Lecture 7 - Molecular Computing/Nanobots

Question 1

What is DNA?

Answer 1

Deoxyribonucleic acid

Question 2

Four nucleotides that make up DNA?

Answer 2

Adenine, Guanine, Thymine, and Cytosine.

Question 3

What are two huge advantages of using DNA as storage?

Answer 3

Durability - designed for the future and not expected to ever be out of functionality (unlike floppy disks etc)
Storage size - The theoretical limit of storage using DNA is above 1 EB/mm3 (A lot of memory in a tiny space)

Question 4

One disadvantage of DNA storage?

Answer 4

Access time is extremely high relative to other storage devices

Question 5

Three pros of DNA computing?

Answer 5

Information density - With 1 LB of DNA you have more computing power than all the computers ever made (apparently)
Parallel Processing - Good to solve complex problems quickly
Low Power - The only power needed it to keep DNA from denaturing

Question 6

Cons of DNA computing?

Answer 6

Expensive
Error prone and sometimes difficult to reproduce
Application specific - hard to engineer - and hard to understand output
Simple problems are better solved with a regular computer
Manual intervention is often required

Question 7

How can you use DNA computing to solve the travelling salesman problem?

Answer 7

Chain of nucleotides code for a chain of cities, these are then put in a test tube and replicated to come up with millions of different sequences. The right answer will be one of the sequences (but will need to be analysed via a computer, i think)

Question 8

What is MAYA made up of?

Answer 8

X AND Y ANDNOT Z logic gates

Question 9

What do the logic gates in MAYA do?

Answer 9

Perform Boolean logical operations on more than one input to produce an output

Question 10

What can a single DNA molecule provide for a molecular automaton?

Answer 10

The input data and all of the necessary fuel for the molecular automaton

Question 11

Chemical Computation:

f(x1)=2x1

Answer 11

X1 -> Y + Y

Question 12

Chemical Computation:

min(x1,x2)

Answer 12

X1+X2 -> Y

This shows the minimum as the amount of Y that can be produced is constrained to the minimum amount of X1 and X2

Question 13

Chemical Computation:

X1+X2

Answer 13

X1 -> Y

X2 -> Y

Question 14

Chemical Computation:

Parity of X1

Answer 14

X1+N->Y
X1+Y-> N
My understanding is that this gives the parity by:
if you have even amounts of X1 you will get equal amounts of Y and N.
If you have odd amounts of X1 then you will end up with more Y than N or vice versa

Question 15

Chemical Computation:

X1 > X2

Answer 15

X1 + Y -> N
X2 + N -> Y
If one is bigger than the other then there will be a halt in reactions as they may run out of X2 and thus Y and can no longer produce N etc

Question 16

Intended Learning Outcomes

Answer 16

1) Know of examples of DNA computing.
2) Know the pros and cons of DNA computing compared
to traditional computing.
3) List applications of DNA computing
4) Write out Chemical Reaction Networks

Question 17

If you were to put a book into DNA storage how would you be able to piece information together sequentially?

Answer 17

The DNA sequence which codes for a particular section comes with an address of where it fits.

Question 18

What is used to replicate DNA molecules?

Answer 18

Polymersae chain reaction

Question 19

How to make sure your DNA sequence is of the right length?

Answer 19

Use gel electrophoresis

Question 20

Examples of DNA computing

Answer 20

Chess
Travelling salesman
tic tac toe

Question 21

How does DNA chess work? (basic algorithm)

Answer 21

1. Create all logical statements
2. Destroy chains which contain illegal statments
3. Read output (remaining chains are legal)

Question 22

What is DNA origami?

Answer 22

Using knowledge of how different strands of DNA bind together to create shapes

Question 23

What are some advantages of nanobots for cancer treatment?

Answer 23

Better targeted drug delivery

Better identification of tumours

Question 24

What done to some nanobots to allow for better cell penetration into tumours?

Answer 24

Encapsulate the nanobots in a non-sticky case