Writing and compiling code into biochemistry.

Area of Science:

• Biochemistry
• Computational Biology
• Synthetic Biology

Background:

• High-level programming constructs are difficult to directly implement in biological systems.
• Translating computational logic into biochemical processes is a key challenge in synthetic biology.

Purpose of the Study:

• To develop a methodology for translating iterative arithmetic computations into biochemical reactions.
• To enable the synthesis of proteins that perform computational operations based on input quantities.

Main Methods:

• Generating biochemical reactions from input/output specifications for arithmetic operations (addition, subtraction, scalar multiplication).
• Implementing iterative constructs (loops) using protein quantity transfer and a clocking mechanism.
• Conceptual synthesis of abstract biochemical reactions followed by mapping to specific library reactions (compilation analogy).

Main Results:

• Demonstrated compilation of iterative functions including multiplication, exponentiation, discrete logarithms, and linear transforms.
• Validated designs through transient stochastic simulation of chemical kinetics.
• Exploration of DNA-based computation using strand displacement as a potential experimental platform.

Conclusions:

• The proposed methodology effectively translates high-level computational tasks into biochemical reaction systems.
• The approach allows for the creation of complex protein-based computations.
• This work lays the foundation for advanced DNA-based computing architectures.