Cubic Defects: Comparing the Eight-State-System with its Two-Level-Approximation

Substitutional defects in a cubic symmetry (such as a lithium defect in a KCl host crystal) can be modeled appropriately by an eight-state-system. Usually this tunneling degree of freedom is approximated by a two-level-system. We investigate the observable differences between the two models in three contexts. First we show that the two models predict different relations between the temperature dependence of specific heat and static susceptibility. Second we demonstrate that in the presence of external forces (pressure and electric field) the eight-state-system shows features that cannot be understood within the framework of the two-level-approximation. In this context we propose an experiment for measuring the parameter for tunneling along the face diagonal. Finally we discuss the differences between the models appearing for strongly coupled pairs. Geometric selection rules and particular forms of asymmetry lead to clear differences between the two models.Comment: 19 pages, Latex, submitted to J. of Phys., some small supplement

Elastic response of [111]-tunneling impurities

We study the dynamic response of a [111] quantum impurity, such as lithium or cyanide in alkali halides, with respect to an external field coupling to the elastic quadrupole moment. Because of the particular level structure of a eight-state system on a cubic site, the elastic response function shows a biexponential relaxation feature and a van Vleck type contribution with a resonance frequency that is twice the tunnel frequency $\Delta/\hbar$. This basically differs from the dielectric response that does not show relaxation. Moreover, we show that the elastic response of a [111] impurity cannot be reduced to that of a two-level system. In the experimental part, we report on recent sound velocity and internal friction measurements on KCl doped with cyanide at various concentrations. At low doping (45 ppm) we find the dynamics of a single [111] impurity, whereas at higher concentrations (4700 ppm) the elastic response rather indicates strongly correlated defects. Our theoretical model provides a good description of the temperature dependence of $\delta v/v$ and $Q^{-1}$ at low doping, in particular the relaxation peaks, the absolute values of the amplitude, and the resonant contributions. From our fits we obtain the value of the elastic deformation potential $\gamma_t=0.192$ eV.Comment: 19 pages, 5 figure

Radical-induced purine lesion formation is dependent on DNA helical topology

AbstractHerein we report the quantification of purine lesions arising from gamma-radiation sourced hydroxyl radicals (HO•) on tertiary dsDNA helical forms of supercoiled (SC), open circular (OC), and linear (L) conformation, along with single-stranded folded and non-folded sequences of guanine-rich DNA in selected G-quadruplex structures. We identify that DNA helical topology and folding plays major, and unexpected, roles in the formation of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG) and 8-oxo-7,8-dihydro-2'-deoxyadenosine (8-oxo-dA), along with tandem-type purine lesions 5′,8-cyclo-2′-deoxyguanosine (5′,8-cdG) and 5′,8-cyclo-2′-deoxyadenosine (5′,8-cdA). SC, OC, and L dsDNA conformers together with folded and non-folded G-quadruplexes d[TGGGGT]4 (TG4T), d[AGGG(TTAGGG)3] (Tel22), and the mutated tel24 d[TTGGG(TTAGGG)3A] (mutTel24) were exposed to HO• radicals and purine lesions were then quantified via stable isotope dilution LC-MS/MS analysis. Purine oxidation in dsDNA follows L > OC ≫ SC indicating ..

Biomimetic Models of Radical Stress and Related Biomarkers

The biological consequences of free radical production is the central subject of a very lively scientific debate, focusing on the estimation of the type and extent of damage, as well as the efficiency of the protective and repair systems. When studying free radical based chemical mechanisms, it is very important to establish biomimetic models, which allow the experiments to be performed in a simplified environment, but suitably designed to be in strict connection with cellular conditions. The biomimetic modeling approach has been coupled with physical organic chemistry methodologies and knowledge of free radical reactivity. Molecular basis of important processes have been identified, building up molecular libraries of products concerning unsaturated lipids, sulfur-containing proteins and nucleic acids, to be developed as biomarkers. Ongoing projects in our group deal with lipidomics, genomics and proteomics of free radical stress and some examples will be described

A 5\u27, 8-cyclo-2\u27-deoxypurine lesion induces trinucleotide repeat deletion via a unique lesion bypass by DNA polymerase β.

5′,8-cyclo-2′-deoxypurines (cdPus) are common forms of oxidized DNA lesions resulting from endogenous and environmental oxidative stress such as ionizing radiation. The lesions can only be repaired by nucleotide excision repair with a low efficiency. This results in their accumulation in the genome that leads to stalling of the replication DNA polymerases and poor lesion bypass by translesion DNA polymerases. Trinucleotide repeats (TNRs) consist of tandem repeats of Gs and As and therefore are hotspots of cdPus. In this study, we provided the first evidence that both (5′R)- and (5′S)-5′,8-cyclo-2′-deoxyadenosine (cdA) in a CAG repeat tract caused CTG repeat deletion exclusively during DNA lagging strand maturation and base excision repair. We found that a cdA induced the formation of a CAG loop in the template strand, which was skipped over by DNA polymerase β (pol β) lesion bypass synthesis. This subsequently resulted in the formation of a long flap that was efficiently cleaved by flap endonuclease 1, thereby leading to repeat deletion. Our study indicates that accumulation of cdPus in the human genome can lead to TNR instability via a unique lesion bypass by pol β

New insights into the reaction paths of hydroxyl radicals with purine moieties in DNA and double-stranded oligodeoxynucleotides

The reaction of hydroxyl radical (HO•) with DNA produces many primary reactive species and many lesions as final products. In this study, we have examined the optical spectra of intermediate species derived from the reaction of HO• with a variety of single- and double-stranded oligodeoxynucleotides and ct-DNA in the range of 1 µs to 1 ms by pulse radiolysis using an Intensified Charged Coupled Device (ICCD) camera. Moreover, we applied our published analytical protocol based on an LC-MS/MS system with isotopomeric internal standards to enable accurate and precise measurements of purine lesion formation. In particular, the simultaneous measurement of the four purine 50,8-cyclo-20-deoxynucleosides (cPu) and two 8-oxo-7,8-dihydro-20-deoxypurine (8-oxo-Pu) was obtained upon reaction of genetic material with HO• radicals generated either by γ-radiolysis or Fenton-type reactions. Our results contributed to the debate in the literature regarding absolute level of lesions, method of HO• radical generation, 50R/50S diastereomeric ratio in cPu, and relative abundance between cPu and 8-oxo-Pu.Fil: Chatgilialoglu, Chryssostomos. Istituto Per la Sintesi Organica E la Fotoreattivita, Bologna; ItaliaFil: Krokidis, Marios G.. Consiglio Nazionale delle Ricerche; ItaliaFil: Masi, Annalisa. Consiglio Nazionale delle Ricerche; ItaliaFil: Barata Vallejo, Sebastian. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay; ArgentinaFil: Ferreri, Carla. Consiglio Nazionale delle Ricerche; ItaliaFil: Terzidis, Michael A.. Consiglio Nazionale delle Ricerche; ItaliaFil: Szreder, Tomasz. Institute of Nuclear Chemistry and Technology; PoloniaFil: Bobrowski, Krzysztof. Institute of Nuclear Chemistry and Technology; Poloni

Supported Gold Nanoparticle-Catalyzed Selective Reduction of Multifunctional, Aromatic Nitro Precursors into Amines and Synthesis of 3,4-Dihydroquinoxalin-2-Ones

The synthesis of 3,4-dihydroquinoxalin-2-ones via the selective reduction of aromatic, multifunctional nitro precursors catalyzed by supported gold nanoparticles is reported. The reaction proceeds through the in situ formation of the corresponding amines under heterogeneous transfer hydrogenation of the initial nitro compounds catalyzed by the commercially available Au/TiO2-Et3SiH catalytic system, followed by an intramolecular C-N transamidation upon treatment with silica acting as a mild acid. Under the present conditions, the Au/TiO2-TMDS system was also found to catalyze efficiently the present selective reduction process. Both transfer hydrogenation processes showed very good functional-group tolerance and were successfully applied to access more structurally demanding products bearing other reducible moieties such as chloro, aldehyde or methyl ketone. An easily scalable (up to 1 mmol), low catalyst loading (0.6 mol%) synthetic protocol was realized, providing access to this important scaffold. Under these mild catalytic conditions, the desired products were isolated in good to high yields and with a TON of 130. A library analysis was also performed to demonstrate the usefulness of our synthetic strategy and the physicochemical profile of the derivatives

Dynamical models for sand ripples beneath surface waves

We introduce order parameter models for describing the dynamics of sand ripple patterns under oscillatory flow. A crucial ingredient of these models is the mass transport between adjacent ripples, which we obtain from detailed numerical simulations for a range of ripple sizes. Using this mass transport function, our models predict the existence of a stable band of wavenumbers limited by secondary instabilities. Small ripples coarsen in our models and this process leads to a sharply selected final wavenumber, in agreement with experimental observations.Comment: 9 pages. Shortened version of previous submissio

Design agency:prototyping multi-agent systems in architecture

This paper presents research on the prototyping of multi-agent systems for architectural design. It proposes a design exploration methodology at the intersection of architecture, engineering, and computer science. The motivation of the work includes exploring bottom up generative methods coupled with optimizing performance criteria including for geometric complexity and objective functions for environmental, structural and fabrication parameters. The paper presents the development of a research framework and initial experiments to provide design solutions, which simultaneously satisfy complexly coupled and often contradicting objectives. The prototypical experiments and initial algorithms are described through a set of different design cases and agents within this framework; for the generation of façade panels for light control; for emergent design of shell structures; for actual construction of reciprocal frames; and for robotic fabrication. Initial results include multi-agent derived efficiencies for environmental and fabrication criteria and discussion of future steps for inclusion of human and structural factors