Detailed Information on Publication Record
2018
Implementing efficient concerted rotations using Mathematica and C code
TUBIANA, L., Miroslav JURÁSEK and I. COLUZZABasic 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
Language
English
Type of outcome
Článek v odborném periodiku
Country of publisher
United States of America
Confidentiality degree
není předmětem státního či obchodního tajemství
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.
Změněno: 7/9/2020 17:50, RNDr. Daniel Jakubík
Abstract
V originále
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.