Compilation of student projects from the Junction 2015 program, organized by the MIT Educational Studies Program: https://esp.mit.edu/learn/Junction/index.html
Uploaded on January 22, 2016.

© All Rights Reserved

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Compilation of student projects from the Junction 2015 program, organized by the MIT Educational Studies Program: https://esp.mit.edu/learn/Junction/index.html
Uploaded on January 22, 2016.

© All Rights Reserved

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You are on page 1of 113

esp.mit.edu

Cover page design by Lucia Lam

Typesetting by Sara Freed Sussman and Herng Yi Cheng

The views expressed in this journal represent those of the student, and

not necessarily those of ESP.

Contents

P REFACE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iii

J UNCTION P ROJECTS AND PARTICIPANTS . . . . . . . . . . . . . . . . . . . . . . . . . vii

Hackenbush and its Variations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Ahaan S. Rungta, mentored by Lane Gunderman

Anusha Datar, mentored by Elizabeth Berg

Ariel Azbel, mentored by Herng Yi Cheng

Applications of Knot Theory to DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

David Li, mentored by Herng Yi Cheng

Teaching Coding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Garrett Mallinson, mentored by Lane Gunderman

On Quantum Mechanics and Computation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Junlin Mo and Trevor Pennypacker, mentored by Lane Gunderman

On the Configurations of Hats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Karen Ying, mentored by Herng Yi Cheng

DNA Sequence Analysis Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

Karen Zhou, mentored by Lane Gunderman

Control Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

Keren Shao, mentored by Christopher Harmon

Visualizing Light Patterns of Flat-Folding Origami . . . . . . . . . . . . . . . . . . . . . . . 65

Ria Das, mentored by Herng Yi Cheng

Understanding and Preventing the Formation of Suicide Pacts

Among Younger Population in both China and the United States . . . . . . . . . . . . . 77

Tianyu (Christina) Lin, mentored by Evan Kuras

Humanity throughout the Holocaust . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

Vineetha Yadlapalli, mentored by Elizabeth Berg

i

Preface

What is Junction?

Junction is a program organized by MITs Educational Studies Program (ESP) where 41

middle and high school students worked on summer-long independent study projects that they

had proposed themselves. Students completed their projects under the guidance of their Junction mentor. Junction 2015 students were between the ages of 13 and 18 from diverse educational backgrounds, coming from areas as close as the city of Boston and as far as Fujian, China.

Some students came to Junction as aspiring novelists, researchers, painters, educators,

game designers, civil engineers or conservationists; others sought meaning within poetry, computer science, design, linguistics, music or mathematics. Some students proposed Junction

projects in fields that were completely new to them, curious about a pattern that they noticed

or a topic that kept appearing in the books they read. Others found project inspiration in their

attempts to understand the experiences of a friend. Still others saw Junction as an opportunity

to express passions that they had already harbored for years.

Junction began with two months of student project development between each student

and their individual mentor as they communicated via email and video chat. To culminate the

summers efforts, from August 10 to 21 all mentors and students assembled on MITs campus for

an intensive program of events. Each student dove into further work on their project, met daily

with their mentor to discuss ideas, progress and feedback, and participated in four multi-day

Seminar classes and ten one-shot Sprinkler classes held on topics such as Russian Language

and Culture, Cheesecake Crafting and Climate Change Science, among many others. Most

classes were taught by the Junction mentors and directors; other teachers included undergraduates from MIT and Northeastern.

The six mentors of Junction 2015 Elizabeth Berg, Herng Yi Cheng, Lane Gunderman,

Christopher Harmon, Evan Kuras and Lucia Lam are current undergraduate and graduate

students pursuing various fields of study. Each mentor is profiled in the Junction Projects and

Participants section of the Journal. In addition to their mentoring and teaching responsibilities, the team used their ingenuity to think up and lead additional activities for Junction students throughout the program.

The mentors devised a puzzle hunt for the first day where students worked in teams to

solve puzzles that featured each mentors areas of expertise. During program down time, they

got to know students through card games and frisbee. Students satisfied their curiosity about

the mentors by having their anonymous questions answered at the mentors Ask Me Anything

lunchtime activity.

The mentors encouraged Junction students to venture out into their surroundings and

iii

P REFACE

bond as a community. A group of students constructed their projects at MITs Edgerton Center

Student Laboratory. The Urban Ecology Sprinkler class took students outside to investigate

the campus and the Gentrification and the Future of Cities Seminar traveled to South Boston

on a walking tour. Students, mentors and directors came together for lunchtime and afterprogram activities such as impromptu five-minute Firestorm classes, a jam session and walks

by the Charles River.

To prepare students for presenting their projects, mentors also developed workshops in

communication, as well as typesetting and editing papers. Also, mentors encouraged students

to practice public speaking and thinking on their feet through improvised presentation games.

On August 21, Junction held its Final Project Showcase at MITs Stata Center. At the showcase,

20 students gave formal talks on their projects to family and friends of the Junction participants, and many more presented informational posters, art pieces and demonstrations that

represented their projects.

Every Junction student had the option to submit excerpts of their work to the Junction

Journal, a formal compilation of the 2015 projects that aims to portray the student diversity,

passion and individual commitment that inspired our mentor and director team. Though the

Journal represents the final product of some students work, behind each entry lies the students unique process of investigation, struggle and refinement, which we also ask the reader to

keep in mind.

It is important to note that not every student submitted to the Journal. Many students

undertook impressive projects that were not text-based and were therefore not as easy to represent on the printed page. We encourage the reader to look over the full list of student projects in

the Junction Projects and Participants section. We are especially grateful to Junction mentor

Herng Yi for editing the Journal, and to Junction mentor Lucia for designing the journal cover

art.

Junction focused on maximizing the learning experiences of middle and high school students mentored by college students. As such, all results from student projects should be interpreted as exploratory in nature.

Acknowledgements

First and foremost the directors wish to thank the 2015 Junction mentor team: Elizabeth

Berg, Herng Yi Cheng, Lane Gunderman, Christopher Harmon, Evan Kuras and Lucia Lam. The

amount of work that they each put into Junction was at times nothing short of astounding, and

we continue to appreciate their perspectives and contributions. We wish to acknowledge the

other Junction Seminar and Sprinkler teachers for their energy and creativity: Crystal Wang,

Taylor Sutton, Arkadiy Frasinich and William Navarre from MIT, as well as Gina Asipenko from

Northeastern. We wish to thank ESP members Emily Tencate, Anthony Lu and Favyen Bastani

for helping out at Junction almost every day. We are grateful to the 2015 ESP chairs, Megan

Belzner and Lisa Ho, for being sources of expertise and advice from the time we began to deiv

P REFACE

velop this years program in January 2015 until Junctions last day in August. We are also indebted to Dr. James Bales for offering mentors and students the use of MITs Edgerton Center

Student Laboratory to work on projects involving electronics and light mechanical tools, and to

librarian Forrest Larson for offering time and materials so that a Junction student could learn

about sound engineering and music production at MITs Lewis Music Library.

We are ultimately grateful to the Junction Class of 2015 and their families for providing us

with much to learn about, reflect on and enjoy. Thank you for sharing your outstanding work

with us this summer. We hope that you take pride in reading the array of explorations ahead.

Sara Freed Sussman and Corinn Herrick

MIT Educational Studies Program

Cambridge, MA

Projects Listed by Mentor

Christopher Harmon studies Mechanical Engineering at the Massachusetts Institute of

Technology (MIT). He has worked on a number of projects involving robotics, electrical engineering, prototyping, and design analysis. He also enjoys composing music.

Alex Yu

Da-Jin Chu

Joel Saint-Eloi

Keren Shao

Long Do

Rudd Dantes

Sarah Kim

Viraz Mahanti

Learning CAD

Building a RC Plane

Control Theory

Building a Quadcopter

Building a RC Car

Bridge Building

The Fruit Chopper

Elizabeth Berg studies Earth, Atmospheric, and Planetary Sciences, as well as Literature

at MIT. Her pursuits span race and gender, atmospheric and oceanic physics, science writing,

environmental science and policy, teaching and cooking.

Anusha Datar

Experiments for Young Students

Claire August

Tina Lu

Tyler Wolfe

Vineetha Yadlapalli

Wendy Matt

Smog in China

Humanity throughout the

Holocaust

The International Banquet

vii

Evan Kuras is enrolled in a Masters program in Environmental Conservation at UMass

Amherst, and has conducted biodiversity research in the Amazon rainforest. His interests include ecology, public health, urban studies and sociology.

Christina Lin

Suicide Pacts Among Younger Population in both

China and the United States

Danielle Gillerin

Jorie Coe

Mady Eori

Olivia Garrahan

Alexander

Lee-Papastavros

Through Song

Haveesh Viswanatha

Herng Yi Cheng is a Mathematics major at MIT who likes investigating the mathematics

behind origami, the art of folding paper. His interests span mathematics, origami, their respective histories, as well as theoretical computer science and science communication.

Ariel Azbel

David Li

Farid A. Azar Len

John Namgung

Karen Ying

Ria Das

Applications of Knot Theory to DNA

Notes on Set Theory and Functions

Machine Learning in Relation to Number Sets

On the Configurations of Hats

Visualizing Light Patterns of Flat-Folding Origami

Lane Gunderman studies Chemistry and Physics at MIT and has done research on biological simulations. He enjoys reading plays and learning about computational, physical and

theoretical chemistry, together with game theory and physics.

Ahaan S. Rungta

Charlie Kip

Garrett Mallinson

Junlin Mo &

Trevor Pennypacker

Designing a Mythology Based Card Game

Teaching Coding

On Quantum Mechanics and Computation

Karen Zhou

Logan Troy

Theorized Game Behavior

viii

Lucia Lam is a Mechanical Engineering major at MIT who enjoys writing, as well as finding trends and common themes throughout history, linguistics or other forms of data. She is

especially intrigued by trends across cultural, geographic and disciplinary boundaries.

Davon Dowie

Jennifer Yu

Hannah Parrott

Owen Tellalian

Pallavi Krishnamurthy

Shashvat Srivastava

William Hu

Juggling for Brains: Achieving Effective Focus

Linguistic Similarities

Effects of Smell on Taste

Gender and the Criminal Mind

The Perception of Time

Dysphemisms: An Overview

The Directors

Corinn Herrick is a senior at MIT majoring in Computer Science. She has been involved

in ESP since her freshman year, serving as Splash Director, Spring HSSP Director and ESP Chair.

She really enjoyed getting to know all of the students at Junction and seeing all of their impressive work.

Sara Freed Sussman is a current sophomore visiting undergraduate at Harvard College

studying physics and math, originally from Lesley University. She likes learning about particles

and studying abstract algebra. She has worked at the Food Project and City Year Boston in

Dorchester, and has also directed Spring HSSP for ESP.

ix

Ahaan S. Rungta

mentored by Lane Gunderman

Abstract

Hackenbush is a mathematical game concerning graphs and thus falls under

the categories of game theory and graph theory. The below study was conducted to further understand and formalize past research on the strategies and

mathematical notation used for Hackenbush, with hopes to perform extensive

research in the future.

1 Introduction

We, first, introduce the notion of a legal initial position, on which the game of Hackenbush

is played. We draw a ground line and a graph G under the following conditions, under the

assumption that all edges are line segments:

All the segments of G are either blue or red.

We say that G is a union of n disconnected graphs, and we call them I 1 , I 2 , . . . , I n , where

n 1.

For each I i , exactly one of its vertices must lie on the ground line.

For example, the graph shown in Figure 1 consists of three disconnected graphs and is a

legal initial position G for blue-red Hackenbush.

Ahaan S. Rungta

On the other hand, the graph in Figure 2 is not legal, since one disconnected graph is not

attached to the ground line.

There are two players. One owns the color red call this the red player and the other

owns the color blue call this the blue player. A legal move is one where a player removes at

least one edge of the color that they own. After a legal move, if the resulting graph contains a

disconnected graph that does not share a vertex with the ground line (an illegal initial position),

then that disconnected graph is removed altogether. The game goes as follows:

One player begins the game by making a legal move.

The other player makes a legal move on the new graph.

The players alternate moves until one of the players have no legal moves to make. This

player is declared the loser and the player who made the last move is declared the winner.

Finally, we define a Hackenbush value v(G) of a position G to be a numerical value given to

a Hackenbush game such that it satisfies some mathematical properties of surreal numbers,

described below.

2 Known facts

It is known that two-player Hackenbush is a combinatorial game, because it satisfies the

four conditions for a combinatorial game:

i. Two players alternately move, the owner of each color.

ii. There is no factor of luck involved and both players have perfect information; in other

words, it is a fair game whose result is determined based on the moves that are made.

iii. The game must terminate, since there are a finite number of vertices and edges.

iv. There is no draw, since the winner is determined by the last person with a move, and we

know that this exists because of condition (iii).

2

Ahaan S. Rungta

VARIATIONS

3 Variations

3.1 3-color Hackenbush

Consider, now, a game of Hackenbush, also with two players and with the same set of legal

moves. However, now suppose there are also black edges, which either player can remove. A

special case of such a three-player game is one where there are no edges owned by either the

red player or the blue player; i.e. all the edges are black. In this case, at any point in the game, the

two players have the same set of legal moves available to them. A black-red-blue Hackenbush

game with only black edges is also called impartial Hackenbush.

We denote n to be the impartial game that starts with an initial position of n black segments chained from the ground, as shown in Figure 3.

Theorem. Given any finite impartial game position G, there is a unique integer n 0 such that

v (G + n) = 0.

4 Relation to Nim

4.1 The game of Nim

In the game of Nim, we begin with m piles of stones. The i th stone has n i heaps. For

example, in the case of m = 3, we have three piles, each with n 1 , n 2 , and n 3 stones. A move is

defined as a removal of m i stones from pile i , where 1 m i n i . Two players alternate moves

until all the stones have been removed. The last player to take a stone is declared the winner.

The other player is declared the loser.

3

Ahaan S. Rungta

Definition. Let m and n be two integers such that, in binary, we have

)

a k a k1 a 0 2 ,

(

)

n = b k b k1 b 0 .

m =

(

)

m n = c k c k1 c 0 2 ,

where c i {0, 1} is the the remainder when a i + b i is divided by 2.

For example,

13 7 = 11012 01112

= 10102 .

The above is also known as bitwise addition.

The default starting configuration of a Nim game usually has a Nim sum of zero. The winning strategy is well-known. The player that starts the game must always leave a non-zero Nim

sum after the first move, which the second player can take advantage of. Therefore, you are

always at a disadvantage if you start the game first at the default configuration.

Towards the end of the game, the method does break down For example, if you have two

piles with one stone each, this position has a Nim Sum of zero, but the player who moves first

in this position wins. More precisely, the Nim strategy changes only when normal play would

result in at most one stone in each pile. In that case, the correct move is to leave an odd number

of piles with one stone (in normal play, the correct move would be to leave an even number of

piles with one stone).

4.3 Nimbers

A nimber is a position n for some ordinal number n, where 0 = {} and (n + 1) = n

{n}. Let G, H be positions positions and let G + H be a position in a combined game where a

current player can choose either to move in G or in H . Computation of G+H is done by repeated

application of the rule

G + H = {G + h | h H } {g + H | g G}.

In other words, position addition is commutative and assosciative.

Theorem. Let the nimber value of game positions G, H be N (G), N (H ). Then,

N (G + H ) = N (G) N (H ).

Ahaan S. Rungta

Consider a union of graphs of the form n.

to a Nim game with original piles with 1, 3, 5, and 7 stones, respectively.

We claim that there is a bijection between a game of Nim with piles of stone with counts

n 1 , n 2 , . . . , n m and a Hackenbush position consisting of chains n 1 , n 2 , . . . , n m . consistent with

the following result.

Theorem. (Sprague-Grundy) Every impartial game under normal play convention is equivalent

to a nimber.

We use a similar type of arithmetic as we did for Nim and impartial Hackenbush. Again,

we let v(G) be the Hackenbush value assigned to a position G, such that v(G) satisfies nimber

properties and the following rule holds.

Definition. (The Simplicity Rule) Let b be the largest value of any position to which blue can

move. Let r be the smallest value of any position to which red can move. (Due to convention,

b < r is always true.) If there is an integer n satsifying b < n < r , then v(G) is the closest such

integer to 0. Otherwise, v(G) is the unique rational number x satsifying b < x < r whose denominator is the smallest power of 2.

Again, v(G + H ) = v(G) + v(H ) for positions G, H . In other words, we think of the Hackenbush value v exactly as we did for Nim values N .

6 Future goals

Ideally, it would be helpful to find a direct relation between some properties of an initial

position and the numerical Hackenbush value of the graph, since the value is immediately related to which player has the winning strategy for the game.

5

Ahaan S. Rungta

We would also like to be able to tackle specifically complicated cases, using the facts we

know about simple ones. For example, cycles in graphs are harder to deal with and can affect

the way the value of a graph relates to just the degrees of vertices.

Also, we could consider infinite games using set theory and perhaps find a homomorphism

between Hackenbush and other more popular mathematical games.

Acknowledgements

Thank you to MIT ESPs program Junction for providing the opportunity to conduct the

above studies and to my mentor Lane Gunderman for assistance, advice, and guidance with the

project. Also thank you to Richard Stanleys Transparencies lecture collection available online

for reference materials.

Inquiry Is Elementary:

Science Experiments for Young Students

Anusha Datar

mentored by Elizabeth Berg

About

After the frustrating experience of being taught science through rote instruction and labs

that were like recipes, many students find themselves annoyed at and confused by the nature of

the subject itself. Students typically do not design their own experiments and solutions until the

later years of their high school education. I created a blog at http://inquiryiselementary.

blogspot.com/ to combat this custom; scientific inquiry should be an important part of curricula for all students, as it will inspire them to pursue and appreciate science and systematic

thought processes. Hopefully, this site will be a valuable resource for educators and parents

hoping to inspire future scientists.1

Grades: K2, 35

Subject: Physics, Engineering

Time: 30 minutes

Anusha Datar

I NQUIRY I S E LEMENTARY

In this activity, students will learn about conductors and insulators in an exciting setting.

With the element of competition, they will be motivated to work effectively and tweak their

designs in order to come up with the best solution.

This is an exciting engineering challenge in which students will learn about insulators

and heat transfer in a competitive and exciting setting. While this experiment works with any

amount of students at any age level, it works best with ten to twenty kids separated into teams,

though it also works with just an individual.

Some materials are very good at deflecting heat, allowing them to keep cold objects cold

and hot objects hot. These materials are called insulators, and they are an essential part of

everyday technology, from coolers to lunchboxes. In contrast, some materials are effective at

allowing heat to pass through them, such as metals.

1.3 Materials

(Should have enough for each group to use):

Aluminum Foil

Masking or Duct Tape

Printer Paper

Newspaper

Parchment/Wax Paper

Cardboard Boxes

Cotton Balls

Rubber Bands

Additional conductors/insulators

Ice Cubes (1 per group/person and 1 separate control)

First, ask the students what they know about ice and what happens as ice cubes melt.

Where does the heat go? What happens to the ice cube? Is this similar to how humans react to

heat?

Then, distribute all of the materials except for the ice cube to the student(s).

After these materials have been handed out, present them with the problem they have to

solve: Using the given materials, they need to build a place where the ice cube could be kept

so that it would not melt. It would be ideal to either weigh or take pictures of the initial cubes.

Afterwards, give the students time to build their structures. Encourage them to plan what they

8

Anusha Datar

O N A R OLL

want to build and which materials they want to use before they start. After they have finished

building, give each group an ice cube to place into their structures. Additionally, place an ice

cube on a bowl or plate without the structure so that students can compare their experimental

results with a controlled group that has no structure. After about thirty minutes, have students

compare the ice cubes in their structures to the ice cube in the bowl.

After deciding who the winner is, discuss the strengths and weaknesses of the different

designs. What materials were useful? Why were they useful? What could we do to make the best

structure? Where is this applicable in real life?

Covers MA 35 Physical Science Standards #6

2 On a Roll

Grades: K2

Subject: Physics

Time: 1520 minutes

This activity is designed to help students understand the properties of different objects

based on their size, shape, and distribution of weight. By experimenting with different ideas,

students will be able to clearly understand the effects of an objects physical properties on how

it acts. This activity is ideal when students work in small groups so that they can effectively

discuss their ideas, but its also okay if they work alone.

Many different three-dimensional objects react to force, or a push or pull, in different ways.

For example, dropping a tennis ball on the ground is very different from dropping a bowling ball

on the ground. In this lesson, we will discover the way that different shapes respond the forces

when they are rolled.

9

Anusha Datar

I NQUIRY I S E LEMENTARY

2.3 Materials

(Should have enough for each group to use):

Construction Paper

Glue/Tape

After introducing students to the materials, present them with the problem that they have

to solve: They need to design one object that rolls in a straight line, and one object that rolls in a

circle. Allow them to try many different combinations in order to decide which one works best.

If some students finish quickly, ask them to design more objects that also meet these conditions.

When all of the students have come up with their shapes, have them discuss why their

designs were effective. What is different about the two objects? Where is the weight centered?

How does this affect how each of the objects roll?

Covers MA K2 Physical Science Standards #3

3 Be a Beaver

Grades: 35

Subject: Biology, Engineering

Time: 30 minutes

This activity integrates both biology and engineering so that students can effectively learn

about the amazing structures animals are able to construct. Students can either work in groups

or individually, though it may be better for them to work in groups so that they can discuss their

ideas.

Beavers are rodents that live both in and out of water. They are threatened by predators

such as wolves and coyotes, and they need a safe place to store their food during the winter.

For this reason, beavers work together to build huge structures made of wood, rocks, and mud.

These structures give them a protective home. Dams also block the rivers that they are built on,

but they allow some water through. In this activity, we will construct our own beaver dams.

10

Anusha Datar

B E A B EAVER

3.3 Materials

Container for sand

Plastic Storage Bin or similar

Aquarium or similar

Sandbox

Sand

Water

Building materials

Popsicle sticks/Skewers

Straws

Rocks

Etc.

After explaining the background information to the students, distribute the materials to

them.

Have the students fill their containers with sand. Then, have them carve a river in the sand

by digging a path through it that is at least two or three inches deep and two or three inches

wide. Have them each pick a location for their dam on the river. Ideally, the dam should only let

a little bit of water through. Students can look at photographs of actual beaver dams for ideas.

Next, let each group construct their dams. Remind them that water pressure is higher as

the water gets deeper, so the bottom of their dam will have to be stronger than the top of the

dam. When students believe that they have finished, allow them to test their dams by pouring

water down the river. If the dam is not effective, let them decide on and accordingly make the

appropriate changes.

After the students have finished with the dam, ask them what they think they did well and

what they think they could have improved on. What was the best shape for the dam to be? What

materials worked best? Where was the best location to build the dam? How do real beaver dams

reflect this?

Covers MA 35 Earth and Space Science #12

For more activities, visit: http://inquiryiselementary.blogspot.com/ or

tinyurl.com/junctioninquiry.

11

Ariel Azbel

mentored by Herng Yi Cheng

1 Introduction

For centuries mathematicians have been fascinated with the vast applications of one particular number. This famous number is known as e. A Scottish physicist, John Napier, first

presented this irrational constant in the world of mathematics four hundreds years ago, and to

this day it is still widely used in calculus. This constant is approximately equivalent to 2.718, but

it goes on infinitely. Other than compound interest, I was not aware of any other application of

the number e. I became fascinated in this mysterious number when I started to learn calculus.

The number appeared in many areas of calculus, causing me to expand my interest in it.

When most math students think of the number e they think of its application in compound

interest and continuous interest formulas. The formula for calculating the compound interest

(

j )nt

is S = P 1 + n . This formula is deceptively simple because the variables have very straightforward meanings. P is the starting amount of money you have, S is the value after t periods, j

is the annual interest rate, n is the number of times the interest is compounded per year, and t

is number of years the money is borrowed for. When you plug in one for t and j while n is approaching infinity the limit is equivalent to the number e. This fascinating mathematical fact is

how John Napier discovered this irrational constant. Surely enough, the adventure of the number e does not stop here. Another common citing of the number e is in the base of the natural

logarithm. When mathematicians were deriving logarithms they would not get nice numbers,

rather they would get strange decimals and fractions. After years of testing they discovered one

number that could be used as a base for the logarithm, and once it was differentiated, it would

give you a good answer. This number was e, and when you differentiate log base e, also known

as the natural logarithm, you get 1/x because the natural logarithm of e is equal to 1. This astounded the math community, since such a strange, irrational number could give you such a

good answer.

13

Ariel Azbel

T HE M AGICAL N UMBER : e

One of the first concepts most students learn in calculus is how to calculate a derivative.

To clarify, a derivative of a function is the slope at a particular point on that graph. The number

e has an immense role in derivatives because once you differentiate the function e x you get e x .

This is the only function in all of mathematics where this happens. If you were to graph the

function e x and find the slope of each point on that graph it would give you that same function.

Moreover, the derivative of C e x is also C e x for any constant C , and when x = 0 the function

needs to evaluate to 1. Therefore the only function whose derivative is itself, and satisfies f (x) =

1, is f (x) = e x . The function e x has many other interesting applications, such as the Taylor and

Mclaurin series. The Taylor series is function that is represented by an infinite sum of terms

that are based on the derivatives of that function at a certain point. The Mclaurin series is

equivalent to the Taylor series, except the point that you are calculating the functions derivative

at is 0. Here are a few important examples of the Mclaurin series:

(1)n

x2 x4

x 2n

= 1

+

2! 4!

n=0 (2n)!

(1)n 2n+1

x3 x5

sin x =

x

=x

+

3! 5!

n=0 (2n + 1)!

cos x =

for all x

for all x

From these series we can derive one of the most beautiful formulas in all of math known

as Eulers Identity e i + 1 = 0, which is equivalent to Eulers Formula e i = cos + i sin , except

x is substituted by . The way you get this identity from the three Mclaurin series previously

mentioned is by using the following steps: first, you take the series with the function e x and

(i )2

(i )3

plug in i for x, and you would get: e i = 1 + i

1! + 2! + 3! + . We still want to prove how the

sum of other two series is equal to the first series, so you take the sin x function, multiply it by

3

5

+ i 5!

. Finally, you take the cos x

i , and input , so it should look like this: i sin = i1! i 3!

2

function, and plug in , making it equal the following: cos = 1 2! + 4! . Now, if you add

the cos and i sin functions the outcome would be equivalent to the e i . We have proven that

e i = cos + i sin , so there is only one more step to prove that e i + 1 = 0. You need to plug in

for , and you will receive e i = cos + i sin . If you simplify this you will get e i = 1 + 0,

and now it is very clear that e i + 1 = 0. You may be confused why all this work was done in

order to prove some small formula, but e i +1 = 0 has great value in it because it is know as the

most beautiful formula in mathematics. Most mathematicians claim this because the formula

is made up of every important constant used in math.

4 Conclusion

The number e has bewildered the math and science community with its application, since

the time of its discovery. In the future I hope to learn the application of e in other sciences more

in depth. I also hope to some how apply my research to another project that can be used in a

science fair. So far I have conducted research on the number e, but I have not applied it to a real

world problem.

14

guided by mentor Christopher Harmon (center). The completed

music is available at https://soundcloud.com/yushuf/

yushuf-chris-harmon-junction.

(right) testing a mythology-based

card game designed by Charlie

in his project.

David Li

mentored by Herng Yi Cheng

Abstract

DNA topology is an unavoidable characteristic when dealing with virtually any

natural DNA molecule. It is an essential part of DNA replication, gene expression, non-homologous end joining, and other processes in molecular biology.

Its study using knot theory has led to the development of several important

medicines and provided insight into many of these fundamental processes.

This report briefly explains some of the basics of knot theory, DNA, and their

intersection. Some of the interesting results we obtained are also included in

this report.

Topology is the study of properties unaffected by the continuous deformations of shape or

size of figures. Knot theory is a subfield of topology that studies mathematical knots. Conventional knots are not mathematical knots because the ends must be joined together in a mathematical knot. This means that mathematical knots cannot be undone. In mathematical jargon,

a knot is an embedding of a circle in R3 with no self intersections. Any modification to the knot,

as long as the strand doesnt break or pass through itself, is equivalent to the original knot. The

simplest knot is just an unknotted circle, which is named the unknot or the trivial knot. The first

real knot is the trefoil knot (Figure 1). The real trefoil knot is in three dimensional space, but

studying two dimensional images is easier so mathematicians use pictures like the one below.

These pictures are called projections.

Figure 1: A Projection of the Trefoil Knot (Adapted from The Knot Book by Colin

Adams [1])

17

David Li

The crossings of a given projection are the places where the knot crosses itself in the image.

The trefoil knot above has three crossings. We say that the trefoil knot has a crossing number

of three because there is not a projection of the trefoil knot with less crossings. Officially, the

crossing number is defined as the smallest number of crossings in any projection of the knot.

To distinguish if a projection is equivalent to the trefoil knot or any other kind of knot, deformations must be used. One basic deformation is planar isotopy which consists of stretching

the length of sides without altering the crossings. In 1926, a set of three very important deformations on knots were defined and listed in a paper written by Kurt Reidemeister [2]. They are

referred to as Reidemeister moves. A Type I Reidemeister move is the addition or removal of

a twist in the knot. A Type II Reidemeister move is the addition or removal of two crossings

(Figure 2). A Type III Reidemeister move is the sliding of a strand of the knot from one side of a

crossing to the other side of the crossing. Using these three moves and planar isotopy, you can

determine conclusively if two projections are equivalent.

Crossing number is a knot invariant because Reidemeister moves and planar isotopy do

not affect it. Currently, all knots with a crossing number of sixteen or less have been identified.

These knots are denoted in Alexander-Briggs notation, which consists of its crossing number

and then a subscript.

Figure 3: All of the Knots with Crossing Number 7 or Less (Adapted from The

Knot Book by Colin Adams [1])

18

David Li

DNA

A link is a set of knotted loops all tangled together. Two links are considered to be the same

if one link can by deformed to the other without ever having any of the loops intersect itself. For

simplicity, all links in this report will have two components.

One specific topological invariant of links is known as the linking number. To calculate the

linking number, you first choose an arbitrary orientation on each component of the link. Then

at each of the crossings, one of the pictures in the figure below will hold. You count a 1 for each

crossing of the third and fourth type and a +1 for any crossing of the first or second type. Next,

you take the sum of the +1s and 1s over all the crossings between the components of the link

and divide the sum by 2. This is the linking number. All linking numbers must be integers. One

example is shown in Figure 5.

Figure 5: The Linking Number of this Link is 2 (Adapted from the Wikimedia

Commons)

2 DNA

DNA, deoxyribonucleic acid, is the molecule that stores genetic information in all living organisms. It is a polymer of repeating subunits called nucleotides. Each nucleotide is composed

of a 5 carbon 2-deoxyribose sugar, which contains a 3 hydroxyl group, 1-3 phosphate groups,

and one of four heterocyclic bases: Guanine, Adenine, Thymine, or Cytosine. A phosphodiester

bond links together the phosphate groups and hydroxyl groups of two adjacent nucleotides

to form a single strand of DNA. Hydrogen bonding between corresponding bases allows two

strands of DNA to base pair, which can form various structures. Adenine forms two hydrogen

bonds with Thymine and Cytosine forms three hydrogen bonds with Guanine.

In cells, DNA is most commonly found as the famous double helix structure [4]. This is

also known as B-DNA. This double helix structure is stabilized by pi-pi interactions between

the cyclic rings in each of the nucleotides and hydrogen bonding between corresponding bases

19

David Li

Figure 6: Primary Structure of DNA (Adapted from DNA Topology by Bates and

Maxwell [3])

[10]. B-DNA is a right-handed helix with 10.4 base pairs per turn of the helix when fully relaxed and a repeat distance between each nucleotide of 3.4 Angstroms. This means that one full

turn of DNA is approximately 35 Angstroms long [14, 26]. The phosphate backbones of the two

strands of single stranded DNA form what looks like the rails of a spiral staircase and the bases

look like the steps up the staircase. The true conformation of B-DNA in vitro depends on the

hydrophobicity of bases, the solution pH, temperature, and many other factors.

Figure 7: B-DNA (Adapted from Molecular Biology of the Gene by Watson et. al.)

20

David Li

Other structures can also form as a result of base pairing including cruciforms [8], triplexes

[11, 13], and even quadruplexes [5, 13].The first structure in Figure 8, is a type of DNA triplex

called H-DNA. It consists of a triple-stranded region and a single-stranded region. It is strongly

favored in solutions with low pH [12]. A Holliday Junction is shown in the second image. It is a

result of homologous recombination and can also form in strands with palindrome sequences

[15]. G-Quadruplexes and i-Motifs form in single stranded DNA with long sequences of only

guanine and only cytosine respectively [13].

Micromechanics by Qu Yuanyuan)

DNA is normally a very long molecule compared to its diameter, and in order for it to be

replicated the strands must be separated to serve as templates for daughter strands at the replication fork. However, separating the two strands requires the DNA double helix to spin ahead

of the spitting strands. The twisting of the helix will tighten ahead of the replication fork which

will induce some strain. This strain leads the helix to coil on itself. This is known as supercoiling. There are two types of supercoiling, negative and positive, as shown in Figure 9. When the

DNA is overwound, or has less than 10.4 base pairs per turn, it will positively supercoil. When

the DNA has more than 10.4 base pairs per turn, it is underwound and will negatively supercoil.

Within each type, the DNA can coil either plectonemically or toroidally [16, 17].

DNA supercoiling is crucial for some processes and inhibits others. Supercoiling is the

first step in DNA compactification in both eukaryotes and prokaryotes. After the DNA is supercoiled, it is wrapped around histones before being assembled into nucleosomes and packaged

into chromatin. Supercoiling also helps proteins access the major and minor grooves of DNA.

Supercoiling is energetically unfavorable for most DNA structures so supercoiled DNA has more

energy that proteins or other molecules can harness [26].

To measure DNA supercoiling quantitatively, F. Fuller [7], G. Calugareanun [25], and James

White [9] developed the Calugareanu-White-Fuller Theorem:

Lk = T w + W r

21

(1)

David Li

In the Calugareanu-White-Fuller Theorem, Tw stands for Twist, Wr stands for Writhe,

and Lk stands for Linking Number. The Twist describes the number of times the individual

strands of DNA coil around the central axis of the helix. The Twist Equation is shown in Figure 10. The Writhe is a measure of how many times the double helix coils around itself. It is

given by the equation in Figure 11 [26]. The Linking Number is the same as the Linking Number

invariant from Section 1. Because it is an invariant, any change in Twist must also manifest as a

change in Writhe.

1

Tw =

2

ds +

[] X

=T +N

2

1

Wr =

4

C C

d r1 d r2

r1 r2

|r1 r2 |3

Once we have calculated the linking number, we just need a couple more equations to

quantify the supercoiling. We define Lk to be the linking number of relaxed DNA. The equation

for Lk is given in Equation 2. It is calculated by dividing the number of base pairs N by the

proper number of base pairs per turn for a piece of relaxed DNA h. This means that Lk is

defined with a base unit of turns. Because Lk does not have to be an integer, it isnt a true

linking number. From this definition we have Lk which is equal to the difference between Lk

and Lk.

N

h

Lk = Lk Lk

Lk =

(2)

(3)

From above, we know that the introduction of supercoils into a DNA molecule corresponds

to the introduction of torsional stress. The larger Lk is, the more torsional stress there will be.

22

David Li

Additionally, a given Lk will generate less torsional stress the larger the number of bases N is,

so we must normalize it. This gives us the specific linking difference .

=

Lk Lk Lk

=

Lk

Lk

(4)

We now have a specific number that we can use to compare the supercoiling of different

DNA molecules. For example, natural covalently-closed circular DNA molecules from E. Coli

have on average a specific linking difference of around 0.06 [3].

DNA molecules with the same length and sequence but differ in Lk are known as topoisomers. From some thermodynamics equations, we can calculate the concentration of a certain

topoisomer. The concentration of DNA with a linking number Lk is:

(

)

K (Lk Lk )2

1

[Lk] = exp

Z

RT

(5)

where R is Boltzmanns constant, T is the temperature in Kelvin, and Z is a normalization constant. The distribution of topoisomers follow a Gaussian distribution with Lk as the center [18].

To maintain this distribution, cells have certain enzymes called topoisomerases that can interconvert between topoisomers. There are two classes of topoisomerases, known as Type I and

Type II. Within each of the types of topoisomerases, there are subclasses of topoisomerases.

Type I topoisomerases have 3 distinct subclasses (A, B and C) and Type II topoisomerases have

2 distinct subclasses (A, and B).

Type IA topoisomerases can only relax negative supercoiling. Type IA topoisomerases resemble a padlock and operate through a strand-passage mechanism. First, a single DNA strand

is cleaved and opened by a catalyic tyrosine. A second DNA strand is navigated through the gap

and then the broken strand is resealed. Topo 1, Topo 3, and Reverse Gyrase are all in this class.

Interestingly, Reverse Gyrase can positively supercoil DNA away from topological equilibrium

using ATP hydrolysis. This is extremely common in organisms that thrive in environments with

extreme heat because the positive supercoiling helps protect the DNA.

Type IB topoisomerases (swivelases) can relax both negative and positive supercoiling.

Type IB topoisomerases pretty much just nick the DNA and let it spin around itself. Friction

between the enzyme and DNA keeps it from spinning too much and the DNA is resealed.

Type IC topoisomerases act very much like Type IB topos but have a different protein fold.

Suprisingly, there is only one protein in this class (Topo V).

Type IIA topoisomerases can relax both positive and negative superoiling. They function

much like Type IA topoisomerases except they require ATP or an alternate energy source. They

also employ a strand passage mechanism but cleave both strands of a double stranded DNA

duplex and pass a second duplex through the break. This class includes Gyrase, Topo II, and

Topo IV. Gyrase is particularly special in the fact that it can introduce negative supercoiling

while other topoisomerases can not.

Type IIB topoisomerases act very much like Type IIA topoisomerases even using the same

mechanism, but the structural arrangement differs greatly. There is only one topoisomerase in

this class, Topo VI. [19]

Topoisomerases are the target of many cancer medicines because without topoisomerase,

DNA replication cannot occur. For example, one specific class of antibiotic drugs, quinolones,

23

David Li

block the reformation of the covalent bonds after a Type II topoisomerase has split a DNA segment. This leads to fatal double-stranded breaks which make quinolones potent antibacterial

agents [20]. Some other topoisomerase inhibition mechanisms are shown in Figure 12. Knot

Theory can also be used to study other enzymes [2124, 26].

Tangled Up: how cells direct, manage and exploit topoisomerase function [19])

4 Rational Tangles

A tangle is a region of a knot or link projection that is surrounded by a circle such that

the knot or link crosses the circle exactly four times. We will think of the four points where the

strands cross as occurring in the four compass directions NW, NE SW, and SE [1]. As with knots,

two tangles are equivalent if we can get from one to the other by a series of Reidemeister moves

and planar isotopy.

The tangle in the upper left corner of Figure 13 is the 0 tangle. It is one of the most basic

tangles. The tangle in the upper right corner of Figure 13 is the 2 tangle because it is only different from the 0 tangle by 2 counter clockwise twists. If they were clockwise twists it would have

notation 2. Another way to determine whether the twist is positive or negative is to look at the

overstrand. If the overstrand has a negative slope, it is a negative twist. If the overstrand has

a positive slope, it is a positive twist. To continue constructing the tangle, you must reflect the

tangle over the NW and SE diagonal line. Next, you take the two new NE and SE strands of the

24

David Li

R ATIONAL TANGLES

tangle and twist how ever many times you want. In Figure 13, the strands are twisted two times.

Any tangle that can be constructed in this manner is known as a rational tangle. With rational

tangles there is a very easy way to tell if two rational tangles are equivalent. All you have to do

is calculate the continued fraction corresponding a tangles tangle notation. For example, the

final tangle in Figure 13 has a tangle notation of 3, 1, 2. The continued fraction corresponding

1

to 3, 1, 2 is 2 +

which simplifies down to 72 . The continued fraction corresponding to

1

1 + 3

1

4, 5, 7, 1 is 1 +

which simplifies down to 156

137 .

7+ 11

5+ 4

The closure of a tangle leads to the formation of a knot or a catenane. There are two types

of closure operations, numerator and denominator, which are commonly denoted by N and D

respectively. K is also used to denote the numerator closure of a tangle [1, 26]. When you write

down the Conway notation for a knot, you use the tangle that forms the knot when under a

numerator closure operation. Both operations are shown in Figure 14. To check if two closures

are the same knot requires the use of the tangle fraction. Suppose you have two rational tangles

(p )

( p )

p

p

with simplified tangle fractions q and q . If K q and K q denote the corresponding rational

(p )

( p )

knots obtained by taking the closures of these tangles, then K q and K q are topologically

equivalent if and only if p = p and either q q (mod p) or q q 1 (mod p) [26, 27].

We developed a program that can calculate all two twist rational tangles that will form a

p

certain knot using Python. The program first uses a given q to generate all tangle fractions

( )

( )

p

p

p

. This is calculated using modular arithmetic and the

that

fit

the

equation

K

=

K

q

q

q

constraint that p must be greater than q for the tangle fraction to be a valid tangle fraction.

Once this list has been calculated, the program iterates through this list and finds solutions for

25

David Li

Applying Rational Knots and Rational Tangles by Kaufman et. al.)

each specific tangle fraction. If a specified tangle fraction is equivalent to an integer , there are

always three solutions. These solutions are (0, ), (1, 1), and (1, +1). Solutions for fractions

that arent integers are calculated using the floor and ceiling functions. The program was ran

on all the knots from 31 to 814 . Interestingly, on one of the knots the program ran on, 62 , we

managed to produce a solution, 4, 3 that was even simpler than the one in a standard knot

table. We created a physical model of the closed tangle and tried to deform it into the knot 62 . It

took multiple attempts and quite a bit of time, but in the end we managed to deform it into the

knot 62 . It turns out that you have to rotate the closed tangle 180 to see the desired knot. It was

also special because the solution, (4, 3), has a total of seven crossings at the beginning which

is more than our target knot. All of the solutions we found are in Figures 15 and 16 below.

26

David Li

R ATIONAL TANGLES

You might be wondering how this is related to molecular biology. We attacked this problem

because two twist DNA substrates can be designed and synthesized. Most of the biological

background is based off of one paper Construction and Electrophoretic Migration of SingleStranded DNA Knots and Catenanes written by Alexander Bucka [28]. The synthesis process is

shown in Figure 17. It is suprisingly effective and efficient. It starts with the formation of a DNA

loop by base pairing of homologous sequences. Upon formation, this loop is bound by the two

ends of the DNA. DNA ligase then joins the ends with a phosphodiester bond which effectively

closes the knot.

27

David Li

Figure 17: Single-stranded DNA Knot and Catenane Synthesis (Adapted from

Electrophoretic Migration of Single-Stranded DNA Knots and Catenanes by

Alexander Bucka [28])

28

David Li

B IOLOGICAL C ONSEQUENCES

5 Biological Consequences

DNA supercoiling is an attribute of almost all in vitro DNA. It helps with DNA compaction,

replication, and directly influences the interactions between specific proteins and DNA. Many

interactions can be modeled by individual steps, each impacted by supercoiling. These include

the binding of topoisomerases, recombinases, and strand-transfer proteins. Because rewinding

negatively supercoiled DNA brings it toward equilibrium, separation of strands and increased

twisting are both energetically favorable. This makes DNA replication favorable in negative

supercoiled DNA. Supercoiling also affects the secondary structure of DNA and will encourage

the formation of Z-DNA.

In all biological systems, replication of DNA proceeds from specific sites known as origins of replication. In bacteria, only one origin is present in the entire genome. In eukaryotes,

there are multiple replication origins. Negative supercoiling opens up the origin for binding

and actually stabilize the region. In yeast, the presence of negatively supercoiled DNA activates

unwinding of various autonomously replicating sequences. Normally, at the end of replication,

the end product is a catenane of some sort. Type II topoisomerases will then come over and

decatenate the structure resulting in two identical DNA rings.

DNA topology is also a factor that controls gene expression. The binding of transcription

factors or RNA polymerase to DNA will also significantly impact the topology of the DNA. In

transcription initiation, a RNA polymerase holoenzyme is formed and binds to the DNA which

stabilizes the negative supercoiling and promotes strand seperation. Initiation is a complicated

process that involves a number of phases. This equates to many opportunities to implement

control mechanisms. Various regulatory proteins also depend on the topology of local DNA.

6 Future Research

In the future, maybe the formation of various catenanes could be modeled and synthesized in real life. Deriving a equation for the electrophoretic mobility of a molecule is also a

interesting pursuit. Studying the structure of topoisomerases and analyzing the results of topoisomerases on various knots would also be possible areas to delve deeper into. Performing wet

lab work involving DNA topology also seems interesting.

Bibliography

[1] Adams, C. (2004). The Knot Book: An Elementary Introduction to the Mathematical Theory

of Knots. Providence, R.I.: American Mathematical Society.

[2] Reidemeister, K. (1932). Knotentheorie. Eregebnisse Der Matematik Und Ihrer Grenzgebiete,

1(1).

[3] Bates, A., & Maxwell, A. (2005). DNA Topology. New York: Oxford University Press.

[4] Watson, J., & Crick, F. (1974). Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid. Nature, 171, 737-738.

29

David Li

[5] Lam, E., Beraldi, D., Tannahill, D., & Balasubramanian, S. (2013). G-quadruplex structures

are stable and detectable in human genomic DNA. Nature Communications, 4, 1796.

[6] Valentin V. Rybenkov, Alexander V. Vologodskii, and Nicholas R. Cozzarelli The Effect of

Ionic Conditions on DNA Helical Repeat, Effective Diameter and Free Energy of Supercoiling

Nucleic Acids Res. (1997) 25 (7): 1412-1418

[7] Fuller, F. (1978). Decomposition of the linking number of a closed ribbon: A problem from

molecular biology. Proc. Natl. Acad. Sci. USA, 75(8), 3557-3561.

[8] Brzda, V., Laister, R., Jagelsk, E., & Arrowsmith, C. (2011). Cruciform structures are a

common DNA feature important for regulating biological processes. BMC Molecular Biology, 12, 33-49. doi:10.1186/1471-2199-12-33

[9] Bauer, W. R., Crick, F. H. C. and White, J. H. (1980). Supercoiled DNA. Scientific American

243, 118-133.

[10] Matta, C., Castillo, N., & Boyd, R. (2005). Extended Weak Bonding Interactions in DNA: Stacking (BaseBase), BaseBackbone, and BackboneBackbone Interactions. The Journal of

Physical Chemistry B J. Phys. Chem. B, 110(1), 563-578. doi:10.1021/jp054986g

[11] Jain, A., Wang, G., & Vasquez, K. (2008). DNA triple helices: Biological consequences and

therapeutic potential. Biochimie, 90(8), 1117-1130. doi:10.1016/j.biochi.2008.02.011

[12] Frank-Kamenetskii, M., & Mirkin, S. (1995). Triplex DNA Structures. Annual Review of Biochemistry, 64, 65-95.

[13] Gilbert, D., & Feigon, J. (1999). Multistranded DNA structures. Current Opinion in Structural Biology, 9(3), 305-314. doi:10.1016/S0959-440X(99)80041-4

[14] Wing, R., Drew, H., Takano, T., Broka, C., Tanaka, S., Itakura, K., & Dickerson, R.

(1980). Crystal structure analysis of a complete turn of B-DNA. Nature, 287, 755-758.

doi:10.1038/287755a0

[15] Shinagawa, H., & Iwasaki, H. (1996). Processing the holliday junction in homologous recombination. Trends in Biochemical Sciences, 21(3), 107-111. doi:10.1016/S09680004(96)10014-1

[16] Boles, T., White, J., & Cozzarelli, N. (1990). Structure of plectonemically supercoiled DNA.

Journal of Molecular Biology, 213(4), 931-951. doi:10.1016/S0022-2836(05)80272-4

[17] Calladine, C. (1980). Toroidal elastic supercoiling of DNA. Biopolymers, 1(10), 1705-1713.

doi:10.1002/bip.1980.360191002

[18] Depew, D., & Wang, J. (1975). Conformational fluctuations of DNA helix. Proceedings of the

National Academy of Sciences, 72(11), 4275-4279.

[19] Vos, S., Tretter, E., Schmidt, B., & Berger, J. (2011). All tangled up: How cells direct, manage

and exploit topoisomerase function. Nature Reviews Molecular Cell Biology, (12), 827-841.

doi:10.1038/nrm3228

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David Li

BIBLIOGRAPHY

[20] Laponogov, I., Pan, X., Veselkov, D., Mcauley, K., Fisher, L., & Sanderson, M. (2010). Structural Basis of Gate-DNA Breakage and Resealing by Type II Topoisomerases. PLoS ONE,

5(6). doi:10.1371/journal.pone.0011338

[21] Misra, J., Mukherjee, S., & Das, A. (2004). A mathematical model for enzymatic action on DNA knots and links. Mathematical and Computer Modelling, 39(14), 1423-1430.

doi:10.1016/j.mcm.2004.07.001

[22] Darcy, I., Chang, J., Druivenga, N., McKinney, C., Medikonduri, R., Mills, S., . . . Thompson,

T. (2006). Coloring the Mu transpososome. BMC Bioinformatics, 4(435). doi:10.1186/14712105-7-435

[23] Crisona, N., Weinberg, R., Peter, B., Sumners, D., & Cozzarelli, N. (1999). The Topological Mechanism of Phage Integrase. Journal of Molecular Biology, (4), 747-775.

doi:10.1006/jmbi.1999.2771

[24] Ernst, C., & Sumners, D. (1990). A calculus for rational tangles: Applications to DNA recombination. Mathematical Proceedings of the Cambridge Philosophical Society, 108(3),

489-515. doi:10.1017/S0305004100069383

[25] Calugareanu, G. (1959). Lintgrale de Gauss et lAnalyse des nuds tridimensionnels. Rev.

Math. Pures Appl., 4,5-20.

[26] Monastyrsky, M. (Ed.). (2007). Topology in molecular biology (1st ed.). Berlin: SpringerVerlag Berlin Heidelberg.

[27] Schubert, H. (1956). Knoten mit zwei Brcken, Math. Zeitschrift, 65, 133-170.

[28] Alexander, B., & Andrzej, S. (2002). Construction and electrophoretic migration of

single-stranded DNA knots and catenanes. Nucleic Acids Research, 30(6), 24-24.

doi:10.1093/nar/30.6.e24

31

Mentor Evan Kuras (red cap) exploring the urban ecology of MIT with students.

Teaching Coding

Garrett Mallinson

mentored by Lane Gunderman

1 Introduction

I plan to start a coding club at my school. I will need to learn more python in order to

teach it to others. I plan to create class curriculum and I will also learn effective methods to

teach coding to small groups. Over the summer I took coding classes, in which I expanded

my programming skills and looked at their teaching methods. At Junction, I planned my class

curriculum. In the beginning of the school year I will implement my curriculum when I start

my coding club.

2 Lesson Plans

Day 1

Create list of everything the students think coding is

Create a list on how coding is used in everyday life

Show coding video https://www.youtube.com/watch?v=uEdyTlI3BAA

Explain what python and coding are

(if time permits) show how to download python

Create another list on what students think coding is now

Day 2

teach students basic python (if statements, strings, for loops etc...)

Day 3

have the students try to fix a text adventure

33

Garrett Mallinson

T EACHING C ODING

Day 4

have the students try to fix the syntax errors in droids

Day 5

have students create their own text adventure (contest for who can make the best text

adventure)

Resources

http://www.cheatography.com/davechild/cheat-sheets/python/

http://www.dummies.com/how-to/content/python-for-dummies-cheat-sheet.html

http://www.astro.ufl.edu/~warner/prog/python.html

http://learnpythonthehardway.org/

34

Junlin Mo and Trevor Pennypacker

mentored by Lane Gunderman

In everyday life, we intuitively understand how the world works. Throw an object up, and

it will come down, as per the law of gravity. If you attempt to walk through a wall you will fail,

as two objects cannot occupy the same space at the same time. Until the turn of the twentieth

century, scientists believed that these basic laws applied to everything in the universe. However,

as technology improved, scientists realized that many of these principles fail on the atomic

level. Thus, scientists developed a new branch of physics known as quantum mechanics to

better understand the way tiny particles move and interact. Quantum mechanics, put simply,

is the study of very, very, very small things.

The fundamental equation of quantum mechanics is the Schrdinger Equation. It reads

i

= H ,

t

H =

2 2

+ V.

2m

H = E ,

where E is the eigenvalue.

The Schrdinger Equation, when given certain parameters and solved, gives the wave

function of a particle. Denoted by , the wave function provides information as to the density of the particle. Specifically,

b

a

35

Junlin Mo

Since the total probability of an event is always 1, we know that

|(x, t )|2 d x = 1.

Take a particle that is completely free, except at two ends where an infinite potential prevents it from escaping. This scenario is also called the Particle in a Box", and is shown in Figure 1.

So what would the wave function look like for this particle? Lets first start with the timeindependent Schrdinger equation.

2 d 2

+ V = E .

2m d x 2

Like the name connotes, the time-independent Schrdinger equation is a variant of the

Schrdinger equation that remains constant as time progresses, making the equation much

easier to solve. Since the particle is free-floating, we can substitute 0 for V (x) to get

2 d 2

= E ,

2m d x 2

or

d 2

= k 2 where k =

d x2

2mE

.

This is the simple harmonic oscillator equation, which has the general solution

(x) = A sin(kx) + B cos(kx).

It is possible to solve for a particular solution when given some boundary conditions, but

well leave the solution in its general form for simplicity.

36

Trevor Pennypacker

F OURIER T RANSFORMATIONS

When given a set of boundary conditions, it is possible to solve the general simple harmonic oscillator equation to get a particular solution. Take Figure 1 for example, where the

bounds are at x = 0 and x = a. (0) = 0, and thus

(0) = A sin(0) + B cos(0) = B,

so B = 0, and therefore (x) = A sin(kx). The boundary conditions also maintain that (a) = 0,

and thus ka is an integer multiple of . Another way of writing this is

kn =

n

, with n = 1, 2, 3, . . .

a

make the total probability density equal to 1.

a

a

2

|A|2 sin2 (kx)d x = |A|2 = 1, so |A|2 = .

2

a

0

The solutions then are

n (x) =

( n )

2

sin

.

a

a

The solutions to the infinite square well problem are mutually orthogonal, or orthonormal, meaning

m (x) n (x)d x = mn ,

{

mn = 0 m = n

mn = 1 m = n.

3 Fourier Transformations

Unlike the simple harmonic oscillator, some signals are not so easy to work with. However, any continuous periodic function can be modeled by a linear combination of sinusoidal

functions, and the Fourier Transformation provides a method of doing so.

Let g (t ) be the Fourier approximation of a function f (t ). The general Fourier decomposition for g (t ) is given by

)

(

)

(

2nt

2nt

+

A m cos

.

g (t ) =

A n sin

T

T

m=0

n=1

37

Junlin Mo

The constants A n and A m determine the relative weights for each of the sinusoids, and become

infinitely small as m and n become large, and can be solved for using the following equations:

2

An =

T

)

2nt

dt

f (t ) sin

T

2

Am =

T

T

0

)

2mt

dt.

f (t ) cos

T

Or, utilizing Eulers Identity e i x = cos(x) + i sin(x), the Fourier decomposition equation

can be rewritten as

g (t ) =

cn e i

2nt

T

where c n =

n=

1

T

f (t )e i

2nt

T

dt.

Take for instance a saw function, as shown in Figure 2. A function like this is difficult

to work with, and thus it is helpful to use a Fourier transform. As seen in the following diagrams, the Fourier decomposition models the sawtooth function more precisely as the number

of terms increases.

As with the solutions to the simple harmonic oscillator, the sinusoids in a Fourier series

are orthogonal, making them ideal to work with.

(a)

(b)

(c)

(d)

Figure 2: (a) Saw function. (b) Approximation with three terms. (c) Approximation with seven terms. (d) Approximation with 41 terms.

38

Trevor Pennypacker

To properly study Quantum Computation, one must study the fundamentals of classical

computation. A classical computer is a device that can store and process data. Computers process data by executing algorithms. These algorithms provide a set of instructions for the computer to follow. In addition to being well-defined, algorithms need to be able to be translated

into a physical task.

Currently, classical computers have been developed to the point where billions of processes per second can occur within commercial computers.

When studying computers, it is important to remember the relationship between computation and physics. As we dive deeper into the field of quantum computing, the laws of physics

will begin to devise and set limits to principles of computation. Classical and realistic computers exist in a physical space and must obey the laws of that physical space, as opposed to

common idealized computational models .

5 Classical Computing

The foundation of all classical computing is a simple logic gatea system capable of being

switched on and off, true and false, 1 and 0, etc. From this basic unit we begin to develop and

build upon more difficult concepts. Modern computing is built upon hundreds of layers of

systems, from binary to the coding languages used to program the applications that we use.

5.1 Gates

A logic gate performs a logical operation on one or more logical inputs and produces a

single logical output. Logic gates are the fundamental building blocks to circuits, which may

contain strings of gates in succession.

The NOT gate is a standard gate of classical computation. The NOT gate operates on one

input. For input A The NOT gate will output the opposite value of the input. (See Figure 3)

The OR gate requires 2 inputs. From these 2 inputs, OR will check if any of them is 1. If so,

it outputs a 1. (See Figure 4)

39

Junlin Mo

Likewise, the AND gate also require 2 inputs. The AND gate will only output a 1 of both

inputs are 1. (See Figure 5)

6 Qubits

Qubits are essentially a pair of orthogonal states. Unlike regular bits, Qubits can represent

0, 1, or a superposition of 0 and 1. A bit can only represent 0 or 1, or 21 pieces of information.

A qubit is able to represent 0, 1, or a superposition of 0 or 1. This can be represent 22 pieces of

information. With this property, qubits are able to transmit more information at one time. In

essence, a qubit bears remarkable similarity to the particle in a box problem presented earlier

(see Figure 1). Similar to how the particle in a box can be decomposed into sine and cosine

waves using the Fourier Transform, a qubit can be decomposed into superpositions of binary

states.

This is a common representation of the qubit.

7 Quantum Gates

One of of the most common gates used in quantum computation is the Hadamard Gate.

The Hadamard gate, represented by H , takes a a vector (bit) of 0 or 1 and produces a superposition with it:

H |0 = p1 (|0 + |1)

H |1 =

2

1

p (|0 |1)

2

40

Trevor Pennypacker

In addition to producing a superposition of the vector 0 or 1, the Hadamard Gate is its own

inverse. This means that H = H 1 . Therefore, when applied to the created superposition of the

vector 0 or 1, it will revert the superposition back into the binary vector of 0 or 1:

(

)

H p1 (|0 + |1) = |0

( 2

)

H = H 1 =

H p1 (|0 |1) = |1

2

The Quantum Fourier Transform, also known as Quantum Phase Estimation, is a linear

transformation on qubits. The Quantum Fourier Transform obtains a good estimate of the

phase parameter, , of a periodic state. Consider the two-qubit state:

1

1 2

e 2i y |y

p

2 y=0

2

x 2 can be determined from the first qubit by applying a Hadamard gate. In turn, x 1 has

to be determined from the second qubit. If x 2 = 0, then the 0 is negligible because it does not

affect the binary decimal value of . Therefore, we can determine x 1 by applying a Hadamard

gate second qubit since would just equal 0.x 1 . If x 2 = 1, we will need to apply a phase rotation

operator, R 2 :

[

] [

]

1

0

1

0

R2 =

2 =

0 e 2i (0.01)

0 e 2i /2

Notice the 0.01 in the exponent. This exponent is written in base 2 decimal form, (i.e. 0.01 =

22 ). The inverse of R 2 also will use base 2 in the exponent.

[

]

1

0

1

R2 =

0 e 2i (0.01)

In order to execute the phase estimation, the binary representation of the decimal is taken.

Then, the right most digit of the decimal is checked. If said digit is 1, it activates the controlled

rotation gate. If the digit is 0, it does not activate the rotation gate. Either way, it returns the 0

or 1 and it tells you the coefficient of the negative power of 2. The rotation gate will essentially

change the right most digit to 0. This will iterate until the frequency is obtained or one runs out

of qubits. (See Figure 7)

41

Junlin Mo

9 Time Complexity

The time complexity of any given algorithm is the amount of resources used by a computer

to complete the algorithm. Two very important resources for computers are time and space.

We measure the amount of a resources used in a computation for solving a given problem as

a function of the length of the input of an instance of that problem. For example, a computer

may take 4n 2 +2n units of time to solve the problem. We would say that the running time of that

algorithm for these computer is O(n 2 ). Time Complexity is often referred to in O notation. An

algorithm is generally considered efficient if the amount of the resource used is O(n k ) for some

k. We call these algorithms polynomial with respect to the resource. If an algorithms running

time is in O(n) or O(log n), we call these linear and logarithmic, respectively. These algorithms

are all considered efficient.

As a note, O( f (n)) represents an upper bound of the running time. This means that algorithms in O(n) or O(n 2 ) are also in O(n 3 ). is used for lower bounds. Algorithms that use (c n )

for some constant, c, resources are considered exponential and inefficient. This is because, at

some point (or amount of resources), an exponential algorithms will exceed the running time

of even the largest polynomial algorithms.

10 Modern Implications

One of the largest subject of algorithms of interest in the field of quantum computing are

prime factorization algorithms. These algorithms are of large interest because of their applications in the RSA. The RSA cryptosystem is a public key protocol commonly used in government

and corporations in order to encrypt sensitive information. The security of RSA relies upon the

assumption that that factoring large numbers on computers is a difficult and strenuous process.

That being said, currently, there is no known classical computer prime factorization algorithm

that has a polynomial running time, O(n k ). If an algorithm were to be found, it wound undermine the security of RSA.

However, there are quantum prime factorization algorithms that are vastly more efficient

than classical computation algorithms (See Figure 8). Both Shors algorithms and a minimization algorithm have been used to factor large numbers in a timely manor. For example, Shors

algorithms running time is O((log n)2 (log log n)(log log log n)). One thing to note is that these

algorithms have also only run on ten or less qubits.

Moores Law is essentially an observation on the rate of change in silicon-based processors.

Gordon E. Moore, co-founder of Intel, observed that the number of transistors in a dense integrated circuit had doubled approximately every two years. After 50 years of evidence, Moores

Law has been a reference point in the advancement of computing (See Figure 9). However, in

accordance to Moores Law, there are only so many transistors that we can fit into a dense integrated circuit before it becomes physically impossible to add more. Quantum computers already use subatomic particles as bits because they rely on the quantum mechanical properties

of subatomic particles, such as superposition, to process information. Looking into the future,

42

Trevor Pennypacker

M ODERN I MPLICATIONS

society may change their reliance from silicon-based computing to other forms of computing,

quantum computing being a possible alternative in x amount of years.

43

Junlin Mo

Sources

Kaye, Phillip, Raymond Laflamme, and Michele Mosca. An Introduction to Quantum Computing. Oxford: Oxford UP, 2007. Print.

Griffiths, David J. Introduction to Quantum Mechanics. Upper Saddle River, NJ: Pearson Prentice Hall, 2005. Print.

44

Karen Ying

mentored by Herng Yi Cheng

1 Introduction

In this paper, well be exploring a collection of logic puzzles in which a number of people

are given colored hats and asked to guess the color of the hat on their head (which they cannot

see) based on the information that is presented to them.

The solutions to these puzzles relate to information theory and data transmission. Additionally, these puzzles are common interview questions at large companies such as Google and

Jane Street Capital.

n people stand in a circle, each with either a white or a black hat and are given

a deterministic strategy (i.e. the strategy cannot be to guess randomly) to guess

the color of his own hat by observing the other n 1 hats. All players must use the

same strategy, which they agreed on beforehand. Let us represent a black hat as

1 and a white hat as 0 [1].

Theorem 1. For n = 2 and a particular strategy, there will always be a hat assignment that guarantees no one guesses correctly.

Proof. For n = 2, there are only the following four strategies:

1. Guess 0.

2. Guess 1.

3. Guess the same color as what the other person is wearing.

4. Guess the opposite color of what the other person is wearing.

45

Karen Ying

For each of these strategies, we can assign the hats in a way that no one guesses their hat

color correctly:

1. [1, 1]

2. [0, 0]

3. [0, 1] or [1, 0]

4. [0, 0] or [1, 1]

What if n > 2? How many people can guess correctly? We find that at least one person can

always guess their hat correctly.

Theorem 2. n > 2 a strategy where at least one person guesses correctly.

Proof by Construction. We will use the following two rules which form our strategy:

1. When n is even and you see an alternating pattern of hats, guess the hat color that fits in

the alternating pattern (i.e. guess the color of the person sitting two spaces to the right of

you).

2. In all other cases, guess the color of the hat to your immediate right.

With this strategy, we have the following cases:

Case 1. n is odd: We need the following lemma.

Lemma 2.1. If n is odd, there is always at least one pair of adjacent people with the same

color hats.

Proof. Assume there are n = 2m + 1 people and that there are no pairs of adjacent same

color hat people. Pick a person, without loss of generality, assume his hat is black. Then

the people immediately next to him have the same color hats, white. More generally, the

people k spaces to the left and k spaces to the right have the same colors. However, the

people m spaces to the left and m spaces to the right sit next to each other and have the

same color hat.

Since there is at least one adjacent same color pair in any odd hat assignment, rule 2

guarantees that at least one person guesses correctly.

Case 2. n is even and the hat assignment is alternating: By rule 1, everyone guesses correctly.

Case 3. n is even and the hat assignment is alternating with one error, e.g. 0101010111: In this

case, the error will see an alternating pattern of hats and guess wrongly. The other n 1

people will use rule 2, and guess the color of the hat to their right. The person sitting to

the left of the error will be the only one who guesses correctly.

46

Karen Ying

Case 4. n is even and the hat assignment is not Case 2 or 3, so every other hat assignment: Since

the pattern is not alternating, there is at least one pair of people with the same color hat

sitting right next to each other. Thus rule 2 guarantees that at least one person guess

correctly.

n

2

Proof. Let us calculate the expected value of the number of correct guesses given out in a random hat assignment, N :

N=

number of people that guess correctly in x

x{0,1}n

=

=

1

2n

1

2n

x{0,1}n ppeople

ppeople x{0,1}n

Going through all x, we see y {0, 1}n1 , 0 y or 1 y . For each y, an assignment of the rest of

the hats, one time ps hat is guessed correctly based on the strategy and one time it is not. Thus,

N=

1

2n

2n1 =

ppeople

1

n

n 2n1 = .

n

2

2

In general, the minimum of a set is less than or equal to the expected value, or average,

with equality when, in this case, all hat assignments give the same number of correct guesses.

Consider the assignment of all white hats without loss of generality. This assignments means

everyone guesses the same thing. Either n people guess correctly or no one guesses correctly.

Thus the minimum does not equal the average which means that the minimum number of hats

is less than n2 .

Theorem 4. 2n a strategy such that at least n 1 people guess correctly.

Proof by Construction. Among everyone, there is either an odd or even number of black hats.

If one knows the parity of black hats, he is able to figure out the color of his hat and guess

accordingly. Thus if n people think that theres an odd number of black hats and the other

n people think that theres an even number, exactly n people will guess the color of their hat

correctly.

Since theres an even number of people standing in a circle, we are able to pair everyone

up with the person standing directly across from them, forming n pairs. Within each pair, the

two people will either have the same color hats, call them same color pair or different color

hats, different color pair. Suppose there are m different color pairs.

The strategy works as follows:

1. If you observe the rest of the n 1 pairs as same color pairs, then guess your partners

color hat.

47

Karen Ying

2. If you observe at least one different color pair out of the n1 pairs, find the person nearest

clockwise to you who is part of a different color pair. If his hat is black, judge the total

number of black hats as odd and make your guess accordingly. If his hat is white, judge

the total number of black hats as even and guess accordingly.

Thus we have the follow 3 cases:

Case 1. m = 0: By rule 1, 2n people are correct.

Case 2. m = 1: By rule 1, the two people in the one different color pair will both be wrong.

However for the rest of the n 1 pairs, exactly one out of the two people will be correct

since the two people will make different observations about the parity of the black hats.

Thus n 1 people will guess correctly.

Case 3. m > 1: By rule 2, n pairs, two people in each pair will make different judgments about

the parity of black hats. Exactly n people will be correct about the parity and thus guess

the color of their hat correctly.

This strategy works for even numbers of people. However, what if theres an odd number?

Can we generalize, or do even better?

Theorem 5 (From [2]). n a strategy in which n2 1 people guess correctly.

Proof by Construction. We define two configurations of hats adjacent if flipping a single hat in

one results in the other. In addition, we define a configuration of hats to be symmetric if rotating

each hat m people around the circle for some m < n produces the same configuration. We are

going to need the following lemma to construct our strategy which begins our transition into

graph theory.

Lemma 5.1. Given a multigraph G with minimum degree 2m, for each edge we can choose one

of its vertices such that every vertex is chosen at least m times.

Proof. First if there are any cycles of edges v 1 v 2 , v 2 v 3 , . . . , v r 1 v r , v r v 1 , we can choose the vertices of the cycle in a direction along the cycle. Do this until the edges left to be assigned have

no cycles and thus form a forest.

Let degT (x) be the degree of vertex x after cycle deletion i.e. the number of edges coming

out x that are not part of cycles. For each tree T , pick a vertex v T such that degT (v T ) = 1 and

orient T so that every edge in the tree points away from v T . Every vertex with degree one after

cycle deletion originally had degree at least 2m + 1 and has been already chosen by at least m

edges. Every other vertex u T , is chosen at least degT (u) 1 times. If u is not part of any

cycles then degT (u) = deg(u) 2m and it is chosen degT (u) 1 times which is at least m times.

However if u is part of c cycles in addition to to T , u is chosen degT (u) 1 + c times total, which

is m:

degT (u) + 2c

m

deg(u) = degT (u) + 2c 2m =

2

Simplifying the LHS we have:

degT (u) + 2c degT (u)

=

+c

2

2

48

Karen Ying

We know,

degT (u)

2

degT (u) 1

Thus,

degT (u)

2

Every vertex in a multigraph is either only part of cycles or part of cycles and a tree. If a

vertex is only part of cycles, its degree is 2m and is chosen m times. If a vertex u is part of

cycles and a tree, weve shown above that u is chosen at least m times as well. This concludes

our lemma.

Back to the strategy. We deal with the symmetric hat assignments by having the people

implement the following strategy: if there is a color and a person such that the configuration

would be symmetric if that person has that color hat, the person guesses that color. This ensures

that for symmetric configurations, every person will guess correctly.

And now for non-symmetric configurations, we construct a multigraph whose vertices are

equivalence classes, v i , of n-bit non-symmetric strings under rotation. First connect every adjacent hat configuration with a line. We can summarize and simplify these lines connecting

adjacent configurations in different rotation classes by an edge in this way: The number of

edges connecting v i to v j is equal to the number of adjacent hat configurations a i v i has in

v j and a j v j has in v i . Then label these edges with (n 1)-bit strings which represent the hat

configurations one person would possibly see if he looks clockwise around the circle such that

he knows which two equivalence classes the actual hat assignment may belong to.

E.g. for n = 5:

49

Karen Ying

Orient the multigraph as described in the lemma above, and then simplify the equivalence

classes into vertices.

E.g. for n = 5:

Finally, our strategy is: Have everyone agree on a multigraph representation for n people

beforehand and memorize it. Look clockwise around the circle. You see an (n 1)-bit string

which corresponds to an edge in the multigraph. This edge chooses a vertex in the multigraph.

Thus the chosen vertex represents the equivalence class you guess the hat configuration is in.

Guess the hat color that would make the configuration in the equivalence class complete. By

the previous

will be chosen

n lemma, we can assign a vertex to each edge G such that each

nvertex

at least 2 times

n which agrees with Theorem 3. This means at least 2 people guess correctly because 2 people chose that the hat configuration equivalence class correctly and thus

guessed correctly.

There is also the case of a symmetric hat configuration with one error. The error looks

around and sees a symmetric configuration and therefore guesses the wrong color. The other

n 1 people see a non-symmetric

configuration and use the multigraph strategy. This is why

n

we can only guarantee that 2 1 people guess correctly.

50

Karen Ying

n people stand in a line, wearing either a black hat or a white hat. These people

can see all the hats in front of them but not the hat on their head nor the hats

on the heads of the people behind them. They guess in the order in which they

are standing, starting with the person in the very back. Everyone can hear each

others guesses. Again, assign a black hat the number 1 and a white hat, 0.

Theorem 6. n a strategy such that n 1 people will always guess their hat color correctly.

Proof by Construction. We build the following strategy: The person all the way in the back cannot gain any information about the color of their hat, so he sacrifices himself for the greater

good of mathematics. However, he is able to convey information to the rest of the n 1 people.

He takes the sum of the number representation of the hats in front of him mod 2 and that is his

guess. This guess conveys the parity of the black hats to the people in front of him. The other

n 1 people can deduce their hat color because they know the parity of the black hats in front

of them from the guesses of the people behind them. Thus the other n 1 people are able to

guess their hat color correctly.

A countably infinite number of people stand in a line, wearing either a black hat

or a white hat. These people can see all the hats in front of them but not the hat

on their head nor the hats on the heads of the people behind them. They guess in

the order in which they are standing, starting with the person in the very back.

Everyone can hear each others guesses. Assign a black hat the number 1 and a

white hat, 0.

For any n > 0 we proved before that only one out of every n people fails to guess correctly.

Thus for an infinite number of people, we can just divide everyone into groups of size n and

have them implement the finite strategy sown above. However, we can do better and have only

a finite number of people guess incorrectly.

Theorem. For an infinite number of people standing in a line, all but finitely many people can

guess their hat color correctly.

Proof by Construction. Let S = {(a 1 , a 2 . . .) | a i Z2 }, the set of hat assignments. We need to define an equivalence relation on the hat assignments. For s, s S, we say s s if they eventually

agree in every place (e.g. (11111111 . . .) 01111111 . . .).

Before everyone lines up, they agree to invoke the axiom of choice and choose a single

element from each equivalence class in S and memorize each element.

Person i in the line sees:

s = (. . . a i +1 , a i +2 . . .)

51

Karen Ying

He doesnt know the first i elements but he can determine the equivalence class of s by

observing the hats in front of him. He then recalls from his memory the element that everyone agreed to memorize from the equivalence class of s and guesses the i th element of the

sequence.

If everyone in the line implements this strategy, only a finite amount of people will guess

incorrectly since two hat assignments in the same equivalence class will only differ in a finite

number of places before converging.

5 Applications

Hamming codes are a type of efficient single error correcting codes, giving 2k 1-bit messages, where k-bits are redundant and the rest of the 2k k 1-bits are data. A property of single

error correcting Hamming codes is that it either is a valid message or one error away from being

a valid message [3] .

Tying this back to our puzzles, suppose we have n = 2k 1 people in a circle wearing either

a black (1) or a white color hat (0). They guess the color of their hat by observing the other n 1

people. We have everyone assume that the assignment is not a valid Hamming encoded message, e.g. if a person knows that him having a black hat makes the assignment a valid message,

he guesses white. Unfortunately, the strategy breaks down when the configuration is a valid

Hamming encoded message. But for every valid message there are n invalid messages (since

there are n bits that you can change in the string to result in an invalid message) which

means

n

n

n2

that the probability of success is for every person is n+1 , averaging n+1 n = n+1 correct

guesses.

6 More Directions

Now that you have a feel for some of the types of hat logic puzzles that exist and their

solutions, what if we have many different color hats instead of just black and white? n colored

hats? What if theres an infinite number of people in a circle? What if people standing in a line

had to make their guesses simultaneously? What generalizations can you make about these

puzzles?

Bibliography

[1] Canada/USA Mathcamp, cited 2015: Qualifying Quiz,

http://www.mathcamp.org/prospectiveapplicants/quiz/index.php

[3] Alex Zorn, cited 2013: Colored Hats and Logic Puzzles,

http://mathcircle.berkeley.edu/archivedocs/2012_2013/lectures/

1213lecturespdf/BMC_Int_Jan22_2013_HatsAndLogicPuzzles.pdf

52

Karen Zhou

mentored by Lane Gunderman

Abstract

Bioinformatics is the application of mathematics and computer science to develop methods of analyzing and studying biological data. Programs that compare and analyze DNA sequences are important for the sake of scientific and

medical progress. They are useful in researching genetics, identifying evolutionary history, studying epidemiology, and more. This purpose of this project

was to develop a basic DNA sequence analysis program using the C++ programming language. Specifically, it would input two files of DNA sequences, use the

word method to compare their sequences, align the files and display the results, and provide more information about the sequences. Additional features

and functions will be added after the duration of Junction.

1 Introduction

There exist several DNA sequence alignment and analysis programs; one such program is

called basic local alignment search tool, or BLAST. BLAST was first implemented in 1990 (Kumar, 2005). It works by parsing nucleotide sequences into query words, performing character

string comparison against all sequences in the target database, and identifying statistically significant matches. BLAST uses an identity matrix and applies a scoring system to get a raw score

of how similar two sequences are. Then it uses statistics to convert the raw score into a bit score

(BLAST, 2007). Programs like BLAST are useful for studying gene families, analyzing evolutionary patterns, identifying species, and more. BLAST served as inspiration for this project.

The purpose of my research project was to develop a C++ computer program that analyzed

similarities in DNA sequences. The program would read in two FASTA files of nucleotides. This

program would first assign values of 0, 1, 2, and 3 for A, C, T, and G respectively. Then, similarly

to the blastn program of BLAST for nucleotide-nucleotide comparison, it would parse the nucleotide sequences in both files into query words of size 8. The parsed words would be hashed

and stored in a hash table. Then the hash tables of both files would be compared to each other.

A function would align the sequences based on similar sequences and their positions. Finally,

the program would show additional information about the files, such as the percentage of similarities and the number of different base pairs.

53

Karen Zhou

I was inspired to do this project because I had previously used bioinformatic programs

like BLAST and Seaview, and phylogenetics programs like BEAST. Because bioinformatics combined two things I enjoyed, biology and programming, I decided to look more into it. Junction

was the perfect opportunity to further explore bioinformatics, especially because it is not typically taught in a high school setting. I wanted to gain insight into how the programs worked by

creating one of my own. It is my intention to continue this project after the duration of Junction,

potentially for science fair, and to improve my computer program. I hope to eventually use my

program for actual genetics research.

2 Methods

The materials required for this project include:

C++ Programming

Computer/Laptop

Programming software (Eclipse or Windows Visual Studio 2013)

Seaview (to check alignment)

Two FASTA files of nucleotide sequences

USB drive or other method of backing up work

(optional) BitBucket or other code repository site

Before beginning the project, I researched existing DNA analysis programs, like BLAST.

Then I downloaded the necessary programming software: Eclipse for C++, as well as Seaview.

I opened the Eclipse workspace and began a new C++ project. In the source folder, I added a

header file, named Hash.h, which was then included in the main.cpp. The majority of functions

were written in the header file. In Hash.h, I declared a class called Hash. Then I declared and

created functions that read in FASTA files, converted the sequences in the files (A 0, C 1, T

2, G 3), and parsed the converted files into words of size 8 bp. Then I wrote a function that

hashed the parsed words. The hash function converted each base-4 parsed word into a base-10

integer. This integer value, known as the hash value, was then stored in a hash table (see Figure 1). The hash table was generated in another function. Each hash value, which represented

a parsed sequence, was stored in a space in the hash table that corresponded with its position

in the original sequence. Then I created functions that compared the hash tables of each file

by searching for matching hash values (see Figure 2). Matching hash values meant the both

sequences contained that particular sequences. The differences in locations of matching hash

values were then used to align the files. More functions converted the hash values back into

sequences of nucleotide bases, and displayed the final alignment. In the main.cpp, I created

a new Hash variable, so that I could apply the functions from the header to the sequence files.

When the program ran, it asked the user to input the file names. Then it displayed the aligned

result, along with base-pair differences and percentage similarity. I backed up my work onto a

USB drive every time I made a major update (e.g. after creating a successful function, before

creating a new function). Debugging occurred throughout this whole process.

54

Karen Zhou

R ESULTS

Position

0

1

2

...

n

Hash Value

10062

40248

29923

...

7523

Figure 1: Hash table visualized. The hash value is stored relative to its position

in the sequence.

the corresponding positions of the hash tables and show mismatches. Green

arrows show matching hash values. When matches are found, the differences

in position of the hash values are used to align the sequences. For example, the

difference in position for hash value 10062 is 1 0 = 1, which implies a shift of

1 in the alignment.

3 Results

Figure 3: This screenshot of the console shows the resulting alignment after

two FASTA files are inputted. The differences are highlighted in yellow.

55

Karen Zhou

Figure 4: This screenshot shows the end of the alignment. The dashes represent gaps where deletions or insertions may have occurred.

Figure 5: This screenshot shows the additional info provided by the programs

analysis of the two DNA sequences. The program counted the number of different base pairs and calculated the percentage of similarity between the two

files.

Figure 6: This screenshot of the header file shows the various functions that

were created to ultimately display the alignment and other information. There

were several hundred lines of code in this program.

56

Karen Zhou

D ISCUSSION

4 Discussion

There were several challenges that I faced while conducting this project. Brainstorming

and implementing the most efficient methods was a time-consuming process. Many bugs rose

along the way, especially as the code got longer, as it got harder to determine the source of

error in the multitude of lines. There were also software issues; for a while I had to switch to

Windows Visual Studio because Eclipses compiler was not functioning correctly. Furthermore,

my original hash table was of size 29,425,664, and running the program while comparing each

value of the two 29,425,664 sized hash tables took over 40 minutes.

Hash Value + 48 (Pos)

0

...

10062 + 48 (1) = 75, 598

...

(48 1) + 48 448 = 29, 425, 663

Exists? (Yes = 1, No = 0)

1

...

1

...

0

Figure 7: Original hash table visualized. The size of the entire hash table was

29,425,664. If a particular sequence was contained in a specific position in a

file, then a 1 was stored in that hash table index. If it was not contained in the

file, a 0 was stored.

Then the hash table was shortened to 48, or 65,536. This increased the speed significantly.

However, because this new hash table stored positions relative to hash values, it was difficult to

analyze the locations of sequences and to align them accordingly.

Hash Value

0

1

...

10062

...

48 1 = 65, 535

is found (if not found 1)

1

1

...

1, 17

...

35

Figure 8: Revised hash table visualized. Now the hash table is of size 48 or

65,536. Because certain strings of bases can be found in multiple areas of a

sequence, multiple positions could be stored relative to hash value.

Finally, the hash table was changed to store hash values relative to their position. So the

size was now the total number of parsed words obtained from the file (see Figure 1). The files I

used each yielded 441 parsed words, so their hash tables were of size 441. This not only ensured

that the program would be faster, but it also simplified the alignment process. The time limit

was another obstacle that prevented me from adding more features to my program. Some additional features I could add in the future include displaying locations of differences, making the

57

Karen Zhou

alignment more accurate, and identifying specific genes. Furthermore, I used the word method

of comparison in my project, but dynamic programming is another method of sequence alignment that I could explore in the future. Ultimately, this project was challenging, but rewarding,

and I gained a lot of knowledge and insight into bioinformatics.

Acknowledgements

Id like to thank my mentor, Lane Gunderman, the Junction directors, the other Junction

mentors and students, and my friends and family for all their contributions to these amazing two weeks. Id also like to thank my AP Biology teacher, Dr. Offner, for first introducing

me to BLAST and thus opening my world to bioinformatics, and my programming teacher,

Ms. Knecht, for teaching me the coding skills I used for my project.

References

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). Basic local alignment

search tool. Journal of molecular biology, 215(3), 403-410.

Beringer, K. (2014, June 21). C++ tutorial: Intro to hash tables. Retrieved from

http://pumpkinprogrammer.com/2014/06/21/c-tutorial-intro-to-hashtables/

gov/Class/MLACourse/Modules/BLAST/slide_list.html

[Rolling Hash (Rabin-Karp Algorithm)] [Lecture notes]. (2011, February 18). Retrieved from

http://courses.csail.mit.edu/6.006/spring11/rec/rec06.pdf

bioinformaticsweb/

58

Control Theory

Keren Shao

mentored by Christopher Harmon

Keren was interested in the analysis of real, dynamic systems and how to control them. These systems include many things, from a cruise controller in a

vehicle to the stabilization of large aircraft. But with any of these systems, there

remains exactly one goal: using an input to have a desired effect on an output.

For simplicity, he focused on SISO (single input, single output) systems, and

conducted tests using different controllers to command a copper flywheel to

spin at various speeds. The goal was to devise a method of achieving a system

that would respond to changes in its state quickly and accurately when given a

command signal. Then the goal was to improve that method using feedback

control analysis techniques. The following exposition by Keren outlines the

theory and general process he used.

1 Block Diagram

It wont be extremely complicated to describe a system if we use the following:

Since there is an ordinary differential equation in our plant, we transfer the system into

the frequency domain (and do easy algebra!)

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Keren Shao

C ONTROL T HEORY

2 Laplace Transform

Using Partial Integral,

L( f (t )) = F (s) =

e st f (t ) d t

0

L( f (t )) =

e st f (t ) d t = sF (s) f (0)

0

L( f (t )) = F (s)

L( f (t )) = sF (s)

L( f (t )) = s 2 F (s)

Now we transform the ODE in the flywheel

J + B = T

J s(s) + B (s) = T

1

=

T

Js +B

Hooray! The time of graphs and algebra! Based on the block diagram, we can get the Error

Function E (s) = (s)K t .

KQ

=

T (transfer function) =

d J s + B + KQ

(

)

Kt Ka Km

Kd

Q=

and K = K p + K i s +

N

s

If K =

Kp

a

Ki s

b

Kd

sc

then

T=

K (as + b + cs 2 )Q

J s 2 + B s + K (as + b + cs 2 )Q

3 Analysis

3.1 Response Curve

Since

(

T = KQ

c

J +KQc

s2 +

s2 +

a

J +K Qc

s + J +Kb Qc

B +KQa

K Qb

J +K Qc s + J +K Qc

Wn =

K Qb

J + KQc

B + K Qa

(4KQb)(J + K Qc)

frequency, is the damping ratio and W d is the damping frequency

satisfying W d = W n 1 2 ,

60

Keren Shao

A NALYSIS

Figure 2: O A is the time constant, OB is the rise time, OC is the peak time, DF

is the overshoot, and OE is the settling time.

Important parameters:

= 1 e 1

Tr =

(1 cos1 )

2

1

Tp =

1 2

p

2

OS = e / 1

I n(%)

Ts =

W n

T=

K Q(cs 2 + as + b)

(J + K Q)s 2 + (B + K Qa)s + K Qb

When the numerator is 0, we get zeros. When the denominator is 0, we get poles. Assumption:

for the sake of god and algebra, we set a = 2, c = 1, b = 5, and J = B = Q = 1. The numerator is 0

when s = 1 + 2i or 1 2i , and the denominator is 0 when s = 0 or 1.

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Keren Shao

C ONTROL T HEORY

Is this system stable...? (Probably) Does it respond quickly? (No)

4 Improvement

1. Try to move the Zeros to more negative area with respect to The Real Axis (Asjust a, b, c)

2. Try to use P/PI/PD controllers for this system? (In fact, P seems to be the best controller

for this system if we do not have a bad motor?)

62

Keren Shao

I MPROVEMENT

63

Above: Long Do with a quadcopter that he built for his project. Below: A cheesecake-making class!

of Flat-Folding Origami

Ria Das

mentored by Herng Yi Cheng

1.1 Origami and its importance in mathematics and science

Origami is the ancient Japanese art of paperfolding. Thousands of years old, it has given

us such wonders of art and physics as the paper crane, paper elephants, and many other impressive models. Yet, besides being a form of art, origami also has a lot of intersection with

mathematics and science. The mathematics behind origami models allows one to come up

with novel origami designs, to explain the foldability of a given design, and to create algorithms

for use in computer programs that make it much easier to design origami models and visualize

the folded state of a given design. The precise specification of crease patterns in origami has led

scientists to explore its application in diverse scientific pursuits, such as in the folding of large

space telescopes that could make it possible to transport them in size-limited spacecraft [1],

and in manufacturing synthetic DNA using folding techniques that best resemble the folding

involved in natural DNA synthesis [2].

Tessellations are repeating patterns of geometric shapes that cover the plane with no gaps

or overlaps. These are used in wallpaper designs, mosaics, and so on. Origami tessellations

are repeating patterns of geometric shapes folded by using pleats and twists from a single

sheet of paper [3]. A popular type of basic flat-folding origami tessellations is considered the

brainchild of Japanese origamist Shuzo Fujimoto. The design produced after folding the pleats

and twists is flat that is, it can be expressed using two-dimensional geometry. At the same

time, different points in the folded paper may have a varying number of layers of paper on it.

Thus, if the sheet of paper is semi-transparent, then the folded design, when held against bright

light, will have different amounts of light coming through its different parts.

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Ria Das

The following picture shows a Five-and-Four folded origami tessellation against the outside light. Some of the gaps between darker bands were caused by slight inaccuracies in folding.

This MIT ESP Junction project was an independent study with the aim of understanding

the mathematics behind origami and origami tessellations, as well as an attempt to write algorithms based on computational geometry and graph theory that would allow a computer

program, given a crease pattern, to show on a monitor or in a printout the light pattern that

would result if the folding was carried out. The availability of such a tool makes it easier and

faster to visualize the light patterns of origami tessellations.

2.1 Input: Vertices

The vertices are specified in a text file with each line being of the form:

<vertex-label-name> <x-coordinate> <y-coordinate>

66

Ria Das

1A 0 0

2X -2 0

3P -2 1

The faces of a crease pattern are polygons bounded by the crease patterns lines that do not

overlap each other and together cover the entire paper. Each face is specified by a face name

(for reference) followed by a list of vertices specified in a single line. Each vertex in the list is

identified by its position (calculated as the line number minus 1) in the vertex input file. The

first line of the face input file, however, is used just for specifying the fixed, starting face for

folding and hence contains only a single face name.

Specifically, the first line of the face text file has the following format:

<face-label-name-to-be-used-as-the-fixed-face-in-the-model>

Each subsequent line has the following format (the vertex-index-number is the line number of the vertex in the vertex file minus 1, to allow for 0-based indexing):

<face-label-name> <vertex-index-number> <vertex-index-number> ...

The first few lines of a sample face input file are shown below:

Face-AXMV

Face-ABC 0 6 7

Face-BCYST 6 7 8 13 5

Face-ADB 0 3 6

The information in the transformation input file is used for positioning and making duplicate copies of the main origami pattern on the screen. Each line of the file contains a label

followed by one or more transformations, as follows:

<label> <reflection or translation or scale> ...

m b <isVertical>

where m and b are numbers representing the slope and y-intercept of the reflection line y =

mx + b.

The <isVertical> component can either be true or false. If true, m can take any numeric

value, and b is the x-intercept of the vertical line x = b.

Translations (x, y) 7 (x + a, y + b) are specified in the following format:

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Ria Das

a b translate

A scale (x, y) 7 (ax, a y) is represented by the following line:

a 0 scale

Finally, the three possible labels at the start of a line are old, new, and all.

old applies the following transformations to the crease pattern/folded model specified by the

new makes a duplicate copy of the old-transformed unit, and apply the following transforma-

tions to it.

all makes duplicate copies of the old-transformed and all the new-transformed units on the

screen, eliminate the common boundary lines between those transformed units, and apply the transformations specified in this line to them.

(Note: There must be exactly one old label in the transformation file, followed by zero or

more new-labeled lines and at least one all-labeled lines, in that order.)

Here are the lines in a sample transformation input file:

old

new

new

new

all

all

all

all

all

all

all

all

0 0 true

0 0 false

0 0 true 0 0 false

5 0 translate

-5 0 translate

0 5 translate

0 -5 translate

5 5 translate

-5 -5 translate

-5 5 translate

5 -5 translate

3.1 Overall algorithm

1. Read the following from the input files: vertices (label and coordinates), faces (fixed face

name, each face name and its list of vertex numbers), and positioning information (for

replication, translation, and scaling).

2. Determine the list of adjacent faces for each face.

3. Starting from the designated fixed face, compute a Hamiltonian path (if one exists); otherwise, find a spanning tree.

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Ria Das

4. For each face, traverse back along the path to the fixed face (root). Multiply the sequence

of transformation matrices corresponding to the edges being traversed to compute the

final conversion matrix for the face.

5. For each face, use its final conversion matrix and its original vertices to obtain the coordinates of the vertices after the folding.

6. Display the faces on the screen, before folding (show crease pattern) or after folding

(show folded model), using semi-transparent fill of the interior of the faces. Areas where

multiple faces overlap become darker in appearance.

7. If the user specifies a test points coordinates, compute the number of layers at that point

by using a variation of PNPoly algorithm that considers proximity to sides and vertices of

a face.

1. Finding an adjacency list for the faces: The adjacency of a pair of faces is determined by

checking to see if they share a line segment. This is determined by checking for common

subsequence in the two faces circular sequences of vertices, possibly reversed. For example, faces ABCD and DCEF are determined to be adjacent because they share the CD line

segment. This adjacency information is used in modeling a crease pattern as a graph and

generating the folding sequence and transformation matrices for each face, as explained

below.

2. Modeling a crease pattern as a graph: In graph theory, a graph is a mathematical structure made up of nodes and line segments called edges that connect them. The specified crease pattern is modeled as a graph in the program with each face represented as

a node, and the line segment shared between each pair of faces represented as an edge

connecting two nodes. This representation allows use of graph theoretical algorithms and

analysis, in particular for the path finding purposes described below.

3. Hamiltonian path finding: A Hamiltonian path in a graph is a simple path that visits

every vertex exactly once [4, p. 1066]. Upon modeling the crease pattern as a graph, the

program attempts to find a Hamiltonian path starting from the fixed face specified in the

face input file. If one exists, then it performs transformations for folding the faces in the

reverse path order. The line containing the line-segment shared between a consecutive

pair of faces is used as the line of reflection that represents the folding action. The specific

algorithm used for finding the Hamiltonian path, if one exists, is shown later.

4. Spanning Tree finding: A spanning tree connects all of the nodes of a graph without any

cycles, such that there is exactly one path connecting every pair of nodes. If a Hamiltonian

path cannot be found starting from a fixed node (face), a spanning tree is computed using

an algorithm shown later.

5. Determining the transformations for each face: Consider the sequence of edges, representing the shared line-segments between each consecutive nodes on the path from each

69

Ria Das

node to the fixed node. A face undergoes a fold, that is, a reflection, on each such crease.

Such reflections are represented as affine transformations [5]. Left multiplication of the

33 identity matrix with the sequence of affine transformation matrices provides us with

the single conversion matrix to be used to left-multiply the vertices of the face.

6. Compute the new coordinates of the face vertices: The conversion matrix computed

above for each face is used to left-multiply the matrix representing the vertices of the face

to obtain the coordinates for the vertices after folding.

7. Finding the number of layers of paper present at a given point: Due to folding, the number of layers of paper at a given point may vary from 0 (if outside the folded area) to n,

where n is the total number of faces in the crease pattern. For a given point, the number

of layers is determined by using a variation of the PNPoly algorithm [6] that allows specification of an error tolerance value to handle approximation of values in double arithmetic

computation.

3.3 Combined algorithm for finding Hamiltonian path (if present) and

finding a spanning tree

The following stack-based algorithm finds a Hamiltonian path starting from a fixed face,

if one exists. While looking for a Hamiltonian path, it also computes a spanning tree with the

fixed face as the root, by recording a (single) parent node for each node in the graph.

String HpSt (Node N, Stack<Node> Path) {

P <- Path.peek(); // find parent of node N - may be null (if N is root)

if (not(visited(N))) {

visited(N) <- true;

parent(N) <- P;

}

if (Path.contains(N)) return false; // LOOP detected

else {

Path.push(N);

if (Path.length() == nodeCount) return true;

// found Hamiltonian path

// iterate over each adjacent node except parent // SUCCESS if any child succeeds

for (each node M in adjacencyList(N) AND M != P)

if (HpSt(M, Stack Path)) return true; // found Hamiltonian path

// backtrack - FAILURE because all children failed

Path.pop();

return false;

}

}

70

Ria Das

that a face goes through

Each reflection that a face goes through is of one of two types: against a non-vertical line

and against a vertical line. The affine transformation matrix used for these two cases is shown

below. The general formulas in the two cases differ only in 1st and 2nd rows of the 3rd column.

Table 1: Affine transformation matrices from fold line equations

Non-vertical line: y = mx + b

angle A = tan1 m

Non-vertical line: x = b

angle A = /2

Affinetransformation matrix:

cos 2A sin 2A

b sin 2A

0

0

1

Affinetransformation matrix:

cos 2A sin 2A

2b

sin 2A cos 2A

0

0

0

1

by fold1 , fold2 , . . . , foldm and the corresponding affine transformation matrices are denoted by

M (fold1 ), M (fold2 ), . . . , M (foldm ), then the final conversion matrix M (foldfinal ) is computed as

M (foldfinal ) = M (foldm )M (foldm1 ) M (fold2 )M (fold1 ).

To compute the coordinates of the transformed face, the 3 3 conversion matrix, denoted

by M (foldfinal ), is multiplied with the 3 N matrix representing the sequence of vertices of the

original face. If the vertices of the face are (x 1 , y 1 ), (x 2 , y 2 ), . . . , (x n , y n ), then the original face

matrix M (faceoriginal ) is

x 1 x 2 x N 1 x N

M (faceoriginal ) = y 1 y 2 y N 1 y N

1 1

1

1

The matrix M (facetransformed ) representing the vertices of the transformed face is then

M (facetransformed ) = M (foldfinal )M (faceoriginal )

To calculate the number of layers of paper at a given point in the crease pattern or folded

model, a slight modification of W. Randolph Franklins PNPoly algorithm is used [6].

The PNPoly algorithm employs a ray-casting method, looping over each edge of the face,

to determine whether a given point is strictly inside a polygon. In each iteration of the loop, if

the horizontal ray extending from the test point to the right intersects the edge of the polygon

(at a single point), then it toggles a Boolean variable which gets set to true if this is the n th time

we found such a case and n is odd.

In this light pattern visualization tool, a special requirement added to compensate for

slight inaccuracies in the values of tan1 m made while computing transformation matrices

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Ria Das

was to consider a point that was on or very close to a side of a face as within the face. In order to

implement this, if a point is not strictly within a face, it is checked if the point is within a certain

ERROR distance from any edge of the face, for the very small ERROR value of 106 units (see

Figure 2). If the point is indeed inside this error margin, it is considered to be inside the face,

and an additional layer is added to the layer count.

the polygon, check if it is within ERROR distance of each edge (blue area), where

ERROR = 106 units (diagram not to scale)

4 Results

The outputs generated by the computer program upon clicks of the show crease pattern

and show folded model buttons are shown below.

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Ria Das

F UTURE W ORK

The extent of darkness of an area reflects the number of layers covering that area of the

paper. The exact number of layers covering a point may be found by entering the coordinates

of the point and clicking the Calculate number of layers button.

5 Future Work

In the future, I would like to improve the program in several ways, including:

using a dynamic programming based algorithm for finding Hamiltonian path [7] to reduce its worst case running time from O(n!) to O(n 2 2n )

showing generated transformation matrices

showing the layers visually with the face labels

enhancing the GUI: coordinate plane zoom in/out, changing the paper color

From a conceptual perspective, I would like to explore the following areas:

additional mathematics behind origami tessellations

3D origami tessellations

3D computer graphics and affine transformations

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Ria Das

Bibliography

[1] Robert J. Lang. Origami: Science, mathematics, and technology.

http://www.langorigami.com/science/science.php

[2] Erik D. Demaine and Joseph ORourke. Geometric Folding Algorithms. Cambridge University Press, 2007.

[3] Eric Gjerde. Origami Tessellations: Awe-Inspiring Geometric Designs. Boca Raton, FL: CRC

Press, 2009.

[4] Thomas H. Cormen, Charles E. Leiserson, Ronald L. Rivest, and Clifford Stein. Introduction

to Algorithms. MIT Press, 2009.

[5] John Choate. Reflections.

http://www.zebragraph.com/Geometers_Corner_files/Reflection.pdf

http://www.ecse.rpi.edu/Homepages/wrf/Research/Short_Notes/pnpoly.html

[7] ShreevatsaR. Answer to What is the dynamic programming algorithm for finding a Hamiltonian cycle in a graph?, last modified September 7, 2009. http://stackoverflow.com/

a/1387823

74

a cookbook with recipes

from around the world.

the Formation of Suicide Pacts

Among Younger Population in

both China and the United States

Tianyu (Christina) Lin

mentored by Evan Kuras

Abstract

A suicide pact is an agreement between a small group of people to commit suicide together.

Cases of suicide pacts were found through searching for news articles in Chinese searching engine Baidu and American searching engine Google. In the investigation, cases of suicide

pacts in China and the United States between those who were under 30 years old were gathered

(5 in the United States and 10 in China). Demographics, traditional or cybersuicide, method of

suicide pact formation, outcome of suicide, and geographic location of victims were taken note

of. Categorization and statistical analysis were used to process the data. For demographics, it

was found that victims of suicide pacts in China were generally in an age group from 20 to 25

and were older than victims in suicide pacts in the United States. There were no cybersuicide

cases in the United States. In fact, suicide pacts in the United States were formed between people who were familiar with each other in real life but never blood-kin; on the other hand, the

number of suicide pacts formed through QQ chat rooms was significantly higher than other

methods, possibly due to the herd mentality that instigated participants in the chatroom to

commit suicide. Since the victims in many suicide pacts in China formed suicide pacts under

the influence of other on the Internet, the number of cases with victims that backed out was significantly higher than those in the United States. Geography seemed to play an important role

at the same time. The provinces in which there were many suicide victims were provinces that

produced many immigrant workers, indicating the importance of improving migrant workers

mental health in preventing the formation of suicide pacts. In order to better understand suicide pacts in the younger population in both China and the United States, more cases would be

necessary, and such cases could be possibly obtained through research institutions and local

law enforcements.

Key Words: suicide pact, suicide prevention, cross-continental comparison

77

U NDERSTANDING AND P REVENTING THE F ORMATION OF S UICIDE PACTS Tianyu (Christina) Lin

1 Introduction

Suicide is the act of intentionally causing ones own death. Such events are tragic and

even more so when people take such actions together. There are two recognized categories of

group suicides. The first is mass suicide, in which a larger number of people kill themselves together for the same ideological reason. One example would be the mass suicide in Jonestown in

1978, when Jim Jones, the churchman who founded Peoples Temple, led his followers to commit suicide in Guyana, a nation in South Africa (Mass suicide at Jonestown). The other type

of group suicide is the suicide pact, which involves a small group of people whose motivations

are typically non-ideological. Those who commit suicide in the same subdistrict, a defined administration area, and within three days of each other are considered parties in a suicide pact

in England and Wales (Rajagopal).

There are two types of suicide pacts. One is traditional: the participants are already familiar with each other in real life. The other is a cybersuicide pact: the participants meet over

the Internet. What made suicide pacts known to the general public was two separate pacts that

killed nine individuals in October 2004. Participants in both suicide pacts were strangers who

met in suicide-related chatrooms online and then ended their lives together near Mount Fuji in

Japan (Huus).

Statistically, less than 1% of all suicides are suicide pacts. However, the prevention of suicide pacts can be crucial in saving lives, because usually one party of the pact is not as willing

to commit suicide and could be saved. In suicide pact cases where the instigator is more determined to end his or her life than the other victims of the suicide pact, the instigator is usually the

one who is deceased, and the survivor is usually the person who is compelled by the instigator

to participate in the pact (Rajagopal).

Past research has compared suicide pacts in Eastern and Western countries. In one particular study published in Journal of Clinical Psychiatry in 1985, 20 cases of suicide pacts in

Florida were compared to cases in England, Japan, and India. It was found that suicide pacts

occur more frequently in Japan. Lover pacts, spouse pacts, and friend pacts are more prevalent

in Japan, England, and India, respectively (International Comparisons).

Although states and cities in different cultures have been studied, countries, such as the

United States and China, are not systematically studied as a whole. Also, suicide pacts form an

integral, though not very well-known, part of the tragic deaths that occur each year in China.

The number of suicide pacts has been on the rise in both China and the United States in recent

years. In China, for instance, news articles concerning new suicide pact cases in Baidu have

risen from 66 (April to December 2014) to 194 (January to August 2015) (data gathered by the

author). Also, traditional suicide pacts have been between individuals within families or in

romantic relationships. However, with the rising popularity and prevalence of the Internet, now

cybersuicide pacts constitute a fair percent of all the suicide pact cases.

Although some research has been done to analyze the act of individual suicide, suicide

pacts remain as an area that is poorly investigated although their occurrence is increasing.

Also, despite some research on the cultural differences of suicide pacts, the research remains

limited. Most importantly, suicide pacts between young people, or those in their twenties or

younger, have not been studied, yet suicides are the most preventable form of death for teens.

Understanding and being able to prevent the formation of suicide pacts among the younger

78

M ETHODS

In order to understand the formation of suicide pacts in young people in both China and

the United States, demographics, how the pacts were formed, outcome of the pacts, as well as

whether the suicide pact was a traditional or cybersuicide pact were factors that were taken

note of and analyzed in suicide pact cases. Finding ways to prevent the formation of suicide

pacts in two countriesChina and the United Statesis another part of the project.

2 Methods

2.1 Procedure

Cases of suicide pacts in China were gathered by searching the keyword ,

meaning suicide pact in Chinese, in the Baidu search engine, specifically under news. Cases

of suicide pacts in the United States were gathered by searching the keyword suicide pact in

the Google search engine, specifically under news. Only online news articles were used because

it was the venue in which the latest suicide pact cases were reported. Only cases that happened

in either China or the United States involving individuals in their twenties or younger were included in this investigation. All available cases within 5 years (20102015) were gathered since

the data collected in such time frame is current and relevant to the situation today. The following factors were studied in each case: demographics (age of the victims of suicide pact), whether

the pact was a traditional or cybersuicide pact, how the victims formed the suicide pacts, and

the outcome of the pacts. Also, for cases in China, the origin of victims was taken note of as well

as the place of suicide. For cases in the United States, only the pace of suicide was taken note of

because the origin information was largely unavailable.

2.2 Analysis

Based on notes, the total number of cases that fall under each category of each variable

for both China and the United States was compiled. For demographics, the categories are 15

and under, 16 to 20, 20 to 25, and 26 to 30. For the different types of suicide pact, there are two

categories-traditional suicide pacts and cybersuicide pacts. For the ways that victims formed

suicide pacts, the categories are classmates, family, friends, colleagues, couples, through QQ

groups, through online forums, and other. For outcomes of the suicide pacts, the categories

are all dead, one rescued, one backed out, all rescued, and all backed out. After obtaining the

total numbers, the percent of each category in each factor was calculated by dividing the total

number of each category by the total number of cases (5 for data on United States and 10 for

data on China) or total number of victims in the case of demographics.

Chi-square test was performed on all factors (Lancaster). The expected value was the average of all the categories, and the null hypothesis was that the cases in factor are evenly distributed throughout all the categories.

79

U NDERSTANDING AND P REVENTING THE F ORMATION OF S UICIDE PACTS Tianyu (Christina) Lin

3 Results

3.1 Demographics

Figure 1: The percent of participants (sample size: 10 for the United States and

26 for China) of the suicide pact in each age group in both China and the United

States.

Although the victims in the United States are spread relatively evenly through the first three

age groups, none were in the oldest age group. There are significant differences between the

percent of people in the suicide pacts in China and the United States in the first two age groups,

which are considred as stages for teenagers and young adults in both countries. However, the

percent of victims who fall under the category of 21 to 25 is on average fifty percent higher

than the other three categories. Age of participants in the suicide act does not affect percent

of participants in the United States (p > 5%) but does affect percent of participants in China

(p < 5%).

80

R ESULTS

None of the suicide pacts in the United States are cybersuicides. More than half of the suicide pacts in China are cybersuicide pacts. Two cases that are worth noting in China. One is a

pact that was not formed via the Internet, but the participants in the pact are barely acquainted.

Another is one in which there is a combination of traditional and cybersuicide pacts. The category of the suicide act does affect percent of participants in the United States (p < 5%) but does

not affect percent of participants in China (p > 5%).

Figure 2: The percent of suicide pacts (sample size: 5 for the United States and

10 for China) in both China and the United States that are either traditional

suicide pacts or cybersuicide pacts.

From Figure 2, it is already known that gathered suicide pacts formed in the United States

are all traditional. The specific breakdown of the formation show that there are equal numbers

of pacts that are formed between friends and couples. For suicides in China, however, there was

no pact that was formed between couples. The numbers of pacts formed between classmates,

family, and friends are even. The highest number of suicide pacts are formed through QQ chat

groups, chat groups formed on a popular web-based instant messenger in China. Some were

formed through suicide forum. The two methods in others were roommates who did not really

know each other and online but specific method was not mentioned. The method used to form

suicide pact does affect percent of participants in the United States (p < 5%) but does affect

percent of participants in China (p < 5%).

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U NDERSTANDING AND P REVENTING THE F ORMATION OF S UICIDE PACTS Tianyu (Christina) Lin

Figure 3: Percent of pacts (sample size: 5 for the United States and 10 for China)

that used different methods to form suicide pacts in both China and the United

States.

Figure 4: Percent of different outcomes of the suicide pacts in both China and

the United States (sample size: 5 for the United States and 10 for China).

The mortality of the suicide pacts in the United States was significantly higher than that

in China. In fact, no one in the suicide pacts in the United States backed out. The percent of

situations in which one party in the suicide pact backed out was higher in China than the United

States. The number of rescues in China was also higher than the United States. The condition

of all participants after the suicide pact does affect percent of participants in the United States

(p < 5%) but does affect percent of participants in China (p < 5%).

82

R ESULTS

were used to geographically distinguish cases because they are conventions

that are economically and culturally different. The location is not where the

location where the victims committed suicide but where the victims were originally from. The highest number of victims is in Sichuan, Shanxi, Shandong,

and Hunan. The cases were all in the general area of south-east of China. The

provinces with the most cases surround the other provinces that had just individuals of cases.

The provinces with the highest number of suicidesShanxi, Shandong, and

Zhejiangwere coastal provinces.

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U NDERSTANDING AND P REVENTING THE F ORMATION OF S UICIDE PACTS Tianyu (Christina) Lin

Figure 7: States in which the suicide pacts took place. There were no suicides in

the central area of the United States. Other than the suicide pact in Minnesota,

all the pacts were in coastal areas (East coast and West coast)

4.1 Demographics

The victims of suicide in China that were in the 21 to 25 age group were 50% more than

the victims in any other age groupe. It is important to note that 21 to 25 is around the time

that students in China graduate from college and start job-hunting; the high number of suicide

pacts in this age group indicates that the intense pressure of finding jobs in China has triggered

the formation of many suicide pacts, indicating the necessity of counseling effort for newly

graduated Chinese students. In the United States, on the other hand, the victims of suicide

pacts were younger than the victims in China.There were no victims of suicide pact in the age

group of 25 to 30. At the same time, Chi-square rejected null hypothesis, which shows that age

does not affect the percent of victims in suicide pacts in the United States.

The lack of cybersuicide in the United States suggested that those in the United States

prefered to die with someone he or she loves and is close to. However, the higher number of cybersuicide pacts in China demonstrated that some victims in suicide pacts in China just wished

to die while in the company of someone, no matter who his or her companion may be. The fact

that two of the traditional suicide pact cases also involved strangers or people who were barely

acquaintances further supported this conclusion.

The highest percent of cases in the United States between classmates, friends, couples,

which were all people that were close to one another in real life. However, interestingly, none

of the cases involved people who were related by blood. This absence of suicide pact between

84

blood-kins may suggest that many of the suicide victims were aware of their suicides impact on

their families. Therefore, one possible method to persuade people from joining suicide pacts is

through the comfort and persuasion of the families.

In China, The highest percent method used to form suicide pact is QQ groups. First of all

QQ groups are extremely prevalent in the China and are not strictly controlled by Tencent. Inc,

the company that provides the service of the QQ app, thus there were suicide pact chatrooms

available (ji zhe wo de) as the easy way to find someone to accompany one to commit suicide.

According to a Chinese nationally recognized counselor, the pessimistic view of the world is

very easily spread through QQ groups (ji zhe wo de). Although committing suicide is an act

that requires a lot of determination, when even one person expresses such negative thoughts

or when a group of people discuss methods of committing suicide in the chatroom, the onlookers desire to commit suicide can grow stronger and can lead to eventual execution of the

suicide pact (ji zhe wo de). The herd mentality can also explain the prevalence of the formation

of suicide pacts via QQ groups. In a study regarding the herd mentality of college students, it

was noted that the herd mentality allows one to feel less guilty about the wrongful thing that

one has done, which in this case would be committing suicide (da xue sheng cong).

The fact that there are more rescues in China is either caused by coincidence or the victims

usually choose places that are easier to find and methods that are reversible. Such a high possibility of termination of suicide pact mid way correspond to the fact that many suicide pacts

in China are formed with strangers and QQ groups thus they agreed to be in the suicide pact

because of factors such as herd mentality.

In China, two of the provinces where the highest number of suicide pact victims were originally fromShanxi and Sichuanas well as other provinces, such as Jiangxi and Hubei, are

provinces that historically produce a lot of immigrant workers. Thus, the high number of suicide pact victims from these victims could be caused by migrant workers. In fact, in one of

the cases, three victims in a suicide pact in China were specifically listed as migrant workers in

the news article. This conjecture is supported by the fact that Zhejiang, one of the wealthiest

provinces in China (2014 nian zhong guo), became the province where the highest number of

suicide victims decided to commit suicide, suggesting that some migrant workers from other

provinces and work in Zhejiang committed suicide in where they work. Also, there had been research done on the mental health of immigrant workers, and it turned out that the state of mental health of migrant workers is worrisome due to financial pressure and the constant stress of

being from a different province (da gong zu xin). In the research, it was found that one in four

migrant worker has some degree of mental health issue. Also, 98.76% of the migrant workers

interviewed for the investigation are not happy with their life. Another mental health problem

that migrant workers created in their province of origin was the the children that the left behind.

In fact, according to a recent study, children who are left-behind were 18% more likely to have

some form of mental disorder than those who are not (da xue sheng cong).

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U NDERSTANDING AND P REVENTING THE F ORMATION OF S UICIDE PACTS Tianyu (Christina) Lin

In the United States, 80% of the victims are from the coastal states (either east coast or

west coast) and no victims from the central areas of the country. Trying to analyze by looking at

wealth of each state did not yield any noticeable patterns.

One major problem encountered during the investigation was the scarcity of cases reported in the news, especially in the United States. All 35 pages of Google searching results

were looked through and only 5 cases were found. In order to gather more cases in the future,

it is possible to contact local law enforcement or perhaps research facilities for suicide.

5 Conclusions

In conclusion, through data analysis of suicide pacts, several patterns were found regarding suicide pacts in younger people in China and the United States. For demographics, there

were many victims of suicide pacts in the age group of 20 to 25, suggesting the pressure of finding jobs after graduating college in China. There were more cybersuicide pacts in China and

many of these pacts were formed via QQ chatrooms, suggesting the herd mentality that could

cause victims to commit suicide when they do not fully want to. The fact that more victims

of suicides backed out of suicide pacts further support the proposition that many suicide pact

victims in China were not fully ready to commit suicide. In the United States, although many

people chose to form traditional suicide pacts with people they knew, the pacts were never between close kin. In terms of geographic locations, it is possible that migrant workers played a

big role in the existence of suicide pacts and counseling these migrant workers can play an important role in stopping the formation of future suicide pacts. In the United States, most of the

victims were from the east coast or the west coast. However, in order to more fully investigate

the formation of suicide pacts in China and the United States, a bigger sample size would be

necessary.

6 Acknowledgements

I would like to thank Evan Kuras, my mentor, who supported my idea from its initiation

and provided me with helpful feedback and ideas. He also had the right combination of compassion and humor that helped me through this serious yet sometimes mood-crushing investigation, and I could not ask for a better mentor. I would also like to thank MIT Junction for

giving me the opportunity to work on a project that I wanted to investigate for a long time and

the platform on which I can present my work to the world.

86

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New Civil Rights Movement. N.p., 21 Apr. 2011. Web. 11 Aug. 2015.

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com.cn/system/2011/10/19/010158194.shtml

da xue sheng cong zhong xin li yu xing wei de yan jiu yu fen xi

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wenku.baidu.com. N.p., Jan 15. 2015. Web.

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Fishbain, Da, and Te Aldrich. Suicide Pacts: International Comparisons. Journal of Clinical

Psychiatry 46.1 (1985): n. pag. Print.

Gatlin, Allison. Salinas Man Pleads Not Guilty in Alleged Suicide Pact. The Californian.

N.p., 5 Dec. 2014. Web. 11 Aug. 2015.

http://www.thecalifornian.com/story/news/local/2014/12/04/salinas-manpleads-guilty-alleged-suicide-pact/19918919/

[left-behind childrens mental health issues cannot be ignored]news.qq.com. N.p., Jun

12. 2015. Web. http://view.news.qq.com/original/intouchtoday/n3188.html

Huus, Kari. Japans Chilling Internet Suicide Pacts. msnbc.com. N.p., n.d. Web. 18 Aug.

2015.

http://www.nbcnews.com/id/3340456/t/japans-chilling-internet-suicidepacts/

ji zhe wo de zi sha qun dui hua chu mu jing xin quan dao hao wu xiao guo

[journalists go undercover in suicide groups with scary

conversations, talking to participants yield no result] xinhuanet.com. N.p., Oct 25. 2013.

Web. 11 Aug. 2015. http://news.xinhuanet.com/photo/2013-10/25/c_125596665.

htm

liang ge jiu ling hou xong wai di xiang yue ji nan xiao lv guan nei shao tan zi sha 90

[two born in 1990s from other cities meet in

Jinan; commit suicide by burning coal in a small motel] liaocheng.dom. N.p., Jan 14.

2015. Web. 11 Aug. 2015. http://liaocheng.dzwww.com/sdxw/201501/t20150114_

11725283.htm

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U NDERSTANDING AND P REVENTING THE F ORMATION OF S UICIDE PACTS Tianyu (Christina) Lin

liang ming nv wang you xiang yue yi di zi sha jiu dian shao tan shi bei jiu xia

two females who met over the internet formed suicide pact

but were rescued when they burnt coal in a hotel room] sina.com. N.p., Jun 29. 2015. Web.

11 Aug. 2015. http://news.sina.com.cn/s/2015-06-29/061932030894.shtml?_t=t

Mass suicide at Jonestown HISTORY.com. N.p., 18 June 2015. Web. 11 Aug. 2015. http:

//www.history.com/this-day-in-history/mass-suicide-at-jonestown

the suicide pact between strangers] tuxi.com N.p., 6 Jun. 2013. Web. 11 Aug. 2015. http:

//news.tuxi.com.cn/news/84/843827.html

nv yan jiu sheng he wang you xiang yue zi sha [female graduate

student makes suicide pact with someone she met online] 163.com. N.p., July 5. 2015.

Web. 11 Aug. 2015. http://news.163.com/15/0705/12/ATOTMUMI00014Q4P.html

qq qun xiang yue zi sha bei ju cha dian you shang yan QQ

[Formation of suicide pact in QQ group; Tragedy almost happened again] xinhuanet.com.

N.p., 26 Oct. 2014. Web. 11 Aug. 2015. http://www.cq.xinhuanet.com/2014-06/20/

c_1111229172.htm

Rare Teen Suicide Pact Leaves Lots of Questions in Interboro Towns. Daily Times News. N.p.,

10 Mar. 2010. Web. 11 Aug. 2015.

http://www.delcotimes.com/general-news/20100305/rare-teen-suicide-pactleaves-lots-of-questions-in-interboro-towns

Rajagopal, Sundararajan. Suicide Pacts and the Internet. British Medical Journey 329.7478

(2004): 1298-99. Print.

Report: Men Died in Murder-suicide Pact. WMUR. N.p., 2 Aug. 2013. Web. 11 Aug. 2015.

http://www.wmur.com/news/nh-news/report-men-died-in-murdersuicidepact/21307902

san ming jiu ling hou da gong zhe wang luo xiang yue zi sha liang ren shen wang 90

[three workers born in the 90s made a pact online to

commit suicide and two passed away] sina.com. N.p., 11 May. 2010. Web. 11 Aug. 2015.

http://news.sina.com.cn/s/p/2010-05-11/051120244071.shtml

shan xi wu ming xue sheng xiang yue he nong yao zi sha sir en shi liu shou er tong. 5

4 [Five students in Shanxi made a pact to drink

pesticide; four of them are left-behind children] ubetween.com. N.p., 11 Jun. 2015. Web.

11 Aug. 2015. http://news.ubetween.com/2015/hotnews_0611/76300.html

Torres, John A. Torres: Suicide Pact Teen Chose Life. Florida Today. N.p., 18 June 2015.

Web. 11 Aug. 2015. http://www.floridatoday.com/story/news/local/2015/06/17/

torres-suicide-pact-teen-chose-life/28870511/

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xiang yue zi sha chun cui shi wei le zhao ci ji [Making suicide

pact just for the excitement] shrb.com. N.p., 6 Jun. 2013. Web. 11 Aug. 2015. http:

//shrb.qlwb.com.cn/shrb/content/20150520/ArticelA10002JQ.htm

xue sheng xiang yue zi sha: bu rong hu shi de xing hao [students form suicide pacts: a signal that cannot be ignored] people.com. N.p., 26 Oct. 2014.

Web. 11 Aug. 2015. http://edu.people.com.cn/n/2014/1026/c1053-25909192.html

zheng jiang li shui fa yuan pan ding QQ xiang yue zi sha an teng xun gong sib u dan ze

QQ [Court in Lishui, Zhejiang rules that

Tencent.Co is not responsible in the formation of suicide pacts via QQ] cnr.com. N.p.,

10 Feb. 2012. Web. 11 Aug. 2015. http://native.cnr.cn/city/201202/t20120210_

509147923_1.shtml

2014 nian zhong guo 31 ge sheng shi GDP he cai li pai ming 2014 31 GDP

[2014 ranking of GDP and wealth of the 31 provinces and major cities in China]

eastmoney.com.N.p., Mar 10. 2015. Web. 11 Aug. 2015. http://stock.eastmoney.com/

news/1406,20150310484436192.html

89

Vineetha Yadlapalli

mentored by Elizabeth Berg

What qualities make one human? Does being human mean to always hold ones beliefs?

Does being human mean to abandon all in order to achieve survival? The meaning of being

human is debatable, and the definition depends on context and opinion. The humanity of people always changed throughout history, but one time, humanitys beliefs were put to the test:

during the Holocaust. It was a period of genocide led by German Nazi leader Adolf Hitler, who

targeted many groups of people he considered worthless. The victims included Jews, Gypsies,

the physically and mentally disabled, homosexuals, and many other groups of people, whether

targeted because of religion, ethnicity or political beliefs, resulting in 11 million deaths. These

deaths were the murders of innocent people (when excluding the criminals). In the time of the

Holocaust, the victims had to cope with the cruel environment of a concentration camp governed by SS officials. People died due to starvation, exhaustion from overworking, hangings,

gas chambers, and crematoriums. This situation forced each victim to face the struggles and

deal with that everyday life or to succumb to the escape of death. Thus, the humanity in them

changed.

While in the camps, people questioned parts of their humanity, such as why they were

placed in the concentration camps, the absence of Gods aid, and more. These questions need

to be answered in order to evaluate this difficult time in history. This paper will address various

aspects of humanity present or absent in camp life, and will answer questions like: How does

the peoples humanity change in a situation where it does not seem to exist? How harsh does

dehumanization get and what does it do? How was the Holocaust an example of how people

are affected mentally by the actions and beliefs of people around them? These questions will

be explored by examining memoirs written by Holocaust victims and survivors: Night by Elie

Wiesel, The Diary of a Young Girl by Anne Frank, and Survival in Auschwitz by Primo Levi.

Night, written years after the Holocaust by a Romanian Jew named Elie Wiesel, reflects

upon his struggle as he travels through various concentration camps at the age of fifteen with

his father. The Diary of a Young Girl, written by a victim who was a thirteen-year-old girl named

Anne Frank, gives a look into hiding in the upper parts of a building from discovery during the

Holocaust. Lastly, Survival in Auschwitz was written after the Holocaust ended by an Italian

chemist, Primo Levi. He was twenty five when he entered a concentration camp, and he spends

about a year in camps before his liberation. He explains his experience and thoughts in the

book.

Humanity has two different, but complementary definitions: being kind and compassion91

Vineetha Yadlapalli

ate towards others, and the state of being human. Dehumanization is the psychological process

of making someone seem less than human, and unworthy of being treated as one, which results

in the victim themselves believing they arent human either. This certain concept will be delved

into later.

Different types of people who existed in the camps viewed humanity differently there. On

a literal level, the types of people included the oppressed and the oppressors. The oppressed

were victims like Jews, Poles, and prisoners of war, while the oppressors included the officials

that ran the genocide, ranging from Hitler and the Nazis, to the SS officials and Germans. How

the oppressors could orchestrate such a horrific event, and how they could hurt people without

regret or feeling is still something to be thought about today.

The Nazis and SS officials and German civilians, the main oppressors of the victims besides

Hitler, varied in positions. The SS were the people that controlled the German police forces and

the concentration camp system (USHMM para. 2) and the Nazis were the people of Hitlers

political party called the National Socialist German Workers Party . . . or Nazi party . . .

(USHMM para. 4). The German civilians were the people living in Germany under Hitlers rule.

The SS officials would deliver whipping blows to the working victims in the camp and order

them around, exhausting them to the final breath. But, they showed momentary hesitation in

rare scenarios, like when it came to painful situations and the victims impacted them in some

way. For example, in Night, the camp people are forced to watch hangings to enforce discipline.

One hanging that Wiesel sees is different from the others he has seen before. It is the hanging

of a young boy. The boy is tied in the gallows along with two older men while the camp people

stare in horror. Wiesel notices the SS seemed more preoccupied, more worried, than usual.

To hang a child . . . was not a small matter . . . This time, the Lagerkapo refused to act

as executioner (Wiesel 64). Kapo is a German term for a leader of a group of people in the

concentration camp. It could be a Nazi, SS, or a promoted prisoner. Despite the SS officials

cruel attitude, they could feel guilt for their actions. This is important because it was proof they

had sympathy. In someone that appears to be inhumane, refusing to hang an individual or hurt

someone contradicts their supposed beliefs.

Also, earlier in Night, a Polish official tells Wiesel, Dont lose hope . . . Have faith in life .

. . Hell does not last forever . . . Help each other. That is the only way to survive. (Wiesel 41)

They could also provide hope, something unexpected for these people. I think that one thing

to infer about the SS officers is they were psychologically affected by the Holocaust as they had

murdered people, while in reality they felt guilt and shame each time for their actions. They

may have not been fully compassionless, from showing pity on the victims or reluctance to

carry out tasks, showing that they may have taken on a certain look on humanity with prejudice

and racial purity, but really felt differently, despite being the oppressors. Though they cannot

be excused for their atrocious acts, it does not mean they all lacked compassion.

In his experience, Primo Levi states there were two kinds of people that exist: the saved

and the drowned. Other pairs of opposites . . . are considerably less distinct . . . this division is much less evident in ordinary life; for there it rarely happens that a man loses himself

(Levi 100). The saved were the people who created contacts with others, gained knowledge and

respect, and had a good way to survive. For example, the saved could mean the Jews or Poles

who survived by adapting, like learning camp rules or rationing their food supply. The saved

could even be the non-Jewish civilians, Nazi party members, and soldiers, because they were

not targeted. On the contrary, the drowned were the ones who did not find a way to live in the

92

Vineetha Yadlapalli

camp quickly enough and were doomed to die inevitably. They were labeled as the muselmann:

the weak, the inept, those doomed to selection. (Levi 100) The drowned were the victims, and

could be Jews, Poles, and more. Another way to categorize people would be the Holocaust

camp survivors and the victims. Yet, the term survivor would apply to people that physically

lived through the Holocaust, as most people did not survive inside. They lost who they used to

be before they were taken to the camps. Their past identities slipped away.

Many types of people were targeted, and when they were all placed together in a concentration camp, it was challenging to understand others linguistically and socially to survive. The

camp victims had to learn to understand the German commands the SS gave, and they had to

adjust to other cultures ways, whether the people they met be Italian or Romanian or more.

This constant reminder to survive led to the regression in the humanity of people there.

What exactly was lost in humanity because of the environment of inhumanity? Much was,

because to survive in the face of driving necessity and physical disabilities many social habits

and instincts [were] reduced to silence (Levi 93). Civilization enforces social habits to live by,

and even though civilization is not present in the concentration camp, social habits vanish due

to the need to survive, which surpasses the importance of social habits and humane respect.

One aspect of humanity in civilization that is always encouraged but is discarded here is morality. Morality is a system where right and wrong or good and bad is distinct. Being moral means

to uphold good and right behavior and living by the rules one sets. Yet in the camps, there were

unclear meanings of good and bad or just and unjust in there. For example, theft in Buna,

punished by the civil direction, is authorized and encouraged by the SS; theft in camp, severely

repressed by the SS . . . (Levi 92). The ordinary moral world could not survive in the camp because of the instinct of survival. Levi adapts to this lifestyle free of typical rules, and says that .

. . if I find a spoon lying around, a piece of string, anything which I can acquire without danger

of punishment, I pocket them and consider them mine by full right (Levi 33). This enforces the

necessity of giving up morals to live in a situation where one could either save himself or drown.

Because as Levi says, Survival without renunciation of any part of ones own moral world . . .

was conceded only to very few superior individuals . . . (Levi 99). Their humanity changes because their moral beliefs must be shed to live. But what is unacceptable is the mistreatment of

people, especially the women. Anne Frank writes in her diary about how she hears that Men,

women, and children all sleep together. One hears of frightful immorality because of this; and

a lot of the women, and even girls, who stay there any length of the time of expecting babies

(Frank 50). The camp breeds an environment of immorality, and raping someone would be

to invade ones privacy and dignity, something they have not lost, unlike everything else they

have. Part of being oneself is to have independence and the ability to control themselves. To

take that away by this mistreatment is taking away ones humanity. In addition, to rape and

have no shame doing so shows the uncivilized and immoral attitudes the people adopted; their

humanity had altered due to the land of inhumanity.

On another note, savagery erupts in the conditions they live in, as everyone regresses from

civilized to savage, turning on each other. For example, a full-scale battle for food bursts between the Jews on a train that Wiesel is traveling on. Some German civilians decide to toss

bread onto the train where the packed, starving Jews watch. In the wagon where the bread

had landed, a battle had ensued. Men were hurling themselves against each other, trampling,

tearing at and mauling each other. Beasts of prey unleashed, animal hate in their eyes . . .

and the spectators observed these emaciated creatures ready to kill for a crust of bread (Wiesel

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Vineetha Yadlapalli

101). The Jews are all fighting like uncivilized creatures in order to get food and survive, uncivilized here meaning without typical rules. Food was not given by the SS officials before the train

started, showing how uncompassionate the SS could be by not helping the victims, causing the

humanity of the Jews to diminish too like when they fight for example. In addition, family loyalty and connections cease to matter when it comes to survival in its worst. Everyone forgets

who they are fighting with, battling just to get food. Among them are a father and his son, Meir.

During the bread fight, Meirs father is able to acquire a piece of bread, and he intends to share

with Meir, when he is killed by his own son. The father cries Meir! My little Meir! Dont you

recognize me . . . Youre killing your father . . . I have bread . . . for you too . . . for you too. . . .

(Wiesel 101). Meir kills him for bread, and moments later, he dies as well when two other men

kill him, therefore killing his father for nothing. Here, Meir betrays his father and goes against

family loyalty to gain food for himself, showing that family connections do not matter anymore,

and one is mostly on their own in the situation.

Later, Wiesel discovers the difficulty of resisting the urge to abandon. He promises himself

to have the strength to not betray his father. However, after the train, he feels guilt whenever

he thinks he would rather keep food he gives to his father for himself, so he can survive. In

the beginning of the novella, Wiesel cares deeply for his father. He still does now, but because

of survival, Wiesel acquires a selfish side. For example, he does not cry when his father dies,

making him ashamed of his selfishness. Selfishness and survival win out over family, showing

how everything important from before must go to live. It is hard to keep civil aspects from the

past with one when the situation demands the loss of all that to survive.

Despite the loss of morality, civility, and savagery, some remained kind. Some camp inmates help out others by encouragement. For example, Wiesel tells how he is beaten up for no

reason by a camp official and lies in the corner, trying to recover from the blows, when he feels

a cold hand wiping the blood from my forehead. It was the French girl. She . . . slipped me a

crust of bread . . . she said Bite your lips, little brother . . . Dont cry. . . (Wiesel 53). This

demonstrates the seldom acts of kindness inmates did, despite all the cruelty they face. Some

remember to keep their kindness with them, which can go a long way. Levi also encounters

understanding when he converses with another person in the camp. He explains the situation

of his Italian mother in hiding, and says how the listener timidly embraces me . . . I have not

forgotten his serious and gentle face of a child, which welcomed me on the threshold of the

house of the dead (Levi 27). Levi can still recall this moment of sympathy, showing the power

kindness can have. These seldom outliers have great impact on others.

Levi also receives help from a German civilian on the other side of the barbed wire, saying

himself that without the Germans assistance, he would not have survived. Civilians did have

the kindness to help. Also, in Anne Franks diary, Frank writes of the German civilians she encounters in public. Jews could not drive, so they had to walk. She writes how You could see

by [the Germans] faces how sorry they were they couldnt offer us a lift; the gaudy yellow star

spoke for itself (Frank 27). The Jews were required to wear badges to be identified. These

stars were a psychological [tactic] aimed at isolating and dehumanizing the Jews . . . directly

marking them as being different . . . to everyone else. It allowed for the easier facilitation of

their separation from society . . . (Arsenault para. 3). The star had power over the Jews and

Germans: it degraded the Jews, and resulted in no help from Germans, even if they wanted to.

They could not in fear of discovery. Other Germans though, like Levis helper, gave assistance

though it was punishable. Only a few of the kind Germans had the courage to do the right thing

94

Vineetha Yadlapalli

People do have the kindness to act and help others, one of the most vital traits to possess,

because kindness gives a reason to others to still believe in the good of humanity. Everyone

must help each other to survive together, although survival there did not occur mainly on that

trait: cleverness, wit, and connections were the way to pass selections, endure the days work,

bargain for materials and more. Because survival to them was more important than kindness,

Jews fought against other Jews for things. Though they should have been allies in the situation,

the kindness and respect for one another diminished, being replaced with natural survival instincts. The SS were the real issue. This is dangerous because if the victims turn on each other,

the Germans in charge have won, and they fulfill the twisted SS perspective of the Jews being

less than human.

The Nazis and SS viewed Jews and other targeted groups with disgust and hate; the victims

were not human to them. The SS made it their goal to enforce dehumanization on the victims,

because they believed they were not human to begin with. There are levels to this process,

and with each, the human is degraded further. In the Holocaust, dehumanization reached the

ultimate low, as victims lost who they used to be in the process. One thing it did was giving

no respect for the camp victims there. In Night, Wiesels father is suffering a colic attack, so

he got up and asked politely, in German, Excuse me . . . Could you tell me where the toilets

are located? The Gypsy stared at him . . . as if he wished to ascertain that the person . . .

was actually . . . a human being . . . he slapped [him] with such force that he fell down .

. . (Wiesel 39). Though Wiesels father addresses the guard in the language which the guard

uses and asks with respect, he is treated like he is not worthy of fulfilling basic human needs

and is instead treated with violence in return. The victims lose respect in the eyes of the SS,

and because of this, they build up fear of mistreatment and feel the pain of the incident. The

scar for Wiesels father to bear is physical and mental. Respect no longer exists for the people.

Something notable is that in normal circumstances, being slapped in such a way would bring

shame upon the victim of such violence. Yet here, Wiesels father shows no humiliation to his

son when he comes crawling back. This shows that dignity is not important here, as everyone

is equal and less than human. In addition, part of their identity is stolen when they are forced

to strip and wear new uniforms and shave their hair off. The new uniforms are thrown at the

people carelessly, further showing the lack of respect for them. Wiesel recounts on this moment

by saying Our clothes were to be thrown on the floor at the back of the barrack . . . For us

it meant true equality: nakedness . . . (Wiesel 35). Nakedness means true equality to them

because any past societal position associated with their clothing is stripped away, leaving them

equal. Clothes give one uniqueness and freedom of expression. Clothes can also represent

status in a class or society. But, the removal of their clothes symbolizes the loss of expression

and belonging in a place of civilized society. They all feel the same, as the hierarchy of society

from the past no longer exists here. But, this can make them feel distant from a familiar humanmade system that everyone belongs to, and that can take away from them.

One major aspect that is taken away from all the victims concerning identity is their name,

which can affect one greatly. Each person received a tattooed number on their arm, symbolizing the permanent reminder they are not worthy of being called by their real name, and they

are nothing but a number, even on them post-Holocaust, just like the SS and Nazis would have

liked. Some people even forget their real name while there in the camp. Levi writes of a fellow

person that worked with him during the day for some time, saying He is Null Achtzehn. He is

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Vineetha Yadlapalli

not called anything except that, Zero Eighteen . . . everyone was aware that only man is worthy

of a name, and that Null Achtzehn is no longer a man, I think that even he has forgotten his

name . . . (Levi 41). Ones identity defines who they are, and for them to lose who they are because of others is the worst of dehumanization, because identity gives one purpose to live, to be,

to be human. This shows that the SS symbolically took away their actual names, which enforced

dehumanization further, because when one no longer has a name, they cease to be a human.

Also, the numbers each camp victim was branded with were prison-like, which would imply

guilt for wrongdoing. However, the irony is most of the people in the concentration camps were

innocent. This criminal branding could have changed the way they viewed themselves (as good

or bad, human or not), which makes dehumanization strike harder.

Another thing Holocaust victims faced because of dehumanization was the loss of their

possessions and themselves. When people entered the concentration camps, they were separated from family, causing one to lose hope and worry constantly. It wounded them to know

their beloved ones were dead or in pain, and they could not do anything to help them, causing

psychological effects on their minds through pain and guilt. When entering, they lost clothing

from their past lives and all their valuables, such as gold, only for the SS officials gratification

by gaining wealth. For example, Wiesel is forced to give up his tooths gold crown to a doctor.

Wiesel escapes the encounter . However, a fellow inmate demands he give the gold crown and

a ration of bread to him afterwards. Wiesel exclaims What? My ration of bread so that you can

have my crown? (Wiesel 56). This interaction shows the injustice that occurred. Having possessions gives a victim a sense of ownership as well as memories, but when it is stripped away,

they can feel empty without it, since possessions make one feel important of owning something

and being human by having that right to own it.

Holocaust victims also lost who they used to be by no longer holding individual identity.

After the Holocaust ends, Wiesel decides to look into a mirror for the first time since he lived in

the ghettos long ago. Wiesel says I had not seen myself since the ghetto. From the depths of

the mirror, a corpse was contemplating me. The look in his eyes as he gazed at me has never

left me (Wiesel 115). Wiesel saw a corpse, not the boy he used to be. He could not recognize

himself, showing how people would lose themselves because of dehumanization, so they were

degraded and eventually lost themselves.

A joy of being human is the freedom. Yet, in the Holocaust, freedom is taken away. For one,

all the victims were forced into an unsanitary, confined concentration camp, surrounded by

guards. They also lost the freedom of expression by stripping their old clothes. In addition, their

freedom was restricted when they lost their rights and had rules. According to Frank, she writes

of how Jews, including her, must wear a yellow star . . . Jews are banned from trans[portation]

and are forbidden to drive . . . Youre scared to do anything because it may be forbidden.

Our freedom was strictly limited . . . (Frank 14). Jews were denied from basic property and

rights, and were singled out like wrongdoers when they wore stars. Freedoms absence allowed

dehumanization to occur further.

The SS treated the victims like animals. The Jews and other sufferers were beaten frequently, whether for no reason or for punishment. They were even beaten by fellow Jew inmates. Wiesel says that Dozens of inmates were there to receive us, sticks in hand, striking

anywhere . . . Strip! Hurry up! Raus! (Wiesel 35). The fact that Jews beat fellow Jews shows

they were emotionally stripped, and without emotion, people would act like animals. They

were treated as animals too as they were caged by barbed wire in the small camp, and were

96

Vineetha Yadlapalli

called items, not people. For example, the SS addressed them as items. Levi says how the Germans held the roll-call. At the end, the officer asked Wieviel Stuck? The corporal . . . replied

that there were six hundred and fifty pieces. . . (Levi 10). To the SS, the victims were to be used

to work or if unable, worthless and to die. He will be a hollow man . . . whose life and death

can be lightly decided with no sense of human affinity . . . on the basis of pure judgement of

utility . . . (Levi 22). They were treated like objects for work and like animals, not people.

The Jews and the other Holocaust targets reached the limit of dehumanization. Even Levi

acknowledges it, as he says we became aware that our language lacks words to express this

offence, the demolition of a man . . . We had reached the bottom . . . no human condition

is more miserable than this, nor could it be conceivably be so. Nothing belongs to us . . .

They will even take away our name . . . (Levi 22). Unfortunately, they had reached the limit,

losing everything. They suffered humiliation, isolation from society, denial of rights, and were

separated from possessions and their beloved.

Something vital to the Jews that they lost was religion. Throughout the Holocaust, as people kept praying for the end of their suffering, they gradually lost their faith in God because of

the lack of response to their prayers. Before the Holocaust, religion was everything to Wiesel.

But, during the stay in the concentration camp, he goes through so much he loses that faith. As

he sees the hanging of a child in the gallows, he hears someone say For Gods sake, where is

God? And from within me, I heard a voice answer: Where he is? This is where - hanging here

from this gallows. . . (Wiesel 65). Religion gives hope that somehow, everything will turn out

alright. Wiesel says that God died, which shows the point where his faith is shattered.

There could be three possible explanations to why God did not respond to the Jews. One

is that he did not care for his devotees, so he did not help. This could cause anger as well as loss

of faith. But, the second possible explanation is more dangerous: God simply could not help.

This would mean that the SS had more power than God himself, terrifying to the religious. This

shook their faith and brought the belief they would suffer a punishment by the SS more powerful

than Gods force. Also, the Jews may have thought God did not help because they deserved it: a

twisted, yet possible reason the devotees could have conjured up in their desperation to try to

explain their suffering. If God did not care and thought they did not deserve his help, they would

believe they were worthless and less than human, enforcing dehumanization more. Because

they lost their faith, many were shaken severely by this revelation. They lost a massive aspect of

their past lives and culture, so they lose hope and succumb to dehumanization.

The aspects of the victims previous lives came to use for camp survival. For example, they

made an economy called the Market, where chaos and noise occurred as people bargained for

items and food from many different types of people. Levi describes the Market as very active.

Although every exchange (in fact, every form of possession) is explicitly forbidden . . . the

northeast corner of the Lager . . . is permanently occupied by a tumultuous throng . . . (Levi

84). They were able to make an economy with currencies and bargaining. The system is similar

to the outside societys economy. Another aspect that helped was their past lifes profession.

Some would use their skills to their advantage. One person who does so is Engineer Kardos, a

man who moves around the bunks, tending to wounded feet . . . That is his trade. There is

no one who will not willingly renounce a slice of bread . . . in this manner, honestly, engineer

Kardos solves the problem of living (Levi 59). Many different skilled people were able to put

their knowledge to use so they could survive, which shows the importance of aspects of their

past lives in aiding their survival in the camp.

97

Vineetha Yadlapalli

The past aspects also reminded them of what they did not have. The victims dreamt of

food and the desire to consume it, which was always interrupted by the reality of having to

consume few small portions of stale bread and watery soup instead. This aspect of recalling

food can lead to ones downfall, as they could go mad by recalling such fantasies.

Throughout this paper, humanity in the Holocaust was explored, from the change of peoples humanity, which resulted in the loss of morality, family loyalty, and kindness, and savagery

spreading, to the effects of dehumanization on people, and how cruel it got (identity loss, possessions, respect, themselves, animal regression, religious faith). Three books shed light with

first-hand accounts of the authors experiences: Night by Elie Wiesel, The Diary of a Young Girl

by Anne Frank, and Survival in Auschwitz by Primo Levi. The Holocaust was a dark and confusing time for many people, victims and non-victims alike. This paper has hopefully explained

various concepts from that time.

Despite it all, Germans could not take away the victims memories, as long as they held on

to them and kept remembering. As Levi says, We know where we come from. The memories

of the world outside crowd our sleeping and our waking hours; we become aware, with amazement, that we have forgotten nothing; every memory evoked rises in front of us painfully clear

(Levi 55). These memories were a blessing to recall, yet torture, because to remember meant to

regret. They had memories of their past lives and the Holocaust with them.

Holocaust memories bring up the importance of the Holocaust. What is the most important about this event is the necessity to remember that it happened and to prevent such a

tragedy from occurring again. Human hate should cease and instead all should respect each

other for who they are, by supporting one another. Also, it is crucial to acknowledge and understand the Holocaust, but to not empathize with the victims. The reason for this is that one in

the modern world is incapable to empathize. One cannot compare their ordinary experiences

to something else on a whole different level. By trying to empathize, one will minimize the situations severity. To reduce the level of what the event really was is the worse one could do to

victims. By avoiding empathy and discouraging hate, such an atrocity can remain an anomaly.

The world must remember the Holocaust, because like Wiesel said, if everyone forgets, we are

guilty, we are accomplices (Wiesel 118).

Works Cited

Frank, Anne. The Diary of a Young Girl. New York: Doubleday, 2001. Print.

Levi, Primo. Survival in Auschwitz: If This is a Man. New York: bnpublishing, 2008. Print.

Wiesel, Elie. Night. New York: Hill and Wang, 2006. Print.

SS. United States Holocaust Memorial Museum. United States Holocaust Memorial Museum, 20 June 2014. Web. 18 Aug 2015. http://www.ushmm.org/wlc/en/article.php?

ModuleId=10007400

Arsenault, Joshua. Holocaust Badges.Holocaust Memorial Center Zekelman Family Campus. Holocaust Memorial Center, n.d. Web. 18 Aug 2015.

http://www.holocaustcenter.org/holocaust-badges

98

The MIT Educational Studies Program (ESP) is a student group at the Massachusetts Institute of Technology that recruits MIT students and community members to teach classes for

high school and middle school students from the Boston area and beyond.

We are all MIT undergraduates, graduate students, alumni, and community members who

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programs that range in size, scope, and style from the single-weekend Splash and Spark,

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esp.mit.edu. If you have additional questions, please email us at esp@mit.edu.

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