Orientation and shape of flexible polymers in a slit

Abstract

The shape and orientation of a polymer in a good solvent confined between two parallel plates is investigated by Monte Carlo simulations of self-avoiding random walks on a simple cubic lattice. Decreasing the width of the slit, the coil starts, due to its anisotropic shape, to orient long before its shape changes. Only after the longest principal axis is aligned considerably parallel to the plates, the coil is squeezed. Using a scaled distance between the plates, a corresponding state behavior as a function of chain length is found. The results are in good agreement with predictions based on an analytical rigid ellipsoid model with principal axes’ lengths set equal to the span lengths along the principal axes of inertia of the self-avoiding random walk.

Effect of confinement on DNA dynamics in microfluidic devices

“…Simple scaling arguments 8 give XϰN k H Ϫ2/3 for a chain in a good solvent; this scaling has been previously verified by Monte Carlo simulations. 8,9 Figure 4 shows the dimensionless equilibrium stretch, X*ϭ͗X͘ eq /X b , as a function of the inverse dimensionless channel width, 1/H*ϭS b /H. Chains ranging from 4.2 m (N s ϭ1) to 420 m (N s ϭ200) are considered.…”

“…8,9 Much less theoretical or computational work is available on the dynamics of confined chains, either in equilibrium or flow, in spite of their practical importance. [10][11][12][13][14][15] Qualitatively, one might envision two effects of confinement on the dynamics of a dissolved chain.…”

Double-Stranded DNA Diffusion in Slitlike Nanochannels

“…55,56 However, above we have ensemble averaged many anisotropic configurations and used the isotropy of the resulting distribution to cancel hydrodynamic interactions by symmetry. In the low-Reynolds number limit, the solvent velocity field forms instantaneously compared to the rearrangement (relaxation) time of the polymer.…”

The Shape of Confined Polymer Chains

“…The m ai n di˜erence i s the l ocati on of the mi mi ma deno ted as d Ê , whi ch are shi fted to wards hi gher val ues of d for l ong er chai ns. The sam e b ehavi or was fo und f or other model s of conÙned l i near pol ym er [3,5] and recentl y f or l atti ce star-bra nched chai ns [7]. The expl ana ti on of thi s pheno m enon seems to b e simpl e: the di a meter of a chai n can b e esti m ated as 2 h S 2 i 1 = and the p oi nt d i s l ocated near thi s val ue.…”

“…V an Vl i et and ten Bri nke carri ed out Mo nte Ca rl o sim ula ti ons of l atti ce m odel s of p ol ym er chai ns [3]. They f ound tha t the size of a p ol ym er chai n exhi bi ts a uni versa l b ehavi or di sregardi ng i ts l ength.…”