The development of synthetic biology relies heavily on various biological modeling techniques and methods. Models enable researchers to design experiments and analyze results more efficiently.

This year, to validate the effectiveness of the modules in our designed Whole-Cell Immobilization Platform TasAnchor, our dry lab exploratory experiments consist of four parts:

1. Adhesion Module Simulation;

2. Function Test Module Simulation;

3. Safety Module Simulation;

4. Protein Modeling.

These experiments aim to assist in the design of wet lab experiments and further explore the feasibility and limitations of our project design through in silico simulations.

Using mathematical modeling, we simulated and compared two bacterial adhesion strategies (a fusion protein system vs. the SpyTag-SpyCatcher system) for wastewater treatment. The simulation demonstrated the SpyTag-SpyCatcher system's superiority, achieving higher long-term bacterial density and stronger biofilm stability due to its lower metabolic burden, guiding the selection of the optimal strategy for subsequent wet lab experiments.

Wet experiments showed Bacillus subtilis grows differently under cadmium stress vs. normal conditions, with few heavy metal stress models for engineered bacteria. We used data at varied cadmium concentrations to fit curves with 4 classical primary models, comparing to the control. As classical models failed to capture nonlinear growth (e.g., prolonged lag phase, biphasic traits), we added cadmium stress correction terms, and via parameter iteration/verification (R, SSE, AIC), built a more accurate cadmium-adapted model. Finally, 2 secondary models fitted parameters and cadmium concentrations, exploring parameter significance and guiding cadmium tolerance mechanism studies.

To validate the effectiveness of our designed density-dependent switch in practical fluid environments, we developed three interconnected mathematical models: an ODE-based threshold model to establish critical density limits, a PDE-based spatial distribution model to analyze positional effects, and a fluid cloak model to enhance robustness against environmental perturbations. The simulations identified precise suicide thresholds and demonstrated effective containment strategies under various conditions, providing a quantitative framework for biosafety applications in synthetic biology.

Protein modeling was performed to evaluate TasA fusion strategies for enhanced polystyrene adsorption. Constructs included TasA fused to polystyrene-binding peptides (PSBP-R, PS-1, PS-2) or mussel foot proteins (Mefp-1, Mefp-5), and assemblies using SpyTag/SpyCatcher covalent pairing. Rather than molecular dynamics, a lightweight, mechanistic pipeline combined AlphaFold-3 structure prediction and AIUPred disorder profiling with interpretable scores: context-aware exposure of adhesive residues (6 Å neighborhood weighting), tethered reachability across an 8–12 nm gap (worm-like-chain proxy), and split-only ligation efficiency with an occlusion penalty. Composite rankings prioritized designs with strong exposure and reliable assembly, guiding wet-lab construction toward high-affinity polystyrene immobilization.