From molecular dynamics to fluorescence anisotropy of fluorophores bound to oriented structures

Molecular dynamics are often used to analyze and interpret fluorophore motions in relation to observed fluorescence anisotropy measurements. The Soleillet method allows computation of fluorescence anisotropy from molecular dynamics for isotropically oriented fluorophores, but not for oriented fluorophores, such as might be used to study oriented bacterial cultures, oriented, functionalized nanotubes, or oriented, stacked planar bilayers. A numerical approach to distribute molecular dynamics systems appropriately into a larger experimental frame context, allowing prediction of time-resolved and steady-state anisotropies for fluorophores distributed in the crystal-like arrays, is presented. The classical principles of absorption selectivity and motional effects on fluorescence anisotropy for isotropically distributed fluorophores are confirmed. Fluorescence anisotropy for fluorophores distributed on oriented cylinders are predicted to show a rich cylinder-angle dependence.