Implementing efficient concerted rotations using Mathematica and C code

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Authors

TUBIANA L. JURÁSEK Miroslav COLUZZA I.

Year of publication 2018
Type Article in Periodical
Magazine / Source EUROPEAN PHYSICAL JOURNAL E
MU Faculty or unit

Central European Institute of Technology

Citation
Doi http://dx.doi.org/10.1140/epje/i2018-11694-7
Keywords INTRINSICALLY UNSTRUCTURED PROTEINS; MONTE-CARLO SIMULATIONS; COARSE-GRAINED MODELS; MOLECULAR-DYNAMICS; SYSTEMS; ALGORITHM
Attached files
Description 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.
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