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.

Kinematics of the Sicily and Calabria Subduction System from Elastic Block Modeling of GPS Data

We use data from about 700 GPS stations in the EuroMediterranen region to investigate the present-day behavior of the the Calabrian subduction zone within the Mediterranean-scale plates kinematics and to perform local scale studies about the strain accumulation on active structures. We focus attenction on the Messina Straits and Crati Valley faults where GPS data show extentional velocity gradients of ∼3 mm/yr and ∼2 mm/yr, respectively. We use dislocation model and a non-linear constrained optimization algorithm to invert for fault geometric parameters and slip-rates and evaluate the associated uncertainties adopting a bootstrap approach. Our analysis suggest the presence of two partially locked normal faults. To investigate the impact of elastic strain contributes from other nearby active faults onto the observed velocity gradient we use a block modeling approach. Our models show that the inferred slip-rates on the two analyzed structures are strongly impacted by the assumed locking width of the Calabrian subduction thrust. In order to frame the observed local deformation features within the present- day central Mediterranean kinematics we realyze a statistical analysis testing the indipendent motion (w.r.t. the African and Eurasias plates) of the Adriatic, Cal- abrian and Sicilian blocks. Our preferred model confirms a microplate like behaviour for all the investigated blocks. Within these kinematic boundary conditions we fur- ther investigate the Calabrian Slab interface geometry using a combined approach of block modeling and χ2ν statistic. Almost no information is obtained using only the horizontal GPS velocities that prove to be a not sufficient dataset for a multi-parametric inversion approach. Trying to stronger constrain the slab geometry we estimate the predicted vertical velocities performing suites of forward models of elastic dislocations varying the fault locking depth. Comparison with the observed field suggest a maximum resolved locking depth of 25 km.

Micro-FEM models based on micro-CT reconstructions for the in vitro characterization of the elastic properties of trabecular bone tissue.

This master’s thesis describes the research done at the Medical Technology Laboratory (LTM) of the Rizzoli Orthopedic Institute (IOR, Bologna, Italy), which focused on the characterization of the elastic properties of the trabecular bone tissue, starting from october 2012 to present. The approach uses computed microtomography to characterize the architecture of trabecular bone specimens. With the information obtained from the scanner, specimen-specific models of trabecular bone are generated for the solution with the Finite Element Method (FEM). Along with the FEM modelling, mechanical tests are performed over the same reconstructed bone portions. From the linear-elastic stage of mechanical tests presented by experimental results, it is possible to estimate the mechanical properties of the trabecular bone tissue. After a brief introduction on the biomechanics of the trabecular bone (chapter 1) and on the characterization of the mechanics of its tissue using FEM models (chapter 2), the reliability analysis of an experimental procedure is explained (chapter 3), based on the high-scalable numerical solver ParFE. In chapter 4, the sensitivity analyses on two different parameters for micro-FEM model’s reconstruction are presented. Once the reliability of the modeling strategy has been shown, a recent layout for experimental test, developed in LTM, is presented (chapter 5). Moreover, the results of the application of the new layout are discussed, with a stress on the difficulties connected to it and observed during the tests. Finally, a prototype experimental layout for the measure of deformations in trabecular bone specimens is presented (chapter 6). This procedure is based on the Digital Image Correlation method and is currently under development in LTM.

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.

On moduli spaces of semistable sheaves on K3 surfaces

Ich untersuche die nicht bereits durch die Arbeit "Singular symplectic moduli spaces" von Kaledin, Lehn und Sorger (Invent. Math. 164 (2006), no. 3) abgedeckten Fälle von Modulräumen halbstabiler Garben auf projektiven K3-Flächen - die Fälle mit Mukai-Vektor (0,c,0) sowie die Modulräume zu nichtgenerischen amplen Divisoren - hinsichtlich der möglichen Konstruktion neuer Beispiele von kompakten irreduziblen symplektischen Mannigfaltigkeiten. Ich stelle einen Zusammenhang zu den bereits untersuchten Modulräumen und Verallgemeinerungen derselben her und erweitere bekannte Ergebnisse auf alle offenen Fälle von Garben vom Rang 0 und viele Fälle von Garben von positivem Rang. Insbesondere kann in diesen Fällen die Existenz neuer Beispiele von kompakten irreduziblen symplektischen Mannigfaltigkeiten, die birational über Komponenten des Modulraums liegen, ausgeschlossen werden.

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.

Thermal inflation and the cosmological moduli problem

Ho studiato la possibilità di soluzione per il problema cosmologico dei moduli (CMP) presente a causa della compattificazione delle dimensioni extra tramite un periodo di inflazione a basse energie (Thermal Inflation). L'elaborato consta di cinque capitoli. Il primo introduce il lettore alla problematica dei moduli partendo dalla teoria Kaluza-Klein. Il secondo riguarda interamente il CMP e altri problemi cosmologici associati ai moduli. Nel terzo viene descritta la thermal inflation e le condizioni di funzionamento. Nel quarto capitolo viene preso in esame il problema di stabilizzazione dei moduli nella teoria di stringa tipo IIB: vengono descritti sia il meccanismo KKTL che il LVS. L'ultimo capitolo consiste nel calcolo della diluizione dei moduli, enunciata prima in un contesto generale e infine applicata al LVS, tramite la thermal inflation. Viene altresì presa in esame la possibilità di due epoche di thermal inflation, al fine di ottenere una diluizione più efficiente dei moduli. In LVS sono presenti due moduli, differenti per massa e vita media. Il più leggero è soggetto al CMP e si trova che, anche dopo due periodi di thermal inflation vi è ancora un numero eccessivo di tali campi, in quanto se da un lato la thermal inflation ne diliusca la densità iniziale, dall'altro ne causa una forte riproduzione, dovuta essenzialmente alle caratteristiche del modulo

Moduli spaces of (G,h)-constellations

Given a reductive group G acting on an affine scheme X over C and a Hilbert function h: Irr G → N_0, we construct the moduli space M_Ө(X) of Ө-stable (G,h)-constellations on X, which is a common generalisation of the invariant Hilbert scheme after Alexeev and Brion and the moduli space of Ө-stable G-constellations for finite groups G introduced by Craw and Ishii. Our construction of a morphism M_Ө(X) → X//G makes this moduli space a candidate for a resolution of singularities of the quotient X//G. Furthermore, we determine the invariant Hilbert scheme of the zero fibre of the moment map of an action of Sl_2 on (C²)⁶ as one of the first examples of invariant Hilbert schemes with multiplicities. While doing this, we present a general procedure for the realisation of such calculations. We also consider questions of smoothness and connectedness and thereby show that our Hilbert scheme gives a resolution of singularities of the symplectic reduction of the action.

Behaviour and applications of elastic waves in structures and metamaterials

The present thesis focuses on elastic waves behaviour in ordinary structures as well as in acousto-elastic metamaterials via numerical and experimental applications. After a brief introduction on the behaviour of elastic guided waves in the framework of non-destructive evaluation (NDE) and structural health monitoring (SHM) and on the study of elastic waves propagation in acousto-elastic metamaterials, dispersion curves for thin-walled beams and arbitrary cross-section waveguides are extracted via Semi-Analytical Finite Element (SAFE) methods. Thus, a novel strategy tackling signal dispersion to locate defects in irregular waveguides is proposed and numerically validated. Finally, a time-reversal and laser-vibrometry based procedure for impact location is numerically and experimentally tested. In the second part, an introduction and a brief review of the basic definitions necessary to describe acousto-elastic metamaterials is provided. A numerical approach to extract dispersion properties in such structures is highlighted. Afterwards, solid-solid and solid-fluid phononic systems are discussed via numerical applications. In particular, band structures and transmission power spectra are predicted for 1P-2D, 2P-2D and 2P-3D phononic systems. In addition, attenuation bands in the ultrasonic as well as in the sonic frequency regimes are experimentally investigated. In the experimental validation, PZTs in a pitch-catch configuration and laser vibrometric measurements are performed on a PVC phononic plate in the ultrasonic frequency range and sound insulation index is computed for a 2P-3D phononic barrier in the sonic frequency range. In both cases the numerical-experimental results comparison confirms the existence of the numerical predicted band-gaps. Finally, the feasibility of an innovative passive isolation strategy based on giant elastic metamaterials is numerically proved to be practical for civil structures. In particular, attenuation of seismic waves is demonstrated via finite elements analyses. Further, a parametric study shows that depending on the soil properties, such an earthquake-proof barrier could lead to significant reduction of the superstructure displacement.