TUBIANA, L., Miroslav JURÁSEK and I. COLUZZA. Implementing efficient concerted rotations using Mathematica and C code. EUROPEAN PHYSICAL JOURNAL E. NEW YORK: SPRINGER, vol. 41, No 7, p. 87-95. ISSN 1292-8941. 2018.
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Basic information
Original name Implementing efficient concerted rotations using Mathematica and C code
Authors TUBIANA, L. (40 Austria), Miroslav JURÁSEK (203 Czech Republic, guarantor, belonging to the institution) and I. COLUZZA (724 Spain).
Edition EUROPEAN PHYSICAL JOURNAL E, NEW YORK, SPRINGER, 2018, 1292-8941.
Other information
Original language English
Type of outcome Article in a journal
Country of publisher United States of America
Confidentiality degree is not subject to a state or trade secret
RIV identification code RIV/00216224:14740/18:00101714
Organization Středoevropský technologický institut – Repository – Repository
UT WoS 000439642100001
Keywords in English INTRINSICALLY UNSTRUCTURED PROTEINS; MONTE-CARLO SIMULATIONS; COARSE-GRAINED MODELS; MOLECULAR-DYNAMICS; SYSTEMS; ALGORITHM
Links GA17-11571S, research and development project. LM2015085, research and development project. LQ1601, research and development project. 692068, interní kód Repo.
Changed by Changed by: RNDr. Daniel Jakubík, učo 139797. Changed: 7/9/2020 17:50.
Abstract
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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  • a concrete person Mgr. Jolana Surýnková, uco 220973
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