The effect of solvent on the collapse dynamics of polymers is studied using computer simulation. Two cases are investigated, one where the solvent is incorporated through a pairwise additive attraction between the polymer beads and a random force on each polymer bead, and another where the solvent is incorporated in an explicit fashion as a second component. Brownian dynamics and molecular dynamics simulations are used in the former and latter model, respectively, with intermolecular interactions chosen so that the equilibrium size of the polymer is similar in both models at similar conditions. In the Brownian dynamics simulations, at short times local blobs of monomers are found separated by linear segments. With time the blobs grow in size and coalesce to form sausage like shapes. These sausages gradually become thicker and shorter until the final shape of a spherical globule is reached. The first stage is rapid whereas the second sausage-sphere stage is slow. In this stage the polymer often gets trapped in local minima and the change in size with time occurs through discrete jumps, and the equilibrium conformation is often not reached. In contrast, in the molecular dynamics simulations with explicit solvent, the size of the polymer changes smoothly with time, and the polymer does not get trapped in local minima for the cases investigated, although the sequence of polymer shapes is similar. This suggests that incorporating solvent molecules explicitly is important in the computer simulations of collapse and folding of polymers.
Fully stretched DNA molecules are becoming a fundamental component of new systems for comprehensive genome analysis. Among a number of approaches for elongating DNA molecules, nanofluidic molecular confinement has received enormous attentions from physical and biological communities for the last several years. Here we demonstrate a well-optimized condition that a DNA molecule can stretch almost its full contour length: the average stretch is 19.1 μm ± 1.1 μm for YOYO-1 stained λ DNA (21.8 μm contour length) in 250 nm × 400 nm channel, which is the longest stretch value ever reported in any nanochannels or nanoslits. In addition, based on Odijk’s polymer physics theory, we interpret our experimental findings as a function of channel dimensions and ionic strengths. Furthermore, we develop a Monte Carlo simulation approach using a primitive model for the rigorous understandings of DNA confinement effects. Collectively, we present more complete understanding of nanochannel confined DNA stretching via the comparisons to computer simulation results and Odijk’s polymer physics theory.
Geometric factors affecting the enhanced electrocatalysis on nanoporous Pt (L2-ePt) were examined by electrochemical methods and computer simulations. The experimental results revealed that the electrochemical enhancement of O2 and H2O2 does not come only from expansion of the active surface area (so-called roughness factor, f R) of L2-ePt. The presence of extra contribution was verified by the fact that significant enhancement in electrocatalytic reactions remained even after the effect of the f R was eliminated from the electrochemical redox behavior of O2 and H2O2 on L2-ePt electrodes. Not only the voltammetric observation but also potentiometric pH responses of L2-ePt suggested the presence of unique nanoporous effects other than the surface enlargement in regard to heterogeneous electrochemical reactions. L2-ePt showed near Nernstian behavior, faster response time, and less hysteresis even if the real surface area was smaller than that of flat Pt. Increased residence time near the electrode surface due to extremely confined space of nanoporous structure was proposed as possible origins and examined by the Monte Carlo simulations of simple model electrodes. The theoretical approaches indicated that long residence time of reactant at electrode surface by confinement effect of the nanoporous environment well accounted for the experimental results.
Molecular dynamic simulations are reported for the static and dynamic properties of hard sphere fluids in matrices (or media) composed of quenched hard spheres. The effect of fluid and matrix density, matrix structure, and fluid to matrix sphere size ratio on the static and dynamic properties is studied using discontinuous molecular dynamics. The matrix density has a stronger effect on the self-diffusion coefficient than the fluid density, especially at high matrix densities where the geometric constraints due to the quenched spheres are significant. When the ratio of the size of the fluid spheres to that of the matrix spheres is equal to or greater than one, the diffusion increases as the fluid density is increased, at constant total volume fraction. This trend is however reversed if the ratio is smaller than one. Different methods of generating the matrix have a very strong effect on the dynamic properties even though the static correlations are similar. An analysis of the single-chain structure factor of the particle trajectories shows a change in the particle diffusive behavior at different time scales, suggestive of a hopping mechanism, although normal diffusion is recovered at long times. At high matrix densities, there is considerable heterogeneity in the diffusion of the fluid particles. The simulations demonstrate that the correlations in the matrix play a significant role on the diffusion of fluid spheres. For example, the diffusion constant in matrices constructed by different methods can be an order of magnitude different even though the pair correlation functions are almost identical.
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