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Implementing efficient concerted rotations using Mathematica and C code

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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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Original name Implementing efficient concerted rotations using Mathematica and C code
Authors TUBIANA, L., Miroslav JURÁSEK and I. COLUZZA.
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
Organization Středoevropský technologický institut - 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.
Changed by Changed by: RNDr. Daniel Jakubík, učo 139797. Changed: 14/3/2019 00:55.
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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Tubiana2018_Article_ImplementingEfficientConcerted.pdf   File version 26. 2. 2019

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Tue 26. 2. 2019 00:58

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  • a concrete person Mgr. Lucie Vařechová, uco 106253
  • a concrete person RNDr. Daniel Jakubík, uco 139797
  • a concrete person Mgr. Jolana Surýnková, uco 220973
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