Implementing efficient concerted rotations using Mathematica and C code

  • Luca TubianaEmail author
  • Miroslav Jurásek
  • Ivan Coluzza
Open Access
Regular Article
Part of the following topical collections:
  1. Advances in Computational Methods for Soft Matter Systems


In this article we demonstrate a general and efficient metaprogramming implementation of concerted rotations using Mathematica. Concerted rotations allow the movement of a fixed portion of a polymer backbone with fixed bending angles, like a protein, while maintaining the correct geometry of the backbone and the initial and final points of the portion fixed. Our implementation uses Mathematica to generate a C code which is then wrapped in a library by a Python script. The user can modify the Mathematica notebook to generate a set of concerted rotations suited for a particular backbone geometry, without having to write the C code himself. The resulting code is highly optimized, performing on the order of thousands of operations per second.

Graphical abstract


Topical issue: Advances in Computational Methods for Soft Matter Systems 



Open Access funding provided by University of Vienna.


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Copyright information

© The Author(s) 2018

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Authors and Affiliations

  • Luca Tubiana
    • 1
    Email author
  • Miroslav Jurásek
    • 2
    • 3
  • Ivan Coluzza
    • 4
  1. 1.Computational Physics DepartmentUniversity of ViennaViennaAustria
  2. 2.Faculty of ScienceMasaryk UniversityBrnoCzech Republic
  3. 3.CEITEC - Central European Institute of TechnologyBrnoCzech Republic
  4. 4.CIC biomaGUNE Parque Cientfico y Tecnolgico de GipuzkoaDonostia / San Sebastin, GipuzkoaSpain

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