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We investigate modifications of a stochastic polymer picture through a shift in the boundary between the system and an external environment. A conventional bead-and-spring model serving as the coarse-graining model is given by the Langevin equation for all the monomers subject to white noise. However, stochastic motion for only a tagged monomer is observed to occur in the presence of colored noise. The qualitative change in the observations arises from the boundary shift decided by the observer. The Langevin dynamics analyses interpret the colored noise as the emergence of the polymeric elastic force, resulting in additional heat in the tagged monomer observation. Being distinguished from coarse-graining based on scale separation, the projection of comparable internal degrees of freedom is also discussed in light of the fluctuation theorem and the stochastic polymer thermodynamics.
The rectification of unbiased fluctuations, also known as the ratchet effect, is normally obtained under statistical non-equilibrium conditions. Here we propose a new ratchet mechanism where a thermal bath solicits the random rotation of an asymmetri
Structural changes in giant DNA induced by the addition of the flexible polymer PEG were examined by the method of single-DNA observation. In dilute DNA conditions, individual DNA assumes a compact state via a discrete coil-globule transition, wherea
Glass transition process gets affected in ultrathin films having thickness comparable to the size of the molecules. We observe systematic broadening of glass transition temperature (Tg) as the thickness of the polymer film reduces below the radius of
We investigate the dynamics of nanoparticles in semidilute polymer solutions when the nanoparticles are comparably sized to the polymer coils using explicit- and implicit-solvent simulation methods. The nanoparticle dynamics are subdiffusive on short
The topological effects on the thermal properties of several knot configurations are investigated using Monte Carlo simulations. In order to check if the topology of the knots is preserved during the thermal fluctuations we propose a method that allo