Perturbation theory analysis for electronic response of DNA base pairs

Reaction-diffusion wave model for self-assembled network formation of poly(dA)·poly(dT) DNA on mica and HOPG surfaces

Deoxyribonucleic acid (DNA) is a vital molecule for life since it contains genetic information. However, DNA has recently been reported to have unique properties that make it suitable for bionanoelectronic applications, such as the possibility of electrical conductivity and self-organisation. Self-assembled DNA network structures have been observed on several substrates, but the detailed self-assembly mechanism has yet to be determined. The present study investigates self-assembled structures of DNA both theoretically and experimentally. We developed a reaction-diffusion model and used it to investigate pattern formations observed by atomic force microscopy. The computational results qualitatively replicate the network patterns of DNA molecules based on a quantitative agreement with the surface size and timescale. The model can account for the effect of the DNA concentration on pattern formation. Furthermore, peculiar geometric patterns are simulated for mica and highly oriented pyrolytic graphite surfaces.

Characterization of polymer structures based on Burnside's lemma

Polymer structure modeling is a trend of recent material sciences. Developments of computational science and nanotechnology make it possible to predict properties of complicated molecular structures. Many theoretical and computational methods have succeeded in elucidating the nature of polymer structures. It is not always best to model whole complicated structures depending on computer capabilities. Significant properties of materials may be manifested in simple structural aspects. In the present study, characteristics of a polymer structure are investigated by applying Burnside's lemma to the modeling procedure. This method is expected to be available to model polymers or molecular crystals in which functional groups play an important role in expressing their functions. Every structure under the symmetry and periodicity is counted completely and the energy distribution caused by the conformations of functional groups can be clarified. The detailed procedure is introduced and the present method is applied to a problem for investigating molecular structures of sulfonated poly(ether ether ketone) (SPEEK). SPEEK is focused on a candidate for proton exchange membranes in polymer electrolyte fuel cells. Sulfonic groups have a significant role in proton exchange membranes to make proton conduction channels. From our analysis, it is found that sulfonic groups tend to be dispersed in SPEEK membranes at their stable conditions. These are unfavorable characteristics for proton exchange membranes due to their difficulty to form desirable water channels inevitable for the high proton conductivity. This is one reason why SPEEK membranes are inferior to Nafion® membranes that express the highest performance as proton exchange membranes. Using the present method, experimental and theoretical results previously reported are confirmed and detailed characteristics are discussed in terms of structural simplicities.

Molecular dynamics study of solvation effect on diffusivity changes of DNA fragments

DNA sequence analyzing and base pair separation techniques have attracted much attention, such as denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and capillary electrophoresis. However, details of sequence separation mechanisms in electrophoresis are not clarified enough. Understanding and controlling flow characteristics of DNA are important not only for fundamental research but also for further developments of bio-nano technologies. In the present study, we theoretically discuss the relationship between diffusivity and hydrated structures of DNA fragments in water solvent using molecular dynamics methods. In particular, influence of base pair substitutions on the diffusivity is investigated, focusing on an adenine-thymine (AT) rich B-DNA decamer 5'-dCGTATATATA-3'. Consequently, it is found that water molecules that concentrate on dissociated base pairs form hydrated structures and change the diffusivity of DNA decamers. The diffusion coefficients are affected by the substitution of GC for AT because of the different manner of interactions between the base molecules and water solvent. This result predicts a possibility of base pair separation according to differences in the diffusivity.