Related papers: Crowding induces entropically-driven changes to DN…
Formation of a pseudoknot in the conserved RNA core domain in the ribonucleoprotein human telomerase is required for function. In vitro experiments show that the pseudoknot (PK) is in equilibrium with an extended hairpin (HP) structure. We…
Macromolecular crowding affects biophysical processes as diverse as diffusion, gene expression, cell growth, and senescence. Yet, there is no comprehensive understanding of how crowding affects reactions, particularly multivalent binding.…
Previous numerical investigations of an one-dimensional DNA model with an extended modified coupling constant by transcripting enzyme are integrated to longer time and demonstrated explicitly the trapping of breathers by DNA chains with…
The structure and function of polymers in confined environments, e.g., biopolymers in the cytoplasm of a cell, are strongly affected by macromolecular crowding. To explore the influence of solvent quality on conformations of crowded…
Using molecular dynamics simulations, we investigate the aggregation behavior of neutral stiff (rod-like) and flexible polymer chains mediated by attractive crowders. Attractive crowders serve as bridging agents, inducing aggregation…
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…
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 investigate the effects of crowding on the conformations and assembly of confined, highly charged, and thick polyelectrolyte brushes in the osmotic regime. Particle tracking experiments on increasingly dense suspensions of colloids…
Protein dynamics in cells may be different from that in dilute solutions in vitro since the environment in cells is highly concentrated with other macromolecules. This volume exclusion due to macromolecular crowding is predicted to affect…
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments…
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…
We derive an analytical pair potential of mean force for Brownian molecules in the liquid-state. Our approach accounts for many-particle correlations of crowding particles of the liquid, and for diffusive transport across the spatially…
We study the effect of the crowded nature of the cellular cytoplasm on the translocation of a polymer through a pore in a membrane. By systematically treating the entropic penalty due to crowding, we show that the translocation dynamics are…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…
We use X-ray scattering and molecular simulations to investigate the structural properties of complexes of multivalent cationic lipids and DNA molecules. At low mole fraction of neutral lipids (NLs), $\Phi_{\rm NL}$, the complexes show…
Macromolecular diffusion in strongly confined geometries and crowded environments is still to a large extent an open subject in soft matter physics and biology. In this paper, we employ large-scale Langevin dynamics simulations to…
The work presented in this paper essentially focuses at providing a scientific theory to explain the growth of information bearing molecules (size and information contents) without the need of any enzymatic system. It infers the footprints…
The unconstrained genomic DNA of bacteria forms a coil, which volume exceeds 1000 times the volume of the cell. Since prokaryotes lack a membrane-bound nucleus, in sharp contrast with eukaryotes, the DNA may consequently be expected to…
Tethered Particle Motion (TPM) is a single molecule technique, which consists in tracking the motion of a nano-particle (NP) immersed in a fluid and tethered to a glass surface by a DNA molecule. The present work addresses the question of…
DNA is increasingly employed for bio and nanotechnology thanks to its exquisite versatility and designability. Most of its use is limited to linearised and torsionally relaxed DNA but non-trivial architectures and torsionally constrained --…