Symmetry reduced dynamics of charged molecular strands

DOI10.1007/S00205-010-0305-YzbMATH Open1333.70029arXiv0901.2959OpenAlexW2008172887MaRDI QIDQ717161FDOQ717161

Authors: David C. P. Ellis, François Gay-Balmaz, D. D. Holm, Vakhtang Putkaradze, T. S. Ratiu 

Publication date: 27 September 2011

Published in: Archive for Rational Mechanics and Analysis (Search for Journal in Brave)

Abstract: Euler-Poincare equations are derived for the dynamical folding of charged molecular strands (such as DNA) modeled as flexible continuous filamentary distributions of interacting rigid charge conformations. The new feature is that the equations of motion for the dynamics of such molecular strands are nonlocal when the screened Coulomb interactions, or Lennard-Jones potentials between pairs of charges are included. These nonlocal dynamical equations are derived in the convective representation of continuum motion by using modified Euler-Poincare and Hamilton-Pontryagin variational formulations that illuminate the various approaches within the framework of symmetry reduction of Hamilton's principle for exact geometric rods. In the absence of nonlocal interactions, the equations recover the classical Kirchhoff theory of elastic rods in the spatial representation. The motion equations in the convective representation are shown to be affine Euler-Poincare equations relative to a certain cocycle. This property relates the geometry of the molecular strands to that of complex fluids. An elegant change of variables allows a direct passage from the infinite dimensional point of view to the covariant formulation in terms of Lagrange-Poincare equations. In another revealing perspective, the convective representation of the nonlocal equations of molecular strand motion is transformed into quaternionic form.

Full work available at URL: https://arxiv.org/abs/0901.2959

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Mathematics Subject Classification ID

Dynamical systems in biology (37N25) Symmetries and conservation laws, reverse symmetries, invariant manifolds and their bifurcations, reduction for problems in Hamiltonian and Lagrangian mechanics (70H33) Strings (74K05) Statistical mechanics of polymers (82D60) Hamilton's principle (70H25)

Cites Work

• Reduction in principal bundles: covariant Lagrange-Poincaré equations
• Nonholonomic mechanics and control. With the collaboration of J. Baillieul, P. Crouch, and J. Marsden. With scientific input from P. S. Krishnaprasad, R. M. Murray, and D. Zenkov.
• Lagrangian reduction by stages
• Title not available (Why is that?)
• The Euler-Poincaré equations and semidirect products with applications to continuum theories
• Title not available (Why is that?)
• Hamiltonian reduction by stages
• The Hamiltonian structure of nonlinear elasticity: The material and convective representations of solids, rods, and plates
• Kirchhoff's theory of rods
• Towards a classification of Euler–Kirchhoff filaments
• The geometric structure of complex fluids
• Semidirect Products and Reduction in Mechanics
• A new Lagrangian dynamic reduction in field theory
• A double-strand elastic rod theory
• Variational principles for spin systems and the Kirchhoff rod
• The analogy between spin glasses and Yang–Mills fluids
• Elastic rods, rigid bodies, quaternions and the last quadrature
• Title not available (Why is that?)
• Title not available (Why is that?)
• Geometric mechanics. Part II: Rotating, translating and rolling
• Nonlocal orientation-dependent dynamics of charged strands and ribbons

Cited In (34)

• A geometric formulation of Schaefer's theory of Cosserat solids
• Multisymplectic Lie group variational integrator for a geometrically exact beam in \(\mathbb{R}^3\)
• Poisson-Poincaré reduction for field theories
• Swirling fluid flow in flexible, expandable elastic tubes: variational approach, reductions and integrability
• Equivalent theories of liquid crystal dynamics
• Discrete variational Lie group formulation of geometrically exact beam dynamics
• Exact geometric theory of dendronized polymer dynamics
• Geometric theory of flexible and expandable tubes conveying fluid: equations, solutions and shock waves
• Euler-Poincaré approaches to nematodynamics
• Euler-Poincaré reduction in principal bundles by a subgroup of the structure group
• Nonlocal orientation-dependent dynamics of charged strands and ribbons
• Lagrange-Poincaré field equations
• Multisymplectic variational integrators and space/time symplecticity
• Cotangent bundle reduction and Routh reduction for polysymplectic manifolds
• A multisymplectic integrator for elastodynamic frictionless impact problems
• Variational Methods for Fluid-Structure Interactions
• Symmetry reduction, integrability and reconstruction in \(k\)-symplectic field theory
• Invariant higher-order variational problems
• Poincaré's equations for Cosserat media: application to shells
• Invariant higher-order variational problems. II
• Multisymplectic variational integrators for nonsmooth Lagrangian continuum mechanics
• On a Lagrangian reduction and a deformation of completely integrable systems
• Dirac reduction for nonholonomic mechanical systems and semidirect products
• On flexible tubes conveying fluid: geometric nonlinear theory, stability and dynamics
• Helical states of nonlocally interacting molecules and their linear stability: a geometric approach
• Hamel's formalism for classical field theories
• \(G\)-strands
• The problem of Lagrange on principal bundles under a subgroup of symmetries
• Lie-Poisson neural networks (LPNets): data-based computing of Hamiltonian systems with symmetries
• Hamel's formalism for infinite-dimensional mechanical systems
• Lagrangian reduction by stages in field theory
• Hamiltonian coupling of electromagnetic field and matter
• Dynamics of elastic strands with rolling contact
• Stochastic variational principles for dissipative equations with advected quantities

Uses Software

• APBS

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