Detailed Information on Publication Record

TUBIANA, L., Miroslav JURÁSEK and I. COLUZZA. Implementing efficient concerted rotations using Mathematica and C code. EUROPEAN PHYSICAL JOURNAL E. NEW YORK: SPRINGER, 2018, vol. 41, No 7, p. 87-95. ISSN 1292-8941.

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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.

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.