ECM-Mechanics-Regulate-Cancer-Cell-State

ECM Mechanics Regulate Cancer Cell Morphological Fate via Energy Minimization

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Running the simulations using the three-dimensional computational cell model

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Steps to run the simulations are provided here.

Prerequisites:

Ensure you have the following software installed and linked:

• Abaqus
• Visual Studio
• Intel Parallel Studio XE (Instructions to find the compatible versions of Visual Studio and Intel Fortran and properly link Abaqus with Fortran can be found online)

Instructions:

1. Download and extract the Simulations folder: After downloading the Simulations folder, extract its contents to a directory of your choice.

2. Open Windows command prompt: Open the Windows command prompt by either opening the Start menu and searching for "cmd" or pressing the Windows key + R, typing "cmd" or "cmd.exe" in the Run command box, and pressing Enter.

3. Navigate to the simulation folder: Use the command prompt to navigate to the drive and the path where you extracted the Simulations folder. For example:

C: cd path\to\the\simulation\folder

4. Run Abaqus simulation: Execute any of the "***.inp" files from the command prompt:

abaqus job=*** user=CellMatrixModel_20241204

Each of the "***.inp" files is the input file for the simulation of each case. Please note that the file "CellMatrixModel_20241204.for" contains a user subroutine UMAT code, which is based on the theoretical model for defining cell material properties. Each section of the UMAT code is explained with annotations for clarity and ease of understanding.

5. Verify simulation completion: Check the last line in the ".log" file to ensure the Abaqus job "" is completed.

6. Open simulation results in Abaqus: Open the "***.odb" file generated by the simulation.

7. Adjust visualization settings to calculate cell energy terms:

• From the Results Tree on the left, navigate to Output Databases > ***.odb > Instances
• Right-click on the PART-CELL-1 and pick Replace
• From the Menu bar, navigate to Report > Field Output
• In the Variable tab, pick Centroid for Position. Then pick any of the SDVs below: SDV77: Total cell energy SDV78: Mechanical energy SDV79: Chemical energy SDV80: Motor-work energy
• Navigate to Setup tab. Put a name for the report file. Make sure to uncheck "Append to file" and click on OK.
• Open the report file (located at the Abaqus working directory by default) using a text editor software. Find the total value on the last line of the report file. (Note that, for the cluster case, the total value is the sum of values for each cell.)
• Divide the total value by the total number of cell elements (equal to the number of the last element) to have the average of the elements. (Note that, for the cluster case, the total number of elements is the sum of the number of elements for each cell.)
• Multiply the average by the cell volume. Steps to calculate the cell volume are provided below.
• To have the cell volume, from the menu bar, navigate to Tools > Query > Mass properties
• In Select elements dialogue, pick Part instances. Select the cell part, and click on Done.

8. Adjust visualization settings to calculate ECM energy term:

• From the Results Tree on the left, navigate to Output Databases > ***.odb > Instances
• Right-click on the PART-MATRIXVOID-1 and pick Replace
• From the Menu bar, navigate to Report > Field Output
• In the Variable tab, pick Centroid for Position. Then pick SDV77 for total ECM energy.
• Navigate to Setup tab. Put a name for the report file. Make sure to uncheck "Append to file" and click on OK.
• Open the report file.
• Find the total value on the last line of the report file.
• Divide the total value by the total number of ECM elements.
• Multiply the average by the ECM volume. Steps to calculate the ECM volume are provided below.
• To have the ECM volume, from the menu bar, navigate to Tools > Query > Mass properties
• In Select elements dialogue, pick Part instances. Select the ECM part, and click on Done.
• To have the ECM energy due to cell expansion, repeat part 8 for associated simulations named Job-7 to Job-10

Files Included:

• "Jobs 1 to 10".inp: Abaqus input file for simulations of all cases.
• CellMatrixModel_20241204.for: User subroutine UMAT code based on the theoretical model to define cell material properties and behavior.