How are cell concentrations implicated in activity and selectivity of antimicrobial peptides?
Azadeh Bagheri University of Waterloo
PIRSA:13120020
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Dynamic Force Patterns of an Undulatory Microswimmer
Rafael Shulman McMaster University
PIRSA:13120038 -
The viscoelastic properties of the nematode C. elegans
Matilda Backholm McMaster University
PIRSA:13120019 -
Dynamics of the magnetic disc in nematic liquid crystal under the action of magnetic field
Alena Antipova Western University
PIRSA:13120018 -
BBN and the Unnatural Weak Scale
David Pinner University of California, Berkeley
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From spin foams to anyons and back again - Joint Condensed Matter/Quantum Gravity Seminar
Bianca Dittrich Perimeter Institute for Theoretical Physics
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Slow Melting and Fast Crystals
PIRSA:13120015 -
Using the Higgs as a Direct Probe of New Physics
Michael Park Rutgers University
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Circumferential gap propagation in an anisotropic elastic bacterial sacculus
Andrew Rutenberg Dalhousie University
PIRSA:13120014 -
Predicting plasticity with soft vibrational modes: from dislocations to glasses
Joerg Rottler University of British Columbia
PIRSA:13120013
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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 appear -
Polymer translocation : alternative driving forces
Gary Slater University of Ottawa
PIRSA:13120016TBA -
Slow 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. -
Using the Higgs as a Direct Probe of New Physics
Michael Park Rutgers University
The discovery of the Higgs boson marks the first direct probe into the mechanism of electroweak symmetry breaking. All evidence currently points to the fact that electroweak symmetry is broken by at least one fundamental scalar, and naturalness remains the most compelling reason to expect additional degrees of freedom at the weak scale. This talk will describe some ideas for how to utilize powerful and proven experimental techniques, in conjunction with the fact that observables directly related to the Higgs boson are now experimentally accessible, to make concrete statements about the existence of possible new degrees of freedom at the weak scale. -
Circumferential gap propagation in an anisotropic elastic bacterial sacculus
Andrew Rutenberg Dalhousie University
PIRSA:13120014We 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. -
Predicting plasticity with soft vibrational modes: from dislocations to glasses
Joerg Rottler University of British Columbia
PIRSA:13120013We 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.