Electron-scale electrostatic solitary waves and shocks: the role of superthermal electrons

The propagation of electron-acoustic solitary waves and shock structures is investigated in a plasma characterized by a superthermal electron population. A three-component plasma model configuration is employed, consisting of inertial (“cold”) electrons, inertialess ? (kappa) distributed superthermal (“hot”) electrons and stationary ions. A multiscale method is employed, leading to a Korteweg-de Vries (KdV) equation for the electrostatic potential (in the absence of dissipation). Taking into account dissipation, a hybrid Korteweg-de Vries-Burgers (KdVB) equation is derived. Exact negative-potential pulse- and kink-shaped solutions (shocks) are obtained. The relative strength among dispersion, nonlinearity and damping coefficients is discussed. Excitations formed in superthermal plasma (finite ?) are narrower and steeper, compared to the Maxwellian case (infinite ?). A series of numerical simulations confirms that energy initially stored in a solitary pulse which propagates in a stable manner for large ? (Maxwellian plasma) may break down to smaller structures or/and to random oscillations, when it encounters a small-? (nonthermal) region. On the other hand, shock structures used as initial conditions for numerical simulations were shown to be robust, essentially responding to changed in the environment by a simple profile change (in width).

Electron-acoustic solitary waves in the presence of a suprathermal electron component

The nonlinear dynamics of electron-acoustic localized structures in a collisionless and unmagnetized plasma consisting of “cool” inertial electrons, “hot” electrons having a kappa distribution, and stationary ions is studied. The inertialess hot electron distribution thus has a long-tailed suprathermal (non-Maxwellian) form. A dispersion relation is derived for linear electron-acoustic waves. They show a strong dependence of the charge screening mechanism on excess suprathermality (through ?). A nonlinear pseudopotential technique is employed to investigate the occurrence of stationary-profile solitary waves, focusing on how their characteristics depend on the spectral index ?, and the hot-to-cool electron temperature and density ratios. Only negative polarity solitary waves are found to exist, in a parameter region which becomes narrower as deviation from the Maxwellian (suprathermality) increases, while the soliton amplitude at fixed soliton speed increases. However, for a constant value of the true Mach number, the amplitude decreases for decreasing ?.

Molecular rearrangement reactions in the gas phase triggered by electron attachment

Bond formation and rearrangement reactions in gas phase electron attachment were studied through dissociative electron attachment (DEA) to pentafluorotoluene (PFT), pentafluoroaniline (PFA) and pentafluorophenol (PFP) in the energy range 0-14 eV. In the case of PFA and PFP, the dominant processes involve formation of [M - HF](-) through the loss of neutral HF. This fragmentation channel is most efficient at low incident electron energy and for PFP it is accompanied by a substantial conformational change of the anionic fragment. At higher energy, HF loss is also observed as well as a number of other fragmentation processes. Thermochemical threshold energies have been computed for all the observed fragments and classical trajectories of the electron attachment process were calculated to elucidate the fragmentation mechanisms. For the dominant reaction channel leading to the loss of HF from PFP, the minimum energy path was calculated using the nudged elastic band method.

Charge steering of laser plasma accelerated fast ions in a liquid spray - Creation of MeV negative ion and neutral atom beams

The scenario of electron capture and loss has been recently proposed for the formation of negative ion and neutral atom beams with up to MeV kinetic energy [S. Ter-Avetisyan, Appl. Phys. Lett. 99, 051501 (2011)]. Validation of these processes and of their generic nature is here provided in experiments where the ion source and the interaction medium have been spatially separated. Fast positive ions accelerated from a laser plasma source are sent through a cold spray where their charge is changed. Such formed neutral atom or negative ion has nearly the same momentum as the original positive ion. Experiments are released for protons, carbon, and oxygen ions and corresponding beams of negative ions and neutral atoms have been obtained. The electron capture and loss phenomenon is confirmed to be the origin of the negative ion and neutral atom beams. The equilibrium ratios of different charge components and cross sections have been measured. Our method is general and allows the creation of beams of neutral atoms and negative ions for different species which inherit the characteristics of the positive ion source.

Energetic beams of negative and neutral hydrogen from intense laser plasma interaction

We present observations of intense beams of energetic negative hydrogen ions and fast neutral hydrogen atoms in intense (5 × 10 W/cm) laser plasma interaction experiments, which were quantified in numerical calculations. Generation of negative ions and neutral atoms is ascribed to the processes of electron capture and loss by a laser accelerated positive ion in the collisions with a cloud of droplets. A comparison with a numerical model of charge exchange processes provides information on the cross section of the electron capture in the high energy domain.

Electron-induced hydrogen loss in uracil in a water cluster environment

Low-energy electron-impact hydrogen loss due to dissociative electron attachment (DEA) to the uracil and thymine molecules in a water cluster environment is investigated theoretically. Only the A'-resonance contribution, describing the near-threshold behavior of DEA, is incorporated. Calculations are based on the nonlocal complex potential theory and the multiple scattering theory, and are performed for a model target with basic properties of uracil and thymine, surrounded by five water molecules. The DEA cross section is strongly enhanced when the attaching molecule is embedded in a water cluster. This growth is due to two effects: the increase of the resonance lifetime and the negative shift in the resonance position due to interaction of the intermediate negative ion with the surrounding water molecules. A similar effect was earlier found in DEA to chlorofluorocarbons. 

Electron rescattering in strong-field photodetachment of F-

We present ab initio studies of photoelectron spectra for above threshold detachment (ATD) of F- anions in short, 1300 nm and 1800 nm laser pulses. We identify and assess the importance of electron rescattering in strong-field photodetachment of a negative ion through comparison with an analytic, Keldysh-type approach, demonstrating the capability of ab-initio computation in the challenging near-IR regime. We further assess the influence of the strong electron correlation on the photodetachment.

Electron-acoustic solitons in an electron-beam plasma system with kappa-distributed electrons

Interaction of a stream of high-energy electrons with the background plasma plays an important role in the astrophysical phenomena such as interplanetary and stellar bow shock and Earth's foreshock emission. It is not yet fully understood how electrostatic solitary waves are produced at the bow shock. Interestingly, a population of energetic suprathermal electrons were also found to exist in those environments. Previously, we have studied the properties of negative electrostatic potential solitary structures exist in such a plasma with excess suprathermal electrons. In the present study, we investigate the existence conditions and propagation properties of electron-acoustic solitary waves in a plasma consisting of an electron beam fluid, a cold electron fluid, and hot suprathermal electrons modeled by a kappa-distribution function. The Sagdeev pseudopotential method was used to investigate the occurrence of stationary-profile solitary waves. We have determined how the electron-acoustic soliton characteristics depend on the electron beam parameters. It is found that the existence domain for solitons becomes narrower with an increase in the suprathermality of hot electrons, increasing the beam speed, decreasing the beam-to-cold electron population ratio. These results lead to a better understanding of the formation of electron-acoustic solitary waves observed in those space plasma systems characterized by kappa-distributed electrons and inertial drifting (beam) electrons.

New source of MeV negative ion and neutral atom beams

The scenario of "electron-capture and -loss" was recently proposed for the formation of negative ion and neutral atom beams with MeV kinetic energies. However, it does not explain why the formation of negative ions in a liquid spray is much more efficient than with an isolated atom. The role of atomic excited states in the charge-exchange processes is considered, and it is shown that it cannot account for the observed phenomena. The processes are more complex than the single electron-capture and -loss approach. It is suggested that the shell effects in the electronic structure of the projectile ion and/or target atoms may influence the capture/loss probabilities.

Fast atom bombardment and electron impact mass spectrometry studies of some aryltin compounds and ferrocenes

Both El MS and FAB MS behavior of two groups of compounds, aryltin and ferrocene compounds, have been studied. For the aryltin compounds, the effect of substituent group position, substituent group type and ligand type on the El spectra have been explored in the El MS studies. The fragmentation mechanism has been investigated under El with linked scans, such as fragment ion scans(BJE), parent ion scans(B2JE) and constant neutral radical loss scans(B2(1-E)JE2). In the FAB MS studies, matrix optimization experiments have been carried out. The positive ion FAB MS studies focused on the effect of substituent group position, substituent group type and ligand type on the spectra. The fragmentation mechanisms of all the samples under positive ion FAB have been studied by means of the linked scans. The CA positive ion FAB fragmentation studies were also carried out for a typical sample. Negative ion FAB experiments of all the compounds have been done. And finally, the comparison of the El MS and FAB MS has been made. For ferrocenes, the studies concentrated on the fragmentation mechanism of each compound under El with linked scan techniques in the first field-free region and the applicability of positive/negative ion FAB MS to this group of compounds. The fragmentation mechanisms under positive ion FAB of those ferrocenes which can give positive ion FAB MS spectra were studied with the linked scan techniques. The CA +ve F AB fragmentation studies were carried out for a typical sample. Comparison of the E1 MS and FAB MS has been made.

Orientation of Non-Native 2-Monosubstituted and 2,3-Disubstituted 1,4-Naphthoquinones in the A1 binding site of PSI and the effect on the rate of electron transfer : an electron paramagnetic resonance spectroscopy study

The proce-ss ofoxygenic photosynthesis is vital to life on Earth. the central event in photosynthesis is light induced electron transfer that converts light into energy for growth. Ofparticular significance is the membrane bound multisubunit protein known as Photosystem I (PSI). PSI is a reaction centre that is responsible for the transfer of electrons across the membrane to reduce NADP+ to NADPH. The recent publication ofa high resolution X-ray structure of PSI has shown new information about the structure, in particular the electron transfer cofactors, which allows us to study it in more detail. In PSI, the secondary acceptor is crucial for forward electron transfer. In this thesis, the effect of removing the native acceptor phylloquinone and replacing it with a series of structurally related quinones was investigated via transient electron paramagnetic resonance (EPR) experiments. The orientation of non native quinones in the binding site and their ability to function in the electron transfer process was determined. It was found that PSI will readily accept alkyl naphthoquinones and anthraquinone. Q band EPR experiments revealed that the non-native quinones are incorporated into the binding site with the same orientation of the headgroup as in the native system. X band EPR spectra and deuteration experiments indicate that monosubstituted naphthoquinones are bound to the Al site with their side group in the position occupied by the methyl group in native PSI (meta to the hydrogen bonded carbonyl oxygen). X band EPR experiments show that 2, 3- disubstituted methyl naphthoquinones are also incorporated into the Al site in the same orientation as phylloquinone, even with the presence of a halogen- or sulfur-containing side chain in the position normally occupied by the phytyl tail ofphylloquinone. The exception to this is 2-bromo-3-methyl --.- _. -. - -- - - 4 _._ _ _ - _ _ naphthoquinone which has a poorly resolved spectrum, making determination of the orientation difficuh. All of the non-native quinones studied act as efficient electron acceptors. However, forward electron transfer past the quinone could only be demonstrated for anthraquinone, which has a more negative midpoint potential than phylloquinone. In the case of anthraquinone, an increased rate of forward electron transfer compared to native PSI was found. From these results we can conclude that the rate ofelectron transfer from Al to Fx in native PSI lies in the normal region ofthe Marcus Curve.

X-ray diffraction of a gram-negative bacterial membrane mimetic

This thesis applies x-ray diffraction to measure he membrane structure of lipopolysaccharides and to develop a better model of a LPS bacterial melilbrane that can be used for biophysical research on antibiotics that attack cell membranes. \iVe ha'e Inodified the Physics department x-ray machine for use 3.'3 a thin film diffractometer, and have lesigned a new temperature and relative humidity controlled sample cell.\Ve tested the sample eel: by measuring the one-dimensional electron density profiles of bilayers of pope with 0%, 1%, 1G :VcJ, and 100% by weight lipo-polysaccharide from Pse'udo'lTwna aeTuginosa. Background VVe now know that traditional p,ntibiotics ,I,re losing their effectiveness against ever-evolving bacteria. This is because traditional antibiotic: work against specific targets within the bacterial cell, and with genetic mutations over time, themtibiotic no longer works. One possible solution are antimicrobial peptides. These are short proteins that are part of the immune systems of many animals, and some of them attack bacteria directly at the membrane of the cell, causing the bacterium to rupture and die. Since the membranes of most bacteria share common structural features, and these featuret, are unlikely to evolve very much, these peptides should effectively kill many types of bacteria wi Lhout much evolved resistance. But why do these peptides kill bacterial cel: '3 , but not the cells of the host animal? For gramnegative bacteria, the most likely reason is that t Ileir outer membrane is made of lipopolysaccharides (LPS), which is very different from an animal :;ell membrane. Up to now, what we knovv about how these peptides work was likely done with r !10spholipid models of animal cell membranes, and not with the more complex lipopolysa,echaricies, If we want to make better pepticies, ones that we can use to fight all types of infection, we need a more accurate molecular picture of how they \vork. This will hopefully be one step forward to the ( esign of better treatments for bacterial infections.

Large is fast, small is tight: determinants of speed and affinity in subunit capture by a periplasmic chaperone

The chaperone/usher pathway assembles surface virulence organelles of Gram-negative bacteria, consisting of fibers of linearly polymerized protein subunits. Fiber subunits are connected through 'donor strand complementation': each subunit completes the immunoglobulin (Ig)-like fold of the neighboring subunit by donating the seventh β-strand in trans. Whereas the folding of Ig domains is a fast first-order process, folding of Ig modules into the fiber conformation is a slow second-order process. Periplasmic chaperones separate this process in two parts by forming transient complexes with subunits. Interactions between chaperones and subunits are also based on the principle of donor strand complementation. In this study, we have performed mutagenesis of the binding motifs of the Caf1M chaperone and Caf1 capsular subunit from Yersinia pestis and analyzed the effect of the mutations on the structure, stability, and kinetics of Caf1M-Caf1 and Caf1-Caf1 interactions. The results suggest that a large hydrophobic effect combined with extensive main-chain hydrogen bonding enables Caf1M to rapidly bind an early folding intermediate of Caf1 and direct its partial folding. The switch from the Caf1M-Caf1 contact to the less hydrophobic, but considerably tighter and less dynamic Caf1-Caf1 contact occurs via the zip-out-zip-in donor strand exchange pathway with pocket 5 acting as the initiation site. Based on these findings, Caf1M was engineered to bind Caf1 faster, tighter, or both faster and tighter. To our knowledge, this is the first successful attempt to rationally design an assembly chaperone with improved chaperone function.

Modelling negative feedback networks for activating transcription factor 3 predicts a dominant role for miRNAs in immediate early gene regulation

Activating transcription factor 3 (Atf3) is rapidly and transiently upregulated in numerous systems, and is associated with various disease states. Atf3 is required for negative feedback regulation of other genes, but is itself subject to negative feedback regulation possibly by autorepression. In cardiomyocytes, Atf3 and Egr1 mRNAs are upregulated via ERK1/2 signalling and Atf3 suppresses Egr1 expression. We previously developed a mathematical model for the Atf3-Egr1 system. Here, we adjusted and extended the model to explore mechanisms of Atf3 feedback regulation. Introduction of an autorepressive loop for Atf3 tuned down its expression and inhibition of Egr1 was lost, demonstrating that negative feedback regulation of Atf3 by Atf3 itself is implausible in this context. Experimentally, signals downstream from ERK1/2 suppress Atf3 expression. Mathematical modelling indicated that this cannot occur by phosphorylation of pre-existing inhibitory transcriptional regulators because the time delay is too short. De novo synthesis of an inhibitory transcription factor (ITF) with a high affinity for the Atf3 promoter could suppress Atf3 expression, but (as with the Atf3 autorepression loop) inhibition of Egr1 was lost. Developing the model to include newly-synthesised miRNAs very efficiently terminated Atf3 protein expression and, with a 4-fold increase in the rate of degradation of mRNA from the mRNA/miRNA complex, profiles for Atf3 mRNA, Atf3 protein and Egr1 mRNA approximated to the experimental data. Combining the ITF model with that of the miRNA did not improve the profiles suggesting that miRNAs are likely to play a dominant role in switching off Atf3 expression post-induction.

Oxygen-mediated electron transport through hybrid silicon-organic interfaces

We investigate from first principles the electronic and transport properties of hybrid organic/silicon interfaces of relevance to molecular electronics. We focus on conjugated molecules bonded to hydrogenated Si through hydroxyl or thiol groups. The electronic structure of the systems is addressed within density functional theory, and the electron transport across the interface is directly evaluated within the Landauer approach. The microscopic effects of molecule-substrate bonding on the transport efficiency are explicitly analyzed, and the oxygen-bonded interface is identified as a candidate system when preferential hole transfer is needed.