Paper Citing NAMD - Abstract
Yamamoto, Takenori; Uda, Tsuyoshi; Yamasaki, Takahiro; Ohno, Takahisa
Hydration effect on the optical property of a DNA fiber: First-principles and molecular dynamics studies
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:9300-9311, 2010
We have studied the theoretical hydration effect on the optical property of a deoxyribonucleic acid (DNA) double helix fiber. First-principles electronic structure and molecular dynamics simulations reveal that the electronic structure of the DNA fiber varies according to the amount of hydration or the relative humidity. We show that ultraviolet optical conductivity is influenced by hydration structure and DNA deformation, and our findings agree with other theoretical results and experimental observations. Infrared (IR) optical conductivity is estimated by the molecular dynamics approach. The humidity dependence of optical conductivity due to dipole relaxation of water is in close agreement with experimental observations. The theoretical IR absorption spectrum due to DNA vibrations agrees with the experimental spectrum. We discuss deformation and screening effects of the DNA fiber on humidity dependence of the optical spectra.
