Hairpins in the conformations of a confined polymer

If a semiflexible polymer confined to a narrow channel bends around by 180 degrees, the polymer is said to exhibit a hairpin. The equilibrium extension statistics of the confined polymer are well understood when hairpins are vanishingly rare or when they are plentiful. Here we analyze the extension statistics in the intermediate situation via experiments with DNA coated by the protein RecA, which enhances the stiffness of the DNA molecule by approximately one order of magnitude. We find that the extension distribution is highly non-Gaussian, in good agreement with Monte Carlo simulations of confined discrete wormlike chains. We develop a simple model that qualitatively explains the form of the extension distribution. The model shows that the tail of the distribution at short extensions is determined by conformations with one hairpin.Comment: Revised version. 22 pages, 7 figures, 2 tables, supplementary materia

A phenomenological density-scaling approach to lamellipodial actin dynamics

The integration of protein function studied in vitro in a dynamic system like the cell lamellipodium remains a significant challenge. One reason is the apparent contradictory effects that perturbations of some proteins can have on the overall lamellipodium dynamics, depending on exact conditions. Theoretical modeling offers one approach for understanding the balance between the mechanisms that drive and regulate actin network growth and decay. Most models use a \bottom-up" approach, involving explicitly assembling biochemical components to simulate observable behaviour. Their correctness therefore relies on both the accurate characterisation of all the components and the completeness of the relevant processes involved. To avoid potential pitfalls due to this uncertainty, we used an alternative \top-down" approach, in which measurable features of lamellipodium behaviour, here observed in two different cell types (HL60 and B16-F1), directly inform the development of a simple phenomenological model of lamellipodium dynamics. We show that the kinetics of F-actin association and dissociation scales with the local F-actin density, with no explicit location dependence. This justifies the use of a simplified kinetic model of lamellipodium dynamics that yields predictions testable by pharmacological or genetic intervention. A length-scale parameter (the lamellipodium width), emerges from this analysis as an experimentally accessible probe of network regulatory processes

Angular distribution studies on the two-photon ionization of hydrogen-like ions: Relativistic description

The angular distribution of the emitted electrons, following the two-photon ionization of the hydrogen-like ions, is studied within the framework of second order perturbation theory and the Dirac equation. Using a density matrix approach, we have investigated the effects which arise from the polarization of the incoming light as well as from the higher multipoles in the expansion of the electron--photon interaction. For medium- and high-Z ions, in particular, the non-dipole contributions give rise to a significant change in the angular distribution of the emitted electrons, if compared with the electric-dipole approximation. This includes a strong forward emission while, in dipole approxmation, the electron emission always occurs symmetric with respect to the plane which is perpendicular to the photon beam. Detailed computations for the dependence of the photoelectron angular distributions on the polarization of the incident light are carried out for the ionization of H, Xe$^{53+}$, and U$^{91+}$ (hydrogen-like) ions.Comment: 16 pages, 4 figures, published in J Phys

Quantifizierung von Goethit in Mischproben mit FTIR-Spektroskopie

Infrarot (IR)-spektroskopische Untersuchungen ermöglichen eine gleichzeitige und unkomplizierte Analyse von anorganischen und organischen Bestandteilen komplexen Mischproben (z.B. Boden). Aufgrund der Überlagerung von Absorptionsbanden werden die IR-Spektren solcher Proben überwiegend auf qualitativer Basis interpretiert. Bei quantitativen Ansätzen, wie z.B. der Berechnung von Bandenverhältnissen, besteht die Gefahr, dass Hintergrundsignale und deren Variabilität nur unzureichend berücksichtigt werden. Die vorliegende Studie präsentiert einen chemometrischen Ansatz, um einzelne Substanzen in komplexen IR-Spektren voneinander reproduzierbar zu diskriminieren. Hierbei erfolgt mittels Positiver Matrixfaktorisierung (PMF) die Zerlegung der IR-Spektren in eine Linearkombination aus Gehalt und Spektrum von Einzelkomponenten. Bei Bedarf können dabei bekannte Spektren von Referenzsubstanzen benutzt werden, um die der Faktorenanalyse inherente Uneindeutigkeit zu begrenzen. Zudem können die Eindeutigkeit und Reproduzierbarkeit der PMF-Lösungen durch komplementäre statistische Parameter überwacht werden. Dieser Ansatz wurde bzgl. der Wiederfindung von kolloidalem Goethit in Grundwasser erprobt. Der Anteil Goethit-induzierter Banden konnte dabei von Banden anorganischer (Quarz, Kaolinit etc.) und organischer Verbindungen (autochthoner und allochthoner OM) in den IR-Spektren von getrockneten Grundwasserproben erfolgreich diskriminiert und quantifiziert werden. Abhängig von der Fragestellung könnten demnach auch weitere Grundwasserbestandteile neben Goethit quantifiziert werden. PMF ist damit ein geeigneter Ansatz, um IR-Spektren reproduzierbar in einzelne Komponenten zu zerlegen, die Spektrum und Gehalt der Einzelsubstanzen in Mischproben reflektieren

Structure of adsorbed Fe on Ni{111}

Using photoelectron diffraction in the scanned energy mode we have established that Fe atoms adsorb in the fcc hollow sites of the Ni{111} surface even at low temperatures. Total-energy calculations had suggested that the hcp hollow sites were more stable

Direct visualization of magnetic vortex pinning in superconductors

We study the vortex structure in a Pb film deposited on top of a periodic array of ferromagnetic square microrings by combining two high resolution imaging techniques: Bitter decoration and scanning Hall probe microscopy (SHPM). The periodicity and strength of the magnetic pinning potential generated by the square microrings are controlled by the magnetic history of the template. When the square rings are in the magnetized dipolar state, known as the onion state, the strong stray field generated at the domain walls prevents the decoration of vortices. SHPM images show that the stray field generated by the dipoles is much stronger than the vortex field in agreement with the results of simulations. Real space vortex imaging has revealed that, in the onion state, the corners of the square rings act as effective pinning centers for vortices.Comment: To be published in Phys. Rev.

Fragmentation and systematics of the Pygmy Dipole Resonance in the stable N=82 isotones

The low-lying electric dipole (E1) strength in the semi-magic nucleus 136Xe has been measured which finalizes the systematic survey to investigate the so-called pygmy dipole resonance (PDR) in all stable even N=82 isotones with the method of nuclear resonance fluorescence using real photons in the entrance channel. In all cases, a fragmented resonance-like structure of E1 strength is observed in the energy region 5 MeV to 8 MeV. An analysis of the fragmentation of the strength reveals that the degree of fragmentation decreases towards the proton-deficient isotones while the total integrated strength increases indicating a dependence of the total strength on the neutron-to-proton ratio. The experimental results are compared to microscopic calculations within the quasi-particle phonon model (QPM). The calculation includes complex configurations of up to three phonons and is able to reproduce also the fragmentation of the E1 strength which allows to draw conclusions on the damping of the PDR. Calculations and experimental data are in good agreement in the degree of fragmentation and also in the integrated strength if the sensitivity limit of the experiments is taken into account