A new computational machine is invented, called a clock machine, that is a novel alternative to computing machines (digital computers) based on logic gates. In an embodiment, computation is performed with one or more clock machines that use time. In an embodiment, a cryptographic cipher is implemented with random clock machines, constructed from a non-deterministic process, wherein the compiled set of instructions (i.e., the implementation of the cryptographic procedure) is distinct on each device or chip that executes the cryptographic cipher. In an embodiment, by using a different set of clock machines to execute two different instances of the same cryptographic procedure, each execution of a procedure looks different to malware that may try to infect and subvert the cryptographic procedure. This cryptographic process also makes timing attacks more challenging. In an embodiment, a detailed implementation of the Midori cipher with random clock machines is described.