The word "enitity" intrigues me: the epitet "physical" also. I assume you mean something like "a separate bunch of atoms" here, correct?
I mean physical.
Software is encoded in the state of the computer that is running it; But you can't take the software out of the computer, because it is a (large) collection of interacting states; it is not a physical object that is added to the computer, which contains the same number of atoms, electrons, quarks, etc. whether or not Windows is installed and/or running.
Patterns require physical material to exist, but they are distinct from those materials. A really simple example is a wave in the ocean - we can watch a wave from a long way off in the distance, and see it approach the shore, crest, and break. It is observably real - an "entity"; an object we can use and discuss - we can interact with it as an entity (for example by riding it on a surfboard - a surfer rides waves, not just water, otherwise millponds would be full of Californians in wetsuits).
The water molecules that are part of the wave offshore remain offshore. And the water molecules that are part of the breaking wave on the beach are totally different water molecules. The wave is a property of the materials of which it is constructed - and those materials change constantly. It is not a material object in its own right. The wave cannot continue on, up the beach and into the hinterland; Without water, the wave ceases to exist. Similarly, consciousness, thought, mind, thinking etc. are patterns in the brain - they depend on the brain to exist, and cannot survive without it; but there are no 'thoughts' that you can remove from a brain with a scalpel; There is no 'soul' that can live on after death, any more than there are ocean waves still propagating a hundred miles inland, and for the same basic reason - the things that people ascribe to souls: Consciousness, thought, mind, self, etc. - require a brain in order to exist, just as an ocean wave requires water in order to exist.