Pipelined Algorithm to Calculate Gibb’s Free Energy for Mutational Robustness

Abstract

Robustness is a fundamental property of biological systems which expresses a system’s ability to maintain function in the face of mutational or environmental challenges.. To measure the robustness of a DNA strand we calculate its energy by subtracting its initial and final state, this is also known as Gibbs Free Energy. On a typical mutational robustness algorithm, there is a great number of operations O(n^2) that must be executed per population. Because the values increment given a bigger number of generation and population, faster implementations are required to run this program. Since computations on population members are data independent, this algorithm is a good candidate for improvement by using the parallelism available in field programmable gate arrays (FPGAs).