Implementing efficient concerted rotations using Mathematica and C code

Varování

Publikace nespadá pod Ekonomicko-správní fakultu, ale pod Středoevropský technologický institut. Oficiální stránka publikace je na webu muni.cz.

Autoři	TUBIANA L. JURÁSEK Miroslav COLUZZA I.
Rok publikování	2018
Druh	Článek v odborném periodiku
Časopis / Zdroj	EUROPEAN PHYSICAL JOURNAL E
Fakulta / Pracoviště MU	Středoevropský technologický institut
Citace
Doi	http://dx.doi.org/10.1140/epje/i2018-11694-7
Klíčová slova	INTRINSICALLY UNSTRUCTURED PROTEINS; MONTE-CARLO SIMULATIONS; COARSE-GRAINED MODELS; MOLECULAR-DYNAMICS; SYSTEMS; ALGORITHM
Přiložené soubory	Tubiana2018_Article_ImplementingEfficientConcerted.pdf
Popis	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.
Související projekty:	BISON - Bridging Structural Biology with Biological Synthesis and Self Assembly to Reveal Key Processes in Living Systems CERIT Scientific Cloud CEITEC 2020 Amphiphilic Peptides at Phospholipid Membranes