I had a hard time understanding how prayer might work until I flipped the figure and ground: it’s not that prayer is mediated by run of the mill physical transactions, but vice versa.
Each entity has its causal influence upon its successors in virtue of its own urgency toward some final state of affairs, that is beyond its own powers alone to procure in itself. For, every actual event is effectually a proposal for the appropriation and adoption of its character by its subsequents as at least an element in their own. When an event behaves in way x, it effectually proposes that x is an appropriate way to behave for occasions of its own general sort in its approximate circumstances.
So, the transfer of energy between two particles can be understood as a prayer by the transferor for that transfer to occur, which is answered in the affirmative by a transferee.
Prayer then is not extraphysical. Rather, the physical is intraprecarial. We have difficulty accounting for prayer in merely physical terms because we are undertaking the project the wrong way: prayer cannot be accounted for in the economy of physics; but physics can be accounted for in the economy of prayer, as a sort thereof.
The metaphysical prolegomenae to this notion are fleshed out in How I Got Religion.