Three-dimensional quantized spaces are newly introduced. Four three-dimensional quantized spaces with total 12 dimensions are used to explain the universes including ours. The warped three-dimensional quantized spaces with the quantum time width (t=tq) (see Fig. 4B) are applied to explain the origin of the charges and evolution of the universe. Also, the warped quantized time with the quantum space size (x=xq) of the three-dimensional spaces (see Fig. 4C) is used to explain the magnetic charges. In the present work, the positive energy has the positive time momentum (E/c>0) flowing toward the positive time direction and the negative energy has the negative time momentum (-E/c<0) flowing toward the negative time direction (see section 17). The birth of our positive energy matter universe is justified from the production of the positive and negative energy warped space pair. This birth is the beginning of the physical universe with the big bang. The energy is newly defined as the space-time volume of E = ctV in the present work. It is shown that the quantum length (xq) and time (tq) of our universes are 2x_p^2 = 5.223 10-70 m and xq/c = 1.7422 10-78 s, respectively, which give the present masses of the elementary particles. The time is originated from the unobservable quantum space fluctuation. There are many physical problems which we do not know how to solve. Based on the present model, those problems are discussed in the present work. Those problems are including the matter universe question, three generations of the leptons and quarks, the quark confinement, the proton decay, Majorana particle, dark matter, dark energy, dark flow, magnetic monopoles, graviton, hadronization, time before the big bang, a black hole, relative theory, very high energy cosmic rays, hard x-rays, high temperature superconductor, quantum entanglement, quantum wave function collapse, neutrino oscillations, CP violations and proton spin crisis. Also, it is shown for the first time that the wave function in the quantum mechanics is closely connected to the energy of the warped space caused by the moving elementary particles.