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Matlab Codes: 1 Inertial Regime

This document provides MatLab code functions to simulate particle dynamics under different regimes: inertial, diffusive, and trapped particle regimes. The codes implement fundamental equations of motion for particles undergoing Brownian motion. Input parameters and output results are specified for each function. The functions can be modified to explore more complex simulation cases.

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debdip1993
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60 views4 pages

Matlab Codes: 1 Inertial Regime

This document provides MatLab code functions to simulate particle dynamics under different regimes: inertial, diffusive, and trapped particle regimes. The codes implement fundamental equations of motion for particles undergoing Brownian motion. Input parameters and output results are specified for each function. The functions can be modified to explore more complex simulation cases.

Uploaded by

debdip1993
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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MatLab codes

Giorgio Volpe and Giovanni Volpe

Below, we provide the key MatLab codes to perform the simulations pre-
sented in the article. These codes can be modified by the readers themselves
to explore more complex cases. In each subsection, we present a function
that implements one of the FDE presented above and we suggest some pa-
rameters to run the codes. Note that we use thoroughly SI measurements
units.

1 Inertial regime
This function implements Eq. (8). Inputs: number of samples N [1e+5],
timestep Dt [1e-8 s], initial positions x1,x2 [0 m, 0 m], particle radius
R [1e-6 m], temperature T [300 K], fluid viscosity eta [0.001 Pa s -
water], and density d [2.6e+3 kg/m3]. Outputs: particle position x [m]
and time t [s].

function [x,t]=inertial(N,Dt,x1,x2,R,T,eta,d)
kB = 1.38e-23; % Boltzmann constant [J/K]
gamma = 6*pi*R*eta; % friction coefficient
m = 4/3*pi*R^3*d; % particle mass
tau = m/gamma; % momentum relaxation time

x(1)=x1; x(2)=x2; % initial conditions


for i = 3:1:N
x(i) = (2+Dt*gamma/m)/(1+Dt*gamma/m)*x(i-1) ...
- 1/(1+Dt*gamma/m)*x(i-2) ...
+ sqrt(2*kB*T*gamma)/(m+Dt*gamma)*randn();
end
t = [0:Dt:(N-1)*Dt];

1
figure
plot(t,x)
xlabel(’time [s]’)
ylabel(’x [m]’)

2 Diffusive regime
This function implements Eq. (10). Inputs: number of samples N [1e+5],
timestep Dt [1e-3 s], initial position x1 [0 m], particle radius R [1e-6
m], temperature T [300 K], and fluid viscosity eta [0.001 Pa s - water].
Outputs: particle position x [m] and time t [s].

function [x,t]=diffusive(N,Dt,x1,R,T,eta)
kB = 1.38e-23; % Boltzmann constant [J/K]
gamma = 6*pi*R*eta; % friction coefficient
D = kB*T/gamma; % diffusion coefficient

x(1)=x1; % initial condition


for i = 2:1:N
x(i) = x(i-1) + sqrt(2*D*Dt)*randn();
end
t = [0:Dt:(N-1)*Dt];

figure
plot(t,x)
xlabel(’time [s]’)
ylabel(’x [m]’)

3 Velocity autocorrelation function


This function implements Eq. (12). Inputs: particle position x [m] and
timestep Dt [s]. Outputs: velocity autocorrelation function x [m] and de-
lay time s [s].

function [r,s]=acf(x,Dt)

v = (x(2:end)-x(1:end-1))/Dt; % average speed

2
r = xcorr(v,ceil(sqrt(length(x))),’unbiased’);
s = Dt*[0:1:length(r)-1];

figure
plot(s,r)
xlabel(’s [s]’)
ylabel(’R [m^2]’)

4 Mean square displacement


This function implements Eq. (14). Inputs: particle position x [m] and
timestep Dt [s]. Outputs: mean square displacement msd [m2] and delay
time s [s].

function [msd,s] = MSD(x,Dt)

for n = 0:1:sqrt(length(x))
msd(n+1) = mean((x(n+1:end)-x(1:end-n)).^2);
end
s = Dt*[0:1:length(msd)-1];

figure
plot(s,msd)
xlabel(’s [s]’)
ylabel(’MSD [m^2]’)

5 Trapped particle
This function implements Eq. (16). Inputs: number of samples N [1e+5],
timestep Dt [1e-3 s], initial position x1,x2,x3 [0 m, 0 m, 0 m], particle
radius R [1e-6 m], temperature T [300 K], fluid viscosity eta [0.001 Pa
s - water], and trap stiffness kx,ky,kz [1e-6 N/m, 1e-6 N/m, 0.2e-6
N/m]. Outputs: particle position x,y,z [m] and time t [s].

function [x,y,z,t]=...
trapped(N,Dt,x1,y1,z1,R,T,eta,kx,ky,kz)
kB = 1.38e-23; % Boltzmann constant [J/K]

3
gamma = 6*pi*R*eta; % friction coefficient
D = kB*T/gamma; % diffusion coefficient

x(1)=x1;y(1)=y1;z(1)=z1; % initial condition


for i = 2:1:N
% Deterministic step
x(i) = x(i-1) - kx*Dt/gamma*x(i-1);
y(i) = y(i-1) - ky*Dt/gamma*y(i-1);
z(i) = z(i-1) - kz*Dt/gamma*z(i-1);
% Diffusive step
x(i) = x(i) + sqrt(2*D*Dt)*randn();
y(i) = y(i) + sqrt(2*D*Dt)*randn();
z(i) = z(i) + sqrt(2*D*Dt)*randn();
end
t = [0:Dt:(N-1)*Dt];

figure
plot3(x,y,z)
xlabel(’x [m]’)
ylabel(’y [m]’)
zlabel(’z [m]’)
axis equal

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