Waterloo Soft Matter Theory

37 talks

December 05, 2013 - December 05, 2013

C13037

Collection TypeConference/School

Source RepositoryPIRSA

DescriptionWaterloo Soft Matter Theory 2013

Displaying 1 - 12 of 37

O Topology

Randall Kamien University of Pennsylvania

December 05, 2013

PIRSA:13120008
Monte Carlo Field-Theoretic Simulations Applied to Block Copolymer Melts

Mark Matsen University of Waterloo

December 05, 2013

PIRSA:13120009
Transition Pathways Connecting Stable and Metastable Phases

An-Chang Shi McMaster University

December 05, 2013

PIRSA:13120010
Building Colloidal Crystals in Anisotropic Media

Colin Denniston Western University

December 05, 2013

PIRSA:13120011
Modelling Materials Microstructure Across Scales using Phase Field Methods

Nikolas Provatas McGill University

December 05, 2013

PIRSA:13120012
Predicting plasticity with soft vibrational modes: from dislocations to glasses

Joerg Rottler University of British Columbia

December 05, 2013

PIRSA:13120013
Circumferential gap propagation in an anisotropic elastic bacterial sacculus

Andrew Rutenberg Dalhousie University

December 05, 2013

PIRSA:13120014
Slow Melting and Fast Crystals

December 05, 2013

PIRSA:13120015
Polymer translocation : alternative driving forces

Gary Slater University of Ottawa

December 05, 2013

PIRSA:13120016
Inferring the spatiotemporal DNA replication program from noisy data

December 05, 2013

PIRSA:13120017
Dynamics of the magnetic disc in nematic liquid crystal under the action of magnetic field

Alena Antipova Western University

December 05, 2013

PIRSA:13120018
The viscoelastic properties of the nematode C. elegans

Matilda Backholm McMaster University

December 05, 2013

PIRSA:13120019

O Topology

Randall Kamien University of Pennsylvania

December 05, 2013

PIRSA:13120008

Yes, quite. But also with some applications.
Monte Carlo Field-Theoretic Simulations Applied to Block Copolymer Melts

Mark Matsen University of Waterloo

December 05, 2013

PIRSA:13120009

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, ce. The resulting S(k) matches the predictions of renormalized one-loop (ROL) calculations over the full range of ceN 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 (ceN)ODT follows the predicted N-1/3 scaling over our range of N.
Transition Pathways Connecting Stable and Metastable Phases

An-Chang Shi McMaster University

December 05, 2013

PIRSA:13120010

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.
Building Colloidal Crystals in Anisotropic Media

Colin Denniston Western University

December 05, 2013

PIRSA:13120011

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.
Modelling Materials Microstructure Across Scales using Phase Field Methods

Nikolas Provatas McGill University

December 05, 2013

PIRSA:13120012

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.
Predicting plasticity with soft vibrational modes: from dislocations to glasses

Joerg Rottler University of British Columbia

December 05, 2013

PIRSA:13120013

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.
Circumferential gap propagation in an anisotropic elastic bacterial sacculus

Andrew Rutenberg Dalhousie University

December 05, 2013

PIRSA:13120014

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.
Slow Melting and Fast Crystals

December 05, 2013

PIRSA:13120015

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.
Polymer translocation : alternative driving forces

Gary Slater University of Ottawa

December 05, 2013

PIRSA:13120016

TBA
Inferring the spatiotemporal DNA replication program from noisy data

December 05, 2013

PIRSA:13120017

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

Alena Antipova Western University

December 05, 2013

PIRSA:13120018

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 (<10G) the disc will rotate to equilibrate the magnetic torque and the elastic torque due to the distortion of the nematic director. When the magnetic field rotates the disc so that the angle between normal to the surface of the disc and director of the liquid crystal becomes greater than the disc goes through the transition in which . The analysis of this behavior was performed.
The viscoelastic properties of the nematode C. elegans

Matilda Backholm McMaster University

December 05, 2013

PIRSA:13120019

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. Here we present a novel experimental technique where the deflection of a force-calibrated micropipette is used to directly probe the viscoelastic material properties of C. elegans. The worm was shown to have a self-similar elastic structure as well as a surprising shear-thinning viscous component (M. Backholm W. S. Ryu and K. Dalnoki- Veress PNAS 110 (2013)). The excellent force (pN) and time (ms) resolution provided by the micropipette deflection technique also enables measurements of the drag forces experienced by the microswimmer as it moves through a liquid. This direct experimental characterisation of C. elegans provides guidance for theoretical treatments of undulatory locomotion in general.

Title	Speaker(s)	Date	Talk Type	Info
O Topology	Randall Kamien	2013-12-05	Conference	View details
Monte Carlo Field-Theoretic Simulations Applied to Block Copolymer Melts	Mark Matsen	2013-12-05	Conference	View details
Transition Pathways Connecting Stable and Metastable Phases	An-Chang Shi	2013-12-05	Conference	View details
Building Colloidal Crystals in Anisotropic Media	Colin Denniston	2013-12-05	Conference	View details
Modelling Materials Microstructure Across Scales using Phase Field Methods	Nikolas Provatas	2013-12-05	Conference	View details
Predicting plasticity with soft vibrational modes: from dislocations to glasses	Joerg Rottler	2013-12-05	Conference	View details
Circumferential gap propagation in an anisotropic elastic bacterial sacculus	Andrew Rutenberg	2013-12-05	Conference	View details
Slow Melting and Fast Crystals		2013-12-05	Conference	View details
Polymer translocation : alternative driving forces	Gary Slater	2013-12-05	Conference	View details
Inferring the spatiotemporal DNA replication program from noisy data		2013-12-05	Conference	View details
Dynamics of the magnetic disc in nematic liquid crystal under the action of magnetic field	Alena Antipova	2013-12-05	Conference	View details
The viscoelastic properties of the nematode C. elegans	Matilda Backholm	2013-12-05	Conference	View details

Supported by

Waterloo Soft Matter Theory

Format results

O Topology

Monte Carlo Field-Theoretic Simulations Applied to Block Copolymer Melts

Transition Pathways Connecting Stable and Metastable Phases

Building Colloidal Crystals in Anisotropic Media

Modelling Materials Microstructure Across Scales using Phase Field Methods

Predicting plasticity with soft vibrational modes: from dislocations to glasses

Circumferential gap propagation in an anisotropic elastic bacterial sacculus

Slow Melting and Fast Crystals

Polymer translocation : alternative driving forces

Inferring the spatiotemporal DNA replication program from noisy data

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

The viscoelastic properties of the nematode C. elegans

O Topology

Monte Carlo Field-Theoretic Simulations Applied to Block Copolymer Melts

Transition Pathways Connecting Stable and Metastable Phases

Building Colloidal Crystals in Anisotropic Media

Modelling Materials Microstructure Across Scales using Phase Field Methods

Predicting plasticity with soft vibrational modes: from dislocations to glasses

Circumferential gap propagation in an anisotropic elastic bacterial sacculus

Slow Melting and Fast Crystals

Polymer translocation : alternative driving forces

Inferring the spatiotemporal DNA replication program from noisy data

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

The viscoelastic properties of the nematode C. elegans