CS/Math 4414: Issues in Scientific Computing - Spring 2022

Tue/Thu 5.00 - 6.15 MCB 136 (zoom when necessary, link on CANVAS)


"All is number", Pythagoras

"The purpose of computing is insight, not numbers", R. H. Hamming


Instructor:        Alexey Onufriev
Office:              2160C Torgersen Hall
Phone:              (540)231-4237
Email:               onufriev@cs.vt.edu
Office Hours:    Wed. 2-4 pm, by request.
GTAs: Niteya Shah (Hws and Unix Issues only) and Dan Folescu (Project related issues, including AMBER and visualization)          
Office:               ask GTA
Niteya' Email: niteya@vt.edu               niteya@vt.edu
Office Hours: Tue/Thu 3.30 - 4.30 until further notice.    

Dan's Email: dan1345@vt.edu                dan1345@vt.edu
Office Hours: by request.    
Recommended Texts:
Syllabus: PDF
Instructor Lectures:
  • Class project introduced
  • Proteins 101
  • The Energy Function to be minimized.
  • Finding minimum of a function in 1D: Newton's method.
  • Intro to mutidimensional optimization: steepest descent, conjugate gradient. Notes on why global optimization is so difficult.
  • Advanced Optimization: Simulated Annealing (lecture notes on Canvas).
  • Advanced Optimization: Nelder-Mead method (lecture notes on Canvas).
  • Advanced Optimization: Genetic Algorithm (lecture notes on Canvas).
  • The new way of supercomputing: GPU. Introduction.
  • Scientific Visualization
  • Advanced Scientific Software Libraries: Num. Recipies, GLS, NetLib.
  • In class: quick estimates of what is computationally feasible
  • Computational thinking. Laplace's Daemon. Philosophical notes on computation.
  • Student presentations of select research papers (see options below).

    Student Presentations. One presentation per group, ~25 mins. Each group picks one topic from the list below. 25 points. Due: In class, April 26, carry over to May 3rd.
  • Ten Simple Rules for Making Good Oral Presentations
  • Example Presentations:
  • Evaluations of student talks
    UNIX Basics. Each student submits 3 separate solutions via Canvas.
    Homeworks. Group work (unless otherwise stated). **Each** group member submits groups' work (PDF), with his/her name, amd names of all the partners indicated. Individual work (when specified): each student submits his/her work (PDF). Submission to canvas in all cases.
  • HW1. Explore a model of the pandemic. Due Feb 14, 11 pm. GROUP WORK. Submit via Canvas
  • HW2. Playing with the energy (objective) function: simple examples. INDIVIDUAL WORK. Due March 28, 11 pm. Submit via Canvas.
  • HW3. Pitfalls of numerical optimization. INDIVIDUAL WORK. Due TBA, 11 pm. Submit via Canvas.
    Homework Solution Hints will be available on CANVAS within about a week after due date.

    The Project:
  • Brief project info. Read this first.
  • What to present, when, and how
  • Final report template
  • Final report template files



    Project Milestones and Due Dates: Project-specific notes and deliverables.
    Computer Resources