Related papers: Why Does the Rouse Model Works at Least Satisfacto…
The internal dynamics of macro-molecular systems is characterized by widely separated time scales, ranging from fraction of ps to ns. In ordinary molecular dynamics simulations, the elementary time step dt used to integrate the equation of…
In recent past, experiments and simulations have suggested that apart from the solvent friction, friction arising from the protein itself plays an important role in protein folding by affecting the intra-chain loop formation dynamics. This…
We study the dynamics of the contact-process, one of the simplest nonequilibrium stochastic processes, taking place on a scale-free network. We consider the network topology as annealed, i.e. all links are rewired at each microscopic time…
Entropy production in stochastic mechanical systems is examined here with strict bounds on its rate. Stochastic mechanical systems include pure diffusions in Euclidean space or on Lie groups, as well as systems evolving on phase space for…
The localization kinetics of a regular block-copolymer of total length $N$ and block size $M$ at a selective liquid-liquid interface is studied in the limit of strong segregation between hydrophobic and polar segments in the chain. We…
New exact completely closed homogeneous Generalized Master Equations (GMEs), governing the evolution in time of equilibrium two-time correlation functions for dynamic variables of a subsystem of s particles (s<N) selected from N>>1…
The behavior of polymers in combined flow and electric fields underlies many manufacturing processes but remains poorly understood. To address this, we model charged polymers across scales. We extend the original Rouse model for a…
Linear polymers are represented as chains of hopping reptons and their motion is described as a stochastic process on a lattice. This admittedly crude approximation still catches essential physics of polymer motion, i.e. the universal…
Using molecular dynamics simulations, we determine the linear and nonlinear viscoelastic properties of a model polymer melt in the unentangled regime. Several approaches are compared for the computation of linear moduli, including…
We investigate theoretically a diffusion-limited reaction between a reactant attached to a Rouse polymer and an external fixed reactive site in confinement. The present work completes and goes beyond a previous study [T. Gu\'erin, O.…
Polymer Physics: Phenomenology of Polymeric Fluid Simulations is a review volume that I am writing. I anticipate it will take a while to complete, so I am supplying individual chapters when each is more-or-less completed. This Chapter…
The measured time series from complex systems are renowned for their intricate stochastic behavior, characterized by random fluctuations stemming from external influences and nonlinear interactions. These fluctuations take diverse forms,…
We consider statistical mechanical properties of the primitive chain network (PCN) model for entangled polymers from its dynamic equations. We show that the dynamic equation for the segment number of the PCN model does not reduce to the…
Motivated by renewed interest in the physics of branched polymers, we present here a complete characterization of the connectivity and spatial properties of $2$ and $3$-dimensional single-chain conformations of randomly branching polymers…
A simple analytic expression for the first cumulant of the dynamic structure factor of a polymer coil in the Rouse model is derived. The obtained formula is exact within the usual assumption of the continuum distribution of beads along the…
We study the relaxation dynamics of a coarse-grained polymer chain at different degrees of stretching by both analytical means and numerical simulations. The macromolecule is modelled as a string of beads, connected by anharmonic springs,…
We derive the stochastic equations of motion for a tracer that is tightly attached to a semiflexible polymer and confined or agitated by an externally controlled potential. The generalised Langevin equation, the power spectrum, and the…
The crossover to Rouse-like behavior for the self-diffusion constant D, the viscosity $\eta$, and the equilibrium structural statistics of n-alkanes $(6 \le n \le 66)$ is studied numerically. For small n the chains are non-Gaussian and the…
Whereas the original Boltzmann's $H$-theorem applies to elastic collisions, its rigorous generalization to the inelastic case is still lacking. Nonetheless, it has been conjectured in the literature that the relative entropy of the velocity…
We study the translocation of polymers across varying-section channels. Using systematic approximations, we derive a simplified model that reduces the problem of polymer translocation through varying-section channels to that of a point-like…