Related papers: Competitive ligand binding kinetics to linear poly…
Cell competition in multicellular organisms has been shown to play a critical role during the development of organisms, cancer progression, and in the establishment and maintenance of tissue homeostasis. Various mechanisms of cell…
By means of Monte Carlo computer simulations in the isothermal-isobaric ensemble, we investigated the interaction of a hydrophobic ligand with the hydrophobic surfaces of various curvatures (planar, convex and concave). A simple…
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,…
In biology, ligand mediated transitions (LMT), where the binding of a molecular ligand onto the binding site of a receptor molecule leads to a well-defined change in the conformation of the receptor, are often referred to as 'the second…
The equilibrium behavior of binary mixtures can be understood through the competition of energy scales, which classifies their corresponding phase diagrams into distinct topological regimes (Types I-IV). However, in many soft-matter…
We present Monte Carlo computer simulations for melts of semiflexible randomly knotted and randomly concatenated ring polymers on the fcc lattice and in slit confinement. Through systematic variation of the slit width at fixed melt density,…
The kinetic behavior of a three-dimensional off-lattice heteropolymer model is studied in terms of the time dependence of the average mean-square displacement between configurations. It is found that at short time-scales similar behavior is…
This note considers a system in which three ligands can independently bind to a scaffold. Such systems arise in diverse applications, including immunotherapy and synthetic biology. It is shown that there are unique steady states in each…
Cells in multicellular organisms adhere to the extracellular matrix through two-dimensional clusters spanning a size range from very few to thousands of adhesion bonds. For many common receptor-ligand systems, the ligands are tethered to a…
Indentation is a common experimental technique to study the mechanics of polymeric materials. The main advantage of using indentation is because this provides a direct correlation between the microstructure and the small-scale mechanical…
Protein-ligand interactions are crucial for a wide range of physiological processes. Many cellular functions result in these non-covalent `bonds' being mechanically strained, and this can be integral to proper cellular function. Broadly,…
By means of contact-density chain-growth simulations, we investigate a simple lattice model of a flexible polymer interacting with an attractive substrate. The contact density is a function of the numbers of monomer-substrate and…
Multivalent particles competing for binding on the same surface can exhibit switch-like behaviour, depending on the concentration of receptors on the surface. When the receptor concentration is low, energy dominates the free energy of…
We propose a model of mass-conserving heterogeneous nucleation to describe the dynamics of ligand-receptor binding in closed cellular compartments. When the ligand dissociation rate is small, competition among receptors for free ligands…
We present molecular dynamics simulations on the structural relaxation of a simple bead-spring model for polymer blends. The introduction of a different monomer size induces a large time scale separation for the dynamics of the two…
A model of protein-ligand binding kinetics in which slow solvent dynamics results from hydrophobic drying transitions is investigated. Molecular dynamics simulations show that solvent in the receptor pocket can fluctuate between wet and dry…
A coarse-grained molecular simulation approach originally developed for entangled polymeric liquids is extended to model the mechanical behavior of long-fiber networks. The model, based on the slip-link picture of chain entanglements,…
With the help of a simple two-dimensional model we simulate the tribological properties of a thin lubricant film consisting of linear (chain) molecules in the ordinary soft-lubricant regime. We find that friction generally increases with…
The coexistence of multiple types of interactions within social, technological and biological networks has moved the focus of the physics of complex systems towards a multiplex description of the interactions between their constituents.…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…