Programming physical realizations of quantum computers

We study effects of the physical realization of quantum computers on their logical operation. Through simulation of physical models of quantum computer hardware, we analyze the difficulties that are encountered in programming physical realizations of quantum computers. Examples of logically identical implementations of the controlled-NOT operation and Grover's database search algorithm are used to demonstrate that the results of a quantum computation are unstable with respect to the physical realization of the quantum computer. We discuss the origin of these instabilities and discuss possibilities to overcome this, for practical purposes, fundamental limitation of quantum computers.