Talk:CH391L/S13/DNA Computing

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*'''[[User:Kevin Baldridge|Kevin Baldridge]] 16:39, 1 April 2013 (EDT)''':How did he select against those which were not applicable? The combinatorial approach that gave all possible answers yields so many possibilities, I don't see how this is any improvement over traditional computer brute force approach if you can't eliminate the problem of selecting possible answers.
*'''[[User:Kevin Baldridge|Kevin Baldridge]] 16:39, 1 April 2013 (EDT)''':How did he select against those which were not applicable? The combinatorial approach that gave all possible answers yields so many possibilities, I don't see how this is any improvement over traditional computer brute force approach if you can't eliminate the problem of selecting possible answers.
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**'''[[User: Siddharth Das|Siddharth Das]] 16:39, 1 April 2013 (EDT): Granted this methodology isn't an elegant as computations conducted by normal computers, but "brute force" allows find solutions for highly combinatorial problems. In other words, DNA computing vs electronic computing is in essence memory vs. time, respectively. The amount of memory an electronic computer needs to allocate to solve a problem would never fulfill the requirements to screen for solutions such as combinatorial, factorization, and etc. For example in RSA cryptography, basically packages of data are stored in prime numbers (795028841 X 25209506681 = 20042284878777186721) shared between two parties. As an "eavesdropper", the number 20042284878777186721 (lock) means nothing to you  and thus prompts you to factorize the incredibly huge number. Without using the RSA algorithm (key), the eavesdropper must rely on simply "brute forcing" the decryption process which is where DNA computing would be advantageous.
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**'''[[User: Siddharth Das|Siddharth Das]] 16:39, 1 April 2013 (EDT)''': Granted this methodology isn't an elegant as computations conducted by normal computers, but "brute force" allows find solutions for highly combinatorial problems. In other words, DNA computing vs electronic computing is in essence memory vs. time, respectively. The amount of memory an electronic computer needs to allocate to solve a problem would never fulfill the requirements to screen for solutions such as combinatorial, factorization, and etc. For example in RSA cryptography, basically packages of data are stored in prime numbers (795028841 X 25209506681 = 20042284878777186721) shared between two parties. As an "eavesdropper", the number 20042284878777186721 (lock) means nothing to you  and thus prompts you to factorize the incredibly huge number. Without using the RSA algorithm (key), the eavesdropper must rely on simply "brute forcing" the decryption process which is where DNA computing would be advantageous.
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*'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 16:42, 1 April 2013 (EDT)''':DNA cryptography?
*'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 16:42, 1 April 2013 (EDT)''':DNA cryptography?
**'''[[User:Siddharth Das|Siddharth Das]] 16:45, 1 April 2013 (EDT)''':  
**'''[[User:Siddharth Das|Siddharth Das]] 16:45, 1 April 2013 (EDT)''':  
**'''[[User:Benjamin Gilman|Benjamin Gilman]] 17:15, 3 April 2013 (EDT)''': It's kind of out there, but DNA sequences could be pretty useful as key pads for decrypting a [http://en.wikipedia.org/wiki/Vernam_cipher Vernam Cipher].  DNA pieces can be generated randomly, copied accurately, and destroyed if necessary.  Although it's not truly random, just taking an existing sequence block (like a chunk of a genome from NCBI) would be close enough to make the cipher difficult to break.  Maybe someday spies will be carrying tubes of DNase around with them.
**'''[[User:Benjamin Gilman|Benjamin Gilman]] 17:15, 3 April 2013 (EDT)''': It's kind of out there, but DNA sequences could be pretty useful as key pads for decrypting a [http://en.wikipedia.org/wiki/Vernam_cipher Vernam Cipher].  DNA pieces can be generated randomly, copied accurately, and destroyed if necessary.  Although it's not truly random, just taking an existing sequence block (like a chunk of a genome from NCBI) would be close enough to make the cipher difficult to break.  Maybe someday spies will be carrying tubes of DNase around with them.
*'''[[User:Kevin Baldridge|Kevin Baldridge]] 16:45, 1 April 2013 (EDT)''':I think I might have shared this paper before, but it is very directly related to some of the topics you discuss here [http://www.ncbi.nlm.nih.gov/pubmed/22722847 Single Cell Programmable Biocomputers]
*'''[[User:Kevin Baldridge|Kevin Baldridge]] 16:45, 1 April 2013 (EDT)''':I think I might have shared this paper before, but it is very directly related to some of the topics you discuss here [http://www.ncbi.nlm.nih.gov/pubmed/22722847 Single Cell Programmable Biocomputers]
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*'''[[User:Alvaro E. Rodriguez M.|Alvaro E. Rodriguez M.]] 17:24, 4 April 2013 (EDT)''':Here is the NPR news article about the [http://www.npr.org/2013/03/29/175604770/tiny-dna-switches-aim-to-revolutionize-cellular-computing "Tiny DNA Switches Aim To Revolutionize 'Cellular' Computing"], there is a 4 min download that we could listen too in class. Also could you add a small section/ or talk about in class?.
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*'''[[User:Neil R Gottel|Neil R Gottel]] 20:40, 4 April 2013 (EDT)''':During class, we were wondering why Church didn't use a two-bits-per-nucleotide system (such as G=00, C=01, T=10, A=11). It doubles the storage requirement, but there's a very good reason: if parts of your data have 2-bit repeats (like 10101010101010 or 00000000000000), then you're gonna have a hell of a time during sequencing, because it's difficult for next-gen sequencers to differentiate between something like TTTTTTT and TTTTTTTT. Assigning two nucleotides to a single bit allows you to arbitrarily "complicate" the 2-bit repeated region into a sequence that won't mess up your sequencing results.

Revision as of 20:42, 4 April 2013

  • Kevin Baldridge 16:39, 1 April 2013 (EDT):How did he select against those which were not applicable? The combinatorial approach that gave all possible answers yields so many possibilities, I don't see how this is any improvement over traditional computer brute force approach if you can't eliminate the problem of selecting possible answers.
    • Siddharth Das 16:39, 1 April 2013 (EDT): Granted this methodology isn't an elegant as computations conducted by normal computers, but "brute force" allows find solutions for highly combinatorial problems. In other words, DNA computing vs electronic computing is in essence memory vs. time, respectively. The amount of memory an electronic computer needs to allocate to solve a problem would never fulfill the requirements to screen for solutions such as combinatorial, factorization, and etc. For example in RSA cryptography, basically packages of data are stored in prime numbers (795028841 X 25209506681 = 20042284878777186721) shared between two parties. As an "eavesdropper", the number 20042284878777186721 (lock) means nothing to you and thus prompts you to factorize the incredibly huge number. Without using the RSA algorithm (key), the eavesdropper must rely on simply "brute forcing" the decryption process which is where DNA computing would be advantageous.
  • Jeffrey E. Barrick 16:42, 1 April 2013 (EDT):DNA cryptography?
    • Siddharth Das 16:45, 1 April 2013 (EDT):
    • Benjamin Gilman 17:15, 3 April 2013 (EDT): It's kind of out there, but DNA sequences could be pretty useful as key pads for decrypting a Vernam Cipher. DNA pieces can be generated randomly, copied accurately, and destroyed if necessary. Although it's not truly random, just taking an existing sequence block (like a chunk of a genome from NCBI) would be close enough to make the cipher difficult to break. Maybe someday spies will be carrying tubes of DNase around with them.
  • Kevin Baldridge 16:45, 1 April 2013 (EDT):I think I might have shared this paper before, but it is very directly related to some of the topics you discuss here Single Cell Programmable Biocomputers
  • Alvaro E. Rodriguez M. 17:24, 4 April 2013 (EDT):Here is the NPR news article about the "Tiny DNA Switches Aim To Revolutionize 'Cellular' Computing", there is a 4 min download that we could listen too in class. Also could you add a small section/ or talk about in class?.
  • Neil R Gottel 20:40, 4 April 2013 (EDT):During class, we were wondering why Church didn't use a two-bits-per-nucleotide system (such as G=00, C=01, T=10, A=11). It doubles the storage requirement, but there's a very good reason: if parts of your data have 2-bit repeats (like 10101010101010 or 00000000000000), then you're gonna have a hell of a time during sequencing, because it's difficult for next-gen sequencers to differentiate between something like TTTTTTT and TTTTTTTT. Assigning two nucleotides to a single bit allows you to arbitrarily "complicate" the 2-bit repeated region into a sequence that won't mess up your sequencing results.
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