Module dna 

High-performance DNA strand displacement pipeline.

Accelerates three critical hot paths from sc_neurocore.bridges.dna_mapper:

1. Sequence design — GC-balanced, homopolymer-free, orthogonal oligo generation
2. Cross-hybridization — O(n²) pairwise alignment scoring (rayon-parallelized)
3. Kinetic simulation — RK4 mass-action integrator with Arrhenius scaling

Structs

DnaGateSpec

A gate in the DNA circuit.

KineticConfig

Kinetic simulation configuration.

Enums

DnaGateType

Gate types for kinetic simulation.

Constants

ALPHABET 🔒

DEFAULT_TOEHOLD 🔒

GC_HIGH 🔒

GC_LOW 🔒

MAX_HOMOPOLYMER 🔒

R_GAS 🔒

Functions

alignment_score 🔒

Pairwise alignment score between two sequences.

arrhenius_scale 🔒

Arrhenius temperature scaling.

check_cross_hybridization

Check all pairs for dangerous cross-hybridization. Returns vec of (i, j, score) for pairs above threshold.

complement

Watson-Crick complement.

compute_k_eff 🔒

Compute effective rate constant for a gate.

design_orthogonal_set

Generate multiple orthogonal sequences.

design_sequence

Generate a GC-balanced, homopolymer-free DNA sequence.

detect_hairpins

Detect hairpins in a sequence. Returns vec of (stem_start, stem_len, loop_len).

gc_content 🔒

longest_common_substring 🔒

reverse_complement

Reverse complement.

simulate_kinetics

Run kinetic simulation, returning time traces per output.