The Trie isn't needed anymore as it provided by the VM

package.json

@@ -10,7 +10,6 @@
     "es6-shim": "^0.35.1",
     "ethereumjs-block": "^1.2.2",
     "ethereumjs-vm": "^1.4.0",
-    "merkle-patricia-tree": "^2.1.2",
     "ethereumjs-util": "^4.4.0",
     "ethereumjs-tx": "^1.1.1",
     "ethereumjs-abi": "^0.6.1",

src/universal-dapp.js

@@ -1,6 +1,5 @@
 var $ = require('jquery');
 var EthJSVM = require('ethereumjs-vm');
-var Trie = require('merkle-patricia-tree');
 var ethJSUtil = require('ethereumjs-util');
 var EthJSTX = require('ethereumjs-tx');
 var ethJSABI = require('ethereumjs-abi');
@@ -24,8 +23,7 @@ function UniversalDApp (contracts, options) {
         this.accounts = {};
 
         this.BN = ethJSUtil.BN;
-        this.stateTrie = new Trie();
+        this.vm = new EthJSVM(null, null, { activatePrecompiles: true });
-        this.vm = new EthJSVM(this.stateTrie, null, { activatePrecompiles: true });
 
         this.addAccount('3cd7232cd6f3fc66a57a6bedc1a8ed6c228fff0a327e169c2bcc5e869ed49511');
         this.addAccount('2ac6c190b09897cd8987869cc7b918cfea07ee82038d492abce033c75c1b1d0c');