High-resolution Theory Research Articles

DNA, Flexibly Flexible

Investigators have constructed dsDNA molecules with several different base modifications and have characterized their bending and twisting flexibilities using atomic force microscopy, DNA ring closure, and single-molecule force spectroscopy with optical tweezers. The three methods provide persistence length measurements that agree semiquantitatively, and they show that the persistence length is surprisingly similar for all of the modified DNAs. The circular dichroism spectra of modified DNAs differ substantially. Simple explanations based on base stacking strength, polymer charge, or groove occupancy by functional groups cannot explain the results, which will guide further high-resolution theory and experiments.

Surface Forces at Restricted Equilibrium, in Solutions Containing Finite or Infinite Semiflexible Polymers

We use density functional theory to investigate how the presence of polymers influence the interactions between adsorbing or nonadsorbing flat surfaces, forming a slit geometry. The study is primarily made under “restricted equilibrium” conditions, i.e., below a threshold separation, the chains are allowed to equilibrate conformationally between the surfaces, but they are unable to diffuse into or out from the slit. This is believed to be a reasonable model for commonly encountered experimental situations, when the surfaces are large and adsorbing and the polymers are long. Using a recently presented density functional theory, we are able to compare predictions for chains of finite and infinite length. A major advantage of the infinite chain formulation is that it is a high resolution theory, and predictions from the finite length version will exactly approach the ones for infinite chains, when the degree of polymerization becomes large enough. Our study spans across a relatively large number of relevant system parameters, such as bulk concentration, surface adsorption strength, polymer length, and chain flexibility. The response in terms of the net surface interaction, to a change of a system parameter, is often nonmonotonic. We also make comparisons with predictions at full equilibrium, where the diffusion constraint has been relaxed. We give a specific example of how a diffusion-limited process can lead to hysteresis effects, similar to those observed in many surface force measurements. Finally, in a separate section of this work, we have included some direct experimental comparisons, demonstrating the relevance and applicability of restricted equilibrium conditions to “real world” scenarios. The computational power of the density functional approach is here highlighted, with calculations including semiflexible 20000-mers.

Principle and practice of high-resolution imaging with a field-emission TEM

High-resolution imaging with a LaB6 instrument is limited by the spatial and temporal coherence, with little contrast remaining beyond the point resolution. A Field Emission Gun (FEG) reduces the incidence angle by a factor 5 to 10 and the energy spread by 2 to 3. Since the incidence angle is the dominant limitation for LaB6 the FEG provides a major improvement in contrast transfer, reducing the information limit to roughly one half of the point resolution. The strong improvement, predicted from high-resolution theory, can be seen readily in diffractograms (Fig. 1) and high-resolution images (Fig. 2). Even if the information in the image is limited deliberately to the point resolution by using an objective aperture, the improved contrast transfer close to the point resolution (Fig. 1) is already worthwhile.