Oral Sessions 2015

Talks are 15 minutes in length followed by 5 minutes for questions and speaker set-up. You will need to upload your talk via a USB in pdf or ppt format to site computer on Thursday July 30th during the lunch or poster session. More info on uploading talks will be given on Thursday during the conference. If you can’t attend Thursday, you can email your presentation ahead of time to wipc2015@physics.utoronto.ca.

Oral Session 1: Including Biophysics and Condensed Matter Physics

Location: Fields Institute, James Stewart Library

10:30-10:50: Madeleine Bonsma, University of Toronto:

Building bacteria-phage interaction networks using the CRISPR locus

10:50-11:10: Philippa Krahn, University of Toronto

Magnetic resonance characterization of acute cardiac RF ablation lesions

11:10-11:30: Ling Yao Yu, Laval University:

Optical and mechanical analysis on the biological cell in the optical tweezers

11:30-11:50 Mercedes Martinson, University of Saskatchewan:

Phase Preserving Beam Expander for Biomedical X-ray Imaging

11:50-12:10: Amany Raslan, Trent University:

Modelling of LaAlO3/SrTiO3 interfaces

12:10-12:30: Laila Obied, Brock University:

Ge:Mn thick films


Oral Session 2: Including Astronomy, Particle and Chemical Physics

Location: Fields Institute, Room 230

10:30-10:50: Kathleen Sampson, University of Toronto:

Alteration of Organic Semiconductor Chemical Structure to Fine Tune Electronic Properties for Organic Electronic Applications

10:50-11:10: Janet Rumleskie, Laurentian University:

Rn-222 assay systems for the SNO+ experiment

11:10-11:30: Caitlyn Darrach, Laurentian University:

A supernova calibration source for SNO+

11:30-11:50: Parshati Patel, University of Western Ontario:

Investigating inner gaseous disks around young, massive (Herbig Be) stars

11:50-12:10: Heather Fong, University of Toronto:

Detecting gravitational waves with LIGO

12:10-12:30: Laura Chajet, York University:

AGNs: Line width distribution of MHD disc winds

 Abstracts (Alphabetical)

“Building bacteria-phage interaction networks using the CRISPR locus”
Madeleine Bonsma and Sidhartha Goyal
University of Toronto
Bacteria-phage interaction networks provide an important window into the functioning and ecology of microbiomes. Here we utilize the CRISPR locus to build and analyze the structure of such networks.
Prokaryotes and their phage predators are abundant in many environments and can strongly impact their environments. Importantly, recent evidence links bacteria and archaea in the human microbiome to such phenomena as obesity [1], cancer [2], and immune disorders [3]. Phages influence their hosts in turn, producing population-level effects such as gene transfer [4] and mediation of pathogenic bacteria outbreaks [5]. The construction and interpretation of phage-bacteria interaction networks has wide-ranging implications for understanding the role of microbiomes in their environments.
Recently discovered prokaryotic adaptive immune system CRISPR-Cas [6–9] provides another window into bacteria-phage networks. Bacteria and archaea that possess a CRISPR-Cas system can develop a memory of past phage infections by incorporating small samples of phage DNA, called spacers, into a specific CRISPR locus.
Previous work to probe interactions has largely consisted of direct experiments with cultured bacteria and phages (Ref [10] compiles 38 such studies). This method, while yielding detailed and accurate results, is time-consuming to the point of being unfeasible for large networks. As well, only a small fraction of the microorganisms in natural environments can be cultured in a laboratory at all [11], meaning that a significant portion of microbial ecosystems remains inaccessible by this technique.
In this work, we propose and demonstrate phage-bacteria interaction networks constructed using the information contained in the CRISPR locus. To the extent that CRISPR-Cas is utilized in a bacterial strain, the CRISPR locus provides a detailed snapshot of phage interaction history, which can be used to construct an interaction map. Displaying bacteria-phage relationships in this way facilitates comparison to previous experimental infection studies and opens the door to ecological analysis of microbiomes using existing network analysis metrics such as modularity (how well a network can be divided into subgroups) and nestedness (to what extent the interaction ranges of members are subsets of other interaction ranges) [10,12–14].
We construct CRISPR-based networks by aligning spacers using BLAST to a compilation of phage databases and recording high-scoring matches. We investigate clustering in these networks using a traditional modularity measure as well as a measure of clustering consistency on repeated trials. Clustering between sub-groups of bacteria and phage is potentially indicative of ecologically distinct groups of interacting bacteria and phages.
CRISPR-based networks require much less experimental effort to construct than experimental infection studies and could provide a new way of investigating natural microbial systems. This approach is promising as a method of teasing out the important parameters in interacting bacteria-phage networks.
Acknowledgements: much of the code used to analyze data was contributed through open-source collaborations – see collaborators list. https://github.com/goyalsid/phageParser/graphs/contributors
1Department of Physics, University of Toronto, Toronto, Canada.
[1] P. J. Turnbaugh, R. E. Ley, M. a Mahowald, V. Magrini, E. R. Mardis, and J. I. Gordon, Nature 444, 1027 (2006). [2] R. F. Schwabe and C. Jobin, Nat. Rev. Cancer 13, 800 (2013). [3] S. K. Mazmanian, H. L. Cui, A. O. Tzianabos, and D. L. Kasper, Cell 122, 107 (2005). [4] E. Sano, S. Carlson, L. Wegley, and F. Rohwer, Appl. Environ. Microbiol. 70, 5842 (2004). [5] S. M. Faruque, M. J. Islam, Q. S. Ahmad, a S. G. Faruque, D. a Sack, G. B. Nair, and J. J. Mekalanos, Proc. Natl. Acad. Sci. U. S. A. 102, 6119 (2005). [6] A. Bolotin, B. Quinquis, A. Sorokin, and S. Dusko Ehrlich, Microbiology 151, 2551 (2005). [7] C. Pourcel, G. Salvignol, and G. Vergnaud, Microbiology 151, 653 (2005). [8] K. S. Makarova, N. V Grishin, S. a Shabalina, Y. I. Wolf, and E. V Koonin, Biol. Direct 1, 7 (2006). [9] F. J. M. Mojica, C. Díez-Villaseñor, J. García-Martínez, and E. Soria, J. Mol. Evol. 60, 174 (2005). [10] C. O. Flores, J. R. Meyer, S. Valverde, L. Farr, and J. S. Weitz, Proc. Natl. Acad. Sci. U. S. A. 108, E288 (2011). [11] E. R. Mardis, Trends Genet. 24, 133 (2008). [12] M. J. Barber, Phys. Rev. E – Stat. Nonlinear, Soft Matter Phys. 76, 066102 (2007). [13] M. E. J. Newman, Proc. Natl. Acad. Sci. U. S. A. 103, 8577 (2006). [14] J. S. Weitz, T. Poisot, J. R. Meyer, C. O. Flores, S. Valverde, M. B. Sullivan, and M. E. Hochberg, Trends Microbiol. 21, 82 (2013).

“AGNs: Line width distribution of MHD disc winds”
Laura S. Chajet, Patrick B. Hall
York University
It has been recently found that there is a supermassive black hole (SMBH) at the centre of all sufficiently massive galaxies. Moreover, it has been shown that there is a tight relationship between the black hole masses and the galaxy bulges, suggesting their co-evolution. In a fraction of those galaxies, collectively known as active galactic nuclei (AGN), the central region releases enormous amounts of energy at virtually all wavelengths from radio to the X-ray (and in some cases, the gamma-ray) range. These active nuclei are so luminous that they often outshine the rest of the galaxy.
AGN are powered by mass accreting into the central SMBH. In the current paradigm, the accreting structure, assumed to be disc-like, is responsible for most of the ultraviolet (UV) and optical continuum emission. The broad emission lines (BELs), a dominant feature in the UV/optical spectrum of many AGNs, are produced by photoionisation of dense gas surrounding the central engine. The central region is embedded in an dusty molecular torus that obscures some lines of sight to the nucleus, accounting for the diversity in the AGN phenomenon. It is now increasingly accepted that AGN broad emission forms in winds emerging from the accretion disc. This wind picture naturally explains many of the BELs characteristics. In addition, those outflows off er a plausible feedback mechanism by the SMBHs to their host galaxy, thus regulating their co-evolution.
Accurate emission line models are important to determine AGN black hole masses and accretion rates. We study AGN emission line pro files with a model that combines an improved version of the accretion disc wind model of Murray & Chiang (1997) with the magnetohydrodynamic driving (MHD) of Emmering et al. (1992). We have compared the dispersions in our model Civ linewidth distributions to observational upper limit on that dispersion, that translates into an upper limit to the half-opening angle of the putative torus.
For a set of diff erent masses and luminosities, we constructed a series of models parametrised by two angles: inclination of the disc to our line of sight and the wind launching angle and found hints suggesting that the dispersion of the linewidth (and, thus, the torus half-opening angle) compatible with the observations depends on both the accretion rate and the mass alone.

“A supernova calibration source for SNO+”
Caitlyn Darrach, C. Virtue, C. Kraus
Laurentian University
A supernova calibration system is currently being developed for the SNO+ experiment housed at the underground facilities of SNOLAB at Creighton Mine, Sudbury, Ontario. SNO+ is a kilotonne liquid scintillator neutrino detector primarily focused on neutrinoless double beta decay studies. It will also be sensitive to supernova neutrinos once online. SNO+ plans to participate in the Supernova Early Warning System (SNEWS), which will alert the astronomical community in the event of a galactic supernova. More than 99% of the gravitational binding energy released during a core-collapse supernova is in the form of a brief burst of neutrinos of all flavors. The SNO+ detector requires calibration to ensure that a burst of supernova neutrino events can be reliably read out and recorded by the electronics and data acquisition system in the event of a nearby supernova. During a supernova event, the directives of SNO+ involve recording the data, sending a timely alert to SNEWS, and quickly analyzing and interpreting the data. The Supernova Calibration Source for SNO+ (SNC+) will simulate the interactions of neutrinos from a core-collapse supernova with the liquid scintillator using pulsed visible light from a laser diode. The SNC+ is a data-driven pulser capable of producing 2 ns, 0-200mW, 405nm pulses with repetition rates up to 12.5 MHz. An ASCII “burst” file of up to 256K 32-bit entries speci es a burst of photon pulses simulating a supernova, with each photon pulse capable of simulating a deposited energy of up to 70 MeV within the liquid scintillator of the SNO+ detector. The light from the SNC+ laser diode is delivered isotropically within the SNO+ detector by fiber optics and a di ffusing ball.

“Detecting gravitational waves with LIGO”
Heather Fong, Prayush Kumar, Tony Chu, Harald Pfeiffer
University of Toronto
The Laser Interferometer Gravitational-wave Observatory (LIGO) has finally completed its major upgrades in instrument sensitivity, and will commence observations this September 2015. In order to detect gravitational wave signals from binary black holes, LIGO uses a technique known as matched-filtering that depends on having a vast collection of highly accurate gravitational waveforms. I will summarize the results of our error analysis of contemporary gravitational-wave models using a new set of numerically generated waveforms, and I will also discuss whether or not these waveform models are sufficiently accurate for gravitational wave detections and parameter estimation.

“Magnetic resonance characterization of acute cardiac RF ablation lesions”
Philippa Krahn, Venkat Ramanan, Jennifer Barry, Bonny Biswas, Kevan Anderson, Robert Xu, Nicolas Yak, Sheldon Singh, Mihaela Pop, Graham A. Wright
University of Toronto
Ventricular tachycardia (VT), an abnormally fast heart rhythm initiated in the ventricles, is a leading cause of sudden cardiac death (SCD). 300 000-400 000 people succumb to SCD annually in the US alone. Radio-frequency (RF) ablation provides a cure for ongoing VT via small, carefully targeted lesions (burns) created in the cardiac muscle using energy delivered by a catheter. Placed accurately, the electrically-unexcitable lesions block the abnormal electrical pathways responsible for VT. Unfortunately, approximately 37% of patients treated successfully with RF ablation therapy experience VT recurrence. Recurrence suggests that the ablated tissue may be comprised of irreversible and reversible regions of injury. Understanding these regions of tissue injury may be crucial to effectively preventing VT.
One solution to this problem may be provided by Magnetic Resonance Imaging (MRI), which is a novel and powerful tool to visualize RF lesions. MRI affords the high soft-tissue contrast and flexible contrast mechanisms to enable differentiation between reversible and irreversible tissue injury caused by RF ablation. This study aims to characterize the intrinsic MR properties of RF lesions to contribute to the understanding of injured tissue structure and inflammation after ablation.

“Phase Preserving Beam Expander for Biomedical X-ray Imaging”
Mercedes Martinson, Nazanin Samadi, Bassey Bassey, Ariel Gomez and Dean Chapman
University of Saskatchewan
The BioMedical Imaging and Therapy beamlines at the Canadian Light Source are used by many re-searchers to capture phase-based imaging data. These experiments have so far been limited by a small vertical beam size, requiring vertical scanning of biological samples in order to image their full vertical extent. Previous work has been done to develop a Bent Laue Beam Expanding Monochromator [1] for use at these beamlines, however the first attempts exhibited significant distortion in the diffraction plane, in-creasing the beam divergence and eliminating the monochromator’s usefulness for phase-related imaging techniques. Recent work has been done to more carefully match the polychromatic and geometric focal lengths in a so-called “magic condition” that preserves the divergence of the beam and enables full-field phase-based imaging techniques. The new experimental parameters, namely asymmetry and Bragg an-gles, were evaluated by analysing knife-edge and in-line phase images to determine the effect on beam divergence in both vertical and horizontal directions, using the beamline’s flat Bragg double-crystal mon-ochromator as a baseline. The results show that by using the magic condition, the difference between the two monochromator types is less than 10% in the diffraction plane. Phase fringes visible in test images of a biological sample demonstrate that this difference is small enough to enable in-line phase imaging, de-spite operating at a sub-optimal energy for the wafer and asymmetry angle that was used. References: [1] M. Martinson, N. Samadi, G. Belev, B. Bassey, R. Lewis, G. Aulakh, D. Chapman, Development of a bent Laue beam-expanding double-crystal monochromator for biomedical X-ray imaging, Journal of Synchrotron Radiation, 21 (2014) 479-483.

“Ge:Mn thick films”
Laila Obied, Sjoerd Roorda and David Crandles
Brock University
Dilute magnetic semiconductors (DMS) are of great interest for their potential applications in
spintronics. We decided to study Mn doped Ge because it is a simple system representative of
this important class of materials. Several Ge:Mn samples were prepared using ion implantation at
77 K into a single crystal Ge wafer. The implantation was done at ion energy of 4.76 MeV with a
fluence of 2×1016 cm-2 which yielded amorphous layers approximately 4 μm thick with
maximum Mn concentration at 2.5 μm. Different samples were annealed at 200°C (168 hours),
330°C (33 hours) and 600°C (35 minutes) in a tube furnace to achieve a solid phase epitaxial
regrowth of the amorphous implanted layer.
X-ray diffraction (XRD) of the sample annealed at 330°C showed a polycrystalline layer. The
sample annealed at 600°C showed XRD peaks corresponding to an unknown phase in addition to
peaks from amorphous and polycrystalline Ge. Annealing at 200°C showed little effect on the
morphology of the implanted layer. Secondary ion mass spectroscopy (SIMS) revealed that some
Mn diffused to the surface during annealing at 330°C. A SQUID was used to measure the
magnetic properties of all samples. The as-implanted sample exhibited paramagnetic behaviour
due to a dominant Mn2+ state. A magnetic hysteresis at 5K and up to 200K was observed for the
samples annealed at 330°C and 200°C which indicate the existence of a ferromagnetic phase in
the sample after annealing. The 600°C annealed sample showed no ferromagnetic response and a
significant reduction in the paramagnetic response at low temperature compared to the asimplanted
The temperature dependent optical transmission spectra were measured in the mid-infrared range
for different Mn-implanted samples and a self-implanted Ge sample. While the transmission of
pure Ge (measured at low resolution to remove Fabry-Perot oscillations) exhibits absorption
features due to lattice vibrations and the band gap absorption, spectra of the as-implanted sample
and the self-implanted Ge exhibited additional oscillations indicating a change in the index of
refraction and density between the implanted layer and the thick Ge substrate. The annealed
sample at 330°C showed a metallic-like absorption.

“Investigating inner gaseous disks around young, massive (Herbig Be) stars”
Parshati Patel, Aaron Sigut and John D. Landstreet
University of Western Ontario
Stars form from giant molecular clouds which are larger collections of gas and dust. During the star formation, the inherited material settles into a disk. The studies of such disks have garnered a lot of interests as they are the site of planet formation. Extensive work has been done in understanding the physics of these disks especially around low mass stars, like our Sun, and older massive stars. However, disks around very young massive stars (called Herbig Ae/Be stars) are comparatively poorly understood, especially the inner gaseous region, as the star and the inner disk are blocked by the outer dusty disk. In this talk, I will discuss how a combination of computer modelling and observations can help us understand not only the structure and kinematics of these inner gaseous disks, giving an insight into the formation and evolution of the young massive stars.

“Modelling of LaAlO3/SrTiO3 interfaces”
Amany Raslan and W. A. Atkinson
Trent University
The two-dimensional electron gas at the LaAlO_3/SrTiO_3 interface has an interesting phase diagram: it exhibits metallic, superconducting, and magnetic behaviours. From first principles, we develop a simple model to study the temperature dependence of the SrTiO_3 band structure. In our model, we consider the strong dependence of the dielectric constant of SrTiO_3 on the temperature and electric field. By solving a set of self-consistent equations for the charge density and the lattice displacement, we obtain the band structure as a function of temperature. We find that as the temperature decreases, the charge density is less confined to the interface.

“Rn-222 assay systems for the SNO+ experiment”
Janet Rumleskie
Laurentian University
SNO+ is a large, underground neutrino detector, redesigned from the SNO detector. Three separate phases (H2O loaded, liquid scintillator loaded, and Te-loaded scintillator) of SNO+ will allow for a diverse study of neutrinos, with one phase speci cally dedicated to the search of neutrinoless double beta decay in 130Te. Observing the process would con firm the Majorana property of the neutrino and conclude the neutrino as its own antiparticle. At a depth of 2 km underground (6000 m.w.e), SNO+ is shielded from many cosmogenics, yet the decay of 238U within the surrounding rock leads to high (3.54 pCi/L) levels of 222Rn. With a halflife of 3.8 days and a gaseous form, 222Rn possesses a mobility which could cripple the detector from signi cant ingress. A large cavity surrounding the detector contains ultrapure water shielding, and an existing cryo-trapping system within the cavity water puri fication plant is capable of assaying and monitoring the H2O, ensuring the target level of 3.5×10^13 g 238U/g H2O is met. Unused since SNO, the system is undergoing improvements and background runs and will soon be online for cavity H2O. A purfii cation plant for the liquid scintillator also exists, and an improved 222Rn trapping system coupled to the plant is under construction to measure the anticipated 222Rn levels of 1017 g/g within the SNO+ detecting medium. Both 222Rn trapping systems separate liquid (H2O or scintillator) from gas via degassing columns and commercially purchased cooling systems, then separate out 222Rn by freezing it inside vacuum tubing packed with brass wool and submerged within LN2. 222Rn is cryo-pumped to a compressing trap, then transfered into a custom Lucas cell via volume sharing. Once full, Lucas cells are placed inside a speci cally designed counting unit to measure alpha production from 222Rn and progeny. Assays of this method have proven to be successful in the past, and the systems will be a complementary ex-situ detection method for monitoring backgrounds within SNO+.

“Alteration of Organic Semiconductor Chemical Structure to Fine Tune Electronic Properties for Organic Electronic Applications”
Kathleen L. Sampson, Yiying Li, Zheng-Hong Lu, Timothy P. Bender
University of Toronto
The energy levels (highest occupied molecular orbital, HOMO, and lowest unoccupied molecular orbital, LUMO) of organic semiconductor materials and their spacing relative to other semiconductors within an organic electronic device is an important design criteria to ensure proper and thermodynamically favourable transfer of charge within a device. One class of organic semiconducting materials that is of interest to our laboratory is boron subphthalocyanines (BsubPcs). BsubPcs have intense and narrow light absorption and emission within the visible spectrum. The properties of BsubPcs can be altered by making BsubPc derivatives using the vastness of organic chemistry. One derivative of particular interest is pentafluorophenoxy-BsubPc (F5BsubPc). F5BsubPc has been shown to have a lower than expected HOMO energy level attributed to the pentafluorophenoxy substituent1. This presentation will focus on our recent investigation on whether the electronic properties (HOMO/LUMO energy levels) of F5BsubPc analog compounds could be systematically altered and finely tuned by changing the number and position of fluorines on the phenoxy-BsubPc.
Seven fluorophenoxy-BsubPc compounds were synthesized with various number and position of fluorines on the phenoxy group. All compounds maintained a similar absorbance, emission, and solid state arrangement. However, there were fine changes in the electronic properties as seen by electrochemistry techniques and HOMO energy level calculations by ultraviolet photoelectron spectroscopy (UPS). The various fluorophenoxy-BsubPc’s had reduction potentials between that of phenoxy-BsubPc (PhO-BsubPc, no fluorines) and F5BsubPc (all five fluorines). The meta position (3rd and 4th position) on the phenoxy group had the least effect on reducing the reduction potential and was closest to that of PhO-BsubPc. This trend was matched by UPS HOMO energy level results. As a result, one or more of the fluorophenoxy-BsubPc compounds can be integrated into organic electronic devices to facilitate efficient charge extraction based on the fine-tuned energy levels of the various fluorophenoxy-BsubPc compounds. This level of fine tuning of organic electronic materials is unprecedented within the field. References: 1. Morse, G. E.; Helander, M. G.; Stanwick, J.; Sauks, J. M.; Paton, A. S.; Lu, Z.-H.; Bender, T. P., J. Phys. Chem. C 2011, 115 (23), 11709-11718.

“Optical and mechanical analysis on the biological cell in the optical tweezers”
Lingyao Yu and Yunlong Sheng
Laval University
Mechanical manipulation of the biological cell by the optical tweezers is of great interest to test the cellular mechanical properties. We firstly used a two-way coupled model with the finite element method to compute the cell deformation in the dual-trap optical tweezers as a function of the two beam separation. It is a widely accepted process to use the optical tweezers in the time-sharing regime to replace the static optical multi-trap for the flexible manipulation of the biological cell in experiment. We demonstrated that in the time-sharing optical tweezers the local stress and local strain are jumping in each cycle all the time and at all the locations independently on the jumping frequency and the viscosity of the material. The effect of the force jumping therefore must be considered in the experiments. We also demonstrated that in the mechanical testing, the 3D cell shape has significant effects on the creeping behavior of the cell and on the final deformation of the cell in the equilibrium state in the optical tweezers and stretcher. The 3D shape of the cell then must be considered in the future experiments. However, the loss tangent in the dynamic testing of the cell is less sensitive to the 3D shape of the cell.