Biological Cell Cluster

Contest Ended, Winner(s) have been selected.
Description:
I am looking to obtain a 3D CAD model of a biological cell cluster in order to transfer it to a multiphysics simulation software (COMSOL). The cluster will consist of 120 'cells' in the shape of a hyper-dodecahedron (theory.org/geotopo/120-cell/ ). Each side of each dodecahedron must measure ~5um.
Wants:
In order to better emulate physiological cell models, I require the faces of each dodecahedron (when the dodecahedrons are joined) to be concave with a protrusion in the middle to resemble two cells connecting by a gap junction of ~100nm. Here is a figure showing two sides of two decahedrons joined: http://imgur.com/2E2hdod
Software:
  1. SolidWorks
  2. AutoCAD

Entries

1st Winner
#9 Hyper-D Connected by mariusp
2013-04-08 15:03:50
#1 sample image only by Steven
image of cell. showing repeating gaps
more
2013-03-15 17:04:10
#2 image only by Steven
the 5 unit face limits distortion of the elements. Which keeps them from locking together on all faces. The only way to make this work is to deform each layer into a more and more flattened element. This will create an element with variable face sizes.
more
2013-03-15 18:04:39
#3 Hyper-D model by mariusp
Hi there - i need to know if the starts it's ok for you. Thanks
more
2013-03-18 16:18:50
#4 Hyper-D First Layer by mariusp
2013-03-19 16:23:09
#5 Hyper-D by mariusp
119 cells Hyper-D
more
2013-03-25 17:51:34
#6 Hyper-D (177 cells) by mariusp
Layer0 - 1cell
L1 - 12cells
L2 - 32cells
L3 - 132cells
T = 177cells
more
2013-04-01 11:41:17
#7 Hyper-P by mariusp
L1 - 1 cell
L2 - 12 cells
L3 - 32 cells
L4 - 42 cells
L5 - 162 cells
Total - 249 cells
the last layer has a a few cells more like a pyrmaid
if you want me, i can delete them
more
2013-04-02 17:03:21
#8 12D_demo by poppy
2013-04-04 15:03:19
#10 Hyper-D 3rd Layer by mariusp
2013-04-09 15:34:44

Discussion

mariusp

Designer

Thu, 28 Mar 2013 07:38:45 +0000
hi Jamal,
as far as i understood from whatever I read on the internet it is true that the Hyper D has 120 cells, but that happens only in 4D
now, since we do not have a tool to draw in 4D, the only way to represent your model is the way I’ve drew it – of course we can vary some distance parameters but in the end you will obtain a 3D molecule with 119 cells

to be a little bit more clear please check this:
http://www.georgehart.com/rp/rp.html

if there is something that i do not understood (and it could happen) please write to me

thanks

Jamal

Buyer

Mon, 25 Mar 2013 20:51:19 +0000
Hi mariusp,

Thanks for the upload. I took at look at the work, you are on the right track but it is not quite what I'm looking for. There are indeed 120 cells in the final hyper dodecahedron structure. Also, the final structure should resemble a spherical shape. I will repost here the original site I listed in the contest description as well as another site that should be used as a guideline.

https://theory.org/geotopo/120-cell/
http://eusebeia.dyndns.org/4d/120-cell

I hope this helps out.

Jamal

mariusp

Designer

Mon, 25 Mar 2013 17:52:58 +0000
are u sure that there are 120 and not 119?
pleae check the model that i ve uploaded and tell me if its working for you

Jamal

Buyer

Wed, 20 Mar 2013 23:28:36 +0000
Hi mariusp,

yes indeed the dodecahedron shape is compulsory for the model to work since it is a 120 'cell' hyper-dodecahedron.

As for the purpose, it is to basically simulate in COMSOL the reaction of a cellular cluster - in our case epithelial cell clusters - to an external electric field for biosensing purposes.

Thanks for all your effort,
Jamal

mariusp

Designer

Wed, 20 Mar 2013 14:20:51 +0000
thanks Jamal
so the dodecahedron is compulsory

now a last question if is not to much
what kind of biological cells? (i m asking this question just for ethical purposes)

thanks

Jamal

Buyer

Tue, 19 Mar 2013 17:32:59 +0000
Hi mariusp

I think I answered your question as I understood it. Only the first central dodecahedron is a perfect one (ie. all sides of every face are the same length of 5um). All dodecahdra that come after are imperfect, so yes, you can of course use irregulat polyhedrons to build up the model (but they have to be dodecahedra, in this case though not all faces or sides are equal, hence the irregularity).

As for the purpose, the cluster is supposed to emulate an aggregate of biological cells to be later used as part of COMSOL multiphysics simulations.

Jamal

mariusp

Designer

Tue, 19 Mar 2013 16:27:49 +0000
hi
i understood that
actually you haven't answered my questions
please review them and answer here
thanks

ps: if its possible could you please tell us: what exactly is this cluster about? what does it stands for?
thanks

Jamal

Buyer

Mon, 18 Mar 2013 20:26:38 +0000
Hi mariusp

As indicated in my last response, only the middle dodecahedron is perfect while the rest are irregular dodecahedron. So the answer to your question is yes you must use irregular polyhedra following the central dodecahedron.

Please let me know if more clarification is needed.

Cheers
Jamal

mariusp

Designer

Mon, 18 Mar 2013 19:40:14 +0000
hi Jamal,
thanks for your clarifications
now:
please tell me if we can use other polyhedrons for your model
if the answer is no:
please perform a section and check the model that i ve posted here, and tell me if if the faces that i ve designed for your model fit in what you wanted us to design
thanks

Jamal

Buyer

Mon, 18 Mar 2013 16:58:11 +0000
Hi mariusp,

Absolutely, I am aware that a perfect dodecahedron will not be able to form uniform assembly past the central dodecahderon. The following dodechedra must be 'unperfect' in that the side dimensions have to change to be able to fit (as demonstrated in the link in the contest description). The ~5um dimensions for the sides are for the central dodecahedron only, the rest of the layers have to be around that ballpark but it is inevitable that irregular dodecahedrons must be designed to fit all the layers in building the 120 'cells'.

Please let me know if further clarification is required.

Thanks,
Jamal

mariusp

Designer

Mon, 18 Mar 2013 16:25:01 +0000
hi there
there are conectivity problems in the second layer ...

it is possible to propose a different polyhedron?
if the dodecahedron is compulsory than the second & the tird cell layers will have to have irregular dodecahedrons

so, what's the path that we have to follow?
thanks in advance for your answer

Jamal

Buyer

Sat, 16 Mar 2013 20:51:08 +0000
Hi aghisilaos,

A solid in AutoCAD is preferred. Also, if this is done as parts + assembly then both part and assembly files would be great as it leaves room for future modifications.

Thanks, please let me know if you have any other inquiries.
Sat, 16 Mar 2013 12:44:50 +0000
do you want this to be a solid in auto cad or just planes and meshes?

Jamal

Buyer

Fri, 15 Mar 2013 23:08:02 +0000
Hello,

Thank you for your interest. I realize that this model can be difficult to visualize so I'll attempt my best at trying to explain. Please also feel free to ask more question for clarification.

In order to help clarify a bit, I posted attachements of a sample dodecahedron face (and sample attachement of 2 faces) of the central dodecahedron, which according to the earlier link in the project description is a perfect dodecahedron. I drew these using AutoCAD Inventor and included the .dwg files as well.

Basically, the most important aspect is that there should be a 'gap junction' or hole (I drew it as a protrusion from the middle of the face) of ~100 nm in which all volumes of adjacent dodecahedra are connected. So technically the final design will have one big interconnected volume, although there will be 120 'cells'. It is also important to have the 'cells' glued together at the edges as I illustrated in the attachements (and the cross-section provided at http://imgur.com/2E2hdod), leaving 'empty spaces' between connected 'cells'.

@aghisilaos: If we assume the central red dodecahedron is a sphere, then a diameter of ~10um would be ideal.

@Gabriela: Yes i mean the sides of the dodecahedron should measure ~5um. This will be easy for the central dodecahedron because all faces are equal. However, it will vary for other dodecahedra as the model builds to become a hyper dodecahedron. The dimensions then can vary as long as they're within this range.

@Phil Keane: I hope the illustrations I provided can give a good guide. I can provide more information if needed.

@Steven: Thank you so much for your entries. I am aware that perfect dodecahedra won't interlock past the first layer. I don't even think they interlock when building around the central perfect dodecahedra. The key is to be able to get the dimensions right as to be able to build up to the hyper-dodecahedron. Anything past the first central dodecahedron is not perfect.

As a general note, I'd like to mention that the dimensions need not be completely exact. As long as the ball park figure of ~5um sides (which will vary of course when dodecahedra become very 'unperfect') and ~100nm gap junctions connecting the 'cells'. The rest of the dimensions are not vital as long as the final CAD model contains 120 'cells' that make up a single interconnected volume.

And as a side note, since this is a part of a project that will be used in a scientific publications. The appropriate acknowledgement in the publication will of course be mentioned.

Steven

Designer

Fri, 15 Mar 2013 18:07:17 +0000
the size limitations prevents the model from fitting together properly.

Steven

Designer

Fri, 15 Mar 2013 16:56:40 +0000
perfect dodecahedra wont interlock past the first layer. The gap between them gets wider and wider. Is that ok?
Fri, 15 Mar 2013 16:49:20 +0000
and what size you want the green cells to be in depth?
Fri, 15 Mar 2013 16:39:25 +0000
can u put more details please? specifically show an illustration of where u want the concave part. also, show in detail what you want the protrusion to look like.
Fri, 15 Mar 2013 16:10:52 +0000
When you say "each side... measure ~5um" do you mean each edge measure ~5um?
Fri, 15 Mar 2013 15:30:46 +0000
lets say that the first cell (the red one) is a sphere....what would be the diameter if this sphere?

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