ECE 455 Engineering of Nanobiotechnological

Systems

ECE 750: Nanobiotechnological Systems

Instructor: Jie Chen

Department of Electrical and Computer Engineering
University of Alberta

© Copyright: Jie Chen

 General Course Overview

• ECE 750 is very much a “big picture” course, in that the topics are
about the general applications of micro/nanoelectronic circuits and
microfluidic devices in solving bio/nanotechnology problems.

• Topics in the course range from basic genetics, forces, microfluidics,

nanoparticles to DNA structure.

• There is no required textbook, but there are recommended readings

(especially if you don’t have experience with biology or
biochemistry).
 Instructor & TA
Jie Chen, E-mail: jchen@ece.ualberta.ca
URL:
http://www.ece.engineering.ualberta.ca/en/FacultyStaff/FacultyAcade
mic/JieChen.aspx
Tel: 780-492-9820
Office hours: by appointment
For lab questions, please contact Lab TA, Xianglou Chen
(xianglou@ualberta.ca)
*3 (fi 8) (either term, 3-0-0) Microfluidic and nanobiotechnological
devices. Fabrication techniques for devices: self-assembly, lithographic
technologies. Applications of nanobiotechnology in computing,
electronics, human health, environment and manufacture.
 Grade Grades
Distributions

Class location: ECERF W3-87

Lecture time: 12:00 – 13:20PM (M, W )
In-class quiz 15%

Assignments 10%
(solutions will be posted) *No late homework
will be accepted
Computer Labs 20%

Design Project 15%

2 hours final exam 40%

(To be determined)
ECE 750: Nanobiotechnological Systems
(Chapter 1: Forces, Laws and Math)
 1.1 Forces
1.1.1 Overview
Generally speaking, there are four fundamental forces
1. The strong nuclear force (strongest force, short range)
It holds the nuclei of atoms together
2. The electromagnetic force (stronger force, infinite range)
e.g. repulsion between like electrical charges or the interaction of bar magnets
3. The weak nuclear force (next weakest force, short range)
e.g. radioactive decay, neutrino interactions.
4. Gravity (weakest force, infinite range)
The weak nuclear and strong nuclear force are effective only within a
very short range at the level of subatomic particles.
Gravity and the electromagnetic force have infinite range.

For more readings, please refer to

https://www.clearias.com/four-fundamental-forces-of-nature/
Question: In the class, we have mentioned four different forces
(gravity, electromagnetism, weak nuclear force and strong nuclear
force). Which one of the following statement is incorrect?

1. Electromagnetism affects only particles with an electric charge

2. Gravity is the strongest
3. Radioactivity is caused by weak nuclear force
4. Strong nuclear force holds protons and neutrons inside the nucleus of
an atom.

https://www.clearias.com/four-fundamental-forces-of-nature/
 Quiz
Question: In the class, we have mentioned four different forces
(gravity, electromagnetism, weak nuclear force and strong nuclear
force). Which one of the following statement is incorrect?

1. Electromagnetism affects on particles with an electric charge

2. Gravity is the strongest
3. Radioactivity is caused by weak nuclear force
4. Strong nuclear force holds protons and nutrons inside the nuclear of
an atom.

https://www.clearias.com/four-fundamental-forces-of-nature/
https://www.clearias.com/four-fundamental-forces-of-nature/
 1.1 Forces
1.1.1.1 Gravity
-- Gravity is the weakest force of the previously mentioned four
fundamental forces, however, it is long range and universal.
-- It acts between any two pieces of matter in the Universe

F = Gm1m2/r2

where F is the force due to gravity, between two masses (m1 and m2),
which are a distance r apart; G is the gravitational constant.
-- The main role gravity will play in microsystems is in the pressure it
exerts in a vertical column of liquid.
-- The pressure at the bottom of a column of liquid is
 1.1.1.2 Dipole-dipole forces (Generally very weak)

Intermolecular forces are weaker

than intramolecular forces

Intramolecular forces vs. intermolecular forces

Ammonia gas
(NH3)

https://study.com/academy/lesson/hydrogen-bonding-dipole-dipole-ion-dipole-forces-
strong-intermolecular-forces.html
 1.1.1.2 Dipole-dipole forces (Generally very weak)

Molecules have to stay close to

each other.

https://study.com/academy/lesson/hydrogen-bonding-dipole-dipole-ion-dipole-forces-
strong-intermolecular-forces.html
 Van der Waals’ forces
• Bond lengths in molecules are determined by the Lennard-
Jones Potential, described by the equation

V(r)

ε is the depth of the potential well.

The minimum energy of the σ
0 r
Lennard-Jones potential is –ε.
–ε
σ is the “hard-shell” diameter of the ~0.3nm
potential. It is the distance at which
the potential of the system is 0
(the x-intercept of the graph).
1.1.1.3 H-bonding
– An especially strong dipole-dipole force.
– Important in DNA linkages between A-T and G-C
Note: G-C bonding is stronger than A-T bonding

A-T bonding
(double bonding)

G-C bonding
(triple bonding)

DNA double
helix structure
https://www.researchgate.net/figure
For more reading, please refer to https://en.wikipedia.org/wiki/Photon
Who is the Nobel Prize Winner in Physics of 2018?
(a)Arthur Ashkin
(b)Andre Geim
(c)Albert Einstein
(d)John H. Hall

What is the contribution of Nobel

Prize Winner in Physics of 2018?
(a) Optical Tweezer
(b) Carbon Nanotube
(c) Optical Coherence
(d) Optical Comb Technique
Who is the Nobel Prize Winner in Physics of 2018?
(a)Arthur Ashkin
(b)Andre Geim
(c)Albert Einstein
(d)John H. Hall

What is the Contribution of Nobel Prize Winner in Physics of 2018?

(a)Optical Tweezer
(b)Carbon Nanotube
(c)Theory of Relativity
(d)Optical Comb Technique
Why can this technology change biology?
• Photons carry energy and light pressure can be used to move
and manipulate small molecules.

Light pressure Video: Optical Tweezers in Action

From http://www.youtube.com/watch?v=ju6wENPtXu8
 1.2 Thermodynamics

1.2.1 Energy diagram

• Energy diagrams: Shown here is the “energy landscape” for a

given system (e.g. silica particles at different temperatures)

Configuration
• At equilibrium and at a low
enough temperature, the
population is located at the E
energy minima.

Configuration
• Systems will generally try to take the lowest energy
configuration (populate the lowest energy minima), but
this is not always the case…
• If the system is heated to a high temperature (energy is added)
and then cooled quickly, the population will not be able to
occupy the lowest minima, but rather settle into the local
minima. This is the case when liquid silica is snap-cooled to
form glass (an amorphous crystal).

Snap-Cooling

E
• However, if the same system is cooled slowly, the population
is able to get to the lower minima. This is the case when liquid
silica is cooled very slowly to form a perfect crystal (the
lowest energy state).

Slow Cooling Even Slower Cooling

E
E
 Cartesian Coordinates (Review)
Cartesian coordinates of three-dimensional space

https://mathinsight.org/cartesian_coordinates#3dspace
 Cylindrical Cooridnates (Review)
Cylindrical coordinates are the extension of two-dimensional polar
coordinates.

https://mathinsight.org/cartesian_coordinates#3dspace
 Spherical Coordinates (Review)
Another coordinates is called spherical coordinates.

The relationship between

spherical coordinates and
Cartesian coordinates

https://mathinsight.org/cartesian_coordinates#3dspace
Unit Vectors (Review)

https://www.cpp.edu/~ajm/materials/delcyl.pdf
Unit Vectors (Review)

0 0 0 0 0

https://www.cpp.edu/~ajm/materials/delcyl.pdf
Gradient Operation (Review)

https://www.cpp.edu/~ajm/materials/delcyl.pdf
Laplacian Operation (Review)

https://www.cpp.edu/~ajm/materials/delcyl.pdf
1.2.2 Heat Equation
In general, the heat equation is

is the specific heat capacity, k is the thermal conductivity, S

is the heat generation per unit volume and is the mass
density.
For example: consider a block of a material which is being heated
on one side …

The heating describes the “S” term. The solution to the

differential equation will give the Temperature of the material as
a function of space and time
Originally, in Cartesian coordinates the heat equation was:
Next, taking the time independent solution (steady
state)

To maintain the equality, the source term of the temperature

distribution must be the negative of the input heat. That is, all of
the heat must be accounted for (total is zero)
For our purposes in this course, we primarily deal with
cylindrical channels where a heating source is applied to one
side of the capillary.
Changing the spatial coordinates to cylindrical coordinates (with
r being the direction radially outward from the center of the
channel, φ being the angle around the capillary and z being the
direction along the capillary), the heat equation becomes (still
assuming that the thermal conductivity is spatially invariant in
the channel):

At steady state, the left term = 0.

Because there is only variation along the r direction (radially
from the center of the capillary:

This equation is for the steady state temperature distribution (that

is, time independent) which eliminates the time derivative of the
temperature from the equation.
1.2.3 Joule heating in a cylindrical capillary

•Let us consider the source term (S) when there is a constant applied
voltage on the capillary. To do this, we treat the capillary as a resistor
(with its resistance determined by the electrical resistivity of the fluid
in the capillary) and find the power dissipation given the applied
voltage:

!!
Here the resistance is ! = !" = !
!

!"
!= !
!
!
where d is the length of the capillary and A is the cross sectional

area of the capillary.

 ! !!
!= !
!"

!
Remember that the term S is defined as the power per unit volume, so
to get that we have to divide the total power above by the total
volume of the capillary.
! !! !!
!= = = !!
!" !! ! !
• Replacing this in the heat equation:

we get
• For a capillary with radius (with a fixed temperature at
the surface of ), the temperature in the capillary is
therefore (through some quick derivations):

Note: The proof is left as a homework question

 Example question

What is the maximum voltage that can be applied across a

cylindrical microchannel that has a radius of 200µm and is 5cm
long if the microchannel is filled a water-like liquid with an
electrical resistivity of ρE=102 Ωm, boiling point at 100°C and
a thermal conductivity of 0.6 W/(K*m)? (Assume the outer
wall of the microchannel is a perfect heat sink held at 25°C)
Solution:

Here we assume that the limiting factor in the applied voltage is

Joule heating of the liquid in the capillary. For the sake of
simplicity, we will assume that nothing in the system flows until
the liquid reaches its boiling point. The temperature of the liquid
based on Joule heating is:

From this equation, the maximum temperature is at the center of

the channel (r=0). Also, the electric field across the channel is
calculated as E= V/d with d being the length of the channel.
Therefore:
Here

The maximum voltage is therefore:

1.3 Mechanical Forces

1.3.1 Newton’s law of viscosity

•A Newtonian fluid, by definition, has a sheer stress (F/A) which
is proportional to the velocity gradient (with the proportionality
constant being the viscosity, represented by η)

•A plate (area A) is moved with constant velocity v on a layer of

the liquid with thickness y and the force is the drag force exerted
by the liquid.
• The fluid can be visualized layers of atoms between the two
plates. The top layer sticks perfectly to the top plate (no slip
condition).
• When the top plate is moved, it drags the top layer of
molecules in the fluid with it, and this drags the next layer at a
different rate.
• The viscosity of the fluid is determined by how well each layer
moves the next along.
• A fluid with infinite viscosity (eg. a solid) has dv/dy =0 (from
the equation), so each layer moves the one below it perfectly
with no delay.
• In a fluid with zero viscosity, only the top layer moves and
does not drag any other layer along with it at all.
 Reynolds Experiments

Flow can be laminar,

transitional and turbulent
depending on the speed of
flow.

At the low speed, flow

tends to be laminar.

At the high speed, flow

tends to be turbulent.
Reynolds Experiment

http://www-
mdp.eng.cam.ac.uk/web/library/enginfo/aerothermal_dvd_only/aero/fprops/pipeflow/node8.html
 Reynolds Number

Pa or Pascal unit in SI base unit: kg⋅m−1⋅s−2

https://study.com/academy/lesson/reynolds-number-definition-equation.html
1.3.2 Laminar flow
• Turbulent vs. Laminar flow

Reynolds Number <2300 Laminar flow

>4000 Turbulent flow
between Transitional flow
1.3.3 Surface Effects
• Contact angle
Dews on leaves
– Contact angle is a property of a surface and describes its
“wetting” ability.
Solid-vapor interfacial energy

L: liquid phase
S: solid phase
G (or V): vapor phase

Schematic diagram of contact angle

Young’s equation
https://en.wikipedia.org/wiki/Contact_angle
• Young’s equation

In this equation, γ is the surface tension (between the liquid

and solid, solid and vapor or the vapor and liquid) and θ is the
contact angle
• In general, surface interactions (e.g. liquid interacting with the glass
walls of a capillary) are unfavorable energetically compared to
interactions at internal locations. This energy minimization creates a
force (called surface tension).
• Consider a hemispherical segment of fluid with a radius r (like the
profile of a liquid in a capillary)

• The liquid naturally forms this kind of profile through energy

minimization with the surface. To counteract the pressure difference
at the liquid/air interface, the walls of the capillary must exert a force-
per-unit circumference on the capillary (proportional to the amount of
surface the edge of the liquid is in contact with). This surface tension
is denoted by gamma (γ) and has units of N/m.
• Therefore the total force exerted by this surface interaction to
counter balance the pressure difference and maintain the liquid’s
profile) is:
(assuming a circular cross section capillary)

• There is another factor to consider as well: the contact angle of

the liquid on the surface. This forms a meniscus and limits the
interaction between the surface and the liquid. An interface with a
0 degree contact angle will have no impedance to the surface
interactions, whereas one with a 90 degree angle will have no
surface interaction at all. This leads to the consine dependence in
the final equation:

(Please refer to “Microsystem Design” by Stephen D. Senturia

for further details).
• Capillary forces
• For a capillary with a circular cross section the capillary
force is:

• This leads to an equivalent pressure in the capillary of:

• For a rectangular capillary (width w and height h)

 Example question

A square microchannel with edge length 100µm is attached to a vertical

supply well. The mircochannel is 5cm long. The fabrication process has
led to a contact angle (with water) of 110° (Use a value of 72 milliN/m
for the water-air surface energy). To what height must water be filled in
the well for the microchannel to fill?

w=h
 Solution
The pressure required to fill a square microchannel is calculated by:

(Note: The negative value for the answer just indicated that this is a
required pressure, not an actual negative pressure)

This threshold pressure is caused by the gravitational force of the water

in the well. Therefore, the required height of water in the well can be
calculated.