Hi Mayank,
There's nothing like that in any of the PhET common-code repositories. But if would be relatively easy to create your own.
But first... If it's important that the user sees these alerts, you might reconsider the approach that you've described. What if a user looks away from the screen and doesn't see the alert before it fades out? If the message is something that the user MUST see in order to prevent confusion, then a modal dialog, which the user has to explicitly close, is probably most appropriate. That said...
For the dialog, you could either use sun.Dialog, or scenery-phet.OopsDialog. Dialog is very general, the base class used for all dialogs. OopsDialog is intended for notifying the user when something has gone wrong ("Oops! ...") but you can change the message and the image. Dialog demos are in sun/js/demo/DialogsScreenView.js. OopsDialog demo is in scenery-phet/js/demo/DialogsScreenView.js.
PhET currently supports only modal dialogs, which dim the rest of the screen and make it impossible to interact with the sim while it's displayed. If you want something different, you could use a sun.Panel and create your own "information popup". This approach might be more appropriate for an "alert" that allows the user to keep interacting with the sim, and then fades out.
For fading out the alert, see the PhET twixt repository. This is PhET's animation library, and it includes classes for fading things out. Run twixt/twixt_en.html and see twixt/js/demo/ for examples. There are additional examples in many of the PhET sims, search for "twixt/js/" in .js files. If you use twixt, not that you'll need to add it to package.json, then run "grunt update", because it is not one of the libraries used by all PhET sims.
I hope this helps!
Chris Malley
PixelZoom, Inc.