Thesis chapter engineering

Thesis Chapter Engineering

Build chapters around research questions, not around available file types.

Before drafting

1. Load thesis.project.json, scope, terminology, and authority record.
2. Read current school rules and at least one accepted local exemplar for structure and presentation patterns. Do not copy wording.
3. Load only verified evidence relevant to the chapter.
4. Create a chapter contract using references/chapter-contract.md.
5. Validate the contract before prose expansion.

Research-chapter pattern

Follow the school and supervisor decision. When methods are chapter-specific, prefer:

1. Chapter introduction and research question.
2. Materials/reagents relevant to this chapter.
3. Sample preparation or computational setup.
4. Characterization/evaluation methods with complete conditions.
5. Results and discussion organized by claims and figures.
6. Chapter summary containing only established conclusions.

Do not create an independent universal methods chapter when the confirmed thesis structure integrates methods into each research chapter.

Paragraph construction

For each analytical paragraph:

1. State the observation and point to a figure/table/equation.
2. Quantify the relevant comparison when data exist.
3. Distinguish sample, condition, time, and panel.
4. Give the explanation at the evidence-appropriate strength.
5. Compare with verified literature when useful.
6. State the consequence for the chapter question.

Avoid paper-by-paper lists in reviews. Organize by mechanism, method, scale, disagreement, or design variable.

Figure-led writing

Do not describe a group figure generically. Map every panel first, then write comparisons such as (a) versus (c) only when the actual panel identities and conditions are verified.

Route caption and figure quality work to thesis-figure-table-audit.

Language rules

Read references/language-and-logic.md. Remove production traces such as “PPT shows”, “small paper”, “provided later”, “current version”, or “the user supplied”. Replace them only with scientifically accurate source descriptions, not invented provenance.

Use concrete nouns. Replace vague umbrella terms with the actual object when the scope supports it, for example water/glycerol molecules, tobacco fibers, heating conditions, or mesoporous silica.

Cross-chapter closure

Before finalizing a chapter:

• verify methods cover every reported result;
• verify every retained figure/table is discussed;
• verify every conclusion appears in results;
• verify the next chapter follows from a stated unresolved question;
• verify abstract and final conclusions use the same sample mapping and evidence strength.

Tool

python scripts/validate_chapter_contract.py chapter-contract.json \
  --project-root /path/to/project --report reports/chapter-contract.json

Read references/stem-chapter-patterns.md for introduction, review, experiment, simulation, and conclusion patterns.