Appendix A: Model Generating GUI Documentation A.1 Setup Instructions

1. Uncompress Matlab files in desired working folder. 2. Set the same folder as the working directory in Abaqus CAE, “File > Set

Work Directory”. 3. Open GUI_1.m for suspended cell or GUI_2.m for spread cell and run

script. Select “Change Folder” to set the current folder as the Matlab working directory.

Figure A.1. Prompt window for step 3.

4. Input desired simulation parameters (see section A.3) and select “Generate Model” (macro text file “abaqusmacro.py” is created in the folder).

5. In Abaqus CAE, select “File > Macro Manager > Macro1 > Run” to run the macroinstructions that generates the model according to the parameters and starts the simulation automatically (refer to section A.4 for error troubleshooting).

Figure A.2. Abaqus macro manager.

o Abaqus will first generate 5 components (nucleus, membrane, cytoplasm, cytoskeleton, indenter), create interaction properties, mesh the parts, and apply boundary conditions and indentation conditions.

Figure A.3. Abaqus status window indicating complete model generation.

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o Abaqus will then analyse create a job file for analysis for errors. Upon completion, it will automatically start the simulation.

o At this point of time, the simulation processes the indentation in small increments until it reaches the final indentation distance.

o The simulation process can be monitored in “Jobs > Jobs Manager”.

o It is normal to see “warnings”, which will still allow the simulation to complete. However, “errors” will result in the simulation stopping (refer to section A.4 for error troubleshooting).

o Time to complete depends on the mesh coarseness and the indentation distance (approx. 20 to 40 minutes running on Linux OS in TLC).

A.2 Obtaining Results from the Simulation

1. When simulation job is complete, it will be indicated in the status window of Abaqus CAE.

Figure A.4. Abaqus status window indicating complete simulation.

2. Access the results in Abaqus CAE by selecting “Results” in Job Manager. This will bring you to the “Visualisation” Panel.

Figure A.5. Abaqus job manager indicating complete simulation, results available.

3. Double-click “XYData” in the side panel, select “ODB History Output” and then “Continue”.

Figure A.6. Abaqus status window indicating complete model generation.

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4. The simulation produces 2 main outputs: (1) Reaction forces at the indenter “Reaction Force: RF2 PI: Part 5-1 Node 1 in NSET AFM”, (2) Indentation Distance “Spatial Displacement: U2 PI: PART 2-1 Node 2 in NSET Indentation Point”.

Figure A.7. Abaqus history outputs window.

5. Select “Save As…” and click “OK” for each output to generate “XYData-1” and “XYData-2”.

Figure A.8. Abaqus output saving window.

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6. Right clicking “XYData-1” and “XYData-2” individually and selecting “Edit” produces two data tables containing the reaction forces (left) and indentation distances (right) at each increment. The units of the reaction forces and indentation distances are Newtons and nanometres respectively. The X-column of each table shows the fraction of each increment from zero (0 nm indentation) to one (final indentation distance), while the Y-column shows the data at each increment.

Figure A.9. Abaqus status window indicating complete model generation.

7. Transfer the data the respective columns in the excel sheet provided “Data Sheet.xlsx” to obtain elastic modulus and stiffness data.

Figure A.10. Excel data sheet requires output data from Abaqus.

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A.3 Functionality Documentation

Figure A.11. Spread Cell Finite Element Model Generator GUI.

Figure A.12. Suspended Cell Finite Element Model Generator GUI.

As the focus of the project is the analysis of the cell adherent on a substrate, the suspended cell generator supports less features is was only used as an early proof-of-concept algorithm. The suspended cell generator only supports point-loading conditions, compressing/stretching at the top and bottom nodes of the cell. This documentation section focuses on the spread cell generator.

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Figure A.13. Cellular Level Settings Panel.

• Cell Shape: Switch between Suspended Cell and Spread Cell Generator. • Cell Height: Enter height of cell centre from substrate. • Substrate Contact Length: Enter length of cell in contact with substrate. • Prestressing: Enable/disable prestressing algorithm to calculate and model

the force vectors (due to strain as the elements stretch/compress from their suspended state) on the end nodes of each tensegrity element. Turns simulation to nlgeom=OFF, which may result in decreased accuracy.

Figure A.14. Indentation Settings Panel.

• Distance: Vertical Indentation Distance. • Offset: Lateral Indentation Offset from Cell Centre. • Point Load/Spherical/Cylindrical Indenter Settings: Select Indentation

Type/Shape. • Radius: Input indenter radius for spherical/cylindrical indenters.

Figure A.15. Sub-Cellular Level Settings Panel.

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• Dimensions: input values for dimensions for sub-cellular components. o No. of filaments (top/bottom): input number of microfilaments in a

cell (top), input number of microtubules in a cell (bottom). o X-section area (top/bottom): input average cross-sectional area of

each microfilament (top) and microtubule (bottom) in a cell. o Thickness: Input plasma membrane thickness. o Vertical Height: Input vertical height of nucleus. o Lateral Length: Input lateral length of nucleus.

• Modulus: Input Young’s modulus of each sub-cellular component. • Poisson’s Ratio: Input Poisson’s Ratio of each sub-cellular component.

Figure A.16. Meshing Controls Panel.

It is recommended to maximise number of seeds for the software license (20,000 total nodes for academic license).

• Nucleus (Seeds): Input Global Size of Nucleus (smaller = finer mesh). • Cytoplasm (Seeds): Input number of seeds on Cytoplasm vertical edge. Seeds

are biased towards the cell centre (figure A.17). • Cytoskeleton (Elements): Input number of elements per tensegrity element

(recommended: 1) (figure A.17). • Membrane Seeds: Input number of seeds on the cells top edges (figure A.17).

Figure A.17. Seeding configurations. Membrane Seeds (orange) determines the

number of seeds at the outer edge, Cytoplasm Seeds (red) determines the number of seeds at the vertical edge, Nucleus Seeds (blue) determines the number of seeds at the nucleus edge, Cytoskeleton Elements (green) determines the number of elements that

make up a single strut/cable.

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Figure A.18. Computation Panel.

• Generate Model: Run Algorithm to print Macro to generate model in Abaqus.

• Status Box: Reports Model Generated when complete. • Cell Volume: Presents calculated cell volume for the dimensions input. To be

used as reference if cell volume is desired to be kept constant.

A.4 Error Troubleshooting

As there is a large permutation of possible settings, it was unable to exhaustively test the model generator GUI. The GUI functions as designed using the default input parameters. Any large deviation from the default parameters may cause the simulation to fail. Any minor alteration of the GUI script is likely to cause the macroinstruction to be unusable by Abaqus. As such, it is recommended that a user have good understanding of the scripting process before alterations are made. Minor alterations to the model may be made within Abaqus CAE without much risk of a failed simulation. The following is a list of factors that may contribute to the failure of simulation within Abaqus:

• Excessive number of seeds in meshing may cause the model to generate a total number of nodes that exceeds the academic license (20,000 nodes). Reduce the number of seeds and regenerate model to resolve.

• Large indentation distances may cause the simulation to run for excessively long periods. This is due to the software reducing the increment size as the problem becomes more complex. At large indentations, a large number of elements are being calculated. As such, the simulation may fail before it reaches the final indentation distance. However, all data up to the failure point can still be used and accessed. Reduce the indentation distance to resolve.

• Simulation may fail if the microfilament/microtubule count is increased and a large indentation is made directly on a tensegrity vertex. This is due to the relatively high modulus of the tensegrity structure, and a large deformation causes an unexpectedly large deformation to the structure. Adjust the indentation offset to ensure that indentation is not too close to a tensegrity vertex to resolve.

• Model generation failures may result if the input dimensions generate impossible geometries (i.e. nucleus vertical height larger than cell height). The algorithm produces a macro that instructs Abaqus to generate the model by following set steps. Check input dimensions or start by making small changes to default parameters to resolve. Alternatively, checking the point at which the Abaqus model generation fails may help to narrow down the cause of the error.