Single polymer chains in poor solvent: Using the bond fluctuation method with explicit solvent

Abstract

We use the bond fluctuation model with explicit solvent to study single polymer chains under poor solvent conditions. Static and dynamic properties of the bond fluctuation model with explicit solvent are compared with the implicit solvent model, and the Θ-temperatures are determined for both solvent models. We show that even in the very poor solvent regime, dynamics is not frozen for the explicit solvent model. We investigate some aspects of the structure of a single collapsed globule and show that rather large chain lengths are necessary to reach the scaling regime of a dense sphere. The force-extension curve of a single polymer chain under poor solvent conditions in the fixed end-to-end distance ensemble is analyzed. We find that the transition of the tadpole conformation to the stretched chain conformation is rather smooth because of fluctuation effects, which is in agreement with recent experimental results.

Thermal Tunneling of Homopolymers through Amphiphilic Membranes

“…In Figure we show the frequency of polymer translocation, T R ≡ 1/τ, on the basis of the inverse mean first escape time. There, we also include simulation results on the number of polymer translocations detected during MC simulations. , Excellent agreement is found for all chain lengths using the diffusion constant D ∝ 1/ N of the chain and rescaling the time by a factor of order unity. The results demonstrate further that introduction of Γ ∝ N –1/3 is sufficient to reproduce the chain-length dependence as determined by the globular conformations.…”

“…Inspection of radial globule density distributions reveals that the total diameter of the diffuse surface layer can be of the order of the membrane thickness. 20,21 Length scales are not sufficiently separated to treat the polymer either as an inert sphere or as a random coil only. We note further that the interface of the globule exposes sections of fluctuating strands that obey nearly Gaussian statistics.…”

“…Polymers in the regime of interest, H ≳ 1/2, are compatible neither with the membrane core nor with solvent but found in a globular state. , In this case, the fraction of monomers exposed to the external potential decreases with the increasing chain length, N , as ∝ N –1/3 assuming an ideal spherical globule surface, and we set Γ = N –1/3 . For the interesting range of hydrophobicity 0.6 ≤ H ≤ 0.7 polymer globules are far from Θ-conditions ,, both in solvent and in the bilayer’s core, and the screened potential is too weak to break up the globule state. Nevertheless, a statistical description of polymer conformations is essential: a polymer globule does not have an ideal spherical surface but possesses shape and density fluctuations at its surface.…”

“…Nevertheless, a statistical description of polymer conformations is essential: a polymer globule does not have an ideal spherical surface but possesses shape and density fluctuations at its surface. Inspection of radial globule density distributions reveals that the total diameter of the diffuse surface layer can be of the order of the membrane thickness. , Length scales are not sufficiently separated to treat the polymer either as an inert sphere or as a random coil only. We note further that the interface of the globule exposes sections of fluctuating strands that obey nearly Gaussian statistics.…”

Crumpled globule formation during collapse of a long flexible and semiflexible polymer in poor solvent

“…28 We believe that the usage of explicit solvent and hydrodynamic interactions is very important and a key to find crumpled globule after the collapse. Sommer et al recently presented the results of the coil-to-globule transition with explicit solvent particles 31 and have shown that only explicit solvent allows to simulate polymer behavior in a very poor solvent.…”