Note that due to US laws, we are not able to discuss the implementation of AES in this forum. However, your question does not depend upon the implementation of AES, so it can be discussed.
You will need to pack your bits together into 8 bit bytes and encrypt the sequence of bytes; then unpack the sequence of encrypted bytes to form a sequence of bits.
ByteVector = bin2dec( char(reshape(BitVector, 8, []).' + '0') );
But first you have to pad BitVector out to a multiple of 8 bits.
Then you can encrypt ByteVector. Then afterwards
EncryptedBitVector = reshape( dec2bin( EncryptedByteVector, 8) .' - '0', 1, [])
This will almost certainly be longer than the original vector due to the way that AES works.
