Fluorescence modulation of eosin Y in a PMMA film by diarylethene switching

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Electron injection into DNA: synthesis and spectroscopic properties of pyrenyl-modified oligonucleotides

The nucleoside 5-(1-pyrenyl)-2'-deoxyuridine (1) was prepared by a Suzuki-Miyaura cross-coupling reaction and subsequently used as a DNA building block in order to prepare a range of modified oligonucleotides using phosphoramidite chemistry. The DNA duplexes contain a pyrenyl group covalently attached to the nucleobase uracil. Upon excitation at 340 nm an intramolecular electron transfer from the pyrenyl group to the uracil moiety takes place which represents an injection of an excess electron into the DNA base stack. Based on the results obtained by steady-state fluorescence and time-resolved pump-probe laser spectroscopy it was possible to show that base-to-base electron transfer can occur from the Py-dU group only to adjacent thymines.     

Novel design of multicapillary arrays for high-throughput DNA sequencing

A novel approach to design and optimize linear multicapillary arrays (LMCAs) for high-throughput DNA sequencing is proposed. A significant increase in the number of capillary lanes is obtained due to the use of composite insertions alternately placed between working capillaries of the array and a specific combination of refractive indices of the DNA separation matrix, capillary glass, the insertions and a medium which surrounds the capillary array. Theoretical and experimental studies showed that in conjunction with a dual-side laser illumination scheme, the proposed LMCA design allows a simultaneous uniform irradiation of as many as 550 working capillaries.     

Analysis of nucleation ability of cluster configurations with Monte Carlo simulations of argon

We determine the nucleation ability of argon clusters from Monte Carlo simulations. The nucleation rate appears to be defined by a sole characteristic of the clusters, namely, the stability. The stability is calculated as the ratio of grand canonical growth and decay rates and can be assigned to individual cluster configurations. We study the connection between the stability of the cluster configurations and their volume and total potential energy. Neither the potential energy nor the volume of a cluster configuration has a clear relation to its stability, and thus to the nucleation ability. On the other hand, we show that it is possible to use a specific volume for each cluster size to calculate the work of the cluster formation. These clusters with a unique volume have the same average stability as the full set of clusters. Our simulation method allows us to study the effect of possible deviations from equilibrium in the cluster configuration distributions. We argue that the nucleation process itself can produce a source for such a deviation. We show that even a small deviation from equilibrium in the cluster configuration distribution can lead to a dramatic deceleration of the nucleation rate. Although our simulations may overestimate the magnitude of the effect, they give qualitative estimates for its importance.     

Periodic “weighted” operators

Consider the periodic weighted operator Ty=−ρ⁻²(ρ²y′)′ in , where the real function ρ is 1-periodic positive, and let q=ρ′/ρ∈L²(0,1). The spectrum of T consists of intervals separated by gaps γ_n,n?1, with the lengths |γ_n|. Let h_n be a height of the corresponding slit in the quasimomentum domain and let g_n,n?1, be the gap with the length |g_n| of the operator . The following results are obtained: (i) the quasimomentum k for the weighted operator T is constructed and the basic properties of k are studied, (ii) two-sided estimates of ?² norms of the sequences {|γ_n|/n}₁^∞,{h_n}₁^∞,{|g_n|}₁^∞, in terms of , (iii) the asymptotics of the gap length |γ_n| as n→∞, are determined. The proofs are based on the analysis of the quasimomentum as a conformal mapping, embedding theorems and the identities between the quasimomentum and the potential. In order to prove these results the asymptotics of the fundamental solutions and the Lyapunov function are obtained at high energy.     

Monte Carlo simulations of critical cluster sizes and nucleation rates of water

We have calculated the critical cluster sizes and homogeneous nucleation rates of water at temperatures and vapor densities corresponding to experiments by Wolk and Strey [J. Phys. Chem B 105, 11683 (2001)]. The calculations have been done with an expanded version of a Monte Carlo method originally developed by Vehkamaki and Ford [J. Chem. Phys. 112, 4193 (2000)]. Their method calculates the statistical growth and decay probabilities of molecular clusters. We have derived a connection between these probabilities and kinetic condensation and evaporation rates, and introduce a new way for the calculation of the work of formation of clusters. Three different interaction potential models of water have been used in the simulations. These include the unpolarizable SPC/E [J. Phys. Chem. 91, 6269 (1987)] and TIP4P [J. Chem. Phys. 79, 926 (1983)] models and a polarizable model by Guillot and Guissani [J. Chem. Phys. 114, 6720 (2001)]. We show that TIP4P produces critical cluster sizes and a temperature and vapor density dependence for the nucleation rate that agree well with the experimental data, although the magnitude of nucleation rate is constantly overestimated by a factor of 2 x 10(4). Guissani and Guillot's model is somewhat less successful, but both the TIP4P and Guillot and Guissani models are able to reproduce a much better experimental temperature dependency of the nucleation rate than the classical nucleation theory. Using SPC/E results in dramatically too small critical clusters and high nucleation rates. The water models give different average binding energies for clusters. We show that stronger binding between cluster molecules suppresses the decay probability of a cluster, while the growth probability is not affected. This explains the differences in results from different water models.     

Surface interactions during polyelectrolyte multilayer buildup. 1. Interactions and layer structure in dilute electrolyte solutions

We report the investigation of surface forces between polyelectrolyte multilayers of poly(allylamine hydrochloride) (PAH) and poly(styrenesulfonate sodium salt) (PSS) assembled on mica surfaces during film buildup using a surface force apparatus. Up to four polyelectrolyte layers were prepared on each surface ex situ, and the surface interactions were measured in 10(-4) M KBr solutions. The film thickness under high compressive loads (above 2000 microN/m) increased linearly with the number of deposited layers. In all cases, the interaction between identical surfaces at large separations (>100 A from contact) was dominated by electrostatic double-layer repulsion. By fitting DLVO theory to the experimental force curves, the apparent double-layer potential of the interacting surfaces was calculated. At shorter separations, an additional non-DLVO repulsion was present due to polyelectrolyte chains extending some distance from the surface into solution, thus generating an electrosteric type of repulsion. Forces between dissimilar multilayers (i.e., one of the multilayers terminated with PSS and the other with PAH) were attractive at large separations (30-400 A) owing to a combination of electrostatic attraction and polyelectrolyte bridging.     

Resonant neutral-particle emission after collisions of electrons with base-stacked oligonucleotide cations in a storage ring

Electron-cation collisions have been studied for various protonated deoxyoligonucleotide monocations, using an electrostatic storage ring equipped with a merged-electron-beam device. Resonant neutral-particle emissions have been observed at a collision energy of about 4.5 eV for some of them. The resonance parameters depend on DNA base composition and sequence, and the resonances occur only in oligonucleotide monocations with base stacking. The resonance widths increase with oligonucleotide length, but saturate at trimers. Quantum-chemical estimations performed here help explain these results.