Vol3D

To overcome the limitations with slice models a volumetric construction strategy was needed. Unfortunately, existing software did not constrain the components such that the local ordering was preserved. Thus Vol3D was created in collaboration with Dr. Justin Watson. The user defines the distribution of molecules, stacks, and pores using Fringe3D, they define the volume (x, y, z) of a box. The components are treated as volume elements and added to the box such that overlap is not permitted (volume exclusion). Inherent porosity is created due to the stacking and placement of the volume elements. Once this quantity is determined additional porosity can be included in the distribution and the pore size distribution captured. Again as the placement is simply volume elements the construction is rapid taking minutes for a 50,000 atom model.

Publications:

Wang, C.; Watson, J. K.; Louw, E.; Mathews, J. P., A construction strategy for atomistic models of coal chars capturing stacking diversity and pore size distribution. Energy Fuels 2015, 29, 4814–4826.

Xin, H.; Wang, C.; Louw, E.; Wang, D.; Mathews, J. P., Atomistic simulation of coal char isothermal oxy-fuel combustion: char reactivity and behavior. Fuel 2016, 182, 935-943.

Combustion / Oxy-Fuel Combustion / Gasification Reactivity Simulations

Using Vol3D we are able to capture the char structure with ease. However, there are challenges in examining the char reactivity by traditional approached due to the large-scale required by the structural diversity and pore size distribution. Thus, we created a simplistic simulation within Materials Studio with scripts running the sequential process and aiding in capturing the structural transformations. The steps include:

1. Place char into a periodic boundary box surrounded by oxygen (or reactive molecule)
2. Allow reactive gas to diffuse via molecular dynamics (char remains fixed)
3. For the reactive gas molecules that are within the specified distance of a reactive carbon: delete the carbon but retain the reactive gas molecule
4. Repeat the sequence but with an additional clean-up of ring fragments

The behavior is dependent upon the char structure, and the sequence is repeatable so the impact of changes in the structure on reactivity can be determined. The information captured is

1. Number of reactive and reacting atoms (the rate)
2. Where the atoms are being deleted
3. The size of the char
4. Via PoreBlazer the density, pore location, and pore size distribution

Here is a movie (no sound) showing the oxy-fuel combustion progression for a 40,000 atom structure (automation and simulation credit Haihui Xin).

Publications:

Xin, H.; Wang, C.; Louw, E.; Wang, D.; Mathews, J. P., Atomistic simulation of coal char isothermal oxy-fuel combustion: char reactivity and behavior. Fuel 2016, 182, 935-943.

Louw, E. Structure and combustion reactivity of inertinite-rich and vitrinite-rich South African coal chars: quantification of the structural factors contributing to reactivity differences. Ph.D., John and Willie Leone Family Department of Energy and Mineral Engineering, The Pennsylvania State University, 2013.

Automation of Construction and Evaluation via Scripts (Within Materials Studio)

We use the tools Fringe3D etc. to create basic aromatic structures (or we could use name molecules also). These we can change into the appropriate molecules (addition of heteroatoms in the correct functionality) etc. as well as change the molecular weight distribution via cross-linking etc. Thus our strategy is to build to suit rather than go through a multi-step evaluation process (this is thus much quicker). We perform structural evaluations in the same way and can control the distributions by manipulating the structures within select ranges. Examples include:

Construction

Mixture of molecules to individual files

H to OH

H to CH3

Heteroatoms addition

Cleave cross-links

Example of ring additon in Fringe3D

Cross-linking example

Oxydation example

Cleave cross-links (aliphatic) example

Evaluation

Molecular weight distribution

H to OH

Count the number of molecules

NMR parameters (Solum et al. 21 parameters

Molecule solubility prediction (Painter et al.)

Ring counting (5-, 6-, and 7-membered)

Publications:

Ramachandran, V.; Castro-Marcano, F.; Van Niekerk, D.; Ferdandez-Alos, V.; Alvares Rojas, Y. E.; Pou, J. O.; Watson, J. K.; Mathews, J. P., Construction, structural evaluation, and exploring chemical transformations of coal molecular models using scripting, International Conference on Coal Science & Technology, 2013, The Pennsylvania State University, PA, USA, 1015-26

Castro-Marcano, F.; Lobodin, V. V.; Rodgers, R. P.; McKenna, A. M.; Marshall, A. G.; Mathews, J. P., A molecular model for the Illinois no. 6 Argonne Premium coal: moving towards capturing the continuum structure. Fuel 2012, 95, 35-49.

Visualization

Because our structures are so large we often need visualization aids to help view and identify structural features and their transformations.
Publications:

Pou, J. O.; Alvarez, Y. E.; Watson, J. K.; Pisupati, S.; Mathews, J. P., Co-primary thermolysis molecular modeling simulation of lignin and subbituminous coal via a reactive coarse-grained simplification. Journal of Analytical and Applied Pyrolysis 2012, 95, 101-111.

Alvarez, Y. E.; Moreno, B. M.; Klein, M. T.; Watson, J. K.; Castro-Marcano, F.; Mathews, J. P., A novel simplification approach for large-scale structural models of coal: 3D molecules to 2D lattices. 3. Reactive lattice simulations. Energy and Fuels 2013, 27, 2915-2922.

Alvarez, Y. E.; Watson, J. K.; Pou, J. O.; Mathews, J. P., A novel simplification approach for large-scale structural models of coal: 3D molecules to 2D lattices. 2. Visualization capabilities. Energy & Fuels 2012, 26, 4946-4952.

Alvarez, Y. E.; Watson, J. K.; Mathews, J. P., A novel simplification approach for large-scale structural models of coal: 3D molecules to 2D lattices. 1. Lattice creation. Energy & Fuels 2012, 26, 4938-4945.