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We investigated the viscoelastic response of model interphase chromosomes by tracking the three-dimensional motion of hundreds of dispersed Brownian particles of sizes ranging from the thickness of the chromatin fiber up to slightly above…
We theoretically investigate the kinetics of the folding transition of a single semiflexible polymer. In the folding transition, the growth rate decrease with an increase in the number of monomers in a collapsed domain, suggesting that the…
The emergence of nanoscience has increased the importance of experiments able to probe the very local structure of materials, especially for disordered and heterogeneous systems. This is technologically important; for example, the nanoscale…
Collective behavior occurs ubiquitously in nature and it plays a key role in bacterial colonies, mammalian cells or flocks of birds. Here, we examine the average density and velocity of self-propelled particles, which are described by a…
Using molecular dynamics simulations we examine the dynamics of a family of model polymers with varying chain length and torsional potential barriers. We focus on features of the dynamics of polymers that are seen experimentally but absent…
We study the segmental dynamics of poly(ethylene oxide) (PEO) from microscopic simulations in the neat polymer and a polymer electrolyte (PEO/LiBF$_4$) by analyzing the normal modes. We verify the applicability of the Rouse theory,…
Plastic deformation of crystals is a physical phenomenon, which has immensely driven the development of human civilisation since the onset of the Chalcolithic period. This process is primarily governed by the motion of line defects, called…
The chromosome is a key player of cell physiology, and its dynamics provides valuable information about its physical organization. In both prokaryotes and eukaryotes, the short-time motion of chromosomal loci has been described as a Rouse…
In recent years the functionality of synthetic active microparticles has edged even closer to that of their biological counterparts. However, we still lack the understanding needed to recreate at the microscale key features of autonomous…
We study the relation between short-time vibrational modes and long-time relaxational dynamics in a kinetically constrained lattice gas with harmonic interactions between neighbouring particles. We find a correlation between the location of…
We generalize the Vicsek model to describe the collective behaviour of polar circle swimmers with local alignment interactions. While the phase transition leading to collective motion in 2D (flocking) occurs at the same interaction to noise…
We study the role of hydrodynamic interactions for the relaxation of segments' orientations in dendrimers. The dynamics is considered in the Zimm framework. It is shown that inclusion of correlations between segments' orientations plays a…
We employ mesoscopic simulations to study active polymers in a solvent via multi-particle collision dynamics. We investigate linear chains in which either the head or tail monomer exerts an active force, directed away from or towards its…
Reptation theory has been highly successful in explaining the unusual material properties of entangled polymer solutions. It reduces the complex many-body dynamics to a single-polymer description where each polymer is envisaged to be…
In recent years, fluorescence correlation spectroscopy has been increasingly applied for the study of polymer dynamics on the nanometer scale. The core idea is to extract, from a measured autocorrelation curve, an effective mean-square…
Self-mated hydrogel contacts show extremely small friction coefficients at low loads but a distinct velocity dependence. Here we combine mesoscopic simulations and experiments to test the polymer-relaxation hypothesis for this velocity…
The translocation of a polymer through a pore in a membrane separating fluids of different viscosities is studied via several computational approaches. Starting with the polymer halfway, we find that as a viscosity difference across the…
We show, through analytical theory and rigorous numerical calculations, that optical binding can organize a collection of particles into stable one-dimensional lattice. This lattice, as well as other optically-bound structures, are shown to…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
Conventional molecular dynamics simulations macromolecules require long computational times because the most interesting motions are very slow compared with the fast oscillations of bond lengths and bond angles that limit the integration…