Scientists from the Science and Technology Center for Quantitative Cell have created the most detailed simulation yet of a living cell’s life cycle — opening a new window into the fundamental processes that make life possible.

The team, led by QCB Director and University of Illinois Urbana-Champaign chemistry professor Zan Luthey-Schulten, built a 4D whole-cell model — three dimensions of space plus time. Their computer simulation tracks how every essential molecule in a minimal cell behaves during its 105-minute life cycle, from birth to growth to division. Unlike earlier models, this simulation places molecules in realistic 3D positions.

The breakthrough, reported in the journal Cell, focuses on one of the simplest living organisms ever created: a living “minimal cell” called JCVI-syn3A developed at the J. Craig Venter Institute in California. This bacterium contains only about 500 genes — far fewer than most cells — but it can still grow, copy its DNA, divide and perform other life functions.

Collaborative effort
In addition to the Luthey-Schulten team, other QCB members contributed heavily to this discovery. The J. Craig Venter Institute who supplied the Syn3A minimal cell. Angad Mehta, a QCB team leader and professor of chemistry at Illinois and Taekjip Ha of Boston Children’s Hospital and Harvard Medical School, generated experimental data that allowed the team to accurately simulate and validate numerous aspects of cell function. The National Center for Supercomputing Applications at Illinois provided 15,000 GPU hours of compute time on their Delta supercomputer to run the 50 simulations. Each simulation took four to six days of computational time of two high-performance computing GPUs per cell cycle.

Although the model still has limitations — for example, it does not yet include every molecular interaction — it represents a major step toward building a complete, physics-based simulation of life, opening a new window into the fundamental processes that make life possible.

Learn more. 

Pictured Above: Simulating an entire cell requires multiple types of computer simulations. This picture shows the same point in time for a single cell, but 4 different components. Top left is DNA (red/blue) and ribosomes (yellow/purple), bottom left is protein molecules, top right is cubic representation of cytoplasm (light blue/white) and ribosomes (yellow/red), and bottom right is cubic representation of cell membrane.