Miracle-dz/UniFAR-FTUs huggingface dataset:
Hexapole state-selection and orientation of asymmetric top molecules: CH2F2

Molecular beams of the b-type asymmetric top molecule methylenefluoride (CH2F2) were focused and rotationally state-selected with an electrostatic hexapole. The focusing behavior is mediated by the dependence of rotational energy on electric field strength, the Stark effect. The matrix quantum theory needed to calculate the rotational energies of asymmetric top molecules within an electric field are summarized. These Stark energies were calculated and parameterized for the lowest 165|JτM〉 rotational levels of CH2F2. Excellent agreement was found between classical trajectory simulations incorporating these calculated energies and experimentally measured hexapole focusing spectra. Based on this agreement, the rotational state distribution transmitted by the hexapole as a function of hexapole voltage has been ascertained. Comparisons are made with simulated focusing spectra of the a-type rotor, formaldehyde (H2CO). The theoretical formalism needed to describe the orientational probability distribution functi.
DC Glow Discharge in Atmospheric Air as a Source for Volatile Organic Compounds Abatement

Summary: In this article, a direct-current (DC) discharge in atmospheric pressure air as a source for pollution control is presented. The investigated continuous discharge occurring between two metal electrodes is of the glow type. The discharge generated a highly ionized, non-equilibrium air plasma with gas temperatures of 1 500-2 500 K. Single and multiple discharges of this type were successfully tested in glass and copper tube reactors for the abatement of selected VOCs (cyclohexanone and toluene). Depending on the reactor type, discharge parameters and the energy density, abatement efficiencies of 30-95 % were obtained, with energy costs of 200-1 000 eV/molecule. The thermal VOC decomposition in the discharge was coupled with radical-induced volume reactions. It was found that extending the radical-dominated decomposition phase yielded a better performance. The VOCs tested were converted to some gaseous and some condensed products. Copper electrode surfaces influenced the character of the condensed products and seemed to have a certain catalytic effects on the process.
Molecular modeling of hydrophobic effects in complex biomolecular systems : from simple mixtures to protein-interface aggregation

Hydrophobicity is a term commonly used to discuss the formation of molecular structures in aqueous solution, and since water is ubiquitous in cellular systems, it may be applied in virtually every biomolecular context. Hydrophobicity is not a first-principle parameter but an abstract concept to describe the “behavior” of molecules in aqueous environments. The terminology of hydrophobicity is misleading, because it implies repulsion or a lack of attraction between nonpolar groups and water, when in fact attractive interactions persist due to atom dipoles. Although it has long been recognized that the driving force of structure formation in aqueous environments is founded in water’s “narcissism”, i.e., water self-preference, rather than in a general “fear of water”, the term hydrophobicity has established itself ever since Kautzmann related protein stability to hydrophobic interactions. Due to its false implications, hydrophobicity can be a cause of confusion and the culprit of misleading deductions. Presented in this dissertation is the author’s work on the structural and dynamical characterization of hydrophobic effects in biomolecular systems in the broadest sense, whereby molecular systems on three different size scales are covered: binary mixtures of methanol and water, aggregation of triglyceride droplets in aqueous solution and enzymes that interact with triglyceride-water interfaces of large-scale triglyceride aggregates. Hydrophobizitat ist ein Begriff, der die Bildung molekularer Strukturen im wassrigen Milieu beschreibt und findet daher in nahezu jedem biomolekularen Kontext Anwendung. Hydrophobizitat lasst sich nicht durch einen prazisen Formalismus begrunden; es handelt sich dabei um ein abstraktes Konzept, welches das strukturbildende “Verhalten” von Molekulen in Wechselwirkung mit Wasser beschreibt. Die Terminologie ist dabei irrefuhrend, da eine Abstosung zwischen unpolaren Molekulgruppen und Wasser impliziert wird, wobei in der Tat anziehende Krafte vorliegen, die sich auf atomare Dipole zwischen Elektronen und Protonen zuruckfuhren lassen. Obwohl es langst als gesichert gilt, dass sich die zentrale Triebkraft von Hydrophobizitat nicht auf die „Scheu vor Wasser“ sondern eher auf eine Art „Narzissmus des Wassers“, d.h. auf die praferierte Interaktion von Wassermolekulen mit ihresgleichen, zuruckfuhren lasst, ist der Begriff Hydrophobizitat im wissenschaftlichen Sprachgebrauch fest etabliert. Dies lasst sich auf die Arbeiten von Kautzmann zuruckfuhren, in denen Proteinstabilitat mit hydrophoben Wechselwirkungen korreliert wurde. Gegenstand dieser Dissertation sind im weitesten Sinne die Arbeiten des Autors bezuglich struktureller und dynamischer Charakterisierung hydrophober Effekte in biomolekularen Systemen, wobei Systeme in drei verschiedenen Grosenordnungen untersucht wurden: Binare Methanol-Wasser Mischungen, die Aggregation von Triglyzeridtropfchen in wassriger Losung, sowie die Interaktion von Enzymen mit grosflachigen Triglyzerid-Wasser-Grenzflachen.
1/f noise and Luttinger liquid phenomena in carbon nanotubes

Title of Document: 1/f NOISE AND LUTTINGER LIQUID PHENOMENA IN CARBON NANOTUBES David Andrew Tobias, Doctor of Philosophy, 2007 Directed By: Associate Professor Michael S. Fuhrer and Professor Christopher J. Lobb, Department of Physics Carbon nanotubes (CNTs) provide an ideal medium fo r testing the behavior of one-dimensional electron systems and are promising ca didates for electronic applications such as sensors or field-effect transi stors. This thesis describes the use of low frequency resistance fluctuations to measure bo th the properties of the onedimensional electron system in CNTs, and the sensit ivity of CNT devices to their environment. Low frequency noise was measured in CNTs in field effect transistor (FET) geometry. CNTs have a large amount of surface area relative to their volume and are expected to be strongly affected by their environme t, l ading to speculation that CNTs should have large amounts of 1/f noise. My mea surements indicate that the noise level is in the same range as that of traditi onal FETs, an encouraging result for possible electronic applications. The temperature d ependence of 1/f noise from 1.2 K to 300 K can be used to extract the characteristic energies of the fluctuators responsible for the noise. The characteristic energ ies allows for the elimination of structural and electronic transitions within the CN T itself as possible sources of 1/f noise in CNTs, leaving the motion of defects in the gate dielectric, or possibly strongly physisorbed species, as the likely culprit s. Another form of low frequency noise found in CNTs is random telegraph signal (RTS), which manifests as the alternation be twe n two current states at a stable voltage bias. In CNTs, this phenomenon occurs due t o the tunneling of electrons into and out of the CNT from a nearby defect, and thus p rovides a way to probe the tunneling density of states of the CNT itself. The tunneling density of states in turn provides information on the strength of the electro n-electron interaction in CNTs. Due to the one-dimensional structure of CNTs their electronic state is expected to be a Luttinger liquid, which should manifest as a powe r-law suppression of the tunneling density of states at the Fermi energy. The power law exponent is measured in both the temperature dependence and energy dependence of the tunneling rates. In agreement with theory, the power-law exponent is si gnificantly larger in semiconducting CNTs than found in previous experime nts on metallic CNTs. The RTS can also be used as a “defect thermometer” to p robe the electron temperature of the CNT. The effect of the bias voltage on the elec tron temperature provides a means to determine the energy relaxation length for the e lectrons in the CNT. 1/f NOISE AND LUTTINGER LIQUID PHENOMENA IN CARBON NANOTUBES
Organic and inorganic waste treatment and simultaneous photoproduction of hydrogen by immobilized photosynthetic bacteria

Photosynthetic bacterial strains isolated from tropical and subtropical marine environments that have high growth and hydrogen production were selected and immobilized in agar. Immobilization significantly stabilized H/sub 2/ production by preventing the inhibitory effect from O/sub 2/. Immobilized Chromatium sp. removed sulfide from medium effectively and simultaneously produced H/sub 2/. Immobilized Rhodopseudomonas sp. , which had wide organic substrate specificity, were also used to treat waste water from an orange-processing plant. Removal of total organic carbon (TOC), near-complete reduction of BOD, and simultaneous H/sub 2/ photoproduction were also demonstrated. Continuous H/sub 2/ photoproduction was carried out for several weeks with periodic addition of waste in indoor artificial light. These experiments were successfully applied in outdoor natural sunlight conditions. These data clearly demonstrated that immobilized selected strains of photosynthetic bacteria can be effectively used simultaneously for waste treatment and clean energy (H/sub 2/) production. 31 references, 6 figures, 1 table.
Electrochemically generated base synthesis of thiazolidine-2-thiones

The electrolysis of secondary β-amino alcohols in the presence of carbon disulfide using an electrogenerated base (EGB) to promote the reaction of the synthesis of thiazolidine-2-thione is reported. The EGB was prepared by probase-free electrolysis of acetonitrile under galvanostatic conditions using a sacrificial magnesium anode. The reaction produces the corresponding heterocyclic thiazolidine-2-thiones in satisfactory yields. The compounds thus obtained were fully characterized by IR, 1H, 13C NMR spectroscopy, HRMS and elementary analysis. GRAPHICAL ABSTRACT
Theoretical study of ultrafast index dynamics in semiconductor optical amplifiers

We proposed a novel extended semiconductor optical amplifier (SOA) model for applications in femtosecond pulse transmission, in which the various ultra-fast nonlinear effects, such as gain dispersion, group velocity dispersion (GVD) were taken into account. We use the extended SOA model to analyze the refractive index in response to variation of the input current and the length of SOA. In addition, the impact of carrier density pulsation and carrier heating on the refractive index dynamics of SOA was discussed respectively. The refraction index dynamics that occur in bulk InGaAsP SOA in response to femtosecond pulse (Full width at half maximum is 200fs) are studied numerically. We use the alpha factors (α-factors) to calculate the phase shift from the gain variations, which are related to the refractive index changes. We have considered the effects of carrier heating (CH), and spectrum hole burning (SHB) to analyze the impact of intra-band carrier dynamics on nonlinear refraction index. We also consider the impact of the length of SOA and operation condition on the refraction dynamics.
Assimilable Organic Carbon as an Indicator of Bacterial Regrowth

The relationship between the level of regrowth of heterotrophic bacteria and the level of easily assimilable organic carbon (AOC) was determined by collecting and examining a series of distribution water samples from 20 supplies during two summer and autumn periods. The AOC concentration of distribution system water decreased with increasing distance from the treatment plant, but AOC uptake was limited at concentrations <10 jig C/L. A significant correlation was found between the concentration of AOC in water leaving the treatment plant and the geometric mean of the counts of heterotrophic bacteria in distribution water as determined on diluted broth agar medium. At AOC concentrations <10 jig C/L, the geometric mean of the colony counts on plate count agar medium (incubated at 22°C) remained below the guideline value of 100 cfu/mL.
Improved sample preparation and quality control for the characterisation of titanium dioxide nanoparticles in sunscreens using flow field flow fractionation on-line with inductively coupled plasma mass spectrometry

Titanium dioxide in nanoparticulate form is used in large scale in a variety of consumer products including sunscreens. There is an increasing need for methodology for the reliable characterisation of the particle size and size dependent elemental composition in these complex matrices. Such measurement capability is essential for underpinning safety assessments, for quality control of existing products and for correlation of nanoparticle characteristics with biological effects observed in toxicity tests. This work describes the first systematic comparison and optimisation of extraction methods for titanium dioxide nanoparticles in sunscreen samples. Sunscreens were selected because of their wide use, high fat content and matrix of high complexity. Defatting of the sample with hexane followed by bath sonication with an aqueous extractant was found to provide stable suspensions of secondary titanium dioxide particles for their size characterisation by flow field flow fractionation on-line with element selective detection by inductively coupled plasma mass spectrometry. Further addition of a small amount of hexane to the aqueous extractant resulted in particle disaggregation and thus allowed for characterisation of the primary particle size. A novel approach based on sample spiking with aluminium-labelled titanium dioxide reference particles of known size was used to study the effect of extraction and separation conditions on particle size distribution in the presence of the real sample matrix. The developed methodology was applied to analysis of commercial sunscreens with various sun protection factors. Titanium extraction efficiency, particle size distribution and titanium dioxide recovery from the FFF channel were determined for each product.
Approaches to modelling uranium(VI) adsorption on natural mineral assemblages

Component additivity (CA) and generalised composite (GC) approaches to deriving a suitable surface complexation model for description of U(VI) adsorption to natural mineral assemblages are pursued in this paper with good success. A single, ferrihydrite-like component is found to reasonably describe uranyl uptake to a number of kaolinitic iron-rich natural substrates at pH > 4 in the CA approach with previously published information on nature of surface complexes, acid-base properties of surface sites and electrostatic effects used in the model. The GC approach, in which little pre-knowledge about generic surface sites is assumed, gives even better fits and would appear to be a method of particular strength for application in areas such as performance assessment provided the model is developed in a careful, stepwise manner with simplicity and goodness of fit as the major criteria for acceptance.
Mechanism of actin polymerization with yeast formin Bni1p: effect of the KCl concentration on the FH2 mediated actin nucleation

Formin proteins are actin nucleators and elongators which can be found in most eukaryotic cells. In this work, structure-function relationships between yeast formin Bni1p and actin polymerization were studied. In the first part of this work, it was attempted to clone and express formin constructs derived from yeast Bni1p (Saccharomyces cerevisiae), including the key FH2 domain and a modified FH1 domain. Biomathematical models involving both diffusion and concentration-limited actin recruitment kinetics could be tested with such proteins. Cloning was mostly successful, but only the FH2 domain alone was expressed. In the second part of this work, a salt effect on FH2 mediated actin nucleation was discovered by means of pyrene assays and epifluorescence microscopy. Potassium chloride (KCl) is a downregulator of FH2 nucleation activity: a higher KCl concentration leads to a significantly lower actin polymerization speed (kp, m), to a bigger lag time (tlag) and to a bigger t1/2, with the respective actin filament length distributions. The salt effect was shown to be significant in a KCl concentration range from 10 mM to 90 mM at two different FH2 concentration, but not in absence of FH2. The critical KCl concentration is lowered in the presence of FH2. Some initial experiments with sodium chloride point to a non-specific nature of this salt. This is in agreement with the electrostatic nature of the salt effect, which was studied further by computational means: A decrease of the KCl concentration leads to lower binding free energies of the protein-protein interactions in the crystallographically characterized actin-FH2 complex 1Y64. This is especially the case for the electrostatic Coulomb interaction of a specific area ("lasso" site). ANCHOR calculation results of solvent accessible surface areas (SASAs) corroborate the importance of this site. The experimentally found downregulation of FH2 mediated actin nucleation by KCl can therefore be explained by reduced actin recruitment by the FH2 dimer: KCl diminishes the surface charge of FH2 and actin and thus weakens electrostatic Coulomb interactions. In future, this newly discovered salt effect should be considered in experiments on formins, for example when performing in vitro screens for FH2 inhibitors. The relevance of this new salt effect in vivo remains to be demonstrated.
Magnetic nanoparticles as a catalyst vehicle for simple and easy recycling

The surface of magnetic ferrite nanoparticles (CoFe2O4) was coated with a Rh-based cationic complex, [Rh(cod)(η6-benzoic acid)]BF4, to make them homogeneously dispersable and thermodynamically stable without an excess amount of surface capping molecules in normal organic solvents. Since magnetic nanoparticles themselves have strong magnetic properties and could be considered as a nanometer-sized solid support for the surface-anchored Rh-based catalyst, the ferrite nanoparticle-supported Rh catalyst showed very effective catalytic activity toward the hydroformylation reaction of olefins and could be easily recovered from the reaction mixture by magnetic decantation to be used for subsequent reactions.
Application of Nanoparticle Iron Oxide in Cigarette for Simultaneous CO and NO Removal in the Mainstream Smoke

Abstract Based on the unique temperature and oxygen profiles in a burning cigarette, a novel approach is proposed in this paper to use a single oxidant/catalyst in the cigarette filler for simultaneous removal of carbon monoxide (CO) and nitric oxide (NO) in mainstream smoke. A nanoparticle iron oxide is identified as a very active material for this application due to its multiple functions as a CO catalyst, as a CO oxidant, and in its reduced forms as a NO catalyst. The multiple functions of the nanoparticle iron oxide are characterized in a flow tube reactor and the working mechanisms of these multiple functions for CO and NO removal in a burning cigarette are explained. The effect of smoke condensate on the catalyst are examined and discussed. The advantage of in situ generation of the catalyst during the cigarette burning process is illustrated. The test results of nanoparticle iron oxide for CO and NO removal in cigarettes are presented.
Preparation of a protein–chitin nanofiber complex from crab shells and its application as a reinforcement filler or substrate for biomineralization

A protein–chitin nanofiber complex was successfully prepared from crab shells by a mechanical treatment after the removal of CaCO3. One step in the conventional series of treatments—i.e., the removal of proteins—was omitted to bring down the production cost of the nanofibers. The obtained protein–chitin nanofibers had uniform width of approximately 20 nm and a high aspect ratio. These characteristics were similar to conventional chitin nanofibers. The optically transparent protein–chitin nanofiber composite was fabricated with acrylic resin. The nanofibers reinforced the acrylic resin film and thereby increased its mechanical properties. Proteins on the chitin nanofiber surface affected the biomineralization of CaCO3 in the crab shell. Mineralization of CaCO3 on the protein–chitin nanofiber was carried out by the gas-diffusion method. Protein molecules on the chitin NFs increased the chances for biomineralization to occur. The protein molecules stabilized the formation of vaterite and inhibited the transformation of vaterite to calcite.
Microsensor for in situ flow measurements in benthic boundary layers at submillimeter resolution with extremely slow flow

The currents in the lowest few millimeters of the bottom boundary layer of lakes are highly important for the dissipation of kinetic energy and for chemical processes such as oxygen transfer into the sediment. So far, no high‐resolution flow velocity profiles close to the sediment‐water interface have been reported for such systems because a suitable flow meter was lacking. This article introduces a novel sensor for the measurement of extremely low‐flow velocities. The sensor is based on a gas transducer surrounded by a gas reservoir. It measures the change in the partial pressure of a tracer gas outside the reservoir tip due to advective transport. The sensor is suitable for measurements of velocities smaller than 1 mm s−1, with a spatial resolution of 100 to 250 µm. The flow measurements prove to be insensitive to temperature changes between 5 and 15 °C. The sensor is robust against relative pressure changes, and angular differences in the sensitivity can be calibrated. We present high‐resolution in situ measurements at the bottom of a pre‐alpine lake with shear velocities as low as 0.13 ± 0.02 cm s−1. The velocity profile nicely resolves the transition zone between the viscous and the logarithmic boundary layer.
Self-assembled monolayers of bifunctional periodic mesoporous organosilicas for cell adhesion and cellular patterning

Periodic mesoporous organosilicas (PMOs), an important class of inorganic–organic functional hybrid materials, find numerous potential applications in nano- and biotechnologies due to their porous nature, large surface area (internal and external surfaces) and the structural diversity of their organosilica frameworks. In this contribution we report on the selective functionalization of both the internal and the external surfaces of PMOs with a fluorescent dye and bioactive molecules, respectively. Subsequently we used these unique bifunctionalized PMO nanoparticles for the preparation of non-patterned and patterned self-assembled monolayers (SAMs) on glass. In cell experiments we showed that these new biomaterial surfaces enhance cell adhesion. We were able to determine the position of the inside dye substituted PMOs of the biomolecule functionalized surface in relation to the position of the stained cells by fluorescence microscopy as well. Patterned SAMs of bifunctionalized PMOs lead to selective cellular patterning along the stripes (texture of the surface).
Compositional bowing of band energies and their deformation potentials in strained InGaAs ternary alloys: a first-principles study

Using first-principles calculations, we show that the conduction and valence band energies and their deformation potentials exhibit a non-negligible compositional bowing in strained ternary semiconductor alloys such as InGaAs. The electronic structure of these compounds has been calculated within the framework of local density approximation and hybrid functional approach for large cubic supercells and special quasi-random structures, which represent two kinds of model structures for random alloys. We find that the predicted bowing effect for the band energy deformation potentials is rather insensitive to the choice of the functional and alloy structural model. The direction of bowing is determined by In cations that give a stronger contribution to the formation of the In$_{x}$Ga$_{1-x}$As valence band states with $x\gtrsim 0.5$, compared to Ga cations.