相关论文: Proteins and polymers
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
The transport of polymers with folded configurations across membrane pores is investigated theoretically by analyzing simple discrete stochastic models. The translocation dynamics is viewed as a sequence of two events: motion of the folded…
Chain-like macromolecules in solution, whether biological or synthetic, transform from an extended conformation to a compact one when temperature or other system parameters change. This collapse transition is relevant in various phenomena,…
Partitioning of (bio)materials in polymeric mixtures is a key phenomenon both in cellular environments, as well as in industrial applications. In cells, several macromolecules are suspended within different biomolecular phases. On the other…
If many micelles adsorb onto the same polymer molecule then they are said to form a necklace. A minimal model of such a necklace is proposed and shown to be almost equivalent to a 1-dimensional fluid with nearest-neighbour interactions. The…
We study the structure and interfacial properties of model athermal mixtures of colloids and excluded volume polymers. The colloid particles are modeled as hard spheres whereas the polymer coils are modeled as chains formed from…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…
The configurations taken by polymers embedded in out-of-equilibrium baths may have broad effects in a variety of biological systems. As such, they have attracted considerable interest, particularly in simulation studies. Here we analyze the…
We discuss structural correlations in mixtures of free polymer and colloidal particles based on a microscopic, 2-component liquid state integral equation theory. Whereas in the case of polymers much smaller than the spherical particles the…
Protein chains of the (FG)$_n$ ($n \simeq$ 300) type cap the cytoplasmatic side of the nucleopore complex, which connects the nucleus to the remainder of an eukaryotic cell. We study the properties of three fundamental polymer models that…
We have studied the thermodynamics of isolated homopolymer chains of varying stiffness using a lattice model. A complex phase behaviour is found; phases include chain-folded `crystalline' structures, the disordered globule and the coil. It…
Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…
The aim of this paper is to investigate the distribution of a continuous polymer in the presence of an attractive finitely supported potential. The most intricate behavior can be observed if we simultaneously and independently vary two…
We study the geometric properties of the energy landscape of coarse-grained, off-lattice models of polymers by endowing the configuration space with a suitable metric, depending on the potential energy function, such that the dynamical…
Inspired by recent experiments on chromosomal dynamics, we introduce an exactly solvable model for the interaction between a flexible polymer and a set of motor-like enzymes. The enzymes can bind and unbind to specific sites of the polymer…
The structures of proteins exhibit secondary elements composed of helices and loops. Comparison of several water-only hydrophobicity scales with the functionalities of two repeat proteins shows that these secondary elements possess…
Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions $\phi \approx 0.75$, a value that is similar to close packing equal-sized spheres. A limitation…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession…
The motion of active polymers in a porous medium is shown to depend critically on flexibilty, activity and degree of polymerization. For given Peclet number, we observe a transition from localisation to diffusion as the stiffness of the…