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
Tumour development and progression45 nm super-resolution microscopy!
Prof. Virginijus Barzda – Nonlinear microscopy of biological systems
Muscle contraction Chicken embryo heart muscle
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