the shape and structure of this object.
the mechanical properties of the materials, of which this object consists.
into a numerical model the behavior of the object using the fundamental laws of physics.
the model, by creating a code that is capable of simulating the cell behavior.
the model parameters using experimental measurements of basic cell manipulation.
the computational model against more complex physiological experiments.
the validated model to predict outcomes of other experiments and to formulate hypotheses.
Chapter 2 describes an introductory simulation that presents a computer script. It explains some of the possibilities and available features step by step. If you are interested mainly in building a model or if you have previous experience with cell modeling, this chapter may be skipped. It is primarily meant for readers not familiar with these topics to illustrate basic outcomes and to make it a bit clearer what we are trying to achieve.
Chapter 3 contains the modeling core of the book. Here, we establish the cell model, first with some hidden flaws but then revisited and improved. The modeling part is complemented with section, which discusses the fluid solver and section, which addresses the cell-cell interactions. The cell model is then discussed within the context of other approaches.
To link the biological reality with the developed model, we first review and derive theoretical foundations and then we use the theory as a starting point for direct comparison of model and real-world experiments with cells. Data from experiments need to be approached carefully and we point out several issues that should be considered.
Now the model is ready for practical use, but before we actually use it, we point out some issues that may arise. These include strategies for seeding of dense simulations or suitable discretisations.
We describe some - with absolutely no intention of being exhaustive - applications of the presented model. We show how this model may be used for computing capture rates of circulating tumor cells in microfluidic devices or for evaluating collision rates during deterministic lateral displacement in periodic obstacle arrays. The knowledge of individual cell deformation during the passage of the device may be used for evaluation of the blood damage index and for design optimisation of ventricular assist devices. The user-friendly open-source approach in computer implementation of the model has also led to its use for optimisation of micro-roughness of channel surfaces.
The model, or more precisely, the force-based approach to cell modeling, is flexible enough that several other biological phenomena, such as cell adhesion, inclusion of a cell’s inner structure or modeling of stiff cells can be tried.
Chapter 8 does not contain either Conclusions or Summary. In it we discuss, where the modeling may lead some time in the future. While writing this chapter, we have unleashed our imagination a little bit and we have replaced the sci-entific context with a sci-fiction context.
Computational Blood Cell Mechanics: Road towards models and biomedical applications is available at Amazon and CRC Press. It is part of the Chapman and Hall Mathematical and Computational Biology Series. While it is not a textbook, certain portions of it are suitable as a supplementary material for a course on computational blood cell modeling.
ESPResSo is an open-source Extensible Simulation Package for Research of Soft Matter. The 4.0 release (September 2018) is available here. The computational core is developed mainly at the Institute of Computational Physics in Stuttgart, Germany. It contains a lattice-Boltzmann solver for fluid.
Object-in-fluid is a computational framework developed in Žilina, Slovakia as part of ESPResSo. It lets the user model and simulate closed elastic objects using python scripts. The documentation and current information is available at Cell-in-fluid Research Group website and the latest version can be downloaded from here.
Here you can watch animations from simulations that use the model described in the book. Some of the videos are proof-of-concept works for various applications.