Related papers: Simulating the Entropic Collapse of Coarse-Grained…
We investigate the collapse kinetics of charged polymers (polyelectrolytes) induced by counterion condensation using coarse-grained molecular dynamics simulations. Under good solvent conditions, polyelectrolytes above the critical charge…
We report molecular dynamics simulations of the segregation of two overlapping chains in cylindrical confinement. We find that the entropic repulsion between the chains can be sufficiently strong to cause segregation on a time scale that is…
Conformational properties of a single flexible polyelectrolyte chain in a poor solvent are studied using constant temperature molecular dynamics simulation. The effects of counterions are explicitly taken in to account. Structural…
We propose a highly coarse-grained simulation model for crystalline polymer solids with crystalline lamellar structures. The mechanical properties of a crystalline polymer solid are mainly determined by the crystalline lamellar structures.…
Given the ubiquity of depletion effects in biological and other soft matter systems, it is desirable to have coarse-grained Molecular Dynamics simulation approaches appropriate for the study of complex systems. This paper examines the use…
We present a scaling theory describing the collapse of a homopolymer chain in poor solvent. At time t after the beginning of the collapse, the original Gaussian chain of length N is streamlined to form N/g segments of length R(t), each…
The rapid collapse of a polymer, due to external forces or changes in solvent, yields a long-lived `crumpled globule.' The conjectured fractal structure shaped by hierarchical collapse dynamics has proved difficult to establish, even with…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
We perform extensive molecular dynamics simulations of a highly charged flexible polyelectrolyte (PE) chain in a poor solvent for the case when the chain is in a collapsed state and the electrostatic interactions, characterized by the…
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such…
We study the Brownian dynamics of flexible and semiflexible polymer chains densely grafted on a flat substrate, upon rapid quenching of the system when the quality of solvent becomes poor and chains attempt collapse into a globular state.…
We investigate the dynamics of the collapse of a single copolymer chain, when the solvent quality is suddenly quenched from good to poor. We employ Brownian dynamics simulations of a bead-spring chain model and incorporate fluctuating…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
During the eukaryotic cell cycle, chromatin undergoes several conformational changes, which are believed to play key roles in gene expression regulation during interphase, and in genome replication and division during mitosis. In this…
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…
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
Recent experimental results suggest that the E. coli chromosome feels a self-attracting interaction of osmotic origin, and is condensed in foci by bridging interactions. Motivated by these findings, we explore a generic modeling framework…
Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular-dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N=40…
We study the effects of the shear force on the rupture mechanism on a double stranded DNA. Motivated by recent experiments, we perform the atomistic simulations with explicit solvent to obtain the distributions of extension in hydrogen and…
Using Brownian dynamics (BD) simulations and an analytical approach we investigate the shear-induced, nonequilibrium dynamics of dense colloidal suspensions confined to a narrow slit-pore. Focusing on situations where the colloids arrange…