Category Archives: Media Hunt #4

Enigma Machine

The Enigma Machine was used by the Germans during WWI to encrypt messages electrically.  It looks  a lot like a typewriter.  On the front, there is a plugboard where you can plug in different wires into different letters.  The Germans would switch up these letters everyday.  This is where a lot of randomness can play into the encryption.  There are also 3 rotors, which you can change to any number from 1 to 26.  Each day, the rotors are set to a different code and the wires in the plugboard are also changed daily.  When you type a letter, the different coded letter will light up on the machine.  Each time you type a letter, the rotor changes one position.  There are many different places where the operator can change the settings.  This makes the encryption code very chaotic and difficult to break.

Ecological Patterns in Coral Reefs

As covered in this week’s reading, a number of natural ecological patterns can be seen in coral reef ecosystems.   The video below gives a brief overview of coral reefs and their dynamics.  It does not specifically address the different spacial patterns that occur, but it shows a wide variety of coral reef footage that does display the different patterns that emerge.  The reading for this week mentioned some types of patterns that can occur in coral reefs, such as regularly spaced coral plates and reef islands that form.  The coral naturally exhibits individual growth symmetry and pattern, which then lead to larger growth patterns once other outside factors become involved.  These factors can include the flow path of water, the available nutrients of an ecosystem and its distribution, and the dispersion of other organisms that directly influence the coral.  These types of small scale and large scale patterns, and some of their influences, can be seen in the following video after the first 25 seconds or so.

Spatial Self-Organization in a Mussel Bed

The mussel bed shown in the video above demonstrates how an ecosystem can reveal spatial self-organization. In the reading, spatial self-organization is described as “the process where large-scale ordered spatial patterns emerge from disordered initial conditions through local interactions.” It is clear that this mussel bed possesses all of the qualities given in this definition. The mussels begin in a disordered state. They are simply spread out all over the surface with no concern about their position in the system. Then as time elapses, the mussels begin to interact with each other and group together. This grouping occurs locally at certain places but spreads throughout the entire system. As a result of this grouping, the mussel bed forms a pattern similar to that of a activator-inhibitor system than was presented in the reading. The reading also describes how this system corresponds to an activator-inhibitor: “the activation results from local cooperative behavior and the inhibition from resource depletion.”

Activator-Inhibitor Model

This clip demonstrates the activator-inhibitor model as presented by Alan Turing. While the video itself is very short, it shows the concept quite well. Relative to the reading, the blue color would represent the I compound, diffusing much more quickly away from the centers of diffusion and creating a negative feedback loop for the red color. The red/yellow centers represent the A compound, diffusing slowly and creating a positive feedback loop at the centers of diffusion.

Ecological Patterns: Critical Biodiversity



This video discusses the growing rate at which extinctions are occurring in all ecosystems across the world.  The name of the video (Critical Biodiversity) really drew me in; is there a critical point in which our ecosystems cannot sustain such extinctions, and begin to fall into rapid decline?  The connotations and connections with nonlinearity here show that if this is the case, small fluctuations on animal populations or even in the abiotic factors that govern these populations could result in dire consequences for biodiversity, which the video correctly notes as an area that every single world economy and livelihood is based on.  Will symmetry breaking in ecology result in a barren, lifeless earth?  Let’s hope it doesn’t come to that.

Electric beats: Pacemakers and the human heart

This video shows how heart arrhythmias can be treated by different types of pacemakers.  The heart does have a natural pacemaker which is the sinus node but there are times when that cardiac rhythm generating area can become out of sync and throw the heart out of its natural rhythm.  This video shows how pacemakers can get the heart beating in a more steady rhythm or with more complicated arrhythmias restart the heart.

Heart Attack by Rupture

The majority of videos and sites I looked at about heart attacks discussed a heart attack occuring when an artery was clogged by the build up of plaque.  This generally happened either by a complete block by the plaque itself, or by cells getting caught on some plaque and those building up.  The heart attack described in this video happens in mostly the same fashion, however it was a little bit different in that rather than plaque just building up overtime, there is a bit of plaque build up on one wall of the artery which at some point ruptures and the plaque rushes out of the rupture and quickly fills up the artery, blocking all flow.  It would be interesting to look at how the initial conditions of the artery and amount of plaque play a role in determining in what manner a blockage will occur or even if the plaque will build up enough to cause an attack.

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


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. [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.

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.