A Novel Technique for Generating a Band Diagonal Matrix in Tight-Binding DNA Analysis

POSTER

Abstract

There exist numerous selection sequence techniques for creating a coupling integral matrix for the calculation of transmission of an electron through a DNA molecule. However, these techniques typically create a matrix which requires a significant amount of computer time and memory, especially for large DNA models. Presented here is a novel technique that generates a band diagonal coupling integral matrix which reduces the computer time and memory required for the calculations. To illustrate the benefits, Poly(G)-Poly(C) 4-channel DNA models for 3-basepairs, 5-basepairs, and 7-basepairs are used to compare the CPU calculation time of the different models. A graphical representation will reveal the benefit of using this novel technique.

Authors

  • Dale Igram

    Cornell University, Air Force Research Labs, The Center for Photochemical Sciences and Department of Physics, BGSU, Department of Physics, BGSU, Department of Physics and Astronomy, Ball State University, Miami University, Johannes-Gutenberg-Universitat, Mainz, Germany, Martin-Luther-Universitat, Halle, Germany, The Ohio State University, Department of Physics, Columbus, OH 43210, USA, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA, Ohio Northern University, The Ohio State University, Department of Physics, Columbus, OH 43210, Sciprint.org, Ball State University, Department of Physics and Materials Research Institute, Pennsylvania State University, University Park, PA 16802

  • Dale Igram

    Cornell University, Air Force Research Labs, The Center for Photochemical Sciences and Department of Physics, BGSU, Department of Physics, BGSU, Department of Physics and Astronomy, Ball State University, Miami University, Johannes-Gutenberg-Universitat, Mainz, Germany, Martin-Luther-Universitat, Halle, Germany, The Ohio State University, Department of Physics, Columbus, OH 43210, USA, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA, Ohio Northern University, The Ohio State University, Department of Physics, Columbus, OH 43210, Sciprint.org, Ball State University, Department of Physics and Materials Research Institute, Pennsylvania State University, University Park, PA 16802

  • Yong Joe

    Dept. of Physics \& Astronomy, Ball State University, Department of Physics and Astronomy, Ball State University, Department of Physics and Astrnomy, Ball State University