Live briefing
Everything about Smoldyn
Smoldyn is an open-source software application for cell-scale biochemical simulations. It uses particle-based simulation, meaning that it simulates each molecule of interest individually, in order to capture natural stochasticity and yield nanometer-scale spatial resolution. Simulated molecules diffuse, react, are confined by surfaces, and bind to membranes in similar manners as in real biochemical systems. Wikipedia →
🧠Start here: a 6-step reading path
- Read the overview: SmoldynA 5-minute orientation
- Pick up a classic book: Bacterial molecular networksThe most-reprinted book on the subject
- Read the landmark paper: Detailed Simulations of Cell Biology with Smoldyn 2.1Cited 308 times
- Go sideways: List of systems biology modeling softwareA closely related topic
- Go sideways: Multi-state modeling of biomoleculesA closely related topic
đź“– Definitions
No dictionary entry for this exact phrase.
🗂️ The subject at a glance
🏆 Landmark papers (most cited)
Detailed Simulations of Cell Biology with Smoldyn 2.1
Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface
Multiscale reaction-diffusion simulations with Smoldyn
Smoldyn on Graphics Processing Units: Massively Parallel Brownian Dynamics Simulations
Enabling surface dependent diffusion in spatial simulations using Smoldyn
Python interfaces for the Smoldyn simulator
Correction to: Python interfaces for the Smoldyn simulator
đź“š Books worth reading
Bacterial molecular networksJacques van Helden, Ariane Toussaint · 2012
Ranked by number of editions on Open Library, a rough measure of how lasting a book is.
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