Monthly Archives: October 2010

Media Hunt 4 – “How Does A Heart Attack Happen?”

Heart attacks occur when the inside of heart arteries develop plaques made of various substances. This narrows the arteries, which means there is less room for blood to carry oxygen through. This kills the surrounding areas. It seems like the process could be very sensitive to initial conditions. If plaque develops in slightly different ways it could mean the heart attack occurs sooner.

Holy Heart Attack, Batman!

Heart attacks are initiated by the clotting of arteries. To better predict heart attacks, then, doctors have to know what causes the clots to form. As the video shows, the build-up of atheroma (the clotting agent) is reminiscent of some of the non-linear systems we’ve studied. Somewhat like the DLA models we studied, the build-up of blood platelets forms a cluster that makes further aggregation more likely. I suspect that this non-linearity makes heart attacks especially hard to predict. Certain factors increase one’s risk for heart attacks, but no individual is 100% safe.

What happens during a heart attack.

So this video came up as one of my first youtube search results. I had to post it because it very accurately and realistically shows what happens during a heart attack. You can clearly see the disorder in the blood flow caused by the clot formation. This results in an irregular wave excitation in the heart leading to muscle damage.

Quantum Computing

My understanding for this Media Hunt was how we are trying to use the nano-scale and its effects in the macrosopic region, to improve our technologies

Most of us know of Moore’s Law. Us techies Love and Hate it. Meaning what we just bought,  next year will be worthless. Windows Vista is a good example. Also the iPhone. However we now that it will be better stronger, and faster than ever before the next time around.

So Computers have been developing for some time and we are reaching the point were silicon by itself is becoming the limiting factor.

However companies such as Intel and AMD or still pushing the envelope. The best CPU you can get is the i7-980X [a hexa-core Intel masterpiece] it has 1.17 billion transistors crammed into a die that fits in the palm of your hand, yeah smaller than your phone. the picture below is of the yet to be coated i7-970 the younger brother to the 980 and it too use the 32nm building technology. You heard right, your computer is using nanometer technology to control the electron flow making decisions for what to do with that facebook post you are typing.

Over a billion transistors

OH THE PIXELS REFRESH SO FAST!!!

Silicon is nearing the limit that it can be controlled for this manufacturing process. The next leap in computer is to remove the one to 12 calculations at a time [hyperthreading a hex core gives 12 threads of actual computation] and move to doing all calculations simultaneously in the array. This is the Quantum Computer.

Taking pieces of atoms and intertwining them so we can use them to do calculations. This is considered the ideal computer, to increase efficiency you find better ways to remove the heat generated.

http://www.nature.com/news/2010/100929/full/467513a.html [still cannot figure this GUI out for doing URL links]

This goes into how the qubits are made and why three is needed. It is like a Raid 5 array were three disks are used to store the data. Two hold it and the third is a parity disk that allows for one of the disks to be damaged and/or lost and then have the data reconstructed on a new disk. However in a quantum computer two qubits do the calculation and the third is there to make sure they stay in the proper configuration for the calculation.

To get a better understanding of how tedious it is to really build a CPU the video below is of a game known as Minecraft. In this video, the person has built a working 16 bit ALU (no firmware yet unless you count the operation control bits). imagine that each block is ~16nm that means every gate that he built is ~32nm which is the scale that the newest processors use.

The video is a little long so jump to these key parts:
0:10 the size of the thing (not as good as Intel but it is okay)
1:24 the control bits
4:30 the logic gates for interfacing the working part of the ALU into a readout

The rest of the video is him running through it showing some of the things he made for it

The second video gives a better idea of just how tedious nano-manufacturing can be.

this one is not hyperlinked cause it is not really the key point of this post

The future is asking us to increase performance will decreasing input, essential to building the perfect machine. Quantum computing brings us really close. When we get that one figured out we will be set for another decade or so but until then we will have to get the Interns to use the nano-tweezers and install those 1.17 billion transistors for us.

Emulsion Formation

This video demonstrates a concept in Biological Physics by Philip Nelson.  He explains how certain substances can act as surfactants, and create emulsion to stabilize oil in water.  A surfactant belongs to the class of materials called amphiphiles which have a hydrophobic and a hydrophilic part.  The hydrophobic parts are attracted to the oil and the hydrophilic part is attracted to the water.  An oil droplet can be surrounded by these hydrophobic parts which creates a sphere showing only hydrophilic heads on the outside while the hydrophobic tails hide the oil on the inside.  This video shows the formation of the sphere on a nanoscale.  You can see in the end that all the heads are the only thing you can see on the outside as the tails are hidden.

 

http://www.youtube.com/watch?v=6vabRDBMPRE&NR=1

3d Visualization of Virus Self-Assembly

The following video shows a simplified model for virus assembly. Presumably, the flat part of the pieces represents the hydrophilic part of the molecules, while the pointy part is the hydrophobic end.

As was mentioned in the article “Biomolecules and Nanotechnology”, structures on the microscopic level are strongly affected by thermal vibrations — ie. the “random shaking” in this video. Correctly designed “pieces” can even use these random fluctuations to do work, like self-assembly.

DNA Mutation

This video is kind of self-explanatory, but it follows the replication of DNA and shows how an incorrect amino acid can be coded for. Once the double-stranded DNA strand is cut apart, the single strands are matched with complementary nucleotides. Sometimes this does not happen correctly, either the wrong nucleotide is matched or their is one nucleotide on the strand left uncoded. This affects which amino acid the sequence codes for, and sometimes one change codes for a different nucleotide. This is an example of how small fluctuations can have large repercussions on the nanoscale in Biology.

Self-Assembly of a Membrane

The video below shows a computer simulation of the self-assembly of a lipid bilayer.  Specifically, it simulates what happens when the phospholipid Dipalmitoylphosphatidylcholine (DPPC) is exposed to water.  DPPC acts very much like the surfactants described in Section 8.4 of Biological Physics as each molecule of DPPC has a polar (hydrophilic) head and a hydrophobic tail.  When this substance is placed in water, the molecules arrange themselves so that the hydrophobic tails point toward each other and only the polar heads come in contact with the water.  The result of the natural tendency to arrange in this manner is alternating “layers” of phospholipid and water.  The phospholipid layers are called bilayers because they consist of two rows of DPPC molecules with their tails facing one another.  Most cell membranes are made of a very similar lipid bilayer.  Ultimately, these membranes are able to self-assemble because of the chemical properties of the molecules they consist of.

Viruses and Nanotechnology

This video, though it does not focus on the particulars of how viruses self assemble, is a nice general overview to supplement the material in the readings. The narrator gives a rather interesting, sarcastic, but down to earth explanation of what viruses are and why they should be considered as nature’s form of nanotechnology. It focuses on the unique features of these not-quite alive microscopic particles, such as their ability to bind to cells, inject their own DNA, and cause diseases in your body as a result (while also corrupting your DNA). Studies have shown that a significant part of the human genome has been encoded by virus-like particles. He claims that viruses are “programmed” for infection in that they take advantage of your own enzymes’ ability to read DNA, and he stresses that viruses by themselves cannot hurt you. He also goes into detail about how your body attempts to fight off these infections, focusing particularly on the interactions between white blood cells and macrophages carrying the virus’ DNA. Overall, this video showcases the typical interactions between the cells in your body and these viruses at the nanoscale.

Mandelbrot

Not to be morbid on the eve of our paper submission, but did anyone else see this? I thought it was relevant…
(I’m not sure why the link isn’t showing up but click the “Published..” below)

Sierpinski / Menger Sponge

The Menger Sponge, also known as the Sierpinski Sponge, is an example of a fractal. It is created by dividing a cube into 27 smaller cubes, and removing the center cube and the middle cube on each face. In the image above, we see a plain cube and the first 3 iterations or levels of the fractal.

The Menger Sponge is a three-dimensional extension of the Sierpinski Carpet, which is a 2D shape created by removing the center square from a square divided into 9 parts.

This shape has a fractal dimension [Hausdorff dimension] of approximately 2.726833.

Media Hunt #2: Fractals and Jackson Pollock

Who’s familiar with Jackson Pollock?  Pollock was a very interesting American abstract artist who created art by essentially splattering paint onto the canvas in a seemingly random pattern.  This somewhat psychedelic video I found starts out rather generally giving information about fractals that we’ve already learned in class, but things get more interesting at about 2:15 when Jackson Pollock himself is addressed.  Many examples of Pollock’s paintings are then shown.  Interestingly, with such great controversy surrounding the legitimacy of his work, only Pollock’s paintings contain fractals, whereas the imitators of such work do not.

link: http://www.youtube.com/watch?v=Rs1GZxmdT6swatch?v=Rs1GZxmdT6s

Burning Ship

 

The burning ship fractal was first described by Michael Michelitsch and Otto Rossler in 1992.  This fractal is created by iterations of the equations:

Xn+1 = Xn^2 – Yn^2 – Cx

Yn+1 = 2 * absvalue( Xn*Yn) – Cy

This video zooms in on a fractal that resembles a burning ship.  As you zoom in closer and closer, you start to see the repeated pattern of the burning ship.  This is much like the Mendelbrot set, since each time you zoomed in you would see a smaller version of the original shape.  I would like to explore the burning ship fractal more to see if there are any other repeated shapes.  For example, this video only zooms in the the area on the right.  I wonder if the “swirly smoke” also has this kind of repeated pattern.

 

For more info:  Burning Ship Fractal

Mandelbulb

The Mandelbulb is a 3-dimensional analog of the Mandelbrot set, created by Daniel White and Paul Nylander. Since the 2d Mandelbrot set exists in the space of complex numbers (a + bi, where i is the square root of 2), the 3d Mandelbrot must occupy a space of “hypercomplex” numbers.

The hypercomplex algebra is complicated, but the important thing is that the Mandelbulb uses the map z -> z^n + c    (different values of n generate different Mandelbulbs). The most well-known Mandelbulb seems to be the one generated by n=8:

Just like the Mandelbrot set, the Mandelbulb displays “pseudo-fractal” morphology. There don’t appear to be any exact repetitions, but there are bulbs upon bulbs upon bulbs……. Additionally, we cannot discern our level of zoom just by looking at the level of detail.

Here is a video of a zoom into the Mandelbulb:

For more information, see http://en.wikipedia.org/wiki/Mandelbulb and http://www.skytopia.com/project/fractal/mandelbulb.html

Fractal Carrots

Many plants in nature produce fractal growth patterns, and a plant called Queen Anne’s Lace is one of them.  Queen Anne’s Lace is the special name given to wild carrots, and its floral arrangement displays certain characteristics of a fractal.  From the main stem, each blossom produces smaller iterative blooms, so that each blossom looks just like a copy of the main stem.  In this way, Queen Anne’s Lace shows self-similarity, at least up to a point.  As a biological/physical object, the flower’s fractal characteristics are not infinite, only showing a handful of iterations.  However, its self-budding still gives Queen Anne’s Lace its characteristic, large-scale fractal qualities.

Top View

Bottom View

Broccoli

Broccoli is not only my favorite vegetable but also a fractal.  Broccoli is an example of one of the naturally occurring fractals in the environment.  Broccoli meets the characteristics of being a fractal because it has a small-scale structure, it is split into parts that are smaller than the origin and it can not be described in regular geometric terms because of its irregular structure.    A piece of broccoli would be difficult to measure because of its small structure and infinite complexity.

Media Hunt #2: Fractal Diamonds

    Here is a picture of a diamond fractal (self-named by the author; taken from deviantart.com drawn by JASONQUANTUM1). It is a self- similar pattern, one of the characteristics of fractals. Mathematically, you could find a way to draw this pattern.  What I would like to discuss in class is if real diamonds could be considered fractals? They have very sharp lines inside that cross planes; however, there are no examples in our readings of them. Given that most people have had interaction with diamonds, they probably should be a go-to example. And if we determine that diamonds are not in fact fractals, what makes them different from crystals?

Diamond vs. Crystal

(Diamond picture from jewishjournal.com article; crystal from USDA file found on wikimedia.com)

Falling Sand Game

When looking at the many branch patterns we discussed in class, I couldn’t help but remember a game I played a few years ago. This one was called Falling Sand. It is a complete game of emergence, as there is no progression. All one does is add different types of particles and see how they interact. The interaction that relates to out subject matter is that between the Water and Plant. Water is blue and falls down until it leaves the screen. Plant is green and stays in the same place on the screen. When a blue particle touches a green particle, it stops and turns green, making the plant “grow”. The branching pattern occurs when you place a spout (light blue) above a plant. The spout stays still, but produces water at a seemingly random timing.

The water falls and hits the plant, making it grow. The spots that get more water grow faster and expand, cutting off water to lower parts. This can be furthered by segmenting the spout (as seen in the image) or can be minimized by starting all points at the same time. Here’s the link to try it out yourself:

http://fallingsandgame.com/sand/pyro.html

Media Hunt #2: Peacock Feathers

While it may not seem evident at first, the feathers of a peacock, or any bird feather, show some amount of a fractal pattern.  A feather’s fractal nature does not repeat infinitely, only a few times.  The feather has a main vein off which many barbs extend.  Off of these barbs, extend barbules, and then off the barbules are tiny hooklets.  It is these hooklets which hold the barbules, and therefore the barbs, together giving the feather the shape that we see.  Fractals can be found everywhere in nature, and here we see them found in birds.  The peacock is an especially beautiful bird where the feathers themselves are not only fractals, but also create an exquisite pattern with the other feathers.

Media Hunt 2: Mandelbrot TED Talk

The following is a video of Mandelbrot himself explaining the concept of roughness and how he found regularity within roughness. In the beginning he goes through how a cauliflower, for example, has a repetitive morphology; the more you cut it, the smaller yet same cauliflowers you have. What’s really amazing is how he is able to estimate, just by looking, the fractal dimension of a certain picture. He also talks about how he came up with certain assumptions that were correct, though he had no proofs for them (his friends later found the proofs).

In the video, Mandelbrot  describes himself as “constructing a geometry, a geometry of things which had no geometry” which I thought was pretty interesting.

He also talks about the use of his findings in CGI images in movies, the debate over how large the area of a lung is, and other interesting facts about his career and the Mandelbrot set. He is a really funny guy and the video was very entertaining to watch.