scholarly journals Generation of Novel-Substrate-Accepting Biphenyl Dioxygenases through Segmental Random Mutagenesis and Identification of Residues Involved in Enzyme Specificity

2006 ◽  
Vol 72 (3) ◽  
pp. 2191-2199 ◽  
Author(s):  
Marco Zielinski ◽  
Silke Kahl ◽  
Christine Standfuß-Gabisch ◽  
Beatriz Cámara ◽  
Michael Seeger ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Random Mutagenesis ◽  
Major Influence ◽  
Enzyme Specificity ◽  
Three Dimensional Model ◽  
Wild Type Enzyme ◽  
High Frequencies ◽  
Burkholderia Xenovorans ◽  
Function Relationship

ABSTRACT Aryl-hydroxylating dioxygenases are of interest for the degradation of persistant aromatic pollutants, such as polychlorobiphenyls (PCBs), or as catalysts for the functionalization of aromatic scaffolds. In order to achieve dioxygenation of technical mixtures of PCBs, enzymes with broadened or altered substrate ranges are essential. To alter the substrate specificity of the biphenyl dioxygenase (BphA) of Burkholderia xenovorans LB400, we applied a directed evolution approach that used structure-function relationship data to target random mutageneses to specific segments of the enzyme. The limitation of random amino acid (AA) substitutions to regions that are critical for substrate binding and the exclusion of AA exchanges from positions that are essential for catalytic activity yielded enzyme variants of interest at comparatively high frequencies. After only a single mutagenic cycle, 10 beneficial variants were detected in a library of fewer than 1,000 active enzymes. Compared to the parental BphA, they showed between 5- and 200-fold increased turnover of chlorinated biphenyls, with substituent patterns that rendered them largely recalcitrant to attack by BphA-LB400. Determination of their sequences identified AAs that prevent the acceptance of specific PCBs by the wild-type enzyme, such as Pro334 and Phe384. The results suggest prime targets for subsequent cycles of BphA modification. Correlations with a three-dimensional model of the enzyme indicated that most of the exchanges with major influence on substrate turnover do not involve pocket-lining residues and had not been predictable through structural modeling.

Conjugate Flow and Heat Transfer Investigation of a Turbo Charger: Part I — Numerical Results

2003 ◽  
Author(s):  
Dieter Bohn ◽  
Tom Heuer ◽  
Karsten Kusterer
Keyword(s):  
Heat Transfer ◽  
Three Dimensional ◽  
Heat Fluxes ◽  
Inlet Temperature ◽  
Three Dimensional Model ◽  
Flow And Heat Transfer ◽  
Turbine Inlet ◽  
Turbo Charger ◽  
Conjugate Calculation

In this paper a three-dimensional conjugate calculation has been performed for a passenger car turbo charger. The scope of this work is to investigate the heat fluxes in the radial compressor which can be strongly influenced by the hot turbine. As a result of this, the compressor efficiency may deteriorate. Consequently, the heat fluxes have to be taken into account for the determination of the efficiency. To overcome this problem a complex three-dimensional model has been developed. It contains the compressor, the oil cooled center housing, and the turbine. 12 operating points have been numerically simulated composed of three different turbine inlet temperatures and four different mass flows. The boundary conditions for the flow and for the outer casing were derived from experimental test data (part II of the paper). Resulting from these conjugate calculations various one-dimensional calculation specifications have been developed. They describe the heat transfer phenomena inside the compressor with the help of a Nusselt number which is a function of an artificial Reynolds number and the turbine inlet temperature.

Numerical modelling of a microreactor for thermocatalytic decomposition of toxic compounds

2011 ◽  
Vol 32 (3) ◽  
pp. 215-227 ◽  
Author(s):  
Paweł Jóźwik ◽  
Michał Karcz ◽  
Janusz Badur
Keyword(s):  
Numerical Modelling ◽  
Knudsen Diffusion ◽  
Three Dimensional ◽  
Operating Conditions ◽  
Three Dimensional Model ◽  
Toxic Compounds ◽  
Slip Boundary ◽  
Standard Models ◽  
Thermocatalytic Decomposition

Numerical modelling of a microreactor for thermocatalytic decomposition of toxic compounds In this paper a three-dimensional model for determination of a microreactor's length is presented and discussed. The reaction of thermocatalytic decomposition has been implemented on the base of experimental data. Simplified Reynolds-Maxwell formula for the slip velocity boundary condition has been analysed and validated. The influence of the Knudsen diffusion on the microreactor's performance has also been verified. It was revealed that with a given operating conditions and a given geometry of the microreactor, there is no need for application of slip boundary conditions and the Knudsen diffusion in further analysis. It has also been shown that the microreactor's length could be practically estimated using standard models.

HIGH-FREQUENCY DIFFRACTION BY A SPHERE

1961 ◽  
Vol 39 (10) ◽  
pp. 1486-1494
Author(s):  
C. L. Tang
Keyword(s):  
Plane Wave ◽  
High Frequency ◽  
Rotational Symmetry ◽  
Asymptotic Series ◽  
Three Dimensional ◽  
Shadow Region ◽  
High Frequencies ◽  
Present Procedure ◽  
Dimensional Object

A systematic procedure is given for the determination of the asymptotic series directly from the Helmholtz equation and the boundary conditions for the field in the shadow region of a sphere illuminated by a plane wave at high frequencies. The first two terms in the series for the shadow region, including the regions near the axial caustic and the boundary layer near the surface of the sphere, are explicitly evaluated. The present procedure can be generalized to any smooth convex three-dimensional object with a rotational symmetry, illuminated by a plane wave in the direction of the axis of rotational symmetry.

scholarly journals КОМП’ЮТЕРНА ТЕХНОЛОГІЯ АНАЛІЗУ ТА ДИЗАЙНУ ПРЕДМЕТНОГО СЕРЕДОВИЩА З ПОЗИЦІЇ ВІЗУАЛЬНОГО СПРИЙНЯТТЯ

2020 ◽  
pp. 39-48
Author(s):  
Т. В. Булгакова ◽  
О. В. Полякова ◽  
С. С. Кисіль ◽  
О. Є. Шмельова
Keyword(s):  
Visual Perception ◽  
Quantitative Determination ◽  
Three Dimensional ◽  
Geometrical Model ◽  
Human Being ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Three Dimensional Objects ◽  
Computer Technologies

The purpose of the investigation is the development of computer technology of analysis and design of built environment from the point of its visual perception in the space of its three-dimensional model without using the perspective projections. The methodology were used to achieve the purpose: analysis of the scientific publications on the topic of object environment composition; applied geometry methods, method of division of the geometrical object into simplexes (triangulation), methods of advanced algebra and analytical geometry; computer modeling for construction of the model of visual perception of the environment. Methods of analysis of the three-dimensional model on the basis of modeling of visual perception by means of computer technologies directly in the area of the model without using perspective projections are developed. It is offered to analyze the visual perception of any objects and their relations by means of using the solid angles with the vertices placed in the point of view and the surfaces that surround the visible contours of three-dimensional objects. This approach gives the opportunity to analyze the objects simultaneously regardless their position according to the observer; apart of that, the objects, which are accepted similarly in the reality, will have the same geometrical features during the modeling of visual perception and beside that, the refusal of using of the perspective projections will make possible to avoid the distortion of the images. The algorithm of determination of the solid angles to three-dimensional objects, which is the basis of computer methods of compositional analysis of the object environment from the position of visual perception without the use of perspective projections, is developed. The geometrical model of visual perception by a human being from the certain point of perception is built. It makes possible to define correctly visual features of the object environment and gives the opportunity to analyze the whole surrounding of the observer in the area of 360 degrees. Scientific novelty of the investigation means that the methods of analysis of the three-dimensional model on the basis of modeling of visual perception by means of computer technologies directly in the area of the model without using perspective projections are developed for the first time. The concept of the geometrical model of visual perception by a human being from the certain point of perception is developed. The further development of the methodology of quantitative determination of characteristics of object environment by means of computer technologies is defined. Practical significance shows that the results of the scientific investigation can be used for analysis and judgments of the aesthetic peculiarities of the object environment by means of computer technologies with quantitative determination of characteristics of object environment from the point of its visual perception. Such approach gives the opportunity to develop and create the further certain recommendations and instructions for correction of the existing environment and for the development of the new one.

A Model for the Fast Determination of Modal Sound Transmission of Large Rectangular Opening

2020 ◽  
Vol 142 (6) ◽  
Author(s):  
Jiazhu Li ◽  
Rui Zhang ◽  
Shen Chen ◽  
Can Li ◽  
Jian Chen
Keyword(s):  
Wave Equations ◽  
Three Dimensional ◽  
Sound Transmission ◽  
Computational Effort ◽  
Sound Insulation ◽  
Fast Determination ◽  
High Frequencies ◽  
Higher Order Modes ◽  
Insulation Performance

Abstract The existence of openings affects the sound insulation performance of structures significantly. The determination of sound transmission through large rectangular openings is often time-consuming, because of the large number of modes, especially if there is a need to go to high frequencies. A model is proposed and detailed based on three-dimensional wave equations, the transfer matrix method, and modal superposition. The viscous and thermal boundary layer effects have been concerned; hence, the model accuracy for narrow slits was improved. The computational effort is significantly decreased by neglecting the cross-modal sound transmission. The accuracy of this model is validated by comparing it with the existing model, the measurement, and the acoustic finite element method. The study of sound transmission behavior of higher-order modes is performed. The modal sound transmission is predicted and compared for several modes. The phenomenon that is different from that of the plane wave situation is found and discussed.

Synthesis of Three-Dimensional Models from Drawings Based on Spectral Graph Theory

2015 ◽  
Vol 756 ◽  
pp. 598-603 ◽  
Author(s):  
Aleksey Zakharov ◽  
Arkady Zhiznyakov
Keyword(s):  
Graph Theory ◽  
Three Dimensional ◽  
Spectral Graph Theory ◽  
Boundary Representation ◽  
Three Dimensional Model ◽  
Three Dimensional Objects ◽  
Spectral Graph ◽  
Dimensional Models ◽  
Three Dimensional Models

Task of automatic reconstruction of three-dimensional objects by drawing views presented. The algorithm based on a boundary representation of three-dimensional models. The algorithm consists of the following steps: automatic separation of the drawing per the views, determination of three-dimensional coordinates of vertices, definition and marking of wire model primitives, reconstruction of model faces and model elements. The fundamental concept of the algorithm is to find the structural elements of three-dimensional model with usage of pre-specified patterns. The templates are described by means of matrices. Matching algorithm uses spectral graph theory. Reconstruction results are presented.

A three-dimensional model of the human airway tree

1999 ◽  
Vol 87 (6) ◽  
pp. 2207-2217 ◽  
Author(s):  
Hiroko Kitaoka ◽  
Ryuji Takaki ◽  
Béla Suki
Keyword(s):  
3D Model ◽  
Human Lung ◽  
Three Dimensional ◽  
Deterministic Algorithm ◽  
Three Dimensional Model ◽  
Fluid Delivery ◽  
Human Airway ◽  
Airway Tree ◽  
Function Relationship ◽  
Good Agreement

A three-dimensional (3D) model of the human airway tree is proposed using a deterministic algorithm that can generate a branching duct system in an organ. The algorithm is based on two principles: 1) the amount of fluid delivery through a branch is proportional to the volume of the region it supplies; and 2) the terminal branches are arranged homogeneously within the organ. These principles define the basic process of branching: generation of the dimensions and directionality of two daughter branches is governed by the properties of the parent branch and the region the parent supplies. The algorithm is composed of nine basic rules and four complementary rules. When the contour of an organ and the position of the trunk are specified, branches are successively generated by the algorithm. Applied to the human lung, the algorithm generates an airway tree that consists of ∼54,000 branches. Its morphometric characteristics are in good agreement with those reported in the literature. The algorithm and the 3D airway model are useful for studying the structure-function relationship in the lung.

scholarly journals Modelling and mutational analysis of Aspergillus nidulans UreA, a member of the subfamily of urea/H + transporters in fungi and plants

Open Biology ◽  
2014 ◽  
Vol 4 (6) ◽  
pp. 140070 ◽  
Author(s):  
Manuel Sanguinetti ◽  
Sotiris Amillis ◽  
Sergio Pantano ◽  
Claudio Scazzocchio ◽  
Ana Ramón
Keyword(s):  
Amino Acids ◽  
Aspergillus Nidulans ◽  
Vibrio Parahaemolyticus ◽  
Mutational Analysis ◽  
Three Dimensional ◽  
Random Mutagenesis ◽  
Membrane Transporters ◽  
Substrate Selectivity ◽  
Dimensional Model ◽  
Three Dimensional Model

We present the first account of the structure–function relationships of a protein of the subfamily of urea/H + membrane transporters of fungi and plants, using Aspergillus nidulans UreA as a study model. Based on the crystal structures of the Vibrio parahaemolyticus sodium/galactose symporter (vSGLT) and of the Nucleobase-Cation-Symport-1 benzylhydantoin transporter from Microbacterium liquefaciens (Mhp1), we constructed a three-dimensional model of UreA which, combined with site-directed and classical random mutagenesis, led to the identification of amino acids important for UreA function. Our approach allowed us to suggest roles for these residues in the binding, recognition and translocation of urea, and in the sorting of UreA to the membrane. Residues W82, Y106, A110, T133, N275, D286, Y388, Y437 and S446, located in transmembrane helixes 2, 3, 7 and 11, were found to be involved in the binding, recognition and/or translocation of urea and the sorting of UreA to the membrane. Y106, A110, T133 and Y437 seem to play a role in substrate selectivity, while S446 is necessary for proper sorting of UreA to the membrane. Other amino acids identified by random classical mutagenesis (G99, R141, A163, G168 and P639) may be important for the basic transporter's structure, its proper folding or its correct traffic to the membrane.

scholarly journals Automatic determination of an anatomical coordinate system for a three-dimensional model of the human patella

2013 ◽  
Vol 46 (12) ◽  
pp. 2093-2096 ◽  
Author(s):  
Michael J. Rainbow ◽  
Daniel L. Miranda ◽  
Roy T.H. Cheung ◽  
Joel B. Schwartz ◽  
Joseph J. Crisco ◽  
...  
Keyword(s):  
Coordinate System ◽  
Three Dimensional ◽  
Dimensional Model ◽  
Automatic Determination ◽  
Three Dimensional Model

Conjugate Flow and Heat Transfer Investigation of a Turbo Charger

2005 ◽  
Vol 127 (3) ◽  
pp. 663-669 ◽  
Author(s):  
Dieter Bohn ◽  
Tom Heuer ◽  
Karsten Kusterer
Keyword(s):  
Heat Transfer ◽  
Three Dimensional ◽  
Heat Fluxes ◽  
Inlet Temperature ◽  
Three Dimensional Model ◽  
Flow And Heat Transfer ◽  
Turbine Inlet ◽  
Turbo Charger ◽  
Conjugate Calculation

In this paper a three-dimensional conjugate calculation has been performed for a passenger car turbo charger. The scope of this work is to investigate the heat fluxes in the radial compressor, which can be strongly influenced by the hot turbine. As a result of this, the compressor efficiency may deteriorate. Consequently, the heat fluxes have to be taken into account for the determination of the efficiency. To overcome this problem a complex three-dimensional model has been developed. It contains the compressor, the oil cooled center housing, and the turbine. Twelve operating points have been numerically simulated composed of three different turbine inlet temperatures and four different mass flows. The boundary conditions for the flow and for the outer casing were derived from experimental test data (Bohn et al.). Resulting from these conjugate calculations various one-dimensional calculation specifications have been developed. They describe the heat transfer phenomena inside the compressor with the help of a Nusselt number, which is a function of an artificial Reynolds number and the turbine inlet temperature.

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