scientific-writing

name

scientific-writing

description

Scientific writing assistant for biophysics and soft matter manuscripts. Writes, edits, and revises LaTeX research papers for physics journals (PRL, PRE, Biophysical Journal, Soft Matter). Uses IMRAD structure with combined Results and Discussion. Handles figure captions, LaTeX equations (revtex4-2), numbered APS citations, and terminology consistency. Use when: writing or editing paper sections, drafting figure captions, formatting equations, checking terminology, revising prose, responding to reviewer comments, or any task involving the manuscript.

Scientific Writing Assistant

Overview

Edit and improve the LaTeX manuscript at: Percolation-Driven Compaction of Cell-Matrix Networks/paper/main.tex

Bibliography: Percolation-Driven Compaction of Cell-Matrix Networks/paper/references.bib

Writing Process

Follow a two-stage process:

1. Outline: List key points and logical flow for the section
2. Draft: Convert outline into full, flowing paragraphs

Always write in complete paragraphs with flowing prose. Never leave bullet points or outlines in the final manuscript. Every paragraph must have a topic sentence, supporting evidence, and a transition to the next idea.

Author's Voice

• Concise and direct — avoid verbosity, get to the point
• Physics-grounded — frame biological phenomena using physics principles
• Active voice — "Cells form networks" not "Networks are formed by cells"
• Quantitative — specific values, not vague descriptions

Remove unnecessary qualifiers ("very", "quite", "rather", "crucial"). Avoid nominalization: "We analyzed" not "We performed an analysis of". Avoid throat-clearing: "Our simulations show that..." not "It is interesting to note that the results of our simulation demonstrate that..."

Apply AI pattern checks before delivering any prose — see references/deslop-scientific.md.

Epistemic language — match certainty to evidence (see references/epistemic-language.md for full guide):

• Strong ("demonstrates", "shows") — only for direct, unambiguous results
• Moderate ("suggests", "is consistent with") — most mechanistic claims belong here
• Speculative ("may", "could") — extrapolating beyond data
• Simulations demonstrate sufficiency, not necessity. A model that reproduces an observation is consistent with an explanation, not proof of it
• Separate what the simulation does (state confidently) from what it means for biology (hedge appropriately)
• Weave model limitations into claims: "Within the assumptions of our model, this suggests..."

Section Quick Reference

For section structure, paragraph templates, and format targets by journal, see references/paper-structure.md.

Verb Tense

Section	Tense	Example
Model description	Present	"The network consists of..."
Simulation procedure	Past	"We performed 20 realizations..."
Established facts	Present	"Collagen gels exhibit strain-stiffening..."
Specific results	Past	"The compaction parameter decreased sharply..."
Interpretation	Present	"This coincidence suggests that..."
Figure references	Present	"Figure 2 shows..."

Figure Captions

See references/figure-caption-guide.md for the six principles, deconstructed examples, a bad-caption case study, and a rewritten model caption.

Equations and LaTeX

• Use $$..$$ for mathematical symbols and short inline equations
• Use display equations (\begin{equation}) for key force laws, equations of motion, and definitions
• Number all important equations for cross-referencing
• Use revtex4-2 document class with \bibliography{references}
• APS numbered citations: [1], [2], [3,4]
• Multi-panel figures labeled (a), (b), (c)

Reference Index

Load these files as needed based on the task:

Task	File to load
Improving prose quality, revision	references/writing-principles.md
Removing AI patterns from prose	references/deslop-scientific.md
Structuring sections, paragraph templates	references/paper-structure.md
Writing figure captions	references/figure-caption-guide.md
Formatting citations, bibliography	references/citation-styles.md
Epistemic language, hedging, causal claims	references/epistemic-language.md
Need writing style exemplar	references/examples/doha-2022.md, references/examples/peng-2025.md, or references/examples/zakharov-2021.md

Example papers (in references/examples/):

• doha-2022.md — Primary experimental reference (Doha et al. 2022, disorder-to-order transition)
• peng-2025.md — Writing style reference (Peng et al. 2025, fiber recruitment phase transition)
• zakharov-2021.md — Writing style reference (Zakharov et al. 2021, clot elasticity)

Quick Editing Checklist

• First sentence states the main point clearly
• Results are quantified with specific values
• Active voice; subject performs the action
• Sentences connect logically; smooth transitions
• Physical/mechanistic interpretation is clear
• Technical terms defined on first use
• Parameter values consistent between Model and Results
• Equation formatting correct (proper LaTeX syntax)