ours is a battery simulator(a model behaves like a real battery),not a charger.

By our program, after getting the current value from ADC,We calculate the pulse width sent to the Timer.By varying the pulse width
we can vary the voltage ouput.

the problem is:

say,first it senses a current value.
then it calculates the resistence.
it generates the PWM.
then our program again comes to the current sensing part.(within few micro sec.)
but time delay to generate voltage output,filtering,Scaling ,A/D conversion is much larger than the program delay(pwm generation and current sensing)

So i asked how to synchronise these time delays.