How can i make Nano scale - Meta particle in EDEM?
Hi, I am very new to EDEM.
I recently purchased an Altair license and am trying to use EDEM to model and simulate nanoscale structures, particularly DNA double helix bundles. However, I’m facing significant difficulties in modeling such nanoscale structures within EDEM.
My objective is to represent a DNA double helix strand using the Bonding V2 model or the Fiber Bonding model, where the DNA strand is constructed as a long chain of bonded particles. To achieve this, I need to create nanoscale particles within EDEM.
However, when I try to create particles on the nanometer scale in EDEM, several issues arise, and I’m struggling to resolve them. Below are the attempts I have made and the corresponding outcomes:
- Fiber Bonding Model using Sphero-Cylinder Particles:
I tried to model sphero-cylinder-shaped particles to construct the Fiber Bonding model. Since I wanted to represent a cross-section of 6 DNA strands, I needed the particle radius (R) to be 4 nm, which is a fixed value in my problem setup.
Since EDEM’s unit system uses micrometers as the smallest unit, I set Physicla Radius ( R value in sphero cylinder) to4.0e-3 [μm]and the cylinder length to8.0e-3 [μm]. However, with these settings, the particles did not appear in the simulation.
—> Result when i set the R = 4.0e-3[um]
L = 8.0e-3 [um]
When I increased the length (L value), the cylindrical caps dose not showing up, and only the side surface became visible.
When I increased the physical radius to about0.013 [μm], the cylindrical cap started to appear, but in a distorted shape.
(My guess is that this issue stems from the fact that my target scale is finer than the minimum meshing resolution supported by EDEM.) - Bonding V2 Model using Custom Polyhedral Particles:
I next attempted to use the Bonding V2 model by importing a thin cylindrical shape as a custom polyhedral particle via CAD. In the CAD model, I set the radius to 4 [mm] and the height to 0.24 [mm], and tried to import this model into EDEM using the "Import Custom Particle Shape" function. However, EDEM returned an error and failed to import the shape. ( I succeeded when I imported it using millimeter units. )
—> The option setting that i used when i tried to import CAD.
—> Error message i got when i tried to import CAD in micrometer scale as above setting. - Using Built-in Polyhedral Particles:
Lastly, I tried using one of EDEM’s built-in polyhedral particle shapes instead of importing a CAD model.
However, I noticed that EDEM does not allow setting the dimensions of polyhedral particles below 1 μm as below picture, which makes it impossible to reach the nanoscale range I need.
These are the methods I have tried so far to model DNA strands in EDEM.
Based on these experiences, I suspect that EDEM is fundamentally designed for macroscopic-scale DEM simulations, and although micrometer-scale simulations may be possible for powder materials, the software may not be specialized for nanoscale meshing and modeling.
Nevertheless, I am currently in a situation where I must use EDEM to model and simulate DNA strands.
If there is any feasible method to generate particles at the nanoscale and connect them into a meta-particle (such as a strand) in EDEM—whether it builds upon the methods I’ve tried above or involves a completely different approach—I would greatly appreciate it if you could let me know.
Among the methods I’ve tried, my preferred priority is 1 → 2 → 3, in that order.
Any suggestions or insights would be greatly appreciated. Thank you in advance!
Hi
There are more concerns that what you have found out, with this approach.
EDEM is not able to resolve a meshed particle with that low of a resolution. You can always use spherical particles, and bond multiple spherical particles to form your shape (I realize it is more cumbersome), and that should work for creating the shape, since there is no mesh for a spherical particle within EDEM.
Moving on to other concerns with this approach - at such a small scale of the particle, there are other motions that come into play that EDEM cannot resolve. EDEM resolves classical mechanics for the particles, but at this scale, you may also encounter Brownian motion/diffusion of the particles in reality, which EDEM will not be able to resolve.
Also, EDEM cannot resolve contacts for particles which are lower than 1 micron. Forces for particle sizes as low as 1 nm, will be accurately calculated from the 2025.1 release.
Finally, I would recommend that you scale up your particle sizes (if you are able), so that you get reasonable accuracy, and run times for your case.
Hope this helps.
Thanks,
Jerrin Job
Hello,
First of all, Thank you very much for your thorough and helpful explanation.
After reading your response, I have summarized my current understanding as follows:
Below is what I currently understand:
I would be grateful if you could kindly confirm whether the above points reflect your explanation accurately.
I have also learned that EDEM does not provide built-in models for Brownian motion or viscous damping in solution. Nevertheless, I understand that the EDEM API allows users to define custom forces. My intention is to apply a random force—sampled from a Gaussian distribution—to each nanoparticle at every time step (for example, by bonding ten spherical particles with the Bonding V2 model to create one meta-particle, then applying the random force separately to each of the ten constituent particles).
Could you advise whether implementing such a force via the API is feasible?
Thank you once again for your kind assistance.
I greatly appreciate your time and any further guidance you can provide.
Thanks,