problem whit pause command

hi I need control relay using microcontroller. mirocontroller accept to byte. first pin_number and second pin_value. this is the matlab code

% % the micro controller just take the Pin_Number and Pin_value, and assign  Pin_value to Pin_Number
Active=1;
Deactive=0;
S=serial(COM3);
fopen(S);
%%%%%%%
if (hObject,'value') ; %%if user  prees start(command) botton;

PinNumber=get(handles.popup_PinNumber,'value');  %%get PinNumber from an popupmenu in GUI  {8 9  or 10}
Active_TIME=get(handles.popup_Active_TIME,'value');  %%get  Active_TIME the time from an popupmenu in GUI  { 10 20 30 40 50 }
%%command to microcontroller to active pin
fwrite(S,pin); 
fwrite(S,Active); %%0=Pin_
%%waite for Active_TIME
pause(Active_TIME);
%%command to microcontroller to deactive pin
fwrite(S,pin); 
fwrite(S,Deactive)
end

the main code is a GUI and i supress that hear to essentially parts. my problem is that i can't control 2 pin in a same time. in otherwords, the program stop until the Active_TIME become end. I know that the PAUSE() command cause this problem but i have not any replacement solution. any idea can be very helpful. tnx.