Topology and kinetic pathways of colloidosome assembly and disassembly
Data files
Sep 01, 2025 version files 33.06 GB
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AllClosedColloidosomes.zip
9.03 GB
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Code.zip
646.42 KB
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EncapsilationImages.zip
149.20 KB
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ExtendingVesicle.zip
2.21 GB
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PendantColloidosomes.zip
17.19 GB
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README.md
6.50 KB
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SinglePoreUnwrapping.zip
3.06 GB
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TwoPoreOpening.zip
1.58 GB
Abstract
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.
Dataset DOI: 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.