1. Overview

This repository contains:

• Finite Element (FE) simulations using Abaqus
• Neural response simulations using a Leaky Integrate-and-Fire (LIF) model implemented in MATLAB
• Processed results used to generate the figures in the manuscript

2. Folder Structure

Project_Root/ | |----- FE_model/ | |----- stimulus1_probe/ | |----- stimulus2_braille/ | |----- stimulus3_dot_texture/ | |----- stimulus4_single_dot/ | |----- LIF_model/ | |----- stimulus1_probe/ | |----- stimulus2_braille/ | |----- stimulus3_dot_texture/ | |----- stimulus4_single_dot/

Folder Description

FE_model/ Abaqus finite element model files (.inp).

LIF_model/ MATLAB scripts (.m) implementing the neural response (LIF) model and corresponding simulation output for each simulation condition.

stimulusXX_XX/ Each folder corresponds to one simulation condition described in the manuscript.

3. Software Requirements

Finite Element Simulation Abaqus Version: Abaqus 2016 and Abaqus 2022

Neural Simulation MATLAB Version: R2024b Required toolboxes: Global Optimization Toolbox

4. Overall Workflow

The simulation pipeline consists of the following steps:

1. Run Abaqus FE simulation (.inp)
2. Extract strain enelgy density data from FE output (extracted data: abaqusXX.rpt and fXX-X.xlsx, stored in LIF_model/stimulusXX_XX/fingerXX/)
3. Run the MATLAB-based LIF simulation using the extracted FE data as input (.m)
4. Neural response outputs

5. Detailed Execution Procedure

5.1 Stimulus1

1. Multi-objective Optimization

• Navigate to: LIF_model/stimulus1_probe/
• Run: multiObj_Pareto.m
• Output (variables): popSol: Identified parameter sets (saved in param.mat) popCost: Pareto-optimal solutions. Exported as probe_pareto_sol.csv (stored in result1/). Used to generate Fig. 2 in the manuscript.

2. Probe stimulation

• Navigate to: LIF_model/stimulus1_probe/
• Run: mainProbe.m
• Output (variables): spikeTime: Calculated spike timing. Exported as probe_spiketrain_param_XX_ps_XX-XX.csv (stored in result2/). Here, param_XX denotes the parameter set number, and ps_XX-XX denotes the probe indentation speed. Used to generate Fig. 3.

5.2 Stimulus2

• Navigate to: LIF_model/stimulus2_braille/
• Run: mainBrailleRA.m (for RA responses) mainBrailleSA1.m (for SA1 responses)
• Output (variables): allSpikeTime: Calculated spike timing. Exported as braille_sep_param_XX.csv (stored in result1/). Here, param_XX denotes the parameter set number for RA responses, whereas braille_sep_sa1.csv corresponds to SA1 responses. Used to generate Fig. 6.

5.3 Stimulus3

• Navigate to: LIF_model/stimulus3_braille/
• Run: mainDotTexRA.m (for RA responses) mainDotTexSA1.m (for SA1 responses)
• Output (variables): allSpikeTime: Calculated spike timing. Exported as dot_texture_sep_param_XX_ds_XX-XX.csv (stored in result1/). Here, param_XX denotes the parameter set number for RA responses, whereas dot_texture_sep_sa1_ds_XX-XX.csv corresponds to SA1 responses. ds_XX-XX denotes the dot spacing. Used to generate Fig. 7. vec_allFiringRateHistogramArray: Calculated firing rate. Exported as dot_texture_firerate_sim.csv (stored in result2/). Used to generate Fig. 8(A-1). Fig. 9(A) was generated using dot_texture_firerate_diff2.csv. The results in XX_diff.csv are sorted in ascending order of the parameter set number, whereas the results in XX_diff2.csv are sorted in ascending order of ΔFST. vec_tempoVariArray: Calculated temporal variation. Exported as dot_texture_tempvar_sim.csv (stored in result2/). Used to generate Fig. 8(A-2). Fig. 9(B) was generated using dot_texture_tempvar_diff2.csv. setFiringRateRMSE: Calculated RMSE for firing rate. Exported as dot_texture_firerate_rmse.csv (stored in result2/). The results in XX_rmse.csv are sorted in ascending order of the parameter set number, whereas the results in XX_rmse2.csv are sorted in ascending order of ΔFST. Fig. 8(B) was generated using XX_rmse2.csv. setTempoVariRMSE: Calculated RMSE for temporal variation. Exported as dot_texture_tempvar_rmse.csv (stored in result2/). Fig. 8(B) was generated using XX_rmse2.csv.

5.4 Stimulus4

• Navigate to: LIF_model/stimulus4_single_dot/
• Run: mainSingleDotRA.m (for RA responses) mainSingleDotSA1.m (for SA1 responses)
• Output (variables): allSpikeTime: Calculated spike timing. Exported as single_dot_sep_param_XX_dw_XX-XX.csv (stored in result1/). Here, param_XX denotes the parameter set number for RA responses, whereas single_dot_sep_sa1_dw_XX-XX.csv corresponds to SA1 responses. dw_XX-XX denotes the dot width. Used to generate Fig. 10. setRespWidth: Calculated response width. Exported as single_dot_respwidth.csv (stored in result2/). The results in XX_respwidth.csv are sorted in ascending order of the parameter set number, whereas the results in XX_respwidth2.csv are sorted in ascending order of ΔFST. In addition, the response widths in XX_respwidth2.csv represent the differences between the simulation results and the experimental data. Fig. 11 was generated using XX_respwidth2.csv.