Non-thermal Plasma Exposure Rapidly Attenuates Bacterial AHL-Dependent Quorum Sensing and Virulence.

The antimicrobial activity of atmospheric pressure non-thermal plasma has been exhaustively characterised, however elucidation of the interactions between biomolecules produced and utilised by bacteria and short plasma exposures are required for optimisation and clinical translation of cold plasma technology. This study characterizes the effects of non-thermal plasma exposure on acyl homoserine lactone (AHL)-dependent quorum sensing (QS). Plasma exposure of AHLs reduced the ability of such molecules to elicit a QS response in bacterial reporter strains in a dose-dependent manner. Short exposures (30-60 s) produce of a series of secondary compounds capable of eliciting a QS response, followed by the complete loss of AHL-dependent signalling following longer exposures. UPLC-MS analysis confirmed the time-dependent degradation of AHL molecules and their conversion into a series of by-products. FT-IR analysis of plasma-exposed AHLs highlighted the appearance of an OH group. In vivo assessment of the exposure of AHLs to plasma was examined using a standard in vivo model. Lettuce leaves injected with the rhlI/lasI mutant PAO-MW1 alongside plasma treated N-butyryl-homoserine lactone and n-(3-oxo-dodecanoyl)-homoserine lactone, exhibited marked attenuation of virulence. This study highlights the capacity of atmospheric pressure non-thermal plasma to modify and degrade AHL autoinducers thereby attenuating QS-dependent virulence in P. aeruginosa.

Measurement of electromagnetic pulses generated during interactions of high power lasers with solid targets

A target irradiated with a high power laser pulse, blows off a large amount of charge and as a consequence the target itself becomes a generator of electromagnetic pulses (EMP) owing to high return current flowing to the ground through the target holder. The first measurement of the magnetic field induced by the neutralizing current reaching a value of a few kA was performed with the use of an inductive target probe at the PALS Laser Facility (Cikhardt et al. Rev. Sci. Instrum. 85 (2014) 103507). A full description of EMP generation should contain information on the spatial distribution and temporal variation of the electromagnetic field inside and outside of the interaction chamber. For this reason, we consider the interaction chamber as a resonant cavity in which different modes of EMP oscillate for hundreds of nanoseconds, until the EMP is transmitted outside through the glass windows and EM waves are attenuated. Since the experimental determination of the electromagnetic field distribution is limited by the number of employed antennas, a mapping of the electromagnetic field has to be integrated with numerical simulations. Thus, this work reports on a detailed numerical mapping of the electromagnetic field inside the interaction chamber at the PALS Laser Facility (covering a frequency spectrum from 100 MHz to 3 GHz) using the commercial code COMSOL Multiphysics 5.2. Moreover we carried out a comparison of the EMP generated in the parallelepiped-like interaction chamber used in the Vulcan Petawatt Laser Facility at the Rutherford Appleton Laboratory, against that produced in the spherical interaction chamber of PALS.

Towards optical polarization control of laser-driven proton acceleration in foils undergoing relativistic transparency

Control of the collective response of plasma particles to intense laser light is intrinsic to relativistic optics, the development of compact laser-driven particle and radiation sources, as well as investigations of some laboratory astrophysics phenomena. We recently demonstrated that a relativistic plasma aperture produced in an ultra-thin foil at the focus of intense laser radiation can induce diffraction, enabling polarization-based control of the collective motion of plasma electrons. Here we show that under these conditions the electron dynamics are mapped into the beam of protons accelerated via strong charge-separation-induced electrostatic fields. It is demonstrated experimentally and numerically via 3D particle-in-cell simulations that the degree of ellipticity of the laser polarization strongly influences the spatial-intensity distribution of the beam of multi-MeV protons. The influence on both sheath-accelerated and radiation pressure-accelerated protons is investigated. This approach opens up a potential new route to control laser-driven ion sources.

Thomson scattering on non-thermal atmospheric pressure plasma jets

To characterize non-thermal atmospheric pressure plasmas experimentally, a large variety of methods and techniques is available, each having its own specific possibilities and limitations. A rewarding method to investigate these plasma sources is laser Thomson scattering. However, that is challenging. Non-thermal atmospheric pressure plasmas (gas temperatures close to room temperature and electron temperatures of a few eV) have usually small dimensions (below 1 mm) and a low degree of ionization (below 10^-4). Here an overview is presented of how Thomson scattering can be applied to such plasmas and used to measure directly spatially and temporally resolved the electron density and energy distribution. A general description of the scattering of photons and the guidelines for an experimental setup of this active diagnostic are provided. Special attention is given to the design concepts required to achieve the maximum signal photon flux with a minimum of unwanted signals. Recent results from the literature are also presented and discussed.

L'impact du glissement en fréquence lors de l'accélération directe d'électrons par le faisceau laser

L’accélération directe d’électrons par des impulsions ultrabrèves de polarisation radiale fortement focalisées démontre un grand potentiel, notamment, pour la production de paquets d’électrons ultrabrefs. Plusieurs aspects de ce schéma d’accélération restent toutefois à être explorés pour en permettre une maîtrise approfondie. Dans le cadre du présent mémoire, on s’intéresse à l’ajout d’une dérive de fréquence au champ de l’impulsion TM01 utilisée. Les expressions exactes des composantes du champ électromagnétique de l’impulsion TM01 sont établies à partir d’une généralisation du spectre de Poisson. Il s’agit, à notre connaissance, du premier modèle analytique exact pour la description d’une impulsion avec une dérive de fréquence. Ce modèle est utilisé pour étudier l’impact du glissement en fréquence sur le schéma d’accélération, grâce à des simulations “particule test” unidimensionnelles, considérant en premier lieu une énergie constante par impulsion, puis un champ maximum constant. Les résultats révèlent que le glissement en fréquence diminue le gain en énergie maximum atteignable dans le cadre du schéma d’accélération à l’étude ; une baisse d’efficacité de plusieurs dizaines de pourcents peut survenir. De plus, les simulations mettent en évidence certaines différences reliées à l’utilisation d’impulsions avec une dérive vers les basses fréquences ou avec une dérive vers les hautes fréquences : il se trouve que, pour un glissement en fréquence de même grandeur, l’impulsion avec une dérive vers les basses fréquences conduit à un gain en énergie cinétique maximum plus élevé pour l’électron que l’impulsion avec une dérive vers les hautes fréquences.

Studies of Protein-Protein and Protein-Water Interactions by Small Angle X-Ray Scattering, Terahertz Spectroscopy, ASMOS, And Computer Simulation

The protein folding problem has been one of the most challenging subjects in biological physics due to its complexity. Energy landscape theory based on statistical mechanics provides a thermodynamic interpretation of the protein folding process. We have been working to answer fundamental questions about protein-protein and protein-water interactions, which are very important for describing the energy landscape surface of proteins correctly. At first, we present a new method for computing protein-protein interaction potentials of solvated proteins directly from SAXS data. An ensemble of proteins was modeled by Metropolis Monte Carlo and Molecular Dynamics simulations, and the global X-ray scattering of the whole model ensemble was computed at each snapshot of the simulation. The interaction potential model was optimized and iterated by a Levenberg-Marquardt algorithm. Secondly, we report that terahertz spectroscopy directly probes hydration dynamics around proteins and determines the size of the dynamical hydration shell. We also present the sequence and pH-dependence of the hydration shell and the effect of the hydrophobicity. On the other hand, kinetic terahertz absorption (KITA) spectroscopy is introduced to study the refolding kinetics of ubiquitin and its mutants. KITA results are compared to small angle X-ray scattering, tryptophan fluorescence, and circular dichroism results. We propose that KITA monitors the rearrangement of hydrogen bonding during secondary structure formation. Finally, we present development of the automated single molecule operating system (ASMOS) for a high throughput single molecule detector, which levitates a single protein molecule in a 10 µm diameter droplet by the laser guidance. I also have performed supporting calculations and simulations with my own program codes.

Plasma kinetic theory

Kinetic theory studies the macroscopic properties of large numbers of particles, starting from their (classical) equations of motion while the thermodynamics describes the equilibrium behavior of macroscopic objects in terms of concepts such as work, heat, and entropy. The phenomenological laws of thermodynamics tell us how these quantities are constrained as a system approaches its equilibrium. At the microscopic level, we know that these systems are composed of particles (atoms, particles), whose interactions and dynamics are reasonably well understood in terms of more fundamental theories. If these microscopic descriptions are complete, we should be able to account for the macroscopic behavior, i.e. derive the laws governing the macroscopic state functions in equilibrium. Kinetic theory attempts to achieve this objective. In particular, we shall try to answer the following questions [1]: How can we define equilibrium for a system of moving particles? Do all systems naturally evolve towards an equilibrium state? What is the time evolution of a system that is not quite in equilibrium?

Human Ezrin: Prediction of the 3D structure and interactions with mTOR

The protein Ezrin, is a member of the ERM family (Ezrin, Radixin and Moesin) that links the F-actin to the plasma membrane. The protein is made of three domains namely the FERM domain, a central α-helical domain and the CERMAD domain. The residues in Ezrin such as Ser66, Tyr145, Tyr353 and Tyr477 regulate the function of the protein through phosphorylation. The protein is found in two distinct conformations of active and dormant (inactive) state. The initial step during the conformation change is the breakage of intramolecular interaction in dormant Ezrin by phosphorylation of residue Thr567. The dormant structure of human Ezrin was predicted computationally since only partial active form structure was available. The validation analysis showed that 99.7% residues were positioned in favored, allowed and generously allowed regions of the Ramachandran plot. The Z-score of Ezrin was −7.36, G-factor was 0.1, and the QMEAN score of the model was 0.61 indicating a good model for human Ezrin. The comparison of the conformations of the activated and dormant Ezrin showed a major shift in the F2 lobe (residues 142-149 and 161-177) while changes in the conformation induced mobility shifts in lobe F3 (residues 261 to 267). The 3D positions of the phosphorylation sites Tyr145, Tyr353, Tyr477, Tyr482 and Thr567 were also located. Using targeted molecular dynamic simulation, the molecular movements during conformational change from active to dormant were visualized. The dormant Ezrin auto-inhibits itself by a head-to-tail interaction of the N-terminal and C-terminal residues. The trajectory shows the breakage of the interactions and mobility of the CERMAD domain away from the FERM domain. Protein docking and clustering analysis were used to predict the residues involved in the interaction between dormant Ezrin and mTOR. Residues Tyr477 and Tyr482 were found to be involved in interaction with mTOR.

Análisis teórico del contacto plasma-superficie y sus aplicaciones industriales

Actualmente, la física de plasmas constituye una parte importante de la investigación en física que está siendo desarrollada. Su campo de aplicación varía desde el estudio de plasmas interestelares y cósmicos, como las estrellas, las nebulosas, el medio intergaláctico, etc.; hasta aplicaciones más terrenales como la producción de microchips o los dispositivos de iluminación. Resulta particularmente interesante el estudio del contacto de una superficie metálica con un plasma. Siendo la razón que, la dinámica de la interfase formada entre un plasma imperturbado y una superficie metálica, resulta de gran importancia cuando se trata de estudiar problemas como: la implantación iónica en una oblea de silicio, el grabado por medio de plasmas, la carga de una aeronave cuando atraviesa la ionosfera y la diagnosis de plasmas mediante sondas de Langmuir. El uso de las sondas de Langmuir está extendido a través de multitud de aplicaciones tecnológicas e industriales como método de diagnosis de plasmas. Algunas de estas aplicaciones han sido mencionadas justo en el párrafo anterior. Es más, su uso también es muy popular en la investigación en física de plasmas, por ser una de las pocas técnicas de diagnosis que proporciona información local sobre el plasma. El equipamiento donde es habitualmente implementado varía desde plasmas de laboratorio de baja temperatura hasta plasmas de fusión en dispositivos como tokamaks o stellerators. La geometría más popular de este tipo de sondas es cilíndrica, y la principal magnitud que se usa para diagnosticar el plasma es la corriente recogida por la sonda cuando se encuentra polarizada a un cierto potencial. Existe un interes especial en diagnosticar por medio de la medida de la corriente iónica recogida por la sonda, puesto que produce una perturbación muy pequeña del plasma en comparación con el uso de la corriente electrónica. Dada esta popularidad, no es de extrañar que grandes esfuerzos se hayan realizado en la consecución de un modelo teórico que explique el comportamiento de una sonda de Langmuir inmersa en un plasma. Hay que remontarse a la primera mitad del siglo XX para encontrar las primeras teorías que permiten diagnosticar parámetros del plasma mediante la medida de la corriente iónica recogida por la sonda de Langmuir. Desde entonces, las mejoras en estos modelos y el desarrollo de otros nuevos ha sido una constante en la investigación en física de plasmas. No obstante, todavía no está claro como los iones se aproximan a la superficie de la sonda. Las dos principales, a la par que opuestas, aproximaciones al problema que están ampliamente aceptadas son: la radial y la orbital; siendo el problema que ambas predicen diferentes valores para la corriente iónica. Los experimentos han arrojado resultados de acuerdo con ambas teorías, la radial y la orbital; y lo que es más importante, una transición entre ambos ha sido recientemente observada. La mayoría de los logros conseguidos a la hora de comprender como los iones caen desde el plasma hacia la superficie de la sonda, han sido llevados a cabo en el campo de la dinámica de fluidos o la teoría cinética. Por otra parte, este problema puede ser abordado mediante el uso de simulaciones de partículas. La principal ventaja de las simulaciones de partículas sobre los modelos de fluidos o cinéticos es que proporcionan mucha más información sobre los detalles microscópicos del movimiento de las partículas, además es relativamente fácil introducir interacciones complejas entre las partículas. No obstante, estas ventajas no se obtienen gratuitamente, ya que las simulaciones de partículas requieren grandísimos recursos. Por esta razón, es prácticamente obligatorio el uso de técnicas de procesamiento paralelo en este tipo de simulaciones. El vacío en el conocimiento de las sondas de Langmuir, es el que motiva nuestro trabajo. Nuestra aproximación, y el principal objetivo de este trabajo, ha sido desarrollar una simulación de partículas que nos permita estudiar el problema de una sonda de Langmuir inmersa en un plasma y que está negativamente polarizada con respecto a éste. Dicha simulación nos permitiría estudiar el comportamiento de los iones en los alrededores de una sonda cilíndrica de Langmuir, así como arrojar luz sobre la transición entre las teorías radiales y orbitales que ha sido observada experimentalmente. Justo después de esta sección introductoria, el resto de la tesis está dividido en tres partes tal y como sigue: La primera parte está dedicada a establecer los fundamentos teóricos de las sondas de Langmuir. En primer lugar, se realiza una introducción general al problema y al uso de sondas de Langmuir como método de diagnosis de plasmas. A continuación, se incluye una extensiva revisión bibliográfica sobre las diferentes teorías que proporcionan la corriente iónica recogida por una sonda. La segunda parte está dedicada a explicar los detalles de las simulaciones de partículas que han sido desarrolladas a lo largo de nuestra investigación, así como los resultados obtenidos con las mismas. Esta parte incluye una introducción sobre la teoría que subyace el tipo de simulaciones de partículas y las técnicas de paralelización que han sido usadas en nuestros códigos. El resto de esta parte está dividido en dos capítulos, cada uno de los cuales se ocupa de una de las geometrías consideradas en nuestras simulaciones (plana y cilíndrica). En esta parte discutimos también los descubrimientos realizados relativos a la transición entre el comportamiento radial y orbital de los iones en los alrededores de una sonda cilíndrica de Langmuir. Finalmente, en la tercera parte de la tesis se presenta un resumen del trabajo realizado. En este resumen, se enumeran brevemente los resultados de nuestra investigación y se han incluido algunas conclusiones. Después de esto, se enumeran una serie de perspectivas futuras y extensiones para los códigos desarrollados.

Geographic Provenancing of Unprocessed Cotton Using Elemental Analysis and Stable Isotope Ratios

Cotton is the most abundant natural fiber in the world. Many countries are involved in the growing, importation, exportation and production of this commodity. Paper documentation claiming geographic origin is the current method employed at U.S. ports for identifying cotton sources and enforcing tariffs. Because customs documentation can be easily falsified, it is necessary to develop a robust method for authenticating or refuting the source of the cotton commodities. This work presents, for the first time, a comprehensive approach to the chemical characterization of unprocessed cotton in order to provide an independent tool to establish geographic origin. Elemental and stable isotope ratio analysis of unprocessed cotton provides a means to increase the ability to distinguish cotton in addition to any physical and morphological examinations that could be, and are currently performed. Elemental analysis has been conducted using LA-ICP-MS, LA-ICP-OES and LIBS in order to offer a direct comparison of the analytical performance of each technique and determine the utility of each technique for this purpose. Multivariate predictive modeling approaches are used to determine the potential of elemental and stable isotopic information to aide in the geographic provenancing of unprocessed cotton of both domestic and foreign origin. These approaches assess the stability of the profiles to temporal and spatial variation to determine the feasibility of this application. This dissertation also evaluates plasma conditions and ablation processes so as to improve the quality of analytical measurements made using atomic emission spectroscopy techniques. These interactions, in LIBS particularly, are assessed to determine any potential simplification of the instrumental design and method development phases. This is accomplished through the analysis of several matrices representing different physical substrates to determine the potential of adopting universal LIBS parameters for 532 nm and 1064 nm LIBS for some important operating parameters. A novel approach to evaluate both ablation processes and plasma conditions using a single measurement was developed and utilized to determine the “useful ablation efficiency” for different materials. The work presented here demonstrates the potential for an a priori prediction of some probable laser parameters important in analytical LIBS measurement.

Rogue waves generation via nonlinear soliton collision in multiple-soliton state of a mode-locked fiber laser

We report for the first time, rogue waves generation in a mode-locked fiber laser that worked in multiple-soliton state in which hundreds of solitons occupied the whole laser cavity. Using real-time spatio-temporal intensity dynamics measurements, it is unveiled that nonlinear soliton collision accounts for the formation of rogue waves in this laser state. The nature of interactions between solitons are also discussed. Our observation may suggest similar formation mechanisms of rogue waves in other systems.

Statistical properties of radiation of multiwavelength random DFB fiber laser

In the presented paper, the temporal and statistical properties of a Lyot filter based multiwavelength random DFB fiber laser with a wide flat spectrum, consisting of individual lines, were investigated. It was shown that separate spectral lines forming the laser spectrum have mostly Gaussian statistics and so represent stochastic radiation, but at the same time the entire radiation is not fully stochastic. A simple model, taking into account phenomenological correlations of the lines' initial phases was established. Radiation structure in the experiment and simulation proved to be different, demanding interactions between different lines to be described via a NLSE-based model.