Computational mass spectrometry of linear binary synthetic copolymers

The accurate characterization of synthetic polymer sequences represents a major challenge in polymer science. We present a computational approach to quantify the abundances of all sequences in a measured copolymer sample. The first step in our workflow is transforming mass spectra into copolymer fingerprints. Our method is based on linear programming and is capable of automatically resolving overlapping isotopes and isobaric ions. Peak intensities in matrix-assisted laser desorption/ionization spectra are influenced by mass and composition-dependent ionization. We demonstrate a method to correct the abundance bias. The second step in our workflow is interpreting the computed copolymer fingerprints using new Markov chain models for copolymerization kinetics: The Bernoulli and Geometric models. In contrast to previous Markov chain approaches to copolymerization, both models take variable chain lengths and time-dependent monomer probabilities into account and allow computing sequence likelihoods and copolymer fingerprints. We find that computing the models is fast and memory efficient. Then, we focus on the Geometric copolymerization model with reactivity parameters. First, several approaches to identify the optimal model parameters from observed fingerprints are evaluated using Monte-Carlo simulated data. A compromise between robustness and running time is found by exploiting the relationship between ordinary differential equations and the Geometric model. Second, we show that the model is also useful for copolymerizations involving termination and depropagation reactions. We then compute several copolymer statistics and compared them to the statistics obtained from Monte-Carlo simulations. Last but not least, we present our software framework COCONUT, which implements all algorithms presented in this thesis. Our software is freely available and provides a graphical user interface. COCONUT represents a step towards comprehensive computational support in polymer science

Exploring the limits of the geometric copolymerization model

The geometric copolymerization model is a recently introduced statistical Markov chain model. Here, we investigate its practicality. First, several approaches to identify the optimal model parameters from observed copolymer fingerprints are evaluated using Monte Carlo simulated data. Directly optimizing the parameters is robust against noise but has impractically long running times. A compromise between robustness and running time is found by exploiting the relationship between monomer concentrations calculated by ordinary differential equations and the geometric model. Second, we investigate the applicability of the model to copolymerizations beyond living polymerization and show that the model is useful for copolymerizations involving termination and depropagation reactions

Systematic evaluation of particle loss during handling in the percutaneous transluminal angioplasty for eight different drug-coated balloons

Paclitaxel drug coated balloons (DCBs) should provide optimal drug transfer exclusively to the target tissue. The aim of this study was to evaluate the particle loss by handling during angioplasty. A robotic arm was developed for systematic and reproducible drug abrasion experiments. The contact force on eight different commercially available DCB types was gradually increased, and high-resolution microscopic images of the deflated and inflated balloons were recorded. Three types of DCBs were classified: no abrasion of the drug in both statuses (deflated and inflated), significant abrasion only in the inflated status, and significant abrasion in both statuses. Quantitative measurements via image processing confirmed the qualitative classification and showed changes of the drug area between 2.25 and 45.73% (13.28 ± 14.29%) in the deflated status, and between 1.66 and 40.41% (21.43 ± 16.48%) in the inflated status. The structures and compositions of the DCBs are different, some are significantly more susceptible to drug loss. Particle loss by handling during angioplasty leads to different paclitaxel doses in the target regions for same DCB types. Susceptibility to involuntary drug loss may cause side effects, such as varying effective paclitaxel doses, which may explain variations in studies regarding the therapeutic outcome

Strong anisotropy in surface kinetic roughening: analysis and experiments

We report an experimental assessment of surface kinetic roughening properties that are anisotropic in space. Working for two specific instances of silicon surfaces irradiated by ion-beam sputtering under diverse conditions (with and without concurrent metallic impurity codeposition), we verify the predictions and consistency of a recently proposed scaling Ansatz for surface observables like the two-dimensional (2D) height Power Spectral Density (PSD). In contrast with other formulations, this Ansatz is naturally tailored to the study of two-dimensional surfaces, and allows to readily explore the implications of anisotropic scaling for other observables, such as real-space correlation functions and PSD functions for 1D profiles of the surface. Our results confirm that there are indeed actual experimental systems whose kinetic roughening is strongly anisotropic, as consistently described by this scaling analysis. In the light of our work, some types of experimental measurements are seen to be more affected by issues like finite space resolution effects, etc. that may hinder a clear-cut assessment of strongly anisotropic scaling in the present and other practical contexts

Mechanical Stress Inference for Two Dimensional Cell Arrays

Many morphogenetic processes involve mechanical rearrangement of epithelial tissues that is driven by precisely regulated cytoskeletal forces and cell adhesion. The mechanical state of the cell and intercellular adhesion are not only the targets of regulation, but are themselves likely signals that coordinate developmental process. Yet, because it is difficult to directly measure mechanical stress {\it in vivo} on sub-cellular scale, little is understood about the role of mechanics of development. Here we present an alternative approach which takes advantage of the recent progress in live imaging of morphogenetic processes and uses computational analysis of high resolution images of epithelial tissues to infer relative magnitude of forces acting within and between cells. We model intracellular stress in terms of bulk pressure and interfacial tension, allowing these parameters to vary from cell to cell and from interface to interface. Assuming that epithelial cell layers are close to mechanical equilibrium, we use the observed geometry of the two dimensional cell array to infer interfacial tensions and intracellular pressures. Here we present the mathematical formulation of the proposed Mechanical Inverse method and apply it to the analysis of epithelial cell layers observed at the onset of ventral furrow formation in the {\it Drosophila} embryo and in the process of hair-cell determination in the avian cochlea. The analysis reveals mechanical anisotropy in the former process and mechanical heterogeneity, correlated with cell differentiation, in the latter process. The method opens a way for quantitative and detailed experimental tests of models of cell and tissue mechanics

Differences between Ca2+ and Mg2+ in DNA binding and release by the SfiI restriction endonuclease: implications for DNA looping

Many enzymes acting on DNA require Mg2+ ions not only for catalysis but also to bind DNA. Binding studies often employ Ca2+ as a substitute for Mg2+, to promote DNA binding whilst disallowing catalysis. The SfiI endonuclease requires divalent metal ions to bind DNA but, in contrast to many systems where Ca2+ mimics Mg2+, Ca2+ causes SfiI to bind DNA almost irreversibly. Equilibrium binding by wild-type SfiI cannot be conducted with Mg2+ present as the DNA is cleaved so, to study the effect of Mg2+ on DNA binding, two catalytically-inactive mutants were constructed. The mutants bound DNA in the presence of either Ca2+ or Mg2+ but, unlike wild-type SfiI with Ca2+, the binding was reversible. With both mutants, dissociation was slow with Ca2+ but was in one case much faster with Mg2+. Hence, Ca2+ can affect DNA binding differently from Mg2+. Moreover, SfiI is an archetypal system for DNA looping; on DNA with two recognition sites, it binds to both sites and loops out the intervening DNA. While the dynamics of looping cannot be measured with wild-type SfiI and Ca2+, it becomes accessible with the mutant and Mg2+

Measurement of Exclusive rho^0 rho^0 Production in Two-Photon Collisions at High Q^2 at LEP

Exclusive rho rho production in two-photon collisions involving a single highly virtual photon is studied with data collected at LEP at centre-of-mass energies 89GeV < \sqrt{s} < 209GeV with a total integrated luminosity of 854.7pb^-1 The cross section of the process gamma gamma^* -> rho rho is determined as a function of the photon virtuality, Q^2 and the two-photon centre-of-mass energy, Wgg, in the kinematic region: 1.2GeV^2 < Q^2 < 30GeV^2 and 1.1GeV < Wgg < 3GeV

K0s K0s Final State in Two-Photon Collisions and Implications for Glueballs

The K0s K0s final state in two-photon collisions is studied with the L3 detector at LEP. The mass spectrum is dominated by the formation of the f_2'(1525) tensor meson in the helicity-two state with a two-photon width times the branching ratio into K Kbar of 76 +- 6 +- 11 eV. A clear signal for the formation of the f_J(1710) is observed and it is found to be dominated by the spin-two helicity-two state. No resonance is observed in the mass region around 2.2 GeV and an upper limit of 1.4 eV at 95% C.L. is derived for the two-photon width times the branching ratio into K0s K0s for the glueball candidate xi(2230)

Search for Branons at LEP

We search, in the context of extra-dimension scenarios, for the possible existence of brane fluctuations, called branons. Events with a single photon or a single Z-boson and missing energy and momentum collected with the L3 detector in e^+ e^- collisions at centre-of-mass energies sqrt{s}=189-209$ GeV are analysed. No excess over the Standard Model expectations is found and a lower limit at 95% confidence level of 103 GeV is derived for the mass of branons, for a scenario with small brane tensions. Alternatively, under the assumption of a light branon, brane tensions below 180 GeV are excluded

Study of Spin and Decay-Plane Correlations of W Bosons in the e+e- -> W+W- Process at LEP

Data collected at LEP at centre-of-mass energies \sqrt(s) = 189 - 209 GeV are used to study correlations of the spin of W bosons using e+e- -> W+W- -> lnqq~ events. Spin correlations are favoured by data, and found to agree with the Standard Model predictions. In addition, correlations between the W-boson decay planes are studied in e+e- -> W+W- -> lnqq~ and e+e- -> W+W- -> qq~qq~ events. Decay-plane correlations, consistent with zero and with the Standard Model predictions, are measured