Feature/3rd module

[meganrm]

Problem

Estimated review size: Medium

closes #207 and #204

Solution

Added the written content for the 3rd module and updated the simulation to handle a new Agent, D

Type of change

Please delete options that are not relevant.

• New feature (non-breaking change which adds functionality)

Steps to Verify:

1. bun dev
2. click on Competitive Binding on the progress bar to go to that section
3. follow the instructions

there are still more things to do to finish this module

[Copilot]

Pull request overview

This PR adds support for a third module on competitive binding by introducing Agent D and updating the simulation system to handle multiple complex formations. The changes extend the existing two-agent binding system to support a competitive inhibitor that can bind to the same target as Agent B.

Key changes:

• Added Agent D as a competitive inhibitor with its own binding characteristics
• Refactored the simulation to track multiple complex types (AB, AC, AD) separately
• Updated the UI and content to guide users through the competitive binding experiment

Reviewed changes

Copilot reviewed 14 out of 14 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
src/types/index.ts	Added new agent types (D, Adjustable_2, Complex_3), product name (AD), and ViewType enum
src/simulation/context.tsx	Added viewport type state and setter to simulation context
src/simulation/PreComputedSimulationData.ts	Renamed AgentFunction to AgentType, updated method names
src/simulation/LiveSimulationData.ts	Added Agent D configuration, restructured concentrations by module, added competitive binding logic
src/simulation/ISimulationData.ts	Updated interface to reflect AgentType rename and method signature changes
src/simulation/BindingSimulator2D.ts	Refactored to track multiple complex types with individual colors, removed unused productColor parameter
src/simulation/BindingInstance.ts	Modified unbinding to return the released child instance
src/content/LowAffinity.tsx	Fixed typo in completion message
src/content/Competitive.tsx	Added complete content flow for competitive binding module
src/components/main-layout/LeftPanel.tsx	Hidden events over time plot for competitive binding module
src/components/concentration-display/LiveConcentrationDisplay.tsx	Fixed Math.min to Math.max for step calculation
src/components/concentration-display/ConcentrationSlider.tsx	Added decimal number formatting for slider marks
src/components/ViewSwitch.tsx	Refactored to use context-based view state instead of local state
src/App.tsx	Added experiment initialization, view state management, and module-specific concentration handling

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[Copilot]

Pull request overview

Copilot reviewed 14 out of 14 changed files in this pull request and generated 3 comments.

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[Copilot]

Pull request overview

Copilot reviewed 14 out of 14 changed files in this pull request and generated 2 comments.

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[Copilot]

Pull request overview

Copilot reviewed 14 out of 14 changed files in this pull request and generated 3 comments.

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[Copilot]

[nitpick] The conditional formatting logic for decimal marks is unclear and fragile. Consider extracting this to a named function with a descriptive name like formatSliderMark to improve readability and make the intent explicit.

[Copilot]

Pull request overview

Copilot reviewed 14 out of 14 changed files in this pull request and generated 1 comment.

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[Copilot]

Two consecutive page entries have identical title, content, layout, section, and actionButton. The only difference is progressionElement (START_EXPERIMENT_ID vs PLAY_BUTTON_ID). This duplication should be eliminated by either combining into one entry or extracting common content.

Suggested change

	title: "Start the experiment",
	content: (
	<>
	We cannot directly measure the formation of <AD /> (which is why
	it's shown in grey). To figure out how strongly <D /> binds to{" "}
	<A /> we're going to keep track of how adding more <D /> affects
	the amount of <AB /> formed.
	</>
	),
	layout: LayoutType.LiveSimulation,
	section: Section.Introduction,
	actionButton: <StartExperiment />,
	progressionElement: PLAY_BUTTON_ID,
	callToAction: (
	<>
	Click the <strong>Start experiment</strong> button to reset the
	simulation and begin by pressing <strong>play</strong>!
	</>
	),
	},
	{