PPT-High Throughput Parallel Molecular Dynamics

HTPMD Steve Cox RENCI Engagement Overview High Throughput Parallel Computing Molecular Dynamics First User Solution Bigger Challenges Workflow and Hybrid Computing Objectives Exploit parallel processing . microlens. array. Antony Orth and Kenneth . Crozier. 8 . May. CLEO . 2012. Microscopy with lens arrays. What is high . thoughput. microscopy?. Experimental setup – . confocal. system. Lens array characteristics, resolution. High-speed Networks. Esma. . Yildirim. Data Intensive Distributed Computing Laboratory. University at Buffalo (SUNY). Condor Week 2011 . Motivation. Data grows larger hence the need for speed to transfer it. FORMATION. Konstantinos Tassis. Collaborators: . Karen Willacy, Harold . Yorke. , Neal Turner (JPL/Caltech) . . . Talayeh. . Hezareh. (. MPIfR. ). University of Crete. The Initial . Denise Chac. 10 October 2014. Immunology. The study of the human immune system . Lymphocytes. B Cells. Membrane bound antibody. Activation: bind to pathogen and triggered by helper T cells. MHC II proteins present antigen peptide on cell surface. Yu-Shan . Lin (YSL). Department of . Chemistry. Tufts . University. Simulate how molecules move. Molecular dynamics simulations. km. hr. v. . (0). = . =. . 100. = 1000 kg. = . −. 7000 N. m. s. 2. MMPBSA. D. G. free. D. G. bound. (1) Use free energy perturbation methods to estimate relative free energies. . DD. G =. D. G. free. - . D. G. bound. how to estimate free energies?. D. G?. ?. (2) Estimate potential of mean force along pathway? (but, what. Luke Winslow. OWI a-la-carte. Overview. What is Parallel Computing. Example Uses. Intro to Condor. Demo. Parallel Computing. Cluster. Why would I need this?. Dealing with Large Datasets. Lake Shape Characteristics. Frictional . Contact: Differential . Variational . Inequality Approaches. Final Thoughts, ME751. April 20, . 2010. © Dan Negrut, . 2010. ME751. , UW-Madison. “. All you need is ignorance and confidence and the success is sure. Ananth Grama. . Computer Science, Purdue University. ayg@cs.purdue.edu. Outline. Introduction. Molecular Dynamics Methods vs. ReaxFF. Sequential Realization: SerialReax. Algorithms and Numerical Techniques. Physics 5403: Computational Physics. Physics. 5403: . Computational. . Physics. - . Chapter. 6: . Molecular. Dynamics. 1. 6.0 Overview. What is molecular dynamics (MD)?. Numerical method for studying many-particle systems such as molecules, clusters, and even macroscopic systems such as gases, liquids and solids . Understanding New Tools from Federal Chemical Testing Programs . Linda Birnbaum. , Ph.D., D.A.B.T., A.T.S.. Director, National Institute of Environmental Health Sciences and National Toxicology Program. A CERN . openlab. / Intel collaboration. Niko Neufeld, CERN/PH-Department. niko.neufeld@cern.ch. HTCC in a nutshell. Apply upcoming Intel technologies in an Online / Trigger & DAQ context. Application domains: L1-trigger, data acquisition and event-building, accelerator-assisted processing for high-level trigger. Frontend. Dan Bradley. Center for High Throughput Computing. Condor Flocking. CHTC. Condor. Pool. CS. Nuclear Eng.. Genomics. CMS Tier 2. Atlas Tier 3. Chemical Engineering. IceCube. Medical. Physics. Anna Maria Nardiello. 1,. *, Lucia Sessa. 1,2. , Jacopo Santoro. 1. and Stefano Piotto. 1,2. 1. . Department of Pharmacy, University of Salerno, . Fisciano. , 84084, Italy. 2. . Research. Centre for .