Related papers: Lattice models for protein organization throughout…
Cytoskeletal networks, which are essentially motor-filament assemblies, play a major role in many developmental processes involving structural remodeling and shape changes. These are achieved by nonequilibrium self-organization processes…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
We present a two channel driven lattice gas model with oppositely directed species moving on two parallel lanes with lane switching processes. We study correlated lane switching mechanism for particles so that switching may occur with…
We report on a lattice based algorithm, completely vectorized for molecular dynamics simulations. Its algorithmic complexity is of the order O(N), where $N$ is the number of particles. The algorithm works very effectively when the particles…
Mechanical loading in articular cartilage drives interstitial fluid flow through the porous collagen proteoglycan matrix, generating electrokinetic signals. We investigate whether the structural organization of cartilage histology can be…
The dynamic of complex ordering systems with active rotational degrees of freedom exemplified by protein self-assembly is explored using a machine learning workflow that combines deep learning-based semantic segmentation and rotationally…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
We study a kinetically constrained lattice glass model in which continuous local densities are randomly redistributed on neighbouring sites with a kinetic constraint that inhibits the process at high densities, and a random bias accounting…
Cell spreading is investigated at various scales in order to understand motility of living cells which is essential for a range of physiological activities in higher organisms as well as in microbes. At a microscopic scale, it has been seen…
Membrane organization is essential for cellular functions such as signal transduction and membrane trafficking. A major challenge is to understand the lateral heterogeneous structures in membranes and membrane fluidity in the presence of…
Mixtures of lipids and cholesterol are commonly used as model systems for studying the formation of liquid-ordered ($L_o$) domains in heterogeneous biological membranes. The simplest model system exhibiting coexistence between $L_o$ domains…
We report on a lattice based algorithm, completely vectorized for molecular dynamics simulations. Its algorithmic complexity is of the order $O(N)$, where $N$ is the number of particles. The algorithm works very effectively when the…
In order to grasp the features arising from cellular discreteness and individuality, in large parts of cell tissue modelling agent-based models are favoured. The subclass of off-lattice models allows for a physical motivation of the…
We investigate the hydrodynamic stability and the formation of patterns in a continuum model of epithelial layers, able to account for the interplay between mechanical activity, lateral adhesion and the $6-$fold orientational order…
Determining the middle of the bacteria cell and the proper placement of the septum is essential to the division of the bacterial cell. In E. coli, this process depends on the proteins MinC, MinD, and MinE. Here, the Lattice Boltzmann method…
The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations of specific proteins have been reported in a variety of…
A cell membrane can be simply regarded as composite material consisting of lipid bilayer, membrane cytoskeleton beneath lipid bilayer, and proteins embedded in lipid bilayer and linked with membrane cytoskeleton if one only concerns its…
In living cells, proteins involved in specialized biochemical functions are often spatially organized within biomolecular condensates. Increasing evidence suggests that some of these condensates, including DNA repair condensates, emerge…
We consider a lattice polymer model (random walk), in which the walk is allowed to visit lattice bonds at most twice. Such a model might have some relevance to describe statistical properties of RNA molecules. In order to mimic base…
We present results for a lattice model of bio-polymers where the type of $\beta$-sheet formation can be controlled by different types of hydrogen bonds depending on the relative orientation of close segments of the polymer. Tuning these…