Simulating Macroions: Obtaining Characteristics & Gender

[Majid Rezaei]

Hi dear all
I am working on electrophoretic flow and I want to simulate macroions which are large complex molecules consisting charged atoms. As I know we can consider that a macroion is a large sphere (or cylindrical) particle with a hydrodynamic radius with the net charge of forming atoms.
But there is a question and that is how can I specify the gender of macroion. I am using lennard-jones potential which needs σ and ε coefficients and I don't know how to obtain them.
In papers that I read they specify the diameter, mass, charge, and lennard jones coefficients of an sphere macroion without saying anything about what is this macroion and it consist how many particles and what is its gender. also they show the effect of varying σ and ε on results. So what is your idea for me to simulate true macroions. Do you think this is better to simulate polymers or no I can consider sphere particles? And if I can, How can I obtain its characteristics?
please give me suggestions with refrences.
Thanks alot
Best regard
Majid

 

[eljose79]

Hi Majid,

Thank you for your question. Simulating macroions can be a complex task, but there are some guidelines and considerations that can help you accurately represent these large complex molecules in your simulations.

Firstly, it is important to note that the term "gender" in this context typically refers to the shape of the macroion, rather than its actual gender. For example, a "rod-like" macroion would have a cylindrical shape, while a "spherical" macroion would have a more spherical shape. These different shapes can have an impact on the behavior of the macroion in an electrophoretic flow.

In terms of obtaining the σ and ε coefficients for your simulations, these can vary depending on the specific type of macroion you are trying to simulate. One approach could be to use experimental data or theoretical calculations to estimate these values for your particular macroion. Alternatively, you could also try using molecular dynamics simulations to obtain these values, as they can provide a more accurate representation of the interactions between particles.

In terms of determining the characteristics of your macroion, such as its diameter, mass, and charge, this will also depend on the specific molecule you are trying to simulate. However, you could refer to previous studies or experimental data on similar macroions to get an idea of the expected values for these parameters.

As for whether it is better to simulate polymers or spheres, this will depend on your research goals and the specific system you are studying. Both approaches have their advantages and disadvantages, so it is important to carefully consider your research objectives and choose the approach that best suits your needs.

I hope this helps. If you have any further questions, please feel free to ask. Good luck with your research!