Working definition
Molecular computing uses chemical species, binding, reactions, synthesis, separation, or sequencing to encode and transform information. DNA computing can exploit massive molecular parallelism, but practical assessment must include material preparation, error correction, reaction time, laboratory operations, readout, waste, and instance-specific encoding—not merely the number of simultaneous molecules.
Mechanism
- Encode an instance into molecular species.
- Apply reactions and selection operations.
- Read out and verify candidate solutions.
Measurements
- Yield and error rate
- Wall-clock and laboratory effort
- Material, energy, and readout cost
Reproducibility controls
- Version hardware, software, firmware, and analysis code.
- Declare dataset, preprocessing, random seeds, and measurement boundary.
- Report repeated runs, variation, exclusions, and failed trials.
Limits and failure modes
- Wet-lab parallelism has substantial overhead.
- One encoded problem is not a programmable computer.
Mathematical connection
Formal structure without substrate erasure
Molecular candidate filtering
Represent encoded candidate solutions and the laboratory operations intended to eliminate invalid states.
Inputs
- Problem constraints
- Molecular encoding
- Reaction and selection error
Outputs
- Candidate pool
- Expected false positives
- Readout burden
Limit: The abstraction omits wet-lab preparation, reaction kinetics, material scale, contamination, sequencing, and human labor unless explicitly modeled.
Technical and governance sources
- [1]Molecular computation of solutions to combinatorial problems · Science
Establishes: A foundational experiment using molecular biology operations and DNA strands to encode and recover a solution to one small directed Hamiltonian-path instance.
Boundary: The experiment demonstrates a bounded molecular computation. It does not establish practical general-purpose DNA computing, favorable end-to-end energy or latency, autonomous operation, or scalability beyond the reported instance.