Bio_Computing

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Bio_Computing

  1. 1. DNA COMPUTERS By V.Meera C.Meenakshi (St.Peter’s Engineering college)
  2. 2. CONTENTS <ul><li>Why DNA Computers </li></ul><ul><li>DNA-In a nut shell </li></ul><ul><li>DNA structure </li></ul><ul><li> Advantages </li></ul><ul><li>Features of DNA computers </li></ul><ul><li> Memory </li></ul><ul><li> Parallelism </li></ul><ul><li> Power Generation </li></ul><ul><li> Operations in DNA </li></ul><ul><li>Silicon Computers Vs DNA Computers <Similarities and Difference> </li></ul><ul><li>Applications </li></ul><ul><li>Conclusions </li></ul>
  3. 3. Why DNA Computers? <ul><li>Moore’s Law states that silicon microprocessors double in complexity roughly every two years. </li></ul><ul><li>To overcome the limitations of Current Computing Technology. BIO-Chips made up of DNA is used as a substitute for sillicon chips. </li></ul>
  4. 4. DNA-In a Nut Shell <ul><li>DNA -D eoxyribo N ucleic A cid </li></ul><ul><li>All organisms on this planet are made of the same type of genetic blueprint. </li></ul><ul><li>Within the cells of any organism is a substance called DNA which is a double-stranded helix of nucleotides. </li></ul><ul><li>DNA carries the genetic information of a cell.<Memory in DNA computers> </li></ul>
  5. 5. DNA Structure <ul><li>Each strand is based on 4 bases: </li></ul><ul><li>>Adenine (A) </li></ul><ul><li>>Thymine (T) </li></ul><ul><li>>Cytosine (C) </li></ul><ul><li>>Guanine (G) </li></ul>
  6. 6. DNA Structure… <ul><li>Due to the hybridization reaction, A is complementary with T and C is complementary with G. </li></ul>
  7. 7. Features Of DNA Computers <ul><li>PARALLELISM </li></ul><ul><li>The process of carrying out different operations in different strands at the same time. </li></ul><ul><li>Replication </li></ul><ul><li>Reason for Enormous parallelism of DNA computers . </li></ul>
  8. 8. Replication
  9. 9. Parallelism…… <ul><li>If forced to behave sequentially, DNA loses its appeal . </li></ul><ul><li>Eg: </li></ul><ul><li>Will doubling the clock speed or doubling </li></ul><ul><li>your RAM give you better performance? </li></ul>
  10. 10. Parallelism…… <ul><li>Proof: </li></ul><ul><li>Read and write rate of DNA: </li></ul><ul><li><DNA of Bacteria is taken as sample> </li></ul><ul><li>Case 1: If single copy of the replication enzymes to work in sequential manner. </li></ul><ul><li>Case 2: If many copies of the replication </li></ul><ul><li>enzymes to work on DNA in parallel. </li></ul>
  11. 11. Memory <ul><li>The 1 gram of DNA can hold about 1x1014 MB of data. </li></ul><ul><li>A test tube of DNA can contain trillions of strands. Each operation on a test tube of DNA is carried out on all strands in the tube in parallel ! </li></ul><ul><li>Check this out……. We Typically use </li></ul>
  12. 12. No More Viruses
  13. 13. Virus Resistance <ul><li>In DNA Computers </li></ul><ul><li>> Here viruses effects the base pairs of the DNA . </li></ul><ul><li>> There are various error correction mechanisms that autocorrects the base pairs. </li></ul><ul><li>>PCR detects a erroneous DNA strand. </li></ul><ul><li>>Err in one DNA does not affect the whole system. </li></ul><ul><li>So Adieu Anti-Virus!!! </li></ul>
  14. 14. Power Generation <ul><li>A DNA polymer molecule stores significant amount of energy relative to the same polymer broke into little pieces - its monomers. The DNA computer uses this energy to drive a useful process, namely computation . </li></ul>
  15. 15. Operations In DNA Computers… <ul><li>Logical operations in DNA computers: </li></ul><ul><li>DNA logic gates pick up various fragments </li></ul><ul><li>single of a genome as input before creating a </li></ul><ul><li>output from the fragments </li></ul>
  16. 16. Logical Operations in DNA Computers <ul><li>Typical logic gate operations can be explained as below : </li></ul><ul><li>OR: </li></ul><ul><li>- pouring together DNA solutions containing </li></ul><ul><li>specific sequences . </li></ul><ul><li>AND: </li></ul><ul><li>- Separating DNA strands according to their </li></ul><ul><li>sequences </li></ul>
  17. 17. Logical Operations in DNA Computers.. <ul><li>EX-OR: </li></ul><ul><li>- If the DNA at the input is a complementary strand they combine to give a 1. </li></ul>
  18. 18. Operations In DNA Computers <ul><li>Steps to perform the logic operations: </li></ul><ul><li>STEP 1: </li></ul><ul><li>Chemical structure of the DNA is found. </li></ul>
  19. 19. Operations In DNA Computers… <ul><li>STEP 2: </li></ul><ul><li>The DNA strands are separated and placed in a solid substrate or in a liquid. This is the reference strand . </li></ul>
  20. 20. Operations In DNA Computers… <ul><li>STEP 3: </li></ul><ul><li>Another DNA strand to which the operation is to be done is introduced. </li></ul>
  21. 21. Operations In DNA Computers… <ul><li>STEP 4: </li></ul><ul><li>After the hybridization a bond is formed between two strands which yields the result. </li></ul>
  22. 22. The truth table for DNA logic gates <ul><li>The truth table in a DNA computers uses a three-level scheme. </li></ul><ul><li>An operation is represented in terms of DNA hybridisation. </li></ul><ul><li>For each binary operation the two bit strings are represented with two different DNA single strands. </li></ul><ul><li>The first string is called the “input” and the second is the “operand”. </li></ul>
  23. 23. Truth table for DNA Computers…. <ul><li>Each bit is represented with a dinucleotide unit, and a bit string with a sequence of dinucleotides </li></ul><ul><li>Bases used in encoding are </li></ul><ul><li>>A-Adenine </li></ul><ul><li>>T-Thymine </li></ul><ul><li>>U-Uracil </li></ul><ul><li> >P-2,6-diaminopurine </li></ul>
  24. 24. Truth table encoding using “dinucleotide” bits .
  25. 25. Sample operation <ul><li>Eg: 1001 NAND 0101 </li></ul><ul><li>Input string:1001 </li></ul><ul><li>Operand :0101 </li></ul>
  26. 26. Conventional Computers Vs DNA Computers
  27. 27. Applications <ul><li>DNA fingerprinting. </li></ul><ul><li>Airline and communication routing <NP –Problem> </li></ul><ul><li>DNA chips. </li></ul><ul><li>Genetic programming. </li></ul><ul><li>Pharmaceutical applications. </li></ul><ul><li>Cracking of coded messages </li></ul>
  28. 28. NP Problem made easy <ul><li>E.g.: </li></ul><ul><li>Hamiltonian Problem </li></ul><ul><li>Statement: </li></ul><ul><li>Given a graph with directed edges, find a Hamiltonian Path, i.e. a path which starts at one node, finishes at another, and goes through all other nodes exactly once. </li></ul>
  29. 29. NP Problem made easy….. <ul><li>Edges represent non-stop flights </li></ul><ul><li>Determine whether there is a Hamiltonian Path starting in Atlanta,ending in Detroit </li></ul>
  30. 30. Steps to solve the problem <ul><li>Step 1: Encode this graph in a DNA. </li></ul>
  31. 31. Steps to solve the problem.. <ul><li>Step 2: Vertices are assigned a random DNA sequence </li></ul><ul><li>o Atlanta: ACTT GCAG </li></ul><ul><li>o Boston: TCGG ACTG </li></ul>
  32. 32. Steps to solve the problem.. <ul><li>Step 3: </li></ul><ul><li>Edges (flights) are formed by concatenating </li></ul><ul><li>the 2nd half of the originating city and the 1st </li></ul><ul><li>half of the destination city </li></ul><ul><ul><li>>Atlanta-Boston: GCAG TCGG </li></ul></ul><ul><li>Step 4: </li></ul><ul><li>Use Polymerase Chain Reaction (PCR) to </li></ul><ul><li>replicate DNA with the correct start and end </li></ul><ul><li>city. </li></ul>
  33. 33. Steps to solve the problem.. <ul><li>Step 5: </li></ul><ul><li>Put one primer on Atlanta and one primer on </li></ul><ul><li>Detroit. </li></ul><ul><li>Step 6: </li></ul><ul><li>The right answer is replicated exponentially, </li></ul><ul><li>while the wrong paths are replicated linearly or </li></ul><ul><li>not at all. </li></ul>
  34. 34. Steps to solve the problem.. <ul><li>Step 7: </li></ul><ul><li>Use gel electrophoresis to identify the molecules with the right length. </li></ul><ul><li>Step 8: </li></ul><ul><li>Finally, use affinity separation procedure to </li></ul><ul><li>weed out paths without all the cities. </li></ul>
  35. 35. Steps to solve the problem.. <ul><li>Step 9: </li></ul><ul><li>Probe molecules attached on iron balls attract </li></ul><ul><li>the correct strands; the rest is poured out. </li></ul><ul><li>Step 10: </li></ul><ul><li>If any DNA is left in the tube, it is the Hamiltonian Path. </li></ul>
  36. 36. Applications <ul><li>DNA fingerprinting. </li></ul><ul><li>Airline and communication routing <NP –Problem> </li></ul><ul><li>DNA chips. </li></ul><ul><li>Genetic programming. </li></ul><ul><li>Pharmaceutical applications. </li></ul><ul><li>Cracking of coded messages </li></ul>
  37. 37. Conclusions <ul><li>DNA computers showing enormous </li></ul><ul><li>potential, especially for medical as well </li></ul><ul><li>as data processing applications. </li></ul><ul><li>Still lots of work resources required to </li></ul><ul><li>develop it into a fully fledged product. </li></ul>
  38. 38. QUERIES???

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