User:Di Wu

Di Wu (an artistic interpretation)

About Me

Di Wu. I graduated with an Honours degree in Comp Sci at Monash University, right now doing a second degree in Cell Biology major at Melbourne. I hope you will enjoy our iGEM project!

Education

• Columbia University (M.S. in Computational Biology, Sep 2009 - Dec 2010)
• Melbourne University (B.S.)
• Columbia University (Stopped in the middle of M.S. Comp. Sci. because I really like biomedical sciences)
• Monash University (B.Comp.Sci Hon)

Current Work

I'm currently working at the St. Vincent's Institute of Medical Research as a UROP student. My focus is on Cancer Structural Biology, under the supervision of Professor Michael Parker. The main idea is to use crystallography to analyse structures of cancer causing/related proteins and find ways to inhibit them.

Oh, and I can't just walk away without telling you about my other interests, which is on insects! I'll put some photos and vidoes clips of my favourate insect pets. I bet you'll enjoy them.

Reserch Interests

• Cancer, Cancer Stem Cell, cell cycle, signalling regulation

• Biomedical informatics

• And off course our Melbourne iGEM!

Contact

ever_wudi@yahoo.com, diw@student.unimelb.edu.au

A Feasible implementation of Bacteria Counter

Hi Friends,

I know we are at the stage of brainstorming. I just thought about a feasible way of implementating a "bacteria counter", just to put it here in case I forgot, not intending to confuse or distract anyone. If not feeling like to read it now, just skip it or come back later. The "bacteria counter" not only can be used for "biological clock" but also could be used for related topics which we might come up later. Just as a proposed idea.

We could use the strategy of binary counting in biological counting systems. Before I start, I shall give a very brief idea (and that's all we need to know) on binary counting (I'm sure some people already knew this via mathematics, computer science, physics, engineering etc):

Binary counting (based on 2) is done in the same a way as decimal counting (based on 10, as we do everyday). For example,

if we want to represent number 3 in binary numbers (bits), [math]\displaystyle{ 3 = 1\times 2 + 1\times 1 = 1\times 2^1 + 1\times2^0 = 11~(base ~2) }[/math]

to represent number 4 in binary, [math]\displaystyle{ 4 = 1\times2^2 + 0\times2^1 + 0\times2^0 = 100~(base ~2) }[/math]

to represent number 5 in binary, [math]\displaystyle{ 5 = 1\times4 + 0\times2^1 + 1\times1 = 1\times2^2 + 1\times2^0 = 101~(base~ 2) }[/math]

Binary numbers can represent arbitarily large numbers just as digital numbers, e.g. if we have a binary number 1011011,

[math]\displaystyle{ 2^6 }[/math]	[math]\displaystyle{ 2^5 }[/math]	[math]\displaystyle{ 2^4 }[/math]	[math]\displaystyle{ 2^3 }[/math]	[math]\displaystyle{ 2^2 }[/math]	[math]\displaystyle{ 2^1 }[/math]	[math]\displaystyle{ 2^0 }[/math]
1	0	1	1	0	1	1

= [math]\displaystyle{ 1\times2^6 + 0\times2^5 + 1\times2^4 + 1\times2^3 + 0\times2^2 + 1\times2^1 + 1\times2^0 = 64 + 0 + 16 + 8 + 0 + 2 + 1 = 91~(base~10) }[/math]

Implementing Binary expression on "bacteria counter"

Ok, so how can we implement this in bacteria systems? Say we have 3 bacteria: B2 B1 B0, each with its own characteristic colour (or other traits) when its expression is turned on, e.g. B2=red B1=green, B0=blue. Also, each B(n) needs the expression outcome only from B(n-1) plus a toggle control to express its own gene. Then we can read off the current number just by reading the color combinations (or other characteristic traits). For example,

B2	B1	B0	Binary	Decimal(time)
clear	clear	clear	000	0
clear	clear	blue	001	1
clear	green	clear	010	2
clear	green	blue	011	3
red	clear	clear	100	4
red	clear	blue	101	5
red	green	clear	110	6
red	green	blue	111	7

So for instance if our colour combination is red, green, blue, then we know our current time is 7, if colour combination is just red, we know it's time 4. Every expression of B(n) depends only on input from B(n-1) plus another toggle control. So the only bacteria determining counting speed is B0 (just like in a stop watch where the counting speed is entirely dependent on the last digit). Maybe we can race the real clock by adjusting the expression rates!

As we know ALU (Arithmetic Logical Unit) is also based on binary number operation. This idea could be extended to be implemented on binary addition, substitution, multiplication.

This is just 1 out of the many thoughts we've put. We have the whole bucket of great ideas from other brilliant brainstormers!