Paper Citing NAMD - Abstract
Guzman, Dora L.; Roland, Jason T.; Keer, Harindar; Kong, Yen Peng; Ritz, Thorsten; Yee, Albert; Guan, Zhibin
Using steered molecular dynamics simulations and single-molecule force spectroscopy to guide the rational design of biomimetic modular polymeric materials
POLYMER, 49:3892-3901, AUG 26 2008
This article describes results on using steered molecular dynamics (SMD) simulations and experimental single-molecule force spectroscopy (SMFS) to investigate the relationship between hydrogen bonding and mechanical stability of a series of homodimeric beta-sheet mimics. The dimers consisting of 4, 6, and 8 H-bonding sites were modeled in explicit chloroform solvent and the rupture force was studied using constant velocity SMD. The role of solvent structuring on the conformation of the dimers was analyzed and showed no significant contribution of chloroform molecules in the rupture event. The simulated stability of the dimers was validated by force data obtained with atomic force microscopy (AFM)-based SMFS in toluene. The computational model for the 8H dimer also offered insight into a possible mismatched dimer intermediate that may contribute to the lower than expected mechanical stability observed by single-molecule AFM force studies. In addition, atomic level analysis of the rupture mechanism verified the dependence of mechanical strength on pulling trajectory due to the directional nature of chemical bonding under an applied force. The knowledge gained from this basic study will be used to guide further design of modular polymers having folded nanostructures through strategic programming of weak, non-covalent interactions into polymer backbones. Published by Elsevier Ltd.
