From 1 cell to 2, researchers have simulated the entire cell division process
A 4D computer simulation accurately shows every single molecule and reaction inside a cell as it divides over the course of about 100 minutes
Have you ever wondered what goes on inside a living cell? Researchers supported by the U.S. National Science Foundation have produced the most detailed computer-generated simulation of a dividing cell ever made. The work is a breakthrough in computer vision, unlocking a deeper understanding of cellular activity.
The subject of the simulation is a "minimal" bacterial cell that has a tiny genome consisting of only 493 genes. By comparison, the fruit fly genome has nearly 14,000 genes. The "minimal" cell was designed to have the fewest genes needed to program and coordinate cell growth and division. This pared-down size reduced the complexity of the simulation.
The results of the study are published in the journal Cell.
The study builds on years of experimental results that systematically modeled the essential metabolism and other subcellular networks of a cell. Using this accumulated data, researchers determined the identity, location and function of thousands of molecules inside the cell and created 3D spatial views of the crowded cellular interior.
By adding time as a fourth dimension across the 105 minutes it takes for the cell to grow and divide, the team gained unprecedented insights into cellular dynamics. The resulting 4D simulated cell captures how cellular components are made and degraded, how they function and move, and how they partition into daughter cells.
The results of this study represent a significant advance over earlier simulations published by the team, which only modeled growth over a 20-minute period. Lengthening the simulation timeframe to cover the entire cell cycle permits much more detailed observation of cellular processes. Commenting on the work, Susan Marqusee, assistant director of the NSF Directorate for Biological Sciences, said, "Being able to model a cell with this exquisite detail enables us for the first time to ask questions at the molecular level about how cellular processes work, and to explore hypotheses that we cannot do with direct experiments."
Achieving this advance required overcoming two major challenges. The first was to figure out how to simulate moving molecules and processes occurring at the same time in different parts of the cell. The second challenge was the tremendous computing capacity needed for the simulation, with each run taking four to six days. This was made possible by high-performance NVIDIA A100 graphics processing units on the Delta advanced computing and data resource. Delta is jointly supported by NSF and the state of Illinois as part of the University of Illinois National Center for Supercomputing Applications.
Cellular simulations have broad applications for both education and advanced study. The team has previously produced tools that allow students to visualize structures of normal and cancer cells using the video game Minecraft, making complex cellular processes more accessible. Marqusee commented, "The cell simulations using Minecraft are great education tools to help explain biological complexity inside cells to students at all levels." For future experimentation, the latest simulations open the door to study cellular behaviors under changing conditions, for example, by altering growth conditions or treating with antibiotics or other drugs that disrupt cell division.
This article was originally published by the University of Illinois Urbana-Champaign.
Read the full story: Team simulates a living cell that grows and divides