Waterloo Soft Matter Theory Conference

Conference Date: 
Thursday, December 5, 2013 (All day)
Pirsa Collection: 
Scientific Areas: 
Condensed Matter

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
O Topology

Theatre

9:15-9:35am

Mark Matsen, University of Waterloo
Monte Carlo Field-Theoretic Simulations Applied to Block Copolymer Melts

Theatre

9:35-9:55am

An-Chang Shi, McMaster University
Transition Pathways Connecting Stable and Metastable Phases

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
Building Colloidal Crystals in Anisotropic Media

Theatre

10:50-11:10am

Nikolas Provatas, McGill University
Modelling Materials Microstructure Across Scales using Phase Field Methods

Theatre

11:10-11:30am

Joerg Rottler, University of British Columbia
Predicting plasticity with soft vibrational modes: from dislocations to glasses

Theatre

11:30-11:50

Andrew Rutenberg, Dalhousie University
Circumferential gap propagation in an anisotropic elastic bacterial sacculus

Theatre

11:50-1:40pm

Lunch

Bistro – 1st Floor

 

Chair:  Bae-Yeun Ha, University of Waterloo

 

1:40-2:20pm

David Weitz, Harvard University
Slow Melting and Fast Crystals

Theatre

2:20-2:40pm

Gary Slater, University of Ottawa
Polymer translocation : alternative driving forces

Theatre

2:40-3:00pm

John Bechhoefer, Simon Fraser University
Inferring the spatiotemporal DNA replication program from noisy data

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
Dynamics of the magnetic disc in nematic liquid crystal under the action of magnetic field

Theater

3:26-3:32pm

Matilda Backholm, McMaster University
The viscoelastic properties of the nematode C. elegans

Theater

3:32-3:38pm

Rafael Schulman, McMaster University
Dynamic Force Patterns of an Undulatory Microswimmer

Theater

3:38-3:44pm

Azadeh Bagheri, University of Waterloo
How are cell concentrations implicated in activity and selectivity of antimicrobial peptides?

Theater

3:44-3:50pm

Behnaz Bagheri Varnousfaderani,
University of Waterloo
Transport in molecular scale

Theater

3:50-3:56pm

Drew Bennett, University of Waterloo
Thermodynamics of pore formation in lipid bilayers

Theater

3:56-4:02pm

Aidan Brown, Dalhousie University
Double twist liquid crystal model of collagen structure

Theater

4:02-4:08pm

Mykyta Chubynsky, University of Ottawa
"Diffusing diffusivity": A model of "anomalous yet Brownian" diffusion

Theater

4:08-4:14pm

Ashkan Dehghan, McMaster University
Emergence of Hierarchical Morphologies in
Binary Blends of Diblock Copolymers

Theater

4:14-4:20pm

Trang Do, University of Waterloo
Studying protein adsorption on bone surfaces using molecular simulations

Theater

4:20-4:26pm

Jie Gao, University of Waterloo
Phase behavior of long worm-like chain
confined in a cavity

Theater

4:26-4:32pm

Mohamed Amine Gharbi,
University of Pennsylvania
Assembly of microparticles on thin smectic films

Theater

4:32-4:38pm

Mona Habibi, University of Western Ontario
Effect of wetting on micelle fragmentation in
confined channels

Theater

4:38-4:44pm

Mark Ilton, McMaster University
Quantized contact angles in the dewetting of a
structured liquid

Theater

4:44-4:50pm

Chanil Jeon, University of Waterloo
Spatial organization of a ring copolymer confined in a cylindrical space

Theater

4:50-4:56pm

Yuriy Khalak, University of Waterloo
Improving the Martini model: coarse-graining with dynamic charges and polarization

Theater

4:56-5:02pm

Norman Lam, University of Toronto
Electrostatics

Theater

5:02-5:08pm

Yao Li, Tsinghua University
Topological defects of tetratic liquid-crystal order on a soft spherical surface

Theater

5:08-5:14pm

Bin Liu, University of Waterloo
Molecular dynamics studies of Langmuir
monolayers of cationic/PC lipids

Theater

5:14-5:20pm

Anna Mkrtchyan, University of Western Ontario
A Study on Dynamics of Tissue Growth Using
Single Cell Based Model

Theater

5:20-5:26pm

Mostafa Nategh, University of Guelph
The rocky road from non-equilibrium work to free energy

Theater

5:26-5:32pm

Benoit Palmieri, McGill University
Phase-field model for cellular monolayers :
a cancer cell migration studyauthors :
Benoit Palmieri and Martin Grant

Theater

5:32-5:38pm

Tyler Shendruk, University of Ottawa
Electrophoretic Mobility within a Confining Well

Theater

5:38-5:44pm

Russell Spencer, University of Guelph
Dynamical simulation of disordered micelles in a diblock copolymer melt with fluctuations

Theater

5:44-5:50pm

Yu-Cheng Su, University of Waterloo
Budding transition of a self-avoiding polymer confined by a soft membrane adhering onto a flat wall

Theater

5:50-5:56pm

John Tatini Titantah,
University of Western Ontario
Ab initio insight in supercooled water

Theater

5:56-6:02pm

Shaghayegh Vafaei, University of Guelph
Calculating the free energy of antimicrobial peptide (HHC-36) dimerization in bulk

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.

 

 

Thursday Dec 05, 2013

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.

Collection/Series: 

 

Thursday Dec 05, 2013
Speaker(s): 

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.

Collection/Series: 

 

Thursday Dec 05, 2013

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.

Collection/Series: 

 

Thursday Dec 05, 2013
Speaker(s): 

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.

Collection/Series: 

 

Thursday Dec 05, 2013
Speaker(s): 

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.

Collection/Series: 

 

Thursday Dec 05, 2013
Speaker(s): 

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.

Collection/Series: 

 

Thursday Dec 05, 2013
Speaker(s): 

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 (

Collection/Series: 

 

Thursday Dec 05, 2013
Speaker(s): 

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.

Collection/Series: 

 

Thursday Dec 05, 2013

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.

Collection/Series: 

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