Allan Variance Analysis as Useful Tool to Determine Noise in Various Single-Molecule Setups

One limitation on the performance of optical traps is the noise inherently present in every setup. Therefore, it is the desire of most experimentalists to minimize and possibly eliminate noise from their optical trapping experiments. A step in this direction is to quantify the actual noise in the system and to evaluate how much each particular component contributes to the overall noise. For this purpose we present Allan variance analysis as a straightforward method. In particular, it allows for judging the impact of drift which gives rise to low-frequency noise, which is extremely difficult to pinpoint by other methods. We show how to determine the optimal sampling time for calibration, the optimal number of data points for a desired experiment, and we provide measurements of how much accuracy is gained by acquiring additional data points. Allan variances of both micrometer-sized spheres and asymmetric nanometer-sized rods are considered.Comment: 14 pages, 6 figures, presented at SPIE Optics+Photonics 2009 in San Diego, CA, US

Myxococcus xanthus gliding motors are elastically coupled to the substrate as predicted by the focal adhesion model of gliding motility

Myxococcus xanthus is a model organism for studying bacterial social behaviors due to its ability to form complex multi-cellular structures. Knowledge of M. xanthus surface gliding motility and the mechanisms that coordinate it are critically important to our understanding of collective cell behaviors. Although the mechanism of gliding motility is still under investigation, recent experiments suggest that there are two possible mechanisms underlying force production for cell motility: the focal adhesion mechanism and the helical rotor mechanism which differ in the biophysics of the cell-substrate interactions. Whereas the focal adhesion model predicts an elastic coupling, the helical rotor model predicts a viscous coupling. Using a combination of computational modeling, imaging, and force microscopy, we find evidence for elastic coupling in support of the focal adhesion model. Using a biophysical model of the M. xanthus cell, we investigated how the mechanical interactions between cells are affected by interactions with the substrate. Comparison of modeling results with experimental data for cell-cell collision events pointed to a strong, elastic attachment between the cell and substrate. These results are robust to variations in the mechanical and geometrical parameters of the model. We then directly measured the motor-substrate coupling by monitoring the motion of optically trapped beads and find that motor velocity decreases exponentially with opposing load. At high loads, motor velocity approaches zero velocity asymptotically and motors remain bound to beads indicating a strong, elastic attachment

MesonNet Workshop on Meson Transition Form Factors

The mini-proceedings of the Workshop on Meson Transition Form Factors held in Cracow from May 29th to 30th, 2012 introduce the meson transition form factor project with special emphasis on the interrelations between the various form factors (on-shell, single off-shell, double off-shell). Short summaries of the talks presented at the workshop follow.Comment: 69 pages, 14 figures; all talks can be found at https://sites.google.com/site/mesonnetwork/home/activities/form-factor-workshop-2012; v2: workshop link updated (as the page had to be moved to a commercial server), table 6 correcte

Determination of the eta'-proton scattering length in free space

Taking advantage of both the high mass resolution of the COSY-11 detector and the high energy resolution of the low-emittance proton-beam of the Cooler Synchrotron COSY we determine the excitation function for the pp --> pp eta' reaction close-to-threshold. Combining these data with previous results we extract the scattering length for the eta'-proton potential in free space to be Re(a_{p eta'}) = 0+-0.43 fm and Im(a_{p eta'}) = 0.37(+0.40)(-0.16) fm.Comment: 5 pages, 3 figures, accepted for publication in Phys. Rev. Let

Poly(3-alkylthiophenes): new sorption materials for solid phase microextraction of drugs isolated from human plasma

A novel sorbent in solid phase microextraction (SPME) method based on poly(3-alkylthiophenes) was used in the isolation of linezolid from human plasma samples following liquid chromatography determination. The effect of extraction time on the sorption capacity of the SPME process was studied and pointed at 10 min both for adsorption and desorption. Poly(3-methylthiophene) and poly(3-nonylthiophene) were applied for the extraction of linezolid from water solutions. In plasma samples, four coatings including polythiophene and poly(3-penthylthiophene) were investigated. With these measurements, correlation coefficients were calculated in the range from 0.9820 to 0.9995, and the relative standard deviations were below 15%. That allowed claiming that the synthesized and described materials can be successfully applied in the analysis of linezolid also from other matrices such as urine or blood

Single-molecule observations of topotecan-mediated TopIB activity at a unique DNA sequence

The rate of DNA supercoil removal by human topoisomerase IB (TopIB) is slowed down by the presence of the camptothecin class of antitumor drugs. By preventing religation, these drugs also prolong the lifetime of the covalent TopIB–DNA complex. Here, we use magnetic tweezers to measure the rate of supercoil removal by drug-bound TopIB at a single DNA sequence in real time. This is accomplished by covalently linking camptothecins to a triple helix-forming oligonucleotide that binds at one location on the DNA molecule monitored. Surprisingly, we find that the DNA dynamics with the TopIB–drug interaction restricted to a single DNA sequence are indistinguishable from the dynamics observed when the TopIB–drug interaction takes place at multiple sites. Specifically, the DNA sequence does not affect the instantaneous supercoil removal rate or the degree to which camptothecins increase the lifetime of the covalent complex. Our data suggest that sequence-dependent dynamics need not to be taken into account in efforts to develop novel camptothecins

Eta and eta' mesons production at COSY-11

The low emittance and small momentum spread of the proton and deuteron beams of the Cooler Synchrotron COSY combined with the high mass resolution of the COSY-11 detection system permit to study the creation of mesons in the nucleon-nucleon interaction down to the fraction of MeV with respect to the kinematical threshold. At such small excess energies, the ejectiles possess low relative momenta and are predominantly produced with the relative angular momentum equal to zero. Taking advantage of these conditions we have performed investigations aiming to determine the mechanism of the production of eta and eta' mesons in the collision of hadrons as well as the hadronic interaction of these mesons with nucleons and nuclei. In this proceedings we address the ongoing studies of the spin and isospin dependence for the production of the eta and eta' mesons in free and quasi-free nucleon-nucleon collisions. New results on the spin observables for the vec(p)p --> pp eta reaction, combined with the previously determined total cross section isospin dependence, reveal a statistically significant indication that the excitation of the nucleon to the S11(1535) resonance, the process which intermediates the production of the eta meson in the nucleon-nucleon interactions, is predominantly due to the exchange of the pi meson between the colliding nucleons.Comment: Invited talk at MESON 2006: 9th International Workshop on Meson Production, Properties and Interactions, Cracow, Poland, 9-13 Jun 200

Dynamics of the near threshold eta meson production in proton-proton interaction

We present the results of measurements of the analysing power for the p(pol)p --> pp eta reaction at the excess energies of Q=10 and 36 MeV, and interpret these results within the framework of the meson exchange models. The determined values of the analysing power at both excess energies are consistent with zero implying that the eta meson is produced predominantly in s-wave.Comment: 3 pages, 3 figures, Presented at the Workshop on the physics of excited nucleons (NSTAR 2007), 5-8 September 2007, Bonn, German