@article{33031,
   author = {Tubiana, L. and Jurásek, Miroslav and Coluzza, I.},
   article_location = {NEW YORK},
   article_number = {7},
   keywords = {INTRINSICALLY UNSTRUCTURED PROTEINS; MONTE-CARLO SIMULATIONS; COARSE-GRAINED MODELS; MOLECULAR-DYNAMICS; SYSTEMS; ALGORITHM},
   language = {eng},
   issn = {1292-8941},
   journal = {EUROPEAN PHYSICAL JOURNAL E},
   title = {Implementing efficient concerted rotations using Mathematica and C code},
   volume = {41},
   year = {2018}
}

TY  - JOUR
ID  - 33031
AU  - Tubiana, L. - Jurásek, Miroslav - Coluzza, I.
PY  - 2018
TI  - Implementing efficient concerted rotations using Mathematica and C code
JF  - EUROPEAN PHYSICAL JOURNAL E
VL  - 41
IS  - 7
SP  - 87
EP  - 87
PB  - SPRINGER
SN  - 1292-8941
KW  - INTRINSICALLY UNSTRUCTURED PROTEINS
KW  - MONTE-CARLO SIMULATIONS
KW  - COARSE-GRAINED MODELS
KW  - MOLECULAR-DYNAMICS
KW  - SYSTEMS
KW  - ALGORITHM
N2  - 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.
ER  - 

TUBIANA, L., Miroslav JURÁSEK a I. COLUZZA. Implementing efficient concerted rotations using Mathematica and C code. \textit{EUROPEAN PHYSICAL JOURNAL E}. NEW YORK: SPRINGER, roč.~41, č.~7, s.~87-95. ISSN~1292-8941. 2018.