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Notes Lecture

This document presents Lecture 5 of BENG 221, focusing on the use of partial differential equations (PDEs) in bioengineering, specifically linear diffusion. It includes MATLAB code for solving a homogeneous PDE using finite differences and the built-in 'pdepe' function, along with initial and boundary conditions. The document also features graphical representations of the solutions obtained from both methods.

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Chico Thenawijaya
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11 views9 pages

Notes Lecture

This document presents Lecture 5 of BENG 221, focusing on the use of partial differential equations (PDEs) in bioengineering, specifically linear diffusion. It includes MATLAB code for solving a homogeneous PDE using finite differences and the built-in 'pdepe' function, along with initial and boundary conditions. The document also features graphical representations of the solutions obtained from both methods.

Uploaded by

Chico Thenawijaya
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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BENG 221: Mathematical Methods in Bioengineering

Lecture 5

Introduction: PDEs in Linear Space and Time

References

Haberman APDE, Ch. 1.


Haberman APDE, Ch. 4.
Haberman APDE, Ch. 6.
function lindiff
%%% Homogeneous PDE: Linear (1-D) Diffusion
%%% BENG 221 example, 9/29/2011, updated 11/4/2017

% diffusion constant
global D
D = 0.001;

% domain
global dx
dx = 0.02; % step size in x dimension
dt = 0.1; % step size in t dimension
xmesh = -1:0.02:1; % domain in x
tmesh = 0:0.1:10; % domain in t

% solution using finite differences (see Week 5 class notes)


nx = length(xmesh); % number of points in x dimension
nt = length(tmesh); % number of points in t dimension
stepsize = D * dt / dx^2; % stepsize for numerical integration
sol_fd = zeros(nt, nx);
sol_fd(1, :) = (xmesh == 0)/dx; % initial conditions; delta impulse at center
sol_fd(:, 1) = 0; % left boundary conditions; zero value
sol_fd(:, nx) = 0; % right boundary conditions; zero value
for t = 1:nt-1
for x = 2:nx-1
sol_fd(t+1, x) = sol_fd(t, x) + stepsize * ...
(sol_fd(t, x-1) - 2 * sol_fd(t, x) + sol_fd(t, x+1));
end
end

figure(1)
surf(tmesh,xmesh,sol_fd')
title('Finite differences')
xlabel('t')
ylabel('x')
zlabel('u(x,t)')

% solution using Matlab's built in "pdepe"


% See: http://www.mathworks.com/help/techdoc/ref/pdepe.html
% Also: https://mse.redwoods.edu/darnold/math55/DEProj/sp02/AbeRichards/paper.pdf
help pdepe
sol_pdepe = pdepe(0,@pdefun,@ic,@bc,xmesh,tmesh);

figure(2)
surf(tmesh,xmesh,sol_pdepe')
title('Matlab pdepe')
xlabel('t')
ylabel('x')
zlabel('u(x,t)')

% function definitions for pdepe:


% --------------------------------------------------------------

function [c, f, s] = pdefun(x, t, u, DuDx)


% PDE coefficients functions

global D
c = 1;
f = D * DuDx; % diffusion
s = 0; % homogeneous, no driving term

% --------------------------------------------------------------

function u0 = ic(x)
% Initial conditions function

global dx
u0 = (x==0)/dx; % delta impulse at center

% --------------------------------------------------------------

function [pl, ql, pr, qr] = bc(xl, ul, xr, ur, t)


% Boundary conditions function

pl = ul; % zero value left boundary condition


ql = 0; % no flux left boundary condition
pr = ur; % zero value right boundary condition
qr = 0; % no flux right boundary condition
Finite differences

50

40

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u(x,t)

20

10

0
1

0.5 10
8
0
6
-0.5 4
2
x -1 t
0
Matlab pdepe

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40

30
u(x,t)

20

10

0
1

0.5 10
8
0
6
-0.5 4
2
x -1 t
0

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