Multiscale Bayesian-Mechanical Framework for Oral Biofilm

GitHub · Wiki · Discussions · Release (all PDFs)

Pipeline Overview

In vitro Data 4 cond × 5 spp TMCMC 20-param Bayesian Hamilton ODE 5-species + Hill DI → E(DI) 28× stiffness 3D FEM Abaqus T23 Stress / UQ σ, u, CI bands DeepONet 384× speedup
5
Species
20
Parameters
4
Conditions
28×
Stiffness Range
~80×
DeepONet Speedup
19
Paper Figures

Paper Draft

Main Paper (LaTeX Draft v1)

Bridging microbial ecology and continuum mechanics: A TMCMC-based multiscale framework for oral biofilm stress analysis. 45 pages, 19 figures.

Paper 2026-02-25 · 520 KB
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Algorithm Documentation

TMCMC + TSM-ROM Algorithm (EN)

Full algorithm: Hamilton ODE, TMCMC Bayesian inference, Taylor Series ROM, complex-step Jacobian.

Algorithm EN · 2.1 MB
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TMCMC + TSM-ROM Algorithm (JA)

Same content in Japanese.

Algorithm JA · 1.1 MB
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TSM-ROM-TMCMC Pseudocode

Compact pseudocode for the linearisation-based TMCMC pipeline.

Algorithm EN · 267 KB
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Presentation

Research Presentation Slides

Full presentation: biofilm ecology, TMCMC inference, multiscale FEM, DeepONet surrogate.

Slides 11.6 MB
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FEM Reports

FEM Pipeline Report

JAX-FEM + Abaqus eigenstrain pipeline, DI-based material model, 3D stress fields.

FEM
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3-Tooth Biofilm Analysis

Patient T23 tooth, conformal C3D4 mesh, tie constraint, cross-condition comparison.

FEM
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Abaqus Implementation

Eigenstrain (thermal analogy) approach, INP generation, boundary conditions.

FEM
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Klempt 2024 Benchmark

Nutrient PDE validation against Klempt et al. (2024), Thiele modulus comparison.

FEM
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Paper Figures (19)