Study on the coil–globule transition and dynamics of polymer chain confined in slit

Abstract

The coil-globule transition and dynamics of a lattice self-avoiding bond fluctuation polymer chain confined in slit are studied by Monte Carlo simulations. The coil-globule transition temperature of polymer chain is increased at intermediate slit height H (H $ R G0 with R G0 the radius of gyration of polymer in dilute solution) due to the squeeze of the polymer in the repulsive slit, but it is decreased by surface attraction as the polymer is extended along the surface. We have compared the difference between the rotational relaxation time s R for the reorientation of end-to-end vector and the relaxation time s for the polymer diffusing over a distance of the size of polymer. We find that s R is clearly distinct from s as they have different scaling exponents in their slit height-dependent behaviors s R $ H 2aR and s $ H 2a for the polymer in the extended coil state, that is, a R > a. And both exponents increase with an increase in the intrapolymer attraction and surface attraction. However, these scaling relations are destroyed by strong surface attraction when the polymer is adsorbed on surfaces.

Melting of confined DNA: static and dynamic properties

“…[45][46][47][48] This nonmonotonic behaviour in melting temperature is profound in earlier polymer studies within slit-like confinement. [45][46][47][48] There is also the emergence of non-monotonicity in melting profile and ejection time of polymer within wedge-shape confinement. 55,56 In our study, the transition temperature shifts from 0.89 (where the size of DNA 4 slit width) to 0.75 (where the size of DNA B slit width) for the middle region and at last approaches the bulk value 0.78 (size of DNA o slit width).…”

“…The non-monotonic behaviour again shows its signature in the hR x i variation. 45,46 Douwe Jan Bonthuis et al evidenced a similar non-monotonic trend in the shape of l-phage DNA confined within a slit by laser fluorescence microscopy. 58 Upon heating, local denaturation zones or bubbles often act as a precursor to DNA melting at T m .…”

“…41,42 Theoretical approaches also reinstate the fact that there exists a critical width of confinement where thermodynamic observables of the polymer exhibit a minimum. [43][44][45][46][47][48] Our goal is to explore any non-monotonic response of dsDNA subjected to system properties (temperature, degree of confinement, etc.) in the equilibrium and quasi-equilibrium regime.…”

Monte–Carlo simulation of crystallization in single‐chain square‐well homopolymers

“…The crystallization is controlled by the monomer connectivity and interactions. In computer simulations several classes of interactions are commonly used: lattice models 1–3 and off‐lattice interactions using the Lennard–Jones 4–9 or square well potential 10–14 . Bonded interactions can be chosen to give freely jointed 10–12 or semi flexible chains 4,6,8,13–15 .…”

“…However, simulating long chains presents computational challenges. Long chains, of 256 monomers, have long been possible for lattice simulations 1–3 and more recently the free energy landscape of the coil to crystal transition for lattice chains of up to 1024 monomers was simulated by dynamic Monte–Carlo (MC) methods, combined with parallel tempering 16,17 . There has also been recent progress with off‐lattice simulations of Lennard Jones chains, where chains of up to 724 monomers have been successfully simulated 5 .…”