Related papers: General coarse-grained red blood cell models: I. M…
Many methods to computationally predict red blood cell damage have been introduced, and among these are Lagrangian methods which track the cells along their pathlines. Such methods typically do not explicitly include cell-cell interactions.…
This chapter summarizes several approaches combining theory, simulation and experiment that aim for a better understanding of phenomena in lipid bilayers and membrane protein systems, covering topics such as lipid rafts, membrane mediated…
Thrombosis is a common complication following the surgical implantation of blood contacting devices, and is strongly influenced by the phenomenon of near-wall enrichment of platelets. This paper describes a multi-constituent continuum…
Investigation of cell structure is hardly imaginable without bright-field microscopy. Numerous modifications such as depth-wise scanning or videoenhancement make this method being state-of-the-art. This raises a question what maximal…
Increasing the efficiency of materials design and discovery remains a significant challenge, especially given the prohibitively large size of chemical compound space. The use of a chemically transferable coarse-grained model enables…
Finding coarse-grained, low-dimensional descriptions is an important task in the analysis of complex, stochastic models of gene regulatory networks. This task involves (a) identifying observables that best describe the state of these…
The non-linear behavior of human erythrocytes subjected to shear stress was analyzed using data series from the Erythrocyte Rheometer and a theoretical model was developed. Linear behavior was eliminated by means of a slot filter and a…
A coarse-grained molecular model, which consists of a spherical particle and an orientation vector, is proposed to simulate lipid membrane on a large length scale. The solvent is implicitly represented by an effective attractive interaction…
Restricted Boltzmann machines (RBMs) are endowed with the universal power of modeling (binary) joint distributions. Meanwhile, as a result of their confining network structure, training RBMs confronts less difficulties (compared with more…
In this work, we introduce a novel computational framework that we developed to use numerical simulations to investigate the complexity of brain tissue at a microscopic level with a detail never realised before. Directly inspired by the…
We consider the motion of red blood cells and other non-spherical microcapsules dilutely suspended in a simple shear flow. Our analysis indicates that depending on the viscosity, membrane elasticity, geometry and shear rate, the particle…
Centrifugation of biological matter in density gradient solutions is a standard method for separating cell types or components. It is also used to separate red blood cells (RBCs) by age, as they lose water and become denser over their…
Cell detection and cell type classification from biomedical images play an important role for high-throughput imaging and various clinical application. While classification of single cell sample can be performed with standard computer…
Prototype-based classification learning methods are known to be inherently interpretable. However, this paradigm suffers from major limitations compared to deep models, such as lower performance. This led to the development of the so-called…
We construct a coarse-grained (CG) model for dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayers and apply it to large-scale simulation studies of lipid membranes. Our CG model is a two-dimensional representation of the membrane,…
We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and…
Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps…
Blood cell classification and counting are vital for the diagnosis of various blood-related diseases, such as anemia, leukemia, and thrombocytopenia. The manual process of blood cell classification and counting is time-consuming, prone to…
Red blood cells are highly deformable and present in various shapes. In blood cell disorders, only a subset of all cells is morphologically altered and relevant for the diagnosis. However, manually labeling of all cells is laborious,…
We investigate the properties of membranes under tension by Monte-Carlo simulations of a generic coarse-grained model for lipid bilayers. We give a comprising overview of the behavior of several membrane characteristics, such as the area…