I am looking for papers or any other information discussing how fast dsDNA can be melt into sinlge strands at denaturation temperature. What are the characteristic timescales - nanoseconds, microseconds or rather miliseconds? What are the differences between short (12bp), medium (100bp) or long (10000bp) DNA chains? Many thanks for any information!
Hello, PhD Sun. What is the PBD model(s)? Can the PDB model be used to simulate DNA melting. In order to achieve a larger time scale, such as multi-us and even ms, I think reasonable parameterized coarse-grained simulation is a good choice.
Thank you Zhaoxi Sun, thank you Zhengwei Han,
the first link I found on the Peyrard–Bishop–Dauxois (PBD) model is "A nonlinear dynamic model of DNA with a sequence-dependent stacking term", this paper is in open access. On the first glance they did not mention exact times, except for the bubble formation durung melting (ps timescale), but I will read it more accurately and look for similar works.
Zhengwei Han, what do you mean by "In order to achieve a larger timescale...", does it mean there exists indeed a known relationship between melting times and oligo length?
Zhaoxi Sun , Professor Sun. I just remember. Previously, I seem to have seen the PBD model used in an article about the software package ESPResSo(an extensible software package for simulating soft matter systems). I want to say, there are some other software packages or codes to achieve the PBD model. Thank you for your reply
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