docs: updated inrenal structure part (#4047)

* Update README.md

* Update packages/vm/README.md

Co-authored-by: acolytec3 <[email protected]>

* Update README.md

* Update packages/vm/README.md

---------

Co-authored-by: acolytec3 <[email protected]>
Co-authored-by: Scorbajio <[email protected]>

Author: 3 people

packages/vm/README.md

@@ -373,8 +373,8 @@ The following loggers are currently available:
 | Logger      | Description                                                        |
 | ----------- | ------------------------------------------------------------------ |
 | `vm:block`  | Block operations (run txs, generating receipts, block rewards,...) |
-| `vm:tx`     |  Transaction operations (account updates, checkpointing,...)       |
-| `vm:tx:gas` |  Transaction gas logger                                            |
+| `vm:tx`     |  Transaction operations (account updates, checkpointing,...)       |
+| `vm:tx:gas` |  Transaction gas logger                                            |
 | `vm:state`  | StateManager logger                                                |
 
 Note that there are additional EVM-specific loggers in the [@ethereumjs/evm](https://github.com/ethereumjs/ethereumjs-monorepo/tree/master/packages/evm) package.
@@ -413,20 +413,32 @@ DEBUG=ethjs,vm:tx,vm:evm,vm:ops:sstore,vm:*:gas tsx test.ts
 
 ## Internal Structure
 
-The VM processes state changes at many levels.
-
-- **runBlockchain**
-  - for every block, runBlock
-- **runBlock**
-  - for every tx, runTx
-  - pay miner and uncles
-- **runTx**
-  - check sender balance
-  - check sender nonce
-  - runCall
-  - transfer gas charges
-
-TODO: this section likely needs an update.
+The VM processes state changes at several levels:
+
+- **[`runBlock`](./src/runBlock.ts)**: Processes a single block.
+  - Performs initial setup: Validates hardfork compatibility, sets the state root (if provided), applies DAO fork logic if necessary.
+  - Manages state checkpoints before and after processing.
+  - Iterates through transactions within the block:
+    - For each transaction, calls `runTx`.
+  - Processes withdrawals (post-Shanghai/EIP-4895).
+  - Calculates and assigns block rewards to the miner (and uncles, pre-Merge).
+  - Finalizes the block state (state root, receipts root, logs bloom).
+  - Commits or reverts state changes based on success.
+- **[`runTx`](./src/runTx.ts)**: Processes a single transaction.
+  - Performs pre-execution checks: Sender balance sufficient for gas+value, sender nonce validity, transaction gas limit against block gas limit, EIP activations (e.g., 2930 Access Lists, 1559 Fee Market, 4844 Blobs).
+  - Warms up state access based on Access Lists (EIP-2929/2930).
+  - Pays intrinsic gas cost.
+  - Executes the transaction code using `vm.evm.runCall` (or specific logic for contract creation).
+  - Calculates gas used and refunds remaining gas.
+  - Transfers gas fees to the fee recipient (recipient receives all pre EIP-1559, base fee is burned post EIP-1559).
+  - Generates a transaction receipt.
+  - Manages state checkpoints and commits/reverts changes for the transaction.
+- **[`vm.evm.runCall`](../evm/src/evm.ts)** (within `@ethereumjs/evm`): Executes the EVM code for a transaction (message call or contract creation).
+  - Steps through EVM opcodes.
+  - Manages memory, stack, and storage changes.
+  - Handles exceptions and gas consumption during execution.
+
+Note: The process of iterating through the blockchain (block by block) is typically managed by components outside the core VM package, such as `@ethereumjs/blockchain` or a full client implementation, which then utilize the VM's `runBlock` method.
 
 ## Development