WestGrid Seminars - Fall 2010

Wednesday, October 6, 2010
Getting Started: An Introduction to WestGrid
Speaker: Doug Phillips, Scientific Computing Consultant, IT, UofC
This introductory seminar focuses on utilizing WestGrid Systems and will provide an overview of WestGrid operations, including an introduction to Compute Canada and the national HPC landscape.

To view the online documentation, click here

To download the archived videoclick here


Wednesday, October 20, 2010
Watching Biomolecules Move: Computer Simulations of Lipids and Membrane Proteins
Speaker: Peter Tieleman, Professor, Department of Biological Sciences, UofC
Direct simulation of complex biomolecules such as proteins, nucleic acids, and lipids has become a powerful and useful method to study details of how such molecules interact with each other, with water, ions, and with other molecules. Computer simulations of atoms and molecules have a firm basis in physical chemistry, particularly statistical mechanics and thermodynamics. Over 30 years ago the first simulation of a small protein was published in Nature. At the time, there was one computer in Europe powerful enough for this type of calculation. The average modern cell phone is orders of magnitude more powerful than this computer; the stunning increase in computer power over the past decades has been a major driving force in an incredible increase in the use of computer simulations. They are now widely used in all research areas that deal with atoms and molecules, including biochemistry and biophysics, drug design, and materials research. We are primarily interested in processes that involve lipids: the properties of cell membranes, membrane proteins, and monolayers such as those formed by lung surfactant. I will give a brief introduction of the principles behind modern biomolecular simulation, focusing on the widely used molecular dynamics method. I will illustrate the power of these simulations with a number of recent applications, including the interactions of fullerenes with a model membrane, the behavior of lung surfactant, and the interactions between cholesterol and phospholipids.

To view the presentation slides, click here <still to come...>

To download the archived videoclick here 

 

Wednesday, November 3, 2010
Molecular Simulations of Biomolecules
Gurpreet Singh, PDF, UofC

This introductory seminar will provide an overview of the most commonly used computational tools for studying biomolecules, mainly focusing on potential energy function and its evaluation, general molecular dynamic simulation algorithm, and current methods for free energy calculations implemented in molecular simulation package GROMACS. This session will build upon Dr. Tieleman’s presentation. From the early use of computers to study various aspects of liquids and gases by modeling them as hard spheres, computer simulations now days are routinely used to study dynamics of complex molecules such as proteins, carbohydrates, nucleic acids, and lipid membranes. Computer simulations have became a useful tool in understanding the dynamics and mechanism of function of these molecules with atomistic details. New sampling methods coupled with increased computational resources have made it possible to simulate the folding of small peptides and proteins. The underlying parameters or force-fields used in atomistic representation have matured to the point that free energies calculated using computer simulations methods are in quantitative agreements with experiments.

 

To view the presentation slides, click here

To download the archived video, click here 

 

 

Wednesday, November 17, 2010
Multi-sensory Exploration of Large Scientific Data Using Virtual Reality
Speaker: Pierre Boulanger, Professor, Department of Computing Science, UofA

By exploiting our visual abilities, traditional scientific visualization aims at offering engineers and scientists various ways to assist them at exploring complex phenomenon. What Virtual Reality (VR) technologies has to offer is to put an expert user at the center of the exploration process that utilise not only his visual abilities but also his multi-sensory senses such as touch and sound. To improve the effectiveness of the traditional data exploration process, many researchers has focused on the development of more intuitive interaction techniques that exploits the sensory-motor capacity of humans to deal with complex environments. To achieve this goal two conditions need to be respected. First, exploitation of different modalities must not oppose one another, and each sensory
channel must be rendered in a way that fits with human abilities. During this talk, I will explore how VR can create a true multi-sensory interface by using high-resolution displays, haptics, and sound. We will explore the current state of the art and discuss our implementation for a virtual wind tunnel application and the exploration of medical data.

To view the presentation slides, click here

To download the archived video, click here 

 

 

Wednesday, December 1, 2010
Recent Developments of Closed-loop Simluation and Visualization Interfaces Using GPU
Speaker: Pierre Boulanger, Professor, Department of Computing Science, UofA

Abstract: This introductory seminar will focus on the use of GPUs for programming and computation. This session will build upon Dr. Boulanger's presentation. The recent advances of Graphic Processing Unit (GPU) capable of performing not only graphic calculations but also general computing at order of magnitude faster than the traditional CPU has revolutionized the way Engineers and Scientists can explore complex phenomena. The processing power of GPU is an unprecedented revolution in computing by offering large scale parallel multi-treads computing and true high-speed interconnects at low cost. Today's GPU can now help us bridge the gap between simulation and visualization, allowing us to develop true computational steering environments. In this talk, we will review the most recent advances in GPU development and describe how it can be used for closed-loop simulation and visualization.

 

To view the presentation slides, click here

To download the archived video, click here