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Simulating the Capture and Translocation of Rigid fd Viruses though a Nanopore
Hendrick de Hann University of Ontario Institute of Technology
PIRSA:14050036Recent advances in the search for complementary sequences
Ilias Kotsireas Wilfrid Laurier University
PIRSA:14050040Anomalies of discrete symmetries and Symmetry Protected Topological Phases
Anton Kapustin California Institute of Technology (Caltech) - Division of Physics Mathematics & Astronomy
Noncommutative geometry and the symmetries of the standard model
Fedele Lizzi University of Naples Federico II
The Case for an Alternative Cosmology
Jayant Narlikar IUCAA - The Inter-University Centre for Astronomy and Astrophysics
John Paul Robinson: Art, Science and Myth
PIRSA:14050062
Biological graph dissimilarity characterization using graph theory
PIRSA:14050043Many biological data sets and relationships can be modeled as graphs. Understanding how structure of these graphs relates to biological function is essential for understanding underlining mechanisms of disease and for aiding drug discoveries. Vertices of biological graphs represent individual entities such as genes and proteins. Edges represent the relationship between two cellular components such as physical and functional interactions. A challenging problem in the post-genomic era is graph comparisons as they are large typed complex and evolving. Comparing graph structures helps to gain insights into the underlying signaling mechanisms and treatments for complex diseases. With technological advancement biological data will continue to grow and so will the size and complexity of graphs.Large graph comparisons are computationally intensive as they involve the subgraph isomorphism problem which is NP-complete. Therefore graph comparison algorithms need to be efficient scalable and be able to systematically capture biologically meaningful graph structure differences. Efficient graph comparison algorithms are necessary for many types of biological graphs e.g. protein-protein interaction drug-target microRNA-gene gene-regulatory and co-expression graphs. Furthermore graph comparison algorithms are extremely useful for many applications such as comparing graphs characterizing different diseases representing different cancer subtypes or different drug treatment responses. There are two main categories of graph properties used for comparing biological graphs global graph properties and local graph properties. Global graph properties study the overall graph while local graph properties focus on local structures of the graph. Our objective is to develop an efficient scalable graph comparison algorithm such that graph structure differences between any two states can be obtained systematically. We achieve the objective in two steps. First we propose an algorithm such that graph structure differences are systematically obtained and verified that the differences are biologically meaningful. Then we develop a heuristic to improve upon the proposed algorithm in the first step in terms of efficiency and scalability. While our approaches are generic we apply it on non-small cell lung cancer data sets. The non-small cell lung cancer datasets are used to construct normal and tumor co-expression graphs. Global graphs properties do not contain the detail needed to capture the structural characteristics of biological graphs thus we used a local property graphlets. Graphlets are all non-isomorphic connected induced graphs on a specific number of vertices. By definition graphlets have the ability to capture all the local structures on a certain number of vertices. Results showed that our graphlet approach returns graph structure differences between normal and tumor conditions that correspond to biological knowledge. We then introduce a heuristic to identify areas that are likely to be different between the normal and tumor graph and perform graph comparisons on the identified areas only. The heuristic was able to achieve interesting results that were successfully validated in vitro.Modelling Surface Driven Flows in the Ocean
Eric Bembenek University of Waterloo
PIRSA:14050047Buoyancy driven flows at the top of the ocean or bottom of the atmosphere are inherently different from their interior dynamics. Oneidealized model that has recently become very popular to idealizethese surface flows with strong rotation is Surface Quasi-Geostrophic (SQG) dynamics. This model is appropriate for large-scale dynamics and assumes the motion is in near geostrophic and hydrostatic balance. Many of the numerical simulations of SQG have shown thatvortices are frequently generated at very small scales scales thatare well beyond the SQG limits.In this talk we examine the dynamics of a rotating three-dimensionalelliptic vortex in both the SQG model and a more general and muchmore complicated primitive equation model. In order to compute highresolution solutions to the three dimensional primitive equations we make use of Sharcnet resources. We find that in the case of strongrotation (small Rossby number) we confirm the predictions from SQG.With weaker rotation (moderate Rossby number) we see the non-SQG effects that arise and find that the regime where SQG can beappropriate can be very limited. We conclude that some of thepredictions that arise from the SQG model might not be very accuratein idealizing geophysical flows at the surface.Solving initial-boundary value problems without numerical differentiation
PIRSA:14050042The numerical solution of nonlinear partial differential equations with nontrivial boundary conditions is central to many areas of modelling. When high accuracy is required (pseudo) spectral methods are usually the first choice. Typically in this approach we search for the pre-image under a linear operator which represents a combination of spatial derivatives along with the boundayr conditions in every time step. This operator can be quite ill-conditioned. On a basis of Chebyshev polynomials for instance the condition number increases algebraically with the number of basis functions. I will present an alternative method based on recent work by Viswanath and Tobasco which avoids numerical differentiation entirely through the use of Green's functions. I will demonstrate this method on the Kuramoto-Sivashinsky equation with fixed boundary conditions.HPC Application in Large Eddy Simulation of Fuel Spray / Air Jet interaction
PIRSA:14050046Along with the development of computational resources computational fluid dynamics (CFD) has evolved in resolving the finest length scales and smallest time scales of the flow. Direct numerical simulation (DNS) resolves the finest flow scales known as Kolmogorov length scales which are responsible for the dissipation of the energy transferred from the large and intermediate length scales. However DNS simulations are computationally costly and demand very powerful resources which are not widely available to this day. Large eddy simulation (LES) is a more feasible tool to resolve the large flow scales and model the sub-grid scales using a Reynolds averaged modeling. High performance computing tools make it possible to perform high fidelity large eddy simulations which reasonably (almost twelve times the Kolmogorov length scale) resolve the flow structures.In the present study large eddy simulation is utilized to simulate interaction of a high speed compressible round air jet with a group of sprays injected from a six-hole nozzle injector into the shear layer of the air jet. Fuel sprays are injected with 10 and 15 MPa injection pressures in the jet cross flows of 125 and 215 m/s. Simulations are performed using 64 processors and 240 GB of memory. The focus of the study is on the spray atomization assisted by air jet cross-flow. Consequent processes of fuel/air mixing are also investigated by focusing on the role of vortical structures resolved using large eddy simulation.New insights into polymer-induced drag reduction in turbulent flows
PIRSA:14050041Polymer additives are known to cause significant reduction in turbulent friction drag and reduce the energy dissipation rate of fluid transport. This effect is however bounded by a universal upper limit the maximum drag reduction (MDR) asymptote that does not change with polymer properties. Understanding MDR remains an important unsolved problem in the areas of turbulence and non-Newtonian fluid mechanics. Dynamical trajectories on the boundary in state space between laminar and turbulent plane channel flow - edge states - are computed for Newtonian and viscoelastic fluids. Viscoelasticity has a negligible effect on the properties of these solutions and at least at a low Reynolds number their mean velocity profiles correspond closely to experimental observations for polymer solutions in the MDR regime. These results confirm the existence of weak turbulence states that cannot be suppressed by polymer additives explaining the fact that there is an upper limit for polymer-induced drag reduction.Simulating the Capture and Translocation of Rigid fd Viruses though a Nanopore
Hendrick de Hann University of Ontario Institute of Technology
PIRSA:14050036The passage of long biological molecules from one side of a membrane to the other through a nanoscale hole has been the subject of intense research in recent years. Motivated by the possibility of new sequencing technologies the focus of this work has been studying the translocation of DNA across biological and synthetic membranes. In this talk I will present results from a joint experimental-simulation study examining the translocation of rod-like fd viruses through a nanopore. While DNA is relatively flexible the fd virus has a persistence length that is over twice that of its contour length and is thus stiff. In principle translocation in this rod-like limit is much easier to model. However I will show that experimental results for the distribution of translocation times exhibit significant deviations from the expected result. I will present a model for fd translocation that was developed to probe these results. Simulations based on this model yield insight into previously unclear experimental results including i) details of how the polymer is capture by the pore at different external fields ii) a correlation between the translocation time and the conformation at capture and iii) sources for the increased dispersion in the translocation time distributions.Recent advances in the search for complementary sequences
Ilias Kotsireas Wilfrid Laurier University
PIRSA:14050040We will present recent developments in the search for complementary sequences namely new theoretical and algorithmic progress. SHARCNET resources are used quite heavily in this project.Scattering of emerging excitations in Matrix Product States
Jutho Haegeman Ghent University
We review the formalism of matrix product states and one of its recent generalisations which allows to variationally determine the dispersion relation of elementary excitations in generic one-dimensional quantum spin chains. These elementary excitations dominate the low energy effective behaviour of the system. We discuss recent work where we show how we can also describe the effective interaction between these excitations – as mediated by the strongly correlated ground state – and how we can extract the corresponding S matrix. With these two ingredients, we can already build a highly non-trivial low-energy description of any microscopic Hamiltonian by assuming that higher order scattering processes are negligible. This allows to extract accurate information about the behaviour of the system under perturbations or at finite temperature, as we illustrate using the spin 1 Heisenberg model.Anomalies of discrete symmetries and Symmetry Protected Topological Phases
Anton Kapustin California Institute of Technology (Caltech) - Division of Physics Mathematics & Astronomy
There is a close connection between Symmetry Protected Topological Phases and anomalies: a surface of an SPT phase typically has a global symmetry with a nonvanishing 't Hooft anomaly which is canceled by the anomaly inflow from the bulk. This observation together with the known results about the classification of SPT phases suggest that anomalies are much more ubiquitous than thought previously and do not require chiral fermions We elucidate the physical mechanism of anomalies and give examples of bosonic theories with 't Hooft anomalies in various dimensions.Noncommutative geometry and the symmetries of the standard model
Fedele Lizzi University of Naples Federico II
I will describe Connes approach to the standard model based on spectral noncommutative geometry with particular emphasis on the symmetries. The model poses constraints which are satisfied by the standard model group, and does not leave much room for other possibilities. There is however a possibility for a larger symmetry (the ``grand algebra'') which may also be instrumental to obtain the correct mass of the Higgs.The Case for an Alternative Cosmology
Jayant Narlikar IUCAA - The Inter-University Centre for Astronomy and Astrophysics
This talk will describe the Quasi-Steady State Cosmology proposed in 1993 by Fred Hoyle, Geoffrey Burbidge and Jayant Narlikar. Starting with the motivation for this exercise, a formal field theoretic framework inspired by Mach’s principle is shown to lead to this model. The model is a generalization of the classical steady state model in the sense that it is driven by a scalar field which causes creation in explosive form. Such ‘minicreation events’ lead to a universe with a long term de Sitter expansion superposed with oscillations of shorter time scales. It is shown that this cosmology explains all the observed cosmological features and that there exist potential tests to distinguish between this cosmology and the standard big bang cosmology.John Paul Robinson: Art, Science and Myth
PIRSA:14050062Canadian glass artist and Renaissance man, John Paul Robinson, explores the mythic potential of science. Explaining that, “This is the idea that scientific discovery is changing our mythology by changing our understanding of the world and our place in it.” Backed with a firm understanding of the science he references, his sculptures poetically interpret such theoretical phenomena as wave particles, string mathematics and black holes. Most people, especially scientists see mythology and science as mutually exclusive and many believe that a scientific understanding of the world will eventually eliminate the need for myth. This idea is based on a misunderstanding as to what myth really is and it’s relationship to science. Myth is not superstition, fairy tail or lies nor is it truth, history or fact. Myth is Art. Myth is a picture, a story, a map; we use to navigate the world. Not the external material world but the world we all create and hold in our minds. In every human mind is a mythic picture of the world that provides the stage for all we experience. This picture not only helps us navigate our world but also performs the critical function of informing our sense of place and belonging within that world. Science cannot replace myth but it can inform it for mythology deals not with the mysteries generated by our ignorance of how the world works but by our understanding of how the world works. The mathematics of string theory is a powerful tool to describe the world but even physicists have to close their eyes and picture in their minds the world their equations are describing. The equation is pure logic and reason, but the picture of tiny strings playing the music that creates the universe is pure mythology. Award-winning glass artist and instructor John Paul Robinson was educated at the Georgian College of Arts and Technology in Barrie, Ontario, and the Ontario College of Art, where he subsequently taught for a number of years. His work has been exhibited in solo shows throughout Canada and the United States, in cities such as Montreal, Toronto and Chicago. Robinson’s works are held in the collections of The Museum of Civilization in Ottawa, Ontario, the Museum of American Glass in Millville, New Jersey and the Musée des Beaux-arts de Montréal, Québec. He has also created the Amber Archive, an annual participatory art project to communicate our existence and creative endeavours (by artists, designers and scientists) to beings millions of years in the future.