Multiscale approach to radiation damage induced by ion beams: complex DNA damage and effects of thermal spikes

We present the latest advances of the multiscale approach to radiation damage caused by irradiation of a tissue with energetic ions and report the calculations of complex DNA damage and the effects of thermal spikes on biomolecules. The multiscale approach aims to quantify the most important physical, chemical, and biological phenomena taking place during and following irradiation with ions and provide a better means for clinically-necessary calculations with adequate accuracy. We suggest a way of quantifying the complex clustered damage, one of the most important features of the radiation damage caused by ions. This quantification allows the studying of how the clusterization of DNA lesions affects the lethality of damage. We discuss the first results of molecular dynamics simulations of ubiquitin in the environment of thermal spikes, predicted to occur in tissue for a short time after an ion’s passage in the vicinity of the ions’ tracks.     

Molecular dynamics study of structural damage in amorphous silica induced by swift heavy-ion radiation

In this paper, the radiation defects induced by the swift heavy ions and the recoil atoms in amorphous SiO₂ were studied. The energy of recoil atoms induced by the incident Au ions in SiO₂ was calculated by using Monte Carlo method. Results show that the average energies of recoils reach the maximum (200?eV for Si and 130?eV for O, respectively) when the incident energy of Au ion is 100?MeV. Using Tersoff/zbl potential with the newly built parameters, the defects formation processes in SiO₂ induced by the recoils were studied by using molecular dynamics method. The displacement threshold energies (E_d) for Si and O atoms are found to be 33.5 and 16.3?eV, respectively. Several types of under- and over-coordinated Si and O defects were analyzed. The results demonstrate that Si₃, Si₅, and O₁ are the mainly defects in SiO₂ after radiation. Besides, the size of cylindrical damage region produced by a single recoil atom was calculated. The calculation shows that the depth and the radius are up to 2.0 and 1.4?nm when the energy of recoils is 200?eV. Finally, it is estimated that the Au ion would induce a defected track with a diameter of 4?nm in SiO₂.     

Acoustic impedance changes in cartilage and subchondral bone due to primary arthrosis

This study aimed at assessing elastic changes of cartilage and subchondral bone in sections from osteoarthritic human tibia plateaus using a 50-MHz scanning acoustic microscope (SAM). Samples were obtained from 28 human individuals during alloplastic implant surgery. Sagittal sections were explored using a time-resolved acoustic microscope in hyperosmolar (2.5 molar) saline solution at 25 degrees C. Cartilage and bone impedance distributions were evaluated as a function of the distance to the cartilage-bone interface. The degree of cartilage degeneration was derived from histological and immunohistochemical analyses. The mean impedance value in cartilage was 2.12+/-0.02 Mrayl. The layered cartilage structure was revealed by means of distinctly different impedance values in most samples. Generally, values were higher close to the bone interface and decreased continuously towards the cartilage surface. Higher grades of degeneration show a loss of the layered structure and remarkable cartilage surface undulations. The mean impedance value in subchondral bone was 6.28+/-0.54 Mrayl. A significant increase of the acoustic impedance within the first 150 microm relative to cartilage-bone interface was observed in 65.5% of the investigated sections. We hypothesize that the impedance increase close to the bone cartilage boundary is an indicator for subchondral sclerosis.     

Enhanced photocatalytic activity of ultra-high aspect ratio ZnO nanowires due to Cu induced defects

We report the synthesis of ZnO nanowires in ambient air at 650°C by a single-step vapor transport method using two different sources Zn (ZnO nanowires-I) and Zn:Cu (ZnO nanowires-II). The Zn:Cu mixed source co-vaporize Zn with a small amount of Cu at temperatures where elemental Cu source does not vaporize. This method provides us a facile route for Cu doping into ZnO. The aspect ratio of the grown ZnO nanowires-II was found to be higher by more than five times compared ZnO nanowires-I. Photocatalytic activity was measured by using a solar simulator and its ultraviolet-filtered light. The ZnO nanowires-II shows higher catalytic activity due to increased aspect ratio and higher content of surface defects because of incorporation of Cu impurities.     

Thickness induced structural changes in polystyrene films

Changes to the structure of polystyrene melt films as measured through the spectrum of density fluctuations have been observed as a function of film thickness down to the polymer radius of gyration (Rg). Films thicker than 4Rg show bulklike density fluctuations. Thinner films exhibit a peak in S(q) near q=0 which grows with decreasing thickness. This peak is attributed to a decreased interpenetration of chains resulting in an enhanced compressibility. Measurements were made using small angle x-ray scattering in a standing wave geometry designed to enhance scattering from the interior of the film compared to interface scattering.     

DNA damage induced by laser-hematoporphyrin derivative

Irradiation caused DNA single-strand breaks in S180 cells in the presence oflaser-hematoporphyrin derivative(HPD).The number of single strand breaks was 3.69 ×10~(10)break dolton~(-1).The analysis of base composition of DNA showed that the effect of laser-HPDirradiation on guanine was the highest,being 5-12 times as high as those of the three others(adenine,cytosine and thymine).It was different from the nature of DNA damage caused by γ-ray irradiation.     

A fluorescence based assay for DNA damage induced by radiation,chemical mutagens and enzymes

A simple and rapid assay to detect DNA damage is reported. This novel assay is based on changes in melting/annealing behavior and facilitated using certain dyes that increase their fluorescence upon association with double stranded (ds)DNA. Damage caused by ultraviolet (UV) radiation, chemical mutagens or restriction enzymes produced an assay response. UV radiation at 254 nm (approximating UV-C) and 360 nm (approximating UV-A) were used to induce the damage in dsDNA. Chemical damage was induced using several compounds with known effects on nucleic acids. Restriction enzymes Hind III, Msp1, Sau 3A1 were used to cut the plasmid (pUC19) at specific sequences in addition to the non-specific endonuclease DNase I. The effects of these types of damage on repeated melting and annealing of dsDNA were observed in real time using several fluorescence indicator dyes. Low concentrations of dsDNA (between 10 and 100 ng/ml) and small volumes (20 μl) were required for this assay. Repeated measures yielded a coefficient of variation of 2% (CV%). In addition to measuring various DNA damaging agents, the potential application of this assay to study the efficiency of various sun blocking agents against UV-induced DNA damage is discussed.     

Electronically induced changes in structural properties of solid Kr

Excitation of the electron subsystem is shown to affect the structural properties of solid Kr at low temperatures. An electronically induced stable point defect formation has been observed. Experiments were performed under irradiation by electrons of subthreshold energy. Defects were detected by means of vacuum ultraviolet luminescence spectroscopy. The results obtained reveal an excited-state mechanism of defect formation when the defect is formed during the lifetime of the excited state. Self-trapping of excitons in the long-lived electronic state ³Σ⁺_u is shown to be a stimulating factor.     

Specific radiation damage to acidic residues and its relation to their chemical and structural environment

Intense synchrotron radiation produces specific structural and chemical damage to crystalline proteins even at 100 K. Carboxyl groups of acidic residues (Glu, Asp) losing their definition is one of the major effects observed. Here, the susceptibilities to X‐ray damage of acidic residues in tetrameric malate dehydrogenase from Haloarcula marismortui are investigated. The marked excess of acidic residues in this halophilic enzyme makes it an ideal target to determine how specific damage to acidic residues is related to their structural and chemical environment. Four conclusions are drawn. (i) Acidic residues interacting with the side‐chains of lysine and arginine residues are less affected by radiation damage than those interacting with serine, threonine and tyrosine side‐chains. This suggests that residues with higher pK_a values are more vulnerable to damage than those with a lower pK_a. However, such a correlation was not found when calculated pK_a values were inspected. (ii) Acidic side‐chains located in the enzymatic active site are the most radiation‐sensitive ones. (iii) Acidic residues in the internal cavity formed by the four monomers and those involved in crystal contacts appear to be particularly susceptible. (iv) No correlation was found between radiation susceptibility and solvent accessibility.     

Computational determination of radiation damage effects on DNA structure

Molecular dynamics (MD) studies of several radiation originated lesions on the DNA molecules are presented. The pyrimidine lesions (cytosinyl radical, thymine dimer, thymine glycol) and purine lesion (8-oxoguanine) were subjected to the MD simulations for several hundred picoseconds using MD simulation code AMBER 5.0 (4.0). The simulations were performed for fully dissolved solute molecules in water. Significant structural changes in the DNA double helical structure were observed in all cases which may be categorized as: a) the breaking of hydrogen bonds network between complementary bases and resulted opening of the double helix (cytosinyl, radical, 8-oxoguanine); b) the sharp bending of the DNA helix centered at the lesion site (thymine dimer, thymine glycol); and c) the flippingout of adenine on the strand complementary to the lesion (8-oxoguanine). These changes related to the overall collapsing of the double helical structure around the lesion, are expected to facilitate the docking of the repair enzyme into the DNA in the formation of DNA-enzyme complex. The stable DNA-enzyme complex is a necessary condition for the onset of the enzymatic repair process. In addition to structural changes, specific values of electrostatic interaction energy were determined at several lesion sites (thymine dimer, thymine glycol and 8-oxoguanine). This lesion-specific electrostatic energy is a factor that enables repair enzyme to discriminate lesion from the native site during the scanning of the DNA surface.     

Features of structural changes due to the formation of the boride crystal structure in steels

A mechanism of the transformation of crystal lattices of borides under liquid boronizing of steels has been investigated. It has been shown that nonstoichiometric borides with an FeB or Fe₂B structure were the structure-formation element of phases in the hardened layer. The origin of the high rate of the formation of borides at the initial stage of chemical-thermal treatment at 800–1100°C has been elucidated. It has been established that the transformation of the Fe₂B-FeB lattices was due to the enrichment of the FeB lattice by the boron vacancies.     

Shear flow induced structural changes in polymeric liquid crystals

A conformation tensor rheological model of polymeric liquid crystals is introduced. Both stiff and semiflexible macromolecular chains are considered. Equilibrium and rheological properties implied by the model are derived.     

Gamma radiation induced changes in nuclear waste glass containing Eu

Gamma radiation induced changes were investigated in sodium-barium borosilicate glasses containing Eu. The glass composition was similar to that of nuclear waste glasses used for vitrifying Trombay research reactor nuclear waste at Bhabha Atomic Research Centre, India. Photoluminescence (PL) and electron paramagnetic resonance (EPR) techniques were used to study the speciation of the rare earth (RE) ion in the matrix before and after gamma irradiation. Judd-Ofelt (J-O) analyses of the emission spectra were done before and after irradiation. The spin counting technique was employed to quantify the number of defect centres formed in the glass at the highest gamma dose studied. PL data suggested the stabilisation of the trivalent RE ion in the borosilicate glass matrix both before and after irradiation. It was also observed that, the RE ion distributes itself in two different environments in the irradiated glass. From the EPR data it was observed that, boron oxygen hole centre based radicals are the predominant defect centres produced in the glass after irradiation along with small amount of E’ centres. From the spin counting studies the concentration of defect centres in the glass was calculated to be 350 ppm at 900 kGy. This indicated the fact that bulk of the glass remained unaffected after gamma irradiation up to 900 kGy.     

Anharmonic pulses due to transition radiation

The possibility of using the transition radiation of an electron bunch to generate nonstationary anharmonic pulses in free space and in a dispersive medium is demonstrated. It is shown that the transition radiation of the bunch gives rise to an infinite train of nonstationary anharmonic pulses described by solutions to the Klein-Gordon equation. The polarization of the resulting field at its leading edge appears to be different from the field polarization at the interface. The leading edge becomes steeper with time. It is shown that the bunch density longitudinal distribution and the parameters of the dispersive medium can be determined from the values of the fields and their derivatives near the leading edge of the resulting signal.     

Raman study of activated quasi-modes due to misorientation of ZnO nanowires

We present Raman scattering study of wurtzite ZnO nanowires deposited by metal–organic chemical vapor deposition (MOCVD) on (0001) sapphire. It is shown that the misorientation of the nanowires, i.e. the inclination with respect to the vertical direction, mixes A1 and E1 Raman modes, giving rise to new modes for which the propagation directions make various angles with the C-axis of ZnO nanowires. Two particular bands depending on the tilt of the nanowires are observed at 400 and 585 cm^?1. They are attributed to TO and LO quasi-phonons, and explained using Loudon's model. Morphological information of the nanowires was extracted and an average orientation of nanowires is calculated.     

Computational mechanistic investigation of radiation damage of adenine induced by hydroxyl radicals

The radiation damage of adenine base was studied by B3LYP and MP2 methods in the presence of hydroxyl radicals to probe the reactivities of five possible sites of an isolated adenine molecule. Both methods predict that the C8 site is the more vulnerable than the other sites. For its bonding covalently with the hydroxyl radicals, B3 LYP predicts a barrierless pathway, while MP2 finds a transition state with an energy of 106.1 kJ/mol. For the hydroxylation at the C2 site, the barrier was calculated to be 165.3 k J/mol using MP2 method. For the dehydrogenation reactions at five sites of adenine, B3 LYP method predicts that the free energy barrier decreases in the order of H8 H2 HN62 HN61 HN9.     

Acoustic radiation impedance of duct-nozzle system

A method is described to evaluate the radiation impedance spectra of a duct-nozzle system with and without mean flow by using measured reflection coefficient data. In this method the impedance at the junction of the duct and nozzle is first evaluated by using complex reflection coefficient data measured experimentally with an impulse technique. This impedance is then transferred to the nozzle exit by using a solution of the wave equation appropriate for the duct-nozzle system. The application of this method is described and results are presented to show the effect of nozzle geometry and the effect of mean flow on the radiation impedance of the duct-nozzle system. The results derived by using this method are compared with the similar results derived by using some approximate methods.     

Plasmid DNA damage induced by helium atmospheric pressure plasma jet

Recently demonstrated ghost interference using correlated photons of different frequencies, has been theoretically analyzed. The calculation predicts an interesting nonlocal effect: the fringe width of the ghost interference depends not only on the wave-length of the photon involved, but also on the wavelength of the other photon with which it is entangled. This feature, arising because of different frequencies of the entangled photons, was hidden in the original ghost interference experiment. This prediction can be experimentally tested in a slightly modified version of the experiment.