"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:
Numerical Mathematics and Computing, Cheney & Kincaid (the basics of numerical methods, a refresher course )
Computational Physics: Problem Solving with Computers, Rubin H. Landau, Manuel J. Páez and Cristian C. Bordeianu (an intro text with lots of examples worked out in detail. Scientific computing focused on the problem, rather than method )
Numerical Recipes in C (or C++), W. H. Press, et al. (The bible
of scientific computing for those who approach the subject from the application perspective, i.e. physicists, chemists, etc. )
The beginner's guide to Mathematica, J. Glynn et al. (A really good, albeit somewhat dated, intro into Mathematica. Lots of cool, easy to follow and non-trivial examples ).
Introduction to UNIX, D. Schwartz . (A nice thin book with lots of detailed examples. Perfect for those not on first name basis with UNIX )
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.
Alpha-fold: A Deep Learning micracle [Base your discussion on this blog, which gives a 30 thousand feet view of the algorithm and its main chievements ]
Discuss "Folding at home" (what that is, the main idea, success stories, current state).
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.
Brainstorming results due in class, Due Feb 17. No more than 15
min. per group presentation + 3 min discussion
with the rest of the class. For details,
including the format, and how many points you can earn,
see "what to present, when and how", above.
For deliverables, see "Starting notes" below.
Mid-term progress reports (15 mins. per group. + 2 mins for questions)
due in class, March 31. For details of
the format, and how many points you can earn,
see "what to present, when and how", above. Deliverables are outlined in
"Starting notes", and detailed in Mid-term specific notes below.
Pre-final progress reports due in class, April 28 For details,
including the format and how many points you can earn,
see "what to present, when and how", below.
Final report: see "what to present, when and how", above. Deliverables are outlined in "Starting notes", and detailed in Final report
specific notes below. Submit via
VT Canvas. Due by May 9, 9pm. No exceptions under any circumstance.