Read the equation
This relation defines E_cross(i,j) in the source section “IX. 44-BOND ENERGY FUNCTIONS · E_cross(i,j)”. It specifies the displayed relationship between the named quantities or parameters. Its interpretation depends on the source’s stated variables and conditions; this record does not assign an unprovided physical or cognitive meaning to them.
Terms & definitions
The recovered passage does not supply a separate symbol table. Read the source context for the notation used in this version; familiar letters may carry different meanings in other builds.
How it works
Read E_cross(i,j) as the quantity being defined or updated by this relation.
Substitute the source-defined variables or recorded values and follow the displayed arithmetic and indexing exactly.
Use this version’s variable definitions and update order. The same symbol may be assigned a different meaning in another build.
Assumptions & limits
This source expression was recovered from the pinned code revision. Its presence does not establish that the associated program was built, run, or scientifically validated.
Original context
Read the surrounding source passage
double dd = d_k - D0_INTER;
double harmonic = 0.5 * kappa_inter_ * dd * dd;
double periodic = epsilon_ * std::cos(TWIST_ANGLE_RAD * k);
return harmonic + periodic;
}
// Cross-helix energy (Bonds 33-44) - Lennard-Jones:
// E_cross(i,j) = -ε_cross/d_{ij}⁶ + σ_cross/d_{ij}¹²
double cross_helix_energy(double d_ij) const {
double d6 = std::pow(d_ij, 6);
double d12 = d6 * d6;
return -epsilon_cross_ / d6 + sigma_cross_ / d12;
}
// 10.6 periodicity energy:
// E_10.6 = -κ_period · cos(2πN/10.6)
double periodicity_energy(int N) const {
return -kappa_period_ * std::cos(2.0 * M_PI * N / BASE_PAIRS_PER_TURN);Exact original notation
E_cross(i,j) = -ε_cross/d_{ij}⁶ + σ_cross/d_{ij}¹²