Double twist liquid crystal model of collagen structure
Aidan Brown Dalhousie University
PIRSA:13120023
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Thermodynamics of pore formation in lipid bilayers
Drew Bennett University of Waterloo
PIRSA:13120022How are cell concentrations implicated in activity and selectivity of antimicrobial peptides?
Azadeh Bagheri University of Waterloo
PIRSA:13120020Dynamic Force Patterns of an Undulatory Microswimmer
Rafael Shulman McMaster University
PIRSA:13120038The viscoelastic properties of the nematode C. elegans
Matilda Backholm McMaster University
PIRSA:13120019Dynamics of the magnetic disc in nematic liquid crystal under the action of magnetic field
Alena Antipova Western University
PIRSA:13120018BBN and the Unnatural Weak Scale
David Pinner University of California, Berkeley
From spin foams to anyons and back again - Joint Condensed Matter/Quantum Gravity Seminar
Bianca Dittrich Perimeter Institute for Theoretical Physics
Slow Melting and Fast Crystals
PIRSA:13120015
Double twist liquid crystal model of collagen structure
Aidan Brown Dalhousie University
PIRSA:13120023Collagen 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. We numerically minimize mean-field Frank free energy in the bulk to solve for the liquid crystal orientation as a function of radial distance (r). By also considering surface terms the overall energy per fibril area is minimized to find the optimal fibril radius R and molecule orientation on the fibril surface (R) both of which may be compared to experimental measurements.Thermodynamics of pore formation in lipid bilayers
Drew Bennett University of Waterloo
PIRSA:13120022Lipid 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. The free energy barrier is due to an unfavourable change in entropy while the enthalpy of pore formation is favourable. These results have implications on a wide range of biological and biotechnological applications such as drug delivery antimicrobial peptides and transmembrane structure and stability.Transport in molecular scale
Behnaz Bagheri Varnousfaderani University of Waterloo
PIRSA:13120021Recently 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. Our theoretical goal is to predict quantum transport properties of molecular nanodevices including their I-V characteristics from first principle theoretical method.How are cell concentrations implicated in activity and selectivity of antimicrobial peptides?
Azadeh Bagheri University of Waterloo
PIRSA:13120020Antimicrobial 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
Rafael Shulman McMaster University
PIRSA:13120038C. 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. Using a micropipette deflection technique in conjunction with high speed imaging we have directly measured the time-varying forces generated by C elegans during swimming. Furthermore by analyzing the bodys kinematics over time and applying a simple model of locomotion we can compute the theoretical force curves. We observe excellent agreement between the measured and calculated forces. The success of this simple model has important implications in the understanding of microswimming in general.The viscoelastic properties of the nematode C. elegans
Matilda Backholm McMaster University
PIRSA:13120019Undulatory 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.Dynamics of the magnetic disc in nematic liquid crystal under the action of magnetic field
Alena Antipova Western University
PIRSA:13120018We 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.BBN and the Unnatural Weak Scale
David Pinner University of California, Berkeley
The discovery of a perturbatively-coupled, 125 GeV Higgs, together with the absence of LHC signals for supersymmetry, places the principle of naturalness under tension. In this talk I will discuss the possibility that the weak scale is unnatural, with its value determined environmentally in the landscape. In particular, this environmental selection may be driven by BBN: as the weak scale is increased, the abundance of Hydrogen in the early universe is rapidly depleted. That our own universe contains an O(1) fraction of primordial Helium arises as a conspiracy among the weak scale, the neutron-proton mass difference, and the planck scale.Inferring the spatiotemporal DNA replication program from noisy data
PIRSA:13120017In 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.From spin foams to anyons and back again - Joint Condensed Matter/Quantum Gravity Seminar
Bianca Dittrich Perimeter Institute for Theoretical Physics
Spin foams provide models for quantum gravity and hence quantum space time. One of the key outstanding questions is to show that they reproduce smooth space time manifolds in a continuum limit.I will start with a very short introduction to spin foams and the structure of quantum space time they encode. I will explain how the investigation of the continuum limit via coarse graining and renormalization techniques led as to consider anyonic spin chains and a classification of ground states in systems with quantum group symmetries.I will then present new results on the continuum limit of spin net models, that allow us to draw first conclusions about the large scale dynamics of spin foams.
Based on: B.D., W. Kaminski, Topological lattice field theories from intertwiner dynamics, arXiv:1311.1798, B.D., S. Steinhaus, Time evolution as refining, coarse graining and entangling, to appear, B.D. M. Martin-Benito, S. Steinhaus, The refinement limit of quantum group spin net models, to appearPolymer translocation : alternative driving forces
Gary Slater University of Ottawa
PIRSA:13120016TBASlow Melting and Fast Crystals
PIRSA:13120015This 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.