Title :
Parallel Monte Carlo study on caffeine-DNA interaction in aqueous solution
Author :
Kalugin, M.D. ; Teplukhin, A.V.
Author_Institution :
Inst. of Syst. Programming, Russian Acad. of Sci., Moscow, Russia
Abstract :
Monte Carlo simulation of the caffeine-DNA interaction in aqueous solution at room temperature was carried out using parallel calculations on supercomputer. Very large simulation boxes were used containing superhelical B-DNA fragment surrounded by caffeine and water molecules. The most probable binding sites of caffeine molecules on the DNA surface as well as structural features of the respective caffeine-DNA complexes were revealed for several solutions´ concentrations.
Keywords :
DNA; Monte Carlo methods; biology computing; molecular biophysics; parallel algorithms; aqueous solution; binding sites; caffeine-DNA interaction; parallel Monte Carlo simulation; superhelical B-DNA fragment; Aggregates; Computational modeling; Computer simulation; DNA; Drugs; Geometry; Mathematical programming; Monte Carlo methods; Sampling methods; Temperature;
Conference_Titel :
Parallel & Distributed Processing, 2009. IPDPS 2009. IEEE International Symposium on
Conference_Location :
Rome
Print_ISBN :
978-1-4244-3751-1
Electronic_ISBN :
1530-2075
DOI :
10.1109/IPDPS.2009.5160925
