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DNA Simulation using Knots |
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 A rendering of a DNA loop (polygonal knot) in an area of gel. The violet sticks model the gel and are stationary. The green sticks model the DNA loop and move within the gel. The red spheres are the vertices of the knot. |
Although the study of polygonal knots is inetesting as a purely mathematical notion there has been a great deal of work in recent years in attempting to correlate polygonal knot behavior with that of DNA. Of particular interest to this research project is the possible correlation between the behavior of physically real polygonal knots and that of DNA loops in gel electrophoresis experiments. In gel electrophoresis an electric current is applied to the ends of a tube of gel and DNA loops are introduced at one end of the tube. The loops are then pulled through the gel by the electrostatic potential which move through the gel in a manner dependent upon their physical properties. The resulting spectrum can then be used to analyze the DNA. This software performs a gel electrophoresis simulation using polygonal knots as a proxy for DNA. The computational model was developed jointly by Professor Jon Simon of the University of Iowa and Professor Kenny Hunt of the University of Wisconsin - LaCrosse. The software is under development and will be made freely available once it is developed Select the images below for high-fidelity MPEG movies of various trefoil knot simulations. Note that each file is between about 25Mb and 50Mb in size. |
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| The software supports numerous output formats including Mathematica, POV, and OpenInventor. | ||||||
| The software is written in C/C++ and supports numerous options for experimentation. | ||||||
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Simulation 1 |
Simulation 2 |
Simulation 3 |
Simulation 4 |
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