Goyal Group:Collective dynamics of large population of cells

Co-evolutionary dynamics in microbes (viruses and bacteria)

• Ue-Yu, experiments• Dominique Soutiere, theory• Madeleine Bonsma, data analysis

30C

Time(hr)

Frac

on

Popula

on(10^x)

30C 37C 42C

Time (hrs)

Cellular aging and mitochondrial population genetics

• Chris Nunn theory and experiments

Within cell dynamics

Asymmetricsegregation

Cellular fitness

Aging

Clonal dynamics of blood and stem cells

• Phenomenological models for blood regeneration

• Sophie McGibbon-Gardner, cellular reprogramming

Goyal Group:Collective dynamics of large population of cells

Nuclear pore complexes Secretion mechanisms in

bacteria and drug resistance

Prof. Zilman Quantitative biology and biological physics

Biological “nano-machines”

Mechanisms of targeted drug delivery: design and transport

T cell

Dendritic cellRecognition and

activation

T cell proliferation

Kill

Infected

cells

UptakePathogen

organisms

Dynamics of the immune system: stochastic population dynamics

Dynamics of the immune system: single molecule signaling

How to reliably model stochastic, non-linear

and complex processes in biology?

Dealing with unknown dragons: modelling complex biological processes

http://hilfinger.group

How to reliably model stochastic, non-linear

and complex processes in biology?

Dealing with unknown dragons: modelling complex biological processes

http://hilfinger.group

Establish

performance bounds

Robust data

analysis

Fluctuation

Theorems

http://hilfinger.group

Theorem Generating

Machine

Open for business!

Computational Biophysics —Rauscher Lab @ UTM

Our Focus: Disordered Proteins

• Disordered proteins are involved in many diseases (e.g. cancer, HIV, Alzheimer’s).• They represent ~30% of human proteins.• Disordered proteins are very challenging to study because they adopt many conformations.

Computational Biophysics —Rauscher Lab @ UTM

Our Approach:

• We use molecular dynamics simulations to describe the structure, interactions, and dynamics of disordered proteins in all-atom detail.

Our research is:

• collaborative — working closely with experimental groups

• interdisciplinary —physics/bio./chem.

Shine on you crazy…molecule

Get to Know Us Weekend 2018

Ultrasensitive bioanalytics

G protein coupled receptors

Polymer-lipid nanoparticles

Intrinsically disordered proteins

Quantum dot biosensors

Commercial application: DNA ladder

Milstein Laboratory for Biological Physics Research at the interface of the physical and life sciences

Biomechanics of Gene Expression

Optical Tweezers Super-Resolution Microscopy

Conformational DNA Dynamics

Bacterial DNA Segregation Dynamics

Prof. Robin Marjoribanks – Interaction of biological tissue with ultrashort laser pulses

• An exciting field at the interface between physics and biology: the chance to conduct experiments at all levels, from investigating fundamental physics of laser-interactions, to applications in medicine

• Three in-house high-intensity burst-mode femtosecond lasers dedicated to project

• Physics of laser-matter interaction in biologically relevant environments

• Laser induced breakdown in solids and liquids

• Shockwave generation

• Laser induced bubble formation and cavitation

• Ablative cooling – claw-back of absorbed energy

• What are the basic effects of intense ultrafast lasers or high repetition rate on cell biology?

• Reduction of cell death due heat diffusion?

• How to limit negative impacts of ionizing radiation?

• Control and ‘recycling’ of residual energy and plasma

• How can knowledge of this physics control the ways that laser surgery is improved?

• Full-time collaboration with biologists and hospital surgeons to develop new surgical methods

• Use of world-leading Advanced Optical Microscopy Facility (AOMF) at MaRS

• Your chance to be involved from early development through to clinical trials

a) Large volume removal of

porcine cartilage (section).

b) Cross-section of same

sample, no damage or

carbonisation visible.

c) Live (green) and dead

(red) cells imaged using

confocal fluorescent

microscopy. Short necrosis

ranges make this ideal for

graft-bed preparation.

d) State of the art Optical

Coherence Tomography

(OCT) is used to measure

accurate surface profiles

a) b)

c)

d)

Prof. Virginijus Barzda – Nonlinear microscopy of biological systems

Laser development

Nonlinear microscopedevelopment

Biological tissueinvestigation

Virgis.barzda@utoronto.ca

Tumour development and progression45 nm super-resolution microscopy!

Prof. Virginijus Barzda – Nonlinear microscopy of biological systems

Muscle contraction Chicken embryo heart muscle

Virgis.barzda@utoronto.ca

Biophysics and biophotonics positions available!

C. elegans muscles

Ryu Lab: Sensory Biophysics & Behavior

5

10

15

20

25

C. elegans neurophysiologyC. elegans locomotory behavior

How do single cells and small networks of neurons measure inputs and compute outputs?

McMillen: Systems and synthetic biology• Synthetic biology (controlling cells):

– Design and construct genetic networks, insert them into living cells, model and test their behaviour (control cells for medical, biotech purposes)

– Projects: integral feedback controllers, digital logic with RNA and proteins, engineering bacteria for waste-water treatment

• Systems biology (understanding cells):

– Dynamics of cellular processes: how does the internal state of a cell evolve over time? What are the relevant levels of description?

Promoter gene x

Protein X

Protein Y17

Experimental and modelling work:

you’re welcome to do either, or both