QCB is a combined computational and experimental center. We seek to quantitatively describe the physical and chemical processes that define the functional state of a cell. We use experimental techniques as well as computer modeling and simulation.
What is a minimal cell?
According to a plain language summary from the National Institutes of Health’s PubMed® page on the paper: “One way that researchers can test whether they understand a biological system is to see if they can accurately recreate it as a computer model. The more they learn about living things, the more the researchers can improve their models and the closer the models become to simulating the original. In this approach, it is best to start by trying to model a simple system.
Biologists have previously succeeded in creating ‘minimal bacterial cells’. These synthetic cells contain fewer genes than almost all other living things and they are believed to be among the simplest possible forms of life that can grow on their own. The minimal cells can produce all the chemicals that they need to survive – in other words, they have a metabolism. Accurately recreating one of these cells in a computer is a key first step toward simulating a complete living system.
Tools We Use
We are fine-tuning the experimental tools that will accelerate our challenging computational work. We’re using a state-of-the-art MINFLUX microscope, allowing live-cell tracking of single molecules with a spatial resolution of 2 nm for minutes, while maintaining sub-ms time-resolution. We have obtained preliminary results, both on-site and with remote access, including data from our partners.
Combined with existing cryo-electron tomography (for cell shape and architecture) and newly developed label-free infrared microscopy (providing spatial mapping of chemical compositions and metabolites inside the cell), we now have the data needed to continue improving our computer models.
As our models develop, we will simulate biological processes such as gene expression, metabolism, organelle dynamics and cell division under the influence of the environment, from the underlying molecular diffusion and chemical reactions within the cell.