Watanabe T. – TechConnect Briefs

Phonon Scattering in Doped Silicon by Molecular Dynamics Simulation

Yao M., Watanabe T., Phillpot S.R., Schelling P.K., Keblinski P., Cahill D.G., University of Florida, US

Molecular dynamics simulation is used to study the scattering of phonon wave packets of well–defined frequency . The simulation system is 22 unit cells in the direction normal to phonon propagation and 3000 unit cells [...]

DNA and Estrogen Receptor Interaction Revealed by the Fragment Molecular Orbital Method -Implementation of SCF Convergence-

Watanabe T., Inadomi Y., Tanaka S., Nagashima U., National Institute of Advanced Industrial and Science and Technology, JP

The fragment molecular orbital (FMO) method was applied to evaluate the interaction between estrogen response element (ERE) in DNA and DNA binding domain (DBD) of estrogen receptor (ER). In order to calculate the whole electronic [...]

Molecular Simulation of DNA Microarrays – an Application of 2D particle mesh Ewald algorithm

Watanabe T., Kawata M., Nagashima U., National Institute of Advanced Industrial and Science and Technology, JP

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 [...]