2A18 Abstracts 2015

Below is a list of abstracts by second-year students in the Integrated Science Program:


James Lai – A mathematical model of circumstellar and circumplanetary habitable zones accounting for multiple heat sources.

Supervisor: Dr. George Dragomir
The habitable zone is the range of orbital radii at which a celestial body’s temperature is conducive to liquid water. It is influenced by factors including stellar radiation and tidal heating. The ability to predict exoplanetary habitability can improve understanding of the range of orbital parameters that may allow life to develop and survive.

I combine elements of mathematical models developed in the literature to determine energy contributions by stellar radiation and tidal heating, producing a Maple 18 model accounting for both circumstellar and circumplanetary habitability. Using input star, planet, and moon properties, the model outputs calculated temperatures for both the planet and moon, as well as coloured maps representing the habitable zone.

Using this model, I assess the effect on the habitable zone when tidal heating is considered in addition to stellar radiation, giving a better understanding of how these factors influence habitability. Specifically, tidal heating may pushes both edges of the habitable zone outward, but whether the habitable zone size changes is unclear. Additionally, it is expected that accounting for the circumplanetary habitable zone will expand the overall habitable zone.

By synthesizing a single model from existing literature models, a more accurate prediction of exoplanetary system habitability may be obtained, allowing scientists to better determine which exoplanets are more likely to have life and target these for further study. The model is therefore applied to existing exoplanet data to demonstrate this application of the model in predicting exoplanet and exomoon temperatures.

Tristan Goodwill – Geodesics in general relativity.

Supervisor: Dr. George Dragomir
General relativity is a theory that attempts to explain the universe at very large scales by treating gravity as a geometric property of spacetime. The fact that spacetime is curved in the presence of massive bodies and gravity is interpreted as the manifestation of this curvature is one of the central ideas of general relativity. As a consequence of this fact, spacetime is no longer flat and the geometry is no longer Euclidean. Due to this curved geometry, the mathematics behind general relativity is notoriously arduous. This project attempts to gain an intuitive understanding of the geometry of spacetime through studying its geodesic structure. In general relativity, geodesics are the trajectories of free particles and they can be thought of as the straightest paths through spacetime. The behaviour of geodesics depends on the curvature of spacetime. In the vicinity of spherically symmetric, non-rotating massive objects, such as black holes, the geometric structure of spacetime is given by the so-called Schwarzschild metric. In non-Euclidean geometry, defining such a metric allows one to measure distances and angles in spacetime in very much the same way the dot product is used for such measurements in Euclidean geometry. This project describes the geodesics of this specific metric in an attempt to understand the geometry of spacetime near a black hole.

Deep Inamdar – Geometric analysis of tonality in the chord space.

Supervisor: Dr. George Dragomir
Tonality is a property that is fundamental to Western music. The term is used to define any musical composition that arranges pitches and chords in a manner that generates a perceptually appealing sequence of auditory stabilities. Over the years, composers have identified a variety of components which are believed to contribute to tonality. These include the following: conjunct melodic motion, acoustic consonance, harmonic consistency, limited macroharmony, and centricity. To date, the scientific community has yet to fully understand the relation between the identified elements and tonality. The purpose of the study was to analyze these components through the construction of an orbifold model that has the ability to display all possible chords and voice leadings in two dimensions. This was done by mapping a variety of voice leadings to the orbifold model. In the results, specific orbifold parameters were associated with the components that contribute to tonality. The findings suggest that it may be possible to develop music on a mathematical basis, without the need of a musical instrument at all.

Lucia Krivankova-Smal and Supriya Singh – Reconstruction of the geological and paleoenvironmental history of the island Marcus.

Supervisor: Dr. Carolyn Eyles
Geologic processes have continued to shape our planet from the Precambrian to current day. Understanding these processes is significant in the comprehension of the physical world, as well as the history of life and our planet. Geologists use their knowledge of Earth’s history in the exploration for minerals, reservoirs of hydrocarbons, and water. The objective of this activity is to create a hypothetical island where the geological and paleoenvironmental history is reconstructed using cross-sections and geologic maps. The stratigraphy, fossils, and mineral deposits will provide evidence to create a timeline of events of the creation of the island. The island Marcus has an initial tectonic setting of two island arc subduction zones with volcanism. After accretion onto a continental landmass, the margins become passive. This collision causes a build-up of sediments in an accretionary wedge forming an ophiolite. Additionally, this leads to the formation of a greenstone belt that is rich in minerals and certain ores including Cu-pyrite, ZnCu, and Pb-Zn-Cu massive sulfide deposits. A rift valley forms, causing the separation of Marcus from the continental crust. This sequence of events has created favourable conditions for mineral exploration similar to that of the greenstone belts in Canada. Through the reconstruction the geological history of Marcus, current island and greenstone belt formation can be better understood.

Mindy Chapman – Synthesis of RNA from mononucleotides in different environments.

Supervisor: Dr. Maikel Rheinstädter
One of the fundamental questions of biology is how nucleotides were first assembled and incorporated into cells. Before the DNA-dominated world of today, it is hypothesized that RNA was used to store genetic information and as a catalyst for chemical reactions. RNA is a polymer of nucleotides linked by a ribose-phosphate backbone. We hope that by learning under what conditions RNA can be synthesized in a laboratory setting, we will gain an understanding of how RNA formed on Earth four billion years ago. In this study, we used X-ray scattering to investigate base stacking of 5′-adenosine monophosphate (AMP) and 5′-uridine monophosphate (UMP) mononucleotides concentrated by evaporation in different matrices, including a multilamellar phospholipid matrix, nanoscopic films, ammonium chloride salt crystals and Montmorillonite clay. Two contributions from the nucleotides were observed in diffraction pattern of all the materials, one corresponding to a nearest neighbor distance of ~4.6 Å and a second at a smaller distance of 3.45 Å. While the 3.45 Å distance agrees well with the distance between stacked base pairs in RNA, the 4.6 Å can be attributed to nucleotides that have not undergone stacking. From the strength of the two contributions, the effectiveness of the different environments for producing RNAlike base stacking can be quantified for the first time.

By learning under which conditions RNA begins to form, we gain a better understanding of how life formed on Earth.


Thomas Burrows, Kylee Innes, Martyn Siek, and Jacqueline Watt – Creative video representation of critical period plasticity and its applications.

Supervisor: Dr. Deda Gillespie
Neuroplasticity is one of the hallmarks of the nervous system and is essential for enabling our body to perform the functions we use on a daily basis. One of the most important times for neuroplasticity in the brain is during a child’s development: this is known as critical period plasticity. During this period, the brain forms and strengthens all of the necessary synapses to function while eliminating the weakened, non-essential ones. The goal of this project is to share the knowledge of this essential feature of the nervous system with a general audience through a video presentation. The video will highlight research based on critical period plasticity, and the experiments of David Hubel and Torsten Wiesel regarding synaptic plasticity in the visual cortex and how their theory relates to patch therapy. Additionally, the video will discuss current research studying synaptic plasticity in adult brains in the form of drug addiction. Understanding the intricacy of the brain’s functions, as well as key concepts about neuroscience, is important for further understanding in the neuroscience field. Hopefully this video will allow us to enlighten viewers of key neurological concepts, and inspire the future scientists of tomorrow.

Biran Falk-Dotan – Exploration, activity, and sociality in Drosophila melanogaster larvae.

Supervisor: Dr. Reuven Dukas
Social animals can often benefit from public information. For example, animals may follow others to available food patches rather than exploring individually. Consequently, highly social individuals may rely less on their own exploration, suggesting a negative correlation between sociality and individual exploration. My research compared fruit fly larvae (Drosophila melanogaster) from different genotypes of the Drosophila Genetic Research Panel (a collection of nearly homozygous fruit fly lines) in their patterns of exploration and activity shortly after hatching. Based on data from a previous project characterizing sociality, we chose 5 highly social genotypes and 5 genotypes of low sociality. We assessed the exploration tendencies of these 10 genotypes by placing eggs in a food patch in the centre of an otherwise uniform arena and video-recording larval movement patterns after hatching. Movement outside of the patch can be considered exploration, as the larvae leave a suitable environment in search of a more favourable environment. We compared these to movement patterns of corresponding larvae in arenas with no food patch to control for baseline activity levels. We tested the prediction that larvae of more social genotypes will have a lower tendency to explore individually because they are more reliant on other larvae to find food patches. More generally, our data allows us to characterize genetic variation in exploration and activity levels, which may ultimately lead to the identification of genes responsible for exploration in fruit flies and other animals.

Angelico Obille – Investigating the relationship between variance of transition temperatures.

Supervisor: Russ Ellis
Colligative properties are properties of impurities. Most substances are mixtures since it is difficult to maintain a completely pure substance. The effects of a solute on the properties of a substance include freezing point depression (FPD) and boiling point elevation (BPE). These properties are due to the impurity lowering the mole fraction of the solvent, consequently decreasing its chemical potential. This stabilizes the liquid state and causes the solvent to exist as a liquid for a wider range of temperatures at constant pressures. The purpose of this study is to investigate a general relationship between FPD and BPE. Specifically, the study aims to provide a method in determining a proportionality between the transition constants of a general solvent. The transition constants represent how much the variance of transition temperatures change against varying concentrations of solute. The transition constants (Kfp and Kbp) are determined for water with varying concentrations of dissolved acetic acid, sucrose, and sodium chloride. The freezing point and boiling point of the solutions are determined with analysis of cooling and heating curves, and the variance of transition temperature is determined upon comparison with pure controls. Boiling point elevation has been found to be positively correlated with freezing point depression, increasing by a factor of 0.36 (±0.08 s.d.). The experiments designed in this study provide a simple reproducible way to demonstrate and support the fundamental principles underlying colligative properties.

Timothy Fernandes – The implications of quantum mechanics in insect and bird communication, migration, and physiology from an ecological and evolutionary perspective.

Supervisor: Dr. Chad Harvey and Dr. Duncan O’Dell
Throughout the animal kingdom, many species have developed unique physiological adaptations to promote evolutionary fitness. In particular, the European honeybee and European robin have evolved to use the unique properties of Earth’s magnetic field and light polarization to increase the efficiency of migration and transportation routes. It has also been proposed that both of these species use quantum particle characteristics to communicate and navigate effectively. To investigate the evolution of these unique physiological adaptations, potential selective pressures were identified and analyzed to further understand how they are used by collective bird and insect species. A meta-analysis of current literature on both insect and bird physiology in relation to migratory route and communicatory method selection has been completed. Furthermore, through an analysis of the current and historical literature pertaining to bird and insect evolution, the direct and indirect mechanisms involved in the evolution of the physiological adaptations in question will be discussed. Analyzing the current literature and providing an integrative review of insect and bird quantum biology may suggest a novel mechanism of convergent evolution. Through this physiological and evolutionary analysis, it is possible to suggest improvement of navigation and communication devices, including automated vehicles and data encryption.


Ball, P., 2011. Physics of life: The dawn of quantum biology. Nature, 474, pp. 272-274.

Landgraf, T., Rojas, R., Nguyen, H., Kriegel, F. and Stettin, K., 2011. Analysis of the waggle dance motion of honeybees for the design of a biomimetic honeybee robot. PLOS One, DOI: 10.1371/journal.pone.0021354.

Ritz, T., 2011. Quantum effects in biology: bird navigation. Elsevier, 3(1), pp. 26

Nafis Wazed – Understanding drug discovery using computational platforms.

Supervisor: Russ Ellis
Computational biochemistry has become a fundamental concept in drug design. As the complexity of drug development increases, there is a need for computational platforms to simplify and aid in understanding the properties of drugs. It has long been accepted by the drug design community that the structure of a protein determines its function. Computational platforms such as PyMOL allows for structure visualization of different proteins and ligands, to enable correlation between structural properties and the protein function. This project will involve designing a lab to serve as an extension to the “Minimum Inhibitory Concentration (MIC) Lab” in the Drug Discovery Project in the Integrated Science 2A18 course at McMaster University. PyMOL will be used to allow undergraduates to examine the structures of the different proteins they will be testing. Students will use this software to hypothesize how the structure of a protein affects its resistance to different antibiotics. The focus will be on the structure of dihydrofolate reductase (DHFR) and on how different inhibitors interact with DHFR to block its function. Students will also be tasked with comparing wild-type DHFR with a F98Y mutant DHFR and analyze the structural differences that lead to an increased resistance in the mutant. Students will use their understanding of drug discovery to hypothesize the effectiveness of the ligands and mutations and perform a MIC test to assess their hypothesis. This project will focus on teaching undergraduate Integrated Science students the importance of computational biochemistry and how it pertains to drug discovery as a whole.