Paper Citing NAMD - Abstract
Varghese, Anoop; Vemparala, Satyavani; Rajesh, R.
Force fluctuations in stretching a tethered polymer
PHYSICAL REVIEW E, 88 Art. No. 022134, AUG 19 2013
The recently proposed fluctuation relation in unfolding forces [Phys. Rev. E 84, 060101(R) (2011)] is reexamined taking into account the explicit time dependence of the force distribution. The stretching of a tethered Rouse polymer is exactly solved and the ratio of the probabilities of positive to negative forces is shown to be an exponential in force. Extensive steered molecular dynamics simulations of unfolding of deca alanine peptide confirm the form of fluctuation relation proposed earlier, but with explicit correct time dependence of unfolding forces taken into account. From exact calculations and simulations, a linear dependence of the constant in the exponential of the fluctuation relation on average unfolding forces and inverse temperature is proposed.
