System and method that allow utilize machine learning algorithms to move a micro-object to a desired position are described. A sensor such as a high speed camera or capacitive sensing, tracks the locations of the objects. A dynamic potential energy landscape for manipulating objects is generated by controlling each of the electrodes in an array of electrodes. One or more computing devices are used to: estimate an initial position of a micro-object using the sensor; generate a continuous representation of a dynamic model for movement of the micro-object due to electrode potentials generated by at least some of the electrodes and use automatic differentiation and Gauss quadrature rules on the dynamic model to derive optimum potentials to be generated by the electrodes to move the micro-object to the desired position; and map the calculated optimized electrode potentials to the array to activate the electrodes.