A user ready, well documented software package PyOIF contains an implementation of a robust validated computational model for cell flow modelling. The software is capable of simulating processes involving biological cells immersed in a fluid. The examples of such processes are flows in microfluidic channels with numerous applications such as cell sorting, rare cell isolation or flow fractionation. Besides the typical usage of such computational model in the design process of microfluidic devices, PyOIF has been used in the computer-aided discovery involving mechanical properties of cell membranes. With this software, single cell, many cell, as well as dense cell suspensions can be simulated. Many cell simulations include cell-cell interactions and analyse their effect on the cells. PyOIF can be used to test the influence of mechanical properties of the membrane in flows and in membrane-membrane interactions. Dense suspensions may be used to study the effect of cell volume fraction on macroscopic phenomena such as cell-free layer, apparent suspension viscosity or cell degradation. The PyOIF module is based on the official ESPResSo distribution with few modifications and is available under the terms of the GNU General Public Licence. PyOIF is based on Python objects representing the cells and on the C++ computational core for fluid and interaction dynamics. The source code is freely available at GitHub repository, runs natively under Linux and MacOS and can be used in Windows Subsystem for Linux. The communication among PyOIF users and developers is maintained using active mailing lists. This work provides a basic background to the underlying computational models and to the implementation of interactions within this framework. We provide the prospective PyOIF users with a practical example of simulation script with reference to our publicly available User Guide.

The main aim of our work is future optimization of microfluidic devices used for capture of rare cells, for instance circulating tumour cells. Since the manufacture of such devices and performing biological experiments are complicated and time consuming, in silico experiments are preferable for this purpose. But first a simulation model has to be properly verified. In this article we propose statistical characteristics for comparison of simulation and biological experiments of red blood cells moving in a fluid. At the same time these characteristics allow better understanding of the course of the simulation and the behaviour of its individual components. In the first part we explore the sensitivity of some of the characteristics formulated on the grounds of the previous research to various topologies of the microfluidic channel with one solid hematocrit. The second part of the article analyzes the entire blood cell group; it focuses on their position (orientation) in the channel. To analyze the orientation, we use the principal component analysis (PCA), by means of which we can determine the statistical distribution of the directions of a blood cell set with a certain channel geometry. This characteristics describes the qualities of blood cells during a simulation, which are interesting when we are analyzing, as a targeted value, the possibility of the largest number possible of blood cells getting to the wall of the channel. We have tested the characteristics for various simulation parameters, and we have obtained interesting results.

The sorting of biological cells or particles immersed in a fluid is a frequent goal in the domain of microfluidics. One approach for such sorting is in using the inertial effects that are present in curved channels. In this study, we propose a new approach of inertial focusing of cells in microfluidic devices. The investigated channels had the form of a helical channel with a circular cross-section, and the cells were spherical. We identified the key parameters that influence the cell sorting results through multiple computational simulations using a modelling tool PyOIF within the package ESPResSo. We found that spherical cells could be sorted with respect to their size in helical channels since their stabilised positions are located in different parts of the channel cross section. The location of the stabilised position is a function of the fluid parameters, the geometrical parameters of the helical device, and the size of the immersed cells.

In this work, we examine the volumetric flow rate of microfluidic devices. The volumetric flow rate is a parameter which is necessary to correctly set up a simulation of a real device and to check the conformity of a simulation and a laboratory experiments [1]. Instead of defining the volumetric rate at the beginning as a simulation parameter, a parameter of external force is set. The proposed hypothesis is that for a fixed set of other parameters (topology, viscosity of the liquid, …) the volumetric flow rate is linearly dependent on external force in typical ranges of fluid velocity used in our simulations. To confirm this linearity hypothesis and to find numerical limits of this approach, we test several values of the external force parameter. The tests are designed for three different topologies of simulation box and for various haematocrits. The topologies of the microfluidic devices are inspired by existing laboratory experiments [3 - 6]. The linear relationship between the external force and the volumetric flow rate is verified in orders of magnitudes similar to the values obtained from laboratory experiments.