相关论文: Proteins and polymers

We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…

The Flory theory for a single polymer chain is derived as the lowest order of a cumulant expansion. In this approach, the full original Flory free energy (including the logarithmic term), is recovered. %This term does not change the…

Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…

The beautiful structures of single and multi-domain proteins are clearly ordered in some fashion but cannot be readily classified using group theory methods that are successfully used to describe periodic crystals. For this reason, protein…

We propose a method for the theoretical investigation of polymer translocation through composite pore structures possessing arbitrarily specified geometries. Translocation through each constituent part of the composite is treated as being…

The fracture and severing of polymer chains plays a critical role in the failure of fibrous materials and the regulated turnover of intracellular filaments. Using continuum wormlike chain models, we investigate the fracture of semiflexible…

Semiflexible polymers in poor solvents exhibit a rich variety of collapsed morphologies, including globules, toroids, and rodlike bundles, arising from the competition between attractive interactions and chain stiffness. Computer…

Mesh-like structures, such as mucus gel or cytoskeleton networks, are ubiquitous in biological systems. These intricate structures are composed of cross-linked, semi-flexible bio-filaments, crucial to numerous biological processes. In many…

Proteins work only if folded in their native state, but changes in temperature T and pressure P induce their unfolding. Therefore for each protein there is a stability region (SR) in the T-P thermodynamic plane outside which the biomolecule…

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…

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…

As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and…

We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…

We propose a simple friction model for isolated polymer chains on a solid substrate. The chains are pulled at constant velocity by one end, the other end can be trapped on the solid substrate on localised sites. We focus on the energy…

Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…

One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of…

Polymer-coated pores play a crucial role in nucleo-cytoplasmic transport and in a number of biomimetic and nanotechnological applications. Here we present Monte Carlo and Density Functional Theory approaches to identify different collective…

We study the conformational behavior of polarizable polymer chain under an external homogeneous electric field within the Flory type self-consistent field theory. We consider the influence of electric field on the polymer coil as well as on…

Understanding protein self-assembly is important for many biological and industrial processes. Proteins can self-assemble into crystals, filaments, gels, and other amorphous aggregates. The final forms include virus capsids and condensed…

We explore the interplay between the protein-protein interactions network and the expression of the interacting proteins. It is shown that interacting proteins are expressed in significantly more similar cellular concentrations. This is…