Functionals linear in curvature and statistics of helical proteins

DOI10.1016/J.NUCLPHYSB.2004.10.062zbMATH Open1119.82342arXivcond-mat/0211415OpenAlexW2058799758MaRDI QIDQ874560FDOQ874560

A. Feoli, V. V. Nesterenko, Gaetano Scarpetta

Publication date: 10 April 2007

Published in: Nuclear Physics B (Search for Journal in Brave)

Abstract: The effective free energy of globular protein chain is considered to be a functional defined on smooth curves in three dimensional Euclidean space. From the requirement of geometrical invariance, together with basic facts on conformation of helical proteins and dynamical characteristics of the protein chains, we are able to determine, in a unique way, the exact form of the free energy functional. Namely, the free energy density should be a linear function of the curvature of curves on which the free energy functional is defined. We briefly discuss the possibility of using the model proposed in Monte Carlo simulations of exhaustive searching the native stable state of the protein chain. The relation of this model to the rigid relativistic particles and strings is also considered.

Full work available at URL: https://arxiv.org/abs/cond-mat/0211415

zbMATH Keywords

complete integrabilityprotein foldinghelicesgeometry of curvesparticles with rigidityrigid stringsemi-flexible polymers

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Statistical mechanics of polymers (82D60) Applications of variational problems in infinite-dimensional spaces to the sciences (58E50) Quantum theory (81-XX)

Cites Work

• Massless particle with rigidity as a model for the description of bosons and fermions
• Title not available (Why is that?)
• Field theory of paths with a curvature-dependent term
• Singular Lagrangians with higher derivatives
• Dynamics of relativistic particles with Lagrangians dependent on acceleration
• Title not available (Why is that?)
• Exterior differential systems and the calculus of variations
• Title not available (Why is that?)
• Title not available (Why is that?)
• Title not available (Why is that?)
• Title not available (Why is that?)
• Title not available (Why is that?)
• Complete integrability for Lagrangians dependent on acceleration in a spacetime of constant curvature
• Title not available (Why is that?)
• Classical dynamics of the rigid string from the Willmore functional
• Colloquium: Geometrical approach to protein folding: a tube picture
• Curvature and torsion of the world curve in the action of the relativistic particle
• On a model of a relativistic particle with curvature and torsion

Cited In (19)

• A conformal variational approach for helices in nature
• Elastic strips along isotropic curves in complex 3-spaces
• Helices for mathematical modelling of proteins, nucleic acids and polymers
• Geometric effects of cross sections on equilibrium of helical and twisted ribbon
• Relativistic particles with torsion in three-dimensional non-vacuum spacetimes
• Rigid particle revisited: Extrinsic curvature yields the Dirac equation
• Lagrangian curves in a 4-dimensional affine symplectic space
• A variational characterization and geometric integration for Bertrand curves
• Normal mode analysis of molecular motions in curvilinear coordinates on a non-Eckart body-frame: an application to protein torsion dynamics
• A Review of Mathematical and Mechanical Modelling in Nanotechnology
• On the energy density of helical proteins
• On the geometry and dynamics of relativistic particles in generalized Robertson-Walker spacetimes
• Curvature-dependent energies minimizers and visual curve completion
• Dynamics of relativistic particles with torsion in certain non-flat spacetimes
• EXTERNAL FIELD INFLUENCE ON SEMIFLEXIBLE MACROMOLECULES: GEOMETRIC COUPLING
• Epicycloids generating Hamiltonian minimal surfaces in the complex quadric
• HELFIT: Helix fitting by a total least squares method
• B- to Z-DNA transition probed by the Feoli's formalism for a Kirchhoff model
• The slant helix solutions of the equilibrium shape equations for the biopolymer chains

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