Latest revision as of 14:51, 6 October 2016

Modeling - TAS Taipei iGEM Wiki

PROJECT

Background

Achievements

Collaborations

Parts

Cataracts - the leading cause of blindness. Find out how we can noninvasively treat and prevent cataract formation.
EXPERIMENTAL

Lens Cataract Model

Prevention and Treatment Constructs

Delivery Prototype

Notebook

We don't just come up with great ideas. We show they work. Follow along our discovery of exciting science!
MODEL

Cataract Damage

GSR/25HC Pathway

Nanoparticle Degradation

Eyedrop Model

Computational Biology provides us models that we cannot easily test. Click to find out the results of our modeling, and if you want, the math behind it!
HUMAN PRACTICE

Research

Outreach

Impact

We don't just grow cool bacteria. We make a difference. Find out how we tackled social aspects of this project.
BIOSAFETY

Researcher Safety

Environmental Safety

Biobrick Safety

Local Safety

Safety first. Especially in a lab. Here's how we maintained and investigated the integrity and security of our work environment.
TEAM

Members

About

Attributions

Wiki Standard Pages

Behind every tough iGem project lies a hard-working yet cheerful group of students. Meet the team!

C◎UNTERACTS

Modeling

Abstract

We answer two questions: How much GSR to maintain in the lens, and how to maintain that amount? We find the amount of GSR needed in the lens (Model 2) to limit crystallin damage so the resulting cataract is less than LOCS 2.5 (Model 1). Then, we find the optimal design of eyedrops (Model 4) and nanoparticles that will maintain this amount of GSR in the lens (Model 3). These models allow our team to understand the impact of adding GSR-loaded nanoparticles into the lens, and to design a full treatment plan on how to prevent and treat cataracts.

Achievements

Designed a simple calculator to find amount of GSR or 25HC eyedrops needed for a patient's LOCS score.
Bridged the gap between the medical, biological, and chemical measurement of crystallin damage.
Predicted impact of adding GSR and 25HC on the amount of crystallin damage in the lens.
Created Nanoparticle Customizer for doctors to find a full treatment plan.
Generalized our Customizer to allow other iGEM teams who wish to use nanoparticle drug delivery
Analyzed sensitivity of prototype, and suggested insights into optimal manufacturing and clinical use of our prototype.
Used Experimental data to develop Models 1 and 3.

Outline

Introduction

Why Model?

In the lab, biologists are often unable to test everything experimentally. For example, in our cataracts project, cataract prevention occurs in the long-term, from 20-50 years. Obviously, although short experiments can provide us an idea of what prevention may look like, the power of computational biology allows us to model into the future. As a result, our modeling has been crucial in developing a prototype.

Focus

Most iGEM teams perform modeling on gene expression, which we accomplish in model 5. However, as our construct is not directly placed into the eyes, how our synthesized protein impacts the eyes after it is seperately transported is much more interesting. As a result, we spent the majority of our models on understanding the impacts on the eye.

Guiding Questions

How much GSR do we want inside the lens?
How do we use nanoparticles to control the amount of GSR in the lens?
How do we synthesize GSR, package into NP, and send it into the eye?

Model 1: Crystallin Damage

Abstract

In our experiments, absorbance measurements are meaningless without understanding how severe a cataract that absorbance measurement means. We use literature research to relate LOCS, the physician's scale of cataract severity) to absorbance, which is how we quantified crystallin damage in experiments. We use experimental data to understand how crystallin damage can be quantified by measuring absorbance. With this model, we can calculate how much crystallin damage we have to limit to reduce LOCS to an acceptable level.

Purpose

How much do we need to limit crystallin damage so surgery is not needed?

Measurement of Cataract Severity

There are four ways of measuring cataract severity, each used for a different purpose.

Lens Optical Cataract Scale (LOCS): Physicians use this scale, from 0 – 6, to grade the severity of cataracts.
Opacity (%): This is the physical, quantitative property of the LOC scale.
Absorbance at 397.5 nm: This is the experimental method, used by our team in the lab (c.d.).
Crystallin Damage: This is a chemical definition. We quantify cataract severity as a function of how much oxidizing agents there are, as well as how long crystalline is exposed to oxidizing agents. We define 1 crystallin damage unit as the damage done to human crystallin when exposed to 1 M hydrogen peroxide, the main oxidizing agent, for 1 hour.

<

We use the unit of crystallin damage to connect cataract severity with the amount of GSR we add (in Model 2). We want to lower c.d. below so that the resulting cataract is of LOCS 2.5. For the rest of the model, our task is simple: relate each point of the LOCS scale to c.d., in order to connect to Model 2.

LOCS Equivalence to Absorbance: Literature Research

Past studies have done numerous studies on how absorbance measurements can be converted to the LOC scale that physicians end up using. With the results of ________ and ________, we construct the first three columns in Table 2.

Absorbance Equivalence to Crystallin Damage: Experimental Data

We use experimental data from our team’s Cataract Lens Model (link). In each trial, they added H2O2 to crystallin, and measured the resulting absorbance. The data used are shown in Table 1. We can calculate the theoretical c.d., and graph absorbance vs. crystallin damage in Figure 2.

With this relation in Figure 2, we calculate the equivalent crystallin damage to each LOCS rating and its equivalent absorbance.

Error Analysis

It may be surprising that only around 1 M-h is required to induce moderately severe cataracts. Remember that this is done in the absence of antioxidation systems (GSR) and at an extremely high oxidizing concentration of H2O2 (1M of H2O2). In the lens, H2O2 has a much lower concentration, so severe cataracts are induced over months to years.

There are some limitations of the model that arise from our assumptions. We assume that fish and human lens contain similar crystallin proteins that are degraded in the similar manner (Assumption 4). In addition, we made a rough adjustment of data based our diluting procedure. For better results to create a human cataract model, experiments will need to be done on human lens, even better if done in vitro, without any dilutions.

**Table 2: Results of Model 1 – Equivalent values for LOCS, Opacity, Absorbance, and Crystallin Damage.**
LOCS	Opacity (%)	Absorbance (@397.5 nm)	Crystallin Damage (M-h)
0.0	0.00	0.0000	0.0000
0.5	3.24	0.0143	0.1327
1.0	6.65	0.0299	0.2774
1.5	10.81	0.0497	0.4610
2.0	15.88	0.0751	0.6966
2.5	21.95	0.1076	0.9981
3.0	29.07	0.1492	1.3840
4.0	46.37	0.2706	2.5101
5.0	66.05	0.4691	4.3514

Background

There are four ways to measure cataract severity (how blurred the lens is):

Lens Optical Cataract Scale III (LOCS) - a scale from 0-6 used by physicians.
Opacity (%) - used to calculate the LOC scale
Absorbance at 397.5 nm - measurable in the lab.
Crystallin Damage - used to quantify how much crystallin has been reacted with hydrogen peroxide to create insoluble, damaged crystallin. The following definition of crystallin damage is used:

\[c.d.(t) = \int_{0}^{\infty} [H_2O_2]_t dt\]

In other words, 1 unit of crystallin damage, in M-h, is equal to the damage caused by 1 molar concentration of hydrogen peroxide reacting crystallin in the eyes for 1 hour.

LOCS Scale

Assumptions

Definition of crystallin damage: Crystallin damage is proportional to the concentration of hydrogen peroxide, and the time of exposure. This is a valid assumption, supported by the fact that the reaction between cysteine (molecules on crystallin) and hydrogen peroxide is linear.
We assume that the amount of crystallin is far greater than the amount oxidized. Our product is meant for long-term cataract prevention and minor treatment, and is not suggested for patients with extremely severe cataracts.
When the experiments diluted the cataract lens protein, the amount of crystallin is diluted. However, the final absorbance of degraded crystallin is also diluted, so we assume any errors in absorbance is canceled out.
We assume that fish and human lens contain similar crystallin proteins.

Procedure

In the first part, we find how the absorbance measurements in the lab are related to the severity of the cataracts. Through literature data, we can relate LOCS to the opacity of the lens. Then, via physical calculations, we can relate the opacity of the lens to the absorbance of the lens at 400 nm.
Then, we use our team’s experimental data in the cataract model. For each trial, the concentration of H2O2 and the length of exposure are given, so we can calculate the theoretical crystallin damage using the definition above and the assumptions we made. In each trial we also measured the absorbance, so we have a relation between crystallin damage and absorbance.
However, we need to make a minor adjustment, because absorbance is affected by dilution. When the fish lens was isolated, they were placed in Tris buffer and diluted. We calculate the ratio of volumes from diluted volume to the Tris buffer, and multiply each absorbance measurement by this value.

LOCS Scale

Results

**Table 1: Results of Model 1 - Equivalent values for LOCS, Opacity, Absorbance, and Crystallin Damage.**
LOCS	0.0	0.5	1.0	1.5	2.0	2.5	3.0	4.0	5.0
Degree	None	Trace		Mild			Moderate		Severe
Opacity (%)	0	3.24	6.65	10.81	15.88	21.95	29.07	46.37	66.05
Absorbance (a.u.)	0.0000	0.0143	0.0299	0.0497	0.0751	0.1076	0.1492	0.2706	0.4691
Crystallin Damage (c.d.)	0.0000	0.1327	0.2774	0.4610	0.6966	0.9981	1.3840	2.5101	4.3514

**Table 2: Experimental Data used for Model 1 from Cataract Lens Model (TAS) - Absorbance vs. Crystallin Damage**
Trial	H2O2 Concentration (M)	Exposure Time (h)	Crystallin Damage (c.d.)	Measured Absorbance (abs @400 nm)
1	0.100	24.0	2.40	0.105
2	0.100	46.5	4.65	0.451
3	0.100	72.0	7.20	0.0.695
4	0.100	20.0	2.00	0.089
5	0.100	42.0	4.20	0.392
6	0.100	15.0	1.50	0.093
7	0.100	42.0	0.340	0.340
8	0.100	67.0	6.70	0.563

Discussion

Model Result

The model successfully relates LOCS, opacity of lens, absorbance measurements, and the equivalent crystallin damage of the lens. The purpose of relating LOCS to crystallin damage, is that in Model 2, we will use chemical kinetics to determine how adding GSR to the lens will decrease the amount of crystallin damage. Exactly how much crystallin damage we need to decrease is determined by the desired LOCS. For example, if we want to have a LOCS rating of less than 2.5, then we must lower crystalline damage to only 0.9981 M-h.

Model Adjustment

When determining the relationship between absorbance and crystallin, in Figure 1 the best fit line has a x – intercept that is nonzero. However, when converting each absorbance rating to equivalent crystallin damage in Table 2, we ignore the constant term. When doing the experiments, the fish lens may have contained GSH that is still active, so the fact that the crystallin is exposed to H2O2, the degradation reaction does not happen until all GSH is depleted, and crystallin damage begins to form. We subtract around 1 unit of crystallin damage from all values.

Error Analysis

It may be surprising that only around 1 M-h is required to induce moderately severe cataracts. Remember that this is done in the absence of antioxidation systems (GSR) and at an extremely high oxidizing concentration of H2O2 (1M of H2O2). In the lens, H2O2 has a much lower concentration, so severe cataracts are induced over months to years.

There are some limitations of the model that arise from our assumptions. We assume that fish and human lens contain similar crystallin proteins that are degraded in the similar manner (Assumption 4). Also, to simplify the experiments, the lens were diluted in Tris buffer. Because of this dilution, the actual crystallin damage is much lower, but so is the actual absorbance. We assume that the decrease in crystallin damage and absorbance is the same, so no adjustments need to be made for the relation between crystallin damage and absorbance (Assumption 3). For better results to create a human cataract model, experiments will need to be done on human lens, even better if done in vitro, without any dilutions.

Conclusion

For surgery to not be needed, the LOCS value has to be below 2.5. This is equivalent to 21.95% in light opacity or 0.1076 abs units. Based on the results of our experiments, this is equivalent to 0.9981 units of crystallin damage, the damage done to crystallin if exposed to 0.9981 M of H2O2 for 1 hr. For future models, this value 0.9981 units of c.d. will be called the crystallin damage threshold for LOCS 2.5.

Model 2: GSR/25HC Chemical Pathway

Abstract

The key question: How much GSR to add? Now that we know how much we need to limit crystallin damage, we use systems of ordinary differential equation to model the GSR Pathway. We calculate the necessary GSR concentration to be maintained over 50 years so that the resulting cataract is below LOCS 2.5./p>

Purpose

How much GSR do we need to maintain in the lens so that the crystallin damage recorded over 50 years is below the threshold for LOCS 2.5?

Chemical Kinetics Model: Differential Equations

By the Law of Mass Action, Michaelis-Menten Enzyme kinetics, Ping-pong mechanism, and the Law of Passive Diffusion, we build a system of 10 differential equations based on 6 chemical reactions. All parameters, constants, and initial conditions are based off literature data. Estimates made are also shown with assumptions and reasoning. The details are shown in the collapsible for interested readers.

Blackbox Approach: Testing GSR Impact

Image

We will vary the input, Initial GSR concentration, from 0 to 100 uM, holding all other variables constant, and numerically solve for the amount of hydrogen peroxide over time. With this graph, we can find the amount of crystallin damage accumulated over 20 to 50 years if different levels of GSR is maintained.

Background

The following 6 reactions describe the antioxidant system inside the cortex and nucleus.

$$GP_{xr}+[H_2O_2]_{in}+H^+ \xrightarrow[]{k_1} GP_{xo}+H_2O ...(1)$$ $$GP_{xo}+GSH+H^+ \xrightarrow[]{k_2} [GS-GP_x]+H_2O ...(2)$$ $$[GS-GP_x] + GSH \xrightarrow[]{k_3} GP_{xr}+GSSG+H^+ ...(3)$$ $$NADPH \xrightarrow[GSR]{k4, K_{4M}} NADP^+ ...(4)$$ $$GSSG \xrightarrow[GSR']{k_5, K_{5M}} 2GSH ...(5)$$ $$[H_2O_2]_{out} \xrightarrow[]{k_5} [H_2O_2]_{in} ...(6)$$

Each reaction will be discussed in detail, and we will derive rate equations.

Reaction 1:As hydrogen ions are numerous are negligible in the reaction, we will ignore it. By the law of mass action, the rate of this reaction is: $$r_1=k_1[GP_{xr}][H_2O_2]_{in}$$

Reaction 2: By the law of mass action, the rate of this reaction is: $$r_2=k_2[GP_{xo}][GSH]$$

Reaction 3: By the law of mass action, the rate of this reaction is: $$r_3=k_3[GS-GP_x][GSH]$$

Summary of Reaction 1-3:In these reactions, hydrogen peroxide is reduced to water. GSH is consumed to recycle the enzyme GPx back into reduced form, to neutralize more hydrogen peroxide.

Reaction 4: ByMichaelis-Menten kinetics and the Ping-Pong mechanism, the rate of this reaction, with rate constant k4, and Michaelis-Menten constant Km4, is: $$r_4=k_4\frac{[NADPH]}{K_{4M}+[NADPH]}$$

Reaction 5: ByMichaelis-Menten kinetics and the Ping-Pong mechanism, the rate of this reaction, with rate constant k5, and Michaelis-Menten constant Km5, is: $$r_5=k_5\frac{[GSSG]}{K_{4M}+[GSSG]}$$

Summary of Reaction 4-5: In these, GSSG is reduced back to form GSH, using the enzyme GSR. This is necessary for antioxidation to continue as reaction 1 is constantly using GSH, converting them to GSSG.

Reaction 6: By the Law of Passive Diffusion, the rate of diffusion into the cortex and lens is: is: $$r_6=k_6([H_2O_2]_{out}-[H_2O_2]_{in})$$

Differential Equations

We have six reaction rates derived from above. Now, we will form differential equations, where every time a species is used as a reactant, the reaction rate will be subtracted from the species’ derivative, while each time it is formed as a product, the reaction rate will be added to the species’ derivative. We will go through each species in detail:

Substituting the rate of each reaction, we get the following system of differential equations.

$$\frac{d[GP_{xr}]}{dt}=k_3[GS-GP_x][GSH]-k_1[GP_{xr}][H_2O_2]_{in}$$ $$\frac{d[H_2O_2]}{dt}=k_6[[H_2O_2]_{out}-{H_2O_2]_{in}]-k_1[GP_{xr}][H_2O_2]_{in}$$ $$\frac{d[H_2O_2]}{dt}=k_1([H_2O_2]_{out} - [H_2O_2]_{in})-k_1[GP_{xr}][H_2O_2]_{in}$$ $$\frac{d[GP_{x0}]}{dt}=k_1[GP_{xr}][H_2O_2]_{in}-k_2[GP_{xo}][GSH]$$ $$\frac{d[H_2O]}{dt}=k_1[GP_{xr}][H_2O_2]_{in}+k_2[GP_{xo}][GSH]$$ $$\frac{d[GSH]}{dt}=2k_5[GSR']\frac{[GSSG]}{K_{5M}+[GSSG]}-k_2[GP_{xo}][GSH]-k_3[GS-GP_x][GSH]$$ $$\frac{d[GS-GP_x]}{dt}=k_2[GP_{xo}][GSH]-k_3[GS-GP_x][GSH]$$ $$\frac{d[GSSG]}{dt}=k_3[GS-GP_x][GSH]-k_5[GSR']\frac{[GSSG]}{K_{5M}+[GSSG]}$$ $$\frac{d[NADPH]}{dt}=-k_4[GSR]\frac{[NADPH]}{K_{4M}+[NADPH]}$$ $$\frac{d[GSR]}{dt}=k_5[GSR']\frac{[GSSG]}{K_{5M}+[GSSG]}-k_4[GSR]\frac{[NADPH]}{K_{4M}+[NADPH]}$$ $$\frac{d[GSR']}{dt}=k_4[GSR]\frac{[NADPH]}{K_{4M}+[NADPH]}-k_5[GSR']\frac{[GSSG]}{K_{5M}+[GSSG]}$$

Part 1 Results

**Table 1: Data obtained from XXX relating each value of the LOCS scale, to opacity values.**
LOCS	0.0	0.5	1.0	2.0	3.0	4.0	5.0	6.0
Degree	None		Trace	Mild	Surgery Suggested	Moderate	Severe	Very Severe
Opacity (%)	0.34	4.24	5.80	18.88	23.60	49.14	65.61	90+
Absorbance (a.u.)	0.001	0.019	0.026	0.091	0.117	0.294	0.464	1.3+

We wish to remain below clinically significant levels, so we will reach attempt to lower the LOCS rating of a cataract to below grade 2.5, which means we want to control GSR such that the crystallin damage results in less than 0.108 a.u. at absorbance at 397.5 nm.

Menu 3

Eaque ipsa quae ab illo inventore veritatis et quasi architecto beatae vitae dicta sunt explicabo.

When determining the relationship between absorbance and crystallin, in Figure 1 the best fit line has a x – intercept that is nonzero. However, when converting each absorbance rating to equivalent crystallin damage in Table 2, we ignore the constant term. When doing the experiments, the fish lens may have contained GSH that is still active, so the fact that the crystallin is exposed to H2O2, the degradation reaction does not happen until all GSH is depleted, and crystallin damage begins to form. We subtract around 1 unit of crystallin damage from all values.

Conclusion

Model 3: Nanoparticles

Abstract

Purpose

Background

There are three quantifiers of how severe cataract formation is, two are measurable, one is not.

Absorbance @ 397.5 nm, which is measured with lab equipment.
LOCS scale, subjectively measured by physicians on a scale from 0 - 6.
Crystallin Damage, which we define as the following (for any time $t$)

\[c.d.(t) = \int_{0}^{\infty} [H_2O_2]_t dt\]

In other words, 1 unit of crystallin damage, in M-h, is equal to the damage caused by 1 molar concentration of hydrogen peroxide reacting crystallin in the eyes for 1 hour.

In making this definition, we assume that crystallin damage is directly proportional to the amount of time crystallin is exposed to hydrogen peroxide. Hydrogen peroxide causes damage by forming disulfide bridges within cysteine molecules on crystallin. This changes the structure of crystallin, causing misfolding and cataract damage. Our linear assumption is valid because the rate for this reaction is first order with respect to hydrogen peroxide concentration.

Method

We will relate the three by doing the following:

Relate LOCS scale to opacity via literature research.
Relate opacity to light transmittance via literature research.
Relate light transmittance to absorbance via physical calculations.
Relate absorbance to crystallin damage via experimental data.

Part 1 Results

**Table 1: Data obtained from XXX relating each value of the LOCS scale, to opacity values.**
LOCS	0.0	0.5	1.0	2.0	3.0	4.0	5.0	6.0
Degree	None		Trace	Mild	Surgery Suggested	Moderate	Severe	Very Severe
Opacity (%)	0.34	4.24	5.80	18.88	23.60	49.14	65.61	90+
Absorbance (a.u.)	0.001	0.019	0.026	0.091	0.117	0.294	0.464	1.3+

We wish to remain below clinically significant levels, so we will reach attempt to lower the LOCS rating of a cataract to below grade 2.5, which means we want to control GSR such that the crystallin damage results in less than 0.108 a.u. at absorbance at 397.5 nm.

Menu 3

Eaque ipsa quae ab illo inventore veritatis et quasi architecto beatae vitae dicta sunt explicabo.

Conclusion

Model 4: Eyedrops

Abstract

Purpose

Background

There are three quantifiers of how severe cataract formation is, two are measurable, one is not.

Absorbance @ 397.5 nm, which is measured with lab equipment.
LOCS scale, subjectively measured by physicians on a scale from 0 - 6.
Crystallin Damage, which we define as the following (for any time $t$)

\[c.d.(t) = \int_{0}^{\infty} [H_2O_2]_t dt\]

In other words, 1 unit of crystallin damage, in M-h, is equal to the damage caused by 1 molar concentration of hydrogen peroxide reacting crystallin in the eyes for 1 hour.

In making this definition, we assume that crystallin damage is directly proportional to the amount of time crystallin is exposed to hydrogen peroxide. Hydrogen peroxide causes damage by forming disulfide bridges within cysteine molecules on crystallin. This changes the structure of crystallin, causing misfolding and cataract damage. Our linear assumption is valid because the rate for this reaction is first order with respect to hydrogen peroxide concentration.

Method

We will relate the three by doing the following:

Relate LOCS scale to opacity via literature research.
Relate opacity to light transmittance via literature research.
Relate light transmittance to absorbance via physical calculations.
Relate absorbance to crystallin damage via experimental data.

Part 1 Results

**Table 1: Data obtained from XXX relating each value of the LOCS scale, to opacity values.**
LOCS	0.0	0.5	1.0	2.0	3.0	4.0	5.0	6.0
Degree	None		Trace	Mild	Surgery Suggested	Moderate	Severe	Very Severe
Opacity (%)	0.34	4.24	5.80	18.88	23.60	49.14	65.61	90+
Absorbance (a.u.)	0.001	0.019	0.026	0.091	0.117	0.294	0.464	1.3+

We wish to remain below clinically significant levels, so we will reach attempt to lower the LOCS rating of a cataract to below grade 2.5, which means we want to control GSR such that the crystallin damage results in less than 0.108 a.u. at absorbance at 397.5 nm.

Menu 3

Eaque ipsa quae ab illo inventore veritatis et quasi architecto beatae vitae dicta sunt explicabo.

Conclusion

Yay

@@ Line 3: / Line 3: @@
 <head>
-	<title>Project Description - TAS Taipei iGEM Wiki</title>
+	<title>Modeling - TAS Taipei iGEM Wiki</title>
   <style type='text/css'>
        #top_title, #sideMenu{
@@ Line 44: / Line 44: @@
 <style type='text/css'>
-p{font-family: Lato !important; font-size:15px !important;}
+p{font-family: Lato !important; font-size:18px !important;}
 h1{font-size:40-px !important;}
 body{font-family:Lato !important;}
@@ Line 57: / Line 57: @@
 			}, 500);
 });
 </script>
-    <script>
-		$(document).ready(function() {
-			var bio_data = [
-			{"name":"Dylan Chiu","photo_url":"https://static.igem.org/mediawiki/2015/c/c3/DChiu.JPG","question_1":"I signed up iGem due to my passion for computer science and biology. Computer science allowed me to engineer anything with the simple mechanics of \"if\" and \"else\", while biology allowed me to study the energy and structure of all forms of life. Synthetic biology allowed me to do both. Plus, it sounds really cool.","question_2":"Something along the lines of being a programmer."},
-			{"name":"Bryan Tseng","photo_url":"https://static.igem.org/mediawiki/2015/e/e0/BTseng.JPG","question_1":"I became interested in iGem and synthetic biology because I am amazed by how engineering can be used as an approach to understand biology. The diverse range of ideas that iGem spurs is also phenomenal.","question_2":"Something impactful to the world"},
-			{"name":"Andrew Chen","photo_url":"https://static.igem.org/mediawiki/2015/b/b4/AWiggins.JPG","question_1":"I was given an opportunity to intern under a immuno-therapy professor. I really liked working under him so I decided to give iGEM a shot.","question_2":"I would like to become an entrepreneur/ businessman so I could put my creativity and knowledge into creating things that can benefit or improve the lives of others."},
-			{"name":"Joseph Chuang","photo_url":"https://static.igem.org/mediawiki/2015/2/25/JChuang.JPG","question_1":"I appreciate the interdisciplinary aspect of iGEM. Aside from its strong focus on science which I really enjoyed, iGEM also incorporates human, design and technological elements. I learned what synthetic biology meant for humanity as a whole.","question_2":"Go on Mars and not get stranded"},
-			{"name":"Daphne Liu","photo_url":"https://static.igem.org/mediawiki/2015/2/2f/DLiu.JPG","question_1":"Every time I passed by the lab last year, I saw iGEMers mesmerized, cheered and frustrated over bottles of water-like liquid. I asked myself “what kind of magic portion is that? I have to find out!”  So I joined iGEM.  (turns out to be E. coli- not disappointed) I also joined iGEM because of the growing role synthetic biology plays in health, food, and environmental issues. Rather than passively letting it seep into my life, I joined iGEM to be a part of current and future trend!","question_2":" I have many ambitions and I am open to all opportunities. I am fascinated by many occupations such as \"pharmacist\", \"biotechnology patent lawyer\", \"big data scientist\" and \"WHO agent\". I will stay proactive, committed and flexible to find out what is right for me. Above all, I want to embrace my family motto \"Do what you love, and Love what you do.\" My life goal is to balance between career and personal hobbies, and do something spontaneous and crazy once in a while!"},
-			{"name":"Leon Yim","photo_url":"https://static.igem.org/mediawiki/2015/8/8e/LYim.JPG","question_1":"I first heard about iGEM from our instructor, Mr. Clapper. At the time, he was putting in orders for primers and explaining how you can literally synthesize DNA fragments if needed. Since then, I thought of iGEM as building new animals or hacking DNA to create your own super power. The power to play was available.","question_2":"I would like to become a scientist. Maybe I'll be a researcher in a lab. I want to live long doing what I love: science."},
-			{"name":"Evonne Pei","photo_url":"https://static.igem.org/mediawiki/2015/4/4b/EPei.jpg","question_1":"Through iGEM, I am able to create, plan, and build together a SynBio project with people of the same passion. I've always been interested in biology, and synthetic biology just takes it to the next level. It is amazing how we can use biology to assemble parts and create things that can help the people around us or the environment we are in.","question_2":"Have 10 pugs and a big backyard. Not exactly kidding about the previous statement- but to add to that, I would like to have a job in a biology related field."},
-			{"name":"Monica Lu","photo_url":"https://static.igem.org/mediawiki/2015/b/bf/MLu.jpg","question_1":"During the summer before my senior year, I was interning at a research lab at NYMU and found it quite interesting so I wanted to continue it somehow during the school year. From that experience, I found out that I wanted to be part of the whole research process, including coming up with the project which was something I did not get to do at NYMU. So I found that I would be able to get that opportunity by joining iGEM. And to me, synthetic biology just sounded fun in the sense that I could learn to manipulate genes to allow us to make bacteria do things that they were not originally able to do. So, I decided to give iGEM a try.","question_2":"Musician!"},
-			{"name":"Jonathan Chen","photo_url":"https://static.igem.org/mediawiki/2015/a/a8/JChen.jpg","question_1":"I got involved in iGem and synthetic biology because I like the topic of biology and I thought syn-bio could provide me with more knowledge and understanding on the subject. Also iGem made me feel like I'm part of a team working towards one goal; it's something very special.","question_2":"Professional baller"},
-			{"name":"Paul Chevassus","photo_url":"https://static.igem.org/mediawiki/2015/b/b2/PChevassus.jpg","question_1":"I got interested in the program via the iGEM club at our school. The science that was being presented captivated me and therefore I joined the program. ","question_2":"Not sure yet"},
-			{"name":"Kevin Huang","photo_url":"https://static.igem.org/mediawiki/2015/2/20/KHuang.jpg","question_1":"Synthetic biology is the forefront of STEM and - more importantly - the future of the medicine in the greater picture. My natural interest in biology is a key stepping stone that got me interested in iGEM, as it represents the best medium that bridges me with synthetic biology.","question_2":"Unnamed/Be Happy"},
-			{"name":"Phillip Teng","photo_url":"https://static.igem.org/mediawiki/2015/5/5b/PTeng.png","question_1":"It was a coincidence. I had to swim after school so I couldn't go off campus for research. As I started learning more and more about synthetic biology, I fell in love with it, and this is my second year participating in the iGEM competition!","question_2":"My dream career is to work on automating medical diagnosis and treatment. My life goal is to be a good person and hopefully influence a few people around me to live a meaningful life."},
-			{"name":"Jude Clapper","photo_url":"https://static.igem.org/mediawiki/2015/3/33/JClapper.JPG","question_1":"I'm a chemist by training, but I really got interested in synthetic biology because of the relatively straightforward approach to designing biological contructs.  I really enjoy the engineering aspect to synthetic biology and iGEM is the perfect competition in which to test yourself.","question_2":"Dream career is to be a scuba diving instructor in the South Pacific islands."},
-			{"name":"Teresa Chiang","photo_url":"https://static.igem.org/mediawiki/2015/0/04/TChiang.jpg","question_1":"My passion is in cellular and molecular biology, and I love the process of research: coming up with a fresh idea, designing (and redesigning) experiments to solve a problem, and finally getting an answer. iGEM offers students an amazing opportunity, not only to learn and grow as a researcher, but also to have fun!","question_2":"What I'm doing now-- teaching research!"},
-			{"name":"Edward \"Sabotage\" Hsieh","photo_url":"https://static.igem.org/mediawiki/2015/8/87/EHsieh.png","question_1":"Taking a class in the STEM fields which did not entail just learning material.    You have to think so much more in research than in other science classes, which makes it all the more interesting.","question_2":"As of now some sort of engineer, researcher, or health professional but might change given that I'm a freshman in college.  It's all about finding your passion."},
-			{"name":"Richard Brundage","photo_url":"https://static.igem.org/mediawiki/2015/4/43/RBrundage.jpg","question_1":"I got interested in synthetic biology because both of my parents work in pharmaceuticals and because I really enjoyed seeing what our students were doing in the lab. I thought this was impossibly cool; how can I be a part of it?","question_2":"My life goal is to leave the world a better place than I found it."},
-			{"name":"Sean Tsao","photo_url":"https://static.igem.org/mediawiki/2015/7/72/STsao.jpg","question_1":"iGEM is fun and creative!","question_2":"My life goal is to travel around the world."}
-			];
-			$('#portrait_container img').click(function() {
-				index = $(this).data('index');
-				$("#spotlight_question_1 p").show();
-				$("#spotlight_question_2 p").show();
-				$("#spotlight_question_3 p").show();
-				$("#spotlight_image").show();
-				$("#spotlight_name").show();
-				$("#spotlight_question_intro").hide();
-				$("#spotlight_question_1").removeClass('intro_large');
-				$("#spotlight_question_2").removeClass('intro_large');
-				$("#spotlight_question_3").removeClass('intro_large');
-				$("#spotlight_name").html(bio_data[index]["name"]);
-				$("#spotlight_question_1 p").html(bio_data[index]["question_1"]);
-				$("#spotlight_question_2 p").html(bio_data[index]["question_2"]);
-				$("#spotlight_image").attr('src', bio_data[index]["photo_url"]);
-			});
-		});
-</script>
 	<div class="container" style='z-index:10;position:relative;'>
 		<div class="row center-block" style = "text-align: left;">
@@ Line 157: / Line 110: @@
 			</li>
 			<li class="dropdown">
-				<a href="https://2016.igem.org/Team:TAS_Taipei/Model"><h4 class='dropdown-toggle disabled' data-toggle="dropdown"><b>MODEL</b></h4></a>
+				<a href="https://2016.igem.org/Team:TAS_Taipei/Modeling"><h4 class='dropdown-toggle disabled' data-toggle="dropdown"><b>MODEL</b></h4></a>
 				<div class="dropdown-menu">
 					<div class='subcategories_container'>
@@ Line 274: / Line 227: @@
 				<div id="category_navbar">
 					<ul class="nav nav-list" data-spy="affix" data-offset-top="160" style='-webkit-transform: translateZ(0);width:160px;margin-left:0' >
-						<li><a href="#members">Members</a></li>
+						<li><a href="#overview">Overview</a></li>
-						<li><a href="#aboutTAS">About TAS</a></li>
+						<li><a href="#crystallin">Crystallin</a></li>
-						<li><a href="#aboutLab">About the Lab</a></li>
+						<li><a href="#gsr25hc">GSR/25HC</a></li>
+						<li><a href="#nanoparticle">Nanoparticles</a></li>
+						<li><a href="#eyedrop">Eyedrop</a></li>
 					</ul>
 				</div>
@@ Line 283: / Line 238: @@
-			<div class="col-lg-10">
+			<div class="col-sm-10" style="padding-right:5%;">
 				<div class="row">
-					<div class="col-lg-12">
+					<div class="col-sm-12">
-						<h1>Team</h1>
+                                                <body>
-						<p> We are the Taipei American School iGEM team, Taiwan's first high school team. Our team consists of 14 dedicated members, 9 of whom will be attending the jamboree in MIT. This is our second year participating in the iGEM competition, and we look forward to continuing for years to come!</p>
-					</div>
-				</div>
-				<div class="row" id='members'>
+						<h1 id='overview'>Modeling</h1>
-					<div class="col-lg-12">
-						<h2 id="members">Members</h2>
-						<p>Click and scroll down for descriptions</p>
+                        <div class="row">
-					</div>
+                            <div class="col-sm-6" >
-				</div>
+                                <div class="col-sm-12">
+                                    <h3> Abstract </h4>
+ 						                 <p>We answer two questions: How much GSR to maintain in the lens, and how to maintain that amount?  We find the amount of GSR needed in the lens (Model 2) to limit crystallin damage so the resulting cataract is less than LOCS 2.5 (Model 1). Then, we find the optimal design of eyedrops (Model 4) and nanoparticles that will maintain this amount of GSR in the lens (Model 3). These models allow our team to understand the impact of adding GSR-loaded nanoparticles into the lens, and to design a full treatment plan on how to prevent and treat cataracts. </p>
+                                </div>
+                            </div>
+                            <div class="col-sm-6" >
+                                <div class="col-sm-12">
+                                    <h3>Achievements</h4>
+                                    <ul style="font-size:15px">
+                                        <li>Designed a simple calculator to find amount of GSR or 25HC eyedrops needed for a patient's LOCS score.</li>
+                                        <li>Bridged the gap between the medical, biological, and chemical measurement of crystallin damage.</li>
+                                        <li>Predicted impact of adding GSR and 25HC on the amount of crystallin damage in the lens.</li>
+                                        <li>Created Nanoparticle Customizer for doctors to find a full treatment plan.</li>
+                                        <li>Generalized our Customizer to allow other iGEM teams who wish to use nanoparticle drug delivery </li>
+                                        <li>Analyzed sensitivity of prototype, and suggested insights into optimal manufacturing and clinical use of our prototype.</li>
+                                        <li>Used Experimental data to develop Models 1 and 3.</li>
+                                    </ul>
+                                </div>
+                            </div>
+                        </div>
-				<div class="row">
+						<h3> Outline </h3>
-					<div class="col-lg-12 col-md-6 col-sm-6" id="portrait_container">
-						<div class="row">
-							<img data-index='0' src="https://static.igem.org/mediawiki/2015/c/c3/DChiu.JPG">
-							<img data-index='1' src="https://static.igem.org/mediawiki/2015/e/e0/BTseng.JPG">
-							<img data-index='2' src="https://static.igem.org/mediawiki/2015/b/b4/AWiggins.JPG">
-							<img data-index='3' src="https://static.igem.org/mediawiki/2015/2/25/JChuang.JPG">
-							<img data-index='4' src="https://static.igem.org/mediawiki/2015/2/2f/DLiu.JPG">
-							<img data-index='5' src="https://static.igem.org/mediawiki/2015/8/8e/LYim.JPG">
-							<img data-index='6' src="https://static.igem.org/mediawiki/2015/4/4b/EPei.jpg">
-							<img data-index='7' src="https://static.igem.org/mediawiki/2015/b/bf/MLu.jpg">
-							<img data-index='8' src="https://static.igem.org/mediawiki/2015/a/a8/JChen.jpg">
-							<img data-index='9' src="https://static.igem.org/mediawiki/2015/b/b2/PChevassus.jpg">
-							<img data-index='10' src="https://static.igem.org/mediawiki/2015/2/20/KHuang.jpg">
-							<img data-index='11' src="https://static.igem.org/mediawiki/2015/5/5b/PTeng.png">
-							<img data-index='12' src="https://static.igem.org/mediawiki/2015/3/33/JClapper.JPG">
-							<img data-index='13' src="https://static.igem.org/mediawiki/2015/0/04/TChiang.jpg">
-							<img data-index='14' src="https://static.igem.org/mediawiki/2015/8/87/EHsieh.png">
-							<img data-index='15' src="https://static.igem.org/mediawiki/2015/4/43/RBrundage.jpg">
-							<img data-index='16' src="https://static.igem.org/mediawiki/2015/7/72/STsao.jpg">
-						</div>
-						<div class="row">
-						</div>
-					</div>
-					<div class="col-lg-12" id='member_spotlight'>
-						<div class="row">
-							<div class="col-lg-4">
-								<div class="col-lg-12">
-									<img id='spotlight_image' src="https://static.igem.org/mediawiki/2014hs/a/ae/Chris_s.png" style='display:none;width:70%;margin-left:15%;'>
-								</div>
-								<div class="col-lg-12">
-									<h3 id='spotlight_name' style='text-align:center;display:none;'>Christopher Yen</h3>
-								</div>
-							</div>
-							<div class="col-lg-8">
-								<div class='intro_large col-lg-6' id='spotlight_question_1'>
-									<h5 style=''>What got you interested in synthetic biology?</h5>
-									<p style='display:none;'></p>
-								</div>
-								<div class='intro_large col-lg-6' id='spotlight_question_2'>
-									<h5 style=''>Dream career or lifegoal?</h5>
-									<p style='display:none;'></p>
-								</div>
-								<div class='intro_large col-lg-6' id='spotlight_question_intro'>
-									<h5 style=''>Click on each member to see their responses!</h5>
-									<p style='display:none;'></p>
-								</div>
-							</div>
-						</div>
-					</div>
+						<h2>Introduction</h2>
-				</div>
+  						<h3> Why Model? </h3>
+						<p>In the lab, biologists are often unable to test everything experimentally. For example, in our cataracts project, cataract prevention occurs in the long-term, from 20-50 years. Obviously, although short experiments can provide us an idea of what prevention may look like, the power of computational biology allows us to model into the future. As a result, our modeling has been crucial in developing a prototype.</p>
-				<div class="row" id='tas'>
+  						<h3> Focus </h3>
-					<div class="col-lg-12">
+						<p>Most iGEM teams perform modeling on gene expression, which we accomplish in model 5. However, as our construct is not directly placed into the eyes, how our synthesized protein impacts the eyes after it is seperately transported is much more interesting. As a result, we spent the majority of our models on understanding the impacts on the eye.</p>
-						<h2 id="aboutTAS">About Taipei American School</h2>
-					</div>
+						<h3>Guiding Questions </h3>
-				</div>
+						<ol>
-				<div class="row">
+						      <li>How much GSR do we want inside the lens?</li>
-					<div class="col-lg-3">
+						      <li>How do we use nanoparticles to control the amount of GSR in the lens?</li>
-						<img src="https://static.igem.org/mediawiki/2014hs/0/03/Tas_logo.png" style='float:right;width:150px;'>
+						      <li>How do we synthesize GSR, package into NP, and send it into the eye?</li>
-                        <h4>Head of Model</h4>
+					        </ol>
-					</div>
-					<div class="col-lg-8">
-						<p>Taipei American School is a private independent school with an American-based curriculum located in Tianmu (T'ien-mu), Shilin District (Shih-lin), Taipei City. Most graduates of TAS go on to attend colleges and universities in United States, although some choose to attend schools in other countries. TAS strives to stay ahead of the curve in STEAM education. An important aspect of STEAM education is the 'E': Engineering. Our iGEM team represents the application of engineering beyond robotics.</p>
-					</div>
-				</div>
-				<div class="row" id='the_lab'>
-					<div class="col-lg-12">
-						<h2 id="aboutLab">About The Lab</h2>
-					</div>
 				</div>
-				<div class="row">
+                </div>
-					<div class="col-lg-11">
-						<img src="https://static.igem.org/mediawiki/2015/1/18/Team_page.JPG" style='float: right;width: 263px;margin: 10px;'>
-						<p>We work in the Sandy R. Puckett Memorial Research Lab, which was completely renovated in 2013 to provide a research laboratory for on-campus student research in synthetic biology and nanotechnology. It is fully equipped with lab tools for research for the iGEM competition. The students have the opportunity to be creative and exploratory in many areas of scientific research at TAS.</p>
+<div class = "row">
+		<div class="col-sm-12">
+				<h2 id = 'crystallin'>Model 1: Crystallin Damage</h2>
+                        <h3>Abstract</h3>
+                        <p>In our experiments, absorbance measurements are meaningless without understanding how severe a cataract that absorbance measurement means. We use literature research to relate LOCS, the physician's scale of cataract severity) to absorbance, which is how we quantified crystallin damage in experiments. We use experimental data to understand how crystallin damage can be quantified by measuring absorbance. With this model, we can calculate how much crystallin damage we have to limit to reduce LOCS to an acceptable level.</p>
+ 						<h3> Purpose </h3>
+ 						<p> How much do we need to limit crystallin damage so surgery is not needed? </p>
+                        <h3>Measurement of Cataract Severity</h3>
+                        <div class="row">
+                            <div class="col-sm-12">
+                                    <p>
+                                        There are four ways of measuring cataract severity, each used for a different purpose.
+                                        <ol>
+                                            <li><b>Lens Optical Cataract Scale (LOCS):</b> Physicians use this scale, from 0 – 6, to grade the severity of cataracts.</li>
+                                            <li><b>Opacity (%):</b> This is the physical, quantitative property of the LOC scale.</li>
+                                            <li><b>Absorbance at 397.5 nm:</b> This is the experimental method, used by our team in the lab (c.d.).</li>
+                                            <li><b>Crystallin Damage: </b>This is a chemical definition. We quantify cataract severity as a function of how much oxidizing agents there are, as well as how long crystalline is exposed to oxidizing agents. We define 1 crystallin damage unit as the damage done to human crystallin when exposed to 1 M hydrogen peroxide, the main oxidizing agent, for 1 hour.</li>
+                                        </ol>
+                                    </p>
+                            <</div>
+                        </div>
+                        <p>We use the unit of crystallin damage to connect cataract severity with the amount of GSR we add (in Model 2). We want to lower c.d. below so that the resulting cataract is of LOCS 2.5. For the rest of the model, our task is simple: relate each point of the LOCS scale to c.d., in order to connect to Model 2.</p>
+                        <h3>LOCS Equivalence to Absorbance: Literature Research</h3>
+                        <p>Past studies have done numerous studies on how absorbance measurements can be converted to the LOC scale that physicians end up using. With the results of ________ and ________, we construct the first three columns in Table 2.</p>
+                        <h3>Absorbance Equivalence to Crystallin Damage: Experimental Data</h3>
+                        <div class="row">
+                            <div class="col-sm-7">
+                                <div class="col-sm-12" >
+                                    <p>
+                                        We use experimental data from our team’s Cataract Lens Model (link).  In each trial, they added H2O2 to crystallin, and measured the resulting absorbance. The data used are shown in Table 1. We can calculate the theoretical c.d., and graph absorbance vs. crystallin damage in Figure 2.
+                                    </p>
+                                    <p>With this relation in Figure 2, we calculate the equivalent crystallin damage to each LOCS rating and its equivalent absorbance.</p>
+                                    <h3>Error Analysis</h3>
+                                    <p>It may be surprising that only around 1 M-h is required to induce moderately severe cataracts. Remember that this is done in the absence of antioxidation systems (GSR) and at an extremely high oxidizing concentration of H2O2 (1M of H2O2). In the lens, H2O2 has a much lower concentration, so severe cataracts are induced over months to years.</p>
+                                    <p>There are some limitations of the model that arise from our assumptions. We assume that fish and human lens contain similar crystallin proteins that are degraded in the similar manner (Assumption 4). In addition, we made a rough adjustment of data based our diluting procedure. For better results to create a human cataract model, experiments will need to be done on human lens, even better if done in vitro, without any dilutions.</p>
+                                </div>
+                            </div>
+                            <div class="col-sm-5" style="margin:0px">
+                                <div class="col-sm-12">
+                                    <p>
+                                        <table class="table table-bordered" style='width: 80%;margin-left:0%;'>
+							                 <caption style='caption-side:top;'><b>Table 2: Results of Model 1 – Equivalent values for LOCS, Opacity, Absorbance, and Crystallin Damage.</caption>
+							                 <thead>
+								                <tr>
+                                                    <th>LOCS</th>
+                                                    <th>Opacity (%)</th>
+                                                    <th>Absorbance (@397.5 nm)</th>
+                                                    <th>Crystallin Damage (M-h)</th>
+                                                </tr>
+                                            </thead>
+                                            <tr>
+                                                <th>0.0</th>
+                                                <th>0.00</th>
+                                                <th>0.0000</th>
+                                                <th>0.0000</th>
+                                            </tr>
+                                            <tr>
+                                                <th>0.5</th>
+                                                <th>3.24</th>
+                                                <th>0.0143</th>
+                                                <th>0.1327</th>
+                                            </tr>
+                                            <tr>
+                                                <th>1.0</th>
+                                                <th>6.65</th>
+                                                <th>0.0299</th>
+                                                <th>0.2774</th>
+                                            </tr>
+                                            <tr>
+                                                <th>1.5</th>
+                                                <th>10.81</th>
+                                                <th>0.0497</th>
+                                                <th>0.4610</th>
+                                            </tr>
+                                            <tr>
+                                                <th>2.0</th>
+                                                <th>15.88</th>
+                                                <th>0.0751</th>
+                                                <th>0.6966</th>
+                                            </tr>
+                                            <tr>
+                                                <th>2.5</th>
+                                                <th>21.95</th>
+                                                <th>0.1076</th>
+                                                <th>0.9981</th>
+                                            </tr>
+                                            <tr>
+                                                <th>3.0</th>
+                                                <th>29.07</th>
+                                                <th>0.1492</th>
+                                                <th>1.3840</th>
+                                            </tr>
+                                            <tr>
+                                                <th>4.0</th>
+                                                <th>46.37</th>
+                                                <th>0.2706</th>
+                                                <th>2.5101</th>
+                                            </tr>
+                                            <tr>
+                                                <th>5.0</th>
+                                                <th>66.05</th>
+                                                <th>0.4691</th>
+                                                <th>4.3514</th>
+                                            </tr>
+                                        </table>
+                                    </p>
+                                </div>
+                            </div>
+                        </div>
+<button class="accordion">Background, Method, Results, Discussion</button>
+<div class="panel">
+	<div class="accordionmenu1" class ="col-sm-12" >
+  		<ul class="nav nav-tabs">
+   			 <li class="active"><a data-toggle="tab" href="#cryshome">Background</a></li>
+   			 <li><a data-toggle="tab" href="#crysmenu1">Assumptions</a></li>
+   			 <li><a data-toggle="tab" href="#crysmenu2">Procedure</a></li>
+   			 <li><a data-toggle="tab" href="#crysmenu3">Results</a></li>
+   			 <li><a data-toggle="tab" href="#crysmenu4">Discussion</a></li>
+ 		 </ul>
+  		<div class="tab-content">
+   			 <div id="cryshome" class="tab-pane fade in active">
+      			<h3>Background</h3>
+                <div class="row">
+                    <div class="col-sm-8">
+                        <div class="col-sm-12" style="border:1px solid black">
+                            <p>There are four ways to measure cataract severity (how blurred the lens is):
+					           <ol>
+						          <li>Lens Optical Cataract Scale III (LOCS) - a scale from 0-6 used by physicians.</li>
+						          <li>Opacity (%) - used to calculate the LOC scale</li>
+						          <li>Absorbance at 397.5 nm - measurable in the lab.	</li>
+                                    <li>Crystallin Damage - used to quantify how much crystallin has been reacted with hydrogen peroxide to create insoluble, damaged crystallin. The following definition of crystallin damage is used:</li>
+					           </ol>
+                                \[c.d.(t) = \int_{0}^{\infty} [H_2O_2]_t dt\]
+				            </p>
+				            <p> In other words, 1 unit of crystallin damage, in M-h,  is equal to the damage caused by 1 molar concentration of hydrogen peroxide reacting crystallin in the eyes for 1 hour.</p>
+                        </div>
+                    </div>
+                    <div class="col-sm-4" style="background-color:lightpink;margin:0px">
+                        <div class="col-sm-12" style="border:1px solid black">
+                            <h3>LOCS Scale</h3><br> <br> <br><br> <br> <br> <br><br><br><br>
+                        </div>
+                    </div>
+                </div>
+   			 </div>
+    		<div id="crysmenu1" class="tab-pane fade">
+     			 <h3>Assumptions</h3>
+                <div class="row">
+                    <div class="col-sm-12">
+                        <div class="col-sm-12">
+                            <p>
+                                <ol>
+                                       <li>Definition of crystallin damage: Crystallin damage is proportional to the concentration of hydrogen peroxide, and the time of exposure. This is a valid assumption, supported by the fact that the reaction between cysteine (molecules on crystallin) and hydrogen peroxide is linear. </li>
+                                       <li>We assume that the amount of crystallin is far greater than the amount oxidized. Our product is meant for long-term cataract prevention and minor treatment, and is not suggested for patients with extremely severe cataracts. </li>
+                                       <li>When the experiments diluted the cataract lens protein, the amount of crystallin is diluted. However, the final absorbance of degraded crystallin is also diluted, so we assume any errors in absorbance is canceled out.</li>
+                                       <li>We assume that fish and human lens contain similar crystallin proteins.</li>
+                                </ol>
+      			           </p>
+                        </div>
+                    </div>
+                </div>
+   			 </div>
+   			 <div id="crysmenu2" class="tab-pane fade">
+      			<h3>Procedure</h3>
+                <div class="row">
+                    <div class="col-sm-8">
+                        <div class="col-sm-12" style="border:1px solid black">
+                            <p>
+                                <ol>
+                                    <li>In the first part, we find how the absorbance measurements in the lab are related to the severity of the cataracts. Through literature data, we can relate LOCS to the opacity of the lens. Then, via physical calculations, we can relate the opacity of the lens to the absorbance of the lens at 400 nm.</li>
+                                    <li>Then, we use our team’s experimental data in the cataract model. For each trial, the concentration of H2O2 and the length of exposure are given, so we can calculate the theoretical crystallin damage using the definition above and the assumptions we made. In each trial we also measured the absorbance, so we have a relation between crystallin damage and absorbance. </li>
+                                    <li>However, we need to make a minor adjustment, because absorbance is affected by dilution. When the fish lens was isolated, they were placed in Tris buffer and diluted. We calculate the ratio of volumes from diluted volume to the Tris buffer, and multiply each absorbance measurement by this value.</li>
+                                </ol>
+      			           </p>
+                        </div>
+                    </div>
+                    <div class="col-sm-4" style="background-color:lightpink;margin:0px">
+                        <div class="col-sm-12" style="border:1px solid black">
+                            <h3>LOCS Scale</h3><br> <br> <br><br> <br> <br> <br><br><br><br>
+                        </div>
+                    </div>
+                </div>
+   			 </div>
+   			 <div id="crysmenu3" class="tab-pane fade">
+                <h3>Results</h3>
+      			<table class="table table-bordered" style='width: 70%;margin-left:15%;'>
+                    <caption style='caption-side:top;'><b>Table 1: Results of Model 1 - Equivalent values for LOCS, Opacity, Absorbance, and Crystallin Damage. </b> </caption>
+							<tbody>
+								<tr>
+									<td>LOCS</td>
+									<td>0.0</td>
+									<td>0.5</td>
+									<td>1.0</td>
+                                    <td>1.5</td>
+									<td>2.0</td>
+                                    <td>2.5</td>
+									<td>3.0</td>
+									<td>4.0</td>
+									<td>5.0</td>
+								</tr>
+								<tr>
+									<td>Degree</td>
+									<td>None</td>
+									<td colspan="2">Trace</td>
+									<td colspan="3">Mild</td>
+									<td colspan="2">Moderate</td>
+									<td>Severe</td>
+								</tr>
+								<tr>
+									<td>Opacity (%)</td>
+									<td>0</td>
+                                    <td>3.24</td>
+									<td>6.65</td>
+									<td>10.81</td>
+									<td>15.88</td>
+									<td>21.95</td>
+									<td>29.07</td>
+									<td>46.37</td>
+									<td>66.05</td>
+								</tr>
+								<tr>
+									<td>Absorbance (a.u.)</td>
+									<td>0.0000</td>
+									<td>0.0143</td>
+									<td>0.0299</td>
+									<td>0.0497</td>
+									<td>0.0751</td>
+									<td>0.1076</td>
+									<td>0.1492</td>
+									<td>0.2706</td>
+                                    <td>0.4691</td>
+								</tr>
+                                <tr>
+									<td>Crystallin Damage (c.d.)</td>
+									<td>0.0000</td>
+									<td>0.1327</td>
+                                    <td>0.2774</td>
+									<td>0.4610</td>
+									<td>0.6966</td>
+									<td>0.9981</td>
+									<td>1.3840</td>
+									<td>2.5101</td>
+									<td>4.3514</td>
+								</tr>
+							</tbody>
+				</table>
+                 <br><br><br>
+                <table class="table table-bordered" style='width: 70%;margin-left:15%;'>
+                    <caption style='caption-side:top;'><b>Table 2: Experimental Data used for Model 1 from Cataract Lens Model (TAS) - Absorbance vs. Crystallin Damage </b></caption>
+							<tbody>
+                                <thead>
+                                    <td>Trial</td>
+									<td>H2O2 Concentration (M)</td>
+									<td>Exposure Time (h)</td>
+									<td>Crystallin Damage (c.d.)</td>
+                                    <td>Measured Absorbance (abs @400 nm)</td>
+                                </thead>
+								<tr>
+                                    <td>1</td>
+                                    <td>0.100</td>
+                                    <td>24.0</td>
+                                    <td>2.40</td>
+                                    <td>0.105</td>
+								</tr>
+                                <tr>
+                                    <td>2</td>
+                                    <td>0.100</td>
+                                    <td>46.5</td>
+                                    <td>4.65</td>
+                                    <td>0.451</td>
+								</tr>
+                                <tr>
+                                    <td>3</td>
+                                    <td>0.100</td>
+                                    <td>72.0</td>
+                                    <td>7.20</td>
+                                    <td>0.0.695</td>
+								</tr>
+                                <tr>
+                                    <td>4</td>
+                                    <td>0.100</td>
+                                    <td>20.0</td>
+                                    <td>2.00</td>
+                                    <td>0.089</td>
+								</tr>
+                                <tr>
+                                    <td>5</td>
+                                    <td>0.100</td>
+                                    <td>42.0</td>
+                                    <td>4.20</td>
+                                    <td>0.392</td>
+								</tr>
+                                <tr>
+                                    <td>6</td>
+                                    <td>0.100</td>
+                                    <td>15.0</td>
+                                    <td>1.50</td>
+                                    <td>0.093</td>
+								</tr>
+                                <tr>
+                                    <td>7</td>
+                                    <td>0.100</td>
+                                    <td>42.0</td>
+                                    <td>0.340</td>
+                                    <td>0.340</td>
+								</tr>
+                                <tr>
+                                    <td>8</td>
+                                    <td>0.100</td>
+                                    <td>67.0</td>
+                                    <td>6.70</td>
+                                    <td>0.563</td>
+								</tr>
+							</tbody>
+				</table>
+   			 </div>
+   			 <div id="crysmenu4" class="tab-pane fade">
+     			 <h3>Discussion</h3>
+                 <h4>Model Result</h4>
+      			    <div class="row">
+                        <div class="col-sm-6">
+                            <div class="col-sm-12" >
+                                <p>
+                                    The model successfully relates LOCS, opacity of lens, absorbance measurements, and the equivalent crystallin damage of the lens. The purpose of relating LOCS to crystallin damage, is that in Model 2, we will use chemical kinetics to determine how adding GSR to the lens will decrease the amount of crystallin damage. Exactly how much crystallin damage we need to decrease is determined by the desired LOCS. For example, if we want to have a LOCS rating of less than 2.5, then we must lower crystalline damage to only 0.9981 M-h.
+                                </p>
+                            </div>
+                        </div>
+                        <div class="col-sm-6" style="background-color:lightpink;margin:0px">
+                            <div class="col-sm-12">
+                                <p>
+                                    <br><br><br><br><br>
+                                </p>
+                            </div>
+                        </div>
+                    </div>
+                 <h4>Model Adjustment</h4>
+                    <div class="row">
+                        <div class="col-sm-6" style="background-color:lightpink;margin:0px">
+                            <div class="col-sm-12" >
+                                <p>
+                                    <br><br><br><br><br>
+                                </p>
+                            </div>
+                        </div>
+                        <div class="col-sm-6" >
+                            <div class="col-sm-12">
+                                <p>
+                                    When determining the relationship between absorbance and crystallin, in Figure 1 the best fit line has a x – intercept that is nonzero. However, when converting each absorbance rating to equivalent crystallin damage in Table 2, we ignore the constant term. When doing the experiments, the fish lens may have contained GSH that is still active, so the fact that the crystallin is exposed to H2O2, the degradation reaction does not happen until all GSH is depleted, and crystallin damage begins to form. We subtract around 1 unit of crystallin damage from all values.
+                                </p>
+                            </div>
+                        </div>
+                    </div>
+                 <h4>Error Analysis</h4>
+                 <div class="row">
+                        <div class="col-sm-12">
+                            <div class="col-sm-12" >
+                                <p>
+                                    It may be surprising that only around 1 M-h is required to induce moderately severe cataracts. Remember that this is done in the absence of antioxidation systems (GSR) and at an extremely high oxidizing concentration of H2O2 (1M of H2O2). In the lens, H2O2 has a much lower concentration, so severe cataracts are induced over months to years.
+                                </p>
+                            </div>
+                        </div>
+                    </div>
+                 <div class="row">
+                        <div class="col-sm-12">
+                            <div class="col-sm-12" >
+                                <p>
+                                    There are some limitations of the model that arise from our assumptions. We assume that fish and human lens contain similar crystallin proteins that are degraded in the similar manner (Assumption 4). Also, to simplify the experiments, the lens were diluted in Tris buffer. Because of this dilution, the actual crystallin damage is much lower, but so is the actual absorbance. We assume that the decrease in crystallin damage and absorbance is the same, so no adjustments need to be made for the relation between crystallin damage and absorbance (Assumption 3). For better results to create a human cataract model, experiments will need to be done on human lens, even better if done in vitro, without any dilutions.
+                                </p>
+                            </div>
+                        </div>
+                    </div>
+    			</div>
+ 		 </div>
+	</div>
+</div>  <!-- End Menu -->
+ 			    <h3> Conclusion</h3>
+ 						<div class="row">
+                        <div class="col-sm-6" style="background-color:lightpink;margin:0px">
+                            <div class="col-sm-12" >
+                                <p>
+                                    <br><br><br><br><br>
+                                </p>
+                            </div>
+                        </div>
+                        <div class="col-sm-6">
+                            <div class="col-sm-12">
+                                <p>
+                                    For surgery to not be needed, the LOCS value has to be below 2.5. This is equivalent to 21.95% in light opacity or 0.1076 abs units. Based on the results of our experiments, this is equivalent to 0.9981 units of crystallin damage, the damage done to crystallin if exposed to 0.9981 M of H2O2 for 1 hr.
+                                    For future models, this value 0.9981 units of c.d. will be called the crystallin damage threshold for LOCS 2.5.
+                                </p>
+                            </div>
+                        </div>
+                    </div>
+	</div> <!-- Container -->
+</div> <!-- Container -->
+<div class = "row">
+		<div class="col-sm-12">
+						<h2 id = 'gsr25hc'>Model 2: GSR/25HC Chemical Pathway</h2>
+                        <div class="row">
+                                <div class="col-sm-6" >
+                                        <h3> Abstract </h3>
+                                        <p> The key question: <b>How much GSR to add?</b> Now that we know how much we need to limit crystallin damage, we use systems of ordinary differential equation to model the GSR Pathway. We calculate the necessary GSR concentration to be maintained over 50 years so that the resulting cataract is below LOCS 2.5./p>
+                                        </p>
+                                </div>
+                                <div class="col-sm-6" >
+                                        <h3> Purpose </h3>
+                                        <p> How much GSR do we need to maintain in the lens so that the crystallin damage recorded over 50 years is below the threshold for LOCS 2.5? </p>
+                                </div>
+                        </div>
+                        <h3> Chemical Kinetics Model: Differential Equations </h3>
+                        <div class="row">
+                                <div class="col-sm-12" >
+                                        <p> By the Law of Mass Action, Michaelis-Menten Enzyme kinetics, Ping-pong mechanism, and the Law of Passive Diffusion, we build a system of 10 differential equations based on 6 chemical reactions. All parameters, constants, and initial conditions are based off literature data. Estimates made are also shown with assumptions and reasoning. The details are shown in the collapsible for interested readers. </p>
+                                </div>
+                        </div>
+                        <div class="row">
+                                <div class="col-sm-6" >
+                                        <h3>Blackbox Approach: Testing GSR Impact </h3>
+                                        <p> Image</p>
+                                </div>
+                                <div class="col-sm-6" >
+                                        <h3>  </h3>
+                                        <p> We will vary the input, Initial GSR concentration, from 0 to 100 uM, holding all other variables constant, and numerically solve for the amount of hydrogen peroxide over time. With this graph, we can find the amount of crystallin damage accumulated over 20 to 50 years if different levels of GSR is maintained.  </p>
+                                </div>
+                        </div>
+    </div>
+<button class="accordion">Background, Method, Results, Discussion</button>
+<div class="panel">
+	<div class="accordionmenu1" class ="col-sm-12" >
+  		<ul class="nav nav-tabs">
+   			 <li class="active"><a data-toggle="tab" href="#gsrhome">Background</a></li>
+   			 <li><a data-toggle="tab" href="#gsrmenu1">Method</a></li>
+   			 <li><a data-toggle="tab" href="#gsrmenu2">Results Part 1</a></li>
+   			 <li><a data-toggle="tab" href="#gsrmenu2">Results Part 2</a></li>
+   			 <li><a data-toggle="tab" href="#gsrmenu3">Discussion</a></li>
+ 		 </ul>
+  		<div class="tab-content">
+   			 <div id="gsrhome" class="tab-pane fade in active">
+      			<h4>Background</h4>
+				<p> The following 6 reactions describe the antioxidant system inside the cortex and nucleus.</p>
+$$GP_{xr}+[H_2O_2]_{in}+H^+ \xrightarrow[]{k_1} GP_{xo}+H_2O ...(1)$$
+$$GP_{xo}+GSH+H^+ \xrightarrow[]{k_2} [GS-GP_x]+H_2O ...(2)$$
+$$[GS-GP_x] + GSH \xrightarrow[]{k_3} GP_{xr}+GSSG+H^+ ...(3)$$
+$$NADPH \xrightarrow[GSR]{k4, K_{4M}} NADP^+ ...(4)$$
+$$GSSG \xrightarrow[GSR']{k_5, K_{5M}} 2GSH ...(5)$$
+$$[H_2O_2]_{out} \xrightarrow[]{k_5} [H_2O_2]_{in} ...(6)$$
+				<p> Each reaction will be discussed in detail, and we will derive rate equations.</p>
+                 <p><b>Reaction 1:</b>As hydrogen ions are numerous are negligible in the reaction, we will ignore it. By the <b>law of mass</b> action, the rate of this reaction is: $$r_1=k_1[GP_{xr}][H_2O_2]_{in}$$</p>
+                 <p><b>Reaction 2:</b> By the <b>law of mass</b> action, the rate of this reaction is: $$r_2=k_2[GP_{xo}][GSH]$$</p>
+                 <p><b>Reaction 3:</b> By the <b>law of mass</b> action, the rate of this reaction is: $$r_3=k_3[GS-GP_x][GSH]$$</p>
+                 <p><b>Summary of Reaction 1-3:</b>In these reactions, hydrogen peroxide is reduced to water. GSH is consumed to recycle the enzyme GPx back into reduced form, to neutralize more hydrogen peroxide.</p>
+                 <br>
+                 <p><b>Reaction 4:</b> By<b>Michaelis-Menten kinetics </b>and the <b>Ping-Pong mechanism</b>, the rate of this reaction, with rate constant k4, and Michaelis-Menten constant Km4, is: $$r_4=k_4\frac{[NADPH]}{K_{4M}+[NADPH]}$$</p>
+                 <p><b>Reaction 5:</b> By<b>Michaelis-Menten kinetics </b>and the <b>Ping-Pong mechanism</b>, the rate of this reaction, with rate constant k5, and Michaelis-Menten constant Km5, is: $$r_5=k_5\frac{[GSSG]}{K_{4M}+[GSSG]}$$</p>
+                 <p><b>Summary of Reaction 4-5</b>: In these, GSSG is reduced back to form GSH, using the enzyme GSR. This is necessary for antioxidation to continue as reaction 1 is constantly using GSH, converting them to GSSG.</p>
+                 <br>
+                 <p><b>Reaction 6:</b> By the <b>Law of Passive Diffusion</b>, the rate of diffusion into the cortex and lens is: is: $$r_6=k_6([H_2O_2]_{out}-[H_2O_2]_{in})$$</p>
+   			 </div>
+    		<div id="gsrmenu1" class="tab-pane fade">
+     			 <h4>Differential Equations</h4>
+      			<p>We have six reaction rates derived from above. Now, we will form differential equations, where every time a species is used as a reactant, the reaction rate will be subtracted from the species’ derivative, while each time it is formed as a product, the reaction rate will be added to the species’ derivative. We will go through each species in detail:</p>
+                <p>Substituting the rate of each reaction, we get the following system of differential equations. </p>
+     			<p>
+                    $$\frac{d[GP_{xr}]}{dt}=k_3[GS-GP_x][GSH]-k_1[GP_{xr}][H_2O_2]_{in}$$
+                    $$\frac{d[H_2O_2]}{dt}=k_6[[H_2O_2]_{out}-{H_2O_2]_{in}]-k_1[GP_{xr}][H_2O_2]_{in}$$
+                    $$\frac{d[H_2O_2]}{dt}=k_1([H_2O_2]_{out} - [H_2O_2]_{in})-k_1[GP_{xr}][H_2O_2]_{in}$$
+                    $$\frac{d[GP_{x0}]}{dt}=k_1[GP_{xr}][H_2O_2]_{in}-k_2[GP_{xo}][GSH]$$
+                    $$\frac{d[H_2O]}{dt}=k_1[GP_{xr}][H_2O_2]_{in}+k_2[GP_{xo}][GSH]$$
+                    $$\frac{d[GSH]}{dt}=2k_5[GSR']\frac{[GSSG]}{K_{5M}+[GSSG]}-k_2[GP_{xo}][GSH]-k_3[GS-GP_x][GSH]$$
+                    $$\frac{d[GS-GP_x]}{dt}=k_2[GP_{xo}][GSH]-k_3[GS-GP_x][GSH]$$
+                    $$\frac{d[GSSG]}{dt}=k_3[GS-GP_x][GSH]-k_5[GSR']\frac{[GSSG]}{K_{5M}+[GSSG]}$$
+                    $$\frac{d[NADPH]}{dt}=-k_4[GSR]\frac{[NADPH]}{K_{4M}+[NADPH]}$$
+                    $$\frac{d[GSR]}{dt}=k_5[GSR']\frac{[GSSG]}{K_{5M}+[GSSG]}-k_4[GSR]\frac{[NADPH]}{K_{4M}+[NADPH]}$$
+                    $$\frac{d[GSR']}{dt}=k_4[GSR]\frac{[NADPH]}{K_{4M}+[NADPH]}-k_5[GSR']\frac{[GSSG]}{K_{5M}+[GSSG]}$$
+      			</p>
+   			 </div>
+   			 <div id="gsrmenu2" class="tab-pane fade">
+      			<h4>Part 1 Results</h4>
+      			<table class="table table-bordered" style='width: 70%;margin-left:15%;'>
+							<caption style='caption-side:top;'><b>Table 1: Data obtained from XXX<b> relating each value of the LOCS scale, to opacity values. </caption>
+							<tbody>
+								<tr>
+									<td>LOCS</td>
+									<td>0.0</td>
+									<td>0.5</td>
+									<td>1.0</td>
+									<td>2.0</td>
+									<td>3.0</td>
+									<td>4.0</td>
+									<td>5.0</td>
+									<td>6.0</td>
+								</tr>
+								<tr>
+									<td>Degree</td>
+									<td>None</td>
+									<td></td>
+									<td>Trace</td>
+									<td>Mild</td>
+									<td>Surgery Suggested</td>
+									<td>Moderate</td>
+									<td>Severe</td>
+									<td>Very Severe</td>
+								</tr>
+								<tr>
+									<td>Opacity (%)</td>
+									<td>0.34</td>
+									<td>4.24</td>
+									<td>5.80</td>
+									<td>18.88</td>
+									<td>23.60</td>
+									<td>49.14</td>
+									<td>65.61</td>
+									<td>90+</td>
+								</tr>
+								<tr>
+									<td>Absorbance (a.u.)</td>
+									<td>0.001</td>
+									<td>0.019</td>
+									<td>0.026</td>
+									<td>0.091</td>
+									<td>0.117</td>
+									<td>0.294</td>
+									<td>0.464</td>
+									<td>1.3+</td>
+								</tr>
+							</tbody>
+						</table>
+<p> We wish to remain below clinically significant levels, so we will reach attempt to lower the  LOCS rating of a cataract to below grade 2.5, which means we want to control GSR such that the crystallin damage results in less than 0.108 a.u. at absorbance at 397.5 nm. </p>
+   			 </div>
+   			 <div id="gsrmenu3" class="tab-pane fade">
+   			 </div>
+   			 <div id="gsrmenu4" class="tab-pane fade">
+     			 <h4>Menu 3</h4>
+      			<p>Eaque ipsa quae ab illo inventore veritatis et quasi architecto beatae vitae dicta sunt explicabo.</p>
+    			</div>
+ 		 </div>
+	</div>
+</div>  <!-- End Menu -->
+                        <h3></h3>
+                        <div class="row">
+                            <div class="col-sm-6">
+                                <div class="col-sm-12" >
+                                    <p>
+                                        <br><br><br><br><br>
+                                    </p>
+                                </div>
+                            </div>
+                            <div class="col-sm-6" >
+                                <div class="col-sm-12">
+                                    <p>
+                                        When determining the relationship between absorbance and crystallin, in Figure 1 the best fit line has a x – intercept that is nonzero. However, when converting each absorbance rating to equivalent crystallin damage in Table 2, we ignore the constant term. When doing the experiments, the fish lens may have contained GSH that is still active, so the fact that the crystallin is exposed to H2O2, the degradation reaction does not happen until all GSH is depleted, and crystallin damage begins to form. We subtract around 1 unit of crystallin damage from all values.
+                                    </p>
+                                </div>
+                            </div>
+ 						<h4> Conclusion</h4>
+ 						<p> Conclusion</p>
+	</div> <!-- Container -->
+</div> <!-- Container -->
+<div class = "row">
+		<div class="col-sm-12">
+						<h2 id = 'nanoparticle'>Model 3: Nanoparticles</h2>
+ 						<h4> Abstract </h4>
+ 						<p> Abstract </p>
+ 						<h4> Purpose </h4>
+ 						<p> Purpose </p>
+<button class="accordion">Background, Method, Results, Discussion</button>
+<div class="panel">
+	<div class="accordionmenu1" class ="col-sm-12" >
+  		<ul class="nav nav-tabs">
+   			 <li class="active"><a data-toggle="tab" href="#nphome">Background</a></li>
+   			 <li><a data-toggle="tab" href="#npmenu1">Method</a></li>
+   			 <li><a data-toggle="tab" href="#npmenu2">Results Part 1</a></li>
+   			 <li><a data-toggle="tab" href="#npmenu2">Results Part 2</a></li>
+   			 <li><a data-toggle="tab" href="#npmenu3">Discussion</a></li>
+ 		 </ul>
+  		<div class="tab-content">
+   			 <div id="home" class="tab-pane fade in active">
+      			<h4>Background</h4>
+				<p>There are three quantifiers of how severe cataract formation is, two are measurable, one is not.
+					<ol>
+						<li>Absorbance @ 397.5 nm, which is measured with lab equipment.</li>
+						<li>LOCS scale, subjectively measured by physicians on a scale from 0 - 6.
+</li>
+						<li>Crystallin Damage, which we define as the following (for any time $t$)																														    </li>
+					</ol>
+				</p>
+\[c.d.(t) = \int_{0}^{\infty} [H_2O_2]_t dt\]
+				<p> In other words, 1 unit of crystallin damage, in M-h,  is equal to the damage caused by 1 molar concentration of hydrogen peroxide reacting crystallin in the eyes for 1 hour.</p>
+                               <p> In making this definition, we assume that crystallin damage is directly proportional to the amount of time crystallin is exposed to hydrogen peroxide. Hydrogen peroxide causes damage by forming disulfide bridges within cysteine molecules on crystallin. This changes the structure of crystallin, causing misfolding and cataract damage. Our linear assumption is valid because the rate for this reaction is first order with respect to hydrogen peroxide concentration. </p>
+   			 </div>
+    		<div id="npmenu1" class="tab-pane fade">
+     			 <h4>Method</h4>
+      			<p>We will relate the three by doing the following:
+     				 <ol>
+                                       <li>Relate LOCS scale to opacity via literature research. </li>
+                                       <li>Relate opacity to light transmittance via literature research. </li>
+                                       <li>Relate light transmittance to absorbance via physical calculations. </li>
+                                       <li>Relate absorbance to crystallin damage via experimental data. </li>
+     				 </ol>
+      			</p>
+   			 </div>
+   			 <div id="npmenu2" class="tab-pane fade">
+      			<h4>Part 1 Results</h4>
+      			<table class="table table-bordered" style='width: 70%;margin-left:15%;'>
+							<caption style='caption-side:top;'><b>Table 1: Data obtained from XXX<b> relating each value of the LOCS scale, to opacity values. </caption>
+							<tbody>
+								<tr>
+									<td>LOCS</td>
+									<td>0.0</td>
+									<td>0.5</td>
+									<td>1.0</td>
+									<td>2.0</td>
+									<td>3.0</td>
+									<td>4.0</td>
+									<td>5.0</td>
+									<td>6.0</td>
+								</tr>
+								<tr>
+									<td>Degree</td>
+									<td>None</td>
+									<td></td>
+									<td>Trace</td>
+									<td>Mild</td>
+									<td>Surgery Suggested</td>
+									<td>Moderate</td>
+									<td>Severe</td>
+									<td>Very Severe</td>
+								</tr>
+								<tr>
+									<td>Opacity (%)</td>
+									<td>0.34</td>
+									<td>4.24</td>
+									<td>5.80</td>
+									<td>18.88</td>
+									<td>23.60</td>
+									<td>49.14</td>
+									<td>65.61</td>
+									<td>90+</td>
+								</tr>
+								<tr>
+									<td>Absorbance (a.u.)</td>
+									<td>0.001</td>
+									<td>0.019</td>
+									<td>0.026</td>
+									<td>0.091</td>
+									<td>0.117</td>
+									<td>0.294</td>
+									<td>0.464</td>
+									<td>1.3+</td>
+								</tr>
+							</tbody>
+						</table>
+<p> We wish to remain below clinically significant levels, so we will reach attempt to lower the  LOCS rating of a cataract to below grade 2.5, which means we want to control GSR such that the crystallin damage results in less than 0.108 a.u. at absorbance at 397.5 nm. </p>
+   			 </div>
+   			 <div id="npmenu3" class="tab-pane fade">
+   			 </div>
+   			 <div id="npmenu4" class="tab-pane fade">
+     			 <h4>Menu 3</h4>
+      			<p>Eaque ipsa quae ab illo inventore veritatis et quasi architecto beatae vitae dicta sunt explicabo.</p>
+    			</div>
+ 		 </div>
+	</div>
+</div>  <!-- End Menu -->
+ 						<h4> Conclusion</h4>
+ 						<p> Conclusion </p>
+	</div> <!-- Container -->
+</div> <!-- Container -->
+<div class = "row">
+		<div class="col-sm-12">
+						<h2 id = 'eyedrop'>Model 4: Eyedrops</h2>
+ 						<h4> Abstract </h4>
+ 						<p> Abstract </p>
+ 						<h4> Purpose </h4>
+ 						<p> Purpose </p>
+<button class="accordion">Background, Method, Results, Discussion</button>
+<div class="panel">
+	<div class="accordionmenu1" class ="col-sm-12" >
+  		<ul class="nav nav-tabs">
+   			 <li class="active"><a data-toggle="tab" href="#eyehome">Background</a></li>
+   			 <li><a data-toggle="tab" href="#eyemenu1">Method</a></li>
+   			 <li><a data-toggle="tab" href="#eyemenu2">Results Part 1</a></li>
+   			 <li><a data-toggle="tab" href="#eyemenu2">Results Part 2</a></li>
+   			 <li><a data-toggle="tab" href="#eyemenu3">Discussion</a></li>
+ 		 </ul>
+  		<div class="tab-content">
+   			 <div id="eyehome" class="tab-pane fade in active">
+      			<h4>Background</h4>
+				<p>There are three quantifiers of how severe cataract formation is, two are measurable, one is not.
+					<ol>
+						<li>Absorbance @ 397.5 nm, which is measured with lab equipment.</li>
+						<li>LOCS scale, subjectively measured by physicians on a scale from 0 - 6.
+</li>
+						<li>Crystallin Damage, which we define as the following (for any time $t$)																														    </li>
+					</ol>
+				</p>
+\[c.d.(t) = \int_{0}^{\infty} [H_2O_2]_t dt\]
+				<p> In other words, 1 unit of crystallin damage, in M-h,  is equal to the damage caused by 1 molar concentration of hydrogen peroxide reacting crystallin in the eyes for 1 hour.</p>
+                               <p> In making this definition, we assume that crystallin damage is directly proportional to the amount of time crystallin is exposed to hydrogen peroxide. Hydrogen peroxide causes damage by forming disulfide bridges within cysteine molecules on crystallin. This changes the structure of crystallin, causing misfolding and cataract damage. Our linear assumption is valid because the rate for this reaction is first order with respect to hydrogen peroxide concentration. </p>
+   			 </div>
+    		<div id="eyemenu1" class="tab-pane fade">
+     			 <h4>Method</h4>
+      			<p>We will relate the three by doing the following:
+     				 <ol>
+                                       <li>Relate LOCS scale to opacity via literature research. </li>
+                                       <li>Relate opacity to light transmittance via literature research. </li>
+                                       <li>Relate light transmittance to absorbance via physical calculations. </li>
+                                       <li>Relate absorbance to crystallin damage via experimental data. </li>
+     				 </ol>
+      			</p>
+   			 </div>
+   			 <div id="eyemenu2" class="tab-pane fade">
+      			<h4>Part 1 Results</h4>
+      			<table class="table table-bordered" style='width: 70%;margin-left:15%;'>
+							<caption style='caption-side:top;'><b>Table 1: Data obtained from XXX<b> relating each value of the LOCS scale, to opacity values. </caption>
+							<tbody>
+								<tr>
+									<td>LOCS</td>
+									<td>0.0</td>
+									<td>0.5</td>
+									<td>1.0</td>
+									<td>2.0</td>
+									<td>3.0</td>
+									<td>4.0</td>
+									<td>5.0</td>
+									<td>6.0</td>
+								</tr>
+								<tr>
+									<td>Degree</td>
+									<td>None</td>
+									<td></td>
+									<td>Trace</td>
+									<td>Mild</td>
+									<td>Surgery Suggested</td>
+									<td>Moderate</td>
+									<td>Severe</td>
+									<td>Very Severe</td>
+								</tr>
+								<tr>
+									<td>Opacity (%)</td>
+									<td>0.34</td>
+									<td>4.24</td>
+									<td>5.80</td>
+									<td>18.88</td>
+									<td>23.60</td>
+									<td>49.14</td>
+									<td>65.61</td>
+									<td>90+</td>
+								</tr>
+								<tr>
+									<td>Absorbance (a.u.)</td>
+									<td>0.001</td>
+									<td>0.019</td>
+									<td>0.026</td>
+									<td>0.091</td>
+									<td>0.117</td>
+									<td>0.294</td>
+									<td>0.464</td>
+									<td>1.3+</td>
+								</tr>
+							</tbody>
+						</table>
+<p> We wish to remain below clinically significant levels, so we will reach attempt to lower the  LOCS rating of a cataract to below grade 2.5, which means we want to control GSR such that the crystallin damage results in less than 0.108 a.u. at absorbance at 397.5 nm. </p>
+   			 </div>
+   			 <div id="eyemenu3" class="tab-pane fade">
+   			 </div>
+   			 <div id="eyemenu4" class="tab-pane fade">
+     			 <h4>Menu 3</h4>
+      			<p>Eaque ipsa quae ab illo inventore veritatis et quasi architecto beatae vitae dicta sunt explicabo.</p>
+    			</div>
+ 		 </div>
+	</div>
+</div>  <!-- End Menu -->
+ 						<h4> Conclusion</h4>
+ 						<p> Conclusion</p>
+	</div> <!-- Container -->
+</div> <!-- Container -->
+				<div class = "row">
+					<div class="col-sm-12">
+						<h2 id ="X">Conclusion</h2>
+						<p class="col-sm-12">Yay</p>
 					</div>
 				</div>
-				<div class="row" id='synthetic_biology'>
-					<div class="col-lg-12">
-						<h2>Synthetic Biology</h2>
+				<div class = "row">
+					<div class="col-sm-12">
+						<h3>Citations</h3>
+					        <br> <br>  <br>  <br>  <br>  <br>  <br>  <br>
 					</div>
 				</div>
-				<div class="row">
-					<div class="col-lg-11">
-						<p>The fusion between biological research and engineering has culminated in the creation of synthetic biology. This interdisciplinary area was facilitated by the recent advances in technology, allowing humans to actually design and construct biological devices as if they were machinery. However, the advent of synthetic biology has raised concerns with biosafety and biosecurity, which is why iGEM places such importance on "safety".</p>
-					</div>
-				</div>
-                <div class="alert alert-danger">
-                    <a href="#" class="close" data-dismiss="alert" aria-label="close">&times;</a>
-                    <strong>Danger!</strong> This alert box could indicate a dangerous or potentially negative action.
-                </div>
 			</div>
-		</div>
+		</div>
 	</div>
 	<br>
 <br><br>
-<canvas id="canvas-container" style = "z-index:-1"></canvas>
-<script type="text/javascript" src='https://2015.igem.org/Template:TAS_Taipei/js/field?action=raw&ctype=text/javascript'></script>
-</body>
@@ Line 602: / Line 1,485: @@
               Eyedrops
      </h2>
-    </div>
-</div>
-<div id="slideoutco">
-    <div id="slidecontentco">
      </div>
 </div>
@@ Line 621: / Line 1,497: @@
      top: 30%;
      right:-150px;
-    padding-left: 60px;
-    z-index:30;
-    border-radius: 25px;
-}
-#slideoutco {
-    background: #FFD700;
-    position: fixed;
-    height: 300px;
-    width: 200px;
-    top: 70%;
-    right:200px;
      padding-left: 60px;
      z-index:30;

Difference between revisions of "Team:TAS Taipei/Modeling"

Latest revision as of 14:51, 6 October 2016

C◎UNTERACTS

Modeling

Abstract

Achievements

Outline

Introduction

Why Model?

Focus

Guiding Questions

Model 1: Crystallin Damage

Abstract

Purpose

Measurement of Cataract Severity

LOCS Equivalence to Absorbance: Literature Research

Absorbance Equivalence to Crystallin Damage: Experimental Data

Error Analysis

Background

LOCS Scale

Assumptions

Procedure

LOCS Scale

Results

Discussion

Model Result

Model Adjustment

Error Analysis

Conclusion

Model 2: GSR/25HC Chemical Pathway

Abstract

Purpose

Chemical Kinetics Model: Differential Equations

Blackbox Approach: Testing GSR Impact

Background

Differential Equations

Part 1 Results

Menu 3

Conclusion

Model 3: Nanoparticles

Abstract

Purpose

Background

Method

Part 1 Results

Menu 3

Conclusion

Model 4: Eyedrops

Abstract

Purpose

Background

Method

Part 1 Results

Menu 3

Conclusion

Conclusion

Citations

Prevention

GSR Eyedrop

Treatment

25HC Eyedrop

LOCS: 0

Eyedrops