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NewtonBioMorphX v1.0.0

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@jahanbak jahanbak released this 09 Oct 23:25
v1.0.0
661e60a

NewtonBioMorphX v1.0.0

A GPU-accelerated framework for mechanical morphogenesis.

First public release of NewtonBioMorphX, an open-source application for simulating the tissue-scale mechanics of morphogenesis, developed at the Laboratory of Artificial and Natural Evolution (LANE), University of Geneva.

NewtonBioMorphX brings together the finite element formulation behind our studies of crease networks in mammalian noses, skin folding in chicken reticulate scales, and the mechanical patterning of head scales in crocodiles and tortoises, all in a single graphical interface. You can build geometries, define tissue mechanics, prescribe growth, run GPU simulations and watch them evolve in real time, without editing or recompiling any code. It is designed for biologists and physicists alike, and works well as a teaching tool.

Highlights

Modeling

  • Built-in mesh generator: box, disk, tube, cone, sphere and torus, with adjustable layers, dimensions, thickness and resolution. VTK meshes can also be imported.
  • Multilayer tissues: each layer gets its own properties, and any layer can be set as rigid to represent bone or a substrate.
  • Material model: Young's modulus, Poisson's ratio, viscosity and plasticity, from fully elastic to fully plastic behavior.
  • Fibers and active forces: up to four passive collagen-like fiber families per layer, plus active contractile forces that can be directional, spatially variable and time dependent.
  • Growth functions: isotropic or anisotropic growth, defined independently along each direction and varying freely in space and time.
  • Boundary conditions: traction, free, fixed and tangential slide.
  • Seven coordinate systems: normal/tangent, Cartesian, cylindrical (Z and Y), cone-adapted, spherical and toroidal.
  • Analytical expressions: every parameter accepts formulas using coordinates, time, standard math functions, and vector or tensor notation.

Solver

  • GPU-accelerated finite element solver, with each model compiled on the fly into CUDA kernels.
  • Self-contact handling for strongly folded tissues.
  • F-bar formulation to prevent volumetric locking in nearly incompressible materials.
  • Automatic stability control: the solver rolls back to the last stable state and reduces the time step when needed.
  • Automatic stopping on energy convergence or an iteration limit.

Visualization and analysis

  • Real-time rendering while the simulation runs, with surface, section and clip modes.
  • Scalar field maps: layers, von Mises stress, pressure, velocity, growth and plastic deformation, and material parameters.
  • Line-glyph display of growth directions, active filaments and passive fibers.
  • Mesh-quality histogram, perspective or orthographic views, and fixed view orientations for comparing results.
  • A live information panel showing domain size, time step, energy convergence, mesh statistics and solver speed.

Saving and export

  • Plain-text project files that store the complete setup and can be reloaded.
  • MP4 movie recording straight from the rendering window.
  • Export to VTK (mesh plus mechanical state, for ParaView, VisIt or Python) and PLY (surface, for Blender or MeshLab), as single snapshots or automatic frame series.

Getting started

Twelve ready-to-run presets are included, progressing from folding on an elastic box to fiber-reinforced tori, multilayer spheres and periodic growth patterns. We recommend working through them in order. The User Manual explains each panel in detail and includes an FAQ.

Downloads

Linux:

  • NewtonBioMorphX-1.0.0-x86_64.AppImage. Make it executable (chmod +x NewtonBioMorphX-x86_64.AppImage)

Windows (choose one):

  • Installer (recommended): NewtonBioMorphX-1.0.0-win64.exe installs the application and adds it to the Start menu.
  • Portable: NewtonBioMorphX-1.0.0-win64.zip runs without installation; just unzip it anywhere and run bin/NewtonBioMorphX.exe.

Requirements

  • NVIDIA GPU, Turing generation or newer (RTX 20-series or later)
  • Recent NVIDIA driver (R560 or newer recommended)
  • 64-bit Windows 10/11, or a Linux distribution from roughly 2022 onward

Citation

If you use NewtonBioMorphX in your research, please cite:
NewtonBioMorphX: a computational framework for simulating tissue-scale mechanics of morphogenesis (DOI).

Authors

Ebrahim Jahanbakhsh and Michel C. Milinkovitch, LANE, University of Geneva
Logo: Fabrice Berger, Gregory Loichot, Ebrahim Jahanbakhsh and Michel C. Milinkovitch
Project website: https://www.lanevol.org/projects/NewtonBioMorphX

License

GNU General Public License v3.0

What's Changed

New Contributors

Full Changelog: https://github.com/LANEvol/NewtonBioMorphX/commits/v1.0.0

Contributors

jahanbak
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