christoffer; Lerdrup, Linda; Plath, Niels
2014-08-01
Here, we present the pharmacological characterisation of Lu AF64280, a novel, selective, brain penetrant phosphodiesterase (PDE) 2A inhibitor, in in vitro/in vivo assays indicative of PDE2A inhibition, and in vivo models/assays relevant to cognitive processing or antipsychotic-like activity. The in vitro selectivity of Lu AF64280 was determined against a panel of PDE enzymes and 3',5'-cyclic guanosine monophosphate (cGMP) levels in the hippocampus were determined using in vivo microdialysis. Lu AF64280 potently inhibited hPDE2A (Ki = 20 nM), 50-fold above moderate inhibition of both hPDE9A (Ki = 1,000 nM) and hPDE10A (Ki = 1,800 nM), and displayed a >250-fold selectivity over all other full-length human recombinant PDE family members (Ki above 5,000 nM). Lu AF64280 (20 mg/kg) significantly increased cGMP levels in the hippocampus (p < 0.01 versus vehicle-treated mice), attenuated sub-chronic phencyclidine-induced deficits in novel object exploration in rats (10 mg/kg, p < 0.001 versus vehicle-treated), blocked early postnatal phencyclidine-induced deficits in the intradimensional/extradimensional shift task in rats (1 and 10 mg/kg, p < 0.001 versus vehicle-treated) and attenuated spontaneous P20-N40 auditory gating deficits in DBA/2 mice (20 mg/kg, p < 0.05 versus vehicle-treated). In contrast, Lu AF64280 failed to attenuate phencyclidine-induced hyperactivity in mice, and was devoid of antipsychotic-like activity in the conditioned avoidance response paradigm in rats, at any dose tested. Lu AF64280 represents a novel tool compound for selective PDE2A inhibition that substantiates a critical role of this enzyme in cognitive processes under normal and pathological conditions.
DISC1–ATF4 transcriptional repression complex: dual regulation of the cAMP-PDE4 cascade by DISC1
Soda, T; Frank, C; Ishizuka, K; Baccarella, A; Park, Y-U; Flood, Z; Park, S K; Sawa, A; Tsai, L-H
2013-01-01
Disrupted-In-Schizophrenia 1 (DISC1), a risk factor for major mental illnesses, has been studied extensively in the context of neurodevelopment. However, the role of DISC1 in neuronal signaling, particularly in conjunction with intracellular cascades that occur in response to dopamine, a neurotransmitter implicated in numerous psychiatric disorders, remains elusive. Previous data suggest that DISC1 interacts with numerous proteins that impact neuronal function, including activating transcription factor 4 (ATF4). In this study, we identify a novel DISC1 and ATF4 binding region in the genomic locus of phosphodiesterase 4D (PDE4D), a gene implicated in psychiatric disorders. We found that the loss of function of either DISC1 or ATF4 increases PDE4D9 transcription, and that the association of DISC1 with the PDE4D9 locus requires ATF4. We also show that PDE4D9 is increased by D1-type dopamine receptor dopaminergic stimulation. We demonstrate that the mechanism for this increase is due to DISC1 dissociation from the PDE4D locus in mouse brain. We further characterize the interaction of DISC1 with ATF4 to show that it is regulated via protein kinase A-mediated phosphorylation of DISC1 serine-58. Our results suggest that the release of DISC1-mediated transcriptional repression of PDE4D9 acts as feedback inhibition to regulate dopaminergic signaling. Furthermore, as DISC1 loss-of-function leads to a specific increase in PDE4D9, PDE4D9 itself may represent an attractive target for therapeutic approaches in psychiatric disorders. PMID:23587879
Megens, Anton A H P; Hendrickx, Herman M R; Mahieu, Michel M A; Wellens, Annemie L Y; de Boer, Peter; Vanhoof, Greet
2014-01-01
The enzyme phosphodiesterase 10A (PDE10A) regulates the activity of striatal, medium spiny neurons (MSNs), which are divided into a behaviorally stimulating, Gs-coupled D1 receptor-expressing “direct” pathway and a behaviorally suppressant, Gi-coupled D2 receptor-expressing “indirect” pathway. Activating both pathways, PDE10A inhibitors (PDE10AIs) combine functional characteristics of D2 antagonists and D1 agonists. While the effects of PDE10AIs on spontaneous and stimulated behavior have been extensively reported, the present study investigates their effects on suppressed behavior under various conditions of reduced dopaminergic neurotransmission: blockade of D1 receptors with SCH-23390, blockade of D2 receptors with haloperidol, or depletion of dopamine with RO-4-1284 or reserpine. In rats, PDE10AIs displayed relatively low cataleptic activity per se. After blocking D1 receptors, however, they induced pronounced catalepsy at low doses close to those required for inhibition of apomorphine-induced behavior; slightly higher doses resulted in behavioral stimulant effects, counteracting the catalepsy. PDE10AIs also counteracted catalepsy and related behaviors induced by D2 receptor blockade or dopamine depletion; catalepsy was replaced by behavioral stimulant effects under the latter but not the former condition. Similar interactions were observed at the level of locomotion in mice. At doses close to those inhibiting d-amphetamine-induced hyperlocomotion, PDE10AIs reversed hypolocomotion induced by D1 receptor blockade or dopamine depletion but not hypolocomotion induced by D2 receptor blockade. It is concluded that PDE10AIs stimulate or inhibit motor behavior dependent on the relative activation state of the direct and indirect striatal output pathways. PMID:25505601
Zhang, Liyun; Xiang, Lue; Liu, Yiwen; Venkatraman, Prahatha; Chong, Leelyn; Cho, Jin; Bonilla, Sylvia; Jin, Zi-Bing; Pang, Chi Pui; Ko, Kam Ming; Ma, Ping
2016-01-01
Retinal degeneration is often progressive. This feature has provided a therapeutic window for intervention that may extend functional vision in patients. Even though this approach is feasible, few promising drug candidates are available. The scarcity of new drugs has motivated research to discover novel compounds through different sources. One such example is Schisandrin B (SchB), an active component isolated from the five-flavor fruit (Fructus Schisandrae) that is postulated in traditional Chinese medicines to exert prophylactic visual benefit. This SchB benefit was investigated in this study in pde6cw59, a zebrafish retinal-degeneration model. In this model, the pde6c gene (phosphodiesterase 6C, cGMP-specific, cone, alpha prime) carried a mutation which caused cone degeneration. This altered the local environment and caused the bystander rods to degenerate too. To test SchB on the pde6cw59 mutants, a treatment concentration was first determined that would not cause morphological defects, and would initiate known physiological response. Then, the mutants were treated with the optimized SchB concentration before the appearance of retinal degeneration at 3 days postfertilization (dpf). The light sensation of animals was evaluated at 6 dpf by the visual motor response (VMR), a visual startle that could be initiated by drastic light onset and offset. The results show that the VMR of pde6cw59 mutants towards light onset was enhanced by the SchB treatment, and that the initial phase of the enhancement was primarily mediated through the mutants’ eyes. Further immunostaining analysis indicates that the treatment specifically reduced the size of the abnormally large rods. These observations implicate an interesting hypothesis: that the morphologically-improved rods drive the observed VMR enhancement. Together, these investigations have identified a possible visual benefit of SchB on retinal degeneration, a benefit that can potentially be further developed to extend
Zhang, Liyun; Xiang, Lue; Liu, Yiwen; Venkatraman, Prahatha; Chong, Leelyn; Cho, Jin; Bonilla, Sylvia; Jin, Zi-Bing; Pang, Chi Pui; Ko, Kam Ming; Ma, Ping; Zhang, Mingzhi; Leung, Yuk Fai
2016-01-01
Retinal degeneration is often progressive. This feature has provided a therapeutic window for intervention that may extend functional vision in patients. Even though this approach is feasible, few promising drug candidates are available. The scarcity of new drugs has motivated research to discover novel compounds through different sources. One such example is Schisandrin B (SchB), an active component isolated from the five-flavor fruit (Fructus Schisandrae) that is postulated in traditional Chinese medicines to exert prophylactic visual benefit. This SchB benefit was investigated in this study in pde6cw59, a zebrafish retinal-degeneration model. In this model, the pde6c gene (phosphodiesterase 6C, cGMP-specific, cone, alpha prime) carried a mutation which caused cone degeneration. This altered the local environment and caused the bystander rods to degenerate too. To test SchB on the pde6cw59 mutants, a treatment concentration was first determined that would not cause morphological defects, and would initiate known physiological response. Then, the mutants were treated with the optimized SchB concentration before the appearance of retinal degeneration at 3 days postfertilization (dpf). The light sensation of animals was evaluated at 6 dpf by the visual motor response (VMR), a visual startle that could be initiated by drastic light onset and offset. The results show that the VMR of pde6cw59 mutants towards light onset was enhanced by the SchB treatment, and that the initial phase of the enhancement was primarily mediated through the mutants' eyes. Further immunostaining analysis indicates that the treatment specifically reduced the size of the abnormally large rods. These observations implicate an interesting hypothesis: that the morphologically-improved rods drive the observed VMR enhancement. Together, these investigations have identified a possible visual benefit of SchB on retinal degeneration, a benefit that can potentially be further developed to extend
Polymorphisms in PDE4D are associated with a risk of COPD in non-emphysematous Koreans.
Yoon, Hyoung-Kyu; Hu, Hae-Jin; Rhee, Chin-Kook; Shin, Seung-Hoon; Oh, Yeon-Mok; Lee, Sang-Do; Jung, Seung-Hyun; Yim, Seon-Hee; Kim, Tae-Min; Chung, Yeun-Jun
2014-12-01
Despite extensive effort, only a few chronic obstructive pulmonary disease (COPD)-associated genes have been suggested, indicating that there must be additional risk-associated loci. Here we aimed to identify additional COPD-associated SNPs and to explore the potential relationship between COPD subgroups and the SNPs in the Korean population. We performed a genome-wide association study (GWAS) with 990 Korean individuals; 102 COPD cases and 544 controls for GWAS using Affymetrix SNP array 5.0, and 173 COPD cases and 171 controls for replication. After validating the candidate single nucleotide polymorphisms (SNP), we performed subgroup analysis by disease phenotype. Through GWAS, we identified a novel SNP in the phosphodiesterase-4D (PDE4D) gene [rs16878037 (C>T), p = 1.66 ◊ 10(-6)] that was significantly associated with COPD. This signal in PDE4D was successfully replicated in the independent set (p = 0.041). When we combined the discovery and replication data, the association signal became more significant (p = 5.69 ◊ 10(-7)). In the COPD subgroup analysis, the T allele of rs16878037 was significantly more frequent in COPD patients without severe diffusion capacity impairment (mild mixed and obstruction-dominant group) than in patients with severe impairment (severe mixed and emphysema-dominant groups). This result supports that PDE4D polymorphisms might be involved in the susceptibility to COPD especially in non-emphysematous individuals and that they could also affect the responsiveness of the PDE4 inhibitor treatment. PMID:24926854
The center for multiscale plasma dynamics
Kevrekidis, Yannis G
2015-01-20
This final report describes research performed in Princeton University, led by Professor Yannis G. Kevrekidis, over a period of six years (August 1, 2014 to July 31, 2010, including a one-year, no-cost extension) as part of the Center for Multiscale Plasma Dynamics led by the University of Maryland. The work resulted in the development and implementation of several multiscale algorithms based on the equation-free approach pioneered by the PI, including its applications in plasma dynamics problems. These algoriithms include coarse projective integration and coarse stability/bifurcation computations. In the later stages of the work, new links were made between this multiscale, coarse-graining approach and advances in data mining/machine learning algorithms.
Generalized multiscale radial basis function networks.
Billings, Stephen A; Wei, Hua-Liang; Balikhin, Michael A
2007-12-01
A novel modelling framework is proposed for constructing parsimonious and flexible multiscale radial basis function networks (RBF). Unlike a conventional standard single scale RBF network, where all the basis functions have a common kernel width, the new network structure adopts multiscale Gaussian functions as the bases, where each selected centre has multiple kernel widths, to provide more flexible representations with better generalization properties for general nonlinear dynamical systems. As a direct extension of the traditional single scale Gaussian networks, the new multiscale network is easy to implement and is quick to learn using standard learning algorithms. A k-means clustering algorithm and an improved orthogonal least squares (OLS) algorithm are used to determine the unknown parameters in the network model including the centres and widths of the basis functions, and the weights between the basis functions. It is demonstrated that the new network can lead to a parsimonious model with much better generalization property compared with the traditional single width RBF networks.
Multiscale Computational Models of Complex Biological Systems
Walpole, Joseph; Papin, Jason A.; Peirce, Shayn M.
2014-01-01
Integration of data across spatial, temporal, and functional scales is a primary focus of biomedical engineering efforts. The advent of powerful computing platforms, coupled with quantitative data from high-throughput experimental platforms, has allowed multiscale modeling to expand as a means to more comprehensively investigate biological phenomena in experimentally relevant ways. This review aims to highlight recently published multiscale models of biological systems while using their successes to propose the best practices for future model development. We demonstrate that coupling continuous and discrete systems best captures biological information across spatial scales by selecting modeling techniques that are suited to the task. Further, we suggest how to best leverage these multiscale models to gain insight into biological systems using quantitative, biomedical engineering methods to analyze data in non-intuitive ways. These topics are discussed with a focus on the future of the field, the current challenges encountered, and opportunities yet to be realized. PMID:23642247
Sutcliffe, Jane S.; Beaumont, Vahri; Watson, James M.; Chew, Chang Sing; Beconi, Maria; Hutcheson, Daniel M.; Dominguez, Celia; Munoz-Sanjuan, Ignacio
2014-01-01
Cyclic adenosine monophosphate (cAMP) signalling plays an important role in synaptic plasticity and information processing in the hippocampal and basal ganglia systems. The augmentation of cAMP signalling through the selective inhibition of phosphodiesterases represents a viable strategy to treat disorders associated with dysfunction of these circuits. The phosphodiesterase (PDE) type 4 inhibitor rolipram has shown significant pro-cognitive effects in neurological disease models, both in rodents and primates. However, competitive non-isoform selective PDE4 inhibitors have a low therapeutic index which has stalled their clinical development. Here, we demonstrate the pro-cognitive effects of selective negative allosteric modulators (NAMs) of PDE4D, D159687 and D159797 in female Cynomolgous macaques, in the object retrieval detour task. The efficacy displayed by these NAMs in a primate cognitive task which engages the corticostriatal circuitry, together with their suitable pharmacokinetic properties and safety profiles, suggests that clinical development of these allosteric modulators should be considered for the treatment of a variety of brain disorders associated with cognitive decline. PMID:25050979
Boomkamp, S D; McGrath, M A; Houslay, M D; Barnett, S C
2014-01-01
Background and Purpose cAMP and pharmacological inhibition of PDE4, which degrades it, are promising therapeutic targets for the treatment of spinal cord injury (SCI). Using our previously described in vitro SCI model, we studied the mechanisms by which cAMP modulators promote neurite outgrowth and myelination using enantiomers of the PDE4-specific inhibitor rolipram and other modulators of downstream signalling effectors. Experimental Approach Rat mixed neural cell myelinating cultures were cut with a scalpel and treated with enantiomers of the PDE4-specific inhibitor rolipram, Epac agonists and PKA antagonists. Neurite outgrowth, density and myelination were assessed by immunocytochemistry and cytokine levels analysed by qPCR. Key Results Inhibition of the high-affinity rolipram-binding state (HARBS), rather than the low-affinity rolipram binding state (LARBS) PDE4 conformer promoted neurite outgrowth and myelination. These effects were mediated through the activation of Epac and not through PKA. Expression of the chemokine CXCL10, known to inhibit myelination, was markedly elevated in astrocytes after Rho inhibition and this was blocked by inhibition of Rho kinase or PDE4. Conclusions and Implications PDE4 inhibitors targeted at the HARBS conformer or Epac agonists may provide promising novel targets for the treatment of SCI. Our study demonstrates the differential mechanisms of action of these compounds, as well as the benefit of a combined pharmacological approach and highlighting potential promising targets for the treatment of SCI. These findings need to be confirmed in vivo. PMID:24467222
Modelling of platelet-fibrin clot formation in flow with a DPD-PDE method.
Tosenberger, A; Ataullakhanov, F; Bessonov, N; Panteleev, M; Tokarev, A; Volpert, V
2016-02-01
The paper is devoted to mathematical modelling of clot growth in blood flow. Great complexity of the hemostatic system dictates the need of usage of the mathematical models to understand its functioning in the normal and especially in pathological situations. In this work we investigate the interaction of blood flow, platelet aggregation and plasma coagulation. We develop a hybrid DPD-PDE model where dissipative particle dynamics (DPD) is used to model plasma flow and platelets, while the regulatory network of plasma coagulation is described by a system of partial differential equations. Modelling results confirm the potency of the scenario of clot growth where at the first stage of clot formation platelets form an aggregate due to weak inter-platelet connections and then due to their activation. This enables the formation of the fibrin net in the centre of the platelet aggregate where the flow velocity is significantly reduced. The fibrin net reinforces the clot and allows its further growth. When the clot becomes sufficiently large, it stops growing due to the narrowed vessel and the increase of flow shear rate at the surface of the clot. Its outer part is detached by the flow revealing the inner part covered by fibrin. This fibrin cap does not allow new platelets to attach at the high shear rate, and the clot stops growing. Dependence of the final clot size on wall shear rate and on other parameters is studied.
AAV-mediated Gene Therapy Halts Retinal Degeneration in PDE6β-deficient Dogs.
Pichard, Virginie; Provost, Nathalie; Mendes-Madeira, Alexandra; Libeau, Lyse; Hulin, Philippe; Tshilenge, Kizito-Tshitoko; Biget, Marine; Ameline, Baptiste; Deschamps, Jack-Yves; Weber, Michel; Le Meur, Guylène; Colle, Marie-Anne; Moullier, Philippe; Rolling, Fabienne
2016-05-01
We previously reported that subretinal injection of AAV2/5 RK.cpde6β allowed long-term preservation of photoreceptor function and vision in the rod-cone dysplasia type 1 (rcd1) dog, a large animal model of naturally occurring PDE6β deficiency. The present study builds on these earlier findings to provide a detailed assessment of the long-term effects of gene therapy on the spatiotemporal pattern of retinal degeneration in rcd1 dogs treated at 20 days of age. We analyzed the density distribution of the retinal layers and of particular photoreceptor cells in 3.5-year-old treated and untreated rcd1 dogs. Whereas no rods were observed outside the bleb or in untreated eyes, gene transfer halted rod degeneration in all vector-exposed regions. Moreover, while gene therapy resulted in the preservation of cones, glial cells and both the inner nuclear and ganglion cell layers, no cells remained in vector-unexposed retinas, except in the visual streak. Finally, the retinal structure of treated 3.5-year-old rcd1 dogs was identical to that of unaffected 4-month-old rcd1 dogs, indicating near complete preservation. Our findings indicate that gene therapy arrests the degenerative process even if intervention is initiated after the onset of photoreceptor degeneration, and point to significant potential of this therapeutic approach in future clinical trials.
Modelling of thrombus growth in flow with a DPD-PDE method.
Tosenberger, A; Ataullakhanov, F; Bessonov, N; Panteleev, M; Tokarev, A; Volpert, V
2013-11-21
Hemostatic plug covering the injury site (or a thrombus in the pathological case) is formed due to the complex interaction of aggregating platelets with biochemical reactions in plasma that participate in blood coagulation. The mechanisms that control clot growth and which lead to growth arrest are not yet completely understood. We model them with numerical simulations based on a hybrid DPD-PDE model. Dissipative particle dynamics (DPD) is used to model plasma flow with platelets while fibrin concentration is described by a simplified reaction-diffusion-advection equation. The model takes into account consecutive stages of clot growth. First, a platelet is weakly connected to the clot and after some time this connection becomes stronger due to other surface receptors involved in platelet adhesion. At the same time, the fibrin mesh is formed inside the clot. This becomes possible because flow does not penetrate the clot and cannot wash out the reactants participating in blood coagulation. Platelets covered by the fibrin mesh cannot attach new platelets. Modelling shows that the growth of a hemostatic plug can stop as a result of its exterior part being removed by the flow thus exposing its non-adhesive core to the flow.
Instantaneous stroke volume by PDE during and after constant LBNP (-50 torr)
NASA Technical Reports Server (NTRS)
1980-01-01
Six male subjects were exposed to -50 torr lower body negative pressure (LBNP) for 10 min while stroke volume was recorded beat by beat at regular intervals before, during and after release of LBNP. Stroke volume was calculated from the systolic velocity integral in the ascending aorta by pulsed Doppler echocardiography (PDE) and the cross sectional area of the vessel by M mode echocardiography. Changes in leg volume were recorded continuously and blood pressure was taken every minute. Stroke volume dropped by 51% of the control in the first 33 sec of LBNP and continued to decline slowly to -62% toward the end. Heart rate increased by 15% in the first 10 sec and was 22% above control at the end of exposure. The resulting cardiac output closely followed the course of stroke volume (-47% at 33 sec, -53% at 8 min) showing that the modest increase in heart rate did little to offset the drop in stroke volume. Leg volume increased markedly within the first 10 sec with a more gradual rise reaching +3.5% at the end. Upon sudden release of LBNP, leg volume dropped significantly during the first 3 sec simultaneously with an increase in stroke volume followed by a substantial decline in heart rate below the baseline.
Multiscale Modeling of Cortical Neural Networks
NASA Astrophysics Data System (ADS)
Torben-Nielsen, Benjamin; Stiefel, Klaus M.
2009-09-01
In this study, we describe efforts at modeling the electrophysiological dynamics of cortical networks in a multi-scale manner. Specifically, we describe the implementation of a network model composed of simple single-compartmental neuron models, in which a single complex multi-compartmental model of a pyramidal neuron is embedded. The network is capable of generating Δ (2 Hz, observed during deep sleep states) and γ (40 Hz, observed during wakefulness) oscillations, which are then imposed onto the multi-compartmental model, thus providing realistic, dynamic boundary conditions. We furthermore discuss the challenges and chances involved in multi-scale modeling of neural function.
Multiscale Modeling of Ceramic Matrix Composites
NASA Technical Reports Server (NTRS)
Bednarcyk, Brett A.; Mital, Subodh K.; Pineda, Evan J.; Arnold, Steven M.
2015-01-01
Results of multiscale modeling simulations of the nonlinear response of SiC/SiC ceramic matrix composites are reported, wherein the microstructure of the ceramic matrix is captured. This micro scale architecture, which contains free Si material as well as the SiC ceramic, is responsible for residual stresses that play an important role in the subsequent thermo-mechanical behavior of the SiC/SiC composite. Using the novel Multiscale Generalized Method of Cells recursive micromechanics theory, the microstructure of the matrix, as well as the microstructure of the composite (fiber and matrix) can be captured.
Michie, A M; Rena, G; Harnett, M M; Houslay, M D
1998-01-01
We have previously shown that the major cAMP phosphodiesterase (PDE) isoforms present in murine thymocytes are the cGMP-stimulated PDE activity (PDE-2) and the cAMP-specific PDE activity (PDE-4), and that these isoforms are differentially regulated following ligation of the TCR (Michie, A.M., Lobban, M. D., Mueller, T., Harnett, M. M., and Houslay, M.D. [1996] Cell. Signalling 8, 97-110). We show here that the anti-CD3-stimulated elevation in PDE-4 activity in murine thymocytes is dependent on protein tyrosine kinase and protein kinase C (PKC)-mediated signals as the TCR-coupled increase in PDE-4 activity can be abrogated by both the tyrosine kinase inhibitor, genistein, and the PKC selective inhibitors chelerythrine and staurosporine. Moreover, the PKC-activating phorbol ester, phorbol-12-myristate, 13-acetate (PMA) caused an increase in PDE-4 activity, similar to that observed in cells challenged with anti-CD3 monoclonal antibodies and which was not additive with cochallenge using anti-CD3 antibodies. Both the PMA- and the anti-CD3 antibody-mediated increases in PDE-4 activity were blocked by treatment with either cycloheximide or actinomycin D. Despite the upregulation of PDE-4 activity consequent to TCR ligation, intracellular cAMP levels increased on challenge of thymocytes with anti-CD3 antibody, indicating that adenylate cyclase activity was also increased by TCR ligation. It is suggested that the anti-CD3-mediated increase in PDE-4 activity was owing to a rapid PKC-dependent induction of PDE-4 activity following crosslinking of the TCR complex. This identifies "crosstalk" occurring between the PKA and PKC signaling pathways initiated by ligation of the antigen receptor in murine thymocytes. That both adenylate cyclase and PDE-4 activities were increased may indicate the presence of compartmentalized cAMP responses present in these cells. PMID:9515165
Multiscale modeling of nucleosome dynamics.
Sharma, Shantanu; Ding, Feng; Dokholyan, Nikolay V
2007-03-01
Nucleosomes form the fundamental building blocks of chromatin. Subtle modifications of the constituent histone tails mediate chromatin stability and regulate gene expression. For this reason, it is important to understand structural dynamics of nucleosomes at atomic levels. We report a novel multiscale model of the fundamental chromatin unit, a nucleosome, using a simplified model for rapid discrete molecular dynamics simulations and an all-atom model for detailed structural investigation. Using a simplified structural model, we perform equilibrium simulations of a single nucleosome at various temperatures. We further reconstruct all-atom nucleosome structures from simulation trajectories. We find that histone tails bind to nucleosomal DNA via strong salt-bridge interactions over a wide range of temperatures, suggesting a mechanism of chromatin structural organization whereby histone tails regulate inter- and intranucleosomal assemblies via binding with nucleosomal DNA. We identify specific regions of the histone core H2A/H2B-H4/H3-H3/H4-H2B/H2A, termed "cold sites", which retain a significant fraction of contacts with adjoining residues throughout the simulation, indicating their functional role in nucleosome organization. Cold sites are clustered around H3-H3, H2A-H4 and H4-H2A interhistone interfaces, indicating the necessity of these contacts for nucleosome stability. Essential dynamics analysis of simulation trajectories shows that bending across the H3-H3 is a prominent mode of intranucleosomal dynamics. We postulate that effects of salts on mononucleosomes can be modeled in discrete molecular dynamics by modulating histone-DNA interaction potentials. Local fluctuations in nucleosomal DNA vary significantly along the DNA sequence, suggesting that only a fraction of histone-DNA contacts make strong interactions dominating mononucleosomal dynamics. Our findings suggest that histone tails have a direct functional role in stabilizing higher-order chromatin
Feng, Yanguo; Cheng, Dejun; Zhang, Chaofeng; Li, Yuchun; Zhang, Zhiying; Wang, Juan; Shi, Yuzhong
2016-01-01
Background The PDE4B single nucleotide polymorphisms (SNPs) have been reported to be associated with schizophrenia risk. However, current findings are ambiguous or even conflicting. To better facilitate the understanding the genetic role played by PDE4B in susceptibility to schizophrenia, we collected currently available data and conducted this meta-analysis. Methods A comprehensive electronic literature searching of PubMed, Embase, Web of Science and Cochrane Library was performed. The association between PDE4B SNPs and schizophrenia was evaluated by odds ratios (ORs) and 95% confidence intervals (CIs) under allelic, dominant and recessive genetic models. The random effects model was utilized when high between-study heterogeneity (I2 > 50%) existed, otherwise the fixed effects model was used. Results Five studies comprising 2376 schizophrenia patients and 3093 controls were finally included for meta-analysis. The rs1040716 was statistically significantly associated with schizophrenia risk in Asian and Caucasian populations under dominant model (OR = 0.87, 95% CI: 0.76–0.99, P = 0.04). The rs2180335 was significantly related with schizophrenia risk in Asian populations under allelic (OR = 0.82, 95% CI: 0.72–0.93, P = 0.003) and dominant (OR = 0.75, 95% CI: 0.64–0.88, P < 0.001) models. A significant association was also observed between rs4320761 and schizophrenia in Asian populations under allelic model (OR = 0.87, 95% CI: 0.75–1.00, P = 0.048). In addition, a strong association tendency was found between rs6588190 and schizophrenia in Asian populations under allelic model (OR = 0.87, 95% CI: 0.76–1.00, P = 0.055). Conclusion This meta-analysis suggests that PDE4B SNPs are genetically associated with susceptibility to schizophrenia. However, due to limited sample size, more large-scale, multi-racial association studies are needed to further clarify the genetic association between various PDE4B variants and schizophrenia. PMID:26756575
The SX Solver: A Computer Program for Analyzing Solvent-Extraction Equilibria: Version 3.0
Lumetta, Gregg J.
2002-01-17
A new computer program, the SX Solver, has been developed to analyze solvent-extraction equilibria. The program operates out of Microsoft Excel and uses the built-in Solver function to minimize the sum of the square of the residuals between measured and calculated distribution coefficients. The extraction of nitric acid by tributyl phosphate has been modeled to illustrate the programs use.
A block iterative LU solver for weakly coupled linear systems. [in fluid dynamics equations
NASA Technical Reports Server (NTRS)
Cooke, C. H.
1977-01-01
A hybrid technique, called the block iterative LU solver, is proposed for solving the linear equations resulting from a finite element numerical analysis of certain fluid dynamics problems where the equations are weakly coupled between distinct sets of variables. Either the block Jacobi iterative method or the block Gauss-Seidel iterative solver is combined with LU decomposition.
T2CG1, a package of preconditioned conjugate gradient solvers for TOUGH2
Moridis, G.; Pruess, K.; Antunez, E.
1994-03-01
Most of the computational work in the numerical simulation of fluid and heat flows in permeable media arises in the solution of large systems of linear equations. The simplest technique for solving such equations is by direct methods. However, because of large storage requirements and accumulation of roundoff errors, the application of direct solution techniques is limited, depending on matrix bandwidth, to systems of a few hundred to at most a few thousand simultaneous equations. T2CG1, a package of preconditioned conjugate gradient solvers, has been added to TOUGH2 to complement its direct solver and significantly increase the size of problems tractable on PCs. T2CG1 includes three different solvers: a Bi-Conjugate Gradient (BCG) solver, a Bi-Conjugate Gradient Squared (BCGS) solver, and a Generalized Minimum Residual (GMRES) solver. Results from six test problems with up to 30,000 equations show that T2CG1 (1) is significantly (and invariably) faster and requires far less memory than the MA28 direct solver, (2) it makes possible the solution of very large three-dimensional problems on PCs, and (3) that the BCGS solver is the fastest of the three in the tested problems. Sample problems are presented related to heat and fluid flow at Yucca Mountain and WIPP, environmental remediation by the Thermal Enhanced Vapor Extraction System, and geothermal resources.
Experimental validation of GADRAS's coupled neutron-photon inverse radiation transport solver.
Mattingly, John K.; Mitchell, Dean James; Harding, Lee T.
2010-08-01
Sandia National Laboratories has developed an inverse radiation transport solver that applies nonlinear regression to coupled neutron-photon deterministic transport models. The inverse solver uses nonlinear regression to fit a radiation transport model to gamma spectrometry and neutron multiplicity counting measurements. The subject of this paper is the experimental validation of that solver. This paper describes a series of experiments conducted with a 4.5 kg sphere of {alpha}-phase, weapons-grade plutonium. The source was measured bare and reflected by high-density polyethylene (HDPE) spherical shells with total thicknesses between 1.27 and 15.24 cm. Neutron and photon emissions from the source were measured using three instruments: a gross neutron counter, a portable neutron multiplicity counter, and a high-resolution gamma spectrometer. These measurements were used as input to the inverse radiation transport solver to evaluate the solver's ability to correctly infer the configuration of the source from its measured radiation signatures.
A High-Order Direct Solver for Helmholtz Equations with Neumann Boundary Conditions
NASA Technical Reports Server (NTRS)
Sun, Xian-He; Zhuang, Yu
1997-01-01
In this study, a compact finite-difference discretization is first developed for Helmholtz equations on rectangular domains. Special treatments are then introduced for Neumann and Neumann-Dirichlet boundary conditions to achieve accuracy and separability. Finally, a Fast Fourier Transform (FFT) based technique is used to yield a fast direct solver. Analytical and experimental results show this newly proposed solver is comparable to the conventional second-order elliptic solver when accuracy is not a primary concern, and is significantly faster than that of the conventional solver if a highly accurate solution is required. In addition, this newly proposed fourth order Helmholtz solver is parallel in nature. It is readily available for parallel and distributed computers. The compact scheme introduced in this study is likely extendible for sixth-order accurate algorithms and for more general elliptic equations.
High-performance equation solvers and their impact on finite element analysis
NASA Technical Reports Server (NTRS)
Poole, Eugene L.; Knight, Norman F., Jr.; Davis, D. Dale, Jr.
1990-01-01
The role of equation solvers in modern structural analysis software is described. Direct and iterative equation solvers which exploit vectorization on modern high-performance computer systems are described and compared. The direct solvers are two Cholesky factorization methods. The first method utilizes a novel variable-band data storage format to achieve very high computation rates and the second method uses a sparse data storage format designed to reduce the number of operations. The iterative solvers are preconditioned conjugate gradient methods. Two different preconditioners are included; the first uses a diagonal matrix storage scheme to achieve high computation rates and the second requires a sparse data storage scheme and converges to the solution in fewer iterations that the first. The impact of using all of the equation solvers in a common structural analysis software system is demonstrated by solving several representative structural analysis problems.
Perturbative forward solver software for small localized fluorophores in tissue
Martelli, F.; Bianco, S. Del; Di Ninni, P.
2011-01-01
In this paper a forward solver software for the time domain and the CW domain based on the Born approximation for simulating the effect of small localized fluorophores embedded in a non-fluorescent biological tissue is proposed. The fluorescence emission is treated with a mathematical model that describes the migration of photons from the source to the fluorophore and of emitted fluorescent photons from the fluorophore to the detector for all those geometries for which Green’s functions are available. Subroutines written in FORTRAN that can be used for calculating the fluorescent signal for the infinite medium and for the slab are provided with a linked file. With these subroutines, quantities such as reflectance, transmittance, and fluence rate can be calculated. PMID:22254165
Blade design and analysis using a modified Euler solver
NASA Technical Reports Server (NTRS)
Leonard, O.; Vandenbraembussche, R. A.
1991-01-01
An iterative method for blade design based on Euler solver and described in an earlier paper is used to design compressor and turbine blades providing shock free transonic flows. The method shows a rapid convergence, and indicates how much the flow is sensitive to small modifications of the blade geometry, that the classical iterative use of analysis methods might not be able to define. The relationship between the required Mach number distribution and the resulting geometry is discussed. Examples show how geometrical constraints imposed upon the blade shape can be respected by using free geometrical parameters or by relaxing the required Mach number distribution. The same code is used both for the design of the required geometry and for the off-design calculations. Examples illustrate the difficulty of designing blade shapes with optimal performance also outside of the design point.
AN ADAPTIVE PARTICLE-MESH GRAVITY SOLVER FOR ENZO
Passy, Jean-Claude; Bryan, Greg L.
2014-11-01
We describe and implement an adaptive particle-mesh algorithm to solve the Poisson equation for grid-based hydrodynamics codes with nested grids. The algorithm is implemented and extensively tested within the astrophysical code Enzo against the multigrid solver available by default. We find that while both algorithms show similar accuracy for smooth mass distributions, the adaptive particle-mesh algorithm is more accurate for the case of point masses, and is generally less noisy. We also demonstrate that the two-body problem can be solved accurately in a configuration with nested grids. In addition, we discuss the effect of subcycling, and demonstrate that evolving all the levels with the same timestep yields even greater precision.
GPU accelerated FDTD solver and its application in MRI.
Chi, J; Liu, F; Jin, J; Mason, D G; Crozier, S
2010-01-01
The finite difference time domain (FDTD) method is a popular technique for computational electromagnetics (CEM). The large computational power often required, however, has been a limiting factor for its applications. In this paper, we will present a graphics processing unit (GPU)-based parallel FDTD solver and its successful application to the investigation of a novel B1 shimming scheme for high-field magnetic resonance imaging (MRI). The optimized shimming scheme exhibits considerably improved transmit B(1) profiles. The GPU implementation dramatically shortened the runtime of FDTD simulation of electromagnetic field compared with its CPU counterpart. The acceleration in runtime has made such investigation possible, and will pave the way for other studies of large-scale computational electromagnetic problems in modern MRI which were previously impractical.
Perturbative forward solver software for small localized fluorophores in tissue.
Martelli, F; Del Bianco, S; Di Ninni, P
2012-01-01
In this paper a forward solver software for the time domain and the CW domain based on the Born approximation for simulating the effect of small localized fluorophores embedded in a non-fluorescent biological tissue is proposed. The fluorescence emission is treated with a mathematical model that describes the migration of photons from the source to the fluorophore and of emitted fluorescent photons from the fluorophore to the detector for all those geometries for which Green's functions are available. Subroutines written in FORTRAN that can be used for calculating the fluorescent signal for the infinite medium and for the slab are provided with a linked file. With these subroutines, quantities such as reflectance, transmittance, and fluence rate can be calculated. PMID:22254165
Using parallel banded linear system solvers in generalized eigenvalue problems
NASA Technical Reports Server (NTRS)
Zhang, Hong; Moss, William F.
1994-01-01
Subspace iteration is a reliable and cost effective method for solving positive definite banded symmetric generalized eigenproblems, especially in the case of large scale problems. This paper discusses an algorithm that makes use of two parallel banded solvers in subspace iteration. A shift is introduced to decompose the banded linear systems into relatively independent subsystems and to accelerate the iterations. With this shift, an eigenproblem is mapped efficiently into the memories of a multiprocessor and a high speedup is obtained for parallel implementations. An optimal shift is a shift that balances total computation and communication costs. Under certain conditions, we show how to estimate an optimal shift analytically using the decay rate for the inverse of a banded matrix, and how to improve this estimate. Computational results on iPSC/2 and iPSC/860 multiprocessors are presented.
Using parallel banded linear system solvers in generalized eigenvalue problems
NASA Technical Reports Server (NTRS)
Zhang, Hong; Moss, William F.
1993-01-01
Subspace iteration is a reliable and cost effective method for solving positive definite banded symmetric generalized eigenproblems, especially in the case of large scale problems. This paper discusses an algorithm that makes use of two parallel banded solvers in subspace iteration. A shift is introduced to decompose the banded linear systems into relatively independent subsystems and to accelerate the iterations. With this shift, an eigenproblem is mapped efficiently into the memories of a multiprocessor and a high speed-up is obtained for parallel implementations. An optimal shift is a shift that balances total computation and communication costs. Under certain conditions, we show how to estimate an optimal shift analytically using the decay rate for the inverse of a banded matrix, and how to improve this estimate. Computational results on iPSC/2 and iPSC/860 multiprocessors are presented.
Aeroelastic analysis of advanced propellers using an efficient Euler solver
NASA Technical Reports Server (NTRS)
Srivastava, R.; Reddy, T. S. R.; Mehmed, O.
1992-01-01
A 3D Euler solver is coupled with a 3D structural dynamics model to investigate flutter of propfans. A hybrid scheme is used to reduce computational time for the Euler equations and a normal mode analysis is used for flutter calculations. Experimental and calculated flutter results are compared for an advanced propeller propfan which experienced flutter at transonic tip relative velocities. The predicted flutter calculations are in close agreement with the experimental data. A structural damping value of 0.5 percent was required to predict the behavior observed in the experiment. Computations show that the flutter behavior is dominated by the second mode, but coupling with the first mode is required. The addition of other modes to the calculations did not affect the flutter behavior.
Progress in developing Poisson-Boltzmann equation solvers
Li, Chuan; Li, Lin; Petukh, Marharyta; Alexov, Emil
2013-01-01
This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nano-objects, the last one referring to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules. The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task provided the specific definition of the system to be modeled and as a physical problem aiming to better capture the phenomena occurring in the real experiments. In addition, specific attention is paid to methods to extend the capabilities of the existing solvers to model large systems toward applications of calculations of the electrostatic potential and energies in molecular motors, mitochondria complex, photosynthetic machinery and systems involving large nano-objects. PMID:24199185
Application of sparse matrix solvers as effective preconditioners
Young, D.P.; Melvin, R.G.; Johnson, F.T.; Bussoletti, J.E.; Wigton, L.B.; Samant, S.S. )
1989-11-01
In this paper the use of a new out-of-core sparse matrix package for the numerical solution of partial differential equations involving complex geometries arising from aerospace applications is discussed. The sparse matrix solver accepts contributions to the matrix elements in random order and assembles the matrix using fast sort/merge routines. Fill-in is reduced through the use of a physically based nested dissection ordering. For very large problems a drop tolerance is used during the matrix decomposition phase. The resulting incomplete factorization is an effective preconditioner for Krylov subspace methods, such as GMRES. Problems involving 200,000 unknowns routinely are solved on the Cray X-MP using 64MW of solid-state storage device (SSD).
Extending the QUDA Library with the eigCG Solver
Strelchenko, Alexei; Stathopoulos, Andreas
2014-12-12
While the incremental eigCG algorithm [ 1 ] is included in many LQCD software packages, its realization on GPU micro-architectures was still missing. In this session we report our experi- ence of the eigCG implementation in the QUDA library. In particular, we will focus on how to employ the mixed precision technique to accelerate solutions of large sparse linear systems with multiple right-hand sides on GPUs. Although application of mixed precision techniques is a well-known optimization approach for linear solvers, its utilization for the eigenvector com- puting within eigCG requires special consideration. We will discuss implementation aspects of the mixed precision deflation and illustrate its numerical behavior on the example of the Wilson twisted mass fermion matrix inversions
A three-dimensional fast solver for arbitrary vorton distributions
Strickland, J.H.; Baty, R.S.
1994-05-01
A method which is capable of an efficient calculation of the three-dimensional flow field produced by a large system of vortons (discretized regions of vorticity) is presented in this report. The system of vortons can, in turn, be used to model body surfaces, container boundaries, free-surfaces, plumes, jets, and wakes in unsteady three-dimensional flow fields. This method takes advantage of multipole and local series expansions which enables one to make calculations for interactions between groups of vortons which are in well-separated spatial domains rather than having to consider interactions between every pair of vortons. In this work, series expansions for the vector potential of the vorton system are obtained. From such expansions, the three components of velocity can be obtained explicitly. A Fortran computer code FAST3D has been written to calculate the vector potential and the velocity components at selected points in the flow field. In this code, the evaluation points do not have to coincide with the location of the vortons themselves. Test cases have been run to benchmark the truncation errors and CPU time savings associated with the method. Non-dimensional truncation errors for the magnitudes of the vector potential and velocity fields are on the order of 10{sup {minus}4}and 10{sup {minus}3} respectively. Single precision accuracy produces errors in these quantities of up to 10{sup {minus}5}. For less than 1,000 to 2,000 vortons in the field, there is virtually no CPU time savings with the fast solver. For 100,000 vortons in the flow, the fast solver obtains solutions in 1 % to 10% of the time required for the direct solution technique depending upon the configuration.
Domain decomposed preconditioners with Krylov subspace methods as subdomain solvers
Pernice, M.
1994-12-31
Domain decomposed preconditioners for nonsymmetric partial differential equations typically require the solution of problems on the subdomains. Most implementations employ exact solvers to obtain these solutions. Consequently work and storage requirements for the subdomain problems grow rapidly with the size of the subdomain problems. Subdomain solves constitute the single largest computational cost of a domain decomposed preconditioner, and improving the efficiency of this phase of the computation will have a significant impact on the performance of the overall method. The small local memory available on the nodes of most message-passing multicomputers motivates consideration of the use of an iterative method for solving subdomain problems. For large-scale systems of equations that are derived from three-dimensional problems, memory considerations alone may dictate the need for using iterative methods for the subdomain problems. In addition to reduced storage requirements, use of an iterative solver on the subdomains allows flexibility in specifying the accuracy of the subdomain solutions. Substantial savings in solution time is possible if the quality of the domain decomposed preconditioner is not degraded too much by relaxing the accuracy of the subdomain solutions. While some work in this direction has been conducted for symmetric problems, similar studies for nonsymmetric problems appear not to have been pursued. This work represents a first step in this direction, and explores the effectiveness of performing subdomain solves using several transpose-free Krylov subspace methods, GMRES, transpose-free QMR, CGS, and a smoothed version of CGS. Depending on the difficulty of the subdomain problem and the convergence tolerance used, a reduction in solution time is possible in addition to the reduced memory requirements. The domain decomposed preconditioner is a Schur complement method in which the interface operators are approximated using interface probing.
High Energy Boundary Conditions for a Cartesian Mesh Euler Solver
NASA Technical Reports Server (NTRS)
Pandya, Shishir; Murman, Scott; Aftosmis, Michael
2003-01-01
Inlets and exhaust nozzles are common place in the world of flight. Yet, many aerodynamic simulation packages do not provide a method of modelling such high energy boundaries in the flow field. For the purposes of aerodynamic simulation, inlets and exhausts are often fared over and it is assumed that the flow differences resulting from this assumption are minimal. While this is an adequate assumption for the prediction of lift, the lack of a plume behind the aircraft creates an evacuated base region thus effecting both drag and pitching moment values. In addition, the flow in the base region is often mis-predicted resulting in incorrect base drag. In order to accurately predict these quantities, a method for specifying inlet and exhaust conditions needs to be available in aerodynamic simulation packages. A method for a first approximation of a plume without accounting for chemical reactions is added to the Cartesian mesh based aerodynamic simulation package CART3D. The method consists of 3 steps. In the first step, a components approach where each triangle is assigned a component number is used. Here, a method for marking the inlet or exhaust plane triangles as separate components is discussed. In step two, the flow solver is modified to accept a reference state for the components marked inlet or exhaust. In the third step, the flow solver uses these separated components and the reference state to compute the correct flow condition at that triangle. The present method is implemented in the CART3D package which consists of a set of tools for generating a Cartesian volume mesh from a set of component triangulations. The Euler equations are solved on the resulting unstructured Cartesian mesh. The present methods is implemented in this package and its usefulness is demonstrated with two validation cases. A generic missile body is also presented to show the usefulness of the method on a real world geometry.
Multiscale information modelling for heart morphogenesis
NASA Astrophysics Data System (ADS)
Abdulla, T.; Imms, R.; Schleich, J. M.; Summers, R.
2010-07-01
Science is made feasible by the adoption of common systems of units. As research has become more data intensive, especially in the biomedical domain, it requires the adoption of a common system of information models, to make explicit the relationship between one set of data and another, regardless of format. This is being realised through the OBO Foundry to develop a suite of reference ontologies, and NCBO Bioportal to provide services to integrate biomedical resources and functionality to visualise and create mappings between ontology terms. Biomedical experts tend to be focused at one level of spatial scale, be it biochemistry, cell biology, or anatomy. Likewise, the ontologies they use tend to be focused at a particular level of scale. There is increasing interest in a multiscale systems approach, which attempts to integrate between different levels of scale to gain understanding of emergent effects. This is a return to physiological medicine with a computational emphasis, exemplified by the worldwide Physiome initiative, and the European Union funded Network of Excellence in the Virtual Physiological Human. However, little work has been done on how information modelling itself may be tailored to a multiscale systems approach. We demonstrate how this can be done for the complex process of heart morphogenesis, which requires multiscale understanding in both time and spatial domains. Such an effort enables the integration of multiscale metrology.
Collaboratory for Multiscale Chemical Science (CMCS)
Allison, Thomas C
2012-07-03
This document provides details of the contributions made by NIST to the Collaboratory for Multiscale Chemical Science (CMCS) project. In particular, efforts related to the provision of data (and software in support of that data) relevant to the combustion pilot project are described.
Joe, I-Seul; Cho, Goang-Won
2016-08-01
Increased intracellular cyclic adenosine monophosphate (cAMP) can promote axonal elongation and facilitate neuronal repair, while decreased cAMP is associated with losses in neuronal regenerative capacity. Rolipram, which upregulates intracellular cAMP by blocking phosphodiesterase-4 (PDE4) enzyme activity, can mitigate diverse neurological disorders. In this study, we investigated whether rolipram induces neuronal differentiation of human bone marrow-mesenchymal stem cells (hBM-MSCs). Rolipram-treated MSCs (Roli-MSCs) had significantly increased expression of the neuroprogenitor proteins Nestin, Musashi, GFAP, and Sox-2. When Roli-MSCs were differentiated with neuronal induction media (Roli-dMSCs), they exhibited cell body and dendritic morphologies similar to those of neurons. The neurite number and length of Roli-dMSCs were significantly increased compared to those of differentiated MSCs (dMSCs). Compared with undifferentiated hBM-MSCs, the Roli-dMSCs and dMSCs showed significantly increased expression of the neuronal-specific marker genes Nestin, Musashi, CD133, GFAP, NF-M, MAP-2, KCNH1, KCNH5, SCN3A, and CACNA1A, and decreased expression of other lineage-specific markers Adiponectin, ALP, FABP4, and MMP13. The Roli-dMSCs also showed a higher expression of the neuronal markers Nestin, Musashi, Sox-2, NF-M, and Tuj-1 compared to those of the undifferentiated hBM-MSCs, measured by immunocytochemistry and immunoblotting assay. Thus, we have shown that rolipram ameliorates neuronal differentiation by the regulation of neuroprogenitor expression in hBM-MSCs, and rolipram treatment of MSCs may improve the therapeutic efficacy of stem cell therapy for neurodegenerative disorders. PMID:27459581
Meyers, John A.; Taverna, Josephine; Chaves, Jorge; Makkinje, Anthony; Lerner, Adam
2009-01-01
Purpose Type 4 cAMP phosphodiesterase (PDE4) inhibitors, compounds that activate cAMP-mediated signaling by inhibiting cAMP catabolism, potentiate glucocorticoid-mediated apoptosis in chronic lymphocytic leukemia (CLL) cells but the mechanism by which this occurs is unknown. In this study, we sought to address whether PDE4 inhibitors alter expression of glucocorticoid receptor (GRα) in CLL cells. Experimental Design CLL cells or normal hematopoietic cells were treated with PDE4 inhibitors followed by analysis of GRα transcript and protein by real-time PCR and Western analysis. Results PDE4 inhibitors up-regulate glucocorticoid receptor transcript levels in CLL cells but not normal circulating T cells, B cells, monocytes or neutrophils. As GRα transcript half-life does not vary in CLL cells treated with the prototypic PDE4 inhibitor rolipram, the four-fold increase in GRα mRNA levels observed within four hours of rolipram treatment appears to result from an increase in transcription. Rolipram treatment increases levels of transcripts derived from the 1A3 promoter to a greater extent than the 1B promoter. Treatment of CLL cells with cilomilast and roflumilast, two PDE4 inhibitors previously studied in clinical trials also augments GRα transcript levels and glucocorticoid-mediated apoptosis. Washout studies demonstrate that simultaneous treatment with both drug classes irreversibly augments apoptosis over the same time frame that glucocorticoid receptor up-regulation occurs. While treatment of CLL cells with glucocorticoids reduces basal GRα transcript levels in a dose-related manner, co-treatment with rolipram maintained GRα transcript levels above baseline. Conclusion Our results suggest that PDE4 inhibitors may sensitize CLL cells to glucocorticoid-induced apoptosis by augmenting GRα expression. PMID:17699872
Yuen, P.S.T.; Walseth, T.F.; Panter, S.S.; Sundby, S.R.; Graeff, R.M.; Goldberg, N.D.
1987-05-01
cGMP binding proteins in toad ROS were identified by direct photoaffinity labeling (PAL) with /sup 32/P-cGMP and quantified by retention of complexes on nitrocellulose filters. By PAL, high affinity sites were present on the ..cap alpha.. and ..beta.. subunits of the cGMP-specific phosphodiesterase (PDE) which have MW/sub app/ of 94 and 90 kDa. A doublet was deduced from its photolabeling properties to represent PDE/sub ..gamma../ photocrosslinked with PDE/sub ..cap alpha../ or PDE/sub ..beta../, respectively. cGMP prebound to these high affinity sites was released by light-activated G-protein or its ..cap alpha.. subunit complexed with GTP..gamma..S; this inhibition of cGMP binding to PDE did not result from decreased cGMP availability due to enhanced hydrolysis. A low affinity cGMP binding component identified by PAL is tightly associated with ROS membranes. Apparent ATP/light-dependent stimulation of cGMP binding was shown to result from light activated cGMP hydrolysis in conjunction with ATP-promoted conversion of GMP to GDP/GTP and increased GDP/GTP binding. These findings coincide with a model for light-related regulation of cGMP binding and metabolism predicted from intact and cellfree kinetic measurements: in the dark state the cGMP hydrolic rate is constrained by the availability of cGMP because of its binding to high affinity sites on PDE. Light activated G-protein releases cGMP from these sites and allows for its redistribution to lower affinity sites represented by PDE catalytic site(s) and possible cGMP-dependent membrane cation channels.
Wood, Edgar R.; Bledsoe, Randy; Chai, Jing; Daka, Philias; Deng, Hongfeng; Ding, Yun; Harris-Gurley, Sarah; Kryn, Luz Helena; Nartey, Eldridge; Nichols, James; Nolte, Robert T.; Prabhu, Ninad; Rise, Cecil; Sheahan, Timothy; Shotwell, J. Brad; Smith, Danielle; Tai, Vince; Taylor, J. David; Tomberlin, Ginger; Wang, Liping; Wisely, Bruce; You, Shihyun; Xia, Bing; Dickson, Hamilton
2015-01-01
2′,5′-Oligoadenylate synthetase (OAS) enzymes and RNase-L constitute a major effector arm of interferon (IFN)-mediated antiviral defense. OAS produces a unique oligonucleotide second messenger, 2′,5′-oligoadenylate (2–5A), that binds and activates RNase-L. This pathway is down-regulated by virus- and host-encoded enzymes that degrade 2–5A. Phosphodiesterase 12 (PDE12) was the first cellular 2–5A- degrading enzyme to be purified and described at a molecular level. Inhibition of PDE12 may up-regulate the OAS/RNase-L pathway in response to viral infection resulting in increased resistance to a variety of viral pathogens. We generated a PDE12-null cell line, HeLaΔPDE12, using transcription activator-like effector nuclease-mediated gene inactivation. This cell line has increased 2–5A levels in response to IFN and poly(I-C), a double-stranded RNA mimic compared with the parental cell line. Moreover, HeLaΔPDE12 cells were resistant to viral pathogens, including encephalomyocarditis virus, human rhinovirus, and respiratory syncytial virus. Based on these results, we used DNA-encoded chemical library screening to identify starting points for inhibitor lead optimization. Compounds derived from this effort raise 2–5A levels and exhibit antiviral activity comparable with the effects observed with PDE12 gene inactivation. The crystal structure of PDE12 complexed with an inhibitor was solved providing insights into the structure-activity relationships of inhibitor potency and selectivity. PMID:26055709
Quantifying prediction fidelity in multiscale multiphysics simulations.
Adalsteinsson, Helgi
2010-04-01
Multiscale multiphysics problems arise in a host of application areas of significant relevance to DOE, including electrical storage systems (membranes and electrodes in fuel cells, batteries, and ultracapacitors), water surety, chemical analysis and detection systems, and surface catalysis. Multiscale methods aim to provide detailed physical insight into these complex systems by incorporating coupled effects of relevant phenomena on all scales. However, many sources of uncertainty and modeling inaccuracies hamper the predictive fidelity of multiscale multiphysics simulations. These include parametric and model uncertainties in the models on all scales, and errors associated with coupling, or information transfer, across scales/physics. This presentation introduces our work on the development of uncertainty quantification methods for spatially decomposed atomistic-to-continuum (A2C) multiscale simulations. The key thrusts of this research effort are: inference of uncertain parameters or observables from experimental or simulation data; propagation of uncertainty through particle models; propagation of uncertainty through continuum models; propagation of information and uncertainty across model/scale interfaces; and numerical and computational analysis and control. To enable the bidirectional coupling between the atomistic and continuum simulations, a general formulation has been developed for the characterization of sampling noise due to intrinsic variability in particle simulations, and for the propagation of both this sampling noise and parametric uncertainties through coupled A2C multiscale simulations. Simplified tests of noise quantification in particle computations are conducted through Bayesian inference of diffusion rates in an idealized isothermal binary material system. A proof of concept is finally presented based on application of the present formulation to the propagation of uncertainties in a model plane Couette flow, where the near wall region is
Vezzosi, Delphine; Libé, Rossella; Baudry, Camille; Rizk-Rabin, Marthe; Horvath, Anelia; Levy, Isaac; René-Corail, Fernande; Ragazzon, Bruno; Stratakis, Constantine A.; Vandecasteele, Grégoire
2012-01-01
Context: Phosphodiesterases (PDEs) are key regulatory enzymes of intracellular cAMP levels. PDE11A function has been linked to predisposition to adrenocortical tumors. Objective: The aim of the study was to study the PDE11A gene in a large cohort of patients with ACTH-independent macronodular adrenal hyperplasia (AIMAH) and in control subjects. Design: The PDE11A entire coding region was sequenced in 46 patients with AIMAH and 192 controls. Two variants found in AIMAH patients were transiently expressed in HEK 293 and adrenocortical H295R cells for further functional studies. Results: The frequency of all PDE11A variants was significantly higher among patients with AIMAH (28%) compared to controls (7.2%) (P = 5 × 10−5). Transfection of the two PDE11A variants found in AIMAH patients only (D609N or M878V) showed that cAMP levels were higher, after forskolin stimulation, in cells transfected with the PDE11A mutants, compared to cells transfected with the wild-type PDE11A in HEK 293 cells (P < 0.05). Moreover, transfection with mutants PDE11A increased transcriptional activity of a cAMP-response element reporter construct compared to wild-type PDE11A in HEK 293 cells (P < 0.0004 for D609N and P < 0.003 for M878V) and in the adrenocortical H295R cells (P < 0.05 for D609N and M878V). In addition, analysis of cAMP levels in intact living culture cells by fluorescence resonance energy transfer probes showed increased cAMP in forskolin-treated cells transfected with PDE11A variants compared with wild-type PDE11A (P < 0.05). Conclusion: We conclude that PDE11A genetic variants may increase predisposition to AIMAH. PMID:22996146