Three-body recombination in ultracold systems: Prediction of weakly-bound atomic trimer energies

The three-body recombination coefficient of an ultracold atomic system, together with the corresponding two-body scattering length a, allow us to predict the energy E 3 of the shallow trimer bound state, using a universal scaling function. The production of dimers in trapped Bose-Einstein condensates, from three-body recombination processes, in the regime of short magnetic pulses near a Feshbach resonance, is also studied in line with the experimental observation.

BF Integrase Genes of HIV-1 Circulating in Sao Paulo, Brazil, with a Recurrent Recombination Region

Although some studies have shown diversity in HIV integrase (IN) genes, none has focused particularly on the gene evolving in epidemics in the context of recombination. The IN gene in 157 HIV-1 integrase inhibitor-naive patients from the Sao Paulo State, Brazil, were sequenced tallying 128 of subtype B (23 of which were found in non-B genomes), 17 of subtype F (8 of which were found in recombinant genomes), 11 integrases were BF recombinants, and 1 from subtype C. Crucially, we found that 4 BF recombinant viruses shared a recurrent recombination breakpoint region between positions 4900 and 4924 (relative to the HXB2) that includes 2 gRNA loops, where the RT may stutter. Since these recombinants had independent phylogenetic origin, we argue that these results suggest a possible recombination hotspot not observed so far in BF CRF in particular, or in any other HIV-1 CRF in general. Additionally, 40% of the drug-naive and 45% of the drug-treated patients had at least 1 raltegravir (RAL) or elvitegravir (EVG) resistance-associated amino acid change, but no major resistance mutations were found, in line with other studies. Importantly, V151I was the most common minor resistance mutation among B, F and BF IN genes. Most codon sites of the IN genes had higher rates of synonymous substitutions (dS) indicative of a strong negative selection. Nevertheless, several codon sites mainly in the subtype B were found under positive selection. Consequently, we observed a higher genetic diversity in the B portions of the mosaics, possibly due to the more recent introduction of subtype F on top of an ongoing subtype B epidemics and a fast spread of subtype F alleles among the B population.

Relationship between B-Cell-specific moloney murine leukemia virus integration site 1 (BMI-1) and homologous recombination regulatory genes in invasive ductal breast carcinomas

B-cell-specific Moloney murine leukemia virus integration site 1 (Bmi-1) is a Polycomb group protein that is able to induce telomerase activity, enabling the immortalization of epithelial cells. Immortalized cells are more susceptible to double-strand breaks (DSB), which are subsequently repaired by homologous recombination (HR). BRCA1 is among the HR regulatory genes involved in the response to DNA damage associated with the RAD51 protein, which accumulates in DNA damage foci after signaling H2AX, another important marker of DNA damage. Topoisomerase III beta (topoIII beta) removes HR intermediates before chromosomal segregation, preventing damage to cellular DNA structure. In breast carcinomas positive for BMI-1 the role of proteins involved in HR remains to be investigated. The aim of this study was to evaluate the association between BMI-1 and homologous recombination proteins. Using tissue microarrays containing 239 cases of primary breast tumors, the expression of Bmi-1, BRCA-1, H2AX, Rad51, p53, Ki-67, topoIII beta, estrogen receptors (ER), progesterone receptors (PR), and HER-2 was analyzed by immunohistochemistry. We observed high Bmi-1 expression in 66 cases (27.6%). Immunohistochemical overexpression of BMI-1 was related to ER (p=0.004), PR (p<0.001), Ki-67 (p<0.001), p53 (p=0.003), BRCA1 (p=0.003), H2AX (p=0.024) and topoIII beta (p<0,001). Our results show a relationship between the expression of BMI-1 and HR regulatory genes, suggesting that Bmi-1 overexpression might be an important event in HR regulation. However, further studies are necessary to understand the mechanisms in which Bmi-1 could regulate HR pathways in invasive ductal breast carcinomas.

Dependence of Generation-Recombination Noise With Gate Voltage in FD SOI MOSFETs

A model for computing the generation-recombination noise due to traps within the semiconductor film of fully depleted silicon-on-insulator MOSFET transistors is presented. Dependence of the corner frequency of the Lorentzian spectra on the gate voltage is addressed in this paper, which is different to the constant behavior expected for bulk transistors. The shift in the corner frequency makes the characterization process easier. It helps to identify the energy position, capture cross sections, and densities of the traps. This characterization task is carried out considering noise measurements of two different candidate structures for single-transistor dynamic random access memory devices.

Autoionizing states and their relevance in electron-ion recombination

Atomic physics plays an important role in determining the evolution stages in a wide range of laboratory and cosmic plasmas. Therefore, the main contribution to our ability to model, infer and control plasma sources is the knowledge of underlying atomic processes. Of particular importance are reliable low temperature dielectronic recombination (DR) rate coefficients. This thesis provides systematically calculated DR rate coefficients of lithium-like beryllium and sodium ions via ∆n = 0 doubly excited resonant states. The calculations are based on complex-scaled relativistic many-body perturbation theory in an all-order formulation within the single- and double-excitation coupled-cluster scheme, including radiative corrections. Comparison of DR resonance parameters (energy levels, autoionization widths, radiative transition probabilities and strengths) between our theoretical predictions and the heavy-ion storage rings experiments (CRYRING-Stockholm and TSRHeidelberg) shows good agreement. The intruder state problem is a principal obstacle for general application of the coupled-cluster formalism on doubly excited states. Thus, we have developed a technique designed to avoid the intruder state problem. It is based on a convenient partitioning of the Hilbert space and reformulation of the conventional set of pairequations. The general aspects of this development are discussed, and the effectiveness of its numerical implementation (within the non-relativistic framework) is selectively illustrated on autoionizing doubly excited states of helium.

Charge generation, transport and recombination in organic solar cells

This thesis presents a study of the charge generation, transport, and recombination processes in organic solar cells performed with time-resolved experimental techniques. Organic solar cells based on polymers can be solution-processed on large areas and thus promise to become an inexpensive source of renewable energy. Despite significant improvements of the power conversion efficiency over the last decade, the fundamental working principles of organic solar cells are still not fully understood. It is the aim of this thesis to clarify the role of different performance limiting processes in organic solar cells and to correlate them with the molecular structure of the studied materials, i.e. poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl C61 butyric acid methyl ester (PCBM). By combining time-of-flight charge transport measurements, transient absorption spectroscopy, a newly developed experimental technique called time delayed double pulse experiment and drift-diffusion simulations a comprehensive analysis of the working principles of P3HT:PCBM solar cells could be performed. It was found that the molecular structure of P3HT (i.e. the regioregularity) has a pronounced influence on the morphology of thin films of pristine P3HT and of blends of P3HT with PCBM. This morphology in turn affected the charge transport properties as well as the charge generation and recombination kinetics. Well-ordered regioregular P3HT was found to be characterized by a high charge carrier mobility, efficient charge generation and low but field-dependent (non-geminate) recombination. Importantly, the charge generation yield was found to be independent of temperature and applied electric field as opposed to the expectations of the Onsager-Braun model that is commonly applied to describe the temperature and field dependence of charge generation in organic solar cells. These properties resulted in a reasonably good power conversion efficiency. In contrast to this, amorphous regiorandom P3HT was found to show poor charge generation, transport and recombination properties that combine to a much lower power conversion efficiency.

Mechanistic study of cell death induction by O 6-methylating agents, focusing on the role of homologous recombination as a molecular target for sensitization of tumor cells to chemotherapeutic alkylating agents

Chemotherapeutic SN1‑methylating agents are important anticancer drugs. They induce several covalent modifications in the DNA, from which O6‑methylguanine (O6MeG) is the main toxic lesion. In this work, different hypotheses that have been proposed to explain the mechanism of O6MeG‑triggered cell death were tested. The results of this work support the abortive processing model, which states that abortive post‑replicative processing of O6MeG‑driven mispairs by the DNA mismatch repair (MMR) machinery results in single‑strand gaps in the DNA that, upon a 2nd round of DNA replication, leads to DNA double‑strand break (DSB) formation, checkpoint activation and cell death. In this work, it was shown that O6MeG induces an accumulation of cells in the 2nd G2/M‑phase after treatment. This was accompanied by an increase in DSB formation in the 2nd S/G2/M‑phase, and paralleled by activation of the checkpoint kinases ATR and CHK1. Apoptosis was activated in the 2nd cell cycle. A portion of cells continue proliferating past the 2nd cell cycle, and triggers apoptosis in the subsequent generations. An extension to the original model is proposed, where the persistence of O6MeG in the DNA causes new abortive MMR processing in the 2nd and subsequent generations, where new DSB are produced triggering cell death. Interestingly, removal of O6MeG beyond the 2nd generation lead to a significant, but not complete, reduction in apoptosis, pointing to the involvement of additional mechanisms as a cause of apoptosis. We therefore propose that an increase in genomic instability resulting from accumulation of mis‑repaired DNA damage plays a role in cell death induction. Given the central role of DSB formation in toxicity triggered by chemotherapeutic SN1‑alkylating agents, it was aimed in the second part of this thesis to determine whether inhibition of DSB repair by homologous recombination (HR) or non‑homologous end joining (NHEJ) is a reasonable strategy for sensitizing glioblastoma cells to these agents. The results of this work show that HR down‑regulation in glioblastoma cells impairs the repair of temozolomide (TMZ)‑induced DSB. HR down‑regulation greatly sensitizes cells to cell death following O6‑methylating (TMZ) or O6‑chlorethylating (nimustine) treatment, but not following ionizing radiation. The RNAi mediated inhibition in DSB repair and chemo‑sensitization was proportional to the knockdown of the HR protein RAD51. Chemo‑sensitization was demonstrated for several HR proteins, in glioma cell lines proficient and mutated in p53. Evidence is provided showing that O6MeG is the primary lesion responsible for the increased sensitivity of glioblastoma cells following TMZ treatment, and that inhibition of the resistance marker MGMT restores the chemo‑sensitization achieved by HR down‑regulation. Data are also provided to show that inhibition of DNA‑PK dependent NHEJ does not significantly sensitized glioblastoma cells to TMZ treatment. Finally, the data also show that PARP inhibition with olaparib additionally sensitized HR down‑regulated glioma cells to TMZ. Collectively, the data show that processing of O6MeG through two rounds of DNA replication is required for DSB formation, checkpoint activation and apoptosis induction, and that O6MeG‑triggered apoptosis is also executed in subsequent generations. Furthermore, the data provide proof of principle evidence that down‑regulation of HR is a reasonable strategy for sensitizing glioma cells to killing by O6‑alkylating chemotherapeutics.

Charge generation and recombination in hybrid organic,inorganic solar cells

This thesis deals with the investigation of exciton and charge dynamics in hybrid solar cells by time-resolved optical spectroscopy. Quasi-steady-state and transient absorption spectroscopy, as well as time-resolved photoluminescence spectroscopy, were employed to study charge generation and recombination in solid-state organic dye-sensitized solar cells, where the commonly used liquid electrolyte is replaced by an organic solid hole transporter, namely 2,2′7,7′-tetrakis-(N,N-di-p-methoxyphenyl-amine)-9,9′-spirobifluorene (spiro-MeOTAD), and polymer-metal oxide bulk heterojunction solar cells, where the commonly used fullerene acceptor [6,6]-phenyl C61 butyric acid methyl ester (PCBM) is replaced by zinc oxide (ZnO) nanoparticles. By correlating the spectroscopic results with the photovoltaic performance, efficiency-limiting processes and processes leading to photocurrent generation in the investigated systems are revealed. rnIt is shown that the charge generation from several all-organic donor-π-bridge-acceptor dyes, specifically perylene monoimide derivatives, employed in solid-state dye-sensitized solar cells, is strongly dependent on the presence of a commonly used additive lithium bis(trifluoromethanesulphonyl)imide salt (Li-TFSI) at the interface. rnMoreover, it is shown that charges can not only be generated by electron injection from the excited dye into the TiO2 acceptor and subsequent regeneration of the dye cation by the hole transporter, but also by an alternative mechanism, called preceding hole transfer (or reductive quenching). Here, the excited dye is first reduced by the hole transporter and the thereby formed anion subsequently injects an electron into the titania. This additional charge generation process, which is only possible for solid hole transporters, helps to overcome injection problems. rnHowever, a severe disadvantage of solid-state dye-sensitized solar cells is re-vealed by monitoring the transient Stark effect on dye molecules at the inter-face induced by the electric field between electrons and holes. The attraction between the negative image charge present in TiO2, which is induced by the positive charge carrier in the hole transporter due to the dielectric contrast between the organic spiro-MeOTAD and inorganic titania, is sufficient to at-tract the hole back to the interface, thereby increasing recombination and suppressing the extraction of free charges.rnBy investigating the effect of different dye structures and physical properties on charge generation and recombination, design rules and guidelines for the further advancement of solid-state dye-sensitized solar cells are proposed.rnFinally, a spectroscopic study on polymer:ZnO bulk heterojunction hybrid solar cells, employing different surfactants attached to the metal oxide nanoparticles, was performed to understand the effect of surfactants upon photovoltaic behavior. By applying a parallel pool analysis on the transient absorption data, it is shown that suppressing fast recombination while simultaneously maintaining the exciton splitting efficiency by the right choice of surfactants leads to better photovoltaic performances. Suppressing the fast recombination completely, whilst maintaining the exciton splitting, could lead to a doubling of the power conversion efficiency of this type of solar cell.

Charge separation and recombination in novel polymeric absorber materials for organic solar cells : a photophysical study

In dieser Dissertation wird die Ladungsträgergeneration und -rekombination in neuen polymeren Absorbermaterialien für organische Solarzellen untersucht. Das Verständnis dieser Prozesse ist wesentlich für die Entwicklung neuer photoaktiver Materialsysteme, die hohe Effizienzen erzielen und organische Solarzellen konkurrenzfähig im Bereich der erneuerbaren Energien machen. Experimentell verwendet diese Arbeit hauptsächlich die Methode der transienten Absorptionsspektroskopie, die sich für die Untersuchung photophysikalischer Prozesse auf einer Zeitskala von 100 fs bis 1 ms als sehr leistungsfähig erweist. Des Weiteren wird eine soft-modeling Methode vorgestellt, die es ermöglicht, photophysikalische Prozesse aus einer gemessenen transienten Absorptions-Datenmatrix zu bestimmen, wenn wenig a priori Kenntnisse der Reaktionskinetiken vorhanden sind. Drei unterschiedliche Donor:Akzeptor-Systeme werden untersucht; jedes dieser Systeme stellt eine andere Herangehensweise zur Optimierung der Materialien dar in Bezug auf Lichtabsorption über einen breiten Wellenlängenbereich, effiziente Ladungstrennung und schnellen Ladungstransport. Zuerst wird ein Terpolymer untersucht, das aus unterschiedlichen Einheiten für die Lichtabsorption und den Ladungstransport besteht. Es wird gezeigt, dass es möglich ist, den Fluss angeregter Zustände vom Chromophor auf die Transporteinheit zu leiten. Im zweiten Teil wird der Einfluss von Kristallinität auf die freie Ladungsträgergeneration mit einer Folge von ternären Mischungen, die unterschiedliche Anteile an amorphem und semi-kristallinem Polymer enthalten, untersucht. Dabei zeigt es sich, dass mit steigendem amorphen Polymeranteil sowohl der Anteil der geminalen Ladungsträgerrekombination erhöht als auch die nicht-geminale Rekombination schneller ist. Schlussendlich wird ein System untersucht, in dem sowohl Donor als auch Akzeptor Polymere sind, was zu verbesserten Absorptionseigenschaften führt. Die Rekombination von Ladungstransferzuständen auf der unter 100 ps Zeitskala stellt hier den hauptsächliche Verlustkanal dar, da freie Ladungsträger nur an Grenzflächen erzeugt werden können, an denen Donor und Akzeptor face-to-face zueinander orientiert sind. Darüber hinaus wird festgestellt, dass weitere 40-50% der Ladungsträger durch die Rekombination von Grenzflächenzuständen verloren gehen, die aus mobilen Ladungsträgern geminal gebildet werden.

Charge generation and recombination in solid-state dye-sensitized solar cells

Diese Doktorarbeit befasst sich mit Ladungsgeneration und – rekombination in Feststoff-Farbstoffsolarzellen, die spiro-OMeTAD als Lochleiter verwenden. Die vorliegende Arbeit ist in drei Fallstudien unterteilt: i.) Kern-erweiterte Rylen-Farbstoffe, ii.) ein Perylenmonoimid-Farbstoff und iii.) Donor-π verbrückte (Cyclopentadithiophen)-Akzeptor-Farbstoffe. Trotz ihres hohen molaren Extinktionskoeffizienten und der hohen Absorbanz der sensibilisierten Filme, zeigen einige dieser Farbstoffmoleküle nur geringe photovoltaischen Effizienzen. Um den Ursprung des geringen Wirkungsgrades herauszufinden, wurde breitbandige, ultraschnelle transiente Absorptionsspektroskopie an Solarzellen durchgeführt.rnInsbesondere die Auswirkungen verschiedender Ankergruppen, Dipolmomente, Photolumineszenzlebenszeiten, Lithium-Kationensensitivität und Ladungsträgerdynamik, die alle einen großen Einfluss auf den Wirkungsgrad der Solarzelle besitzen, wurden untersucht. In der ersten Fallstudie zeigte ein kurzer Rylen-Farbstoff aufgrund deutlich verlängerter Lebenszeiten die beste Effizienz im Vergleich zu größeren Kern-erweiterten Rylen-Farbstoffen. Die Lebenszeit wurde weiter reduziert, wenn Maleinsäure als Ankergruppe unter einer Ringöffnungsreaktion an die mesoporöse Oberfläche des Metalloxid-Halbleiters adsorbierte. Dies konnte mit Hilfe von Berechnungen mittels der Dichtefunktionaltheorie (DFT, B3LYP) auf die Differenz des Dipolmoments zwischen Grundzustand und angeregtem Zustand zurückgeführt werden. Die Berechnungen bekräftigen die unvorteilhafte Injektion von Ladungen durch die Änderung der Richtung des Dipolmoments, wenn eine Ringöffnung der Anhydridgruppe stattfindet. In der zweiten Studie zeigte das Perylenmonoimid-Derivat ID889 einen Wirkungsgrad von 4.5% in Feststoff-Farbstoffsolarzellen, wobei ID889 sogar ohne Zuhilfenahme eines Additivs in der Lage ist langlebige Farbstoffkationen zu bilden. Die Verwendung von Lithium-Kationen stabilisiert jedoch sowohl den Prozess der Ladungsgeneration als auch den der Ladungsregeneration. Des Weiteren wurde in ID889-sensitivierten Bauteilen kein reduktives Löschen beobachtet. Dabei wurde die Dynamik der Exzitonen mittels einer soft-modelling Methode Kurvenanalyse aus den Daten der transienten Absorptionsspektroskopie gewonnen. Zuletzt wurden Strukturen mit Cyclopentadithiophen(CPDT)-Baustein untersucht, die eine typische D-π-A Molekülstruktur bilden. FPH224 und 233 zeigten dabei eine bessere Effizienz als FPH231 und 303 aufgrund einer großen Injektionseffizienz (IE) und längerer Lebenszeit der angeregten Zustände. Dies kann auf reduktives Löschen in FPH231 und 303 zurückgeführt werden, wohingegen FPH224 und 233 einen moderaten Zerfall des Spirokationensignals zeigten.

MET inhibition in tumor cells by PHA665752 impairs homologous recombination repair of DNA double strand breaks

Abnormal activation of cellular DNA repair pathways by deregulated signaling of receptor tyrosine kinase systems has broad implications for both cancer biology and treatment. Recent studies suggest a potential link between DNA repair and aberrant activation of the hepatocyte growth factor receptor Mesenchymal-Epithelial Transition (MET), an oncogene that is overexpressed in numerous types of human tumors and considered a prime target in clinical oncology. Using the homologous recombination (HR) direct-repeat direct-repeat green fluorescent protein ((DR)-GFP) system, we show that MET inhibition in tumor cells with deregulated MET activity by the small molecule PHA665752 significantly impairs in a dose-dependent manner HR. Using cells that express MET-mutated variants that respond differentially to PHA665752, we confirm that the observed HR inhibition is indeed MET-dependent. Furthermore, our data also suggest that decline in HR-dependent DNA repair activity is not a secondary effect due to cell cycle alterations caused by PHA665752. Mechanistically, we show that MET inhibition affects the formation of the RAD51-BRCA2 complex, which is crucial for error-free HR repair of double strand DNA lesions, presumably via downregulation and impaired translocation of RAD51 into the nucleus. Taken together, these findings assist to further support the role of MET in the cellular DNA damage response and highlight the potential future benefit of MET inhibitors for the sensitization of tumor cells to DNA damaging agents.

Selection and recombination drive the evolution of MHC class II DRB diversity in ungulates

Major histocompatibility complex (MHC) antigen-presenting genes are the most variable loci in vertebrate genomes. Host-parasite co-evolution is assumed to maintain the excessive polymorphism in the MHC loci. However, the molecular mechanisms underlying the striking diversity in the MHC remain contentious. The extent to which recombination contributes to the diversity at MHC loci in natural populations is still controversial, and there have been only few comparative studies that make quantitative estimates of recombination rates. In this study, we performed a comparative analysis for 15 different ungulates species to estimate the population recombination rate, and to quantify levels of selection. As expected for all species, we observed signatures of strong positive selection, and identified individual residues experiencing selection that were congruent with those constituting the peptide-binding region of the human DRB gene. However, in addition for each species, we also observed recombination rates that were significantly different from zero on the basis of likelihood-permutation tests, and in other non-quantitative analyses. Patterns of synonymous and non-synonymous sequence diversity were consistent with differing demographic histories between species, but recent simulation studies by other authors suggest inference of selection and recombination is likely to be robust to such deviations from standard models. If high rates of recombination are common in MHC genes of other taxa, re-evaluation of many inference-based phylogenetic analyses of MHC loci, such as estimates of the divergence time of alleles and trans-specific polymorphism, may be required.