We introduce a spectral parameter into the geometrically exact Hamiltonian equations for the elastic rod in a way that creates a Lax pair. This assures integrability and permits application of the inverse scattering transform solution method. If the method can be carried through, the solution of the original problem is recovered by setting the spectral parameter to zero.
In previous work, the dynamics of the elastic rod was recast in a Lax pair formulation, with fiducial arc length s and time t as continuous independent variables. However, the solution of these equations cannot apply directly to a system where the fiducial arc length s is a discrete variable. In this paper, we show how to discretize the continuous s variable in a way that preserves the integrability of the original system. The t parameter is not discretized, so this algorithm will be especially useful for solutions of the s-discrete and t-continuous elastic rod problem, as may occur in problems where the polymeric structure of the DNA is made explicit.
Hirotas bilinear approach is a very effective method to construct solutions for soliton systems. In terms of this method, the nonlinear equations can be transformed into linear equations, and can be solved by using perturbation method. In this paper, we study the bilinear Boussinesq equation and obtain its bilinear B{a}cklund transformation. Starting from this bilinear B{a}cklund transformation, we also derive its Lax pair and test its integrability.
We consider two infinite classes of ordinary difference equations admitting Lax pair representation. Discrete equations in these classes are parameterized by two integers $kgeq 0$ and $sgeq k+1$. We describe the first integrals for these two classes in terms of special discrete polynomials. We show an equivalence of two difference equations belonged to different classes corresponding to the same pair $(k, s)$. We show that solution spaces $mathcal{N}^k_s$ of different ordinary difference equations with fixed value of $s+k$ are organized in chain of inclusions.
We consider equations in the modified KdV (mKdV) hierarchy and make use of the Miura transformation to construct expressions for their Lax pair. We derive a Lagrangian-based approach to study the bi-Hamiltonian structure of the mKdV equations. We also show that the complex modified KdV (cmKdV) equation follows from the action principle to have a Lagrangian representation. This representation not only provides a basis to write the cmKdV equation in the canonical form endowed with an appropriate Poisson structure but also help us construct a semianalytical solution of it. The solution obtained by us may serve as a useful guide for purely numerical routines which are currently being used to solve the cmKdV eqution.
To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations in these trajectories we obtain estimates of the bend and twist persistence lengths, and the underlying bend and twist elastic moduli and couplings between them. Only on length scales beyond those associated with the spacings between the interhelix crossovers do the bending fluctuations behave like those of a worm-like chain. The obtained bending persistence lengths are much larger than that for double-stranded DNA and increase non-linearly with the number of helices, whereas the twist moduli increase approximately linearly. To within the numerical error in our data, the twist-bend coupling constants are of order zero. That the bending persistence lengths we obtain are generally somewhat higher than in experiment probably reflects both that the simulated origami have no assembly defects and that the oxDNA extensional modulus for double-stranded DNA is too large.
Yaoming Shi Dept. ofn Chemistry
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(2001)
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"A Lax Pair for the Dynamics of DNA Modeled as a Shearable and Extensible Elastic Rod"
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William Martin McClain
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