DOI: 10.5061/dryad.sbcc2frdf
title: Direct observation of phase transitions in truncated tetrahedral microparticles under quasi-2D confinement

description: Colloidal crystals are used to understand fundamentals of atomic
 rearrangements in condensed matter and build complex metamaterials with
 unique functionalities. Simulations predict a multitude of self-assembled
 crystal structures from anisotropic colloids, but these shapes have been
 challenging to fabricate. Here, we use two-photon lithography to fabricate
 Archimedean truncated tetrahedrons and self-assemble them under quasi-2D
 confinement. These particles self-assemble into a hexagonal phase under an
 in-plane gravitational potential. Under additional gravitational
 potential, the hexagonal phase transitions into a quasi-diamond two-unit
 basis. In-situ imaging reveal this phase transition is initiated by an
 out-of-plane rotation of a particle at a crystalline defect and causes a
 chain reaction of neighboring particle rotations. Our results provide a
 framework of studying different structures from hard-particle
 self-assembly and demonstrates the ability to use confinement to induce
 unusual phases.
description: # Direct observation of phase transitions in truncated tetrahedral
 microparticles under quasi-2D confinement
 This dataset contains the
 images, .csv files, and code needed to reproduce the results to support
 the conclusion of the manuscript. ### Files and Folders The file structure
 is ordered relative to the dataset collected for each main figure in the
 manuscript, as well as some of the supplemental information data. Each
 folder can contain images (.png, .tif), .csv files, and Jupyter notebooks
 (.ipynb) that will help reproduce the dataset in the main manuscript. Each
 folder that has code has a `README.md` that helps facilitate installing
 and running the code. #### **/Figure 1** * *README.md* * Markdown (.md)
 file that has details for installing a conda python environment to run the
 necessary analysis code for the data in Figure 1. * *environment.yml* *
 YAML (.yml) file that declares all necessary python libraries to run the
 analysis code (*orderParams.py and OrderParameterAnalysis.ipynb*) *
 *orderParams.py* * Python (.py) file containing necessary functions to run
 analysis code (*OrderParameterAnalysis.ipynb)* *
 *OrderParameterAnalysis.ipynb* * Jupyter notebook (.ipynb) file that
 contains the analysis code to generate the spatial pair distribution
 function, *g(r)*, and the bond order parameter image found in Figure 1. *
 *WP-008-H11.png* * Portable Network Graphics (.png) file of truncated
 tetrahedrons assembled on a 2D surface at a low gravitational field. This
 is the raw data/image used to run the analysis code on
 *(OrderParameterAnalysis.ipynb).* * *WP-008-H11_centers.csv* * Comma
 separated valued (.csv) file of the centers of the particles found in
 *WP-008-H11.png*. The first column is the x-pixel value and the second
 column is the y-pixel value. This is needed to run the analysis code
 (*OrderParameterAnalysis.ipynb*). ##### **/Figure 2** * *README.md* *
 Markdown (.md) file that has details for installing a conda python
 environment to run the necessary analysis code for the data in Figure 2. *
 *environment.yml* * YAML (.yml) file that declares all necessary python
 libraries to run the analysis code (*orderParams.py and
 OrderParameterAnalysis.ipynb*) * *orderParams.py* * Python (.py) file
 containing necessary functions to run analysis code
 (*OrderParameterAnalysis.ipynb)* * *OrderParameterAnalysis.ipynb* *
 Jupyter notebook (.ipynb) file that contains the analysis code to generate
 the spatial pair distribution function, *g(r)*, graph and the bond order
 parameter image in Figure 2. * *SUM_WP-008-H11_001.png* * Portable Network
 Graphics (.png) file of truncated tetrahedrons assembled on a 2D surface
 at a higher gravitational field. This is the raw image used to run the
 analysis code *(OrderParameterAnalysis.ipynb).* * *SUM_WP-008-H11_001.czi*
 * .CZI file of truncated tetrahedrons assembled on a 2D surface at a
 higher gravitational field. This is the raw confocal image with multiple
 z-planes. * *SUM_WP-008-H11_001_centers.csv* * Comma separated valued
 (.csv) file of the centers of the particles found in
 *SUM_WP-008-H11_001.png*. The first column is the x-coordinate (in
 microns) and the second column is the y -coordinate (in microns). This is
 needed to run the analysis code (*OrderParameterAnalysis.ipynb*). #####
 **/Figure 3** * *README.md* * Markdown (.md) file that has details for
 installing a conda python environment to run the necessary analysis code
 to generate data in Figure 3. * *environment_entropy.yml* * YAML (.yml)
 file that declares all necessary python libraries to run the entropy model
 analysis code (*EntropyModel.ipynb*) * *EntropyModel.ipynb* * Jupyter
 notebook (.ipynb) file that contains the code to generate the single-cell
 occupancy free energy curves as a function of packing fraction seen in
 Figure 3. * *environment_hpmc.yml* * YAML (.yml) file that declares all
 the necessary python libraries to run the hard-particle Monte Carlo (hpmc)
 simulations (*hpmc.ipynb)* * *hpmc.ipynb* * Jupyter notebook (.ipynb) file
 that contains the code to generate the hard-particle Monte Carlo
 simulations seen in Figure 3. * *ATT_centered.stl* * 3D model (.STL) file
 of an Archimedean truncated tetrahedron that is used for the hard-particle
 Monte Carlo simulations (*hpmc.ipynb).* ##### /Supplemental\_Avrami *
 *README.md* * Markdown (.md) file that has details for installing a conda
 python environment to run the necessary analysis code to generate data in
 Supplementary Figure 5. * *environment.yml* * YAML (.yml) file that
 declares all necessary python libraries to run the entropy model analysis
 code (*grainAnalysis.ipynb*) * *grainAnalysis.ipynb* * Jupyter notebook
 (.ipynb) file that contains the code to estimate the number of particles
 in either a 3-fold or 6-fold bond order configuration for the data found
 in Supplementary Figure 5. * */output* * Empty folder for the generated
 output image data generated from *grainAnalysis.ipynb*. *
 *WP-009-L14_timelapse_10x002-3.tif* * Multi-image file (.tif) of raw data
 for calculating the number of particles in either a 3-fold or 6-fold bond
 order configuration. This is the same file as the Supplementary Video 3.
 Each frame corresponds to ~5 seconds. This is needed to run the analysis
 code (*grainAnalysis.ipynb)* * *WP-009-L14_timelapse_10x002-3_centers.csv*
 * Comma separated valued (.csv) file of the centers of the particles found
 in *WP-009-L14_timelapse_10x002-3.tif* for each frame. Each particle is
 denoted by an ID (Column B), which has a unique x coordinate (in pixels),
 Column E "POSITION_X", and y coordinate (in pixels), Column F
 "POSITION_Y" . Each frame can be identified by the Column I
 "FRAME". This is needed to run the analysis code
 (*grainAnalysis.ipynb*). ## Code/Software The code run on each dataset is
 provided in each folder in the form of a `Jupyter notebook` that is tested
 in a `conda` environment. The dependencies are given in the form of a
 `.yml` file. Each folder that has code has an individual `README.md` that
 helps facilitate installing and running the code. Each code was tested on
 11/28/2023 by author(s) and the output cells that are available in the
 `notebook` reflect the code run on the dataset given.