COVID-19 information for PI Residents and Visitors
This is a new one-day conference on soft matter theory. This will bring in Canadian researchers and graduate students in this area to showcase their research projects and promote collaborations. The relevant topics include polymers, membranes, materials, and nano-science. The overall format will be two keynote speakers (one morning and one afternoon) and seven invited speakers. There will be a special 90-minute session, where the graduate students can make short oral presentations on their research projects. Lunch will be provided by the Black Hole Bistro.
Registration for the conference is now closed.
Keynote Speakers:
Randall Kamien, University of Pennsylvania
David Weitz, Harvard University
Invited Speakers:
John Bechhoefer, Simon Fraser University
Colin Denniston, University of Western Ontario
Mark Matsen, University of Waterloo
Nikolas Provatas, McGill University
Joerg Rottler, University of British Columbia
Andrew Rutenberg, Dalhousie University
An-Chang Shi, McMaster University
Gary Slater, University of Ottawa
- Dmitry Abanin, Perimeter Institute
- Nasser Mohieddin Abukhdeir, University of Waterloo
- Arash Ahmadi, McMaster University
- Alena Antipova, University of Western Ontario
- Matilda Backholm, McMaster University
- Azadeh Bagheri, University of Waterloo
- Mehran Bagheri, University of Ottawa
- Behnaz Bagheri Varnousfaderani, University of Waterloo
- Solomon Barkley, McMaster University
- John Bechhoefer, Simon Fraser University
- Drew Bennett, University of Waterloo
- Martin Bertrand, University of Ottawa
- Aidan Brown, Dalhousie University
- Jeff Chen, University of Waterloo
- Mykyta Chubnysky, University of Ottawa
- Alexandre Day, University of Waterloo
- John de Bruyn, University of Western Ontario
- Hendrick de Haan, University of Ontario Institute of Technology
- Ashkan Dehghan, McMaster University
- Colin Denniston, University of Western Ontario
- Trang Do, University of Waterloo
- Jess Fallone, University of Waterloo
- James Forrest, University of Waterloo
- Paul Fowler, McMaster University
- Jie Gao, University of Waterloo
- Mohamed Amine Gharbi, University of Pennsylvania
- Michel Gingras, University of Waterloo
- Doug Grzetic, University of Guelph
- Bae-Yeun Ha, University of Waterloo
- Mona Habibi, Universityof Western Ontario
- Paul Higgs, McMaster University
- Mark Ilton, McMaster University
- Chanil Jeon, University of Waterloo
- Randall Kamien, University of Pennsylvania
- Mikko Karttunen, University of Waterloo
- Yuriy Khalak, University of Waterloo
- Grigoriy Kimaev, University of Waterloo
- Norman Lam, University of Toronto
- Yao Li, Tsinghua University
- Apichart Linhananta, Lakehead University
- Bin Liu, University of Waterloo
- Zheng Ma, University of Ottawa
- Frances Mackay, University of Western Ontario
- Pranav Madhikar, University of Waterloo
- Pendar Mahmoudi, Universityof Waterloo
- Mark Matsen, University of Waterloo
- Han Miao, Shanghai Jiatong University
- Anna Mkrtchyan, University of Western Ontario
- Mostafa Nategh, University of Guelph
- Benoit Palmieri, McGill University
- Robert Peters, McMaster University
- Ganna Piatkovska, University of Western Ontario
- Nikolas Provatas, McGill University
- Joerg Rottler, University of British Columbia
- Andrew Rutenberg, Dalhousie University
- Rafael Schulman, McMaster University
- David Sean, University of Ottawa
- Tyler Shendruk, University of Ottawa
- An-Chang Shi, McMaster University
- Gary Slater, University of Ottawa
- Russell Spencer, University of Guelph
- Yu-Cheng Su, University of Waterloo
- Russell Thompson, University of Waterloo
- John Tatini Titantah, University of Western Ontario
- Shaghayegh Vafaei, University of Guelph
- Qianshi Wei, University of Waterloo
- David Weitz, Harvard University
- Robert Wickham, University of Guelph
Time |
Event |
Location |
8:00-8:30am |
Registration |
Reception |
8:30-8:35am |
Jeff Chen to introduce Dmitry Abanin, Perimeter Institute, for opening remarks |
Theatre |
|
Chair: Russell Thompson, University of Waterloo |
|
8:35-9:15am |
Randall Kamien, University of Pennsylvania |
Theatre |
9:15-9:35am |
Mark Matsen, University of Waterloo |
Theatre |
9:35-9:55am |
An-Chang Shi, McMaster University |
Theatre |
9:55-10:00am |
Conference Photo |
Atrium |
10:00-10:30am |
Coffee Break |
Bistro – 1st Floor |
|
Chair: Mikko Karttunen, University of Waterloo |
|
10:30-10:50am |
Colin Denniston, University of Western Ontario |
Theatre |
10:50-11:10am |
Nikolas Provatas, McGill University |
Theatre |
11:10-11:30am |
Joerg Rottler, University of British Columbia |
Theatre |
11:30-11:50 |
Andrew Rutenberg, Dalhousie University |
Theatre |
11:50-1:40pm |
Lunch |
Bistro – 1st Floor |
|
Chair: Bae-Yeun Ha, University of Waterloo |
|
1:40-2:20pm |
David Weitz, Harvard University |
Theatre |
2:20-2:40pm |
Gary Slater, University of Ottawa |
Theatre |
2:40-3:00pm |
John Bechhoefer, Simon Fraser University |
Theatre |
3:00-3:20pm |
Coffee Break |
Bistro – 1st Floor |
|
Chair: Jeff Chen, University of Waterloo |
|
3:20-6:02pm |
PDF & Graduate Student Presentations |
Theatre |
3:20-3:26pm |
Alena Antipova, University of Western Ontario |
Theater |
3:26-3:32pm |
Matilda Backholm, McMaster University |
Theater |
3:32-3:38pm |
Rafael Schulman, McMaster University |
Theater |
3:38-3:44pm |
Azadeh Bagheri, University of Waterloo |
Theater |
3:44-3:50pm |
Behnaz Bagheri Varnousfaderani, |
Theater |
3:50-3:56pm |
Drew Bennett, University of Waterloo |
Theater |
3:56-4:02pm |
Aidan Brown, Dalhousie University |
Theater |
4:02-4:08pm |
Mykyta Chubynsky, University of Ottawa |
Theater |
4:08-4:14pm |
Ashkan Dehghan, McMaster University |
Theater |
4:14-4:20pm |
Trang Do, University of Waterloo |
Theater |
4:20-4:26pm |
Jie Gao, University of Waterloo |
Theater |
4:26-4:32pm |
Mohamed Amine Gharbi, |
Theater |
4:32-4:38pm |
Mona Habibi, University of Western Ontario |
Theater |
4:38-4:44pm |
Mark Ilton, McMaster University |
Theater |
4:44-4:50pm |
Chanil Jeon, University of Waterloo |
Theater |
4:50-4:56pm |
Yuriy Khalak, University of Waterloo |
Theater |
4:56-5:02pm |
Norman Lam, University of Toronto |
Theater |
5:02-5:08pm |
Yao Li, Tsinghua University |
Theater |
5:08-5:14pm |
Bin Liu, University of Waterloo |
Theater |
5:14-5:20pm |
Anna Mkrtchyan, University of Western Ontario |
Theater |
5:20-5:26pm |
Mostafa Nategh, University of Guelph |
Theater |
5:26-5:32pm |
Benoit Palmieri, McGill University |
Theater |
5:32-5:38pm |
Tyler Shendruk, University of Ottawa |
Theater |
5:38-5:44pm |
Russell Spencer, University of Guelph |
Theater |
5:44-5:50pm |
Yu-Cheng Su, University of Waterloo |
Theater |
5:50-5:56pm |
John Tatini Titantah, |
Theater |
5:56-6:02pm |
Shaghayegh Vafaei, University of Guelph |
Theater |
6:10pm |
Conference Banquet |
Bistro – 1st Floor |
John Bechhoefer, Simon Fraser University
Inferring the spatiotemporal DNA replication program from noisy data
In eukaryotic organisms, DNA replication is initiated at “origins,” launching “forks” that spread bidirectionally to replicate the genome. The distribution and firing rate of these origins and the fork progression velocity form the “replication program.” With Antoine Baker, I generalize a stochastic model of DNA replication to allow for space and time variations in origin-initiation rates, characterized by a function I(x,t). We then address the inverse problem of inferring I(x,t) from experimental data concerning replication in cell populations. Previous work based on curve fitting depended on arbitrarily chosen functional forms for I(x,t), with free parameters that were constrained by the data. We introduce a model-free, non-parametric method of inference that is based on Gaussian process regression, a well-known inference technique from the machine-learning community. The method replaces specific assumptions about the functional form of the initiation rate with more general prior expectations about the smoothness of variation of this rate, along the genome and in time. Using this inference method, we can recover simulated replication schemes with data that are typical of current experiments without having to know or guess the functional form for the initiation rate I(x,t). I will argue that Gaussian process regression has many other potential applications to physics.
Colin Denniston, University of Western Ontario
Building Colloidal Crystals in Anisotropic Media
Colloids in a liquid crystal matrix exhibit very anisotropic interactions. Further, these interactions can be altered by both properties of the colloid and of the liquid crystal. This gives a potential for creating specific colloidal aggregates and crystals by manipulating the interactions between colloids. However, modelling these interacting colloids in a liquid crystal is very challenging. We use a hybrid particle-lattice Boltzmann scheme that incorporates hydrodynamic forces and forces from the liquid crystal field. I will discuss configurations that we have studied, including chains and a potentially stable colloidal crystal with a diamond lattice structure.
Randall Kamien, University of Pennsylvania
O Topology
Yes, quite. But also with some applications
Mark Matsen, University of Waterloo
Monte Carlo Field-Theoretic Simulations Applied to Block Copolymer Melts
Monte Carlo field-theoretic simulations (MC-FTS) are performed on melts of symmetric diblock copolymer for invariant polymerization indexes extending down to experimentally relevant values of N=104. The simulations are performed with a fluctuating composition field, W-(r), and a pressure field, W+(r), that follows the saddle-point approximation. Our study focuses on the disordered-state structure function, S(k), and the order-disorder transition (ODT). Although short-wavelength fluctuations cause an ultraviolet (UV) divergence in three dimensions, this is readily compensated for with the use of an effective Flory-Huggins interaction parameter, e. The resulting S(k) matches the predictions of renormalized one-loop (ROL) calculations over the full range of eN and N examined in our study, and agrees well with Fredrickson-Helfand (F-H) theory near the ODT. Consistent with the F-H theory, the ODT is discontinuous for finite N and the shift in (eN)ODT follows the predicted N-1/3 scaling over our range of N.
Nikolas Provatas, McGill University
Modelling Materials Microstructure Across Scales using Phase Field Methods
Phase field crystal models and their recent extension will be summarized. Their application to non-equilibrium kinetics and phase transformations in materials will be reviewed. In particular, we review new results from applications of this modeling paradigm to solute trapping during rapid solidification of alloys, defect-mediated solid-state precipitation, and magneto-crystalline interactions. We close with a discussion of new complex amplitude representations of PFC models and how these can be used for multi-scale simulations using adaptive mesh refinement methods.
Joerg Rottler, University of British Columbia
Predicting plasticity with soft vibrational modes: from dislocations to glasses
We show how to utilize soft modes in the vibrational spectrum as a universal tool for the identification of defects in solids. Perfect crystals with isolated dislocations exhibit single phonon modes that localize at the dislocation core, and their polarization pattern predicts the motion of atoms during elementary dislocation glide in two and three dimensions in great detail. A superposition of soft modes can be used to construct a population of soft spots that predict the location of local plastic rearrangements at the grain boundaries of polycrystals and in amorphous solids. Additionally, we find a significant correlation between the soft directions of the polarization fields and the atomic displacements that result from elementary shear events.
Andrew Rutenberg, Dalhousie University
Circumferential gap propagation in an anisotropic elastic bacterial sacculus
We have modelled stress concentration around small gaps in anisotropic elastic sheets, corresponding to the peptidoglycan sacculus of bacterial cells, under loading corresponding to the effects of turgor pressure in rod-shaped bacteria. We find that under normal conditions the stress concentration is insufficient to mechanically rupture bacteria, even for gaps up to a micron in length. We then explored the effects of stress-dependent smart-autolysins, as hypothesised by Arthur L Koch. We show that the measured anisotropic elasticity of the PG sacculus can lead to stable circumferential propagation of small gaps in the sacculus. This is consistent with the recent observation of circumferential propagation of PG-associated MreB patches in rod-shaped bacteria. We also find a bistable regime of both circumferential and axial gap propagation, which agrees with behavior reported in cytoskeletal mutants of B. subtilis. We conclude that the elastic anisotropies of a bacterial sacculus, as characterised experimentally, may be relevant for maintaining rod-shaped bacterial growth.
An-Chang Shi, McMaster University
Transition Pathways Connecting Stable and Metastable Phases
Phase transitions are ubiquitous in nature. Understanding the kinetic pathways of phase transitions has been a challenging problem in physics and physical chemistry. From a thermodynamics point of view, the kinetics of phase transitions is dictated by the characteristics of the free energy landscape. In particular, the emergence of a stable phase from a metastable phase follows specific paths, the minimum energy paths, on the free energy landscape. I will describe the characteristics of the minimum energy paths and introduce an efficient method, the string method, to construct them. I will use self-assembled phases of block copolymers as examples to demonstrate the power of the method. In particular, I will show how precisely determined transition pathways provide understanding and surprises when we try to connect the different ordered phases of block copolymers.
Gary Slater, University of Ottawa
Polymer translocation : alternative driving forces
David Weitz, Harvard University
Slow Melting and Fast Crystals
This talk will focus on the behavior of colloidal crystals, and will describe both the nucleation and growth of crystals and their melting. The nucleation and growth of colloidal crystals is experimentally observed to be much faster than expected theoretically or through simulation. The discrepancy can be as much as 10150! I will describe some new experiments that suggest a possible reason for this. I will also describe the melting of colloidal crystals formed with highly charged particles that form a Wigner lattice. I will show that this melting resembles a second-order phase transition, and follows the prediction of Born for a catastrophic collapse of the elastic constant.
Double twist liquid crystal model of collagen structure
Collagen is the main component of connective tissue and the most abundant protein in mammals. The structure of collagen is hierarchical with the triple-helical molecules organizing into fibrils and fibrils contained in higher-order arrangements. A fibril may be considered as a liquid crystal of individual triple helices. Their chiral molecular structure can lead to a macroscopic helical arrangement known as the cholesteric phase which has been observed in fragments of collagen fibrils. The cholesteric orientation can vary with radial distance in the fibril as a double twist.
Thermodynamics of pore formation in lipid bilayers
Lipid bilayers form the basic structure of cellular membranes creating a semi-permeable barrier necessary for separating distinct chemical environments. Hydrophilic pores can form in bilayers that breach the barrier potentially causing cell death or enhance the uptake of hydrophilic molecules. We use molecular dynamics simulations and free energy calculations to investigate pore formation in model bilayers. The free energy barrier for pore formation is much lower in thinner phosphatidylcholine bilayers compared to thicker bilayers.
Transport in molecular scale
Recently there has been a large growth of research effort for nanoelectronic devices.Investigations of quantumly coherent nano-meter scale systems whose fabrication has been made possible by recent advances in experimental and sample preparation techniques have revealed that transport properties could be non-Ohmic and G could be quantized. Understanding electron conduction in such devices is an extremely active research topic.
How are cell concentrations implicated in activity and selectivity of antimicrobial peptides?
Antimicrobial peptides (AMPs) are known to be active against a wide range of microbes. Cell selectivity is an important quality of AMPs which enables them to preferentially bind to and kill the microbes over host cells. Despite its significance in determining the cell selectivity however the cell-concentration dependence of AMP activity has not been criticality examined. Here we present a coarse-grained model for describing how cell concentrations are implicated in AMP's membrane-perturbing activity and selectivity.
Dynamic Force Patterns of an Undulatory Microswimmer
C. elegans is a millimeter-sized nematode which has served as a model organism in biology for several decades primarily due to its simple anatomy. Using an undulatory form of locomotion this worm is capable of propelling itself through various media. Due to the small length scales involved swimming in this regime is qualitatively different from macroscopic locomotion because the swimmers can be considered to have no inertia. In order to understand the microswimming that this worm exhibits it is crucial to determine the viscous forces experienced during its motion.
The viscoelastic properties of the nematode C. elegans
Undulatory motion is utilized by crawlers and swimmers such as snakes and sperm at length scales spanning more than seven orders of magnitude. The understanding of this highly efficient form of locomotion requires an experimental characterisation of the passive material properties of the organism as well as of its active force output on the surrounding medium. The millimeter-sized nematode Caenorhabditis elegans provides an excellent biophysical system for both static and dynamic biomechanical studies.
Dynamics of the magnetic disc in nematic liquid crystal under the action of magnetic field
We simulated Ni disc immersed in a liquid crystal using a lattice Boltzmann algorithm for liquid crystals. In the absence of external torques discs with homeotropic anchoring align with their surface normal parallel to the director of the nematic liquid crystal. In the presence of a weak magnetic field (
Inferring the spatiotemporal DNA replication program from noisy data
In eukaryotic organisms, DNA replication is initiated at “origins,” launching “forks” that spread bidirectionally to replicate the genome. The distribution and firing rate of these origins and the fork progression velocity form the “replication program.” With Antoine Baker, I generalize a stochastic model of DNA replication to allow for space and time variations in origin-initiation rates, characterized by a function I(x,t). We then address the inverse problem of inferring I(x,t) from experimental data concerning replication in cell populations.
Polymer translocation : alternative driving forces
Slow Melting and Fast Crystals
This talk will focus on the behavior of colloidal crystals, and will describe both the nucleation and growth of crystals and their melting. The nucleation and growth of colloidal crystals is experimentally observed to be much faster than expected theoretically or through simulation. The discrepancy can be as much as 10150! I will describe some new experiments that suggest a possible reason for this. I will also describe the melting of colloidal crystals formed with highly charged particles that form a Wigner lattice.
Pages
Scientific Organizers:
Jeff Z. Y. Chen, University of Waterloo
Bae-Yeun Ha, University of Waterloo
Mikko Karttunen, University of Waterloo
Russell Thompson, University of Waterloo