STRANDS are thin elastic solids that are visually well approximated as smooth curves, and yet possess essential physical behaviors characteristic of solid objects such as twisting. Common examples in computer graphics include: sutures, catheters, and tendons in surgical simulation; hairs, ropes, and vegetation in animation. Physical models based on spring meshes or 3D finite elements for such thin solids are either inaccurate or inefficient for interactive simulation. In this paper we show that models based on the Cosserat theory of elastic rods are very well suited for interactive simulation of these objects. The physical model reduces to a system of spatial ordinary differential equations that can be solved efficiently for typical boundary conditions. The model handles the important geometric non-linearity due to large changes in shape. We introduce Cosserat-type physical models, describe efficient numerical methods for interactive simulation of these models, and implementation results.

In this paper we give precise definitions of different, properly invariant notions of mean or average rotation. Each mean is associated with a metric in SO(3). The metric induced from the Frobenius inner product gives rise to a mean rotation that is given by the closest special orthogonal matrix to the usual arithmetic mean of the given rotation matrices. The mean rotation associated with the intrinsic metric on SO(3) is the Riemannian center of mass of the given rotation matrices. We show that the Riemannian mean rotation shares many common features with the geometric mean of positive numbers and the geometric mean of positive Hermitian operators. We give some examples with closed-form solutions of both notions of mean.

Simulating one-dimensional elastic objects such as threads, ropes or hair strands is a difficult problem, especially if material torsion is considered. In this paper, we present CORDE(french ’rope’), a novel deformation model for the dynamic interactive simulation of elastic rods with torsion. We derive continuous energies for a dynamically deforming rod based on the Cosserat theory of elastic rods. We then discretize the rod and compute energies per element by employing finite element methods. Thus, the global dynamic behavior is independent of the discretization. The dynamic evolution of the rod is obtained by numerical integration of the resulting Lagrange equations of motion. We further show how this system of equations can be decoupled and efficiently solved. Since the centerline of the rod is explicitly represented, the deformation model allows for accurate contact and self-contact handling. Thus, we can reproduce many important looping phenomena. Further, a broad variety of different materials can be simulated at interactive rates. Experiments underline the physical plausibility of our deformation model.

This article considers the design and implementation of variable-timestep methods for simulating holonomically constrained mechanical systems. Symplectic variable stepsizes are briefly discussed, we then consider time-reparameterization techniques employing a time-reversible (symmetric) integration method to solve the equations of motion. We give several numerical examples, including a simulation of an elastic (inextensible, unshearable) rod undergoing large deformations and collisions with the sides of a bounding box. Numerical experiments indicate that adaptive stepping can significantly smooth the numerical energy and improve the overall efficiency of the simulation.

Abstract. The classical Euler problem on stationary configurations of elastic rod in the plane is studied in detail by geometric control techniques as a left-invariant optimal control problem on the group of motions of a two-dimensional plane E(2). The attainable set is described, the existence and boundedness of optimal controls are proved. Extremals are parametrized by the Jacobi elliptic functions of natural coordinates induced by the flow of the mathematical pendulum on fibers of the cotangent bundle of E(2). The group of discrete symmetries of the Euler problem generated by reflections in the phase space of the pendulum is studied. The corresponding Maxwell points are completely described via the study of fixed points of this group. As a consequence, an upper bound on cut points in the Euler problem is obtained. 1.

The classical Kirchhoff elastic-rod model applied to DNA is extended to account for sequence-dependent intrinsic twist and curvature, anisotropic bending rigidity, electrostatic force interactions, and overdamped Brownian motion in a solvent. The zero-temperature equilibrium rod model is then applied to study the structural basis of the function of the lac repressor protein in the lac operon of Escherichia coli. The structure of a DNA loop induced by the clamping of two distant DNA operator sites by lac repressor is investigated and the optimal geometries for the loop of length 76 bp are predicted. Further, the mimicked binding of catabolite gene activator protein (CAP) inside the loop provides solutions that might explain the experimentally observed synergy in DNA binding between the two proteins. Finally, a combined Monte Carlo and Brownian dynamics solver for a worm-like chain model is described and a preliminary analysis of DNA loop-formation kinetics is presented.

We calculate the probability of DNA loop formation mediated by regulatory proteins such as Lac repressor (LacI), using a mathematical model of DNA elasticity. Our model is adapted to calculating quantities directly observable in Tethered Particle Motion (TPM) experiments, and it accounts for all the entropic forces present in such experiments. Our model has no free parameters; it characterizes DNA elasticity using information obtained in other kinds of experiments. It assumes a harmonic elastic energy function (or wormlike chain type elasticity), but our Monte Carlo calculation scheme is flexible enough to accommodate arbitrary elastic energy functions. We show how to compute both the “looping J factor” (or equivalently, the looping free energy) for various DNA construct geometries and LacI concentrations, as well as the detailed probability density function of bead excursions. We also show how to extract the same quantities from recent experimental data on tethered particle motion, and then compare to our model’s predictions. In particular, we present a new method to correct observed data for finite camera shutter time and other experimental effects. Although the currently available experimental data give large uncertainties, our firstprinciples predictions for the looping free energy change are confirmed to within about

. This article describes the design and implementation of a variable timestep method for simulating time-reversible constrained dynamical systems. Based on the Adaptive Verlet method of Huang and Leimkuhler [14], and the SHAKE [23] and RATTLE [1] discretizations, the new method (VRATTLE) defines a mapping of the constraint manifold which preserves the reversible structure. It achieves this through the solution of a single additional scalar nonlinear equation at each timestep, together with the equations of constraint. As a nontrivial application, we simulate the dynamics of an elastic (inextensible, unshearable) rod undergoing large deformations and collisions with the sides of a bounding box. Numerical experiments indicate that adapting the stepsize using VRATTLE can smooth the numerical energy and improve the overall efficiency of the simulation. Key words. symplectic methods, time-reversible methods, adaptive timestepping, variable stepsize methods, nonlinear elastic dynamics, rod ...

$EVWUDFW We treat certain classes of material symmetry in straight nonlinearly elastic rods in the presence of a uniform helical microstructure � In particular, we consider rods with chirality or ññhandednessòò � This is a natural setting for manufactured ropes and cables and for biological filaments such as DNA strands � First we propose a novel definition of transverse material symmetry, enabling, e�g�, a clear distinction to be made between hemitropic and isotropic rods � The former category can be realized from a simple spatial average of uniform helical symmetry � We show that hemitropic rods naturally exhibit mechanical coupling between extension and twist � Next we obtain an explicit representation theorem for the stored energy of rods with uniform helical symmetry (without averaging) � We also study rods with dihedralïhelical symmetry � This characterizes most manufactured ropes and cables, which are typically composed of two or more uniformly wound helical strands � Finally, we treat prismatic rods with transverse dihedral symmetry� 1

We present a generalized approach to stability of static equilibria of nonlinearly elastic rods, subjected to general loading, boundary conditions and constraints (of both point-wise and integral type), based upon the linearized dynamics stability criterion. Discretization of the governing equations leads to a non-standard (singular) generalized eigenvalue problem. A new efficient sparse-matrix-friendly algorithm is presented to determine its few left-most eigenvalues, which, in turn, yield stability/instability information. For conservative problems, the eigenvalue problem arising from the linearized dynamics stability criterion is also shown to be equivalent to that arising in the determination of constrained local minima of the potential energy. We illustrate the method with several examples. A novel variational formulation for extensible and unshearable rods is also proposed within the context of one of the example problems. 1