Choose normalized energy eigenstates of a time-independent Hamiltonian operator, with , and assume first that they form a complete orthonormal basis. For a pure state and an observable ,
The column index labels the input basis vector, and row labels the output component. Self-adjointness gives , so a finite example is a Hermitian matrix. A matrix element can be negative or complex; by itself it is not generally a probability. The Born rule assigns measurement probabilities using the eigenstates of , which need not be energy eigenstates. For an unbounded observable, these expressions require a suitable operator domain; a system with continuous spectrum also needs the corresponding spectral integrals.
In the Heisenberg picture, an observable without explicit time dependence has
Here is the reduced Planck constant. An emitted photon on a transition with has positive angular frequency . The sign of the array's quantum phase follows its index convention; it is not a negative measured photon frequency. The frequencies involve differences of energy levels, rather than the absolute values . Adding a constant to leaves these frequencies unchanged.
Insert the complete orthonormal basis between two linear operators:
The sum runs over intermediate states. The second identity follows by cancellation of ; it makes every term in the product acquire the same time factor . This is a useful reason for matrix multiplication: it composes the two indexed arrays consistently with the addition of transition frequencies. It does not multiply matching entries independently. Swapping and generally changes the intermediate-state sum and hence the result.
Consider an original ideal quantum system with positive scales and
Interpret as one component of an electric dipole moment, so its coupling to the corresponding electric field is the electric-dipole interaction . The gaps are , but : this interaction has no direct first-order coupling. The nonzero squared matrix elements are and . These are coupling weights; actual spectral line intensities also depend on populations and radiation factors. In particular, there is no promise that an experiment populates the upper state of every allowed transition.
Figure 1.
Matrix mechanics: three energy levels, an observable array and two nonzero coupling weights
. Original ideal three-state model. The gap exists even though its electric dipole matrix element vanishes. The plotted weights are squared couplings, not measured emission intensities. Details.
A measurement of itself has possible outcomes , since
These are eigenvalues of , not the energy eigenvalues . Moreover, although : two factors connect through . This algebraic statement does not turn into a nonzero direct coupling. Higher-order probability amplitudes for transitions require the appropriate dynamical calculation.

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