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COMPUTATIONAL BIOPHYSICS

UNIVERSITY OF TWENTE
THE NETHERLANDS
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polymer physics amphiphilic systems rod-like colloids reaction rates
alpha-synuclein clathrin

Polymer Physics

coarse graining

An atomistic polyethylene chain and its coarse-grain representation Fully atomistic potentials have proven to be very useful in the simulation of numerous systems. They are, however, less suited for simulating larger systems on longer time scales due to their computational requirements. It then proves advantageous to describe the system on a "higher" coarse grained level, where particles represent entire groups of atoms. We have developed two systematic methods for deriving the effective interactions between particles representing large fragments of a polymer. The first approach is based on representing the structural properties on the coarse level as good as possible, while the second approach aims at reproducing the free energy of the underlying atomic system, i.e. the system that one really wants to describe, as good as possible.

entanglements

An important feature of a melt of long polymers is that the bonds of the chains can not cross each other. This seemingly simple fact has a large impact on the long time dynamics and rheology of the material. In coarse grained polymer models, where a polymer is reduced to a chain of soft particles, this effect is lost. Hence, the coarse-grained melt no longer behaves like a real melt. We have developed the TWENTANGLEMENT algorithm to re-introduce the uncrossability of chains, by explicitly keeping track of when and where chains entangle. A repulsive force is introduced for every crossed pair, to gradually drive the pair back to the uncrossed state. The effect of these entanglements on the dynamics and rheology of the system has been studied.

melt dynamics

Simulations of polyethyline (PE) melts using TWENTANGLEMENT, based on coarse-grained potentials derived from atomistic simulations of short polymers, have enabled us to calculate the rheological properties of PE melts for polymers up to 1000 carbons. The additional order in length scale relative to atomistic simulations achieves the cross-over from the non-entangled Rouse regime to the strongly entangled reptation regime. We find a diffusion coefficient scaling with chain-length to the power -2 and a viscosity scaling with the power -3.5. These results are in spectacular agreement with experiments.

Lecture notes on polymer physics

W.J. Briels Theory of polymer dynamics October 1998 (PostScript, pdf)