Probabilistic Phase Space Trajectory Description for Anomalous Polymer Dynamics
Debabrata Panja
备注：
8 pages, two figures, 3 eps figure files, minor changes, supplementary material included moved to the appendix, references expanded, to appear in J. Phys.: Condens. Matter
It has been recently shown that the phase space trajectories for the anomalous dynamics of a tagged monomer of a polymer --- for single polymeric systems such as phantom Rouse, self-avoiding Rouse, Zimm, reptation, and translocation through a narrow pore in a membrane; as well as for many-polymeric system such as polymer melts in the entangled regime --- is robustly described by the Generalized Langevin Equation (GLE). Here I show that the probability distribution of phase space trajectories for all these classical anomalous dynamics for single polymers is that of a fractional Brownian motion (fBm), while the dynamics for polymer melts between the entangled regime and the eventual diffusive regime exhibits small, but systematic deviations from that of a fBm.
For reproducing the anomalous -- i.e., sub- or super-diffusive -- behavior in some stochastic dynamical systems, the Generalized Langevin Equation (GLE) has gained considerable popularity in recent years. Motivated by the question whether or not a system with anomalous dynamics can have the GLE formulation, here I consider polymer physics, where sub-diffusive behavior is commonplace. I provide an exact derivation of the GLE for phantom Rouse polymers, andby identifying polymeric response to local strains, I argue the case for the GLE formulation for self-avoiding polymers and polymer transloca…
Any first course on polymer physics teaches that the dynamics of a tagged monomer of a polymer is anomalously subdiffusive, i.e., the mean-square displacement of a tagged monomer increases as $t^α$ for some $α<1$ until the terminal relaxation time $τ$ of the polymer. Beyond time $τ$ the motion of the tagged monomer becomes diffusive. Classical examples of anomalous dynamics in polymer physics are single polymeric systems, such as phantom Rouse, self-avoiding Rouse, self-avoiding Zimm, reptation, translocation through a narrow pore in a membrane, and many-polymeric systems such as polymer melts…
We investigate a model of self-avoiding walk exhibiting a first-order coil-globule transition. This first-order nature, unravelled through the coexistence of distinct coil and globule populations, has observable consequences on the scaling properties. A thorough analysis of the size dependence of the mean radius of gyration evidences a breakdown of the plain tricritical scaling behaviour. In some regimes, anomalous exponents are observed in the transition region and logarithmic corrections arise along the coexistence curve.
The way tension propagates along a chain is a key to govern many of anomalous dynamics in macromolecular systems. After introducing the weak and the strong force regimes of the tension propagation, we focus on the latter, in which the dynamical fluctuations of a segment in a long polymer during its stretching process is investigated. We show that the response, i.e., average drift, is anomalous, which is characterized by the nonlinear memory kernel, and its relation to the fluctuation is nontrivial. These features are discussed on the basis of the generalized Langevin equation, in which the rol…
We study the translocation dynamics of a polymer chain threaded through a nanopore by an external force. By means of diverse methods (scaling arguments, fractional calculus and Monte Carlo simulation) we show that the relevant dynamic variable, the translocated number of segments $s(t)$, displays an {\em anomalous} diffusive behavior even in the {\em presence} of an external force. The anomalous dynamics of the translocation process is governed by the same universal exponent $α= 2/(2ν+2 - γ_1)$, where $ν$ is the Flory exponent and $γ_1$ - the surface exponent, which was established recently fo…
From the spread of pollutants in the atmosphere to the transmission of nutrients across cell membranes, anomalous diffusion processes are ubiquitous in natural systems. The ability to understand and control the mechanisms guiding such processes across various scales has important application to research in materials science, finance, medicine, and energetics. Here we present a numerical study of anomalous diffusion of light through a semi-crystalline polymer structure where transport is guided by random disorder and nonlocal interactions. The numerical technique examines diffusion properties i…
The translocation dynamics of a polymer chain through a nanopore in the absence of an external driving force is analyzed by means of scaling arguments, fractional calculus, and computer simulations. The problem at hand is mapped on a one dimensional {\em anomalous} diffusion process in terms of reaction coordinate $s$ (i.e. the translocated number of segments at time $t$) and shown to be governed by an universal exponent $α= 2/(2ν+2-γ_1)$ whose value is nearly the same in two- and three-dimensions. The process is described by a {\em fractional} diffusion equation which is solved exactly in the…
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We consider a polymer of length $N$ translocating through a narrow pore in the absence of external fields. Characterization of its purportedly anomalous dynamics has so far remained incomplete. We show that the polymer dynamics is anomalous until the Rouse time $τ_{R}\sim N^{1+2ν}$, with a mean square displacement through the pore consistent with $t^{(1+ν)/(1+2ν)}$, with $ν\approx0.588$ the Flory exponent. This is shown to be directly related to a decay in time of the excess monomer density near the pore as $t^{-(1+ν)/(1+2ν)}\exp(-t/τ_{R})$. Beyond the Rouse time translocation becomes diffusiv…
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Machine learning (ML) and artificial intelligence (AI) have the remarkable ability to classify, recognize, and characterize complex patterns and trends in large data sets. Here, we adopt a subclass of machine learning methods viz., deep learnings and develop a general-purpose AI tool - dPOLY for analyzing molecular dynamics trajectory and predicting phases and phase transitions in polymers. An unsupervised deep neural network is used within this framework to map a molecular dynamics trajectory undergoing thermophysical treatment such as cooling, heating, drying, or compression to a lower dimen…
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