🔬 Core Theory

DiffBiophys is based on several foundational biophysical principles:

1. Natural Extension Reference Frame (NeRF)

NeRF converts internal coordinates (bond lengths, angles, dihedrals) to Cartesian coordinates. By using JAX, we can differentiate through this conversion to optimize protein backbones.

2. Debye Scattering

The Debye formula calculates SAXS intensity by summing interference between all atom pairs: $\(I(q) = \sum_i \sum_j f_i(q) f_j(q) \frac{\sin(qr_{ij})}{qr_{ij}}\)$ Our GPU-accelerated implementation makes this \(O(N^2)\) calculation viable for large complexes.

3. Saupe Alignment Tensor

RDCs are calculated using the Saupe tensor approach, which describes the partial alignment of a molecule in an anisotropic medium.