Logical data is how your applications see the data, and how they query data.
In the case of a relational database, the design of tables, along with their columns and relationships, is the logical model. In other database models the logical level could be queues, collections, or any type of data structure used by applications.
But how are those data structures written to disks (and to memory)? That is the physical layer. It is the set of files written to disk to contain data, and the format used to represent data.
So what is the independence between physical and logical layers? It is the principle that states that programs which query a database don't need to know how it stored data physically. For example, an SQL query mentions table and columns, not files and bytes from that file.