Related papers: Lattice models for protein organization throughout…
Protein aggregation on the plasma membrane (PM) is of critical importance to many cellular processes such as cell adhesion, endocytosis, fibrillar conformation, and vesicle transport. Lateral diffusion of protein aggregates or clusters on…
The adhesion of biomembranes is mediated by the binding of membrane-anchored receptor and ligand proteins. The proteins can only bind if the separation between apposing membranes is sufficiently close to the length of the protein complexes,…
Many cellular organelles are membrane-bound structures with complex membrane composition and shape. Their shapes have been observed to depend on the metabolic state of the organelle, and the mechanisms that couple biochemical pathways and…
We theoretically investigate the dynamics of a floating lipid bilayer membrane coupled with a two-dimensional cytoskeleton network, taking into explicitly account the intermonolayer friction, the discrete lattice structure of the…
The formation and dynamics of a wide variety of binary two-dimensional ordered structures and superlattices are investigated through a phase field crystal model with sublattice ordering. Various types of binary ordered phases, the phase…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
Recent advances in high-resolution experimental methods have highlighted the significance of cell signal pathway crosstalk and localised signalling activity in the development and disease of numerous biological systems. The investigation of…
In silico, cell based approaches for modeling biological morphogenesis are used to test and validate our understanding of the biological and mechanical process that are at work during the growth and the organization of multi-cell tissues.…
The organization of lipids in biological membranes is essential for cellular functions such as signal transduction and membrane trafficking. A major challenge is how to control lateral lipid composition in supported membranes which are…
We study segregation and stratification of mixtures of grains differing in size, shape and material properties poured in two-dimensional silos using a microscopic lattice model for surface flows of grains. The model incorporates the…
A chloroplast is a subcellular organelle of photosynthesis in plant and algal cells. A chloroplast genome encodes proteins of the photosynthetic electron transport chain and ribosomal proteins required to express them. Chloroplast-encoded…
A contemporary procedure to grow artificial tissue is to seed cells onto a porous biomaterial scaffold and culture it within a perfusion bioreactor to facilitate the transport of nutrients to growing cells. Typical models of cell growth for…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
We present a simple model which allows to investigate equilibrium aspects of molecular recognition between rigid biomolecules on a generic level. Using a two-stage approach, which consists of a design and a testing step, the role of…
The thermodynamic, dynamic and structural behavior of a water-like system confined in a matrix is analyzed for increasing confining geometries. The liquid is modeled by a two dimensional associating lattice gas model that exhibits density…
Membrane particles such as proteins and lipids organize into zones that perform unique functions. Here, I introduce a topological and category-theoretic framework to represent particle and zone intra-scale interactions and inter-scale…
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Go interactions. By means of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal component…
Biological membranes are complex, dynamic structures essential for cellular compartmentalization, signaling, and mechanical integrity. The molecular organization of eukaryotic membranes has been extensively studied, including the lipid…
Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibriums measured in vitro with purified DNA and protein components. Recently, a new field of applications…
Plasma membranes appear as deformable systems wherein molecules are free to move and diffuse giving rise to condensed microdomains (composed of ordered lipids, transmembrane proteins and cholesterol) surrounded by disordered lipid…