Department Calendar of Events

Redesigning Drug Design by Dr. John Chodera
Wednesday, December 8th @ 10:00AM
Zoom Link: https://utoronto.zoom.us/j/87130346324
Passcode: 398523
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As machine learning and physical modeling technologies are reaching maturity, a new era of technological innovation in computer-driven drug discovery is dawning. In this talk, we highlight an exciting new generation of tools that blend machine learning with physical modeling to accelerate structure-enabled drug discovery programs, with the goal of ultimately enabling fully autonomous drug discovery. We also highlight the role these tools have played in the COVID Moonshot, an open science global collaborative effort to discover a novel patent-free oral SARSCoV-2 antiviral with the goal of rapid, global, and equitable access.

John Chodera’s research focuses on reimagining the way we develop small molecule drugs and pair therapeutics with individual patient tumors by bringing physical modeling and structure-informed machine learning into the cancer genomics era. By combining novel algorithmic advances to achieve orders-of-magnitude efficiency gains with powerful but inexpensive GPU hardware, machine learning, and distributed computing technologies, the Chodera lab is developing next-generation approaches and open source software for predicting small molecule binding affinities, designing small molecules with desired properties, predicting drug sensitivity or resistance of clinical mutations, and understanding the detailed structural mechanisms underlying oncogenic mutations. The Chodera lab co-develops the OpenMM GPU-powered molecular simulation framework, which powers numerous biomolecular modeling and simulation applications using physical modeling and machine learning. As a core member of the Folding@home Consortium, the lab harnesses the largest computing platform in the world—the first to reach an exaFLOP/s—pooling the efforts of a million volunteers around the world to study functional implications of mutations and new opportunities for therapeutic design against cancer targets and global pandemics. Dr. Chodera co-founded the Open Force Field Initiative, a scientific collaboration funded by the NIH and an industry consortium consisting of dozens of scientists working to develop modern open source infrastructure for building and applying high-quality biomolecular force fields. Dr. Chodera is a co-founder of the COVID Moonshot, a radical open science patent-free drug discovery effort aiming to develop an inexpensive small molecule therapy effective against COVID-19 and future coronavirus. Using automated biophysical measurements, the Chodera laboratory collects new experimental data targeted to advance the quantitative accuracy of our methodologies, and gather new insight into drug susceptibility and resistance in kinases and other cancer targets. Their work makes extensive use of scalable Bayesian statistical inference, machine learning via probabilistic programming, and information theoretic principles for designing experiments and quantifying error. Dr. Chodera is passionate about open science, disseminating scientific best practices, and maximizing research reproducibility

Coming soon is a special iFAST Symposium to celebrate Prof. Perry L. McCarty‘s 90th birthday and honor his outstanding contributions to Environmental Biotechnology.  We invite you to attend this remarkable tribute.  

This special symposium will be spread among three days, December 16-18, 2021, 2.5 hours each day, 3:00 pm-5:30 pm UTC/GMT.  Here is the information you need to know to join the symposium:

Dates:    December 16-18, 2021
Times:   3:00 pm – 5:30 pm UTC/GMT
               10:00 am – 12:30 pm EST
               7:00 am – 9:30 am PST
               11:00 pm – 1:30 am China

Zoom link:  https://zoom.us/j/93481422012

Please see the agenda and check for the latest updates at our event webpage: https://www.ou.edu/ieg/seminars/ifast2112.

 If you have any questions, please contact us at ieg@ou.edu.

On behalf of iFAST and the Symposium Organizing Committee:
Bruce Rittmann (chair), Kenneth Williamson, Craig Criddle, Jaeho Bae, Elizabeth Edwards, & Alison Cupples

Upcoming SOCAAR Seminar:

EnVISIONing reGENEration WITHIN tissues by enhancing cell-based plasticity

Please register via Zoom.

Cindi Morshead to give land acknowledgement and opening remarks

11:05am-11:35am
Penney Gilbert introduces Sally Temple
Sally Temple, Scientific Director, Neural Stem Cell Institute
Using stem cell technology to combat age-related neurodegenerative disease

Cell transplantation therapy to restore vision

11:55am-12:25pm
Valerie Wallace introduces Rachael Pearson
Rachael Pearson, Professor, King’s College London
Stem cell-derived cone photoreceptor transplantation to restore vision

12:40pm-12:50pm
Arturo Ortin-Martinez, Scientific Associate, Krembil Research Institute
Modulating intracellular material transfer in transplanted photoreceptors

12:50pm-1:00pm
Margaret Ho, PhD Student, University of Toronto
A hyaluronan and methylcellulose-based hydrogel to perturb photoreceptor material transfer

1:00pm-1:10pm
Madison Gray, PhD Student, University of Toronto
Tracing synaptic connections in normal and regenerating retina

Gene therapy to promote neuroplasticity

1:20pm-1:50pm
Maryam Faiz introduces Shane Liddelow
Shane Liddelow, Assistant Professor, New York University
Reactive astrocyte heterogeneity in Inflammation and neurodegenerative disease

2:05pm-2:15pm
Justine Bajohr, PhD Student, University of Toronto
Astrocyte reprogramming for brain repair

2:15pm-2:25pm
Rikke Kofoed, Postdoctoral Fellow, Sunnybrook Research Institute
Kate Noseworthy, MSc student, University of Toronto
Focused ultrasound mediates brain plasticity and viral vector delivery

2:25pm-2:35pm
Hussein Ghazale, Postdoctoral Fellow, University of Toronto
Glia to neuron conversion in a mouse model of amyotrophic lateral sclerosis

Stimulating endogenous repair in neural and muscle tissue

2:45pm-3:15pm
Julie Lefebvre introduces Joshua Sanes
Joshua Sanes, Professor, Harvard University
Enhancing neuronal survival and regeneration after retinal injury: insights from single cell
transcriptomics

3:30pm-3:40pm
Emily Gilbert, Postdoctoral Fellow, University of Toronto
Metformin-mediated recovery following spinal cord injury: Sex-dependent effects on
inflammation and neural precursor cells

3:40pm-3:50pm
Erik Jacques, PhD Student, University of Toronto
Engineered bio-mimetic niche supports muscle stem cell quiescence

3:50pm-4:00pm
Danielle Jeong, PhD Student, University of Toronto
Characterization of neural stem cells and their niche during CNS remyelination

Molly Shoichet to give closing remarks

Information and registration via Zoom.

Cell Therapy Mini Symposium Poster (Portrait) – updated Jan 18, 2022:

Upcoming SOCAAR Seminar:

External members were required to register to receive the link and passcode. Registration closed at 9am on February 14. 

Prineha Narang, Harvard

Host: Prof. Frank Gu

Quantum systems host spectacular nonequilibrium effects and unconventional transport phenomena, but many of these remain challenging to predict and consequently, technologically unexplored. My group’s research focuses on how quantum systems behave, particularly away from equilibrium, and how we can harness emergent effects in these systems. By creating predictive theoretical and computational approaches to study dynamics, decoherence and correlations in molecules and materials, our work enables technologies that are inherently more powerful than their classical counterparts, ranging from scalable quantum information processing to ultra-high efficiency optoelectronic and energy conversion systems. Capturing these phenomena poses unique computational and theoretical challenges. In fact, the simultaneous contributions of processes that occur on many time and length-scales has eluded state-of-the-art computational physics and model Hamiltonian approaches alike, necessitating a new lens. In this context, I will focus on our work on approaches to describe excited-states in quantum matter, including electron-electron and electron-phonon interactions beyond leading order, and predicting emergent states introduced by external drives. Our approach brings quantum chemistry, quantum optics and condensed matter together to create unexpected and useful properties, including surprisingly long coherence times and propagation lengths, as well as enabling new quantum probes of correlations. I will also discuss our methods in spatially-resolved non-equilibrium transport in quantum matter. By introducing GPU-accelerated large-scale transport frameworks that retain microscopic scattering, we are overcoming long-standing barriers in the field and taking transport in matter to exascale computing. Finally, I will share our vision for the future towards crossing the finite-extended system divide, and leveraging the power of both classical high-performance computing and quantum computation paradigms in predicting new phenomena.
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Professor Prineha Narang came to Harvard University from the Massachusetts Institute of Technology where she worked as a Research Scholar in Condensed Matter Theory in the Department of Physics. She received an M.S. and Ph.D. in Applied Physics from the California Institute of Technology (Caltech). Prineha’s work has been recognized by many awards and special designations, including a Friedrich Wilhelm Bessel Research Award from the Alexander von Humboldt Foundation, a Max Planck Sabbatical Award from the Max Planck Society, and the IUPAP Young Scientist Prize in Computational Physics in 2021, an NSF CAREER Award in 2020, being named a Moore Inventor Fellow by the Gordon and Betty Moore Foundation for pioneering innovations in quantum science, CIFAR Azrieli Global Scholar by the Canadian Institute for Advanced Research, and a Top Innovator by MIT Tech Review (MIT TR35).

View the complete 2021-22 LLE schedule

Questions? Please contact Delicia Ansalem, Communications Officer & External Relations Liaison delicia.ansalem@utoronto.ca

BioZone will be hosting Professor Amanda Wright, from the Department of Human Health and Nutritional Sciences, at the University of Guelph on Thursday, February 24th from 3 pm – 4:30 pm.

Abstract

Functional foods deliver health benefits beyond basic nutrition. Natural health product (NHP) is the Canadian regulatory term for over-the-counter supplements that contain health-promoting molecules derived from foods, e.g., vitamins, minerals, herbals, probiotics. Together, these product categories encompass so much of the science and technology surrounding foods and nutrition. Our group works at the food-nutrition interface to support the evidence-basis for a variety of functional foods and NHPs. We have specialized interests in dietary lipids and in understanding how the structure of foods and food ingredients influences bioavailability and metabolic response, mediated by events in the gastrointestinal tract.

For example, what role does triacylglycerol crystallinity play in determining postprandial lipemia and what does this mean for saturated fatty acids? This talk will discuss our application of in vitro digestion and human research methods to relate emulsion properties to gastric microstructure, emptying, and postprandial satiety and lipemia (a risk factor for cardiometabolic diseases) to highlight the benefits of integrated food-nutrition research. Examples drawing on other functional foods will also be presented. Foods have always been functional. Focusing specifically on food structure and applying a physical property lens to what happens in the gastrointestinal tract paves the way for better understanding the nuanced relationships between foods and health, and ultimately to realize the potential for efficacious functional foods and NHPs.

Bridging the gap between microbiology and chemistry in built environments

Prof. Sarah Haines, Assistant Professor
Department of Civil & Mineral Engineering
University of Toronto

We spend the majority of our time indoors where the built environment has important implications for human health, particularly for those with asthma. Asthma disproportionately impacts low-socioeconomic communities due to poor quality housing associated with mold and moisture exposure. One of the main exposures to mold in housing is through the resuspension of floor dust. Microbes grow in carpet dust at elevated relative humidity conditions and release microbial volatile organic compounds (mVOCs). However, we do not know how the influence of moisture may drive species composition and chemical emissions from microbes in dust and on common building materials. Understanding
these interactions in the indoor environment is the next frontier in environmental engineering and has the potential to lead to substantial improvements in public health.

Utilizing cutting edge techniques, my work has ranged from collecting dust in carpet from homes in Ohio to analyzing dust particles from the International Space Station. Ultimately, results from my work have demonstrated that microbial growth can be quantitatively modeled in buildings, and for the first time demonstrated interactions between chemicals and microbes in house dust under elevated relative humidity conditions. My future work will link climate change, social justice, and viruses to contribute to healthy indoor environments.

Microsoft Teams meeting:
Join on your computer or mobile app
Click here to join the meeting

Or call in (audio only)
+1 647-794-1609,,691691226#   Canada, Toronto

Phone Conference ID: 691 691 226#
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External members were required to register to receive the link and passcode. Registration closed at 9am on March 7.

Desmond Moser, Western

Host: Prof. Jane Howe

The characterization of long-lived minerals, including natural metal deposits of copper, and their corrosion behaviours is an area of shared interest among geo- and materials scientists. This is particularly true in regard to transdisciplinary efforts to improve the design of multi-barrier Deep Geological Repositories for spent nuclear fuel. Examples of our application of micro- and nano-characterization techniques (e.g. EBSD, SIMS, Atom Probe Tomography) will be presented for a range of geomaterials including > 4 billion-year-old weakly-radioactive minerals in Martian meteorites and 1 billion-year-old copper from Earth.

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Professor Desmond Moser has spent most of his career unraveling the evolution of ancient planetary crusts using weakly radioactive and highly resilient microminerals. Increasingly his group is directing their expertise to help understand all aspects of the long-lived natural materials important to designing multi-barrier Deep Geological Repositories for spent nuclear fuel.

Prof. Moser conducts solid Earth and planetary science research using Western’s nationally unique Zircon and Accessory Phase Laboratory (ZAPLab). Micromineral crystal growth and deformation analysis (e.g. CL, EBSD) is integrated with field mapping, microchemical (EDS, WDS), petrologic and mass spectrometry measurements (radiogenic and stable isotopes) at Western and partner institutes. His active projects investigate meteorites, crustal cross-sections, kimberlite xenoliths, sedimentary basins and impact structures in the Americas, Africa and Europe. His ZAPLab team is advancing our knowledge of the timing and nature of processes that form and modify planetary crusts and ore deposits while advancing the growing sub-discipline of accessory mineral science.

View the complete 2021-22 LLE schedule

Questions? Please contact Delicia Ansalem, Communications Officer & External Relations Liaison delicia.ansalem@utoronto.ca