Speaker
Description
Folding or collapse transitions are prominent examples of rare events, during which a biomolecule (protein or polymer) transforms from one stable state to another. The transition is typically few orders of magnitude faster than the lifetime of the stable states, resulting in poor sampling efficiency of direct MD simulations. In contrast to well defined protein native fold, rich ensemble of globular states must be considered for polymers. Moreover traditional variables used in polymer physics describe polymer collapse pathways only crudely. Consequently, one of the present challenges in field of smart materials is to gain the quantitative microscopic insight in the kinetics of thermoresponsive polymer transitions.
In this contribution we utilized a purely hydrophobic polymer to investigate the generic collapse transition in aqueous solutions 1. Employing long direct MD simulations, the high-dimensional data (hundreds of polymer state descriptors) were transformed using time-lagged independent component analysis (TICA) method into few collective variables [2]. Next, using converged replica-exchange MD low-dimensional free energy landscapes were constructed, suggesting two distinct mechanisms to overcome the barrier between the collapsed and swollen state (see black, and gray routes in the Figure 1). Pathway-specific and average kinetic properties were calculated by transition interface sampling technique [3]. This work presents a first step towards quantitative investigation of kinetic properties of role model thermoresponsive polymer PNIPAM, which quantitative force-field was developed only recently [4].
References:
1) Athawale M.V.; Goel G.; Ghosh T.; Truskett T.M.; Garde S.; Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water, PNAS 2007, 104, 733-738.
2) Noe F.; http://docs.markovmodel.org/lecture_tica.html
3) Dellago, C.; Bolhuis, P. G.; Csajka, F. S.; Chandler, D.; Transition path sampling and the calculation of rate constants. The Journal of Chemical Physics 1998, 108, 1964–1977.
4) Palivec, V; Zadrazil, D.; Heyda, J; All-atom REMD simulation of poly-N-isopropylacrylamide thermodynamics in water: a model with a distinct 2-state behavior. 2018, arXiv:1806.05592
Figure 1
Free energy landscape in two major collective variables constructed by TICA. Two distinct collapse pathways, depicted in black and gray, are shown along with polymer configurations.
