Related papers: General coarse-grained red blood cell models: I. M…
Recognizing the types of white blood cells (WBCs) in microscopic images of human blood smears is a fundamental task in the fields of pathology and hematology. Although previous studies have made significant contributions to the development…
Conjugated organic molecules play a central role in a wide range of optoelectronic devices, including organic light-emitting diodes, organic field-effect transistors, and organic solar cells. A major bottleneck in the computational design…
We introduce a closure model for coarse-grained kinetic theories of polar active fluids. Based on a quasi-equilibrium approximation of the particle distribution function, the model closely captures important analytical properties of the…
Non-particulate continuum descriptions allow for computationally efficient modeling of suspension flows at scales that are inaccessible to more detailed particulate approaches. It is well known that the presence of particles influences the…
We developed a physics-based analytical model to describe the nonlinear mechanical response of aspirated elastic shells. By representing the elastic energy through a stretching modulus, $K$, and a dimensionless ratio, $\delta$, capturing…
Building a good generative model for image has long been an important topic in computer vision and machine learning. Restricted Boltzmann machine (RBM) is one of such models that is simple but powerful. However, its restricted form also has…
Recent clinical results indicate that aberrant erythrocyte aggregation in hematological disorders is accompanied by endothelial damage and glycocalyx disruption, but the underlying biophysical mechanisms remain unclear. This study uses…
Coarse-grained (CG) models are simplified representations of soft matter systems that are commonly employed to overcome size and time limitations in computational studies. Many approaches have been developed to construct and parametrise…
Coarse-grained (CG) models provide an effective route to reducing the complexity of molecular simulations (MD), but conventional approaches depend heavily on long all-atom MD trajectories to adequately sample configurational space. This…
The measurement of cellular traction forces on soft elastic substrates has become a standard tool for many labs working on mechanobiology. Here we review the basic principles and different variants of this approach. In general, the…
In the paper we extend the Multiple-Relaxation-Time (MRT) Lattice Boltzmann (LB) model proposed in [Europhys. Lett. \textbf{90}, 54003 (2010)] so that it is suitable also for incompressible flows. To decrease the artificial oscillations,…
We preset a computational study of bending models for the curvature elasticity of lipid bilayer membranes that are relevant for simulations of vesicles and red blood cells. We compute bending energy and forces on triangulated meshes and…
We present a numerical analysis of the rheology of a suspension of red blood cells (RBCs) for different volume fractions in a wall-bounded, effectively inertialess, small amplitude oscillatory shear (SAOS) flow for a wide range of applied…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
The study of protein mass transport via atomistic simulation requires time and length scales beyond the computational capabilities of modern computer systems. The raspberry model for colloidal particles in combination with the mesoscopic…
We present the first deep implicit 3D shape model of the female breast, building upon and improving the recently proposed Regensburg Breast Shape Model (RBSM). Compared to its PCA-based predecessor, our model employs implicit neural…
Coarse-graining has become an area of tremendous importance within many different research fields. For molecular simulation, coarse-graining bears the promise of finding simplified models such that long-time simulations of large-scale…
We investigate two different types of non-Markovian coarse-grained models extracted from a linear, non-equilibrium microscopic system, featuring a tagged particle coupled to underdamped oscillators. The first model is obtained by…
Equilibrium aspects of molecular recognition of rigid biomolecules are investigated using coarse-grained lattice models. The analysis is carried out in two stages. First an ensemble of probe molecules is designed with respect to the target…
Brute-force simulations for dynamics on very large networks are quite expensive. While phenomenological treatments may capture some macroscopic properties, they often ignore important microscopic details. Fortunately, one may be only…