PPT-Survey of Molecular Dynamics Simulations

By Will Welch For Jan Kubelka CHEM 45605560 Spring 2017 University of Wyoming Why Molecular Dynamics 1 Scale Large collections of interacting particles that cannot and should not be studied by quantum mechanics . FORMATION. Konstantinos Tassis. Collaborators: . Karen Willacy, Harold . Yorke. , Neal Turner (JPL/Caltech) . . . Talayeh. . Hezareh. (. MPIfR. ). University of Crete. The Initial . Damjan. . Temelkovski. Dr.. . Tamas. Kiss. Dr.. Gabor . Terstyanszky. University of Westminster. Molecular Docking. a.k.a. . in-. silico. docking. Simulating the interaction between two molecules: . By Will Welch. For Jan . Kubelka. CHEM 4560/5560. Fall, 2014 . University of Wyoming. Forces on each particle are calculated at time t. The forces provide trajectories, which are propagated for a . small duration of time, . 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. Bridging Length Scales. Sara M. Hashmi, Ph.D.. Director, Facility for Light Scattering. 786. Asphaltenes. Most aromatic component of petroleum fluids. Industrial nuisance. Form pickering emulsions in oil spills. 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. Z.T. Wang, Y.G. Wang, R. Mu, Y. Yoon, A. Dahal, G.K. Schenter, V.A. Glezakou, R. Rousseau, I. Lyubinetsky, and Z. Dohnálek, . PNAS. . Embargo release Feb. 6th.. Detailed measurements coupled with theoretical calculations provide unprecedented level of detail about water deprotonation. 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 . CO J =1-0 + J =3-2 map (Oka+ 1999, 2007) Galactic Center Kunihiko Tanaka (1) , Tomoharu Oka (1) , Shinji Matsumura (1) , Kazuhisa Kamegai (2) , Makoto Nagai (3) , Testuo Hasegawa (4) (1) Keio University (2) ISAS/JAXA(3) KEK (4) Joint Alma Office Aqueous Solvation in Extreme Conditions: Accurate Calculations when Accurate Measurements are not PossiblePresented by…William L. HaseWelch Professor, Department of Chemistry & BiochemistryTexas 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 . A.L. Gillian-Daniel, B. L. Taylor. Materials Research Science and Engineering Center (MRSEC) . University of Wisconsin-Madison. Nanotechnology. is the understanding and control of matter . 1 to 100 nanometers in size. 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 .