What would happen to the samples in the following PCR reactions ?

 I think following happens.

I guess question is what happens to samples biochemically..rather than just heat and cool down.

So, Before I go on .I assume you have DNA template......Forward and reverse oligos, polymerase and dNTPs at right amount (oh ya, buffer, mg++ too), 

then, 

lid 85deg ; Wait; Auto--> Pre heat.and lid is always at 85, while the samples are at varied temp
95deg 5min--> denature the DNA 
95deg 30 sec-->denature the DNA
40deg 60 sec-->>attach the forward and reverse oligo's , It may actually vary according to melting temp of oligo, isn't 40 too low...may get some unwanted items tooo 
72deg 30 sec-->extention , work of polymerase to extend oligo by adding DNTPs
Goto 2 rep 40 times -> repeat 40 times, so, 2**40 fragments.
72deg 5 minutes -->> final extention and stabalise 
Hold 4 deg--> hold for temporary storage, in case you don't come back in time to store the plate in refrigerator after you go for some coffee or beer......

Shiva nagar is i guess right,
40 degrees is too low for a 20 mer primer with workable proportion of GC and AT
also depends on what enzyme you are using, Taq, pfu or phusion., kappa etc  phusion requires more Tm and pfu less. In either case 40 is low

you are expected to get
1. primer binding to itself
2. more non specific product
3. no product at all

read the answers above from other users if you are looking for a basic PCR reaction mechanism

Thanks !

 @aakashconky timilai chine jasto lagyo...genetics class kasto bhai ra cha ta ..ha ha :P 

Maile pani timilai ekchoti Mai Chine, Jaso taso chali ra cha !