Modelling and Design

Biochip with Integrated Vertical Emitting Light Source
Introduction
Optical interrogation is a useful, non-contact, means of examining the contents of a microfluidic channel. Such
interrogation could involve measuring the optical transmission, absorbance or fluorescence of the channel contents.
Since the sample is moving within the channel, the measured signal will be an average response of the volume of
sample that passes through the interrogating light beam in the measurement period. There are many advantages, such
as reducing the averaging effect, in making the beam size as small as possible. For instance, in a fluorescence
measurement the sample is excited with a beam of one wavelength causing fluorescence at a different wavelength. If
the excitation and fluorescence wavelength are similar, a narrow exciting beam a short distance from the measurement
point can reduce the errors caused by stray pick-up of the exciting beam. Also, tightly focused, high intensity light
beams can be used to trap microscopic particles. The region of highest intensity, usually the focal point, acts as the
equivalent of the high field region in positive dielectrophoresis and attracts the particles. Once trapped, these particles
can be examined over time as they take part in chemical reactions within the biochip.
1.1. Overview
Semiconductor-based light sources such as LEDs and VCSELs allow very narrow light beams to be created within
biochips. Typically the light emitting aperture is <20?m in size. Including the top and bottom contact areas, devices can
be <1 millimetres in each dimension. Wire bonding is often used to form an electrical contact to the top surface.
However, the emitted beam is very divergent (typically >20o) so within the vertical distance of the wire bond the beam
becomes significantly larger than the output aperture. Additionally, the vertical height of the loop of wire forming the
bond can vary from device to device. If the device is mounted under a polymer microfluidic channel, the height of this
wire limits how close the light source can be placed to the edge of the channel and so limits the width of the beam
entering the channel.
To overcome this uncertainty, microfabrication methods can be used to allow semiconductor light sources to be
repeatedly mounted in close proximity to the edge of the channel. The mounting of the small emitter devices is as
follows.
Step 1: The emitter device is placed aperture downwards on a freshly cured
planar PDMS surface along with any additional electrical contact pads. The PDMS
forms a temporary seal against the surface of the device and pads. The second
device contact is bonded to the back surface of the device.
Step 2: The device and pads are encapsulated in an optical epoxy which forms a
flat planar surface against the cured PDMS.
Step 3: After curing the epoxy, the PDMS is removed from the inverted structure
to reveal a flat surface containing the light emitting aperture and the additional
contact. The epoxy forms a strong bond around the edges of the device and
contact by does not encroach onto the surface of either component because of
the PDMS seal in place during curing.
Step 4: Next, the epoxy surface is coated with an evaporated metal which is
subsequently pattered to expose the light emitting aperture of the device. The
metal layer forms an electrical connection between the upper surface of the
device and the embedded electrical contact so allowing both upper and lower
contacts of the device to be accesses from the rear of the device.
Step 5: Finally, a precise layer of epoxy, typically 2?m thick, is spin coated over
the device to provide electrical insulation and mechanical robustness. Microfluidic
channels are subsequently fabricated on the upper surface of this epoxy layer. In
doing so, the lower surface of the channel is within 2?m of the light emitting
aperture so reducing divergence effects and optimally delivering light to the
channel.
Calculations
The process of generating light from the current flowing through a semiconductor device causes such small devices to
significantly heat up. This heat must be dissipated and a proportion will be conducted through the epoxy into the
microfluidic channel. At the same time, proteins and cells which may be within the sample must be kept at a regulated
temperature and typically not exceeding 37oC. The task of this assignment is to use Comsol Multiphysics to calculate
the change in temperature at the bottom surface (top of the thin epoxy layer) of the microfluidic channel over time. To
reduce the temperature rise, the device can be driven from a pulsed voltage source where the duty cycle and frequency
are chosen to allow heat generated in the device ‘on-time’ to be dissipated before the next pulse. Use your model to
find an appropriate pulse width for a 10% on time duty cycle to limit the temperature rise at the lower surface of the
channel above the emitter aperture to 0.5oC.
Figure 1. View of the complete model geometry
The geometry used in this assignment represents the semiconductor (R2), encapsulating epoxy (R6), thin epoxy layer
(R1), fluidic channel (R4), channel upper wall (R5) and the active region of the semiconductor (R3). This geometry
should be modelled in 2D with the overall length of the model being 5mm and the total height being 1.5mm. The top of
the channel is 100?m above the surface of the semiconductor with a 2?m epoxy layer separating the channel from the
device. The device is 2mm long and 300?m high. The active region is located in the centre of the upper surface of the
device and is 40?m wide and 2?m high and positioned to be 1.5mm from the start of the channel. It can be assumed
that all the current flows from the upper surface of the active region to the lower surface of this region so limiting the
heat generation to the active region.
To create the model for this assignment you will need to combine fluid flow, thermal and electrical physics regimes to
calculate the effect of Ohmic heating on a sample undergoing laminar flow in the channel. Assume that the channel
contains water and that fluid flow only occurs within the channel subdomain. Current can be assumed to only flow
through the active region which has a conductivity of 17Sm-1. Heat will be dissipated through all parts of the model. The
following thermal properties can be assumed.
Subdomain Density Thermal Conductivity Specific Heat Capacity
Thin Epoxy Layer (R1) 1300 0.15 1100
Device (R2) 5316 33 550
Active Region (R3) 5316 33 550
Channel (R4) 1000 0.6 4200
Channel Upper Wall (R5) 1300 0.15 1100
Encapsulating Epoxy (R6) 1300 0.15 1100
Figure 1. Expanded view of the
active region of the model geometry.
Note: To define the device voltage you will need to define a voltage pulse. Comsol Multiphysics contains the functions
to create steps etc in the definitions node. These functions allow realistic pulses with a defined switch on time to be
defined.
Tasks.
Produce a written report on your modelling work. This report should draw on knowledge from other modules where
appropriate and should consist of:
? An introduction describing the aim of the project.
? A background theory section briefly describing any essential background physics or mathematics required to
understand the problem.
? A method section describing how your model was created along with any boundary and subdomain settings.
You should explain why each boundary and subdomain parameter has been chosen
? A Results section presenting your findings in a clear and concise manner. The data that answers any specific
questions in this document should be presented here along with simulations that have been used to
understand the operation of the vortex chamber.
? A discussion section presenting a more detailed explanation for your observations from the modelling
exercise. You should also include in your discussion any evidence from literature that confirms or contradicts
your findings. This section should also explain the answers to any specific questions asked in this document
? A conclusions section that summarises the work carried out and key findings from the work
? A references section containing full reference to any information sources you will of course have used in
your work.
You will notice that your report should have a similar structure to a journal publication or book chapter. It may help you
to imagine that the report is to become a published paper. Ask yourself what information is necessary for someone else
to reproduce your work and what is the best way to present and fully explain your findings? The descriptions of the
example models in the Comsol Multiphysics User Guide show a good way of presenting only the methods section of
your work.
You are strongly encouraged to use scientific journal publications and text books to acquire a broad knowledge of the
subject you are modelling. Such an investigation will help you further understand the physics behind this assignment
and assist in creating an accurate model. While the internet is a good source of general information, you must not rely
on this information and cannot use it in your references – find the original source. Additionally, your report will be
subject to the University of Wales, Bangor plagiarism rules which are explained in your student handbook.
This assignment will contribute towards 40% of your final module mark. A typical student is expected you spend 150
hours of study for this module. Your report and model should reflect this expected effort. Ask questions where
necessary and make use of the Blackboard discussion forums to share ideas.
This assignment is to be carried out working in pairs with your individual assignment report being submitted through
Blackboard by 5:00pm on Friday 21th December 2012. Please also submit your Comsol files on a CD and a printed copy
of your report to the School office by the same deadline.

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