The key to this problem is that the physical sciences produce models of the world; they do not access the world as such. When we talk about subatomic particles — proteins, electrons, neutrons, quarks, or what you will — we are applying concepts defined within a model that largely works to describe the events we see. We cannot see the particles directly, but we can see indirectly see effects on the world that we can attribute to these particles within this model, Therefore the particles are phenomena. In other words:
- We assert that a table is an 'object' because we can place a cup on it, and the cup won't fall through to the floor (as opposed to, say, a hologram of a table). If we were to make a table out of a perfectly transparent material, we could still assert it was an object, because we could still place a cup on it without the cup falling to the floor. The cup not falling as a phenomenal experience that points to the existence of an object.
- We assert that a quark is an 'object' because we can perform certain (highly technical) actions and produce consistent with the model that defined quarks. It doesn't matter that we can't 'see' them directly; like the transparent table, we see an effect that implies the existence of an object.
We don't really 'know' what's happening 'in reality' on the subatomic level. That's all noumena, beyond our grasp. We see certain phenomena; we build models that attempt to encapsulate that phenomena systematically; those models define arguable/argumentative objects that ostensible encapsulate meaningful elements of Ding an Sich. But there is always an insurmountable gap of knowledge between those modeled objects and Ding an Sich itself.