Simulating Chemistry, Biochemistry and Materials
Science
Syllabus
General Information:
Instructor: Maria Alexandra Gomez
Class Hours: MWF 10:00-10:50 AM in Kendade 303
Office hours: M, F 1-2PM; Tu, Th 11AM-12PM or by appointment.
Office Location: G22C Carr Laboratory
Email: magomez@mtholyoke.edu
Web Page: http://www.mtholyoke.edu/courses/magomez/SimulatingChemistry
This course introduces the concepts of computational chemistry, biochemistry,
and materials science through a sequence of projects. The projects are linked
by a common theme. This semester's theme is understanding chronic beryllium
disease.
Exposure to beryllium
oxide by inhalation from beryllium, beryllium oxide, and
beryllium/copper alloy processing plants has been linked to chronic
beryllium disease (CBD). Once the beryllium oxide
particulates are deposited on the lung membrane, macrophages engulf the
particles. In the low pH (about 4.8) of the macrophage's
lysosomal digestive fluid,
beryllium oxide dissolves. Infected macrophages aggregate and form granulomas at the surface of the lungs. Scar tissue from the granulomar formation
and inflamation from the immune response reduce the breathable lung tissue.
This causes breathing difficulties and eventually death. Currently, there
is no cure.
In a series of projects, we will study the material structure of beryllium
oxide, the chemistry of beryllium oxide dissolution,
and finally how the beryllium oxide dissolved products interact with
common biomolecules in macrophages. As we do this, we will learn some of
the standard algorithms in computational sciences and explore the pathway to
the disease.
Grading Policy:
- Projects 60%
- Reviews 20%
- Term Paper 20%
This course is composed of a series of projects and a final term paper.
After you complete each
project, you will write a scientific article for submission to a
journal. Your peers will serve as reviewers. After you receive
their review, you can revise your article and turn in a final
manuscript for grading. Articles on projects are due for review on dates followed by an "A" at the start of class. Reviews are due on dates followed by an "R" at
the start of class. Final submissions are due on dates followed
by an "F." The final submissions and the reviews will be graded.
Requirements for each project paper will be discussed on project discussion days.
No work is accepted after the due date. Articles not submitted
by the due date are not eligible for a final submission.
Finally, there is a term paper on your view of chronic beryllium disease. The term paper is in lieu of a final which is due during the final examination period.
Schedule:
| Topic | Date |
| I. Introduction |
Chronic beryllium disease | 9/8 |
| Using library resources | 9/11 |
| Sources of beryllium and likely structure inhaled | 9/13 |
| Project 1: Structure of beryllium oxide and its surfaces | 9/15, 9/18 |
| Guest Lecturer: Sharon Stranford | 9/20 |
| Writing articles for publication and project discussion | 9/22, 9/25 |
|
| II. Potential energy surface structure | Minima and saddle points
| 9/27 |
| Introduction to unix | 9/29A |
| Project 2: Hydroxylation of the BeO (100) and (001) surfaces | 10/2, 10/4R,10/6,10/11F,10/13 |
| Project 2 discussion | 10/16 |
|
| III. Moving on the potential energy surface |
Molecular dynamics and Monte Carlo | 10/18 |
| Project 3:
Search for BeO dissolution products
| 10/20A, 10/23, 10/25R |
| IV. Solvation |
Dielectrics
| 10/30F |
| Quasi-chemical theory
| 11/1 |
|
Further analysis of project 3 data
| 11/3, 11/8, 11/15,11/17, 11/19 |
| V. Considering equilibrium thermodynamics |
Coupled equilibrium reactions
| 11/27 |
|
Project 4: Finding the most probable beryllium complexes in solution at lysosomal digestive fluid pH.
| 11/29, 12/1, 12/4 |
| Project 4 discussion
| 12/6A |
| VI. Interaction with amino acids |
Amino acid structure and pH
| 12/8R |
|
Putting it all together - planning sessions for term paper
| 12/11F, 12/13 |
|
