2013 AAAS Annual Meeting--> Boston Trip

On the 14th of February, Mr. Calos, Mr. Evans, Ms. Hatton, few of the science interns and I went to the AAAS meeting at Boston. The first night we had a really nice dinner at Joe's and the next day we woke up at 7:00 am ready to attend the meeting. As a person who lacks a sense of direction (except underground), I was not surprise when we got lost the minute we got to Hynes Convention Center, which was connected to our hotel. However, we got registered and went to forums that each of us are interested in.

2/15
Symposia that I went:
1) Is Beauty Truth? Mathematics in Physics from Dirac to the Higgs Boson and Beyond (went to this because I just read an article online that talked about the Higgs Boson, which was a newly discovered particle. Also because I am interning at the Particle Physics department and want to know more about the topics).
2) The Science of Uncertainty in Genomic Medicine
3) More Than Pretty Pictures: How the Process of Making Science Images and Graphics Clarifies Understanding
//Poster Sessions for 20 minutes//
4)Science Advances and New Strategies for Reconstruction of Oral and Facial Tissues.
5)Stroke Research: New Concepts and Innovative Solutions
6) Sherry Turkle: The Robotic Moment: What Do We Forget When We Talk to Machines.
//Dinner and rest//

Because there were so many talks that I wanted to go, I barely have time to rest and go outside. Sherry and I (we went as a team because I do not own a cellphone) sat through all of the talks except for the Facial Reconstruction one because it was overlapped with the Stroke Research presentations. During the half hour break we had in the morning (in between two talks) Sherry and I went to the exhibitions. We talked to several people and got a lot of souvenirs. :)

2/16
1)The Connectome: From the Synapse to Brain Networks in Health and Disease.
2) Family Science--> this was lots of fun, I saw a lot of demonstrations and attempted to ask a really hard question for the "Ask an Engineer" booth but failed, partly because of the lack of time (only had 10 minutes in the Family Science Event).

I don't know why.. but Sherry and I found extra time to go to the exhibitions again. This time we listened a lecture at NASA's booth and talked to a person from Wolfram who introduced us to Mathemetica and a search engine (the "mother" of Siri)--> more souvenirs ensued~

Sharing time~
The two talks that are easier to explain with only words and are also very interesting are:
1) A Data Driven Pathway to Genomic Medicine (Robert C. Green)
Dr. Green from Partners Center for Personalized Genetic Medicine. As technology advances "personalization" of health care using one's genetic code has became a new possibility. Dr. Green talks about G2P "Genomes to People" which is a research in Translational Genomics and Health outcomes. He focuses on the REVEAL study (Risk Evaluation and Education for Alzheimer's Disease). In the study, each individual has their genes coded and the researchers found out that as individual possess one or more copies of APOE (E₄ ) genotype he/she is more likely to develop Alzheimer's Disease. It turns out that APOE gene is also linked to the Heart Disease which is reasonable since Alzheimer's is due to the lack of blood flow. The results also show that after the individuals got their results back, they have increased their exercise and improved their diet. People handled the data well. However, the insurance companies will be at risk after the "personalization" of health care become publicized because they are going to loose a lot of money.
--> a counterargument was presented by James P. Evans (Jim) from University of North Carolina. He said that genomics in clinical medicine may only be useful when the the disease is rare because they have less factors, whereas the common diseases has too many etiologic factors and risk alleles that are going to be hard to predict the possibility of actually getting that disease.

2)Molecules and Mechanisms Involving in Synaptic Plasticity in Health and Disease (Mark F. Bear, MIT)
Dr. Bear talked bout the plasticity of the synapses that leads to Amblyopia and Autism. In my blog I am going to focus on the Autism part.
Fragile X Syndrome: a intellectual disability, a cause of Autism. Has
LTD (Long Term Depressing): serves to selectively weaken specific synapses in order to make constructive use of synaptic strengthening caused by LTP (wikipedia).--> enhanced--> Autism. LTD is enhanced by unusually amount of AMPAR internalization (see figure below) which is due to a lack of FMRP protein that acts as a initiator of the AMPAR internalization and also a negative feedback inhibitor that stops more FMRP protein generation therefore stops the internalization of AMPAR.

http://www.sciencedirect.com/science/article/pii/S0304416509000348

A. In normal brains, FMRP is produced normally, making good amounts of AMPA receptor when mGluR5 receptor is activated. 

B. in Fragile X Syndrome FMRP is silenced therefore there is an abundance of AMPAR internalization causing LTD to be enhanced (causing abnormal dendrites spines to be formed in patients with Fragile X Syndrome, less contact with other neurons, neurons weakened--> mental disability)

C. in therapy MPEP is used to silence mGluR5 which slows down the internalization of AMPA (not in his talk but from the website). What he said was only to inhibit mGluR5 but I did not hear things about MPEP.

Dark Matter Simulation Step 1

Today, we finished the interactive button pressing projectile motion simulation (which surprisingly only took about ten minutes) and posted on our website. http://www.sos.siena.edu/~mbellis/ew_processing/final_projectile.html

You can click on the button on the upper-right corner and stop the ball. Place the mouse on the ball to see the location of the ball. One thing you'll have to be aware of is that Processing's coordinate system is different than the ordinary coordinating system (see figure below).

So when you are looking at the location make sure to find the relative position based on the starting point's location. 

The next thing we did was to start making the Dark Matter Simulation!!! (a moment I've been waiting for so long!)

Dr. Bellis wants me to start with making the sun rotate around the center of the Milky Way Galaxy which I represented as a circle in the middle. It was perplexing at first because I did not have any experience on making circular motion before.  Dr. Bellis gave me a hint.. that is: the equation of a circle r^2=x^2+y^2 and I related it to x=rcos(theta) and y=rsin(theta) which I can use for the center of the circle as it moves. To create motion I have to increase the theta as time goes by so the code I made was x=rcos(theta+t*0.1) and similarly with y-coordinate. As for the "r" I made it a float (variable) so that we can modify it whenever we want.

I also added a few increasing transparency circles in the simulation to show the density of the stars in the Galaxy. 

Orange= Sun, Black= Center of the Galaxy

Code:

int windowHeight= 800;

int windowWidth= 800;

float radius= 20;

float t=0.0; 

float x0= 32;

float y0= 32;

float theta=3.142/6;

float meters2pixels= 10;

float pixels2meters= 1/meters2pixels;

int frameRateSpeed= 30;

void setup() {

    size(windowWidth, windowHeight);  

    noStroke();     

    frameRate(frameRateSpeed);   

}

void draw() { 

    

    background(255);  

    float g= 9.8;

    float x=cos(theta+t*.5)*radius+x0;

    float y=sin(theta+t*.5)*radius+y0;

    float ellipse_width=20;

    float ellipse_height=20;

    

    x = meters2pixels*x;

    y = meters2pixels*y;

    

    

    ellipseMode(CENTER);

    fill(230);

    ellipse(320,320,500,500);

    fill(200);

    ellipse(320,320,250,250);

    fill(150);

    ellipse(320,320,120,120);

    fill(0);

    ellipse(320,320,20,20);

    fill(240,127,70);

    ellipse(x,y,ellipse_width,ellipse_height);

    

    PFont f;

    f = createFont("Microsoft Sans Serif", 16, true);

    textFont (f, 24);

    

   fill (182,132,222); 

    String time_text = "time: "+nf(t,1,2);

   text (time_text, 10, 580);

   fill (83,130,229);

   textFont (f,18);

   text("Center of Galaxy", 260,360);

    t= t+(1.0/frameRateSpeed);

    

   

   if (t>400)

   { 

     t= 0;

   }

   if (y>=windowHeight)

   {t=0;}

  

   

}

The next meeting I'll add Earth to our simulation which will rotate around the sun while the sun rotates around the center of the universe.

Because I finished this step early I asked Dr. Bellis about Higgs Boson and the Higgs Mechanism that I read on a website (http://case.ntu.edu.tw/blog/?p=12593#more-12593 ==in Chinese). During our conversation I learned that he was involved in the experiment. The Higgs Boson was found recently by CERN (a large particle physics lab) using the LHC (Large Electron-Positron Collider, so big that it goes across the border of France and Switzerland-underground 27km circumference). It was really interesting to me because the LHC uses the same idea behind PET scan which is a scan used for detecting blood flow in brain (which I just read about a day ago for Neuroscience class). The machine shoots out a position (e+) which is an anti-matter, when it collides with an electron (e-) the collision produces two protons (p+) that shoot out in opposite directions. The circular machine then detects the protons that hit the wall and form a graph/image from the impacts it receive. For PET scan, the patient injects a radioactive substance (collides with positron and shoots out proton) in their blood so when there is more blood flow in a particular area in the brain, the PET scan can sense it. 

LHC and the route the particles travel

LHC air view

A PET scan for brain imaging 

Learning about Dark Matter

Today Dr. Bellis posted my simulations on a website so other people can view it~~ :)
Link: http://www.sos.siena.edu/~mbellis/ew_processing/spring_2013.html

It was really fascinating to watch him make the webpage... I couldn't play with it because the program was on his computer. With HTML codes. While he was making the webpage, I searched about HTML codes, maybe next time I can try to get it on my computer (the codes are not that complex), and added mouse tracker for the projectile motion simulation. Our goal is to place a button that will start and stop the ball on the simulation and be able to place the mouse on the ball to see it's location at different times (which I have already done, but not the buttons... still discovering how to do that).


The next thing that I did was to do the worksheet on GoogleDoc about Dark Matter, because we are going to start making the Dark Matter simulations soon. My mentor has a meeting from 3:30 to the end of my internship, so I did the worksheet while he was away.
Here is the work that I've done:

For this assignment, I’ve given you some questions to answer that will hopefully teach you a bit about Dark Matter. You need only answer in a few sentences...or a paragraph at most. Feel free to use Wikipedia or other website, but put the link in this document from where you got the material. Let me know if you have any questions!

Who was Vera Rubin? (picture from Wikipedia)

Vera Rubin is a woman who discovered the galaxy rotation problem (the discrepancy between the predicted angular motion of galaxies and the observed motion) by studying galaxy rotation curves which led to the theory of Dark Matter.
A: Predicted value
B: Observed value.

The link to galaxy rotation problem: http://www.popscicoll.org/dark-matter/galaxy-rotation-problem.html
Theory for the rotational speed claimed that as the stars are farther out from the center the speed will be less but in reality the speed did not change. → Raises the question that there might be some kind of matter that exerts an extra pull on the stars to cause it to have a higher speed.

Who was Fritz Zwicky?
Published extreme concepts of the 1930s—neutron stars, galactic gravitational lensing, supernovas.

Discovered and named the concept of “Dark Matter”.

While observing the rotation of galaxies (which do not orbit around a central heavy object like the sun) and wanting to determine the velocity of the galaxies, he applied the virial theorem. “A straightforward application of classical mechanics, the virial theorem relates the velocity of orbiting objects to the amount of gravitational force acting on them. Isaac Newton's theory tells us that gravitational force is proportional to the masses of the objects involved, so Zwicky was able to calculate the total mass of the Coma Cluster from his measured galactic velocities. Zwicky also measured the total light output of all the cluster's galaxies, which contain about a trillion stars altogether. When he compared the ratio of the total light output to the mass of the Coma Cluster with a similar ratio for the nearby Kapteyn stellar system, he found the light output per unit mass for the cluster fell short of that from a single Kapteyn star by a factor of over 100. He reasoned that the Coma Cluster must contain a large amount of matter not accounted for by the light of the stars. He called it "dark matter." -http://www.learner.org/courses/physics/unit/text.html?unit=10&secNum=2

What is a WIMP, as it pertains to dark matter?
WIMPs are the subatomic particles which are not made up of ordinary matter. They are "weakly interacting" because they can pass through ordinary matter without any effects. They are "massive" in the sense of having mass (whether they are light or heavy depends on the particle).
Source: http://imagine.gsfc.nasa.gov/docs/teachers/galaxies/imagine/dark_matter.html

It is a candidate of the Dark Matter because Dark Matter also does not interact with other matters which is similar to the characteristics of WIMPs.

How big is the Milky Way galaxy?
The Milky Way is a barred spiral galaxy 100,000–120,000 light-years in diameter containing 200–400 billion stars. (Wikipedia).

How far is our sun from the center of our galaxy?
26,000 light years away from the center of Milky Way galaxy.
http://www.enchantedlearning.com/subjects/astronomy/solarsystem/where.shtml

How fast does the sun rotate around the center of the galaxy? (velocity in m/s)
The orbital speed of the Solar System about the center of the Galaxy is approximately 251 km/s. (Wikipedia)

How fast does the Earth rotate around the sun? (velocity in m/s)
The orbital speed of the Earth around the Sun averages about 30 km/s (108,000 km/h).
(Wikipedia)



:)