Guilin Sun
Ansys Employee
Basically, FDTD can simulate phenomina that can be described by Maxwell's Equations. As long as you have the material property, such as refractive index or permittivity, FDTD can simulate. However, how sensitive FDTD can get the change will depend on your settings. for example using higher accuracy mesh with proper PML can lead highly accurate transmission or reflection to the power of 1e-5 or smaller. But it will need time and skill to do convergence testing.
Q1. The graphene material, when made like a cylinder,has the same properties as a carbon nanotube right?
A: Please search some information to make sure the current graphene material mode can represent the carbon nanotube. btw: there are 2D sheet and 3D bulk graphene material modes. I guess you mean 2D sheet: Graphene surface conductivity material model
Q2. What is the best way to do receptor studies? How do I input material properties in MODE and FDTD so that our receptor will only accept one gas but not air for instance? Since materials in MODE and FDTD are like bulk materials with bulk properties. 
A: you can either use the material in the database, if it is good represent. or you can import your own material data:
However, nothing can prevent or specify what material can accept one gas, except that you design the device carefully.
Q3. Is there a kind of material that will allow us to study material interactions with a specific gas and another?
A: This is by your design, not by setting a material.
anyway, It is the designer's duty to optimize the device to response to certain environmental material, either gas or acceptor or antibody, or other liquid, as desired. Just a reminder, FDTD is to simulate light-matter interaction with given device configuration, which will need the designer's effort to optize the performance.