Faculty of Science

Undergraduate Symposium 2022

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Presentation Layout
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Psychology
A Comparative Analysis of Surgical
Treatments to Prevent Neuroma Formation
Aline Thorkelsson Psychology
16
Co-authors: Dr. Christine Webber, Paige Hardy, Shirley Dua, Leah Acton
Abstract: Up to one-third of the wounded warriors and people with amputations will experience
painful symptomatic neuromas, a type of neuropathic pain (NP), which can be attributed to
residual limb pain. This pain arises from injury to pain-processing (nociceptive) neurons in the
peripheral or central nervous system, is exceptionally debilitating and, unfortunately, is almost
always resistant to opioid and other currently developed medication treatments. Targeted
muscle reinnervation (TMR) is a surgical technique to treat chronic neuroma- driven NP. It
involves transferring a proximal stump of an amputated peripheral nerve to a nearby redundant
target muscle to encourage neuromuscular innervation and thus prevent neuroma formation
and NP. The Regenerating Peripheral Nerve Interface (RPNI) involves wrapping a denervated
muscle around the cut nerve stump to promote muscle reinnervation instead of forming a
painful neuroma. As TMR and RPNI are becoming more common in clinical situations where
amputation is necessary, we will examine the efficacy of TMR and RPNI at preventing neuroma
formation and NP in rats and quantify the muscle reinnervation.

An eye for an egg: Investigating how an

object’s social value impacts visual attention
and memory
Arianna Cook Psychology
18
Co-authors: Dana Hayward
Abstract: The current paradigm in social attention research presumes that all objects lack
social value; consequently, objects are used as control stimuli in experiments. Thus, although
evidence suggests that objects can communicate social information, no known research has
explored if attentional biases exist for objects with a social vs. non-social value. In this
experiment, 84 participants engaged in a visual search task and a memory task that included
objects belonging to one of three social categories: identity, situation, or neutral. Identity
objects—such as a menorah—are affiliated with an individual’s identity, situation objects—such
as a food platter—are used in social situations, while neutral objects—such as a toothbrush—are
not reflective of one’s identity nor used in social situations. Further, 43 of the participants
received a social prime, where participants were informed that the goal was to analyze the
relationship between an object’s social value and attention. We predicted that participants
would be faster to find the identity and situation objects, remember their location better, and
those who received the social prime would show enhanced performance. Participants were
faster to locate identity and situation objects compared to neutral objects. However, memory
accuracy was only significantly worse for the neutral objects when compared to the situation
objects. Surprisingly, the prime had no effect on participant performance. These findings
suggest that non-social objects should not be treated as equal, which has implications for the
current methods used in attention research.
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Physics
High Quality Superconducting Thin Films
Harmon Bovee Physics
1
Co-authors: Matt Rudd, Emil Varga, Marvin Hirschel, John Davis

Abstract: Optomechanical devices provide a platform for highly sensitive measurement devices.
One use case is the measurement of magnetic properties of materials with so-called optome-
chanical torque magnetometry. Iron and permalloy have been measured with such devices;
however, an interesting class of materials lies in superconductors, particularly at mesoscopic
scales (many-atom systems with non-classical behaviour). The measurement of mesoscopic
superconductors requires thin film deposition recipes that are clean and free of defects which
may produce undesirable effects during measurement. To develop such high quality test films,
deposition methods and parameters are varied, and tested for microscopic structure, resistiv-
ity, and superconducting properties. In this work physical vapour deposition (PVD) is used
to create test films on cleaned and diced silicon nitride wafers; characterization is done with
scanning electron and atomic force microscopy (SEM and AFM), four-point probe resistivity
measurements, and low temperature four-point probe resistivity measurements; a relationship
between fast deposition speeds and higher superconductor quality is found; and further steps
are identified.

Isolating the Sound of Dark Matter: Our

HELIOS Suspension
Noah Baker Physics
3
Co-authors: John Davis, Marvin Hirschel

Abstract: There are several candidates in the broad search for dark matter. Prevalent among
them is an ultralight particle interacting via some scalar field, which would induce an isotropic
strain on all condensed bodies. Our dark matter detector (HELIOS) aims to measure this effect
in the 2 kHz frequency range, and thus requires strong vibration isolation in that range. We
have created a new kind of vibration isolation suspension, which uses circular catherine-wheel
springs cut out of oxygen-free copper sheets. These springs utilize significantly less vertical
height, meaning more isolation stages can fit above the shell of our dilution refrigerator. This
increases the overall attenuation. Since stainless-steel coil springs also have very poor thermal
conduction, similar suspensions are generally thermally bypassed using copper wires or rods.
This implementation is unnecessary with this new design, as the entire suspension is made out
of copper. Strong attenuation was measured in the desired frequency range, as well as clear
improvement in overall attenuation as more stages were added.
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Experimental setup for the observation of

Majorana fermions in 3He-B
Aymar, Muhikira Physics
5
Co-authors: Alex Shook, John P Davis

Abstract: The B phase of superfluid 3He is theorised to exhibit Majorana modes as edge states
on its surface. In a confined geometry, these Majorana modes can be suppressed by applying
a magnetic field. As the quasi-particles lead to a power-law suppression of the superfluid
mass current, observing the different forms of the mass current without a magnetic field and
with a magnetic field could lead to a direct signature of these edge states. This project is
concerned with the design of the different components to be assembled into a system to detect
said signature. The magnetic field is generated by a solenoid, and different parameters of the
coil are studied to get the optimal design. The mass current is to be measured using two-basin
nanofluidic capacitors, and such devices are assembled in a cell and characterised. The next
stages of the project are then presented.

A Graph Database Solution For Tracking The

Deployment And Layout Of A Large Radio
Interferometer
Dhananjhay Bansal Physics
7
Co-authors: Adam D. Hincks, Anatoly Zavyalov

Abstract: The Hydrogen Intensity and Real-Time Analysis eXperiment (HIRAX) is a 21 cm

intensity mapping experiment in the Karoo region of South Africa that will consist of 1,024
six meter dishes operating interferometrically from 400 to 800 MHz; an initial 256-dish ar-
ray is funded. The full experiment will have over 2,000 signal chains, each consisting of many
individual components—dual-polarization antennas, amplifiers, filters, cables, etc.—whose con-
nections, locations and states need to be tracked as the experiment is deployed and modified.
Data analysis requires accurate information about the physical location of each antenna and
which digital channel it is connected to at any given moment in the observatory’s history. Iden-
tifying the particular components within each signal chain, which in principle can have unique
calibration information, may also be needed in order to reach the high levels of precision re-
quired by HIRAX. This complex bookkeeping task requires specialized software. Padloper is
a package under active development to meet this need and record the physical configuration
of HIRAX through time. It uses JanusGraph, an open source graph database, to represent
hardware components as vertices and their connections as edges of a graph. A custom-written
Python API populates the database and can be used to query the database for the experiment
configuration at a given date and time. A web interface built with React interfaces to this API
via a Flask server for user-friendly access and provides useful visualization tools. Padloper is
open source and could easily be deployed for any experiment that needs to track signal chains,
such as the upcoming CHORD and PUMA radio interferometers.
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Quantum Plane Waves on Lattices in

Hyperbolic Space; An Anomalous Behaviour
Davidson Noby Joseph Physics
9
Co-authors: Igor Boettcher, Santanu Dey

Abstract: Picture this, you stand on a beach, watching over the waves. Beneath, to your feet
are waves that are rather chaotic, however waves far off are more tranquil; they (more or less)
move in parallel towards the shore. Quantum particles with a fixed momentum are akin to these
plane waves, but the wave function is Complex. Plane waves in regular space can be rather
boring after a while, so to spice things up, we bring in Hyperbolic Space. This bizarre space
has a plethora of properties, one of which include the fact that parallel lines never intersect!
In this space, we can talk about Hyperbolic Plane waves, akin to our regular Plane waves.
Moreover, we can also embed lattices in this Hyperbolic space, which we call Hyperbolic Lat-
tices. Why bother with what seems like a mathematical muse? Because these Hyperbolic Lat-
tices have been realized in ground-breaking experiments with both superconducting resonators
(2019; Kollar, Fitzpatric et al) and topoelectrical circuits (2021; Lenggenhager, Stegmaier,
Boettcher et al) over the last four years. Importantly, the propagation of Quantum or Classical
wave packets is the central experimental probe in these experiments. Given the novelty of the
setups, not much is known about these dynamics either analytically or numerically.
We study the propagation of a Hyperbolic Quantum plane wave through the hyperbolic lat-
tices. Plane waves with fixed momenta would remain plane waves without the lattice. However,
this is no longer true when one sends a plane wave through the hyperbolic lattices.
We utilize first order Borne approximation scheme to derive an integral equation for the
eigenfunctions of the hopping Hamiltonian H = −∆+ϵQ on the order ϵ = 0.27, which is a fixed
lattice constant and Q is an operator arising from the lattice. We show the wave dynamics
through simulations in time by expanding the Time Evolution Operator for small t. Finally,
we study the momenta distribution that appears through time evolution.

Using a Monte Carlo Event Generator to

Model String Resonances in Proton-Proton
Collisions
Kenny Moc Physics
11
Co-authors: Doug Gingrich, Jack Lindon

Abstract: Strings may exist at a low-energy scale in specific models of string theory. In such
cases, proton-proton collisions at the LHC could generate string resonances that would differ
from our theories of quantum chromodynamics; which govern the interactions between quarks
and gluons. We can detect this resonance by analyzing the particle jets generated by the quarks
and gluons. We form simulations of these collisions using a Monte Carlo event generator with
and without the string resonance. Our objective is to aid in the search for particles beyond the
standard model.
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Statistical Analysis of Fluctuations in Energy

Transport in a Magnetized Plasma
Cassandra Mckenna Physics
21
Co-authors: R. D. Sydora, S. Karbashewski
Abstract: The goal of this research project was to study fluctuations and energy transport in a
magnetized plasma experiment which was facilitated by the creation of a graphical user inter-
face for analysis of large data sets. By studying the higher moments of a probability distribution
function (PDF) obtained from the density and temperature fluctuations, we characterized these
fluctuations (distinguishing coherent or sinusoidal versus quasi-coherent and chaotic) along with
the associated energy transport. The data was collected from the Large Plasma Device (LaPD)
located at UCLA. In this device, the main plasma is created by a cathode-anode discharge
and within that large plasma volume there is another smaller cathode-anode electron beam
source that thermalizes and produces a localized magnetized plasma pressure filament. Within
this filament, there are fluctuations in temperature and density created by the pressure gradi-
ent associated with the filamentary structure. These fluctuations induce anomalous transport
(wave-driven) of energy and particles and the properties of these fluctuations are analyzed sta-
tistically. From the moments of PDF – mean, standard deviation, skew, kurtosis – we found
relationships between them and uncovered evidence of intermittency and non-diffusive energy
transport both temporally and spatially.

Optimizing Deployable Boom Designs For

Stable Operation of Nano-Satellites
Andre Ulliac Physics
22
Co-authors: Katelyn Ball, Jari Swanson, Mike Lipsett, Dan Sameoto, Ian Mann
Abstract: Many satellites require the use of deployable booms for various applications, such as
separating a scientific payload from magnetic noise sources on the vehicle. However, their use on
cube- and nano-satellites presents a number of challenges. These booms can significantly alter
the inertial properties and therefore rotational stability of the system, which can be significantly
destabilising for small satellites with limited control torques. Here we outline a process for using
the boom to tune the inertial parameters of the boom plus spacecraft bus system to optimize
stability. The investigation builds on previous work designing an articulated deployable boom
for CubeSatellite applications.
A simple deployable boom design that readily permits modifications of the spacecraft inertial
properties during the design phase has been prototyped and is ready to fly on 3 upcoming
University of Alberta student-led CubeSatellite missions: Ex-Alta 2, AuroraSat, and YukonSat.
The boom has a two-member design, is mounted on the exterior of the spacecraft, and utilizes
two joints to achieve a total length approximately twice that of the longest face of the CubeSat.
It uses two machined features to control the angle at which the elbow and shoulder joints rest
in their respective fully deployed positions. Work is currently ongoing to characterize the flight-
model mass properties of the system and to characterize the affect of the boom on spacecraft
stability via simulation.
This abstract was adapted from an abstract presented at the Canadian Society for Me-
chanical Engineering International Congress 2021, and reflects the continuation of the same
research.
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Detection of Mechanical Resonances through

Torque Magnetometry
Jaren Wheeler Physics
23
Co-authors: Mark Freeman, Katryna Fast

Abstract: Electrons have an intrinsic form of angular momentum known as spin, which governs
the electron’s reaction to torque from magnetic fields. There are two different types of magnetic
torque that are of interest, the most common is cross product torque and the other is the
Einstein-de Haas (EdH) torque. Cross product torques depend primarily on external DC fields
whereas EdH torques depend linearly on frequency.
In this research, we present a prototype for a mechanical sensor to measure magnetic torques
simultaneously at multiple frequencies. The sensor prototype is fabricated from a bulk silicon
wafer, and is loaded with a small disk of ferrite as the magnetic specimen.
To generate AC magnetic torque, the sample is magnetized with a DC magnetic field and
an AC field is applied in tandem. The AC torque is used to search for points of mechanical
resonance. The deflection of the rod is detected using optical interferometry based on the
relative motion of the silicon device and a fixed optical fibre. In sweeping over frequencies,
only two strong mechanical resonance peaks have been observed so far. Because of the high
amplitudes and low frequency range of measurement it is concluded that these resonances are
due to cross product torques. Finite-element simulations indicate that the intended nature of
higher frequency mechanical modes in the prototype has been strongly modified by coupling to
the surrounding silicon.
Once the mechanical frequency can be increased to a sufficiently high level (material- depen-
dent), the linear relationship should break down when the required speed of angular momentum
transfer between electrons and the lattice becomes too great for the lattice to handle. This will
provide important insight into the mechanism of angular momentum transfer in materials.

Fluxgate Magnetometry and Space Weather

Science from the Northern SPIRIT CubeSat
Constellation
Jari Swanson Physics
24
Co-authors: Katelyn Ball , Andy Kale, David Milling, David Barona Arias, David Miles, Miroslaw
Ciurzynski, Andre Ulliac, Michael Lipsett, Ian Mann

Abstract: A miniature fluxgate magnetometer has been developed for cube satellites (CubeSats)
to study space weather from low Earth orbit. This sensor has remarkably low volume with a
greatest dimension of 4 cm, 500 mW power draw, and total mass less than 250 g, while retaining
high resolution and low noise. The first generation was flown successfully on AlbertaSat’s Ex-
Alta 1 satellite developed at the University of Alberta; a second generation instrument has been
developed and tested for flight on three upcoming CubeSat missions in the Northern SPIRIT
collaboration between U. Alberta, Yukon U., and the Auroral Research Institute (NWT) within
the Canadian Space Agency (CSA) Canadian CubeSat Project. The instrument consists of
three main components: a PC104 electronics board, a 2-member 60 cm deployable boom, and
the sensor head. A new assembly method for the high-permeability permalloy cores has been
developed to avoid spot welding the material which drastically reduces the noise floor, from
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over 150 √pT

Hz
to about 40 √pT
Hz
. The sensor head’s mechanical housing has been redesigned to
accommodate the new sensor’s geometry while still allowing it to be stowed within a CubeSat.
A cutout has been added to the PC104 board which allows it to be placed directly beneath the
stowed sensor. The boom was updated following its flight on Ex-Alta 1 and subsequent testing
in microgravity on a parabolic aircraft flight. A hinge has been added to the joint between
the primary and secondary boom members, constraining the boom’s motion on deployment
which reduces the risk of impacting other components, and ensures the sensor deploys into a
consistent orientation. The deployment angles of both boom joints can be adjusted to finely
tune the spacecraft’s moments of inertia, which is critical for stabilization of the attitude
determination and control system (ADCS).

Soap Film Surface Fluctuations under Electric

Field
Samiha Ali Physics
25
Co-authors: Daniel Charlebois, Prashant Waghmare

Abstract: This projects aims to uses an understanding of electric fields to model the effects of
electric fields on catenoids. It builds on the works of Moulton, who set up a cylindrical electrode
along the axis of a soap film catenoid, and exposed the film to high voltage potential. However,
there was slight asymmetry in the soap film which was amplified from stronger electric fields
towards one side of the catenoid film. This was resulting from the distance from the soap
membrane to the inner electrode at the midplane not being identical on the left and right side.
Our goal was to derive the azimuthal asymmetric perturbation on the catenoid experimentally.
To do this, we examined the changes in radii of curvature of the soap film using ImagePro.
We also observed the soap film began to pulsate as the voltage was increased, with increasing
frequency, so this behaviour is also further explored.

On Quantum Fields in Conformal and

Quantum Field Theory
Rene Payne Physics
27
Co-authors: Raphael Belliard, Thomas Creutzig

Abstract: We begin with the definition of a Quantum Field Theory through a categorical
formulation. Also presenting the required axioms that are to be satisfied. We then discuss the
perturbative approach to Quantum Field Theory, that is, The Feynman Diagrams, and also
discussing Twistors and how they aid. Following this, we discuss non-perturbative approaches
to Quantum Field Theory. We then conclude with the introduction to 2Dimensional Conformal
Field Theory, which includes the Ward Identities, Operator Product Expansion, and we present
some examples.
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Coupling of Internal Waves Generated by

Turbulence
Akash Kav Physics
28
Co-authors: Bruce Sutherland

Abstract: Internal waves which occur within a stratified fluid, which has increasing density
with depth. The interaction of internal waves with turbulence has been a long-standing issue in
physics, as the waves are launched a specific frequency of oscillation, which may be correlated to
resonant structures within the turbulence. Throughout the course of this research, the coupling
of internal waves with turbulence is explored through the study of a turbulent jet impinging
upon a medium of stratified fluid, through numerical studies using modern turbulence models.
The structures of turbulence and the waves are then analyzed using mathematical techniques
which separate the rotational parts of the fluid from the irrotational part, in order to find
the coupling between the turbulence and the waves. It was found that lower frequencies of
oscillation occurred at the top boundary of the turbulent jet, corresponding to the frequency
of oscillation of the internal waves, and that higher frequencies of oscillation correspond to the
base of the turbulent jet impinging upon the medium. As weather models do not currently
account for the effects of internal waves generated by turbulence, these discoveries could lead
to improved weather and climate forecasting. This research will furthermore have implications
for any environment which can behave as a stratified fluid, such as the inside of stars.

Surface effects in unconventional

superconductors
Sean Chen Physics
29
Co-authors: Frank Marsiglio, Pramodh Senarath Yapa

Abstract: We study the order parameters corresponding to different pairing symmetries on a

square lattice using the extended Hubbard model and compare how properties on the surface
differ from those of the bulk.

Active magnetic field cancellation system

Yeh-In Kang Physics
30
Co-authors: Lindsay Leblanc, Arina Tashchilina

Abstract: The purpose of this project was to implement an active magnetic field cancellation
system in one-axis. The system consists of 2 Honeywell HMC 1021Z magnetoresistive sensors
that sit opposite to each other at the edges of a control zone that is contained between a pair
of Helmholtz coils. The field generated by these coils are controlled using the sensors and
a proportional controller. This system is best suited to compensate for uniform DC or low
frequency stray fields such as Earth’s magnetic field and fields emanating from power lines.
This system can be used to increase the consistency of magnetic fields in the trap region of
a Bose-Einstein Condensate(BEC) apparatus resulting in increased consistency in the atom
count of the trap and more robust experiments.
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The Hubbard Model: a tutorial in electronic

properties of solids
Alcantara-Tangonan Roger Felix Physics
31
Co-authors: Mason Protter, Pramodh Senarath Yapa Arachchige, Frank Marsiglio

Abstract: The Hubbard model describes the physics of many-electron systems. This model
reduces the complexities of electron interactions to just a few parameters; these control ef-
fects such as the repulsion between like charges and the energy required for the electrons to
move. This conceptually simple model encapsulates electronic properties of solids ranging from
conduction and insulation, to superconductivity. Despite its simplicity, undergraduate and
graduate students still face a steep learning curve when computationally solving the Hubbard
model. With an instructive and pedagogical approach, we present an introduction to the Hub-
bard model and employing its numerical methods. Since we can describe physical systems
using simple mathematical structures known as matrices, we show how matrix mechanics can
be applied to calculate the properties of electronic materials. Since matrices are simply ordered
lists of numbers, computers are well suited to perform these tedious calculations with ease.
This becomes especially significant when working with increasingly large systems. We hope
that this introduction makes the Hubbard model an accessible tool in studying and computing
electronic properties like the spectral weight function and density of states.

Biological Effects of Intense Terahertz Pulses

On Synthetic Gene Circuits.
Sanjina Aurin Physics
32
Co-authors: Frank Hegmann, Daniel Charlebois, Harold flohr, Sam Ruttiman, Nils Refvik.

Abstract: The effects of intense Terahertz (1011 − 1012 Hz) pulses on biological systems have
been observed previously such as disassembling microtubules, expression of multiple genes as-
sociated with cancer and inflammatory skin diseases. However, the cause of these effects are
yet to be discovered. We do not have a working mechanism to demonstrate these effects of
Terahertz pulses. Thus, it is very important to conduct experiments with a well-characterized
and controlled biological system such as genetically engineered yeast strains (i.e., the PF strain)
to understand this phenomenon. In our experiment we grew 3 different genetically engineered
yeast cells out of which some were exposed to the intense Terahertz pulses whereas others
served as control to the experiment. The effects on the growth cycle of the cell was then ana-
lyzed using a cell cytometer. In addition to the effects of the cell growth, we also observed the
effects on the gene expression. The results of the experiment performed are as follows: with
the lower concentration of the inducer, on the 24th hour the exposed cells were more successful
in expressing the gene at an exposure duration of 20 minutes. Similar results were obtained
with an exposure duration of 40 minutes. Exploring the effects caused by the radiation will
provide fundamental and valuable insight in the mechanism of the biological effects of intense
Terahertz pulses.
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Mathematical & Statistical Sciences

Modelling COVID-19 and Influenza
Lawrence Martinez Mathematical & Statistical Sciences
19
Co-authors: Michael Li, Xuyuan Wang
Abstract: Efforts to reduce the spread of COVID-19 may have changed the dynamics of other
infectious diseases such as influenza. Early influenza case data show a rise in cases during late
spring and early summer, uncharacteristic of the typical influenza season. As well, data trends
of COVID-19 and influenza appear to not align. With the world returning to a pre-pandemic
normal, creating a model that can accurately predict when new infectious cases will rise is vital
information. In this project, we train a mathematical model using COVID-19 and influenza
data from Alberta Health Services to determine the dynamics of both infectious diseases and
predict when new cases are expected to rise. For each disease, we create a model that considers
the contact of individuals within and between age groups and the case infection ratio, a time-
dependent parameter. We also consider vaccinated and unvaccinated populations in our model.
Then, we fit the remaining parameters of the model using diffusive nested sampling. While we
are still waiting for the results of this model fitting, the process of creating and training an
effective mathematical prediction model has significant implications in the field of public health.

Hybrid Dealiasing Convolutions

Robert Joseph George Mathematical & Statistical Sciences
52
Co-authors: John Bowman, Noel Murasko
Abstract: The convolution theorem provides a method for efficiently computing convolutions
using Fast Fourier Transforms (FFTs), with the caveat that the convolution is periodic. Many
applications such as nonlinear PDEs require a linear convolution, which can be computed using
the convolution theorem, provided that the data is sufficiently padded with zeros. Implicit
dealiasing provides an alternative to explicit dealiasing: the FFTs are formulated to implicitly
take account of the known zero values, avoiding the need for explicit zero padding. Recently,
implicit dealiasing has been extended to handle arbitrary data and padding lengths. To max-
imize performance, the padding is chosen to be fully implicit, fully explicit, or somewhere in
between. We offer unique solutions that expand hybrid dealiasing to issues with uneven input
or minimum padded sizes, reducing memory and computation time. We also expand this to
1D/2D scenarios (3D is still in process), where we now have image convolution and construct the
first hybrid dealiasing solution, which is around 10 times quicker than typical explicit padding
approaches. We also expand this to multi-convolution, applying the convolution to a sequence
of data, N arrays rather than just two, and demonstrate a conventional grid search hyperpa-
rameters search strategy that selects the optimal hyperparameters that result in the shortest
convolution time. Finally, we are developing them for existing state-of-the-art fast Fourier
transform libraries such as FFTW++, which can result in low memory FFT algorithms that
are faster, and we are comparing the performance of our approach to the standard approach in
Convolution Neural Networks, Machine Learning, turbulence simulations, signal filtering, PDEs
etc. Therefore, we expect hybrid dealiasing to become the standard method for convolutions
in the future and hope to develop hybrid dealiased convolutions for computing sparse Fourier
Transforms, fractional phase, and partial Fourier transforms.
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Studies of Turing pattern formation by the

Tulip breaking virus
Aidan Wong Mathematical & Statistical Sciences
20
Co-authors: Gustavo Carrero and Thomas Hillen
Abstract: The Tulip breaking virus creates striped petals. Using its biological processes, we
created a mathematical model for the pattern formation of pigments in broken tulips. Our
model used reaction diffusion equations guided by the work of both A. Turing and L. Wolpert.
We applied tulip-like domain growth into the model and investigated how it affected pattern
formation.

Modelling Leukemia Relapse following

Immunotherapy
Nat Kendal-Freedman Mathematical & Statistical Sciences
35
Co-authors: Thomas Hillen and Jay Newby
Abstract: Immunotherapies are a new class of cancer treatments that focus on bolstering the
immune system’s ability to fight cancer. Chimeric Antigen Receptor (CAR) T-cell therapy
is a type of immunotherapy that has proven very successful in patients with relapsed B-Cell
Acute Lymphoblastic Leukemia (B-ALL). We develop an Ordinary Differential Equation model
of CAR T-cell therapy for B-ALL including T-regulatory cells and demonstrate that it can
explain relapse in the absence of CAR T-cells. Furthermore, we do a bifurcation analysis which
provides an explicit condition under which relapse will occur following the extinction of CAR
T-cells.

Quantum symmetric super-pairs

Coleton Kotch Mathematical & Statistical Sciences
36
Co-authors: Nicolas Guay
Abstract: Quantum groups, and in particular quantized enveloping algebras of Lie algebras,
have been of interest to mathematicians and theoretical physicists since the 1980’s. Over the
past twenty years, the related theory of quantum symmetric pairs has been developed and has
gained in popularity. Another branch of Lie theory that is of importance in mathematical
physics is the theory of Lie superalgebras. Symmetric pairs of Lie superalgebras have been
studied, but there is nothing in the literature so far about quantum symmetric super-pairs.
This is a topic worth investigating, starting with the basic question of how to define these.
There should be two ways to construct them: either as co-ideal subalgebras of quantized en-
veloping superalgebras or via the reflection equation and a symmetry relation. The proof of
the equivalence of these two definitions should rely on a matrix solution of the reflection equa-
tion and the main goal of this research project is to find such suitable solutions. Once this is
achieved, it should be possible to find bases for these co-ideal subalgebras. The first superpair
to consider is the one consisting of the general linear Lie superalgebra and its orthosymplectic
sub-superalgebra, as there are some papers devoted to the classical (non-super) analogue of this
pair. Quantum symmetric pairs were first introduced to help study certain special functions:
it would be interesting to see if a similar connection can be established for Lie superalgebras.
 14

Periodic solutions of second-order differential

equations
Joshua George Mathematical & Statistical Sciences
37
Co-authors: Mohammad Ali Niksirat

Abstract: In this project we prove the existence of a periodic solution to the following second
order differential solution : x′′ = f (t, x, x′ ) where f is ω-periodic with respect to t, that is,
f (t + ω, x, x′ ) = f (t, x, x′ ). To do so we first construct a Green function G(t, s) for the following
equation  ′′
 x + λ2 x = δ(t − s)
x(0) = x(ω) .
 ′ ′
x (0) = x (ω)
After that, the given differential equation is reduced to the following integral equation
Z ω
G(t, s) f (s, x(s), x′ (s)) − λ2 x(s) ds.

x(t) =
0

The existence of a periodic solution to the given differential equation is reduced to the existence
of a solution for the obtained integral equation. To do so we prove the Brouwer Fixed Point
Theorem using Degree Theory and the Schauder Fixed Point Theorem.

Detecting Heavy Tails and Long Range

Dependence in Time Series
Edmond Tuong Mathematical & Statistical Sciences
50
Co-authors: MA Kouritzin

Abstract: For a linear process xk = ∞

P
l=1 ck−l ξl with coefficients cl and i.i.d. zero-mean in-
novations ξl , cl often decays slow enough to have long-range dependence, and the distribution
of ξl can also have heavy polynomial tails. The standard tests for either of these extreme
properties require the absence of the other. Here, we will investigate the use of Marcinkiewicz
strong laws of large numbers capable of estimating both properties simultaneously in a neural
network, calibrating it with simulated data, and testing it on real-world financial data. We also
try a topological neural network, involving precomposition of the linear process with a metric
function.
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Cross-Sectional Analysis of Loan Market

Returns Using Machine Learning Methods
Kailash Seshadri Mathematical & Statistical Sciences
51
Co-authors: Christoph Frei, Hamed Ghanbari

Abstract: We analyze the performance of Random Regression Forests for the canonical problem
of measuring risk premiums and asset pricing in the syndicated loan market. We compare re-
sults between traditional linear regressional methods from literature with tree-based regression
methods from machine learning to better understand the price of different sources of risk in
investments. We demonstrate much higher predictability when using tree-based methods over
traditional linear regression, with Regression Forests providing an average predictive R2 of 0.37
compared to the mean Adj − R2 of 0.30 managed by traditional methods. This increase in
predictability results in significant gains for investors, who can make more educated choices on
investments and enjoy higher average returns.

Computing Science
Making Reinforcement Learning Experiments
More Reproducible and Computationally
Efficient
Robert Joseph George Computing Science
53
Co-authors: Martha White, Adam White, Samuel Neumann

Abstract: The Arcade Learning Environment (ALE) is a well-known testing ground for re-
inforcement learning agents. MinAtar, short for miniature Atari, was introduced in 2018 by
researchers at the University of Alberta and Google Brain/Deepmind as a new set of envi-
ronments that capture the general mechanics of specific Atari games while simplifying the
representational complexity to focus more on the behavioral challenges. Seaquest, Breakout,
Asterix, Freeway, and Space Invaders are all counterparts of Atari games in MinAtar. Cur-
rently, the implementation of these gaming environments is slow, and we refactored the whole
codebase to reduce training time by roughly 50% across all environments and also included a
Just in time compiler (Numba) that makes the code even faster. This is a huge improvement
for researchers to train their algorithms on these environments and get the results faster. Sec-
ondly, we propose a new approach to select the best hyperparameters after a hyperparameter
sweep wherein the old method just used to choose the best hyper that resulted in largest area
under the learning curve (AUC) but suffered from not taking into account the hyperparameter
sensitivity etc. We compare the Soft Actor Critic (SAC) Discrete CNN and Vanilla Actor-
Critic (VAC) Discrete CNN agents’ mean learning curves in several contexts utilizing this new
approach. We hope to compare various other algorithms in the future and create a benchmark
for MinAtar so researchers can compare their algorithms on these environments. Lastly we also
hope to add more games from ALE to the MinAtar codebase for further testing. We hope that
MinAtar and this new hyperparameter approach can allow researchers to use it as a testbed
for reinforcement learning.
 16

Meta Learning Objectives

Haruto Tanaka Computing Science
13
Co-authors: Alex Lewandowski, Dale Schuurmans

Abstract: Meta-learning is a class of algorithms that learn to improve other learning problems,
and is often used in few-shot learning problems. Historically, research on meta-learning is highly
focused on searching the optimal parameter initialization or optimizer. Although, interestingly,
meta-learning the objective function has been less focused, while it is one of the chief compo-
nents in gradient-based learning. Due to this lack of research, facts related to the properties
of learned objective function remains unexplored. In this project, we attempt to unveil the
hidden properties of learned objective function, trained with meta-gradients. Analysis mainly
include the quantitative comparison between the learned objective function and the well-known
objective function, and geometric properties of learned objective. We also discuss the possible
future directions based on the qualitative analysis of outcomes.

A Character-Level Length Control Algorithm

for Non-Autoregressive Sentence
Summarization
Xiang Zhang Computing Science
33
Co-authors: Puyuan Liu, Xiang Zhang, Lili Mou

Abstract: Sentence summarization aims at compressing a long sentence into a short one that
keeps the main gist, and has extensive real-world applications such as headline generation. In
previous work, researchers have developed various approaches to improve the ROUGE score,
which is the main evaluation metric for summarization, whereas controlling the summary length
has not drawn much attention. In our work, we address a new problem of explicit character-
level length control for summarization, and propose a dynamic programming algorithm based
on the Connectionist Temporal Classification (CTC) model. Results show that our approach
not only achieves higher ROUGE scores but also yields more complete sentences.

Mechanic Maker
Vardan, Saini Computing Science
34
Co-authors: Matthew Guzdial

Abstract: Developing games is challenging as it requires expertise in programming skills and

game design. This process is costly and consumes a great deal of time. In this paper we
describe a tool we developed to help decrease this burden: Mechanic Maker. Mechanic Maker
is designed to allow users to make 2D games without programming. A user interacts with a
machine learning AI agent, which learns game mechanics by demonstration.
 17

Sum Coloring Chordal Graphs

Ian DeHaan Computing Science
54
Co-authors: Zachary Friggstad

Abstract: The Sum Coloring (SC) problem is a graph problem which can be used to find the
minimum average completion time for a set of equal length tasks, some pairs of which cannot
be done concurrently. SC is NP-hard, even on well-structured graph types such as chordal
graphs. We use a linear program rounding scheme to get an improved approximation for the
Maximum k-Colorable Subgraph Problem on chordal graphs. We then use this to give a 1.796-
approximation for SC on chordal graphs, improving the previous best 3.592-approximation.
 18

Chemistry
Optimizing halogen uptake on
self-decontaminating textile finish
Jemma Forgie Chemistry
38
Co-authors: Forgie, J.; Arredondo, O. R.; Labonno, A. A.; De La Mata, P.; Harynuk, J. J.;
Batcheller, J.; Dolez, P. I.

Abstract: Halogens have become a popular additive in textile finishing as they contribute broad-
spectrum self-decontaminating behaviours against chemical and biological hazards, which may
be used in a variety of occupational settings. However, their efficacy as decontaminating agents
relies on a secure bond to the fabric surface and an even finish application. Different factors
may impact halogen-fabric bonds such as previous coating conditions, drying time and temper-
atures, and halogen type. Furthermore, conditions in-use such as textile storage, UV exposure,
abrasion, and laundering can cause deterioration of halogen-fabric bonds over time. This re-
search focuses on optimizing coating conditions to allow for sufficient uptake of halogens on the
fabric surface. A cotton-polyester blend fabric was treated with a polymer coating and then
exposed to different solutions containing halogens, which served as an active decontaminating
compound on the fabric surface. The coated fabrics were then titrated using an iodometric
method to assess halogen concentration. With one exception, the examined halogens showed
similar uptake levels and even distribution on the fabric surface. Discrepancies were also seen in
the effect of the halogens on the fabric dye, with the different halogens causing unique changes
in colour intensity and direction following halogenation.

Influence of water ratio on autooxidation of

glycols
Ya-Chun Chan Chemistry
39
Co-authors: Ya-Chun Chan, Xinyang Guo, Ran Zhao

Abstract: Glycol is of many commercial and industrial applications. It is mixed with water at
varied ratio acting as the base of both e-cigarette juice and fog machine juice, with the latter
commonly employed in theatre and concert settings. Recently, our lab discovered the formation
of toxic carbonyl compounds during glycol storage, which, we proposed to be due to autoox-
idation. Prolonged exposure to these substances may lead to adverse health consequences.
Despite the increasing studies on the properties and behaviours of glycols, the autooxidation
of glycol is not fully understood, representing a need for further investigation. The overarching
goal of this project to understand the autooxidation of glycols and its risk to the consumers.
Specifically, we want to quantify both the intermediate, total peroxide content, and terminal
products, formaldehyde and glycoaldehyde, of autooxidation. Secondly, we aim to explore how
the ratio of water-glycol mixtures influences autooxidation. In addition, we intend to examine
the efficacy of antioxidants on impeding autooxidation. I first develop and optimize a method
allowing determination and quantification of target species. While the total peroxide content is
determined by iodometry, 2,4-dinitrophenylhydrazine derivatization coupled with liquid chro-
matography mass spectrometry is employed to characterize carbonyls compounds. Second,
 19

water-glycol mixtures at various glycol volume ratios were prepared. The formation of selected
species is monitored over course of six weeks and compared to a control group where the air
exposure is minimized thus the autooxidation. To examine the efficacy of antioxidants, an
additional glycol sample spiked with an antioxidant was also monitored over the same period.
Preliminary results showed growth of formaldehyde and glycolaldehyde over three weeks. In
particular, we found non-linear relationship between water-glycol ratio and the level of toxic
substance formed; 50% water-glycol ratio gives rise to the fastest growth of carbonyl species
which happens to be the ratio of commercial fog juices. The result of experiments involving
antioxidants will also be discussed in the poster. This project is the first to systematically
investigate autooxidation of glycols and the subsequent formation of toxic compounds. The
findings of this project have the potential to provide insight into a novel chemistry which not
only provides guidance to policies relating to occupational health but also ensure that con-
sumers are made aware of the precaution to be taken with water-glycol products appealing to
public health.

Genetically Encoded Fragment-Based

Discovery of Covalent Peptide Macrocycle
Inhibitors of PKM2 with Extended in-vivo
Circulation
Ryan Qiu Chemistry
40
Co-authors: Arunika I. Ekanayake, Ratmir Derda

Abstract: Peptides and peptide-derived therapeutics (PDT) have the potential to engage targets
that cannot be addressed by small-molecule therapeutics (aka “undruggable targets”). PDTs
can provide highly selective interactions with drug targets, rendering them favorable binders
for therapeutically important proteins. The high specificity of peptides can be combined with
electrophilic chemical fragments to generate irreversibly reacting PDTs that can interact with
active and allosteric site nucleophilic amino acid residues such as cysteines. Using a method-
ology developed in our group, we can create libraries of covalently reactive ligands that can
provide highly specific interactions with the target by grafting electrophilic compounds onto
genetically encoded phage-displayed macrocyclic libraries. This serves as a method to identify
novel PDTs bearing electrophilic modalities. Pyruvate kinase muscle isozyme 2 (PKM2) ex-
hibits two catalytic cysteine sites addressable by electrophilic fragments and binding pockets
targetable by peptide sequences.
The metabolic role of PKM2 is applied when cancer cells switch to a glycolytic phenotype
known as the Warburg effect. Therefore, PKM2 is an interesting biomarker for cancer and a
therapeutic target for tumorigenesis. While PDTs provide many desirable properties as drugs,
they present several caveats, such as short half-life in the bloodstream and poor kidney reten-
tion. The binding of peptides to abundant serum proteins such as human serum albumin (HSA)
can aid in addressing these drawbacks, increasing the circulation of PDTs by delaying renal
excretion from the bloodstream. Previously, we discovered macrocyclization with a perfluori-
nated aromatic linchpin that provides an amphiphilic scaffold recognizable by the hydrophobic
binding site of HSA in-vivo. By linking both peptides together, creating a small macrocyclic
antibody-like scaffold (SMALS), we can add circulation extension properties to our therapeutic
peptide macrocycle.
 20

Synthesis and reactivity of tetraaryl

[4]cumulenes
Jakob A. Meckes Chemistry
41
Co-authors: Matthew A. Johnson, Michael J. Ferguson, Rik R. Tykwinski

Abstract: [n]Cumulenes are linear sp-hybridized molecules that contain multiple cumulated
double bonds. They fall into two classes, even and odd, depending on the number of double
bonds. Cumulenes with an odd number of double bonds are generally more stable and better
understood than even [n]cumulenes. Currently, the longest isolated even [n]cumulene derivatives
contain 4 cumulated double bonds.
In order to synthesize and isolate longer even [n]cumulenes, one requires a better under-
standing of the stability of these molecules and the ways in which they can decompose. There-
fore, synthesizing and comparing [4]cumulenes with different aryl end-groups and studying side
product formation will allow for future work in making longer, stable even [n]cumulenes.

Investigating the Photostability of Silicon

Quantum Dots Upon Exposure to UV Light
Yifan Yang Chemistry
42
Co-authors: I Teng Cheong, Kevin M. O’Connor, Jonathan G.C. Veinot

Abstract: Quantum dots are nanosized semiconductor particles that exhibit tunable size-
dependant luminescent properties throughout the visible and infrared spectral regions. Silicon
quantum dots (SiQDs) are an attractive subclass of these materials because of their natural
abundance and biocompatibility having potential applications in luminescent solar concentra-
tors and biological labelling applications which rely on stable photoluminescence.1 Despite
impressive advances, the photostability of SiQDs remains as an outstanding challenge. In fact,
reports have shown a 40% decrease in SiQD photoluminescence quantum yield (PLQY) with
prolonged UV exposure in air.2 Improving SiQD photostability can lead to advancements in
longer lasting optoelectronic devices. Non-radiative carrier trapping within regions of struc-
tural disorder found in the nanoparticle core, as well as defects at the particle surface have been
proposed as causes for the PL decrease of SiQDs.3 The Staebler-Wronski effect (SWE) offers
a potential source of non-radiative defects via UV-induced homolytic cleavage of Si-H or Si-Si
bonds.4,5 Thiessen et al. reported that thermal processing of hydrogen silsesquioxane provides
SiQDs bearing a disordered amorphous shell and an ordered crystalline core.6 The amorphous
layer can be partially removed by with ethanolic hydrofluoric acid. We are investigating the
role of the amorphous Si shell and if its removal or presence could provide a viable approach
toward decreasing the impact of UV exposure and by extension the SWE. This poster will
present our latest results and points to the amorphous shell playing a role in photostability.
 21

Mapping in-vivo organ specific glycan binding

preferences using genetically encoded
multivalent Liquid Glycan Array (LiGA)
Ellen Hayhoe Chemistry
43
Co-authors: Ellen Hayhoe, Chih Lan Lin, Susmita Sarkar, Mirat Sojitra, Matthew S. Macauley,
Ratmir Derda

Abstract: Introduction: The discovery of glycan binding preferences of organs in vivo is a

current challenge in glycobiology due to the non-template-based glycan synthesis in cells. Pre-
viously reported Liquid Glycan Array (LiGA) introduces a 1:1 correspondence between DNA
barcodes and glycans. LiGA employs M13 bacteriophages equipped with silent DNA barcodes
and a defined multivalent display of glycans on their coat proteins. LiGA has been successfully
used to characterize the structure and density of the glycans recognized by glycan binding
proteins in vitro, on the surface of living cells and in vivo.
Objectives: We aim to successfully map the localization of glycans displayed on the phage
particles and to profile homing preferences for each glycan. Fundamental mapping of spe-
cific glycan-target interactions in vivo can give insight into cell-cell communication and disease
progression. This can potentially lead to significant therapeutic advances, including the devel-
opment of improved inhibitors, vaccines, and targeted delivery of drugs.
Methodology: In order to probe the organ-specific glycan binding preferences in vivo, we
injected LiGA containing 250 glycan-linked phage conjugates into a mouse. Mouse organs were
isolated and the organ homogenate was mixed with bacteria. The organ-bound phages were
amplified by the bacteria along with the DNA barcode present in the phage. This amplification
allows for the successful recovery of barcodes that were present in the organ-bound phage. Deep
sequencing of phage DNA allows for the identification of glycans that localize to a specific organ.
Results: Major findings of this experiment show that glycans with a terminal Gal-Nac show
significant enrichment in the liver when compared to other organs.
Conclusions and future research: Future research includes the development of improved
next-generation encoded vectors in the phage that will allow for digital detection of glycans.
This will be used in order to provide sufficient specificity to eliminate sequencing bias and
improve accuracy to unambiguously determine glycan diversity binding to cells within each
organ.

Creation of Neuraminidase Knockouts using

CRISPR-Cas9
Benjamin Bekkema Chemistry
44
Co-authors: Amran Howlander; Chris Cairo

Abstract: The human neuraminidase enzymes (NEU; also called sialidase) are glycosyl hydro-
lase enzymes that modify glycoprotein and glycolipid substrates. These enzymes cleave terminal
N-acetyl-neuraminic acid (also known as sialic acid), leading to modified glycan epitopes. Sialic
acids are common features of membrane glycoproteins and often act as important recognition
elements in protein-protein and cell-cell interactions. Our group has been investigating the role
of NEU in regulating cell migration and adhesion, processes that are critical for understanding
immune response and cancer. We have observed that inhibition or knock-down of expression
 22

of human NEU can have dramatic effects on the migration of endothelial and leukocyte cells
in vitro. This project has worked to characterize the processes involved in these changes by
knocking out individual NEU enzymes using CRISPR-Cas9. We used leukocytes and endothe-
lial cells (Jurkat and HEK), which are sensitive to changes in NEU activity. Cultured cells
were transfected with lentiviral CRISPR vectors. Knockouts were achieved through the cre-
ation of indels in NEU genes through errors in the repair of DNA using non-homologous end
joining repair systems as a result of CRISPR-Cas9 cleavage. Cell colonies were screened using
PCR amplification and T7 endonuclease mismatch assay. Following screening, mutations were
confirmed using sanger sequencing. These Knockout cell lines will help to further explore the
specific biochemical changes for which NEU enzymes are responsible and will enable future
work to investigate applications of these results in inflammation and other diseases

A Comprehensive Fatty Acid Profiling of

Skincare Oils by GC×GC
Kavitha Elisha Chemistry
45
Co-authors: Nathaniel McCallum, Michael D.S. Armstrong, Trevor A. Johnson, A. Paulina de la
Mata, James J. Harynuk

Abstract: Plant-based oils have many uses including manufacturing soap and detergent, foods,
nutritional supplements, and in the formulation of skincare and cosmetic products. Plant-
based oils in skincare products have grown in popularity in recent times for therapeutic benefits
treating acne, improving skin dryness and anti-aging effects. Current research suggests that the
fatty acid composition and concentration of these skincare oils play a role in their effectiveness.
For example, linoleic acid helps provide moisture to the skin while alpha-lipoic acid purports
anti-aging properties. Three different plant oils (rosehip seed oil, sea buckthorn oil, and jojoba
oil) from five different brands were analyzed for their fatty acid composition. In order to
characterize the fatty acid composition of these oils, the fatty acids were derivatized to fatty
acid methyl esters (FAMEs). Samples of derivatized oils were then introduced to a GC×GC-
TOFMS for separation and identification. Peaks in the oil chromatograms were positively
identified by comparison to an authentic FAME standard mix. The FAME profile obtained is
useful for selecting plant oils that contain the desirable fatty acid composition for skin repair
and potentially improve the cosmeceutical formulation of skincare oils.

Analysis of Plant Volatiles in Vivo using

GC×GC-TOFMS
Ewenet Mesfin Chemistry
46
Co-authors: S.A. Schmidt; A. P. de la Mata; J.J. Harynuk

Abstract: Volatile organic compounds (VOCs) are one of the most important groups of metabo-
lites produced by plants. Plant VOCs belong to various chemical classes and they are spon-
taneously emitted. Plant VOCs are involved in plant communication to, for example, attract
beneficial insects, or repel pests. They are also key constituents of the flavours and aromas
of plants. Given the importance of plant VOCs, there is great interest in their study. These
compounds are generally analyzed by gas chromatography (GC) coupled to mass spectrometry
 23

(MS). VOCs are often sampled by solid-phase microextraction (SPME) or active sampling onto
a sorbent trap. Previous work in our laboratory relied on using SPME to sample plant VOCs
coupled to comprehensive two-dimensional gas chromatography (GC×GC) with time-of-flight
mass spectrometry (TOFMS). SPME has difficulties trapping highly volatile analytes and can
also impart some selectivity to the analysis due to the fibre chemistry.1 In this study, we op-
timized a method for in vivo sampling of different types of plants using a headspace system
and active sampling onto sorbent tubes. These tubes were then thermally desorbed into the
GC×GC-TOFMS for analysis. The key purpose of this study is to be able to identify different
volatile organic compounds (metabolomic profile) that are present in various species of plant.
In this research, four types of different plants were sampled; mint (Mojito sp.), one blueberry
(Patriot Spec) plant, and two different varieties of tomato (little Napoli and sugar rush sp.).

Chemometric Analysis of the Fatty Acids

beyond C18:1∆9 and C18:2∆9,12 in Skin Care
Oils using GC× GC-TOFMS/FID
Nathaniel McCallum Chemistry
47
Co-authors: Kavitha Elisha, Michael Armstrong, Trevor Johnson, A. Paulina de la Mata, James
Harynuk

Abstract: Skin care oil (SCO) use has grown in popularity due to its ability to alleviate dry-
ness, treat acne, and help maintain the skin’s moisture barrier. A main contributor is the fatty
acid (FA) make-up of the SCOs, as they are essential contributors to the health of the skin.
Current research hypothesizes that a SCO’s effectiveness could be related to the SCO’s linoleic-
to-oleic acid ratio (C18:2∆ 9,12 to C18:1∆ 9), but this relationship is not well understood. We
were instead interested in exploring the variation arising from the fatty acids in lower abun-
dance to give potential reason for an SCO’s effectiveness compared to the others. This was
explored using comprehensive two-dimensional gas chromatography time of flight mass spec-
trometry/flame ionization detection (GC×GC-TOFMS/FID), which is advantageous due to its
low detection limits and superior resolution power. Samples from five commercial suppliers
of each ofSimmondsia chinensis (Link) C.K. (Jojoba), Hippophae rhamnoides L. (Sea Buck-
thorn), and Rosa canina L. (Rosehip) oil were collected. We obtained comprehensive profiling
of these samples by GC×GC-TOFMS/FID that allowed for less abundant relevant features to
be identified that differentiate one SCO type from another. The chemical differences in the
types of SCOs were explored by PCA.
 24

Rapid, Sensitive and Robust Determination of

Sweeteners Acesulfame and Sucralose in
Wastewater for Surveillance
Minh Chau Chemistry
48
Co-authors: Caley Craven, Kristin Carroll, Nicholas Wawryk, and Xing-Fang Li
Abstract: Wastewater based surveillance (WBS) is a powerful tool for monitoring SARS-CoV-2
infections in the community, complementing clinical testing. The viruses are shed in the feces
flowing into sewer systems. A number of factors including temperature, flow rate, and dilution
by other water sources going to the sewer systems can cause large variation in the viral loads in
wastewater samples. Normalization is required for the estimate of community infections. How-
ever, it is difficult to normalize SARS-CoV-2 measurements. Artificial sweeteners acesulfame
(ACE) and sucralose (SUC) are widely used and completely excreted to urine and faeces, and
they are stable in the wastewater. Therefore, we propose to use the sweeteners as the markers
for WBS normalization. To achieve this, we developed a simple, rapid and sensitive HPLC-
MS/MS method for determination of ACE and SUC in wastewater. Our method provides limits
of quantification (LOQ) of 0.1 ug/L for ACE and 5.0 ug/L for SUC. The total runtime is 6
minutes. We have successfully analyzed 350 wastewater samples and demonstrated this method
is reliable, efficient, and robust analysis. This method is useful for future WBS applications.

Solvent Selection for Extraction of

Environmental Solid Samples for Subsequent
Analysis by GC×GC-TOFMS
Dylan Long Chemistry
49
Co-authors: M.S. Armstrong, T. A. Johnson, A.P. de la Mata, and J.J. Harynuk
Abstract: Petroleum hydrocarbon contamination of soils is common and arises due to spills,
leaks, and emissions during the production, processing, transport, and use of petroleum. Ef-
fective methods for the detailed characterization of contamination are critical for accurate as-
sessment of contamination and the efficacy of remediation efforts. Tools for profiling petroleum
in solid samples can also be useful for characterizing petroleum deposits. Thermal desorption
(TD) can be used as an extraction/sample introduction technique for the characterization of
volatile and semi-volatile compounds in soils and sediments. The extracts are then analyzed
by gas chromatography (GC) or two-dimensional gas chromatography (GC×GC) coupled with
mass spectrometry (MS). TD extraction provides a nearly exhaustive extraction of a sample’s
volatile components; however, this extraction method has a large up-front cost which may pre-
vent many from utilizing it. Using shale as a reference sample, the goal of the study was to
develop a comprehensive solvent extraction method that approaches the efficacy of TD and
allows for a more widely available, cheaper extraction.
Samples and extracts were injected into a GC×GC-TOFMS by either TD or liquid injection.
After collection of the data, the abundances of five different classes of petroleum hydrocarbons
was examined using ions based on the ASTM E1412-19 method for characterization of ignitable
liquid residues. These ion traces were used to compare the efficacy of each solvent system to TD
using multivariate statistical tools. Seven different solvents were tested: hexane, methyl tert-
butyl ether, toluene, ethyl acetate, dichloromethane, hexane/acetone (50:50 v:v) and t-butyl
alcohol/acetone (50:50 v:v).
 25

Hybrid Electrolyte for Optimizing Mechanical

Strength and Ion Conductivity
Kay Lin Chemistry
59
Co-authors: Jiwei He; Jesli Tadina; Fuwei Wen; Andy Cao; Lingzi Sang

Abstract: Hybrid electrolytes are emerging as a promising candidate to integrate high ionic
conductivity, optimal mechanical flexibility, great interfacial performance, and wide electro-
chemical stability window for all solid-state lithium batteries (ASSLB). A halide-type solid
electrolyte, Li3InCl6, was reported with a great Li+ conductivity of 2.04 · 10–3 Scm−1 at 25°C
and relatively good air stability. However, it suffers from poor mechanical strength as the
pellet for Li3InCl6 electrolyte shatter easily during preparations. On top of the high ionic
conductivity of Li3InCl6, the addition of polymer matrix can bring in higher flexibility and
mechanical reinforcement to a hybrid electrolyte system. The efforts by Zhang and co-workers
were performed PVDF-HFP as a matrix for Li7La3Zr2O12 solid electrolyte. The resulting
thin films showed a high Li+ conductivity of 1.1 · 10–4 Scm–1 at room temperature with good
mechanical strength. Previous efforts in our group revealed that Li3InCl6 can be strengthened
by mechano-mixing with polyvinylidene fluoride (PVDF) powder. Other polymer candidates
such as poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-HFP), cellulose, polyethylene
oxide (PEO), and poly(methyl methacrylate) (PMMA) were also investigated for mechano-
mixing with Li3InCl6. Our current progress on hybrid electrolyte focuses on fabricating thin
films with industrial-scalable procedure. A prototype of the hybrid film is composed of polymer
matrix and Li3InCl6 with well-tailored composition. Electrochemical characterizations such as
cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) for the film were
conducted. A preliminary result of our hybrid film prototype showed a good ionic conductivity
of 2.95 · 10–4 as well as mechanical robustness. The electrochemical investigation of Li+ mi-
gration within the hybrid electrolyte and the morphology characterization are currently under
investigation.

Effects of dynamical disorder on the storage

efficiency of an excitonic quantum battery
Jalal Tarabishi Chemistry
60
Co-authors: Gabriel Hanna; Zohreh Khodadad

Abstract: In recent years, there has been a great deal of theoretical work on developing ar-
chitectures for quantum batteries (QBs) - quantum systems that store and discharge energy
to power nanoscale devices. One of the main obstacles in developing an effective QB is the
leakage of energy from the QB to its environment. Recently, the Hanna group demonstrated
the possibility of storing excitation energy (or exciton) with 100% efficiency in a fixed network
of atoms coupled to two thermal environments. This was achieved by storing the exciton in the
“dark state” of a network possessing structural exchange symmetries, which effectively decou-
ples the QB from its environments. At finite temperatures, however, the network undergoes
fluctuations that may disrupt its symmetries and thereby reduce the QB’s storage efficiency.
Therefore, in this work, we introduce different types and magnitudes of dynamical disorder into
the QB model, and gauge to what extent the storage efficiency is affected.
 26

ProAlanase as a Complement to Trypsin for

Protein Sequencing by Mass
Spectrometry-based Proteomics
Jonathan Walter Chemistry
61
Co-authors: Yasmine Rais; Andrei Drabovich

Abstract: While trypsin is the most commonly used protease for digestion of proteins for study
in mass spectrometry-based proteomics, some of the resulting peptides are not able to be
detected. Alternative proteases to complement trypsin digestion are needed for complete se-
quencing of the human proteome. Of particular note are proteins with a high proline content or
few arginine or lysine residues available for trypsin digestion, such as histone proteins. Another
application is sequencing of the variable regions of antibodies, which could facilitate charac-
terization and development of novel monoclonal antibody therapies. ProAlanase, a protease
that cleaves proteins at the C-terminal to proline and alanine, has been shown to be useful for
specific proteomic applications such as locating disulfide bonds in monoclonal antibodies and
sequencing histone proteins. To evaluate the potential of ProAlanase for protein sequencing, we
performed shotgun analysis with nano-liquid chromatography followed by tandem mass spec-
trometry to compare the performance of ProAlanase to trypsin in digestion of bovine serum
albumin, LNCaP prostate adenocarcinoma cell line, and human immunoglobulin G (IgG) puri-
fied from serum. The number of successfully identified proteins and peptides were evaluated by
MaxQuant and revealed that ProAlanase generated high quality peptides that may have the
potential to complement trypsin in proteomic analysis.

The Silicon Nanoparticle Puzzle: Piecing

Together the Anomalous High-Temperature
Thermal Behaviour of Hydrogen Silsesquioxane
Abbie Rubletz Chemistry
62
Co-authors: Abbie T. Rubletz; Kevin M. O’Connor; Jonathan G. C. Veinot

Abstract: Silicon nanoparticles (SiNPs) have long been of interest due to their size dependent
optical and electronic properties. A common method of producing SiNPs for these applications
involves the thermally induced disproportionation of hydrogen silsesquioxane (HSQ; HSiO3/2).
This process yields nanocrystalline domains of elemental silicon within an SiO2-like matrix,
which can then be liberated for further functionalization upon exposure to HF. Previous work
by the Veinot group has suggested that particle evolution occurs through a continuous, bottom-
up mechanism with larger SiNPs attained by increasing processing temperatures and/or dwell
times. However, recent attempts to produce big (d > 75 nm) nanoparticles have uncovered
a high-temperature anomaly where this previously established explanation fails. Composites
processed between 1500-1600℃ experience significant losses of both elemental silicon content
and overall sample mass, but predicted trends re-emerge at 1700℃. These unusual results align
with a number of phase changes within the composite, including the crystallization and eventual
softening of the silica matrix, and melting of the silicon domains within it [SiO2 crystallization
point: ca. 1470 ℃, melting point: ca. 1710 ℃; Si melting point: ca. 1414 ℃]. Further, these
occur alongside the consumption of any SiNPs through the silicon-assisted reduction of SiO2
 27

to SiO. Our ongoing research efforts involve further investigating and quantifying the nature
of the interaction between the SiNPs and their matrix to explain the behavior of HSQ at high
temperatures. This will provide the basis for a modified mechanism for SiNP evolution.

Investigating the Stability and Tolerance of

Diazaborines to Common Reactions Used in
Medicinal
Warren Wong Chemistry
63
Co-authors: Jake J. Blackner, Dennis G. Hall*

Abstract: The importance of organic heterocycles is evident given the frequency in which nature
incorporates them into complex molecular architectures. Heterocycle-containing natural prod-
ucts inspire drug design, acting as a synthetic starting point for biologically relevant molecules.
For instance, 59% of unique small-molecule drugs contain a nitrogen heterocycle, while oxygen-
heterocycles are present in 27% of U.S. FDA-approved drugs. Even with the ubiquity of hetero-
cyclic compounds, there are still many unaddressed challenges concerning medicine and human
health. In this regard, boron-containing heterocycles have gained significant attention, with
Vaborbactam recognized as an essential medicine by the World Health Organization. Despite
the success of boranol (B-OH) containing species, they remain predominantly underexplored.
Phenols and their derivatives are aromatic moieties widely present in natural products
such as resveratrol and tyrosine and are core components for numerous pharmaceuticals, dyes,
and fragrances. Therefore, the design of phenol isosteres may provide access to molecular
species with unique and desirable properties and biological activity. Herein, we report efficient
synthetic access to diazaborines, a novel class of boron-heterocycles and an unexplored phenolic
isostere. In order to investigate the stability and general synthetic utility of the novel borocyclic
species, the prepared compounds were subjected to various transition metal-catalyzed reaction
conditions and other frequent transformations employed in the pharmaceutical industry. This
is important due to the known reactivity of C-B bonds, emphasized in the Nobel prize-winning
Suzuki-Miyaura cross-coupling. Tolerance to common reactions used in medicinal chemistry
can expand chemical diversity for developing novel drug chemotypes with improved physical
and biological properties.

Urine 3 Ways: Comparing Urine Metabolomics

Sampling using Derivatization, Dynamic
Headspace, and Solid-Phase Microextraction
Dosoftei Sebastian Chemistry
64
Co-authors: Ryland T. Giebelhaus, A. Paulina de la Mata, James J. Harynuk

Abstract: Through the analysis of metabolites in biological systems, metabolomics offers insight
into the mechanisms of diseases, aiding in developing diagnostic tools and treatment strate-
gies. Urine is often utilized in metabolomics due to its rich metabolite content and stability.
Gas chromatography-mass spectrometry (GC-MS) is used for metabolomics due to its ability
to detect hundreds of volatile metabolites at low concentrations in a single analysis. Two-
dimensional GC time-of-flight MS (GC×GC-TOFMS) is increasingly used for metabolomics
 28

as the additional dimension of separation provides improved sensitivity, resolution, and selec-
tivity. Urinary metabolomics typically employs derivatization, where metabolites of interest
are chemically modified, increasing their volatility for GC analysis. Derivatization introduces
errors through the loss of volatile metabolites. Dynamic headspace (DHS) and solid-phase mi-
croextraction (SPME) are two techniques which permit the detection of volatile metabolites
without derivatization. In both, the sample is placed in a vial and heated. To sorb volatiles in
DHS, the sample headspace is purged with inert gas, transporting the headspace to a sorbent
bed; in SPME, a sorbent coated fibre is exposed to the headspace. To desorb volatiles into the
GC in DHS, the sorbent is heated; in SPME, the fibre is exposed to the heated inlet.
DHS is exhaustive as volatiles in the sample are continuously partitioned into the headspace,
purged, and collected on the sorbent, whereas SPME is not as it relies on the equilibrium be-
tween the volatiles and the fibre to trap metabolites, and only a fraction of the analytes are ex-
tracted. We present a comparison of SPME, DHS, and derivatization-based urine metabolomics
workflows. Derivatization revealed the most metabolites; SPME and DHS complement deriva-
tization by permitting the detection of various volatile metabolites. Together, these method-
ologies provide nearly complete global coverage of the urine metabolome, which will contribute
to future urinary metabolomics studies, and thereby new screening assays and therapeutics.

Octahedral Tilting and Spin-Orbit Coupling in

A2SnX6 (A+= K, Rb; X= Cl, Br, I)
Materials- a Solid-State NMR and Quantum
Chemical Investigation
Brayden Glockzin Chemistry
65
Co-authors: Abhoy Karmakar, Meagan Oakley, Aaron Mitchell, Mariusz Klobukowski, Arkadii
Pominov, and Vladimir K. Michaelis*

Abstract: Perovskites have both interesting structural characteristics and strong potential for
applications in devices such as solar cells and light-emitting diodes. While not true perovskites,
A2SnX6 (A+= K, Rb; X= Cl, Br, or I) materials are relatives of traditional ABX3 perovskites
that commonly adopt the K2PtCl6 structure type. To date, A2SnX6 materials have been
studied extensively using diffraction techniques, and a handful Nuclear Quadrupole Resonance
(NQR) studies have also been undertaken. However, the local structure of the A- and B-sites
has remained relatively unexplored. Herein, we use solid-state Nuclear Magnetic Resonance
(NMR) spectroscopy to explore the influence of Group 1 (alkali) and Group 17 (halide) substi-
tutions on the local chemical environments of the A- and B-sites in A2SnX6 materials. NMR
experiments on the two challenging quadrupolar nuclei 39K and 87Rb reveal the presence of size-
able quadrupolar coupling constants (CQs) and considerable chemical shift anisotropy (CSA)
for these nuclei in the monoclinic K2SnBr6 and tetragonal Rb2SnI6. High and ultra-high field
analysis also enables successful resolution of the relative orientations between the EFG and CSA
tensors for 39K and 87Rb in these non-cubic systems. We also explore the B-site polyhedral
environment throughout the compositional range via 119Sn NMR spectroscopy, demonstrating
that the 119Sn chemical shift follows a normal halide dependence (NHD). Analysis of quantum
chemical computations at the triple-Zeta/ZORA level of theory show that the NHD is driven
almost entirely by spin-orbit effects. We also reinforce the necessity of proper relativistic treat-
ment of heavy-atom containing systems by demonstrating that a standard approach to NMR
computations at the scalar ZORA level in CASTEP yields inferior results.
 29

Combating heart disease: synthesis and

comparison of a small-molecule APJ receptor
agonist and metabolically stable
apelin-analogues
Anjalee Wijewardane Chemistry
66
Co-authors: Bethan Donnelly, Kleinberg Fernandez, Gavin Oudit, John Vederas

Abstract: In Canada, heart disease is the 2nd leading cause of death and the primary cause of
hospitalization. The Apelin peptide-APJ receptor system has been identified to play an impor-
tant role in cardiovascular homeostasis by protection against myocardial ischemic reperfusion
injury. However, native apelin peptides have limited use as pharmacological tools against car-
diovascular diseases as they have short half-lives. The Vederas group has synthesized an active
apelin analog, Cbz-PEG6, that is resistant to serum proteases with a half-life of 18 h in hu-
man blood. Another clinical candidate is an orally bioavailable small-molecule APJ receptor
agonist, BMS-986224 discovered by Bristol Myers Squibb. To study and compare the cardio-
physiological effects of both candidates, the small-molecule APJ receptor agonist needs to be
synthesized.
The purpose of this project is two-fold: firstly, to synthesize the small-molecule APJ recep-
tor agonist and secondly to perform biological assays that provide a side-by-side comparison of
the pharmacological and cardio-physiological effects of the drugs. Thus far, we have successfully
synthesized the biaryl pyridinone core and the pyridyl side chain of BMS-986224 using chemical
synthesis methods. The construction of the pyridinone core involved ortho-metallation, alkyla-
tion, condensation, amination, and intramolecular cyclization reactions. The pyridyl side chain
relied on a nucleophilic aromatic substitution followed by decarboxylation. The intermediates
of the small molecule were characterized using HR-MS (high-resolution mass spectrometry)
and 13C and 1H NMR (nuclear magnetic resonance) spectroscopy. High purity was achieved
using column chromatography with yields comparable to published data. Upon the completion
of synthesizing the agonist BMS-986224, biological assays will be conducted to evaluate and
compare the pharmacological effects of the apelin-analogue and the BMS small-molecule with
our collaborator in UA Cardiology, Dr Gavin Oudit.

Chelating Frustrated Lewis Pair Ligands and

Their Ability to Form and Stabilize Adducts
with Different Main Group Group 14 and 15
Elements
Hannah Dokken Chemistry
67
Co-authors: Brandon Frenette, Eric Rivard

Abstract: Frustrated Lewis pairs (FLPs) are a combination of a Lewis acid and a Lewis base,
in which the classical Lewis acid-base interaction is prevented by steric or electronic controls
(2006, Welch, Stephan et al), (2015, Stephan, Erker). FLPs open new pathways for main-group
compounds to bind and activate small molecules. The Rivard group recently showed that the
phosphinoborane FLP ligand, PB [ iPr2 P(C6 H4 )BCy2 (Cy=cyclohexyl)], forms complexes with
group 14 elements (Si, Ge) that, upon mild heating, deposit thin films of silicon or germanium
 30

and regenerate PB (2021, Omaña, Rivard et al). The Rivard group has also shown that the PB
ligandforms adducts with nitrogen, allowing access to a stable complex of the parent nitrene,
NH (2021, Frenette, Rivard et al). This research focuses on extending this FLP chemistry
towards the heavier group 15 elements P and Bi, while also probing the reactivity of alternative
FLP ligands. We show how the in situ reduction of phosphorus(III) precursors in the presence
of PB is a viable path to stable phosphorus(I) complexes. We also showcase a novel FLP ligand,
PBFl [ iPr2 P(C13 H8 )BCy2 ] which features a smaller bite angle than PB (4-membered chelate vs.
5-membered) and its preliminary reactivity toward group 14 and group 15 elements. This work
will lead to new precursors for low-valent group 14 and 15 elements for a variety of synthetic
and materials applications.

Chemometrics with AWS

Wenwen Li Chemistry
68
Co-authors: W.Li, M.S. Armstrong1, A.P. de la Mata1, and J.J. Harynuk1

Abstract: Instrumental output provides an abundance of chemical information, but properly

interpreting these data requires computationally expensive statistical and machine learning
tools. Our research has focused on extracting features from raw Gas Chromatography - Mass
Spectrometry (GC-MS) signals using PARAFAC2, and extracting the resultant features using
a wrapper function called Feature Selection by Cluster Resolution (FSCR). We are sharing
how to build, deploy, and manage computationally expensive chemometric pipelines, on web
applications using the popular cloud computing platform Amazon Web Service (AWS).
PARAFAC2 relaxes some of the assumptions of a standard PARAFAC model, such that
chromatographic drift between multiple samples is accounted for. In essence, chemical infor-
mation that is indexed differently across the retention modes within a 3rd-order tensor can be
identified and quantified without a separate alignment step. A drawback of this technique is
that it is slow, making cross-validation for component number estimation largely impractical.
Splitting each training and validation subset onto multiple instances on AWS can be used to
help this problem.
PyCR (Cluster Resolution in Python) is an advanced implementation of the FSCR algorithm
built on AWS. Like FSCR, PyCR is a variable selection algorithm that examines the effect of
each variable in a dataset within the context of highly-ranked variables by measuring the
maximum confidence interval over which two or more clusters are separable within principal
component space. This measurement is defined as cluster resolution (ξ for binary class problems,
or Ξ for 3 or more classes). As a wrapper function, multiple redundant iterations are required,
which can make it impractical for local deployment. Using AWS to run the function online can
be used to mitigate this issue.
 31

Electrochemical Synthesis of Lignin Derived

Carbon Quantum Dots Under Mild Conditions
Mia Dolanjski Chemistry
69
Co-authors: Jeffrey M. Stryker, Robin J. Hamilton

Abstract: Carbon quantum dots (CQD) are a relatively new form of nanocarbon materials gain-
ing plenty of interest due to their abundance and fascinating fluorescence properties. CQDs
can be fabricated using either bottom-up or top-down approaches. One of the most com-
mon approaches to CQD syntheses is the bottom-up, hydrothermal method. Unfortunately,
the hydrothermal method uses strong acids, often boiling sulfuric, and thus possesses multiple
health, safety, and environmental hazards. We designed a bottom-up electrochemical synthe-
sis of CQDs from waste material, which is safer, greener, and a more sustainable bottom-up
alternative.
Lignin, a highly complex aromatic organic polymer, is regarded as waste material in the
paper and pulp industry. As such, it exhibits minimal purpose in the production of paper. We
found that CQDs can be made from lignin under oxidative electrochemical conditions using
common electrodes, electrolytes, and solvents. Further, amine additives and pH have profound
effect on the photoluminescent (PL) properties of the CQDs, affording various colours. These
new CQDs are easily scalable and have the potential for various bio-medical and environmental
applications.

Properties and Applications of DNA

functionalized Nanoparticles
Boris Stevanovic Chemistry
70
Co-authors: Boris Stevanovic; Nahida Akter; Cole Butler; I Teng Cheong; Julianne Gibbs; Jonathan
Veinot

Abstract: Nanoparticles are an emerging field of research that is generating a lot of excitement
due to the tunable properties of nano based materials. Often formed from group 14 elements or
transition metals, Nanoparticles can have many different shapes such as spheres, wires, sheets
and more. Furthermore, based on the size and shape, Nanoparticles can have varying optical
and conductive properties. All this variability allows for many potential applications in fields of
electronics, medicine and more. Lastly, the surface of these Nanoparticles can be functionalized
with different chemical groups such as alkyl chains or with structures such as DNA. Due to its
basic binding properties, based on the hydrogen bonding between the bases: A, T, C, G, DNA
has emerged as a method to assemble nanoparticles allowing for control over the position and
movement of the nanoparticles. By binding and unbinding DNA bound Nanoparticles, they
are able to be moved in and out of solution; this has promising applications in sensing devices
as the change of color could indicate the presence of a specific strand of DNA, (i.e viral DNA).
This poster shows many of the properties that DNA functionalized nanoparticles, specifically
those of Gold and Silicon, exhibit and the processes used to attach DNA onto Nanoparticles.
 32

Developing an Efficient Magnetic Beads-Based

Automated Miniprep Protocol for pCDNA and
pBAD Plasmids
Eric Fan-Lou Chemistry
71
Co-authors: Shuce Zhang, Robert Campbell

Abstract: Plasmid purification (“miniprep” for small scale) is an essential molecular biology
procedure for many downstream applications, such as cloning and transfection. Although
miniprep has been commercialized and widely used for decades, the complex nature of the E.
coli lysate typically necessitates multiple manually performed steps using the traditional silica-
membrane spin columns. This study aims to establish a robust automated protocol for plasmid
miniprep using magnetic beads-based commercial kits with a KingFisherTM instrument. We
first programmed a standardized procedure for the KingFisherTM Duo Prime instrument to
minimize manual intervention. Using this program, we systematically evaluated two commer-
cially available magnetic bead-based miniprep kits with both high-yield and low-yield plasmids.
The concentration, purity, and DNA conformation of the eluate were measured to evaluate the
performance. We show that automated miniprep using magnetic beads-based kits can perform
as comparably and robustly as the traditionally column-based method while substantially re-
ducing manual handling time. Automated plasmid miniprep provides a promising solution to
high throughput library screening in protein engineering.

Synthesis of Glycosylated Macrocycle Peptides

by the Knorr-Pyrazole Reaction
Linda Tran Chemistry
72
Co-authors: Arunika Ekanayake, Michael Downey, Ryan Qiu, Danial Yazdan and Ratmir Derda

Abstract: Peptide-derived therapeutics (PDTs) have the ability to target diseases such as can-
cer. Compared to small molecule therapeutics, PDTs have the ability to target traditionally
“undruggable” proteins. Traditional antibody therapeutics are significantly larger resulting in
decreased bio-distribution inside tumours and other non-vascularized tissues. Functionalization
of PDTs using glycans and other natural products, such as biotin, are methods of enhancing
binding affinity and target specificity. Current methods used to access this class of molecules
require the use of protecting groups and toxic environmentally damaging organic solvents. We
aim to develop green, water-based synthesis platforms for glycosylated peptide macrocycles.
Successful pathways will provide a foundation for chemically grafting glycans onto genetically
encoded phage-displayed libraries. These chemically modified libraries incorporate billion-scale
diversity in one chemical step that can be screened in parallel to yield drug candidates. This
poster will discuss our progress toward streamlined synthetic methodology based on unpro-
tected peptide and sugar building blocks in water by the Knorr-pyrazole reaction to provide
glycosylated macrocycles.
 33

Biological Sciences
Broad spectrum therapeutics targeting -1PRF
activity against corona-viruses
Sandaru Ileperuma Biological Sciences
2
Co-authors: Krishna Neupane- Research associate and Micheal Woodside- Principle investigator

Abstract: Coronaviruses employ Programmed Ribosomal Frameshifting (PRF) to encode two

different protein products that are crucial to the virus’s replication cycle. Due to its importance,
this activity remains relatively conserved through different strains of the virus. Preventing this
translational event from occurring can potentially help halt the virus’s replication cycle. My
work primarily focuses on screening potential drugs that have been computationally discovered
that inhibit -1PRF activity, using a cell-free dual luciferase assay against various coronaviral
frameshifting elements.

Severity of Rickets and Surgical Intervention in

Children with X-linked hypophosphatemia
Irene Chen Biological Sciences
4
Co-authors: Chelsey Grimbly

Abstract: Phosphate is a mineral that is crucial for bone development and strength. X-linked
hypophosphatemia (XLH) is a rare condition where the kidneys deposit phosphate. XLH
often leads to rickets, which causes bone deformities and slowed childhood growth. The bone
deformities may be severe enough that children need surgery. In this project, we aim to explore
associations between the severity of rickets in children with XLH and a greater need for surgery.
We will do this by collecting data on children with XLH who did and didn’t require surgery.
We will then evaluate if the children that needed surgery had blood work that showed more
bone problems, including more renal phosphate depletion, increased alkaline phosphatase, worse
signs of rickets, slower growth, and the need for more medication. In doing this, we expect to
have a better understanding of why certain children with XLH need surgery so we can possibly
manage their condition differently and determine risk factors for surgical intervention.
 34

Fool me twice: Personality-related recapture

bias in black-capped chickadees (Poecile
atricapillus)
Megan Froese Biological Sciences
6
Co-authors: Kimberley Mathot

Abstract: Within populations, individuals exhibit repeatable differences in behaviour, known

as animal personality. These among-individual differences in behaviour can have ecological
and evolutionary consequences, such as (re-)capture bias, where individuals with certain be-
havioural types have a greater probability of being captured and/or recaptured for study. Po-
tential personality-related (re-)capture bias is important to assess, as it can lead to biased
population-level inferences. Using a sample of previously captured black-capped chickadees
(Poecile atricapillus), we explored whether recapture probability is affected by sex and five
behavioural traits. We found no evidence that recapture probability varied as a function of
exploration, handling aggression or sampling behaviour. However, we found some support for
an effect of sex, with males being less likely to be recaptured compared to females. Further,
there was moderate support for an effect of both feeding rate and latency to resume feeding
after predation risk exposure. We also found that individuals with higher feeding rates and
individuals with shorter feeding latencies had a greater tendency to be recaptured. Consistent
with findings from a range of taxa, this may indicate that individuals with higher energetic
needs, demonstrated by greater foraging activity in both benign and high perceived predation
risk contexts, have greater opportunity to be recaptured. Given that among-individual differ-
ences in energy requirements are ubiquitous and have been shown to co-vary with a range of
traits, we suggest that such re-capture biases may be the norm rather than the exception and
propose solutions to mitigate the extent of foraging-related recapture bias.

Evaluating the Antimicrobial Activity of

Nanocrystalline Silver Dressings
Payton LeBlanc Biological Sciences 8
Co-authors: Robert Burrell

Abstract: Antimicrobial resistance (AMR) is an ongoing global crisis in which antibiotics are
becoming ineffective and novel technologies are urgently required to treat antibiotic resistant
infections. Nanocrystalline silver dressings present an exciting opportunity to fight AMR as
studies have shown they target antibiotic resistant bacteria as well as provide anti-inflammatory
properties in wound healing. This study will determine the bactericidal activity of commer-
cially available and lab synthesized nanocrystalline silver dressings. Methods to identify the
effectiveness of each dressing will include log reduction and silver analyses assays. Log reduc-
tions will determine the number of bacteria killed while the silver analyses will establish the
specific silver species released into solution, which will determine the mechanism by which the
dressings are antimicrobial. Overall, nanocrystalline silver dressings are an innovative approach
to treating microbial infections, though further research is required to determine how they can
be solutions for site specific treatment of infections (e.g. bladder infections).
 35

G-Quadruplex’s–A novel therapy for targeting

the chronic from of Hepatitis B Virus
Emmanuelle Kasinyabo Biological Sciences
10
Co-authors: Vanessa Meier-Stephenson

Abstract: Hepatitis B virus (HBV) chronically infects about 300 million people worldwide.
Covalently closed circular DNA (cccDNA) is the chronic form of HBV that persists in the
nucleus of infected cells and is not targeted by current therapies. Recently a unique target,
a G4-quadruplex (GQ) was found in a key promoter region in this chronic form and may be
a novel approach to blocking HBV replication at its root. GQs are guanine rich secondary
structures that are associated with nucleic acids such as DNA and RNA. GQs may play a role
in biological processes such as transcription, translation, and DNA replication. In this study, we
want to know if known GQ-binders TMPyP4 and BRACO19 can also bind and impact HBV’s
replication. A cell culture model was employed where cells are infected and then treated with
different concentrations of GQ-binding agents, as well as a known HBV therapy, tenofovir, as a
control. After harvesting the samples, the amount of viral DNA, RNA and protein produced in
each scenario were studied to determine the effects of the therapy. Methods such as quantitative
polymerase chain reaction (qPCR) and enzyme-linked immunosorbent assay (ELISA) were used
to determine the amounts of nucleic acids or proteins, respectively, present in the samples.
Using GQ-binders to block GQs was expected to decrease the amount of the viral nucleic acids
and protein production. While the results for the protein measurements were inconclusive,
the qPCR results suggested that quantities of viral nucleic acids had been reduced in both
TMPyP4 and BRACO19 treated infected cells thus, TMPyP4 and BRACO19 may have the
ability to terminate HBV replication. This work will provide some of the initial studies to
support targeting this G4Q in HBV and may show promise in itself, or for future prospects
towards advancements in creating better binders.

The Effect of Alpha-B Crystallin on Peripheral

Nerve Regeneration
Paige Hardy Biological Sciences
12
Co-authors: Christine Webber

Abstract: AlphaB Crystallin (ABC) is a small heat shock protein that is found in neurons
and supporting cells in the peripheral nervous system. ABC has been suggested to impact
peripheral nerve regeneration through immunomodulation and remyelination after injury. In
our study, we aimed to determine if ABC had an impact on the extent of axon regeneration
in peripheral nerves. Using a knockout ABC mouse model, we applied a crush lesion to the
sciatic nerve to allow degeneration to occur. After 10 days, a 5mm graft of the sciatic nerve
distal to the crush site was transected into the sciatic nerve of either a ABC knockout or
wildtype mouse. This process was repeated for wildtype (WT) mice. These surgeries resulted
in 4 graft conditions: WT grafts coapted into WT mice (WTWTWT), WT grafts coapted
into ABC mice (ABCWTABC), ABC grafts coapted into WT mice (WTABCWT) and ABC
grafts coapted into ABC mice (ABCABCABC). 7 days after transection, the second cohort
of mice was euthanized and their sciatic nerve was harvested. Nerve tissue was fixed, frozen,
and sectioned, and immunohistochemistry was performed to visualize the regenerating axons.
 36

Analysis was performed under the microscope to determine axon count every 0.5mm, and to
determine length of regeneration for each condition. Statisitcal analysis revealed no significant
difference between conditions in axon count or axon length, suggesting that ABC does not play
a significant role in determining the extent of peripheral nerve regeneration after injury.

The Circadian Clock Regulates the

Transcription of the 26S Proteasome in
Arabidopsis thaliana
Dash Zhong Biological Sciences
14
Co-authors: Qiaomu Li, R. Glen Uhrig

Abstract: The 26S proteasome is a cytoprotective protein complex that prevents proteotoxicity
accumulation in cells [1]. The proteasome degrades misfolded or specific proteins and recycles
them into their constitutive amino acids. Through bioinformatic analyses of the promoter
region sequences, we identified transcription factor binding sites in the proteasome genes of
Arabidopsis thaliana. Transcription factors are regulatory proteins produced by genes of the
circadian clock, an internal regulatory oscillator that accounts for external changes during plant
growth and development[2][3]. We find that removing different circadian clock genes results
in varying levels of impairment to mutant growth when proteasome inhibition is applied. Our
results suggest that LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK
ASSOCIATED1 (CCA1) are the two major regulators that influence the expression of the
proteasome subunits. At the protein level, we also analyzed the changes in the abundance of
proteasome subunits in some circadian clock mutants. We reaffirmed our findings by comparing
them to the expression data of proteasome genes documented on Diurnal DB, a public database.

Development of anatomical and molecular 3D

models to enhance learning in university
classrooms
Dustin Doty Biological Sciences
15
Co-authors: Brian Chwyl, Kim Rans, Susan Fawcett, Paul LaPointe

Abstract: Spatial awareness and learning are large hurdles students face throughout their de-
gree. Whether visualizing chemical structures in chemistry or interpreting a patient’s MRI scan,
many students fail to sufficiently grasp these concepts. The immense volume of 3D structures
that students in the Bsc. Radiation Therapy program have to understand and interpret has
informed out project. To improve students spatial learning, we developed an augmented reality
(AR) smartphone application where MRI/CT scans are 3D modelled and can be summoned by
the student by scanning a 2D flashcard. The objects summoned can be viewed at all angles,
and upon bringing the phone closer to the object, a clipping plane is applied to allow visualiza-
tion of internal structures. The brain, heart, and abdomen have been modelled thus far, and
our current goal is to model disease progression in the context of cervical cancer. Models of
enzymes such as myoglobin and various molecules have also been created to expand outside of
 37

radiology. For further accessibility, we also have uploaded our models onto the web-based ap-
plication SketchFab. This website can create links that can be embedded in other websites like
eClass, allowing students to view these models at any time. In the web viewer, a user interface
allows for the toggling of text written by the instructor including links to outside resources.
We aim to create an object library that instructors can take from, and artists to upload to, and
a smartphone template that users can plug these models into to have customizable apps. Our
application will be rolled out in small cohorts of Bsc. Radiology students Fall 2022 to measure
its impact on learning.

Effect of Hydraulic Fracturing Wastewater on

Brain and Behaviour Development in Zebrafish
Kayla Lottin Biological Sciences
17
Co-authors: Connor Stewart, Tamzin Blewett, Zachary Hall

Abstract: Hydraulic fracturing is a method of oil and gas extraction from non-porous rock.
Flowback and produced water (FPW) is the wastewater generated by hydraulic fracturing and
is composed of fracturing fluid, oil, and formation-derived components. Spills during the col-
lection, transport, and storage of FPW from hydraulic fracturing sites poses a contamination
risk to nearby aquatic habitats. However, the effects of FPW on the developmental biology
of aquatic species is understudied. To address the gap in our understanding, I am testing the
effects of FPW on brain and behaviour development in a lab model for aquatic vertebrates, the
zebrafish. I exposed groups of zebrafish embryos to aquatic facility water, FPW, or saltwater
(FPW and saltwater concentrations ranged from 5%-35% in facility water). Embryos were
scored for lethal and non-lethal effects over a 96-hour exposure period to identify treatment
concentrations for subsequent brain and behaviour analysis. I will then expose groups of ze-
brafish embryos to identified FPW and saltwater treatment concentrations to sample the impact
of FPW on swimming after 96-hours. Following swim tracking, brains will be collected from
zebrafish and histologically processed labelling gross anatomy and cell proliferation to char-
acterize changes in brain growth associated with FPW exposure. I predict exposure to FPW
will reduce swim behaviour and decrease brain growth by impairing cell proliferation. Further
investigations will include chemical analysis of FPW, physiological measurements (spine curva-
ture and body length), use of additional immunostaining markers, and the interplay between
brain and behaviour.
 38

Characterization of patients with pulmonary

hypertension in Alberta
Stefan Iordache Biological Sciences
55
Co-authors: Rhea Varughese and Jason Weatherald

Abstract: My project analyzes Albertan pulmonary arterial hypertension (PAH) and chronic
thromboembolic pulmonary hypertension (CTEPH) patients while contributing to the Cana-
dian Pulmonary Hypertension Registry (CPHR). This study looks at consenting adult PAH
and CTEPH patients that are followed by the pulmonary hypertension (PH) clinics in Edmon-
ton and Calgary. Data is collected from electronic health records. Descriptive statistics and
survival analysis will be performed to understand this patient population. We expect to under-
stand the demographics of PAH and CTEPH patients in Alberta, what medications they use
for their lung disease, how many are referred for lung transplantation, and their mortality. We
anticipate that our results will be similar to Canadian and international data. This information
will be used to understand the needs of Albertan PH patients, leading to quality improvement
and future research.

Splicing Efficiency of Q24P, an insight into the

SF3b4 mutant function
Ishrat Meghla Biological Sciences
56
Co-authors: Andrew M. MacMillan, Ayat R Omar.

Abstract: The spliceosome is a large RNA-protein complex in eukaryotes responsible for excision
of introns from pre-mRNAs and ligation of exons to yield the mature mRNA. The splicing factor
SF3b4 is an essential U2 snRNP protein component that cross-links to the intron upstream to
the branch Adenosine.
Several SF3b4 mutations have been identified and the phenotypes among these mutants are
distinct. Clinically, one mutant named Q24P (Glutamine to Proline substitution at position 24)
is associated with a developmental disease called Nager syndrome. For this project, we used S.
cerevisiae as a model organism to study the effect of this particular mutant on SF3b4 function
and splicing efficiency (SE). Hsh49 protein, a human SF3b49/SAP49 homolog in S. cerevisiae,
is used for this purpose. We cultured both the Wild-Type (WT) and the Q24P Mutant-Type
(MuT) strains in a Yeast-extract Peptone Dextrose (YPD) rich medium and collected splicing
extracts and carried out splicing assays. We monitored the splicing efficiency for both phases
for the WT and MuT strains at certain time intervals and drafted splicing efficiency graphs.
We also performed PhosphorImaging of the splicing assays of pre-mRNA substrates grown in a
rich YPD medium. Analysis of the data revealed that there is no significant difference in the SE
for both the steps between the two strains. MuT behaved similarly to the WT when no stress
conditions were applied in an abundance of nutrients. This is a clear contrast to the minimal
media (MM) where the MuT exhibited enhanced splicing efficiency in both steps compared to
WT for both log and stationary phase. These findings explain the effects of Q24P with respect
to observed yeast growth defects. WT yeast repress splicing under starvation conditions which
down-regulates expression of Ribosomal Protein Genes (RPGs). This reduces translation and
nutrient consumption to conserve energy for cell survival. The strong splicing in MuT extracts
mimicking starvation (MM) leads to reduced viability under those conditions.
 39

Alternative Toxin Assembly in Salmonella

bongori
Antonio Chemello Biological Sciences
57
Co-authors: Casey Fowler

Abstract: Bacteria within the Salmonella genus can cause many diseases including gastroen-
teritis to typhoid fever. An important virulence factor of Salmonella enterica subspecies typhi
is a holotoxin, typhoid toxin. Typhoid toxin is an A2B5 toxin, composed of 2 distinct active
subunits and 5 identical binding subunits (pltB). However, the toxin not only assembles with
the binding subunit within the toxin islet, pltB, but also with an isolated and unrelated binding
subunit, pltC. Therefore typhoid toxin exists in two different subtypes that exhibit different
characteristics. S. bongori, a related species, contains the typhoid toxin and an unrelated B
subunit, pltD. It is hypothesized that the active subunits of typhoid toxin assemble with pltD
to form a unique typhoid toxin subtype.
The genetic expression of relevant genes will be determined via qPCR and western blotting
strains that have tagged proteins. Conditions tested will include those known to induce toxin
expression in S. typhi, like low concentrations of magnesium. Additionally, an important reg-
ulating system of the typhoid toxin in S. typhi, phoPQ, will be deleted in strains to determine
its role in regulating typhoidal genes and pltD in S. bongori. As well, protein purification via
nickel columns will be conducted on S. bongori strains with his-6 tagged active subunits under
inducing conditions. This will help determine what the active subunits are binding to.
Preliminary qPCR data and western blots analysis show that the typhoid toxin genes and
pltD are all expressed in low magnesium conditions. In contrast, pltD (or any typhoid toxin
genes) are not expressed when cells are treated with mitomycin C, an inducing condition for the
ancestral gene of pltD, artB. These results illustrate that typhoid toxin and pltD are expressed
at the same time and under the same conditions, making it likely that they could form a unique
typhoid toxin subtype.

Improving efficacy of chemotherapeutic

cisplatin by mitigating serious side-effects such
as ototoxicity.
Sakina Mithaiwala Biological Sciences
58
Co-authors: W. Ted Allison (PI), Aaron Fox (Graduate Student Supervisor), Frederick West and
Amit Bhavsar (co-collaborators)

Abstract: Cisplatin is a highly effective chemotherapeutic treatment for many solid tumours
in pediatric as well as adult patients but causes serious adverse drug reactions such as oto-
toxicity and nephrotoxicity. Previous studies have proposed a cisplatin metabolism model in
kidney cells using cysteine-S-conjugate β lyase (CCBL) and γ-glutamyl transferase (GGT).
This model is based on chemical inhibitors to CCBL (aminooxyacetic acid or AOAA) and
GGT (Acivicin) protecting kidney cells from cisplatin-induced toxicity. While this model has
been demonstrated to be implicated in nephrotoxicity, it has not been researched in the con-
text of ototoxicity. Preliminary data has shown that treatment of the murine inner ear cell
line HEI-OC1 with Acivicin increases their viability in the presence of cisplatin and reduces
cisplatin-induced IL-6 expression. Therefore, in this project we examined the otoprotective
 40

potential of inhibiting cisplatin metabolism using Acicivin in a zebrafish model in order to gain
important insights into how cisplatin is metabolized into an ototoxin in the inner ear. Zebrafish
are an established model for ototoxic drug screening and for studying CIO due to the external
mechanosensory hair cells they possess in their inner ear and posterior Lateral Line (pLL) in
clusters called neuromasts. These hair cells are developmentally, morphologically and physio-
logically homologous to mammalian hair cells and are highly accessible and easily visualized
with fluorescent vital dyes. We found that concomitant application of Acivicin with cisplatin
via bath application provided protection to the hair cells along the pLL of zebrafish larvae.
This research project has provided support for the hypothesis that cisplatin may be converted
to an ototoxin through the previously described cisplatin metabolism model and important in-
sights into potential therapeutic strategies for mitigating CIO, particularly in pediatric cancer
patients.