Automated Mesoporous Synthesis

This repository is a companion to the paper, "Open-hardware automation platform for accelerated sol-gel nanomaterial synthesis". It contains the execution code used to run the automated synthesis experiments as well as a tutorial walk-through detailing how to reproduce the synthesis workflow.

Repository contents

automated-mesoporous-silica
├── synthesis_experiment_files/
|   ├── fully_automated_execution/                    # Fully automated synthesis–characterization experiments
│   |    ├── 2025_03_28_BaselineSampling.ipynb        # Uses NIST-AFL sample loader
│   |    ├── Sobol_baseline_sample_generation.ipynb   # Constrained Sobol sampling
│   |    ├── Mesoporous_SobolBaseline_APS_*.csv       # Sample compositions
│   |    ├── 2025_03_28_BaselineSampling.log          # Experiment log file
│   |    ├── Mesoporous_constants_APS.json            # Parameter space constants
│   |    └── systemconfig.json                        # AFL and system config
|   |
│   └── batch_synthesis/                              # Batch-mode synthesis (main paper experiments)
│        ├── 2025_03_29_BatchSynthesis.ipynb
│        ├── Sobol_baseline_sample_generation_batchmode.ipynb
│        ├── Mesoporous_SobolBaseline_APS_BatchMode_*.csv
│        ├── Mesoporous_constants_APS_batch.json
│        ├── APS_batchSynthesis_2025_03_29.log
│        └── systemconfig.json
│
├── tutorial/                                         # Instructional walkthrough
│   ├── tutorial.md
│   └── TutorialWalkthrough.ipynb
│
├── usaxs_integration/                                # Automated USAXS integration
│   ├── usaxs_integration.md
│   └── beamline_control_script.py
│
├── sample_utilities/                                 # Sample selection + volume calculations
│   └── samples.py
│
├── scattering_data
│   ├── SAXS_reduced_data
│   ├── usaxs_raw_data
│   └── usaxs_reduced_data
|
├── stober_synthesis_utils.py                         # Reactant transfer and mixing utilities
├── usaxs_utils.py                                    # USAXS instrument client integration
└── sample_composition_information                    # Sample reference including composition and associated scattering filenames

Procedure tutorial

For an explanatory walk-through of the steps needed to set up and execute the synthesis described in the paper, check out the tutorial

Instrument integration

More information on the APS 12-ID-E USAXS and Xenocs SAXS instrument integrations is available here.

Included scattering data

Collected scattering data for the batch parameter space exploration synthesis experiment are included in scattering_data

• SAXS_reduced_data contains data collected on a Xenocs Xeuss 3.0, with high resolution in the high-q region corresponding to scattering from the porous interior of particles. This data has been reduced as described in the manuscript.
• usaxs_raw_data contains non-reduced USAXS data in .h5 file format. The files are named in format {Cartridge plate well}{scan number}{Instrument incremental ID}.h5. Refer to the sample composition information file to determine which scattering data goes with which sample.
• usaxs_reduced data contains the reduced usaxs data. The nonreduced usaxs data can be reduced using Igor Pro 8.04. The appropriate empty container background is A2_1_2035.h5 for samples with instrument ID below 2081 and A3_0_c2_2108.h5 for samples with instrument ID of 2109 and above.

Additional hardware documentation

The science-jubilee platform, including the Digital Pipette syringe tools, is fully documented here

The NIST-AFL sample changer implementation is documented here.