Related papers: Structural motifs of biomolecules
We investigate a set of design principles that link specific features of interparticle interactions to predictable structural and dynamic outcomes in two-dimensional self-assembly, a framework relevant to soft matter and biological…
The shape of the building blocks plays a crucial role in directing self-assembly towards desired architectures. Out of the many different shapes, helix has a unique position. Helical structures are ubiquitous in nature and a helical shape…
We describe a computational model for studying the complexity of self-assembled structures with active molecular components. Our model captures notions of growth and movement ubiquitous in biological systems. The model is inspired by…
Carbon nanotubes are modeled as point particle configurations in the framework of Molecular Mechanics, where interactions are described by means of short range attractive-repulsive potentials. The identification of local energy minimizers…
Building structures with hierarchical order through the self-assembly of smaller blocks is not only a prerogative of nature, but also a strategy to design artificial materials with tailored functions. We explore in simulation the…
DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and…
The structural parameters of alpha helix and some forms of DNA-structures are determined by methods of algebraic topology. These structures are locally periodic and correspond to the bifurcation point for minimal surfaces given by…
A simple phenomenological model for describing the conformational dynamics of biological macromolecules via the nonlinearity-induced instabilities is proposed. It is shown that the interaction between charges and bending degrees of freedom…
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages,…
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…
Living cells are soft bodies of a characteristic form, but endowed with a capacity for a steady turnover of their structures. Both of these material properties, i.e. recovery of the shape after an external stress has been imposed and…
Soft particles such as microgels and core-shell particles can undergo significant and anisotropic deformations when adsorbed to a liquid interface. This, in turn, leads to a complex phase behavior upon compression. Here we develop a…
Molecular self-assembly on surfaces constitutes a powerful method for creating tailor-made surface structures with dedicated functionalities. Varying the intermolecular interactions allows for tuning the resulting molecular structures in a…
We study the self-assembly behaviour of patchy particles with `protein-like' interactions that can be considered as a minimal model for the assembly of viral capsids and other shell-like protein complexes. We thoroughly explore the…
A cubic structure of polymer colloid complexes is studied. The technique of the research includes i) an analysis of well-known literature SAXS data; on this base, at some assumptions, ii) constructing a simple model to estimate geometric…
Phase separation within polymer networks plays a central role in shaping the structure and mechanics of both synthetic materials and living cells, including the formation of biomolecular condensates within cytoskeletal networks. Previous…
Motivated by intracellular phase separation, we theoretically investigate how molecular orientation and multi-component nature affect phase behavior. We construct a minimal model for a ternary mixture composed of isotropic (I), anisotropic…
Spinodal decomposition process in the system of immiscible PbTe/CdTe compounds is analyzed as an example of a self-organizing structure. The immiscibility of the constituents leads to the observed morphological transformations like…
We review the theoretical analyses and simulations of the interactions between curvature-inducing proteins and biomembranes. Laterally isotropic proteins induce spherical budding, whereas anisotropic proteins, such as Bin/Amphiphysin/Rvs…
We show that the formation of membrane tubes (or membrane tethers), which is a crucial step in many biological processes, is highly non-trivial and involves first order shape transitions. The force exerted by an emerging tube is a…