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@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 and I. COLUZZA. Implementing efficient concerted rotations using Mathematica and C code. \textit{EUROPEAN PHYSICAL JOURNAL E}. NEW YORK: SPRINGER, 2018, vol.~41, No~7, p.~87-95. ISSN~1292-8941.
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