Related papers: Crossover from Reptation to Rouse dynamics in the …
Molecular dynamics simulations are performed to investigate the plastic response of a model glass to a local shear transformation in a quiescent system. The deformation of the material is induced by a spherical inclusion that is gradually…
The scaling of the viscosity of polymer melts is investigated with regard to the molecular weight. We present a generalization of the Rubinstein-Duke model, which takes constraint releases into account and calculate the effects on the…
We study the effect of the crowded nature of the cellular cytoplasm on the translocation of a polymer through a pore in a membrane. By systematically treating the entropic penalty due to crowding, we show that the translocation dynamics are…
Superexponential systems are characterized by a potential where dynamical degrees of freedom appear in both the base and the exponent of a power law. We explore the scattering dynamics of many-body systems governed by superexponential…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
A kinetic Monte Carlo method was used to simulate the diffusion of reptating polymer chains across the interface. A time-resolved fluorescence technique conjunction with direct energy transfer method was used to measure the extend of…
We propose a method for the theoretical investigation of polymer translocation through composite pore structures possessing arbitrarily specified geometries. Translocation through each constituent part of the composite is treated as being…
The transport of polymers with folded configurations across membrane pores is investigated theoretically by analyzing simple discrete stochastic models. The translocation dynamics is viewed as a sequence of two events: motion of the folded…
The recrossing correction to the transition state theory estimate of a thermal rate can be difficult to calculate when the energy barrier is flat. This problem arises, for example, in polymer escape if the polymer is long enough to stretch…
We study the implications of coupling Langmuir kinetics (LK) process with the dynamics of an extending lattice. The model that we consider couples dynamically extending exclusion process (DEEP) with the process of random attachment and…
We consider an arbitrarily charged polymer driven by a weak field through a gel according to the rules of the Rubinstein-Duke model. The probability distribution in the stationary state is related to that of the model in which only the head…
The Rouse model can be regarded as the standard model to describe the dynamics of a short polymer chain under melt conditions. In this contribution, we explicitly check one of the fundamental assumptions of this model, namely that of a…
Using a generalized Rubinstein-Duke model we prove rigorously that kinematic disorder leaves the prediction of standard reptation theory for the scaling of the diffusion constant in the limit for long polymer chains $D \propto L^{-2}$…
A novel principle is presented which allows for the proof of bounded weak solutions to a class of physically relevant, strongly coupled parabolic systems exhibiting a formal gradient-flow structure. The main feature of these systems is that…
We study the static and dynamical properties of a harmonically confined Rouse polymer coupled to a fluctuating correlated medium, which affect each other reciprocally during their stochastic evolution. The medium is modeled by a scalar…
Lattice-based random walk models are widely used to study populations of migrating cells with motility bias and proliferation. Crowding is typically represented by volume exclusion, where each lattice site can be occupied by at most one…
Quasielastic neutron scattering and molecular dynamics simulation data from PEO/PMMA blends found that for short times the self-dynamics of PEO chain follows the Rouse model, but at longer times past tc=1 to 2 ns it becomes slower and…
Size, morphology and distributions of pores in organic matters of shale matrix are discussed based on high resolution images from experiments in the literature. 150 nanoscale structures of the organic matters are then reconstructed by…
Polymer dynamics is analyzed through the lens of linear dimensionality reduction methods, in particular principal (PCA) and time-lagged independent component analysis (tICA). For a polymer undergoing ideal Rouse dynamics, the slow modes…
We discuss simulations of a simple model for polymer blends in the framework of the Rouse model. At odds with standard predictions, large dynamic asymmetry between the two components induces strong non-exponentiality of the Rouse modes for…