Confinement-induced phase transition in a DNA-lipid hydrated complex

We study the effect of the soft confinement by fluid lipid bilayers on the spatial organisation of DNA molecules in a DNA-zwitterionic lipid hydrated lamellar complex. The confinement is increased by dehydrating the complex in a controlled way, which leads to a decrease of the water channel thickness separating the periodically stacked bilayers. Using grazing-incidence small-angle X-ray scattering on an oriented thin film, we probe in situ as dehydration proceeds the structure of the DNA-lipid complex. A structural phase transition is evidenced, where an apparently disordered phase of DNA rods embedded within the one-dimensionally ordered lipid lamellar phase observed at high hydration is replaced by a 2D hexagonal structure of DNA molecules intercalated between the lipid bilayers. Copyright (C) EPLA, 2010

Critical discontinuous phase transition in the threshold contact process

We analyze a threshold contact process on a square lattice in which particles are created on empty sites with at least two neighboring particles and are annihilated spontaneously. We show by means of Monte Carlo simulations that the process undergoes a discontinuous phase transition at a definite value of the annihilation parameter, in accordance with the Gibbs phase rule, and that the discontinuous transition exhibits critical behavior. The simulations were performed by using boundary conditions in which the sites of the border of the lattice are permanently occupied by particles.

An extinction-survival-type phase transition in the probabilistic cellular automaton p182-q200

We investigate the critical behaviour of a probabilistic mixture of cellular automata (CA) rules 182 and 200 (in Wolfram`s enumeration scheme) by mean-field analysis and Monte Carlo simulations. We found that as we switch off one CA and switch on the other by the variation of the single parameter of the model, the probabilistic CA (PCA) goes through an extinction-survival-type phase transition, and the numerical data indicate that it belongs to the directed percolation universality class of critical behaviour. The PCA displays a characteristic stationary density profile and a slow, diffusive dynamics close to the pure CA 200 point that we discuss briefly. Remarks on an interesting related stochastic lattice gas are addressed in the conclusions.

Gas-Phase Acylium Ion Transfer Reactions Mediated by a Proton Shuttle Mechanism

The mechanism and the energy profile of the gas-phase reaction that mimics esterification under acidic conditions have been investigated at different levels of theory. These reactions are known to proceed with rate constants close to the collision limit in the gas-phase and questions have been raised as to whether the typical addition-elimination mechanism via a tetrahedral intermediate can explain the ease of these processes. Because these reactions are common to many organic and biochemical processes it is important to understand the intrinsic reactivity of these systems. Our calculations at different levels of theory reveal that a stepwise mechanism via a tetrahedral species is characterized by energy barriers that are inconsistent with the experimental results. For the thermoneutral exchange between protonated acetic acid and water and the exothermic reaction of protonated acetic acid and methanol our calculations show that these reactions proceed initially by a proton shuttle between the carbonyl oxygen and the hydroxy oxygen of acetic acid mediated by water, or methanol, followed by displacement at the acylium ion center. These findings suggest that the reactions in the gas-phase should be viewed as an acylium ion transfer reaction. (C) 2010 Wiley Periodicals, Inc. Int J Quantum Chem 111: 1596-1606, 2011

Selectivity and Mechanisms Driven by Reaction Dynamics: The Case of the Gas-Phase OH-+CH3ONO2 Reaction

Well-established statistical approaches such as transition-state theory based on high-level calculated potential energy profiles are unable to account for the selectivity observed in the gas-phase OH- + CH3ONO2 reaction. This reaction can undergo bimolecular nucleophilic displacement at either the carbon center (S(N)2@C) or the nitrogen center (S(N)2@N) as well as a proton abstraction followed by dissociation (E(CO)2) pathway. Direct dynamics simulations yield an S(N)2:E(CO)2 product ratio in close agreement with experiment and show that the lack of reactivity at the nitrogen atom is due to the highly negative electrostatic potential generated by the oxygen atoms in the ONO2 group that scatters the incoming OH-. In addition to these dynamical effects, the nonstatistical behavior of these reactions is attributed to the absence of equilibrated reactant complexes and to the large number of recrossings, which might be present in several ion-molecule gas-phase reactions.

Cerium oxide nanoparticle uptake kinetics from the gas-phase into lung cells in vitro is transport limited

Nowadays, aerosol processes are widely used for the manufacture of nanoparticles (NPs), creating an increased occupational exposure risk of workers, laboratory personnel and scientists to airborne particles. There is evidence that possible adverse effects are linked with the accumulation of NPs in target cells, pointing out the importance of understanding the kinetics of particle internalization. In this context, the uptake kinetics of representative airborne NPs over 30 min and their internalization after 24 h post-exposure were investigated by the use of a recently established exposure system. This system combines the production of aerosolized cerium oxide (CeO(2)) NPs by flame spray synthesis with its simultaneous particle deposition from the gas-phase onto A549 lung cells, cultivated at the air-liquid interface. Particle uptake was quantified by mass spectrometry after several exposure times (0, 5, 10, 20 and 30 min). Over 35% of the deposited mass was found internalized after 10 min exposure, a value that increased to 60% after 30 min exposure. Following an additional 24 h post-incubation, a time span, after which adverse biological effects were observed in previous experiments, over 80% of total CeO(2) could be detected intracellularly. On the ultrastructural level, focal cerium aggregates were present on the apical surface of A549 cells and could also be localized intracellularly in vesicular structures. The uptake behaviour of aerosolized CeO(2) is in line with observations on cerium suspensions, where particle mass transport was identified as the rate-limiting factor for NP internalization.

Experimental and Theoretical Study of the OH Vibrational Spectra and Overtone Chemistry of Gas-Phase Vinylacetic Acid

In this study we present the gas-phase vibrational spectrum of vinylacetic acid with a focus on the ν = 1−5 vibrational states of the OH stretching transitions. Cross sections for ν = 1, 2, 4 and 5 of the OH stretching vibrational transitions are derived on the basis of the vapor pressure data obtained for vinylacetic acid. Ab initio calculations are used to assist in the band assignments of the experimental spectra, and to determine the threshold for the decarboxylation of vinylacetic acid. When compared to the theoretical energy barrier to decarboxylation, it is found that the νOH = 4 transition with thermal excitation of low frequency modes or rotational motion and νOH = 5 transitions have sufficient energy for the reaction to proceed following overtone excitation.

Adaptive liquid-crystal phase-only passive devices

This PhD work is focused on liquid crystal based tunable phase devices with special emphasis on their design and manufacturing. In the course of the work a number of new manufacturing technologies have been implemented in the UPM clean room facilities, leading to an important improvement in the range of devices being manufactured in the laboratory. Furthermore, a number of novel phase devices have been developed, all of them including novel electrodes, and/or alignment layers. The most important manufacturing progress has been the introduction of reactive ion etching as a tool for achieving high resolution photolithography on indium-tin-oxide (ITO) coated glass and quartz substrates. Another important manufacturing result is the successful elaboration of a binding protocol of anisotropic conduction adhesives. These have been employed in high density interconnections between ITO-glass and flexible printed circuits. Regarding material characterization, the comparative study of nonstoichiometric silicon oxide (SiOx) and silica (SiO2) inorganic alignment layers, as well as the relationship between surface layer deposition, layer morphology and liquid crystal electrooptical response must be highlighted, together with the characterization of the degradation of liquid crystal devices in simulated space mission environment. A wide variety of phase devices have been developed, with special emphasis on beam steerers. One of these was developed within the framework of an ESA project, and consisted of a high density reconfigurable 1D blaze grating, with a spatial separation of the controlling microelectronics and the active, radiation exposed, area. The developed devices confirmed the assumption that liquid crystal devices with such a separation of components, are radiation hard, and can be designed to be both vibration and temperature sturdy. In parallel to the above, an evenly variable analog beam steering device was designed, manufactured and characterized, providing a narrow cone diffraction free beam steering. This steering device is characterized by a very limited number of electrodes necessary for the redirection of a light beam. As few as 4 different voltage levels were needed in order to redirect a light beam. Finally at the Wojskowa Akademia Techniczna (Military University of Technology) in Warsaw, Poland, a wedged analog tunable beam steering device was designed, manufactured and characterized. This beam steerer, like the former one, was designed to resist the harsh conditions both in space and in the context of the shuttle launch. Apart from the beam steering devices, reconfigurable vortices and modal lens devices have been manufactured and characterized. In summary, during this work a large number of liquid crystal devices and liquid crystal device manufacturing technologies have been developed. Besides their relevance in scientific publications and technical achievements, most of these new devices have demonstrated their usefulness in the actual work of the research group where this PhD has been completed. El presente trabajo de Tesis se ha centrado en el diseño, fabricación y caracterización de nuevos dispositivos de fase basados en cristal líquido. Actualmente se están desarrollando dispositivos basados en cristal líquido para aplicaciones diferentes a su uso habitual como displays. Poseen la ventaja de que los dispositivos pueden ser controlados por bajas tensiones y no necesitan elementos mecánicos para su funcionamiento. La fabricación de todos los dispositivos del presente trabajo se ha realizado en la cámara limpia del grupo. La cámara limpia ha sido diseñada por el grupo de investigación, es de dimensiones reducidas pero muy versátil. Está dividida en distintas áreas de trabajo dependiendo del tipo de proceso que se lleva a cabo. La cámara limpia está completamente cubierta de un material libre de polvo. Todas las entradas de suministro de gas y agua están selladas. El aire filtrado es constantemente bombeado dentro de la zona limpia, a fin de crear una sobrepresión evitando así la entrada de aire sin filtrar. Las personas que trabajan en esta zona siempre deben de estar protegidas con un traje especial. Se utilizan trajes especiales que constan de: mono, máscara, guantes de látex, gorro, patucos y gafas de protección UV, cuando sea necesario. Para introducir material dentro de la cámara limpia se debe limpiar con alcohol y paños especiales y posteriormente secarlos con nitrógeno a presión. La fabricación debe seguir estrictamente unos pasos determinados, que pueden cambiar dependiendo de los requerimientos de cada dispositivo. Por ello, la fabricación de dispositivos requiere la formulación de varios protocolos de fabricación. Estos protocolos deben ser estrictamente respetados a fin de obtener repetitividad en los experimentos, lo que lleva siempre asociado un proceso de fabricación fiable. Una célula de cristal líquido está compuesta (de forma general) por dos vidrios ensamblados (sándwich) y colocados a una distancia determinada. Los vidrios se han sometido a una serie de procesos para acondicionar las superficies internas. La célula se llena con cristal líquido. De forma resumida, el proceso de fabricación general es el siguiente: inicialmente, se cortan los vidrios (cuya cara interna es conductora) y se limpian. Después se imprimen las pistas sobre el vidrio formando los píxeles. Estas pistas conductoras provienen del vidrio con la capa conductora de ITO (óxido de indio y estaño). Esto se hace a través de un proceso de fotolitografía con una resina fotosensible, y un desarrollo y ataque posterior del ITO sin protección. Más tarde, las caras internas de los vidrios se acondicionan depositando una capa, que puede ser orgánica o inorgánica (un polímero o un óxido). Esta etapa es crucial para el funcionamiento del dispositivo: induce la orientación de las moléculas de cristal líquido. Una vez que las superficies están acondicionadas, se depositan espaciadores en las mismas: son pequeñas esferas o cilindros de tamaño calibrado (pocos micrómetros) para garantizar un espesor homogéneo del dispositivo. Después en uno de los sustratos se deposita un adhesivo (gasket). A continuación, los sustratos se ensamblan teniendo en cuenta que el gasket debe dejar una boca libre para que el cristal líquido se introduzca posteriormente dentro de la célula. El llenado de la célula se realiza en una cámara de vacío y después la boca se sella. Por último, la conexión de los cables a la célula y el montaje de los polarizadores se realizan fuera de la sala limpia (Figura 1). Dependiendo de la aplicación, el cristal líquido empleado y los demás componentes de la célula tendrán unas características particulares. Para el diseño de los dispositivos de este trabajo se ha realizado un estudio de superficies inorgánicas de alineamiento del cristal líquido, que será de gran importancia para la preparación de los dispositivos de fase, dependiendo de las condiciones ambientales en las que vayan a trabajar. Los materiales inorgánicos que se han estudiado han sido en este caso SiOx y SiO2. El estudio ha comprendido tanto los factores de preparación influyentes en el alineamiento, el comportamiento del cristal líquido al variar estos factores y un estudio de la morfología de las superficies obtenidas.

Adaptive and phase transition behavior in performance of discrete multi-articular actions by degenerate neurobiological systems

The identification of attractors is one of the key tasks in studies of neurobiological coordination from a dynamical systems perspective, with a considerable body of literature resulting from this task. However, with regards to typical movement models investigated, the overwhelming majority of actions studied previously belong to the class of continuous, rhythmical movements. In contrast, very few studies have investigated coordination of discrete movements, particularly multi-articular discrete movements. In the present study, we investigated phase transition behavior in a basketball throwing task where participants were instructed to shoot at the basket from different distances. Adopting the ubiquitous scaling paradigm, throwing distance was manipulated as a candidate control parameter. Using a cluster analysis approach, clear phase transitions between different movement patterns were observed in performance of only two of eight participants. The remaining participants used a single movement pattern and varied it according to throwing distance, thereby exhibiting hysteresis effects. Results suggested that, in movement models involving many biomechanical degrees of freedom in degenerate systems, greater movement variation across individuals is available for exploitation. This observation stands in contrast to movement variation typically observed in studies using more constrained bi-manual movement models. This degenerate system behavior provides new insights and poses fresh challenges to the dynamical systems theoretical approach, requiring further research beyond conventional movement models.

Mechanism of dehydroxylation temperature decrease and high temperature phase transition of coal-bearing strata kaolinite intercalated by potassium acetate

The thermal decomposition and dehydroxylation process of coal-bearing strata kaolinite–potassium acetate intercalation complex (CSKK) has been studied using X-ray diffraction (XRD), infrared spectroscopy (IR), thermal analysis, mass spectrometric analysis and infrared emission spectroscopy. The XRD results showed that the potassium acetate (KAc) have been successfully intercalated into coal-bearing strata kaolinite with an obvious basal distance increase of the first basal peak, and the positive correlation was found between the concentration of intercalation regent KAc and the degree of intercalation. As the temperature of the system is raised, the formation of KHCO3, KCO3 and KAlSiO4, which is derived from the thermal decomposition or phase transition of CSKK, is observed in sequence. The IR results showed that new bands appeared, the position and intensities shift can also be found when the concentration of intercalation agent is raised. The thermal analysis and mass spectrometric analysis results revealed that CSKK is stable below 300 °C, and the thermal decomposition products (H2O and CO2) were further proved by the mass spectrometric analysis. A comparison of thermal analysis results of original coal-bearing strata kaolinite and its intercalation complex gives new discovery that not only a new mass loss peak is observed at 285 °C, but also the temperature of dehydroxylation and dehydration of coal bearing strata kaolinite is decreased about 100 °C. This is explained on the basis of the interlayer space of the kaolinite increased obviously after being intercalated by KAc, which led to the interlayer hydrogen bonds weakened, enables the dehydroxylation from kaolinite surface more easily. Furthermore, the possible structural model for CSKK has been proposed, with further analysis required in order to prove the most possible structures.

Liquid-vapour phase change : nucleate boiling of pure fluid and nanofluid under different gravity levels

This research was a step towards the comprehension of the nano-particles interaction with bubbles created during boiling. It was aimed at solving the controversies of whether the heat transfer is enhanced or deteriorated during the boiling of the nanofluid. Experiments were conducted in normal gravity and reduced gravity environments on-board the European Space Agency Parabolic Flight Program. The local modification of the thermo-physical properties of the fluid and moreover the modification experienced in the liquid microlayer under the growing vapour bubble were the dominant factors in explaining the mechanisms of the boiling behaviour of the nanofluid.

Ultraviolet action spectroscopy of iodine labeled peptides and proteins in the gas phase

Structural investigations of large biomolecules in the gas phase are challenging. Herein, it is reported that action spectroscopy taking advantage of facile carbon-iodine bond dissociation can be used to examine the structures of large molecules, including whole proteins. Iodotyrosine serves as the active chromophore, which yields distinctive spectra depending on the solvation of the side chain by the remainder of the molecule. Isolation of the chromophore yields a double featured peak at ∼290 nm, which becomes a single peak with increasing solvation. Deprotonation of the side chain also leads to reduced apparent intensity and broadening of the action spectrum. The method can be successfully applied to both negatively and positively charged ions in various charge states, although electron detachment becomes a competitive channel for multiply charged anions. In all other cases, loss of iodine is by far the dominant channel which leads to high sensitivity and simple data analysis. The action spectra for iodotyrosine, the iodinated peptides KGYDAKA, DAYLDAG, and the small protein ubiquitin are reported in various charge states. © 2012 American Chemical Society.

Direct Detection of a Persistent Carbonyloxyl Radical in the Gas Phase

Long lived: Carbonyloxyl radicals (RCO2 .) are reactive intermediates that play key roles in initiating polymerization reactions. This reactivity also makes their direct observation difficult. For the first time a persistent organic RCO2 . radical is detected in the gas phase, its extraordinary longevity is attributed to the high barrier towards fragmentation owing to the endothermicity of the decarboxylation products. Grant Numbers ARC/DP0986738, ARC/DP120102922, ARC/DE120100467

Hydroxyl radical formation in the gas phase oxidation of distonic 2-methylphenyl radical cations

The reactions of distonic 4-(N, N, N-trimethylammonium)-2-methylphenyl and 5-(N, N, N-trimethylammonium)-2-methylphenyl radical cations (m/z 149) with O-2 are studied in the gas phase using ion-trap mass spectrometry. Photodissociation (PD) of halogenated precursors gives rise to the target distonic charge-tagged methylphenyl radical whereas collision-induced dissociation (CID) is found to produce unreactive radical ions. The PD generated distonic radicals, however, react rapidly with O-2 to form \[M + O2](center dot+) and \[M + O-2 - OH](center dot+) ions, detected at m/z 181 and m/z 164, respectively. Quantum chemical calculations using G3SX(MP3) and M06-2X theories are deployed to examine key decomposition pathways of the 5-(N, N, N-trimethylammonium)-2-methylphenylperoxyl radical and rationalise the observed product ions. The prevailing product mechanism involves a 1,5- H shift in the peroxyl radical forming a QOOH-type intermediate that subsequently eliminates (OH)-O-center dot to yield charge-tagged 2-quinone methide. Our study suggests that the analogous process should occur for the neutral methylphenyl + O-2 reaction, thus serving as a plausible source of (OH)-O-center dot radicals in combustion environments. Grants: ARC/DP0986738, ARC/DP130100862