Paper Citing NAMD - Abstract
Abolbashari, M. H.; Ameli, S.
Mechanical unfolding of titin I27 domain: Nanoscale simulation of mechanical properties based on virial theorem via steered molecular dynamics technique
SCIENTIA IRANICA, 19:1526-1533, DEC 2012
The mechanical properties of a single titin immunoglobulin-like domain (I27) are studied, based on the virial stress definition, via steered molecular dynamics simulation. Moreover, the effects of biological conditions on the obtained results are investigated. Due to different viewpoints on virial stress definition, the role of kinetic stress in virial stress definition is elucidated. The obtained Young's modulus is about 0.7 +/- 0.1 GPa. It is found that the ultimate stress decreases nonlinearly and the Young's modulus decreases almost linearly with an increase in temperature. It is observed that the mechanical properties decrease with a decrease in the strain rate. The mechanical properties are not sensitive to small unfolding forces, but they rise up with an increase in the force magnitude afterwards. Considering the kinetic stress term in calculation of virial stress increases the accuracy of the results, but does not have a significant effect on mechanical properties, especially at low temperatures. This implies that the kinetic stress term can be ignored at low temperatures. This study furnishes a basis for the I27 domain, where mechanical properties must be taken into account. (C) 2012 Sharif University of Technology. Production and hosting by Elsevier B. V. All rights reserved.
