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Synthetic polymers are versatile and widely used materials. Similar to small organic molecules, a large chemical space of such materials is hypothetically accessible. Computational property prediction and virtual screening can accelerate…
Scaffold proteins organize cellular processes by bringing signaling molecules into interaction, sometimes by forming large signalosomes. Several of these scaffolds are known to polymerize. Their assemblies should therefore not be understood…
The characterization of protein-nanoparticle assemblies in solution remains a challenge. We demonstrate a technique based on a graphene microelectrode for structural-functional analysis of model systems composed of nanoparticles enclosed in…
A theoretical analysis of the unfolding pathway of simple modular proteins in length- controlled pulling experiments is put forward. Within this framework, we predict the first module to unfold in a chain of identical units, emphasizing the…
The endoplasmic reticulum (ER) is the largest continuous membrane-bound organelle in the cell and plays a central role in the synthesis and turnover of many lipids and proteins. It connects directly to the nucleus through specialized…
We present an analytical theory for heteropolymer deformation, as exemplified experimentally by stretching of single protein molecules. Using a mean-field replica theory, we determine phase diagrams for stress-induced unfolding of typical…
The extent of coupling between the folding of a protein and its binding to a substrate varies from protein to protein. Some proteins have highly structured native states in solution, while others are natively disordered and only fold fully…
Multiple loop formation in polymer macromolecules is an important feature of the chromatin organization and DNA compactification in the nuclei. We analyze the size and shape characteristics of complex polymer structures, containing in…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Multiblock copolymer chains in implicit nonselective solvents are studied by Monte Carlo method which employs a parallel tempering algorithm. Chains consisting of 120 $A$ and 120 $B$ monomers, arranged in three distinct microarchitectures:…
In the past years, the folding kinetics of many small single-domain proteins has been characterized by mutational Phi-value analysis. In this article, a simple, essentially parameter-free model is introduced which derives folding routes…
We use the lattice model of directed walks to investigate the conformational as well as the adsorption properties of a semiflexible homopolymer chain immersed in a good solvent in two and three dimensions. To account for the stiffness in…
Electrochemical phenomena in biology often unfold in confined geometries where micrometer- to millimeter-scale domains coexist with nanometer-scale interfacial diffuse charge layers. We analyze a model lipid membrane-electrolyte system…
We investigate the voltage-driven translocation of an inhomogeneously charged polymer through a nanopore by utilizing discrete and continuous stochastic models. As a simplified illustration of the effect of charge distribution on…
We present a method to probe molecular and nanoparticle diffusion within thin, solvated polymer coatings. The device exploits the confinement with well-defined geometry that forms at the interface between a planar and a hemi-spherical…
A simple model for the formation of the polymer-enzyme conjugates has been proposed and described using corresponding extension of the Wertheim's first-order thermodynamic perturbation theory (TPT1) for the system of associating chain…
We study the driven translocation of a flexible polymer through an interacting conical pore using Langevin dynamics simulations. We find that, for a fixed value of externally applied force and pore polymer interaction strength, the mean…
Entropic repulsion between DNA ring polymers under confinement is the key mechanism governing the spatial segregation of bacterial chromosomes, although it remains incompletely understood how proteins aid the process of entropic…
In this paper we present simulations of a surface-adsorbed polymer subject to an elongation force. The polymer is modelled by a self-avoiding walk on a regular lattice. It is confined to a half-space by an adsorbing surface with attractions…
In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors…