CS/Math 4414: Issues in Scientific Computing - Spring

Tue/Thu 2:00 - 3.15 pm WHIT 257 (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:    by request.
GTA: Dan Folescu (Project related issues, including AMBER and visualization)          
Office:               ask GTA

Dan's Email: dan1345@vt.edu                dan1345@vt.edu
Office Hours: by request.    
Recommended Texts:
Syllabus: PDF
Instructor Lectures (the order may change) :
  • Class project introduced (Notes on Canvas)
  • 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, TBA (late April).
  • Ten Simple Rules for Making Good Oral Presentations
  • Example Presentations:
  • Evaluations of student talks
    Homeworks. Individual work and Group work. For group work assignments, **Each** group member submits groups' work (PDF), with his/her name, group number, and the names of all the partners indicated. Individual work (when specified): each student submits his/her work (PDF). Submission to canvas in all cases.
  • First HW. Playing with the energy (objective) function: simple examples. GROUP WORK. Due Feb. Submit via Canvas.
  • HW3. Pitfalls of numerical optimization. GROUP WORK. Due TBA, 11 pm. Submit via Canvas.
  • HW. Explore a model of the pandemic. Due TBA, 11 pm. INDIVIDUAL WORK. Submit via Canvas
    Homework Solution Hints will be available on CANVAS within about two weeks 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