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Biomolecular dynamic detection method under the mirror model of ellipsoidal cavity

A technology of dynamic detection and biomolecules, applied in special data processing applications, instruments, electrical digital data processing, etc., can solve problems such as low efficiency

Active Publication Date: 2016-05-18
YANCHENG INST OF TECH
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Problems solved by technology

[0003] The problem to be solved by the present invention is that in the biomolecular simulation, the detection of the electrostatic interaction of non-spherical biomacromolecules is inefficient in the traditional spherical cavity mixed image solvent model

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  • Biomolecular dynamic detection method under the mirror model of ellipsoidal cavity
  • Biomolecular dynamic detection method under the mirror model of ellipsoidal cavity
  • Biomolecular dynamic detection method under the mirror model of ellipsoidal cavity

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Embodiment Construction

[0015] The present invention will be described in further detail below in conjunction with the accompanying drawings of the description.

[0016] 1. Solvent model structure of mixed mirror image in ellipsoidal cavity

[0017] Ellipsoid cavity mixed mirror solvent model, such as figure 1 As shown, including ellipsoid 1 and truncated octahedron 2. The truncated octahedron 2 is located inside the ellipsoid 1 . The three-axis radii of the ellipsoid 1 are denoted as R c , R c , R f ,,R c with R f The conditions are met between: . in , . The ellipsoid 1 can be expressed as: . On the XOZ section, the truncated octahedron 2 is a regular inscribed octahedron of the ellipsoid 1, such as figure 1 shown. The three-dimensional structure of the truncated octahedron 2 is as follows figure 2 As shown, a parallel polyhedron with 14 sides surrounded by 8 hexagons and 6 quadrilaterals. Expressed mathematically, the planes of the 8 hexagons of the truncated octahedron 2 sati...

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Abstract

The invention discloses a biological molecular dynamics detection method under an ellipsoidal-cavity mirror image model. The method is implemented mainly through the construction of the ellipsoidal-cavity mirror image mixed solvent model; the model comprises an ellipsoid and a truncated octahedron arranged in the ellipsoid; the truncated octahedron is a 14-sided polyhedron formed by 6 quadrangles and 8 hexagons. Compared with an existing spherical-cavity mirror image solvent model, the structure of the ellipsoidal-cavity mirror image mixed solvent model, provided by the invention, is more effective in biological macromolecular dynamics simulation of some slender biological macromolecules such as actin and DNA.

Description

technical field [0001] The invention relates to dynamic detection of biological macromolecules. Background technique [0002] Under the existing technology, in biomolecular simulation, the spherical cavity mixed image solvent model is usually used to deal with the electrostatic interaction of heterogeneous systems (Y. Lin, A. Baumketner, S. Deng, Z. Xu, D. Jacobs, W. Cai, An image-based reaction field method for electrostatic interactions in molecular dynamics simulations so faqueous solutions, J. Chem. Phys. 131 (2009) 154103). However, for non-spherical biomacromolecules (such as actin and DNA), the efficiency of using spherical cavity is not high. The use of irregularly shaped cavities containing only a few layers of solvent around the macromolecule can greatly reduce the size of the system. But the problem of using irregularly shaped cavity is how to accurately and efficiently calculate the reaction field in such irregularly shaped cavity at each simulation time step. ...

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G06F19/16
Inventor 薛长峰
Owner YANCHENG INST OF TECH
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