{"id":146,"date":"2016-07-26T11:57:54","date_gmt":"2016-07-26T11:57:54","guid":{"rendered":"http:\/\/mech.sharif.ir\/~nejat\/?p=146"},"modified":"2019-06-11T10:52:40","modified_gmt":"2019-06-11T10:52:40","slug":"introduction-to-computational-nanoscience","status":"publish","type":"post","link":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/2016\/07\/26\/introduction-to-computational-nanoscience\/","title":{"rendered":"Introduction to Computational Nanoscience"},"content":{"rendered":"
\n

Syllabus:<\/strong>\u00a0<\/strong><\/span><\/p>\n

Molecular Dynamics<\/strong><\/span><\/p>\n

Introduction to the Application of the Molecular Dynamics for Modeling of the Nano-scale Systems<\/span><\/p>\n

Interatomic Potentials<\/span><\/p>\n

Energy Minimization and Related Methods for Exploring Energy Surfaces<\/span><\/p>\n

Computer Simulation Methods<\/span><\/p>\n

Molecular Dynamics Simulations Methods<\/span><\/p>\n

Introduction to Coarse Graining Methods<\/span><\/p>\n

Monte Carlo<\/strong><\/p>\n

Finite Difference Applications\u00a0for PDEs<\/strong><\/p>\n

 <\/p>\n

\n

References:<\/strong><\/p>\n

    \n
  1. A. R. Leach, Molecular Modelling: Principles and Applications, Prentice Hall, 2001.<\/li>\n<\/ol>\n
      \n
    1. J. M. Haile, Molecular Dynamics Simulation: Elementary Methods, \u00a0Wiley-Interscience<\/li>\n<\/ol>\n
        \n
      1. D. C. Rapaport , \u201cThe Art of Molecular Dynamics Simulation\u201d, Cambridge University Press, 2004.<\/li>\n<\/ol>\n
          \n
        1. W. Humphrey, A. Dalke, and K. Schulten, \u201cVMD \u2013 Visual Molecular Dynamics\u201d, Journal of Molecular Graphics, vol. 14, p. 33-38, 1996.<\/li>\n<\/ol>\n
            \n
          1. J. C. Phillips et al., \u201cScalable molecular dynamics with NAMD,\u201d Journal of computational chemistry, vol. 26, no. 16, p. 1781, 2005. \u201cNAMD A Parallel Object-Oriented Molecular Dynamics Program\u201d<\/li>\n<\/ol>\n
              \n
            1. \u201cLAMMPS Molecular Dynamics Simulator\u201d. Sandia National Laboratories. Retrieved 2010-10-03.<\/li>\n<\/ol>\n

              introductory-finite-difference-methods-for-pdes<\/a><\/p>\n

              MATLAB Primer<\/a><\/p>\n

              \n

              Codes<\/span><\/span><\/p>\n<\/div>\n

              Parabolic PDE<\/a><\/p>\n

              ode_RK4<\/a><\/p>\n

              Hyperbolic PDE<\/a><\/p>\n

              Elliptic PDE<\/a><\/p>\n

              \n

              Slides:<\/p>\n

              Chapter1<\/a><\/p>\n

              Chapter2<\/a><\/p>\n

              Chapter3<\/a><\/p>\n

              Chapter4<\/a><\/p>\n

              Chapter5_2<\/a><\/p>\n

              Chapter6 – Monte Carlo1<\/a><\/p>\n

              \n

               <\/p>\n

              HW:<\/p>\n

              HW1<\/a><\/p>\n

              HW2_N<\/a><\/p>\n

              HW3_Nano<\/a><\/p>\n

              HW4:\u00a0VMD_HM<\/a><\/p>\n

              HW 5:\u00a0HW5_N<\/a><\/p>\n

              HW 6:\u00a0HW6N_MD<\/a><\/p>\n

              HW7:\u00a0HW7_NAMD<\/a><\/p>\n

              HW8:\u00a0LAMMPS<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

              Syllabus:\u00a0 Molecular Dynamics Introduction to the Application of the Molecular Dynamics for Modeling of the Nano-scale Systems Interatomic Potentials Energy Minimization and Related Methods for Exploring Energy Surfaces Computer Simulation Methods Molecular Dynamics Simulations Methods Introduction to Coarse Graining Methods Monte Carlo Finite Difference Applications\u00a0for PDEs   References: A. R. Leach, Molecular Modelling: Principles and[…]<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[9],"tags":[],"_links":{"self":[{"href":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/wp-json\/wp\/v2\/posts\/146"}],"collection":[{"href":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/wp-json\/wp\/v2\/comments?post=146"}],"version-history":[{"count":29,"href":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/wp-json\/wp\/v2\/posts\/146\/revisions"}],"predecessor-version":[{"id":853,"href":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/wp-json\/wp\/v2\/posts\/146\/revisions\/853"}],"wp:attachment":[{"href":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/wp-json\/wp\/v2\/media?parent=146"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/wp-json\/wp\/v2\/categories?post=146"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/mech.sharif.edu\/~nejat\/index.php\/wp-json\/wp\/v2\/tags?post=146"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}