Centre for Mathematical Biology (CMB) July1, 2011 to June 30, 2012

  1. Overview

During 2011-2012, the Centre was home to 8 undergraduates, 19 graduate students, 4 postdoctoral fellows, 2 research associates, 4 core faculty members and many affiliated faculty. Dr. Dawes accepted an Assistant Professor position in the Department of Molecular Genetics at Ohio State University in July 2011.

Again, constructive collaborations flourished with federal and provincial governments, Mathematics in Information Technology and Complex Systems (MITACS), NSERC networks, NGOs, industry, academic researchers within campus, and academic researchers worldwide.

The Centre was active in hosting 14 seminar speakers and 3 short-term visitors

  1. Scientific Activities & Infrastructure

There were 4 core investigators for the Centre, (Lewis, de Vries, Hillen, and Wang). (Also see Appendix A). Scientific activities at the Centre are defined as the activities of these core investigators.

(a)Current Major Multidisciplinary Research Collaborations

Ongoing and new collaborative major multidisciplinary projects are listed.

Animal Movement Modelling (AMM): This work models animal movement, using mechanistically detailed processes describing how animals respond to environmental, resource and conspecific cues. There are a variety of sub-projects, ranging from state space models for wolf movement in the Alberta foothills to tracking polar bear movement over ice sheets, to more abstract models for swarming and group formation. One article and one book chapter were published during this year. The article appears in Royal Society Interface Focus and the book is entitled Dispersal, Individual Movement and Spatial Ecology: A Mathematical Perspective.

Canadian Aquatic Invasive Species Network (CAISNII): This Canada-wide network of researchers study spread and control of aquatic invaders. It involves interactions between academics and the Department of Fisheries and Oceans and is funded by an NSERC Network grant. A new network, CAISN II, has been funded by NSERC and partners at an amount of $6,560,000 for the period of April 2011 to March 2016. Four articles have been published in Biological Invasions this year.

Cell Movement (CM): The mathematical modelling of cell movement on petri dishes and in tissues is a major focus of Dr. Hillen’s research. Qualitative properties of chemotaxis models have been analysed through international collaborations with Kevin Painter, Heriot-Watt University, Edinburgh. A chapter in the book, Dispersal, Individual Movement and Spatial Ecology: A Mathematical Perspective, was published this year.

Coral Reef Preservation and Restoration (CRPR): This work involves investigatory preservation and restoration of natural coral reefs using a group of newly developed refuge-dependant models. An article was published in Journal of Biological Systems this year.

Development of Instructional Modules in Mathematical Biology (IMMB); This project fits under the auspices of the CRYSTAL-Alberta program. The researchers are developing a collection of interactive web-based instructional models in the area of mathematical biology, with the goal of conveying how mathematical techniques and mathematical thinking contribute to contemporary scientific research in the biological and life sciences. The audience is primarily senior high school students and beginning undergraduate students.

Dynamics of Insect Populations (DIP): Mathematical modelling to investigate dynamics of insect populations includes modelling dynamics of forest caterpillars and analysis of two-cycle dynamics in the Rocky Mountain Apollo butterfly under climate change. This work was continued in an international working group funded at the US National Institute for Mathematical and Biological Synthesis (NIMBios).

Evolution of Cell Size and Body Size (ECB): This workhas two subprojects: evolution of cell sizes of phytoplankton and zooplankton with random or growth-dependent mutations and evolution of body size phenotypes of lemmings. One article was published in Canadian Applied Math Quarterly this year.

Ecological Stoichiometry (ES): Ecological stoichiometry is the study of the balance of energy and nutrient elements in ecological systems. Stoichiometry theory provides an important lens to understand and model ecological interactions with successful applications in plant-herbivore interactions and competition for multiple nutrients. There are a variety of subprojects, ranging from mechanistically modelling limiting factors – light and phosphorus – in algae-daphnia microcosm experiments, and stoichiometric control of invasive daphnia species in aquatic ecosystems, to modelling nutrient limitations on lemming population cycles in terrestrial ecosystems. One article was published in Ecological Modeling this year.

F1000: Includes reviews for Faculty 1000 on new research papers. Faculty 1000 is a small group of invited scientists that review and recommend research papers internationally. One review was completed during this year.

Habitat Destruction (HD):The study of the number and rank of species extinction after habitat destruction.

Infectious Disease Modelling (IDM): Modelling infectious disease transmissionincludes three subprojects: modelling indirectly transmitted infectious diseases such as cholera, devising a new algorithm to recover the time-dependent transmission rate from epidemiological data via an inverse method and abstract modelling of infectious disease transmission with waning immunity. This year, three articles were published in Canadian Applied Math Quarterly, Journal of Biological Dynamics and Proceedings of the Royal Society B.

Instream Flow Needs: A Mechanistic Model-based Approach (IFN): This project focuses on impacts of changing water flow on the biological interactions in Alberta Rivers. This year, twoarticles were published in theJournal of Mathematical Biology and SIAM Journal on Applied Mathematics.

Mathematical Models for Industrial-scale Composting (MMIC):This project investigates mathematical models for industrial-scale composting processes. The research is exploring opportunities to validate the models with researchers at the Edmonton Waste Management Centre of Excellence.

Mathematical Models of Radiotherapy in Cancer Research (RCR):Dr. Hillen leads this study of optimization of radiation treatment of cancer. An article has been published this year in Mathematical Models and Methods in Applied Sciences.

Microbiology (MB): Modelling bacterial population dynamics, behaviours and functioning is a major focus of Dr. Wang’s research. Subprojects include; bacterial colony and community formation, bacterial competition and coexistence, bacteria-driven organic matter decomposition and nutrient regeneration.

Modelling Primary Succession on Mount St. Helens (MSH): Since the eruption of Mount St Helens in May 1980, researchers have been monitoring the progression of primary succession on its slopes. Many mechanisms have been proposed to explain how primary succession unfolds, though few have been explored in mechanistic models. Working with former MSc student, Justin Marleau, (now a PhD student at McGill), John Bishop (Washington State University), and Bill Fagan (University of Maryland), models have been developed to test the importance of these mechanisms on Mount St Helens. Insights gleaned from these models could, one day, be applied to restore ecosystems damaged by mining and natural disasters. One article has been published in American Naturalist.

Mountain Pine Beetle Modelling (MPB): This project is a collaboration between Dr.Lewis and Canadian Forest Service scientist, Barry Cooke and research associate, Mario Pineda-Krch, as part of the Alberta MPB Genomics TRIA Project.

Other (OTH): One article on fitting a structured juvenile-adult model for green tree frogs to population estimates from capture-mark-recapture field data was published in Bulletin of Mathematical Biology. As well, achapter about phenotypic plasticity appears in the book, The Sourcebook in Theoretical Ecology.

Polar Bear Reproductive Dynamics Under Sex-selective Harvest and Climate Change (PBR):. There are three projects: mathematical models to predict the effects of a sex-selective harvest on polar bear population dynamics, mathematical models to predict the effects of climate warming on the reproduction and body condition of polar bears, and impact of ice movement on polar bear foraging and fitness.

Population Cycles (PC): This project focuses on impacts of physiological or behavioral parameters and environmental factors on small mammal population fluctuations.

Risk Assessment of Oil Sands Related Contaminants to Aquatic Biodiversity (RAOSC): The main goal of this project is to assess the effects environmental contaminants have on the aquatic ecosystems and what risks are posed to individuals and populations of a variety of species within the oil sands area of northeast Alberta.

Sea Lice in Salmon (SLS): This work involves researchers from Alberta, Victoria, Salmon Coast Research Station, University of Washington, Dalhousie University and Simon Fraser University. Here, the ability to analyze the system using mathematical and statistical models has been key in the ability to understand complex dynamics. One project investigated the evolutionary dynamics of sea lice under pesticide control. Several other projects assess the impact of sea lice on conservation of wild salmon. Three articles were published this year, one in Proceedings of the National Academy of Sciences, another in American Naturalist and the last in Canadian Journal of Fisheries and Aquatic Sciences.

Spatio-Temporal Dynamics of Cellular Proteins (DCP): This project aims to provide theoretical support for the quantitative interpretation of data obtained from experiments that are designed to probe the spatio-temporal dynamics of biomolecules such as proteins in living cells.

Theory of Delay Differential Equations (TDDE): This work focuses on developing new mathematical theorems for delay differential equations with applications in biological models.

Projects with no Centre publications are typically in their first few years, with papers currently in the submission/review stage. Many of the projects involve additional trainees not at the Centre. For simplicity of presentation, only the Centre trainees are shown.

Project / Senior Researchers / Centre Trainees / Centre Publications / Funding Agencies
Dept / Campus / Off-Campus
AMM / 3 / 2 / 4 / 3 / 9, 22 / NSERC & PIMS
CAISNII / 2 / 1 / 6 / 3 / 12, 14, 18, 19 / NSERC & partners
CM / 1 / 1 / 20 / NSERC
CRPR / 1 / 3 / 15
DCP / 1 / 1 / 2 / 3 / NSERC USRA & NSERC Discovery
DIP / 1 / 1 / 2 / NSERC & AIF
ECB / 1 / 1 / 16 / NSERC
ES / 1 / 5 / 1 / 17 / NSERC
F1000 / 1 / 1 / 6
HD / 1 / 1 / 1 / NSERC
IDM / 2 / 1 / 4 / 5 / 7, 11, 13 / NSERC & UofAStartup
IFN / 1 / 1 / 5 / 1 / 3, 8 / AIF Fellowship
Project / Senior Researchers / Centre Trainees / Centre Publications / Funding Agencies
Dept / Campus / Off-Campus
IMMB / 1 / 1 / 2
MB / 1 / 7 / 2 / NSERC
MMIC / 1 / 1 / 1
MPB / 2 / 3 / 1 / 1 / NSERC
MSH / 1 / 3
OTH / 4 / 2 / 1, 21
PBR / 1 / 1 / 1 / 1 / NSERC
PC / 1 / 2 / NSERC & UA Startup
RAOSC / 2 / 1 / 1 / AB Environment & MITACS
RCR / 2 / 3 / 2 / 2 / NSERC
SLS / 2 / 7 / 1 / 4, 5, 10 / NSERC, ITGC & MITACS Discovery
TDDE / 2 / 2 / 1 / NSERC & UofAStartup
Totals¹

¹The units here are person times projects. In other words, individuals participating in more than one project are counted for each project they participate in.

(b)Educational Projects and Initiatives

PIMS International Graduate Training Centre (IGTC): This program continued to flourish under the auspices of the Pacific Institute for Math Sciences. On August 1, 2011, Professor Dan Coombs, of the University of British Columbia,took over the position of director from Professor Mark Lewis. Details of the program can be found at

Mathematical Biology Journal Club: Hillen, Dawes and de Vries hosted a weekly seminar meeting at the Centre, to discuss CMB student’s work in progress, to meet with visitors and to read pertinent journal papers.

Wang Research Group:

Wang Research Group consists of 6 graduate students and 1 postdoctoral fellow. Besides weekly individual meetings, they hold regular group meetings to discuss several areas of mathematical biology as diverse as modeling stoichiometry-based ecological interactions, microbiology, infectious diseases, habitat destruction and biodiversity, risk assessment of oil sands pollution. Mathematical models include ODE, DDE, PDE, SDE, IDE.

Dr. Wang, his students and postdocs also had joint activities with other groups in the Centre.

Lewis Research Group:

The Lewis Research Group consists of5 graduate students, 1 visiting summer student, 2 postdoctoral fellows and 2 research associates. Dr. Lewisand his lab members held weekly lab meetings to discuss their research and to touch base on Centre activities. Visitors to the Centre were invited to participate in lab meetings held during the time of their visit.

(c)Research Resources

In 2011-2012, $312.16 was spent on toner for the printer in the Centre. An additional $55.00 was paid to AICT for maintenance and $182.97 was spent for the computing site licence.

(d)Personnel

Faculty:

There are four core faculty members (Gerda de Vries, Thomas Hillen, Mark Lewis and Hao Wang).

This year Dr. de Vriesreceived the President’s Achievement Award “Dare to Discover” for overall achievement for Science 100 Learning Beyond Boundaries.

Dr. Lewis received the University of Victoria Distinguished Alumni Award and the Killam Research Fellowship which is a national award. The last time a University of Alberta faculty member received this award was in 2004.

Support Staff:

Mark Duller remains the Centre’s part-time Computer Analyst. Cecilia Hutchinson left her position as Research and Administrative Coordinator in March 2011.

Graduate Students, Funding and Awards:

  • Janet Cooper: MSc – continuing

The existence of cancer stem cells and their significance for tumor growth

  • William Davis: MSc – completed

Indirectly transmitted infectious diseases (Nitrogen cycle modeling in aquatic environments)

  • HarunKalayci: MSc – continuing

Mathematical analysis of Single-Particle Tracking (SPT) data

  • Maryam KhajenAlijani:MSc – continuing

Stochasticity in modelling biological systems

  • ChaochaoJin:MSc – continuing

Mathematical inverse problem of infectious disease transmission

  • Xihui (Eric) Lin: MSc – completed

Multiple attracting limit cycles in delay differential equations

(Josephine M. Mitchell Graduate Scholarship)

  • Anastasia Lukyanova: MSc – completed

Mathematical modelling of industrial composting process

(PIMS IGTC Fellowship in Math Biology, Josephine M. Mitchell Graduate Scholarship, R. Pundit Sharma Scholarship, Student Oral Presentation Prize (UofA))

  • Nicholas Piazza: MSc – continuing

Infectious disease modelling with seasonal incidence, vaccination and multi-cell spatial spread

  • Aaron Purchase:MSc – withdrew – now in graduate program in Medical Physics
  • Amanda Swan: MSc – continuing

(NSERC Alexander Graham Bell Canada Graduate Scholarship)

  • Marie Auger-Methe: PhD – continuing

State –space models and the analysis movement by Arctic mammals

(Alberta Innovates-Health Solutions, Honorary Izaak Walton Killam Memorial Scholarship and the Steve and ElaineAntoniuk Graduate Scholarship)

  • Andria Dawson: PhD – continuing

Models for mixed wood forests

(Queen Elizabeth II Graduate Scholarship)

  • Jiafen Gong: PhD – completed

Optimization of radiation treatment

  • Jonathan Martin: PhD – continuing

Forest fire research

  • Stephanie Peacock: PhD – continuing

Modelling disease transmission from aquacult to wild salmon

(Vanier Canada Graduate Scholarships, Alberta Innovates Graduate Student Scholarship, D. Alan Birdsall Memorial Scholarship, PIMS IGTC Fellowship in Math Biology (honorary))

  • HarshanaRajankaruna: PhD – continuing

Population viability models for invasive aquatic species

  • Ulrike Schlaegel: PhD – continuing

Modelling wolf movement and researching state-side models

(Alberta Innovates – Technology Futures iCORE Graduate Recruitment Scholarship)

  • SiloginiThanarajah: PhD – continuing

Mathematical models for ecological dynamics

(PIMS IGTC Fellowship in Math Biology)

  • Diana White: PhD – continuing

Mathematical modelling of microtubule dynamics in human columnar epithelial cells

(Best Oral Presentation at the 9th PIMS Young Researchers Conference)

Postdoctoral Researchers, Funding and Awards:

  • Petro Babak: PDF – completed

Forest fire Modelling

  • Qihua Huang: PDF – continuing

Risk assessment of oil sands pollution on fish

(Alberta Environment Internship)

  • Yu Jin: PDF – completed

Development of mechanistic, process-oriented models for stream hydrology and biological interactions. The goal is to understand Instream flow needs for healthy ecosystems.

  • AdityaRaghavan: PDF – continuing

Tree distribution and dynamics under variable environmental conditions

Research Associates/Assistants:

  • Alex Potapov: Research Associate – continuing

Integrated systems for invasive species

  • Mario Pineda-Krch: Research Associate – continuing

Collaborative research on geonomics MPB, in cooperation with government and academic researchers. Duties include modelling and model analysis using computational and other methods.

Undergraduate Students

  • Jeff Bachman: BSc - continuing (NSERC Undergraduate Student Research Award)
  • Neil Borle: Bsc – continuing
  • Dustin Chelen: BSC completed
  • Paul Fritsch: BSc - continuing
  • ShayenneHerder:BSc – continuing
  • Rochelle Nieuwenhuis: BSc – continuing (NSERC Undergraduate Student Research Award)
  • Jeff Zielinski: BSc – continuing
  • Cole Zmurchok: BSc – continuing

(e)Visitor/Seminar Program

The Centre held the PIMS Mathematical Biology Seminar Series each Monday of the Fall and Winter terms. Names of the speakers are listed below and include speakers from Alberta, across Canada, the US, Europe and the Middle East.

Visiting Students

  • Laura Parshotham: MSc (York University) May – August, 2011 – Research/Technical Assistant Effects of oil sand pollution on trout fish population dynamics

Short Term Visitors

  • PhillippeLaurencot, (France) October 3, 2011
  • Rebecca Tyson (British Columbia, Canada) March 19, 2012
  • VlastimilKrivan (Ceske Budejovice, Czech Republic) April 8 – 13, 2012

Visiting Speakers from Universities other than the University of Alberta

  • PhillippeLaurencot – Paul Sabatier University in Toulouse, France

Self-Similar Solutions to a Kinetic Model for Grain Growth

  • Rebecca Tyson - University of British Columbia Okanagan

Predicting Bee-Mediated Movement of Pollen: A Diffusion-Based Approach

  • VlastimilKrivan – Biology Centre and Faculty of Sciences, Czech Republic

Consumer-Resource Dynamics Beyond the Lotka-Volterra Predator-Prey Model

Seminar Speakers from the University of Alberta

  • Thomas Hillen

Anisotropic Diffusion, Brain Tumor Growth and Wolf Movement

  • Qihua Huang

Deterministic and Stochastic Structured Population Models with Application to Green Tree Frogs

  • SiloginiThanarajah

The Role of Motility and Nutrients in Bacterial Colony Formation and Competition