DOI: 10.5061/dryad.g4f4qrg03
title: Topology and kinetic pathways of colloidosome assembly and disassembly

description: Closed capsules, such as lipid vesicles, soap bubbles, and emulsion
 droplets, are ubiquitous throughout biology, engineered matter, and
 everyday life. Their creation and disintegration are defined by a
 singularity that separates a topologically distinct extended liquid film
 from a boundary-free closed shell. Such topology-changing processes are of
 fundamental interest. They are also essential for intercellular transport,
 transcellular communication, and drug delivery. However, studies of
 vesicle formation are challenging because of the rapid dynamics and small
 length scale involved. We develop fluid colloidosomes, micrometer-sized
 analogues of lipid vesicles. The mechanics of colloidosomes and lipid
 vesicles are described by the same theoretical model. We study
 colloidosomes close to their disk-to-sphere topological transition.
 Intrinsic colloidal length and time scales slow down the dynamics to
 reveal colloidosome conformations in real time during their assembly and
 disassembly. Remarkably, the lowest-energy pathway by which a closed
 vesicle transforms into a flat disk involves a topologically distinct
 cylinder-like intermediate. These results reveal aspects of topological
 changes that are relevant to all liquid capsules. They also provide a
 robust platform for the encapsulation, transport, and delivery of
 nanosized cargoes.
description: # Topology and kinetic pathways of colloidosome assembly and disassembly
 Dataset DOI:
 [https://doi.org/10.5061/dryad.g4f4qrg03](https://doi.org/10.5061/dryad.g4f4qrg03) ## Description of the data and file structure The dataset includes the main folder EncapsilationImages.zip containing the following sub-folders: * AllClosedColloidosomes * EncapsulationImages * ExtendingVesicle * PendantColloidosomes * SinglePoreUnwrapping * TwoPoreOpening These were all taken on a spinning disk confocal.  ### Files and variables #### File: Code.zip **Description:** Contains a Python notebook to construct the energy landscapes of the one- and two-pore colloidosomes. Contains a Python notebook to generate the energy-minimizing shapes for closed colloidosomes, pendant colloidosomes, and one-pore and two-pore colloidosomes.  #### File: EncapsulationImages.zip **Description:** Contains raw images used to make Figures 4 B,D. Images formatted as TIFF files. #### File: AllClosedColloidosomes.zip **Description:** Contains raw images of all 42 Litmus colloidosomes from Figures 1 C,D,E,H. Images all formatted as TIFF stacks. Each subfolder contains a single image stack, corresponding to each vesicle.  Essential parameters for analysis are Colloidosome 1: dX = dY = (2*6.45/40) µm, dZ = 0.5 µm Colloidosome 2: dX = dY = (6.45/40) µm, dZ = 0.5 µm Colloidosome 3: dX = dY = (2*6.45/40) µm, dZ = 0.5 µm Colloidosome 4: dX = dY = (2*6.45/40) µm, dZ = 0.5 µm Colloidosome 5: dX = dY = (2*6.45/40) µm, dZ = 0.5 µm Colloidosome 6: dX = dY = (2*6.45/40) µm, dZ = 0.5 µm Colloidosome 7: dX = dY = (2*6.45/40) µm, dZ = 0.5 µm Colloidosome 8: dX = dY = (2*6.45/40) µm, dZ = 0.5 µm Colloidosome 9: dX = dY = (2*6.45/40) µm, dZ = 0.5 µm Colloidosome 10: dX = dY = (2*6.45/40) µm, dZ = 0.5 µm Colloidosome 11: dX = dY = (2*6.45/40) µm, dZ = 0.5 µm Colloidosome 12: dX = dY = (2*6.45/40) µm, dZ = 0.5 µm Colloidosome 13: dX = dY = (2*6.45/40) µm, dZ = 0.5 µm Colloidosome 14: dX = dY = (2*6.45/40) µm, dZ = 0.5 µm Colloidosome 15: dX = dY = (2*6.45/40) µm, dZ = 0.5 µm Colloidosome 16: dX = dY = (2*6.45/40) µm, dZ = 1 µm Colloidosome 17: dX = dY = (2*6.45/40) µm, dZ = 1 µm Colloidosome 18: dX = dY = (6.45/40) µm, dZ = 0.5 µm Colloidosome 19: dX = dY = (6.45/40) µm, dZ = 0.5 µm Colloidosome 20: dX = dY = (6.45/40) µm, dZ = 0.5 µm Colloidosome 21: dX = dY = (6.45/40) µm, dZ = 0.5 µm Colloidosome 22: dX = dY = (2*6.45/40) µm, dZ = 1 µm Colloidosome 23: dX = dY = (6.45/40) µm, dZ = 1 µm Colloidosome 24: dX = dY = (2*6.45/40) µm, dZ = 1 µm Colloidosome 25: dX = dY = (6.45/40) µm, dZ = 0.4 µm Colloidosome 26: dX = dY = (2*6.45/40) µm, dZ = 1 µm Colloidosome 27: dX = dY = (2*6.45/40) µm, dZ = 0.5 µm Colloidosome 28: dX = dY = (2*6.45/40) µm, dZ = 0.5 µm Colloidosome 29: dX = dY = (2*6.45/40) µm, dZ = 0.5 µm Colloidosome 30: dX = dY = (11/40) µm, dZ = 0.5 µm Colloidosome 31: dX = dY = (11/40) µm, dZ = 0.5 µm Colloidosome 32: dX = dY = (22/40) µm, dZ = 0.5 µm Colloidosome 33: dX = dY = (22/40) µm, dZ = 0.5 µm Colloidosome 34: dX = dY = (22/40) µm, dZ = 0.5 µm Colloidosome 35: dX = dY = (22/40) µm, dZ = 0.5 µm Colloidosome 36: dX = dY = (22/40) µm, dZ = 0.5 µm Colloidosome 37: dX = dY = (22/40) µm, dZ = 0.5 µm Colloidosome 38: dX = dY = (22/40) µm, dZ = 0.5 µm Colloidosome 39: dX = dY = (22/40) µm, dZ = 0.5 µm Colloidosome 40: dX = dY = (22/40) µm, dZ = 0.5 µm Colloidosome 41: dX = dY = (22/40) µm, dZ = 0.5 µm Colloidosome 42: dX = dY = (22/40) µm, dZ = 0.5 µm #### File: ExtendingVesicle.zip **Description:** Contain Raw images for three different extending colloidosomes, with the associated mesh files that contour the images. Images all formatted as TIFF stacks, and mesh files are stored in '.ply' format and can be opened using MeshLab.  Essential parameters for analysis are RawImages_1: dX = dY = (6.45/10) µm, dZ = 2.5 µm, dT = 2 min RawImages_2: dX = dY = (6.45/10) µm, dZ = 2.5 µm, dT = 2 min RawImages_3: dX = dY = (6.45/10) µm, dZ = 2.5 µm, dT = 2 min In each folder, images and meshes are numbered in ascending order.  #### File: PendantColloidosomes.zip **Description:** Contain pendent colloidosomes. The subfolder 'non-extending' contains the images for Figure S6. The subfolder 'TearingVesicle' contains raw images for Figures 2 B,C. Images all formatted as TIFF stacks, and mesh files are stored in '.ply' format and can be opened using MeshLab. Essential parameters for analysis are Non-extending: dX = dY = (11/40) µm, dZ = 3 µm, dT = 1.5 min TearingVesicle/Closure: dX = dY = (2*6.45/40) µm, dZ = 0.8 µm, dT = 5 min TearingVesicle/Extending: dX = dY = (2*6.45/40) µm, dZ = 0.622 µm, dT = 2 min In each folder, images and meshes are numbered in ascending order.  #### File: TwoPoreOpening.zip **Description:** Contains raw data for the two-pore disassembly pathway shown in Figures 3 H,I. Images all formatted as TIFF stacks. Essential parameters for analysis are: dX = dY = (2*11/40) µm, dZ = 1 µm, dT = 1 min In each folder, images and meshes are numbered in ascending order.  #### File: SinglePoreUnwrapping.zip **Description:** Contains several raw data sets for the one-pore disassembly pathway, including the one shown in Figures 3 B. Images all formatted as TIFF stacks. Essential parameters for analysis are Set1: dX = dY = (11/40) µm, dZ = 1 µm, dT = 20 s Set2: dX = dY = (11/40) µm, dZ = 1 µm, dT = 20 s Set3: dX = dY = (11/40) µm, dZ = 1 µm, dT = 20 s In each folder, images and meshes are numbered in ascending order.  ## Code/software Code is included in the 'code.zip' file. This includes two subfolders * EnergyLandscapes - TheoreticalShapes EnergyLandscapes is a Python notebook file that generates the energy profiles for the one-pore shape configurations in Figures 3 D,E,F, and the two-pore shape configurations shown in Figures 3 J,K.  TheoreticalShapes is a Python notebook file that minimized the modified Helfrich Hamiltonian, for each of the colloidosome configurations presented in the paper. These include the closed colloidosome contours from Figures 1 F,G, the pendant colloidosomes in Figures 2 D,E and the one- and two-pore shapes in Figure S7. ## Access information Other publicly accessible locations of the data: * NA Data was derived from the following sources: * All data were taken in the Dogic lab at UC Santa Barbara.