Details
| Original language | English |
|---|---|
| Pages (from-to) | 2091–2113 |
| Number of pages | 23 |
| Journal | Biomechanics and Modeling in Mechanobiology |
| Volume | 23 |
| Issue number | 6 |
| Early online date | 30 Sept 2024 |
| Publication status | Published - Dec 2024 |
Abstract
Dense communities of bacteria, also known as biofilms, are ubiquitous in all of our everyday life. They are not only always surrounding us, but are also active inside our bodies, for example in the oral cavity. While some biofilms are beneficial or even necessary for human life, others can be harmful. Therefore, it is highly important to gain an in-depth understanding of biofilms which can be achieved by in vitro or in vivo experiments. Since these experiments are often time-consuming or expensive, in silico models have proven themselves to be a viable tool in assisting the description and analysis of these complicated processes. Current biofilm growth simulations are using mainly two approaches for describing the underlying models. The volumetric approach splits the deformation tensor into a growth and an elastic part. In this approach, the mass never changes, unless some additional constraints are enforced. The density-based approach, on the other hand, uses an evolution equation to update the growing tissue by adding mass. Here, the density stays constant, and no pressure is exerted. The in silico model presented in this work combines the two approaches. Thus, it is possible to capture stresses inside of the biofilm while adding mass. Since this approach is directly derived from Hamilton’s principle, it fulfills the first and second law of thermodynamics automatically, which other models need to be checked for separately. In this work, we show the derivation of the model as well as some selected numerical experiments. The numerical experiments show a good phenomenological agreement with what is to be expected from a growing biofilm. The numerical behavior is stable, and we are thus capable of solving complicated boundary value problems. In addition, the model is very reactive to different input parameters, thereby different behavior of various biofilms can be captured without modifying the model.
Keywords
- Biofilm, Finite Element Simulation, Growth, Hamilton principle, Multi-physics
ASJC Scopus subject areas
- Biochemistry, Genetics and Molecular Biology(all)
- Biotechnology
- Mathematics(all)
- Modelling and Simulation
- Engineering(all)
- Mechanical Engineering
Cite this
- Standard
- Harvard
- Apa
- Vancouver
- BibTeX
- RIS
In: Biomechanics and Modeling in Mechanobiology, Vol. 23, No. 6, 12.2024, p. 2091–2113.
Research output: Contribution to journal › Article › Research › peer review
}
TY - JOUR
T1 - A Hamilton principle-based model for diffusion-driven biofilm growth
AU - Klempt, Felix
AU - Soleimani, Meisam
AU - Wriggers, Peter
AU - Junker, Philipp
N1 - Publisher Copyright: © The Author(s) 2024.
PY - 2024/12
Y1 - 2024/12
N2 - Dense communities of bacteria, also known as biofilms, are ubiquitous in all of our everyday life. They are not only always surrounding us, but are also active inside our bodies, for example in the oral cavity. While some biofilms are beneficial or even necessary for human life, others can be harmful. Therefore, it is highly important to gain an in-depth understanding of biofilms which can be achieved by in vitro or in vivo experiments. Since these experiments are often time-consuming or expensive, in silico models have proven themselves to be a viable tool in assisting the description and analysis of these complicated processes. Current biofilm growth simulations are using mainly two approaches for describing the underlying models. The volumetric approach splits the deformation tensor into a growth and an elastic part. In this approach, the mass never changes, unless some additional constraints are enforced. The density-based approach, on the other hand, uses an evolution equation to update the growing tissue by adding mass. Here, the density stays constant, and no pressure is exerted. The in silico model presented in this work combines the two approaches. Thus, it is possible to capture stresses inside of the biofilm while adding mass. Since this approach is directly derived from Hamilton’s principle, it fulfills the first and second law of thermodynamics automatically, which other models need to be checked for separately. In this work, we show the derivation of the model as well as some selected numerical experiments. The numerical experiments show a good phenomenological agreement with what is to be expected from a growing biofilm. The numerical behavior is stable, and we are thus capable of solving complicated boundary value problems. In addition, the model is very reactive to different input parameters, thereby different behavior of various biofilms can be captured without modifying the model.
AB - Dense communities of bacteria, also known as biofilms, are ubiquitous in all of our everyday life. They are not only always surrounding us, but are also active inside our bodies, for example in the oral cavity. While some biofilms are beneficial or even necessary for human life, others can be harmful. Therefore, it is highly important to gain an in-depth understanding of biofilms which can be achieved by in vitro or in vivo experiments. Since these experiments are often time-consuming or expensive, in silico models have proven themselves to be a viable tool in assisting the description and analysis of these complicated processes. Current biofilm growth simulations are using mainly two approaches for describing the underlying models. The volumetric approach splits the deformation tensor into a growth and an elastic part. In this approach, the mass never changes, unless some additional constraints are enforced. The density-based approach, on the other hand, uses an evolution equation to update the growing tissue by adding mass. Here, the density stays constant, and no pressure is exerted. The in silico model presented in this work combines the two approaches. Thus, it is possible to capture stresses inside of the biofilm while adding mass. Since this approach is directly derived from Hamilton’s principle, it fulfills the first and second law of thermodynamics automatically, which other models need to be checked for separately. In this work, we show the derivation of the model as well as some selected numerical experiments. The numerical experiments show a good phenomenological agreement with what is to be expected from a growing biofilm. The numerical behavior is stable, and we are thus capable of solving complicated boundary value problems. In addition, the model is very reactive to different input parameters, thereby different behavior of various biofilms can be captured without modifying the model.
KW - Biofilm
KW - Finite Element Simulation
KW - Growth
KW - Hamilton principle
KW - Multi-physics
UR - http://www.scopus.com/inward/record.url?scp=85205349655&partnerID=8YFLogxK
U2 - 10.1007/s10237-024-01883-x
DO - 10.1007/s10237-024-01883-x
M3 - Article
C2 - 39347863
AN - SCOPUS:85205349655
VL - 23
SP - 2091
EP - 2113
JO - Biomechanics and Modeling in Mechanobiology
JF - Biomechanics and Modeling in Mechanobiology
SN - 1617-7959
IS - 6
ER -