Related papers: Conformations and diffusion of flexibly linked col…
The structure and dynamics of tissue cultures depend strongly on the physical and chemical properties of the underlying substrate. Inspired by previous advances in the context of inorganic materials, the use of patterned culture surfaces…
Density-dependent diffusion is a widespread phenomenon in nature. We have examined the density-dependent diffusion behavior of some biological processes such as tumor growth and invasion [23]. Here, we extend our previous work by developing…
We study the relaxation dynamics of a coarse-grained polymer chain at different degrees of stretching by both analytical means and numerical simulations. The macromolecule is modelled as a string of beads, connected by anharmonic springs,…
In many physical systems, degrees of freedom are coupled \emph{via} hydrodynamic forces, even in the absence of Hamiltonian interactions. A particularly important and widespread example concerns the transport of microscopic particles in…
We consider a general discrete model for heterogeneous semiflexible polymer chains. Both the thermal noise and the inhomogeneous character of the chain (the disorder) are modeled in terms of random rotations. We focus on the quenched…
We employ molecular dynamics simulations to explore how internal flexibility affects phase transitions in soft-matter systems composed of dimers interacting via a core-softened potential with two characteristic length scales. Monomers are…
Responsive particles, such as biomacromolecules or hydrogels, display a broad and polymodal distribution of conformations and have thus the ability to change their properties (e.g, size, shape, charge density, etc.) substantially in…
By means of classical density functional theory and its dynamical extension, we consider a colloidal fluid with spherically-symmetric competing interactions, which are well known to exhibit a rich bulk phase behavior. This includes complex…
We numerically investigate the self-diffusion coefficient and correlation length of the rigid clusters (i.e., the typical size of the collective motions) in sheared soft athermal particles. Here we find that the rheological flow curves on…
The dynamics of biological polymers, including proteins, RNA, and DNA, occur in very high-dimensional spaces. Many naturally-occurring polymers can navigate a vast phase space and rapidly find their lowest free energy (folded) state. Thus,…
The function of biomolecules such as proteins depends on their ability to interconvert between a wide range of structures or "conformations." Researchers have endeavored for decades to develop computational methods to predict the…
Conformation-dependent design of polymer sequences can be considered as a tool to control macromolecular self-assembly. We consider the monomer unit sequences created via the modification of polymers in a homogeneous melt in accordance with…
Within Kirkwood theory, we study the translational diffusion coefficient of a single polymer chain in dilute solution, and focus on the small difference between the short--time Kirkwood value $D^{(K)}$ and the asymptotic long--time value…
Enhanced colloidal transport beyond the limit imposed by diffusion is usually achieved through external fields. Here, we demonstrate the ballistic transport of a colloidal sphere using internal sources of energy provided by an attached…
The rotational Brownian motion of colloidal spheres in dense suspensions reflects local hydrodynamics and friction, both key to non-linear rheological phenomena such as shear-thickening and jamming, and transport in crowded environments,…
The equilibrium structure and dynamics of a single polymer chain in a thermal solvent is by now well-understood in terms of scaling laws. Here we consider a polymer in a bacterial bath, i.e. in a solvent consisting of active particles which…
Colloidal molecules are designed to mimic their molecular analogues through their anisotropic shape and interactions. However, current experimental realizations are missing the structural flexibility present in real molecules thereby…
We study how the dynamic equilibrium of the reversible protein-protein binding network in yeast Saccharomyces cerevisiae responds to large changes in abundances of individual proteins. The magnitude of shifts between free and bound…
We study the conformational freedom of a protein made by two rigid domains connected by a flexible linker. The conformational freedom is represented as an unknown probability distribution on the space of allowed states. A new algorithm for…
We present an extensive numerical study of dynamical heterogeneities and their influence on diffusion in an athermal mesoscopic model for actively deformed amorphous solids. At low strain rates the stress dynamics are governed by…