Structural and elastic properties of DNA and chromatin

We investigate a chain consisting of two coupled worm-like chains withconstant distance between the strands. The effects due todouble-strandedness of the chain are studied. In a previous analyticalstudy of this system an intrinsic twist-stretch coupling and atendency of kinking is predicted. Even though a local twist structureis observed the predicted features are not recovered. A new model for DNA at the base-pair level is presented. Thebase-pairs are treated as flat rigid ellipsoids and thesugar-phosphate backbones are represented as stiff harmonic springs.The base-pair stacking interaction is modeled by a variant of theGay-Berne potential. It is shown by systematic coarse-graininghow the elastic constants of a worm-like chain are related to thelocal fluctuations of the base-pair step parameters. Even though a lotof microscopic details of the base-pair geometry is neglected themodel can be optimized to obtain a B-DNA conformation as ground stateand reasonable elastic properties. Moreover the model allows tosimulate much larger length scales than it is possible with atomisticsimulations due to the simplification of the force-field and inparticular due to the possibility of non-local Monte-Carlo moves. Asa first application the behavior under stretching is investigated. Inagreement with micromanipulation experiments on single DNA moleculesone observes a force-plateau in the force-extension curvescorresponding to an overstretching transition from B-DNA to aso-called S-DNA state. The model suggests a structure for S-DNA withhighly inclined base-pairs in order to enable at least partialbase-pair stacking. Finally a simple model for chromatin is introduced to study itsstructural and elastic properties. The underlying geometry of themodeled fiber is based on a crossed-linker model. The chromatosomesare treated as disk-like objects. Excluded volume and short rangenucleosomal interaction are taken into account by a variant of theGay-Berne potential. It is found that the bending rigidity and thestretching modulus of the fiber increase with more compact fibers. Fora reasonable parameterization of the fiber for physiologicalconditions and sufficiently high attraction between the nucleosomes aforce-extension curve is found similar to stretching experiments onsingle chromatin fibers. For very small stretching forces a kinkedfiber forming a loop is observed. If larger forces are applied theloop formation is stretched out and a decondensation of the fibertakes place.

Hypersonic elastic excitations in soft mesoscopic structures

This dissertation is devoted to the experimental exploration of the propagation of elastic waves in soft mesoscopic structures with submicrometer dimensions. A strong motivation of this work is the large technological relevance and the fundamental importance of the subject. Elastic waves are accompanied by time-dependent fluctuations of local stress and strain fields in the medium. As such, the propagation phase velocities are intimately related to the elastic moduli. Knowledge of the elastic wave propagation directly provides information about the mechanical properties of the probed mesoscopic structures, which are not readily accessible experimentally. On the other hand, elastic waves, when propagating in an inhomogeneous medium with spatial inhomogeneities comparable to their wavelength, exhibit rather rich behavior, including the appearance of novel physical phenomena, such as phononic bandgap formation. So far, the experimental work has been restricted to macroscopic structures, which limit wave propagation below the KHz range. It was anticipated that an experimental approach capable of probing the interplay of the wave propagation with the controlled mesoscopic structures would contribute to deeper insights into the fundamental problem of elastic wave propagation in inhomogeneous systems. The mesoscopic nature of the structures to be studied precludes the use of traditional methods, such as sound transmission, for the study of elastic wave propagation. In this work, an optical method utilizing the inelastic scattering of photons by GHz frequency thermally excited elastic waves, known as Brillouin light scattering spectroscopy (BLS), was employed. Two important classes of soft structures were investigated: thin films and colloidal crystals. For the former, the main interest was the effect of the one-dimensional (1D) confinement on the wave propagation due to the presence of the free-surface or interface of the layer and the utilization of these waves to extract relevant material parameters. For the second system, the primary interest was the interaction of the elastic wave and the strong scattering medium with local resonance units in a three-dimensional (3D) periodic arrangement.

Investigation of the nuclear matter density distributions of the exotic 12 Be, 14 Be and 8 B nuclei by elastic proton scattering in inverse kinematics

The proton-nucleus elastic scattering at intermediate energies is a well-established method for the investigation of the nuclear matter distribution in stable nuclei and was recently applied also for the investigation of radioactive nuclei using the method of inverse kinematics. In the current experiment, the differential cross sections for proton elastic scattering on the isotopes $^{7,9,10,11,12,14}$Be and $^8$B were measured. The experiment was performed using the fragment separator at GSI, Darmstadt to produce the radioactive beams. The main part of the experimental setup was the time projection ionization chamber IKAR which was simultaneously used as hydrogen target and a detector for the recoil protons. Auxiliary detectors for projectile tracking and isotope identification were also installed. As results from the experiment, the absolute differential cross sections d$sigma$/d$t$ as a function of the four momentum transfer $t$ were obtained. In this work the differential cross sections for elastic p-$^{12}$Be, p-$^{14}$Be and p-$^{8}$B scattering at low $t$ ($t leq$~0.05~(GeV/c)$^2$) are presented. The measured cross sections were analyzed within the Glauber multiple-scattering theory using different density parameterizations, and the nuclear matter density distributions and radii of the investigated isotopes were determined. The analysis of the differential cross section for the isotope $^{14}$Be shows that a good description of the experimental data is obtained when density distributions consisting of separate core and halo components are used. The determined {it rms} matter radius is $3.11 pm 0.04 pm 0.13$~fm. In the case of the $^{12}$Be nucleus the results showed an extended matter distribution as well. For this nucleus a matter radius of $2.82 pm 0.03 pm 0.12$~fm was determined. An interesting result is that the free $^{12}$Be nucleus behaves differently from the core of $^{14}$Be and is much more extended than it. The data were also compared with theoretical densities calculated within the FMD and the few-body models. In the case of $^{14}$Be, the calculated cross sections describe the experimental data well while, in the case of $^{12}$Be there are discrepancies in the region of high momentum transfer. Preliminary experimental results for the isotope $^8$B are also presented. An extended matter distribution was obtained (though much more compact as compared to the neutron halos). A proton halo structure was observed for the first time with the proton elastic scattering method. The deduced matter radius is $2.60pm 0.02pm 0.26$~fm. The data were compared with microscopic calculations in the frame of the FMD model and reasonable agreement was observed. The results obtained in the present analysis are in most cases consistent with the previous experimental studies of the same isotopes with different experimental methods (total interaction and reaction cross section measurements, momentum distribution measurements). For future investigation of the structure of exotic nuclei a universal detector system EXL is being developed. It will be installed at the NESR at the future FAIR facility where higher intensity beams of radioactive ions are expected. The usage of storage ring techniques provides high luminosity and low background experimental conditions. Results from the feasibility studies of the EXL detector setup, performed at the present ESR storage ring, are presented.

Mapping the elastic response of epithelial apical cell membranes suspended across porous array

As the elastic response of cell membranes to mechanical stimuli plays a key role in various cellular processes, novel biophysical strategies to quantify the elasticity of native membranes under physiological conditions at a nanometer scale are gaining interest. In order to investigate the elastic response of apical membranes, elasticity maps of native membrane sheets, isolated from MDCK II (Madine Darby Canine kidney strain II) epithelial cells, were recorded by local indentation with an Atomic Force Microscope (AFM). To exclude the underlying substrate effect on membrane indentation, a highly ordered gold coated porous array with a pore diameter of 1.2 μm was used to support apical membranes. Overlays of fluorescence and AFM images show that intact apical membrane sheets are attached to poly-D-lysine coated porous substrate. Force indentation measurements reveal an extremely soft elastic membrane response if it is indented at the center of the pore in comparison to a hard repulsion on the adjacent rim used to define the exact contact point. A linear dependency of force versus indentation (-dF/dh) up to 100 nm penetration depth enabled us to define an apparent membrane spring constant (kapp) as the slope of a linear fit with a stiffness value of for native apical membrane in PBS. A correlation between fluorescence intensity and kapp is also reported. Time dependent hysteresis observed with native membranes is explained by a viscoelastic solid model of a spring connected to a Kelvin-Voight solid with a time constant of 0.04 s. No hysteresis was reported with chemically fixated membranes. A combined linear and non linear elastic response is suggested to relate the experimental data of force indentation curves to the elastic modulus and the membrane thickness. Membrane bending is the dominant contributor to linear elastic indentation at low loads, whereas stretching is the dominant contributor for non linear elastic response at higher loads. The membrane elastic response was controlled either by stiffening with chemical fixatives or by softening with F-actin disrupters. Overall, the presented setup is ideally suitable to study the interactions of the apical membrane with the underlying cytoskeleton by means of force indentation elasticity maps combined with fluorescence imaging.

Measurement of the elastic electron-proton cross section and separation of the electric and magnetic form factor in the Q 2 range from 0.004 to 1 (GeV/c) 2

The electromagnetic form factors of the proton are fundamental quantities sensitive to the distribution of charge and magnetization inside the proton. Precise knowledge of the form factors, in particular of the charge and magnetization radii provide strong tests for theory in the non-perturbative regime of QCD. However, the existing data at Q^2 below 1 (GeV/c)^2 are not precise enough for a hard test of theoretical predictions.rnrnFor a more precise determination of the form factors, within this work more than 1400 cross sections of the reaction H(e,e′)p were measured at the Mainz Microtron MAMI using the 3-spectrometer-facility of the A1-collaboration. The data were taken in three periods in the years 2006 and 2007 using beam energies of 180, 315, 450, 585, 720 and 855 MeV. They cover the Q^2 region from 0.004 to 1 (GeV/c)^2 with counting rate uncertainties below 0.2% for most of the data points. The relative luminosity of the measurements was determined using one of the spectrometers as a luminosity monitor. The overlapping acceptances of the measurements maximize the internal redundancy of the data and allow, together with several additions to the standard experimental setup, for tight control of systematic uncertainties.rnTo account for the radiative processes, an event generator was developed and implemented in the simulation package of the analysis software which works without peaking approximation by explicitly calculating the Bethe-Heitler and Born Feynman diagrams for each event.rnTo separate the form factors and to determine the radii, the data were analyzed by fitting a wide selection of form factor models directly to the measured cross sections. These fits also determined the absolute normalization of the different data subsets. The validity of this method was tested with extensive simulations. The results were compared to an extraction via the standard Rosenbluth technique.rnrnThe dip structure in G_E that was seen in the analysis of the previous world data shows up in a modified form. When compared to the standard-dipole form factor as a smooth curve, the extracted G_E exhibits a strong change of the slope around 0.1 (GeV/c)^2, and in the magnetic form factor a dip around 0.2 (GeV/c)^2 is found. This may be taken as indications for a pion cloud. For higher Q^2, the fits yield larger values for G_M than previous measurements, in agreement with form factor ratios from recent precise polarized measurements in the Q2 region up to 0.6 (GeV/c)^2.rnrnThe charge and magnetic rms radii are determined as rn⟨r_e⟩=0.879 ± 0.005(stat.) ± 0.004(syst.) ± 0.002(model) ± 0.004(group) fm,rn⟨r_m⟩=0.777 ± 0.013(stat.) ± 0.009(syst.) ± 0.005(model) ± 0.002(group) fm.rnThis charge radius is significantly larger than theoretical predictions and than the radius of the standard dipole. However, it is in agreement with earlier results measured at the Mainz linear accelerator and with determinations from Hydrogen Lamb shift measurements. The extracted magnetic radius is smaller than previous determinations and than the standard-dipole value.

The effect of elastic modulus and equilibrium vapor adsorption on capillary forces

Die Kapillarkraft entsteht durch die Bildung eines Meniskus zwischen zwei Festkörpen. In dieser Doktorarbeit wurden die Auswirkungen von elastischer Verformung und Flϋssigkeitadsorption auf die Kapillarkraft sowohl theoretisch als auch experimentell untersucht. Unter Verwendung eines Rasterkraftmikroskops wurde die Kapillarkraft zwischen eines Siliziumoxid Kolloids von 2 µm Radius und eine weiche Oberfläche wie n.a. Polydimethylsiloxan oder Polyisopren, unter normalen Umgebungsbedingungen sowie in variierende Ethanoldampfdrϋcken gemessen. Diese Ergebnisse wurden mit den Kapillarkräften verglichen, die auf einem harten Substrat (Silizium-Wafer) unter denselben Bedingungen gemessen wurden. Wir beobachteten eine monotone Abnahme der Kapillarkraft mit zunehmendem Ethanoldampfdruck (P) fϋr P/Psat > 0,2, wobei Psat der Sättigungsdampfdruck ist.rnUm die experimentellen Ergebnisse zu erklären, wurde ein zuvor entwickeltes analytisches Modell (Soft Matter 2010, 6, 3930) erweitert, um die Ethanoladsorption zu berϋcksichtigen. Dieses neue analytische Modell zeigte zwei verschiedene Abhängigkeiten der Kapillarkraft von P/Psat auf harten und weichen Oberflächen. Fϋr die harte Oberfläche des Siliziumwafers wird die Abhängigkeit der Kapillarkraft vom Dampfdruck vom Verhältnis der Dicke der adsorbierten Ethanolschicht zum Meniskusradius bestimmt. Auf weichen Polymeroberflächen hingegen hängt die Kapillarkraft von der Oberflächenverformung und des Laplace-Drucks innerhalb des Meniskus ab. Eine Abnahme der Kapillarkraft mit zunehmendem Ethanoldampfdruck hat demnach eine Abnahme des Laplace-Drucks mit zunehmendem Meniskusradius zur folge. rnDie analytischen Berechnungen, fϋr die eine Hertzsche Kontakt-deformation angenommen wurde, wurden mit Finit Element Methode Simulationen verglichen, welche die reale Deformation des elastischen Substrats in der Nähe des Meniskuses explizit berϋcksichtigen. Diese zusätzliche nach oben gerichtete oberflächenverformung im Bereich des Meniskus fϋhrt zu einer weiteren Erhöhung der Kapillarkraft, insbesondere fϋr weiche Oberflächen mit Elastizitätsmodulen < 100 MPa.rn