All the Nodes are assigned with Negative charges.
All but the bigger Node have same negative charge. The Bigger node has a bigger negative charge and so it repels more.
Try to drag the bigger node nearer to other nodes
Modified http://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js to a secure url
https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js