相关论文: Geometry of compact tubes and protein structures

The one-dimensional problem of selecting the triple helix with the highest volume fraction is solved and hence the condition for a helix to be close-packed is obtained. The close-packed triple helix is shown to have a pitch angle of $v_{CP}…

Over the past two decades polymer nanocomposites have received tremendous interest from industry and academia due to their advanced properties comparative to polymer blends. Many computational studies have revealed that the macroscopic…

Advances in experimental techniques and in theoretical models have improved our understanding of protein crystallization. But they have also left open questions regarding the protein phase behavior and self-assembly kinetics, such as why…

Membrane proteins and lipids can self-assemble into membrane protein polyhedral nanoparticles (MPPNs). MPPNs have a closed spherical surface and a polyhedral protein arrangement, and may offer a new route for structure determination of…

We study the protein folding problem on the base of the quantum approach we proposed recently by considering the model of protein chain with nine amino-acid residues. We introduced the concept of distance space and its projections on a…

Shape transformations of hairy nanoparticles under confinement are studied using molecular dynamic simulations. We discuss the behavior of these particles in slits with inert or attractive walls. We assume that only chain-wall interactions…

The shapes of cell membranes are largely regulated by membrane associated, curvature active, proteins. We use a numerical model of the membrane with elongated membrane inclusions, recently developed by us, which posses spontaneous…

The biological activity and functional specificity of proteins depend on their native three-dimensional structures determined by inter- and intra-molecular interactions. In this paper, we investigate the geometrical factor of protein…

We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain…

Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or…

The biological function of a protein stems from its 3-dimensional structure, which is thermodynamically determined by the energetics of interatomic forces between its amino acid building blocks (the order of amino acids, known as the…

The spacial heterogeneity of hydrogels composed of PEGDA and added polymer chains is expected to play a crucial role on their transport properties which can be exploited in filtration or tissue engineering. However little is known about the…

We prove the existence of families of distinct isotopy classes of physical unknots through the key concept of parametrised thickness. These unknots have prescribed length, tube thickness, a uniform bound on curvature, and cannot be…

The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…

The mechanics of complex soft matter often cannot be understood in the classical physical frame of flexible polymers or rigid rods. The underlying constituents are semiflexible polymers, whose finite bending stiffness ($\kappa$) leads to…

Hydrogen bonds are a common feature in protein folding and aggregation. Due to their chemical peculiarities in terms of strength and directionality, a particular attention must be paid to the definition of the hydrogen bond potential…

The self-assembly of particles into organized structures is a key feature of living organisms and a major engineering challenge. While it may proceed through the binding of perfectly matched, puzzle-pieces-like particles, many other…

Polymer materials have the characteristic feature that they are multiscale systems by definition. Already the description of a single molecules involves a multitude of different scales, and cooperative processes in polymer assemblies are…

We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…

Packing problems have been a source of fascination for millenia and their study has produced a rich literature that spans numerous disciplines. Investigations of hard-particle packing models have provided basic insights into the structure…