What are some of the tools and software that you use for nanoscale modeling and simulation in nanotechnology?

I use the ADF/BAND package from SCM for DFT calculations. I really appreciate their use of Slater-type orbitals in the calculations. We have obtained really nice results using their computational tools.

Indeed, FEA can be used to solve quite a few nano-based structures. However, the analysis performed usually give us general information while proper equations have been fed as in Comsol. There are a few FEA-based software that can cope with nanostructures behaviour such as Coventor. It has a few libraries that are based on proper fabrication processes as well as characterisation tools. Another key software to consider is Synopsys, among whole algorithms that it provides a few for either fabrication or analysis are quite interesting and most of the time spot on.

A strength of COMSOL is the ability to combine different types of physics (hence the "Multiphysics" in the name). For example, I simulated the transport of charged nanoparticles under conditions of varying electric fields - I used the AC/DC Module to calculate the field at every time point, and fed that into the Particle Tracing Module to calculate trajectories. This type of simulation could have been programmed in something like MATLAB, but it would require a massive amount of work, especially to implement efficient solvers. Software like COMSOL has a lot of limitations, but comes with efficient solvers pre-built, and is generally friendlier to use.

For complex 3D modeling (e.g., crystal lattices), specialized software can be a good solution. However, for analyzing and visualizing raw simulation data (e.g., particle trajectories), a general purpose tool like MATLAB or Python (with appropriate plotting libraries) can do an excellent job, and give you more control over the exact processing steps and the look of the eventual visualization.

Decent article is as far as mentioning FEA, MD software, visualization tools. But nanotechnology deals with either imaging things on the nanoscale or producing things on the man of scale. So you could probably have a whole lawn discussion on scanning probe microscopy (scanning tunneling microscopy, atomic force microscopy, magnetic force microscopy, and a whole house of other probe based systems dealing with different types of electromagnetic interactions, chem. interactions, between the tip and the surface. One thing to use tools to simulate, or predict the behavior of materials at the nanoscale but to actually be able to image them and look at them under different conditions is equally important. Of course, don't forget SEM/TEM etc

Can't forget the Helium Ion Microscope (HIM). Got trained on the one at the JSNN in Greensboro, NC as a PhD student. It was great but I Love the AFM!!! I remember being amazed that I could image bacteriophage DNA and could see when I was "pressing" to hard with the AFM tip on the DNA. It looked like a cylinder with a crease down the middle long-ways like a split-top loaf of bread. I reduced the amplitude range of the tip and the crease just disappeared. I was imaging the DNA on slivers of mica and had the inherent patterns of the mica to deal with. Of course, at the nanoscale, just imaging the mica by itself was fun since it looked like the surface of the moon or Mars. Especially for something that was considered a "smooth" surface.