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)



:)

Learning about Buttons

Today, I learned how to place buttons on my simulations and how to track the position of my mouse.

My project today: 

Fourth exercise


For this exercise we will work with adding buttons to the simulation. And this will allow us to control the simulation better.
1) Go over the two examples and try to learn how they work. For reference, see the Processing documentation about buttons.
http://processing.org/reference/
http://processing.org/learning/topics/button.html

2) Make a copy of button_exercise_2 and rename it. Modify this new version so that it prints to the window (using the Text stuff you learned last week) the x and y position of the cursor. 

3) Modify the code so that when the button is pressed it displays some new text. Pick whatever text you like!  :)

4) Place some text next to the button that explains what it does.

Dr. Bellis told me to try to figure out what each codes mean by myself, and understand it more as I create one of my own.

It was really confusing at first but as I tried changing the numbers for each code I got the gist of what the codes represent on the simulation. 
For the second question where it asks me to make the window display the x and y positions of the cursor. I used the string method that I did for last internship and put in all the correct codes. The problem is, the texts did not show up on my simulation. I asked Dr. Bellis for help and we found that texts I want to display on the simulation window have to be written under void draw (), whereas before I just wrote the codes on the very bottom of the series of codes.

The outcome is:
Codes for cursor tracking:
PFont f;
 f= createFont("Times New Romans", 16, true);
 textFont (f, 24);
 fill (83,130,229);
 String MouseX_text= "MouseX:"+ nf(mouseX,1,2);          //for X-coordinates
 text (MouseX_text, 10, 400); fill (83, 130, 229);
 String MouseY_text= "MouseY:"+ nf(mouseY,1,2);          //for Y-coordinates
 text (MouseY_text, 10, 420);

The screenshot eliminated my cursor automatically so you can see it, but the mouseX and mouseY shows the coordinates where the cursor is located. 

When the button (the box) is clicked by the cursor, it turns purple. (yea, I had fun with choosing the colors XD)
After this I found that the box button is also draggable... which I think was an interesting unintentional outcome...

As for the second project I added texts to the button so that when one clicks it, it shows "hello" and click it again it shows "bye". I had a little trouble with that too, the same thing with placement, but is was easily solved.

Codes for stimulating a button with words showing:


int windowHeight = 640;              //This sets the size of the window. 
int windowWidth = 700;

float bx;                                        // button x-position
float by;                                       // button y-position
int boxSize = 75;                         //set the size for the box (square with 75 on each side)

boolean overBox = false;            // This tracks whether or not the mouse is over the box.
boolean locked = false;               // This tracks whether or not the box is ``locked". (I was not sure what        "locked means, I am going to find it out on our next meeting)
float xOffset = 0.0;
float yOffset = 0.0;

int background_color = 0;
int display_text = 0;

void setup()
{
    size(640, 360);
    size(windowWidth, windowHeight);  // Size must be the first statement
    bx = 100;
    by = 100;
    //rectMode(RADIUS); //
}

////////////////////////////////////////////////////////////////////////////////
// This is always the part where we deal with all the drawing.
////////////////////////////////////////////////////////////////////////////////
void draw()
{
    background(background_color);

    // Test if the cursor is over the box
    if (mouseX > bx-boxSize && mouseX < bx+boxSize && mouseY > by-boxSize && mouseY < by+boxSize) {               //A command to tell the computer that if the cursor is within the box range, and is clicked the "if()" commands will show. 
        overBox = true;
        if(!locked) {
            stroke(255);        // If we are over the box, change the colors.
            fill(153);
        }
    } else {
        stroke(153);
        fill(153);
        overBox = false;
    }

    // Draw the box
    rect(bx, by, boxSize, boxSize);
    PFont f;
    if (display_text==1)
    {
     f= createFont ("Times New Romans", 16, true);                   //Here is where I added the texts and set the text to display_text= 1. 
      textFont (f, 24);
      fill (224,97,97);
      text ("HELLO~", 100, 240);                                                //Hello will show up when the button is pressed. 
    }
     else if (display_text==2)
     {
            f= createFont ("Times New Romans", 16, true);
            textFont (f, 24);
            fill (56,183,214);
            text ("BYE", 100, 240);                                                  //Same idea here. 
     }
}

////////////////////////////////////////////////////////////////////////////////
// Here is where we tell the program how to deal with:
//   1) When the mouse button is pressed.
////////////////////////////////////////////////////////////////////////////////

// This code tells us what to do when the box is pressed.
void mousePressed() {

    if(overBox) {
        locked = true;
        fill(19, 230, 128);
        if ( background_color == 0 )
        {
                   background_color = 100;
         display_text = 1;                                           //display_text= 1 is the command for calling up the "hello" when the button is pressed. 
      }
        else if ( background_color == 100 )             //When it is clicked again, if background color is 100 (gray) it will change to 0 (black) as written below+ call up display_text= 2 which is the command for "bye". 
     
        {
            background_color = 0;
            display_text = 2;
         
          }
    } else {
        locked = false;
   
    }
    //xOffset = mouseX-bx;
    //yOffset = mouseY-by;

}

Clicked once

Click back. 

For the next meeting, Dr. Bellis and I are going to start discussing our Dark Matter simulations and he is also working with the computer science department to see if we can upload the simulations that I have done on the internet for people to play with. :)

1/16/2012

Today's shuttle to Siena College was canceled due to the large amount of snow. However, I met with my mentor through GChat and e-mail. It was really hard, because I have more than five windows open on my laptop and questions that took a long time to answer.

The homework I did for this meeting was to change units of my simulation to pixels to make it look more realistic. Before we had to change gravity to a small value to make it fit in the screen and make the ball drop slower, but with the conversion gravity can be 9.8 m/s^2 and would still look the same. To do this I had to add two more variables to my simulation:
float pixels2meters=___;
float meters2pixels=___;
In my case my one pixel is equal to 10 meters, and one meter equals to .1 pixel. This did not work so well after all. I sent my simulation to Mr. Bellis so that he could check it for me. We ended up putting more variables in:
float meters2pixels = 10;
float pixels2meters = 1/meters2pixels;
int frameRateSpeed = 30; // frames per second

size(windowWidth, windowHeight);
   noStroke();     
   frameRate(frameRateSpeed);   //set frameRat to the same as frameRate Speed

t = t+(1.0/frameRateSpeed); // Also changed the time so that time increases when one frame goes through (1/30 sec= one frame)
Another homework was to find how to add text to my simulation. It was really fun, because I kept changing the text color to the colors I want. The things I typed to make text appear was:

PFont f;
    f = createFont("Microsoft Sans Serif", 16, true);   //first one was font type (I looked at the font types in my files for word and feel like this is the best one, second one is font size, and third one means anti-aliasing on)
    textFont (f, 24);
    fill (255);
    text("Yvonne Yen", 10, 240);        //text, size, and location (y-coordinate)
    text("Free Fall", 10, 270); 
During the meeting today, I learned how to add timer on my simulation.

String time_text = "time: "+nf(t,1,2);
   text (time_text, 10, 580);
I took this as an example and created a height measurer on my simulation too! :)

String Height_text= "Height:"+ nf(-y+y0,1,2);    //it is -y+y because I want to know how far the ball traveled as it drops so I set the "y" as the negative value (dropping) and add the initial position to exclude it from the measurement. 
   text (Height_text, 10, 610);

I also changed the color of the texts for height and time too~:)

HERE IS THE END PRODUCT:

Looking at this we can know how much the height has dropped in how many sections. I will check if this simulation is accurate later...

Next week, I will have to communicate with my mentor through e-mail again, because it is Emma's MLK service day.

:)

Mentor Out of Town

School commenced today, however, Dr. Bellis was out of town so we will be having our meeting next week 1/16.

For the missing week, Dr. Bellis has assigned me to new assignments:
"I've added a ``Third Exercise" to our shared Google Folder. I've given you a small assignment as a Part 1 on the document. I've also assigned some reading in Part 2, as well as an additional challenge *only* if you have the time. This second part is a bit harder, so feel free to wait until we get together to tackle it. I think you can do Part 1 next Wed, during your research time, even if you are at Emma Willard and I am not around. "

I'll be doing them later this week. :)

During break I learned another new concept called Mirror Stage by Jacques Lacan (a French psychoanalyst) through a novel that I was reading (I was sick for the first week of break, so other than doing college apps I had a lot of free time). The concept became really fascinating as I did some research to understand it more. It states that Mirror stage is a stage in infancy (around one and a half years old) when babies become able to recognized the image in the mirror as themselves, which sets up their 'ego' and their understanding of 'I'. Before then, they think that the their image in the mirror is an ordinary object. The image in the mirror helps babies to acknowledge their existence, however, according to Lacan, their understanding of self is often twisted by the interaction with other people. The image they see in the mirror is shaped in the way they think other people view themselves, or it can also be the idealized version of what we want to look like. At times when we are confident and successful, the image of ourself in the mirror is often prettier/more handsome than before. And at times we are down, we see a worse looking self in the mirror. :)

A picture of Santa Barbara Beach (LA) that I took while we were drive. 

Revels Week- no meeting

12/19/2012

This week, I was at Revels practice (a traditional play played by the whole senior class) so I could not go to Siena College for internship.

The play went through successfully in all three performances. Everyone was crazy when I and the other monks came in doing the Gangnam Style dance with the Mayan Calendar. The screaming was so laud and I enjoyed it very much. :)

We will have our next internship meeting after winter break.