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

The free rigid body dynamics: generalized versus classic

In this paper we analyze the normal forms of a general quadratic Hamiltonian system defined on the dual of the Lie algebra $\mathfrak{o}(K)$ of real $K$ - skew - symmetric matrices, where $K$ is an arbitrary $3\times 3$ real symmetric matrix. A consequence of the main results is that any first-order autonomous three-dimensional differential equation possessing two independent quadratic constants of motion which admits a positive/negative definite linear combination, is affinely equivalent to the classical "relaxed" free rigid body dynamics with linear controls.Comment: 12 page

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

Two-component {CH} system: Inverse Scattering, Peakons and Geometry

An inverse scattering transform method corresponding to a Riemann-Hilbert problem is formulated for CH2, the two-component generalization of the Camassa-Holm (CH) equation. As an illustration of the method, the multi - soliton solutions corresponding to the reflectionless potentials are constructed in terms of the scattering data for CH2.Comment: 22 pages, 3 figures, draft, please send comment

Complete integrability versus symmetry

The purpose of this article is to show that on an open and dense set, complete integrability implies the existence of symmetry

The gradient of potential vorticity, quaternions and an orthonormal frame for fluid particles

The gradient of potential vorticity (PV) is an important quantity because of the way PV (denoted as $q$) tends to accumulate locally in the oceans and atmospheres. Recent analysis by the authors has shown that the vector quantity \bdB = \bnabla q\times \bnabla\theta for the three-dimensional incompressible rotating Euler equations evolves according to the same stretching equation as for \bom the vorticity and \bB, the magnetic field in magnetohydrodynamics (MHD). The \bdB-vector therefore acts like the vorticity \bom in Euler's equations and the \bB-field in MHD. For example, it allows various analogies, such as stretching dynamics, helicity, superhelicity and cross helicity. In addition, using quaternionic analysis, the dynamics of the \bdB-vector naturally allow the construction of an orthonormal frame attached to fluid particles\,; this is designated as a quaternion frame. The alignment dynamics of this frame are particularly relevant to the three-axis rotations that particles undergo as they traverse regions of a flow when the PV gradient \bnabla q is large.Comment: Dedicated to Raymond Hide on the occasion of his 80th birthda

Finite Size Polyelectrolyte Bundles at Thermodynamic Equilibrium

We present the results of extensive computer simulations performed on solutions of monodisperse charged rod-like polyelectrolytes in the presence of trivalent counterions. To overcome energy barriers we used a combination of parallel tempering and hybrid Monte Carlo techniques. Our results show that for small values of the electrostatic interaction the solution mostly consists of dispersed single rods. The potential of mean force between the polyelectrolyte monomers yields an attractive interaction at short distances. For a range of larger values of the Bjerrum length, we find finite size polyelectrolyte bundles at thermodynamic equilibrium. Further increase of the Bjerrum length eventually leads to phase separation and precipitation. We discuss the origin of the observed thermodynamic stability of the finite size aggregates

Lagrangian Reduction, the Euler--Poincar\'{e} Equations, and Semidirect Products

There is a well developed and useful theory of Hamiltonian reduction for semidirect products, which applies to examples such as the heavy top, compressible fluids and MHD, which are governed by Lie-Poisson type equations. In this paper we study the Lagrangian analogue of this process and link it with the general theory of Lagrangian reduction; that is the reduction of variational principles. These reduced variational principles are interesting in their own right since they involve constraints on the allowed variations, analogous to what one finds in the theory of nonholonomic systems with the Lagrange d'Alembert principle. In addition, the abstract theorems about circulation, what we call the Kelvin-Noether theorem, are given.Comment: To appear in the AMS Arnold Volume II, LATeX2e 30 pages, no figure

Tilting mutation of weakly symmetric algebras and stable equivalence

We consider tilting mutations of a weakly symmetric algebra at a subset of simple modules, as recently introduced by T. Aihara. These mutations are defined as the endomorphism rings of certain tilting complexes of length 1. Starting from a weakly symmetric algebra A, presented by a quiver with relations, we give a detailed description of the quiver and relations of the algebra obtained by mutating at a single loopless vertex of the quiver of A. In this form the mutation procedure appears similar to, although significantly more complicated than, the mutation procedure of Derksen, Weyman and Zelevinsky for quivers with potentials. By definition, weakly symmetric algebras connected by a sequence of tilting mutations are derived equivalent, and hence stably equivalent. The second aim of this article is to study these stable equivalences via a result of Okuyama describing the images of the simple modules. As an application we answer a question of Asashiba on the derived Picard groups of a class of self-injective algebras of finite representation type. We conclude by introducing a mutation procedure for maximal systems of orthogonal bricks in a triangulated category, which is motivated by the effect that a tilting mutation has on the set of simple modules in the stable category.Comment: Description and proof of mutated algebra made more rigorous (Prop. 3.1 and 4.2). Okuyama's Lemma incorporated: Theorem 4.1 is now Corollary 5.1, and proof is omitted. To appear in Algebras and Representation Theor

The Hamiltonian structure and Euler-Poincar\'{e} formulation of the Vlasov-Maxwell and gyrokinetic systems

We present a new variational principle for the gyrokinetic system, similar to the Maxwell-Vlasov action presented in Ref. 1. The variational principle is in the Eulerian frame and based on constrained variations of the phase space fluid velocity and particle distribution function. Using a Legendre transform, we explicitly derive the field theoretic Hamiltonian structure of the system. This is carried out with a modified Dirac theory of constraints, which is used to construct meaningful brackets from those obtained directly from Euler-Poincar\'{e} theory. Possible applications of these formulations include continuum geometric integration techniques, large-eddy simulation models and Casimir type stability methods. [1] H. Cendra et. al., Journal of Mathematical Physics 39, 3138 (1998)Comment: 36 pages, 1 figur