Wednesday, May 22, 2013

Some Early Foundational Feasibility Outlines

Spoke with a friend who works with DNA. I had wanted to find out very roughly how DNA strands would behave in clean-room environments (e.g., distilled water). My rationale for these questions is that while we understand how DNA works under natural environments, for the purposes I am gunning for, I'd prefer to consider how DNA would function in artificial environments. This can provide a simple basis for experimental setup to validate statistically-based simulations derived from a computational model with DNA. From this basic model with artificial settings, one can imagine other parameters that can be tuned without concerns about the complexities of natural DNA environments. These can include:
  1. temperature
  2. pressure
  3. density of DNA strands
  4. density of amino acid, protein presence.
The answers so far have been encouraging:

  1. DNA behaves more or less regularly in distilled water, keeping its structure intact. There may be some differences in the way it folds, however and that is important.
  2. DNA will hold under a fair range of temperatures. I'll have to find out what that range is.
  3. It is unclear how DNA will function under different pressures. I imagine they should function without issue over a wide range of pressures, given the presence of deep undersea creatures. Something to find out.
With these parts, it is possible to get started considering computational models under nominal conditions of room temperature and 1 atmosphere of pressure. All that is required is some mechanism for arbitrary DNA sequence construction in a distilled water solution. One of my biggest early interests would be the establishment of a timing mechanism. I would like to see how a mechanism like that could control pulses of "useful work" which can then be observed.

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