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Experiments measuring contact formation between a probe and quencher in disordered chains provide information on the fundamental dynamical timescales relevant to protein folding, but their interpretation usually relies on simplified…
We investigate the role of intra-molecular conformational disorder and inter-molecular electronic interactions on the electronic structure of disorder clusters of poly-p-phenylene vinylene (PPV) oligomers. Classical molecular dynamics is…
Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To…
Short-range interactions and long-range contacts drive the 3D folding of structured proteins. The proteins' structure has a direct impact on their biological function. However, nearly 40% of the eukaryotes proteome is composed of…
Macromolecular crowding can influence polymer shapes, which is important for understanding the thermodynamic stability of polymer solutions and the structure and function of biopolymers (proteins, RNA, DNA) under confinement. We explore the…
The dynamics of units (molecules) with slowly relaxing internal states is studied as an iterated function system (IFS) for the situation common in e.g. biological systems where these units are subjected to frequent collisional interactions.…
While experiments and computer simulations to study biological phenomena are usually performed in diluted in vitro conditions, such phenomena happen inside the cell, an environment densely packed with diverse macromolecules. Here, we revise…
Colloidal mixtures represent a versatile model system to study transport in complex environments. They allow for a systematic variation of the control parameters, namely size ratio, total volume fraction and composition. We study the…
Polydispersity is a universal feature of synthetic polymers and biological molecules in the cytoplasm. However, its quantitative impact on collective behavior remains poorly understood because conventional metrics, such as the…
We computationally investigate the dynamics of a self-propelled Janus probe in crowded environments. The crowding is caused by the presence of viscoelastic polymers or non-viscoelastic disconnected monomers. Our simulations show that the…
The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein-protein interactions is complicated by the fact that the…
In this study, we introduce a minimal model for a collection of polar self-propelled particles (SPPs) on a two-dimensional substrate where each particle has a different ability to interact with its neighbours. The SPPs interact through a…
We study the dynamics of an ideal polymer chain in a crowded, viscoelastic medium and in the presence of active forces. The motion of the centre of mass and of individual monomers is calculated. On time scales that are comparable to the…
We discuss the effects of fluctuations of the local density of charged dopants near a first order phase transition in electronic systems, that is driven by change of charge carrier density controlled by doping level. Using a generalization…
The activity of biological cells is primarily based on chemical reactions and typically modeled as a reaction-diffusion system. Cells are, however, highly crowded with macromolecules, including a variety of molecular machines such as…
We investigate the nonequilibrium dynamics of semiflexible polymers driven by motor proteins (MPs) in two-dimensional motility assays under harmonic confinement. Using a coarse-grained agent-based model that incorporates stochastic motor…
We analyze a model statistical description of the polypeptide chain helix-coil transition, where we take into account the specificity of its primary sequence, as quantified by the phase space volume ratio of the number of all accessible…
We study a strongly interacting crowded system of self-propelled stiff filaments by event-driven Brownian dynamics simulations and an analytical theory to elucidate the intricate interplay of crowding and self-propulsion. We find a…
Polymer translocation in crowded environments is a ubiquitous phenomenon in biological systems. We studied polymer translocation through a pore in free, one-sided (asymmetric), and two-sided (symmetric) crowded environments. Extensive…
{\alpha}-synuclein ({\alpha}-syn) is an intrinsically disordered protein which is considered to be one of the causes of Parkinson's disease. This protein forms amyloid fibrils when in a highly concentrated solution. The fibril formation of…