Ionization of molecular hydrogen in ultrashort intense laser pulses

Energy Technology Data Exchange (ETDEWEB)

Vanne, Yulian V.

2010-03-18

A novel ab initio numerical approach is developed and applied that solves the time-dependent Schroedinger equation describing two-electron diatomic molecules (e.g. molecular hydrogen) exposed to an intense ultrashort laser pulse. The method is based on the fixed-nuclei and the non-relativistic dipole approximations and aims to accurately describe both correlated electrons in full dimensionality. The method is applicable for a wide range of the laser pulse parameters and is able to describe both few-photon and many-photon single ionization processes, also in a non-perturbative regime. A key advantage of the method is its ability to treat the strong-field response of the molecules with arbitrary orientation of the molecular axis with respect to the linear-polarized laser field. Thus, this work reports on the first successful orientation-dependent analysis of the multiphoton ionization of H{sub 2} performed by means of a full-dimensional numerical treatment. Besides the investigation of few-photon regime, an extensive numerical study of the ionization by ultrashort frequency-doubled Ti:sapphire laser pulses (400 nm) is presented. Performing a series of calculations for different internuclear separations, the total ionization yields of H{sub 2} and D{sub 2} in their ground vibrational states are obtained for both parallel and perpendicular orientations. A series of calculations for 800 nm laser pulses are used to test a popular simple interference model. Besides the discussion of the ab initio numerical method, this work considers different aspects related to the application of the strong-field approximation (SFA) for investigation of a strong-field response of an atomic and molecular system. Thus, a deep analysis of the gauge problem of SFA is performed and the quasistatic limit of the velocity-gauge SFA ionization rates is derived. The applications of the length-gauge SFA are examined and a recently proposed generalized Keldysh theory is criticized. (orig.)

Ionization of molecular hydrogen in ultrashort intense laser pulses

International Nuclear Information System (INIS)

Vanne, Yulian V.

2010-01-01

A novel ab initio numerical approach is developed and applied that solves the time-dependent Schroedinger equation describing two-electron diatomic molecules (e.g. molecular hydrogen) exposed to an intense ultrashort laser pulse. The method is based on the fixed-nuclei and the non-relativistic dipole approximations and aims to accurately describe both correlated electrons in full dimensionality. The method is applicable for a wide range of the laser pulse parameters and is able to describe both few-photon and many-photon single ionization processes, also in a non-perturbative regime. A key advantage of the method is its ability to treat the strong-field response of the molecules with arbitrary orientation of the molecular axis with respect to the linear-polarized laser field. Thus, this work reports on the first successful orientation-dependent analysis of the multiphoton ionization of H 2 performed by means of a full-dimensional numerical treatment. Besides the investigation of few-photon regime, an extensive numerical study of the ionization by ultrashort frequency-doubled Ti:sapphire laser pulses (400 nm) is presented. Performing a series of calculations for different internuclear separations, the total ionization yields of H 2 and D 2 in their ground vibrational states are obtained for both parallel and perpendicular orientations. A series of calculations for 800 nm laser pulses are used to test a popular simple interference model. Besides the discussion of the ab initio numerical method, this work considers different aspects related to the application of the strong-field approximation (SFA) for investigation of a strong-field response of an atomic and molecular system. Thus, a deep analysis of the gauge problem of SFA is performed and the quasistatic limit of the velocity-gauge SFA ionization rates is derived. The applications of the length-gauge SFA are examined and a recently proposed generalized Keldysh theory is criticized. (orig.)

Calculated Cross Sections for the Electron Impact Ionization of Molecular Ions

Science.gov (United States)

Deutsch, H.; Becker, K.; Defrance, P.; Onthong, U.; Parajuli, R.; Probst, M.; Matt-Leubner, S.; Maerk, T.

2002-10-01

We report the results of the application of the semi- classical Deutsch-Märk (DM) formalism to the calculation of the absolute electron-impact ionization cross section of the molecular ions H2+, N2+, O2+, CD+, CO+, CO2+, H3O+, and CH4+ for which experimental data have been reported . Where available, we also compare our calculated cross sections with calculated cross sections using the BEB method of Kim and co-workers. The level of agreement between the experimentally determined and calculated cross section is satisfactory in some cases. In all cases, the calculated cross sections exceed the measured cross sections which is not surprising in view of the experimental complications in measuring ionization cross sections of molecular ions due to the presence of competing channels such as ionization dissociative ionization, and dissociative excitation. Work supported in part by FWF, OEAW, and NASA.

Fine- and hyperfine-structure effects in molecular photoionization. II. Resonance-enhanced multiphoton ionization and hyperfine-selective generation of molecular cations

Energy Technology Data Exchange (ETDEWEB)

Germann, Matthias; Willitsch, Stefan, E-mail: stefan.willitsch@unibas.ch [Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel (Switzerland)

2016-07-28

Resonance-enhanced multiphoton ionization (REMPI) is a widely used technique for studying molecular photoionization and producing molecular cations for spectroscopy and dynamics studies. Here, we present a model for describing hyperfine-structure effects in the REMPI process and for predicting hyperfine populations in molecular ions produced by this method. This model is a generalization of our model for fine- and hyperfine-structure effects in one-photon ionization of molecules presented in Paper I [M. Germann and S. Willitsch, J. Chem. Phys. 145, 044314 (2016)]. This generalization is achieved by covering two main aspects: (1) treatment of the neutral bound-bound transition including the hyperfine structure that makes up the first step of the REMPI process and (2) modification of our ionization model to account for anisotropic populations resulting from this first excitation step. Our findings may be used for analyzing results from experiments with molecular ions produced by REMPI and may serve as a theoretical background for hyperfine-selective ionization experiments.

Ionization of one-electron oxygen and fluorine projectiles by molecular hydrogen

International Nuclear Information System (INIS)

Tipping, T.N.; Sanders, J.M.; Hall, J.; Shinpaugh, J.L.; Lee, D.H.; McGuire, J.H.; Richard, P.

1988-01-01

Cross sections for projectile ionization have been measured for hydrogenlike oxygen and fluorine ions incident on a molecular-hydrogen target over a projectile energy range of 0.5--2.5 MeV/amu. The experimental cross sections are compared to the plane-wave Born approximation (PWBA) and to the Glauber-approximation cross sections all of which were calculated for atomic hydrogen and multiplied by 2. The PWBA calculations have a projectile energy dependence similar to the measured cross sections but slightly underestimate them. The Glauber approximation also underestimates the measured projectile-ionization cross sections when the hydrogen target electrons are neglected, while it overestimates the measured cross sections when the effects of the hydrogen target electrons are included. The measured projectile-ionization cross sections for hydrogenlike ions incident on molecular hydrogen are approximately a factor of 2 smaller than previously reported projectile-ionization cross sections for hydrogenlike ions incident on helium. No cross sections are available for atomic hydrogen in this velocity and ion-charge regime

Laser-induced ionization of Na vapor

International Nuclear Information System (INIS)

Wu, R.C.Y.; Judge, D.L.; Roussel, F.; Carre, B.; Breger, P.; Spiess, G.

1982-01-01

The production of Na 2 + ions by off-resonant laser excitation in the 5800-6200A region mainly results from two-photon absorption by the Na 2 molecule to highly excited gerade states followed by (a) direct ionization by absorbing a third photon or (b) coupling to the molecular Na 2 D 1 PIμ Rydberg state which is subsequently ionized by absorbing a third photon. This mechanism, i.e., a two-photon resonance three photon ionization process, explains a recent experimental observation of Roussel et al. It is suggested that the very same mechanism is also responsible for a similar observation reported by Polak-Dingels et al in their work using two crossed Na beams. In the latter two studies the laser-induced associative ionization processes were reported to be responsible for producing the Na 2 + ion. From the ratio of molecular to atomic concentration in the crossed beam experiment of Polak-Dingels et al we estimate that the cross section for producing Na 2 + through laser-induced associative ionization is at least four orders of magnitude smaller than ionization through the two-photon resonance three photon ionization process in Na 2 molecules

Evaluation of ionizing radiation effects in bone tissue by FTIR spectroscopy and dynamic mechanical analysis

International Nuclear Information System (INIS)

Veloso, Marcelo N.; Santin, Stefany P.; Benetti, Carolina; Pereira, Thiago M.; Mattor, Monica B.; Politano, Rodolfo; Zezell, Denise M.

2013-01-01

In many medical practices the bone tissue exposure to ionizing radiation is necessary. However, this radiation can interact with bone tissue in a molecular level, causing chemical and mechanical changes related with the dose used. The aim of this study was verify the changes promoted by different doses of ionizing radiation in bone tissue using spectroscopy technique of Attenuate Total Reflectance - Fourier Transforms Infrared (ATR-FTIR) and dynamic mechanical analysis. Samples of bovine bone were irradiated using irradiator of Cobalt-60 with five different doses between 0.01 kGy, 0.1 kGy,1 kGy, 15 kGy and 75 kGy. To study the effects of ionizing irradiation on bone chemical structure the sub-bands of amide I and the crystallinity index were studied. The mechanical changes were evaluated using the elastic modulus and the damping value. To verify if the chemical changes and the bone mechanic characteristics were related, it was made one study about the correlation between the crystallinity index and the elastic modulus, between the sub-bands ratio and the damping value and between the sub-bands ratio and the elastic modulus. It was possible to evaluate the effects of different dose of ionizing radiation in bone tissue. With ATR-FTIR spectroscopy analysis, it was possible observe changes in the organic components and in the hydroxyapatite crystals organization. Changes were also observed in the mechanical properties. A good correlation between the techniques was found, however, it was not possible to establish a linear or exponential dependence between dose and effect. (author)

Molecular dynamics simulations of matrix assisted laser desorption ionization: Matrix-analyte interactions

International Nuclear Information System (INIS)

Nangia, Shivangi; Garrison, Barbara J.

2011-01-01

There is synergy between matrix assisted laser desorption ionization (MALDI) experiments and molecular dynamics (MD) simulations. To understand analyte ejection from the matrix, MD simulations have been employed. Prior calculations show that the ejected analyte molecules remain solvated by the matrix molecules in the ablated plume. In contrast, the experimental data show free analyte ions. The main idea of this work is that analyte molecule ejection may depend on the microscopic details of analyte interaction with the matrix. Intermolecular matrix-analyte interactions have been studied by focusing on 2,5-dihydroxybenzoic acid (DHB; matrix) and amino acids (AA; analyte) using Chemistry at HARvard Molecular Mechanics (CHARMM) force field. A series of AA molecules have been studied to analyze the DHB-AA interaction. A relative scale of AA molecule affinity towards DHB has been developed.

Collisional energy dependence of molecular ionization by metastable rare gas atoms

International Nuclear Information System (INIS)

Martin, R.M.; Parr, T.P.

1979-01-01

The collisional energy dependence of several molecular total ionization cross sections by metastable rare gas atoms was studied over the thermal energy region using the crossed molecular beam time-of-flight method. Results are reported for the collision systems He, Ne, and Ar ionizing the geometric isomers cis- and trans-dichloroethylene and ortho- and para-dichlorobenzene. The He ionization cross sections oscillate about an energy dependence of E/sup -1/2/ over the energy range 0.004--1.0 eV, and the Ar*+para-dichlorobenzene cross section oscillates about an energy dependence of E/sup -2/5/ over the energy range 0.011--0.64 eV. The remaining systems are characterized by ''bent'' E/sup -m/ dependences with m values of 0.56--0.70 at low energies changing to 0.07--0.29 at higher energies. Comparison with the slopes of the He* systems and the Ar*+para-dichlorobenzene system shows that the ''bent'' and ''oscillating'' energy dependences are similar except for the form of the cross section functions at the lowest energies. No systematic differences are found between the cross section energy dependences for ionization of different geometric isomers or for ionization by the different metastable rare gas atoms

Molecular mechanisms in radiation damage to DNA

International Nuclear Information System (INIS)

Osman, R.

1991-01-01

The objectives of this work are to elucidate the molecular mechanisms that are responsible for radiation-induced DNA damage. The overall goal is to understand the relationship between the chemical and structural changes produced by ionizing radiation in DNA and the resulting impairment of biological function expressed as carcinogenesis or cell death. The studies are based on theoretical explorations of possible mechanisms that link initial radiation damage in the form of base and sugar damage to conformational changes in DNA. These mechanistic explorations should lead to the formulation of testable hypothesis regarding the processes of impairment of regulation of gene expression, alternation in DNA repair, and damage to DNA structure involved in cell death or cancer

In vitro evaluation of ionizing radiation effects in bone tissue by FTIR spectroscopy and dynamic mechanical analysis

International Nuclear Information System (INIS)

Veloso, Marcelo Noronha

2013-01-01

Ionizing radiation from gamma radiation sources or X-ray generators is frequently used in Medical Science, such as radiodiagnostic exams, radiotherapy, and sterilization of haloenxerts. Ionizing radiation is capable of breaking polypeptidic chains and causing the release of free radicals by radiolysis.of water. It interacts also with organic material at the molecular level, and it may change its mechanical properties. In the specific case of bone tissue, studies report that ionizing radiation induces changes in collagen molecules and reduces the density of intermolecular crosslinks. The aim of this study was to verify the changes promoted by different doses of ionizing radiation in bone tissue using Fourier Transform Infrared Spectroscopy (FTIR) and dynamic mechanical analysis (DMA). Samples of bovine bone were irradiated using Cobalt-60 with five different doses: 0.01 kGy, 0.1 kGy, 1 kGy, 15 kGy and 75 kGy. To study the effects of ionizing irradiation on the chemical structure of the bone, the sub-bands of amide I, the crystallinity index and relation of organic and inorganic materials, were studied. The mechanical changes were evaluated using the elastic modulus and the damping value. To verify whether the chemical changes and the mechanical characteristics of the bone were correlated, the relation between the analysis made with spectroscopic data and the mechanical analysis data was studied. It was possible to evaluate the effects of different doses of ionizing radiation in bone tissue. With ATR-FTIR spectroscopy, it was possible to observe changes in the organic components and in the hydroxyapatite crystals organization. Changes were also observed in the elastic modulus and in the damping value. High correlation with statistical significance was observed among (amide III + collagen)/ v1,v3 , PO 4 3- and the delta tangent, and among 1/FHWM and the elastic modulus. (author)

Picosecond multiphoton ionization of atomic and molecular clusters

International Nuclear Information System (INIS)

Miller, J.C.; Smith, D.B.

1990-01-01

High peak-power picosecond laser pulses have been used for the first time to effect nonresonant or resonant multiphoton ionization (MPI) of clusters generated in a supersonic nozzle expansion. The resulting ions are subsequently detected and characterized by time-of-flight mass spectroscopy. Specifically, we present results involving MPI of clusters of xenon and nitric oxide. Previous MPI studies of many molecular clusters using nanosecond lasers have not been successful in observing the parent ion, presumably due to fast dissociation channels. It is proposed that the present technique is a new and rather general ionization source for cluster studies which is complementary to electron impact but may, in addition, provide unique spectroscopic or dynamical information. 23 refs., 5 figs

Quantum-mechanical predictions of DNA and RNA ionization by energetic proton beams.

Science.gov (United States)

Galassi, M E; Champion, C; Weck, P F; Rivarola, R D; Fojón, O; Hanssen, J

2012-04-07

Among the numerous constituents of eukaryotic cells, the DNA macromolecule is considered as the most important critical target for radiation-induced damages. However, up to now ion-induced collisions on DNA components remain scarcely approached and theoretical support is still lacking for describing the main ionizing processes. In this context, we here report a theoretical description of the proton-induced ionization of the DNA and RNA bases as well as the sugar-phosphate backbone. Two different quantum-mechanical models are proposed: the first one based on a continuum distorted wave-eikonal initial state treatment and the second perturbative one developed within the first Born approximation with correct boundary conditions (CB1). Besides, the molecular structure information of the biological targets studied here was determined by ab initio calculations with the Gaussian 09 software at the restricted Hartree-Fock level of theory with geometry optimization. Doubly, singly differential and total ionization cross sections also provided by the two models were compared for a large range of incident and ejection energies and a very good agreement was observed for all the configurations investigated. Finally, in comparison with the rare experiment, we have noted a large underestimation of the total ionization cross sections of uracil impacted by 80 keV protons,whereas a very good agreement was shown with the recently reported ionization cross sections for protons on adenine, at both the differential and the total scale.

On the mechanism of the biological effect of ionizing radiation

International Nuclear Information System (INIS)

Margulis, M.A.; Margulis, I.M.

2005-01-01

The mechanisms of the biological effects of ionizing radiation (IR) and ultrasound (US) were considered. The current views on the nature of toxicity of IR, which is usually assigned to the formation of radicals in living tissues and to the straight-line collision of an ionizing particle with the DNA molecule, were analyzed. It was established that the amount of radicals formed in biological tissues in conditions of ultrasonically induced cavitation can be as large as that for IR; however, the biological effect of US is much softer as compared to IR. It was shown that the contribution of the indirect mechanism to the total biological effect of IR can be estimated by comparing US and IR in their chemical action; the contribution of the indirect mechanism to the biological effect of IR was found to be negligibly small. An alternative mechanism was proposed to explain the biological effect of IR. In accordance with the proposed model, IR with a high linear energy transfer (LET) value breaks through cell walls and biological membranes and causes damage to them, such that the cell can lose its regenerative capacity. Moreover, high-energy heavy ionizing particles perforate cytoplasm to form channels. Ionizing radiation with a low LET value (γ- and X-rays) causes multiple damages to biological membranes. Ionizing particles can also cause damages to membranes of mitochondria thus affecting the mechanism of cellular respiration, which will cause neoplastic diseases. The straight-line collision of an ionizing particle with a DNA molecule was found to be 5-7 orders of magnitude less probable as compared to the collision with a wall or membrane. It was shown that multiple perforations of cell walls and damages to membranes are characteristic only of ionizing particles, which have sufficiently long tracks, and do not occur upon exposure to ultrasonic waves, microwaves, UV radiation, and magnetic fields [ru

Molecular models of zinc phthalocyanines: semi-empirical molecular orbital computations and physicochemical properties studied by molecular mechanics simulations

International Nuclear Information System (INIS)

Gantchev, Tsvetan G.; van Lier, Johan E.; Hunting, Darel J.

2005-01-01

To build 3D-molecular models of Zinc-phthalocyanines (ZnPc) and to study their diverse chemical and photosensitization properties, we performed quantum mechanical molecular orbital (MO) semi-empirical (AM1) computations of the ground, excited singlet and triplet states as well as free radical (ionic) species. RHF and UHF (open shell) geometry optimizations led to near-perfect symmetrical ZnPc. Predicted ionization potentials (IP), electron affinities (EA) and lowest electronic transitions of ZnPc are in good agreement with the published experimental and theoretical data. The computation-derived D 4h /D 2h -symmetry 3D-structures of ground and excited states and free radicals of ZnPc, together with the frontier orbital energies and Mulliken electron population analysis enabled us to build robust molecular models. These models were used to predict important chemical-reactivity entities such as global electronegativity (χ), hardness (η) and local softness based on Fukui-functions analysis. Examples of molecular mechanics (MM) applications of the 3D-molecular models are presented as approaches to evaluate solvation free energy (ΔG 0 ) solv and to estimate ground- and excited- state oxidation/reduction potentials as well as intermolecular interactions and stability of ground and excited state dimers (exciplexes) and radical ion-pairs

Ionization impact on molecular clouds and star formation: Numerical simulations and observations

International Nuclear Information System (INIS)

Tremblin, Pascal

2012-01-01

At all the scales of Astrophysics, the impact of the ionization from massive stars is a crucial issue. At the galactic scale, the ionization can regulate star formation by supporting molecular clouds against gravitational collapse and at the stellar scale, indications point toward a possible birth place of the Solar System close to massive stars. At the molecular cloud scale, it is clear that the hot ionized gas compresses the surrounding cold gas, leading to the formation of pillars, globules, and shells of dense gas in which some young stellar objects are observed. What are the formation mechanisms of these structures? Are the formation of these young stellar objects triggered or would have they formed anyway? Do massive stars have an impact on the distribution of the surrounding gas? Do they have an impact on the mass distribution of stars (the initial mass function, IMF)? This thesis aims at shedding some light on these questions, by focusing especially on the formation of the structures between the cold and the ionized gas. We present the state of the art of the theoretical and observational works on ionized regions (H II regions) and we introduce the numerical tools that have been developed to model the ionization in the hydrodynamic simulations with turbulence performed with the HERACLES code. Thanks to the simulations, we present a new model for the formation of pillars based on the curvature and collapse of the dense shell on itself and a new model for the formations of cometary globules based on the turbulence of the cold gas. Several diagnostics have been developed to test these new models in the observations. If pillars are formed by the collapse of the dense shell on itself, the velocity spectrum of a nascent pillar presents a large spectra with a red-shifted and a blue-shifted components that are caused by the foreground and background parts of the shell that collapse along the line of sight. If cometary globules emerge because of the turbulence of

Ionization in matrix-assisted laser desorption/ionization: singly charged molecular ions are the lucky survivors.

Science.gov (United States)

Karas, M; Glückmann, M; Schäfer, J

2000-01-01

A new model for the ionization processes in UV matrix-assisted laser desorption/ionization (MALDI) which accounts for the major phenomena observed is presented and discussed. The model retains elements of earlier approaches, such as photoionization and photochemical reactions, but it redefines these in the light of new working questions, most importantly why only singly charged ions are detected. Based on experimental evidence, the formation of singly and multiply charged clusters by a deficiency/excess of ions and also by photoionization and subsequent photochemical processes is pointed out to be the major ionization processes, which typically occur in parallel. The generation of electrons and their partial loss into the surrounding vacuum and solid, on the one hand, results in a positively charged ion-neutral plume facilitating a high overall ionization yield. On the other hand, these electrons, and also the large excess of protonated matrix ions in the negative ion mode, induce effective ion reneutralization in the plume. These neutralization processes are most effective for the highly charged cluster ions initially formed. Their fragmentation behaviour is evidenced in fast metastable fragmentation characteristics and agrees well with an electron capture dissociation mechanism and the enthalpy transfer upon neutralization forms the rationale for the prominent fragmentation and intense chemical noise accompanying successful MALDI. Within the course of the paper, cross-correlations with other desorption/ionization techniques and with earlier discussions on their mechanisms are drawn. Copyright 2000 John Wiley & Sons, Ltd.

Angle-dependent strong-field molecular ionization rates with tuned range-separated time-dependent density functional theory

Energy Technology Data Exchange (ETDEWEB)

Sissay, Adonay [Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); Abanador, Paul; Mauger, François; Gaarde, Mette; Schafer, Kenneth J. [Department of Physics and Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); Lopata, Kenneth, E-mail: klopata@lsu.edu [Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803 (United States)

2016-09-07

Strong-field ionization and the resulting electronic dynamics are important for a range of processes such as high harmonic generation, photodamage, charge resonance enhanced ionization, and ionization-triggered charge migration. Modeling ionization dynamics in molecular systems from first-principles can be challenging due to the large spatial extent of the wavefunction which stresses the accuracy of basis sets, and the intense fields which require non-perturbative time-dependent electronic structure methods. In this paper, we develop a time-dependent density functional theory approach which uses a Gaussian-type orbital (GTO) basis set to capture strong-field ionization rates and dynamics in atoms and small molecules. This involves propagating the electronic density matrix in time with a time-dependent laser potential and a spatial non-Hermitian complex absorbing potential which is projected onto an atom-centered basis set to remove ionized charge from the simulation. For the density functional theory (DFT) functional we use a tuned range-separated functional LC-PBE*, which has the correct asymptotic 1/r form of the potential and a reduced delocalization error compared to traditional DFT functionals. Ionization rates are computed for hydrogen, molecular nitrogen, and iodoacetylene under various field frequencies, intensities, and polarizations (angle-dependent ionization), and the results are shown to quantitatively agree with time-dependent Schrödinger equation and strong-field approximation calculations. This tuned DFT with GTO method opens the door to predictive all-electron time-dependent density functional theory simulations of ionization and ionization-triggered dynamics in molecular systems using tuned range-separated hybrid functionals.

Angle-dependent strong-field molecular ionization rates with tuned range-separated time-dependent density functional theory

International Nuclear Information System (INIS)

Sissay, Adonay; Abanador, Paul; Mauger, François; Gaarde, Mette; Schafer, Kenneth J.; Lopata, Kenneth

2016-01-01

Strong-field ionization and the resulting electronic dynamics are important for a range of processes such as high harmonic generation, photodamage, charge resonance enhanced ionization, and ionization-triggered charge migration. Modeling ionization dynamics in molecular systems from first-principles can be challenging due to the large spatial extent of the wavefunction which stresses the accuracy of basis sets, and the intense fields which require non-perturbative time-dependent electronic structure methods. In this paper, we develop a time-dependent density functional theory approach which uses a Gaussian-type orbital (GTO) basis set to capture strong-field ionization rates and dynamics in atoms and small molecules. This involves propagating the electronic density matrix in time with a time-dependent laser potential and a spatial non-Hermitian complex absorbing potential which is projected onto an atom-centered basis set to remove ionized charge from the simulation. For the density functional theory (DFT) functional we use a tuned range-separated functional LC-PBE*, which has the correct asymptotic 1/r form of the potential and a reduced delocalization error compared to traditional DFT functionals. Ionization rates are computed for hydrogen, molecular nitrogen, and iodoacetylene under various field frequencies, intensities, and polarizations (angle-dependent ionization), and the results are shown to quantitatively agree with time-dependent Schrödinger equation and strong-field approximation calculations. This tuned DFT with GTO method opens the door to predictive all-electron time-dependent density functional theory simulations of ionization and ionization-triggered dynamics in molecular systems using tuned range-separated hybrid functionals.

Chemical protection and sensitization to ionizing radiation:molecular investigations

International Nuclear Information System (INIS)

Badiello, R.

1980-01-01

Chemical radioprotection and radiosensitization are induced by the presence of certain chemical compounds, which reduce or enhance the effect of ionizing radiation on living organisms. Such substances are either naturally present or may be artificially introduced in the living cells. Chemical radioprotectors are interesting for possible application in the health protection of both professionally exposed workers and patients treated by radiation for diagnostic and thereapeutic purposes. Interest in chemical radiosensitization has increased recently because of its potential application in the radiotherapy of tumours. Both radioprotection and radiosensitization occur by means of complicated mechanisms, which at first correspond to very fast reactions. The mechanism of the interaction between such substances and radiation-induced biological radicals has been investigated by means of pulse radiolysis and rapid mixing techniques. Examples of the application of these techniques are given to illustrate how information has been obtained on the molecular basis of radiation chemical modi-fication at the cellular level. In particular some interactions between model systems of biological interest (DNA, DNA components, enzymes, amino acids, etc.) and sulphur-containing radioprotectors (glutathione, cysteine, etc.) and/or electroaffinic radiosensitizers, are described. (H.K.)

A four-component Dirac theory of ionization of a hydrogen molecular ion in a super-intense laser field

International Nuclear Information System (INIS)

Faisal, F H M

2009-01-01

In this communication, a four-component Dirac theory of ionization of a hydrogen molecular ion, H + 2 , in a super-intense laser field is presented. Analytic expressions for the spin-specific as well as the total ionization currents emitted from the ground state of the ion are derived. The results are given for arbitrary intensity, frequency, wavenumber and polarization of the field, and for the up or down spin of the bound and ionized states of the electron. They also apply for the case of inner-shell ionization of analogous heavier diatomic molecular ions. The presence of molecular two-slit interference effect, first found in the non-relativistic case, the spin-flip ionization current, and an asymmetry of the up- and down-spin currents similar to that predicted in the atomic case, is found to hold for the present relativistic molecular ionic case as well. The possibility of controlling the spin of the dominant ionization current in any direction by simply selecting the handedness of a circularly polarized incident laser field is pointed out. Finally, we note that the present results obtained within the strong field 'KFR' ansatz open up the way for an analogous fully relativistic four-component treatment for ionization of polyatomic molecules and clusters in super-intense laser fields. (fast track communication)

Kinematic Study of Ionized and Molecular Gases in Ultracompact HII Region in Monoceros R2

Science.gov (United States)

Kim, Hwihyun; Lacy, John H.; Jaffe, Daniel Thomas

2017-06-01

Monoceros R2 (Mon R2) is an UltraCompact HII region (UCHII) surrounded by several PhotoDissociation Regions (PDRs). It is an excellent example to investigate the chemistry and physics of early stage of massive star formation due to its proximity (830pc) and brightness. Previous studies suggest that the wind from the star holds the ionized gas up against the dense molecular core and the higher pressure at the head drives the ionized gas along the shell. In order for the model to work, there should be evidence for dense molecular gas along the shell walls, irradiated by the UCHII region and perhaps entrained into the flow along the walls.We obtained the Immersion Grating INfrared Spectrograph (IGRINS) spectra of Mon R2 to study the kinematic patterns in the areas where ionized and molecular gases interact. The position-velocity maps from the high resolution (R~45,000) H- and K-band (1.4-2.5μm) IGRINS spectra demonstrate that the ionized gases (Brackett and Pfund series, He and Fe emission lines; Δv ≈ 40km/s) flow along the walls of the surrounding clouds. This is consistent with the model by Zhu et al. (2008). In the PV maps of the H2 emission lines there is no obvious motion (Δv ≈ 10km/s) of the molecular hydrogen right at the ionization boundary. This implies that the molecular gas is not taking part in the flow as the ionized gas is moving along the cavity walls.This work used the Immersion Grating Infrared Spectrograph (IGRINS) that was developed under a collaboration between the University of Texas at Austin and the Korea Astronomy and Space Science Institute (KASI) with the financial support of the US National Science Foundation (NSF; grant AST-1229522), of the University of Texas at Austin, and of the Korean GMTProject of KASI.

Molecular mechanisms in radiation damage to DNA. Progress report

International Nuclear Information System (INIS)

Osman, R.

1994-01-01

The objectives of this work are to elucidate the molecular mechanisms that are responsible for radiation-induced DNA damage. The overall goal is to understand the relationship between the chemical and structural changes produced by ionizing radiation in DNA and the resulting impairment of biological function expressed as carcinogenesis or cell death. The studies are based on theoretical explorations of possible mechanisms that link initial radiation damage in the form of base and sugar damage to conformational changes in DNA. These mechanistic explorations should lead to the formulation of testable hypotheses regarding the processes of impairment of regulation of gene expression, alteration in DNA repair, and damage to DNA structure involved in cell death or cancer

Strong eld ionization of naphthalene: angular shifts and molecular potential

DEFF Research Database (Denmark)

Dimitrovski, Darko; Maurer, Jochen; Christensen, Lauge

We analyze the photoelectron momentum distributions from strong eld ionization of xed-in-space naphthalene molecules by circularly polarized laser pulses. By direct comparison between experiment and theory, we show that the angular shifts in the photoelectron momentum distributions are very...... sensitive to the exact form of the molecular potential....

Indirect mechanisms in electron-impact ionization of multiply charged ions

International Nuclear Information System (INIS)

Phaneuf, R.A.; Gregory, D.C.

1986-09-01

The important role of indirect-ionization mechanisms in electron-impact ionization of multiply charged ions has been emphasized by some recent experiments conducted with the ORNL-ECR multicharged ion source. Illustrative examples of investigations of the Mg-isoelectronic and Fe-isonuclear sequences are presented and compared with the results of detailed theoretical calculations. New experimental data is also presented concerning the role of resonance effects in the ionization of Li-like O 5+ and Na-like Fe 15+ ions

Field-dependent molecular ionization and excitation energies: Implications for electrically insulating liquids

Directory of Open Access Journals (Sweden)

N. Davari

2014-03-01

Full Text Available The molecular ionization potential has a relatively strong electric-field dependence as compared to the excitation energies which has implications for electrical insulation since the excited states work as an energy sink emitting light in the UV/VIS region. At some threshold field, all the excited states of the molecule have vanished and the molecule is a two-state system with the ground state and the ionized state, which has been hypothesized as a possible origin of different streamer propagation modes. Constrained density-functional theory is used to calculate the field-dependent ionization potential of different types of molecules relevant for electrically insulating liquids. The low singlet-singlet excitation energies of each molecule have also been calculated using time-dependent density functional theory. It is shown that low-energy singlet-singlet excitation of the type n → π* (lone pair to unoccupied π* orbital has the ability to survive at higher fields. This type of excitation can for example be found in esters, diketones and many color dyes. For alkanes (as for example n-tridecane and cyclohexane on the other hand, all the excited states, in particular the σ → σ* excitations vanish in electric fields higher than 10 MV/cm. Further implications for the design of electrically insulating dielectric liquids based on the molecular ionization potential and excitation energies are discussed.

Quantum statistical mechanics of dense partially ionized hydrogen.

Science.gov (United States)

Dewitt, H. E.; Rogers, F. J.

1972-01-01

The theory of dense hydrogenic plasmas beginning with the two component quantum grand partition function is reviewed. It is shown that ionization equilibrium and molecular dissociation equilibrium can be treated in the same manner with proper consideration of all two-body states. A quantum perturbation expansion is used to give an accurate calculation of the equation of state of the gas for any degree of dissociation and ionization. In this theory, the effective interaction between any two charges is the dynamic screened potential obtained from the plasma dielectric function. We make the static approximation; and we carry out detailed numerical calculations with the bound and scattering states of the Debye potential, using the Beth-Uhlenbeck form of the quantum second virial coefficient. We compare our results with calculations from the Saha equation.

Production of highly ionized recoil ions in heavy ion impact

International Nuclear Information System (INIS)

Tawara, H.; Tonuma, T.; Be, S.H.; Shibata, H.; Kase, M.; Kambara, T.; Kumagai, H.; Kohno, I.

1985-01-01

The production mechanisms of highly ionized recoil ions in energetic, highly charged heavy ion impact are compared with those in photon and electron impact. In addition to the innershell ionization processes which are important in photon and electron impact, the electron transfer processes are found to play a key role in heavy ion impact. In molecular targets are also observed highly ionized monoatomic ions which are believed to be produced through production of highly ionized molecular ions followed by prompt dissociation. The observed N 6+ ions produced in 1.05MeV/amu Ar 12+ ions on N 2 molecules are produced through, for example, N 2 12+ *→N 6+ +N 6+ process. (author)

Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE

Directory of Open Access Journals (Sweden)

Constantinos Yeles

2017-11-01

Full Text Available Ionizing radiation-induced bystander effects (RIBE encompass a number of effects with potential for a plethora of damages in adjacent non-irradiated tissue. The cascade of molecular events is initiated in response to the exposure to ionizing radiation (IR, something that may occur during diagnostic or therapeutic medical applications. In order to better investigate these complex response mechanisms, we employed a unified framework integrating statistical microarray analysis, signal normalization, and translational bioinformatics functional analysis techniques. This approach was applied to several microarray datasets from Gene Expression Omnibus (GEO related to RIBE. The analysis produced lists of differentially expressed genes, contrasting bystander and irradiated samples versus sham-irradiated controls. Furthermore, comparative molecular analysis through BioInfoMiner, which integrates advanced statistical enrichment and prioritization methodologies, revealed discrete biological processes, at the cellular level. For example, the negative regulation of growth, cellular response to Zn2+-Cd2+, and Wnt and NIK/NF-kappaB signaling, thus refining the description of the phenotypic landscape of RIBE. Our results provide a more solid understanding of RIBE cell-specific response patterns, especially in the case of high-LET radiations, like α-particles and carbon-ions.

The molecular basis for cell cycle delays following ionizing radiation. A review

International Nuclear Information System (INIS)

Maity, A.; McKenna, W.G.; Muschel, R.J.

1994-01-01

Exposure of a wide variety of cells to ionizing (X- or γ-) irradiation results in a division delay which may have several components including a G 1 block, a G 2 arrest or an S phase delay. The G 1 arrest is absent in many cells lines, and the S phase delay is typically seen following relatively high doses (>5 Gy). In contrast, the G 2 arrest is seen in virtually all eukaryotic cells and occurs following high and low doses, even under 1 Gy. The mechanism underlying the G 2 arrest may involve suppression of cyclin B1 mRNA and/or protein in some cell lines and tyrosine phosphorylation of p34 cdc2 in others. Similar mechanisms are likely to be operative in the G 2 arrest induced by various chemotherapeutic agents including nitrogen mustard and etoposide. The upstream signal transduction pathways involved in the G 2 arrest following ionizing radiation remain obscure in mammalian cells; however, in the budding yeast the rad9 gene and in the fission yeast the chk1/rad27 gene are involved. There is evidence indicating that shortening of the G 2 arrest results in decreased survival which has led to the hypothesis that during this block, cells repair damaged DNA following exposure to genotoxic agents. In cell lines examined to date, wildtype p53 is required for the G 1 arrest following ionizing radiation. The gadd45 gene may also have a role in this arrest. Elimination of the G 1 arrest leads to no change in survival following radiation in some cell lines and increased radioresistance in others. It has been suggested that this induction of radioresistance in certain cell lines is due to loss of the ability to undergo apoptosis. Relatively little is known about the mechanism underlying the S phase delay. This delay is due to a depression in the rate of DNA synthesis and has both a slow and a fast component. In some cells the S phase delay can be abolished by staurosporine, suggesting involvement of a protein kinase. Understanding the molecular mechanisms behind these delays

Radio-adaptation: cellular and molecular features of a response to low levels of ionizing radiation

International Nuclear Information System (INIS)

Rigaud, O.

1998-01-01

It is well established that sublethal doses of DNA damaging agents induce protective mechanisms against a subsequent high dose treatment ; for instance, the phenomenon of radio-adaptation in the case of ionizing radiations. Since the early observation described in 1984, numerous studies have confirmed the radio-adaptive response in terms of reduction of chromosomal breaks for varied biological models in vitro and in vivo. Evidence for an adaptive response against the induction of gene mutations and the lethal effect is clearly demonstrated. This paper reviews the experimental results describing various aspects of these adaptive responses expressed on these different biological end-points. The molecular mechanism underlying radio-adaptation still remains nuclear. The development of this phenomenon requires de novo synthesis of transcripts and proteins during the time interval between the two doses. Some data are consistent with the hypotheses that these gene products would be involved in the activation of DNA repair pathways and antioxidant systems. However, a major question still remains unanswered; indeed, it is not clear whether or not the radio-adaptation could affect the estimation of cancer risk related with low level exposure to ionizing radiation, a major concern in radioprotection. Until such data are available, it is yet unwise to evoke the beneficial effects of radio-adaptation. (authors)

Effects of Ionizing Radiation on Biological Molecules—Mechanisms of Damage and Emerging Methods of Detection

Science.gov (United States)

Reisz, Julie A.; Bansal, Nidhi; Qian, Jiang; Zhao, Weiling

2014-01-01

Abstract Significance: The detrimental effects of ionizing radiation (IR) involve a highly orchestrated series of events that are amplified by endogenous signaling and culminating in oxidative damage to DNA, lipids, proteins, and many metabolites. Despite the global impact of IR, the molecular mechanisms underlying tissue damage reveal that many biomolecules are chemoselectively modified by IR. Recent Advances: The development of high-throughput “omics” technologies for mapping DNA and protein modifications have revolutionized the study of IR effects on biological systems. Studies in cells, tissues, and biological fluids are used to identify molecular features or biomarkers of IR exposure and response and the molecular mechanisms that regulate their expression or synthesis. Critical Issues: In this review, chemical mechanisms are described for IR-induced modifications of biomolecules along with methods for their detection. Included with the detection methods are crucial experimental considerations and caveats for their use. Additional factors critical to the cellular response to radiation, including alterations in protein expression, metabolomics, and epigenetic factors, are also discussed. Future Directions: Throughout the review, the synergy of combined “omics” technologies such as genomics and epigenomics, proteomics, and metabolomics is highlighted. These are anticipated to lead to new hypotheses to understand IR effects on biological systems and improve IR-based therapies. Antioxid. Redox Signal. 21: 260–292. PMID:24382094

Chapter 6 Quantum Mechanical Methods for Loss-Excitation and Loss-Ionization in Fast Ion-Atom Collisions

Science.gov (United States)

Belkic, Dzevad

Inelastic collisions between bare nuclei and hydrogen-like atomic systems are characterized by three main channels: electron capture, excitation, and ionization. Capture dominates at lower energies, whereas excitation and ionization prevail at higher impact energies. At intermediate energies and in the region of resonant scattering near the Massey peak, all three channels become competitive. For dressed or clothed nuclei possessing electrons, such as hydrogen-like ions, several additional channels open up, including electron loss (projectile ionization or stripping). The most important aspect of electron loss is the competition between one- and two-electron processes. Here, in a typical one-electron process, the projectile emits an electron, whereas the target final and initial states are the same. A prototype of double-electron transitions in loss processes is projectile ionization accompanied with an alteration of the target state. In such a two-electron process, the target could be excited or ionized. The relative importance of these loss channels with single- and double-electron transitions involving collisions of dressed projectiles with atomic systems is also strongly dependent on the value of the impact energy. Moreover, impact energies determine which theoretical method is likely to be more appropriate to use for predictions of cross sections. At low energies, an expansion of total scattering wave functions in terms of molecular orbitals is adequate. This is because the projectile spends considerable time in the vicinity of the target, and as a result, a compound system comprised of the projectile and the target can be formed in a metastable molecular state which is prone to decay. At high energies, a perturbation series expansion is more appropriate in terms of powers of interaction potentials. In the intermediate energy region, atomic orbitals are often used with success while expanding the total scattering wave functions. The present work is focused on

The effect of extreme ionization rates during the initial collapse of a molecular cloud core

Science.gov (United States)

Wurster, James; Bate, Matthew R.; Price, Daniel J.

2018-05-01

What cosmic ray ionization rate is required such that a non-ideal magnetohydrodynamics (MHD) simulation of a collapsing molecular cloud will follow the same evolutionary path as an ideal MHD simulation or as a purely hydrodynamics simulation? To investigate this question, we perform three-dimensional smoothed particle non-ideal MHD simulations of the gravitational collapse of rotating, one solar mass, magnetized molecular cloud cores, which include Ohmic resistivity, ambipolar diffusion, and the Hall effect. We assume a uniform grain size of ag = 0.1 μm, and our free parameter is the cosmic ray ionization rate, ζcr. We evolve our models, where possible, until they have produced a first hydrostatic core. Models with ζcr ≳ 10-13 s-1 are indistinguishable from ideal MHD models, and the evolution of the model with ζcr = 10-14 s-1 matches the evolution of the ideal MHD model within 1 per cent when considering maximum density, magnetic energy, and maximum magnetic field strength as a function of time; these results are independent of ag. Models with very low ionization rates (ζcr ≲ 10-24 s-1) are required to approach hydrodynamical collapse, and even lower ionization rates may be required for larger ag. Thus, it is possible to reproduce ideal MHD and purely hydrodynamical collapses using non-ideal MHD given an appropriate cosmic ray ionization rate. However, realistic cosmic ray ionization rates approach neither limit; thus, non-ideal MHD cannot be neglected in star formation simulations.

Understanding molecular structure from molecular mechanics.

Science.gov (United States)

Allinger, Norman L

2011-04-01

Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

Electron-Impact Ionization and Dissociative Ionization of Biomolecules

Science.gov (United States)

Huo, Winifred M.; Chaban, Galina M.; Dateo, Christopher E.

2006-01-01

It is well recognized that secondary electrons play an important role in radiation damage to humans. Particularly important is the damage of DNA by electrons, potentially leading to mutagenesis. Molecular-level study of electron interaction with DNA provides information on the damage pathways and dominant mechanisms. Our study of electron-impact ionization of DNA fragments uses the improved binary-encounter dipole model and covers DNA bases, sugar phosphate backbone, and nucleotides. An additivity principle is observed. For example, the sum of the ionization cross sections of the separate deoxyribose and phosphate fragments is in close agreement with the C3(sup prime)- and C5 (sup prime)-deoxyribose-phospate cross sections, differing by less than 5%. Investigation of tandem double lesion initiated by electron-impact dissociative ionization of guanine, followed by proton reaction with the cytosine in the Watson-Crick pair, is currently being studied to see if tandem double lesion can be initiated by electron impact. Up to now only OH-induced tandem double lesion has been studied.

III. Penning ionization, associative ionization and chemi-ionization processes

International Nuclear Information System (INIS)

Cermak, V.

1975-01-01

Physical mechanisms of three important ionization processes in a cold plasma and the methods of their experimental study are discussed. An apparatus for the investigation of the Penning ionization using ionization processes of long lived metastable rare gas atoms is described. Methods of determining interaction energies and ionization rates from the measured energy spectra of the originating electrons are described and illustrated by several examples. Typical associative ionization processes are listed and the ionization rates are compared with those of the Penning ionization. Interactions with short-lived excited particles and the transfer of excitation without ionization are discussed. (J.U.)

Automated quantum chemistry based molecular dynamics simulations of electron ionization induced fragmentations of the nucleobases Uracil, Thymine, Cytosine, and Guanine.

Science.gov (United States)

Grimme, Stefan; Bauer, Christopher Alexander

2015-01-01

The gas-phase decomposition pathways of electron ionization (EI)-induced radical cations of the nucleobases uracil, thymine, cytosine, and guanine are investigated by means of mixed quantum-classical molecular dynamics. No preconceived fragmentation channels are used in the calculations. The results compare well to a plethora of experimental and theoretical data for these important biomolecules. With our combined stochastic and dynamic approach, one can access in an unbiased way the energetically available decomposition mechanisms. Additionally, we are able to separate the EI mass spectra of different tautomers of cytosine and guanine. Our method (previously termed quantum chemistry electron ionization mass spectra) reproduces free nucleobase experimental mass spectra well and provides detailed mechanistic in-sight into high-energy unimolecular decomposition processes.

Barium ionization mechanisms in the CRRES G-1 and G-11b releases

International Nuclear Information System (INIS)

Hunton, D.E.

1993-01-01

The G-11b chemical release experiment form the Combined Release and Radiation Effects Satellite (CRRES) was conducted in darkness below the solar UV terminator to test the Critical Ionization Velocity (CIV) hypothesis. The Quadrupole Ion Mass Spectrometer (QIMS) aboard CRRES measured fluxes of barium ions from this darkness release that were only a factor of ten smaller than the G-1 release measurements in full sunlight. Possible mechanisms for this significant barium ionization in darkness include CIV, charge exchange with O + , collisional ionization and associative ionization. The authors have evaluated the relative contributions of the collisional mechanisms by constructing a simple model of barium ions from the darkness release seem to be consistent with recent measurements of the charge transfer cross section. A collective plasma ionization mechanism such as CIV does not seem to necessary in order to explain the large barium ion fluxes observed. However, QIMS could only detect barium ions formed several seconds after the initial detonation of the release canister. A CIV process could still have occurred very early in the expansion of the barium neutral cloud and the mass spectrometer would not have detected these ions

High molecular weight non-polar hydrocarbons as pure model substances and in motor oil samples can be ionized without fragmentation by atmospheric pressure chemical ionization mass spectrometry.

Science.gov (United States)

Hourani, Nadim; Kuhnert, Nikolai

2012-10-15

High molecular weight non-polar hydrocarbons are still difficult to detect by mass spectrometry. Although several studies have targeted this problem, lack of good self-ionization has limited the ability of mass spectrometry to examine these hydrocarbons. Failure to control ion generation in the atmospheric pressure chemical ionization (APCI) source hampers the detection of intact stable gas-phase ions of non-polar hydrocarbon in mass spectrometry. Seventeen non-volatile non-polar hydrocarbons, reported to be difficult to ionize, were examined by an optimized APCI methodology using nitrogen as the reagent gas. All these analytes were successfully ionized as abundant and intact stable [M-H](+) ions without the use of any derivatization or adduct chemistry and without significant fragmentation. Application of the method to real-life hydrocarbon mixtures like light shredder waste and car motor oil was demonstrated. Despite numerous reports to the contrary, it is possible to ionize high molecular weight non-polar hydrocarbons by APCI, omitting the use of additives. This finding represents a significant step towards extending the applicability of mass spectrometry to non-polar hydrocarbon analyses in crude oil, petrochemical products, waste or food. Copyright © 2012 John Wiley & Sons, Ltd.

Proteomic analysis of PC12 cell differentiation induced by ionizing radiation

International Nuclear Information System (INIS)

Zhang Junquan; Gao Ronglian; Chen Xiaohua; Wang Zhidong; Dong Bo; Rao Yalan; Hou Lili; Zhang Hao; Mao Bingzhi

2005-01-01

Objective: To explore the molecular mechanism of PC12 cell differentiation induced by ionizing radiation and screen the molecular target of nervous system injured by irradiation. Methods: PC12 cells were irradiated with 16 Gy 60 Co γ ray. Total proteins of normal and irradiated cells were prepared 48 hours after irradiation and separated with two dimensional gel electrophoresis. Some differential expressed proteins were characterized with mass spectrometry. Results: 876 differential expressed proteins were observed. Up-regulated expression of ubiquitin carboxyl-terminal hydratase L1 was found. Down-regulated expression of new protein similar to HP1α was found. Conclusion: The characterization of some differential expressed proteins through proteomic analysis would benefit the research of molecular mechanism of PC12 cell differentiation induced by ionizing radiation. (authors)

Study on the ionization of 1sσ molecular orbital in slow asymmetric collisions

International Nuclear Information System (INIS)

Sigaud, G.M.

1985-01-01

A model, based on the adiabatic perturbation theory, is proposed to the ionization of the 1sσ molecular orbital in slow asymmetric collisions. The extension of the model to less adiabatic collisions is made by imposing an asymptotic matching with the semiclassical approximation. The transient molecular state wavefunction is evaluated using an effective charge, which is dependent on the internuclear separation distance, for the projectile-target-atom-system. This procedure simulates both the screening due to the external electrons and the modifications on the electronic wavefunction due to the nuclei relative motion. The direct Coulomb ionization cross-section of the 1sσ molecular orbital is calculated for projectiles following hyperbolic paths in terms of this effective charge. At the same time, X-rays production cross-sections for the K-shell of thick targets of Ti and Fe are determined for incident beams of D, He, C, N and O, with energy range between 0,20 and 4,00 MeV. The comparison between the proposed model and the obtained experimental data shows that, for this energy range, two other processes, besides direct ionization, contribute to X-rays production. These processes, namely the recoil of the target-atom in its matrix and the electron capture by the projectile, are discussed in the light of theoretical models existent in the literature. (author)

Hyperthermal surface ionization mass spectrometry of organic molecules: monoterpenes

International Nuclear Information System (INIS)

Kishi, Hiroshi; Fujii, Toshihiro.

1997-01-01

This paper describes an experimental study on the influence of kinetic energy of fast monoterpene molecules on the surface ionization efficiency and on the mass spectral patterns, using rhenium oxide (ReO 2 ) surface. Molecular kinetic energy, given to the molecules through the acceleration in the seeded supersonic molecular beam, ranged from 1 to 10 eV. Hyperthermal surface ionization mass spectra (HSIMS) were taken for various incident kinetic energies and surface temperatures. The observed mass spectra were interpreted in a purely empirical way, by means of evidence from the previous investigations, and they were compared with conventional EI techniques and with the thermal energy surface ionization technique (SIOMS; Surface Ionization Organic Mass Spectrometry). Ionization efficiency (β) was also studied. Under hyperthermal surface ionization (HSI) conditions, many kinds of fragment ions, including quite abundant odd electron ions (OE +· ) are observed. HSIMS patterns of monoterpenes are different among 6-isomers, contrary to those of SIOMS and EIMS, where very similar patterns for isomers are observed. HSIMS patterns are strongly dependent on the molecular kinetic energies. The surface temperature does not affect much the spectral patterns, but it controls the total amount of ion formation. We conclude from these mass spectral findings, HSI-mechanism contains an impulsive process of ion formation, followed by the fragmentation process as a results of the internal energies acquired through the collision processes. (author)

Ionization mechanism of cesium plasma produced by irradiation of dye laser

International Nuclear Information System (INIS)

Yamada, Jun; Shibata, Kohji; Uchida, Yoshiyuki; Hioki, Yoshiaki; Sahashi, Toshio.

1992-01-01

When a cesium vapor was irradiated by a dye laser which was tuned to the cesium atomic transition line, the number of charged particles produced by the laser radiation was observed. Several sharp peaks in the number of charged particles were observed, which corresponded to the atomic transition where the lower level was the 6P excited atom. The ionization mechanism of the laser-produced cesium plasma has been discussed. An initial electron is produced by laser absorptions of the cesium dimer. When the cesium density is high, many 6P excited atoms are excited by electron collisions. The 6P excited atom further absorbs the laser photon and is ionized through the higher-energy state. As the cesium vapor pressure increases, the resonance effect becomes observable. The 6P excited atom plays dominant role in the ionization mechanism of the laser-produced cesium plasma. (author)

Comparative study of the dissociative ionization of 1,1,1-trichloroethane using nanosecond and femtosecond laser pulses

CSIR Research Space (South Africa)

Du Plessis, A

2010-03-01

Full Text Available , but different fragmentation patterns. A general trend is that when using femtosecond laser pulses for ionization, the parent molecular ion is observed but not for nanosecond laser ionization. There is also a fundamental interest in laser...-molecule interactions at the high intensities available from femtosecond lasers [12,13]. These papers describe the multiphoton ionization mechanisms termed ladder climbing and ladder switching, which explain the presence of parent molecular ion in ultrashort pulse...

Electron Impact Excitation-Ionization of Molecules

Science.gov (United States)

Ali, Esam Abobakr A.

In the last few decades, the study of atomic collisions by electron-impact has made significant advances. The most difficult case to study is electron impact ionization of molecules for which many approximations have to be made and the validity of these approximations can only be checked by comparing with experiment. In this thesis, I have examined the Molecular three-body distorted wave (M3DW) or Molecular four-body distorted wave (M4DW) approximations for electron-impact ionization. These models use a fully quantum mechanical approach where all particles are treated quantum mechanically and the post collision interaction (PCI) is treated to all orders of perturbation. These electron impact ionization collisions play central roles in the physics and chemistry of upper atmosphere, biofuel, the operation of discharges and lasers, radiation induced damage in biological material like damage to DNA by secondary electrons, and plasma etching processes. For the M3DW model, I will present results for electron impact single ionization of small molecules such as Water, Ethane, and Carbon Dioxide and the much larger molecules Tetrahydrofuran, phenol, furfural, 1-4 Benzoquinone. I will also present results for the four-body problem in which there are two target electrons involved in the collision. M4DW results will be presented for dissociative excitation-ionization of orientated D2. I will show that M4DW calculations using a variational wave function for the ground state that included s- and p- orbital states give better agreement to the experimental measurements than a ground state approximated as a product of two 1s-type Dyson orbitals.

Quantum-mechanical study of ionization in slow collisions of antiprotons with hydrogen atoms

International Nuclear Information System (INIS)

Sakimoto, Kazuhiro

2004-01-01

The cross sections for the ionization p+H→p+p+e at low collision energies are computed with a complete quantum-mechanical method of time-dependent wave-packet propagation, which was applied to the protonium formation (→pp+e) by the present author [Phys. Rev. A 65, 012706 (2002)]. The ionization process shows very large cross sections even near threshold energy. An impact-parameter semiclassical method, in which the trajectory bending is taken into account by the introduction of the adiabatic potential, is also examined for the calculation of the ionization cross section. The semiclassical results are in good agreement with the quantum-mechanical results

Hydrocarbon analysis using desorption atmospheric pressure chemical ionization

KAUST Repository

Jjunju, Fred Paul Mark; Badu-Tawiah, Abraham K.; Li, Anyin; Soparawalla, Santosh; Roqan, Iman S.; Cooks, Robert Graham

2013-01-01

Characterization of the various petroleum constituents (hydronaphthalenes, thiophenes, alkyl substituted benzenes, pyridines, fluorenes, and polycyclic aromatic hydrocarbons) was achieved under ambient conditions without sample preparation by desorption atmospheric pressure chemical ionization (DAPCI). Conditions were chosen for the DAPCI experiments to control whether ionization was by proton or electron transfer. The protonated molecule [M+H]+ and the hydride abstracted [MH]+ form were observed when using an inert gas, typically nitrogen, to direct a lightly ionized plasma generated by corona discharge onto the sample surface in air. The abundant water cluster ions generated in this experiment react with condensed-phase functionalized hydrocarbon model compounds and their mixtures at or near the sample surface. On the other hand, when naphthalene was doped into the DAPCI gas stream, its radical cation served as a charge exchange reagent, yielding molecular radical cations (M+) of the hydrocarbons. This mode of sample ionization provided mass spectra with better signal/noise ratios and without unwanted side-products. It also extended the applicability of DAPCI to petroleum constituents which could not be analyzed through proton transfer (e.g., higher molecular PAHs such as chrysene). The thermochemistry governing the individual ionization processes is discussed and a desorption/ionization mechanism is inferred. © 2012 Elsevier B.V.

Hydrocarbon analysis using desorption atmospheric pressure chemical ionization

KAUST Repository

Jjunju, Fred Paul Mark

2013-07-01

Characterization of the various petroleum constituents (hydronaphthalenes, thiophenes, alkyl substituted benzenes, pyridines, fluorenes, and polycyclic aromatic hydrocarbons) was achieved under ambient conditions without sample preparation by desorption atmospheric pressure chemical ionization (DAPCI). Conditions were chosen for the DAPCI experiments to control whether ionization was by proton or electron transfer. The protonated molecule [M+H]+ and the hydride abstracted [MH]+ form were observed when using an inert gas, typically nitrogen, to direct a lightly ionized plasma generated by corona discharge onto the sample surface in air. The abundant water cluster ions generated in this experiment react with condensed-phase functionalized hydrocarbon model compounds and their mixtures at or near the sample surface. On the other hand, when naphthalene was doped into the DAPCI gas stream, its radical cation served as a charge exchange reagent, yielding molecular radical cations (M+) of the hydrocarbons. This mode of sample ionization provided mass spectra with better signal/noise ratios and without unwanted side-products. It also extended the applicability of DAPCI to petroleum constituents which could not be analyzed through proton transfer (e.g., higher molecular PAHs such as chrysene). The thermochemistry governing the individual ionization processes is discussed and a desorption/ionization mechanism is inferred. © 2012 Elsevier B.V.

Double and single ionization of He and H2 by slow protons and antiprotons

International Nuclear Information System (INIS)

Kimura, Mineo

1994-01-01

Double and single ionization of He and H 2 by proton (p) and antiproton (bar p)impact in the energy region below 50 keV was studied theoretically by using the semiclassical molecular picture. As the energy decreased, the ratio of the double- to the single-ionization cross section increased for impact and decreased for p impact for both He and H 2 . These trends are consistent with recent measurements for He. Ionization mechanisms differ distinctly for p impact and bar p impact. For p impact, the dominant mechanism for double ionization at the lower energies is sequential ladder climbing by the two electrons through various excited channels and finally into the continuum. For bar p impact, in contrast, the approaching negative charge distorts both the He and H 2 electron clouds toward the other side of the nucleus and decreases the electron binding energies. These effects enhance electron-electron interactions, increasing double ionization. For the H 2 , an effect of molecular orientation is an additional complication in determining the dynamics

Excitation mechanisms in singly ionized krypton laser

International Nuclear Information System (INIS)

El-Sherbini, Th.M.

1982-01-01

Lifetimes for the low lying 4p 4 4d and 4p 4 5s levels of singly ionized krypton laser are calculated, taking into account configuration interaction effects. The results show that some of these levels are metastable. They also suggest a two step excitation from the ground state of the ion (or the atom) to the upper 4p 4 5p laser levels involving some intermediate metastable states as a possible excitation mechanism. (author)

Electron ionization LC-MS with supersonic molecular beams--the new concept, benefits and applications.

Science.gov (United States)

Seemann, Boaz; Alon, Tal; Tsizin, Svetlana; Fialkov, Alexander B; Amirav, Aviv

2015-11-01

A new type of electron ionization LC-MS with supersonic molecular beams (EI-LC-MS with SMB) is described. This system and its operational methods are based on pneumatic spray formation of the LC liquid flow in a heated spray vaporization chamber, full sample thermal vaporization and subsequent electron ionization of vibrationally cold molecules in supersonic molecular beams. The vaporized sample compounds are transferred into a supersonic nozzle via a flow restrictor capillary. Consequently, while the pneumatic spray is formed and vaporized at above atmospheric pressure the supersonic nozzle backing pressure is about 0.15 Bar for the formation of supersonic molecular beams with vibrationally cold sample molecules without cluster formation with the solvent vapor. The sample compounds are ionized in a fly-though EI ion source as vibrationally cold molecules in the SMB, resulting in 'Cold EI' (EI of vibrationally cold molecules) mass spectra that exhibit the standard EI fragments combined with enhanced molecular ions. We evaluated the EI-LC-MS with SMB system and demonstrated its effectiveness in NIST library sample identification which is complemented with the availability of enhanced molecular ions. The EI-LC-MS with SMB system is characterized by linear response of five orders of magnitude and uniform compound independent response including for non-polar compounds. This feature improves sample quantitation that can be approximated without compound specific calibration. Cold EI, like EI, is free from ion suppression and/or enhancement effects (that plague ESI and/or APCI) which facilitate faster LC separation because full separation is not essential. The absence of ion suppression effects enables the exploration of fast flow injection MS-MS as an alternative to lengthy LC-MS analysis. These features are demonstrated in a few examples, and the analysis of the main ingredients of Cannabis on a few Cannabis flower extracts is demonstrated. Finally, the advantages of

Classical electron ionization mass spectra in gas chromatography/mass spectrometry with supersonic molecular beams.

Science.gov (United States)

Gordin, Alexander; Fialkov, Alexander B; Amirav, Aviv

2008-09-01

A major benefit of gas chromatography/mass spectrometry (GC/MS) with a supersonic molecular beam (SMB) interface and its fly-through ion source is the ability to obtain electron ionization of vibrationally cold molecules (cold EI), which show enhanced molecular ions. However, GC/MS with an SMB also has the flexibility to perform 'classical EI' mode of operation which provides mass spectra to mimic those in commercial 70 eV electron ionization MS libraries. Classical EI in SMB is obtained through simple reduction of the helium make-up gas flow rate, which reduces the SMB cooling efficiency; hence the vibrational temperatures of the molecules are similar to those in traditional EI ion sources. In classical EI-SMB mode, the relative abundance of the molecular ion can be tuned and, as a result, excellent identification probabilities and very good matching factors to the NIST MS library are obtained. Classical EI-SMB with the fly-through dual cage ion source has analyte sensitivity similar to that of the standard EI ion source of a basic GC/MS system. The fly-through EI ion source in combination with the SMB interface can serve for cold EI, classical EI-SMB, and cluster chemical ionization (CCI) modes of operation, all easily exchangeable through a simple and quick change (not involving hardware). Furthermore, the fly-through ion source eliminates sample scattering from the walls of the ion source, and thus it offers full sample inertness, tailing-free operation, and no ion-molecule reaction interferences. It is also robust and enables increased column flow rate capability without affecting the sensitivity.

Ionization probes of molecular structure and chemistry

Energy Technology Data Exchange (ETDEWEB)

Johnson, P.M. [State Univ. of New York, Stony Brook (United States)

1993-12-01

Various photoionization processes provide very sensitive probes for the detection and understanding of the spectra of molecules relevant to combustion processes. The detection of ionization can be selective by using resonant multiphoton ionization or by exploiting the fact that different molecules have different sets of ionization potentials. Therefore, the structure and dynamics of individual molecules can be studied even in a mixed sample. The authors are continuing to develop methods for the selective spectroscopic detection of molecules by ionization, and to use these methods for the study of some molecules of combustion interest.

Pitfall in quantum mechanical/molecular mechanical molecular dynamics simulation of small solutes in solution.

Science.gov (United States)

Hu, Hao; Liu, Haiyan

2013-05-30

Developments in computing hardware and algorithms have made direct molecular dynamics simulation with the combined quantum mechanical/molecular mechanical methods affordable for small solute molecules in solution, in which much improved accuracy can be obtained via the quantum mechanical treatment of the solute molecule and even sometimes water molecules in the first solvation shell. However, unlike the conventional molecular mechanical simulations of large molecules, e.g., proteins, in solutions, special care must be taken in the technical details of the simulation, including the thermostat of the solute/solvent system, so that the conformational space of the solute molecules can be properly sampled. We show here that the common setup for classical molecular mechanical molecular dynamics simulations, such as the Berendsen or single Nose-Hoover thermostat, and/or rigid water models could lead to pathological sampling of the solutes' conformation. In the extreme example of a methanol molecule in aqueous solution, improper and sluggish setups could generate two peaks in the distribution of the O-H bond length. We discuss the factors responsible for this somewhat unexpected result and evoke a simple and ancient technical fix-up to resolve this problem.

Ionizing radiation induces PI3K-dependent JNK activation for amplifying mitochondrial dysfunction in human cervical cancer cells

International Nuclear Information System (INIS)

Kim, Min Jung; Choi, Soon Young; Bae, Sang Woo; Kang, Chang Mo; Lee, Yun Sil; Lee, Su Jae

2005-01-01

Ionizing radiation is one of the most commonly used treatments for a wide variety of tumors. Exposure of cells to ionizing radiation results in the simultaneous activation or down regulation of multiple signaling pathways, which play critical role in controlling cell death and cell survival after irradiation in a cell type specific manner. The molecular mechanism by which apoptotic cell death occurs in response to ionizing radiation has been widely explored but not precisely deciphered. Therefore an improved understanding of the mechanisms involved in radiation-induced apoptosis may ultimately provide novel strategies of intervention in specific signal transduction pathways to favorably alter the therapeutic ratio in the treatment of human malignancies. The aim of our investigation was to elucidate molecular mechanisms of the mitochondrial dysfunction mediated apoptotic cell death triggered by ionizing radiation in human cervical cancer cells. We demonstrated that ionizing radiation utilizes PI3K-JNK signaling pathway for amplifying mitochondrial dysfunction and susequent apoptotic cell death: We showed that PI3K-dependent JNK activation leads to transcriptional upregulation of Fas and the phosphorylation/inactivation of Bcl-2, resulting in mitochondrial dysfunction-mediated apoptotic cell death in response to ionizing radiation

Multiphoton ionization/dissociation of osmium tetroxide

International Nuclear Information System (INIS)

Ding, D.; Puretzky, A.A.; Compton, R.N.

1993-01-01

The mechanisms leading to laser multiphoton ionization and dissociation (MPI/MPD) of osmium tetroxide (OsO 4 ) have been investigated from measurements of the kinetic energies of product ions (Os + , Os 2+ , OsO + , O 2 + , O + ) and photoelectrons as a function of the laser wavelength. Neutral channels, intermediate to the dominant Os + ionization channel, such as OsO 4 →OsO 4-n +nO are examined using resonance-enhanced multiphoton ionization (REMPI) of the fast O atoms. Equipartition of the available photon energy among the fragments is observed. The wavelength dependence of the Os + ion signal suggests that one or more of the steps leading to Os + ions involve molecular ions and/or excited neutral atoms. The observed preponderance of very slow ( 2+ is shown to result primarily from REMPI of Os +

Molecular Insights into the pH-Dependent Adsorption and Removal of Ionizable Antibiotic Oxytetracycline by Adsorbent Cyclodextrin Polymers

Science.gov (United States)

Zhang, Yu; Cai, Xiyun; Xiong, Weina; Jiang, Hao; Zhao, Haitong; Yang, Xianhai; Li, Chao; Fu, Zhiqiang; Chen, Jingwen

2014-01-01

Effects of pH on adsorption and removal efficiency of ionizable organic compounds (IOCs) by environmental adsorbents are an area of debate, because of its dual mediation towards adsorbents and adsorbate. Here, we probe the pH-dependent adsorption of ionizable antibiotic oxytetracycline (comprising OTCH2 +, OTCH±, OTC−, and OTC2−) onto cyclodextrin polymers (CDPs) with the nature of molecular recognition and pH inertness. OTCH± commonly has high adsorption affinity, OTC− exhibits moderate affinity, and the other two species have negligible affinity. These species are evidenced to selectively interact with structural units (e.g., CD cavity, pore channel, and network) of the polymers and thus immobilized onto the adsorbents to different extents. The differences in adsorption affinity and mechanisms of the species account for the pH-dependent adsorption of OTC. The mathematical equations are derived from the multiple linear regression (MLR) analysis of quantitatively relating adsorption affinity of OTC at varying pH to adsorbent properties. A combination of the MLR analysis for OTC and molecular recognition of adsorption of the species illustrates the nature of the pH-dependent adsorption of OTC. Based on this finding, γ-HP-CDP is chosen to adsorb and remove OTC at pH 5.0 and 7.0, showing high removal efficiency and strong resistance to the interference of coexisting components. PMID:24465975

Resonance ionization spectroscopy 1990

International Nuclear Information System (INIS)

Parks, J.E.; Omenetto, N.

1991-01-01

The Fifth International Symposium on Resonance Ionization Spectroscopy (RIS) and its Applications was held in Varese, Italy, 16-21 September 1990. Interest in RIS and its applications continues to grow, and RIS is expanding into a more diverse and mature field of study. This maturity was evident in this meeting both in the basic science and understanding of RIS processes and in the number of new and improved applications and techniques. The application of RIS techniques to molecular detection problems made remarkable progress since the last meeting two years ago. Subtle effects pertaining to isotopic discrimination received more theoretical attention, and there now seems to be good understanding of these effects, which can lead to correction procedures and/or methods to avoid isotopic effects. RIS applications were presented in which significant, real world problems were addressed, demonstrating its capability to solve problems that previously could not be accurately solved by other more traditional techniques. The contributions to the conference are grouped under the following major topic headings: physics applications of rare atoms; laser ionization mechanisms - spectroscopy; atomic, molecular and ion sources; molecular RIS; atomic RIS - Rydberg states; environmental trace analysis; biological and medical applications; state selected chemistry; new laser sources and techniques; ultra-high resolution and isotopic selectivity; surface and bulk analysis. (Author)

Optical Imaging of Ionizing Radiation from Clinical Sources.

Science.gov (United States)

Shaffer, Travis M; Drain, Charles Michael; Grimm, Jan

2016-11-01

Nuclear medicine uses ionizing radiation for both in vivo diagnosis and therapy. Ionizing radiation comes from a variety of sources, including x-rays, beam therapy, brachytherapy, and various injected radionuclides. Although PET and SPECT remain clinical mainstays, optical readouts of ionizing radiation offer numerous benefits and complement these standard techniques. Furthermore, for ionizing radiation sources that cannot be imaged using these standard techniques, optical imaging offers a unique imaging alternative. This article reviews optical imaging of both radionuclide- and beam-based ionizing radiation from high-energy photons and charged particles through mechanisms including radioluminescence, Cerenkov luminescence, and scintillation. Therapeutically, these visible photons have been combined with photodynamic therapeutic agents preclinically for increasing therapeutic response at depths difficult to reach with external light sources. Last, new microscopy methods that allow single-cell optical imaging of radionuclides are reviewed. © 2016 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Ionization due to the interaction between two Rydberg atoms

International Nuclear Information System (INIS)

Robicheaux, F

2005-01-01

Using a classical trajectory Monte Carlo method, we have computed the ionization resulting from the interaction between two cold Rydberg atoms. We focus on the products resulting from close interaction between two highly excited atoms. We give information on the distribution of ejected electron energies, the distribution of internal atom energies and the velocity distribution of the atoms and ions after the ionization. If the potential for the atom is not purely Coulombic, the average interaction between two atoms can change from attractive to repulsive giving a Van de Graaff-like mechanism for accelerating atoms. In a small fraction of ionization cases, we find that the ionization leads to a positive molecular ion where all of the distances are larger than 1000 Bohr radii

Monitoring the beam flux in molecular beam epitaxy using laser multiphoton ionization

International Nuclear Information System (INIS)

Chien, R.; Sogard, M.R.

1990-01-01

In this paper, we will describe a method using laser nonresonant multiphoton ionization to measure beam flux in molecular beam epitaxy (MBE) systems. The results were obtained in a test chamber where a focused excimer laser beam was used to photoionize a small fraction of the atomic and molecular beams. The constituents of the beams were identified by a time-of-flight mass spectrometer. Ion signal strength was found to be directly correlated to the temperature of the atomic beam oven. Good stability and sensitivity on gallium, aluminum, and silicon atomic beams was demonstrated. Arsenic was also detected. We demonstrated very sensitive detection of contaminant atomic and molecular constituents of our system. We have also detected the presence of short-term fluctuations in the gallium flux from an effusion source. These fluctuations, previously suspected, can be in excess of ±10%

Condensed tannins from Ficus virens as tyrosinase inhibitors: structure, inhibitory activity and molecular mechanism.

Directory of Open Access Journals (Sweden)

Xiao-Xin Chen

Full Text Available Condensed tannins from Ficus virens leaves, fruit, and stem bark were isolated and their structures characterized by 13C nuclear magnetic resonance spectrometry, high performance liquid chromatography electrospray ionization mass spectrometry, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The results showed that the leaves, fruit, and stem bark condensed tannins were complex mixtures of homo- and heteropolymers of B-type procyanidins and prodelphinidins with degrees of polymerization up to hexamer, dodecamer, and pentadecamer, respectively. Antityrosinase activities of the condensed tannins were studied. The results indicated that the condensed tannins were potent tyrosinase inhibitors. The concentrations for the leaves, fruit, and stem bark condensed tannins leading to 50% enzyme activity were determined to be 131.67, 99.89, and 106.22 μg/ml on monophenolase activity, and 128.42, 43.07, and 74.27 μg/ml on diphenolase activity. The inhibition mechanism, type, and constants of the condensed tannins on the diphenolase activity were further investigated. The results indicated that the condensed tannins were reversible and mixed type inhibitors. Fluorescence quenching, copper interacting, and molecular docking techniques were utilized to unravel the molecular mechanisms of the inhibition. The results showed that the hydroxyl group on the B ring of the condensed tannins could chelate the dicopper irons of the enzyme. Moreover, the condensed tannins could reduce the enzyme product o-quinones into colourless compounds. These results would contribute to the development and design of antityrosinase agents.

Double ionization of the hydrogen sulfide molecule by electron impact: Influence of the target orientation on multiple differential cross sections

Energy Technology Data Exchange (ETDEWEB)

Imadouchene, N. [Laboratoire de Mécanique, Structures et Energétique Université Mouloud Mammeri de Tizi-Ouzou, B.P. 17, Tizi-Ouzou 15000 (Algeria); Aouchiche, H., E-mail: h_aouchiche@yahoo.fr [Laboratoire de Mécanique, Structures et Energétique Université Mouloud Mammeri de Tizi-Ouzou, B.P. 17, Tizi-Ouzou 15000 (Algeria); Champion, C. [Centre d’Etudes Nucléaires de Bordeaux Gradignan, Université Bordeaux, CNRS/IN2P3, Boîte Postale 120, Gradignan 33175 (France)

2016-07-15

Highlights: • The double ionization of the H{sub 2}S molecule is here theoretically studied. • The orientation dependence of the differential cross sections is scrutinized. • The specific double ionizing mechanisms are clearly identified. - Abstract: Multiple differential cross sections of double ionization of hydrogen sulfide molecule impacted by electrons are here investigated within the first Born approximation. In the initial state, the incident electron is represented by a plane wave function whereas the target is described by means of a single-center molecular wave function. In the final state, the two ejected electrons are described by Coulomb wave functions coupled by the Gamow factor, whereas the scattered electron is described by a plane wave. In this work, we analyze the role played by the molecular target orientation in the double ionization of the four outermost orbitals, namely 2b{sub 1}, 5a{sub 1}, 2b{sub 2} and 4a{sub 1} in considering the particular case of two electrons ejected from the same orbital. The contribution of each final state to the double ionization process is studied in terms of shape and magnitude for specific molecular orientations and for each molecular orbital we identified the mechanisms involved in the double ionization process, namely, the Shake-Off and the Two-Step 1.

Investigation of the spectroscopy and relaxation dynamics of benzaldehyde using molecular orbital calculations and laser ionization time-of-flight mass spectroscopy

Science.gov (United States)

da Silva, Maria Cristina Rodrigues

1998-11-01

Molecular orbital methods and laser ionization mass spectrometry measurements are used to investigate the spectroscopy and relaxation dynamics of benzaldehyde following excitation to its S2(/pi/pi/sp/*) state. Energies, equilibrium geometries and vibrational frequencies of ground and low-lying excited states of benzaldehyde neutral and cation determined by ab initio calculations provide a theoretical description of the electronic spectroscopy of benzaldehyde and of the changes occurring on excitation and ionization. The S2(/pi/pi/sp/*)[/gets]S0 excitation spectrum of jet-cooled benzaldehyde acquired using two-color laser ionization mass spectrometry techniques is interpreted with the aid of these calculations. The spectrum is dominated by the origin band and by transitions involving some of the ring modes consistent with the results of the molecular orbital calculations that indicate that the major geometric changes on excitation to S2 are located in the aromatic ring. Ten fundamental vibrations of the S2(/pi/pi/sp/*) state are assigned. The dissociation dynamics of benzaldehyde into benzene and carbon monoxide following excitation to its S2(/pi/pi/sp/*) state are investigated under jet- cooled conditions by two-color laser ionization mass spectrometry using a pump-probe technique. This experimental arrangement allows monitoring the benzaldehyde reactant and the benzene product ion signals as a function of the time delay between the excitation and ionization steps. A kinetic model is proposed to explain the observed biexponential decay of the benzaldehyde signal and the single exponential growth of the benzene product signal in terms of a sequential decay of two excited states of benzaldehyde, one of which leads to formation of benzene molecules in its lowest triplet state. Reactant disappearance and product appearance rates are determined for a number of vibronic transitions of the S2 state. They are found to increase with excitation energy without any indication

Cataracts induced by microwave and ionizing radiation

International Nuclear Information System (INIS)

Lipman, R.M.; Tripathi, B.J.; Tripathi, R.C.

1988-01-01

Microwaves most commonly cause anterior and/or posterior subcapsular lenticular opacities in experimental animals and, as shown in epidemiologic studies and case reports, in human subjects. The formation of cataracts seems to be related directly to the power of the microwave and the duration of exposure. The mechanism of cataractogenesis includes deformation of heat-labile enzymes, such as glutathione peroxide, that ordinarily protect lens cell proteins and membrane lipids from oxidative damage. Oxidation of protein sulfhydryl groups and the formation of high-molecular-weight aggregates cause local variations in the orderly structure of the lens cells. An alternative mechanism is thermoelastic expansion through which pressure waves in the aqueous humor cause direct physical damage to the lens cells. Cataracts induced by ionizing radiation (e.g., X-rays and gamma rays) usually are observed in the posterior region of the lens, often in the form of a posterior subcapsular cataract. Increasing the dose of ionizing radiation causes increasing opacification of the lens, which appears after a decreasing latency period. Like cataract formation by microwaves, cataractogenesis induced by ionizing radiation is associated with damage to the lens cell membrane. Another possible mechanism is damage to lens cell DNA, with decreases in the production of protective enzymes and in sulfur-sulfur bond formation, and with altered protein concentrations. Until further definitive conclusions about the mechanisms of microwaves and ionizing radiation induced cataracts are reached, and alternative protective measures are found, one can only recommend mechanical shielding from these radiations to minimize the possibility of development of radiation-induced cataracts. 74 references

Effects of molecular orientation in the laser ionization of molecules

International Nuclear Information System (INIS)

Xinhua Xie; Gerald Jordan; Christopher Ede; Armin Scrinzi

2006-01-01

Complete test of publication follows. Time-dependent electron momentum distributions are calculated during ionization of linear molecules by a strong laser pulse and upon recollision. For typical experimental laser parameters, we find a strong influence of molecular orientation and initial state symmetry on the total ionization rates and also on momentum distributions, compared to which the effect of electron correlation is less important for simple molecules. The dynamics of electron release and subsequent recollision with the parent ion largely determines the time-frequency structure of harmonic radiation, which underlies the generation of attosecond XUV pulses and the time-resolved imaging techniques for the electronic structure of molecules. In the present work, the effects of orientation and initial orbital symmetry are investigated by solving the time-dependent Schroedinger equation for a two-dimensional diatomic molecule in the single-active electron approximation. As in the presence of strong external fields recolliding electrons cannot be easily separated from bound electrons, the electron wave packet is probed at some distance from where all electrons can be safety considered as detached. We find that momentum distributions strongly depend on molecular size, orientation of the molecular axis, and node structure of the initial state. In order to determine the momentum spectra at the time of electron release and upon recollision, we classically propagate the Wigner distributions of probed wavepackets backward and forward in time, respectively. We find that the times of peak recollision current can vary strongly with the orientation of the molecule. Moreover, correlation effects on the electron spectra are included using the multi-configuration time-dependent Hartree-Fock method. The calculations are performed in three spatial dimensions with the restriction to cylindrical symmetry, where the molecule is aligned with the laser field. Correlation is studied

Performance assessment of semiempirical molecular orbital methods in describing halogen bonding: quantum mechanical and quantum mechanical/molecular mechanical-molecular dynamics study.

Science.gov (United States)

Ibrahim, Mahmoud A A

2011-10-24

The performance of semiempirical molecular-orbital methods--MNDO, MNDO-d, AM1, RM1, PM3 and PM6--in describing halogen bonding was evaluated, and the results were compared with molecular mechanical (MM) and quantum mechanical (QM) data. Three types of performance were assessed: (1) geometrical optimizations and binding energy calculations for 27 halogen-containing molecules complexed with various Lewis bases (Two of the tested methods, AM1 and RM1, gave results that agree with the QM data.); (2) charge distribution calculations for halobenzene molecules, determined by calculating the solvation free energies of the molecules relative to benzene in explicit and implicit generalized Born (GB) solvents (None of the methods gave results that agree with the experimental data.); and (3) appropriateness of the semiempirical methods in the hybrid quantum-mechanical/molecular-mechanical (QM/MM) scheme, investigated by studying the molecular inhibition of CK2 protein by eight halobenzimidazole and -benzotriazole derivatives using hybrid QM/MM molecular-dynamics (MD) simulations with the inhibitor described at the QM level by the AM1 method and the rest of the system described at the MM level. The pure MM approach with inclusion of an extra point of positive charge on the halogen atom approach gave better results than the hybrid QM/MM approach involving the AM1 method. Also, in comparison with the pure MM-GBSA (generalized Born surface area) binding energies and experimental data, the calculated QM/MM-GBSA binding energies of the inhibitors were improved by replacing the G(GB,QM/MM) solvation term with the corresponding G(GB,MM) term.

Quasi free mechanism in single photon double ionization of helium

Energy Technology Data Exchange (ETDEWEB)

Schoeffler, Markus; Stuck, Christian [Frankfurt Univ., Frankfurt am Main (Germany). Inst. fuer Kernphysik; Lawrence Berkeley National Lab, Berkeley, CA (United States); Jahnke, Till; Waitz, Markus; Trinter, Florian; Lenz, Ute; Schmidt-Boecking, Horst; Doerner, Reinhard [Frankfurt Univ., Frankfurt am Main (Germany). Inst. fuer Kernphysik; Jones, Mathew; Landers, Allen [Auburn University, Auburn, AL (United States); Belkacem, Ali; Weber, Thorsten [Lawrence Berkeley National Lab, Berkeley, CA (United States); Cocke, Lew [Kansas State University, Manhattan, KS (United States)

2012-07-01

Double ionization of Helium by a single photon is widely believed to proceed through two mechanisms: knock-off (TS1) or shake-off, with the last one dominating at high photon energies. A new mechanism, termed ''Quasi Free Mechanism'' (QFM) was predicted 35 years ago by Amusia and coworkers, but escaped experimental observation till today. Here we provide the first proof of this mechanism using 800 eV photons from the Advanced Light Source. Fragments (electrons and ions) were measured in coincidence using momentum spectroscopy (COLTRIMS). He{sup (}2+) ions with zero momentum were found - the fingerprint for the QFM.

What Protein Charging (and Supercharging) Reveal about the Mechanism of Electrospray Ionization

Science.gov (United States)

Ogorzalek Loo, Rachel R.; Lakshmanan, Rajeswari; Loo, Joseph A.

2014-10-01

Understanding the charging mechanism of electrospray ionization is central to overcoming shortcomings such as ion suppression or limited dynamic range, and explaining phenomena such as supercharging. Towards that end, we explore what accumulated observations reveal about the mechanism of electrospray. We introduce the idea of an intermediate region for electrospray ionization (and other ionization methods) to account for the facts that solution charge state distributions (CSDs) do not correlate with those observed by ESI-MS (the latter bear more charge) and that gas phase reactions can reduce, but not increase, the extent of charging. This region incorporates properties (e.g., basicities) intermediate between solution and gas phase. Assuming that droplet species polarize within the high electric field leads to equations describing ion emission resembling those from the equilibrium partitioning model. The equations predict many trends successfully, including CSD shifts to higher m/z for concentrated analytes and shifts to lower m/z for sprays employing smaller emitter opening diameters. From this view, a single mechanism can be formulated to explain how reagents that promote analyte charging ("supercharging") such as m-NBA, sulfolane, and 3-nitrobenzonitrile increase analyte charge from "denaturing" and "native" solvent systems. It is suggested that additives' Brønsted basicities are inversely correlated to their ability to shift CSDs to lower m/z in positive ESI, as are Brønsted acidities for negative ESI. Because supercharging agents reduce an analyte's solution ionization, excess spray charge is bestowed on evaporating ions carrying fewer opposing charges. Brønsted basicity (or acidity) determines how much ESI charge is lost to the agent (unavailable to evaporating analyte).

Molecular biological mechanisms I. DNA repair

International Nuclear Information System (INIS)

Friedl, A.A.

2000-01-01

Cells of all living systems possess a variety of mechanisms that allow to repair spontaneous and exogeneously induced DNA damage. DNA repair deficiencies may invoke enhanced sensitivity towards DNA-damaging agents such as ionizing radiation. They may also enhance the risk of cancer development, both spontaneously or after induction. This article reviews several DNA repair mechanisms, especially those dealing with DNA double-strand breaks, and describes hereditary diseases associated with DNA repair defects. (orig.) [de

Influence of ionizing radiation on the mechanical properties of BisGMA/TEGDMA based experimental resin

International Nuclear Information System (INIS)

LMP, Campos; Boaro, LC; LKG, Santos; Parra, DF; Lugão, AB

2015-01-01

Dental restorative composites are activated by visible light and the polymerization process, known as direct technique, is initiated by absorbing light in a specific wavelength range (450–500 nm). However this technique presented some disadvantages. If light is not inserted correctly, layers uncured can cause countless damage to restoration, especially with regard to mechanical properties. A clinical alternative used to reduce the shortcomings of direct application is the use of composite resins for indirect application. These composites are adaptations of resins prepared for direct use, with differences mainly in the healing process. Besides the traditional photoactivation, indirect application composites may be submitted to particular curing conditions, such as a slow curing rate, heating, vacuum, and inert-gas pressure leading to an oxygen-free environment. However few studies have been conducted on the process of post-curing by ionizing radiation at low doses. On this sense the purpose of this study was to evaluate possible interactions of ionizing radiation in the post-curing process of the experimental composites based on BisGMA/TEGDMA filled with silica Aerosil OX-50 silanized. Characterization of the experimental composites was performed by thermogravimetry analysis, infrared spectroscopy, elastic modulus and flexural strength. Statistical analysis of results was calculated by one-way ANOVA/Tukey's test. Cross-linking of the polymeric matrix caused by ionizing radiation, influenced the thermal stability of irradiated specimens. FTIR analysis showed that the ionizing radiation induced a post-cure reaction in the specimens. The irradiation dose influenced directly the mechanical properties that showed a strong positive correlation between flexural strength and irradiation and between modulus strength and irradiation. - Highlights: • Interactions of ionizing radiation in BisGMA/TEGDMA experimental dental composites filled with sylanized silica. �

Magnetic diffusion and ionization fractions in dense molecular clouds: The role of charged grains

International Nuclear Information System (INIS)

Elmegreen, B.G.

1979-01-01

The ionization fraction is determined for dense molecular clouds by considering charge exchange, dissociative recombination, radiative recombination, and collisions between grains and charged species. The inclusion of grains tends to lower the ionization fraction for a given cosmic-ray ionization rate zeta and metal depletion delta. The observed values of the ionization fractions in dense cloud cores (i.e., -8 ) are obtained for reasonable values of zeta=10 -17 s -1 and delta=0.1.For temperatures less than 30 K, each grain alternates in charge between -e and 0. The resulting motion of the grains in a self-graviting cloud that contains a magnetic field will be periodic; their response to electromagnetic forces will depend on their instantaneous charge. This complex motion is calculated in order to determine the average viscous force between the grains and the neutral molecules in the cloud. The grain-neutral viscous force combines with the ion-neutral viscous force to regulate the motion of the neutral molecules relative to the magnetic field. The resultant The result neutral drift leads to a diffusion of the magnetic field out of the cloud. The time scale for this diffusion is calculated. Grain-related viscous forces dominate ion-related forces for ionization fractions less than 5 x 10 -8 . The magnetic diffusion time in a self-gravitating cloud that is supported by an internal magnetic field is shown to be at least 10 times larger thanthe free-fall time even when the ionization fraction is much less than 10 -8

Atomic and Molecular Systems in Intense Ultrashort Laser Pulses

Science.gov (United States)

Saenz, A.

2008-07-01

The full quantum mechanical treatment of atomic and molecular systems exposed to intense laser pulses is a so far unsolved challenge, even for systems as small as molecular hydrogen. Therefore, a number of simplified qualitative and quantitative models have been introduced in order to provide at least some interpretational tools for experimental data. The assessment of these models describing the molecular response is complicated, since a comparison to experiment requires often a number of averages to be performed. This includes in many cases averaging of different orientations of the molecule with respect to the laser field, focal volume effects, etc. Furthermore, the pulse shape and even the peak intensity is experimentally not known with very high precision; considering, e.g., the exponential intensity dependence of the ionization signal. Finally, experiments usually provide only relative yields. As a consequence of all these averagings and uncertainties, it is possible that different models may successfully explain some experimental results or features, although these models disagree substantially, if their predictions are compared before averaging. Therefore, fully quantum-mechanical approaches at least for small atomic and molecular systems are highly desirable and have been developed in our group. This includes efficient codes for solving the time-dependent Schrodinger equation of atomic hydrogen, helium or other effective one- or two-electron atoms as well as for the electronic motion in linear (effective) one-and two-electron diatomic molecules like H_2.Very recently, a code for larger molecular systems that adopts the so-called single-active electron approximation was also successfully implemented and applied. In the first part of this talk popular models describing intense laser-field ionization of atoms and their extensions to molecules are described. Then their validity is discussed on the basis of quantum-mechanical calculations. Finally, some

Oxidation of Carbon Nanotubes in an Ionizing Environment.

Science.gov (United States)

Koh, Ai Leen; Gidcumb, Emily; Zhou, Otto; Sinclair, Robert

2016-02-10

In this work, we present systematic studies on how an illuminating electron beam which ionizes molecular gas species can influence the mechanism of carbon nanotube oxidation in an environmental transmission electron microscope (ETEM). We found that preferential attack of the nanotube tips is much more prevalent than for oxidation in a molecular gas environment. We establish the cumulative electron doses required to damage carbon nanotubes from 80 keV electron beam irradiation in gas versus in high vacuum. Our results provide guidelines for the electron doses required to study carbon nanotubes within or without a gas environment, to determine or ameliorate the influence of the imaging electron beam. This work has important implications for in situ studies as well as for the oxidation of carbon nanotubes in an ionizing environment such as that occurring during field emission.

Sampling Molecular Conformers in Solution with Quantum Mechanical Accuracy at a Nearly Molecular-Mechanics Cost.

Science.gov (United States)

Rosa, Marta; Micciarelli, Marco; Laio, Alessandro; Baroni, Stefano

2016-09-13

We introduce a method to evaluate the relative populations of different conformers of molecular species in solution, aiming at quantum mechanical accuracy, while keeping the computational cost at a nearly molecular-mechanics level. This goal is achieved by combining long classical molecular-dynamics simulations to sample the free-energy landscape of the system, advanced clustering techniques to identify the most relevant conformers, and thermodynamic perturbation theory to correct the resulting populations, using quantum-mechanical energies from density functional theory. A quantitative criterion for assessing the accuracy thus achieved is proposed. The resulting methodology is demonstrated in the specific case of cyanin (cyanidin-3-glucoside) in water solution.

Analysis of multiple scattering contributions in electron-impact ionization of molecular hydrogen

Science.gov (United States)

Ren, Xueguang; Hossen, Khokon; Wang, Enliang; Pindzola, M. S.; Dorn, Alexander; Colgan, James

2017-10-01

We report a combined experimental and theoretical study on the low-energy (E 0 = 31.5 eV) electron-impact ionization of molecular hydrogen (H2). Triple differential cross sections are measured for a range of fixed emission angles of one outgoing electron between {θ }1=-70^\\circ and -130° covering the full 4π solid angle of the second electron. The energy sharing of the outgoing electrons varies from symmetric ({E}1={E}2=8 eV) to highly asymmetric (E 1 = 1 eV and E 2 = 15 eV). In addition to the binary and recoil lobes, a structure is observed perpendicular to the incoming beam direction which is due to multiple scattering of the projectile inside the molecular potential. The absolutely normalized experimental cross sections are compared with results from the time-dependent close-coupling (TDCC) calculations. Molecular alignment dependent TDCC results demonstrate that these structures are only present if the molecule axis is lying in the scattering plane.

CHEMICAL ANALYSIS OF A DIFFUSE CLOUD ALONG A LINE OF SIGHT TOWARD W51: MOLECULAR FRACTION AND COSMIC-RAY IONIZATION RATE

Energy Technology Data Exchange (ETDEWEB)

Indriolo, Nick; Neufeld, D. A. [Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218 (United States); Gerin, M. [LERMA, CNRS, Observatoire de Paris and ENS, F-75231 Paris Cedex 05 (France); Geballe, T. R. [Gemini Observatory, Hilo, HI 96720 (United States); Black, J. H. [Department of Earth and Space Sciences, Chalmers University of Technology, Onsala Space Observatory, SE-43992 Onsala (Sweden); Menten, K. M. [MPI fuer Radioastronomie, D-53121 Bonn (Germany); Goicoechea, J. R. [Departamento de Astrofisica, Centro de Astrobiologia (CSIC-INTA), E-28850 Madrid (Spain)

2012-10-20

Absorption lines from the molecules OH{sup +}, H{sub 2}O{sup +}, and H{sup +} {sub 3} have been observed in a diffuse molecular cloud along a line of sight near W51 IRS2. We present the first chemical analysis that combines the information provided by all three of these species. Together, OH{sup +} and H{sub 2}O{sup +} are used to determine the molecular hydrogen fraction in the outskirts of the observed cloud, as well as the cosmic-ray ionization rate of atomic hydrogen. H{sup +} {sub 3} is used to infer the cosmic-ray ionization rate of H{sub 2} in the molecular interior of the cloud, which we find to be {zeta}{sub 2} = (4.8 {+-} 3.4) Multiplication-Sign 10{sup -16} s{sup -1}. Combining the results from all three species we find an efficiency factor-defined as the ratio of the formation rate of OH{sup +} to the cosmic-ray ionization rate of H-of {epsilon} = 0.07 {+-} 0.04, much lower than predicted by chemical models. This is an important step in the future use of OH{sup +} and H{sub 2}O{sup +} on their own as tracers of the cosmic-ray ionization rate.

Mechanism of Interaction between Ionizing Radiation and Chemicals

International Nuclear Information System (INIS)

Kim, Jin Kyu; Lee, B. H.; Shin, H. S.

2008-03-01

This research project has been carried out jointly with INP (Poland) to develop technologies for 'Mechanism of Interaction between ionizing radiation and chemicals . Several biological end-points were assessed in experimental organisms such as higher plants, rats, cell lines and yeast cells to establish proper bioassay techniques. The Tradescantia somatic cell mutation assay was carried out, and immunohistochemistry and hormone assays were done in Fisher 344 rats and cell lines to analyse the combined effect of ionizing radiation with mercury chloride. Using the common regularities of combined actions of two factors, a theoretical model was established, and applied to the thermo radiation action and synergism between two chemicals, as well. The model approach made it possible to predict the condition under which the maximum synergism could be attained. The research results were published in high standard journals and presented in the scientific conferences to verify KAERI's current technology level. The experience of collaboration can be used as a fundamental tool for multinational collaboration, and make the role of improving relationship between Korea and Poland

Mechanism of Interaction between Ionizing Radiation and Chemicals

Energy Technology Data Exchange (ETDEWEB)

Kim, Jin Kyu; Lee, B H; Shin, H S [and others

2008-03-15

This research project has been carried out jointly with INP (Poland) to develop technologies for 'Mechanism of Interaction between ionizing radiation and chemicals{sup .} Several biological end-points were assessed in experimental organisms such as higher plants, rats, cell lines and yeast cells to establish proper bioassay techniques. The Tradescantia somatic cell mutation assay was carried out, and immunohistochemistry and hormone assays were done in Fisher 344 rats and cell lines to analyse the combined effect of ionizing radiation with mercury chloride. Using the common regularities of combined actions of two factors, a theoretical model was established, and applied to the thermo radiation action and synergism between two chemicals, as well. The model approach made it possible to predict the condition under which the maximum synergism could be attained. The research results were published in high standard journals and presented in the scientific conferences to verify KAERI's current technology level. The experience of collaboration can be used as a fundamental tool for multinational collaboration, and make the role of improving relationship between Korea and Poland.

Mechanism of Interaction between Ionizing Radiation and Chemicals

Energy Technology Data Exchange (ETDEWEB)

Kim, Jin Kyu; Lee, B. H.; Shin, H. S. (and others)

2008-03-15

This research project has been carried out jointly with INP (Poland) to develop technologies for 'Mechanism of Interaction between ionizing radiation and chemicals{sup .} Several biological end-points were assessed in experimental organisms such as higher plants, rats, cell lines and yeast cells to establish proper bioassay techniques. The Tradescantia somatic cell mutation assay was carried out, and immunohistochemistry and hormone assays were done in Fisher 344 rats and cell lines to analyse the combined effect of ionizing radiation with mercury chloride. Using the common regularities of combined actions of two factors, a theoretical model was established, and applied to the thermo radiation action and synergism between two chemicals, as well. The model approach made it possible to predict the condition under which the maximum synergism could be attained. The research results were published in high standard journals and presented in the scientific conferences to verify KAERI's current technology level. The experience of collaboration can be used as a fundamental tool for multinational collaboration, and make the role of improving relationship between Korea and Poland.

Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism

DEFF Research Database (Denmark)

Lonsdale, Richard; Fort, Rachel M; Rydberg, Patrik

2016-01-01

)-mexiletine in CYP1A2 with hybrid quantum mechanics/molecular mechanics (QM/MM) methods, providing a more detailed and realistic model. Multiple reaction barriers have been calculated at the QM(B3LYP-D)/MM(CHARMM27) level for the direct N-oxidation and H-abstraction/rebound mechanisms. Our calculated barriers......The mechanism of cytochrome P450(CYP)-catalyzed hydroxylation of primary amines is currently unclear and is relevant to drug metabolism; previous small model calculations have suggested two possible mechanisms: direct N-oxidation and H-abstraction/rebound. We have modeled the N-hydroxylation of (R...... indicate that the direct N-oxidation mechanism is preferred and proceeds via the doublet spin state of Compound I. Molecular dynamics simulations indicate that the presence of an ordered water molecule in the active site assists in the binding of mexiletine in the active site...

Investigation of the ionization mechanism of polycyclic aromatic hydrocarbons using an ethanol/bromobenzene/chlorobenzene/anisole mixture as a dopant in liquid chromatography/atmospheric pressure photoionization mass spectrometry

KAUST Repository

Amad, Maan H.

2012-09-23

RATIONALE An ethanol-based multicomponent dopant consisting of ethanol/chlorobenzene/bromobenzene/anisole (98.975:0.1:0.9:0.025, v/v/v/v) has been used as a dopant for atmospheric pressure photoionization (APPI) of polycyclic aromatic hydrocarbons (PAHs). In this study the mechanism of ionization of PAHs assisted by the ethanol-based multicomponent dopant is investigated. METHODS The reactant background cluster ions of the ethanol-based multicomponent dopant observed in the positive ion APPI were studied. These studies were performed to investigate the mechanism behind the generation of a molecular radical cation (M +•) for PAHs by APPI assisted by the ethanol-based multicomponent dopant. Full scan and MS/MS analyses were conducted using an LTQ Orbitrap mass spectrometer. The effect of acidification of the mobile phase on the dopant cluster ion formation was also investigated. RESULTS With the ethanol-based multicomponent dopant, a single type of molecular radical cation M +• was observed for the studied PAHs. The characteristic ion signal of the multicomponent dopant mixture consisted of mainly anisole photoions at m/z 108.05697 and its adduct ions at m/z 124.05188 and 164.07061. The anisole ion response at m/z 108.05697 was stable in the presence of acetonitrile, methanol, water and 0.1% formic acid mobile phase composition. CONCLUSIONS The abundance formation of anisole photoions shows the universality of this multicomponent dopant in ionizing compounds with ionization energy ranging from 7.1-8.2 eV. Since the ionization energy of anisole is 8.2 eV and is lower than those of chlorobenzene (9.07 eV) and bromobenzene (9.0 eV), the mechanism of formation of anisole photoions even with its very minute amounts was not only governed by its photoionization by the krypton lamp photon energy (10.0 eV and 10.6 eV), but also by charge transfer from bromobenzene and chlorobenzene radical cations. PAH molecules were mainly ionized by charge transfer reaction from

Investigation of the ionization mechanism of polycyclic aromatic hydrocarbons using an ethanol/bromobenzene/chlorobenzene/anisole mixture as a dopant in liquid chromatography/atmospheric pressure photoionization mass spectrometry

KAUST Repository

Amad, Maan H.; Sioud, Salim

2012-01-01

RATIONALE An ethanol-based multicomponent dopant consisting of ethanol/chlorobenzene/bromobenzene/anisole (98.975:0.1:0.9:0.025, v/v/v/v) has been used as a dopant for atmospheric pressure photoionization (APPI) of polycyclic aromatic hydrocarbons (PAHs). In this study the mechanism of ionization of PAHs assisted by the ethanol-based multicomponent dopant is investigated. METHODS The reactant background cluster ions of the ethanol-based multicomponent dopant observed in the positive ion APPI were studied. These studies were performed to investigate the mechanism behind the generation of a molecular radical cation (M +•) for PAHs by APPI assisted by the ethanol-based multicomponent dopant. Full scan and MS/MS analyses were conducted using an LTQ Orbitrap mass spectrometer. The effect of acidification of the mobile phase on the dopant cluster ion formation was also investigated. RESULTS With the ethanol-based multicomponent dopant, a single type of molecular radical cation M +• was observed for the studied PAHs. The characteristic ion signal of the multicomponent dopant mixture consisted of mainly anisole photoions at m/z 108.05697 and its adduct ions at m/z 124.05188 and 164.07061. The anisole ion response at m/z 108.05697 was stable in the presence of acetonitrile, methanol, water and 0.1% formic acid mobile phase composition. CONCLUSIONS The abundance formation of anisole photoions shows the universality of this multicomponent dopant in ionizing compounds with ionization energy ranging from 7.1-8.2 eV. Since the ionization energy of anisole is 8.2 eV and is lower than those of chlorobenzene (9.07 eV) and bromobenzene (9.0 eV), the mechanism of formation of anisole photoions even with its very minute amounts was not only governed by its photoionization by the krypton lamp photon energy (10.0 eV and 10.6 eV), but also by charge transfer from bromobenzene and chlorobenzene radical cations. PAH molecules were mainly ionized by charge transfer reaction from

Polarization effects in molecular mechanical force fields

Energy Technology Data Exchange (ETDEWEB)

Cieplak, Piotr [Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92120 (United States); Dupradeau, Francois-Yves [UMR CNRS 6219-Faculte de Pharmacie, Universite de Picardie Jules Verne, 1 rue des Louvels, F-80037 Amiens (France); Duan, Yong [Genome Center and Department of Applied Science, University of California, Davis, One Shields Avenue, Davis, CA 95616 (United States); Wang Junmei, E-mail: pcieplak@burnham.or [Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Boulevard, ND9.136, Dallas, TX 75390-9050 (United States)

2009-08-19

The focus here is on incorporating electronic polarization into classical molecular mechanical force fields used for macromolecular simulations. First, we briefly examine currently used molecular mechanical force fields and the current status of intermolecular forces as viewed by quantum mechanical approaches. Next, we demonstrate how some components of quantum mechanical energy are effectively incorporated into classical molecular mechanical force fields. Finally, we assess the modeling methods of one such energy component-polarization energy-and present an overview of polarizable force fields and their current applications. Incorporating polarization effects into current force fields paves the way to developing potentially more accurate, though more complex, parameterizations that can be used for more realistic molecular simulations. (topical review)

Quantum-mechanical predictions of electron-induced ionization cross sections of DNA components

International Nuclear Information System (INIS)

Champion, Christophe

2013-01-01

Ionization of biomolecules remains still today rarely investigated on both the experimental and the theoretical sides. In this context, the present work appears as one of the first quantum mechanical approaches providing a multi-differential description of the electron-induced ionization process of the main DNA components for impact energies ranging from the target ionization threshold up to about 10 keV. The cross section calculations are here performed within the 1st Born approximation framework in which the ejected electron is described by a Coulomb wave whereas the incident and the scattered electrons are both described by a plane wave. The biological targets of interest, namely, the DNA nucleobases and the sugar-phosphate backbone, are here described by means of the GAUSSIAN 09 system using the restricted Hartree-Fock method with geometry optimization. The theoretical predictions also obtained have shown a reasonable agreement with the experimental total ionization cross sections while huge discrepancies have been pointed out with existing theoretical models, mainly developed within a semi-classical framework.

Effects of ionizing radiation on the properties of ultra-high molecular weight polyethylene (PE-UHMW)

International Nuclear Information System (INIS)

Kurth, M.

1990-01-01

Ultra high molecular weight polyethylene (PE-UHMW) is used in most artificial joint replacement devices. Prior to implantation in biological environment, radiatin sterilization by 60 Co or electron beam is common. It is well known that polyethylene exposed to ionizing radiation of any sort undergo physical changes due to chain scission and/or crosslinking. PE-UHMW sheets, 8 mm thick, were either 60 Co or electron beam irradiated, in the range of 10-150 kGy under air or nitrogen atmoshere. The crystallinity of the irradiated samples increases with the irradiation dose. The chain scission/crosslinking events ratio determine the network structure and the sol/gel ratio. The latter was found to depend on irradiation dose, radiation atmosphere and sample thickness. Moreover 60 Co-irradiation is about 5 times more effective in forming PE-UHMW gel than electron-irradiation. Besides the degree of crosslinking, the molecular weight distribution is the main determinant of the structural properties of PE-UHMW. Low molecular weight fractions were also found. Using a dose of 30 kGy ( 60 Co in air), the average molecular weight of the soluble part after extraction decreased from originally 2.3 million g/mol to 170.000 g/mol, corresponding to a factor of about 10. These changes in molecular weight have a strong influence on the mechanical properties of PE-UHMW. Crosslinking slightly increases the yield strength, while the elongation at break decreases. Long-term compressive creep is reduced if the material is irradiated. Obviously, increased crystallinity after oxidative chain scission affects a higher deformation resistance. Radiation crosslinked structures cause a significant increase in abrasion resistance. The above described structural changes occur even upon irradiation of very low doses as used during sterilization. This study will enable to reduce the radiation sterilization damage and thus to gain long term stability of PE-UHMW medical devices. (orig./BBR)

Molecular and Ionized Hydrogen in 30 Doradus. I. Imaging Observations

Science.gov (United States)

Yeh, Sherry C. C.; Seaquist, Ernest R.; Matzner, Christopher D.; Pellegrini, Eric W.

2015-07-01

We present the first fully calibrated H2 1-0 S(1) image of the entire 30 Doradus nebula. The observations were conducted using the NOAO Extremely Wide-field Infrared Imager (NEWFIRM) on the CTIO 4 m Blanco Telescope. Together with a NEWFIRM Brγ image of 30 Doradus, our data reveal the morphologies of the warm molecular gas and ionized gas in 30 Doradus. The brightest H2-emitting area, which extends from the northeast to the southwest of R136, is a photodissociation region (PDR) viewed face-on, while many clumps and pillar features located at the outer shells of 30 Doradus are PDRs viewed edge-on. Based on the morphologies of H2, Brγ, CO, and 8 μm emission, the H2 to Brγ line ratio, and Cloudy models, we find that the H2 emission is formed inside the PDRs of 30 Doradus, 2-3 pc to the ionization front of the H ii region, in a relatively low-density environment <104 cm-3. Comparisons with Brγ, 8 μm, and CO emission indicate that H2 emission is due to fluorescence, and provide no evidence for shock excited emission of this line.

MOLECULAR AND IONIZED HYDROGEN IN 30 DORADUS. I. IMAGING OBSERVATIONS

Energy Technology Data Exchange (ETDEWEB)

Yeh, Sherry C. C. [Subaru Telescope, National Astronomical Observatory of Japan, 650 North A’ohoku Place, Hilo, HI 96720 (United States); Seaquist, Ernest R.; Matzner, Christopher D. [Department of Astronomy and Astrophysics, University of Toronto, 50 St. George Street, Toronto, ON M5S 3H4 (Canada); Pellegrini, Eric W., E-mail: yeh@naoj.org [Department of Physics and Astronomy, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606 (United States)

2015-07-10

We present the first fully calibrated H{sub 2} 1–0 S(1) image of the entire 30 Doradus nebula. The observations were conducted using the NOAO Extremely Wide-field Infrared Imager (NEWFIRM) on the CTIO 4 m Blanco Telescope. Together with a NEWFIRM Brγ image of 30 Doradus, our data reveal the morphologies of the warm molecular gas and ionized gas in 30 Doradus. The brightest H{sub 2}-emitting area, which extends from the northeast to the southwest of R136, is a photodissociation region (PDR) viewed face-on, while many clumps and pillar features located at the outer shells of 30 Doradus are PDRs viewed edge-on. Based on the morphologies of H{sub 2}, Brγ, CO, and 8 μm emission, the H{sub 2} to Brγ line ratio, and Cloudy models, we find that the H{sub 2} emission is formed inside the PDRs of 30 Doradus, 2–3 pc to the ionization front of the H ii region, in a relatively low-density environment <10{sup 4} cm{sup −3}. Comparisons with Brγ, 8 μm, and CO emission indicate that H{sub 2} emission is due to fluorescence, and provide no evidence for shock excited emission of this line.

Deep-down ionization of protoplanetary discs

Science.gov (United States)

Glassgold, A. E.; Lizano, S.; Galli, D.

2017-12-01

The possible occurrence of dead zones in protoplanetary discs subject to the magneto-rotational instability highlights the importance of disc ionization. We present a closed-form theory for the deep-down ionization by X-rays at depths below the disc surface dominated by far-ultraviolet radiation. Simple analytic solutions are given for the major ion classes, electrons, atomic ions, molecular ions and negatively charged grains. In addition to the formation of molecular ions by X-ray ionization of H2 and their destruction by dissociative recombination, several key processes that operate in this region are included, e.g. charge exchange of molecular ions and neutral atoms and destruction of ions by grains. Over much of the inner disc, the vertical decrease in ionization with depth into the disc is described by simple power laws, which can easily be included in more detailed modelling of magnetized discs. The new ionization theory is used to illustrate the non-ideal magnetohydrodynamic effects of Ohmic, Hall and Ambipolar diffusion for a magnetic model of a T Tauri star disc using the appropriate Elsasser numbers.

Effect of Ionizing Beta Radiation on the Mechanical Properties of Poly(ethylene under Thermal Stress

Directory of Open Access Journals (Sweden)

Bednarik Martin

2016-01-01

Full Text Available It was found in this study, that ionizing beta radiation has a positive effect on the mechanical properties of poly(ethylene. In recent years, there have been increasing requirements for quality and cost effectiveness of manufactured products in all areas of industrial production. These requirements are best met with the polymeric materials, which have many advantages in comparison to traditional materials. The main advantages of polymer materials are especially in their ease of processability, availability, and price of the raw materials. Radiation crosslinking is one of the ways to give the conventional plastics mechanical, thermal, and chemical properties of expensive and highly resistant construction polymers. Several types of ionizing radiation are used for crosslinking of polymers. Each of them has special characteristics. Electron beta and photon gamma radiation are used the most frequently. The great advantage is that the crosslinking occurs after the manufacturing process at normal temperature and pressure. The main purpose of this paper has been to determine the effect of ionizing beta radiation on the tensile modulus, strength and elongation of low and high density polyethylene (LDPE and HDPE. These properties were examined in dependence on the dosage of the ionizing beta radiation (non-irradiated samples and those irradiated by dosage 99 kGy were compared and on the test temperature. Radiation cross-linking of LDPE and HDPE results in increased tensile strength and modulus, and decreased of elongation. The measured results indicate that ionizing beta radiation treatment is effective tool for improvement of mechanical properties of LDPE and HDPE under thermal stress.

Ab initio R-matrix/Multi-channel Quantum Defect Theory applied to Molecular Core Excitation and Ionization

International Nuclear Information System (INIS)

Hiyama, M.; Kosugi, N.

2004-01-01

Full text: Ab initio R-matrix/MQDT approach, which is a combination of ab initio R-matrix techniques and the multi channel quantum defect theory (MQDT), has recently been developed by one of the present authors (MH) and Child, to successfully obtain the potential energy curves of Rydberg states converging to not only the lowest but also the higher ionized states. This approach is also applied to estimate the valence state interaction with Rydberg and continuum (ionization) channels. Very recently we have made an original ab initio polyatomic R-matrix/MQDT program package, GSCF4R based on Gaussian type basis functions for the bound and continuum states, to extensively study molecular excitation and ionization in the X-ray region as well as in the VUV region. We are going to report the results for core excitation and ionization of diatomic molecules such as NO and O 2 to show that the R-matrix/MQDT method is indispensable to describe the core-to-Rydberg states with the higher quantum number and the continuum states. These results lead us to the conclusion that the close-coupling approximation augmented with the correlation term within the R-matrix/MQDT formalism is powerful to calculate the Rydberg-valence mixing and the interchannel coupling between several core-ionized states

H ii REGION G46.5-0.2: THE INTERPLAY BETWEEN IONIZING RADIATION, MOLECULAR GAS, AND STAR FORMATION

International Nuclear Information System (INIS)

Paron, S.; Ortega, M. E.; Dubner, G.; Petriella, A.; Giacani, E.; Yuan, Jing-Hua; Li, Jin Zeng; Liu, Hongli; Huang, Ya Fang; Zhang, Si-Ju; Wu, Yuefang

2015-01-01

H ii regions are particularly interesting because they can generate dense layers of gas and dust, elongated columns or pillars of gas pointing toward the ionizing sources, and cometary globules of dense gas where triggered star formation can occur. Understanding the interplay between the ionizing radiation and the dense surrounding gas is very important to explain the origin of these peculiar structures, and hence to characterize triggered star formation. G46.5-0.2 (G46), a poorly studied galactic H ii region located at about 4 kpc, is an excellent target for performing this kind of study. Using public molecular data extracted from the Galactic Ring Survey ( 13 CO J = 1–0) and from the James Clerk Maxwell Telescope data archive ( 12 CO, 13 CO, C 18 O J = 3–2, HCO + , and HCN J = 4–3), and infrared data from the GLIMPSE and MIPSGAL surveys, we perform a complete study of G46, its molecular environment, and the young stellar objects (YSOs) placed around it. We found that G46, probably excited by an O7V star, is located close to the edge of the GRSMC G046.34-00.21 molecular cloud. It presents a horse-shoe morphology opening in the direction of the cloud. We observed a filamentary structure in the molecular gas likely related to G46 and not considerable molecular emission toward its open border. We found that about 10′ to the southwest of G46 there are some pillar-like features, shining at 8 μm and pointing toward the H ii region open border. We propose that the pillar-like features were carved and sculpted by the ionizing flux from G46. We found several YSOs likely embedded in the molecular cloud grouped in two main concentrations: one, closer to the G46 open border consisting of Class II type sources, and another mostly composed of Class I type YSOs located just ahead of the pillar-like features, strongly suggesting an age gradient in the YSO distribution

H II Region G46.5-0.2: The Interplay between Ionizing Radiation, Molecular Gas, and Star Formation

Science.gov (United States)

Paron, S.; Ortega, M. E.; Dubner, G.; Yuan, Jing-Hua; Petriella, A.; Giacani, E.; Zeng Li, Jin; Wu, Yuefang; Liu, Hongli; Huang, Ya Fang; Zhang, Si-Ju

2015-06-01

H ii regions are particularly interesting because they can generate dense layers of gas and dust, elongated columns or pillars of gas pointing toward the ionizing sources, and cometary globules of dense gas where triggered star formation can occur. Understanding the interplay between the ionizing radiation and the dense surrounding gas is very important to explain the origin of these peculiar structures, and hence to characterize triggered star formation. G46.5-0.2 (G46), a poorly studied galactic H ii region located at about 4 kpc, is an excellent target for performing this kind of study. Using public molecular data extracted from the Galactic Ring Survey (13CO J = 1-0) and from the James Clerk Maxwell Telescope data archive (12CO, 13CO, C18O J = 3-2, HCO+, and HCN J = 4-3), and infrared data from the GLIMPSE and MIPSGAL surveys, we perform a complete study of G46, its molecular environment, and the young stellar objects (YSOs) placed around it. We found that G46, probably excited by an O7V star, is located close to the edge of the GRSMC G046.34-00.21 molecular cloud. It presents a horse-shoe morphology opening in the direction of the cloud. We observed a filamentary structure in the molecular gas likely related to G46 and not considerable molecular emission toward its open border. We found that about 10‧ to the southwest of G46 there are some pillar-like features, shining at 8 μm and pointing toward the H ii region open border. We propose that the pillar-like features were carved and sculpted by the ionizing flux from G46. We found several YSOs likely embedded in the molecular cloud grouped in two main concentrations: one, closer to the G46 open border consisting of Class II type sources, and another mostly composed of Class I type YSOs located just ahead of the pillar-like features, strongly suggesting an age gradient in the YSO distribution.

Quantum mechanics/coarse-grained molecular mechanics (QM/CG-MM).

Science.gov (United States)

Sinitskiy, Anton V; Voth, Gregory A

2018-01-07

Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used. However, the QM/MM approach often faces a number of challenges, including the high cost of repetitive QM computations, the slow sampling even for the MM part in those cases where a system under investigation has a complex dynamics, and a difficulty in providing a simple, qualitative interpretation of numerical results in terms of the influence of the molecular environment upon the active QM region. In this paper, we address these issues by combining QM/MM modeling with the methodology of "bottom-up" coarse-graining (CG) to provide the theoretical basis for a systematic quantum-mechanical/coarse-grained molecular mechanics (QM/CG-MM) mixed resolution approach. A derivation of the method is presented based on a combination of statistical mechanics and quantum mechanics, leading to an equation for the effective Hamiltonian of the QM part, a central concept in the QM/CG-MM theory. A detailed analysis of different contributions to the effective Hamiltonian from electrostatic, induction, dispersion, and exchange interactions between the QM part and the surroundings is provided, serving as a foundation for a potential hierarchy of QM/CG-MM methods varying in their accuracy and computational cost. A relationship of the QM/CG-MM methodology to other mixed resolution approaches is also discussed.

Quantum mechanics/coarse-grained molecular mechanics (QM/CG-MM)

Science.gov (United States)

Sinitskiy, Anton V.; Voth, Gregory A.

2018-01-01

Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used. However, the QM/MM approach often faces a number of challenges, including the high cost of repetitive QM computations, the slow sampling even for the MM part in those cases where a system under investigation has a complex dynamics, and a difficulty in providing a simple, qualitative interpretation of numerical results in terms of the influence of the molecular environment upon the active QM region. In this paper, we address these issues by combining QM/MM modeling with the methodology of "bottom-up" coarse-graining (CG) to provide the theoretical basis for a systematic quantum-mechanical/coarse-grained molecular mechanics (QM/CG-MM) mixed resolution approach. A derivation of the method is presented based on a combination of statistical mechanics and quantum mechanics, leading to an equation for the effective Hamiltonian of the QM part, a central concept in the QM/CG-MM theory. A detailed analysis of different contributions to the effective Hamiltonian from electrostatic, induction, dispersion, and exchange interactions between the QM part and the surroundings is provided, serving as a foundation for a potential hierarchy of QM/CG-MM methods varying in their accuracy and computational cost. A relationship of the QM/CG-MM methodology to other mixed resolution approaches is also discussed.

Ghost peaks observed after atmospheric pressure matrix-assisted laser desorption/ionization experiments may disclose new ionization mechanism of matrix-assisted hypersonic velocity impact ionization.

Science.gov (United States)

Moskovets, Eugene

2015-08-30

Understanding the mechanisms of matrix-assisted laser desorption/ionization (MALDI) promises improvements in the sensitivity and specificity of many established applications in the field of mass spectrometry. This paper reports a serendipitous observation of a significant ion yield in a post-ionization experiment conducted after the sample had been removed from a standard atmospheric pressure (AP)-MALDI source. This post-ionization is interpreted in terms of collisions of microparticles moving with a hypersonic velocity into a solid surface. Calculations show that the thermal energy released during such collisions is close to that absorbed by the top matrix layer in traditional MALDI. The microparticles, containing both the matrix and analytes, could be detached from a film produced inside the inlet capillary during the sample ablation and accelerated by the flow rushing through the capillary. These observations contribute some new perspective to ion formation in both laser and laser-less matrix-assisted ionization. An AP-MALDI ion source hyphenated with a three-stage high-pressure ion funnel system was utilized for peptide mass analysis. After the laser had been turned off and the MALDI sample removed, ions were detected during a gradual reduction of the background pressure in the first funnel. The constant-rate pressure reduction led to the reproducible appearance of different singly and doubly charged peptide peaks in mass spectra taken a few seconds after the end of the MALDI analysis of a dried-droplet spot. The ion yield as well as the mass range of ions observed with a significant delay after a completion of the primary MALDI analysis depended primarily on the background pressure inside the first funnel. The production of ions in this post-ionization step was exclusively observed during the pressure drop. A lower matrix background and significant increase in relative yield of double-protonated ions are reported. The observations were partially consistent

Surface-ionization field mass-spectrometry studies of nonequilibrium surface ionization

International Nuclear Information System (INIS)

Blashenkov, Nikolai M; Lavrent'ev, Gennadii Ya

2007-01-01

The ionization of polyatomic molecules on tungsten and tungsten oxide surfaces is considered for quasiequilibrium or essentially nonequilibrium conditions (in the latter case, the term nonequilibrium surface ionization is used for adsorbate ionization). Heterogeneous reactions are supposed to proceed through monomolecular decay of polyatomic molecules or fragments of multimolecular complexes. The nonequilibrium nature of these reactions is established. The dependences of the current density of disordered ions on the surface temperature, electric field strength, and ionized particle energy distribution are obtained in analytical form. Heterogeneous dissociation energies, the ionization potentials of radicals, and the magnitude of reaction departure from equilibrium are determined from experimental data, as are energy exchange times between reaction products and surfaces, the number of molecules in molecular complexes, and the number of effective degrees of freedom in molecules and complexes. In collecting the data a new technique relying on surface-ionization field mass-spectrometry was applied. (instruments and methods of investigation)

Biological effects of ionizing radiation

International Nuclear Information System (INIS)

Heribanova, A.

1995-01-01

The basic principles and pathways of effects of ionizing radiation on living organisms and cells are outlined. The following topics are covered: effects of radiation on living matter (direct effects, radical or indirect effects, dual radiation action, and molecular biological theories); effects of radiation on cells and tissues (cell depletion, changes in the cytogenetic information, reparation mechanisms), dose-response relationship (deterministic effects, stochastic effects), and the effects of radiation on man (acute radiation sickness, acute local changes, fetus injuries, non-tumorous late injuries, malignant tumors, genetic changes). (P.A.). 3 tabs., 2 figs., 5 refs

Mechanisms of alteration of the immune system by ionizing radiations: a basis for radiation protection

Energy Technology Data Exchange (ETDEWEB)

Bourguignon, M. [Direction Generale de la Surete Nucleaire et de la Radioprotection, 75 - Paris (France); Perez, M.; Dubner, D.; Michelin, S. [Autoridad Regulatoria Nuclear, Buenos Aires (Argentina); Carosella, E. [CEA, Service de Recherches en Hemato -Immunologie, 75 - Paris (France)

2006-07-01

the immunological response of the T cells. Immuno-proteasome activity is impaired following irradiation. 7- Immunosuppression and cancer. Malignant cells develop molecular mechanisms, e.g., HLA-G expression, to escape immune recognition. Higher cancer incidence in organ recipients may be attributable to their immunosuppressive treatment and to IR. 8- Autoimmune reactions. Ionizing radiation can break self-tolerance as observed in individuals exposed in Hiroshima and Nagasaki and in children with thyroid disease after Chernobyl accident. 9- Perturbation of immunological homeostasis. Both experimental and epidemiological data have demonstrated that IR disturbs T-cell homeostasis. Conclusion. The effects of IR on the immune system which combine immunosuppression and immuno-modulation, may be responsible for inadequate responses of the body to foreign aggressions allowing for the development of infections or cancers. More attention should be given to the immune system in the context of exposures to IR. (authors)

Mechanisms of alteration of the immune system by ionizing radiations: a basis for radiation protection

International Nuclear Information System (INIS)

Bourguignon, M.; Perez, M.; Dubner, D.; Michelin, S.; Carosella, E.

2006-01-01

the immunological response of the T cells. Immuno-proteasome activity is impaired following irradiation. 7- Immunosuppression and cancer. Malignant cells develop molecular mechanisms, e.g., HLA-G expression, to escape immune recognition. Higher cancer incidence in organ recipients may be attributable to their immunosuppressive treatment and to IR. 8- Autoimmune reactions. Ionizing radiation can break self-tolerance as observed in individuals exposed in Hiroshima and Nagasaki and in children with thyroid disease after Chernobyl accident. 9- Perturbation of immunological homeostasis. Both experimental and epidemiological data have demonstrated that IR disturbs T-cell homeostasis. Conclusion. The effects of IR on the immune system which combine immunosuppression and immuno-modulation, may be responsible for inadequate responses of the body to foreign aggressions allowing for the development of infections or cancers. More attention should be given to the immune system in the context of exposures to IR. (authors)

Effects of ionizing radiation and the molecular and cellular mechanisms

International Nuclear Information System (INIS)

1982-01-01

This symposium with its 60 contributions presents a survey of the current state of the art in molecular radiation biophysics and radiobiology in the FRG. Many contributions show the trend of applying findings in these fields to cancer research. The various sessions have been devoted to: 1) Radiation chemistry of biomolecules; 2) DNA damage and repair; 3) Repair of DNA damage; 4) Cell proliferation and cell inactivation; 5) Cancerogenesis, mutation and chromosomal damage; 6) Effects of heavy ions. (AJ) [de

On the SIMS Ionization Probability of Organic Molecules.

Science.gov (United States)

Popczun, Nicholas J; Breuer, Lars; Wucher, Andreas; Winograd, Nicholas

2017-06-01

The prospect of improved secondary ion yields for secondary ion mass spectrometry (SIMS) experiments drives innovation of new primary ion sources, instrumentation, and post-ionization techniques. The largest factor affecting secondary ion efficiency is believed to be the poor ionization probability (α + ) of sputtered material, a value rarely measured directly, but estimated to be in some cases as low as 10 -5 . Our lab has developed a method for the direct determination of α + in a SIMS experiment using laser post-ionization (LPI) to detect neutral molecular species in the sputtered plume for an organic compound. Here, we apply this method to coronene (C 24 H 12 ), a polyaromatic hydrocarbon that exhibits strong molecular signal during gas-phase photoionization. A two-dimensional spatial distribution of sputtered neutral molecules is measured and presented. It is shown that the ionization probability of molecular coronene desorbed from a clean film under bombardment with 40 keV C 60 cluster projectiles is of the order of 10 -3 , with some remaining uncertainty arising from laser-induced fragmentation and possible differences in the emission velocity distributions of neutral and ionized molecules. In general, this work establishes a method to estimate the ionization efficiency of molecular species sputtered during a single bombardment event. Graphical Abstract GRAPHICAL ABSTRACT TEXT HERE] -->.

Two-center interference effects in (e, 2e) ionization of H2 and CO2 at large momentum transfer

Science.gov (United States)

Yamazaki, Masakazu; Nakajima, Isao; Satoh, Hironori; Watanabe, Noboru; Jones, Darryl; Takahashi, Masahiko

2015-09-01

In recent years, there has been considerable interest in understanding quantum mechanical interference effects in molecular ionization. Since this interference appears as a consequence of coherent electron emission from the different molecular centers, it should depend strongly on the nature of the ionized molecular orbital. Such molecular orbital patterns can be investigated by means of binary (e, 2e) spectroscopy, which is a kinematically-complete electron-impact ionization experiment performed under the high-energy Bethe ridge conditions. In this study, two-center interference effects in the (e, 2e) cross sections of H2 and CO2 at large momentum transfer are demonstrated with a high-statistics experiment, in order to elucidate the relationship between molecular orbital patterns and the interference structure. It is shown that the two-center interference is highly sensitive to the phase, spatial pattern, symmetry of constituent atomic orbital, and chemical bonding nature of the molecular orbital. This work was partially supported by Grant-in-Aids for Scientific Research (S) (No. 20225001) and for Young Scientists (B) (No. 21750005) from the Ministry of Education, Culture, Sports, Science and Technology.

Molecular Theory of the Living Cell Concepts, Molecular Mechanisms, and Biomedical Applications

CERN Document Server

Ji, Sungchul

2012-01-01

This book presents a comprehensive molecular theory of the living cell based on over thirty concepts, principles and laws imported from thermodynamics, statistical mechanics, quantum mechanics, chemical kinetics, informatics, computer science, linguistics, semiotics, and philosophy. The author formulates physically, chemically and enzymologically realistic molecular mechanisms to account for the basic living processes such as ligand-receptor interactions, protein folding, single-molecule enzymic catalysis, force-generating mechanisms in molecular motors, signal transduction, regulation of the genome-wide RNA metabolism, morphogenesis, the micro-macro coupling in coordination dynamics, the origin of life, and the mechanisms of biological evolution itself. Possible solutions to basic and practical problems facing contemporary biology and biomedical sciences have been suggested, including pharmacotheragnostics and personalized medicine.

Atomic and molecular resonance ionization

International Nuclear Information System (INIS)

Botter, R.; Petit, A.

1990-01-01

Published in summary form only the paper recalls the principle of resonance photoionization, transition probability, selectivity and critical parameters. Examples of applications are briefly treated: Trace analysis by resonance ionization mass spectroscopy for detection of Fe in Zr F 4 for fabrication of optical fibers and laser isotopic separation of U 235 and Gd 157 [fr

Chromosomal instability induced by ionizing radiation

International Nuclear Information System (INIS)

Morgan, W.F.; Marder, B.A.; Day, J.P.

1995-01-01

There is accumulating evidence indicating genomic instability can manifest multiple generations after cellular exposure to DNA damaging agents. For instance, some cells surviving exposure to ionizing radiations show delayed reproductive cell death, delayed mutation and / or delayed chromosomal instability. Such instability, especially chromosome destabilization has been implicated in mutation, gene amplification, cellular transformation, and cell killing. To investigate chromosomal instability following DNA damage, we have used fluorescence in situ hybridization to detect chromosomal rearrangements in a human/hamster somatic hybrid cell line following exposure to ionizing radiation. Delayed chromosomal instability was detected when multiple populations of uniquely arranged metaphases were observed in clonal isolates raised from single cells. The relationship between delayed chromosomal destabilization and other endpoints of genomic instability, namely; delayed mutation and gene amplification will be discussed, as will the potential cytogenetic and molecular mechanisms contributing to delayed chromosomal instability

Photoelectron angular distributions from strong-field ionization of oriented molecules

DEFF Research Database (Denmark)

Holmegaard, Lotte; Hansen, Jonas Lerche; Kalhøj, Line

2010-01-01

The combination of ultrafast light sources with detection of molecular-frame photoelectron angular distributions (MFPADs) is setting new standards for detailed interrogation of molecular dynamics. However, until recently measurement of MFPADs relied on determining the molecular orientation after...... ionization, which is limited to species and processes where ionization leads to fragmentation. An alternative is to fix the molecular frame before ionization. The only demonstrations of such spatial orientation involved aligned small linear nonpolar molecules. Here we extend these techniques to the general...... class of polar molecules. Carbonylsulphide and benzonitrile molecules, fixed in space by combined laser and electrostatic fields, are ionized with intense, circularly polarized 30-fs laser pulses. For carbonylsulphide and benzonitrile oriented in one dimension, the MFPADs exhibit pronounced anisotropies...

Molecular mechanics calculations on cobalt phthalocyanine dimers

NARCIS (Netherlands)

Heuts, J.P.A.; Schipper, E.T.W.M.; Piet, P.; German, A.L.

1995-01-01

In order to obtain insight into the structure of cobalt phthalocyanine dimers, molecular mechanics calculations were performed on dimeric cobalt phthalocyanine species. Molecular mechanics calculations are first presented on monomeric cobalt(II) phthalocyanine. Using the Tripos force field for the

Approaches for the analysis of low molecular weight compounds with laser desorption/ionization techniques and mass spectrometry.

Science.gov (United States)

Bergman, Nina; Shevchenko, Denys; Bergquist, Jonas

2014-01-01

This review summarizes various approaches for the analysis of low molecular weight (LMW) compounds by different laser desorption/ionization mass spectrometry techniques (LDI-MS). It is common to use an agent to assist the ionization, and small molecules are normally difficult to analyze by, e.g., matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) using the common matrices available today, because the latter are generally small organic compounds themselves. This often results in severe suppression of analyte peaks, or interference of the matrix and analyte signals in the low mass region. However, intrinsic properties of several LDI techniques such as high sensitivity, low sample consumption, high tolerance towards salts and solid particles, and rapid analysis have stimulated scientists to develop methods to circumvent matrix-related issues in the analysis of LMW molecules. Recent developments within this field as well as historical considerations and future prospects are presented in this review.

H ii REGION G46.5-0.2: THE INTERPLAY BETWEEN IONIZING RADIATION, MOLECULAR GAS, AND STAR FORMATION

Energy Technology Data Exchange (ETDEWEB)

Paron, S.; Ortega, M. E.; Dubner, G.; Petriella, A.; Giacani, E. [Instituto de Astronomía y Física del Espacio (IAFE, CONICET-UBA), CC 67, Suc. 28, 1428 Buenos Aires (Argentina); Yuan, Jing-Hua; Li, Jin Zeng; Liu, Hongli; Huang, Ya Fang; Zhang, Si-Ju [National Astronomical Observatories, Chinese Academy of Sciences, 20 A Datun Road, Chaoyang District, Beijing 100012 (China); Wu, Yuefang, E-mail: sparon@iafe.uba.ar [Department of Astronomy, Peking University, 100871 Beijing (China)

2015-06-15

H ii regions are particularly interesting because they can generate dense layers of gas and dust, elongated columns or pillars of gas pointing toward the ionizing sources, and cometary globules of dense gas where triggered star formation can occur. Understanding the interplay between the ionizing radiation and the dense surrounding gas is very important to explain the origin of these peculiar structures, and hence to characterize triggered star formation. G46.5-0.2 (G46), a poorly studied galactic H ii region located at about 4 kpc, is an excellent target for performing this kind of study. Using public molecular data extracted from the Galactic Ring Survey ({sup 13}CO J = 1–0) and from the James Clerk Maxwell Telescope data archive ({sup 12}CO, {sup 13}CO, C{sup 18}O J = 3–2, HCO{sup +}, and HCN J = 4–3), and infrared data from the GLIMPSE and MIPSGAL surveys, we perform a complete study of G46, its molecular environment, and the young stellar objects (YSOs) placed around it. We found that G46, probably excited by an O7V star, is located close to the edge of the GRSMC G046.34-00.21 molecular cloud. It presents a horse-shoe morphology opening in the direction of the cloud. We observed a filamentary structure in the molecular gas likely related to G46 and not considerable molecular emission toward its open border. We found that about 10′ to the southwest of G46 there are some pillar-like features, shining at 8 μm and pointing toward the H ii region open border. We propose that the pillar-like features were carved and sculpted by the ionizing flux from G46. We found several YSOs likely embedded in the molecular cloud grouped in two main concentrations: one, closer to the G46 open border consisting of Class II type sources, and another mostly composed of Class I type YSOs located just ahead of the pillar-like features, strongly suggesting an age gradient in the YSO distribution.

Quantum Mechanical Study of Atoms and Molecules

Science.gov (United States)

Sahni, R. C.

1961-01-01

This paper, following a brief introduction, is divided into five parts. Part I outlines the theory of the molecular orbital method for the ground, ionized and excited states of molecules. Part II gives a brief summary of the interaction integrals and their tabulation. Part III outlines an automatic program designed for the computation of various states of molecules. Part IV gives examples of the study of ground, ionized and excited states of CO, BH and N2 where the program of automatic computation and molecular integrals have been utilized. Part V enlists some special problems of Molecular Quantum Mechanics are being tackled at New York University.

Numerical simulations of single and double ionization of H2 in short intense laser pulses

International Nuclear Information System (INIS)

Baier, Silvio

2008-01-01

Rescattering is the dominant process leading to double ionization in atoms and molecules interacting with linearly polarized laser pulses with wavelengths around 800 nm and in an intensity regime of 10 14 to 10 15 W/cm 2 . Using numerical integrations of the two-electron Schroedinger equation of the Hydrogen molecule in appropriate reduced dimensions two mechanisms, namely correlated emission of the electrons and excitation followed by field ionization after rescattering, could be identified and characterized. With the help of a planar model in reduced dimensions these mechanisms were quantitatively compared by their dependence on the molecular alignment with respect to the polarization axis. Two additional mechanisms, which are also related to rescattering, could be identified as well. (orig.)

A positive (negative) surface ionization source concept for RIB generation

International Nuclear Information System (INIS)

Alton, G.D.; Mills, G.D.

1995-01-01

A novel, versatile, new concept, spherical-geometry, positive (negative) surface-ionization source has been designed and fabricated which will have the capability of generating both positive- and negative-ion beams without mechanical changes to the source. The source utilizes a highly permeable, high-work-function Ir ionizer (φ∼ = 5.29 eV) for ionizing highly electropositive atoms/molecules; while for negative-surface ionization, the work function is lowered to φ ∼ = 1.43 eV by continually feeding cesium vapor through the ionizer matrix. The use of Cs to effect low work function surfaces for negative ion beam generation has the potential of overcoming the chronic poisoning effects experienced with LaB 6 while enhancing the probability for negative ion formation of atomic and molecular species with low to intermediate electron affinities. The flexibility of operation in either mode makes it especially attractive for RIB applications and, therefore, the source will be used as a complementary replacement for the high-temperature electron impact ionization sources presently in use at the HRIBF The design features and operational principles of the source will be described in this report

Effect of ionization on the oxidation kinetics of aluminum nanoparticles

Science.gov (United States)

Zheng, Yao-Ting; He, Min; Cheng, Guang-xu; Zhang, Zaoxiao; Xuan, Fu-Zhen; Wang, Zhengdong

2018-03-01

Molecular dynamics simulation (MD) of the observed stepwise oxidation of core-shell structured Al/Al2O3 nanoparticles is presented. Different from the metal ion hopping process in the Cabrera-Mott model, which is assumed to occur only at a certain distance from the oxide layer, the MD simulation shows that Al atoms jump over various interfacial gaps directly under the thermal driving force. The energy barrier for Al ionization is found to be increased along with the enlargement of interfacial gap. A mechanism of competition between thermal driving force and ionization potential barrier is proposed in the interpretation of stepwise oxidation behavior.

Molecular Ionization-Desorption Analysis Source (MIDAS) for Mass Spectrometry: Thin-Layer Chromatography

Science.gov (United States)

Winter, Gregory T.; Wilhide, Joshua A.; LaCourse, William R.

2016-02-01

Molecular ionization-desorption analysis source (MIDAS), which is a desorption atmospheric pressure chemical ionization (DAPCI) type source, for mass spectrometry has been developed as a multi-functional platform for the direct sampling of surfaces. In this article, its utility for the analysis of thin-layer chromatography (TLC) plates is highlighted. Amino acids, which are difficult to visualize without staining reagents or charring, were detected and identified directly from a TLC plate. To demonstrate the full potential of MIDAS, all active ingredients from an analgesic tablet, separated on a TLC plate, were successfully detected using both positive and negative ion modes. The identity of each of the compounds was confirmed from their mass spectra and compared against standards. Post separation, the chemical signal (blue permanent marker) as reference marks placed at the origin and solvent front were used to calculate retention factor (Rf) values from the resulting ion chromatogram. The quantitative capabilities of the device were exhibited by scanning caffeine spots on a TLC plate of increasing sample amount. A linear curve based on peak are, R2 = 0.994, was generated for seven spots ranging from 50 to 1000 ng of caffeine per spot.

Conformation analysis of trehalose. Molecular dynamics simulation and molecular mechanics

International Nuclear Information System (INIS)

Donnamaira, M.C.; Howard, E.I.; Grigera, J.R.

1992-09-01

Conformational analysis of the disaccharide trehalose is done by molecular dynamics and molecular mechanics. In spite of the different force fields used in each case, comparison between the molecular dynamics trajectories of the torsional angles of glycosidic linkage and energy conformational map shows a good agreement between both methods. By molecular dynamics it is observed a moderate mobility of the glycosidic linkage. The demands of computer time is comparable in both cases. (author). 6 refs, 4 figs

The mechanism for the primary biological effects of ionizing radiation

International Nuclear Information System (INIS)

Byakov, Vsevolod M; Stepanov, Sergei V

2006-01-01

The primary biological response of living organisms to the passage of fast charged particles is traditionally believed to be dominated by the chemical reactions of the radical products from the radiolysis of cellular water (OH, H, e aq - , O 2 - , H 2 O 2 ) and by the bioradicals that they produce (and which can also result from the direct electronic activation of biomolecules). This understanding has provided insight into how ionizing radiations affect biological systems and, most importantly, what radioprotection and radiosensibilizing effects are produced by chemical compounds introduced into an organism. However, a number of key radiobiological facts remain unexplained by the current theory, stimulating a search for other biologically active factors that may be triggered by radiation. This review examines a fact that is usually ignored in discussing the biological impact of ionizing radiation: the local increase in acidity in the water solution along the track of a charged particle. The acidity in the track is very different from its value for cellular water in a living organism. Biological processes are well-known to be highly sensitive to changes in the environmental acidity. It seems that the biological impact of ionizing radiations is dominated not by the water radiolysis products (mostly radicals) listed above but particles of a different nature, hydroxonium ions H 3 O + , where the term hydroxonium refer to protonated water molecules. This modification of the mechanism of primary radiobiological effects is in good agreement with experimental data. In particular, the extremal dependence of the relative biological efficiency (RBE) of radiations on their ionizing energy losses is accounted for in quantitative terms, as is the increase in the RBE in the relativistic energy range. (reviews of topical problems)

Comparing Laser Desorption Ionization and Atmospheric Pressure Photoionization Coupled to Fourier Transform Ion Cyclotron Resonance Mass Spectrometry To Characterize Shale Oils at the Molecular Level

Science.gov (United States)

Cho, Yunjo; Jin, Jang Mi; Witt, Matthias; Birdwell, Justin E.; Na, Jeong-Geol; Roh, Nam-Sun; Kim, Sunghwan

2013-01-01

Laser desorption ionization (LDI) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was used to analyze shale oils. Previous work showed that LDI is a sensitive ionization technique for assessing aromatic nitrogen compounds, and oils generated from Green River Formation oil shales are well-documented as being rich in nitrogen. The data presented here demonstrate that LDI is effective in ionizing high-double-bond-equivalent (DBE) compounds and, therefore, is a suitable method for characterizing compounds with condensed structures. Additionally, LDI generates radical cations and protonated ions concurrently, the distribution of which depends upon the molecular structures and elemental compositions, and the basicity of compounds is closely related to the generation of protonated ions. This study demonstrates that LDI FT-ICR MS is an effective ionization technique for use in the study of shale oils at the molecular level. To the best of our knowledge, this is the first time that LDI FT-ICR MS has been applied to shale oils.

Dissociation and ionization of molecular ions by ultra-short intense laser pulses probed by coincidence 3D momentum imaging

International Nuclear Information System (INIS)

Ben-Itzhak, Itzik; Wang, Pengqian; Xia, Jiangfan; Max Sayler, A.; Smith, Mark A.; Maseberg, J.W.; Carnes, Kevin D.; Esry, Brett D.

2005-01-01

We have experimentally explored laser-induced dissociation and ionization of diatomic molecular ions using coincidence 3D momentum imaging. The vibrationally excited molecular ion beam (4-8 keV) is crossed by an ultrafast intense laser beam (28-200 fs, 10 13 -10 14 W/cm 2 ). The resulting fragments are recorded in coincidence by a time and position-sensitive detector. Complete angular distributions and kinetic energy release maps are reconstructed from the measured dissociation-momentum vectors. The angular distribution of the H + + H fragments was found to be strongly correlated to their kinetic energy release upon dissociation. Low KER was associated with very narrow angular distributions and high KER with distributions peaking away from the laser polarization. Ionization was found to be smaller than dissociation and increased with laser intensity. The H + + H + fragments have a very narrow angular distribution along the laser polarization

Atomic and molecular science with synchrotron radiation

International Nuclear Information System (INIS)

1989-01-01

This paper discusses the following topics: electron correlation in atoms; atomic innershell excitation and decay mechanisms; timing experiments; x-ray scattering; properties of ionized species; electronic properties of actinide atoms; total photon-interaction cross sections; and molecular physics. 66 refs

Heating and ionization in MHD shock waves propagating into partially ionized plasma

International Nuclear Information System (INIS)

Bighel, L.; Collins, A.R.; Cramer, N.F.; Watson-Munro, C.N.

1975-09-01

A model of the structure of MHD switch-on shocks propagating in a partially ionized plasma, in which the primary dissipation mechanism is friction between ions and neutrals, is here compared favourably with experimental results. Four degrees of upstream ionization were studied, ranging from almost complete to very small ionization. (author)

Heating and ionization in MHD shock wave propagating into partially ionized plasma

International Nuclear Information System (INIS)

Bighel, L.; Collins, A.R.; Cramer, N.F.; Watson-Munro, C.N.

1975-09-01

A model of the structure of MHD switch-on shocks propagating in a partially ionized plasma, in which the primary dissipation mechanism is friction between ions and neutrals, is here compared favourably with experimental results. Four degrees of upstream ionization were studied, ranging from almost complete to very small ionization. (author)

Mechanism of effect of ionizing radiation on bcl-2 protein expression and apoptosis in mouse thymus

International Nuclear Information System (INIS)

Liu Jiamei; Chen Aijun; Chen Dong; Liu Shuzheng

2002-01-01

Objective: To study the mechanism of effect of ionizing radiation in varied doses of X-rays on bcl-2 express and apoptosis in mouse thymus. Methods: Immunohistochemistry, image analysis and transmission electron microscope were used in the study. Results: The expression of bcl-2 protein was limited within thymic medulla, decreased with 2 Gy, however, increased with 0.075 Gy after whole-body irradiation. Some typical apoptotic cells were found in thymic cortex after 2 Gy irradiation. The apoptotic cells decreased and mitotic metaphase increased after 0.075 Gy irradiation. Conclusion: The mechanism of effect of ionizing radiation on apoptosis of thymus was related with the expression of bcl-2 proteins

Excited-state molecular photoionization dynamics

International Nuclear Information System (INIS)

Pratt, S.T.

1995-01-01

This review presents a survey of work using resonance-enhanced multiphoton ionization and double-resonance techniques to study excited-state photoionization dynamics in molecules. These techniques routinely provide detail and precision that are difficult to achieve in single-photon ionization from the ground state. The review not only emphasizes new aspects of photoionization revealed in the excited-state experiments but also shows how the excited-state techniques can provide textbook illustrations of some fundamental mechanisms in molecular photoionization dynamics. Most of the examples are confined to diatomic molecules. (author)

Penning ionization processes studied by electron spectroscopy

International Nuclear Information System (INIS)

Yencha, A.J.

1978-01-01

The technique of measuring the kinetic energy of electrons ejected from atomic or molecular species as a result of collisional energy transfer between a metastable excited rare gas atom and an atom or molecule is known as Penning ionization spectroscopy. Like the analogous photoionization process of photoelectron spectroscopy, a considerable amount of information has been gained about the ionization potentials of numerous molecular systems. It is, in fact, through the combined analyses of photoelectron and Penning electron spectra that affords a probe of the particle-particle interactions that occur in the Penning process. In this paper a short survey of the phenomenon of Penning ionization, as studied by electron spectroscopy, will be presented as it pertains to the ionization processes of simple molecules by metastable excited atoms. (author)

Molecular Mechanisms of Preeclampsia

Directory of Open Access Journals (Sweden)

N. Vitoratos

2012-01-01

Full Text Available Preeclampsia is one of the leading causes of maternal morbidity/mortality. The pathogenesis of preeclampsia is still under investigation. The aim of this paper is to present the molecular mechanisms implicating in the pathway leading to preeclampsia.

In vitro evaluation of ionizing radiation effects in bone tissue by FTIR spectroscopy and dynamic mechanical analysis; Avaliacao in vitro dos efeitos da radiacao ionizante em tecido osseo bovino por espectroscoia ATR-FTIR e analise dinamica-mecanica

Energy Technology Data Exchange (ETDEWEB)

Veloso, Marcelo Noronha

2013-07-01

Ionizing radiation from gamma radiation sources or X-ray generators is frequently used in Medical Science, such as radiodiagnostic exams, radiotherapy, and sterilization of haloenxerts. Ionizing radiation is capable of breaking polypeptidic chains and causing the release of free radicals by radiolysis.of water. It interacts also with organic material at the molecular level, and it may change its mechanical properties. In the specific case of bone tissue, studies report that ionizing radiation induces changes in collagen molecules and reduces the density of intermolecular crosslinks. The aim of this study was to verify the changes promoted by different doses of ionizing radiation in bone tissue using Fourier Transform Infrared Spectroscopy (FTIR) and dynamic mechanical analysis (DMA). Samples of bovine bone were irradiated using Cobalt-60 with five different doses: 0.01 kGy, 0.1 kGy, 1 kGy, 15 kGy and 75 kGy. To study the effects of ionizing irradiation on the chemical structure of the bone, the sub-bands of amide I, the crystallinity index and relation of organic and inorganic materials, were studied. The mechanical changes were evaluated using the elastic modulus and the damping value. To verify whether the chemical changes and the mechanical characteristics of the bone were correlated, the relation between the analysis made with spectroscopic data and the mechanical analysis data was studied. It was possible to evaluate the effects of different doses of ionizing radiation in bone tissue. With ATR-FTIR spectroscopy, it was possible to observe changes in the organic components and in the hydroxyapatite crystals organization. Changes were also observed in the elastic modulus and in the damping value. High correlation with statistical significance was observed among (amide III + collagen)/{sub v1,v3}, PO{sub 4}{sup 3-} and the delta tangent, and among 1/FHWM and the elastic modulus. (author)

Exploring the aqueous vertical ionization of organic molecules by molecular simulation and liquid microjet photoelectron spectroscopy.

Science.gov (United States)

Tentscher, Peter R; Seidel, Robert; Winter, Bernd; Guerard, Jennifer J; Arey, J Samuel

2015-01-08

To study the influence of aqueous solvent on the electronic energy levels of dissolved organic molecules, we conducted liquid microjet photoelectron spectroscopy (PES) measurements of the aqueous vertical ionization energies (VIEaq) of aniline (7.49 eV), veratrole alcohol (7.68 eV), and imidazole (8.51 eV). We also reanalyzed previously reported experimental PES data for phenol, phenolate, thymidine, and protonated imidazolium cation. We then simulated PE spectra by means of QM/MM molecular dynamics and EOM-IP-CCSD calculations with effective fragment potentials, used to describe the aqueous vertical ionization energies for six molecules, including aniline, phenol, veratrole alcohol, imidazole, methoxybenzene, and dimethylsulfide. Experimental and computational data enable us to decompose the VIEaq into elementary processes. For neutral compounds, the shift in VIE upon solvation, ΔVIEaq, was found to range from ≈-0.5 to -0.91 eV. The ΔVIEaq was further explained in terms of the influence of deforming the gas phase solute into its solution phase conformation, the influence of solute hydrogen-bond donor and acceptor interactions with proximate solvent molecules, and the polarization of about 3000 outerlying solvent molecules. Among the neutral compounds, variability in ΔVIEaq appeared largely controlled by differences in solute-solvent hydrogen-bonding interactions. Detailed computational analysis of the flexible molecule veratrole alcohol reveals that the VIE is strongly dependent on molecular conformation in both gas and aqueous phases. Finally, aqueous reorganization energies of the oxidation half-cell ionization reaction were determined from experimental data or estimated from simulation for the six compounds aniline, phenol, phenolate, veratrole alcohol, dimethylsulfide, and methoxybenzene, revealing a surprising constancy of 2.06 to 2.35 eV.

Study of the ionizing radiation effect on the polyamide 6,6 mechanical properties

International Nuclear Information System (INIS)

Colombo, Maria Aparecida da Silva

2004-01-01

Polyamide 6,6 due to its excellent mechanical, thermal and electrical properties and its great performance in multiple industrial applications is considered one of the most important engineering polymers. However, in specific applications, some of its properties need to be improved by means additives or fillers to reach the required properties increasing its final cost. By these considerations, the aim of this work was to apply the ionizing radiation to improve the natural mechanical properties of polyamide 6,6. Also, to evaluate the irradiation parameters, and the mechanical performance of the irradiated polymer in order to use the cross-linking, induced by ionizing radiation, as substitute of additives and fillers. Row polyamide 6,6 samples, for mechanical tests, were prepared by injection molded and then irradiated with high energetic electrons to reach doses of 70, 100, 150, and 200 kGy. The mechanical performance, of non-irradiated and irradiated samples, was evaluated by tensile strength, impact, hardness and wear measurements. Furthermore, hardness and wear tests were carried out with samples, which were immersed in petroleum and sea water for 6 months. The experimental results have shown that, in the studied dose range, the tensile strength increases 25%, the hardness Shore D 15%, the impact values diminished by 80% and the wear values decreased 20 times between 0 and 200 kGy. The effect of the petroleum and sea water were shown mainly in the nonirradiated samples. (author)

Long-term biological effects induced by ionizing radiation--implications for dose mediated risk.

Science.gov (United States)

Miron, S D; Astărăstoae, V

2014-01-01

Ionizing radiations are considered to be risk agents that are responsible for the effects on interaction with living matter. The occurring biological effects are due to various factors such as: dose, type of radiation, exposure time, type of biological tissue, health condition and the age of the person exposed. The mechanisms involved in the direct modifications of nuclear DNA and mitochondrial DNA are reviewed. Classical target theory of energy deposition in the nucleus that causes DNA damages, in particular DNA double-strand breaks and that explanation of the biological consequences of ionizing radiation exposure is a paradigm in radiobiology. Recent experimental evidences have demonstrated the existence of a molecular mechanism that explains the non-targeted effects of ionizing radiation exposure. Among these novel data, genomic instability and a variety of bystander effects are discussed here. Those bystander effects of ionizing radiation are fulfilled by cellular communication systems that give rise to non-targeted effects in the neighboring non irradiated cells. This paper provides also a commentary on the synergistic effects induced by the co-exposures to ionizing radiation and various physical agents such as electromagnetic fields and the co-exposures to ionizing radiation and chemical environmental contaminants such as metals. The biological effects of multiple stressors on genomic instability and bystander effects are also discussed. Moreover, a brief presentation of the methods used to characterize cyto- and genotoxic damages is offered.

Caspase-independent cell death mediated by apoptosis-inducing factor (AIF) nuclear translocation is involved in ionizing radiation induced HepG2 cell death

Energy Technology Data Exchange (ETDEWEB)

Sun, Hengwen [Department of Radiation, Cancer Center of Guangdong General Hospital (Guangdong Academy of Medical Science), Guangzhou, 510080, Guangdong (China); Yang, Shana; Li, Jianhua [Department of Physiology, Guangzhou Medical University, Guangzhou, 510182, Guangdong (China); Zhang, Yajie [Department of Pathology, Guangzhou Medical University, Guangzhou, 510182, Guangdong (China); Gao, Dongsheng [Department of Oncology, Guangdong Medical College Affiliated Pengpai Memorial Hospital, Hai Feng, 516400, Gungdong (China); Zhao, Shenting, E-mail: zhaoshenting@126.com [Department of Physiology, Guangzhou Medical University, Guangzhou, 510182, Guangdong (China)

2016-03-25

Hepatocellular carcinoma (HCC) is the fifth most common cancer in the world. The aim of radiotherapy is to eradicate cancer cells with ionizing radiation. Except for the caspase-dependent mechanism, several lines of evidence demonstrated that caspase-independent mechanism is directly involved in the cell death responding to irradiation. For this reason, defining the contribution of caspase-independent molecular mechanisms represents the main goal in radiotherapy. In this study, we focused on the role of apoptosis-inducing factor (AIF), the caspase-independent molecular, in ionizing radiation induced hepatocellular carcinoma cell line (HepG2) cell death. We found that ionizing radiation has no function on AIF expression in HepG2 cells, but could induce AIF release from the mitochondria and translocate into nuclei. Inhibition of AIF could reduce ionizing radiation induced HepG2 cell death. These studies strongly support a direct relationship between AIF nuclear translocation and radiation induced cell death. What's more, AIF nuclear translocation is caspase-independent manner, but not caspase-dependent manner, in this process. These new findings add a further attractive point of investigation to better define the complex interplay between caspase-independent cell death and radiation therapy. - Highlights: • AIF nuclear translocation is involved in ionizing radiation induced hepatocellular carcinoma cell line HepG2 cell death. • AIF mediated cell death induced by ionizing radiation is caspase-independent. • Caspase-independent pathway is involved in ionzing radiation induced HepG2 cell death.

Caspase-independent cell death mediated by apoptosis-inducing factor (AIF) nuclear translocation is involved in ionizing radiation induced HepG2 cell death

International Nuclear Information System (INIS)

Sun, Hengwen; Yang, Shana; Li, Jianhua; Zhang, Yajie; Gao, Dongsheng; Zhao, Shenting

2016-01-01

Hepatocellular carcinoma (HCC) is the fifth most common cancer in the world. The aim of radiotherapy is to eradicate cancer cells with ionizing radiation. Except for the caspase-dependent mechanism, several lines of evidence demonstrated that caspase-independent mechanism is directly involved in the cell death responding to irradiation. For this reason, defining the contribution of caspase-independent molecular mechanisms represents the main goal in radiotherapy. In this study, we focused on the role of apoptosis-inducing factor (AIF), the caspase-independent molecular, in ionizing radiation induced hepatocellular carcinoma cell line (HepG2) cell death. We found that ionizing radiation has no function on AIF expression in HepG2 cells, but could induce AIF release from the mitochondria and translocate into nuclei. Inhibition of AIF could reduce ionizing radiation induced HepG2 cell death. These studies strongly support a direct relationship between AIF nuclear translocation and radiation induced cell death. What's more, AIF nuclear translocation is caspase-independent manner, but not caspase-dependent manner, in this process. These new findings add a further attractive point of investigation to better define the complex interplay between caspase-independent cell death and radiation therapy. - Highlights: • AIF nuclear translocation is involved in ionizing radiation induced hepatocellular carcinoma cell line HepG2 cell death. • AIF mediated cell death induced by ionizing radiation is caspase-independent. • Caspase-independent pathway is involved in ionzing radiation induced HepG2 cell death.

Ghost peaks observed after AP-MALDI experiment may disclose new ionization mechanism of matrix assisted hypersonic velocity impact ionization

Science.gov (United States)

Moskovets, Eugene

2015-01-01

RATIONALE Understanding the mechanisms of MALDI promises improvements in the sensitivity and specificity of many established applications in the field of mass spectrometry. This paper reports a serendipitous observation of a significant ion yield in a post-ionization experiment conducted after the sample has been removed from a standard atmospheric pressure (AP)-MALDI source. This post-ionization is interpreted in terms of collisions of microparticles moving with a hypersonic velocity into a solid surface. Calculations show that the thermal energy released during such collisions is close to that absorbed by the top matrix layer in traditional MALDI. The microparticles, containing both the matrix and analytes, could be detached from a film produced inside the inlet capillary during the sample ablation and accelerated by the flow rushing through the capillary. These observations contribute some new perspective to ion formation in both laser and laserless matrix-assisted ionization. METHODS An AP-MALDI ion source hyphenated with a three-stage high-pressure ion funnel system was utilized for peptide mass analysis. After the laser was turned off and MALDI sample was removed, ions were detected during a gradual reduction of the background pressure in the first funnel. The constant-rate pressure reduction led to the reproducible appearance of different singly- and doubly-charged peptide peaks in mass spectra taken a few seconds after the end of the MALDI analysis of a dried-droplet spot. RESULTS The ion yield as well as the mass range of ions observed with a significant delay after a completion of the primary MALDI analysis depended primarily on the background pressure inside the first funnel. The production of ions in this post-ionization step was exclusively observed during the pressure drop. A lower matrix background and significant increase in relative yield of double-protonated ions are reported. CONCLUSIONS The observations were partially consistent with a model of

Molecular machines with bio-inspired mechanisms.

Science.gov (United States)

Zhang, Liang; Marcos, Vanesa; Leigh, David A

2018-02-26

The widespread use of molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular machines-which by and large function as switches-and the machines of the macroscopic world, which utilize the synchronized behavior of integrated components to perform more sophisticated tasks than is possible with any individual switch. Should we try to make molecular machines of greater complexity by trying to mimic machines from the macroscopic world or instead apply unfamiliar (and no doubt have to discover or invent currently unknown) mechanisms utilized by biological machines? Here we try to answer that question by exploring some of the advances made to date using bio-inspired machine mechanisms.

Molecular mechanisms in compatibility and mechanical properties of Polyacrylamide/Polyvinyl alcohol blends.

Science.gov (United States)

Wei, Qinghua; Wang, Yanen; Che, Yu; Yang, Mingming; Li, Xinpei; Zhang, Yingfeng

2017-01-01

The objectives of this study were to develop a computational model based on molecular dynamics technique to investigate the compatibility and mechanical properties of Polyacrylamide (PAM)/Polyvinyl alcohol (PVA) blends. Five simulation models of PAM/PVA with different composition ratios (4/0, 3/1, 2/2, 1/3, 0/4) were constructed and simulated by using molecular dynamics (MD) simulation. The interaction mechanisms of molecular chains in PAM/PVA blend system were elaborated from the aspects of the compatibility, mechanical properties, binding energy and pair correlation function, respectively. The computed values of solubility parameters for PAM and PVA indicate PAM has a good miscibility with PVA. The results of the static mechanical analysis, based on the equilibrium structures of blends with differing component ratios, shows us that the elastic coefficient, engineering modulus, and ductility are increased with the addition of PVA content, which is 4/0 PAM/PVAPVAPVAPVAPVA. Moreover, binding energy results indicate that a stronger interaction exists among PVA molecular chains comparing with PAM molecular chains, which is why the mechanical properties of blend system increasing with the addition of PVA content. Finally, the results of pair correlation functions (PCFs) between polar functional groups and its surrounding hydrogen atoms, indicated they interact with each other mainly by hydrogen bonds, and the strength of three types of polar functional groups has the order of O(-OH)>O(-C=O)>N(-NH 2 ). This further elaborates the root reason why the mechanical properties of blend system increase with the addition of PVA content. Copyright © 2016 Elsevier Ltd. All rights reserved.

Development of resonance-enhanced multiphoton ionization system

International Nuclear Information System (INIS)

Naik, P.D.; Upadhyaya, Hari P.; Kumar, Awadhesh; Bajaj, P.N.; Sinha, A.K.; Bhatt, S.; Gupta, M.D.P.

2009-05-01

Radiation and Photochemistry Division has developed a Molecular Beam-Resonance Enhanced Multiphoton Ionization-Time-of-Flight spectrometer, a highly sensitive and selective analytical detection system, for investigation of photodissociation dynamics of isolated molecules. In this system, the molecular beam is intersected in the extraction region of a Wiley-McLaren type Time-of-Flight mass spectrometer by the photolysis laser beam, propagating perpendicular to both the molecular beams and the Time-of-Flight tube. The probe (ionization) laser beam counter propagating to the photolysis beam, ionizes the stable products and the radicals produced on photodissociation. The important features of the system, namely, the resolution and the detection limit, have been determined from the studies of aniline molecular beam, generated by seeding 1% aniline in helium. For the present configuration, using one metre long flight tube, the resolution has been found to be about 400, and detection limit is better than 106 species per cm 3 . The integrity of the set-up is obtained from the photodissociation dynamics studies of bromoform. (author)

Regulation of tumor necrosis factor gene expression by ionizing radiation in human myeloid leukemia cells and peripheral blood monocytes

International Nuclear Information System (INIS)

Sherman, M.L.; Datta, R.; Hallahan, D.E.; Weichselbaum, R.R.; Kufe, D.W.

1991-01-01

Previous studies have demonstrated that ionizing radiation induces the expression of certain cytokines, such as TNF alpha/cachectin. However, there is presently no available information regarding the molecular mechanisms responsible for the regulation of cytokine gene expression by ionizing radiation. In this report, we describe the regulation of the TNF gene by ionizing radiation in human myeloid leukemia cells. The increase in TNF transcripts by x rays was both time- and dose-dependent as determined by Northern blot analysis. Similar findings were obtained in human peripheral blood monocytes. Transcriptional run-on analyses have demonstrated that ionizing radiation stimulates the rate of TNF gene transcription. Furthermore, induction of TNF mRNA was increased in the absence of protein synthesis. In contrast, ionizing radiation had little effect on the half-life of TNF transcripts. These findings indicate that the increase in TNF mRNA observed after irradiation is regulated by transcriptional mechanisms and suggest that production of this cytokine by myeloid cells may play a role in the pathophysiologic effects of ionizing radiation

Influence of ionizing radiation on synthesis and molecular heterogeneity of catalase in tissue culture of Rauwolfia serpentina

International Nuclear Information System (INIS)

Komov, V.P.; Bespalova, E.V.; Strelkova, M.A.

1998-01-01

Changes in activity and molecular heterogeneity of catalase in tissue culture of Rauwolfia serpentina following irradiation in early growth period at the doses of 8 and 50 Gy has been studied. Ionizing radiation accelerate the synthesis and degradation rates of catalase and total protein. A comparative study of changes in enzyme and protein turnover during growth on irradiated and non-irradiated medium has been made [ru

A positive (negative) surface ionization source concept for radioactive ion beam generation

International Nuclear Information System (INIS)

Alton, G.D.; Mills, G.D.

1996-01-01

A novel, versatile, new concept, spherical-geometry, positive (negative) surface-ionization source has been designed and fabricated which will have the capability of generating both positive- and negative-ion beams without mechanical changes to the source. The source utilizes a highly permeable, high-work-function Ir ionizer (φ ≅ 5.29 eV) for ionizing highly electropositive atoms/molecules; while for negative-surface ionization, the work function is lowered by continually feeding a highly electropositive vapor through the ionizer matrix. The use of this technique to effect low work function surfaces for negative ion beam generation has the potential of overcoming the chronic poisoning effects experienced with LaB 6 while enhancing the probability for negative ion formation of atomic and molecular species with low to intermediate electron affinities. The flexibility of operation in either mode makes it especially attractive for radioactive ion beam (RIB) applications and, therefore, the source will be used as a complementary replacement for the high-temperature electron impact ionization sources presently in the use at the Holifield radioactive ion beam facility (HRIBF). The design features and operational principles of the source are described in this report. (orig.)

Quantum mechanical theory of collisional ionization in the presence of intense laser radiation

Science.gov (United States)

Bellum, J. C.; George, T. F.

1978-01-01

The paper presents a quantum mechanical formalism for treating ionizing collisions occurring in the presence of an intense laser field. Both the intense laser radiation and the internal electronic continuum states associated with the emitted electrons are rigorously taken into account by combining discretization techniques with expansions in terms of electronic-field representations for the quasi-molecule-plus-photon system. The procedure leads to a coupled-channel description of the heavy-particle dynamics which involves effective electronic-field potential surfaces and continua. It is suggested that laser-influenced ionizing collisions can be studied to verify the effects of intense laser radiation on inelastic collisional processes. Calculation procedures for electronic transition dipole matrix elements between discrete and continuum electronic states are outlined.

Tunneling Ionization of Diatomic Molecules

DEFF Research Database (Denmark)

Svensmark, Jens Søren Sieg

2016-01-01

When a molecule is subject to a strong laser field, there is a probability that an electron can escape, even though the electrons are bound by a large potential barrier. This is possible because electrons are quantum mechanical in nature, and they are therefore able to tunnel through potential...... barriers, an ability classical particles do not possess. Tunnelling is a fundamental quantum mechanical process, a process that is distinctly non-classical, so solving this tunnelling problem is not only relevant for molecular physics, but also for quantum theory in general. In this dissertation the theory...... of tunneling ionizaion of molecules is presented and the results of numerical calculations are shown. One perhaps surprising result is, that the frequently used Born-Oppenheimer approximation breaks down for weak fields when describing tunneling ionization. An analytic theory applicable in the weak-field limit...

A statistical mechanical model for equilibrium ionization

International Nuclear Information System (INIS)

Macris, N.; Martin, P.A.; Pule, J.

1990-01-01

A quantum electron interacts with a classical gas of hard spheres and is in thermal equilibrium with it. The interaction is attractive and the electron can form a bound state with the classical particles. It is rigorously shown that in a well defined low density and low temperature limit, the ionization probability for the electron tends to the value predicted by the Saha formula for thermal ionization. In this regime, the electron is found to be in a statistical mixture of a bound and a free state. (orig.)

Dielectric barrier discharges applied for soft ionization and their mechanism

Energy Technology Data Exchange (ETDEWEB)

Brandt, Sebastian; Klute, Felix David; Schütz, Alexander; Franzke, Joachim, E-mail: joachim.franzke@isas.de

2017-01-25

Dielectric barrier discharges are used for analytical applications as dissociative source for optical emission spectrometry and for ambient-ionization techniques. In the range of ambient-ionization techniques it has attracted much attention in fields like food safety, biological analysis, mass spectrometry for reaction monitoring and imaging forensic identification. In this review some examples are given for the application as desorption/ionization source as well as for the sole application as ionization source with different sample introductions. It will be shown that the detection might depend on the certain distance of the plasma in reference to the sample or the kind of discharge which might be produced by different shapes of the applied high voltage. Some attempts of characterization are presented. A more detailed characterization of the dielectric barrier discharge realized with two ring electrodes, each separately covered with a dielectric layer, is described. - Highlights: • Dielectric barrier discharge applied as desorption/ionization source. • Dielectric barrier discharge applied solely as ionization source. • Different geometries in order to maintain soft ionization. • Characterization of the LTP probe. • Dielectric barrier discharges with two dielectric barriers (ring-ring shape).

The ATLAS3D project : X. On the origin of the molecular and ionized gas in early-type galaxies

NARCIS (Netherlands)

Davis, Timothy A.; Alatalo, Katherine; Sarzi, Marc; Bureau, Martin; Young, Lisa M.; Blitz, Leo; Serra, Paolo; Crocker, Alison F.; Krajnovic, Davor; McDermid, Richard M.; Bois, Maxime; Bournaud, Frederic; Cappellari, Michele; Davies, Roger L.; Duc, Pierre-Alain; de Zeeuw, P. Tim; Emsellem, Eric; Khochfar, Sadegh; Kuntschner, Harald; Lablanche, Pierre-Yves; Morganti, Raffaella; Naab, Thorsten; Oosterloo, Tom; Scott, Nicholas; Weijmans, Anne-Marie

2011-01-01

We make use of interferometric CO and H i observations, and optical integral-field spectroscopy from the ATLAS3D survey, to probe the origin of the molecular and ionized interstellar medium (ISM) in local early-type galaxies. We find that 36 +/- 5 per cent of our sample of fast-rotating early-type

Ambient ionization mass spectrometry: A tutorial

Energy Technology Data Exchange (ETDEWEB)

Huang, Min-Zong; Cheng, Sy-Chi; Cho, Yi-Tzu [Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, Taiwan (China); Shiea, Jentaie, E-mail: jetea@fac.nsysu.edu.tw [Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, Taiwan (China); Cancer Center, Kaohsiung Medical University, Kaohsiung, Taiwan (China)

2011-09-19

Highlights: {yields} Ambient ionization technique allows the direct analysis of sample surfaces with little or no sample pretreatment. {yields} We sort ambient ionization techniques into three main analytical strategies, direct ionization, direct desorption/ionization, and two-step ionization. {yields} The underlying principles of operation, ionization processes, detecting mass ranges, sensitivity, and representative applications of these techniques are described and compared. - Abstract: Ambient ionization is a set of mass spectrometric ionization techniques performed under ambient conditions that allows the direct analysis of sample surfaces with little or no sample pretreatment. Using combinations of different types of sample introduction systems and ionization methods, several novel techniques have been developed over the last few years with many applications (e.g., food safety screening; detection of pharmaceuticals and drug abuse; monitoring of environmental pollutants; detection of explosives for antiterrorism and forensics; characterization of biological compounds for proteomics and metabolomics; molecular imaging analysis; and monitoring chemical and biochemical reactions). Electrospray ionization and atmospheric pressure chemical ionization are the two main ionization principles most commonly used in ambient ionization mass spectrometry. This tutorial paper provides a review of the publications related to ambient ionization techniques. We describe and compare the underlying principles of operation, ionization processes, detecting mass ranges, sensitivity, and representative applications of these techniques.

Ambient ionization mass spectrometry: A tutorial

International Nuclear Information System (INIS)

Huang, Min-Zong; Cheng, Sy-Chi; Cho, Yi-Tzu; Shiea, Jentaie

2011-01-01

Highlights: → Ambient ionization technique allows the direct analysis of sample surfaces with little or no sample pretreatment. → We sort ambient ionization techniques into three main analytical strategies, direct ionization, direct desorption/ionization, and two-step ionization. → The underlying principles of operation, ionization processes, detecting mass ranges, sensitivity, and representative applications of these techniques are described and compared. - Abstract: Ambient ionization is a set of mass spectrometric ionization techniques performed under ambient conditions that allows the direct analysis of sample surfaces with little or no sample pretreatment. Using combinations of different types of sample introduction systems and ionization methods, several novel techniques have been developed over the last few years with many applications (e.g., food safety screening; detection of pharmaceuticals and drug abuse; monitoring of environmental pollutants; detection of explosives for antiterrorism and forensics; characterization of biological compounds for proteomics and metabolomics; molecular imaging analysis; and monitoring chemical and biochemical reactions). Electrospray ionization and atmospheric pressure chemical ionization are the two main ionization principles most commonly used in ambient ionization mass spectrometry. This tutorial paper provides a review of the publications related to ambient ionization techniques. We describe and compare the underlying principles of operation, ionization processes, detecting mass ranges, sensitivity, and representative applications of these techniques.

Gas chromatography coupled to atmospheric pressure ionization mass spectrometry (GC-API-MS): review.

Science.gov (United States)

Li, Du-Xin; Gan, Lin; Bronja, Amela; Schmitz, Oliver J

2015-09-03

Although the coupling of GC/MS with atmospheric pressure ionization (API) has been reported in 1970s, the interest in coupling GC with atmospheric pressure ion source was expanded in the last decade. The demand of a "soft" ion source for preserving highly diagnostic molecular ion is desirable, as compared to the "hard" ionization technique such as electron ionization (EI) in traditional GC/MS, which fragments the molecule in an extensive way. These API sources include atmospheric pressure chemical ionization (APCI), atmospheric pressure photoionization (APPI), atmospheric pressure laser ionization (APLI), electrospray ionization (ESI) and low temperature plasma (LTP). This review discusses the advantages and drawbacks of this analytical platform. After an introduction in atmospheric pressure ionization the review gives an overview about the history and explains the mechanisms of various atmospheric pressure ionization techniques used in combination with GC such as APCI, APPI, APLI, ESI and LTP. Also new developments made in ion source geometry, ion source miniaturization and multipurpose ion source constructions are discussed and a comparison between GC-FID, GC-EI-MS and GC-API-MS shows the advantages and drawbacks of these techniques. The review ends with an overview of applications realized with GC-API-MS. Copyright © 2015. Published by Elsevier B.V.

Atmospheric pressure ionization of chlorinated ethanes in ion mobility spectrometry and mass spectrometry

Energy Technology Data Exchange (ETDEWEB)

Ewing, Robert G.; Atkinson, David A.; Benson, Michael T.

2015-05-16

This study investigates the APCI mechanisms associated with chlorinated ethanes in an attempt to define conditions under which unique pseudo-molecular adducts, in addition to chloride ion, can be produced for analytical measurements using IMS and MS. The ionization chemistry of chlorinated compounds typically leads to the detection of only the halide ions. Using molecular modeling, which provides insights into the ion formation and relative binding energies, predictions for the formation of pseudo-molecular adducts are postulated. Predicted structures of the chloride ion with multiple hydrogens on the ethane backbone was supported by the observation of specific pseudo-molecular adducts in IMS and MS spectra. With the proper instrumental conditions, such as short reaction times and low temp.

Prediction of mechanical properties for hexagonal boron nitride nanosheets using molecular mechanics model

Energy Technology Data Exchange (ETDEWEB)

Natsuki, Toshiaki [Shinshu University, Faculty of Textile Science and Technology, Ueda (Japan); Shinshu University, Institute of Carbon Science and Technology, Nagano (Japan); Natsuki, Jun [Shinshu University, Institute of Carbon Science and Technology, Nagano (Japan)

2017-04-15

Mechanical behaviors of nanomaterials are not easy to be evaluated in the laboratory because of their extremely small size and difficulty controlling. Thus, a suitable model for the estimation of the mechanical properties for nanomaterials becomes very important. In this study, the elastic properties of boron nitride (BN) nanosheets, including the elastic modulus, the shear modulus, and the Poisson's ratio, are predicted using a molecular mechanics model. The molecular mechanics force filed is established to directly incorporate the Morse potential function into the constitutive model of nanostructures. According to the molecular mechanics model, the chirality effect of hexagonal BN nanosheets on the elastic modulus is investigated through a closed-form solution. The simulated result shows that BN nanosheets exhibit an isotropic elastic property. The present analysis yields a set of very simple formulas and is able to be served as a good approximation on the mechanical properties for the BN nanosheets. (orig.)

Prediction of mechanical properties for hexagonal boron nitride nanosheets using molecular mechanics model

International Nuclear Information System (INIS)

Natsuki, Toshiaki; Natsuki, Jun

2017-01-01

Mechanical behaviors of nanomaterials are not easy to be evaluated in the laboratory because of their extremely small size and difficulty controlling. Thus, a suitable model for the estimation of the mechanical properties for nanomaterials becomes very important. In this study, the elastic properties of boron nitride (BN) nanosheets, including the elastic modulus, the shear modulus, and the Poisson's ratio, are predicted using a molecular mechanics model. The molecular mechanics force filed is established to directly incorporate the Morse potential function into the constitutive model of nanostructures. According to the molecular mechanics model, the chirality effect of hexagonal BN nanosheets on the elastic modulus is investigated through a closed-form solution. The simulated result shows that BN nanosheets exhibit an isotropic elastic property. The present analysis yields a set of very simple formulas and is able to be served as a good approximation on the mechanical properties for the BN nanosheets. (orig.)

Molecular stress response in the CNS of mice after systemic exposureto interferon-alpha, ionizing radiation and ketamine

Energy Technology Data Exchange (ETDEWEB)

Lowe, Xiu R.; Marchetti, Francesco; Lu, Xiaochen; Wyrobek, Andrew J.

2009-03-03

We previously showed that the expression of troponin T1 (Tnnt 1) was induced in the central nervous system (CNS) of adultmice 30 min after treatment with ketamine, a glutamate N-methyl-D-aspartic acid (NMDA) receptor antagonist. We hypothesized that Tnnt 1 expression may be an early molecular biomarker of stress response in the CNS of mice. To further evaluate this hypothesis, we investigated the regional expression of Tnnt 1 in the mouse brain using RNA in situ hybridization 4 h after systemic exposure to interferon-a (IFN-a) and gamma ionizing radiation, both of which have be associated with wide ranges of neuropsychiatric complications. Adult B6C3F1 male mice were treated with either human IFN-a (a single i.p. injection at 1 x 105 IU/kg) or whole body gamma-radiation (10 cGy or 2 Gy). Patterns of Tnnt 1 transcript expression were compared in various CNS regions after IFN-a, radiation and ketamine treatments (previous study). Tnnt 1 expression was consistently induced in pyramidal neurons of cerebral cortex and hippocampus after all treatment regimens including 10 cGy of ionizing radiation. Regional expression of Tnnt 1 was induced in Purkinje cells of cerebellum after ionizing radiation and ketamine treatment; but not after IFN-a treatment. None of the three treatments induced Tnnt 1 expression in glial cells. The patterns of Tnnt 1 expression in pyramidal neurons of cerebral cortex andhippocampus, which are both known to play important roles in cognitive function, memory and emotion, suggest that the expression of Tnnt 1 may be an early molecular biomarker of induced CNS stress.

The ATLAS3D project - X. On the origin of the molecular and ionized gas in early-type galaxies

NARCIS (Netherlands)

Davis, Timothy A.; Alatalo, Katherine; Sarzi, Marc; Bureau, Martin; Young, Lisa M.; Blitz, Leo; Serra, Paolo; Crocker, Alison F.; Krajnović, Davor; McDermid, Richard M.; Bois, Maxime; Bournaud, Frédéric; Cappellari, Michele; Davies, Roger L.; Duc, Pierre-Alain; de Zeeuw, P. Tim; Emsellem, Eric; Khochfar, Sadegh; Kuntschner, Harald; Lablanche, Pierre-Yves; Morganti, Raffaella; Naab, Thorsten; Oosterloo, Tom; Scott, Nicholas; Weijmans, Anne-Marie

2011-01-01

We make use of interferometric CO and H I observations, and optical integral-field spectroscopy from the ATLAS3D survey, to probe the origin of the molecular and ionized interstellar medium (ISM) in local early-type galaxies. We find that 36 ± 5 per cent of our sample of fast-rotating early-type

Molecular-weight distributions of coal and petroleum asphaltenes from laser desorption/ionization experiments

Energy Technology Data Exchange (ETDEWEB)

Ana R. Hortal; Paola Hurtado; Bruno Martinez-Haya; Oliver C. Mullins [Universidad Pablo de Olavide, Seville (Spain). Departamento de Sistemas Fisicos, Quimicos y Naturales

2007-09-15

Molecular-weight distributions (MWDs) of asphaltenes extracted from coal and petroleum have been measured in laser desorption/ionization (LDI) mass spectrometric experiments. The dried-droplet and solvent-free sample preparation methods are compared. The coal asphaltenes have a relatively narrow MWD (full width 150 amu) with an average molecular weight of 340 amu. The petroleum asphaltenes display a broader MWD (full width 300 amu) and are heavier on average (680 amu). The LDI spectra also provide evidence for the formation of noncovalent clusters of the two types of asphaltenes during the desorption process. Petroleum and coal asphaltenes exhibit aggregation as do large model polycyclic aromatic hydrocarbons (PAHs) with five or more fused rings also included in the study. Smaller PAHs (pyrene) exhibit less aggregation, especially when alkane-chain substituents are incorporated to the molecular structure. This indicates that asphaltenes possess large PAHs and, according to the relatively small molecular weights observed, that there is a preponderance of asphaltene molecules with only a single fused ring system. The coal asphaltenes present a significantly smaller propensity toward aggregation than their crude oil counterparts. This finding, coupled with the fact that (1) alkanes inhibit aggregation in LDI and (2) petroleum asphaltenes possess much more alkane carbon, indicates that coal asphaltenes have smaller PAHs on average than petroleum asphaltenes. This is further corroborated by the stronger ultraviolet absorbance of the coal asphaltenes at wavelengths shorter than 400 nm. 32 refs., 8 figs.

Mini-review: Molecular mechanisms of antifouling compounds

KAUST Repository

Qian, Pei-Yuan

2013-04-01

Various antifouling (AF) coatings have been developed to protect submerged surfaces by deterring the settlement of the colonizing stages of fouling organisms. A review of the literature shows that effective AF compounds with specific targets are ones often considered non-toxic. Such compounds act variously on ion channels, quorum sensing systems, neurotransmitters, production/release of adhesive, and specific enzymes that regulate energy production or primary metabolism. In contrast, AF compounds with general targets may or may not act through toxic mechanisms. These compounds affect a variety of biological activities including algal photosynthesis, energy production, stress responses, genotoxic damage, immunosuppressed protein expression, oxidation, neurotransmission, surface chemistry, the formation of biofilms, and adhesive production/release. Among all the targets, adhesive production/release is the most common, possibly due to a more extensive research effort in this area. Overall, the specific molecular targets and the molecular mechanisms of most AF compounds have not been identified. Thus, the information available is insufficient to draw firm conclusions about the types of molecular targets to be used as sensitive biomarkers for future design and screening of compounds with AF potential. In this review, the relevant advantages and disadvantages of the molecular tools available for studying the molecular targets of AF compounds are highlighted briefly and the molecular mechanisms of the AF compounds, which are largely a source of speculation in the literature, are discussed. © 2013 Copyright Taylor and Francis Group, LLC.

Study of the molecular and ionized gas in a possible precursor of an ultra-compact H II region

Science.gov (United States)

Ortega, M. E.; Paron, S.; Giacani, E.; Celis Peña, M.; Rubio, M.; Petriella, A.

2017-10-01

Aims: We aim to study the molecular and the ionized gas in a possible precursor of an ultra-compact H II region to contribute to the understanding of how high-mass stars build-up their masses once they have reached the zero-age main sequence. Methods: We carried out molecular observations toward the position of the Red MSX source G052.9221-00.4892, using the Atacama Submillimeter Telescope Experiment (ASTE; Chile) in the 12CO J = 3-2, 13CO J = 3-2, C18O J = 3-2, and HCO+J = 4-3 lines with an angular resolution of about 22''. We also present radio continuum observations at 6 GHz carried out with the Jansky Very Large Array (JVLA; USA) interferometer with a synthesized beam of 4.8 arcsec × 4.1 arcsec. The molecular data were used to study the distribution and kinematics of the molecular gas, while the radio continuum data were used to characterize the ionized gas in the region. Combining these observations with public infrared data allowed us to inquire about the nature of the source. Results: The analysis of the molecular observations reveals the presence of a kinetic temperature and H2 column density gradients across the molecular clump in which the Red MSX source G052.9221-00.4892 is embedded, with the hotter and less dense gas in the inner region. The 12CO J = 3-2 emission shows evidence of misaligned massive molecular outflows, with the blue lobe in positional coincidence with a jet-like feature seen at 8 μm. The radio continuum emission shows a slightly elongated compact radio source, with a flux density of about 0.9 mJy, in positional coincidence with the Red MSX source. The polar-like morphology of this compact radio source perfectly matches the hourglass-like morphology exhibited by the source in the Ks band. Moreover, the axes of symmetry of the radio source and the near-infrared nebula are perfectly aligned. Thus, based on the presence of molecular outflows, the slightly elongated morphology of the compact radio source matching the hourglass

Biological Applications of Hybrid Quantum Mechanics/Molecular Mechanics Calculation

Directory of Open Access Journals (Sweden)

Jiyoung Kang

2012-01-01

Full Text Available Since in most cases biological macromolecular systems including solvent water molecules are remarkably large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Accordingly, QM calculations that are jointed with MM calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. A UNIX-shell-based interface program connecting the quantum mechanics (QMs and molecular mechanics (MMs calculation engines, GAMESS and AMBER, was developed in our lab. The system was applied to a metalloenzyme, azurin, and PU.1-DNA complex; thereby, the significance of the environmental effects on the electronic structures of the site of interest was elucidated. Subsequently, hybrid QM/MM molecular dynamics (MD simulation using the calculation system was employed for investigation of mechanisms of hydrolysis (editing reaction in leucyl-tRNA synthetase complexed with the misaminoacylated tRNALeu, and a novel mechanism of the enzymatic reaction was revealed. Thus, our interface program can play a critical role as a powerful tool for state-of-the-art sophisticated hybrid ab initio QM/MM MD simulations of large systems, such as biological macromolecules.

Quantum Mechanics/Molecular Mechanics Study of the Sialyltransferase Reaction Mechanism.

Science.gov (United States)

Hamada, Yojiro; Kanematsu, Yusuke; Tachikawa, Masanori

2016-10-11

The sialyltransferase is an enzyme that transfers the sialic acid moiety from cytidine 5'-monophospho-N-acetyl-neuraminic acid (CMP-NeuAc) to the terminal position of glycans. To elucidate the catalytic mechanism of sialyltransferase, we explored the potential energy surface along the sialic acid transfer reaction coordinates by the hybrid quantum mechanics/molecular mechanics method on the basis of the crystal structure of sialyltransferase CstII. Our calculation demonstrated that CstII employed an S N 1-like reaction mechanism via the formation of a short-lived oxocarbenium ion intermediate. The computational barrier height was 19.5 kcal/mol, which reasonably corresponded with the experimental reaction rate. We also found that two tyrosine residues (Tyr156 and Tyr162) played a vital role in stabilizing the intermediate and the transition states by quantum mechanical interaction with CMP.

Atomistic insight into the catalytic mechanism of glycosyltransferases by combined quantum mechanics/molecular mechanics (QM/MM) methods.

Science.gov (United States)

Tvaroška, Igor

2015-02-11

Glycosyltransferases catalyze the formation of glycosidic bonds by assisting the transfer of a sugar residue from donors to specific acceptor molecules. Although structural and kinetic data have provided insight into mechanistic strategies employed by these enzymes, molecular modeling studies are essential for the understanding of glycosyltransferase catalyzed reactions at the atomistic level. For such modeling, combined quantum mechanics/molecular mechanics (QM/MM) methods have emerged as crucial. These methods allow the modeling of enzymatic reactions by using quantum mechanical methods for the calculation of the electronic structure of the active site models and treating the remaining enzyme environment by faster molecular mechanics methods. Herein, the application of QM/MM methods to glycosyltransferase catalyzed reactions is reviewed, and the insight from modeling of glycosyl transfer into the mechanisms and transition states structures of both inverting and retaining glycosyltransferases are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

New excitation and ionization mechanism of ions in dense plasmas

International Nuclear Information System (INIS)

Fujimoto, Takashi; Kato, Takako.

1981-10-01

It is shown that, in dense plasmas, dielectronic capture into doubly excited ionic states followed by the ladder-like excitation-ionization chain becomes important in the excitation-ionization process of ions. For an example of a hydrogen-like ion, its contribution to the excitation 1s → 2s, 2p and also to the ionization has been evaluated by the method of the quasi-steady-state solution to the rate equations. The increase is found to be substantial, i.e., by more than a factor of two both for the excitation and ionization rate coefficients. PACS classification: 52.25., 32.80.D sub(z), 34.80.D. (author)

Substrate binding and catalytic mechanism in phospholipase C from Bacillus cereus. a molecular mechanics and molecular dynamics study

DEFF Research Database (Denmark)

da Graça Thrige, D; Buur, J R; Jørgensen, Flemming Steen

1997-01-01

cereus including a docked substrate molecule was subjected to a stepwise molecular mechanics energy minimization. Second, the location of the nucleophilic water molecule in the active site of the fully relaxed enzyme-substrate complex was determined by evaluation of nonbonded interaction energies between...... water molecule was verified during a 100 ps molecular dynamics simulation. During the simulation the substrate undergoes a conformational change, but retains its localization in the active site. The contacts between the enzyme, the substrate, and the nucleophilic water molecule display some fluctuations...... the strong electrostatic interactions in the active site realistically during energy minimization, delocalization of the charges from the three zinc ions was considered. Therefore, quantum mechanics calculations on the zinc ions and the zinc-coordinating residues were carried out prior to the molecular...

DRIVING TURBULENCE AND TRIGGERING STAR FORMATION BY IONIZING RADIATION

International Nuclear Information System (INIS)

Gritschneder, Matthias; Naab, Thorsten; Walch, Stefanie; Burkert, Andreas; Heitsch, Fabian

2009-01-01

We present high-resolution simulations on the impact of ionizing radiation of massive O stars on the surrounding turbulent interstellar medium (ISM). The simulations are performed with the newly developed software iVINE which combines ionization with smoothed particle hydrodynamics (SPH) and gravitational forces. We show that radiation from hot stars penetrates the ISM, efficiently heats cold low-density gas and amplifies overdensities seeded by the initial turbulence. The formation of observed pillar-like structures in star-forming regions (e.g. in M16) can be explained by this scenario. At the tip of the pillars gravitational collapse can be induced, eventually leading to the formation of low-mass stars. Detailed analysis of the evolution of the turbulence spectra shows that UV radiation of O stars indeed provides an excellent mechanism to sustain and even drive turbulence in the parental molecular cloud.

Chemical effects of ionizing radiation on the individual amino acids within intact and pure protein molecules. Final report

International Nuclear Information System (INIS)

Freidberg, F.

1977-01-01

Progress is reported on the following research projects: gamma radiation induced chemical and molecular weight changes in proteins; the free radical pattern for the irradiated protein; similarities in the mechanism of action of ionizing and of uv radiation; and spin trapping in the study of gamma radiolysis

Simulation with quantum mechanics/molecular mechanics for drug discovery.

Science.gov (United States)

Barbault, Florent; Maurel, François

2015-10-01

Biological macromolecules, such as proteins or nucleic acids, are (still) molecules and thus they follow the same chemical rules that any simple molecule follows, even if their size generally renders accurate studies unhelpful. However, in the context of drug discovery, a detailed analysis of ligand association is required for understanding or predicting their interactions and hybrid quantum mechanics/molecular mechanics (QM/MM) computations are relevant tools to help elucidate this process. In this review, the authors explore the use of QM/MM for drug discovery. After a brief description of the molecular mechanics (MM) technique, the authors describe the subtractive and additive techniques for QM/MM computations. The authors then present several application cases in topics involved in drug discovery. QM/MM have been widely employed during the last decades to study chemical processes such as enzyme-inhibitor interactions. However, despite the enthusiasm around this area, plain MM simulations may be more meaningful than QM/MM. To obtain reliable results, the authors suggest fixing several keystone parameters according to the underlying chemistry of each studied system.

Ionizing radiation effect on physico-mechanical characteristics of thermoplastic polymer materials

International Nuclear Information System (INIS)

Stankevich, V.M.; Pleskachevsky, Yu.M.; Smirnov, V.V.

2001-01-01

Investigation results in the field of ionizing radiation effect on structure and physico-mechanical properties of novel polymer materials are presented. The materials under study are various grades of PETP, PA-6 and polyethylene concentrate of technical carbon (PECC) commercially produced and extensively used in Belarus and abroad. It has been proved using EPR, thermomechanical and gel analyses that a combined effect of ionizing radiation within 0 to 10 MGy of absorbed dose range under different concentrations of mineral fillers (TiO 2 , kaolin, carbon black, graphite) and intensive cross-linking processes in amorphous phase are able to considerably improve strength characteristics of the studied polymers and their compositions. Most informative parameter was found to be breaking strength at rapture (σ r ) which enables to estimate the character of ionizing effect on the targets. At 0.01-0.05 MGy absorbed dose the highest σ r was shown as compared to initial PETP by the following materials: PN grade - 9 times, D - two and a half. When absorbed dose of PETP reached 0.2 MGy, σ r of PN surpassed the initial material 7.8 times, that of D - by 30% and E - by 1,5%. This is the evidence of elevated resistance of named materials to ionizing radiation in contrast to non-filled PETP 215. Growth of σ r in PA-6 has been noticed at absorbed dose above 2 MGy in response to maximum gel-formation values. Abrupt reduction of the studied parameters of PP upon irradiation is attributed to its destruction. Domination of cross-linking processes has been observed in PEVP and PECC which reduces macromolecular mobility and elasticity of the material as a whole but promotes polymer strengthening. Drop of PEVP impact strength can be related to its embrittlement. Presence of the filler (carbon black) in PECC at the initial stage of exposure resulted in improvement of studied parameters. Their further impairment is the result of limited mobility of macromolecules owing to cross-linking in

Quantum mechanics capacitance molecular mechanics modeling of core-electron binding energies of methanol and methyl nitrite on Ag(111) surface.

Science.gov (United States)

Löytynoja, T; Li, X; Jänkälä, K; Rinkevicius, Z; Ågren, H

2016-07-14

We study a newly devised quantum mechanics capacitance molecular mechanics (QMCMM) method for the calculation of core-electron binding energies in the case of molecules adsorbed on metal surfaces. This yet untested methodology is applied to systems with monolayer of methanol/methyl nitrite on an Ag(111) surface at 100 K temperature. It was found out that the studied C, N, and O 1s core-hole energies converge very slowly as a function of the radius of the metallic cluster, which was ascribed to build up of positive charge on the edge of the Ag slab. Further analysis revealed that an extrapolation process can be used to obtain binding energies that deviated less than 0.5 eV against experiments, except in the case of methanol O 1s where the difference was as large as 1.8 eV. Additional QM-cluster calculations suggest that the latter error can be connected to the lack of charge transfer over the QM-CMM boundary. Thus, the results indicate that the QMCMM and QM-cluster methods can complement each other in a holistic picture of molecule-adsorbate core-ionization studies, where all types of intermolecular interactions are considered.

Modeling strong-field above-threshold ionization

International Nuclear Information System (INIS)

Sundaram, B.; Armstrong, L. Jr.

1990-01-01

Above-threshold ionization (ATI) by intense, short-pulse lasers is studied numerically, using the stretched hydrogen atom Hamiltonian. Within our model system, we isolate several mechanisms that contribute to the ATI process. These mechanisms, which involve both excited bound states and continuum states, all invoke intermediate, off-energy shell transitions. In particular, the importance of excited bound states and off-energy shell bound-free processes to the ionization mechanism are shown to relate to a simple physical criterion. These processes point to importance differences in the interpretation of ionization characteristics for short pulses from that for longer pulses. Our analysis concludes that although components of ATI admit of simple, few-state modeling, the ultimate synthesis points to a highly complex mechanism

Electrospray Ionization Mass Spectrometry: A Technique to Access the Information beyond the Molecular Weight of the Analyte

Science.gov (United States)

Banerjee, Shibdas; Mazumdar, Shyamalava

2012-01-01

The Electrospray Ionization (ESI) is a soft ionization technique extensively used for production of gas phase ions (without fragmentation) of thermally labile large supramolecules. In the present review we have described the development of Electrospray Ionization mass spectrometry (ESI-MS) during the last 25 years in the study of various properties of different types of biological molecules. There have been extensive studies on the mechanism of formation of charged gaseous species by the ESI. Several groups have investigated the origin and implications of the multiple charge states of proteins observed in the ESI-mass spectra of the proteins. The charged analytes produced by ESI can be fragmented by activating them in the gas-phase, and thus tandem mass spectrometry has been developed, which provides very important insights on the structural properties of the molecule. The review will highlight recent developments and emerging directions in this fascinating area of research. PMID:22611397

Electrospray ionization mass spectrometry: a technique to access the information beyond the molecular weight of the analyte.

Science.gov (United States)

Banerjee, Shibdas; Mazumdar, Shyamalava

2012-01-01

The Electrospray Ionization (ESI) is a soft ionization technique extensively used for production of gas phase ions (without fragmentation) of thermally labile large supramolecules. In the present review we have described the development of Electrospray Ionization mass spectrometry (ESI-MS) during the last 25 years in the study of various properties of different types of biological molecules. There have been extensive studies on the mechanism of formation of charged gaseous species by the ESI. Several groups have investigated the origin and implications of the multiple charge states of proteins observed in the ESI-mass spectra of the proteins. The charged analytes produced by ESI can be fragmented by activating them in the gas-phase, and thus tandem mass spectrometry has been developed, which provides very important insights on the structural properties of the molecule. The review will highlight recent developments and emerging directions in this fascinating area of research.

Advance of Mechanically Controllable Break Junction for Molecular Electronics.

Science.gov (United States)

Wang, Lu; Wang, Ling; Zhang, Lei; Xiang, Dong

2017-06-01

Molecular electronics stands for the ultimate size of functional elements, keeping up with an unstoppable trend over the past few decades. As a vital component of molecular electronics, single molecular junctions have attracted significant attention from research groups all over the world. Due to its pronounced superiority, the mechanically controllable break junctions (MCBJ) technique has been widely applied to characterize the dynamic performance of single molecular junctions. This review presents a system analysis for single-molecule junctions and offers an overview of four test-beds for single-molecule junctions, thus offering more insight into the mechanisms of electron transport. We mainly focus on the development of state-of-the-art mechanically controlled break junctions. The three-terminal gated MCBJ approaches are introduced to manipulate the electron transport of molecules, and MCBJs are combined with characterization techniques. Additionally, applications of MCBJs and remarkable properties of single molecules are addressed. Finally, the challenges and perspective for the mechanically controllable break junctions technique are provided.

The critical ionization velocity

International Nuclear Information System (INIS)

Raadu, M.A.

1980-06-01

The critical ionization velocity effect was first proposed in the context of space plasmas. This effect occurs for a neutral gas moving through a magnetized plasma and leads to rapid ionization and braking of the relative motion when a marginal velocity, 'the critical velocity', is exceeded. Laboratory experiments have clearly established the significance of the critical velocity and have provided evidence for an underlying mechanism which relies on the combined action of electron impact ionization and a collective plasma interaction heating electrons. There is experimental support for such a mechanism based on the heating of electrons by the modified two-stream instability as part of a feedback process. Several applications to space plasmas have been proposed and the possibility of space experiments has been discussed. (author)

Excitation and Ionization of Ethylene by Charged Projectiles

International Nuclear Information System (INIS)

Zhi-Ping, Wang; Jing, Wang; Feng-Shou, Zhang

2010-01-01

Using the time dependent local density approximation, applied to valence electrons, coupled non-adiabatically to molecular dynamics of ions, the collision process between ethylene and fast charged projectiles is studied in the microscopic way. The impact of ionic motion on the ionization is explored to show the importance of treating electronic and ionic degrees of freedom simultaneously. The number of escaped electrons, ionization probabilities are obtained. Furthermore, it is found that the ionic extensions in different directions show the different patterns. (atomic and molecular physics)

Isotope-selective ionization using four-pulse alignment

International Nuclear Information System (INIS)

Akagi, Hiroshi; Kasajima, Tatsuya; Kumada, Takayuki; Itakura, Ryuji; Yokoyama, Atsushi; Hasegawa, Hirokazu; Ohshima, Yasuhiro

2013-01-01

We have proposed a laser isotope separation method utilizing molecular alignment and non-resonant multiphoton ionization, and demonstrated isotope-selective ionization of 14 N 2 and 15 N 2 isotopomers, using one-pulse alignment. In the present work, we used a train of four identical pulses, instead of one pulse, to obtain the higher selectivity. (author)

MOLECULAR MECHANISMS OF FEAR LEARNING AND MEMORY

Science.gov (United States)

Johansen, Joshua P.; Cain, Christopher K.; Ostroff, Linnaea E.; LeDoux, Joseph E.

2011-01-01

Pavlovian fear conditioning is a useful behavioral paradigm for exploring the molecular mechanisms of learning and memory because a well-defined response to a specific environmental stimulus is produced through associative learning processes. Synaptic plasticity in the lateral nucleus of the amygdala (LA) underlies this form of associative learning. Here we summarize the molecular mechanisms that contribute to this synaptic plasticity in the context of auditory fear conditioning, the form of fear conditioning best understood at the molecular level. We discuss the neurotransmitter systems and signaling cascades that contribute to three phases of auditory fear conditioning: acquisition, consolidation, and reconsolidation. These studies suggest that multiple intracellular signaling pathways, including those triggered by activation of Hebbian processes and neuromodulatory receptors, interact to produce neural plasticity in the LA and behavioral fear conditioning. Together, this research illustrates the power of fear conditioning as a model system for characterizing the mechanisms of learning and memory in mammals, and potentially for understanding fear related disorders, such as PTSD and phobias. PMID:22036561

Molecular mechanisms of fear learning and memory.

Science.gov (United States)

Johansen, Joshua P; Cain, Christopher K; Ostroff, Linnaea E; LeDoux, Joseph E

2011-10-28

Pavlovian fear conditioning is a particularly useful behavioral paradigm for exploring the molecular mechanisms of learning and memory because a well-defined response to a specific environmental stimulus is produced through associative learning processes. Synaptic plasticity in the lateral nucleus of the amygdala (LA) underlies this form of associative learning. Here, we summarize the molecular mechanisms that contribute to this synaptic plasticity in the context of auditory fear conditioning, the form of fear conditioning best understood at the molecular level. We discuss the neurotransmitter systems and signaling cascades that contribute to three phases of auditory fear conditioning: acquisition, consolidation, and reconsolidation. These studies suggest that multiple intracellular signaling pathways, including those triggered by activation of Hebbian processes and neuromodulatory receptors, interact to produce neural plasticity in the LA and behavioral fear conditioning. Collectively, this body of research illustrates the power of fear conditioning as a model system for characterizing the mechanisms of learning and memory in mammals and potentially for understanding fear-related disorders, such as PTSD and phobias. Copyright © 2011 Elsevier Inc. All rights reserved.

Molecular Mechanisms of Renal Ischemic Conditioning Strategies

DEFF Research Database (Denmark)

Kierulf-Lassen, Casper; Nieuwenhuijs-Moeke, Gertrude J; Krogstrup, Nicoline V

2015-01-01

summarizes research on the molecular mechanisms underlying both local and remote ischemic pre-, per- and postconditioning of the kidney. The different types of conditioning strategies in the kidney recruit similar powerful pro-survival mechanisms. Likewise, renal ischemic conditioning mobilizes many...

[Neonatal hyperbilirubinemia and molecular mechanisms of jaundice].

Science.gov (United States)

Jirsa, M; Sticová, E

2013-07-01

The introductory summarises the classical path of heme degradation and classification of jaundice. Subsequently, a description of neonatal types of jaundice is given, known as Crigler Najjar, Gilberts, DubinJohnson and Rotor syndromes, emphasising the explanation of the molecular mechanisms of these metabolic disorders. Special attention is given to a recently discovered molecular mechanism of the Rotor syndrome. The mechanism is based on the inability of the liver to retrospectively uptake the conjugated bilirubin fraction primarily excreted into the blood, not bile. A reduced ability of the liver to uptake the conjugated bilirubin contributes to the development of hyperbilirubinemia in common disorders of the liver and bile ducts and to the toxicity of xenobiotics and drugs using transport proteins for conjugated bilirubin.

Recognition, signaling, and repair of DNA double-strand breaks produced by ionizing radiation in mammalian cells: the molecular choreography.

Science.gov (United States)

Thompson, Larry H

2012-01-01

The faithful maintenance of chromosome continuity in human cells during DNA replication and repair is critical for preventing the conversion of normal diploid cells to an oncogenic state. The evolution of higher eukaryotic cells endowed them with a large genetic investment in the molecular machinery that ensures chromosome stability. In mammalian and other vertebrate cells, the elimination of double-strand breaks with minimal nucleotide sequence change involves the spatiotemporal orchestration of a seemingly endless number of proteins ranging in their action from the nucleotide level to nucleosome organization and chromosome architecture. DNA DSBs trigger a myriad of post-translational modifications that alter catalytic activities and the specificity of protein interactions: phosphorylation, acetylation, methylation, ubiquitylation, and SUMOylation, followed by the reversal of these changes as repair is completed. "Superfluous" protein recruitment to damage sites, functional redundancy, and alternative pathways ensure that DSB repair is extremely efficient, both quantitatively and qualitatively. This review strives to integrate the information about the molecular mechanisms of DSB repair that has emerged over the last two decades with a focus on DSBs produced by the prototype agent ionizing radiation (IR). The exponential growth of molecular studies, heavily driven by RNA knockdown technology, now reveals an outline of how many key protein players in genome stability and cancer biology perform their interwoven tasks, e.g. ATM, ATR, DNA-PK, Chk1, Chk2, PARP1/2/3, 53BP1, BRCA1, BRCA2, BLM, RAD51, and the MRE11-RAD50-NBS1 complex. Thus, the nature of the intricate coordination of repair processes with cell cycle progression is becoming apparent. This review also links molecular abnormalities to cellular pathology as much a possible and provides a framework of temporal relationships. Copyright © 2012 Elsevier B.V. All rights reserved.

Perfect/complete scattering experiments. Probing quantum mechanics on atomic and molecular collisions and coincidences

International Nuclear Information System (INIS)

Lohmann, Bernd; Grum-Grzhimailo, Alexei N.; Kleinpoppen, Hans

2013-01-01

Derives parameters for electrons, photons, atoms, ions, molecules calculated from theory. Delivers the quantum mechanical knowledge of atomic and molecular physics. Presents state-of-the-art experiments in atomic and molecular physics and related theoretical approaches. The main goal of this book is to elucidate what kind of experiment must be performed in order to determine the full set of independent parameters which can be extracted and calculated from theory, where electrons, photons, atoms, ions, molecules, or molecular ions may serve as the interacting constituents of matter. The feasibility of such perfect' and-or 'complete' experiments, providing the complete quantum mechanical knowledge of the process, is associated with the enormous potential of modern research techniques, both, in experiment and theory. It is even difficult to overestimate the role of theory in setting of the complete experiment, starting with the fact that an experiment can be complete only within a certain theoretical framework, and ending with the direct prescription of what, and in what conditions should be measured to make the experiment 'complete'. The language of the related theory is the language of quantum mechanical amplitudes and their relative phases. This book captures the spirit of research in the direction of the complete experiment in atomic and molecular physics, considering some of the basic quantum processes: scattering, Auger decay and photo-ionization. It includes a description of the experimental methods used to realize, step by step, the complete experiment up to the level of the amplitudes and phases. The corresponding arsenal includes, beyond determining the total cross section, the observation of angle and spin resolved quantities, photon polarization and correlation parameters, measurements applying coincidence techniques, preparing initially polarized targets, and even more sophisticated methods. The 'complete' experiment is, until today, hardly to perform

Perfect/complete scattering experiments. Probing quantum mechanics on atomic and molecular collisions and coincidences

Energy Technology Data Exchange (ETDEWEB)

Lohmann, Bernd [Muenster Univ. (Germany). Inst. fuer Theoretische Physik 1; Grum-Grzhimailo, Alexei N. [Moscow State Univ. (Russian Federation). Skobeltsyn Inst. of Nuclear Physics; Kleinpoppen, Hans

2013-07-01

Derives parameters for electrons, photons, atoms, ions, molecules calculated from theory. Delivers the quantum mechanical knowledge of atomic and molecular physics. Presents state-of-the-art experiments in atomic and molecular physics and related theoretical approaches. The main goal of this book is to elucidate what kind of experiment must be performed in order to determine the full set of independent parameters which can be extracted and calculated from theory, where electrons, photons, atoms, ions, molecules, or molecular ions may serve as the interacting constituents of matter. The feasibility of such perfect' and-or 'complete' experiments, providing the complete quantum mechanical knowledge of the process, is associated with the enormous potential of modern research techniques, both, in experiment and theory. It is even difficult to overestimate the role of theory in setting of the complete experiment, starting with the fact that an experiment can be complete only within a certain theoretical framework, and ending with the direct prescription of what, and in what conditions should be measured to make the experiment 'complete'. The language of the related theory is the language of quantum mechanical amplitudes and their relative phases. This book captures the spirit of research in the direction of the complete experiment in atomic and molecular physics, considering some of the basic quantum processes: scattering, Auger decay and photo-ionization. It includes a description of the experimental methods used to realize, step by step, the complete experiment up to the level of the amplitudes and phases. The corresponding arsenal includes, beyond determining the total cross section, the observation of angle and spin resolved quantities, photon polarization and correlation parameters, measurements applying coincidence techniques, preparing initially polarized targets, and even more sophisticated methods. The 'complete' experiment is

XUV ionization of aligned molecules

Energy Technology Data Exchange (ETDEWEB)

Kelkensberg, F.; Siu, W.; Gademann, G. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Rouzee, A.; Vrakking, M. J. J. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Max-Born-Institut, Max-Born Strasse 2A, D-12489 Berlin (Germany); Johnsson, P. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Department of Physics, Lund University, Post Office Box 118, SE-221 00 Lund (Sweden); Lucchini, M. [Department of Physics, Politecnico di Milano, Istituto di Fotonica e Nanotecnologie CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Lucchese, R. R. [Department of Chemistry, Texas A and M University, College Station, Texas 77843-3255 (United States)

2011-11-15

New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO{sub 2} molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

XUV ionization of aligned molecules

International Nuclear Information System (INIS)

Kelkensberg, F.; Siu, W.; Gademann, G.; Rouzee, A.; Vrakking, M. J. J.; Johnsson, P.; Lucchini, M.; Lucchese, R. R.

2011-01-01

New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO 2 molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

Creating a strategy for science-based national policy: Addressing conflicting views on the health risk of low-level ionizing radiation. Final report, Wingspread Conference

International Nuclear Information System (INIS)

McClellan, Roger O.; Apple, Martin A.

1998-01-01

Significant cancer risk for adults exposed to more than 100 millisieverts (10 REM) of ionizing radiation. More research on low-level ionizing radiation is needed in molecular and cellular mechanisms of injury and ongoing exposed populations. Implementation costs should be considered in regulating low-level ionizing radiation. Comparative risk assessment is a powerful tool for risk-based policy formation, and conflicting legal statutes should become harmonized for radiation regulation. More public dialog on low-level radiation is needed. A high level commission should evaluate radiation hazard control practices

Quantification of gene expression modulation at the human genome wide induced by low doses of ionizing radiations

International Nuclear Information System (INIS)

Nosel, Ingrid

2013-01-01

The main goal of this study is to identify the molecular mechanisms involved in the response to low doses of ionizing radiation by using oligonucleotide micro-arrays. The results presented in this study demonstrate the relevance of this tool in the characterization of changes in gene expression at low doses of g radiation. All experimentations conducted were conducted on T CD4+ human lymphocytes. From this model we tried to characterize in 600 minutes after irradiation the molecular players in response to a dose range of 5 and 500 mGy. In this study, we highlight two types of molecular response. First, a dose-dependent response to irradiation involving groups of genes whose proteins are implicated in the response to DNA damage and in the p53 signaling pathway. The expression of the majority of the genes is modulated from 100 mGy. The second type of response is independent of the irradiation dose and the proteins encoded are involved in the mechanism of oxidative phosphorylation. Some of these genes could potentially be regulated by a family of transcription factor with an ETS domain. These ETS factors are known to be potential targets of the MAPKinase pathway. All these genes are modulated from 5 mGy and are therefore potential molecular players involved in the cellular response to ionizing stress with a low intensity. (author)

Molecular pathogenesis and mechanisms of thyroid cancer

Science.gov (United States)

Xing, Mingzhao

2013-01-01

Thyroid cancer is a common endocrine malignancy. There has been exciting progress in understanding its molecular pathogenesis in recent years, as best exemplified by the elucidation of the fundamental role of several major signalling pathways and related molecular derangements. Central to these mechanisms are the genetic and epigenetic alterations in these pathways, such as mutation, gene copy-number gain and aberrant gene methylation. Many of these molecular alterations represent novel diagnostic and prognostic molecular markers and therapeutic targets for thyroid cancer, which provide unprecedented opportunities for further research and clinical development of novel treatment strategies for this cancer. PMID:23429735

An investigation of electronic states of some molecules and molecular cations using mass analyzed threshold ionization and photoinduced Rydberg ionization spectroscopy

Science.gov (United States)

Hofstein, Jason David

1999-11-01

Mass analyzed threshold ionization (MATI) experiments have enabled mapping of the n-dependent Rydberg state survival probability for a series of molecules. Utilizing vacuum and extreme ultraviolet (VUV/XUV) photons, one photon Rydberg manifold spectra of argon, hydrogen chloride, nitrogen, benzene, and oxygen were produced, and the prospects of photoinduced Rydberg ionization (PIRI) experiments examined. It was found that the widths of Rydberg manifolds for the molecules studied are quite different. Hydrogen chloride and nitrogen have the narrowest manifold width, followed by benzene, and then oxygen. These varying widths are most strongly correlated with the angular momentum (i.e., quantum defect) of the initially prepared Rydberg orbital. PIRI experiments required the use of a static cell, rather than a molecular jet assembly, for the more efficient production of higher amounts of VUV/XUV radiation, and hence more Rydberg signal needed to observe PIRI. Armed with the ability to produce tunable VUV/XUV radiation, and to determine the feasibility of a PIRI experiment, the MATI and fragment PIRI spectra of trans-1,3-butadiene (BD) were recorded. The MATI spectrum is vibrationally resolved and was analyzed with the help of ab initio calculations and other published results. The fragment PIRI spectrum of the Aproduction of C3H3+ dominates, but at higher photon energies, C2H4 + is also produced. The production of each fragment showed a definite PIRI wavelength dependence.

Ionization and fragmentation of water clusters by fast highly charged ions

International Nuclear Information System (INIS)

Adoui, L; Cassimi, A; Gervais, B; Grandin, J-P; Guillaume, L; Maisonny, R; Legendre, S; Tarisien, M; Lopez-Tarifa, P; Alcami, M; Martin, F; Politis, M-F; Penhoat, M-A Herve du; Vuilleumier, R; Gaigeot, M-P; Tavernelli, I

2009-01-01

We study the dissociative ionization of water clusters by impact of 12 MeV/u Ni 25+ ions. Cold target recoil ion momentum spectroscopy (COLTRIMS) is used to obtain information about stability, energetics and charge mobility of the ionized water clusters. An unusual stability of the H 9 O + 4 ion is observed, which could be the signature of the so-called Eigen structure in gas-phase water clusters. From the analysis of coincidences between charged fragments, we conclude that charge mobility is very high and is responsible for the formation of protonated water clusters, (H 2 O) n H + , that dominate the mass spectrum. These results are supported by Car-Parrinello molecular dynamics and time-dependent density functional theory simulations, which also reveal the mechanisms of such mobility.

Humidity Effects on Fragmentation in Plasma-Based Ambient Ionization Sources.

Science.gov (United States)

Newsome, G Asher; Ackerman, Luke K; Johnson, Kevin J

2016-01-01

Post-plasma ambient desorption/ionization (ADI) sources are fundamentally dependent on surrounding water vapor to produce protonated analyte ions. There are two reports of humidity effects on ADI spectra. However, it is unclear whether humidity will affect all ADI sources and analytes, and by what mechanism humidity affects spectra. Flowing atmospheric pressure afterglow (FAPA) ionization and direct analysis in real time (DART) mass spectra of various surface-deposited and gas-phase analytes were acquired at ambient temperature and pressure across a range of observed humidity values. A controlled humidity enclosure around the ion source and mass spectrometer inlet was used to create programmed humidity and temperatures. The relative abundance and fragmentation of molecular adduct ions for several compounds consistently varied with changing ambient humidity and also were controlled with the humidity enclosure. For several compounds, increasing humidity decreased protonated molecule and other molecular adduct ion fragmentation in both FAPA and DART spectra. For others, humidity increased fragment ion ratios. The effects of humidity on molecular adduct ion fragmentation were caused by changes in the relative abundances of different reagent protonated water clusters and, thus, a change in the average difference in proton affinity between an analyte and the population of water clusters. Control of humidity in ambient post-plasma ion sources is needed to create spectral stability and reproducibility.

Responses and mechanisms of positive electron affinity molecules in the N2 mode of the thermionic ionization detector and the electron-capture detector

International Nuclear Information System (INIS)

Jones, C.S.

1989-01-01

Very little knowledge has been acquired in the past on the mechanistic pathway by which molecules respond in the N 2 mode of the thermionic ionization detector. An attempt is made here to elucidate the response mechanism of the detector. The basic response mechanisms are known for the electron capture detector, and an attempt is made to identify the certain mechanism by which selected molecules respond. The resonance electron capture rate constant has been believed to be temperature independent, and investigations of the temperature dependence of electron capture responses are presented. Mechanisms for the N 2 mode of the thermionic ionization detector have been proposed by examining the detector response to positive electron affinity molecules and by measurement of the ions produced by the detector. Electron capture mechanisms for selected molecules have been proposed by examining their temperature dependent responses in the electron capture detector and negative ion mass spectra of the samples. In studies of the resonance electron capture rate constant, the relative responses of selected positive electron affinity molecules and their temperature dependent responses were investigated. Positive electron affinity did not guarantee large responses in the N 2 mode thermionic ionization detector. High mass ions were measured following ionization of samples in the detector. Responses in the electron capture detector varied with temperature and electron affinity

Manifestations and mechanisms of non-targeted effects of ionizing radiation

International Nuclear Information System (INIS)

Wright, Eric G.

2010-01-01

A well-established radiobiological paradigm is that the biological effects of ionizing radiation occur in irradiated cells as a consequence of the DNA damage they incur. However, many observations of, so-called, non-targeted effects indicate that genetic alterations are not restricted to directly irradiated cells. Non-targeted effects are responses exhibited by non-irradiated cells that are the descendants of irradiated cells (radiation-induced genomic instability) or by cells that have communicated with irradiated cells (radiation-induced bystander effects). Radiation-induced genomic instability is characterized by chromosomal abnormalities, gene mutations and cell death. Similar effects, as well as responses that may be regarded as protective, have been attributed to bystander mechanisms. The majority of studies to date have used in vitro systems but some non-targeted effects have been demonstrated in vivo and there is also evidence for radiation-induced instability in the mammalian germ line. However, there may be situations where radiation-induced genomic instability in vivo may not necessarily identify genomically unstable somatic cells but the manifestation of responses to ongoing production of damaging signals generated by genotype-dependent mechanisms having properties in common with inflammatory processes. Non-targeted mechanisms have significant implications for understanding mechanisms of radiation action but the current state of knowledge does not permit definitive statements about whether these phenomena have implications for assessing radiation risk.

Secondary-electron-production cross sections for electron-impact ionization of molecular nitrogen

International Nuclear Information System (INIS)

Goruganthu, R.R.; Wilson, W.G.; Bonham, R.A.

1987-01-01

Measurements of the double-differential cross section (DDCS), as a function of the ejected energy, angle, and primary energy for electron-impact ionization of molecular nitrogen are reported at incident energies of 200, 500, 1000, and 2000 eV. The ejection angle was varied from 30 0 to 150 0 in steps of 15 0 . The cross sections were obtained by use of a crossed-beam apparatus with an effusive gas source and a pulsed electron beam. Scattered and ejected electrons were energy analyzed by time-of-flight analysis from below 2 eV to the primary energy. The relative measurements were placed on an absolute scale by matching the experimental elastic differential cross sections to absolute measurements at each primary energy. Comparisons of the DDCS with previous reported values revealed significant differences. The DDCS were fitted to a Legendre polynomial expansion as a function of the ejection angle. Platzman plot analysis was carried out on the energy distributions determined from the fit coefficients. The total ionization cross sections at these primary energies were deduced from this plot. An autoionization feature at 2.3 eV was observed for the first time in measurements of this nature and has been assigned as due to a Rydberg state converging to the B 2 Σ/sub u/ + ionic state which decays to the X 2 Σ/sub g/ + ground state of N 2 + . An analysis of the autoionization lines observed in the present work in the range 0.4--2.5 eV is also presented

Molecularly imprinted polymer (MIP) membrane assisted direct spray ionization mass spectrometry for agrochemicals screening in foodstuffs.

Science.gov (United States)

Pereira, Igor; Rodrigues, Marcella Ferreira; Chaves, Andréa Rodrigues; Vaz, Boniek Gontijo

2018-02-01

Paper spray ionization (PSI) has some limitations such as low sensitivity and ionization suppression when complex samples are analyzed. The use of sample preparation devices directly coupled to MS can avoid these restrictions. Molecularly imprinted polymers (MIPs) are materials widely used as adsorbent in sample preparation methods such as solid-phase extraction and solid-phase microextraction, and they can provide specifics cavities with affinity to a target molecule. Here, we introduce a new MIP membrane spray ionization method combining MIP and PSI. MIP was synthesized directly on a cellulose membrane. Monuron and 2,4,5-T (2,4,5-trichlorophenoxyacetic acid) were used as template molecules in MIP synthesis for diuron and 2,4-D (2,4-dichlorophenoxyacetic acid) analyte sequesters, respectively. Apple, banana and grape methanolic extracts were used as matrices. The MIP membrane spray showed signal intensities of diuron and 2,4-D that were much higher compared to those obtained by non-imprinted polymers(NIP). Calibration curves exhibited R 2 > 0.99 for diuron and 2,4-D in all fruit extracts analyzed. LODs were found less than 0.60µgL -1 and LLOQs were found less than 2.00µgL -1 . The coefficients of variation and relative errors were less than 15% for almost all analyses. The apparent recovery test results ranged between 92,5% and 116.9%. Finally, the MIP membrane spray method was employed for the quantification of diuron and 2,4-D in real samples. Diuron contents were only found in three bananas (4.0, 6.5, and 9.9µgL -1 ). The proposed MIP membrane spray ionization method was straightforward, fast to carry out and provided satisfactory results for analyses of diuron and 2,4-D in apple, banana and grape samples. Copyright © 2017 Elsevier B.V. All rights reserved.

A new instrument of VUV laser desorption/ionization mass spectrometry imaging with micrometer spatial resolution and low level of molecular fragmentation.

Science.gov (United States)

Wang, Jia; Liu, Feng; Mo, Yuxiang; Wang, Zhaoying; Zhang, Sichun; Zhang, Xinrong

2017-11-01

Mass spectrometry imaging (MSI) has important applications in material research, biology, and medicine. The MSI method based on UV laser desorption/ionization (UVLDI) can obtain images of intact samples, but has a high level of molecular fragmentation. In this work, we report a new MSI instrument that uses a VUV laser (125.3 nm) as a desorption/ionization source to exploit its advantages of high single photon energy and small focus size. The new instrument was tested by the mass spectra of Nile red and FGB (Fibrinogen beta chain) samples and mass spectrometric images of a fly brain section. For the tested samples, the VUVDI method offers lower levels of molecular fragmentations and higher sensitivities than those of the UVLDI method and second ion mass spectrometry imaging method using a Bi 3 + beam. The ablation crater produced by the focused VUV laser on a quartz plate has an area of 10 μm 2 . The VUV laser is prepared based on the four-wave mixing method using three collimated laser beams and a heated Hg cell.

A new instrument of VUV laser desorption/ionization mass spectrometry imaging with micrometer spatial resolution and low level of molecular fragmentation

Science.gov (United States)

Wang, Jia; Liu, Feng; Mo, Yuxiang; Wang, Zhaoying; Zhang, Sichun; Zhang, Xinrong

2017-11-01

Mass spectrometry imaging (MSI) has important applications in material research, biology, and medicine. The MSI method based on UV laser desorption/ionization (UVLDI) can obtain images of intact samples, but has a high level of molecular fragmentation. In this work, we report a new MSI instrument that uses a VUV laser (125.3 nm) as a desorption/ionization source to exploit its advantages of high single photon energy and small focus size. The new instrument was tested by the mass spectra of Nile red and FGB (Fibrinogen beta chain) samples and mass spectrometric images of a fly brain section. For the tested samples, the VUVDI method offers lower levels of molecular fragmentations and higher sensitivities than those of the UVLDI method and second ion mass spectrometry imaging method using a Bi3+ beam. The ablation crater produced by the focused VUV laser on a quartz plate has an area of 10 μm2. The VUV laser is prepared based on the four-wave mixing method using three collimated laser beams and a heated Hg cell.

Resveratrol and Calcium Signaling: Molecular Mechanisms and Clinical Relevance

Directory of Open Access Journals (Sweden)

Audrey E. McCalley

2014-06-01

Full Text Available Resveratrol is a naturally occurring compound contributing to cellular defense mechanisms in plants. Its use as a nutritional component and/or supplement in a number of diseases, disorders, and syndromes such as chronic diseases of the central nervous system, cancer, inflammatory diseases, diabetes, and cardiovascular diseases has prompted great interest in the underlying molecular mechanisms of action. The present review focuses on resveratrol, specifically its isomer trans-resveratrol, and its effects on intracellular calcium signaling mechanisms. As resveratrol’s mechanisms of action are likely pleiotropic, its effects and interactions with key signaling proteins controlling cellular calcium homeostasis are reviewed and discussed. The clinical relevance of resveratrol’s actions on excitable cells, transformed or cancer cells, immune cells and retinal pigment epithelial cells are contrasted with a review of the molecular mechanisms affecting calcium signaling proteins on the plasma membrane, cytoplasm, endoplasmic reticulum, and mitochondria. The present review emphasizes the correlation between molecular mechanisms of action that have recently been identified for resveratrol and their clinical implications.

Physics of partially ionized plasmas

CERN Document Server

Krishan, Vinod

2016-01-01

Plasma is one of the four fundamental states of matter; the other three being solid, liquid and gas. Several components, such as molecular clouds, diffuse interstellar gas, the solar atmosphere, the Earth's ionosphere and laboratory plasmas, including fusion plasmas, constitute the partially ionized plasmas. This book discusses different aspects of partially ionized plasmas including multi-fluid description, equilibrium and types of waves. The discussion goes on to cover the reionization phase of the universe, along with a brief description of high discharge plasmas, tokomak plasmas and laser plasmas. Various elastic and inelastic collisions amongst the three particle species are also presented. In addition, the author demonstrates the novelty of partially ionized plasmas using many examples; for instance, in partially ionized plasma the magnetic induction is subjected to the ambipolar diffusion and the Hall effect, as well as the usual resistive dissipation. Also included is an observation of kinematic dynam...

Quantum chemical approaches: semiempirical molecular orbital and hybrid quantum mechanical/molecular mechanical techniques.

Science.gov (United States)

Bryce, Richard A; Hillier, Ian H

2014-01-01

The use of computational quantum chemical methods to aid drug discovery is surveyed. An overview of the various computational models spanning ab initio, density function theory, semiempirical molecular orbital (MO), and hybrid quantum mechanical (QM)/molecular mechanical (MM) methods is given and their strengths and weaknesses are highlighted, focussing on the challenge of obtaining the accuracy essential for them to make a meaningful contribution to drug discovery. Particular attention is given to hybrid QM/MM and semiempirical MO methods which have the potential to yield the necessary accurate predictions of macromolecular structure and reactivity. These methods are shown to have advanced the study of many aspects of substrate-ligand interactions relevant to drug discovery. Thus, the successful parametrization of semiempirical MO methods and QM/MM methods can be used to model noncovalent substrate-protein interactions, and to lead to improved scoring functions. QM/MM methods can be used in crystal structure refinement and are particularly valuable for modelling covalent protein-ligand interactions and can thus aid the design of transition state analogues. An extensive collection of examples from the areas of metalloenzyme structure, enzyme inhibition, and ligand binding affinities and scoring functions are used to illustrate the power of these techniques.

Determination of phosphatidylethanolamine molecular species in various food matrices by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS2).

Science.gov (United States)

Zhou, Li; Zhao, Minjie; Ennahar, Saïd; Bindler, Françoise; Marchioni, Eric

2012-04-01

A liquid chromatographic-electrospray ionization-tandem mass spectrometric (LC-ESI-MS(2)) method has been developed for determination of the molecular species of phosphatidylethanolamine (PE) in four food matrices (soy, egg yolk, ox liver, and krill oil). The extraction and purification method consisted of a pressurized liquid extraction procedure for total lipid (TL) extraction, purification of phospholipids (PLs) by adsorption on a silica gel column, and separation of PL classes by semi-preparative normal-phase HPLC. Separation and identification of PE molecular species were performed by reversed-phase HPLC coupled with electrospray ionization tandem mass spectrometry (ESI-MS(2)). Methanol containing 5 mmol L(-1) ammonium formate was used as the mobile phase. A variety of PE molecular species were detected in the four food matrices. (C16:0-C18:2)PE, (C18:2-C18:2)PE, and (C16:0-C18:1)PE were the major PE molecular species in soy. Egg yolk PE contained (C16:0-C18:1)PE, (C18:0-C18:1)PE, (C18:0-C18:2)PE, and (C16:0-C18:2)PE as the major molecular species. Ox liver PE was rich in the species (C18:0-C18:1)PE, (C18:0-C20:4)PE, and (C18:0-C18:2)PE. Finally, krill oil which was particularly rich in (C16:0(alkyl)-C22:6(acyl))plasmanylethanolamine (PakE), (C16:0-C22:6)PE, and (C16:0-C20:5)PE, seemed to be an interesting potential source for supplementation of food with eicosapentaenoic acid and docosahexaenoic acid.

Structural characterization of saturated branched chain fatty acid methyl esters by collisional dissociation of molecular ions generated by electron ionization[S

Science.gov (United States)

Ran-Ressler, Rinat R.; Lawrence, Peter; Brenna, J. Thomas

2012-01-01

Saturated branched chain fatty acids (BCFA) are present as complex mixtures in numerous biological samples. The traditional method for structure elucidation, electron ionization (EI) mass spectrometry, sometimes does not unambiguously enable assignment of branching in isomeric BCFA. Zirrolli and Murphy (Zirrolli , J. A. , and R. A. Murphy. 1993. Low-energy tandem mass spectrometry of the molecular ion derived from fatty acid methyl esters: a novel method for analysis of branched-chain fatty acids. J. Am. Soc. Mass Spectrom. 4: 223–229.) showed that the molecular ions of four BCFA methyl ester (BCFAME) yield highly characteristic fragments upon collisional dissociation using a triple quadrupole instrument. Here, we confirm and extend these results by analysis using a tabletop 3-D ion trap for activated molecular ion EI-MS/MS to 30 BCFAME. iso-BCFAME produces a prominent ion (30-100% of base peak) for [M-43] (M-C3H7), corresponding to the terminal isopropyl moiety in the original iso-BCFAME. Anteiso-FAME yield prominent ions (20-100% of base peak) corresponding to losses on both side of the methyl branch, [M-29] and [M-57], and tend to produce more prominent m/z 115 peaks corresponding to a cyclization product around the ester. Dimethyl and tetramethyl FAME, with branches separated by at least one methylene group, yield fragment on both sides of the sites of methyl branches that are more than 6 C away from the carboxyl carbon. EI-MS/MS yields uniquely specific ions that enable highly confident structural identification and quantification of BCFAME. PMID:22021637

Improvements in ionization chambers

International Nuclear Information System (INIS)

Whetten, N.R.; Zubal, C.

1980-01-01

A method of reducing mechanical vibrations transmitted to the parallel plate electrodes of ionization chamber x-ray detectors, commonly used in computerized x-ray axial tomography systems, is described. The metal plate cathodes and anodes are mounted in the ionizable gas on dielectric sheet insulators consisting of a composite of silicone resin and glass fibres. (UK)

Surface Ionization and Soft Landing Techniques in Mass Spectrometry

International Nuclear Information System (INIS)

Futrell, Jean H.; Laskin, Julia

2010-01-01

The advent of soft ionization techniques, notably electrospray and laser desorption ionization methods, has extended mass spectrometric methods to large molecules and molecular complexes. This both greatly expands applications of mass spectrometry and makes the activation and dissociation of complex ions an integral part of large molecule mass spectrometry. A corollary of the much greater number of internal degrees of freedom and high density of states associated with molecular complexity is that internal energies much higher than the dissociation energies for competing fragmentation processes are required for observable fragmentation in time scales sampled by mass spectrometers. This article describes the kinetics of surface-induced dissociation (SID), a particularly efficient activation method for complex ions. Two very important characteristics of SID are very rapid, sub-picosecond activation and precise control of ion internal energy by varying ion collision energy. The nature of the surface plays an important role in SID, determining both efficiency and mechanism of ion activation. Surface composition and morphology strongly influence the relative importance of competing reactions of SID, ion capture (soft-landing), surface reaction and neutralization. The important features of SID and ion soft-landing are described briefly in this review and more fully in the recommended reading list.

Health Effects of Non-Ionizing Radiation on Human

International Nuclear Information System (INIS)

Zubaidah-Alatas; Yanti Lusiyanti

2001-01-01

Increases of development and use of equipment that procedures non-ionizing radiant energy such as laser, radar, microwave ovens, power lines and hand phones, bring about public concern about the possible health effects owing to the non-ionizing radiation exposure. Non ionizing electromagnetic radiation compared to ionizing radiation, has longer wavelength, lower frequency, and lower photon energy in its interaction with body tissues. The term on non-ionizing radiation refers to the groups of electromagnetic radiations with energies less than about 10 eV corresponding to wavelengths in the ultraviolet, visible, infra red microwave and radiofrequency spectral regions. This paper describes the current state of knowledge about types of non-ionizing radiation and the health effects at molecular and cellular levels as well as its effects on human health. (author)

Ionizing and non-ionizing radiations

International Nuclear Information System (INIS)

1994-01-01

The monograph is a small manual to get a knowledge of ionizing and non-ionizing radiations. The main chapters are: - Electromagnetic radiations - Ionizing and non-ionizing radiations - Non-ionizing electromagnetic radiations - Ionizing electromagnetic radiation - Other ionizing radiations - Ionizing radiation effects - The Nuclear Safety Conseil

Determination of molecular ionization cross sections in an ICR spectrometer

International Nuclear Information System (INIS)

Takashima, K.; Riveros, J.M.

1976-01-01

Ionization cross sections have been determined for simple gases at 75eV in an ICR spectrometer. Results obtained using a calibrated ion gauge as a pressure indicator yield values which are consistently higher than accepted values by as much as 15%. These results suggest that a more convenient way to measure pressure in ICR experiments might be to record the total ion current and to use the tabulated ionization cross sections where available [pt

Mechanistic insights into Mg2+-independent prenylation by CloQ from classical molecular mechanics and hybrid quantum mechanics/molecular mechanics molecular dynamics simulations.

Science.gov (United States)

Bayse, Craig A; Merz, Kenneth M

2014-08-05

Understanding the mechanism of prenyltransferases is important to the design of engineered proteins capable of synthesizing derivatives of naturally occurring therapeutic agents. CloQ is a Mg(2+)-independent aromatic prenyltransferase (APTase) that transfers a dimethylallyl group to 4-hydroxyphenylpyruvate in the biosynthetic pathway for clorobiocin. APTases consist of a common ABBA fold that defines a β-barrel containing the reaction cavity. Positively charged basic residues line the inside of the β-barrel of CloQ to activate the pyrophosphate leaving group to replace the function of the Mg(2+) cofactor in other APTases. Classical molecular dynamics simulations of CloQ, its E281G and F68S mutants, and the related NovQ were used to explore the binding of the 4-hydroxyphenylpyruvate (4HPP) and dimethylallyl diphosphate substrates in the reactive cavity and the role of various conserved residues. Hybrid quantum mechanics/molecular mechanics potential of mean force (PMF) calculations show that the effect of the replacement of the Mg(2+) cofactor with basic residues yields a similar activation barrier for prenylation to Mg(2+)-dependent APTases like NphB. The topology of the binding pocket for 4HPP is important for selective prenylation at the ortho position of the ring. Methylation at this position alters the conformation of the substrate for O-prenylation at the phenol group. Further, a two-dimensional PMF scan shows that a "reverse" prenylation product may be a possible target for protein engineering.

Ionization of EPA contaminants in direct and dopant-assisted atmospheric pressure photoionization and atmospheric pressure laser ionization.

Science.gov (United States)

Kauppila, Tiina J; Kersten, Hendrik; Benter, Thorsten

2015-06-01

Seventy-seven EPA priority environmental pollutants were analyzed using gas chromatography-mass spectrometry (GC-MS) equipped with an optimized atmospheric pressure photoionization (APPI) and an atmospheric pressure laser ionization (APLI) interface with and without dopants. The analyzed compounds included e.g., polycyclic aromatic hydrocarbons (PAHs), nitro compounds, halogenated compounds, aromatic compounds with phenolic, acidic, alcohol, and amino groups, phthalate and adipatic esters, and aliphatic ethers. Toluene, anisole, chlorobenzene, and acetone were tested as dopants. The widest range of analytes was ionized using direct APPI (66/77 compounds). The introduction of dopants decreased the amount of compounds ionized in APPI (e.g., 54/77 with toluene), but in many cases the ionization efficiency increased. While in direct APPI the formation of molecular ions via photoionization was the main ionization reaction, dopant-assisted (DA) APPI promoted ionization reactions, such as charge exchange and proton transfer. Direct APLI ionized a much smaller amount of compounds than APPI (41/77 compounds), showing selectivity towards compounds with low ionization energies (IEs) and long-lived resonantly excited intermediate states. DA-APLI, however, was able to ionize a higher amount of compounds (e.g. 51/77 with toluene), as the ionization took place entirely through dopant-assisted ion/molecule reactions similar to those in DA-APPI. Best ionization efficiency in APPI and APLI (both direct and DA) was obtained for PAHs and aromatics with O- and N-functionalities, whereas nitro compounds and aliphatic ethers were the most difficult to ionize. Halogenated aromatics and esters were (mainly) ionized in APPI, but not in APLI.

Biology of ionizing radiation effects

International Nuclear Information System (INIS)

Ferradini, C.; Pucheault, J.

1983-01-01

The present trends in biology of ionizing radiation are reviewed. The following topics are investigated: interaction of ionizing radiations with matter; the radiolysis of water and aqueous solutions; properties of the free radicals intervening in the couples O 2 /H 2 O and H 2 O/H 2 ; radiation chemistry of biological compounds; biological effects of ionizing radiations; biochemical mechanisms involving free radicals as intermediates; applications (biotechnological applications, origins of life) [fr

Mechanism of the Glycosidic Bond Cleavage of Mismatched Thymine in Human Thymine DNA Glycosylase Revealed by Classical Molecular Dynamics and Quantum Mechanical/Molecular Mechanical Calculations.

Science.gov (United States)

Kanaan, Natalia; Crehuet, Ramon; Imhof, Petra

2015-09-24

Base excision of mismatched or damaged nucleotides catalyzed by glycosylase enzymes is the first step of the base excision repair system, a machinery preserving the integrity of DNA. Thymine DNA glycosylase recognizes and removes mismatched thymine by cleaving the C1'-N1 bond between the base and the sugar ring. Our quantum mechanical/molecular mechanical calculations of this reaction in human thymine DNA glycosylase reveal a requirement for a positive charge in the active site to facilitate C1'-N1 bond scission: protonation of His151 significantly lowers the free energy barrier for C1'-N1 bond dissociation compared to the situation with neutral His151. Shuttling a proton from His151 to the thymine base further reduces the activation free energy for glycosidic bond cleavage. Classical molecular dynamics simulations of the H151A mutant suggest that the mutation to the smaller, neutral, residue increases the water accessibility of the thymine base, rendering direct proton transfer from the bulk feasible. Quantum mechanical/molecular mechanical calculations of the glycosidic bond cleavage reaction in the H151A mutant show that the activation free energy is slightly lower than in the wild-type enzyme, explaining the experimentally observed higher reaction rates in this mutant.

Molecular mechanics of silk nanostructures under varied mechanical loading.

Science.gov (United States)

Bratzel, Graham; Buehler, Markus J

2012-06-01

Spider dragline silk is a self-assembling tunable protein composite fiber that rivals many engineering fibers in tensile strength, extensibility, and toughness, making it one of the most versatile biocompatible materials and most inviting for synthetic mimicry. While experimental studies have shown that the peptide sequence and molecular structure of silk have a direct influence on the stiffness, toughness, and failure strength of silk, few molecular-level analyses of the nanostructure of silk assemblies, in particular, under variations of genetic sequences have been reported. In this study, atomistic-level structures of wildtype as well as modified MaSp1 protein from the Nephila clavipes spider dragline silk sequences, obtained using an in silico approach based on replica exchange molecular dynamics and explicit water molecular dynamics, are subjected to simulated nanomechanical testing using different force-control loading conditions including stretch, pull-out, and peel. The authors have explored the effects of the poly-alanine length of the N. clavipes MaSp1 peptide sequence and identify differences in nanomechanical loading conditions on the behavior of a unit cell of 15 strands with 840-990 total residues used to represent a cross-linking β-sheet crystal node in the network within a fibril of the dragline silk thread. The specific loading condition used, representing concepts derived from the protein network connectivity at larger scales, have a significant effect on the mechanical behavior. Our analysis incorporates stretching, pull-out, and peel testing to connect biochemical features to mechanical behavior. The method used in this study could find broad applications in de novo design of silk-like tunable materials for an array of applications. Copyright © 2011 Wiley Periodicals, Inc.

Resonantly-enhanced two-photon ionization and mass-analyzed threshold ionization (MATI) spectroscopy of 2-hydroxypyridine

CERN Document Server

Lee, D H; Choi, K W; Choi, Y S; Kim, S K

2002-01-01

Mass-analyzed threshold ionization (MATI) spectra of 2-hydroxypyridines existing as lactims (2-pyridionl) in a molecular beam are obtained via (1+1') two-photon process to give accurate ionization energies of 8.9344 +- 0.0005 and 8.9284 +- 0.0005 eV for 2-pyridinol (2Py-OH) and its deuterated analogue (2Py-OD), respectively. Resonantly-enhanced two-photon ionization spectra of these compounds are also presented to give vibrational structures of their S sub 1 states. Vibrational frequencies of 2Py-OH and 2Py-OD in ionic ground states are accurately determined from MATI spectra taken via various S sub 1 intermediate states, and associated vibrational modes are assigned with the aid of ab initio calculations.

High Resolution Multiphoton Ionization/Dissociation of Molecular Beam of Acetone from 582.60 to 585.80 nm

Science.gov (United States)

Mejia-Ospino, Enrique; Garcia, Gladis; Guerrero, Alfonso; Alvarez, Ignacio; Cisneros, Carmen

2003-05-01

Multiphoton ionization and dissociation of a jet supersonic of acetone at wavelength from 582.60 to 585.80 nm is studied using a Nd:YAG-OPO (optical parametric oscillator) system coupled to time-of-flight mass spectrometer. We present high-resolution (1.5 cm-1) three-photon resonance multiphoton spectra of the acetone 3s CH3CO+), (CH3+) and (COH+), being CH3COCH3+ ---> CH3CO+ + CH3 the more likely channel. The molecular and acetyl ions are observed practically in overall wavelength range.

Inkjet-printed gold nanoparticle surfaces for the detection of low molecular weight biomolecules by laser desorption/ionization mass spectrometry.

Science.gov (United States)

Marsico, Alyssa L M; Creran, Brian; Duncan, Bradley; Elci, S Gokhan; Jiang, Ying; Onasch, Timothy B; Wormhoudt, Joda; Rotello, Vincent M; Vachet, Richard W

2015-11-01

Effective detection of low molecular weight compounds in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is often hindered by matrix interferences in the low m/z region of the mass spectrum. Here, we show that monolayer-protected gold nanoparticles (AuNPs) can serve as alternate matrices for the very sensitive detection of low molecular weight compounds such as amino acids. Amino acids can be detected at low fmol levels with minimal interferences by properly choosing the AuNP deposition method, density, size, and monolayer surface chemistry. By inkjet-printing AuNPs at various densities, we find that AuNP clusters are essential for obtaining the greatest sensitivity. Graphical Abstract ᅟ.

Molecular mechanism of radioadaptive response: A cross-adaptive response for enhanced repair of DNA damage in adapted cells

International Nuclear Information System (INIS)

Takaji Ikushima

1997-01-01

The radioadaptive response (RAR) has been attributed to the induction of a repair mechanism by low doses of ionizing radiation, but the molecular nature of the mechanism is not yet elucidated. We have characterized RAR in a series of experiments in cultured Chinese hamster V79 cells. A 4-h interval is required for the full expression of RAR, which decays with the progression of cell proliferation. Treatments with inhibitors of poly(ADP-ribose) polymerase, protein- or RNA synthesis, and protein kinase C suppress the RAR expression. The RAR cross-reacts on clastogenic lesions induced by other physical and chemical DNA-damaging agents. The presence of newly synthesised proteins has been detected during the expression period. Experiments performed using single-cell gel electrophoresis provided more direct evidence for a faster and enhaced DNA repair rate in adapted cells. Here, using single-cell gel electrophoresis, a cross-adaptive response has been demonstrated for enhanced repair of DNA damage induced by neocarzinostatin in radio-adapted cells. (author)

Chemical protection against ionizing radiation. Final report

International Nuclear Information System (INIS)

Livesey, J.C.; Reed, D.J.; Adamson, L.F.

1984-08-01

The scientific literature on radiation-protective drugs is reviewed. Emphasis is placed on the mechanisms involved in determining the sensitivity of biological material to ionizing radiation and mechanisms of chemical radioprotection. In Section I, the types of radiation are described and the effects of ionizing radiation on biological systems are reviewed. The effects of ionizing radiation are briefly contrasted with the effects of non-ionizing radiation. Section II reviews the contributions of various natural factors which influence the inherent radiosensitivity of biological systems. Inlcuded in the list of these factors are water, oxygen, thiols, vitamins and antioxidants. Brief attention is given to the model describing competition between oxygen and natural radioprotective substances (principally, thiols) in determining the net cellular radiosensitivity. Several theories of the mechanism(s) of action of radioprotective drugs are described in Section III. These mechanisms include the production of hypoxia, detoxication of radiochemical reactive species, stabilization of the radiobiological target and the enhancement of damage repair processes. Section IV describes the current strategies for the treatment of radiation injury. Likely areas in which fruitful research might be performed are described in Section V. 495 references

Chemical protection against ionizing radiation. Final report

Energy Technology Data Exchange (ETDEWEB)

Livesey, J.C.; Reed, D.J.; Adamson, L.F.

1984-08-01

The scientific literature on radiation-protective drugs is reviewed. Emphasis is placed on the mechanisms involved in determining the sensitivity of biological material to ionizing radiation and mechanisms of chemical radioprotection. In Section I, the types of radiation are described and the effects of ionizing radiation on biological systems are reviewed. The effects of ionizing radiation are briefly contrasted with the effects of non-ionizing radiation. Section II reviews the contributions of various natural factors which influence the inherent radiosensitivity of biological systems. Inlcuded in the list of these factors are water, oxygen, thiols, vitamins and antioxidants. Brief attention is given to the model describing competition between oxygen and natural radioprotective substances (principally, thiols) in determining the net cellular radiosensitivity. Several theories of the mechanism(s) of action of radioprotective drugs are described in Section III. These mechanisms include the production of hypoxia, detoxication of radiochemical reactive species, stabilization of the radiobiological target and the enhancement of damage repair processes. Section IV describes the current strategies for the treatment of radiation injury. Likely areas in which fruitful research might be performed are described in Section V. 495 references.

Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks.

Science.gov (United States)

Shen, Lin; Wu, Jingheng; Yang, Weitao

2016-10-11

Molecular dynamics simulation with multiscale quantum mechanics/molecular mechanics (QM/MM) methods is a very powerful tool for understanding the mechanism of chemical and biological processes in solution or enzymes. However, its computational cost can be too high for many biochemical systems because of the large number of ab initio QM calculations. Semiempirical QM/MM simulations have much higher efficiency. Its accuracy can be improved with a correction to reach the ab initio QM/MM level. The computational cost on the ab initio calculation for the correction determines the efficiency. In this paper we developed a neural network method for QM/MM calculation as an extension of the neural-network representation reported by Behler and Parrinello. With this approach, the potential energy of any configuration along the reaction path for a given QM/MM system can be predicted at the ab initio QM/MM level based on the semiempirical QM/MM simulations. We further applied this method to three reactions in water to calculate the free energy changes. The free-energy profile obtained from the semiempirical QM/MM simulation is corrected to the ab initio QM/MM level with the potential energies predicted with the constructed neural network. The results are in excellent accordance with the reference data that are obtained from the ab initio QM/MM molecular dynamics simulation or corrected with direct ab initio QM/MM potential energies. Compared with the correction using direct ab initio QM/MM potential energies, our method shows a speed-up of 1 or 2 orders of magnitude. It demonstrates that the neural network method combined with the semiempirical QM/MM calculation can be an efficient and reliable strategy for chemical reaction simulations.

Inelastic surface collisions and the desorption of massive molecular ions

Energy Technology Data Exchange (ETDEWEB)

Macfarlane, R D [Texas A and M Univ., College Station (USA). Dept. of Chemistry

1983-01-01

The interaction of high energy ions in the region of electronic stopping (1 MeV u/sup -1/) stimulates the desorption of massive molecular ions of biomolecules such as insulin. The experimental details of the measurements are given with some examples of application for analytical mass spectrometry. Studies on the role of the incident ion (accelerator beam experiments) are reviewed as well as the contribution of the matrix to the desorption-ionization process. How the electronic relaxation process couples to desorption-ionization is a central question in understanding the overall mechanism of the process.

Physiological and molecular biochemical mechanisms of bile formation

Science.gov (United States)

Reshetnyak, Vasiliy Ivanovich

2013-01-01

This review considers the physiological and molecular biochemical mechanisms of bile formation. The composition of bile and structure of a bile canaliculus, biosynthesis and conjugation of bile acids, bile phospholipids, formation of bile micellar structures, and enterohepatic circulation of bile acids are described. In general, the review focuses on the molecular physiology of the transporting systems of the hepatocyte sinusoidal and apical membranes. Knowledge of physiological and biochemical basis of bile formation has implications for understanding the mechanisms of development of pathological processes, associated with diseases of the liver and biliary tract. PMID:24259965

Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations.

Science.gov (United States)

Wu, Jingheng; Shen, Lin; Yang, Weitao

2017-10-28

Ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation is a useful tool to calculate thermodynamic properties such as potential of mean force for chemical reactions but intensely time consuming. In this paper, we developed a new method using the internal force correction for low-level semiempirical QM/MM molecular dynamics samplings with a predefined reaction coordinate. As a correction term, the internal force was predicted with a machine learning scheme, which provides a sophisticated force field, and added to the atomic forces on the reaction coordinate related atoms at each integration step. We applied this method to two reactions in aqueous solution and reproduced potentials of mean force at the ab initio QM/MM level. The saving in computational cost is about 2 orders of magnitude. The present work reveals great potentials for machine learning in QM/MM simulations to study complex chemical processes.

Kinetics of molecular transformations in connective tissue hyaluronic acid

International Nuclear Information System (INIS)

Phillips, G.O.

1990-01-01

When exposed to ionizing radiations or inflammatory disease, the glycosaminolycan component of connective tissue is preferentially degraded, probably by a free-radical mediate pathway. The resulting changes in molecular structure adversely change the properties of the matrix. Rooster comb hyaluronic acid of high molecular weight was used to investigate the mechanisms of these structural changes at macro and molecular level. Intrinsic viscosity and gel permeation chromatography measurements are suitable for demonstrating that random chain session occurs. Fast kinetic techniques are necessary to identify the mechanisms of single strand breaks. Pulse conductivity and low-angle laser light scattering pulse radiolysis can quantify the rate and yield of strand breaks. Competitive radical scavenging methods have also allowed the quantification of the rate of spontaneous and alkali-catalyzed hydrolysis of a-hydroxy radicals on polysaccharide chains, which control molecular structure changes

Study of the mechanisms of matrix assisted laser desorption / ionization

International Nuclear Information System (INIS)

Manuelli, Pascal

1995-01-01

This research thesis aims at a better knowledge of some aspects of a complex mechanism: the matrix-assisted laser desorption/ionization (MALDI). The author first proposes a comparative analysis of results obtained by time-of-flight (TOF) mass spectrometry and by Fourier transform mass spectrometry. He reports the study of the matrix role (notably a polymeric matrix) as a matter submitted to laser desorption. In this respect, the influence of the incident wavelength has been studied. The author also reports a comparative of ions produced by matrix laser desorption (study performed by Fourier transform mass spectrometry) and of neutral molecules (study performed by flash pyrolysis coupled with gas chromatography and with mass spectrometry). Finally, results obtained on derivatives and complexes based on beta-cyclodextrins highlight benefits as well as limitations of this technique [fr

Growth of CdTe on Si(100) surface by ionized cluster beam technique: Experimental and molecular dynamics simulation

Energy Technology Data Exchange (ETDEWEB)

Araghi, Houshang, E-mail: araghi@aut.ac.ir [Department of Physics, Amirkabir University of Technology, Tehran (Iran, Islamic Republic of); Zabihi, Zabiholah [Department of Physics, Amirkabir University of Technology, Tehran (Iran, Islamic Republic of); Nayebi, Payman [Department of Physics, College of Technical and Engineering, Saveh Branch, Islamic Azad University, Saveh (Iran, Islamic Republic of); Ehsani, Mohammad Mahdi [Department of Physics, Amirkabir University of Technology, Tehran (Iran, Islamic Republic of)

2016-10-15

II–VI semiconductor CdTe was grown on the Si(100) substrate surface by the ionized cluster beam (ICB) technique. In the ICB method, when vapors of solid materials such as CdTe were ejected through a nozzle of a heated crucible into a vacuum region, nanoclusters were created by an adiabatic expansion phenomenon. The clusters thus obtained were partially ionized by electron bombardment and then accelerated onto the silicon substrate at 473 K by high potentials. The cluster size was determined using a retarding field energy analyzer. The results of X-ray diffraction measurements indicate the cubic zinc blende (ZB) crystalline structure of the CdTe thin film on the silicon substrate. The CdTe thin film prepared by the ICB method had high crystalline quality. The microscopic processes involved in the ICB deposition technique, such as impact and coalescence processes, have been studied in detail by molecular dynamics (MD) simulation.

STATINS AND MYOPATHY: MOLECULAR MECHANISMS

Directory of Open Access Journals (Sweden)

O. M. Drapkina

2012-01-01

Full Text Available The safety of statin therapy is considered. In particular the reasons of a complication such as myopathy are discussed in detail. The molecular mechanisms of statin myopathy , as well as its risk factors are presented. The role of coenzyme Q10 in the myopathy development and coenzyme Q10 application for the prevention of this complication are considered. 

Investigation of mono/competitive adsorption of environmentally relevant ionized weak acids on graphite: impact of molecular properties and thermodynamics.

Science.gov (United States)

Moustafa, Ahmed M A; McPhedran, Kerry N; Moreira, Jesús; Gamal El-Din, Mohamed

2014-12-16

The thermodynamics of adsorption and competitive interactions of five weak acids on a graphite surface was assessed in alkaline solutions. Adsorption of the acids in mono- and multicompound solutions followed their Freundlich isotherms which suggest a diversity of graphite adsorption sites as confirmed by the presence of carboxylic and phenolic groups observed on graphite surfaces. Thermodynamic calculations assigned the formation of the negatively charged assisted hydrogen bond (-CAHB) between ionized solutes and adsorbent surface groups as the possible adsorption mechanism. However, the similar pKa values of current acids resulted in comparable free energies for -CAHB formation (ΔG(-CAHB)) being less than solvation free energies (ΔGSolv). Thus, additional ΔG is supplemented by increased hydrophobicity due to proton exchange of ionized acids with water (ΔΔG Hydrophobicity). Adsorption capacities and competition coefficients indicated that ΔΔG Hydrophobicity values depend on the neutral and ionized acid Kow. Competitive adsorption implies that multilayer adsorption may occur via hydrophobic bonding with the CH3 ends of the self-assembled layer which affects the acid adsorption capacities in mixtures as compared to monocompound solutions. The determination of adsorption mechanisms will assist in understanding of the fate and bioavailability of emerging and classical weak acids released into natural waters.

Gas chromatography coupled to atmospheric pressure ionization mass spectrometry (GC-API-MS): Review

International Nuclear Information System (INIS)

Li, Du-Xin; Gan, Lin; Bronja, Amela; Schmitz, Oliver J.

2015-01-01

Although the coupling of GC/MS with atmospheric pressure ionization (API) has been reported in 1970s, the interest in coupling GC with atmospheric pressure ion source was expanded in the last decade. The demand of a “soft” ion source for preserving highly diagnostic molecular ion is desirable, as compared to the “hard” ionization technique such as electron ionization (EI) in traditional GC/MS, which fragments the molecule in an extensive way. These API sources include atmospheric pressure chemical ionization (APCI), atmospheric pressure photoionization (APPI), atmospheric pressure laser ionization (APLI), electrospray ionization (ESI) and low temperature plasma (LTP). This review discusses the advantages and drawbacks of this analytical platform. After an introduction in atmospheric pressure ionization the review gives an overview about the history and explains the mechanisms of various atmospheric pressure ionization techniques used in combination with GC such as APCI, APPI, APLI, ESI and LTP. Also new developments made in ion source geometry, ion source miniaturization and multipurpose ion source constructions are discussed and a comparison between GC-FID, GC-EI-MS and GC-API-MS shows the advantages and drawbacks of these techniques. The review ends with an overview of applications realized with GC-API-MS. - Highlights: • Atmospheric pressure ion sources (APCI, ESI, APPI, APLC etc) enable the coupling of LC-based high-end MS to GC. • APIs show advantages in selectivity and sensitivity compared with EI in GC-MS. • Accurate mass database in GC-APCI/MS is emerging as an alternative to GC-EI/MS database.

Gas chromatography coupled to atmospheric pressure ionization mass spectrometry (GC-API-MS): Review

Energy Technology Data Exchange (ETDEWEB)

Li, Du-Xin; Gan, Lin; Bronja, Amela [University of Duisburg-Essen, Applied Analytical Chemistry, Universitaetsstr. 5-7, 45141 Essen (Germany); Schmitz, Oliver J., E-mail: oliver.schmitz@uni-due.de [University of Duisburg-Essen, Applied Analytical Chemistry, Universitaetsstr. 5-7, 45141 Essen (Germany)

2015-09-03

Although the coupling of GC/MS with atmospheric pressure ionization (API) has been reported in 1970s, the interest in coupling GC with atmospheric pressure ion source was expanded in the last decade. The demand of a “soft” ion source for preserving highly diagnostic molecular ion is desirable, as compared to the “hard” ionization technique such as electron ionization (EI) in traditional GC/MS, which fragments the molecule in an extensive way. These API sources include atmospheric pressure chemical ionization (APCI), atmospheric pressure photoionization (APPI), atmospheric pressure laser ionization (APLI), electrospray ionization (ESI) and low temperature plasma (LTP). This review discusses the advantages and drawbacks of this analytical platform. After an introduction in atmospheric pressure ionization the review gives an overview about the history and explains the mechanisms of various atmospheric pressure ionization techniques used in combination with GC such as APCI, APPI, APLI, ESI and LTP. Also new developments made in ion source geometry, ion source miniaturization and multipurpose ion source constructions are discussed and a comparison between GC-FID, GC-EI-MS and GC-API-MS shows the advantages and drawbacks of these techniques. The review ends with an overview of applications realized with GC-API-MS. - Highlights: • Atmospheric pressure ion sources (APCI, ESI, APPI, APLC etc) enable the coupling of LC-based high-end MS to GC. • APIs show advantages in selectivity and sensitivity compared with EI in GC-MS. • Accurate mass database in GC-APCI/MS is emerging as an alternative to GC-EI/MS database.

Molecular Mechanisms of Neurodegeneration in Spinal Muscular Atrophy

Directory of Open Access Journals (Sweden)

Saif Ahmad

2016-01-01

Full Text Available Spinal muscular atrophy (SMA is an autosomal recessive motor neuron disease with a high incidence and is the most common genetic cause of infant mortality. SMA is primarily characterized by degeneration of the spinal motor neurons that leads to skeletal muscle atrophy followed by symmetric limb paralysis, respiratory failure, and death. In humans, mutation of the Survival Motor Neuron 1 (SMN1 gene shifts the load of expression of SMN protein to the SMN2 gene that produces low levels of full-length SMN protein because of alternative splicing, which are sufficient for embryonic development and survival but result in SMA. The molecular mechanisms of the (a regulation of SMN gene expression and (b degeneration of motor neurons caused by low levels of SMN are unclear. However, some progress has been made in recent years that have provided new insights into understanding of the cellular and molecular basis of SMA pathogenesis. In this review, we have briefly summarized recent advances toward understanding of the molecular mechanisms of regulation of SMN levels and signaling mechanisms that mediate neurodegeneration in SMA.

A pseudobond parametrization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymes.

Science.gov (United States)

Parks, Jerry M; Hu, Hao; Cohen, Aron J; Yang, Weitao

2008-10-21

The pseudobond method is used in quantum mechanical/molecular mechanical (QM/MM) simulations in which a covalent bond connects the quantum mechanical and classical subsystems. In this method, the molecular mechanical boundary atom is replaced by a special quantum mechanical atom with one free valence that forms a bond with the rest of the quantum mechanical subsystem. This boundary atom is modified through the use of a parametrized effective core potential and basis set. The pseudobond is designed to reproduce the properties of the covalent bond that it has replaced, while invoking as small a perturbation as possible on the system. Following the work of Zhang [J. Chem. Phys. 122, 024114 (2005)], we have developed new pseudobond parameters for use in the simulation of enzymatic systems. Our parameters yield improved electrostatics and deprotonation energies, while at the same time maintaining accurate geometries. We provide parameters for C(ps)(sp(3))-C(sp(3)), C(ps)(sp(3))-C(sp(2),carbonyl), and C(ps)(sp(3))-N(sp(3)) pseudobonds, which allow the interface between the quantum mechanical and molecular mechanical subsystems to be constructed at either the C(alpha)-C(beta) bond of a given amino acid residue or along the peptide backbone. In addition, we demonstrate the efficiency of our parametrization method by generating residue-specific pseudobond parameters for a single amino acid. Such an approach may enable higher accuracy than general purpose parameters for specific QM/MM applications.

Peptidylation for the determination of low-molecular-weight compounds by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

Science.gov (United States)

Tang, Feng; Cen, Si-Ying; He, Huan; Liu, Yi; Yuan, Bi-Feng; Feng, Yu-Qi

2016-05-23

Determination of low-molecular-weight compounds by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has been a great challenge in the analytical research field. Here we developed a universal peptide-based derivatization (peptidylation) strategy for the sensitive analysis of low-molecular-weight compounds by MALDI-TOF-MS. Upon peptidylation, the molecular weights of target analytes increase, thus avoiding serious matrix ion interference in the low-molecular-weight region in MALDI-TOF-MS. Since peptides typically exhibit good signal response during MALDI-TOF-MS analysis, peptidylation endows high detection sensitivities of low-molecular-weight analytes. As a proof-of-concept, we analyzed low-molecular-weight compounds of aldehydes and thiols by the developed peptidylation strategy. Our results showed that aldehydes and thiols can be readily determined upon peptidylation, thus realizing the sensitive and efficient determination of low-molecular-weight compounds by MALDI-TOF-MS. Moreover, target analytes also can be unambiguously detected in biological samples using the peptidylation strategy. The established peptidylation strategy is a universal strategy and can be extended to the sensitive analysis of various low-molecular-weight compounds by MALDI-TOF-MS, which may be potentially used in areas such as metabolomics.

Molecular dynamics and Monte Carlo calculations in statistical mechanics

International Nuclear Information System (INIS)

Wood, W.W.; Erpenbeck, J.J.

1976-01-01

Monte Carlo and molecular dynamics calculations on statistical mechanical systems is reviewed giving some of the more significant recent developments. It is noted that the term molecular dynamics refers to the time-averaging technique for hard-core and square-well interactions and for continuous force-law interactions. Ergodic questions, methodology, quantum mechanical, Lorentz, and one-dimensional, hard-core, and square and triangular-well systems, short-range soft potentials, and other systems are included. 268 references

Effect of ionizing radiation on mechanical and thermal properties of low-density polyethylene containing pro-degradant agents

International Nuclear Information System (INIS)

Bardi, Marcelo A.G.; Kodama, Yasko; Machado, Luci D.B.; Giovedi, Claudia; Rosa, Derval S.

2009-01-01

The wide use of plastics on packages of short-lifetime products has presented harmful consequences for the environment due to their low degradation rate. By this way, improved results to the bio-assimilation of polyolefins have been achieved by the incorporation of pro-oxidant components. The aim of this work is to evaluate the mechanical and thermal behavior of low-density polyethylene (LDPE) modified by those agents and submitted to ionizing radiation by gamma rays. LDPE was modified using a masterbatch containing calcium stearate (CaSt), or magnesium stearate (MgSt) or Clariant R commercial metallic complex. The final amount of stearate in modified LDPE was 0.2%. The films were obtained by compression molding. Samples were gamma irradiated at absorbed doses of 15 kGy and 100 kGy. Differential scanning calorimetry (DSC) and thermogravimetry (TG) were performed on samples, as well as mechanical analysis by universal testing machine. Thermal properties of samples presenting pro-degradant agents were affected by the ionizing radiation in the dose range studied, and some of the mechanical properties were clearly modified by reducing their values of tensile strength at break and elongation at break. (author)

Effect of ionizing radiation on mechanical and thermal properties of low-density polyethylene containing pro-degradant agents

Energy Technology Data Exchange (ETDEWEB)

Bardi, Marcelo A.G.; Kodama, Yasko; Machado, Luci D.B., E-mail: magbardi@ipen.b, E-mail: ykodama@ipen.b, E-mail: lmachado@ipen.b [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil); Giovedi, Claudia, E-mail: giovedi@ctmsp.mar.mil.b [Centro Tecnologico da Marinha em Sao Paulo (CTMSP), Sao Paulo, SP (Brazil); Rosa, Derval S., E-mail: derval.rosa@ufabc.edu.b [Universidade Federal do ABC (UFABC), Santo Andre, SP (Brazil)

2009-07-01

The wide use of plastics on packages of short-lifetime products has presented harmful consequences for the environment due to their low degradation rate. By this way, improved results to the bio-assimilation of polyolefins have been achieved by the incorporation of pro-oxidant components. The aim of this work is to evaluate the mechanical and thermal behavior of low-density polyethylene (LDPE) modified by those agents and submitted to ionizing radiation by gamma rays. LDPE was modified using a masterbatch containing calcium stearate (CaSt), or magnesium stearate (MgSt) or Clariant{sup R} commercial metallic complex. The final amount of stearate in modified LDPE was 0.2%. The films were obtained by compression molding. Samples were gamma irradiated at absorbed doses of 15 kGy and 100 kGy. Differential scanning calorimetry (DSC) and thermogravimetry (TG) were performed on samples, as well as mechanical analysis by universal testing machine. Thermal properties of samples presenting pro-degradant agents were affected by the ionizing radiation in the dose range studied, and some of the mechanical properties were clearly modified by reducing their values of tensile strength at break and elongation at break. (author)

Use of Computational Modeling to Evaluate Hypotheses About the Molecular and Cellular Mechanisms of Bystander Effects

Energy Technology Data Exchange (ETDEWEB)

Zhao, Yuchao; Conolly, Rory B; Andersen, Melvin E.

2006-11-21

This report describes the development of a computational systems biology approach to evaluate the hypotheses of molecular and cellular mechanisms of adaptive response to low dose ionizing radiation. Our concept is that computational models of signaling pathways can be developed and linked to biologically based dose response models to evaluate the underlying molecular mechanisms which lead to adaptive response. For development of quantitatively accurate, predictive models, it will be necessary to describe tissues consisting of multiple cell types where the different types each contribute in their own way to the overall function of the tissue. Such a model will probably need to incorporate not only cell type-specific data but also spatial information on the architecture of the tissue and on intercellular signaling. The scope of the current model was more limited. Data obtained in a number of different biological systems were synthesized to describe a chimeric, “average” population cell. Biochemical signaling pathways involved in sensing of DNA damage and in the activation of cell cycle checkpoint controls and the apoptotic path were also included. As with any computational modeling effort, it was necessary to develop these simplified initial descriptions (models) that can be iteratively refined. This preliminary model is a starting point which, with time, can evolve to a level of refinement where large amounts of detailed biological information are synthesized and a capability for robust predictions of dose- and time-response behaviors is obtained.

Molecular mechanisms of fluoride toxicity.

Science.gov (United States)

Barbier, Olivier; Arreola-Mendoza, Laura; Del Razo, Luz María

2010-11-05

Halfway through the twentieth century, fluoride piqued the interest of toxicologists due to its deleterious effects at high concentrations in human populations suffering from fluorosis and in in vivo experimental models. Until the 1990s, the toxicity of fluoride was largely ignored due to its "good reputation" for preventing caries via topical application and in dental toothpastes. However, in the last decade, interest in its undesirable effects has resurfaced due to the awareness that this element interacts with cellular systems even at low doses. In recent years, several investigations demonstrated that fluoride can induce oxidative stress and modulate intracellular redox homeostasis, lipid peroxidation and protein carbonyl content, as well as alter gene expression and cause apoptosis. Genes modulated by fluoride include those related to the stress response, metabolic enzymes, the cell cycle, cell-cell communications and signal transduction. The primary purpose of this review is to examine recent findings from our group and others that focus on the molecular mechanisms of the action of inorganic fluoride in several cellular processes with respect to potential physiological and toxicological implications. This review presents an overview of the current research on the molecular aspects of fluoride exposure with emphasis on biological targets and their possible mechanisms of involvement in fluoride cytotoxicity. The goal of this review is to enhance understanding of the mechanisms by which fluoride affects cells, with an emphasis on tissue-specific events in humans. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Photoionization studies with molecular beams

International Nuclear Information System (INIS)

Ng, C.Y.

1976-09-01

A molecular beam photoionization apparatus which combines the advantages of both the molecular beam method with photoionization mass spectrometry has been designed and constructed for carrying out some unique photoionization experiments. Rotational cooling during the supersonic expansion has resulted in high resolution photoionization efficiency curves for NO, ICl, C 2 H 2 and CH 3 I. The analysis of these spectra has yielded ionization potentials for these molecules to an accuracy of +- 3 MeV. Detailed autoionization structures were also resolved. This allows the investigation of the selection rules for autoionization, and the identification of the Rydberg series which converge to the excited states of the molecular ions. The degree of relaxation for thermally populated excited states has been examined using NO and ICl as examples. As a result of adiabatic cooling, a small percentage of dimers is also formed during the expansion. The photoionization efficiency curves for (NO) 2 , ArICl, Ar 2 , Kr 2 and Xe 2 have been obtained near the thresholds. Using the known dissociation energies of the (NO) 2 , Ar 2 , Kr 2 and Xe 2 van der Waals molecules, the corresponding dissociation energies for NO-NO + , Ar 2 + , Kr 2 + , and Xe 2 + have been determined. The ionization mechanisms for this class of molecules are examined and discussed

Single photon simultaneous K-shell ionization and K-shell excitation. II. Specificities of hollow nitrogen molecular ions

International Nuclear Information System (INIS)

Carniato, S.; Selles, P.; Andric, L.; Palaudoux, J.; Penent, F.; Lablanquie, P.; Žitnik, M.; Bučar, K.; Nakano, M.; Hikosaka, Y.; Ito, K.

2015-01-01

The formalism developed in the companion Paper I is used here for the interpretation of spectra obtained recently on the nitrogen molecule. Double core-hole ionization K −2 and core ionization-core excitation K −2 V processes have been observed by coincidence electron spectroscopy after ionization by synchrotron radiation at different photon energies. Theoretical and experimental cross sections reported on an absolute scale are in satisfactory agreement. The evolution with photon energy of the relative contribution of shake-up and conjugate shake-up processes is discussed. The first main resonance in the K −2 V spectrum is assigned to a K −2 π ∗ state mainly populated by the 1s→ lowest unoccupied molecular orbital dipolar excitation, as it is in the K −1 V NEXAFS (Near-Edge X-ray Absorption Fine Structure) signals. Closer to the K −2 threshold Rydberg resonances have been also identified, and among them a K −2 σ ∗ resonance characterized by a large amount of 2s/2p hybridization, and double K −2 (2σ ∗ /1π/3σ) −1 1π ∗2 shake-up states. These resonances correspond in NEXAFS spectra to, respectively, the well-known σ ∗ shape resonance and double excitation K −1 (2σ ∗ /1π/3σ) −1 1π ∗2 resonances, all being positioned above the threshold

The Possible Role of Penning Ionization Processes in Planetary Atmospheres

Directory of Open Access Journals (Sweden)

Stefano Falcinelli

2015-03-01

Full Text Available In this paper we suggest Penning ionization as an important route of formation for ionic species in upper planetary atmospheres. Our goal is to provide relevant tools to researchers working on kinetic models of atmospheric interest, in order to include Penning ionizations in their calculations as fast processes promoting reactions that cannot be neglected. Ions are extremely important for the transmission of radio and satellite signals, and they govern the chemistry of planetary ionospheres. Molecular ions have also been detected in comet tails. In this paper recent experimental results concerning production of simple ionic species of atmospheric interest are presented and discussed. Such results concern the formation of free ions in collisional ionization of H2O, H2S, and NH3 induced by highly excited species (Penning ionization as metastable noble gas atoms. The effect of Penning ionization still has not been considered in the modeling of terrestrial and extraterrestrial objects so far, even, though metastable helium is formed by radiative recombination of He+ ions with electrons. Because helium is the second most abundant element of the universe, Penning ionization of atomic or molecular species by He*(23S1 is plausibly an active route of ionization in relatively dense environments exposed to cosmic rays.

Determination of Nerve Agent Metabolites by Ultraviolet Femtosecond Laser Ionization Mass Spectrometry.

Science.gov (United States)

Hamachi, Akifumi; Imasaka, Tomoko; Nakamura, Hiroshi; Li, Adan; Imasaka, Totaro

2017-05-02

Nerve agent metabolites, i.e., isopropyl methylphosphonic acid (IMPA) and pinacolyl methylphosphonic acid (PMPA), were derivatized by reacting them with 2,3,4,5,6-pentafluorobenzyl bromide (PFBBr) and were determined by mass spectrometry using an ultraviolet femtosecond laser emitting at 267 and 200 nm as the ionization source. The analytes of the derivatized compounds, i.e., IMPA-PFB and PMPA-PFB, contain a large side-chain, and molecular ions are very weak or absent in electron ionization mass spectrometry. The use of ultraviolet femtosecond laser ionization mass spectrometry, however, resulted in the formation of a molecular ion, even for compounds such as these that contain a highly bulky functional group. The signal intensity was larger at 200 nm due to resonance-enhanced two-photon ionization. In contrast, fragmentation was suppressed at 267 nm (nonresonant two-photon ionization) especially for PMPA-PFB, thus resulting in a lower background signal. This favorable result can be explained by the small excess energy in ionization at 267 nm and by the low-frequency vibrational mode of a bulky trimethylpropyl group in PMPA.

Multiorbital effects in strong-field ionization and dissociation of aligned polar molecules CH3I and CH3Br

Science.gov (United States)

Luo, Sizuo; Zhou, Shushan; Hu, Wenhui; Li, Xiaokai; Ma, Pan; Yu, Jiaqi; Zhu, Ruihan; Wang, Chuncheng; Liu, Fuchun; Yan, Bing; Liu, Aihua; Yang, Yujun; Guo, Fuming; Ding, Dajun

2017-12-01

Controlling the molecular axis offers additional ways to study molecular ionization and dissociation in strong laser fields. We measure the ionization and dissociation yields of aligned polar CH3X (X =I , Br) molecules in a linearly polarized femtosecond laser field. The current data show that maximum ionization occurs when the laser polarization is perpendicular to the molecular C -X axis, and dissociation prefers to occur at the laser polarization parallel to the C -X axis. The observed angular distributions suggest that the parent ions are generated by ionization from the HOMO. The angular distribution of fragment ions indicates that dissociation occurs mainly from an ionic excited state produced by ionization from the HOMO-1.

Gas chromatography/chemical ionization triple quadrupole mass spectrometry analysis of anabolic steroids: ionization and collision-induced dissociation behavior.

Science.gov (United States)

Polet, Michael; Van Gansbeke, Wim; Van Eenoo, Peter; Deventer, Koen

2016-02-28

The detection of new anabolic steroid metabolites and new designer steroids is a challenging task in doping analysis. Switching from electron ionization gas chromatography triple quadrupole mass spectrometry (GC/EI-MS/MS) to chemical ionization (CI) has proven to be an efficient way to increase the sensitivity of GC/MS/MS analyses and facilitate the detection of anabolic steroids. CI also extends the possibilities of GC/MS/MS analyses as the molecular ion is retained in its protonated form due to the softer ionization. In EI it can be difficult to find previously unknown but expected metabolites due to the low abundance or absence of the molecular ion and the extensive (and to a large extent unpredictable) fragmentation. The main aim of this work was to study the CI and collision-induced dissociation (CID) behavior of a large number of anabolic androgenic steroids (AAS) as their trimethylsilyl derivatives in order to determine correlations between structures and CID fragmentation. Clarification of these correlations is needed for the elucidation of structures of unknown steroids and new metabolites. The ionization and CID behavior of 65 AAS have been studied using GC/CI-MS/MS with ammonia as the reagent gas. Glucuronidated AAS reference standards were first hydrolyzed to obtain their free forms. Afterwards, all the standards were derivatized to their trimethylsilyl forms. Full scan and product ion scan analyses were used to examine the ionization and CID behavior. Full scan and product ion scan analyses revealed clear correlations between AAS structure and the obtained mass spectra. These correlations were confirmed by analysis of multiple hydroxylated, methylated, chlorinated and deuterated analogs. AAS have been divided into three groups according to their ionization behavior and into seven groups according to their CID behavior. Correlations between fragmentation and structure were revealed and fragmentation pathways were postulated. Copyright © 2016 John Wiley

Theoretical calculation of fully differential cross sections for electron-impact ionization of hydrogen molecules

International Nuclear Information System (INIS)

Gao Junfang; Madison, D H; Peacher, J L

2006-01-01

We have recently proposed the orientation averaged molecular orbital (OAMO) approximation for calculating fully differential cross sections (FDCS) for electron-impact ionization of molecules averaged over all molecular orientations. Orientation averaged FDCS were calculated for electron-impact ionization of nitrogen molecules using the distorted wave impulse approximation (DWIA) and the molecular three-body distorted wave (M3DW) approximation. In this paper, we use the same methods to examine the FDCS for ionization of hydrogen molecules. It is found that the DWIA yields reasonable results for high-energy incident electrons. While the DWIA breaks down for low-energy electrons, the M3DW gives reasonable results down to incident-electron energies around 35 eV

Molecular Data for a Biochemical Model of DNA Radiation Damage: Electron Impact Ionization and Dissociative Ionization of DNA Bases and Sugar-Phosphate Backbone

Science.gov (United States)

Dateo, Christopher E.; Fletcher, Graham D.

2004-01-01

As part of the database for building up a biochemical model of DNA radiation damage, electron impact ionization cross sections of sugar-phosphate backbone and DNA bases have been calculated using the improved binary-encounter dipole (iBED) model. It is found that the total ionization cross sections of C3'- and C5'-deoxyribose-phospate, two conformers of the sugar-phosphate backbone, are close to each other. Furthermore, the sum of the ionization cross sections of the separate deoxyribose and phosphate fragments is in close agreement with the C3'- and C5'-deoxyribose-phospate cross sections, differing by less than 10%. Of the four DNA bases, the ionization cross section of guanine is the largest, then in decreasing order, adenine, thymine, and cytosine. The order is in accordance with the known propensity of oxidation of the bases by ionizing radiation. Dissociative ionization (DI), a process that both ionizes and dissociates a molecule, is investigated for cytosine. The DI cross section for the formation of H and (cytosine-Hl)(+), with the cytosine ion losing H at the 1 position, is also reported. The threshold of this process is calculated to be 17.1 eV. Detailed analysis of ionization products such as in DI is important to trace the sequential steps in the biochemical process of DNA damage.

Biological effects of low-level ionizing and non-ionizing radiation

International Nuclear Information System (INIS)

Upton, A.C.

1986-01-01

Early in this century it was recognized that large doses of ionizing radiation could injure almost any tissue in the body, but small doses were generally thought to be harmless. By the middle of the century however it came to be suspected that even the smallest doses of ionizing radiation to the gonads might increase the risk of hereditary disease in subsequently-conceived offspring. Since then the hypothesis that carcinogenic and teratogenic effects also have no threshold has been adopted for purposes of radiological protection. It is estimated nevertheless that the risks that may be associated with natural background levels of ionizing irradiation are too small to be detectable. Hence validation of such risk estimates will depend on further elucidation of the dose-effect relationships and mechanisms of the effects in question, through studies at higher dose levels. In contrast to the situation with ionizing radiation, exposure to natural background levels of ultraviolet radiation has been implicated definitively in the etiology of skin cancers in fair-skinned individuals. Persons with inherited effects in DNA repair capacity are particularly susceptible. Non-ionizing radiations of other types can also affect health at high dose levels, but whether they can cause injury at low levels of exposure is not known

Ab initio dynamics and photoionization mass spectrometry reveal ion-molecule pathways from ionized acetylene clusters to benzene cation.

Science.gov (United States)

Stein, Tamar; Bandyopadhyay, Biswajit; Troy, Tyler P; Fang, Yigang; Kostko, Oleg; Ahmed, Musahid; Head-Gordon, Martin

2017-05-23

The growth mechanism of hydrocarbons in ionizing environments, such as the interstellar medium (ISM), and some combustion conditions remains incompletely understood. Ab initio molecular dynamics (AIMD) simulations and molecular beam vacuum-UV (VUV) photoionization mass spectrometry experiments were performed to understand the ion-molecule growth mechanism of small acetylene clusters (up to hexamers). A dramatic dependence of product distribution on the ionization conditions is demonstrated experimentally and understood from simulations. The products change from reactive fragmentation products in a higher temperature, higher density gas regime toward a very cold collision-free cluster regime that is dominated by products whose empirical formula is (C 2 H 2 ) n + , just like ionized acetylene clusters. The fragmentation products result from reactive ion-molecule collisions in a comparatively higher pressure and temperature regime followed by unimolecular decomposition. The isolated ionized clusters display rich dynamics that contain bonded C 4 H 4 + and C 6 H 6 + structures solvated with one or more neutral acetylene molecules. Such species contain large amounts (>2 eV) of excess internal energy. The role of the solvent acetylene molecules is to affect the barrier crossing dynamics in the potential energy surface (PES) between (C 2 H 2 ) n + isomers and provide evaporative cooling to dissipate the excess internal energy and stabilize products including the aromatic ring of the benzene cation. Formation of the benzene cation is demonstrated in AIMD simulations of acetylene clusters with n > 3, as well as other metastable C 6 H 6 + isomers. These results suggest a path for aromatic ring formation in cold acetylene-rich environments such as parts of the ISM.

Ab initio dynamics and photoionization mass spectrometry reveal ion–molecule pathways from ionized acetylene clusters to benzene cation

Science.gov (United States)

Stein, Tamar; Bandyopadhyay, Biswajit; Troy, Tyler P.; Fang, Yigang; Kostko, Oleg

2017-01-01

The growth mechanism of hydrocarbons in ionizing environments, such as the interstellar medium (ISM), and some combustion conditions remains incompletely understood. Ab initio molecular dynamics (AIMD) simulations and molecular beam vacuum-UV (VUV) photoionization mass spectrometry experiments were performed to understand the ion–molecule growth mechanism of small acetylene clusters (up to hexamers). A dramatic dependence of product distribution on the ionization conditions is demonstrated experimentally and understood from simulations. The products change from reactive fragmentation products in a higher temperature, higher density gas regime toward a very cold collision-free cluster regime that is dominated by products whose empirical formula is (C2H2)n+, just like ionized acetylene clusters. The fragmentation products result from reactive ion–molecule collisions in a comparatively higher pressure and temperature regime followed by unimolecular decomposition. The isolated ionized clusters display rich dynamics that contain bonded C4H4+ and C6H6+ structures solvated with one or more neutral acetylene molecules. Such species contain large amounts (>2 eV) of excess internal energy. The role of the solvent acetylene molecules is to affect the barrier crossing dynamics in the potential energy surface (PES) between (C2H2)n+ isomers and provide evaporative cooling to dissipate the excess internal energy and stabilize products including the aromatic ring of the benzene cation. Formation of the benzene cation is demonstrated in AIMD simulations of acetylene clusters with n > 3, as well as other metastable C6H6+ isomers. These results suggest a path for aromatic ring formation in cold acetylene-rich environments such as parts of the ISM. PMID:28484019

Effects of ionizing radiations on proteins

International Nuclear Information System (INIS)

Maire, M. le; Foresta, B. de; Viel, A.; Thauvette, L.; Beauregard, G.; Potier, M.

1990-01-01

We have reinvestigated the use of ionizing radiations to measure the molecular mass of water-soluble or membrane proteins. Exposure of purified standard proteins to increasing doses of ionizing radiation causes progressive fragmentation of the native protein into defined peptide patterns. The coloured band corresponding to the intact protein was measured on the SDS gel as a function of dose to determine the dose (D 37.t ) corresponding to 37% of the initial amount of unfragmented protein deposited on the gel. This led to a calibration curve and the known molecular mass of the standard proteins. However, we have to conclude that this method is useless to determine the state of aggregation of a protein, since, for all the oligomers tested, the best fit was obtained by using the protomeric molecular mass, suggesting that there is no energy transfer between protomers. Furthermore, SDS greatly increases the fragmentation rate of proteins, which suggests additional calibration problems for membrane proteins in detergent or in the lipid bilayer. The main drawback of the technique is that some proteins behaved anomalously, leading to very large errors in the apparent target size as compared with true molecular mass. It is thus unreliable to apply the radiation method for absolute molecular-mass determination. We then focused on the novel finding that discrete fragmentation of proteins occurs at preferential sites, and this was studied with aspartate transcarbamylase. (author)

Molecular frame photoemission: a probe of electronic/nuclear photo-dynamics and polarization state of the ionizing light

International Nuclear Information System (INIS)

Veyrinas, Kevin

2015-01-01

This is thesis is dedicated to the study and the use of the remarkable properties of the molecular frame photoelectron angular distribution (MFPAD). This observable is a very sensitive probe of both the photoionization (PI) processes in small molecules, through the determination of the magnitudes and relative phases of the dipole matrix elements, and the polarization state of the ionizing light, which is entirely encoded in the MFPAD in terms of the Stokes parameters (s1, s2, s3). MFPAD measurements take advantage of dissociative photoionization (DPI) processes by combining an electron-ion 3D momentum spectroscopy technique with the use of different radiation facilities: SOLEIL synchrotron (DESIRS and PLEIADES beamlines) and the XUV PLFA beamline (SLIC, LIDyL Attophysics group, CEA Saclay) based on the interaction of a strong laser field with a gaseous target called high harmonic generation (HHG). The first part of the thesis is devoted to the complete characterization of the polarization state of an incoming radiation. In this context, an original 'molecular polarimetry' method is introduced and demonstrated by comparison with a VUV optical polarimeter available on the DESIRS beamline. Using this method to determine the full polarization ellipse of HHG radiation generated in different conditions on the XUV PLFA facility leads to original results that include the challenging disentanglement of the circular and unpolarized components of the studied radiation. The second part deals with the study of DPI of the H 2 , D 2 and HD molecules induced by circularly polarized light at resonance with the doubly excited states Q1 and Q2. In this energy region (30-35 eV) where direct ionization, autoionization and dissociation compete on a femtosecond timescale, the photonic excitation gives rise to complex ultrafast electronic and nuclear coupled dynamics. The remarkable asymmetries observed in the circular dichroism in the molecular frame, compared to quantum

On the mechanism of extractive electrospray ionization (EESI) in the dual-spray configuration.

Science.gov (United States)

Wang, Rui; Gröhn, Arto Juhani; Zhu, Liang; Dietiker, Rolf; Wegner, Karsten; Günther, Detlef; Zenobi, Renato

2012-03-01

Dual-spray extractive electrospray ionization (EESI) mass spectrometry as a versatile analytical technique has attracted much interest due to its advantages over conventional electrospray ionization (ESI). The crucial difference between EESI and ESI is that in the EESI process, the analytes are introduced in nebulized form via a neutral spray and ionized by collisions with the charged droplets from an ESI source formed by spraying pure solvent. However, the mechanism of the droplet-droplet interactions in the EESI process is still not well understood. For example, it is unclear which type of droplet-droplet interaction is dominant: bounce, coalescence, disruption, or fragmentation? In this work, droplet-droplet interaction was investigated in detail based on a theoretical model. Phase Doppler anemometry (PDA) was employed to investigate the droplet behavior in the EESI plume and provide the experimental data (droplet size and velocity) necessary for theoretical analysis. Furthermore, numerical simulations were performed to clarify the influence of the sheath gas flow on the EESI process. No coalescence between the droplets in the ESI spray and the droplets in the sample spray was observed using various geometries and sample flow rates. Theoretical analysis, together with the PDA results, suggests that droplet fragmentation may be the dominant type of droplet-droplet interaction in the EESI. The interaction time between the ESI droplet and the sample droplet was estimated to be <5 μs. This work gives a clear picture of droplet-droplet interactions in the dual-spray EESI process and detailed information for the optimization of this method for future applications that require higher sensitivity.

Secondary ionization processes in laser induced breakdown of electronegative gases

International Nuclear Information System (INIS)

Gamal Yosr, E.E.D.; Shafik, M.S.; Abdel-Moneim, H.M.

1990-08-01

This paper presents an investigation of the stepwise ionization processes which occur during the interaction of laser radiation with electronegative gases. Calculations are carried out adopting a modified version of the electron cascade model previously developed by Evans and Gamal. The modifications of the model are performed for the case of molecular oxygen to account for electron attachment losses. Particular attention is devoted to molecular oxygen at a pressure of 2.8 x 10 4 Torr irradiated by 10 ns pulse of Nd:YAG laser (λ=1.064 μm) at a peak intensity of 1.7x10 11 Wcm -2 . The calculations consider the effect of the secondary ionization processes on the electron energy distribution function and its parameters (evolution of the density of the excited molecules, electrons density as well as the electron mean energy during the laser flash). This analysis shows how the removal of slow electrons by attachment to oxygen molecules creates a strong competition between the stepwise ionization processes. These processes namely photoionization and collisional ionization deplete the electronic excited states and contribute eventually to the ionization growth rate in laser induced breakdown of electronegative gases. (author). 7 refs, 6 figs, 1 tab

Computational exploration of single-protein mechanics by steered molecular dynamics

Energy Technology Data Exchange (ETDEWEB)

Sotomayor, Marcos [Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio (United States)

2015-12-31

Hair cell mechanotransduction happens in tens of microseconds, involves forces of a few picoNewtons, and is mediated by nanometer-scale molecular conformational changes. As proteins involved in this process become identified and their high resolution structures become available, multiple tools are being used to explore their “single-molecule responses” to force. Optical tweezers and atomic force microscopy offer exquisite force and extension resolution, but cannot reach the high loading rates expected for high frequency auditory stimuli. Molecular dynamics (MD) simulations can reach these fast time scales, and also provide a unique view of the molecular events underlying protein mechanics, but its predictions must be experimentally verified. Thus a combination of simulations and experiments might be appropriate to study the molecular mechanics of hearing. Here I review the basics of MD simulations and the different methods used to apply force and study protein mechanics in silico. Simulations of tip link proteins are used to illustrate the advantages and limitations of this method.

Molecular mechanisms underlying the emergence of bacterial pathogens: an ecological perspective.

Science.gov (United States)

Bartoli, Claudia; Roux, Fabrice; Lamichhane, Jay Ram

2016-02-01

The rapid emergence of new bacterial diseases negatively affects both human health and agricultural productivity. Although the molecular mechanisms underlying these disease emergences are shared between human- and plant-pathogenic bacteria, not much effort has been made to date to understand disease emergences caused by plant-pathogenic bacteria. In particular, there is a paucity of information in the literature on the role of environmental habitats in which plant-pathogenic bacteria evolve and on the stress factors to which these microbes are unceasingly exposed. In this microreview, we focus on three molecular mechanisms underlying pathogenicity in bacteria, namely mutations, genomic rearrangements and the acquisition of new DNA sequences through horizontal gene transfer (HGT). We briefly discuss the role of these mechanisms in bacterial disease emergence and elucidate how the environment can influence the occurrence and regulation of these molecular mechanisms by directly impacting disease emergence. The understanding of such molecular evolutionary mechanisms and their environmental drivers will represent an important step towards predicting bacterial disease emergence and developing sustainable management strategies for crops. © 2015 BSPP AND JOHN WILEY & SONS LTD.

IONIZATION IN ATMOSPHERES OF BROWN DWARFS AND EXTRASOLAR PLANETS. V. ALFVÉN IONIZATION

International Nuclear Information System (INIS)

Stark, C. R.; Helling, Ch.; Rimmer, P. B.; Diver, D. A.

2013-01-01

Observations of continuous radio and sporadic X-ray emission from low-mass objects suggest they harbor localized plasmas in their atmospheric environments. For low-mass objects, the degree of thermal ionization is insufficient to qualify the ionized component as a plasma, posing the question: what ionization processes can efficiently produce the required plasma that is the source of the radiation? We propose Alfvén ionization as a mechanism for producing localized pockets of ionized gas in the atmosphere, having sufficient degrees of ionization (≥10 –7 ) that they constitute plasmas. We outline the criteria required for Alfvén ionization and demonstrate its applicability in the atmospheres of low-mass objects such as giant gas planets, brown dwarfs, and M dwarfs with both solar and sub-solar metallicities. We find that Alfvén ionization is most efficient at mid to low atmospheric pressures where a seed plasma is easier to magnetize and the pressure gradients needed to drive the required neutral flows are the smallest. For the model atmospheres considered, our results show that degrees of ionization of 10 –6 -1 can be obtained as a result of Alfvén ionization. Observable consequences include continuum bremsstrahlung emission, superimposed with spectral lines from the plasma ion species (e.g., He, Mg, H 2 , or CO lines). Forbidden lines are also expected from the metastable population. The presence of an atmospheric plasma opens the door to a multitude of plasma and chemical processes not yet considered in current atmospheric models. The occurrence of Alfvén ionization may also be applicable to other astrophysical environments such as protoplanetary disks

Mechanisms of chemical modification of neoplastic cell transformation by ionizing radiation

International Nuclear Information System (INIS)

Yang, T.C.; Tobias, C.A.

1985-01-01

During space travel, astronauts will be continuously exposed to ionizing radiation; therefore, it is necessary to minimize the radiation damage by all possible means. The authors' studies show that DMSO (when present during irradiation) can protect cells from being killed and transformed by X rays and that low concentration of DMSO can reduce the transformation frequency significantly when it is applied to cells, even many days after irradiation. The process of neoplastic cell transformation is a complicated one and includes at least two different stages: induction and expression. DMSO apparently can modify the radiation damage during both stages. There are several possible mechanisms for the DMSO effect: (1) changing the cell membrane structure and properties; (2) inducing cell differentiation by acting on DNA; and (3) scavanging free radicals in the cell. Recent studies with various chemical agents, e.g., 5-azacytidine, dexamethane, rhodamin-123, etc., indicate that the induction of cell differentiation by acting on DNA may be an important mechanism for the suppression of expression of neoplastic cell transformation by DMSO

Molecular mechanisms of renal aging.

Science.gov (United States)

Schmitt, Roland; Melk, Anette

2017-09-01

Epidemiologic, clinical, and molecular evidence suggest that aging is a major contributor to the increasing incidence of acute kidney injury and chronic kidney disease. The aging kidney undergoes complex changes that predispose to renal pathology. The underlying molecular mechanisms could be the target of therapeutic strategies in the future. Here, we summarize recent insight into cellular and molecular processes that have been shown to contribute to the renal aging phenotype.The main clinical finding of renal aging is the decrease in glomerular filtration rate, and its structural correlate is the loss of functioning nephrons. Mechanistically, this has been linked to different processes, such as podocyte hypertrophy, glomerulosclerosis, tubular atrophy, and gradual microvascular rarefaction. Renal functional recovery after an episode of acute kidney injury is significantly worse in elderly patients. This decreased regenerative potential, which is a hallmark of the aging process, may be caused by cellular senescence. Accumulation of senescent cells could explain insufficient repair and functional loss, a view that has been strengthened by recent studies showing that removal of senescent cells results in attenuation of renal aging. Other potential mechanisms are alterations in autophagy as an important component of a disturbed renal stress response and functional differences in the inflammatory system. Promising therapeutic measures to counteract these age-related problems include mimetics of caloric restriction, pharmacologic renin-angiotensin-aldosterone system inhibition, and novel strategies of senotherapy with the goal of reducing the number of senescent cells to decrease aging-related disease in the kidney. Copyright © 2017 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.

(e,3e) and (e,3-1e) differential cross sections for the double ionization of water molecule

International Nuclear Information System (INIS)

Mansouri, A.; Dal Cappello, C.; Kada, I.; Champion, C.; Roy, A.C.

2009-01-01

We report new results for differential cross sections for the double ionization of water molecule by 1 keV electron impact. The present calculation is based on the first Born approximation. We describe the water molecule by a single centre wave function of Moccia. For the final state, an approximation of the well-known 3C wave function is used. An extensive study has been made by varying the angles of detection and the energies of each ejected electron. We have investigated the double ionization of each molecular state (1b 1 , 3a 1 , 1b 2 and 2a 1 ) and identified the mechanisms of this process.

Mammalian Tissue Response to Low Dose Ionizing Radiation: The Role of Oxidative Metabolism and Intercellular Communication

Energy Technology Data Exchange (ETDEWEB)

Azzam, Edouard I

2013-01-16

The objective of the project was to elucidate the mechanisms underlying the biological effects of low dose/low dose rate ionizing radiation in organs/tissues of irradiated mice that differ in their susceptibility to ionizing radiation, and in human cells grown under conditions that mimic the natural in vivo environment. The focus was on the effects of sparsely ionizing cesium-137 gamma rays and the role of oxidative metabolism and intercellular communication in these effects. Four Specific Aims were proposed. The integrated outcome of the experiments performed to investigate these aims has been significant towards developing a scientific basis to more accurately estimate human health risks from exposures to low doses ionizing radiation. By understanding the biochemical and molecular changes induced by low dose radiation, several novel markers associated with mitochondrial functions were identified, which has opened new avenues to investigate metabolic processes that may be affected by such exposure. In particular, a sensitive biomarker that is differentially modulated by low and high dose gamma rays was discovered.

Molecular identification of Mucorales in human tissues: contribution of PCR electrospray-ionization mass spectrometry.

Science.gov (United States)

Alanio, A; Garcia-Hermoso, D; Mercier-Delarue, S; Lanternier, F; Gits-Muselli, M; Menotti, J; Denis, B; Bergeron, A; Legrand, M; Lortholary, O; Bretagne, S

2015-06-01

Molecular methods are crucial for mucormycosis diagnosis because cultures are frequently negative, even if microscopy suggests the presence of hyphae in tissues. We assessed PCR/electrospray-ionization mass spectrometry (PCR/ESI-MS) for Mucorales identification in 19 unfixed tissue samples from 13 patients with proven or probable mucormycosis and compared the results with culture, quantitative real-time PCR, 16S-23S rRNA gene internal transcribed spacer region (ITS PCR) and 18S PCR sequencing. Concordance with culture identification to both genus and species levels was higher for PCR/ESI-MS than for the other techniques. Thus, PCR/ESI-MS is suitable for Mucorales identification, within 6 hours, for tissue samples for which microscopy results suggest the presence of hyphae. Copyright © 2015 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Explosives vapour identification in ion mobility spectrometry using a tunable laser ionization source: a comparison with conventional 63Ni ionization

International Nuclear Information System (INIS)

Clark, A.; Deas, R.M.; Kosmidis, C.; Ledingham, K.W.D.; Marshall, A.; Singhal, R.P.

1995-01-01

Laser multiphoton ionization (MPI) is used to produce ions from explosive vapours at atmospheric pressure in air for analysis by ion mobility spectrometry (IMS). In the positive ion mode of detection, NO + ions, generated directly by multiphoton dissociation/ionization of the explosive compounds, show strong variation with laser wavelength. This provides a means of identifying the presence of nitro-containing compounds. Moreover, electrons formed in the MPI of gaseous components in the air carrier stream, primarily O 2 , are transferred via neutral molecular oxygen (O 2 ) to trace explosive vapour, forming negative ions which give rise to characteristic and identifiable ion mobility spectra. Further, negative ion mobility spectra of several explosive vapours are presented using conventional 63 Ni ionization and are compared qualitatively with the laser ionization approach. (author)

Search for a double-collision mechanism as a possible interpretation for ionization by low-energy light-ion impact

International Nuclear Information System (INIS)

Avaldi, L.; Magno, C.; Milazzo, M.; Rota, A.

1981-01-01

In a previous work the authors proposed, in the frame of the binary-encounter approximation (BEA) of the inner-shell atomic ionization by ion bombardment, a correction to the ion energy in order to account for the Coulomb repulsion by the atomic nucleus. Such corrected cross-section values numerically coincide with those of the PWBA model, but, as a consequence of the correction, they obtain a much higher-energy ionization threshold than the binding energy, which has no experimental evidence. In the present work it is shown that ionization below such a threshold can be explained by a double-collision mechanism which involves intermediate electron states and can directly be derived from the impulsive nature of the binary-collision model. Calculations have been performed by supposing a statistical independence between these two collisions. Relativistic corrections have not been taken into account. A remarkable agreement is obtained between the curves corresponding to single- and double-collision classical processes, since they match at the bombarding threshold ion energy. (author)

Progress on untargeted effects of ionizing irradiation

International Nuclear Information System (INIS)

Liu Jing; Chen Jihong; Li Wenjian

2010-01-01

The side effect of ionizing irradiation has been paid more attention with its widely using in tumor treating and mutation breeding. In recent years, untargeted effects induced by ionizing irradiation have become a hotspot of radiobiology. Here, according to reported results, we reviewed the types (genomic instability, bystander effect and adaptive response) and mechanisms of untargeted effects of ionizing irradiation in this paper. (authors)

A coordinated molecular 'fishing' mechanism in heterodimeric kinesin

International Nuclear Information System (INIS)

Hou, Ruizheng; Wang, Zhisong

2010-01-01

Kar3 is a kinesin motor that facilitates chromosome segregation during cell division. Unlike many members of the kinesin superfamily, Kar3 forms a heterodimer with non-motor protein Vik1 or Cik1 in vivo. The heterodimers show ATP-driven minus-end directed motility along a microtubule (MT) lattice, and also serve as depolymerase at the MT ends. The molecular mechanisms behind this dual functionality remain mysterious. Here, a molecular mechanical model for the Kar3/Vik1 heterodimer based on structural, kinetic and motility data reveals a long-range chemomechanical transmission mechanism that resembles a familiar fishing tactic. By this molecular 'fishing', ATP-binding to Kar3 dissociates catalytically inactive Vik1 off MT to facilitate minus-end sliding of the dimer on the MT lattice. When the dimer binds the frayed ends of MT, the fishing channels ATP hydrolysis energy into MT deploymerization by a mechanochemical effect. The molecular fishing thus provides a unified mechanistic ground for Kar3's dual functionality. The fishing-promoted depolymerization differs from the depolymerase mechanisms found in homodimeric kinesins. The fishing also enables intermolecular coordination with a chemomechanical coupling feature different from the paradigmatic pattern of homodimeric motors. This study rationalizes some puzzling experimental observation, and suggests new experiments for further elucidation of the fishing mechanism

Derivatization of Dextran for Multiply Charged Ion Formation and Electrospray Ionization Time-of-Flight Mass Spectrometric Analysis

Science.gov (United States)

Tapia, Jesus B.; Hibbard, Hailey A. J.; Reynolds, Melissa M.

2017-10-01

We present the use of a simple, one-pot derivatization to allow the polysaccharide dextran to carry multiple positive charges, shifting its molecular weight distribution to a lower m/ z range. We performed this derivatization because molecular weight measurements of polysaccharides by mass spectrometry are challenging because of their lack of readily ionizable groups. The absence of ionizable groups limits proton abstraction and suppresses proton adduction during the ionization process, producing mass spectra with predominantly singly charged metal adduct ions, thereby limiting the detection of large polysaccharides. To address this challenge, we derivatized dextran T1 (approximately 1 kDa) by attaching ethylenediamine, giving dextran readily ionizable, terminal amine functional groups. The attached ethylenediamine groups facilitated proton adduction during the ionization process in positive ion mode. Using the low molecular weight dextran T1, we tracked the number of ethylenediamine attachments by measuring the mass shift from underivatized to derivatized dextran T1. Using electrospray ionization time-of-flight mass spectrometry, we observed derivatized dextran chains ranging from two to nine glucose residues with between one and four attachments/charges. Our success in shifting derivatized dextran T1 toward the low m/ z range suggests potential for this derivatization as a viable route for analysis of high molecular weight polysaccharides using electrospray ionization time-of-flight mass spectrometry. [Figure not available: see fulltext.

Sensitivity of clostridium acetobutylicum to oxygen and ionizing radiation

International Nuclear Information System (INIS)

Sozer, A.C.; Adler, H.I.; Machanoff, R.; Haney, S.

1984-01-01

The authors are studying the sensitivity of four strains of the obligate anaerobe, Clostridium acetobutylicum, to oxygen and ionizing radiation. Anaerobic bacteria are useful for such studies because of the absence of elaborate oxygen detoxification mechanisms that are found in aerobes. Their experiments make use of sterile membrane fragments from Escherichia coli that rapidly remove molecular oxygen from media and permit growth of anaerobes without the use of reducing agents or anaerobic chambers. Of the four strains examined for sensitivity to ionizing radiation under anaerobic conditions, one has an LD/sub 50/ of -- 25 krads and the others have an LD/sub 50/ of -- 7 krads. The radiation resistant strain is also relatively resistant to oxygen exposure. Sensitivity to oxygen was determined by diluting cells in buffer at 28 0 and bubbling with air. An exposure to air for 40 min induced only slight inactivation in the radiation resistant strain. All strains are capable of removing oxygen from complex media but there is no apparent correlation between this oxygen consuming reaction and inactivation by either oxygen or radiation

Excitation two-center interference and the orbital geometry in laser-induced nonsequential double ionization of diatomic molecules

International Nuclear Information System (INIS)

Shaaran, T.; Augstein, B. B.; Figueira de Morisson Faria, C.

2011-01-01

We address the influence of the molecular orbital geometry and of the molecular alignment with respect to the laser-field polarization on laser-induced nonsequential double ionization of diatomic molecules for different molecular species, namely N 2 and Li 2 . We focus on the recollision excitation with subsequent tunneling ionization (RESI) mechanism, in which the first electron, upon return, promotes the second electron to an excited state, from where it subsequently tunnels. We assume that both electrons are initially in the highest occupied molecular orbital (HOMO) and that the second electron is excited to the lowest unoccupied molecular orbital (LUMO). We show that the electron-momentum distributions exhibit interference maxima and minima due to the electron emission at spatially separated centers. We provide generalized analytical expressions for such maxima or minima, which take into account s-p mixing and the orbital geometry. The patterns caused by the two-center interference are sharpest for vanishing alignment angle and get washed out as this parameter increases. Apart from that, there exist features due to the geometry of the LUMO, which may be observed for a wide range of alignment angles. Such features manifest themselves as the suppression of probability density in specific momentum regions due to the shape of the LUMO wave function, or as an overall decrease in the RESI yield due to the presence of nodal planes.

Molecular Mechanisms of Neuroplasticity: An Expanding Universe.

Science.gov (United States)

Gulyaeva, N V

2017-03-01

Biochemical processes in synapses and other neuronal compartments underlie neuroplasticity (functional and structural alterations in the brain enabling adaptation to the environment, learning, memory, as well as rehabilitation after brain injury). This basic molecular level of brain plasticity covers numerous specific proteins (enzymes, receptors, structural proteins, etc.) participating in many coordinated and interacting signal and metabolic processes, their modulation forming a molecular basis for brain plasticity. The articles in this issue are focused on different "hot points" in the research area of biochemical mechanisms supporting neuroplasticity.

A combined thermal dissociation and electron impact ionization source for RIB generation

International Nuclear Information System (INIS)

Alton, G.D.; Williams, C.

1995-01-01

The probability for simultaneously dissociating and efficiently ionizing the individual atomic constituents of molecular feed materials with conventional, hot-cathode, electron-impact ion sources is low and consequently, the ion beams from these sources often appear as mixtures of several molecular sideband beams. This fragmentation process leads to dilution of the intensity of the species of interest for RIB applications where beam intensity is at a premium. We have conceived an ion source that combines the excellent molecular dissociation properties of a thermal dissociator and the high ionization efficiency characteristics of an electron impact ionization source that will, in principle, overcome this handicap. The source concept will be evaluated as a potential candidate for use for RIB generation at the Holifield Radioactive Ion Beam Facility (HRIBF), now under construction at the Oak Ridge National Laboratory. The design features and principles of operation of the source are described in this article

Ionization of oriented carbonyl sulfide molecules by intense circularly polarized laser pulses

DEFF Research Database (Denmark)

Dimitrovski, Darko; Abu-Samha, Mahmoud; Madsen, Lars Bojer

2011-01-01

We present combined experimental and theoretical results on strong-field ionization of oriented carbonyl sulfide molecules by circularly polarized laser pulses. The obtained molecular frame photoelectron angular distributions show pronounced asymmetries perpendicular to the direction of the molec......We present combined experimental and theoretical results on strong-field ionization of oriented carbonyl sulfide molecules by circularly polarized laser pulses. The obtained molecular frame photoelectron angular distributions show pronounced asymmetries perpendicular to the direction......-dimensionally-oriented polar molecules, in particular asymmetries in the emission direction of the photoelectrons. In the following article [Phys. Rev. A 83, 023406 (2011)] the focus is to understand strong-field ionization from three-dimensionally-oriented asymmetric top molecules, in particular the suppression of electron...

Ionization chamber

International Nuclear Information System (INIS)

1977-01-01

An improved ionization chamber type X-ray detector comprises a heavy gas at high pressure disposed between an anode and a cathode. An open grid structure is placed next to the anode and is maintained at a voltage intermediate between the cathode and anode potentials. The electric field which is produced by positive ions drifting towards the cathode is thus shielded from the anode. Current measuring circuits connected to the anode are, therefore, responsive only to electron current flow within the chamber and the recovery time of the chamber is shortened. The grid structure also serves to shield the anode from electrical currents which might otherwise be induced by mechanical vibrations in the ionization chamber structure

Conceptual basis of resonance ionization spectroscopy

International Nuclear Information System (INIS)

Payne, M.G.

1984-04-01

Resonance Ionization Spectroscopy (RIS) can b defined as a state-selective detection process in which tunable lasers are used to promote transitions from the selected state of the atoms or molecules in question to higher states, one of which will be ionized by the absorption of another photon. At least one resonance step is used in the stepwise ionization process, and it has been shown that the ionization probability of the spectroscopically selected species can nearly always be made close to unity. Since measurements of the number of photoelectrons or ions can be made very precisely and even one electron (or under vacuum conditions, one ion) can be detected, the technique can be used to make quantitative measurements of very small populations of the state-selected species. Counting of individual atoms has special meaning for detection of rare events. The ability to make saturated RIS measurements opens up a wide variety of applications to both basic and applied research. We view RIS as a specific type of multi-photon ionization in which the goal is to make quantitative measurements of quantum-selected populations in atomic or molecular systems. 16 references

Hyperinsulinemic Hypoglycemia ? The Molecular Mechanisms

OpenAIRE

Nessa, Azizun; Rahman, Sofia A.; Hussain, Khalid

2016-01-01

Under normal physiological conditions, pancreatic β-cells secrete insulin to maintain fasting blood glucose levels in the range 3.5–5.5 mmol/L. In hyperinsulinemic hypoglycemia (HH), this precise regulation of insulin secretion is perturbed so that insulin continues to be secreted in the presence of hypoglycemia. HH may be due to genetic causes (congenital) or secondary to certain risk factors. The molecular mechanisms leading to HH involve defects in the key genes regulating insulin secretio...

Multiple-electron removal and molecular fragmentation of CO by fast F4+ impact

International Nuclear Information System (INIS)

Ben-Itzhak, I.; Ginther, S.G.; Carnes, K.D.

1993-01-01

Multiple-electron removal from and molecular fragmentation of carbon monoxide molecules caused by collisions with 1-MeV/amu F 4+ ions were studied using the coincidence time-of-flight technique. In these collisions, multiple-electron removal of the target molecule is a dominant process. Cross sections for the different levels of ionization of the CO molecule during the collision were determined. The relative cross sections of ionization decrease with increasing number of electrons removed in a similar way as seen in atomic targets. This behavior is in agreement with a two-step mechanism, where first the molecule is ionized by a Franck-Condon ionization and then the molecular ion dissociates. Most of the highly charged intermediate states of the molecule dissociate rapidly. Only CO + and CO 2+ molecular ions have been seen to survive long enough to be detected as molecular ions. The relative cross sections for the different breakup channels were evaluated for collisions in which the molecule broke into two charged fragments as well as for collisions where only a single charged molecular ion or fragment were produced. The average charge state of each fragment resulting from CO Q+ →C i+ +O j+ breakup increases with the number of electrons removed from the molecule approximately following the relationship bar i=bar j=Q/2 as long as K-shell electrons are not removed. This does not mean that the charge-state distribution is exactly symmetric, as, in general, removing electrons from the carbon fragment is slightly more likely than removing electrons from the oxygen due to the difference in binding energy. The cross sections for molecular breakup into a charged fragment and a neutral fragment drop rapidly with an increasing number of electrons removed

Molecular mechanisms of curcumin action: gene expression.

Science.gov (United States)

Shishodia, Shishir

2013-01-01

Curcumin derived from the tropical plant Curcuma longa has a long history of use as a dietary agent, food preservative, and in traditional Asian medicine. It has been used for centuries to treat biliary disorders, anorexia, cough, diabetic wounds, hepatic disorders, rheumatism, and sinusitis. The preventive and therapeutic properties of curcumin are associated with its antioxidant, anti-inflammatory, and anticancer properties. Extensive research over several decades has attempted to identify the molecular mechanisms of curcumin action. Curcumin modulates numerous molecular targets by altering their gene expression, signaling pathways, or through direct interaction. Curcumin regulates the expression of inflammatory cytokines (e.g., TNF, IL-1), growth factors (e.g., VEGF, EGF, FGF), growth factor receptors (e.g., EGFR, HER-2, AR), enzymes (e.g., COX-2, LOX, MMP9, MAPK, mTOR, Akt), adhesion molecules (e.g., ELAM-1, ICAM-1, VCAM-1), apoptosis related proteins (e.g., Bcl-2, caspases, DR, Fas), and cell cycle proteins (e.g., cyclin D1). Curcumin modulates the activity of several transcription factors (e.g., NF-κB, AP-1, STAT) and their signaling pathways. Based on its ability to affect multiple targets, curcumin has the potential for the prevention and treatment of various diseases including cancers, arthritis, allergies, atherosclerosis, aging, neurodegenerative disease, hepatic disorders, obesity, diabetes, psoriasis, and autoimmune diseases. This review summarizes the molecular mechanisms of modulation of gene expression by curcumin. Copyright © 2012 International Union of Biochemistry and Molecular Biology, Inc.

Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.

Science.gov (United States)

Shen, Lin; Yang, Weitao

2018-03-13

Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in a complex environment but also very time-consuming. The computational cost of QM/MM calculations during MD simulations can be reduced significantly using semiempirical QM/MM methods with lower accuracy. To achieve higher accuracy at the ab initio QM/MM level, a correction on the existing semiempirical QM/MM model is an attractive idea. Recently, we reported a neural network (NN) method as QM/MM-NN to predict the potential energy difference between semiempirical and ab initio QM/MM approaches. The high-level results can be obtained using neural network based on semiempirical QM/MM MD simulations, but the lack of direct MD samplings at the ab initio QM/MM level is still a deficiency that limits the applications of QM/MM-NN. In the present paper, we developed a dynamic scheme of QM/MM-NN for direct MD simulations on the NN-predicted potential energy surface to approximate ab initio QM/MM MD. Since some configurations excluded from the database for NN training were encountered during simulations, which may cause some difficulties on MD samplings, an adaptive procedure inspired by the selection scheme reported by Behler [ Behler Int. J. Quantum Chem. 2015 , 115 , 1032 ; Behler Angew. Chem., Int. Ed. 2017 , 56 , 12828 ] was employed with some adaptions to update NN and carry out MD iteratively. We further applied the adaptive QM/MM-NN MD method to the free energy calculation and transition path optimization on chemical reactions in water. The results at the ab initio QM/MM level can be well reproduced using this method after 2-4 iteration cycles. The saving in computational cost is about 2 orders of magnitude. It demonstrates that the QM/MM-NN with direct MD simulations has great potentials not only for the calculation of thermodynamic properties but also for the characterization of

Molecular data for a biochemical model of DNA damage: Electron impact ionization and dissociative ionization cross sections of DNA bases and sugar-phosphate backbone

International Nuclear Information System (INIS)

Huo, Winifred M.; Dateo, Christopher E.; Fletcher, Graham D.

2006-01-01

As part of the database for building up a biochemical model of DNA radiation damage, electron impact ionization cross sections of sugar-phosphate backbone and DNA bases have been calculated using the improved binary-encounter dipole (iBED) model. It is found that the total ionization cross sections of C 3 ' - and C 5 ' -deoxyribose-phosphate, two conformers of the sugar-phosphate backbone, are close to each other. Furthermore, the sum of the ionization cross sections of the separate deoxyribose and phosphate fragments is in close agreement with the C 3 ' - and C 5 ' -deoxyribose-phosphate cross sections, differing by less than 10%, an indication that a building-up principle may be applicable. Of the four DNA bases, the ionization cross section of guanine is the largest, then in decreasing order, adenine, thymine, and cytosine. The order is in accordance with the known propensity of oxidation of the bases by ionizing radiation. Dissociative ionization (DI), a process that both ionizes and dissociates a molecule, is investigated for cytosine. The DI cross section for the formation of H and (cytosine-H1) + , with the cytosine ion losing H at the 1 position, is also reported. The threshold of this process is calculated to be 16.9eV. Detailed analysis of ionization products such as in DI is important to trace the sequential steps in the biochemical process of DNA damage

The Ionization Fraction in the Obscuring ``Torus'' of an Active Galactic Nucleus

Science.gov (United States)

Wilson, A. S.; Roy, A. L.; Ulvestad, J. S.; Colbert, E. J. M.; Weaver, K. A.; Braatz, J. A.; Henkel, C.; Matsuoka, M.; Xue, S.; Iyomoto, N.; Okada, K.

1998-10-01

The LINER galaxy NGC 2639 contains a water vapor megamaser, suggesting the presence of a nuclear accretion disk or torus viewed close to edge-on. This galaxy is thus a good candidate for revealing absorption by the torus of any compact nuclear continuum emission. In this paper, we report VLBA radio maps at three frequencies and an ASCA X-ray spectrum obtained to search for free-free and photoelectric absorptions, respectively. The radio observations reveal a compact (~1.3 × 10-5, which is comparable to the theoretical upper limit derived by Neufeld, Maloney, and Conger for X-ray heated molecular gas. The two values may be reconciled if the molecular gas is very dense: nH2>~109 cm-3. The measured ionization fraction is also consistent with the idea that both absorptions occur in a hot (~6000 K), weakly ionized (ionization fraction a few times 10-2) atomic region that may coexist with the warm molecular gas. If this is the case, the absorbing gas is ~1 pc from the nucleus. We rule out the possibility that both absorptions occur in a fully ionized gas near 104 K. If our line of sight passes through more than one phase, the atomic gas probably dominates the free-free absorption, while the molecular gas may dominate the photoelectric absorption.

A Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) Study on Ornithine Cyclodeaminase (OCD): A Tale of Two Iminiums

Science.gov (United States)

Ion, Bogdan F.; Bushnell, Eric A. C.; De Luna, Phil; Gauld, James W.

2012-01-01

Ornithine cyclodeaminase (OCD) is an NAD+-dependent deaminase that is found in bacterial species such as Pseudomonas putida. Importantly, it catalyzes the direct conversion of the amino acid L-ornithine to L-proline. Using molecular dynamics (MD) and a hybrid quantum mechanics/molecular mechanics (QM/MM) method in the ONIOM formalism, the catalytic mechanism of OCD has been examined. The rate limiting step is calculated to be the initial step in the overall mechanism: hydride transfer from the L-ornithine’s Cα–H group to the NAD+ cofactor with concomitant formation of a Cα=NH2 + Schiff base with a barrier of 90.6 kJ mol−1. Importantly, no water is observed within the active site during the MD simulations suitably positioned to hydrolyze the Cα=NH2 + intermediate to form the corresponding carbonyl. Instead, the reaction proceeds via a non-hydrolytic mechanism involving direct nucleophilic attack of the δ-amine at the Cα-position. This is then followed by cleavage and loss of the α-NH2 group to give the Δ1-pyrroline-2-carboxylate that is subsequently reduced to L-proline. PMID:23202934

A Molecular Dynamics (MD and Quantum Mechanics/Molecular Mechanics (QM/MM Study on Ornithine Cyclodeaminase (OCD: A Tale of Two Iminiums

Directory of Open Access Journals (Sweden)

James W. Gauld

2012-10-01

Full Text Available Ornithine cyclodeaminase (OCD is an NAD+-dependent deaminase that is found in bacterial species such as Pseudomonas putida. Importantly, it catalyzes the direct conversion of the amino acid L-ornithine to L-proline. Using molecular dynamics (MD and a hybrid quantum mechanics/molecular mechanics (QM/MM method in the ONIOM formalism, the catalytic mechanism of OCD has been examined. The rate limiting step is calculated to be the initial step in the overall mechanism: hydride transfer from the L-ornithine’s Cα–H group to the NAD+ cofactor with concomitant formation of a Cα=NH2+ Schiff base with a barrier of 90.6 kJ mol−1. Importantly, no water is observed within the active site during the MD simulations suitably positioned to hydrolyze the Cα=NH2+ intermediate to form the corresponding carbonyl. Instead, the reaction proceeds via a non-hydrolytic mechanism involving direct nucleophilic attack of the δ-amine at the Cα-position. This is then followed by cleavage and loss of the α-NH2 group to give the Δ1-pyrroline-2-carboxylate that is subsequently reduced to L-proline.

Molecular mechanism of Endosulfan action in mammals

Indian Academy of Sciences (India)

Keywords. DNA damage; double-strand break; genomic instability; infertility; MMEJ; NHEJ; pesticides. Abstract. Endosulfan is a broad-spectrum organochlorine pesticide, speculated to be detrimental to human health in areas ofactive exposure. However, the molecular insights to its mechanism of action remain poorly ...

Prediction of Sliding Friction Coefficient Based on a Novel Hybrid Molecular-Mechanical Model.

Science.gov (United States)

Zhang, Xiaogang; Zhang, Yali; Wang, Jianmei; Sheng, Chenxing; Li, Zhixiong

2018-08-01

Sliding friction is a complex phenomenon which arises from the mechanical and molecular interactions of asperities when examined in a microscale. To reveal and further understand the effects of micro scaled mechanical and molecular components of friction coefficient on overall frictional behavior, a hybrid molecular-mechanical model is developed to investigate the effects of main factors, including different loads and surface roughness values, on the sliding friction coefficient in a boundary lubrication condition. Numerical modelling was conducted using a deterministic contact model and based on the molecular-mechanical theory of friction. In the contact model, with given external loads and surface topographies, the pressure distribution, real contact area, and elastic/plastic deformation of each single asperity contact were calculated. Then asperity friction coefficient was predicted by the sum of mechanical and molecular components of friction coefficient. The mechanical component was mainly determined by the contact width and elastic/plastic deformation, and the molecular component was estimated as a function of the contact area and interfacial shear stress. Numerical results were compared with experimental results and a good agreement was obtained. The model was then used to predict friction coefficients in different operating and surface conditions. Numerical results explain why applied load has a minimum effect on the friction coefficients. They also provide insight into the effect of surface roughness on the mechanical and molecular components of friction coefficients. It is revealed that the mechanical component dominates the friction coefficient when the surface roughness is large (Rq > 0.2 μm), while the friction coefficient is mainly determined by the molecular component when the surface is relatively smooth (Rq < 0.2 μm). Furthermore, optimal roughness values for minimizing the friction coefficient are recommended.

State of the Art of Hard and Soft Ionization Mass Spectrometry

International Nuclear Information System (INIS)

Helal, A.I.

2008-01-01

The principles of hard and soft ionization sources, providing some details on the practical aspects of their uses as well as ionization mechanisms are discussed. The conditions and uses of hard ionization methods such as electron impact, thermal ionization and inductively coupled plasma techniques are discussed. Moreover, new generation of soft ionization methods such as matrix-assisted laser desorption/ionization, electro spray ionization and direct analysis in real time are illustrated

Scientific conception on mechanisms of calcium homeostasis disorders under low dose effect of ionizing radiation

International Nuclear Information System (INIS)

Abylaev, Zh.A.; Dospolova, Zh.G.

1997-01-01

Scientific conception of probable consequences of calcium homeostasis disorders in personals, exposed to low dose effect of ionizing radiation has been developed. Principle positions of the conception is that pathologic processes development have different ways of conducting. During predominance of low doses of external gamma-radiation there is leading pathologic mechanism (mechanism 1) of disorder neuroendocrine regulation of both the calcium and the phosphor. In this case sicks have disorders of both the vegetative tonus and the endocrine status. Under internal irradiation (mechanism 2) there is disfunction of organs and systems (bore changes and disorders of hormone status). These changes are considered as consequence of negative action on organism of incorporated long-living radionuclides. Radio-toxic factors action (mechanism 3) provokes the excess of hormones, which acting on bone tissue and could be cause of steroid osteoporosis. Influence of chronic stress factor (mechanism 4) enlarges and burden action on organism of low radiation doses. It is emphasized, that decisive role in development of pathologic processes has mechanism of disturbance of neuroendocrine regulation of calcium exchange

Chemical and mechanical efficiencies of molecular motors and implications for motor mechanisms

International Nuclear Information System (INIS)

Wang Hongyun

2005-01-01

Molecular motors operate in an environment dominated by viscous friction and thermal fluctuations. The chemical reaction in a motor may produce an active force at the reaction site to directly move the motor forward. Alternatively a molecular motor may generate a unidirectional motion by rectifying thermal fluctuations using free energy barriers established in the chemical reaction. The reaction cycle has many occupancy states, each having a different effect on the motor motion. The average effect of the chemical reaction on the motor motion can be characterized by the motor potential profile. The biggest advantage of studying the motor potential profile is that it can be reconstructed from the time series of motor positions measured in single-molecule experiments. In this paper, we use the motor potential profile to express the Stokes efficiency as the product of the chemical efficiency and the mechanical efficiency. We show that both the chemical and mechanical efficiencies are bounded by 100% and, thus, are properly defined efficiencies. We discuss implications of high efficiencies for motor mechanisms: a mechanical efficiency close to 100% implies that the motor potential profile is close to a constant slope; a chemical efficiency close to 100% implies that (i) the chemical transitions are not slower than the mechanical motion and (ii) the equilibrium constant of each chemical transition is close to one

Ionization by a pulsed plasma surface water

International Nuclear Information System (INIS)

Bloyet, E.; Leprince, P.; Marec, J.; Llamas Blasco, M.

1981-01-01

The ionization mechanism is studied of a pulsed surface wave generating a microwave discharge. When the plasma is dominated by collisions, it is found that the velocity of the ionization front depends on the ponderomotive force due to the field gradient in the front. (orig.)

A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules.

Science.gov (United States)

Mendieta-Moreno, Jesús I; Marcos-Alcalde, Iñigo; Trabada, Daniel G; Gómez-Puertas, Paulino; Ortega, José; Mendieta, Jesús

2015-01-01

Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities. Here, we present a detailed explanation of the Fireball method and Fireball/Amber implementation. We also discuss how this tool can be used to analyze reactions in biomolecules using steered molecular dynamics simulations. The potential of this approach is shown by the analysis of a reaction catalyzed by the enzyme triose-phosphate isomerase (TIM). The conformational space and energetic landscape for this reaction are analyzed without a priori assumptions about the protonation states of the different residues during the reaction. The results offer a detailed description of the reaction and reveal some new features of the catalytic mechanism. In particular, we find a new reaction mechanism that is characterized by the intramolecular proton transfer from O1 to O2 and the simultaneous proton transfer from Glu 165 to C2. Copyright © 2015 Elsevier Inc. All rights reserved.

Electron- and photon-impact ionization of furfural

Science.gov (United States)

Jones, D. B.; Ali, E.; Nixon, K. L.; Limão-Vieira, P.; Hubin-Franskin, M.-J.; Delwiche, J.; Ning, C. G.; Colgan, J.; Murray, A. J.; Madison, D. H.; Brunger, M. J.

2015-11-01

The He(i) photoelectron spectrum of furfural has been investigated, with its vibrational structure assigned for the first time. The ground and excited ionized states are assigned through ab initio calculations performed at the outer-valence Green's function level. Triple differential cross sections (TDCSs) for electron-impact ionization of the unresolved combination of the 4a″ + 21a' highest and next-highest occupied molecular orbitals have also been obtained. Experimental TDCSs are recorded in a combination of asymmetric coplanar and doubly symmetric coplanar kinematics. The experimental TDCSs are compared to theoretical calculations, obtained within a molecular 3-body distorted wave framework that employed either an orientation average or proper TDCS average. The proper average calculations suggest that they may resolve some of the discrepancies regarding the angular distributions of the TDCS, when compared to calculations employing the orbital average.

Electron- and photon-impact ionization of furfural

Energy Technology Data Exchange (ETDEWEB)

Jones, D. B. [School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001 (Australia); Ali, E.; Madison, D. H., E-mail: plimaovieira@fct.unl.pt, E-mail: madison@mst.edu, E-mail: michael.brunger@flinders.edu.au [Department of Physics, Missouri University of Science and Technology, Rolla, Missouri 65409 (United States); Nixon, K. L. [Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, MG (Brazil); School of Biology, Chemistry and Forensic Science, University of Wolverhampton, Wolverhampton WV1 1LY (United Kingdom); Limão-Vieira, P., E-mail: plimaovieira@fct.unl.pt, E-mail: madison@mst.edu, E-mail: michael.brunger@flinders.edu.au [Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal); Hubin-Franskin, M.-J.; Delwiche, J. [Départment de Chimie, Université de Liège, Institut de Chimie-Bât. B6C, B-4000 Liège 1 (Belgium); Ning, C. G. [State Key Laboratory of Low-Dimensional Quantum Physics, Department of Physics, Tsinghua University, Beijing 100084 (China); Colgan, J. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Murray, A. J. [Photon Science Institute, School of Physics and Astronomy, University of Manchester, Manchester M13 9PL (United Kingdom); and others

2015-11-14

The He(I) photoelectron spectrum of furfural has been investigated, with its vibrational structure assigned for the first time. The ground and excited ionized states are assigned through ab initio calculations performed at the outer-valence Green’s function level. Triple differential cross sections (TDCSs) for electron-impact ionization of the unresolved combination of the 4a″  +  21a′ highest and next-highest occupied molecular orbitals have also been obtained. Experimental TDCSs are recorded in a combination of asymmetric coplanar and doubly symmetric coplanar kinematics. The experimental TDCSs are compared to theoretical calculations, obtained within a molecular 3-body distorted wave framework that employed either an orientation average or proper TDCS average. The proper average calculations suggest that they may resolve some of the discrepancies regarding the angular distributions of the TDCS, when compared to calculations employing the orbital average.

Electron- and photon-impact ionization of furfural

International Nuclear Information System (INIS)

Jones, D. B.; Ali, E.; Madison, D. H.; Nixon, K. L.; Limão-Vieira, P.; Hubin-Franskin, M.-J.; Delwiche, J.; Ning, C. G.; Colgan, J.; Murray, A. J.

2015-01-01

The He(I) photoelectron spectrum of furfural has been investigated, with its vibrational structure assigned for the first time. The ground and excited ionized states are assigned through ab initio calculations performed at the outer-valence Green’s function level. Triple differential cross sections (TDCSs) for electron-impact ionization of the unresolved combination of the 4a″  +  21a′ highest and next-highest occupied molecular orbitals have also been obtained. Experimental TDCSs are recorded in a combination of asymmetric coplanar and doubly symmetric coplanar kinematics. The experimental TDCSs are compared to theoretical calculations, obtained within a molecular 3-body distorted wave framework that employed either an orientation average or proper TDCS average. The proper average calculations suggest that they may resolve some of the discrepancies regarding the angular distributions of the TDCS, when compared to calculations employing the orbital average

Insight into the Mechanism of Hydrolysis of Meropenem by OXA-23 Serine-β-lactamase Gained by Quantum Mechanics/Molecular Mechanics Calculations.

Science.gov (United States)

Sgrignani, Jacopo; Grazioso, Giovanni; De Amici, Marco

2016-09-13

The fast and constant development of drug resistant bacteria represents a serious medical emergency. To overcome this problem, the development of drugs with new structures and modes of action is urgently needed. In this work, we investigated, at the atomistic level, the mechanisms of hydrolysis of Meropenem by OXA-23, a class D β-lactamase, combining unbiased classical molecular dynamics and umbrella sampling simulations with classical force field-based and quantum mechanics/molecular mechanics potentials. Our calculations provide a detailed structural and dynamic picture of the molecular steps leading to the formation of the Meropenem-OXA-23 covalent adduct, the subsequent hydrolysis, and the final release of the inactive antibiotic. In this mechanistic framework, the predicted activation energy is in good agreement with experimental kinetic measurements, validating the expected reaction path.

Molecular mechanisms of canalization: Hsp90 and beyond

Indian Academy of Sciences (India)

Madhu Sudhan

2007-03-26

Mar 26, 2007 ... clients are essential nodes in signal transduction pathways and regulatory circuits, accounting for the .... respective contributions of genetics versus epigenetics ... authors succeeded in elucidating the molecular mechanism.

Symposium on molecular and cellular mechanisms of mutagenesis

International Nuclear Information System (INIS)

1981-01-01

These proceedings contain abstracts only of the 21 papers presented at the Sympsoium. The papers dealt with molecular mechanisms of mutagenesis and cellular responses to chemical and physical mutagenic agents

Mapping the dissociative ionization dynamics of molecular nitrogen with attosecond resolution

International Nuclear Information System (INIS)

Klinker, M; González-Vázquez, J; Martin, F; Trabattoni, A; Sansone, G; Nisoli, M; Liu, C; Linguerri, R; Hochlaf, M; Klei, J; Vrakking, M J J; Calegari, F

2015-01-01

We wish to understand the processes underlying the ionization dynamics of N 2 as experimentally induced and studied by recording the kinetic energy release (KER) in a XUV-pump/IR-probe setup. To this end a theoretical model was developed describing the ionization process using Dyson Orbitals and, subsequently, the dissociation process using a large set of diabatic potential energy surfaces (PES) on which to propagate. From said set of PES, a small subset is extracted allowing for the identification of one and two photon processes chiefly responsible for the experimentally observed features. (paper)

Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations.

Science.gov (United States)

Monari, Antonio; Rivail, Jean-Louis; Assfeld, Xavier

2013-02-19

Molecular mechanics methods can efficiently compute the macroscopic properties of a large molecular system but cannot represent the electronic changes that occur during a chemical reaction or an electronic transition. Quantum mechanical methods can accurately simulate these processes, but they require considerably greater computational resources. Because electronic changes typically occur in a limited part of the system, such as the solute in a molecular solution or the substrate within the active site of enzymatic reactions, researchers can limit the quantum computation to this part of the system. Researchers take into account the influence of the surroundings by embedding this quantum computation into a calculation of the whole system described at the molecular mechanical level, a strategy known as the mixed quantum mechanics/molecular mechanics (QM/MM) approach. The accuracy of this embedding varies according to the types of interactions included, whether they are purely mechanical or classically electrostatic. This embedding can also introduce the induced polarization of the surroundings. The difficulty in QM/MM calculations comes from the splitting of the system into two parts, which requires severing the chemical bonds that link the quantum mechanical subsystem to the classical subsystem. Typically, researchers replace the quantoclassical atoms, those at the boundary between the subsystems, with a monovalent link atom. For example, researchers might add a hydrogen atom when a C-C bond is cut. This Account describes another approach, the Local Self Consistent Field (LSCF), which was developed in our laboratory. LSCF links the quantum mechanical portion of the molecule to the classical portion using a strictly localized bond orbital extracted from a small model molecule for each bond. In this scenario, the quantoclassical atom has an apparent nuclear charge of +1. To achieve correct bond lengths and force constants, we must take into account the inner shell of

Molecular mechanisms for protein-encoded inheritance

Science.gov (United States)

Wiltzius, Jed J. W.; Landau, Meytal; Nelson, Rebecca; Sawaya, Michael R.; Apostol, Marcin I.; Goldschmidt, Lukasz; Soriaga, Angela B.; Cascio, Duilio; Rajashankar, Kanagalaghatta; Eisenberg, David

2013-01-01

Strains are phenotypic variants, encoded by nucleic acid sequences in chromosomal inheritance and by protein “conformations” in prion inheritance and transmission. But how is a protein “conformation” stable enough to endure transmission between cells or organisms? Here new polymorphic crystal structures of segments of prion and other amyloid proteins offer structural mechanisms for prion strains. In packing polymorphism, prion strains are encoded by alternative packings (polymorphs) of β-sheets formed by the same segment of a protein; in a second mechanism, segmental polymorphism, prion strains are encoded by distinct β-sheets built from different segments of a protein. Both forms of polymorphism can produce enduring “conformations,” capable of encoding strains. These molecular mechanisms for transfer of information into prion strains share features with the familiar mechanism for transfer of information by nucleic acid inheritance, including sequence specificity and recognition by non-covalent bonds. PMID:19684598

Molecular events in the induction of murine tumors by ionizing radiation

International Nuclear Information System (INIS)

Andrews, K.L.

1993-01-01

A new method is presented to identify and clone novel transforming genes from radiation-induced tumors. It involves the creation of a cDNA expression library from radiation-induced tumors. The library is transfected into non-transformed cells, and the nude mouse tumorigenicity assay functionally defines the acquisition of a transformed phenotype. cDNA clones responsible for transformation are rescued by PCR amplification. This method is applicable to a variety of mammalian systems. The only requirement is a functional assay with which to measure the acquisition of an altered phenotype following transfection of a cDNA library. This method has identified a cDNA for the 16 kD subunit of v-H + -ATPase, which has been associated with cellular transformation. Two protocols were used to generate radiation-induced tumors. One experiment utilizing fractionated doses of ionizing radiation had a much greater tumor yield than the second protocol using a single dose of 11.25 Gy. To determine if the mechanism of gene activation is different in radiation- and chemically-induced tumors, the expression pattern of five tumor-associated genes was analyzed. The expression patterns of mals 1-4 were not significantly different. However, transin, a secreted protease, was overexpressed in radiation-induced papillomas and undetectable in chemically-induced papillomas. Transin degrades basement membrane proteins and may be involved in the progression of benign, encapsulated tumors to malignant, invasive squamous cell carcinomas. Isolation and characterization of genes with dominant transforming activity from radiation-induced tumors will provide information to bridge the gap between the initial ionizing radiation event and the subsequent development of malignant tumors. The function of these genes may also provide information about the development of human malignancies. An understanding the natural biology of cells will help elucidate the pathogenesis cancer and other diseases

Symposium on molecular and cellular mechanisms of mutagenesis

Energy Technology Data Exchange (ETDEWEB)

1981-01-01

These proceedings contain abstracts only of the 21 papers presented at the Sympsoium. The papers dealt with molecular mechanisms of mutagenesis and cellular responses to chemical and physical mutagenic agents. (ERB)

Ionizing radiation accidents. Data interpretation

International Nuclear Information System (INIS)

Cascon, Adriana S.

2003-01-01

After a general outlook of the biological effects at the cellular and molecular level, the somatic effects of the ionizing radiation are described. Argentine regulations and the ICRP recommendations on radiological protection of professionally exposed workers are also summarized. The paper includes practical advices for the physician that has to take care of an irradiated patient

Multiscale simulations in face-centered cubic metals: A method coupling quantum mechanics and molecular mechanics

International Nuclear Information System (INIS)

Yu Xiao-Xiang; Wang Chong-Yu

2013-01-01

An effective multiscale simulation which concurrently couples the quantum-mechanical and molecular-mechanical calculations based on the position continuity of atoms is presented. By an iterative procedure, the structure of the dislocation core in face-centered cubic metal is obtained by first-principles calculation and the long-range stress is released by molecular dynamics relaxation. Compared to earlier multiscale methods, the present work couples the long-range strain to the local displacements of the dislocation core in a simpler way with the same accuracy. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

Document authentication at molecular levels using desorption atmospheric pressure chemical ionization mass spectrometry imaging.

Science.gov (United States)

Li, Ming; Jia, Bin; Ding, Liying; Hong, Feng; Ouyang, Yongzhong; Chen, Rui; Zhou, Shumin; Chen, Huanwen; Fang, Xiang

2013-09-01

Molecular images of documents were obtained by sequentially scanning the surface of the document using desorption atmospheric pressure chemical ionization mass spectrometry (DAPCI-MS), which was operated in either a gasless, solvent-free or methanol vapor-assisted mode. The decay process of the ink used for handwriting was monitored by following the signal intensities recorded by DAPCI-MS. Handwritings made using four types of inks on four kinds of paper surfaces were tested. By studying the dynamic decay of the inks, DAPCI-MS imaging differentiated a 10-min old from two 4 h old samples. Non-destructive forensic analysis of forged signatures either handwritten or computer-assisted was achieved according to the difference of the contour in DAPCI images, which was attributed to the strength personalized by different writers. Distinction of the order of writing/stamping on documents and detection of illegal printings were accomplished with a spatial resolution of about 140 µm. A Matlab® written program was developed to facilitate the visualization of the similarity between signature images obtained by DAPCI-MS. The experimental results show that DAPCI-MS imaging provides rich information at the molecular level and thus can be used for the reliable document analysis in forensic applications. © 2013 The Authors. Journal of Mass Spectrometry published by John Wiley & Sons, Ltd.

DMPD: Molecular mechanisms of the anti-inflammatory functions of interferons. [Dynamic Macrophage Pathway CSML Database

Lifescience Database Archive (English)

Full Text Available 18086388 Molecular mechanisms of the anti-inflammatory functions of interferons. Ko....csml) Show Molecular mechanisms of the anti-inflammatory functions of interferons. PubmedID 18086388 Title ...Molecular mechanisms of the anti-inflammatory functions of interferons. Authors K

Comparison of Atmospheric Pressure Chemical Ionization and Field Ionization Mass Spectrometry for the Analysis of Large Saturated Hydrocarbons.

Science.gov (United States)

Jin, Chunfen; Viidanoja, Jyrki; Li, Mingzhe; Zhang, Yuyang; Ikonen, Elias; Root, Andrew; Romanczyk, Mark; Manheim, Jeremy; Dziekonski, Eric; Kenttämaa, Hilkka I

2016-11-01

Direct infusion atmospheric pressure chemical ionization mass spectrometry (APCI-MS) was compared to field ionization mass spectrometry (FI-MS) for the determination of hydrocarbon class distributions in lubricant base oils. When positive ion mode APCI with oxygen as the ion source gas was employed to ionize saturated hydrocarbon model compounds (M) in hexane, only stable [M - H] + ions were produced. Ion-molecule reaction studies performed in a linear quadrupole ion trap suggested that fragment ions of ionized hexane can ionize saturated hydrocarbons via hydride abstraction with minimal fragmentation. Hence, APCI-MS shows potential as an alternative of FI-MS in lubricant base oil analysis. Indeed, the APCI-MS method gave similar average molecular weights and hydrocarbon class distributions as FI-MS for three lubricant base oils. However, the reproducibility of APCI-MS method was found to be substantially better than for FI-MS. The paraffinic content determined using the APCI-MS and FI-MS methods for the base oils was similar. The average number of carbons in paraffinic chains followed the same increasing trend from low viscosity to high viscosity base oils for the two methods.

Molecular Electrical Doping of Organic Semiconductors: Fundamental Mechanisms and Emerging Dopant Design Rules.

Science.gov (United States)

Salzmann, Ingo; Heimel, Georg; Oehzelt, Martin; Winkler, Stefanie; Koch, Norbert

2016-03-15

Today's information society depends on our ability to controllably dope inorganic semiconductors, such as silicon, thereby tuning their electrical properties to application-specific demands. For optoelectronic devices, organic semiconductors, that is, conjugated polymers and molecules, have emerged as superior alternative owing to the ease of tuning their optical gap through chemical variability and their potential for low-cost, large-area processing on flexible substrates. There, the potential of molecular electrical doping for improving the performance of, for example, organic light-emitting devices or organic solar cells has only recently been established. The doping efficiency, however, remains conspicuously low, highlighting the fact that the underlying mechanisms of molecular doping in organic semiconductors are only little understood compared with their inorganic counterparts. Here, we review the broad range of phenomena observed upon molecularly doping organic semiconductors and identify two distinctly different scenarios: the pairwise formation of both organic semiconductor and dopant ions on one hand and the emergence of ground state charge transfer complexes between organic semiconductor and dopant through supramolecular hybridization of their respective frontier molecular orbitals on the other hand. Evidence for the occurrence of these two scenarios is subsequently discussed on the basis of the characteristic and strikingly different signatures of the individual species involved in the respective doping processes in a variety of spectroscopic techniques. The critical importance of a statistical view of doping, rather than a bimolecular picture, is then highlighted by employing numerical simulations, which reveal one of the main differences between inorganic and organic semiconductors to be their respective density of electronic states and the doping induced changes thereof. Engineering the density of states of doped organic semiconductors, the Fermi

Molecular mechanisms in radiation damage to DNA: Final report

International Nuclear Information System (INIS)

Osman, R.

1996-01-01

The objectives of this work were to elucidate the molecular mechanisms that were responsible for radiation-induced DNA damage. The studies were based on theoretical explorations of possible mechanisms that link initial radiation damage in the form of base and sugar damage to conformational changes in DNA

Heating of the solar chromosphere by ionization pumping

Science.gov (United States)

Lindsey, C. A.

1981-01-01

A new theory is proposed to explain the heating of the solar chromosphere, and possibly the corona, by the dissipation of hydrodynamic compression waves. The basis of the dissipative mechanism, here referred to as ionization pumping, is hysteresis caused by irreversible relaxation of the chromospheric medium to ionization equilibrium following pressure perturbations. In the middle chromosphere, where hydrogen is partially ionized, it is shown that ionization pumping will cause strong dissipation of waves whose periods are 200s or less. This could cause heating of the chromosphere sufficient to compensate for the radiative losses. The mechanism retains a high efficiency for waves of arbitrarily small amplitude and, thus, can be more efficient than shock dissipation for small perturbations in pressure. The formation of shocks therefore is not required for the dissipation of waves whose periods are several minutes or less.

Heating of the solar chromosphere by ionization pumping

International Nuclear Information System (INIS)

Lindsey, C.A.

1981-01-01

A new theory is proposed to explain the heating of the solar chromosphere, and possibly the corona, by the dissipation of hydrodynamic compression waves. The basis of the disspative mechanism, here referred to as ''ionization pumping,'' is hysteresis caused by irresversible relaxation of the chromospheric medium to ionization equilibrium following pressure perturbations. In the middle chromosphere, where hydrogen is partially ionized, it is shown that ionization pumping will cause strong dissipation of waves whose periods are approx.200 s or less. This could cause heating of the chromosphere sufficient to compensate for the radiative losses. The mechanism retains a high efficiency for waves of arbitrarily small amplitude and, thus, can be more efficient than shock dissipation for small perturbations in pressure. The formation of shocks therefore is not required for the dissipation of waves whose periods are several minutes or less

Submillisecond Elastic Recoil Reveals Molecular Origins of Fibrin Fiber Mechanics

Science.gov (United States)

Hudson, Nathan E.; Ding, Feng; Bucay, Igal; O’Brien, E. Timothy; Gorkun, Oleg V.; Superfine, Richard; Lord, Susan T.; Dokholyan, Nikolay V.; Falvo, Michael R.

2013-01-01

Fibrin fibers form the structural scaffold of blood clots. Thus, their mechanical properties are of central importance to understanding hemostasis and thrombotic disease. Recent studies have revealed that fibrin fibers are elastomeric despite their high degree of molecular ordering. These results have inspired a variety of molecular models for fibrin’s elasticity, ranging from reversible protein unfolding to rubber-like elasticity. An important property that has not been explored is the timescale of elastic recoil, a parameter that is critical for fibrin’s mechanical function and places a temporal constraint on molecular models of fiber elasticity. Using high-frame-rate imaging and atomic force microscopy-based nanomanipulation, we measured the recoil dynamics of individual fibrin fibers and found that the recoil was orders of magnitude faster than anticipated from models involving protein refolding. We also performed steered discrete molecular-dynamics simulations to investigate the molecular origins of the observed recoil. Our results point to the unstructured αC regions of the otherwise structured fibrin molecule as being responsible for the elastic recoil of the fibers. PMID:23790375

Ionizing radiation-induced metabolic oxidative stress and prolonged cell injury

Science.gov (United States)

Azzam, Edouard I.; Jay-Gerin, Jean-Paul; Pain, Debkumar

2013-01-01

Cellular exposure to ionizing radiation leads to oxidizing events that alter atomic structure through direct interactions of radiation with target macromolecules or via products of water radiolysis. Further, the oxidative damage may spread from the targeted to neighboring, non-targeted bystander cells through redox-modulated intercellular communication mechanisms. To cope with the induced stress and the changes in the redox environment, organisms elicit transient responses at the molecular, cellular and tissue levels to counteract toxic effects of radiation. Metabolic pathways are induced during and shortly after the exposure. Depending on radiation dose, dose-rate and quality, these protective mechanisms may or may not be sufficient to cope with the stress. When the harmful effects exceed those of homeostatic biochemical processes, induced biological changes persist and may be propagated to progeny cells. Physiological levels of reactive oxygen and nitrogen species play critical roles in many cellular functions. In irradiated cells, levels of these reactive species may be increased due to perturbations in oxidative metabolism and chronic inflammatory responses, thereby contributing to the long-term effects of exposure to ionizing radiation on genomic stability. Here, in addition to immediate biological effects of water radiolysis on DNA damage, we also discuss the role of mitochondria in the delayed outcomes of ionization radiation. Defects in mitochondrial functions lead to accelerated aging and numerous pathological conditions. Different types of radiation vary in their linear energy transfer (LET) properties, and we discuss their effects on various aspects of mitochondrial physiology. These include short and long-term in vitro and in vivo effects on mitochondrial DNA, mitochondrial protein import and metabolic and antioxidant enzymes. PMID:22182453

DFT Study on Molecular Structures and ROS Scavenging Mechanisms of Novel Antioxidants from Lespedeza Virgata

Science.gov (United States)

Li, Min-jie; Zhang, Liang-miao; Liu, Wei-xia; Lu, Wen-cong

2011-04-01

The molecular structure and radical scavenging activity of three novel antioxidants from Lespedeza Virgata, lespedezavirgatol, lespedezavirgatal, and lespedezacoumestan, have been studied using density functional theory with the B3LYP and BhandHLYP methods. The optimized geometries of neutral, radical cation, radical and anion forms were obtained at the B3LYP/6-31G(d) level, in which it was found that all the most stable conformations contain intramolecular hydrogen bonds. The same results were obtained from the MP2 method. The homolytic O—H bond dissociation enthalpy and the adiabatic ionization potential of neutral and anion forms for the three new antioxidants and adiabatic electron affinity and H-atom affinity for hydroxyl radical, superoxide anion radical, and hydrogen peroxide radical were determined both in gas phase and in aqueous solution using IEF-PCM and CPCM model with UAHF or Bondi cavity. The antioxidant activities and reactive oxygen species scavenging mechanisms were then discussed, and the results obtained from different methods are consistent. Furthermore, the antioxidant activities are consistent with the experimental findings of the compounds under investigation.

Excitation and ionization of ethylene by charged projectiles

International Nuclear Information System (INIS)

Wang Zhiping; Wang Jing; Zhang Fengshou

2010-01-01

Using the time dependent local density approximation, applied to valence electrons, coupled non-adiabatically to molecular dynamics of ions, the collision process between ethylene and fast charged projectiles is studied in the microscopic way. The impact of ionic motion on the ionization is explored to show the importance of treating electronic and ionic degrees of freedom simultaneously. The number of escaped electrons, ionization probabilities are obtained. Furthermore, it is found that the ionic extensions in different directions show the different patterns. (authors)

Molecular mechanisms of cisplatin resistance in cervical cancer

Directory of Open Access Journals (Sweden)

Zhu H

2016-06-01

Full Text Available Haiyan Zhu, Hui Luo, Wenwen Zhang, Zhaojun Shen, Xiaoli Hu, Xueqiong Zhu Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China Abstract: Patients with advanced or recurrent cervical cancer have poor prognosis, and their 1-year survival is only 10%–20%. Chemotherapy is considered as the standard treatment for patients with advanced or recurrent cervical cancer, and cisplatin appears to treat the disease effectively. However, resistance to cisplatin may develop, thus substantially compromising the efficacy of cisplatin to treat advanced or recurrent cervical cancer. In this article, we systematically review the recent literature and summarize the recent advances in our understanding of the molecular mechanisms underlying cisplatin resistance in cervical cancer. Keywords: cisplatin, epithelial–mesenchymal transition, microRNA, molecular mechanism, resistance

Multiphoton ionization as a probe of molecular photofragmentation: statistical and dynamical energy partitioning in the multiphoton dissociation of nitromethane

International Nuclear Information System (INIS)

Rockney, B.H.

1982-01-01

Multiphoton ionization (MPI) appears in its first use as a probe of laser-induced photofragmentation. Specifically, MPI here reveals the internal and translational energy content of the nascent fragments from the infrared multiphoton dissociation (MPD) of nitromethane (CH 3 NO 2 ). The apparatus for this work consists of a pulsed supersonic molecular beam crossed by two pulsed and focused lasers - a CO 2 laser to induce collision-free unimolecular dissociation of CH 3 NO 2 , and a tunable dye laser following immediately to ionize selectively one of the pair of dissociation fragments for detection by a mass spectrometer and particle multiplier. A computer simulation of each fragment's MPI spectrum, a series of four photon resonances to members of the npsigma/sub u/ Rydberg state of NO 2 and three photon resonances to two vibrational members of the #betta# 1 Rydberg state of CH 3 , aids in determining the fragment's internal energy content. The dye laser is delayed and its focus is traced through a small quarter circle centered at the focus of the CO 2 laser. The flight times of the fragments from the point of dissociation and their laboratory scattering angular distributions at fixed ionizing laser wavelength provide their center of mass recoil velocity distributions. The energy deposited in the fragments evidences a striking mixture of statistical and dynamical energy partitioning. The statistical RRKM theory of unimolecular decomposition accurately predicts the amount of internal energy found in the fragments

Combined quantum and molecular mechanics (QM/MM).

Science.gov (United States)

Friesner, Richard A

2004-12-01

We describe the current state of the art of mixed quantum mechanics/molecular mechanics (QM/MM) methodology, with a particular focus on modeling of enzymatic reactions. Over the past decade, the effectiveness of these methods has increased dramatically, based on improved quantum chemical methods, advances in the description of the QM/MM interface, and reductions in the cost/performance of computing hardware. Two examples of pharmaceutically relevant applications, cytochrome P450 and class C β-lactamase, are presented.: © 2004 Elsevier Ltd . All rights reserved.

Electron-impact ionization of oriented molecules using the time-dependent close-coupling approach

Energy Technology Data Exchange (ETDEWEB)

Colgan, J [Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Pindzola, M S, E-mail: jcolgan@lanl.gov [Department of Physics, Auburn University, Auburn, AL 36849 (United States)

2011-04-01

An overview is given on recent progress on computing triple differential cross sections for electron-impact ionization of the hydrogen molecule using a time-dependent close-coupling approach. Our calculations, when averaged over all molecular orientations, are generally in very good agreement with (e,2e) measurements made on H{sub 2}, where the molecular orientation is unknown, for a range of incident energies and outgoing electron angles and energies. In this paper, we present TDCS for ionization of H{sub 2} at specific molecular orientations. It is hoped that this study will help stimulate future measurements of TDCS from oriented H{sub 2} at medium impact energies.

Optimization and benchmarking of a perturbative Metropolis Monte Carlo quantum mechanics/molecular mechanics program.

Science.gov (United States)

Feldt, Jonas; Miranda, Sebastião; Pratas, Frederico; Roma, Nuno; Tomás, Pedro; Mata, Ricardo A

2017-12-28

In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.

INTERSTELLAR METASTABLE HELIUM ABSORPTION AS A PROBE OF THE COSMIC-RAY IONIZATION RATE

International Nuclear Information System (INIS)

Indriolo, Nick; McCall, Benjamin J.; Hobbs, L. M.; Hinkle, K. H.

2009-01-01

The ionization rate of interstellar material by cosmic rays has been a major source of controversy, with different estimates varying by three orders of magnitude. Observational constraints of this rate have all depended on analyzing the chemistry of various molecules that are produced following cosmic-ray ionization, and in many cases these analyses contain significant uncertainties. Even in the simplest case (H + 3 ), the derived ionization rate depends on an (uncertain) estimate of the absorption path length. In this paper, we examine the feasibility of inferring the cosmic-ray ionization rate using the 10830 A absorption line of metastable helium. Observations through the diffuse clouds toward HD 183143 are presented, but yield only an upper limit on the metastable helium column density. A thorough investigation of He + chemistry reveals that only a small fraction of He + will recombine into the triplet state and populate the metastable level. In addition, excitation to the triplet manifold of helium by secondary electrons must be accounted for as it is the dominant mechanism which produces He* in some environments. Incorporating these various formation and destruction pathways, we derive new equations for the steady state abundance of metastable helium. Using these equations in concert with our observations, we find ζ He -15 s -1 , an upper limit about 5 times larger than the ionization rate previously inferred for this sight line using H + 3 . While observations of interstellar He* are extremely difficult at present, and the background chemistry is not nearly as simple as previously thought, potential future observations of metastable helium would provide an independent check on the cosmic-ray ionization rate derived from H + 3 in diffuse molecular clouds, and, perhaps more importantly, allow the first direct measurements of the ionization rate in diffuse atomic clouds.

Ionization of H2O molecules through second order collisions in an argon-filled flow ionization chamber

International Nuclear Information System (INIS)

Leonhardt, J.

1976-01-01

In an argon-filled ionization chamber with a constant radionuclide radiation source, the ionization of H 2 O through second order collisions with 3sub(p) 2 states of argon excited by field-accelerated electrons is considered within the range of discharge caused by external potentials under atmospheric pressure. It is found that the logarithm of the change of ionization current is proportional to power 3/2 of the electric field strength. Possible formation mechanisms are discussed. Most probable is the ionization of H 2 O through collision with Ar 2 argon dimers originating from excited metastable atoms as a result of triple collision. The production cross section for H 2 O + has been estimated to be sigmasub(H 2 O) approximately 5x10 -15 . (author)

Sperm quality and DNA damage in men from Jilin Province, China, who are occupationally exposed to ionizing radiation.

Science.gov (United States)

Zhou, D D; Hao, J L; Guo, K M; Lu, C W; Liu, X D

2016-03-22

Long-term radiation exposure affects human health. Ionizing radiation has long been known to raise the risk of cancer. In addition to high doses of radiation, low-dose ionizing radiation might increase the risk of cardiovascular disease, lens opacity, and some other non-cancerous diseases. Low- and high-dose exposures to ionizing radiation elicit different signaling events at the molecular level, and may involve different response mechanisms. The health risks arising from exposure to low doses of ionizing radiation should be re-evaluated. Health workers exposed to ionizing radiation experience low-dose radiation and have an increased risk of hematological malignancies. Reproductive function is sensitive to changes in the physical environment, including ionizing radiation. However, data is scarce regarding the association between occupational radiation exposure and risk to human fertility. Sperm DNA integrity is a functional parameter of male fertility evaluation. Hence, we aimed to report sperm quality and DNA damage in men from Jilin Province, China, who were occupationally exposed to ionizing radiation. Sperm motility and normal morphology were significantly lower in the exposed compared with the non-exposed men. There was no statistically significant difference in sperm concentration between exposed and non-exposed men. The sperm DNA fragmentation index was significantly higher in the exposed than the non-exposed men. Chronic long-term exposure to low doses of ionizing radiation could affect sperm motility, normal morphology, and the sperm DNA fragmentation index in the Chinese population. Sperm quality and DNA integrity are functional parameters that could be used to evaluate occupational exposure to ionizing radiation.

Multiphoton ionization of H2+ in xuv laser pulses

International Nuclear Information System (INIS)

Guan Xiaoxu; Secor, Ethan B.; Bartschat, Klaus; Schneider, Barry I.

2011-01-01

We consider the ionization of the hydrogen molecular ion after one-, two-, and three-photon absorption over a large range of photon energies between 9 and 40 eV in the fixed-nuclei approximation. The temporal development of the system is obtained in a fully ab initio time-dependent grid-based approach in prolate spheroidal coordinates. The alignment dependence of the one-photon ionization amplitude is highlighted in the framework of time-dependent perturbation theory. For one-photon ionization as a function of the nuclear separation, the calculations reveal a significant minimum in the ionization probability. The suppressed ionization is attributed to a Cooper-type minimum, which is similar, but not identical, to the cancellation effect observed in photoionization cross sections of some noble-gas atoms. The effect of the nonspherical two-center Coulomb potential is analyzed. For two- and three-photon ionization, the angle-integrated cross sections clearly map out intermediate-state resonances, and the predictions of the current computations agree very well with those from time-independent calculations. The dominant emission modes for two-photon ionization are found to be very similar in both resonance and off-resonance regions.

Molecular mechanism of Danshensu on platelet antiaggregation

Science.gov (United States)

Yu, Chen; Geng, Feng; Fan, Hua-Ying; Luan, Hai-Yun; Liu, Yue; Ji, Kai; Fu, Feng-Hua

2018-04-01

In this study, we detected the effect of Danshensu on PARs-PLCβsignaling pathway to elucidate molecular mechanism of Danshensu on platelet anti-aggregation. Our results demonstrate that Danshensu is able to decrease the levels of IP3, Ca2+ and AA secretion, which indicate that Danshensu may involve in PARs-PLCβ signaling pathways. Molecular docking study shows that Danshesu has similar polar interactions with PAR1 receptors as BMS200261 at the same position. The findings from our study enable a better understanding of Danshensu biological properties, which could ultimately lead to the development of multi-target antiplatelet natural medicine for the treatment and/or prevention of some thrombotic diseases.

Evaluation of carbohydrate molecular mechanical force fields by quantum mechanical calculations

DEFF Research Database (Denmark)

Hemmingsen, Lars Bo Stegeager; Madsen, D.E.; Esbensen, A.L.

2004-01-01

of the (gg, gt and tg) rotamers of methyl alpha-D-glucopyranoside and methyl alpha-D-galactopyranoside are (0.13, 0.00, 0.15) and (0.64, 0.00, 0.77) kcal/mol. respectively. The results of the quantum mechanical calculations are compared with the results of calculations using the 20 second...... for monosaccharide carbohydrate benchmark systems. Selected results are: (i) The interaction energy of the alpha-D-alucopyranose-H2O heterodimer is estimated to be 4.9 kcal/mol, using a composite method including terms at highly correlated (CCSD(T)) level. Most molecular mechanics force fields are in error...

A Model of How Different Biology Experts Explain Molecular and Cellular Mechanisms

Science.gov (United States)

Trujillo, Caleb M.; Anderson, Trevor R.; Pelaez, Nancy J.

2015-01-01

Constructing explanations is an essential skill for all science learners. The goal of this project was to model the key components of expert explanation of molecular and cellular mechanisms. As such, we asked: What is an appropriate model of the components of explanation used by biology experts to explain molecular and cellular mechanisms? Do…

[Molecular Biology on the Mechanisms of Autism Spectrum Disorder for Clinical Psychiatrists].

Science.gov (United States)

Makinodan, Manabu

2015-01-01

While, in general, a certain number of clinical psychiatrists might not be familiar with molecular biology, the mechanisms of mental illnesses have been uncovered by molecular biology for decades. Among mental illnesses, even biological psychiatrists and neuroscientists have paid less attention to the biological treatment of autism spectrum disorder (ASD) than Alzheimer's disease and schizophrenia since ASD has been regarded as a developmental disorder that was seemingly untreatable. However, multifaceted methods of molecular biology have revealed the mechanisms that would lead to the medication of ASD. In this article, how molecular biology dissects the pathobiology of ASD is described in order to announce the possibilities of biological treatment for clinical psychiatrists.

Electronic structure and spectroscopy of nucleic acid bases: Ionization energies, ionization-induced structural changes, and photoelectron spectra

Energy Technology Data Exchange (ETDEWEB)

Bravaya, Ksenia B.; Kostko, Oleg; Dolgikh, Stanislav; Landau, Arie; Ahmed, Musahid; Krylov, Anna I.

2010-08-02

We report high-level ab initio calculations and single-photon ionization mass spectrometry study of ionization of adenine (A), thymine (T), cytosine (C) and guanine (G). For thymine and adenine, only the lowest-energy tautomers were considered, whereas for cytosine and guanine we characterized five lowest-energy tautomeric forms. The first adiabatic and several vertical ionization energies were computed using equation-of-motion coupled-cluster method for ionization potentials with single and double substitutions. Equilibrium structures of the cationic ground states were characterized by DFT with the {omega}B97X-D functional. The ionization-induced geometry changes of the bases are consistent with the shapes of the corresponding molecular orbitals. For the lowest-energy tautomers, the magnitude of the structural relaxation decreases in the following series G > C > A > T, the respective relaxation energies being 0.41, 0.32, 0.25 and 0.20 eV. The computed adiabatic ionization energies (8.13, 8.89, 8.51-8.67 and 7.75-7.87 eV for A,T,C and G, respectively) agree well with the onsets of the photoionization efficiency (PIE) curves (8.20 {+-} 0.05, 8.95 {+-} 0.05, 8.60 {+-} 0.05 and 7.75 {+-} 0.05 eV). Vibrational progressions for the S{sub 0}-D{sub 0} vibronic bands computed within double-harmonic approximation with Duschinsky rotations are compared with previously reported experimental photoelectron spectra.

First-principles investigations on ionization and thermal conductivity of polystyrene for inertial confinement fusion applications

Energy Technology Data Exchange (ETDEWEB)

Hu, S. X., E-mail: shu@lle.rochester.edu; Goncharov, V. N.; McCrory, R. L.; Skupsky, S. [Laboratory for Laser Energetics, University of Rochester, 250 East River Road, Rochester, New York 14623 (United States); Collins, L. A.; Kress, J. D. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

2016-04-15

Using quantum molecular-dynamics (QMD) methods based on the density functional theory, we have performed first-principles investigations of the ionization and thermal conductivity of polystyrene (CH) over a wide range of plasma conditions (ρ = 0.5 to 100 g/cm{sup 3} and T = 15 625 to 500 000 K). The ionization data from orbital-free molecular-dynamics calculations have been fitted with a “Saha-type” model as a function of the CH plasma density and temperature, which gives an increasing ionization as the CH density increases even at low temperatures (T < 50 eV). The orbital-free molecular dynamics method is only used to gauge the average ionization behavior of CH under the average-atom model in conjunction with the pressure-matching mixing rule. The thermal conductivities (κ{sub QMD}) of CH, derived directly from the Kohn–Sham molecular-dynamics calculations, are then analytically fitted with a generalized Coulomb logarithm [(lnΛ){sub QMD}] over a wide range of plasma conditions. When compared with the traditional ionization and thermal conductivity models used in radiation–hydrodynamics codes for inertial confinement fusion simulations, the QMD results show a large difference in the low-temperature regime in which strong coupling and electron degeneracy play an essential role in determining plasma properties. Hydrodynamic simulations of cryogenic deuterium–tritium targets with CH ablators on OMEGA and the National Ignition Facility using the QMD-derived ionization and thermal conductivity of CH have predicted ∼20% variation in target performance in terms of hot-spot pressure and neutron yield (gain) with respect to traditional model simulations.

Photoionization studies with molecular beams

Energy Technology Data Exchange (ETDEWEB)

Ng, C.Y.

1976-09-01

A molecular beam photoionization apparatus which combines the advantages of both the molecular beam method with photoionization mass spectrometry has been designed and constructed for carrying out some unique photoionization experiments. Rotational cooling during the supersonic expansion has resulted in high resolution photoionization efficiency curves for NO, ICl, C/sub 2/H/sub 2/ and CH/sub 3/I. The analysis of these spectra has yielded ionization potentials for these molecules to an accuracy of +- 3 MeV. Detailed autoionization structures were also resolved. This allows the investigation of the selection rules for autoionization, and the identification of the Rydberg series which converge to the excited states of the molecular ions. The degree of relaxation for thermally populated excited states has been examined using NO and ICl as examples. As a result of adiabatic cooling, a small percentage of dimers is also formed during the expansion. The photoionization efficiency curves for (NO)/sub 2/, ArICl, Ar/sub 2/, Kr/sub 2/ and Xe/sub 2/ have been obtained near the thresholds. Using the known dissociation energies of the (NO)/sub 2/, Ar/sub 2/, Kr/sub 2/ and Xe/sub 2/ van der Waals molecules, the corresponding dissociation energies for NO-NO/sup +/, Ar/sub 2//sup +/, Kr/sub 2//sup +/, and Xe/sub 2//sup +/ have been determined. The ionization mechanisms for this class of molecules are examined and discussed.

An investigation on the mechanism of sublimed DHB matrix on molecular ion yields in SIMS imaging of brain tissue.

Science.gov (United States)

Dowlatshahi Pour, Masoumeh; Malmberg, Per; Ewing, Andrew

2016-05-01

We have characterized the use of sublimation to deposit matrix-assisted laser desorption/ionization (MALDI) matrices in secondary ion mass spectrometry (SIMS) analysis, i.e. matrix-enhanced SIMS (ME-SIMS), a common surface modification method to enhance sensitivity for larger molecules and to increase the production of intact molecular ions. We use sublimation to apply a thin layer of a conventional MALDI matrix, 2,5-dihydroxybenzoic acid (DHB), onto rat brain cerebellum tissue to show how this technique can be used to enhance molecular yields in SIMS while still retaining a lateral resolution around 2 μm and also to investigate the mechanism of this enhancement. The results here illustrate that cholesterol, which is a dominant lipid species in the brain, is decreased on the tissue surface after deposition of matrix, particularly in white matter. The decrease of cholesterol is followed by an increased ion yield of several other lipid species. Depth profiling of the sublimed rat brain reveals that the lipid species are de facto extracted by the DHB matrix and concentrated in the top most layers of the sublimed matrix. This extraction/concentration of lipids directly leads to an increase of higher mass lipid ion yield. It is also possible that the decrease of cholesterol decreases the potential suppression of ion yield caused by cholesterol migration to the tissue surface. This result provides us with significant insights into the possible mechanisms involved when using sublimation to deposit this matrix in ME-SIMS.

Molecular mechanisms of the sleep wake cycle : therapeutic applications to insomnia

OpenAIRE

Grima, Melanie; Hunter, Therese; Zhang, Yimeng

2017-01-01

The aim of this review is to explore the molecular mechanism and genetic components of the sleepwake cycle and insomnia. Moreover, we wanted to review the correlation between primary insomnia and its comorbidities. With this aim, a systematic review of recent evidence of the molecular and genetic mechanisms involved in the causation of primary insomnia, along with associations between primary insomnia and other diseases were conducted. Primary insomnia is a complex disorder which accounts for...

Electron angular distributions in He single ionization impact by H2+ ions at 1 MeV

International Nuclear Information System (INIS)

Zhang Shaofeng; Ma Xinwen; Suske, J; Fischer, D; Kuehnel, K U; Voitkiv, A; Najjaril, B; Krauss, A; Moshammer, R; Ullrich, J; Hagmann, S

2009-01-01

For the first time we investigated in a kinematically complete experiment the ionization of helium in collisions with H 2 + -molecular ions at 1 MeV. Using two separate detectors, the orientation of the projectile H 2 + -molecular ions was determined at the instance of the collision. The electron angular distribution was measured by a R eaction Microscope . The observed structures are found in agreement with theoretical calculations, indicating that the ionized electron of He shows a slight preferential emission direction parallel to the molecular axis.

Cell fusion by ionizing radiation

International Nuclear Information System (INIS)

Khair, M.B.

1993-08-01

The relevance and importance of cell fusion are illustrated by the notion that current interest in this phenomenon is shared by scientists in quite varied disciplines. The diversity of cellular membrane fusion phenomena could provoke one to think that there must be a multitude of mechanisms that can account for such diversity. But, in general, the mechanism for the fusion reaction itself could be very similar in many, or even all, cases. Cell fusion can be induced by several factors such as virus Sendai, polyethylene glycol, electric current and ionizing radiation. This article provides the reader with short view of recent progress in research on cell fusion and gives some explanations about fusion mechanisms. This study shows for the first time, the results of the cell fusion induced by ionizing radiations that we have obtained in our researches and the work performed by other groups. (author). 44 refs

Submillisecond elastic recoil reveals molecular origins of fibrin fiber mechanics.

Science.gov (United States)

Hudson, Nathan E; Ding, Feng; Bucay, Igal; O'Brien, E Timothy; Gorkun, Oleg V; Superfine, Richard; Lord, Susan T; Dokholyan, Nikolay V; Falvo, Michael R

2013-06-18

Fibrin fibers form the structural scaffold of blood clots. Thus, their mechanical properties are of central importance to understanding hemostasis and thrombotic disease. Recent studies have revealed that fibrin fibers are elastomeric despite their high degree of molecular ordering. These results have inspired a variety of molecular models for fibrin's elasticity, ranging from reversible protein unfolding to rubber-like elasticity. An important property that has not been explored is the timescale of elastic recoil, a parameter that is critical for fibrin's mechanical function and places a temporal constraint on molecular models of fiber elasticity. Using high-frame-rate imaging and atomic force microscopy-based nanomanipulation, we measured the recoil dynamics of individual fibrin fibers and found that the recoil was orders of magnitude faster than anticipated from models involving protein refolding. We also performed steered discrete molecular-dynamics simulations to investigate the molecular origins of the observed recoil. Our results point to the unstructured αC regions of the otherwise structured fibrin molecule as being responsible for the elastic recoil of the fibers. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Electron-impact ionization of multicharged ions at ORNL: 1985--1992

International Nuclear Information System (INIS)

Gregory, D.C.; Bannister, M.E.

1994-07-01

Absolute cross sections are presented in graphs and tables for single ionization of forty-one ions, multiple ionization of four ions, and for dissociation and ionization of two molecular ions by electron impact. This memo is the third in a series of manuscripts summarizing previously published as well as unpublished ionization cross section measurements at ORNL; contents of the two previous memos are also referenced in this work. All work tabulated in this memo involved ion beams generated in the ORNL-ECR ion source and utilized the ORNL electron-ion crossed beams apparatus. Target ions range from atomic number Z = 8 (oxygen) to Z = 92 (uranium) in initial charge states from +1 to +16. Electron impact energies typically range from threshold to 1500 eV

Numerical simulations of single and double ionization of H{sub 2} in short intense laser pulses; Numerische Simulation zur Einfach- und Doppelionisation von H{sub 2} in kurzen intensiven Laserpulsen

Energy Technology Data Exchange (ETDEWEB)

Baier, Silvio

2008-07-01

Rescattering is the dominant process leading to double ionization in atoms and molecules interacting with linearly polarized laser pulses with wavelengths around 800 nm and in an intensity regime of 10{sup 14} to 10{sup 15} W/cm{sup 2}. Using numerical integrations of the two-electron Schroedinger equation of the Hydrogen molecule in appropriate reduced dimensions two mechanisms, namely correlated emission of the electrons and excitation followed by field ionization after rescattering, could be identified and characterized. With the help of a planar model in reduced dimensions these mechanisms were quantitatively compared by their dependence on the molecular alignment with respect to the polarization axis. Two additional mechanisms, which are also related to rescattering, could be identified as well. (orig.)

Gridded ionization chamber

International Nuclear Information System (INIS)

Houston, J.M.

1977-01-01

An improved ionization chamber type x-ray detector comprises a heavy gas at high pressure disposed between an anode and a cathode. An open grid structure is disposed adjacent the anode and is maintained at a voltsge intermediate between the cathode and anode potentials. The electric field which is produced by positive ions drifting toward the cathode is thus shielded from the anode. Current measuring circuits connected to the anode are, therefore, responsive only to electron current flow within the chamber and the recovery time of the chamber is shortened. The grid structure also serves to shield the anode from electrical currents which might otherwise be induced by mechanical vibrations in the ionization chamber structure

Many-electron phenomena in the ionization of ions

International Nuclear Information System (INIS)

Mueller, A.

2004-01-01

Full text: Single and multiple ionization in ion-atom collisions involve a multitude of complex interactions between the electrons and nuclei of projectile and target. Some of the complexity is avoided in studies of fast collisions when the impulse approximation can be applied and the electrons can be described as independent quasi-free particles with a known momentum distribution. For the detailed investigation of ionization mechanisms that can occur in fast ion-atom collisions, it is illuminating to consider collisions of ions (or atoms) and really free electrons with a narrow energy spread. High energy resolution in electron-ion collision studies provides access to individual, possibly even state-selective, reaction pathways. Even in the simple electron-ion collision system (simple compared with the initial ion-atom problem) single and multiple ionization still involve a multitude of complex mechanisms. Besides the direct removal of one or several electrons from the target by electron impact, resonant and non-resonant formation of intermediate multiply excited states which subsequently decay by electron emission is important in single and multiple ionization of ions and atoms. Direct ionization proceeds via one-step or multi-step knock-off mechanisms which can partly be disentangled by studying effects of different projectile species. The role of multiply excited states in the ionization can be experimentally studied in great detail by a further reduction of the initial ion-atom problem. Multiply excited states of atoms and ions can be selectively populated by photon-ion interactions making use of the potential for extreme energy resolution made available at modern synchrotron radiation sources. In the review talk, examples of studies on single and multiple ionization in electron-ion collisions will be discussed in some detail. Electron-ion collision experiments will also be compared with photon-ion interaction studies. Many-electron phenomena have been observed

Cis-to- Trans Isomerization of Azobenzene Derivatives Studied with Transition Path Sampling and Quantum Mechanical/Molecular Mechanical Molecular Dynamics.

Science.gov (United States)

Muždalo, Anja; Saalfrank, Peter; Vreede, Jocelyne; Santer, Mark

2018-04-10

Azobenzene-based molecular photoswitches are becoming increasingly important for the development of photoresponsive, functional soft-matter material systems. Upon illumination with light, fast interconversion between a more stable trans and a metastable cis configuration can be established resulting in pronounced changes in conformation, dipole moment or hydrophobicity. A rational design of functional photosensitive molecules with embedded azo moieties requires a thorough understanding of isomerization mechanisms and rates, especially the thermally activated relaxation. For small azo derivatives considered in the gas phase or simple solvents, Eyring's classical transition state theory (TST) approach yields useful predictions for trends in activation energies or corresponding half-life times of the cis isomer. However, TST or improved theories cannot easily be applied when the azo moiety is part of a larger molecular complex or embedded into a heterogeneous environment, where a multitude of possible reaction pathways may exist. In these cases, only the sampling of an ensemble of dynamic reactive trajectories (transition path sampling, TPS) with explicit models of the environment may reveal the nature of the processes involved. In the present work we show how a TPS approach can conveniently be implemented for the phenomenon of relaxation-isomerization of azobenzenes starting with the simple examples of pure azobenzene and a push-pull derivative immersed in a polar (DMSO) and apolar (toluene) solvent. The latter are represented explicitly at a molecular mechanical (MM) and the azo moiety at a quantum mechanical (QM) level. We demonstrate for the push-pull azobenzene that path sampling in combination with the chosen QM/MM scheme produces the expected change in isomerization pathway from inversion to rotation in going from a low to a high permittivity (explicit) solvent model. We discuss the potential of the simulation procedure presented for comparative calculation of

Graph-drawing algorithms geometries versus molecular mechanics in fullereness

Science.gov (United States)

Kaufman, M.; Pisanski, T.; Lukman, D.; Borštnik, B.; Graovac, A.

1996-09-01

The algorithms of Kamada-Kawai (KK) and Fruchterman-Reingold (FR) have been recently generalized (Pisanski et al., Croat. Chem. Acta 68 (1995) 283) in order to draw molecular graphs in three-dimensional space. The quality of KK and FR geometries is studied here by comparing them with the molecular mechanics (MM) and the adjacency matrix eigenvectors (AME) algorithm geometries. In order to compare different layouts of the same molecule, an appropriate method has been developed. Its application to a series of experimentally detected fullerenes indicates that the KK, FR and AME algorithms are able to reproduce plausible molecular geometries.

Shock velocity in weakly ionized nitrogen, air, and argon

International Nuclear Information System (INIS)

Siefert, Nicholas S.

2007-01-01

The goal of this research was to determine the principal mechanism(s) for the shock velocity increase in weakly ionized gases. This paper reports experimental data on the propagation of spark-generated shock waves (1< Mach<3) into weakly ionized nitrogen, air, and argon glow discharges (1 < p<20 Torr). In order to distinguish between effects due solely to the presence of electrons and effects due to heating of the background gas via elastic collisions with electrons, the weakly ionized discharge was pulsed on/off. Laser deflection methods determined the shock velocity, and the electron number density was collected using a microwave hairpin resonator. In the afterglow of nitrogen, air, and argon discharges, the shock velocity first decreased, not at the characteristic time for electrons to diffuse to the walls, but rather at the characteristic time for the centerline gas temperature to equilibrate with the wall temperature. These data support the conclusion that the principal mechanism for the increase in shock velocity in weakly ionized gases is thermal heating of the neutral gas species via elastic collisions with electrons

Theory of tunneling ionization of molecules: Weak-field asymptotics including dipole effects

DEFF Research Database (Denmark)

Tolstikhin, Oleg I.; Morishita, Toru; Madsen, Lars Bojer

2011-01-01

The formulation of the parabolic adiabatic expansion approach to the problem of ionization of atomic systems in a static electric field, originally developed for the axially symmetric case [ Phys. Rev. A 82 023416 (2010)], is generalized to arbitrary potentials. This approach is used to rederive...... the asymptotic theory of tunneling ionization in the weak-field limit. In the atomic case, the resulting formulas for the ionization rate coincide with previously known results. In addition, the present theory accounts for the possible existence of a permanent dipole moment of the unperturbed system and, hence......, applies to polar molecules. Accounting for dipole effects constitutes an important difference of the present theory from the so-called molecular Ammosov-Delone-Krainov theory. The theory is illustrated by comparing exact and asymptotic results for a set of model polar molecules and a realistic molecular...

Crosstalk between Apoptosis and Autophagy: Molecular Mechanisms and Therapeutic Strategies in Cancer

Directory of Open Access Journals (Sweden)

Abdelouahid El-Khattouti

2013-01-01

Full Text Available Both apoptosis and autophagy are highly conserved processes that besides their role in the maintenance of the organismal and cellular homeostasis serve as a main target of tumor therapeutics. Although their important roles in the modulation of tumor therapeutic strategies have been widely reported, the molecular actions of both apoptosis and autophagy are counteracted by cancer protective mechanisms. While apoptosis is a tightly regulated process that is implicated in the removal of damaged or unwanted cells, autophagy is a cellular catabolic pathway that is involved in lysosomal degradation and recycling of proteins and organelles, and thereby is considered an important survival/protective mechanism for cancer cells in response to metabolic stress or chemotherapy. Although the relationship between autophagy and cell death is very complicated and has not been characterized in detail, the molecular mechanisms that control this relationship are considered to be a relevant target for the development of a therapeutic strategy for tumor treatment. In this review, we focus on the molecular mechanisms of apoptosis, autophagy, and those of the crosstalk between apoptosis and autophagy in order to provide insight into the molecular mechanisms that may be essential for the balance between cell survival and death as well as their role as targets for the development of novel therapeutic approaches.

[Gas chromatography with a Pulsed discharge helium ionization detector for measurement of molecular hydrogen(H2) in the atmosphere].

Science.gov (United States)

Luan, Tian; Fang, Shuang-xi; Zhou, Ling-xi; Wang, Hong-yang; Zhang, Gen

2015-01-01

A high precision GC system with a pulsed discharge helium ionization detector was set up based on the commercial Agilent 7890A gas chromatography. The gas is identified by retention time and the concentration is calculated through the peak height. Detection limit of the system is about 1 x 10(-9) (mole fraction, the same as below). The standard deviation of 140 continuous injections with a standard cylinder( concentration is roughly 600 x 10(-9)) is better than 0.3 x 10(-9). Between 409.30 x 10(-9) and 867.74 x 10(-9) molecular hydrogen mole fractions and peak height have good linear response. By using two standards to quantify the air sample, the precision meets the background molecular hydrogen compatibility goal within the World Meteorological Organization/Global Atmosphere Watch (WMO/GAW) program. Atmospheric molecular hydrogen concentration at Guangzhou urban area was preliminarily measured by this method from January to November 2013. The results show that the atmospheric molecular hydrogen mole fraction varies from 450 x 10(-9) to 700 x 10(-9) during the observation period, with the lowest value at 14:00 (Beijing time, the same as below) and the peak value at 20:00. The seasonal variation of atmospheric hydrogen at Guangzhou area was similar with that of the same latitude stations in northern hemisphere.

Molecular Mechanisms of Chromium in Alleviating Insulin Resistance

Science.gov (United States)

Hua, Yinan; Clark, Suzanne; Ren, Jun; Sreejayan, Nair

2011-01-01

Type 2 diabetes is often associated with obesity, dyslipidemia, and cardiovascular anomalies and is a major health problem approaching global epidemic proportions. Insulin resistance, a prediabetic condition, precedes the onset of frank type 2 diabetes and offers potential avenues for early intervention to treat the disease. Although lifestyle modifications and exercise can reduce the incidence of diabetes, compliance has proved to be difficult, warranting pharmacological interventions. However, most of the currently available drugs that improve insulin sensitivity have adverse effects. Therefore, attractive strategies to alleviate insulin resistance include dietary supplements. One such supplement is chromium, which has been shown reduce insulin resistance in some, but not all, studies. Furthermore, the molecular mechanisms of chromium in alleviating insulin resistance remain elusive. This review examines emerging reports on the effect of chromium, as well as molecular and cellular mechanisms by which chromium may provide beneficial effects in alleviating insulin resistance. PMID:22423897

Penetration of Cosmic Rays into Dense Molecular Clouds: Role of Diffuse Envelopes

Science.gov (United States)

Ivlev, A. V.; Dogiel, V. A.; Chernyshov, D. O.; Caselli, P.; Ko, C.-M.; Cheng, K. S.

2018-03-01

A flux of cosmic rays (CRs) propagating through a diffuse ionized gas can excite MHD waves, thus generating magnetic disturbances. We propose a generic model of CR penetration into molecular clouds through their diffuse envelopes, and identify the leading physical processes controlling their transport on the way from a highly ionized interstellar medium to the dense interior of the cloud. The model allows us to describe a transition between a free streaming of CRs and their diffusive propagation, determined by the scattering on the self-generated disturbances. A self-consistent set of equations, governing the diffusive transport regime in an envelope and the MHD turbulence generated by the modulated CR flux, is characterized by two dimensionless numbers. We demonstrate a remarkable mutual complementarity of different mechanisms leading to the onset of the diffusive regime, which results in a universal energy spectrum of the modulated CRs. In conclusion, we briefly discuss implications of our results for several fundamental astrophysical problems, such as the spatial distribution of CRs in the Galaxy as well as the ionization, heating, and chemistry in dense molecular clouds. This paper is dedicated to the memory of Prof. Vadim Tsytovich.

Mechanical and molecular studies of biocomposites filled with oil palm empty fruit bunches microfibers

Science.gov (United States)

Nikmatin, S.; Saepulloh, D. R.; Irmansyah; Syafiuddin, A.

2017-05-01

The present work aims to investigate mechanical and molecular characteristics of acrylonitrile butadiene styrene (ABS) composites filled with oil palm empty fruit bunches (OPEFB) microfibers. OPEFB microfibers were produced using mechanical milling. Composite granules were fabricated using single screw extruder. These composites were then used for fabricating helmet according to the Indonesian National Standard (SNI). Mechanical testing confirms that the helmet produced using this biocomposites are suitable to the SNI. Molecular interaction between matrix with OPEFB can be described using orbital hybridization theory. In general, this study has successfully investigated mechanical and molecular properties of the biocomposites.

Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method.

Science.gov (United States)

König, Gerhard; Mei, Ye; Pickard, Frank C; Simmonett, Andrew C; Miller, Benjamin T; Herbert, John M; Woodcock, H Lee; Brooks, Bernard R; Shao, Yihan

2016-01-12

A recently developed MESS-E-QM/MM method (multiple-environment single-system quantum mechanical molecular/mechanical calculations with a Roothaan-step extrapolation) is applied to the computation of hydration free energies for the blind SAMPL4 test set and for 12 small molecules. First, free energy simulations are performed with a classical molecular mechanics force field using fixed-geometry solute molecules and explicit TIP3P solvent, and then the non-Boltzmann-Bennett method is employed to compute the QM/MM correction (QM/MM-NBB) to the molecular mechanical hydration free energies. For the SAMPL4 set, MESS-E-QM/MM-NBB corrections to the hydration free energy can be obtained 2 or 3 orders of magnitude faster than fully converged QM/MM-NBB corrections, and, on average, the hydration free energies predicted with MESS-E-QM/MM-NBB fall within 0.10-0.20 kcal/mol of full-converged QM/MM-NBB results. Out of five density functionals (BLYP, B3LYP, PBE0, M06-2X, and ωB97X-D), the BLYP functional is found to be most compatible with the TIP3P solvent model and yields the most accurate hydration free energies against experimental values for solute molecules included in this study.

A combined thermal dissociation and electron impact ionization source for radioactive ion beam generationa

International Nuclear Information System (INIS)

Alton, G.D.; Williams, C.

1996-01-01

The probability for simultaneously dissociating and efficiently ionizing the individual atomic constituents of molecular feed materials with conventional, hot-cathode, electron-impact ion sources is low and consequently, the ion beams from these sources often appear as mixtures of several molecular sideband beams. This fragmentation process leads to dilution of the intensity of the species of interest for radioactive ion beam (RIB) applications where beam intensity is at a premium. We have conceived an ion source that combines the excellent molecular dissociation properties of a thermal dissociator and the high ionization efficiency characteristics of an electron impact ionization source that will, in principle, overcome this handicap. The source concept will be evaluated as a potential candidate for use for RIB generation at the Holifield Radioactive Ion Beam Facility, now under construction at the Oak Ridge National Laboratory. The design features and principles of operation of the source are described in this article. copyright 1996 American Institute of Physics

Electron ionization and dissociation of aliphatic amino acids

Science.gov (United States)

Papp, P.; Shchukin, P.; Kočíšek, J.; Matejčík, Š.

2012-09-01

We present experimental and theoretical study of electron ionization and dissociative ionization to the gas phase amino acids valine, leucine, and isoleucine. A crossed electron/molecular beams technique equipped with quadrupole mass analyzer has been applied to measure mass spectra and ion efficiency curves for formation of particular ions. From experimental data the ionization energies of the molecules and the appearance energies of the fragment ions were determined. Ab initio calculations (Density Functional Theory and G3MP2 methods) were performed in order to calculate the fragmentation paths and interpret the experimental data. The experimental ionization energies of parent molecules [P]+ 8.91 ± 0.05, 8.85 ± 0.05, and 8.79 ± 0.05 eV and G3MP2 ionization energies (adiabatic) of 8.89, 8.88, and 8.81 eV were determined for valine, leucine, and isoleucine, respectively, as well as the experimental and theoretical threshold energies for dissociative ionization channels. The comparison of experimental data with calculations resulted in identification of the ions as well as the neutral fragments formed in the dissociative reactions. Around 15 mass/charge ratio fragments were identified from the mass spectra by comparison of experimental appearance energies with calculated reaction enthalpies for particular dissociative reactions.

Monte Carlo wave packet approach to dissociative multiple ionization in diatomic molecules

DEFF Research Database (Denmark)

Leth, Henriette Astrup; Madsen, Lars Bojer; Mølmer, Klaus

2010-01-01

A detailed description of the Monte Carlo wave packet technique applied to dissociative multiple ionization of diatomic molecules in short intense laser pulses is presented. The Monte Carlo wave packet technique relies on the Born-Oppenheimer separation of electronic and nuclear dynamics...... and provides a consistent theoretical framework for treating simultaneously both ionization and dissociation. By simulating the detection of continuum electrons and collapsing the system onto either the neutral, singly ionized or doubly ionized states in every time step the nuclear dynamics can be solved....... The computational effort is restricted and the model is applicable to any molecular system where electronic Born-Oppenheimer curves, dipole moment functions, and ionization rates as a function of nuclear coordinates can be determined....

Molecular Mechanisms in Exercise-Induced Cardioprotection

Directory of Open Access Journals (Sweden)

Saeid Golbidi

2011-01-01

Full Text Available Physical inactivity is increasingly recognized as modifiable behavioral risk factor for cardiovascular diseases. A partial list of proposed mechanisms for exercise-induced cardioprotection include induction of heat shock proteins, increase in cardiac antioxidant capacity, expression of endoplasmic reticulum stress proteins, anatomical and physiological changes in the coronary arteries, changes in nitric oxide production, adaptational changes in cardiac mitochondria, increased autophagy, and improved function of sarcolemmal and/or mitochondrial ATP-sensitive potassium channels. It is currently unclear which of these protective mechanisms are essential for exercise-induced cardioprotection. However, most investigations focus on sarcolemmal KATP channels, NO production, and mitochondrial changes although it is very likely that other mechanisms may also exist. This paper discusses current information about these aforementioned topics and does not consider potentially important adaptations within blood or the autonomic nervous system. A better understanding of the molecular basis of exercise-induced cardioprotection will help to develop better therapeutic strategies.

A quantum mechanical/molecular mechanical study of the hydroxylation of phenol and halogeneted derivatives by phenol hydroxylase

NARCIS (Netherlands)

Ridder, L.; Mulholland, A.J.; Rietjens, I.M.C.M.; Vervoort, J.

2000-01-01

A combined quantum mechanical and molecular mechanical (QM/MM) method (AM1/CHARMM) was used to investigate the mechanism of the aromatic hydroxylation of phenol by a flavin dependent phenol hydroxylase (PH), an essential reaction in the degradation of a wide range of aromatic compounds. The model

Survival under stress: molecular mechanisms of metabolic rate ...

African Journals Online (AJOL)

Studies in my laboratory are analysing the molecular mechanisms and regulatory events that underlie transitions to and from hypometabolic states In systems including anoxia-tolerant turtles and molluscs, estivating snails and toads, hibernating small mammals, and freeze tolerant frogs and insects. Our newest research ...

Problems linked to effects of ionizing radiations low doses

International Nuclear Information System (INIS)

Anon.

1995-10-01

The question of exposure to ionizing radiations low doses and risks existing for professional and populations has been asked again, with the recommendations of the International Commission of Radiation Protection (ICRP) to lower the previous standards and agreed as guides to organize radiation protection, by concerned countries and big international organisms. The sciences academy presents an analysis which concerned on epidemiological and dosimetric aspects in risk estimation, on cellular and molecular aspects of response mechanism to irradiation. The observation of absence of carcinogen effects for doses inferior to 200 milli-sieverts and a re-evaluation of data coming from Nagasaki and Hiroshima, lead to revise the methodology of studies to pursue, to appreciate more exactly the effects of low doses, in taking in part, particularly, the dose rate. The progress of molecular and cellular biology showed that the extrapolation from high doses to low doses is not in accordance with actual data. The acknowledge of DNA repair and carcinogenesis should make clearer the debate. (N.C.). 61 refs., 9 annexes

Critical assessment of ionization patterns and applications of ambient desorption/ionization mass spectrometry using FAPA-MS.

Science.gov (United States)

Brüggemann, Martin; Karu, Einar; Hoffmann, Thorsten

2016-02-01

Ambient desorption/ionization mass spectrometry (MS) has gained growing interest during the last decade due to its high analytical performance and yet simplicity. Here, one of the recently developed ambient desorption/ionization MS sources, the flowing atmospheric-pressure afterglow (FAPA) source, was investigated in detail regarding background ions and typical ionization patterns in the positive as well as the negative ion mode for a variety of compound classes, comprising alkanes, alcohols, aldehydes, ketones, carboxylic acids, organic peroxides and alkaloids. A broad range of signals for adducts and losses was found, besides the usually emphasized detection of quasimolecular ions, i.e. [M + H](+) and [M - H](-) in the positive and the negative mode, respectively. It was found that FAPA-MS is best suited for polar analytes containing nitrogen and/or oxygen functionalities, e.g. carboxylic acids, with low molecular weights and relatively high vapor pressures. In addition, the source was used in proof-of-principle studies, illustrating the capabilities and limitations of the technique: Firstly, traces of cocaine were detected and unambiguously identified on euro banknotes using FAPA ionization in combination with tandem MS, suggesting a correlation between cocaine abundance and age of the banknote. Secondly, FAPA-MS was used for the identification of acidic marker compounds in organic aerosol samples, indicating yet-undiscovered matrix and sample surface effects of ionization pathways in the afterglow region. Copyright © 2016 John Wiley & Sons, Ltd.

Understanding the molecular mechanisms of reprogramming

Energy Technology Data Exchange (ETDEWEB)

Krause, Marie N. [Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla 92037, CA (United States); University Hospital of Würzburg, Department of Pediatrics, 2 Josef-Schneiderstrasse, 97080 Würzburg (Germany); Sancho-Martinez, Ignacio [Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla 92037, CA (United States); Centre for Stem Cells and Regenerative Medicine, King' s College London, 28th Floor, Tower Wing, Guy' s Hospital, Great Maze Pond, London (United Kingdom); Izpisua Belmonte, Juan Carlos, E-mail: belmonte@salk.edu [Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla 92037, CA (United States)

2016-05-06

Despite the profound and rapid advancements in reprogramming technologies since the generation of the first induced pluripotent stem cells (iPSCs) in 2006[1], the molecular basics of the process and its implications are still not fully understood. Recent work has suggested that a subset of TFs, so called “Pioneer TFs”, play an important role during the stochastic phase of iPSC reprogramming [2–6]. Pioneer TFs activities differ from conventional transcription factors in their mechanism of action. They bind directly to condensed chromatin and elicit a series of chromatin remodeling events that lead to opening of the chromatin. Chromatin decondensation by pioneer factors progressively occurs during cell division and in turn exposes specific gene promoters in the DNA to which TFs can now directly bind to promoters that are readily accessible[2, 6]. Here, we will summarize recent advancements on our understanding of the molecular mechanisms underlying reprogramming to iPSC as well as the implications that pioneer Transcription Factor activities might play during different lineage conversion processes. - Highlights: • Pioneer transcription factor activity underlies the initial steps of iPSC generation. • Reprogramming can occur by cis- and/or trans- reprogramming events. • Cis-reprogramming implies remodeling of the chromatin for enabling TF accessibility. • Trans-reprogramming encompasses direct binding of Tfs to their target gene promoters.

Newly calculated absolute cross-section for the electron-impact ionization of C2H2+

International Nuclear Information System (INIS)

Deutsch, H.; Becker, K.; Defrance, P.; Probst, M.; Mark, T.D.; Limtrakul, J.

2006-01-01

New measurements of the cross-section for electron impact ionization of the molecular ion C 2 H 2 + have been carried out recently. These data differ significantly from earlier data, because cross-sections corresponding to all the possible dissociative ionization processes were determined. The new data in conjunction with the significant discrepancies between the earlier data and the results of various calculations, which disagreed among themselves by a factor of 3, motivated a renewed attempt to apply the semi-classical Deutsch-Mark (DM) formalism to the calculation of the absolute electron-impact ionization cross-section of this molecular ion. A quantum chemical molecular orbital population analysis for both the neutral molecule and the ion revealed that in the case of C 2 H 2 + the singly occupied molecular orbital (i.e. the 'missing' electron) is highly localized near the site of a C atom in the molecule. This information is explicitly incorporated in our formalism. The results obtained by taking the ionic character directly into account are in excellent agreement with the recent experimental data. (authors)

Compatibility of polyamide 6.6 and low density polyethylene polymeric blend using electron beam ionizing radiation

International Nuclear Information System (INIS)

Feitosa, Marcos Antonio Fernandes

2008-01-01

The plastic industry has recognized that mixture of polymers, called polymeric blends, yields new materials with improve properties and better features of those of the polymer blended. In most of the cases, blends are formed by immiscible components presenting separated phases, micro-structures or morphologies. One of the main factors for good mechanical performance is the interfacial adhesion of the blend components. The improvement of miscibility between the polymer components and the enhancement of blend performance is denominated of compatibility. This compatibility can be achieved by chemical methods or using ionizing radiation. The present work has as a main objective the study of the effect of the ionizing radiation from electron beam in the compatibility of the polyamide (PA) 6.6 and low density polyethylene (LDPE) 75%/25% wt blend, in the range of applied doses from 50 to 250 kGy. The compatibility effect was evaluated by mechanical test, which has shown improvement in the tensile strength and hardness properties and a reduction of the impact resistant. This mechanical behavior can be considered as a combination effect of the cross-linking, induced in the molecular structure on the polymers, and the increase of the miscibility of the blend components. The degree of compatibility was evaluated by the behavior of the glass transition temperatures (T g ) for the blend components obtained by dynamic mechanical analysis (DMA) measurements. The results have shown that the values of T g for PA 6.6 and LDPE get near by 8 deg C showing that the ionizing radiation have promoted a compatibility effect on the irradiated blend. (author)

Biological effects of ionizing radiation

International Nuclear Information System (INIS)

Anon.

1991-01-01

Experiments with small animals, tissue cultures, and inanimate materials help with understanding the effects of ionizing radiation that occur at the molecular level and cause the gross effects observed in man. Topics covered in this chapter include the following: Radiolysis of Water; Radiolysis of Organic Compounds; Radiolysis in Cells; Radiation Exposure and Dose Units; Dose Response Curves; Radiation Effects in Animals; Factors Affecting Health Risks. 8 refs., 3 figs., 5 tabs

Iron oxide nanomatrix facilitating metal ionization in matrix-assisted laser desorption/ionization mass spectrometry.

Science.gov (United States)

Obena, Rofeamor P; Lin, Po-Chiao; Lu, Ying-Wei; Li, I-Che; del Mundo, Florian; Arco, Susan dR; Nuesca, Guillermo M; Lin, Chung-Chen; Chen, Yu-Ju

2011-12-15

The significance and epidemiological effects of metals to life necessitate the development of direct, efficient, and rapid method of analysis. Taking advantage of its simple, fast, and high-throughput features, we present a novel approach to metal ion detection by matrix-functionalized magnetic nanoparticle (matrix@MNP)-assisted MALDI-MS. Utilizing 21 biologically and environmentally relevant metal ion solutions, the performance of core and matrix@MNP against conventional matrixes in MALDI-MS and laser desorption ionization (LDI) MS were systemically tested to evaluate the versatility of matrix@MNP as ionization element. The matrix@MNPs provided 20- to >100-fold enhancement on detection sensitivity of metal ions and unambiguous identification through characteristic isotope patterns and accurate mass (<5 ppm), which may be attributed to its multifunctional role as metal chelator, preconcentrator, absorber, and reservoir of energy. Together with the comparison on the ionization behaviors of various metals having different ionization potentials (IP), we formulated a metal ionization mechanism model, alluding to the role of exciton pooling in matrix@MNP-assisted MALDI-MS. Moreover, the detection of Cu in spiked tap water demonstrated the practicability of this new approach as an efficient and direct alternative tool for fast, sensitive, and accurate determination of trace metal ions in real samples.

Research on the degradation mechanism of dimethyl phthalate in drinking water by strong ionization discharge

Science.gov (United States)

Hong, ZHAO; Chengwu, YI; Rongjie, YI; Huijuan, WANG; Lanlan, YIN; I, N. MUHAMMAD; Zhongfei, MA

2018-03-01

The degradation mechanism of dimethyl phthalate (DMP) in the drinking water was investigated using strong ionization discharge technology in this study. Under the optimized condition, the degradation efficiency of DMP in drinking water was up to 93% in 60 min. A series of analytical techniques including high-performance liquid chromatography, liquid chromatography mass spectrometry, total organic carbon analyzer and ultraviolet-visible spectroscopy were used in the study. It was found that a high concentration of ozone (O3) produced by dielectric barrier discharge reactor was up to 74.4 mg l-1 within 60 min. Tert-butanol, isopropyl alcohol, carbonate ions ({{{{CO}}}3}2-) and bicarbonate ions ({{{{HCO}}}3}-) was added to the sample solution to indirectly prove the presence and effect of hydroxyl radicals (·OH). These analytical findings indicate that mono-methyl phthalate, phthalic acid (PA) and methyl ester PA were detected as the major intermediates in the process of DMP degradation. Finally, DMP and all products were mineralized into carbon dioxide (CO2) and water (H2O) ultimately. Based on these analysis results, the degradation pathway of DMP by strong ionization discharge technology were proposed.

Mechanical properties of polyamide 6,6/low density polyethylene blend by ionizing radiation

International Nuclear Information System (INIS)

Pino, Eddy S.; Feitosa, Marcos A.F.

2007-01-01

Polymer blending is a growing scientific and commercial development activity. In most of the cases, polymeric blends are formed by thermodynamically immiscible components. Such blends require the use of compatibilizers that, often, are copolymers, graft copolymers or any mean that improves the dispersion and adhesion of the blend phases. Compatibility of a polymer blend plays an important role in determining the blend properties for its end use. In this work, the improvement of mechanical properties of PA 6,6/LDPE 75/25% wt/wt composition blend, using electron radiation, was studied. Samples for mechanical test were melt-mixed in an extruder and then injection-molded. These samples were electron irradiated to overall doses of 50, 100, 150, 200 and 250 kGy. Tensile measurements have shown that the strength at break increases with an increase of radiation dose. Hardness Shore D measurements show that this property also increases as a function of radiation dose. On the other hand, Impact Izod tests show that the resistance to impact decreases with the increase of radiation dose. The behavior of these bulk and surface properties implies that ionizing radiation produces changes in the mechanical performance of the irradiated blend due to a combined radiation inducing effects, cross-linking and the compatibility of blend components. (author)

Quantum interference in laser-induced nonsequential double ionization

Science.gov (United States)

Quan, Wei; Hao, XiaoLei; Wang, YanLan; Chen, YongJu; Yu, ShaoGang; Xu, SongPo; Xiao, ZhiLei; Sun, RenPing; Lai, XuanYang; Hu, ShiLin; Liu, MingQing; Shu, Zheng; Wang, XiaoDong; Li, WeiDong; Becker, Wilhelm; Liu, XiaoJun; Chen, Jing

2017-09-01

Quantum interference plays an important role in various intense-laser-driven atomic phenomena, e.g., above-threshold ionization and high-order-harmonic generation, and provides a useful tool in ultrafast imaging of atomic and molecular structure and dynamics. However, it has eluded observation in nonsequential double ionization (NSDI), which serves as an ideal prototype to study electron-electron correlation. Thus far, NSDI usually could be well understood from a semiclassical perspective, where all quantum aspects have been ignored after the first electron has tunneled. Here we perform coincidence measurements for NSDI of xenon subject to laser pulses at 2400 nm. It is found that the intensity dependence of the asymmetry parameter between the yields in the second and fourth quadrants and those in the first and third quadrants of the electron-momentum-correlation distributions exhibits a peculiar fast oscillatory structure, which is beyond the scope of the semiclassical picture. Our theoretical analysis indicates that this oscillation can be attributed to interference between the contributions of different excited states in the recollision-excitation-with-subsequent-ionization channel. Our work demonstrates the significant role of quantum interference in NSDI and may create an additional pathway towards manipulation and imaging of the ultrafast atomic and molecular dynamics in intense laser fields.

Progress in nucleic acid research and molecular biology

International Nuclear Information System (INIS)

Cohn, W.E.; Moldave, K.

1988-01-01

Complementary Use of Chemical Modification and Site-Directed Mutagenesis to Probe Structure-Activity Relationships in Enzymes. Mechanisms of the Antiviral Action of Inteferons. Modulation of Cellular Genes by Oncogenes. DNA Damage Produced by Ionizing Radiation in Mammalian Cells: Identities, Mechanisms of Formation, and Reparability. Human Ferritin Gene Expression. Molecular Biology of the Insulin Receptor. Cap-Binding Proteins of Eukaryotic Messenger RNA: Functions in Initiation and Control of Translation. Physical Monitoring of Meiotic and Mitotic Recombination in Yeast. Early Signals Underlying the Induction of the c-fos and c-myc Genes in Quiescent Fibroblasts: Studies with Bombesin and Other Growth Factors. Each chapter includes references

Programmed necrosis and necroptosis – molecular mechanisms

Directory of Open Access Journals (Sweden)

Agata Giżycka

2015-12-01

Full Text Available Programmed necrosis has been proven vital for organism development and homeostasis maintenance. Its regulatory effects on functional activity of the immune system, as well as on pathways regulating the death mechanisms in cells with diminished apoptotic activity, including malignant cells, have been confirmed. There is also increasing evidence indicating necrosis involvement in many human pathologies. Contrary to previous beliefs, necrosis is not only a passive, pathological, gene-independent process. However, the current knowledge regarding molecular regulation of programmed necrosis is scarce. In part this is due to the multiplicity and complexity of signaling pathways involved in programmed necrosis, as well as the absence of specific cellular markers identifying this process, but also the ambiguous and imprecise international terminology. This review presents the current state of the art on molecular mechanisms of programmed necrosis. In particular, its specific and frequent form, necroptosis, is discussed. The role of RIP1 and RIP3 kinases in this process is presented, as well as the diverse pathways induced by ligation of tumor necrosis factor α, to its receptor, TNFR1, i.e. cell survival, apoptosis or necroptosis.

Advances on molecular mechanism of the adaptive evolution of Chiroptera (bats).

Science.gov (United States)

Yunpeng, Liang; Li, Yu

2015-01-01

As the second biggest animal group in mammals, Chiroptera (bats) demonstrates many unique adaptive features in terms of flight, echolocation, auditory acuity, feeding habit, hibernation and immune defense, providing an excellent system for understanding the molecular basis of how organisms adapt to the living environments encountered. In this review, we summarize the researches on the molecular mechanism of the adaptive evolution of Chiroptera, especially the recent researches at the genome levels, suggesting a far more complex evolutionary pattern and functional diversity than previously thought. In the future, along with the increasing numbers of Chiroptera species genomes available, new evolutionary patterns and functional divergence will be revealed, which can promote the further understanding of this animal group and the molecular mechanism of adaptive evolution.

Study of ionization process of matrix molecules in matrix-assisted laser desorption ionization

Energy Technology Data Exchange (ETDEWEB)

Murakami, Kazumasa; Sato, Asami; Hashimoto, Kenro; Fujino, Tatsuya, E-mail: fujino@tmu.ac.jp

2013-06-20

Highlights: ► Proton transfer and adduction reaction of matrix in MALDI were studied. ► Hydroxyl group forming intramolecular hydrogen bond was related to the ionization. ► Intramolecular proton transfer in the electronic excited state was the initial step. ► Non-volatile analytes stabilized protonated matrix in the ground state. ► A possible mechanism, “analyte support mechanism”, has been proposed. - Abstract: Proton transfer and adduction reaction of matrix molecules in matrix-assisted laser desorption ionization were studied. By using 2,4,6-trihydroxyacetophenone (THAP), 2,5-dihydroxybenzoic acid (DHBA), and their related compounds in which the position of a hydroxyl group is different, it was clarified that a hydroxyl group forming an intramolecular hydrogen bond is related to the ionization of matrix molecules. Intramolecular proton transfer in the electronic excited state of the matrix and subsequent proton adduction from a surrounding solvent to the charge-separated matrix are the initial steps for the ionization of matrix molecules. Nanosecond pump–probe NIR–UV mass spectrometry confirmed that the existence of analyte molecules having large dipole moment in their structures is necessary for the stabilization of [matrix + H]{sup +} in the electronic ground state.

Structure factors for tunneling ionization rates of molecules

DEFF Research Database (Denmark)

Madsen, L.B.; Jensen, F.; Tolstikhin, O.I.

2013-01-01

Within the weak-field asymptotic theory, the dependence of the tunneling ionization rate of a molecule in a static electric field on its orientation with respect to the field is determined by the structure factor for the highest occupied molecular orbital (HOMO). An accurate determination...

Hot-cavity studies for the Resonance Ionization Laser Ion Source

International Nuclear Information System (INIS)

Henares, J.L.; Lecesne, N.; Hijazi, L.; Bastin, B.; Kron, T.; Lassen, J.; Le Blanc, F.; Leroy, R.; Osmond, B.; Raeder, S.; Schneider, F.; Wendt, K.

2016-01-01

The Resonance Ionization Laser Ion Source (RILIS) has emerged as an important technique in many Radioactive Ion Beam (RIB) facilities for its reliability, and ability to ionize target elements efficiently and element selectively. GISELE is an off-line RILIS test bench to study the implementation of an on-line laser ion source at the GANIL separator facility. The aim of this project is to determine the best technical solution which combines high selectivity and ionization efficiency with small ion beam emittance and stable long term operation. The ion source geometry was tested in several configurations in order to find a solution with optimal ionization efficiency and beam emittance. Furthermore, a low work function material was tested to reduce the contaminants and molecular sidebands generated inside the ion source. First results with ZrC ionizer tubes will be presented. Furthermore, a method to measure the energy distribution of the ion beam as a function of the time of flight will be discussed.

Ionized and Molecular Gas Kinematics in a z = 1.4 Star-forming Galaxy

Science.gov (United States)

Übler, H.; Genzel, R.; Tacconi, L. J.; Förster Schreiber, N. M.; Neri, R.; Contursi, A.; Belli, S.; Nelson, E. J.; Lang, P.; Shimizu, T. T.; Davies, R.; Herrera-Camus, R.; Lutz, D.; Plewa, P. M.; Price, S. H.; Schuster, K.; Sternberg, A.; Tadaki, K.; Wisnioski, E.; Wuyts, S.

2018-02-01

We present deep observations of a z = 1.4 massive, star-forming galaxy (SFG) in molecular and ionized gas at comparable spatial resolution (CO 3–2, NOrthern Extended Millimeter Array (NOEMA); Hα, Large Binocular Telescope (LBT)). The kinematic tracers agree well, indicating that both gas phases are subject to the same gravitational potential and physical processes affecting the gas dynamics. We combine the one-dimensional velocity and velocity dispersion profiles in CO and Hα to forward-model the galaxy in a Bayesian framework, combining a thick exponential disk, a bulge, and a dark matter halo. We determine the dynamical support due to baryons and dark matter, and find a dark matter fraction within one effective radius of {f}DM}(≤slant {R}e)={0.18}-0.04+0.06. Our result strengthens the evidence for strong baryon-dominance on galactic scales of massive z ∼ 1–3 SFGs recently found based on ionized gas kinematics alone. Based on observations carried out with the IRAM Interferometer NOEMA. IRAM is supported by INSU/CNRS (France), MPG (Germany), and IGN (Spain). Based on observations carried out with the LBT. The LBT is an international collaboration among institutions in the United States, Italy, and Germany. LBT Corporation partners are: LBT Beteiligungsgesellschaft, Germany, representing the Max-Planck Society, The Leibniz Institute for Astrophysics Potsdam, and Heidelberg University; The University of Arizona on behalf of the Arizona Board of Regents; Istituto Nazionale di Astrofisica, Italy; The Ohio State University, and The Research Corporation, on behalf of The University of Notre Dame, University of Minnesota and University of Virginia.

A Versatile Integrated Ambient Ionization Source Platform

Science.gov (United States)

Ai, Wanpeng; Nie, Honggang; Song, Shiyao; Liu, Xiaoyun; Bai, Yu; Liu, Huwei

2018-04-01

The pursuit of high-throughput sample analysis from complex matrix demands development of multiple ionization techniques with complementary specialties. A versatile integrated ambient ionization source (iAmIS) platform is proposed in this work, based on the idea of integrating multiple functions, enhancing the efficiency of current ionization techniques, extending the applications, and decreasing the cost of the instrument. The design of the iAmIS platform combines flowing atmospheric pressure afterglow (FAPA) source/direct analysis in real time (DART), dielectric barrier discharge ionization (DBDI)/low-temperature plasma (LTP), desorption electrospray ionization (DESI), and laser desorption (LD) technique. All individual and combined ionization modes can be easily attained by modulating parameters. In particular, the FAPA/DART&DESI mode can realize the detection of polar and nonpolar compounds at the same time with two different ionization mechanisms: proton transfer and charge transfer. The introduction of LD contributes to the mass spectrometry imaging and the surface-assisted laser desorption (SALDI) under ambient condition. Compared with other individual or multi-mode ion source, the iAmIS platform provides the flexibility of choosing different ionization modes, broadens the scope of the analyte detection, and facilitates the analysis of complex samples. [Figure not available: see fulltext.

Drugs meeting the molecular basis of diabetic kidney disease: bridging from molecular mechanism to personalized medicine.

Science.gov (United States)

Lambers Heerspink, Hiddo J; Oberbauer, Rainer; Perco, Paul; Heinzel, Andreas; Heinze, Georg; Mayer, Gert; Mayer, Bernd

2015-08-01

Diabetic kidney disease (DKD) is a complex, multifactorial disease and is associated with a high risk of renal and cardiovascular morbidity and mortality. Clinical practice guidelines for diabetes recommend essentially identical treatments for all patients without taking into account how the individual responds to the instituted therapy. Yet, individuals vary widely in how they respond to medications and therefore optimal therapy differs between individuals. Understanding the underlying molecular mechanisms of variability in drug response will help tailor optimal therapy. Polymorphisms in genes related to drug pharmacokinetics have been used to explore mechanisms of response variability in DKD, but with limited success. The complex interaction between genetic make-up and environmental factors on the abundance of proteins and metabolites renders pharmacogenomics alone insufficient to fully capture response variability. A complementary approach is to attribute drug response variability to individual variability in underlying molecular mechanisms involved in the progression of disease. The interplay of different processes (e.g. inflammation, fibrosis, angiogenesis, oxidative stress) appears to drive disease progression, but the individual contribution of each process varies. Drugs at the other hand address specific targets and thereby interfere in certain disease-associated processes. At this level, biomarkers may help to gain insight into which specific pathophysiological processes are involved in an individual followed by a rational assessment whether a specific drug's mode of action indeed targets the relevant process at hand. This article describes the conceptual background and data-driven workflow developed by the SysKid consortium aimed at improving characterization of the molecular mechanisms underlying DKD at the interference of the molecular impact of individual drugs in order to tailor optimal therapy to individual patients. © The Author 2015. Published by

Self-renewal molecular mechanisms of colorectal cancer stem cells.

Science.gov (United States)

Pan, Tianhui; Xu, Jinghong; Zhu, Yongliang

2017-01-01

Colorectal cancer stem cells (CCSCs) represent a small fraction of the colorectal cancer cell population that possess self-renewal and multi-lineage differentiation potential and drive tumorigenicity. Self-renewal is essential for the malignant biological behaviors of colorectal cancer stem cells. While the self-renewal molecular mechanisms of colorectal cancer stem cells are not yet fully understood, the aberrant activation of signaling pathways, such as Wnt, Notch, transforming growth factor-β (TGF-β)/bone morphogenetic protein (BMP) and Hedgehog-Gli (HH-GLI), specific roles mediated by cell surface markers and micro-environmental factors are involved in the regulation of self-renewal. The elucidation of the molecular mechanisms behind self-renewal may lead to the development of novel targeted interventions for the treatment of colorectal cancer.

Molecular Frame Reconstruction Using Time-Domain Photoionization Interferometry.

Science.gov (United States)

Marceau, Claude; Makhija, Varun; Platzer, Dominique; Naumov, A Yu; Corkum, P B; Stolow, Albert; Villeneuve, D M; Hockett, Paul

2017-08-25

Photoionization of molecular species is, essentially, a multipath interferometer with both experimentally controllable and intrinsic molecular characteristics. In this work, XUV photoionization of impulsively aligned molecular targets (N_{2}) is used to provide a time-domain route to "complete" photoionization experiments, in which the rotational wave packet controls the geometric part of the photoionization interferometer. The data obtained is sufficient to determine the magnitudes and phases of the ionization matrix elements for all observed channels, and to reconstruct molecular frame interferograms from lab frame measurements. In principle, this methodology provides a time-domain route to complete photoionization experiments and the molecular frame, which is generally applicable to any molecule (no prerequisites), for all energies and ionization channels.

Reaction Mechanism of Mycobacterium Tuberculosis Glutamine Synthetase Using Quantum Mechanics/Molecular Mechanics Calculations.

Science.gov (United States)

Moreira, Cátia; Ramos, Maria J; Fernandes, Pedro Alexandrino

2016-06-27

This paper is devoted to the understanding of the reaction mechanism of mycobacterium tuberculosis glutamine synthetase (mtGS) with atomic detail, using computational quantum mechanics/molecular mechanics (QM/MM) methods at the ONIOM M06-D3/6-311++G(2d,2p):ff99SB//B3LYP/6-31G(d):ff99SB level of theory. The complete reaction undergoes a three-step mechanism: the spontaneous transfer of phosphate from ATP to glutamate upon ammonium binding (ammonium quickly loses a proton to Asp54), the attack of ammonia on phosphorylated glutamate (yielding protonated glutamine), and the deprotonation of glutamine by the leaving phosphate. This exothermic reaction has an activation free energy of 21.5 kcal mol(-1) , which is consistent with that described for Escherichia coli glutamine synthetase (15-17 kcal mol(-1) ). The participating active site residues have been identified and their role and energy contributions clarified. This study provides an insightful atomic description of the biosynthetic reaction that takes place in this enzyme, opening doors for more accurate studies for developing new anti-tuberculosis therapies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ionization of amphiphilic acidic block copolymers.

Science.gov (United States)

Colombani, Olivier; Lejeune, Elise; Charbonneau, Céline; Chassenieux, Christophe; Nicolai, Taco

2012-06-28

The ionization behavior of an amphiphilic diblock copolymer poly(n-butyl acrylate(50%)-stat-acrylic acid(50%))(100)-block-poly(acrylic acid)(100) (P(nBA(50%)-stat-AA(50%))(100)-b-PAA(100), DH50) and of its equivalent triblock copolymer P(nBA(50%)-stat-AA(50%))(100)-b-PAA(200)-b-P(nBA(50%)-stat-AA(50%))(100) (TH50) were studied by potentiometric titration either in pure water or in 0.5 M NaCl. These polymers consist of a hydrophilic acidic block (PAA) connected to a hydrophobic block, P(nBA(50%)-stat-AA(50%))(100), whose hydrophobic character has been mitigated by copolymerization with hydrophilic units. We show that all AA units, even those in the hydrophobic block could be ionized. However, the AA units within the hydrophobic block were less acidic than those in the hydrophilic block, resulting in the preferential ionization of the latter block. The preferential ionization of PAA over that of P(nBA(50%)-stat-AA(50%))(100) was stronger at higher ionic strength. Remarkably, the covalent bonds between the PAA and P(nBA(50%)-stat-AA(50%))(100) blocks in the diblock or the triblock did not affect the ionization of each block, although the self-association of the block copolymers into spherical aggregates modified the environment of the PAA blocks compared to when PAA was molecularly dispersed.

Atomic and molecular physics of controlled thermonuclear fusion

International Nuclear Information System (INIS)

Joachain, C.J.; Post, D.E.

1983-01-01

This book attempts to provide a comprehensive introduction to the atomic and molecular physics of controlled thermonuclear fusion, and also a self-contained source from which to start a systematic study of the field. Presents an overview of fusion energy research, general principles of magnetic confinement, and general principles of inertial confinement. Discusses the calculation and measurement of atomic and molecular processes relevant to fusion, and the atomic and molecular physics of controlled thermonuclear research devices. Topics include recent progress in theoretical methods for atomic collisions; current theoretical techniques for electron-atom and electronion scattering; experimental aspects of electron impact ionization and excitation of positive ions; the theory of charge exchange and ionization by heavy particles; experiments on electron capture and ionization by multiply charged ions; Rydberg states; atomic and molecular processes in high temperature, low-density magnetically confined plasmas; atomic processes in high-density plasmas; the plasma boundary region and the role of atomic and molecular processes; neutral particle beam production and injection; spectroscopic plasma diagnostics; and particle diagnostics for magnetic fusion experiments

Studying the molecular mechanisms of radiation damage : low-energy electron interactions with biomolecules and medically relevant molecules

International Nuclear Information System (INIS)

Tanzer, K.

2015-01-01

Since it was discovered in the year 2000 that secondary electrons with energies below 20 eV, which are the most abundant secondary species produced upon the interaction of ionizing radiation with biological tissue, can induce severe damages in the DNA such as single and double strand breaks, the interest for the study of the interaction of electrons with essential molecules of the human body has grown immensely. Double strand breaks can lead to cancer and are therefore a substantial threat to human health, however, the radiation research community is not sure how these strand breaks are formed upon interaction with ionizing radiation. The fact that even electrons with energies well below the ionization threshold can induce great damage in biological molecules via a resonant process called dissociative electron attachment (DEA), has even furthered the interest in these electron interactions, as it was shown to be a very efficient decomposition mechanism. A variety of studies, such as DEA studies to components of the DNA, for example, have been undertaken so far to shed more light on the role electrons play in the radiation damage of biomolecules. In this thesis two nucleobases, adenine and hypoxanthine, have been studied by observing their response towards low-energy electrons. It has been found that these nucleobases behave in a similar manner upon low-energy electron interaction, as do other nucleobases, that have been studied previously. The loss of hydrogen is suspected to act as a precursor for the decomposition of the DNA and the nucleobases can also undergo ring cleavage, which will induce substantial damage in the DNA. Furthermore, the search for improved and more efficient methods for the treatment of cancer is as important as ever, considering the ever-rising number of cancer deaths. Radiotherapy has proven to be one of the best treatments for tumors, but was found to be ineffective in hypoxic - oxygen deprived - tumors. Compounds called radiosensitizers

Nanostructure and molecular mechanics of spider dragline silk protein assemblies

Science.gov (United States)

Keten, Sinan; Buehler, Markus J.

2010-01-01

Spider silk is a self-assembling biopolymer that outperforms most known materials in terms of its mechanical performance, despite its underlying weak chemical bonding based on H-bonds. While experimental studies have shown that the molecular structure of silk proteins has a direct influence on the stiffness, toughness and failure strength of silk, no molecular-level analysis of the nanostructure and associated mechanical properties of silk assemblies have been reported. Here, we report atomic-level structures of MaSp1 and MaSp2 proteins from the Nephila clavipes spider dragline silk sequence, obtained using replica exchange molecular dynamics, and subject these structures to mechanical loading for a detailed nanomechanical analysis. The structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly beta-sheet crystal domains, while disorderly regions are formed by glycine-rich repeats that consist of 31-helix type structures and beta-turns. Our structural predictions are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content. Mechanical shearing simulations on selected structures illustrate that the nanoscale behaviour of silk protein assemblies is controlled by the distinctly different secondary structure content and hydrogen bonding in the crystalline and semi-amorphous regions. Both structural and mechanical characterization results show excellent agreement with available experimental evidence. Our findings set the stage for extensive atomistic investigations of silk, which may contribute towards an improved understanding of the source of the strength and toughness of this biological superfibre. PMID:20519206

Molecular mechanisms in gliomagenesis

DEFF Research Database (Denmark)

Hulleman, Esther; Helin, Kristian

2005-01-01

Glioma, and in particular high-grade astrocytoma termed glioblastoma multiforme (GBM), is the most common primary tumor of the brain. Primarily because of its diffuse nature, there is no effective treatment for GBM, and relatively little is known about the processes by which it develops. Therefore......, in order to design novel therapies and treatments for GBM, research has recently intensified to identify the cellular and molecular mechanisms leading to GBM formation. Modeling of astrocytomas by genetic manipulation of mice suggests that deregulation of the pathways that control gliogenesis during normal...... brain development, such as the differentiation of neural stem cells (NSCs) into astrocytes, might contribute to GBM formation. These pathways include growth factor-induced signal transduction routes and processes that control cell cycle progression, such as the p16-CDK4-RB and the ARF-MDM2-p53 pathways...

Effect of an improved molecular potential on strong-field tunneling ionization of molecules

International Nuclear Information System (INIS)

Zhao Songfeng; Jin Cheng; Le, Anh-Thu; Lin, C. D.

2010-01-01

We study the effect of one-electron model potentials on the tunneling ionization rates of molecules in strong fields. By including electron correlation using the modified Leeuwen-Baerends (LB α) model, the binding energies of outer shells of molecules are significantly improved. However, we show that the tunneling ionization rates from the LB α do not differ much from the earlier calculations [Phys. Rev. A 81, 033423 (2010)], in which the local correlation potential was neglected.

Forcefields based molecular modeling on the mechanical and physical properties of emeraldine base polyaniline

NARCIS (Netherlands)

Chen, X.; Yuan, C.A.; Wong, K.Y.; Zhang, G.Q.

2010-01-01

Molecular dynamics (MD) and molecular mechanical (MM) analysis are carried out to provide reliable and accurate model for emeraldine base polyaniline. This study validate the forcefields and model with the physical and mechanical properties of the polyaniline. The temperature effects on non-bond

Epidemiological studies on the effects of low-level ionizing radiation on cancer risk

International Nuclear Information System (INIS)

Akiba, Suminori

2010-01-01

The health effects of low-level ionizing radiation are yet unclear. As pointed out by Upton in his review (Upton, 1989), low-level ionizing radiation seems to have different biological effects from what high-level radiation has. If so, the hazard identification of ionizing radiation should he conducted separately for low- and high-level ionizing radiation; the hazard identification of low-level radiation is yet to be completed. What makes hazard identification of ionizing radiation difficult, particularly in the case of carcinogenic effect, is the difficulty in distinguishing radiation-induced cancer from other cancers with respect to clinicopathological features and molecular biological characteristics. Actually, it is suspected that radiation-induced carcinogenesis involves mechanisms not specific for radiation, such as oxidative stress. Excess risk per dose in medium-high dose ranges can be extrapolated to a low-dose range if dose-response can be described by the linear-non-threshold model. The cancer risk data of atomic-bomb survivors describes leukemia risk with a linear-quadratic (LQ) model and solid-cancer risk with linear non-threshold (LNT) model. The LQ model for leukemia and the LNT model for solid cancer correspond to the two-hit model and the one-hit model, respectively. Although the one-hit model is an unlikely dose-response for carcinogenesis, there is no convincing epidemiological evidence supporting the LQ model or non-threshold model for solid cancer. It should be pointed out, however, even if the true dose response is non-linear various noises involved in epidemiological data may mask the truth. In this paper, the potential contribution of epidemiological studies on nuclear workers and residents in high background radiation areas will be discussed. (author)

New constraints on the escape of ionizing photons from starburst galaxies using ionization-parameter mapping

International Nuclear Information System (INIS)

Zastrow, Jordan; Oey, M. S.; Veilleux, Sylvain; McDonald, Michael

2013-01-01

The fate of ionizing radiation in starburst galaxies is key to understanding cosmic reionization. However, the galactic parameters on which the escape fraction of ionizing radiation depend are not well understood. Ionization-parameter mapping provides a simple, yet effective, way to study the radiative transfer in starburst galaxies. We obtain emission-line ratio maps of [S III]/[S II] for six, nearby, dwarf starbursts: NGC 178, NGC 1482, NGC 1705, NGC 3125, NGC 7126, and He 2-10. The narrowband images are obtained with the Maryland-Magellan Tunable Filter at Las Campanas Observatory. Using these data, we previously reported the discovery of an optically thin ionization cone in NGC 5253, and here we also discover a similar ionization cone in NGC 3125. This latter cone has an opening angle of 40° ± 5° (0.4 sr), indicating that the passageways through which ionizing radiation may travel correspond to a small solid angle. Additionally, there are three sample galaxies that have winds and/or superbubble activity, which should be conducive to escaping radiation, yet they are optically thick. These results support the scenario that an orientation bias limits our ability to directly detect escaping Lyman continuum in many starburst galaxies. A comparison of the star formation properties and histories of the optically thin and thick galaxies is consistent with the model that high escape fractions are limited to galaxies that are old enough (≳3 Myr) for mechanical feedback to have cleared optically thin passageways in the interstellar medium, but young enough (≲5 Myr) that the ionizing stars are still present.

A quantum-mechanics molecular-mechanics scheme for extended systems

International Nuclear Information System (INIS)

Hunt, Diego; Scherlis, Damián A; Sanchez, Veronica M

2016-01-01

We introduce and discuss a hybrid quantum-mechanics molecular-mechanics (QM-MM) approach for Car–Parrinello DFT simulations with pseudopotentials and planewaves basis, designed for the treatment of periodic systems. In this implementation the MM atoms are considered as additional QM ions having fractional charges of either sign, which provides conceptual and computational simplicity by exploiting the machinery already existing in planewave codes to deal with electrostatics in periodic boundary conditions. With this strategy, both the QM and MM regions are contained in the same supercell, which determines the periodicity for the whole system. Thus, while this method is not meant to compete with non-periodic QM-MM schemes able to handle extremely large but finite MM regions, it is shown that for periodic systems of a few hundred atoms, our approach provides substantial savings in computational times by treating classically a fraction of the particles. The performance and accuracy of the method is assessed through the study of energetic, structural, and dynamical aspects of the water dimer and of the aqueous bulk phase. Finally, the QM-MM scheme is applied to the computation of the vibrational spectra of water layers adsorbed at the TiO 2 anatase (1 0 1) solid–liquid interface. This investigation suggests that the inclusion of a second monolayer of H 2 O molecules is sufficient to induce on the first adsorbed layer, a vibrational dynamics similar to that taking place in the presence of an aqueous environment. The present QM-MM scheme appears as a very interesting tool to efficiently perform molecular dynamics simulations of complex condensed matter systems, from solutions to nanoconfined fluids to different kind of interfaces. (paper)

A quantum-mechanics molecular-mechanics scheme for extended systems.

Science.gov (United States)

Hunt, Diego; Sanchez, Veronica M; Scherlis, Damián A

2016-08-24

We introduce and discuss a hybrid quantum-mechanics molecular-mechanics (QM-MM) approach for Car-Parrinello DFT simulations with pseudopotentials and planewaves basis, designed for the treatment of periodic systems. In this implementation the MM atoms are considered as additional QM ions having fractional charges of either sign, which provides conceptual and computational simplicity by exploiting the machinery already existing in planewave codes to deal with electrostatics in periodic boundary conditions. With this strategy, both the QM and MM regions are contained in the same supercell, which determines the periodicity for the whole system. Thus, while this method is not meant to compete with non-periodic QM-MM schemes able to handle extremely large but finite MM regions, it is shown that for periodic systems of a few hundred atoms, our approach provides substantial savings in computational times by treating classically a fraction of the particles. The performance and accuracy of the method is assessed through the study of energetic, structural, and dynamical aspects of the water dimer and of the aqueous bulk phase. Finally, the QM-MM scheme is applied to the computation of the vibrational spectra of water layers adsorbed at the TiO2 anatase (1 0 1) solid-liquid interface. This investigation suggests that the inclusion of a second monolayer of H2O molecules is sufficient to induce on the first adsorbed layer, a vibrational dynamics similar to that taking place in the presence of an aqueous environment. The present QM-MM scheme appears as a very interesting tool to efficiently perform molecular dynamics simulations of complex condensed matter systems, from solutions to nanoconfined fluids to different kind of interfaces.

Endocrine-disrupting Chemicals: Review of Toxicological Mechanisms Using Molecular Pathway Analysis

Science.gov (United States)

Yang, Oneyeol; Kim, Hye Lim; Weon, Jong-Il; Seo, Young Rok

2015-01-01

Endocrine disruptors are known to cause harmful effects to human through various exposure routes. These chemicals mainly appear to interfere with the endocrine or hormone systems. As importantly, numerous studies have demonstrated that the accumulation of endocrine disruptors can induce fatal disorders including obesity and cancer. Using diverse biological tools, the potential molecular mechanisms related with these diseases by exposure of endocrine disruptors. Recently, pathway analysis, a bioinformatics tool, is being widely used to predict the potential mechanism or biological network of certain chemicals. In this review, we initially summarize the major molecular mechanisms involved in the induction of the above mentioned diseases by endocrine disruptors. Additionally, we provide the potential markers and signaling mechanisms discovered via pathway analysis under exposure to representative endocrine disruptors, bisphenol, diethylhexylphthalate, and nonylphenol. The review emphasizes the importance of pathway analysis using bioinformatics to finding the specific mechanisms of toxic chemicals, including endocrine disruptors. PMID:25853100

Using molecular mechanics to predict bulk material properties of fibronectin fibers.

Directory of Open Access Journals (Sweden)

Mark J Bradshaw

Full Text Available The structural proteins of the extracellular matrix (ECM form fibers with finely tuned mechanical properties matched to the time scales of cell traction forces. Several proteins such as fibronectin (Fn and fibrin undergo molecular conformational changes that extend the proteins and are believed to be a major contributor to the extensibility of bulk fibers. The dynamics of these conformational changes have been thoroughly explored since the advent of single molecule force spectroscopy and molecular dynamics simulations but remarkably, these data have not been rigorously applied to the understanding of the time dependent mechanics of bulk ECM fibers. Using measurements of protein density within fibers, we have examined the influence of dynamic molecular conformational changes and the intermolecular arrangement of Fn within fibers on the bulk mechanical properties of Fn fibers. Fibers were simulated as molecular strands with architectures that promote either equal or disparate molecular loading under conditions of constant extension rate. Measurements of protein concentration within micron scale fibers using deep ultraviolet transmission microscopy allowed the simulations to be scaled appropriately for comparison to in vitro measurements of fiber mechanics as well as providing estimates of fiber porosity and water content, suggesting Fn fibers are approximately 75% solute. Comparing the properties predicted by single molecule measurements to in vitro measurements of Fn fibers showed that domain unfolding is sufficient to predict the high extensibility and nonlinear stiffness of Fn fibers with surprising accuracy, with disparately loaded fibers providing the best fit to experiment. This work shows the promise of this microstructural modeling approach for understanding Fn fiber properties, which is generally applicable to other ECM fibers, and could be further expanded to tissue scale by incorporating these simulated fibers into three dimensional

Application of the weak-field asymptotic theory to the analysis of tunneling ionization of linear molecules

DEFF Research Database (Denmark)

Madsen, Lars Bojer; Tolstikhin, Oleg I.; Morishita, Toru

2012-01-01

The recently developed weak-field asymptotic theory [ Phys. Rev. A 84 053423 (2011)] is applied to the analysis of tunneling ionization of a molecular ion (H2+), several homonuclear (H2, N2, O2) and heteronuclear (CO, HF) diatomic molecules, and a linear triatomic molecule (CO2) in a static...... electric field. The dependence of the ionization rate on the angle between the molecular axis and the field is determined by a structure factor for the highest occupied molecular orbital. This factor is calculated using a virtually exact discrete variable representation wave function for H2+, very accurate...... Hartree-Fock wave functions for the diatomics, and a Hartree-Fock quantum chemistry wave function for CO2. The structure factors are expanded in terms of standard functions and the associated structure coefficients, allowing the determination of the ionization rate for any orientation of the molecule...

In situ monitoring of molecular changes during cell differentiation processes in marine macroalgae through mass spectrometric imaging.

Science.gov (United States)

Kessler, Ralf W; Crecelius, Anna C; Schubert, Ulrich S; Wichard, Thomas

2017-08-01

Matrix-assisted laser desorption/ionization mass spectrometric imaging (MALDI-MSI) was employed to discriminate between cell differentiation processes in macroalgae. One of the key developmental processes in the algal life cycle is the production of germ cells (gametes and zoids). The gametogenesis of the marine green macroalga Ulva mutabilis (Chlorophyta) was monitored by metabolomic snapshots of the surface, when blade cells differentiate synchronously into gametangia and giving rise to gametes. To establish MSI for macroalgae, dimethylsulfoniopropionate (DMSP), a known algal osmolyte, was determined. MSI of the surface of U. mutabilis followed by chemometric data analysis revealed dynamic metabolomic changes during cell differentiation. DMSP and a total of 55 specific molecular biomarkers, which could be assigned to important stages of the gametogenesis, were detected. Our research contributes to the understanding of molecular mechanisms underlying macroalgal cell differentiation. Graphical abstract Molecular changes during cell differentiation of the marine macroalga Ulva were visualized by matrix assisted laser desorption/ionization mass spectrometric imaging (MALDI-MSI).

The Effects of Ionizing Radiation on the Oral Cavity.

Science.gov (United States)

de Barros da Cunha, Sandra Ribeiro; Ramos, Pedro Augusto Mendes; Nesrallah, Ana Cristina Aló; Parahyba, Cláudia Joffily; Fregnani, Eduardo Rodrigues; Aranha, Ana Cecília Corrêa

2015-08-01

The aim of this study is to present a literature review on the effects of the ionizing radiation from radiotherapy treatment on dental tissues. Among the effects of increasing global life expectancy and longevity of the teeth in the oral cavity, increasing rates of neoplastic diseases have been observed. One of the important treatment modalities for head and neck neoplastic diseases is radiotherapy, which uses ionizing radiation as the main mechanism of action. Therefore, it is essential for dentists to be aware of the changes in oral and dental tissues caused by ionizing radiation, and to develop treatment and prevention strategies. In general, there is still controversy about the effects of ionizing radiation on dental structures. However, qualitative and quantitative changes in saliva and oral microbiota, presence of oral mucositis and radiation-related caries are expected, as they represent the well-known side effects of treatment with ionizing radiation. Points that still remain unclear are the effects of radiotherapy on enamel and dentin, and on their mechanisms of bonding to contemporary adhesive materials. Ionizing radiation has shown important interaction with organic tissues, since more deleterious effects have been shown on the oral mucosa, salivary glands and dentin, than on enamel. With the increasing number of patients with cancer seeking dental treatment before and after head and neck radiotherapy, it is important for dentists to be aware of the effects of ionizing radiation on the oral cavity.

Molecular medicine of fragile X syndrome: based on known molecular mechanisms.

Science.gov (United States)

Luo, Shi-Yu; Wu, Ling-Qian; Duan, Ran-Hui

2016-02-01

Extensive research on fragile X mental retardation gene knockout mice and mutant Drosophila models has largely expanded our knowledge on mechanism-based treatment of fragile X syndrome (FXS). In light of these findings, several clinical trials are now underway for therapeutic translation to humans. Electronic literature searches were conducted using the PubMed database and ClinicalTrials.gov. The search terms included "fragile X syndrome", "FXS and medication", "FXS and therapeutics" and "FXS and treatment". Based on the publications identified in this search, we reviewed the neuroanatomical abnormalities in FXS patients and the potential pathogenic mechanisms to monitor the progress of FXS research, from basic studies to clinical trials. The pathological mechanisms of FXS were categorized on the basis of neuroanatomy, synaptic structure, synaptic transmission and fragile X mental retardation protein (FMRP) loss of function. The neuroanatomical abnormalities in FXS were described to motivate extensive research into the region-specific pathologies in the brain responsible for FXS behavioural manifestations. Mechanism-directed molecular medicines were classified according to their target pathological mechanisms, and the most recent progress in clinical trials was discussed. Current mechanism-based studies and clinical trials have greatly contributed to the development of FXS pharmacological therapeutics. Research examining the extent to which these treatments provided a rescue effect or FMRP compensation for the developmental impairments in FXS patients may help to improve the efficacy of treatments.

Modern state of the application of ionizing radiation for protection of environment. 1. Ionizing radiation sources. Purification of natural and drinking water (review)

International Nuclear Information System (INIS)

Pikaev, AK.

2000-01-01

Review of modern state of the application of ionizing radiations for protection of environment and natural and drinking water purification is presented. Building of installations with electron accelerators with summarized power of beam ∼0.6 MW signifies that application of ionizing radiation for ecological needs increase. It is pointed out that extensible application of electron accelerators is explained by their safety and efficiency as compared with gamma-sources. New information about ionizing radiation sources, radiation-chemical purification of polluted natural and drinking water, mechanisms of processes taking place during treatment by ionizing radiations are generalized [ru

Investigation and Applications of In-Source Oxidation in Liquid Sampling-Atmospheric Pressure Afterglow Microplasma Ionization (LS-APAG) Source.

Science.gov (United States)

Xie, Xiaobo; Wang, Zhenpeng; Li, Yafeng; Zhan, Lingpeng; Nie, Zongxiu

2017-06-01

A liquid sampling-atmospheric pressure afterglow microplasma ionization (LS-APAG) source is presented for the first time, which is embedded with both electrospray ionization (ESI) and atmospheric pressure afterglow microplasma ionization (APAG) techniques. This ion source is capable of analyzing compounds with diverse molecule weights and polarities. An unseparated mixture sample was detected as a proof-of-concept, giving complementary information (both polarities and non-polarities) with the two ionization modes. It should also be noted that molecular mass can be quickly identified by ESI with clean and simple spectra, while the structure can be directly studied using APAG with in-source oxidation. The ionization/oxidation mechanism and applications of the LS-APAG source have been further explored in the analysis of nonpolar alkanes and unsaturated fatty acids/esters. A unique [M + O - 3H] + was observed in the case of individual alkanes (C 5 -C 19 ) and complex hydrocarbons mixture under optimized conditions. Moreover, branched alkanes generated significant in-source fragments, which could be further applied to the discrimination of isomeric alkanes. The technique also facilitates facile determination of double bond positions in unsaturated fatty acids/esters due to diagnostic fragments (the acid/ester-containing aldehyde and acid oxidation products) generated by on-line ozonolysis in APAG mode. Finally, some examples of in situ APAG analysis by gas sampling and surface sampling were given as well. Graphical Abstract ᅟ.

Molecular imaging of banknote and questioned document using solvent-free gold nanoparticle-assisted laser desorption/ionization imaging mass spectrometry.

Science.gov (United States)

Tang, Ho-Wai; Wong, Melody Yee-Man; Chan, Sharon Lai-Fung; Che, Chi-Ming; Ng, Kwan-Ming

2011-01-01

Direct chemical analysis and molecular imaging of questioned documents in a non/minimal-destructive manner is important in forensic science. Here, we demonstrate that solvent-free gold-nanoparticle-assisted laser desorption/ionization mass spectrometry is a sensitive and minimal destructive method for direct detection and imaging of ink and visible and/or fluorescent dyes printed on banknotes or written on questioned documents. Argon ion sputtering of a gold foil allows homogeneous coating of a thin layer of gold nanoparticles on banknotes and checks in a dry state without delocalizing spatial distributions of the analytes. Upon N(2) laser irradiation of the gold nanoparticle-coated banknotes or checks, abundant ions are desorbed and detected. Recording the spatial distributions of the ions can reveal the molecular images of visible and fluorescent ink printed on banknotes and determine the printing order of different ink which may be useful in differentiating real banknotes from fakes. The method can also be applied to identify forged parts in questioned documents, such as number/writing alteration on a check, by tracing different writing patterns that come from different pens.

Measurement of the ionization probability of the 1s sigma molecular orbital in half a collision at zero impact parameter

International Nuclear Information System (INIS)

Chemin, J.F.; Andriamonje, S.; Guezet, D.; Thibaud, J.P.; Aguer, P.; Hannachi, F.; Bruandet, J.F.

1984-01-01

We have measured, for the first time, the ionization probability Psub(1s sigma) of the 1s sigma molecular orbital in the way into a nuclear reaction (in half a collision at zero impact parameter) in a near symmetric collision 58 Ni + 54 Fe at 230 MeV leads to a compound nucleus of 112 Xe highly excited which decays first by sequential emission of charged particles and then by sequential emission of gamma rays. The determination of Psub(1s sigma) is based on the coincidence measurement between X-rays and γ-rays and the Doppler shift method is used to discrimine the ''atomic'' and ''nuclear'' X-rays

Exact and Optimal Quantum Mechanics/Molecular Mechanics Boundaries.

Science.gov (United States)

Sun, Qiming; Chan, Garnet Kin-Lic

2014-09-09

Motivated by recent work in density matrix embedding theory, we define exact link orbitals that capture all quantum mechanical (QM) effects across arbitrary quantum mechanics/molecular mechanics (QM/MM) boundaries. Exact link orbitals are rigorously defined from the full QM solution, and their number is equal to the number of orbitals in the primary QM region. Truncating the exact set yields a smaller set of link orbitals optimal with respect to reproducing the primary region density matrix. We use the optimal link orbitals to obtain insight into the limits of QM/MM boundary treatments. We further analyze the popular general hybrid orbital (GHO) QM/MM boundary across a test suite of molecules. We find that GHOs are often good proxies for the most important optimal link orbital, although there is little detailed correlation between the detailed GHO composition and optimal link orbital valence weights. The optimal theory shows that anions and cations cannot be described by a single link orbital. However, expanding to include the second most important optimal link orbital in the boundary recovers an accurate description. The second optimal link orbital takes the chemically intuitive form of a donor or acceptor orbital for charge redistribution, suggesting that optimal link orbitals can be used as interpretative tools for electron transfer. We further find that two optimal link orbitals are also sufficient for boundaries that cut across double bonds. Finally, we suggest how to construct "approximately" optimal link orbitals for practical QM/MM calculations.

Illustrating the Molecular Origin of Mechanical Stress in Ductile Deformation of Polymer Glasses.

Science.gov (United States)

Li, Xiaoxiao; Liu, Jianning; Liu, Zhuonan; Tsige, Mesfin; Wang, Shi-Qing

2018-02-16

New experiments show that tensile stress vanishes shortly after preyield deformation of polymer glasses while tensile stress after postyield deformation stays high and relaxes on much longer time scales, thus hinting at a specific molecular origin of stress in ductile cold drawing: chain tension rather than intersegmental interactions. Molecular dynamics simulation based on a coarse-grained model for polystyrene confirms the conclusion that the chain network plays an essential role, causing the glassy state to yield and to respond with a high level of intrachain retractive stress. This identification sheds light on the future development regarding an improved theoretical account for molecular mechanics of polymer glasses and the molecular design of stronger polymeric materials to enhance their mechanical performance.

Illustrating the Molecular Origin of Mechanical Stress in Ductile Deformation of Polymer Glasses

Science.gov (United States)

Li, Xiaoxiao; Liu, Jianning; Liu, Zhuonan; Tsige, Mesfin; Wang, Shi-Qing

2018-02-01

New experiments show that tensile stress vanishes shortly after preyield deformation of polymer glasses while tensile stress after postyield deformation stays high and relaxes on much longer time scales, thus hinting at a specific molecular origin of stress in ductile cold drawing: chain tension rather than intersegmental interactions. Molecular dynamics simulation based on a coarse-grained model for polystyrene confirms the conclusion that the chain network plays an essential role, causing the glassy state to yield and to respond with a high level of intrachain retractive stress. This identification sheds light on the future development regarding an improved theoretical account for molecular mechanics of polymer glasses and the molecular design of stronger polymeric materials to enhance their mechanical performance.

Molecular perspectives in differentiated thyroid cancer.

Science.gov (United States)

Buffet, C; Groussin, L

2015-02-01

Progress in understanding the molecular genetics of thyroid cancer in the last 20 years has accelerated recently with the advent of high-throughput sequencing technologies known as Next-Generation Sequencing. Besides classical molecular abnormalities involving the MAPK (Mitogen Activated Protein Kinase) and PI3K (PhosphoInositide 3-Kinase) pathways that play a key role in follicular-derived thyroid tumorigenesis, new molecular abnormalities have been discovered. The major advances in recent years have been the discovery of new somatic driver gene point mutations (such as RASAL1 [RAS protein activator Like 1] mutations in follicular cancer) and/or mutations that have prognostic value (such as TERT [Telomerase reverse transcriptase] promoter mutations); new chromosomal rearrangements, usually having close connection with exposure to ionizing radiation (such as ALK [Anaplastic Lymphoma Kinase] rearrangements); and deregulation of some gene or microRNA expression representing a molecular signature. Progress made in understanding the molecular mechanisms of thyroid cancer offers new perspectives for the diagnosis of the benign or malignant status of a thyroid nodule, to refine prognosis and offer new perspectives of targeted therapy for radioiodine-refractory cancers. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

The mechanisms of Micrococcus radiodurans radioresistance

International Nuclear Information System (INIS)

Samojlenko, I.I.

1983-01-01

Modern representations on molecular mechanisms of Micrococcus radiodurans viability under the effect of ionizing radiation have been considered. Factors conditioning a high level of micrococcus cell radiostability have been analyzed: peculiarities of structure of a cell wall, DNA, membranes; excess of genetic information; multiplicity of DNA implantation points to a membrane; high level of antioxidation and antiradical systems. It has been shown that on efficiency of accurate, properly balanced system of DNA repair combined with above Micrococcus radiodurant properties provide a high microorganism radioresistance

Nuclear Magnetic Shielding Constants from Quantum Mechanical/Molecular Mechanical Calculations Using Polarizable Embedding: Role of the Embedding Potential

DEFF Research Database (Denmark)

Steinmann, Casper; Olsen, Jógvan Magnus Haugaard; Kongsted, Jacob

2014-01-01

We present NMR shielding constants obtained through quantum mechanical/molecular mechanical (QM/MM) embedding calculations. Contrary to previous reports, we show that a relatively small QM region is sufficient, provided that a high-quality embedding potential is used. The calculated averaged NMR...... shielding constants of both acrolein and acetone solvated in water are based on a number of snapshots extracted from classical molecular dynamics simulations. We focus on the carbonyl chromophore in both molecules, which shows large solvation effects, and we study the convergence of shielding constants...

Molecular Mechanisms Behind the Chemopreventive Effects of Anthocyanidins

Directory of Open Access Journals (Sweden)

De-Xing Hou

2004-01-01

Full Text Available Anthocyanins are polyphenolic ring-based flavonoids, and are widespread in fruits and vegetables of red-blue color. Epidemiological investigations and animal experiments have indicated that anthocyanins may contribute to cancer chemoprevention. The studies on the mechanism have been done recently at molecular level. This review summarizes current molecular bases for anthocyanidins on several key steps involved in cancer chemoprevention: (i inhibition of anthocyanidins in cell transformation through targeting mitogen-activated protein kinase (MAPK pathway and activator protein 1 (AP-1 factor; (ii suppression of anthocyanidins in inflammation and carcinogenesis through targeting nuclear factor kappa B (NF-κB pathway and cyclooxygenase 2 (COX-2 gene; (iii apoptotic induction of cancer cells by anthocyanidins through reactive oxygen species (ROS / c-Jun NH2-terminal kinase (JNK-mediated caspase activation. These data provide a first molecular view of anthocyanidins contributing to cancer chemoprevention.

Interpopulational variability of molecular responses to ionizing radiation in freshwater bivalves Anodonta anatina (Unionidae)

Energy Technology Data Exchange (ETDEWEB)

Falfushynska, H. [Research Laboratory of Comparative Biochemistry and Molecular Biology, Ternopil National Pedagogical University, 2, Kryvonosa Str, Ternopil 46027 (Ukraine); Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223 (United States); Department of General Chemistry, I.Ya. Horbachevsky Ternopil State Medical University, 1, Maidan Voli, Ternopil 46001 (Ukraine); Gnatyshyna, L. [Research Laboratory of Comparative Biochemistry and Molecular Biology, Ternopil National Pedagogical University, 2, Kryvonosa Str, Ternopil 46027 (Ukraine); Department of General Chemistry, I.Ya. Horbachevsky Ternopil State Medical University, 1, Maidan Voli, Ternopil 46001 (Ukraine); Yurchak, I.; Stoliar, O. [Research Laboratory of Comparative Biochemistry and Molecular Biology, Ternopil National Pedagogical University, 2, Kryvonosa Str, Ternopil 46027 (Ukraine); Sokolova, I.M., E-mail: isokolova@uncc.edu [Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223 (United States)

2016-10-15

Freshwater ecosystems are exposed to multiple anthropogenic stressors including chemical pollution and warming that can affect health of the resident organisms and their responses to novel challenges. We investigated the of in situ exposure history on molecular responses to a novel stressor, ionizing radiation, in unionid mollusks Anodonta anatina. Males from pristine (F-), agricultural (A-) sites and a cooling reservoir of a nuclear power plant (N-site) were exposed to acute low dose (2 mGy) X-ray radiation followed by 14 days of recovery (R-groups) or to control conditions (C-groups). Biomarkers of oxidative stress, geno-, cyto- and neurotoxicity were used to assess cellular injury and stress. Control group from the cooling reservoir (CN) had higher background levels of caspase-3 activity, metallothionein concentrations and nuclear lesions and lower levels of superoxide dismutase (SOD) and glutathione in the gills compared to other control groups (CF and CA). Irradiation induced cellular damage in mussels from all three sites including increased levels of nuclear lesions in hemocytes, depletion of caspase-3, suppression of superoxide dismutase and catalase activities, an increase of the lipid peroxidation and oxidized glutathione levels, as well as down-regulation of cholinesterase indicating neurotoxicity. The up-regulation of ethoxyresorufin-O-deethylase activity in the digestive gland and vitellogenin-like protein level in gonads were also found in radiation-exposed groups indicating feminization of males and disturbances of xenobiotic metabolism. The RA-group showed the greatest magnitude of radiation-induced stress responses compared to the other two groups. Overall, unionid mollusks, particularly those from a chronically polluted agricultural site, were highly sensitive to low-dose radiation (2 mGy) indicating limitations of stress protection mechanisms to deal with multiple stressors. - Highlights: • Habitat-specific effects of irradiation were studied

Interpopulational variability of molecular responses to ionizing radiation in freshwater bivalves Anodonta anatina (Unionidae)

International Nuclear Information System (INIS)

Falfushynska, H.; Gnatyshyna, L.; Yurchak, I.; Stoliar, O.; Sokolova, I.M.

2016-01-01

Freshwater ecosystems are exposed to multiple anthropogenic stressors including chemical pollution and warming that can affect health of the resident organisms and their responses to novel challenges. We investigated the of in situ exposure history on molecular responses to a novel stressor, ionizing radiation, in unionid mollusks Anodonta anatina. Males from pristine (F-), agricultural (A-) sites and a cooling reservoir of a nuclear power plant (N-site) were exposed to acute low dose (2 mGy) X-ray radiation followed by 14 days of recovery (R-groups) or to control conditions (C-groups). Biomarkers of oxidative stress, geno-, cyto- and neurotoxicity were used to assess cellular injury and stress. Control group from the cooling reservoir (CN) had higher background levels of caspase-3 activity, metallothionein concentrations and nuclear lesions and lower levels of superoxide dismutase (SOD) and glutathione in the gills compared to other control groups (CF and CA). Irradiation induced cellular damage in mussels from all three sites including increased levels of nuclear lesions in hemocytes, depletion of caspase-3, suppression of superoxide dismutase and catalase activities, an increase of the lipid peroxidation and oxidized glutathione levels, as well as down-regulation of cholinesterase indicating neurotoxicity. The up-regulation of ethoxyresorufin-O-deethylase activity in the digestive gland and vitellogenin-like protein level in gonads were also found in radiation-exposed groups indicating feminization of males and disturbances of xenobiotic metabolism. The RA-group showed the greatest magnitude of radiation-induced stress responses compared to the other two groups. Overall, unionid mollusks, particularly those from a chronically polluted agricultural site, were highly sensitive to low-dose radiation (2 mGy) indicating limitations of stress protection mechanisms to deal with multiple stressors. - Highlights: • Habitat-specific effects of irradiation were studied

Combined quantum mechanical and molecular mechanical reaction pathway calculation for aromatic hydroxylation by p-hydroxybenzoate-3-hydroxylase

NARCIS (Netherlands)

Ridder, L.; Mulholland, A.; Rietjens, I.M.C.M.; Vervoort, J.

1999-01-01

The reaction pathway for the aromatic 3-hydroxylation of p-hydroxybenzoate by the reactive C4a-hydroperoxyflavin cofactor intermediate in p-hydroxybenzoate hydroxylase (PHBH) has been investigated by a combined quantum mechanical and molecular mechanical (QM/MM) method. A structural model for the

Molecular Mechanism of Somite Development

Directory of Open Access Journals (Sweden)

Gulfidan Coskun

2013-06-01

Full Text Available From third week of gestation, notochord and the neural folds begin to gather at the center of the embryo to form the paraxial mesoderm. Paraxial mesoderm separates into blocks of cells called somitomers at the lateral sides of the neural tube of the head region. At the beginning of the third week somitomeres take ring shapes and form blocks of somites from occipital region to caudal region. Although somites are transient structures, they are extremely important in organizing the segmental pattern of vertebrate embryos. Somites give rise to the cells that form the vertebrae and ribs, the dermis of the dorsal skin, the skeletal muscles of the back, and the skeletal muscles of the body wall and limbs. Somitogenesis are formed by a genetic mechanism that is regulated by cyclical expression of genes in the Notch, Wnt and fibroblast growth factor signaling pathways. The prevailing model of the mechanism governing somitogenesis is the “clock and wave front”. Somitogenesis has components of periodicity, separation, epithelialization and axial specification. According to this model, the clock causes cells to undergo repeated oscillations, with a particular phase of each oscillation defining the competency of cells in the presomitic mesoderm to form a somite. Any disruption in this mechanism can be cause of severe segmentation defects of the vertebrae and congenital anomalies. In this review, we discuss the molecular mechanisms underlying the somitogenesis which is an important part of morphogenesis. [Archives Medical Review Journal 2013; 22(3.000: 362-376

Multiphoton ionization of H{sub 2}{sup +} in xuv laser pulses

Energy Technology Data Exchange (ETDEWEB)

Guan Xiaoxu; Secor, Ethan B.; Bartschat, Klaus [Department of Physics and Astronomy, Drake University, Des Moines, Iowa 50311 (United States); Schneider, Barry I. [Office of Cyberinfrastructure, National Science Foundation, Arlington, Virgina 22230 (United States)

2011-09-15

We consider the ionization of the hydrogen molecular ion after one-, two-, and three-photon absorption over a large range of photon energies between 9 and 40 eV in the fixed-nuclei approximation. The temporal development of the system is obtained in a fully ab initio time-dependent grid-based approach in prolate spheroidal coordinates. The alignment dependence of the one-photon ionization amplitude is highlighted in the framework of time-dependent perturbation theory. For one-photon ionization as a function of the nuclear separation, the calculations reveal a significant minimum in the ionization probability. The suppressed ionization is attributed to a Cooper-type minimum, which is similar, but not identical, to the cancellation effect observed in photoionization cross sections of some noble-gas atoms. The effect of the nonspherical two-center Coulomb potential is analyzed. For two- and three-photon ionization, the angle-integrated cross sections clearly map out intermediate-state resonances, and the predictions of the current computations agree very well with those from time-independent calculations. The dominant emission modes for two-photon ionization are found to be very similar in both resonance and off-resonance regions.

The effects of low dose ionizing radiation on the development of rat cerebral cortex, (2)

International Nuclear Information System (INIS)

Matsushita, Koji

1993-01-01

In order to study the molecular mechanisms of neuronal migration on developing rat cerebral cortex, we need a tissue culture system in which neuronal migration can be observed. We prepared a tissue culture system of embryonic rat cerebral cortex starting on embryonic day 16 and cultivating it for 48 hours. The autoradiographic study in this system revealed not only the migration of 3 H-thymidine labeled neurons but also neuronal migration delays from low doses of ionizing radiation of more than 10 cGy. In addition, on immunohistochemical study, cell-cell adhesion molecule N-CAM staining was remarkably decreased in the matrix cell layer. In the tissue culture system where monoclonal anti-N-CAM antibodies were added, neuronal migration delay comparable to that of 20 cGy radiation was found. In conclusion, it was speculated that neuronal migration delay might be caused by disturbed N-CAM synthesis in matrix cells after low dose ionizing radiation. (author)

An update on the mechanisms and pathophysiological consequences of genomic instability with a focus on ionizing radiation

Directory of Open Access Journals (Sweden)

Streffer C

2015-12-01

Full Text Available Christian Streffer Institute for Medical Radiobiology, University Clinics Essen, Essen, Germany Abstract: The genome of eukaryotic cells is generally instable. DNA damage occurs by endogenous processes and exogenous toxic agents. The efficient DNA repair pathways conserve the genetic information to a large extent throughout the life. However, exposure to genotoxic agents can increase the genomic instability. This phenomenon develops in a delayed manner after approximately 20 and more cell generations. It is comparatively thoroughly investigated after the exposure to ionizing radiation. The increase of genomic instability has been observed after exposures to ionizing radiation in vitro and in vivo as well as with many different types of radiation. The effect is induced over a wide dose range, and it has been found with cell death, chromosomal damage, cell transformations, mutations, double-strand breaks, malformations, and cancers. No specific chromosomes or genomic sites have been observed for such events. The increased genomic instability can be transmitted to the next generation. Possible mechanisms such as oxidative stress (mitochondria may be involved, reduced DNA repair, changes in telomeres, epigenetic effects are discussed. A second wave of oxidative stress has been observed after radiation exposures with considerably high doses as well as with cytotoxic agents at time periods when an increased genomic instability was seen. However, the increase of genomic instability also happens to much lower radiation doses. Hypoxia induces an increase of genomic instability. This effect is apparently connected with a reduction of DNA repair. Changes of telomeres appear as the most probable mechanisms for the increase of genomic instability. Syndromes have been described with a genetic predisposition for high radiosensitivity. These individuals show an increase of cancer, a deficient DNA repair, a disturbed regulation of the cell cycle, and an

Cellular and molecular investigations of the adhesion and mechanics of Listeria monocytogenes

Science.gov (United States)

Eskhan, Asma Omar

Atomic force microscopy has been used to quantify the adherence and mechanical properties of an array of L. monocytogenes strains and their surface biopolymers. First, eight L. monocytogenes strains that represented the two major lineages of the species were compared for their adherence and mechanics at cellular and molecular levels. Our results indicated that strains of lineage' II were characterized by higher adhesion and Young's moduli, longer and more rigid surface biopolymers and lower specific and nonspecific forces when compared to lineage' I strains. Additionally, adherence and mechanical properties of eight L. monocytogenes epidemic and environmental strains were probed. Our results pointed to that environmental and epidemic strains representative of a given lineage were similar in their adherence and mechanical properties when investigated at a cellular level. However, when the molecular properties of the strains were considered, epidemic strains were characterized by higher specific and nonspecific forces, shorter, denser and more flexible biopolymers compared to environmental strains. Second, the role of environmental pH conditions of growth on the adhesion and mechanics of a pathogenic L. monocytogenes EGDe was investigated. Our results pointed to a transition in the adhesion energies for cells cultured at pH 7. In addition, when the types of molecular forces that govern the adhesion were quantified using Poisson statistical approach and using a new proposed method, specific hydrogen-bond energies dominated the bacterial adhesion process. Such a finding is instrumental to researchers designing methods to control bacterial adhesion. Similarly, bacterial cells underwent a transition in their mechanical properties. We have shown that cells cultured at pH 7 were the most rigid compared to those cultured in lower or higher pH conditions of growth. Due to transitions observed in adherence and mechanics when cells were cultured at pH 7, we hypothesized that

Molecular dynamics simulations of graphoepitaxy of organic semiconductors, sexithiophene, and pentacene: Molecular-scale mechanisms of organic graphoepitaxy