Single chain properties of polyelectrolytes in poor solvent

Using molecular dynamics simulations we study the behavior of a dilute solution of strongly charged polyelectrolytes in poor solvents, where we take counterions explicitly into account. We focus on the chain conformational properties under conditions where chain-chain interactions can be neglected, but the counterion concentration remains finite. We investigate the conformations with regard to the parameters chain length, Coulomb interaction strength, and solvent quality, and explore in which regime the competition between short range hydrophobic interactions and long range Coulomb interactions leads to pearl-necklace like structures. We observe that large number and size fluctuations in the pearls and strings lead to only small direct signatures in experimental observables like the single chain form factor. Furthermore we do not observe the predicted first order collapse of the necklace into a globular structure when counterion condensation sets in. We will also show that the pearl-necklace regime is rather small for strongly charged polyelectrolytes at finite densities. Even small changes in the charge fraction of the chain can have a large impact on the conformation due to the delicate interplay between counterion distribution and chain conformation.Comment: 20 pages, 27 figures, needs jpc.sty (included), to appear in Jour. Phys. Chem

Stretching and folding processes in the 3D Euler and Navier-Stokes equations

Stretching and folding dynamics in the incompressible, stratified 3D Euler and Navier-Stokes equations are reviewed in the context of the vector \bdB = \nabla q\times\nabla\theta where q=\bom\cdot\nabla\theta. The variable $\theta$ is the temperature and \bdB satisfies \partial_{t}\bdB = \mbox{curl}\,(\bu\times\bdB). These ideas are then discussed in the context of the full compressible Navier-Stokes equations where $q$ takes the two forms q = \bom\cdot\nabla\rho and q = \bom\cdot\nabla(\ln\rho).Comment: UTAM Symposium on Understanding Common Aspects of Extreme Events in Fluid

Continuous and discrete Clebsch variational principles

The Clebsch method provides a unifying approach for deriving variational principles for continuous and discrete dynamical systems where elements of a vector space are used to control dynamics on the cotangent bundle of a Lie group \emph{via} a velocity map. This paper proves a reduction theorem which states that the canonical variables on the Lie group can be eliminated, if and only if the velocity map is a Lie algebra action, thereby producing the Euler-Poincar\'e (EP) equation for the vector space variables. In this case, the map from the canonical variables on the Lie group to the vector space is the standard momentum map defined using the diamond operator. We apply the Clebsch method in examples of the rotating rigid body and the incompressible Euler equations. Along the way, we explain how singular solutions of the EP equation for the diffeomorphism group (EPDiff) arise as momentum maps in the Clebsch approach. In the case of finite dimensional Lie groups, the Clebsch variational principle is discretised to produce a variational integrator for the dynamical system. We obtain a discrete map from which the variables on the cotangent bundle of a Lie group may be eliminated to produce a discrete EP equation for elements of the vector space. We give an integrator for the rotating rigid body as an example. We also briefly discuss how to discretise infinite-dimensional Clebsch systems, so as to produce conservative numerical methods for fluid dynamics

Variational Principles for Lagrangian Averaged Fluid Dynamics

The Lagrangian average (LA) of the ideal fluid equations preserves their transport structure. This transport structure is responsible for the Kelvin circulation theorem of the LA flow and, hence, for its convection of potential vorticity and its conservation of helicity. Lagrangian averaging also preserves the Euler-Poincar\'e (EP) variational framework that implies the LA fluid equations. This is expressed in the Lagrangian-averaged Euler-Poincar\'e (LAEP) theorem proven here and illustrated for the Lagrangian average Euler (LAE) equations.Comment: 23 pages, 3 figure

Regularization modeling for large-eddy simulation

A new modeling approach for large-eddy simulation (LES) is obtained by combining a `regularization principle' with an explicit filter and its inversion. This regularization approach allows a systematic derivation of the implied subgrid-model, which resolves the closure problem. The central role of the filter in LES is fully restored, i.e., both the interpretation of LES predictions in terms of direct simulation results as well as the corresponding subgrid closure are specified by the filter. The regularization approach is illustrated with `Leray-smoothing' of the nonlinear convective terms. In turbulent mixing the new, implied subgrid model performs favorably compared to the dynamic eddy-viscosity procedure. The model is robust at arbitrarily high Reynolds numbers and correctly predicts self-similar turbulent flow development.Comment: 16 pages, 4 figures, submitted to Physics of Fluid

Geodesic boundary value problems with symmetry

This paper shows how left and right actions of Lie groups on a manifold may be used to complement one another in a variational reformulation of optimal control problems equivalently as geodesic boundary value problems with symmetry. We prove an equivalence theorem to this effect and illustrate it with several examples. In finite-dimensions, we discuss geodesic flows on the Lie groups SO(3) and SE(3) under the left and right actions of their respective Lie algebras. In an infinite-dimensional example, we discuss optimal large-deformation matching of one closed curve to another embedded in the same plane. In the curve-matching example, the manifold \Emb(S^1, \mathbb{R}^2) comprises the space of closed curves $S^1$ embedded in the plane $\mathbb{R}^2$. The diffeomorphic left action \Diff(\mathbb{R}^2) deforms the curve by a smooth invertible time-dependent transformation of the coordinate system in which it is embedded, while leaving the parameterisation of the curve invariant. The diffeomorphic right action \Diff(S^1) corresponds to a smooth invertible reparameterisation of the $S^1$ domain coordinates of the curve. As we show, this right action unlocks an important degree of freedom for geodesically matching the curve shapes using an equivalent fixed boundary value problem, without being constrained to match corresponding points along the template and target curves at the endpoint in time.Comment: First version -- comments welcome