Projects / Programmes
| Code |
Science |
Field |
Subfield |
| 1.02.02 |
Natural sciences and mathematics |
Physics |
Theoretical physics |
| Code |
Science |
Field |
| P190 |
Natural sciences and mathematics |
Mathematical and general theoretical physics, classical mechanics, quantum mechanics, relativity, gravitation, statistical physics, thermodynamics |
| Code |
Science |
Field |
| 1.03 |
Natural Sciences |
Physical sciences |
active matter, epithelial tissues, vertex model, machine learning
Researchers (1)
| no. |
Code |
Name and surname |
Research area |
Role |
Period |
No. of publicationsNo. of publications |
| 1. |
36332 |
PhD Matej Krajnc |
Physics |
Head |
2019 - 2021 |
52 |
Organisations (1)
| no. |
Code |
Research organisation |
City |
Registration number |
No. of publicationsNo. of publications |
| 1. |
0106 |
Jožef Stefan Institute |
Ljubljana |
5051606000 |
90,706 |
Abstract
Nature offers many complex materials, that are often in equilibrium or near it, e.g. liquid crystals and wood. In turn, there exist materials, typically of biological nature, that are far from equilibrium. We refer to these materials as active matter. One example of active biological matter are living cells, which are held far from equilibrium by metabolic processes and enzymes, which consume energy to do work, e.g. molecular motors. They generate forces, which deform cells and cause them to migrate. In order to understand how living organisms work and how they develop, it is crucial to first understand the basic underlying biophysical mechanisms governing the material properties and behavior of living materials. A rapid development of eksperimental methods, genetics, and methods of numerical computations using powerful computers enables us to take interdisciplinary approaches to studying these materials. This is especially important for our understanding of the behavior of animal tissues, where we would like to develop more efficient methods for diagnosis and treatment of disease, e.g. cancer. In the proposed research we are going to use methods of mathematical physics and computer simulations to study biological active matter. First, we are going to focus on the formation of epithelial tissue in the early embryonic development of the fruit fly embryo. The nuclei sharing a common cytoplasm get compartmentalized during the so-called process of cellularization. This occurs by invaginations of cell membranes around the nuclei. We are going to be interested in what physical mechanisms govern the robust formation of the epithelium and how different genetic and mechanical perturbations affect cellularization. Next, we are going to study the mechanics of active epithelia, where tension fluctuations at cell-cell junctions drive cell rearrangements and promote fluid-like behavior of the tissue. We are going to look into viscoelastic properties of these active tissues and organization of cells within the tissue. Furthermore, we are going to study tissues consisting of two or more cell types. Here we are going to be interested in how differential mechanical properties between cell types affect cell sorting and drive three-dimensional tissue shape changes. We are also going to develop three-dimensional mathematical models of the fruit fly embryo and folding of intestinal tissues. We are going to study how inter- and intracellular interactions interplay with external forces to drive three-dimensional tissue shape changes. The last part of the proposed project is going to focus on developing computational tools for automatized recognition of behavioral patterns in clusters of active agents. Here we are going to use simple mathematical models of machine learning to develop a computer program, which is going to search for repeating patterns in images from live movies of active agents, e.g. flocs of birds, ants etc., and analyze them. Our tool is going to enable us to improve our quantitative treatment of the mechanics of active materials at the level of their constituents.
Significance for science
Active soft matter physics has been a rapidly growing field of research and is getting more and more attention in scientific community. The systems of interest that it addresses are typically biological by nature and therefore interesting not only from the physics but also from the biology and chemistry perspectives. The theme of the proposed project is mostly going to revolve around the embryonic development and the mechanics of biological tissues and cells. The studies are going to be mostly theoretical, however we are going to be collaborating closely with research groups both from Slovenia and abroad. We are going to present the results of the project in renowned international scientific journals. Our results are going to represent an original and significant scientific contribution that is going to improve our understanding of the basic physical mechanisms behind the dynamics of biological active matter.
Significance for the country
Active soft matter physics has been a rapidly growing field of research and is getting more and more attention in scientific community. The systems of interest that it addresses are typically biological by nature and therefore interesting not only from the physics but also from the biology and chemistry perspectives. The theme of the proposed project is mostly going to revolve around the embryonic development and the mechanics of biological tissues and cells. The studies are going to be mostly theoretical, however we are going to be collaborating closely with research groups both from Slovenia and abroad. We are going to present the results of the project in renowned international scientific journals. Our results are going to represent an original and significant scientific contribution that is going to improve our understanding of the basic physical mechanisms behind the dynamics of biological active matter.
Most important scientific results
Interim report
Most important socioeconomically and culturally relevant results
