J 2018

Implementing efficient concerted rotations using Mathematica and C code

TUBIANA, L., Miroslav JURÁSEK and I. COLUZZA

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

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.

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