52 results on '"M. M. Grigoriev"'
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2. A multi-level boundary element method for Stokes flows in irregular two-dimensional domains
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M. M. Grigoriev and Gary F. Dargush
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Helmholtz equation ,Mechanical Engineering ,Mathematical analysis ,Computational Mechanics ,General Physics and Astronomy ,Mixed boundary condition ,Stokes flow ,Boundary knot method ,Singular boundary method ,Unit square ,Computer Science Applications ,Mechanics of Materials ,Method of fundamental solutions ,Boundary element method ,Mathematics - Abstract
Recently, we have developed multi-level boundary element methods (MLBEM) for the solution of the Laplace and Helmholtz equations that involve asymptotically decaying non-oscillatory and oscillatory singular kernels, respectively. The accuracy and efficiency of the fast boundary element methods for steady-state heat diffusion and acoustics problems have been investigated for square domains. The current work extends the MLBEM methodology to the solution of Stokes equation in more complex two-dimensional domains. The performance of the fast boundary element method for the Stokes flows is first investigated for a model problem in a unit square. Then, we consider an example problem possessing an analytical solution in a rectangular domain with 5:1 aspect ratio, and finally, we study the performance of the MLBEM algorithm in a C-shaped domain.
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- 2005
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3. Accurate Boundary Element Solutions for Highly Convective Unsteady Heat Flows
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Gary F. Dargush and M. M. Grigoriev
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Convection ,Convective heat transfer ,Computer science ,Mechanical Engineering ,Thermodynamics ,Péclet number ,Condensed Matter Physics ,Numerical integration ,Physics::Fluid Dynamics ,Nonlinear system ,symbols.namesake ,Mechanics of Materials ,Heat transfer ,symbols ,Applied mathematics ,General Materials Science ,Convection–diffusion equation ,Boundary element method - Abstract
Several recently developed boundary element formulations for time-dependent convective heat diffusion appear to provide very efficient computational tools for transient linear heat flows. More importantly, these new approaches hold much promise for the numerical solution of related nonlinear problems, e.g., Navier–Stokes flows. However, the robustness of these methods has not been examined, particularly for high Peclet number regimes. Here, we focus on these regimes for two-dimensional problems and develop the necessary temporal and spatial integration strategies. The algorithm takes advantage of the nature of the time-dependent convective kernels, and combines analytic integration over the singular portion of the time interval with numerical integration over the remaining nonsingular portion. Furthermore, the character of the kernels lets us define an influence domain and then localize the surface and volume integrations only within this domain. We show that the localization of the convective kernels becomes more prominent as the Peclet number of the flow increases. This leads to increasing sparsity and in most cases improved conditioning of the global matrix. Thus, iterative solvers become the primary choice. We consider two representative example problems of heat propagation, and perform numerical investigations of the accuracy and stability of the proposed higher-order boundary element formulations for Peclet numbers up to 105.
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- 2005
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4. A boundary element method for steady convective heat diffusion in three-dimensions
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Gary F. Dargush and M. M. Grigoriev
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Convection ,Convective heat transfer ,Iterative method ,Mechanical Engineering ,Mathematical analysis ,Computational Mechanics ,General Physics and Astronomy ,Boundary (topology) ,Geometry ,Boundary knot method ,Computer Science Applications ,Mechanics of Materials ,Heat transfer ,Boundary element method ,Mathematics ,Sparse matrix - Abstract
A higher-order boundary element method recently developed by the current authors [Numer. Heat Trans. Part B: Fundamentals 45 (2004) 109] for two-dimensional steady convective heat diffusion is generalized to three-dimensions. In order to facilitate an accurate and efficient boundary element formulation, we introduce an influence domain due to these convective kernels and then localize the surface integrations only within the domain of influence. The localization of the kernels becomes more prominent as the Peclet number of the flow increases. This, in turn, leads to increasing sparsity and improved conditioning of the global matrix. Consequently, iterative solvers for sparse matrices become the primary choice. In this paper, we consider an example problem with an exact solution and investigate the accuracy and efficiency of the boundary element formulation for Peclet numbers in the range from 10 to 1000. The bi-quartic boundary elements included in this study are shown to provide acceptable levels of resolution.
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- 2005
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5. Fast and Accurate Solutions of Steady Stokes Flows Using Multilevel Boundary Element Methods
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M. M. Grigoriev and Gary F. Dargush
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symbols.namesake ,Gaussian elimination ,Mechanical Engineering ,symbols ,Degrees of freedom (statistics) ,Applied mathematics ,Central processing unit ,Stokes flow ,Boundary element method ,Fast algorithm ,Mathematics - Abstract
Most recently, we have developed a novel multilevel boundary element method (MLBEM) for steady Stokes flows in irregular two-dimensional domains (Grigoriev, M.M., and Dargush, G.F., Comput. Methods. Appl. Mech. Eng., 2005). The multilevel algorithm permitted boundary element solutions with slightly over 16,000 degrees of freedom, for which approximately 40-fold speedups were demonstrated for the fast MLBEM algorithm compared to a conventional Gauss elimination approach. Meanwhile, the sevenfold memory savings were attained for the fast algorithm. This paper extends the MLBEM methodology to dramatically improve the performance of the original multilevel formulation for the steady Stokes flows. For a model problem in an irregular pentagon, we demonstrate that the new MLBEM formulation reduces the CPU times by a factor of nearly 700,000. Meanwhile, the memory requirements are reduced more than 16,000 times. These superior run-time and memory reductions compared to regular boundary element methods are achieved while preserving the accuracy of the boundary element solution.
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- 2005
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6. A fast multi-level convolution boundary element method for transient diffusion problems
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C.-H. Wang, Gary F. Dargush, and M. M. Grigoriev
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Overlap–add method ,Numerical Analysis ,Discrete time and continuous time ,Computational complexity theory ,Applied Mathematics ,General Engineering ,Transient (computer programming) ,Heat equation ,Time domain ,Algorithm ,Boundary element method ,Mathematics ,Convolution - Abstract
A new algorithm is developed to evaluate the time convolution integrals that are associated with boundary element methods (BEM) for transient diffusion. This approach, which is based upon the multi-level multi-integration concepts of Brandt and Lubrecht, provides a fast, accurate and memory efficient time domain method for this entire class of problems. Conventional BEM approaches result in operation counts of order O(N 2 ) for the discrete time convolution over N time steps. Here we focus on the formulation for linear problems of transient heat diffusion and demonstrate reduced computational complexity to order O(N 3/2 ) for three two-dimensional model problems using the multi-level convolution BEM. Memory requirements are also significantly reduced, while maintaining the same level of accuracy as the conventional time domain BEM approach.
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- 2005
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7. Efficiency of boundary element methods for time-dependent convective heat diffusion at high Peclet numbers
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Gary F. Dargush and M. M. Grigoriev
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Convective heat transfer ,Series (mathematics) ,Applied Mathematics ,General Engineering ,Geometry ,Interval (mathematics) ,Range (mathematics) ,Computational Theory and Mathematics ,Orders of magnitude (time) ,Modeling and Simulation ,Convergence (routing) ,Applied mathematics ,Diffusion (business) ,Boundary element method ,Software ,Mathematics - Abstract
A higher-order boundary element method (BEM) recently developed by the current authors (Comput Methods Appl Mech Eng 2003; 192: 4281–4298; 4299–4312; 4313–4335) for time-dependent convective heat diffusion in two-dimensions appears to be a very attractive tool for efficient simulations of transient linear flows. However, the previous BEM formulation is restricted to relatively small time step sizes (i.e. Δt⩽4κ/V2) owing to the convergence issues of the time series for the kernel representation within a time interval. This paper extends the boundary element formulation in a way to allow time step sizes several orders of magnitude larger than in the previous approach. We consider an example problem of thermal propagation, and investigate the accuracy and efficiency of BEM formulations for Peclet numbers in the range from 103 to 105. Copyright © 2005 John Wiley & Sons, Ltd.
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- 2004
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8. Accuracy and efficiency of higher-order boundary element methods for steady convective heat diffusion in three-dimensions
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Gary F. Dargush and M. M. Grigoriev
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Convection ,Convective heat transfer ,Iterative method ,Applied Mathematics ,General Engineering ,Boundary (topology) ,Geometry ,Péclet number ,Computational Mathematics ,symbols.namesake ,Heat transfer ,symbols ,Applied mathematics ,Boundary element method ,Analysis ,Sparse matrix ,Mathematics - Abstract
Higher-order boundary element methods (BEM) are presented for three-dimenisonal steady convective heat diffusion at high Peclet numbers. The boundary element formulation is facilitated by the definition of an influence domain due to convective kernels. This approach essentially localizes the surface integrations only within the domain of influence which becomes more narrowly focused as the Peclet number increases. The outcome of this phenomenon is an increased sparsity and improved conditioning of the global matrix. Therefore, iterative solvers for sparse matrices become a very efficient and robust tool for the corresponding boundary element matrices. In this paper, we consider an example problem with an exact solution and investigate the accuracy and efficiency of the higher-order BEM formulations for high Peclet numbers in the range from 1000 to 100,000. The bi-quartic boundary elements included in this study are shown to provide very efficient and extremely accurate solutions to this problem, even on a single engineering workstation.
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- 2004
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9. A MULTILEVEL BOUNDARY-ELEMENT METHOD FOR TWO-DIMENSIONAL STEADY HEAT DIFFUSION
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M. M. Grigoriev and Gary F. Dargush
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Numerical Analysis ,Mathematical optimization ,Computational complexity theory ,Discretization ,Condensed Matter Physics ,Computer Science Applications ,Matrix (mathematics) ,Mechanics of Materials ,Modeling and Simulation ,Transpose ,Computational mechanics ,Applied mathematics ,Potential flow ,Boundary value problem ,Boundary element method ,Mathematics - Abstract
A fast, accurate, and efficient multilevel boundary-element method (MLBEM) is developed to solve general boundary-value problems arising in computational mechanics. Here we concentrate on problems of two-dimensional steady potential flow and present a fast, direct boundary-element formulation. This novel method extends the pioneering work of Brandt and Lubrecht on multilevel multi-integration (MLMI) in several important ways to address problems with mixed boundary conditions. We utilize bi-conjugate gradient methods (BCGMs) and implement the MLMI approach for fast matrix and matrix transpose multiplication for every iteration loop. After introducing a C-cycle multigrid algorithm, we find that the number of iterations for the bi-conjugate gradient methods is independent of the boundary-element mesh discretization for a broad range of steady-state heat diffusion problems. Here, for a model problem in an L-shaped domain, we demonstrate that the computational complexity of the proposed method approaches the d...
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- 2004
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10. EFFICIENCY AND ACCURACY OF HIGHER-ORDER BOUNDARY-ELEMENT METHODS FOR STEADY CONVECTIVE HEAT DIFFUSION
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M. M. Grigoriev and Gary F. Dargush
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Convection ,Numerical Analysis ,Convective heat transfer ,Mathematical analysis ,Boundary (topology) ,Upwind scheme ,Geometry ,Péclet number ,Condensed Matter Physics ,Computer Science Applications ,Physics::Fluid Dynamics ,symbols.namesake ,Mechanics of Materials ,Modeling and Simulation ,symbols ,Diffusion (business) ,Convection–diffusion equation ,Boundary element method ,Mathematics - Abstract
Higher-order boundary-element methods (BEM) are presented for steady-state convective diffusion problems in two dimensions. The free-space steady convective diffusion fundamental solutions considered in this article provide an analytical upwinding for the entire Peclet number range, from zero to infinity. However, integration of the kernels over the boundary elements requires considerable attention, especially at higher Peclet numbers. We define an influence domain due to these convective kernels and then localize the surface integrations only within the domain of influence. The localization of the kernels becomes more prominent as the Peclet number of the flow increases. This, in turn, leads to increasing sparsity and improved conditioning of the global matrix. Consequently, iterative solvers become the primary choice. We consider an example problem with an exact solution, and investigate the accuracy and efficiency of the higher-order BEM formulations for Peclet numbers in the range from 200 to 200,000....
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- 2004
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11. A fast multi-level boundary element method for the Helmholtz equation
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Gary F. Dargush and M. M. Grigoriev
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Helmholtz equation ,Mechanical Engineering ,Mathematical analysis ,Computational Mechanics ,General Physics and Astronomy ,Mixed boundary condition ,Singular boundary method ,Boundary knot method ,Computer Science Applications ,Mechanics of Materials ,Method of fundamental solutions ,Heat equation ,Boundary value problem ,Boundary element method ,Mathematics - Abstract
Most recently, we have developed a novel multi-level boundary element method (MLBEM) for the solution of the steady heat diffusion equation involving asymptotically decaying non-oscillatory log-singular and strongly singular kernels. This hierarchical approach generalizes the pioneering work of Brandt and Lubrecht on multi-level multi-integration (MLMI) and C-cycle multi-grid to the broader class of mixed boundary value problems. The result is a fast, accurate and efficient boundary element method. The present paper extends this new computational methodology to the solution of the Helmholtz equation involving oscillatory log-singular and strongly singular kernels for two-dimensional problems. We consider a direct boundary element formulation and, due to the nature of the fundamental solutions, split the corresponding boundary integral equation into real and imaginary parts. Then, we introduce double-noded corners to facilitate a patch-by-patch application of the MLMI algorithm for fast matrix–vector and matrix-transpose–vector multiplications within bi-conjugate gradient methods. The performance of the proposed fast MLBEM is investigated using a numerical example that possesses an exact solution. For wave numbers κ=20 and below, we demonstrate that the fast MLBEM algorithm for the Helmholtz equation is robust, accurate, and exceptionally efficient.
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- 2004
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12. Boundary element methods for transient convective diffusion. Part II: 2D implementation
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M. M. Grigoriev and Gary F. Dargush
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Mechanical Engineering ,Multiple integral ,Mathematical analysis ,Computational Mechanics ,General Physics and Astronomy ,Boundary (topology) ,Computer Science Applications ,Volume integral ,Quadratic equation ,Mechanics of Materials ,Quartic function ,Boundary element method ,Kernel (category theory) ,Interpolation ,Mathematics - Abstract
A boundary element method for transient convective diffusion phenomena presented in Part I of the paper is extended to two dimensional problems. We introduce a series representation for the transient convective kernel and perform a time integration for the double integrals to evaluate coefficients of the time-discrete boundary integral equation. The time-integrated kernels are evaluated for the linear, quadratic and quartic time interpolation functions utilized in the paper. Then, linear, quadratic and quartic boundary elements as well as bi-linear, bi-quadratic and bi-quartic volume cells are introduced to ensure proper resolution in space for the two-dimensional formulation. Due to the singular nature of the transient convective diffusion kernels, integration of the kernels over the boundary elements and volume cells requires a considerable effort to maintain a desired level of accuracy. We define influence domains due to time-integrated and time-delayed kernels arising for the surface and volume integrals, respectively. Note that the kernel influences are extremely localized due to the convective nature of the kernels, thus, the surface and volume integrations are performed only within these domains of influence. The localization of the kernels becomes more prominent as the Peclet number of the flow increases. Due to increasing sparsity of the global matrix, iterative solvers become the primary choice for the convective diffusion problems.
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- 2003
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13. Boundary element methods for transient convective diffusion. Part III: Numerical examples
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Gary F. Dargush and M. M. Grigoriev
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Mathematical optimization ,Mechanical Engineering ,Computational Mechanics ,General Physics and Astronomy ,Boundary (topology) ,Upwind scheme ,Computer Science Applications ,Kernel (image processing) ,Mechanics of Materials ,Applied mathematics ,Time domain ,Boundary element method ,Gradient method ,Interpolation ,Mathematics ,Sparse matrix - Abstract
Higher-order boundary element methods (BEM) for transient convective diffusion phenomena presented in Parts I and II of the paper are implemented numerically to examine their performance for a series of model problems. In order to highlight the importance of proper resolution in time and space for the transient problems, we consider both the one- and two-dimensional formulations in this paper. We utilize an implicit time-recurring formulation to advance in the time domain. The use of higher-order time interpolation functions facilitates extremely high resolution with respect to time step sizes, and thus necessitates similar levels of spatial resolution. In this paper, linear, quadratic and quartic boundary elements as well as bi-linear, bi-quadratic and bi-quartic volume cells are implemented to ensure a desired high level of accuracy both in time and in space. In order to investigate the performance of the BEM formulations, we introduce five problems of unsteady convection–diffusion that possess exact solutions. For all five numerical examples considered in this paper, the higher-order BEM demonstrate an extremely high level of accuracy even for predominantly convective flows. It is shown that the use of the convective kernels provide an analytical upwinding for any Peclet number and any mesh orientation with respect to the flow direction. The introduction of the kernel influence domains facilitates a very efficient and robust algorithm for integration over boundary elements and volume cells. Due to the nature of the convective kernels, the resulting global matrix is sparse with the non-zero elements localized around the main diagonal. The preconditioned bi-conjugate gradient method utilized in the paper allows very efficient factorization of the global sparse matrix. Moreover, the efficiency of the BEM formulations increases dramatically with the increase of the Peclet number of the flow.
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- 2003
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14. Boundary element methods for transient convective diffusion. Part I: General formulation and 1D implementation
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Gary F. Dargush and M. M. Grigoriev
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Mechanical Engineering ,Mathematical analysis ,Computational Mechanics ,General Physics and Astronomy ,Boundary (topology) ,Computer Science Applications ,Set (abstract data type) ,Quadratic equation ,Mechanics of Materials ,Quartic function ,Transient (oscillation) ,Representation (mathematics) ,Boundary element method ,Mathematics ,Interpolation - Abstract
A general formulation of higher-order boundary element methods (BEM) is presented for time-dependent convective diffusion problems in one- and multi-dimensions. Free-space time-dependent convective diffusion fundamental solutions originally proposed by Carslaw and Jaeger are used to obtain the boundary integral formulation. Linear, quadratic and quartic time interpolation functions are introduced in this paper for approximate representation of time-dependent boundary temperatures and normal fluxes. Closed form time integration of the kernels is mandatory to attain both accuracy and efficiency of the numerical approach. A complete set of time integrals for the one-dimensional formulation is presented here for the first time in the literature.
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- 2003
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15. Higher-order boundary element methods for transient diffusion problems. Part II: Singular flux formulation
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G. F. Dargush and M. M. Grigoriev
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Numerical Analysis ,Applied Mathematics ,General Engineering - Published
- 2002
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16. Higher-order boundary element methods for transient diffusion problems. Part I: Bounded flux formulation
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M. M. Grigoriev and Gary F. Dargush
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Numerical Analysis ,Rate of convergence ,Heat flux ,Applied Mathematics ,Mathematical analysis ,General Engineering ,Method of fundamental solutions ,Boundary (topology) ,Temporal discretization ,Singular boundary method ,Boundary knot method ,Boundary element method ,Mathematics - Abstract
Despite the significant number of publications on boundary element methods (BEM) for time-dependent problems of heat diffusion, there still remain issues that need to be addressed, most importantly accuracy of the numerical modelling. Although very precise for steady-state problems, the common boundary element methods applied to transient problems do not yield highly accurate numerical solutions. This paper investigates the reasons that prohibit achievement of a high level of accuracy for transient heat diffusion problems with continuous temperature and bounded heat flux solutions. In order to greatly enhance the commonly used boundary element formulations, we propose higher-order time interpolation functions, including quadratic and quartic approximations. We show that the use of higher-order time functions greatly reduces the numerical error concentrated in the corner regions, and results in very good uniformity of the flux and temperature distributions along the boundaries for problems where uniform distributions are expected. In order to highlight the importance of proper resolution both in time and space for the transient problems, we consider one- and two-dimensional formulations in this paper. High-order boundary elements using quartic shape functions, as well as high-order bi-quartic volume cells, are used to attain mesh-independent numerical solutions. We consider four transient heat diffusion problems that possess exact solutions to investigate the convergence rate and accuracy of the higher-order boundary element formulations. A very high level of accuracy is possible for both one- and two-dimensional formulations. Additionally, we show that the accuracy of a commercially available finite-element code is far less than that of the boundary element methods for a given spatial and temporal discretization. Copyright © 2002 John Wiley & Sons, Ltd.
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- 2002
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17. A poly-region boundary element method for incompressible viscous fluid flows
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M. M. Grigoriev and Gary F. Dargush
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Numerical Analysis ,Applied Mathematics ,Numerical analysis ,Mathematical analysis ,General Engineering ,Reynolds number ,Geometry ,Integral equation ,Finite element method ,symbols.namesake ,Compressibility ,symbols ,Galerkin method ,Navier–Stokes equations ,Boundary element method ,Mathematics - Abstract
A boundary element method (BEM) for steady viscous fluid flow at high Reynolds numbers is presented. The new integral formulation with a poly-region approach involves the use of the convective kernel with slight compressibility that was previously employed by Grigoriev and Fafurin [1] for driven cavity flows with Reynolds numbers up to 1000. In order to avoid the overdeterminancy of the global set of equations when using eight-noded rectangular volume cells from that previous work, 12-noded hexagonal volume regions are introduced. As a result, the number of linearly independent integral equations for each node becomes equal to the degrees of freedom of the node. The numerical results for square-driven cavity flow having Reynolds numbers up to 5000 are compared to those obtained by Ghia et al. [2] and demonstrate a high level of accuracy even in resolving the secondary vortices at the corners of the cavity. Next, a comprehensive study is done for backward-facing step flows at Re=500 and 800 using the BEM, along with a standard Galerkin-based finite element methods (FEM). The numerical methods are in excellent agreement with the benchmark solution published by Gartling [3]. However, several additional aspects of the problem are also considered, including the effect of the inflow boundary location and the traction singularity at the step corner. Furthermore, a preliminary comparative study of the poly-region BEM versus the standard FEM indicates that the new method is more than competitive in terms of accuracy and efficiency. Copyright © 1999 John Wiley & Sons, Ltd.
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- 1999
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18. A boundary element method for steady viscous fluid flow using penalty function formulation
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M. M. Grigoriev and A. V. Fafurin
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business.industry ,Applied Mathematics ,Mechanical Engineering ,Mathematical analysis ,Computational Mechanics ,Reynolds number ,Boundary (topology) ,Computational fluid dynamics ,Boundary knot method ,Computer Science Applications ,Physics::Fluid Dynamics ,symbols.namesake ,Rate of convergence ,Mechanics of Materials ,Incompressible flow ,symbols ,business ,Navier–Stokes equations ,Boundary element method ,Mathematics - Abstract
A new boundary element method is presented for steady incompressible flow at moderate and high Reynolds numbers. The whole domain is discretized into a number of eight-noded cells, for each of which the governing boundary integral equation is formulated exclusively in terms of velocities and tractions. The kernels used in this paper are the fundamental solutions of the linearized Navier-Stokes equations with artificial compressibility. Significant attention is given to the numerical evaluation of the integrals over quadratic boundary elements as well as over quadratic quadrilateral volume cells in order to ensure a high accuracy level at high Reynolds numbers. As an illustration, square driven cavity flows are considered for Reynolds numbers up to 1000. Numerical results demonstrate both the high convergence rate, even when using simple (direct) iterations, and the appropriate level of accuracy of the proposed method. Although the method yields a high level of accuracy in the primary vortex region, the secondary vortices are not properly resolved.
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- 1997
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19. Multi-Level Boundary Element Methods for Steady Heat Diffusion in Three-Dimensions
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Gary F. Dargush and M. M. Grigoriev
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Mathematical optimization ,Chemistry ,Heat transfer ,Applied mathematics ,Heat equation ,Thermal conduction ,Thermal diffusivity ,Boundary element method ,Heat kernel ,Domain (mathematical analysis) - Abstract
We have recently developed a novel multi-level boundary element method (MLBEM) for steady heat diffusion in irregular two-dimensional domains (Numerical Heat Transfer Part B: Fundamentals, 46 : 329–356, 2004). This presentation extends the MLBEM methodology to three-dimensional problems. First, we outline a 3-D MLBEM formulation for steady heat diffusion and discuss the differences between multi-level algorithms for two and three dimensions. Then, we consider an example problem that involves heat conduction in a semi-infinite three-dimensional domain. We investigate the performance of the MLBEM formulation using a single-patch approach. The MLBEM algorithms are shown facilitate fast and accurate numerical solutions with no loss of the solution accuracy. More dramatic speed-ups can be achieved provided that patch-edge corrections are also evaluated using multi-level technique.Copyright © 2005 by ASME
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- 2005
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20. A Multi-Level Multi-Integral Algorithm for the Helmholtz Equation
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Gary F. Dargush and M. M. Grigoriev
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symbols.namesake ,Work (thermodynamics) ,Helmholtz equation ,Field (physics) ,Helmholtz free energy ,Polar decomposition ,symbols ,Wavenumber ,Nyquist–Shannon sampling theorem ,Boundary element method ,Algorithm ,Mathematics - Abstract
Previous work on the development of multi-level boundary element methods (MLBEM) has produced dramatic computational efficiencies compared to traditional methods. However, for problems involving the oscillatory kernels associated with the Helmholtz equation, the performance improvements demonstrated to date have been limited due to the presence of coarse mesh Nyquist constraints. In the present paper, we examine an extension of the original Helmholtz MLBEM to remove these limitations, based on a polar decomposition of the kernels and field variables originally proposed by Brandt. In this initial numerical implementation of these ideas, the algorithm is applied to a pair of two-dimensional half-space problems and, therefore, is limited to the fast evaluation of Rayleigh integrals. In general, excellent performance is achieved. For example, in the second problem with a non-dimensional wave number equal to 105 , we obtain speed-up factors of approximately 300,000 versus a traditional BEM approach, while maintaining comparable levels of accuracy.Copyright © 2005 by ASME
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- 2005
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21. A Boundary Element Method for Three-Dimensional Steady Convective Heat Diffusion
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M. M. Grigoriev and Gary F. Dargush
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Convection ,symbols.namesake ,Convective heat transfer ,Mathematical analysis ,symbols ,Boundary (topology) ,Péclet number ,Diffusion (business) ,Boundary knot method ,Boundary element method ,Sparse matrix ,Mathematics - Abstract
Higher-order boundary element methods (BEM) are presented for three-dimensional steady convective heat diffusion at high Peclet numbers. An accurate and efficient boundary element formulation is facilitated by the definition of an influence domain due to convective kernels. This approach essentially localizes the surface integrations only within the domain of influence which becomes more narrowly focused as the Peclet number increases. The outcome of this phenomenon is an increased sparsity and improved conditioning of the global matrix. Therefore, iterative solvers for sparse matrices become a very efficient and robust tool for the corresponding boundary element matrices. In this paper, we consider an example problem with an exact solution and investigate the accuracy and efficiency of the higher-order BEM formulations for high Peclet numbers in the range from 1,000 to 100,000. The bi-quartic boundary elements included in this study are shown to provide very efficient and extremely accurate solutions, even on a single engineering workstation.Copyright © 2004 by ASME
- Published
- 2004
- Full Text
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22. A Higher-Order Poly-Region Boundary Element Method for Steady Thermoviscous Fluid Flows
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M. M. Grigoriev and Gary F. Dargush
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Physics::Fluid Dynamics ,symbols.namesake ,Kernel (image processing) ,Mathematical analysis ,symbols ,Fluid dynamics ,Reynolds number ,Boundary (topology) ,Mixed boundary condition ,Boundary knot method ,Boundary element method ,Integral equation ,Mathematics - Abstract
In this presentation, we re-visit the poly-region boundary element methods (BEM) proposed earlier for the steady Navier-Stokes [1] and Boussinesq [2] flows, and develop a novel higher-order BEM formulation for the thermoviscous fluid flows that involves the definition of the domains of kernel influences due to steady Oseenlets. We introduce region-by-region implementation of the steady-state Oseenlets within the poly-region boundary element fequatramework, and perform integration only over the (parts of) higher-order boundary elements and volume cells that are influenced by the kernels. No integration outside the domains of the kernel influences are needed. Owing to the properties of the convective Oseenlets, the kernel influences are very local and propagate upstream. The localization becomes more prominent as the Reynolds number of the flow increases. This improves the conditioning of the global matrix, which in turn, facilitates an efficient use of the iterative solvers for the sparse matrices [3]. Here, we consider quartic boundary elements and bi-quartic volume cells to ensure a high level resolution in space. Similar to the previous developments [4–6], coefficients of the discrete boundary integral equations are evaluated with the sufficient precision using semi-analytic approach to ensure exceptional accuracy of the boundary element formulation. To demonstrate the attractiveness of the poly-region BEM formulation, we consider a numerical example of the well-known Rayleigh-Benard problem governed by the Boussinesq equations.Copyright © 2004 by ASME
- Published
- 2004
- Full Text
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23. A Time-Space Multi-Level Boundary Element Approach for Time-Dependent Heat Diffusion
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M. M. Grigoriev and Gary F. Dargush
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Physics ,Time space ,Mathematical analysis ,Analytic element method ,Heat equation ,Thermal diffusivity ,Boundary knot method ,Boundary element method - Abstract
A new space-time multi-level boundary element method (MLBEM) is developed for transient heat diffusion problems in two-dimensions. This approach extends the MLBEM approach for steady heat diffusion [1] to accommodate fast time convolution algorithm [2]. The space-time MLBEM algorithm developed in this presentation provides fast, accurate and memory efficient numerical solutions for time-dependent heat diffusion problems. Conventional BEM approaches using M boundary elements result in operation counts of order O(M2N2) for the discrete time convolution over N time steps. Here we focus on the formulation for linear problems of transient heat diffusion and demonstrate reduced computational complexity to order O(M log MN3/2) for a two-dimensional model problem using the multi-level boundary element algorithm. Memory requirements are also significantly reduced, while maintaining the same level of accuracy as the conventional time domain BEM approach.
- Published
- 2004
- Full Text
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24. A Fast Time Convolution Algorithm for Unsteady Heat Diffusion Problems
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M. M. Grigoriev, C. H. Wang, and Gary F. Dargush
- Subjects
Overlap–add method ,Computational complexity theory ,Discrete time and continuous time ,Heat equation ,Transient (computer programming) ,Time domain ,Algorithm ,Boundary element method ,Mathematics ,Convolution - Abstract
A new algorithm is developed to evaluate the time convolution integrals that are associated with boundary element methods (BEM) for transient diffusion. This approach, which is based upon the multi-level multi-integration concepts of Brandt and Lubrecht, provides a fast, accurate and memory efficient time domain method for this entire class of problems. Conventional BEM approaches result in operation counts of order O(N2 ) for the discrete time convolution over N time steps. Here we focus on the formulation for linear problems of transient heat diffusion and demonstrate reduced computational complexity to order O(N3/2 ) for a couple of two-dimensional model problems using the multi-level convolution BEM. Memory requirements are also significantly reduced, while maintaining the same level of accuracy as the conventional time domain BEM approach.Copyright © 2004 by ASME
- Published
- 2004
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25. A Fast Multi-Level Boundary Element Algorithm for Stokes Flows in Two-Dimensions
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Gary F. Dargush and M. M. Grigoriev
- Subjects
Helmholtz equation ,Mathematical analysis ,Method of fundamental solutions ,Mixed boundary condition ,Boundary value problem ,Stokes flow ,Singular boundary method ,Boundary knot method ,Boundary element method ,Algorithm ,Mathematics - Abstract
Recently, we have developed multi-level boundary element methods (MLBEM) for the solution of the Laplace and Helmholtz equations that involve asymptotically decaying non-oscillatory and oscillatory singular kernels, respectively. The accuracy and efficiency of the fast boundary element methods for steady-state heat diffusion and accoustics problems have been investigated for square domains. The current work extends the MLBEM methodology to the solution of Stokes equation in more complex two dimensional domains. The performance of the fast boundary element method for the Stokes flows is first investigated for a model problem in a unit square. Then, we study the performance of the MLBEM algorithm in a C-shaped domain.Copyright © 2004 by ASME
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- 2004
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26. Efficient Multi-Grid Method for the Steady Heat Diffusion Equation
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Gary F. Dargush and M. M. Grigoriev
- Subjects
Matrix (mathematics) ,Work (thermodynamics) ,Discretization ,Transpose ,Mathematical analysis ,MathematicsofComputing_NUMERICALANALYSIS ,Multiplication ,Heat equation ,Boundary value problem ,Boundary element method ,Mathematics - Abstract
An accurate and efficient multi-grid boundary element method is developed to solve steady heat diffusion problems. This novel method extends the pioneering work of Brandt and Lubrecht on multi-level multi-integration in several important ways to address problems with mixed boundary conditions. We utilize bi-conjugate gradient methods and implement the multi-level multi-integration approach for fast matrix and matrix transpose multiplication for e very iteration loop. Furthermore, by introducing a C-c ycle multigrid algorithm, we find that the number of iterations for the bi-conjugate gradient methods is independent of the boundary element mesh discretization.
- Published
- 2003
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27. Boundary Element Methods for Unsteady Convective Heat Diffusion
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M. M. Grigoriev and Gary F. Dargush
- Subjects
Materials science ,Convective heat transfer ,Mechanics ,Diffusion (business) ,Boundary element method - Published
- 2003
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28. A Fast Multi-Level Boundary Element Method for the Steady Heat Diffusion Equation
- Author
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M. M. Grigoriev and Gary F. Dargush
- Subjects
Discretization ,Mathematical analysis ,Method of fundamental solutions ,Mixed boundary condition ,Boundary value problem ,Singular boundary method ,Boundary knot method ,Boundary element method ,Robin boundary condition ,Mathematics - Abstract
A fast, accurate and efficient multi-level boundary element method is developed to solve general boundary value problems. Here we concentrate on problems of two-dimensional steady potential flow and present a fast direct boundary element formulation. This novel method extends the pioneering work of Brandt and Lubrecht on multi-level multi-integration (MLMI) in several important ways to address problems with mixed boundary conditions. We utilize bi-conjugate gradient methods (BCGM) and implement the MLMI approach for fast matrix and matrix transpose multiplication for every iteration loop. Furthermore, by introducing a C-cycle multigrid algorithm, we find that the number of iterations for the bi-conjugate gradient methods is independent of the boundary element mesh discretization for problems of steady-state heat diffusion considered in this paper. As a result, the computational complexity of the proposed method is proportional to only N · log(N), where N is the number of degrees of freedom.Copyright © 2003 by ASME
- Published
- 2003
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29. Efficient Boundary Element Methods for the Time-Dependent Convective Diffusion Equation
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Gary F. Dargush and M. M. Grigoriev
- Subjects
Physics::Fluid Dynamics ,Convection ,symbols.namesake ,Rate of convergence ,Mathematical analysis ,symbols ,Method of fundamental solutions ,Boundary (topology) ,Upwind scheme ,Péclet number ,Boundary knot method ,Boundary element method ,Mathematics - Abstract
Higher-order boundary element methods (BEM) are presented for time-dependent convective diffusion in two dimensions. The time-dependent convective diffusion free-space fundamental solutions originally proposed by Carslaw and Jaeger are used to obtain the boundary integral formulation. Boundary element method solutions up to the Peclet number 106 are obtained for an example problem of unsteady convection-diffusion that possesses an exact solution. We investigate the convergence rate and accuracy of the higher-order boundary element formulations. An extremely high accuracy of the BEM solutions for highly convective flows is demonstrated. Moreover, it is shown that the use of time-dependent convective kernels provides an automatic upwinding for the entire range of Peclet numbers and also leads to very efficient algorithms as the Peclet number increases.Copyright © 2003 by ASME
- Published
- 2003
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30. Boundary element methods for highly convective unsteady flows
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M. M. Grigoriev and Gary F. Dargush
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Physics::Fluid Dynamics ,symbols.namesake ,Quadratic equation ,Quartic function ,Mathematical analysis ,symbols ,Boundary (topology) ,Upwind scheme ,Péclet number ,Summation equation ,Boundary element method ,Mathematics ,Interpolation - Abstract
Publisher Summary Higher-order boundary element methods (BEM) are presented for time-dependent convective diffusion in two dimensions. To facilitate accurate evaluation of the discrete integral equation coefficients over both singular and nonsingular boundary elements because of complex behavior of the time-dependent convective kernels, the chapter develops and implements a semianalytical algorithm. The time-dependent convective-diffusion-free-space fundamental solutions originally proposed by Carslaw and Jaeger are used to obtain the boundary integral formulation. In this chapter, BEM solutions up to the Peclet number 106 are obtained for a problem of unsteady convection-diffusion that possesses an exact solution. An extremely high accuracy of the BEM solutions for highly convective flows is demonstrated. Moreover, it is shown that the use of time-dependent convective kernels provide an automatic upwinding for the entire range of Peclet numbers and also lead to very efficient algorithms as the Peclet number increases. Higher-order boundary element methods for time-dependent convective diffusion problems are also presented. Linear, quadratic, and quartic interpolation functions are utilized for temporal and spatial discretizations of the boundary integral equation.
- Published
- 2003
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31. A fast multi-level multi-grid method for the Laplace equation
- Author
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Gary F. Dargush and M. M. Grigoriev
- Subjects
Biconjugate gradient method ,Matrix (mathematics) ,Mathematical optimization ,Discretization ,Iterative method ,Transpose ,Computational mechanics ,Applied mathematics ,Boundary value problem ,Boundary element method ,Mathematics - Abstract
Publisher Summary This chapter develops a fast, accurate, and efficient multilevel iterative method to solve general boundary value problems arising in computational mechanics. It concentrates on problems of two-dimensional steady potential flow and presents a fast direct boundary element method. This novel method extends the work on multilevel multiintegration (MLMI) in several important ways to address problems with arbitrary geometry and mixed boundary conditions. Researchers use biconjugate gradient methods and implement the MLMI approach for fast matrix and matrix transpose multiplication for every iteration loop. A multigrid algorithm is introduced to find that the number of iterations for the bi-conjugate gradient methods is independent of the boundary-element mesh discretization for problems of steady-state heat diffusion discussed in this chapter. The method can be extended in a straightforward manner to the solution of many problems in science and engineering that result in very large sets of matrix equations when the associated integral equations are discretized.
- Published
- 2003
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32. Multiscale thermomechanical analysis of sliding rings from short-time transients to steady-state
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M. M. Grigoriev, C-H. Wang, Andres Soom, and Gary F. Dargush
- Subjects
Surface (mathematics) ,Steady state (electronics) ,Materials science ,business.industry ,Rotational symmetry ,Thermomechanical analysis ,Transient (oscillation) ,Mechanics ,Surface finish ,Structural engineering ,business ,Boundary element method ,Convolution - Abstract
In order to better understand the performance of clutches, brakes and seals, there is a need to study the multiscale thermomechanical interactions that occur across rough interfacial sliding contacts. While the full three-dimensional problem is at present somewhat beyond reach from a computational standpoint, we can gain some insight into the problem by examining the more idealized axisymmetric case. Here we develop a transient coupled thermomechanical boundary element method to investigate the behaviour of sliding rings with axisymmetric roughness. By incorporating our recently developed fast convolution algorithm, we are able to consider the spatially and temporally localized response at asperity-level contacts, along with the evolution toward a global component-level steady state. In particular, we investigate behaviour for the sliding ring problem by considering surface profiles that incorporate axisymmetric roughness over several orders-of-magnitude. One of the most interesting findings that emerge from these simulations is the development of roughness-dependent steady-state shapes. Details of the short-time transient interactions are found to significantly affect the long-term component level response. This suggests that one may be able to control overall component deformations through the careful specification of surface profiles.
- Published
- 2003
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- View/download PDF
33. Higher-Order Boundary Element Methods for Unsteady Convective Transport
- Author
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Gary F. Dargush and M. M. Grigoriev
- Subjects
Physics ,Order (business) ,Convective transport ,Mechanics ,Boundary element method - Abstract
Higher-order boundary element methods (BEM) are presented for time-dependent convective diffusion problems. The time-dependent convective diffusion free-space fundamental solutions originally proposed by Carslaw and Jaeger are used to obtain the boundary integral formulation. For the linear, quadratic and quartic time interpolation functions considered in this paper, a complete set of closed form time integrals for the one-dimensional formulation are developed. Boundary element method solutions are obtained for four problems of unsteady convection-diffusion, including shock wave propagation. It is shown that the BEM solutions are extremely accurate in contrast to finite-difference and finite-element methods. Moreover, no upwinding is needed for the boundary element methods, even for high Peclet number flows. Finally, the conventional BEM formulation is extended to a problem involving singular flux arising due to a sudden rise of temperature on the boundary. This infinite flux BEM formulation provides significantly more accurate numerical results than the conventional approach.
- Published
- 2001
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34. A poly-region boundary element method for buoyancy-driven flows
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M. M. Grigoriev and Gary F. Dargush
- Subjects
Physics ,Buoyancy ,Pressure-correction method ,Analytic element method ,Mathematical analysis ,engineering ,engineering.material ,Boundary knot method ,Singular boundary method ,Boundary element method ,Discrete element method ,Extended finite element method - Published
- 2001
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35. Guasistationary process conditions of extrusion elastomeric materials on single-screw extruders
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M. M. Grigorieva, D. B. Gorbunov, and A. A. Tatarnikov
- Subjects
Chemistry ,QD1-999 - Abstract
The design procedure of a time characteristic of a single-screw extruder on the channel «a food - productivity» is developed at processing of elastomeric materials. The technique allows to estimate a filtrating ability of a pressure head zone
- Published
- 2008
36. Thermodynamics and structure of actinide(IV) complexes with nitrilotriacetic acid.
- Author
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Bonin L, Guillaumont D, Jeanson A, Den Auwer C, Grigoriev M, Berthet JC, Hennig C, Scheinost A, and Moisy P
- Abstract
Nitrilotriacetic acid, commonly known as NTA (N(CH(2)CO(2)H)(3)), can be considered a representative of the polyaminocarboxylic family. The results presented in this paper describe the thermodynamical complexation and structural investigation of An(IV) complexes with NTA in aqueous solution. In the first part, the stability constants of the An(IV) complexes (An = Pu, Np, U, and Th) have been determined by spectrophotometry. In the second part, the coordination spheres of the actinide cation in these complexes have been described using extended X-ray absorption fine structure spectroscopy and compared to the solid-state structure of (Hpy)(2)[U(NTA)(2)] x (H(2)O). These data are further compared to quantum chemical calculations, and their evolution across the actinide series is discussed. In particular, an interpretation of the role of the nitrogen atom in the coordination mode is proposed. These results are considered to be model behavior of polyaminocarboxylic ligands such as diethylenetriamine pentaacetic acid, which is nowadays the best candidate for a chelating agent in the framework of actinide decorporation for the human body.
- Published
- 2009
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37. Two-step hard X-ray focusing combining Fresnel zone plate and single-bounce ellipsoidal capillary.
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Snigirev A, Bjeoumikhov A, Erko A, Snigireva I, Grigoriev M, Yunkin V, Erko M, and Bjeoumikhova S
- Abstract
A two-step focusing set-up combining a Fresnel zone plate with an ellipsoidal capillary is presented. It is shown that, in addition to the anticipated gain in flux, the employment of the prefocusing micro-optic makes optimal use of the elliptical shape of the capillary by almost eliminating aberrations. A small cross section of the prefocused beam allows a tiny fraction of the capillary surface to be selected, thus reducing the influence of slope errors. An X-ray beam with a 15 keV energy was focused down to a spot size as small as 250 nm, demonstrating the best value that has been achieved up to now for single-bounce capillaries. The use of an ellipsoidal capillary as a micromirror under off-axis illumination by microfocusing optics may open up new opportunities in nanofocusing developments.
- Published
- 2007
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38. Submicrometer hard X-ray focusing using a single-bounce ellipsoidal capillary combined with a Fresnel zone plate.
- Author
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Snigirev A, Bjeoumikhov A, Erko A, Snigireva I, Grigoriev M, Yunkin V, Erko M, and Bjeoumikhova S
- Abstract
A single-bounce capillary with an ellipsoidal shape has been used for two-step focusing in combination with a Fresnel zone plate (FZP). The FZP serves as a first microfocusing element and produces a demagnified micrometer image of the source, before the elliptical capillary makes a last final compression of the beam. With 15 keV X-rays from the European Synchrotron Radiation Facility BM5 bending magnet, the two-step demagnification system produced a focus of about 250 nm with a gain of more than 1000. The use of an ellipsoidal capillary as a micro-mirror under off-axis illumination using micro-prefocusing optics might open up new opportunities in nanofocusing developments.
- Published
- 2007
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39. Single-molecule study of RuvAB-mediated Holliday-junction migration.
- Author
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Dawid A, Croquette V, Grigoriev M, and Heslot F
- Subjects
- Bacterial Proteins metabolism, Bacterial Proteins physiology, Biomechanical Phenomena, DNA Helicases metabolism, DNA, Cruciform metabolism, DNA-Binding Proteins metabolism, Escherichia coli genetics, Escherichia coli Proteins, Kinetics, Macromolecular Substances, Magnetics, Methods, Microspheres, Molecular Motor Proteins, Motion, DNA Helicases physiology, DNA, Cruciform ultrastructure, DNA-Binding Proteins physiology
- Abstract
Branch migration of Holliday junctions is an important step of genetic recombination and DNA repair. In Escherichia coli, this process is driven by the RuvAB complex acting as a molecular motor. Using magnetic tweezers, we studied the RuvAB-directed migration of individual Holliday junctions formed between two approximately 6-kb DNA molecules of identical sequence, and we measured the migration rate at 37 degrees C and 1 mM ATP. We directly demonstrate that RuvAB is a highly processive DNA motor protein that is able to drive continuous and unidirectional branch migration of Holliday junctions at a well defined average speed over several kilobases through homologous sequences. We observed directional inversions of the migration at the DNA molecule boundaries leading to forth-and-back migration of the branch point and allowing us to measure the migration rate in the presence of negative or positive loads. The average migration rate at zero load was found to be approximately 43 bp/sec. Furthermore, the load dependence of the migration rate is small, within the force range of -3.4 pN (hindering force) to +3.4 pN (assisting force).
- Published
- 2004
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40. Involvement of the TIP60 histone acetylase complex in DNA repair and apoptosis.
- Author
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Ikura T, Ogryzko VV, Grigoriev M, Groisman R, Wang J, Horikoshi M, Scully R, Qin J, and Nakatani Y
- Subjects
- Actins chemistry, Adenosine Triphosphatases chemistry, Adenosine Triphosphatases metabolism, Apoptosis radiation effects, Bacterial Proteins chemistry, DNA metabolism, DNA Helicases metabolism, Electrophoresis, Polyacrylamide Gel, HeLa Cells, Histone Acetyltransferases, Humans, Lysine Acetyltransferase 5, Macromolecular Substances, Molecular Weight, Proteins chemistry, Acetyltransferases metabolism, Apoptosis physiology, DNA Repair, Proteins physiology, Saccharomyces cerevisiae Proteins
- Abstract
It is well known that histone acetylases are important chromatin modifiers and that they play a central role in chromatin transcription. Here, we present evidence for novel roles of histone acetylases. The TIP60 histone acetylase purifies as a multimeric protein complex. Besides histone acetylase activity on chromatin, the TIP60 complex possesses ATPase, DNA helicase, and structural DNA binding activities. Ectopic expression of mutated TIP60 lacking histone acetylase activity results in cells with defective double-strand DNA break repair. Importantly, the resulting cells lose their apoptotic competence, suggesting a defect in the cells' ability to signal the existence of DNA damage to the apoptotic machinery. These results indicate that the histone acetylase TIP60-containing complex plays a role in DNA repair and apoptosis.
- Published
- 2000
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41. Crystallographic, X-ray absorption, and IR studies of solid- and solution-state structures of tris(nitrato) N,N,N',N'-tetraethylmalonamide complexes of lanthanides. Comparison with the Americium complex.
- Author
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Den Auwer C, Charbonnel MC, Drew MG, Grigoriev M, Hudson MJ, Iveson PB, Madic C, Nierlich M, Presson MT, Revel R, Russell ML, and Thuéry P
- Abstract
To fine-tune the design of optimized donor ligands for nuclear waste actinide selective extraction, both electronic and molecular structures of the actinide complexes that are formed must be investigated. In particular, to achieve the selective complexation of transplutonium 3+ ions versus lanthanide 3+ ions is one of the major challenges, given the chemical similarities between these two f-element families. In this work, the structure of solvent-phase M(NO3)3(TEMA)2 complexes (Ln = Nd, Eu, Ho, Yb, Lu, Am; TEMA = N,N,N',N'-tetraethylmalonamide) was investigated by liquid-phase spectroscopic methods among which extended X-ray absorption fine structure played a major role. In addition, the crystal structures of the species Nd(NO3)3(TEMA)2 and Yb(NO3)3(TEMA)2 have been determined by X-ray diffraction. Nd(NO3)3(C11N2O2H22)2 crystallizes in the monoclinic system (P2(1) space group; a = 11.2627(4) A, b = 20.5992(8) A, c = 22.2126(8) A; alpha = gamma = 90 degrees, beta = 102.572(1) degrees; Z = 6), and Yb(NO3)3(C11N2O2H22)2 crystallizes in the orthorhombic system (P2(1)2(1)2(1) space group; a = 9.3542(1) A, b = 18.1148(2) A, c = 19.7675(2) A; alpha = beta = gamma = 90 degrees; Z = 4). In the solvent phase, the metal polyhedron was found to be similar to that of the solid-state complex Nd(NO3)3(TEMA)2 for M = Nd to Ho. For M = Yb and Lu, a significant elongation of one nitrate oxygen bond was observed. Comparison with measurements on the Am(NO3)3(TEMA)2 complex in ethanol has shown the similarities between the Nd3+ and Am3+ coordination spheres.
- Published
- 2000
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42. A cruciform structural transition provides a molecular switch for chromosome structure and dynamics.
- Author
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Shlyakhtenko LS, Hsieh P, Grigoriev M, Potaman VN, Sinden RR, and Lyubchenko YL
- Subjects
- Base Pairing genetics, Chromosomes chemistry, Chromosomes genetics, Chromosomes metabolism, DNA, Superhelical genetics, Escherichia coli enzymology, Escherichia coli Proteins, Microscopy, Atomic Force, Models, Genetic, Plasmids chemistry, Plasmids genetics, Plasmids metabolism, Substrate Specificity, DNA Helicases, DNA, Superhelical chemistry, DNA, Superhelical metabolism, DNA-Binding Proteins metabolism, Nucleic Acid Conformation
- Abstract
The interaction between specific sites along a DNA molecule is often crucial for the regulation of genetic processes. However, mechanisms regulating the interaction of specific sites are unknown. We have used atomic force microscopy to demonstrate that the structural transition between cruciform conformations can act as a molecular switch to facilitate or prevent communication between distant regions in DNA. Cruciform structures exist in vivo and they are critically involved in the initiation of replication and the regulation of gene expression in different organisms. Therefore, structural transitions of the cruciform may play a key role in these processes., (Copyright 2000 Academic Press.)
- Published
- 2000
- Full Text
- View/download PDF
43. Migration of a Holliday junction through a nucleosome directed by the E. coli RuvAB motor protein.
- Author
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Grigoriev M and Hsieh P
- Subjects
- Bacterial Proteins chemistry, Base Sequence, DNA Repair, DNA, Bacterial chemistry, DNA-Binding Proteins chemistry, Escherichia coli genetics, Escherichia coli Proteins, Histones metabolism, Models, Molecular, Nucleic Acid Conformation, Nucleic Acid Heteroduplexes chemistry, Nucleic Acid Heteroduplexes metabolism, Protein Conformation, Recombination, Genetic, Bacterial Proteins metabolism, DNA Helicases metabolism, DNA, Bacterial metabolism, DNA-Binding Proteins metabolism, Escherichia coli metabolism, Nucleosomes metabolism
- Abstract
Chromatin plays a critical role in regulating access to DNA by proteins that direct recombination and repair. The E. coli RuvAB protein complex promotes branch migration of the Holliday junction recombination intermediate. The ability of RuvAB to negotiate passage of the junction through nucleosomal DNA is examined. The model system involves the formation of a Holliday junction positioned upstream of a nucleosome. Unassisted, the junction is blocked by a histone octamer. In the presence of RuvAB and ATP, rapid branch migration through the nucleosome is observed. It results in disruption of the histone-DNA interactions leading to the removal of the octamer from the junction intermediate. These results suggest that eukaryotic DNA motor proteins analogous to RuvAB could function during recombination to promote branch migration through chromatin.
- Published
- 1998
- Full Text
- View/download PDF
44. A histone octamer blocks branch migration of a Holliday junction.
- Author
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Grigoriev M and Hsieh P
- Subjects
- Animals, Base Sequence, Chickens, Chromatin chemistry, Chromatin genetics, DNA chemistry, DNA Damage, DNA Primers genetics, DNA Repair, Dinucleotide Repeats, In Vitro Techniques, Macromolecular Substances, Nucleosomes chemistry, Protein Conformation, DNA drug effects, DNA genetics, Histones chemistry, Histones pharmacology, Recombination, Genetic drug effects
- Abstract
The Holliday junction is a key intermediate in genetic recombination. Here, we examine the effect of a nucleosome core on movement of the Holliday junction in vitro by spontaneous branch migration. Histone octamers consisting of H2A, H2B, H3, and H4 are reconstituted onto DNA duplexes containing an artificial nucleosome-positioning sequence consisting of a tandem array of an alternating AT-GC sequence motif. Characterization of the reconstituted branch migration substrates by micrococcal nuclease mapping and exonuclease III and hydroxyl radical footprinting reveal that 70% of the reconstituted octamers are positioned near the center of the substrate and the remaining 30% are located at the distal end, although in both cases some translational degeneracy is observed. Branch migration assays with the octamer-containing substrates reveal that the Holliday junction cannot migrate spontaneously through DNA organized into a nucleosomal core unless DNA-histone interactions are completely disrupted. Similar results are obtained with branch migration substrates containing an octamer positioned on a naturally occurring sequence derived from the yeast GLN3 locus. Digestion of Holliday junctions with T7 endonuclease I establishes that the junction is not trapped by the octamer but can branch migrate in regions free of histone octamers. Our findings suggest that migration of Holliday junctions during recombination and the recombinational repair of DNA damage requires proteins not only to accelerate the intrinsic rate of branch migration but also to facilitate the passage of the Holliday junction through a nucleosome.
- Published
- 1997
- Full Text
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45. Peptide nucleic acids directed to the promoter of the alpha-chain of the interleukin-2 receptor.
- Author
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Praseuth D, Grigoriev M, Guieysse AL, Pritchard LL, Harel-Bellan A, Nielsen PE, and Hélène C
- Subjects
- Binding Sites, DNA Footprinting, DNA, Superhelical metabolism, DNA-Binding Proteins drug effects, DNA-Directed DNA Polymerase, Electrophoresis, Polyacrylamide Gel, Genes, Reporter genetics, Guanosine Triphosphate analogs & derivatives, Guanosine Triphosphate metabolism, Hydrogen Bonding, Nucleic Acid Conformation, Nucleic Acid Synthesis Inhibitors, Oligodeoxyribonucleotides metabolism, Plasmids metabolism, Salts pharmacology, Single-Strand Specific DNA and RNA Endonucleases metabolism, Transcription Factors drug effects, Transcription Factors metabolism, Transcription, Genetic drug effects, Oligodeoxyribonucleotides pharmacology, Peptide Nucleic Acids, Peptides pharmacology, Receptors, Interleukin-2 metabolism
- Abstract
Two 10-mer oligopyrimidine peptide nucleic acids (PNAs) were designed to interfere with IL-2R alpha promoter expression by binding to the regulatory sequences overlapping SRF and NF-kappa B transcription factor sites. Specific complexes were formed on each target sequence, and clearly involved (1) Hoogsteen hydrogen bonds as shown by experiments in which the purine strand of a single or double-stranded target was substituted with 7-deazadeoxyguanosine, (2) P-loop formation on double-helical DNA as evidenced by susceptibility to a single-strand-specific nuclease. When formed on a single-stranded DNA target, these highly stable complexes were responsible for efficient physical blockage of T7 DNA polymerase elongation on the template DNA containing the target oligopurine sequence. On a double-stranded target, these complexes only formed at low ionic strength and were slowly dissociated at physiological ionic strength (pH 6.5) with a t1/2 of 6.5-7 h. The salt-dependent instability of preformed complexes on a plasmid target was probably the critical factor responsible for their lack of significant sequence-specific effect on IL-2R alpha promoter activity inside living cells.
- Published
- 1996
- Full Text
- View/download PDF
46. Detection of covalent triplex within human cells.
- Author
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Guieysse AL, Praseuth D, Grigoriev M, Harel-Bellan A, and Hélène C
- Subjects
- Base Sequence, Cell Line, DNA Adducts, DNA-Directed DNA Polymerase metabolism, Ficusin, Humans, Molecular Sequence Data, Oligodeoxyribonucleotides chemistry, Photochemistry, Plasmids, Receptors, Interleukin-2 genetics, Taq Polymerase, Oligodeoxyribonucleotides analysis
- Abstract
Triple helix-forming oligonucleotides covalently linked to psoralen can be specifically cross-linked to both strands of DNA at the triplex-duplex junction following UV irradiation. We have previously shown that a 15mer psoralen-oligonucleotide conjugate forming a triple helix on the promoter of the alpha subunit gene of the interleukin-2 receptor inhibits transcription of reporter plasmids transfected into living cells after irradiation. In the present work, we directly demonstrate covalent triple helix formation at the target site inside cells. A primer extension assay using Taq polymerase was developed to quantitate the DNA which had reacted with the psoralen of the triple helix-forming oligonucleotide. Photoaddition of the psoralen at the DNA target site was demonstrated, not only when the preformed triplex was electroporated inside cells, but also when the oligonucleotide was added to the culture medium after plasmid electroporation and before irradiation of the cells.
- Published
- 1996
- Full Text
- View/download PDF
47. Oligonucleotide-directed switching of DNA polymerases to a dead-end track.
- Author
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Guieysse AL, Praseuth D, Grigoriev M, Harel-Bellan A, and Hélène C
- Subjects
- Base Sequence, DNA genetics, DNA metabolism, Humans, Molecular Sequence Data, Plasmids genetics, Polymerase Chain Reaction, Receptors, Interleukin-2 genetics, Taq Polymerase, DNA Replication drug effects, DNA-Directed DNA Polymerase metabolism, Oligonucleotides pharmacology
- Abstract
During DNA replication, the presence of oligonucleotides with partial homology to the template strand was shown to induce a switch of the polymerase from the normal template to the oligonucleotide. The latter acted as a dead-end template and led to abortive replication. The only prerequisite was that the oligonucleotide could form 7-9 base pairs with the newly synthesized DNA strand in order to switch templates. The switch occurred when base pairing of the oligonucleotide could take place with the 3'-end of the newly synthesized strand. These results show that oligonucleotides used in antisense or antigene strategies could have unexpected effects on replication. In addition, oligonucleotide-directed abortive replication might play an inhibitory role during PCR experiments on long DNA templates and lead to the amplification of truncated fragments.
- Published
- 1995
- Full Text
- View/download PDF
48. The serum unresponsive Rous sarcoma virus promoter sustains a high serum response factor-dependent transcription in vitro.
- Author
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Trouche D, Grigoriev M, Robin P, and Harel-Bellan A
- Subjects
- 3T3 Cells, Animals, Base Sequence, Binding Sites, DNA Primers, Humans, Leukemia, T-Cell, Mice, Molecular Sequence Data, Nuclear Proteins isolation & purification, Plasmids, Polymerase Chain Reaction, Regulatory Sequences, Nucleic Acid, Repetitive Sequences, Nucleic Acid, Restriction Mapping, Serum Response Factor, Transfection, Tumor Cells, Cultured, Avian Sarcoma Viruses genetics, DNA-Binding Proteins metabolism, Gene Expression Regulation, Viral, Genes, fos, Nuclear Proteins metabolism, Promoter Regions, Genetic, Transcription Factors metabolism, Transcription, Genetic
- Abstract
CArG boxes are cis-regulatory elements which are represented both in serum responsive and unresponsive promoters. Here we show that the RSV Long Terminal Repeat contains two CArG boxes, which were efficiently recognised by purified Serum Response Factor, although they remained unresponsive to serum in transient transfection assays. However, RSV CArG boxes were as efficient as c-fos Serum Response Element in mediating a Serum Response Factor-dependent transcription in vitro. Thus, the fact that a CArG box is able to bind Serum Response Factor in an active form is insufficient for serum responsiveness in vivo.
- Published
- 1993
- Full Text
- View/download PDF
49. Repression of c-fos promoter by MyoD on muscle cell differentiation.
- Author
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Trouche D, Grigoriev M, Lenormand JL, Robin P, Leibovitch SA, Sassone-Corsi P, and Harel-Bellan A
- Subjects
- 3T3 Cells, Animals, Base Sequence, Binding Sites, Cell Differentiation genetics, Cell Line, DNA metabolism, DNA-Binding Proteins genetics, Gene Expression Regulation, Mice, Molecular Sequence Data, Muscles cytology, MyoD Protein, Nuclear Proteins genetics, Rats, Regulatory Sequences, Nucleic Acid, Serum Response Factor, Transcription, Genetic, Transfection, Muscle Proteins metabolism, Muscles metabolism, Promoter Regions, Genetic, Proto-Oncogene Proteins c-fos genetics, Transcription Factors metabolism
- Abstract
Terminal differentiation and cell proliferation are in many cases, as in muscle cells, mutually exclusive processes. While differentiating myoblasts are withdrawn from the cell cycle, myogenesis is inhibited by some mitogens and overexpression of some oncogenes, including proto-oncogene c-fos (which expresses a growth-associated protein constituting the regulatory factor AP-1 in conjunction with c-Jun). MyoD, a muscle-specific transcription factor of the basic helix-loop-helix family, acts at both levels because it triggers a muscle differentiation programme in non-muscle cells, and induces a complete block of cell proliferation. Antagonistic interaction between MyoD and c-Jun has been demonstrated. We here show that c-fos expression greatly decreases upon muscle cell differentiation, concomitant with MyoD-induced activity. We have identified a MyoD-binding site overlapping with the serum-responsive element in the c-fos promoter. We demonstrate that MyoD can act as a negative regulator for c-fos transcription by blocking serum responsiveness through this binding site. These data suggest that the MyoD negative effect on cell growth could be partly mediated by transcriptional inactivation of growth-responsive genes.
- Published
- 1993
- Full Text
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50. Inhibition of gene expression by triple helix-directed DNA cross-linking at specific sites.
- Author
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Grigoriev M, Praseuth D, Guieysse AL, Robin P, Thuong NT, Hélène C, and Harel-Bellan A
- Subjects
- Base Sequence, Cell Line, Chloramphenicol O-Acetyltransferase genetics, Cloning, Molecular, Cross-Linking Reagents, DNA genetics, Gene Expression drug effects, Gene Expression radiation effects, Genes, fos drug effects, Genes, fos radiation effects, HIV Long Terminal Repeat, Human T-lymphotropic virus 1 genetics, Humans, Molecular Sequence Data, Mutagenesis, Site-Directed, NF-kappa B metabolism, Nuclear Proteins isolation & purification, Nuclear Proteins metabolism, Nucleic Acid Conformation, Oligodeoxyribonucleotides chemical synthesis, Plasmids, Promoter Regions, Genetic, Restriction Mapping, Transcription, Genetic radiation effects, Transfection, Furocoumarins pharmacology, Oligodeoxyribonucleotides pharmacology, Receptors, Interleukin-2 genetics, Transcription, Genetic drug effects, Ultraviolet Rays
- Abstract
Synthetic oligodeoxynucleotides represent promising tools for gene inhibition in live systems. Triple helix-forming oligonucleotides, which bind to double-stranded DNA, are of special interest since they are targeted to the gene itself rather than to its mRNA product, as in the antisense strategy. Triple helix-forming oligonucleotides can be coupled to DNA-modifying agents and used to introduce modifications in the DNA target in a highly sequence-specific manner. We have recently designed psoralen-oligonucleotide conjugates, which, upon binding to double-stranded DNA sequences via triple helix formation, may be cross-linked in vitro to both strands of the DNA following UV irradiation. A psoralen-oligonucleotide conjugate was targeted to the promoter of the alpha subunit of the interleukin 2 receptor (IL-2R alpha) gene. The triple helix site overlaps the binding site for the transcription factor NF-kappa B, which activates transcription from the IL-2R alpha promoter. After UV irradiation, the oligonucleotide conjugate becomes cross-linked to the target site and inhibits transcription of reporter plasmids transfected in live cells. Inhibition is observed when UV-induced cross-linking occurs both in vitro (before transfection) and in vivo (after transfection). We directly demonstrate that this inhibitory effect is due to triple helix formation at the target site, since a mutant of the promoter, to which oligonucleotide binding was inhibited, was not affected by the psoralen-oligonucleotide conjugate after UV irradiation. In addition, we demonstrate that site-specific cross-linking upstream of the promoter has no effect on transcription.
- Published
- 1993
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