Related papers: General coarse-grained red blood cell models: I. M…
A coarse-grained version of the Lattice Boltzmann (LB) method is developed with the intent of enhancing its geometrical flexibility so as to be able to tackle a wider class of flows of engineering interest. To this purpose, the original…
We present an extension to the iterative Boltzmann inversion method to generate coarse-grained models with three-body intramolecular potentials that can reproduce correlations in structural distribution functions. The coarse-grained…
A coarse-grained water model is developed using multistate iterative Boltzmann inversion. Following previous work, the k-means algorithm is used to dynamically map multiple water molecules to a single coarse-grained bead, allowing the use…
The ability of cells to undergo reversible shape changes is often crucial to their survival. For Red Blood Cells (RBCs), irreversible alteration of the cell shape and flexibility often causes anemia. Here we show theoretically that RBCs may…
The aim of this paper is to develop suitable models for the phenomenon of cell blebbing, which allow for computational predictions of mechanical effects including the crucial interaction of the cell membrane and the actin cortex. For this…
A coarse-grained cellular automaton is proposed to simulate traffic systems. There, cells represent road sections. A cell can be in two states: jammed or passable. Numerical calculations are performed for a piece of square lattice with open…
Tissue dynamics and collective cell motion are crucial biological processes. Their biological machinery is mostly known, and simulation models such as the "active vertex model" (AVM) exist and yield reasonable agreement with experimental…
The application of machine learning techniques to the medical domain is especially challenging due to the required level of precision and the incurrence of huge risks of minute errors. Employing these techniques to a more complex subdomain…
White blood cells (WBCs) are the most diverse cell types observed in the healing process of injured skeletal muscles. In the course of healing, WBCs exhibit dynamic cellular response and undergo multiple protein expression changes. The…
Plasma proteins such as fibrinogen induce the aggregation of red blood cells (RBC) into rouleaux, which are responsible for the pronounced shear thinning behavior of blood, control the erythro- cyte sedimentation rate (ESR) a common…
The study of thrombosis is crucial to understand and develop new therapies for diseases like deep vein thrombosis, diabetes related strokes, pulmonary embolism etc. The last two decades have seen an exponential growth in studies related to…
Reconstruction of 3D erythrocyte or red blood cell (RBC) morphology from partial observations, such as microscope images, is essential for understanding the physiology of RBC aging and the pathology of various RBC disorders. In this study,…
Ribosomes are critical biomolecular nanomachines responsible for protein synthesis in all known organisms. The function and dynamics of ribosomes can be studied using molecular dynamics computer simulations. Although this task remains…
We present a new method for the geometric reconstruction of elastic surfaces simulated by the immersed boundary method with the goal of simulating the motion and interactions of cells in whole blood. Our method uses parameter-free radial…
creating automated processes in different areas of medical science with the application of engineering tools is a highly growing field over recent decades. In this context, many medical image processing and analyzing researchers use…
For accurate simulations of rarefied gas flows around moving obstacles, we propose a cut cell method on Cartesian grids: it allows exact conservation and accurate treatment of boundary conditions. Our approach is designed to treat Cartesian…
The automatic detection of White Blood Cells (WBC) still remains as an unsolved issue in medical imaging. The analysis of WBC images has engaged researchers from fields of medicine and computer vision alike. Since WBC can be approximated by…
Coarse-grained (CG) force field methods for molecular systems are a crucial tool to simulate large biological macromolecules and are therefore essential for characterisations of biomolecular systems. While state-of-the-art deep learning…
We introduce a general framework for constructing coarse-grained potential models without ad hoc approximations such as limiting the potential to two- and/or three-body contributions. The scheme, called Deep Coarse-Grained Potential…
Motivated by the reported peculiar dynamics of a red blood cell in shear flow, we develop an analytical theory for the motion of a nearly--spherical fluid particle enclosed by a visco--elastic incompressible interface in linear flows. The…