Molecular Simulation of DNA Microarrays - an Application of 2D particle mesh Ewald algorithm -
T. Watanabe, M. Kawata and U. Nagashima
National Institute of Advanced Industrial and Science and Technology, Grid Technology Research Center, JP
Keywords: molecular dynamics, DNA microarrays, 2D particle mesh Ewald
We have developed the two-dimensional particle mesh Ewald (2D-PME) algorithm for molecular dynamics (MD) simulation, and applied it to have knowledge of the behavior of DNA and its interaction on microarrays, which crucial in the design of DNA microarrays. The 2D-PME algorithm can rapidly calculate the Coulomb interaction for a 3D system with 2D periodicity, which is the most time-consuming process in the MD simulation. The MD simulation of DNA microarrays that contain a single DNA molecule in a unit-cell was carried out under the two types of the boundary conditions, 3D systems with the 2D and 3D periodicities, in which the Coulomb interactions were calculated by using 2D-PME and 3D-PME methods, respectively. Effect of the infinite replicas in the vertical direction to the microarray surface in 3D periodic system was examined based on the results of the 3D system with 2D periodicity. Comparison of the computational efficiency and accuracy between the 2D-PME and 3D-PME methods revealed the availability of the 2D-PME method.
Nanotech 2004 Conference Technical Program Abstract