Related papers: Depletion interactions modulate coupled folding an…
The depletion interactions between two colloidal plates or between two colloidal spheres, induced by interacting polymers in a good solvent, are calculated theoretically and by computer simulations. A simple analytical theory is shown to be…
The coupled dynamics of entangled polymers which span a broad time and length scales govern the unique viscoelastic properties of polymers. To follow chain mobility by numerical simulations from the intermediate Rouse and reptation regimes…
Langevin dynamics is employed to study the looping kinetics of self-avoiding polymers both in ideal and crowded solutions. A rich kinetics results from the competition of two crowding-induced effects: the depletion attraction and the…
In bacteria, regulatory proteins search for a specific DNA binding target via "facilitated diffusion": a series of rounds of 3D diffusion in the cytoplasm, and 1D linear diffusion along the DNA contour. Using large scale Brownian dynamics…
Packings of macroscopic granular chains capture some of the essential aspects of molecular polymer systems and have been suggested as a paradigm to understand the physics on a molecular scale. However, here we demonstrate that the…
Connecting the large-scale emergent behaviors of active materials to the microscopic properties of their constituents is a challenge due to a lack of data on the multiscale dynamics and structure of such systems. We approach this problem by…
How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are…
The impact of impenetrable obstacles on the energetics and equilibrium structure of strongly repulsive directed polymers is investigated. As a result of the strong interactions, regions of severe polymer depletion and excess are found in…
Living systems at the sub-cellular, cellular, and multi-cellular level are often crowded systems that contain active particles. The active motion of these particles can also propel passive particles, which typically results in enhanced…
Diffusion of a two component fluid is studied in the framework of differential equations, but where these equations are systematically derived from a well-defined microscopic model. The model has a finite carrying capacity imposed upon it…
Activity and self-generated motion are fundamental features observed in many living and non-living systems. Given that inter-particle adhesive forces are known to regulate particle dynamics, we investigate how adhesion strength controls the…
We report circular dichroism measurements on the helix-coil transition of poly(L-glutamic acid) in solution with polyethylene glycol (PEG) as a crowding agent. Using small angle neutron scattering, PEG solutions have been characterized and…
Despite the diversity of materials designated as active matter, virtually all active systems undergo a form of dynamic arrest when crowding and activity compete, reminiscent of the dynamic arrest observed in colloidal and molecular fluids…
Here, we show by solution nuclear magnetic resonance measurements that the urea-unfolded protein apoazurin becomes elongated when the synthetic crowding agent dextran 20 is present, in contrast to the prediction from the macromolecular…
Using a theoretical model we show that ideal ring polymers are stronger depletants than ideal linear polymers of equal radii of gyration, but not of equal hydrodynamic radii. The difference in the depletion-induced force profile is largely…
Fundamental understanding of the effect of microscopic parameters on the dynamics of probe particles in different complex environments has wide implications. Examples include diffusion of proteins in the biological hydrogels, porous media,…
We investigate the dynamics of a particle moving randomly along a disordered hetero-polymer subjected to rapid conformational changes which induce superdiffusive motion in chemical coordinates. We study the antagonistic interplay between…
By means of molecular dynamics simulations we investigate the formation of single-chain nanoparticles through intramolecular cross-linking of polymer chains, in the presence of their precursors acting as purely steric crowders in…
We study how hydrodynamic interactions affect the collective behaviour of active particles suspended in a fluid at high concentrations, with particular attention to lubrication forces which appear when the particles are very close to one…
The inert polymer polyethylene glycol (PEG) induces a "bundling" phenomenon in F-actin solutions when its concentration exceeds a critical onset value C_o. Over a limited range of PEG molecular weight and ionic strength, C_o can be…