Week 10

Question 1

What are the 4 operations on DNA?

Answer 1

Synthesis
Separation
Gel electrophoresis
Polymerase chain reaction

Question 2

What is synthesis?

Answer 2

Strand may be synthesized by a machine that is supplied with the required sequence of basis.

Question 3

What is separation?

Answer 3

Strands may be separated by a machine that is supplied with a short sequence of bases that they contain.

Question 4

What is Gel Electrophoresis?

Answer 4

Strands may be sorted by size using gel electrophoresis.

Question 5

What is PCR?

Answer 5

PCR quickly amplifies DNA by making copies of a specific region that lies between two known sequences. Note that this target sequence (which may be up to around 3k bases long) may be unknown ahead of time.

Question 6

What is the Hamilton Path problem

Answer 6

Start at node 1 to node 5, visiting each node while following the available edges. (directional) NP.

Question 7

How did the first DNA computation solve the HPP?

Answer 7

Encoding
Computing
Decoding

Question 8

What is encoding in DNA computation?

Answer 8

Each vertex is encoded as short sequences of DNA. (i.e. v1 is encoded as 2 sequences of V1 V1).

Each edge is assigned a 20 nucleotide sequence of DNA made from 2 10-nucleotide sequences that are the complements of the vertices connected.

Question 9

How do we COMPUTE the HPP?

Answer 9

To compute the HPP, simply mix the DNA pieces together in a flask, so performing massively parallel random search using strands of DNA. Use gel electrophoresis to identify sequences of length 6. Use PCR to amplify sequences from V1 to V5

Question 10

Why use DNA computing?

Answer 10

It uses a billion times less energy than silicon computers
It uses a trillion times less space than a silicon computers
It has the ability to self-assemble
It is easily available and cheap.
Living organisms can be used to run programs.

Question 11

What is the Calculus of Communicating systems?

Answer 11

an inactive process 0
an action followed by a process a.P
an identifier naming a process A
a choice of two processes P1+P2
a composition of two processes P1|P2
a renaming of one action as another P[b/a]
a restriction removing an action P\a

Question 12

What is the Gamma language?

Answer 12

Concurrent computation should be expressed as the global result of successive applications of local independent atomic reactions.

Gamma programs are expressed as multisets with transformation rules that alter their components and structure.

Question 13

What is the Chemical Abstract machine?

Answer 13

The CHAM uses the gamma language as the basis of a semantic framework.

multisets = chemical solution
execution rules = chemical reactions

Question 14

Advantages of CHAM

Answer 14

Parallelism

Question 15

What are the components of the CHAM?

Answer 15

Solutions
Reaction rules
Laws

Question 16

What are solutions?

Answer 16

the state of the CHAM is like a chemical solution in which floating molecules are stirred by a magical mixing mechanism that allows for possible contact between them.

Question 17

What is a reaction rule?

Answer 17

A reaction rule changes the information in a solution in an irreversible way.

Question 18

What are CHAM laws?

Answer 18

A heating rule decomposes a single molecule into simpler ones, and a cooling rule recomposes a compound molecule from its components.
A cleanup is performed by a heating rule with no corresponding cooling rule.