DNA based molecular motors

Most of the essential cellular processes such as polymerisation reactions, gene expression and regulation are governed by mechanical processes. Controlled mechanical investigations of these processes are therefore required in order to take our understanding of molecular biology to the next level. Single-molecule manipulation and force spectroscopy have over the last 15 years been developed into extremely powerful techniques. Applying these techniques to the investigation of proteins and DNA molecules has led to a mechanistic understanding of protein function on the level of single molecules. As examples for DNA based molecular machines we will describe single-molecule experiments on RNA polymerases as well as on the packaging of DNA into a viral capsid—a process that is driven by one of the most powerful molecular motors.     

Dispersion of nanospheres on large glass substrate by amorphous or polycrystalline silicon deposition for localized surface plasmon resonance

Nanosphere lithography is a cost-effective way to fabricate noble metal nanostructures for plasmonics. However, dispersing nanospheres on a large area of glass substrate is a difficulty encountered when transparent substrate is required in applications such as localized surface plasmon resonance or surface enhanced Raman spectroscopy. Because poly(diallyldimethyl ammonium chloride) (PDDA) on silicon surface introduces a force that can disperse nanospheres on silicon, in this article, we modify the glass surface through amorphous or polycrystalline silicon deposition and thus well disperse polystyrene or silica nanospheres over a glass area of more than 2 cm × 2 cm. Transmission loss of the glass substrate caused by amorphous or polycrystalline silicon deposition is analyzed with good agreement to experimental spectra, and localized surface plasmon resonance signals generated from the gold nanostructures fabricated on these substrates are measured and yield a sensitivity of 317 nm/RIU, which prove the feasibility and effectiveness of our method.     

Radiolabelling of TiO<Subscript>2</Subscript> nanoparticles for radiotracer studies

Industrially manufactured titanium dioxide nanoparticles have been successfully radiolabelled with ⁴⁸V by irradiation with a cyclotron-generated proton beam. Centrifugation tests showed that the ⁴⁸V radiolabels were stably bound within the nanoparticle structure in an aqueous medium, while X-ray diffraction indicated that no major structural modifications to the nanoparticles resulted from the proton irradiation. In vitro tests of the uptake of cold and radiolabelled nanoparticles using the human cell line Calu-3 showed no significant difference in the uptake between both batches of nanoparticles. The uptake was quantified by Inductively Coupled Plasma Mass Spectrometry and high resolution γ-ray spectrometry for cold and radiolabelled nanoparticles, respectively. These preliminary results indicate that alterations to the nanoparticles’ properties introduced by proton bombardment can be controlled to a sufficient extent that their further use as radiotracers for biological investigations can be envisaged and elaborated.     

Uniform Field Re-entrant Cylindrical TE$$_{01\text {U}}$$ Cavity for Pulse Electron Paramagnetic Resonance Spectroscopy at Q-band

Uniform field (UF) resonators create a region-of-interest, where the sample volume receives a homogeneous microwave magnetic field (\(B_1\)) excitation. However, as the region-of-interest is increased, resonator efficiency is reduced. In this work, a new class of uniform field resonators is introduced: the uniform field re-entrant cylindrical TE\(_{\text {01U}}\) cavity. Here, a UF cylindrical TE\(_{\text {01U}}\) cavity is designed with re-entrant fins to increase the overall resonator efficiency to match the resonator efficiency maximum of a typical cylindrical TE\(_{011}\) cavity. The new UF re-entrant cylindrical TE\(_{\text {01U}}\) cavity is designed for Q-band (34 GHz) and is calculated to have the same electron paramagnetic resonance (EPR) signal intensity as a TE\(_{011}\) cavity, a 60% increase in average resonator efficiency \(\Lambda _\mathrm{ave}\) over the sample, and has a \(B_1\) profile that is 79.8% uniform over the entire sample volume (98% uniform over the region-of-interest). A new H-type T-junction waveguide coupler with inductive obstacles is introduced that increases the dynamic range of a movable short coupler while reducing the frequency shift by 43% during over-coupling. The resonator assembly is fabricated and tested both on the bench and with EPR experiments. This resonator provides a template to improve EPR spectroscopy for pulse experiments at high frequencies.     

An algebraic variational multiscale–multigrid method for large-eddy simulation of turbulent variable-density flow at low Mach number

An algebraic variational multiscale–multigrid method is proposed for large-eddy simulation of turbulent variable-density flow at low Mach number. Scale-separating operators generated by level-transfer operators from plain aggregation algebraic multigrid methods enable the application of modeling terms to selected scale groups (here, the smaller of the resolved scales) in a purely algebraic way. Thus, for scale separation, no additional discretization besides the basic one is required, in contrast to earlier approaches based on geometric multigrid methods. The proposed method is thoroughly validated via three numerical test cases of increasing complexity: a Rayleigh–Taylor instability, turbulent channel flow with a heated and a cooled wall, and turbulent flow past a backward-facing step with heating. Results obtained with the algebraic variational multiscale–multigrid method are compared to results obtained with residual-based variational multiscale methods as well as reference results from direct numerical simulation, experiments and LES published elsewhere. Particularly, mean and various second-order velocity and temperature results obtained for turbulent channel flow with a heated and a cooled wall indicate the higher prediction quality achievable when adding a small-scale subgrid-viscosity term within the algebraic multigrid framework instead of residual-based terms accounting for the subgrid-scale part of the non-linear convective term.     

Raman and SERS study of metoclopramide at different pH values

Conjugate acid–base forms of the drug metoclopramide were investigated by Raman spectroscopy in aqueous solutions and by surface‐enhanced Raman scattering (SERS), when the molecules were adsorbed on colloidal silver surfaces. Raman spectra were recorded at pH values below 8, metoclopramide being poorly water soluble at higher pH values. The SERS spectra of metoclopramide were recorded in the 3–11 pH range, even in spite of its low solubility at basic pH values. The Raman and SERS spectra were assigned by means of density functional theory (DFT) calculations. By monitoring several SERS marker bands, the protonated, neutral or the coexistence of both molecular species adsorbed on the colloidal silver particles could be evidenced. The adsorbate orientation was deduced to be perpendicular to the metal surface for the protonated molecular species and tilted for the neutral metoclopramide molecular species. Copyright © 2009 John Wiley & Sons, Ltd.     

Antenna length and polarization response of antenna-coupled MOM diode infrared detectors

This work focuses on the fabrication and response of dipole antenna-coupled metal–oxide–metal diode detectors to long-wave infrared radiation. The detectors are fabricated using a single electron beam lithography step and a shadow evaporation technique. The detector’s characteristics are presented, which include response as a function of incident infrared power and polarization angle. In addition, the effect of dipole antenna length on detection characteristics for 10.6 μm radiation has been measured to determine resonant lengths. The response of the detector shows a first resonance at a dipole length of 3.1 μm, a second resonance at 9.3 μm, and third at 15.5 μm. The zeros intermediate to the resonances are also evident.     

Ultrafast dynamics and temperature effects on the quantum efficiency of the ring-opening reaction of a photochromic indolylfulgide

The ultrafast ring-opening reaction of the molecular switch 1,2-Dimethyl-3-indolylfulgide dissolved in acetonitrile is investigated by temperature dependent quantum efficiency measurements and time-resolved transient absorption spectroscopy in the ultraviolet and visible spectral range. The photoreaction is found to be thermally activated with an activation energy of about 1640 cm^− 1. The transient absorption signal is bi-exponential with the time constants τ₁ = 0.7 ps and τ₂ = 12 ps. The fast time constant is due to solvation dynamics, while the main component τ₂ is attributed to the excited state lifetime and product formation. A long-lived intermediate state in the photoreaction can be excluded.     

Integer points on hypersurfaces

Very general hypersurfaces in ⁴ contain r ^2+(4/9) integer points in any ball of radiusr>1. As a consequence, an irreducible algebraic hypersurface in ⁿ (wheren4) which is not a cylinder and is of degreed, contains c(d, n)r ^{n–1–(5/9)} integer points in a ball of radiusr. This improves on the known boundc(d, n)r ^n–(3/2).Meinem verehrten Lehrer Professor E. Hlawka zum siebzigsten Geburtstag gewidmetWritten with partial support from NSF-MCS-8211461.     

Local limits and harmonic functions for nonisotropic random walks on free groups

Summary Nearest neighbour random walks on the homogeneous tree representing a free group withs generators (2s) are investigated. By use of generating functions and their analytic properties a local limit theorem is derived. A study of the harmonic functions corresponding to the random walk leads to properties that characterize ther-harmonic function connected with the local limits.