Table 1.

Different methods are used to model biological phenomena, typically depending on the length and time scales of interest, types of interactions involved, and nature of the system

Model type	Scale	Examples	Limitations	Advantages
Molecular Dynamics	Atoms and molecules	1–3	-Small spatiotemporal domain size -No resolution of long-term biological behavior -Computationally costly -Equilibrium system information approximated from nonequilibrium processes in steered molecular dynamics simulations1	High resolution, physics based down to the atomistic level
Coarse-grained agent-based	Large molecular complexes, cytoskeletal and extracellular networks, single and collective cells	4–7	May not produce all biologically relevant phenomena at either small or large scales	Can simulate many interacting components at the scale of interest
Continuum-Based	Single cells and small tissues	8–10	Limited resolution of discrete biological components	-Large physical domain size – Underlying physical principles can be directly experimentally tested
Rule-based	Collective cells and large tissues	11–13	-Mostly phenomenological -Underlying assumptions are difficult to reconcile with physical principles	-Simple rules can produce complex biologically mimicking patterns -Can simulate emergent behaviors not easily attainable by other methods