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Questions related from Berna Erdoğdu
Hi, I've noticed a common practice in publications where multiple Molecular Dynamics (MD) simulations are conducted with varying initial velocities. However, I'm uncertain about the appropriate...
19 April 2024 6,327 2 View
I'm facing difficulties while preparing double agar using the bacteria I initially used to isolate my phage. I wanted to see how different concentrations of these bacteria (measured as OD 0.1,...
17 November 2023 5,829 2 View
Greetings, I have recently isolated a new E.coli phage and during the assessment of its host range, I discovered that this particular phage was effective against Pseudomonas aureginosa and...
30 June 2023 313 4 View
Hi I am using Gromacs 2018 version. I ran the MD simulation for 400 ns at 300K (I didn't change the classic tutorial md.mdp except for nstep). While watching the .xtc file, I noticed that the...
20 May 2023 8,758 1 View
The box size determined for my protein before starting the MD simulation is as in image 1. After 200 ns, some of the protein comes out of the box (image 2). Does this affect the simulation...
03 May 2023 3,973 3 View
When I examined one-step growth curve experiments for bacteriophages, I mainly saw two experimental setups; one is based on bringing bacteria and phage together and precipitating after incubation...
22 July 2022 2,210 2 View
Is it correct to use naming such as phage A1, phage A2, phage A3 when naming phages of the same species but different isolates? Here, I would like to express that phages are the same but different...
01 January 1970 5,187 3 View