Programming for Engineers Course Notes

Title Page [65 KB]

Table of Contents [52 KB]

1. Introduction. Getting Started [121 KB] Introduction to the course. Introduction to programming languages. Introduction to Mathematica. References and resources. Getting started. Exercise: A Tour of Mathematica.

2. Expressions and Evaluation [114 KB] Introduction. Expressions. Evaluation. Assignment. Lists and tables. Problems.

3. Rules and Patterns [87 KB] Introduction. Rules. Patterns. Compound expressions. Problems

4. Writing Functions [82 KB] Introduction. Understanding function definitions. Clearing function definitions. An example with three variables. Summary: The form of a function definition. Problems.

5. Writing Modules [112 KB] Introduction. The need for modules. A template for using a module. How to develop a module. Advanced concept: How modules keep values local. Problems.

6. Functional Programming [114 KB] Introduction. Map. Apply. Thread. Outer. Anonymous functions. Nest. NestList. FixedPoint. Summary: When to use functional programming. Problems.

7. Rule-based Programming [101 KB] Introduction. Constraining rules with simple patterned arguments. Constraining rules with x_Head. Constraining rules through predicates. Constraining rules through conditions. Problems.

8. Graphics Programming [227 KB] Introduction. Showing graphics objects. The FullForm of a graphics object expression. Two dimensional graphics primitives. Graphics options. Style directives. Controlling graphic output. Graphics packages. Graphics arrays. Animation. Problems.

9. Concluding Techniques [107 KB] Introduction. Timing. Printing. Advanced patterns. Recursion. Dynamic programming. Procedural programming. Problems.

A. Packaging Your Program [87 KB] Introduction. Documenting a program. Your workbook. Your journal. The package. The User Guide. Problem. A final note on the art of programming.

B. Programming Project [170 KB] Introduction. Build your model. Setting up your data. Exploring the performance.

C. Past Test Questions [138 KB]

• Teat 1: Expressions evaluation, rules, and patterns
• Test 2: Writing functions
• Test 3: Using modules
• Test 4: Functional programming
• Test 5: Rule-based programming
• Test 6: Graphics programming
• Test 7: Concluding techniques
• Test 8: Packaging your program

Introduction to Metabolic Biochemistry

Overview

• Introduction to Metabolism
• Internet Databases
• How to use KEGG

Lipid Metabolism

• Fatty Acid Metabolism
• Phospholipids and Membrane Biosynthesis
• Glycolipids and Glycoproteins
• Cholesterol, Bile Acids, and Steroid Hormones

Carbohydrate Metabolism

• Glycolysis & Gluconeogenesis
• Glycogen/Starch, Pentose Phosphate Pathway
• Membrane Transport
• Facilitated Glucose Transport
• Mitochondrial Carriers

Energy Metabolism

• Citric Acid Cycle
• Oxidative Phosphorylation
• Photosynthesis
• Nitrogen Metabolism
• Nitrogen Fixation and Urea Cycle
• Amino Acid Metabolism
• Neurotransmitters
• Nucleic Acid Metabolism
• Nitric oxide

Cellml.org - Metabolic Pathways

Understanding the mechanism involved in metabolic regulation has important implications in both biotechnology and in medicine. For example, it is estimated that at least a third of all serious health problems such as coronary heart disease, diabetes and strokes are caused by metabolic disorders. Due to the integrated nature of metabolism, it is often difficult to predict how changing the activity of a single enzyme will affect the entire reaction pathway.

Mathematical kinetic models have been applied to help elucidate the behaviour of biochemical networks. Many of these kinetic models have been published, but presented here are the raw CellML descriptions of metabolic models which have been based on textbook defined pathways. We have assumed that all enzyme-catalysed reactions have Michaelis-Menten kinetics, and that all non-catalysed reactions have mass action kinetics. All metabolites and enzymes have a default concentration of one micromolar, and km, vmax and reaction rate constants also have a default value of one.

• Carbohydrate Metabolism — glycolysis, gluconeogenesis, the pentose phosphate pathway, the electron transport chain and the TCA cycle.
• Lipid Metabolism — fatty acid activation and oxidation, fatty acid synthesis, cholesterol biosynthesis, phospholipid synthesis, glycolipid synthesis and triacylglycerol synthesis.
• Nitrogen Metabolism — transamination, purine and pyrimidine synthesis and degradation, amino acid catabolism, non-essential amino acid synthesis and the urea cycle.

Metabolic Diagrams

Carbohydrate Metabolism

• Figure 1. Glycolysis.glycolysis with encapsulation
• Figure 2. Glycolysis.
• Figure 3. Gluconeogenesis.
• Figure 4. The pentose phosphate pathway.
• Figure 5. The electron transport chain.
• Figure 6. The tricarboxylic acid (TCA) cycle.

Lipid Metabolism

• Figure 7. Fatty acid activation and oxidation.
• Figure 8. Oxidation of odd-chain fatty acids.
• Figure 9. Fatty acid synthesis.
• Figure 10. Cholesterol biosynthesis.
• Figure 11. Phospholipid synthesis.
• Figure 12. Glycolipid synthesis.
• Figure 13. Triacylglycerol synthesis.

Nitrogen Metabolism

• Figure 14. Transamination.
• Figure 15. Pyrimidine nucleotide synthesis.
• Figure 16. Purine nucleotide synthesis.
• Figure 17. Purine nucleotide degradation.
• Figure 18. The conversion of IMP into AMP and GMP.
• Figure 19. Pyrimidine nucleotide degradation (UMP and CMP).
• Figure 20. Pyrimidine nucleotide degradation (dTMP).
• Figure 21. Amino acid catabolism.
• Figure 22. Non-essential amino acid synthesis.