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The aim of this paper is to develop suitable models for the phenomenon of cell blebbing, which allow for computational predictions of mechanical effects including the crucial interaction of the cell membrane and the actin cortex. For this…
Biomolecular condensates are formed via liquid-liquid phase separation of proteins, often together with nucleic acids, typically driven by interactions between low-affinity binding sites. The computational study of such condensates that…
Molecular dynamics simulations of a short-chain polymer melt between two brush-covered surfaces under shear have been performed. The end-grafted polymers which constitute the brush have the same chemical properties as the free chains in the…
We investigate the time evolution of the heteropolymer model introduced by Iori, Marinari and Parisi to describe some of the features of protein folding mechanisms. We study how the (folded) shape of the chain evolves in time. We find that…
Based on a newly developed contact-density chain-growth algorithm, we have simulated a nongrafted peptide in the vicinity of different attractive substrates. We analyzed the specificity of the peptide adsorption by focussing on the…
Because the constant extension ensemble of single chain molecule is not always equivalent with constant force ensemble, a model of double-stranded conformations, as in RNA molecules and $\beta$-sheets in proteins, with fixed extension…
We study the effects of distinct types of quenched disorder in the contact process (CP) with a competitive dynamics on bipartite sublattices. In the model, the particle creation depends on its first and second neighbors and the extinction…
The shapes of liquid polystyrene (PS) droplets on viscoelastic polydimethylsiloxane (PDMS) substrates are investigated experimentally using atomic force microscopy for a range of droplet sizes and substrate elasticities. These shapes, which…
Collective behaviour in suspensions of microswimmers is often dominated by the impact of long-ranged hydrodynamic interactions. These phenomena include active turbulence, where suspensions of pusher bacteria at sufficient densities exhibit…
Molecular dynamics simulations were performed for a polymer melt. In quiescent states, the inter-chain interaction energy supported by each particle takes relatively large values persistently for long times if the particle is close to an…
Diffusive transport of small molecules within the internal structures of biological and synthetic material systems is complex because the crowded environment presents chemical and physical barriers to mobility. We explored this mobility…
Periodically sheared colloids at low densities demonstrate a dynamical phase transition from an inactive to active phase as the strain amplitude is increased. The inactive phase consists of no collisions/contacts between particles in the…
We study the diffusion of a linear polymer in the presence of permeable membranes without excluded volume interactions, using scaling theory and Monte Carlo simulations. We find that the average time it takes for a chain with polymerization…
The endpoint distribution and dynamics of semiflexible fibers is studied by numerical simulation. A brief overview is given over the analytical theory of flexible and semiflexible polymers. In particular, a closed expression is given for…
In this work the diffusion in the quenched trap model with diverging mean waiting times is examined. The approach of randomly stopped time is extensively applied in order to obtain asymptotically exact representation of the disorder…
I study the absorbing-state phase transition in the one-dimensional contact process with mobile disorder. In this model the dilution sites, though permanently inactive, diffuse freely, exchanging positions with the other sites, which host a…
The spreading of polymer droplets is studied using molecular dynamics simulations. To study the dynamics of both the precursor foot and the bulk droplet, large drops of ~200,000 monomers are simulated using a bead-spring model for polymers…
A molecule traveling in a realistic propagation environment can experience stochastic interactions with other molecules and the environment boundary. The statistical behavior of some isolated phenomena, such as dilute unbounded molecular…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
Nonequilibrium molecular dynamics simulations are used to study the deformation behavior of disperse polymer melts by tracking test chains of length N = Mw, the weight average molecular weight, in melts of varying dispersity. At high strain…