Related papers: Combinatorial protein-protein interactions on a po…
In order to understand the nuclei which develop during the course of protein folding and unfolding, we examine phase segregation of a single heteropolymer chain which occurs in equilibrium. These segregated conformations are characterized…
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…
The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a mathematical model is an important challenge…
The ability to tune the microstructures formed by block copolymers using accessible physical approaches provides control for practical material applications. A common strategy involves the addition of homopolymers, which can induce…
The phase-separation occurring in a system of mutually interacting proteins that can bind on specific sites of a chromatin fiber is here investigated. This is achieved by means of extensive Molecular Dynamics simulations of a simple polymer…
The cells and tissues that make up our body juggle contradictory mechanical demands. It is crucial for their survival to be able to withstand large mechanical loads, but it is equally crucial for them to produce forces and actively change…
We study the segregation of motile semiflexible filaments from a background of similar but non-motile filaments. Our Langevin dynamics simulations reveal a wide range of emergent structures governed by filament flexibility and activity,…
Membrane bending is an extensively studied problem from both modeling and experimental perspectives because of the wide implications of curvature generation in cell biology. Many of the curvature generating aspects in membranes can be…
The role of fixed degrees of freedom in soft/granular matter systems has broad applicability and theoretical interest. Here we address questions of the geometrical role that a scaffolding of fixed particles plays in tuning the threshold…
Native protein folds often have a high degree of symmetry. We study the relationship between the symmetries of native proteins, and their designabilities -- how many different sequences encode a given native structure. Using a…
We present a computational study on the folding and aggregation of proteins in aqueous environment, as function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding…
Adsorption of dimers is modelled using random sequential adsorption algorithm. The interaction between molecules is given by screened electrostatic potential. The paper focuses on the properties of adsorbed monolayers as well as the…
Topological entanglements in polymers are mimicked by sliding rings (slip-links) which enforce pair contacts between monomers. We study the force-extension curve for linear polymers in which slip-links create additional loops of variable…
Recent experimental results suggest that the E. coli chromosome feels a self-attracting interaction of osmotic origin, and is condensed in foci by bridging interactions. Motivated by these findings, we explore a generic modeling framework…
The idea of confinement states that in certain systems constituent particles can be discerned only indirectly being bound by an interaction whose strength increases with increasing particle separation. Though the most famous example is the…
Under dehydration conditions, amphipathic Late Embryogenesis Abundant (LEA) proteins fold spontaneously from a random conformation into alpha-helical structures and this transition is promoted by the presence of membranes. To gain insight…
We present a new simulation scheme which allows an efficient sampling of reconfigurable supramolecular structures made of polymeric constructs functionalized by reactive binding sites. The algorithm is based on the configurational bias…
Complex colloidal cluster morphologies are desirable for the fabrication of advanced materials, such as photonic crystals and meta-materials, and can be formed through evaporation-driven packing. By coupling lattice Boltzmann and discrete…
We consider the lateral diffusion of a protein interacting with the curvature of the membrane. The interaction energy is minimized if the particle is at a membrane position with a certain curvature that agrees with the spontaneous curvature…
We consider a model mixture of hard colloidal spheres and non-adsorbing polymer chains in a theta solvent. The polymer component is modelled as a polydisperse mixture of effective spheres, mutually noninteracting but excluded from the…