Paper Citing NAMD - Abstract
Luan, Binquan; Aksimentiev, Aleksei
Strain softening in stretched DNA
PHYSICAL REVIEW LETTERS, 101 Art. No. 118101, SEP 12 2008
The microscopic mechanics of DNA stretching was characterized using extensive molecular dynamics simulations. By employing an anisotropic pressure-control method, realistic force-extension dependences of effectively infinite DNA molecules were obtained. A coexistence of B and S DNA domains was observed during the overstretching transition. The simulations revealed that strain softening may occur in the process of stretching torsionally constrained DNA. The latter observation was qualitatively reconciled with available experimental data using a random-field Ising model.
