Simulation methodology

MultiscaleNano runs real molecular dynamics (OpenMM) for coarse-grained modules and applies documented physical bridges for continuum transport and release. Every completed run includes per-metric equations, references, and 95% confidence intervals from independent MD replicates where applicable.

Simulation modes

Standard MD

5,000 MD steps · 3 replicates · ~30–45 min

Production MD

25,000 MD steps · 5 replicates · hours

Pipeline modules

Encapsulation

OpenMM coarse-grained LJ

Potential energy from Langevin MD trajectory
Encapsulation efficiency from core bead fraction × compactness
Drug retention ΔG from mean potential energy per bead

Replicates: 3 (standard) / 5 (production)

Formation

OpenMM self-assembly MD

Hydrodynamic radius R_H ≈ 2 × R_g from final configuration
Morphology classification (core-shell vs compact-sphere)
Polydispersity from replicate spread

Replicates: 3 / 5

Stability

OpenMM thermal perturbation (+10 K)

Stability score from R_g change under heat stress
Drug leakage rate from energy fluctuation proxy

Replicates: 3 / 5

Transport

Stokes–Einstein continuum bridge

Effective diffusion D = k_B T / (6πηR_H)
Penetration depth x ≈ √(2Dεt) in porous tissue

Replicates: Deterministic from formation MD

Release

Slab diffusion with MD-derived D_eff

Half-life t_½ = R_H² / (2D_eff)
Release profile from exponential cumulative model

Replicates: Deterministic from stability + formation

Protein corona

OpenMM competitive adsorption MD

Adsorbed protein count within 1.2 nm of particle surface

Replicates: 3 / 5

Cell interaction

OpenMM NP–membrane approach MD

Membrane adhesion energy (kT)
Uptake and endosomal escape probabilities from adhesion

Replicates: 3 / 5

Limitations

Results are computational predictions from simplified coarse-grained models. They should supplement — not replace — experimental validation. Screening mode is disabled; all reported metrics require MD simulation.