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KIAM Preprint № 171, Moscow, 2018
Authors: Andreev S. S., Dbar S. A., Lacis A. O., Likhachev I. V., Plotkina E. A., Fialko N. S.
Typical structure of the program for dynamics of one-dimensional DNA molecular chain simulation and its hardware implementation
Abstract:
Many molecular dynamics simulation of one-dimensional models of DNA codes have similar and very simple structure of loops and data dependencies. Together with high computational density, this makes those tasks ideal for acceleration via hardware implementation in FPGA. But, according to the experience of the first of such implementations, the mistakes done by different implementors for the different codes are also very similar and very simple. The ways of making the hardware implementation of such codes efficient, apart from any particular code, are presented in this paper.
Keywords:
DNA molecular dynamics simulation, FPGA, hardware implementation of computations
Publication language: russian,  pages: 16
Research direction:
Programming, parallel computing, multimedia
Russian source text:
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About authors:
  • Andreev Sergey Sergeevich,  orcid.org/0000-0003-2758-9727KIAM RAS
  • Dbar Svetlana Alekseevna,  orcid.org/0000-0003-0172-5321KIAM RAS
  • Lacis Aleksey Ottovich,  orcid.org/0000-0002-9953-2087KIAM RAS
  • Likhachev Ilya Vyacheslavovich,  orcid.org/0000-0002-4926-5654KIAM RAS
  • Plotkina Elena Aronovna,  orcid.org/0000-0002-5946-3646KIAM RAS
  • Fialko Nadezhda Sergeevna,  orcid.org/0000-0001-9850-4036KIAM RAS