Events, Seminars, Colloquia

1 Aug 2017 - 11:30am

Presenter: Laura Liao
Supervisor: Dr. Catherine Beauchemin


In this work, two studies were performed where mathematical models (MM) were used to re-examine and refine quantitative methods based on in vitro assays of influenza A virus infections.

In the first study, we investigated the standard experimental method for counting defective interfering particles (DIPs) based on the reduction in standard virus (STV) yield (Bellett & Cooper, 1959). We found the method is valid for counting DIPs provided that: (1) a STV-infected cell's co-infection window is approximately half its eclipse phase (it blocks infection by other virions before it begins producing progeny virions); (2) a cell co-infected by STV and DIP produces less than 1 STV per 1,000 DIPs; and (3) a high MOI of STV stock (>4 plaque-forming units/cell) is added to perform the assay. Prior work makes no mention of these criteria such that the method has been applied incorrectly in several publications discussed herein. We determined influenza A virus meets these criteria, making the method suitable for counting influenza A DIPs.

In the second study, we compared a MM with an explicit representation of viral release to a simple MM without explicit release, and investigated whether parameter estimation and the estimation of neuraminidase inhibitor (NAI) efficacy were affected by the use of a simple MM. Since the release rate of influenza A virus is not well-known, a broad range of release rates were considered. If the virus release rate is greater than ~0.1 /h, the simple MM provides accurate estimates of infection parameters, but underestimates NAI efficacy, which could lead to underdosing and the emergence of NAI resistance. In contrast, when release is slower than ~0.1 /h, the simple MM accurately estimates NAI efficacy, but it can significantly overestimate the infectious lifespan (i.e., the time a cell remains infectious and producing free virus), and it will significantly underestimate the total virus yield and thus the likelihood of resistance emergence. We discuss the properties of, and a possible lower bound for, the influenza A virus release rate.

Overall, MMs are a valuable tool in the exploration of the known unknowns (i.e., DIPs, virus release) of influenza A virus infection.

Post by Graham, Jul-31-2017
14 Jul 2017 - 8:00am

Presenter: Celina Yang
Doctor of Philosophy, Biomedical Physics
Ryerson University, 2017

Supervisor: Dr. Devika Chithrani and Dr. Michael Kolios

This dissertation presents the effect of peptide-modified 10 nm colloidal gold nanoparticles (GNPs) with chemotherapeutic drugs, bleomycin and cisplatin, and 6 MV X-ray irradiation in a breast cancer cell-line, MDA-MB-231, in vitro. The GNPs were stabilized with a pentapeptide (Cys-Ala-Lys-Asp-Asp) and modified with a peptide sequence containing a ‘RGD’ amino acid motif (H-Cys-Lys-Lys-Lys-Lys-Lys-Lys-Gly-Gly-Arg-Gly-Asp-Met-Phe-Gly-OH). Bleomycin binds to the surface of the GNPs through a thiol bond and cisplatin has no significant interaction with the GNP surface.

Gold nanoparticle concentration used in studies throughout this dissertation was 0.3 nM. No significant toxicity was induced by introducing GNPs to MDA-MB-231 cells at this concentration. To examine the variability of accumulation of GNP constructs with the presence of chemotherapeutics, the amount of gold (Au) atoms were measured with Inductive Coupled Plasma-Atomic Emission Spectroscopy (ICP-AES). There was no significant difference in the accumulation of GNPs in the presence of cisplatin. There was a 5 % decrease in accumulation of GNPs in cells with bleomycin. However, the 5 % decrease with bleomycin was still a 6-fold increase compared to the accumulation of unmodified GNPs in cells. These results suggest that with the peptide modification, the presence of chemotherapeutics do not significantly affect the accumulation of GNPs into cells.

The effect of having GNPs with chemotherapeutics (either bleomycin or cisplatin) was examined through clonogenic and immuofluorscence assays. The conjugation of bleomycin onto peptide modified GNPs decreased the survival of MDA-MB-231 cells by 22.5 % (P < 0.05) compared to treatment with the same concentration of free bleomycin (without GNPs). On the contrary, treating cells with GNPs and cisplatin did not have a significant difference in survival compared to the same concentration of free cisplatin treatment (p = 0.078). This suggests that conjugating chemotherapeutics onto the GNPs can result in a more efficient delivery of the drug. If the drug does not bind to the GNP surface, having GNPs in the media does not interfere with the uptake of the drug.

The effect of radiosensitization in the presence of peptide modified GNPs was studied using 6 MV X-rays. The MDA-MB-231 cells were incubated with 0.3 nM peptide modified GNPs 16 hours prior to irradiation with 2 Gy of 6 MV X-rays. The survival fraction decreased by 23 % (p < 0.05) compared to the cells treated with same volume of phosphate buffed saline (PBS) solution prior to radiation. This confirms radiosensitization from the modified GNPs at a low concentration (0.3 nM) with clinically relevant energies (6 MV).

Lastly, the triple combined effect of modified GNPs, chemotherapeutics, and irradiation was investigated. The MDA-MB-231 cells were treated with modified GNPs, a chemotherapeutic (either bleomycin or cisplatin) and 2 Gy of 6 MV radiation to investigate the effect of triple combined therapy. The presence of GNPs had an advantage to the combined chemotherapy and radiation therapy. Based on results from these studies, peptide-modified GNPs can be used in addition to combined chemotherapy and radiation therapy for improved outcomes in cancer treatment.

Post by Graham, Jun-30-2017
30 Jun 2017 - 10:00am

Presenter: Ermias Woldemichael
M.Sc., Biomedical Physics, Ryerson University, 2017

Supervisor: Dr. Vladislav Toronov


Hyperspectral near infrared spectroscopy (hNIRS) is a noninvasive, real-time imaging modality with an improved quantitative accuracy and increased number of detectable chromophores. It uses the broadband spectrum of light wavelengths in the range of 700 – 1100 nm and is based on the unique absorbance property of molecules and the fact that all biological tissues are relatively transparent to these wavelengths which allow for measuring concentrations of light absorbing molecules such as the Oxy- and Deoxy- hemoglobin and Cytochrome C Oxidase. As opposed to fMRI, PET and SPECT, hNIRS is inexpensive and portable.

The purpose of this thesis project was to employ advantages of hNIRS by developing the multichannel hNIRS set-up for the simultaneous assessment of multiple areas of the brain and to test the system in clinical applications. To achieve these goals, I developed a new optical fiber bundle design providing improvement of the optical power throughput into the hNIRS light detectors. I also developed a novel probe for measurements on hairy areas of the human head. To validate the hNIRS system I used it simultaneously with fMRI, which revealed a good correlation of hNIRS and fMRI BOLD signals from the brain. The multichannel hNIRS set up with the increased signals due to the novel optical fiber bundles was then used during various brain activation protocols, which in the future can allow for the assessment of patients with mild traumatic brain injuries. Finally, the hNIRS system with new fiber bundles was compared with a commercial NIRS system in clinical setting for brain monitoring of patients during the transcatheter aortic valve implantation operation.

Post by Graham, Jun-30-2017
22 Jun 2017 - 10:00am

Presenter: Raphael Jakubovic M.Sc., PhD Candidate
Department of Biomedical Physics
Ryerson University & Sunnybrook Health Sciences Centre

Supervisors: Dr. Victor Yang, Dr. Ana Pejović-Milić


The objective of high dose stereotactic radiotherapy regardless of application is to treat the malignancy while minimizing the dose to the surrounding healthy tissue. In the context of spinal tumours this paradigm is difficult since the rigid dose tolerance of the spinal cord precludes optimal dose coverage of the epidural disease near the spinal cord. To achieve adequate coverage spine separation surgery is performed, increasing the distance from the spinal cord to the malignancy and facilitating adequate radiation treatment planning. This approach has been validated with delivery of maximum tolerable dose and local control rates over 90\%.

The objective of this dissertation is to establish the feasibility of intra-operative, dose guided, spine separation surgery. In the current clinical context, spine separation surgery is performed prior to radiation treatment planning and contours are placed based on post-operative resected tumour volumes. The extent of surgical resection is not dictated by the dosimetric constraints of the spinal cord and relies solely on the clinical expertise of the operating neurosurgeon. Further, though a skilled surgeon can perform precise tumour debulking with or without the aid of millimetre resolution neuro-navigation devices, determination of surgical debulking progress with accuracy comparable to treatment delivery cannot be recognized without intra-operative imaging. To achieve this goal, we introduced pre-surgical dosimetric planning with tracked high frequency ultrasound imaging into the operating theatre to inform the surgeon of the surgical progress while considering the dosimetric objectives.

In this dissertation, we assessed the dosimetric advantage of spine separation surgery on a millimetre by millimetre basis in a retrospective review. Feasibility of intra-operative navigation with submillimetre resolution was established by quantifying the application accuracy of surgical navigation in the context of cranial and spinal surgery. Accuracy quantification was performed, assessing our revolutionary optical surface imaging system and benchmarked versus existing commercially available neuro-navigation systems. Finally, to establish feasibility we integrated a high frequency ultrasound system into the operating theater during spine separation surgery. Thus, by implementing sub-millimetre high-frequency ultrasound imaging and neuro-navigation, incremental gains towards establishing the feasibility of intra-operative dose planning by iteratively updating the extent of tumour resection were recognized.

Post by Graham, Jun-19-2017
27 Mar 2017 - 1:30pm - 3:00pm

Presenter: Chris Meyer
York Mills Collegiate Institute, Toronto
VP Teaching and Learning, Ontario Association of Physics Teachers

We live in an exciting time for teaching physics. Over 30 years of education research by physics professionals is transforming physics teaching from a mystical art into a practical science. In the process, many educational myths have been successfully challenged. Research is providing great insight into the cognitive development of our students’ physics understanding and the accompanying physical changes that take place in the brain. As a result, pedagogical techniques have broken free from the traditions and fads of the past, and are becoming grounded in an empirical understanding of how humans learn. By creating a research-based learning environment, we can literally build better students and build better teachers. In this talk, Chris will share the key results from education research that inspired him to create a lecture-free high school physics program that is now spreading across Ontario.

Chris Meyer leads a reformed grade 11 and 12 physics program at York Mills Collegiate Institute in Toronto. He has presented pedagogical workshops for high schools and universities across southern Ontario, and his classroom resources are used throughout Canada and the United States. Chris is the winner of the 2016 CAP Award for Excellence in Teaching High School/CEGEP Physics (Ontario) and the 2015 Toronto District School Board Teaching Excellence Award. His most recent article, Group Work Test for Context Rich Problems appeared in the May 2016 edition of The Physics Teacher. When Chris takes off his physics hat, he enjoys writing orchestral music, with recent performances by the Toronto Symphony Orchestra and the National Youth Orchestra of Canada. To learn more, please visit:

Post by Graham, Feb-13-2017
20 Mar 2017 - 1:30pm

Presented: Dr. Soo Hyun Byun, Associate Professor
Department of Physics and Astronomy
Radiation Sciences Graduate Program
McMaster University


In order to address the fundamental physics problems encountered in radiation detection and dosimetry, my research group has focused on advanced gaseous radiation detector and signal processing system developments. A gaseous detector is one of the popular radiation detection methods and there has been outstanding progress in its technology in the last decade. Since 2008, my group has been developing THick Gas Electron Multiplier (THGEM) detectors which offer unique features in contrast to traditional gaseous proportional counters. In this talk, I will briefly review the underlying physics on THGEM and present our THGEM detectors geared for imaging and dosimetry. Another amazing project that we are currently working on is “McMaster NEUtron DOSimetry and Exploration (NEUDOSE)”, which aims at designing and building a satellite for measuring neutron and charged particle dose rates in low-Earth orbit. I will present the unique features of the NEUDOSE design and major accomplishments.

For any kind of radiation detectors, the importance of signal processing can never be overemphasized. With the recent progress in digital electronics, detector signal processing has been dramatically improved over the classical analog processing. I will present our recent signal processing systems that have been developed for a variety of radiation detectors.

Post by Graham, Mar-06-2017
23 Feb 2017 - 1:00pm

Presented by: Dr. Julia Bernatska
Hosted by: Dr. Alexandre Douplik

Dr. Julia Bernatska is an Associate Professor (since 2005) and the Chair (since 2014) of Department of Physical and Mathematical Sciences at National University of Kyiv Mohyla Academy (Ukraine). Currently, Dr. Bernatska is a visiting professor of the Department of Mathematics and Statistics at Concordia University, Montreal.

Post by Graham, Feb-23-2017
13 Feb 2017 - 12:00pm

Please join us for the Biomedical Physics Seminar Series.

Student: Xiao Juan Zheng
Supervisor: Dr. Alexandre Douplik

ABSTRACT: Hemoglobin (Hb) molecules present in red blood cells have several critical roles in addition oxygen transportation to tissue. Hb carries photosensitizer substances in photodynamic therapy, though the interaction of the heme group with the light and the substrate resulting in oxygen reactive species. Optical and optoacoustic imaging (OA) are sensitive to different forms of Hb due to the relative strong absorption of Hb. . Light propagation can have significant impact in optical and OA specially in using multi wavelengths approach to detect different forms of Hb. Monitoring hemoglobin (Hb) remains challenging specially in the presence of the reactive oxygen species as it reacts with oxyhemoglobin (oxy-Hb) to form methemoglobin (Met-Hb), another form of hemoglobin. This study will focus on Hb forms conversion in liquid and silicon based phantom. Human Met-Hb sample was obtained by dissolving the lyophilized powder in phosphate buffered saline (PBS), later converted to deoxyhemoglobin (deoxy-Hb) and oxy-Hb. The different Hb forms were validated by measuring its optical absorption (from 300-1000 nm), then compared and confirmed with absorption spectra from Oregon Medical Laser Center (OMLC). Blood containing silicon phantoms with photosensitizer additive were created to conduct photochemical reaction of reducing oxy-Hb to deoxy-Hb. This involved irradiating the phantoms to active the photochemical reaction. The efficiency of various photosensitizer concentrations and irradiation time was determined by measuring the optical absorption (from 300-1000 nm) in each phantom.

Student: Joanna Nguyen
Supervisor: Dr. James Grafe

ABSTRACT: Lanthanum (La) is a rare-earth metal used in phosphate binders in the form of a chewable tablet called lanthanum carbonate (LaC), commercially known as Fosrenol®. The daily high intake of LaC in patients with end-stage kidney disease is needed to reduce serum phosphate concentrations within normal range. Past studies have employed invasive bone biopsy sampling to show La accumulation in bone after long-term administration of LaC. However, the potential risks associated with long-term bone retention of La are unknown. In this work, we investigate the feasibility of using a K X-ray Fluorescence (K-XRF) spectroscopy system to quantitatively and non-invasively measure in vivo bone La. A series of hydroxyapatite (HAp) bone mineral phantoms doped with various concentrations of La were created to represent human bone. The HAp phantoms were placed in a 90° geometry relative to a bulky 1.11 GBq 241Am excitation source and high-purity germanium detector. For a live-time measurement of 2000 s, the initial minimum detection limit (MDL) was calculated to be 2.32 μg La/g Ca or 0.93 μg La/g HAp. However, for a newly acquired lead-collimated 241Am source, the MDL improved to 1.9 μg La/g Ca or 0.75 μg La/g HAp. This improvement in the MDL shows promising results and demonstrates the capabilities of this system as a non-invasive technique to monitor the long-term accumulation of La in bone. To the best of our knowledge, this is the first reported work that seeks to non-invasively measure bone La via in vivo XRF.

Post by Kevin, Feb-09-2017
9 Feb 2017 - 2:00pm

Presenter: Prof. An-Chang Shi
Department of Physics and Astronomy
McMaster University
Hamilton, Ontario, Canada

Abstract: What do plastics, pharmaceuticals, foodstuff and biomaterials have in common? They are all soft matter! Besides their softness, one of the most intriguing properties of soft matter is their ability to self-assemble into complex structures with ordering over many length scales, or hierarchically ordered structures. Understanding the principles governing the self-assembly of hierarchically structured soft materials is paramount to advanced material technology and, more importantly, to biological organisms because we are the perfect example of complex self-assembly. Traditionally, soft matter is a research area populated by chemists and biologists, emphasizing the synthesis and characterization of these materials. Since middle 70’s, many physicists turned their attentions to this important area of research, bringing with them the insights from physics. The infusion of physics ideas into soft matter research has led to many progresses. At the same time, many new physical concepts and ideas emerge from soft matter research. My lecture starts with a brief survey of soft condensed matter and its physical properties, and ends with some of our recent studies in this fascinating research area.

Presenter’s Bio: An-Chang Shi is a professor of physics at McMaster University. He received his B.Sc. in physics from Fudan University in 1982 and his Ph.D. in physics from University of Illinois at Urbana-Champaign in 1988. From 1988 to 1992 he was a Post-Doctoral Fellow and Research Associate at McMaster University. He joined Xerox Research Centre of Canada as a Member of Research Staff in 1992 and moved to McMaster University as an Associate Professor in 1999. He was promoted to Professor in 2004. He received a Premier’s Research Excellent Award in 2000 and was elected to Fellow of American Physical Society in 2010. He has worked on a wide range of topics in condensed matter physics, including crystal shapes, superconductivity and soft matter theory. His current research focuses on the development of theory for polymeric system, the investigation of phase diagrams of block copolymers, and the study of kinetic pathways of transitions between stable and metastable phases.

Post by Graham, Jan-24-2017
9 Feb 2017 - 11:30am

Presenter: Ruben N. Pinto
M. Sc. Biomedical Physics


Significant functional/structural changes of red blood cells (RBCs) have been documented during its in vitro storage. Collectively termed as RBC storage lesions, changes include an increase in RBC oxygen saturation (SO2) and an increase in irreversibly damaged RBCs (spheroechinocytes). In this work, novel optical techniques are presented for determining the spheroechinocyte population as a function of storage time via automated image flow cytometry (IFC) morphology characterization, and the acquisition of RBC SO2 via an in situ photoacoustic (PA) method. Blood gas analysis (BGA) was used as the gold standard SO2 measure. Over the lifespan of seven blood bags, the IFC spheroechinocyte population – PA SO2 correlation was found to be strong (0.60 < r2 < 0.91). These results suggest that monitoring SO2 changes can potentially infer the rate of increase of irreversibly damaged RBCs. A very strong PA SO2 – BGA SO2 correlation (r2 > 0.95) shows high potential for in situ monitoring of RBC storage lesions.

Post by Graham, Feb-06-2017