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Molecular Modeling and Chemical Information

Fall 2017

Instructors:  Carl Dirk and James Salvador

Molecular Modeling assignments will be provided by Dr. Dirk through Blackboard and must be submitted through email to cdirk at utep dot edu.

Chemical Information and Programming assignments must be submitted through the course Moodle.

Week Date Molecular Modeling Chemical Information Programming
1 September 1 Introduction in
2 8 Follow the updated syllabus emailed to you by Dr. Dirk
Video instructions through Blackboard
Email your completed homework to
cdirk at utep dot edu for his assignments only.
Logins Downloading and installing the required software. (4:48)
Introduction to Linear Programming. (12:07)
Introduction to Visual Programming. (16:17)
Introduction to Event Programming. (10:38)
First Challenge Exercise: A Simple calculator. (8:08)
3 15   Introduction to Java Bean Components. (6:16)
Introduction to Drawing. (10:18)
Introduction to Event Driven Drawing. (10:04)
Introduction to Lists. (12:22)
Second Challenge Exercise (8:19)
4 22 Namesake Text Search Introduction to Datatypes. (16:43)
Introduction to Translation or Move. (11:36)
Preparing for Rotation. (13:42)
Introduction to Rotation. (8:34)
Third Challenge Exercise: Changing Modes (5:48)
5 29   Introduction to Rolling. (10:42)
Introduction to Scaling. (5:50)
Introduction to Centering. (8:31)
Introduction to Fit. (7:50)
Fourth Challenge Exercise: New... (3:47)
6 October 6 Drawing Search Introduction to removing event methods. (5:08)
Introduction to the electron and extensions. (6:20)
Introduction to properties and methods of atoms and electrons. (4:41)
Introduction to stitching the atoms and electrons. (11:28)
Introduction to drawing the bonds. (7:17)
Fifth Challenge Exercise: Generalizing methods (3:47)
7 13   Introduction to Libraries. (18:05)
Introduction to Displaying Information (7:44)
Introduction to whichAtom (17:49)
Implementing whichAtom (11:27)
Sixth Challenge Exercise: Fixing Problems with if (2:19)
8 20 Properties Search Introduction to Re-Centering (2:44)
Introduction to Z Sorting (14:56)
Preparing the Periodic Table (7:33)
Seventh Challenge Exercise: Periodic Table (14:27)
9 27   Introduction to the Optimization Problem (10:25)
Introduction to Numerical Analysis: Newton Raphson (13:25)
Application of Newton-Raphson to Optimization (9:29)
Implementing Optimization (19:30)
Eighth Challenge Exercise: New Again (4:02)
10 November 3 Reaction Search Introduction to Thread Programming (9:56)
Introduction to Auto Stop (8:06)
Introduction to Writing Files (17:16)
Introduction to Reading Files (13:39)
Ninth Challenge Exercise: Random (2:23)
11 10    Introduction to drawing polygons. (11:42)
Introduction to lighting. (17:39)
Introduction to a parametric plotter. (13:13)
Implementing arch bonds. (20:48)
Tenth Challenge Exercise: Light (1:10)
12 17 Citation Search
Reference Management
Introduction to hemispheres. (12:52)
Fixing the arches. (5:17)
Introduction to perspective. (9:37)
Fixing perspective input. (9:10)
Eleventh Challenge Exercise: Parallax (5:32)
13 24   Holiday-No Classes
14 December 1   Moving One Atom. (9:46)
Rotate and Roll Around an Atom. (10:07)
Manipulation of one molecule. (21.57)
Twist. (16:42)
Twelfth Challenge Exercise: Templates. (10:10)
15 8   Holiday-No Classes


After being graded, 5 % per day will be deducted for late submissions.  For example, if your work earned a 90 % but you turned it in 2 days late, then your grade for that assignment will be 80 %.

All molecular modeling, chemical information, and programming assignments will be weighted equally. 

Your assignment grades will be averaged to give your course grade as follows:   A > 89.5 %, B > 79.5 %, C > 69.5 %, D > 59.5 %.

 

jsal at utep dot edu

PSCI 203C, 308

Telephone: (915) 747-5704

Office Hours: TR 9:00 to 10:30 am in PSCI 203C or 308