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Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking…
Colloidal gels constitute an important class of materials found in many contexts and with a wide range of applications. Yet as matter far from equilibrium, gels exhibit a variety of time-dependent behaviours, which can be perplexing, such…
The dynamical properties of entangled polymers originate from the dynamic constraints due to the uncrossability between polymer chains. We propose a highly coarse-grained simulation model with transient bonds for such dynamically…
Hybrid particle-field methods are computationally efficient approaches for modelling soft matter systems. So far applications of these methodologies have been limited to constant volume conditions. Here, we reformulate particle-field…
The combination of two techniques (Small Angle X-ray Scattering and Atomic Force Microscopy) has allowed us to measure in reciprocal and real space the correlation length $\xi$ of salt-free aqueous solutions of highly charged hydrophobic…
Molecular dynamics simulations have been employed to study the formation of a physical (thermoreversible) gel by amphiphilic A-B-A triblock copolymers in aqueous solution. In order to mimic the structure of hydrogel-forming polypeptides…
Rigidity analysis using the "pebble game" has been applied to protein crystal structures to obtain information on protein folding, assembly and t he structure-function relationship. However, previous work using this technique has not made…
We report on self-assembly, clustering, and conformational phases of peptides on inorganic semiconductor surfaces. The peptide-covered surface fraction can differ by a factor of 25, depending mainly on surface and peptide polarity. Low…
A self-consistent field theory study of lock and key type interactions between sterically stabilized colloids in polymer solution is performed. Both the key particle and the lock cavity are assumed to have cylindrical shape, and their…
In the present paper we present results of calculations obtained with the use of the theoretical method described in our preceding paper [1] and perform detail analysis of alpha helix-random coil transition in alanine polypeptides of…
We theoretically study the polarizability and the interactions of neutral complexes consisting of a semi-flexible polyelectrolyte adsorbed onto an oppositely charged spherical colloid. In the systems we studied, the bending energy of the…
Small peptides are model molecules for the amino acid residues that are the constituents of proteins. In any bottom-up approach to understand the properties of these macromolecules essential in the functioning of every living being, to…
We examine the phase transition of polymer adsorption as well as the underlying kinetics of polymer binding from dilute solutions on a structureless solid surface. The emphasis is put on the properties of regular multiblock copolymers,…
Chemical crosslinking of collagen is a general strategy to reproduce macroscale tissue properties in physiological environment. However, simultaneous control of protein conformation, material properties and biofunctionality is highly…
A polymer chain tethered to a surface may be compact or extended, adsorbed or desorbed, depending on interactions with the surface and the surrounding solvent. This leads to a rich phase diagram with a variety of transitions. To investigate…
We explore the effect of Couette flow on knotted linear polymer chains with extensive Molecular Dynamics (MD) simulations. Hydrodynamic interactions are accounted for by means of Multi-Particle Collision Dynamics (MPCD). The polymer chain,…
The design of hybrid peptide-solid interfaces for nanotechnological applications such as biomolecular nanoarrays requires a deep understanding of the basic mechanisms of peptide binding and assembly at solid substrates. Here we show by…
We use a coarse-grained molecular dynamics model to study the electrophoretic behaviour of flexible polyelectrolyte chains. We first characterize the static properties of the model with respect to the chain length, the polyelectrolyte…
2D conjugated polyphthalocyanines can be obtained as two distinctly different types of material with specific molecular structures and different morphological properties. It was believed that the temperature is the key factor affecting the…