An Overview of Variational Integrators

The purpose of this paper is to survey some recent advances in variational integrators for both finite dimensional mechanical systems as well as continuum mechanics. These advances include the general development of discrete mechanics, applications to dissipative systems, collisions, spacetime integration algorithms, AVI’s (Asynchronous Variational Integrators), as well as reduction for discrete mechanical systems. To keep the article within the set limits, we will only treat each topic briefly and will not attempt to develop any particular topic in any depth. We hope, nonetheless, that this paper serves as a useful guide to the literature as well as to future directions and open problems in the subject

Point vortices on the sphere: a case with opposite vorticities

We study systems formed of 2N point vortices on a sphere with N vortices of strength +1 and N vortices of strength -1. In this case, the Hamiltonian is conserved by the symmetry which exchanges the positive vortices with the negative vortices. We prove the existence of some fixed and relative equilibria, and then study their stability with the ``Energy Momentum Method''. Most of the results obtained are nonlinear stability results. To end, some bifurcations are described.Comment: 35 pages, 9 figure

Hamiltonian approach to hybrid plasma models

The Hamiltonian structures of several hybrid kinetic-fluid models are identified explicitly, upon considering collisionless Vlasov dynamics for the hot particles interacting with a bulk fluid. After presenting different pressure-coupling schemes for an ordinary fluid interacting with a hot gas, the paper extends the treatment to account for a fluid plasma interacting with an energetic ion species. Both current-coupling and pressure-coupling MHD schemes are treated extensively. In particular, pressure-coupling schemes are shown to require a transport-like term in the Vlasov kinetic equation, in order for the Hamiltonian structure to be preserved. The last part of the paper is devoted to studying the more general case of an energetic ion species interacting with a neutralizing electron background (hybrid Hall-MHD). Circulation laws and Casimir functionals are presented explicitly in each case.Comment: 27 pages, no figures. To appear in J. Phys.

Geometric, Variational Integrators for Computer Animation

We present a general-purpose numerical scheme for time integration of Lagrangian dynamical systems—an important computational tool at the core of most physics-based animation techniques. Several features make this particular time integrator highly desirable for computer animation: it numerically preserves important invariants, such as linear and angular momenta; the symplectic nature of the integrator also guarantees a correct energy behavior, even when dissipation and external forces are added; holonomic constraints can also be enforced quite simply; finally, our simple methodology allows for the design of high-order accurate schemes if needed. Two key properties set the method apart from earlier approaches. First, the nonlinear equations that must be solved during an update step are replaced by a minimization of a novel functional, speeding up time stepping by more than a factor of two in practice. Second, the formulation introduces additional variables that provide key flexibility in the implementation of the method. These properties are achieved using a discrete form of a general variational principle called the Pontryagin-Hamilton principle, expressing time integration in a geometric manner. We demonstrate the applicability of our integrators to the simulation of non-linear elasticity with implementation details

Discrete Lie Advection of Differential Forms

In this paper, we present a numerical technique for performing Lie advection of arbitrary differential forms. Leveraging advances in high-resolution finite volume methods for scalar hyperbolic conservation laws, we first discretize the interior product (also called contraction) through integrals over Eulerian approximations of extrusions. This, along with Cartan's homotopy formula and a discrete exterior derivative, can then be used to derive a discrete Lie derivative. The usefulness of this operator is demonstrated through the numerical advection of scalar fields and 1-forms on regular grids.Comment: Accepted version; to be published in J. FoC

Nonaffine Correlations in Random Elastic Media

Materials characterized by spatially homogeneous elastic moduli undergo affine distortions when subjected to external stress at their boundaries, i.e., their displacements \uv (\xv) from a uniform reference state grow linearly with position \xv, and their strains are spatially constant. Many materials, including all macroscopically isotropic amorphous ones, have elastic moduli that vary randomly with position, and they necessarily undergo nonaffine distortions in response to external stress. We study general aspects of nonaffine response and correlation using analytic calculations and numerical simulations. We define nonaffine displacements \uv' (\xv) as the difference between \uv (\xv) and affine displacements, and we investigate the nonaffinity correlation function $\mathcal{G} =$ and related functions. We introduce four model random systems with random elastic moduli induced by locally random spring constants, by random coordination number, by random stress, or by any combination of these. We show analytically and numerically that $\mathcal{G}$ scales as A |\xv|^{-(d-2)} where the amplitude $A$ is proportional to the variance of local elastic moduli regardless of the origin of their randomness. We show that the driving force for nonaffine displacements is a spatial derivative of the random elastic constant tensor times the constant affine strain. Random stress by itself does not drive nonaffine response, though the randomness in elastic moduli it may generate does. We study models with both short and long-range correlations in random elastic moduli.Comment: 22 Pages, 18 figures, RevTeX

Mapping of serotype-specific, immunodominant epitopes in the NS-4 region of hepatitis C virus (HCV):use of type-specific peptides to serologically differentiate infections with HCV types 1, 2, and 3

The effect of sequence variability between different types of hepatitis C virus (HCV) on the antigenicity of the NS-4 protein was investigated by epitope mapping and by enzyme-linked immunosorbent assay with branched oligopeptides. Epitope mapping of the region between amino acid residues 1679 and 1768 in the HCV polyprotein revealed two major antigenic regions (1961 to 1708 and 1710 to 1728) that were recognized by antibody elicited upon natural infection of HCV. The antigenic regions were highly variable between variants of HCV, with only 50 to 60% amino acid sequence similarity between types 1, 2, and 3. Although limited serological cross-reactivity between HCV types was detected between peptides, particularly in the first antigenic region of NS-4, type-specific reactivity formed the principal component of the natural humoral immune response to NS-4. Type-specific antibody to particular HCV types was detected in 89% of the samples from anti-HCV-positive blood donors and correlated almost exactly with genotypic analysis of HCV sequences amplified from the samples by polymerase chain reaction. Whereas almost all blood donors appeared to be infected with a single virus type (97%), a higher proportion of samples (40%) from hemophiliacs infected from transfusion of non-heat-inactivated clotting factor contained antibody to two or even all three HCV types, providing evidence that long-term exposure may lead to multiple infection with different variants of HCV

Un-reduction

This paper provides a full geometric development of a new technique called un-reduction, for dealing with dynamics and optimal control problems posed on spaces that are unwieldy for numerical implementation. The technique, which was originally concieved for an application to image dynamics, uses Lagrangian reduction by symmetry in reverse. A deeper understanding of un-reduction leads to new developments in image matching which serve to illustrate the mathematical power of the technique.Comment: 25 pages, revised versio

On the use of projectors for Hamiltonian systems and their relationship with Dirac brackets

The role of projectors associated with Poisson brackets of constrained Hamiltonian systems is analyzed. Projectors act in two instances in a bracket: in the explicit dependence on the variables and in the computation of the functional derivatives. The role of these projectors is investigated by using Dirac's theory of constrained Hamiltonian systems. Results are illustrated by three examples taken from plasma physics: magnetohydrodynamics, the Vlasov-Maxwell system, and the linear two-species Vlasov system with quasineutrality

Multisymplectic Geometry and Multisymplectic Preissman Scheme for the KP Equation

The multisymplectic structure of the KP equation is obtained directly from the variational principal. Using the covariant De Donder-Weyl Hamilton function theories, we reformulate the KP equation to the multisymplectic form which proposed by Bridges. From the multisymplectic equation, we can derive a multisymplectic numerical scheme of the KP equation which can be simplified to multisymplectic forty-five points scheme.Comment: 17 papges, 8 figure