A new computer code for tissue mechanics

Biological materials are made up of individual components, including tiny motors that convert fuel into motion. This creates patterns of movement, and matter shapes itself into coherent flows through the continuous consumption of energy. This continuously driven material is called “active material”. The mechanisms of cells and tissues can be described by the theory of active matter, a scientific framework for understanding the form, flows, and shape of living matter. Active matter theory consists of many difficult mathematical equations. Scientists from the Max Planck Institute for Molecular Cell Biology and Genetics (MPI-CBG) in Dresden, the Center for Systems Biology Dresden (CSBD), and TU Dresden have developed an algorithm, implemented in open source supercomputer code, that can for the first time solve matter theory equations. Active in realistic scenarios. These solutions bring us a big step closer to solving the age-old mystery of how cells and tissues get their shape, and to designing artificial biological machines.

Biological processes and behaviors are often very complex. Physical theories provide a precise and quantitative framework for understanding them. Active matter theory provides a framework for understanding and describing the behavior of active matter – materials composed of individual components capable of converting chemical fuels (“food”) into mechanical forces. Several scientists from Dresden were instrumental in developing this theory, including Frank Jülischer, Director of the Max Planck Institute for the Physics of Complex Systems, and Stefan Grill, Director of MPI-CBG. Using these physical principles, the dynamics of active living matter can be described and predicted by mathematical equations. However, these equations are very complex and difficult to solve. Therefore, scientists need the power of supercomputers to understand and analyze living materials. There are different approaches to predicting the behavior of an active substance, with some focusing on small individual molecules, others studying the active substance at the molecular level, and others studying active liquids on a large scale. These studies help scientists figure out how active matter behaves at different levels in space and over time.

Solve complex mathematical equations
Scientists from the research group of Ivo Spalzarini, TU Dresden Professor at the Center for Systems Biology Dresden (CSBD), Research Group Leader at the Max Planck Institute for Molecular Cell Biology and Genetics (MPI-CBG), and Dean of the Faculty of Computer Science at TU Dresden have developed an algorithm Computer to solve active matter equations. Their work has been published in the journal “Fluid Physics” It appeared on the cover. They present an algorithm that can solve complex equations of active matter in three dimensions and in complex shaped spaces. “Our approach can handle different shapes in three dimensions over time,” says Abhinav Singh, one of the study’s first authors, a mathematician who has studied the study. He continues, “Even when data points are not uniformly distributed, our algorithm uses a new numerical approach that works seamlessly with complex biologically realistic scenarios to accurately solve the theory’s equations. Using our approach, we can finally understand the long-term behavior of active materials in both moving and immobile scenarios to predict With its dynamics. Moreover, the theory and simulations can be used to program biological materials or create nano-scale engines to extract useful work. The other first author, Philipp Suhrke, graduate of the Master of Computer Modeling and Simulation at TU Dresden, adds the program: “Thanks to our work, scientists can Now, for example, predicting the shape of tissue or when biological material becomes unstable or irregular, with far-reaching implications in understanding mechanisms of growth and disease.”

Powerful code for everyone to use
The scientists implemented their programs using the open source OpenFPM library, meaning it is freely available for others to use. OpenFPM was developed by the Sbalzarini group to democratize scientific computing at scale. The authors first developed a custom computer language that allows computational scientists to write supercomputer codes by specifying equations in mathematical notation and letting the computer do the work to generate correct program code. As a result, they don’t have to start from scratch every time they write code, effectively reducing code development times in scientific research from months or years to days or weeks, providing huge productivity gains. Given the enormous computational requirements for studying 3D active materials, the new code is scalable on shared-memory, distributed-memory parallel multiprocessor supercomputers, thanks to the use of OpenFPM. Although the application is designed to run on powerful supercomputers, it can also run on regular desktop computers to study 2D materials.

The study’s lead researcher, Ivo Spalzarini, sums up: “Ten years of our research have gone into creating this simulation framework and enhancing the productivity of computational science. All of this now comes together in a tool for understanding the 3D behavior of living materials. Open source, scalable, and capable of Dealing with complex scenarios, our code opens new ways to model active materials. This may finally lead us to understand how cells and tissues get their shape, addressing the fundamental question of morphology that has puzzled scientists for centuries. But it may also help us design machines Synthetic biological with minimal ingredients.

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The computer code supporting the results of this study is openly available in the 3Dactive-hydrodynamics GitHub repository located at https://github.com/mosaic-group/3Dactive-hydrodynamics

The open source framework OpenFPM is available at https://github.com/mosaic-group/openfpm_pdata

Posts related to the embedded computer language and OpenFPM software library:
https://doi.org/10.1016/j.cpc.2019.03.007
https://doi.org/10.1140/epje/s10189-021-00121-x