We calculate effective Hamiltonians and effective electroweak operators with the Okubo-Lee-Suzuki formalism for two-nucleon systems. Working within a harmonic oscillator basis, first without and then with a confining harmonic oscillator trap, we demonstrate the effects of renormalization on observables calculated for truncated basis spaces. We illustrate the renormalization effects for the root-mean-square point-proton radius, electric quadrupole moment, magnetic dipole moment, Gamow-Teller transition and neutrinoless double-beta decay operator using nucleon-nucleon interactions from chiral effective field theory. Renormalization effects tend to be larger in the weaker traps and smaller basis spaces suggesting applications to heavier nuclei with transitions dominated by weakly-bound nucleons would be subject to more significant renormalization effects within achievable basis spaces.

We also develop an {\it ab initio}, non-perturbative, time-dependent basis function method to solve the nuclear structure and scattering problems in a unified manner. We apply this method to a test problem: the Coulomb excitation of a trapped deuteron by an impinging heavy ion. The states of the deuteron system are obtained by the {\it ab initio} nuclear structure calculation implementing a realistic inter-nucleon interaction with a weak external trap to localize the center of mass and to discretize the continuum. The evolution of the internal state of the deuteron system is directly solved using the equation of motion for the scattering. We analyze the excitation mechanism of the deuteron system by investigating its internal transition probabilities and observables as functions of the exposure time and the incident speed. In this investigation, the dynamics of the Coulomb excitation are revealed by the time evolution of the system's internal charge distribution.

Finally, we present the first application of the Basis Light-Front Quantization method to a simple chiral model of the nucleon-pion system as a relativistic bound state for the physical proton. The light-front mass-squared matrix of the nucleon-pion system is obtained within a truncated basis. The mass and the corresponding light-front wave function (LFWF) of the proton are computed by numerical diagonalization of the resulting mass-squared matrix. With the boost invariant LFWF, we evaluate the proton's parton distribution function and Dirac form factor. An improved model, adopting phenomenological corrections for quark contributions, is implemented to calculate the proton's Dirac form factor. The resulting Dirac form factor agrees well with the experimental data below the squared transverse momentum transfer of $0.20$ ${\rm GeV}^{2}$.