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  • Articles  (18)
  • Engineering General  (12)
  • Models, Molecular  (6)
  • 1990-1994  (18)
  • 1955-1959
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  • Articles  (18)
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  • 1
    Publication Date: 1991-12-09
    Description: The three-dimensional structure of an active, disulfide cross-linked dimer of the ligand-binding domain of the Salmonella typhimurium aspartate receptor and that of an aspartate complex have been determined by x-ray crystallographic methods at 2.4 and 2.0 angstrom (A) resolution, respectively. A single subunit is a four-alpha-helix bundle with two long amino-terminal and carboxyl-terminal helices and two shorter helices that form a cylinder 20 A in diameter and more than 70 A long. The two subunits in the disulfide-bonded dimer are related by a crystallographic twofold axis in the apo structure, but by a noncrystallographic twofold axis in the aspartate complex structure. The latter structure reveals that the ligand binding site is located more than 60 A from the presumed membrane surface and is at the interface of the two subunits. Aspartate binds between two alpha helices from one subunit and one alpha helix from the other in a highly charged pocket formed by three arginines. The comparison of the apo and aspartate complex structures shows only small structural changes in the individual subunits, except for one loop region that is disordered, but the subunits appear to change orientation relative to each other. The structures of the two forms of this protein provide a step toward understanding the mechanisms of transmembrane signaling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Milburn, M V -- Prive, G G -- Milligan, D L -- Scott, W G -- Yeh, J -- Jancarik, J -- Koshland, D E Jr -- Kim, S H -- AI 30725/AI/NIAID NIH HHS/ -- DK09765/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1991 Nov 29;254(5036):1342-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1660187" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Aspartic Acid/metabolism ; Binding Sites ; Disulfides/analysis ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; *Receptors, Amino Acid ; Receptors, Cell Surface/*chemistry/metabolism ; Salmonella typhimurium/metabolism ; X-Ray Diffraction
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 1992-03-20
    Description: The highly symmetric pyruvate dehydrogenase multienzyme complexes have molecular masses ranging from 5 to 10 million daltons. They consist of numerous copies of three different enzymes: pyruvate dehydrogenase, dihydrolipoyl transacetylase, and lipoamide dehydrogenase. The three-dimensional crystal structure of the catalytic domain of Azotobacter vinelandii dihydrolipoyl transacetylase has been determined at 2.6 angstrom (A) resolution. Eight trimers assemble as a hollow truncated cube with an edge of 125 A, forming the core of the multienzyme complex. Coenzyme A must enter the 29 A long active site channel from the inside of the cube, and lipoamide must enter from the outside. The trimer of the catalytic domain of dihydrolipoyl transacetylase has a topology identical to chloramphenicol acetyl transferase. The atomic structure of the 24-subunit cube core provides a framework for understanding all pyruvate dehydrogenase and related multienzyme complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mattevi, A -- Obmolova, G -- Schulze, E -- Kalk, K H -- Westphal, A H -- de Kok, A -- Hol, W G -- New York, N.Y. -- Science. 1992 Mar 20;255(5051):1544-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Groningen, The Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1549782" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Azotobacter vinelandii/enzymology ; Chloramphenicol O-Acetyltransferase/genetics ; Humans ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Pyruvate Dehydrogenase Complex/*chemistry/genetics ; Sequence Homology, Nucleic Acid
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 1990-09-07
    Description: A protein crystal structure is usually described by one single structure, which largely omits the dynamical behavior of the molecule. A molecular dynamics method with a time-averaged crystallographic restraint was used to overcome this limitation. This method yields an ensemble of structures in which all possible thermal motions are allowed, that is, in additional to isotropic distributions, anisotropic and anharmonic positional distributions occur as well. In the case of bovine pancreatic phospholipase A2, this description markedly improves agreement with the observed x-ray diffraction data compared to the results of the classical one-model structure description. Time-averaged crystallographically restrained molecular dynamics reveals large mobilities in the loops involved in lipid bilayer association.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gros, P -- van Gunsteren, W F -- Hol, W G -- New York, N.Y. -- Science. 1990 Sep 7;249(4973):1149-52.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BIOSON Research Institute, University of Groningen, The Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2396108" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cattle ; Crystallography ; Hot Temperature ; Models, Molecular ; Motion ; *Phospholipases ; *Phospholipases A ; Phospholipases A2 ; Protein Conformation ; X-Ray Diffraction
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    International Journal for Numerical Methods in Fluids 11 (1990), S. 661-675 
    ISSN: 0271-2091
    Keywords: Finite elements ; Navier-Stokes ; Velocity-vorticity ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: A velocity-vorticity formulation of the Navier-Stokes equations is presented as an alternative to the primitive variables approach. The velocity components and the vorticity are solved for in a fully coupled manner using a Newton method. No artificial viscosity is required in this formulation. The pressure is updated by a method allowing natural imposition of boundary conditions. Incompressible and subsonic results are presented for two-dimensional laminar internal flows up to high Reynolds numbers.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    International Journal for Numerical Methods in Fluids 13 (1991), S. 309-319 
    ISSN: 0271-2091
    Keywords: Viscous-inviscid interaction ; Shock wave-boundary layer interaction ; Boundary layers ; Finite element method for flow problems ; Zonal methods ; Choked viscous flows ; Stream function-vorticity formulation ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: A method is outlined for solving two-dimensional transonic viscous flow problems, in which the velocity vector is split into the gradient of a potential and a rotational component. The approach takes advantage of the fact that for high-Reynolds-number flows the viscous terms of the Navier-Stokes equations are important only in a thin shear layer and therefore solution of the full equations may not be needed everywhere. Most of the flow can be considered inviscid and, neglecting the entropy and vorticity effects, a potential model is a good approximation in the flow core. The rotational part of the flow can then be calculated by solution of the potential, streamfunction and vorticity transport equations. Implementation of the no-slip and no-penetration boundary conditions at the walls provides a simple mechanism for the interaction between the viscous and inviscid solutions and no extra coupling procedures are needed. Results are presented for turbulent transonic internal choked flows.
    Additional Material: 7 Ill.
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  • 6
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    International Journal for Numerical Methods in Fluids 13 (1991), S. 135-144 
    ISSN: 0271-2091
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Finite element solution methods for the incompressible Navier-Stokes equations in primitive variables form are presented. To provide the necessary coupling and enhance stability, a dissipation in the form of a pressure Laplacian is introduced into the continuity equation. The recasting of the problem in terms of pressure and an auxiliary velocity demonstrates how the error introduced by the pressure dissipation can be totally eliminated while retaining its stabilizing properties. The method can also be formally interpreted as a Helmholtz decomposition of the velocity vector.The governing equations are discretized by a Galerkin weighted residual method and, because of the modification to the continuity equation, equal interpolations for all the unknowns are permitted. Newton linearization is used and at each iteration the linear algebraic system is solved by a direct solver. Convergence of the algorithm is shown to be very rapid. Results are presented for two-dimensional flows in various geometries.
    Additional Material: 4 Ill.
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  • 7
    Electronic Resource
    Electronic Resource
    Chichester [u.a.] : Wiley-Blackwell
    International Journal for Numerical Methods in Engineering 36 (1993), S. 765-781 
    ISSN: 0029-5981
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: Kirchhoff plate bending problems were studied by both the Trefftz direct and indirect approximations in which non-singular, complete Trefftz functions are used as the weighting and/or trial functions. The Trefftz direct method involved only the quantities of engineering interest. Numerical results are given to show the efficiency and the excellent accuracy of the present method.
    Additional Material: 10 Ill.
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  • 8
    Electronic Resource
    Electronic Resource
    Chichester [u.a.] : Wiley-Blackwell
    International Journal for Numerical Methods in Engineering 32 (1991), S. 63-78 
    ISSN: 0029-5981
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: The application of the Trefftz method for calculating wave forces on offshore structures is presented. Indirect and direct formulations using complete and non-singular systems of Trefftz functions for the Helmholtz equation are posed in this paper. An effective technique using different interpolation functions for the velocity potential and wave force are suggested to improve the computational accuracy of the wave force. The numerical examples show that the present method is highly efficient and accurate.
    Additional Material: 7 Ill.
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  • 9
    Electronic Resource
    Electronic Resource
    Chichester [u.a.] : Wiley-Blackwell
    International Journal for Numerical Methods in Engineering 30 (1990), S. 1147-1161 
    ISSN: 0029-5981
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: Direct and indirect approximations using sets of non-singular, complete Trefftz functions, i.e. the complete systems of solutions, have been successfully applied to harmonic problems.1 In this paper, the procedure is applied to a more complex situation - plane elasticity problems.The examples show that the present method can avoid the difficulties relating to singular integration and has good accuracy compared with traditional boundary elements.
    Additional Material: 8 Ill.
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Communications in Applied Numerical Methods 8 (1992), S. 511-518 
    ISSN: 0748-8025
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: A second-order explicit method is developed for the numerical solution of the Ricatti (logistic) initial-value problem u′ ≡ du/dt = αu(1 - u), t 〉 0, u(0) = U0, in which α ≠ 0 is a real parameter. The method is based on two first-order methods which appeared in an earlier paper by the authors (Twizell et al.1). In addition to being chaos-free and of higher order, the novel method is seen to converge to the correct, stable, steady-state solution for any value of the parameter α, provided the denominator of the method does not vanish. Convergence is monotonic or oscillatory depending on the magnitude of the product αl, where l is the parameter in the discretization of the independent variable t. This dependence of the type of convergence on αl is likened to the behaviour of the well known Crank-Nicolson method for solving the simple heat equation. Conversion of the numerical method to a reliable, empirical model for predicting the limited growth of successive generations of a population is given. When extended to the numerical solution of Fisher's equation, in which the quadratic polynomial αu(1 - u) appears as the reaction term, the numerical solution is found by solving a linear algebraic system at each time step, as opposed to solving a non-linear system, which often happens when solving non-linear partial differential equations.
    Additional Material: 1 Ill.
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