Start with mechanisms
Define the relationships between growth, environment and process, with traceable parameters and explicit assumptions.
FROM BIOLOGY TO BETTER DECISIONS
Digital twins
for microbial systems.
MicroTwin builds digital twins of microbial systems, connecting growth, environment and process through mechanisms and experimental data. Starting with sourdough fermentation, we aim to explore broader microbial applications.
MECHANISTIC MODELS · EXPERIMENTAL DATA · DIGITAL TWINS
A LIVING SYSTEM, MADE LEGIBLE
01 / THE BIOLOGICAL TWINObserve → Model → Validate
OUR APPROACH
Biological systems have patterns.
We turn them into tools.
Turn experimental observations into traceable, testable models. Understand the mechanisms, calibrate with data, and answer concrete process questions.
Calibrate with data
Preserve batch and raw material differences. Record literature parameters separately from parameters fitted to experiments.
Build trust through validation
Use independent batches to assess error, uncertainty and applicability, so models can support real decisions.
FIRST PRODUCTIN DEVELOPMENT · RESEARCH PREVIEW
DoughTwin®
An understandable digital twin
for fermentation.
Starting with environmental responses of sourdough microorganisms, we explore the connections between temperature, growth and acidification. Our goal is a fermentation process model calibrated with real batches.
Explore the growth model ↗THE DOUGH → THE TWIN
Experimental observations
Temperature · pH · Cell counts⇄Digital model
Mechanisms · Parameters · Responses
Temperature · pH · Cell counts⇄Digital model
Mechanisms · Parameters · Responses
Start with a real process. Return to it for validation.
MODEL 02 / DIET–MICROBIOME DYNAMICSRESEARCH ADAPTATION
GutSim-2-stage
Predict how diet shapes
microbial function.
An individual-agent gut model linking dietary carbon and nitrogen availability to six functional bacterial guilds. The two-period schedule adapts the model to the available experiment.
Explore GutSim-2-stage ↗DIET → RESOURCE USE → FUNCTIONAL bacterial GUILDS
Stage 10–168 hoursFirst dietary environment
→Stage 2168–336 hoursSecond dietary environment
Microbial and nutrient states persist at the switch.
The current 7 + 7-day schedule is a research abstraction. Invited reviewers can run the R model.EXPLORE THE MODEL
When temperature changes,
how does growth respond?
Adjust the temperature to explore published single-factor growth responses for two sourdough microorganisms. These curves use the project’s implemented model 1a.
15 °C40 °C
These are published responses in laboratory medium, not predictions of dough fermentation time or pH. Applicability is limited at low temperatures.
TEMPERATURE RESPONSE μ / h⁻¹
Lactic acid bacteria LTH2581
Yeast H198
SCIENCE & PROGRESS
Transparent progress. Clear boundaries.
Published growth-response baseline
Temperature and environmental response functions have been checked and implemented. The baseline passed 37 scientific and numerical checks, demonstrating implementation consistency.
Acidification and raw material calibration
Time, temperature, pH, cell counts and acid measurements will inform acid production, substrate dynamics and flour buffering relationships.
Predictive performance on real batches
Bakery batch validation is not yet complete. Holding out entire batches and flour lots will help assess prediction error and applicability.
Invited scientists: inspect model structure, principles and assumptions ↗
LET’S BUILD WITH BIOLOGY
The next model starts
with a concrete biological question.
We welcome exploration of DoughTwin with fermentation researchers, bakeries and process development teams. Gather your experimental conditions and key questions to start an evidence-based collaboration discussion.
Open the DoughTwin test workspace ↗Contact MicroTwin ↗Scientific model review ↗Collaboration enquiries: weilan@ualberta.ca
By invitation from Weilan. Model-specific scientific access is separate from bakery testing access.