Related papers: General coarse-grained red blood cell models: I. M…
One of the essential questions in the area of granular matter is, how to obtain macroscopic tensorial quantities like stress and strain from ``microscopic'' quantities like the contact forces in a granular assembly. Different averaging…
In this study, we utilize genetic algorithms to develop a realistic implicit solvent ultra-coarse-grained (PC) membrane model comprising only three interaction sites. The key philosophy of the ultra-CG membrane model SMARTINI3 is its…
We investigate the quality of structural models generated by the Reverse Monte Carlo (RMC) method in a typical application to amorphous systems. To this end we calculate surrogate diffraction data from a Li2O-SiO2 molecular dynamics (MD)…
The development of traction-force microscopy, in the past two decades, has created the unprecedented opportunity of performing direct mechanical measurements on living cells as they adhere or crawl on uniform or micro-patterned substrates.…
We present a novel thermodynamically guided, low-noise, time-scale bridging, and pertinently efficient strategy for the dynamic simulation of microscopic models for complex fluids. The systematic coarse-graining method is exemplified for…
Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. This procedure provides stoichiometries, reaction fluxes (rate laws), and…
The dynamics of single red blood cells (RBCs) determine microvascular blood flow by adapting their shape to the flow conditions in the narrow vessels. In this study, we explore the dynamics and shape transitions of RBCs on the cellular…
In the present article, novel Coarse-Graining (CG) algorithms for the Eulerian-Lagrangian (EL) simulation of particle-laden flows are proposed. These include different variants of Reproducing Kernel Particle Methods (RKPM) and an extended…
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such…
We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered…
Systems biology and whole-cell modelling are demanding increasingly comprehensive mathematical models of cellular biochemistry. These models require the development of simplified models of specific processes which capture essential…
The work analyzes a one-dimensional viscoelastic model of blood vessel growth under nonlinear friction with surroundings, and provides numerical simulations for various growing cases. For the nonlinear differential equations, two sufficient…
This paper provides a new methodology to analyze unobserved heterogeneity when observed characteristics are modeled nonlinearly. The proposed model builds on varying random coefficients (VRC) that are determined by nonlinear functions of…
Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities,…
We have proposed an efficient parameterization method for a recent variant of the Gay-Berne potential for dissimilar and biaxial particles and demonstrated it for a set of small organic molecules. Compared to the previously proposed…
We propose a general method for deriving one-dimensional models for nonlinear structures. It captures the contribution to the strain energy arising not only from the macroscopic elastic strain as in classical structural models, but also…
Accurately and quickly binuclear cell (BC) detection plays a significant role in predicting the risk of leukemia and other malignant tumors. However, manual microscopy counting is time-consuming and lacks objectivity. Moreover, with the…
Erythrocyte Sedimentation Rate (ESR) is a clinical parameter used as a non-specific marker for inflammation, and recent studies have shown that it is linked to the collapse of the gel formed by red blood cells (RBCs) at physiological…
The hyperbolic random graph model (HRG) has proven useful in the analysis of scale-free networks, which are ubiquitous in many fields, from social network analysis to biology. However, working with this model is algorithmically and…
In recent years dynamical modelling has been provided with a range of breakthrough methods to perform exact Bayesian inference. However it is often computationally unfeasible to apply exact statistical methodologies in the context of large…