Week 2: Brownian motion
This is a simulation of the Brownian This is a simulation of the Brownian
motion of 5 particles (yellow) that motion of a big particle (dust particle)
collide with a large set of 800 particles. that collides with a large set of smaller
The yellow particles leave 5 blue trails particles (molecules of a gas) which
of (pseudo) random motion and one of move with different velocities in
them has a red velocity vector. different random directions.
Source: https://en.wikipedia.org/wiki/Brownian_motion
Forces on a Brownian particle
𝑑𝑟⃗
Drag force 𝐹⃗!"#$ = −𝜁𝑢 = −𝜁
𝑑𝑡
Drag
6𝑘% 𝑇𝜁
Brownian force 𝐹⃗% =
Δ𝑡
𝑛
Equation of Motion
𝑑𝑢 Brownian
𝑚 = 𝐹⃗% + 𝐹⃗!"#$ force
𝑑𝑡
0= 𝐹⃗% + 𝐹⃗!"#$ Neglect inertia: Brownian dynamics assumption
𝑛&
𝑑𝑟⃗ 6𝑘% 𝑇𝜁
𝜁 = 𝑛 𝑛 = 𝑛' ; Each component is a random number between -1 and 1
𝑑𝑡 Δ𝑡 𝑛(
Trajectory of a Brownian
particle
Select a length scale equal to
Equation of Motion 𝑑𝑟⃗ 6𝑘% 𝑇𝜁
𝜁 = 𝑛 radius of particle: R
𝑑𝑡 Δ𝑡
𝑟
𝑟∗ =
𝑅
Use non-dimensionless version of the
equation of motion:
𝜁𝑅 *
A relevant time scale:
𝑑𝑟 ∗ 6 𝑘% 𝑇
= 𝑛
𝑑𝑡 ∗ Δ𝑡 ∗ 𝑡 𝑘% 𝑇
𝑡∗ = = 𝑡
𝜁𝑅 * 𝜁𝑅 *
Assume 𝑟 ∗ = 0 at 𝑡 ∗ = 0 (particle starts at origin) 𝑘% 𝑇
𝑑𝑥 ∗ 6 𝑑𝑦 ∗ 6
= 𝑛& = 𝑛' Stokes-Einstein diffusivity:
𝑑𝑡 ∗ Δ𝑡 ∗ 𝑑𝑡 ∗ Δ𝑡 ∗
𝑘% 𝑇
𝐷+, =
𝜁
𝑑𝑧 ∗ 6
∗
= ∗
𝑛( Re-look at the time scale:
𝑑𝑡 Δ𝑡
𝜁𝑅 * 𝑅* 𝑅*
= =
𝑘% 𝑇 𝑘% 𝑇⁄𝜁 𝐷+,
Calculation of Mean Square Displacement
(MSD)
Example trajectory (1D)
MSD(1)=MSD(Δ𝑡 = 1)=AVG[(1-0)2,(2.5-1)2,(4.5-2.5)2,(6.5-4.5)2]
t x*
MSD(1) = [12 + 1.52 + 22 + 22]/4 = 2.81
0 0
MSD(2) = [(2.5-0)2 + (4.5-1)2 + (6.5-2.5)2]/3 = 11.5
1 1
MSD(3) = [(4.5-0)2 + (6.5-1)2]/2 = 25.25
2 2.5
3 4.5 MSD(4) = [(6.5-0)2]/1 = 42.25
4 6.5 MSD(0) = 0, by definition itself
MSD vs time:
𝜟𝒕 MSD
0 0
1 2.81
Slope at t=0 2 11.5
gives the
3 25.25
diffusivity
4 42.25
Exercise
q Consider a particle at origin at t* = 0.
q Consider Brownian dynamics simulation of this particle
q Take Δ𝑡 ∗ = 0.001
q Perform simulations for a total time t* = 100 (105 time steps)
q Write the x*, y*, z* vs t* on a file
q Calculate MSD vs Δ𝑡 ∗ for the trajectory. Plot MSD vs t* (only upto t* = 10)
q Calculate diffusivity. What’s the value you get?
q Take 100 cases, all starting from origin. Perform simulations for a total time t*
= 50 for all cases, while noting their positions at t* = 10, 20, 30, 40 and 50.
Then, for t* = 10, calculate the average distance travelled from origin over all
cases. Repeat for other t*. Plot these average distances with t*. What do you
see? At each of these t*, if you plot the positions of all 100 particles, what do
you observe? (The diffusion of any entity in water that shows up as colored
fronts is related to this exercise. The MSD calculated above is also related.)
