Tuesday, October 30, 2012

Week Eleven Progress (SEM 2)


The plan for this week are to find equations for the flow and the pressure of blood in the arterial tree and to transfer the equations into MATLAB language.

Well I researched and I found an article called "A hybrid one-dimensional/Womersley model of pulsatile blood flow in the entire coronary arterial tree" for "Yunlong Huo and Ghassan S. Kassab" this article is simple and I the blood pressure and flow equation for 1D simulation and I took it as refrence

Quotation from article:

"
The details of the mathematical derivations are outlined in APPENDIX A. Briefly, the governing equations for flow and pressure may be expressed through conservation of mass and momentum asFormula(1)Formula(2)where A is cross-sectional area (CSA) of the vessel, q is volumetric flow rate, ρ is density, Estat is static Young's modulus, h is wall thickness, R0h0, and A0 are original radius of the vessel, original wall thickness, and original CSA, respectively, and ν is kinematic viscosity. 
"


Article http is:
http://ajpheart.physiology.org/content/292/6/H2623.full



Now I have to translate these two equations to MATLAB language.

After I organized the equation I wrote the equation at MATLAB as apeared below

MATLAB APPENDIX for EQUATION 2:


A = ?;
q = ?;
p = ?;
v = ?;
h0 =?;
R0 = ?;
A0 = ?;
Estat = ?;
E = ((-4/3)*(q/A^2)+((A/p)*((Estat*h0)/(R0*A0)));
F = (8/3)*(q/A);
G = v;
K =(dt/dx);
E =(dt^2)/(dx^2));




Week Nine Progress (SEM 2)

This week I was quit busy with my academic stuffs. I had presentations and also I was preparing and sitting for my replaced face tests since I skipped face tests last week (week 8) for temporary leave.
So I have not make a seen progress just I have seen my supervisor Dr Rosmina Jaafar and we discussed about the geometry of upper limb artery issue. She guide me to ignore the geometry of the artery for now because it need long time to study new programming such as ANSYS and I have just four left for the final presentation. She guided me to focus on the blood flow inside that artery.

Lately this week after the meeting with my supervisor. I decided simulated the blood flow not only in the upper limb artery but in whole artery system due that in the beginning I specified my my project in upper limb artery because it very difficult to construct the geometry system and the blood flow for the whole arteries in the body. Since now I am focusing on the blood flow I will extend my project from the blood flow inside the upper limb artery to the whole system artery

Week Eight Progress (SEM 2)

Beginning of this week I decided to stop continuing making MATLAB coding for the project equations for while because I am far away from university's library. secondly to simulate the upper limb artery into MATLAB.

So I began with searching on how to construct the geometry of arterial using MATLAB since a part of my project is to simulate or construct the geometry of upper limp artery besides the blood flow through it.

I made a comprehensive research I went through internet sites and many researches talk about modeling arteries such as (MODELLING THE HEMODYNAMICS IN THE HUMAN CAROTID ARTERY BIFURCATION AND COMPUTER SIMULATION" for Adrian Postelnicu, Dan Minea, Livia Sangeorzan, and Mircea Lupu) and ("MODELING 3-D COMPLIANT BLOOD FLOW WITH FOSLS" for Jeffrey J. Heys, Curt DeGroff, Tom Manteuffel, Steve McCormick and Henry Tufo) and more.

Through my reading I discovered a new obstacle in accomplishing my project that the simulation of blood flow can be done by MATLAB but the geometry of artery it self can not be simulated with MATLAB, it can be simulated by using FOSLS or ANSYS or FLOTRAN but not the MATLAB.

I decided to meet my supervisor Dr Rosmina Jaafar next week since this week I am out of Malaysia in temporary leave; to talk about this issue and how I can handle it.

Week Seven Progress (SEM 2)

Since last week I failed to know how to transfer an inegration equation to matrix form then to MATLAB form. that's mean I failed to transfer the main equation of my project (the Navier-Stoke equation) into matrices then MATLAB.
I decided to get help so I went to see Mr. Syamsul Adlan Mahhir who taught me mathematics four. I went to him in paticular since he is good at mathematics and MATLAB as well. I showed him the equations and I asked him how to change those kind of equations to matrices then to MATLAB. After he saw the equations he told that "it is not easy to achieve that; it long and complex process" and he advised me to read something called Matrix MATLAB. And he Asked me if I faced any problem don't hesitate to come to him again.

I searched on that and I founded it's a really complex process as mister Syamsul said; and there are mathematics researches and master research dedicated only for transferring blood flow equations - which I'm using them too- to MATLAB

I got depressed because knowing how to change blood flow equations (Navier-Stoke -or womresly- and finite) to matrices then MATLAB and there are mathematical researches done by more than researcher only simulating the blood flow.

I decided to intensify my search on the issue. after intesified researched I found a book at BMI library:

called " Introduction to Numerical Analaysis Using MATLAB" to Rizwan Butt 

and the other book called " An Introduction to Numerical Methods A MATLAB Approach" authored by Abdelwahab Kharab and Ronald B. Guenther. 

the beauty of these two books they talk about some numerical methods and they give the general equation for every method then they transfer the equation into matrices after that they give the MATLAB coding for every particular method.

In these to books I found matrices form and the MATLAB coding of the Finite equation -one of equation I use in this project- as appeared in the attachement below.

ATTACHMENT MISSING


notice: those pictures taken from  Introduction to Numerical Analaysis Using MATLAB books

The bad news is I could not found the matrices or the MATLAB coding for Navier-Stoke equation -main equation of the blood flow- in none of the books although the Navier-Stoke equation under numerical method.

So I have to comprehend and intensify my research more in order to know how to matrices the other equations and simulate them in the MATLAB.

Week Six Progress (SEM 2)

As I learnt through the last weeks; we can not code a mathematical equation to MATLAB coding straight away. We have to change the equation to matrix form first then from matrix form to MATLAB coding. This is a must procedure in order to transfer any equation into MATLAB; so I decided firstly gain information, learn and practice how to transfer an equation into matrix form then from matrix form to MATLAB.

There was no big issue in transferring normal equation (first and second order) matrix form but the problem was in transfering defrentiation equations into matrices.
Since the project deals with complex numerical and differential equations -as appeared below-  I really faced a real dilemma in knowing how to transfer those equation into matrices the to MATLAB. the whole week gone in searching and understand how to transfer from numerical to matrices.

appendix: (Navier-Stoke equaion)






Week Five Progress (SEM 2)

NOTICE:


MY ATTACHMENTS FOR THIS WEEK ARE STILL MISSING AS SOON AS THEY BEEN FOUNDED THE POST WILL BE UPDATED

SORRY

Thursday, October 25, 2012

Week Four Progress (SEM 2)

during this week I studied how to apply equation into MATLAB
I started with simple equation. In order to apply any equation to MATLAB we have to convert the equation to matrix form then
X+2Y=5
2X+Y=4














A*Z=B
Z=B/A




RESULT





Sunday, October 7, 2012

Week Three Progress (SEM 2)

I continue mastering the MATLAB:) during this week as well . In this week I focused on the commands of plotting 2D graph and the basic commands of plotting 3D graph


  • Firstly, I learnt how to make 2D plot by using the command 
    • plot(independent variable, dependent variable, ' the property')



  • Then I went through the properties of plotting (colour and line tribe); there are many properties for graph drawing such 'k' for black colour line and '*' for drawing star line.


Example



The Result






  • Then I learnt how to make the graph grid --> by adding 'grid' command after the 'plot' command

  • Then I went through and I understood the 'hold on, hold off and close all' commands
    • hold on & hold off --> to show the last figure or not
    • close off --> to close any figure was opened



  • After that I learnt about 'subplot' command and the different between 'subplot' and 'plotsubplot(number of rows, number of column, the number of the matrix which occupy the figure)


Example for subplot




The Result






  • Then I learnt how to name or label the graph Axis's and title the graph
    • For labeling X Axis we use the command --> xlabel('The of the axis')
    • For labeling Y Axis we use the command --> xlabel('The of the axis')
    • For titling the graph we use the command --> title('The Title of the graph')


Example for Label and Title the Graph



The Result





  • Actually, I went through many related to 2D plotting and I won't be able to mention them all, but I can tell before I ended this post; one the most significant which I learnt during this week that I learnt the basic command of plotting 3D graph
    • The most important two commands in plotting 3D are 'meshgrid' and 'mesh' (which work as plot command in 2D)


Here an Example for 3D Plotting




 The Result



Friday, September 21, 2012

Week Two Progress (SEM 2)

In this week I continued learning about MATLAB and MATLAB's commands

I learnt about
  • matrices 
    • I learnt what the function of comma (,) semicolon (;) space and []
    • Also I learnt how to make commands of addition, subtraction, multiplication, division, exponentiation in matrices
    • Also i learnt the function of other commands such as " min(), max(), prob(), sum(), size(), diag()" and so on



  • Also I studied about M-File and significant of commands like "clc & clear"

  • Also I  knew some important commands like:
    • linspace
    • "linspace(minimum number, maximum number, number of points in between)"



    • randint
    • "randint(number of rows,number of columns,[minimum number,maximum number])"



    • input "input('')"
    • In input we should know about string and character
    • string=a character or word
    • character=a number or group of numbers
    • In order to change from string to character or from chatracter to string "num2str & str2num" 


  • On this week also I had started learning about 2D Plotting in martices
    • Two things we should know when we cross the 2D plotting
    • Dependent Variable    = variable dendening on other value
    • Independent Variable  = its value doesn't on other values



    • example

clc
clear
X=0:0.1:10
Y=sin(x)
polt(X,Y)


    • In this examples 

X is the Independent Variable
Y is the Dependent Variable

Monday, September 10, 2012

Week One Progress (SEM 2)

I started with programming part i was focusing on learn and practice the fundamental of MATLAB. On the week one:

  • I explored about MATLAB command window, workspace, array editor and command history.
  • Then I started to practice simple mathmetical operation commands such as addition, subtraction, multiplication, division, exponentiation square root (+, -, *, /, ^, sqrt).
  • Then I learnt how to address the operation by using (%) command . 
  • After that I discovered what predefined variables (pi, Inf, NaN, i, j) stands for.
  • Also I learnt how to cancel an input command and the output without deleting by using (clear) command.
  • Then enter trigonometric functions commands (sin, cos, tan, sec, csc, cot).
  • Then the inverse trigonometric function commands (asin, acos, atan, asec, acsc, acot) wich usually used in 2D Plotting
  • After that I studied how to enter hyperbolic functions  using (sinh, cosh, tanh, sech, csch, coth) commands
  • Lastly  for week one I learnt how command inverse trigonometric functions (asinh, acosh, asech, acsch, acoth)

Friday, May 4, 2012

The Progress until Now

Located which arteries we going to examine the blood flow inside it >>> Upper Limb Arteries

Figured which utrasound device would be used in scanning the upper limb arteries blood flow and pressure >>> Doppler Ultrasound


Finded Which equations & methods will be used in order to convert the blood flow data into MATLAB language >>> The Navier-Stokes equations, Finite Difference Method, and Numerical Scheme.

WHY & WHY!!!

WHY Blood Flow? - not arteries-

  •  Blood circulation is essential for body. Every cell in the body needs to received oxygen and nutrients. Blood rich in oxygen is sent to the body organs, tissues and cells to nourish them, and the waste products that result are disposed of through the same system.  Simply the body cannot function well without a strong circulatory system.
  • Lack of studies which has been dedicated directly to examine the effect of smoking to the blood flow.

WHY Upper Limb Arteries?

If we look into the arterial system (refer to picture below) we can see that the best place to examine the blood flow is the arteries of upper limb for these reasons:
  • Near to heart so we can see the blood speed and the blood pressure defferences easily.
  • Near to surface (skin) so we can scan it easily and accurately.
  • Branched into to terminal arteries so it is provide us enhancement of reading.


WHY Doppler Ultrasound?


Any regular ultrasounds uses sound waves to produce images, but non of them can show blood flow. Doppler the only one which can measure our blood flow and blood pressure.


WHY MATLAB Simulation?


Becuase MATLAB very familiar and popular engineering field. In 2004, MATLAB had around one million users across industry and academia. MATLAB users come from various backgrounds of engineering, science, and economics. MATLAB is widely used in academic and research institutions as well as industrial enterprises.

Project Main Tools

Simulation >>> MATLAB Software


MATLAB is a high-performance language for technical computing. It integrates computation, visualization, and programming in an easy-to-use environment where problems and solutions are expressed in familiar mathematical notation. MATLAB is widely used in academic and research institutions as well as industrial enterprises.



Examine Area >>> Upper Limb Arteries


Runs from lower border of teres major to neck of radius and ends by dividing into radial and ulnar arteries. Upper limb Arteries contain of three terminal branchs
  • Brachial artery
  • Radial artery
  • Ulnar artery


Blood Flow Test >>> Doppler Utrasound Device


Doppler ultrasound is a noninvasive test that can be used to measure your blood flow and blood pressure by bouncing high-frequency sound waves (ultrasound) off circulating red blood cells.


 

Project Main Idea

  • Bring two young persons one is a smoking person and the other is a non-smoking person.
  • Test and calculate their blood flow.
  • Simulate the result.
  • Compare thier result and see how bad the smoking affects the human blood circulatory.

Thursday, May 3, 2012

Project Motivation



According to Man Health Magazine it has been known since the 1950s that the health effects of smoking cigarettes are devastating and include directly causing lung cancer.

There is overwhelming medical and scientific consensus that smoking cigarettes also causes, heart disease, stroke, emphysema and more than 50 other different diseases and disorders, many fatal.

Half of all long term cigarette smokers are likely to be killed by the harmful effects of cigarette smoking, losing an average of 16 years of life.

Every cigarette shortens your life by 14 minutes.

The number of people under 70 years of age dying from diseases as a result of the effects of smoking cigarettes exceeds the total figure for deaths caused by breast cancer, AIDS, traffic accidents and drug addiction. 

There are more than 4,000 chemicals in cigarette smoke, including 43 known cancer-causing (carcinogenic) compounds and 400 other toxins. 

The Harmful Health Effects of Smoking Cigarettes

  • Smoking cigarettes causes cancer.
  • Smoking cigarettes causes heart disease and stroke. Early signs of these diseases can be found in adolescents who smoke.
  • Cigarette smokers have a lower level of lung function than those persons who have never smoked.
  • Smoking cigarettes reduces the rate of lung growth.
  • Someone who smokes a pack or more of cigarettes each day lives, on average, 7 years less than someone who never smoked.
  • The resting heart rates of young adult cigarette smokers are two to three beats per minute faster than non-smokers. 

That is why I dedicate this project to reflect to people and show them the hazards and danger of smoking ,to the one of most significant circulatory ever -to the human blood circulatory-