Analytical expression of elastic rods at equilibrium under 3D strong anchoring boundary conditions

Abstract A general-purpose method is presented and implemented to express analytically one stationary configuration of an ideal 3D elastic rod when the end-to-end relative position and orientation are imposed. The mechanical equilibrium of such a rod is described by ordinary differential equations and parametrized by six scalar quantities. When one end of the rod is anchored, the analytical integration of these equations lead to one unique solution for given values of these six parameters. When the second end is also anchored, six additional nonlinear equations must be resolved to obtain parameter values that fit the targeted boundary conditions. We find one solution of these equations with a zero-finding algorithm, by taking initial guesses from a grid of potential candidates. We exhibit the symmetries of the problem, which reduces drastically the size of this grid and shortens the time of selection of an initial guess. The six variables used in the search algorithm, forces and moments at one end of the rod, are particularly adapted due to their unbounded definition domain. More than 850 000 tests are performed in a large region of configurational space, and in 99.9% of cases the targeted boundary conditions are reached with short computation time and a precision better than 10 − 5 . We propose extensions of the method to obtain many solutions instead of only one, using numerical continuation or starting from different initial guesses.

[1]  Randy C. Paffenroth,et al.  Interactive computation, parameter continuation, and visualization , 1997 .

[2]  Wilma K. Olson,et al.  The dependence of DNA tertiary structure on end conditions: Theory and implications for topological transitions , 1994 .

[3]  Jean Charles Gilbert,et al.  Numerical Optimization: Theoretical and Practical Aspects , 2003 .

[4]  Mitchell A. Berger,et al.  The writhe of open and closed curves , 2006 .

[5]  C. Hervé du Penhoat,et al.  Solution structure of a truncated anti‐MUC1 DNA aptamer determined by mesoscale modeling and NMR , 2012, The FEBS journal.

[6]  Robert J. Webster,et al.  Guiding Elastic Rods With a Robot-Manipulated Magnet for Medical Applications , 2017, IEEE Transactions on Robotics.

[7]  David Swigon,et al.  Theory of Supercoiled Elastic Rings with Self-Contact and Its Application to DNA Plasmids , 2000 .

[8]  William H. Press,et al.  Numerical recipes: the art of scientific computing, 3rd Edition , 2007 .

[9]  J. Renaud Numerical Optimization, Theoretical and Practical Aspects— , 2006, IEEE Transactions on Automatic Control.

[10]  C. Hervé du Penhoat,et al.  Nucleic acid folding determined by mesoscale modeling and NMR spectroscopy: solution structure of d(GCGAAAGC). , 2009, The journal of physical chemistry. B.

[11]  John H. Maddocks,et al.  Hamiltonian formulations and symmetries in rod mechanics , 1996 .

[12]  Sinan Haliyo,et al.  Classifications of ideal 3D elastica shapes at equilibrium , 2017 .

[13]  W. Press,et al.  Numerical Recipes: The Art of Scientific Computing , 1987 .

[14]  R. Manning A Catalogue of Stable Equilibria of Planar Extensible or Inextensible Elastic Rods for All Possible Dirichlet Boundary Conditions , 2014 .

[15]  Timothy Bretl,et al.  Quasi-static manipulation of a Kirchhoff elastic rod based on a geometric analysis of equilibrium configurations , 2014, Int. J. Robotics Res..

[16]  Liping Liu THEORY OF ELASTICITY , 2012 .

[17]  Alain Goriely,et al.  Towards a classification of Euler–Kirchhoff filaments , 1999 .

[19]  Furong Huang,et al.  Escaping From Saddle Points - Online Stochastic Gradient for Tensor Decomposition , 2015, COLT.

[20]  P. Reis,et al.  Continuation of equilibria and stability of slender elastic rods using an asymptotic numerical method , 2013 .

[21]  J. Cognet,et al.  DNA tri- and tetra-loops and RNA tetra-loops hairpins fold as elastic biopolymer chains in agreement with PDB coordinates. , 2003, Nucleic acids research.

[22]  William H. Press,et al.  Numerical Recipes 3rd Edition: The Art of Scientific Computing , 2007 .

[23]  N. Perkins,et al.  Nonlinear dynamics and loop formation in Kirchhoff rods with implications to the mechanics of DNA and cables , 2005 .

[24]  S. Antman Nonlinear problems of elasticity , 1994 .

[25]  Hideo Tsuru Equilibrium Shapes and Vibrations of Thin Elastic Rod , 1987 .

[26]  Surya Ganguli,et al.  Identifying and attacking the saddle point problem in high-dimensional non-convex optimization , 2014, NIPS.

[27]  E. Grinspun,et al.  Discrete elastic rods , 2008, SIGGRAPH 2008.

[28]  J. Thompson,et al.  Instability and self-contact phenomena in the writhing of clamped rods , 2003 .

[29]  Yves Boubenec,et al.  Whisker Contact Detection of Rodents Based on Slow and Fast Mechanical Inputs , 2017, Front. Behav. Neurosci..

[30]  N. Pugno,et al.  Serpentine locomotion through elastic energy release , 2017, Journal of The Royal Society Interface.

[31]  Klaus Schulten,et al.  Elastic Rod Model of a DNA Loop in the Lac Operon , 1999 .

[32]  S. Timoshenko,et al.  Theory of elasticity , 1975 .

[33]  David Swigon,et al.  THEORY OF THE INFLUENCE OF END CONDITIONS ON SELF-CONTACT IN DNA LOOPS , 1995 .

[34]  J. Stoer,et al.  Introduction to Numerical Analysis , 2002 .

[35]  C.J.F. Ridders,et al.  Accurate computation of F′(x) and F′(x) F″(x) , 1982 .

[36]  S. Neukirch,et al.  Competition between curls and plectonemes near the buckling transition of stretched supercoiled DNA. , 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.

[37]  P Holmes,et al.  An elastic rod model for anguilliform swimming , 2006, Journal of mathematical biology.

[38]  J. Cognet,et al.  Biopolymer Chain Elasticity: A novel concept and a least deformation energy principle predicts backbone and overall folding of DNA TTT hairpins in agreement with NMR distances. , 2003, Nucleic acids research.

[39]  S. Neukirch,et al.  The extended polar writhe: a tool for open curves mechanics , 2016 .

[40]  V.G.A. Goss,et al.  Loading paths for an elastic rod in contact with a flat inclined surface , 2016 .

[41]  Michael E. Henderson,et al.  Classification of the Spatial Equilibria of the Clamped elastica: Numerical Continuation of the Solution Set , 2004, Int. J. Bifurc. Chaos.

[42]  Joel Langer,et al.  Lagrangian Aspects of the Kirchhoff Elastic Rod , 1996, SIAM Rev..

[43]  J. Hearst,et al.  The Kirchhoff elastic rod, the nonlinear Schrödinger equation, and DNA supercoiling , 1994 .