An explicit two-node time integrator
An explicit two-node time integrator
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A single-step time integrator derived from a Petrov–Galerkin weak formulation.
No intrinsic algorithmic dissipation in the undamped limit.
Stable time step grows with physical damping.
GitHub [Link]
Technical details
Formulation: An explicit Petrov-Galerkin time finite element integrator for structural dynamics with physical damping, Computers & Structures (2026) [Link]
SNUPI (Structured NUcleic-acids Programming Interface)
SNUPI (Structured NUcleic-acids Programming Interface)
SNUPI is a multiscale analysis framework based on the finite element model with the intrinsic properties of DNA characterized by molecular dynamics simulations
GitHub [Link]
Technical details
SNUPI framework (static analysis): Rapid computational analysis of DNA origami assemblies at near-atomic resolution, ACS Nano (2021) [Link]
Improved model of single-stranded DNA: Characterizing and harnessing the mechanical properties of short single-stranded DNA in structured assemblies, ACS Nano (2021) [Link]
Partition and relocation framework (free-form structures): Predicting the free-form shape of structured DNA assemblies from their lattice-based design blueprint, ACS Nano (2022) [Link]
Langevin dynamics simulations: A computational model for structural dynamics and reconfiguration of DNA assemblies, Nature Communications (2023) [Link]
EtBr-binding simulations: Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies, Nature Communications (2024) [Link]
Protocol: SNUPI - A computational framework for rapid mechanical analysis of structured DNA assemblies, JACS Au (2025) [Link]
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