Implementing efficient concerted rotations using Mathematica and C code

Varování

Publikace nespadá pod Ústav výpočetní techniky, 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	https://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