[Simulation question]: Chemical stage time end in SBS #52
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Simulation questionHi everyone. My question is about this line in my step-by-step simulations: I have a circular plasmid with 100 base pairs in a box and I have a point source Lu-177 at the center undergoing disintegrations. My question is: what is the best value for this parameter? it is a bit confusing to me as in the manual it says "The end time must be larger than 1 ps (i.e. the time where the chemical stage Thank you a lot in advance. TOPAS-nBio categoryPhysics Code of Conduct
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That parameter dictates the end of the chemistry processes which includes Brownian motion and reactions between chemical species. The products from radiolysis of water (pre-chemical stage) are put in the simulation at 1 ps, thus the time end for the chemistry processes that follow should be greater than 1 ps. Decreasing the time end will cut the transport of chemical species before they reach the plasmid. An example. For your specific application, the time end depends on the scavenging capacity s of the medium (s = k [B]) and the chemical species of interest (e.g., OH) that this medium scavenges. The inverse of s gives you the time at which the concentration of the scavenged species has dropped to 1/e. Thus, for a cellular-like medium with scavenging capacity of c.a. 10^9 /s, the end time is about c.a. ns. For a plasmid suspended in, e.g., DMSO (scavenger of OH, with k~7e9 /M/s), the concentration should be about 0.1 M to mimic roughly the cellular scavenging capacity and thus require the same time end. Therefore, the time end depends on your experimental conditions: type of scavenger and its concentration. |
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Thank you Jose I always appreciate your replies. one quick question: The parameter
in the DBSCAN method, does this mean it is considered that 16% of the scoring volume is occupied by the DNA? (since the DNA geometry is not important in the DBSCAN method) I am trying to have a same volume in both SBS and DBSCAN method to see if I can get similar "direct" DNA damages. Thanks. |
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That parameter dictates the end of the chemistry processes which includes Brownian motion and reactions between chemical species. The products from radiolysis of water (pre-chemical stage) are put in the simulation at 1 ps, thus the time end for the chemistry processes that follow should be greater than 1 ps.
Decreasing the time end will cut the transport of chemical species before they reach the plasmid.
An example. For your specific application, the time end depends on the scavenging capacity s of the medium (s = k [B]) and the chemical species of interest (e.g., OH) that this medium scavenges. The inverse of s gives you the time at which the concentration of the scavenged species has d…