Tension dynamics in semiflexible polymers. II. Scaling solutions and applications

In part I O. Hallatschek , preceding paper, Phys. Rev. E 75, 031905 (2007)] of this contribution, a systematic coarse-grained description of the dynamics of a weakly bending semiflexible polymer was developed. Here, we discuss analytical solutions of the established deterministic partial integro-differential equation for the spatiotemporal relaxation of the backbone tension. For prototypal experimental situations, such as the sudden application or release of a strong external pulling force, it is demonstrated that the tensile dynamics reflects the self-affine conformational fluctuation spectrum in a variety of intermediate asymptotic power laws. Detailed and explicit analytical predictions for the tension propagation and relaxation and corresponding results for common observables, such as the end-to-end distance, are obtained

High frequency non-gyrokinetic turbulence at tokamak edge parameter

First of a kind 6D-Vlasov computer simulations of high frequency ion Bernstein wave turbulence for parameters relevant to the tokamak edge show transport comparable to sub-Larmor-frequency gyrokinetic turbulence. The customary restriction of magnetized plasma turbulence studies to the gyrokinetic approximation may not be based on physics but only a practical constraint due to computational cost

Simulation of ion temperature gradient driven modes with 6D kinetic Vlasov code

With the increase in computational capabilities over the last years it becomes possible to simulate more and more complex and accurate physical models. Gyrokinetic theory has been introduced in the 1960s and 1970s in the need of describing a plasma with more accurate models than fluid equations, but eliminating the complexity of the fast gyration about the magnetic field lines. Although results from current gyrokinetic computer simulations are in fair agreement with experimental results in core physics, crucial assumptions made in the derivation make it unreliable in regimes of higher fluctuations and stronger gradient, such as the tokamak edge. With our novel optimized and scalable semi-Lagrangian solver we are able to simulate ion-temperature gradient modes with the 6D kinetic model including the turbulent saturation. After thoroughly testing our simulation code against analytical computations and gyrokinetic simulations (with the gyrokinetic code GYRO), it has been possible to show first plasma properties that go beyond standard gyrokinetic simulations. This includes the explicit description of the complete perpendicular energy fluxes and the excitation of high frequency waves (around the Larmor frequency) in the nonlinear saturation phase

Propagation and Relaxation of Tension in Stiff Polymers

We present a unified theory for the longitudinal dynamic response of a stiff polymer in solution to various external perturbations (mechanical excitations, hydrodynamic flows, electrical fields, temperature quenches ...) that can be represented as sudden changes of ambient/boundary conditions. The theory relies on a comprehensive analysis of the non--equilibrium propagation and relaxation of backbone stresses in a wormlike chain. We recover and substantially extend previous results based on heuristic arguments. Intriguing new experimental implications are pointed out.Comment: 4 pages, 3 figure

Overdamped Stress Relaxation in Buckled Rods

We present a comprehensive theoretical analysis of the stress relaxation in a multiply but weakly buckled incompressible rod in a viscous solvent. In the bulk two interesting regimes of generic self--similar intermediate asymptotics are distinguished, which give rise to two classes of approximate and exact power--law solutions, respectively. For the case of open boundary conditions the corresponding non--trivial boundary--layer scenarios are derived by a multiple--scale perturbation (``adiabatic'') method. Our results compare well with -- and provide the theoretical explanation for -- previous results from numerical simulations, and they suggest new directions for further fruitful numerical and experimental investigations.Comment: 20 pages, 12 figure

A performance portable implementation of the semi-Lagrangian algorithm in six dimensions

In this paper, we describe our approach to develop a simulation software application for the fully kinetic Vlasov equation which will be used to explore physics beyond the gyrokinetic model. Simulating the fully kinetic Vlasov equation requires efficient utilization of compute and storage capabilities due to the high dimensionality of the problem. In addition, the implementation needs to be extensibility regarding the physical model and flexible regarding the hardware for production runs. We start on the algorithmic background to simulate the 6-D Vlasov equation using a semi-Lagrangian algorithm. The performance portable software stack, which enables production runs on pure CPU as well as AMD or Nvidia GPU accelerated nodes, is presented. The extensibility of our implementation is guaranteed through the described software architecture of the main kernel, which achieves a memory bandwidth of almost 500 GB/s on a V100 Nvidia GPU and around 100 GB/s on an Intel Xeon Gold CPU using a single code base. We provide performance data on multiple node level architectures discussing utilized and further available hardware capabilities. Finally, the network communication bottleneck of 6-D grid based algorithms is quantified. A verification of physics beyond gyrokinetic theory for the example of ion Bernstein waves concludes the work

Tension dynamics in semiflexible polymers. Part I: Coarse-grained equations of motion

Based on the wormlike chain model, a coarse-grained description of the nonlinear dynamics of a weakly bending semiflexible polymer is developed. By means of a multiple scale perturbation analysis, a length-scale separation inherent to the weakly-bending limit is exploited to reveal the deterministic nature of the spatio-temporal relaxation of the backbone tension and to deduce the corresponding coarse-grained equation of motion. From this partial integro-differential equation, some detailed analytical predictions for the non-linear response of a weakly bending polymer are derived in an accompanying paper (Part II, cond-mat/0609638).Comment: 14 pages, 4 figyres. The second part of this article has the preprint no.: cond-mat/060963