The newly developed methods of quantum dynamical manifold theory (QDMT) are used to determine a theory of the differential geometry and topology of the quantum dynamical manifold of the hydrogen nuclear‐electron system. This provides an ab initio theory of the structure of nuclear‐atomic system including the quarks, gluons, and (W+,Z0,W−) in the proton and the atomic orbital electron in a way that treats the strong, electromagnetic, weak, and gravitational forces from a unified QDMT viewpoint. The calculations proposed resemble self‐consistent Green's function ones in Fourier space. The quasi‐particles provide the basis for computing the globally defined connection needed for determining the self‐consistent gauge potentials. This approach allows the simultaneous determination of coupling constants and masses along with the quasi‐particle amplitudes. All integrals needed can be analytically computed using a Gaussian‐type orbital basis. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 80: 369–393, 2000