jQuery is not using CSS 3 yet, probably due to minor issues between browsers in the way they implement custom use cases. So far, not everything is agreed, and sometimes there are errors that are very difficult to circumvent.
However, there are plugins like jQuery Transit that use CSS 3 animations / transitions, etc. With Transit, you can return to using .animate() as follows:
// Delegate .transition() calls to .animate() // if the browser can't do CSS transitions. if (!$.support.transition) $.fn.transition = $.fn.animate;
http://ricostacruz.com/jquery.transit/
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