Typical structure of the program for dynamics of one-dimensional DNA molecular chain simulation and its hardware implementation

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.