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Modeling of RNA Nanotube using Molecular Dynamics Simulation
Shyam Badu Wilfrid Laurier University
PIRSA:14050058Holographic Path to the Turbulent Side of Gravity
Stephen Green University of Nottingham
PIRSA:14050038Motion of disc-shaped colloids and pairs of colloidal discs in a nematic liquid crystal
Alena Antipova Western University
PIRSA:14050057Polycrystalline On-Lattice Kinetic Monte Carlo Simulations of Electrodeposition
Nasser Mohiedden Abukhdeir University of Waterloo
PIRSA:14050055
Critical Behavior of the Classical XY-model on Fractal Structures
PIRSA:14050060There has been considerable interest in determining whether the universality hypothesis extends to systems which are of non-integer dimension or to systems which are scale invariant (fractals). Specifically research into these types of systems is concerned with determining the relevance of topological properties to their critical phenomena. We have performed Monte Carlo simulations for the XY model on three fractal lattices with different topological properties: the Sierpinski pyramid Menger sponge and Sierpinski carpet. We will give an overview of our results and show that while some properties such as the order of ramification are important in determining the critical behavior of these structures the fractal dimension is not.Validation of predicted mRNA splicing mutations using high-throughput transcriptome data
PIRSA:14050059This work has been published:Viner C Dorman SN Shirley BC and Rogan PK (2014)Validation of predicted mRNA splicing mutations using high-throughput transcriptome data [v1; ref status: indexedhttp://f1000r.es/2no]F1000Research20143:8 (doi:10.12688/f1000research.3-8.v1)Additionally this work has been accepted for a highlights presentation at the upcoming Great Lakes Bioinformatics Conference (GLBIO) in Cincinnati Ohio and it was recently presented as a poster at London Health Research Day (LHRD).Abstract:Interpretation of variants present in complete genomes or exomes reveals numerous sequence changes only a fraction of which are likely to be pathogenic. Variants predicted to alter mRNA splicing in particular can be validated by manual inspection of transcriptome sequencing data however this approach is intractable for large datasets. We show that abnormal mRNA splicing patterns are characterized by reads demonstrating either exon skipping cryptic splice site use and high levels of intron inclusion or combinations of these properties. This paper presents Veridical an in silico method for the automatic validation of DNA sequencing variants that alter mRNA splicing. Veridical leverages large numbers of control samples (that lack a putative mutation) applying z-tests to Yeo-Johnson transformed data to normalize read counts of abnormal RNA species in mutant versus non-mutant tissues. With the transformed data the null hypothesis based mainly on either counts of intronic or junctional reads can be rejected for true splicing mutations using conventional parametric statistical methods.Simulations of Binary Neutron Star Mergers
Marcelo Ponce University of Toronto
PIRSA:14050053By numerically solving Einstein equations we are able to study the strong regime of gravity. In many astrophysical scenarios strong gravity plays a fundamental role such as compact binary systems: e.g. Black Hole binaries binary Neutron Stars and Black Hole-Neutron Star systems. In this talk I will discuss the simulations our group has been conducting in binary Neutron Star system where we can study the dynamics and gravitational radiation of the systems but also establish important connections with electromagnetic counterparts and even testing alternatives theories of gravity (i.e. Scalar-Tensor theories).Modeling of RNA Nanotube using Molecular Dynamics Simulation
Shyam Badu Wilfrid Laurier University
PIRSA:14050058We construct the novel RNA nanpclusters- the RNAnanotubes made of several nanorings. We study the struc-tural properties (i.e. the Root Mean Square Deviation (RMSD)the radius of gyration and radial distribution function) ofRNA nanotube up to the size of about 20nm in physilogicalsolution that can be used for drug delivery into human body.We model RNA nanotube by utilizing molecular dynamicssimulation method implemented in NAMD and VMD. Thepatterns of energy and temperature variations of the systemsare also discussed. Furthermore we study the number of ionsaround the tube as a function of time at a particular temper-ature. We find that if the temperature increases the numberof ions increases within certain distance of the tube. We re-port that the number of ions within a certain distance aroundthe tubes decrease in quenched run. This indicates that someions evaporate with decrease in temperature aHolographic Path to the Turbulent Side of Gravity
Stephen Green University of Nottingham
PIRSA:14050038We study the dynamics of a 2 1-dimensional relativistic viscous conformal fluid in Minkowski spacetime. Such fluid solutions arise as duals under the gravity/fluid correspondence to 3 1-dimensional asymptotically antide Sitter (AAdS) black-brane solutions to the Einstein equation. We examine stability properties of shear flows which correspond to hydrodynamic quasinormal modes of the black brane. We find that for sufficiently high Reynolds number the solution undergoes an inverse turbulent cascade to long-wavelength modes. We then map this fluid solution via the gravity/fluid duality into a bulk metric. This suggests a new and interesting feature of the behavior of perturbed AAdS black holes and black branes which is not readily captured by a standard quasinormal mode analysis. Namely for sufficiently large perturbed black objects (with long-lived quasinormal modes) nonlinear effects transfer energy from short- to long-wavelength modes via a turbulent cascade within the metric perturbation. As long-wavelength modes have slower decay this transfer of energy lengthens the overall lifetime of the perturbation. We also discuss various implications of this behavior including expectations for higher dimensions and the possibility of predicting turbulence in more general gravitational scenarios.Tree-Based Cosmological Radiative Transfer
PIRSA:14050052One of the most challenging problems in computational galaxy formation is modeling distant heating and ionization by locally produced radiation. Most Radiative Transfer (RT) techniques are very computationally expensive and limit users to poor resolution or post-processing thus decoupling the radiation from the dynamics of the simulation. We present a new efficient method for RT implemented in the SPH code GASOLINE aimed at full cosmological simulations. The method is tree-based (similar to a gravity solver) scaling as N$_sinklogN_source$ in the optically thin case and as N$_sinklogN_sourcelogN_tot$ in the optically thick case. Applications range from the reionization of the Universe to H$_2$ formation and destruction. First applications focus on FUV and EUV emission from Milky Way-type galaxies and how these affect satellites galaxies.Motion of disc-shaped colloids and pairs of colloidal discs in a nematic liquid crystal
Alena Antipova Western University
PIRSA:14050057In the present work the motion of disc-shaped particles in a nematic liquid crystal was simulated via a Lattice Boltzmann algorithm. Under the action of a rotating magnetic field the colloidal disc with perpendicular surface anchoring immersed in a nematic liquid crystal experiences a torque and continues turning following the field. However when the disc reaches some critical position when the director field around it is highly distorted the disc suddenly flips to minimize the free energy. Analyzing this motion and consequently the behaviour of two discs placed close together we examine the possible uses of this peculiar flip behaviour.A Fourth-Order Solution-Adaptive CENO Scheme for Space-Physics Flows on Three-Dimensional Multi-Block Cubed-Sphere Grids
PIRSA:14050051Accurate efficient and scalable computational methods are highly desirable for large-scale scientific computing applications especially for problems exhibiting spatial and temporal multi-resolution scales non-trivial geometries and complex boundary conditions (BSc). For global magnetohydrodynamics (MHD) modelling of space-physics problemshigh-performance approaches could significantly reduce the grid requirements to achieve targeted solution accuracies thereby enabling more affordable yet accurate predictions of space-plasma flows. Key challenges encountered relate to providing solenoidal magnetic fields accurate discretizations on spherical domains capturing of MHD shocks and implementing accurate BCs. This talk gives an overview of a fourth-order finite-volume discretization procedure in combination with a parallel solution-adaptive algorithm for the computation of MHD space plasmas on cubed-sphere grids. Numerical results to demonstrate the accuracy and capability of the multidimensional high-order solution-adaptive cubed-sphere computational framework are presented.Uses of HPC in radar data processing and analysis
PIRSA:14050056A low troposphere MST type radar located in Costa Rica was used to gather information up to 6 km. With the digital radar technique used thousands of sweeps can be recorded every second. Challenges in processing spectral analysis and radar imaging were addressed with tools provided by HPC.Polycrystalline On-Lattice Kinetic Monte Carlo Simulations of Electrodeposition
Nasser Mohiedden Abukhdeir University of Waterloo
PIRSA:14050055The effects of the microstructure of metal films on device performance and longevity have become increasingly important with the recent advances in nanotechnology. Depending on the application of the metal films and interconnects certain microscopic structures and properties are preferred over others. A common method to produce these films and interconnects is through electrodeposition. As with every process the ability to control the end product requires a detailed understanding of the system and the effect of operating conditions on the resulting product. To address this problem a three-dimensional on-lattice kinetic Monte Carlo (KMC) method is developed to conduct atomistic simulations of polycrystalline metal electrodeposition. The method utilizes the highly descriptive embedded-atom method (EAM) potential to accurately describe the interatomic interaction energy. The EAM potential is a semi-empirical multi-body potential that accounts for the cohesive forces in a metallic system. Its parameters are determined from known experimental data.In the presented study kinetically controlled copper electrodeposition onto polycrystalline copper under potentiostatic conditions is modeled using the aforementioned KMC method. Two plating modes are considered: direct current and pulsed-plating. Three surface processes are considered during electrodeposition: deposition dissolution and surface diffusion. In addition to the surface processes diffusion along grain boundaries is also considered. The KMC method presented in this study is capable of simulating the copper electrodeposition process at the atomic level over long time scales on the order of seconds. The computational requirement of these serial KMC simulations are a fraction (hours versus days) of that required by the parallel molecular dynamics (MD) approach to simulate the same process over the much shorter time scales on the order of nanoseconds. Consequently this KMC method allows for the simulation of electrodeposition processes over time scales that are experimentally-relevant and not feasible using MD.Fast calculation of electro thermo static and elasticity fields in 3D-medium with isolated inclusions using application of Gaussian approximating functions
PIRSA:14050050The problem of calculation of electro and thermo static fields in an infinite homogeneous medium with a heterogeneous isolated inclusion (Kanaun et al) has shown to be reduced to the solution of integral equations for the fields inside the inclusion using Gaussian functions (V. Mazya) for the approximation of the unknown fields. Using this approach coefficients of the matrix of the discretized system will be obtained in closed analytical forms. Only information necessary to carry out the method is the coordinates of the centers of the Gaussian functions (nodes) in the region occupied by the inclusion ie. a mesh-free method. Using a regular grid of nodes the matrix of the discretized problem will have a Teoplitzs structure. Hence Fast Fourier Transform (FFT) technique can be used for the calculation of the matrix-vector products within an iterative solution of the system of linear algebraic equations of the discretized problem. The proposed algorithm is simple fast and does not require much computer memory. In practice this has led to over ten folds reduction in the required computational time and the allocated memory space and enabling consideration of very fine grids not possible with other tried solution methods. Comparisons of the numerical and exact solutions for electrostatic fields inside spherical inclusions with step changing properties are presented here. Second boundary value problem of elasticity for 3D-bodies with cracks is another problem where this approach has been applied successfully. References:S. Kanaun and S. Babaii A numerical method for the solution of thermo and electro static problems for a medium with isolated inclusions Journal of Computational Physics 192 471-493 (2003).V. Mazya Approximate approximation in The Mathematics of Finite Elements and Applications. highlights 1993 edited by J.R. Whitman 77 Wiley Chichester (1994).S. Kanaun A. Markov and S. Babaii An efficient numerical method for the solution of the second boundary value problem of elasticity for 3D- bodies with cracks Int J Fract DOI 10.1007/s10704-013-9885-5