Related papers: Structural symmetry and membrane curvature sensing
We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Fundamental questions about the role of the quaternary structures are addressed using a statistical mechanics off-lattice model of a dimer protein. The model, in spite of its simplicity, captures key features of the monomer-monomer…
Biological and biomimetic membranes often contain aggregates of embedded or adsorbed macromolecules. In this article, the indirect interactions of cylindrical objects adhering to a planar membrane are considered theoretically. The adhesion…
Many closed-cell foams exhibit an elongated cell shape in the foam rise direction, resulting in anisotropic compressive properties. Nevertheless, the underlying deformation mechanisms and how cell shape anisotropy induces this mechanical…
Nonequilibrium membrane pattern formation is studied using meshless membrane simulation. We consider that molecules bind to either surface of a bilayer membrane and move to the opposite leaflet by flip--flop. When binding does not modify…
Understanding the mechanical instabilities of two-dimensional membranes has strong connection to the subjects of structure instabilities, morphology control and materials failures. In this work, we investigate the plastic mechanism…
Cells often migrate on curved surfaces inside the body, such as curved tissues, blood vessels or highly curved protrusions of other cells. Recent \textit{in-vitro} experiments provide clear evidence that motile cells are affected by the…
Several numerical methods for measuring the bending rigidity and the spontaneous curvature of fluid membranes are studied using two types of meshless membrane models. The bending rigidity is estimated from the thermal undulations of planar…
The correlations between the sequence of monomers in a polymer and its three-dimensional structure is a grand challenge in polymer science and biology. The properties and functions of macromolecules depend on their 3D shape that has…
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ…
Recently, we presented a framework for understanding protein structure based on the idea that simple constructs of holding hands or touching of objects can be used to rationalize the common characteristics of globular proteins. We developed…
The detachment dynamics of a fluid membrane with an isotropic spontaneous curvature from a flat substrate are studied by using meshless membrane simulations. The membrane is detached from an open edge leading to vesicle formation. With…
Motivated to understand the behavior of biological filaments interacting with membranes of various types, we study a theoretical model for the shape and thermodynamics of intrinsically-helical filaments bound to curved membranes. We show…
This paper demonstrates how new principles of compressed sensing, namely asymptotic incoherence, asymptotic sparsity and multilevel sampling, can be utilised to better understand underlying phenomena in practical compressed sensing and…
A nematic membrane is a sheet with embedded orientational order, which can occur in biological cells, liquid crystal films, manufactured materials, and other soft matter systems. By formulating the free energy of nematic films using tensor…
Motivated by numerous X-ray scattering studies of lamellar phases with membrane proteins, amphiphilic peptides, polymers, or other inclusions, we have determined the modifications of the classical Caille law for a smectic phase as a…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
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…
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…