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Dynamics of the magnetic disc in nematic liquid crystal under the action of magnetic field
Alena Antipova Western University
PIRSA:13120018 -
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The viscoelastic properties of the nematode C. elegans
Matilda Backholm McMaster University
PIRSA:13120019 -
Dynamic Force Patterns of an Undulatory Microswimmer
Rafael Shulman McMaster University
PIRSA:13120038 -
How are cell concentrations implicated in activity and selectivity of antimicrobial peptides?
Azadeh Bagheri University of Waterloo
PIRSA:13120020 -
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Thermodynamics of pore formation in lipid bilayers
Drew Bennett University of Waterloo
PIRSA:13120022 -
Double twist liquid crystal model of collagen structure
Aidan Brown Dalhousie University
PIRSA:13120023 -
"Diffusing diffusivity": A model of "anomalous yet Brownian" diffusion
Mykyta Chubynsky University of Ottawa
PIRSA:13120024 -
Emergence of Hierarchical Morphologies in Binary Blends of Diblock Copolymers
Ashkan Dehghan McMaster University
PIRSA:13120025 -
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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.
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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. -
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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. -
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. -
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. -
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. -
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. -
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. -
"Diffusing diffusivity": A model of "anomalous yet Brownian" diffusion
Mykyta Chubynsky University of Ottawa
PIRSA:13120024Wang et al. [PNAS 106 (2009) 15160] have found that in several systems, the linear time dependence of mean-square displacement (MSD) of diffusing colloidal particles, typical of normal diffusion, is accompanied by a non-Gaussian displacement distribution (DD), with roughly exponential tails at short times, a situation termed “anomalous yet Brownian” diffusion. We point out that lack of “direction memory” in the particle trajectory (a jump in a particular direction does not change the probability of subsequent jumps in that direction) is sufficient for a strictly linear MSD (assuming that the system is pre-equilibrated), but if at the same time there is “diffusivity memory” (a particle diffusing faster than average is likely to keep diffusing faster for some time), the DD will be non-Gaussian at short times. A gradual change in diffusivity can be due to the environment of the particle changing slowly on its own, the particle moving between different environments, or both. In our model, this is represented by the particle diffusivity itself undergoing a (perhaps biased) random walk (“diffusing diffusivity”). Roughly exponential tails of the DD, as in experiment, are observed in several variants of the model. -
Emergence of Hierarchical Morphologies in Binary Blends of Diblock Copolymers
Ashkan Dehghan McMaster University
PIRSA:13120025The self-assembled structures formed in binary blends of AB/CD diblock copolymers are studied using self-consistent field theory focusing on cases with attractive A/C and repulsive B/D interactions. The attractive A/C interaction prevents macroscopic phase separation whereas the repulsive B/D interaction promotes B/D separation leading to the formation of complex hierarchical structures. The combination of these features makes the AB/CD blend an ideal model system for the study of hierarchical self-assembly. Our results demonstrate that the B/D separation leads to the emergence of modulated and alternate morphologies from the classical lamellar hexagonal spherical and gyroid structures. A common phase transition sequence from the mixed to modulated to alternate B/D structures is observed as a function of B/D interaction strength. The theoretical predictions of our model are consistent with available experiments and more importantly provide an interesting route for the engineering of hierarchically ordered structures using block copolymer blends. -
Studying protein adsorption on bone surfaces using molecular simulations
PIRSA:13120026Mineral-associated proteins have been proposed to play a central role not only in assisting the growth of biomineral crystals in hard tissues but also in preventing or limiting mineral formation in soft tissues. The elucidation of protein-biomineral interactions may lead to the design of mineralized tissues with novel properties and most importantly the development of therapies for common diseases such as kidney stones calcification in blood vessels osteoporosis etc. However the mechanism of the interaction at this unique organic-inorganic interface is still poorly understood. X-ray crystallography techniques have provided important information on the adsorbed states. Unfortunately these methods have limitations in determining the driving forces of the adsorption and the underlying roles played by the lattice ions and ionic solutions. We employ all-atom enhanced-sampling simulations and free-energy calculation techniques to characterize these interactions with the final goal of designing proteins with improved adsorption properties and capacity to prevent or enhance crystal growth.