Related papers: Helices in Biomolecules
Self-assembly at submicroscopic scales is an important but little understood phenomenon. A prominent example is virus capsid growth, whose underlying behavior can be modeled using simple particles that assemble into polyhedral shells.…
A vital constituent of a virus is its protein shell, called the viral capsid, that encapsulates and hence provides protection for the viral genome. Viral capsids are usually spherical, and for a significant number of viruses exhibit overall…
The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path…
In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…
Nature uses elongated shapes and filaments to build stable structures, generate motion, and allow complex geometric interactions. In this Review, we examine the role of biological filaments across different length scales. From the molecular…
A small model polypeptide represented in atomic detail is folded using Monte Carlo dynamics. The polypeptide is designed to have a native conformation similar to the central part of the helix-turn-helix protein ROP. Starting from a…
The halo structure originated in nuclear physics but is now encountered more widely. It appears in loosely bound, clustered systems where the spatial extension of the system is significantly larger than that of the binding potentials. A…
Inside every living cell is the cytoplasm: a fluid mixture of thousands of different macromolecules, predominantly proteins. This mixture is where most of the biochemistry occurs that enables living cells to function, and it is perhaps the…
Based on the competition between members of a hierarchy of length scales in complex multi-scale systems, it is shown how clustering of active quantities into concentrated sets, like bubbles in a Swiss cheese, is a generic property that…
$\alpha$-helices stand out as common and relatively invariant secondary structural elements of proteins. However, $\alpha$-helices are not rigid bodies and their deformations can be significant in protein function ({\it e.g.} coiled coils).…
Autonomous locomotion is a ubiquitous phenomenon in biology and in physics of active systems at microscopic scale. This includes prokaryotic, eukaryotic cells (crawling and swimming) and artificial swimmers. An outstanding feature is the…
Collagen fibrils, cable-like assemblies of long biological molecules, are dominant components of connective tissues. Their determinant morphological and functional roles motivated a large number of studies concerning their formation and…
Hepatitis C virus helicase is a molecular motor that splits nucleic acid duplex structures during viral replication, therefore representing a promising target for antiviral treatment. Hence, a detailed understanding of the mechanism by…
Helices are a key folding motif in protein structure. The question which factors determine helix stability for a given polypeptide or protein is an ongoing challenge. Here we use van der Waals corrected density-functional theory to address…
Rotating clusters or vortices are formations of agents that rotate around a common center. These patterns may be found in very different contexts: from swirling fish to surveillance drones. Here, we propose a minimal model for…
Natural protein molecules are exceptional polymers. Encoded in apparently random strings of amino-acids, these objects perform clear physical tasks that are rare to find by simple chance. Accurate folding, specific binding, powerful…
Results from molecular dynamics simulations of simple, structured particles capable of self-assembling into polyhedral shells are described. The analysis focuses on the growth histories of individual shells in the presence of an explicit…
Microbial flagellates typically inhabit complex suspensions of polymeric material which can impact the swimming speed of motile microbes, filter-feeding of sessile cells, and the generation of biofilms. There is currently a need to better…
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,…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…