Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural Dynamics and Allosteric Signaling in Ionotropic Glutamate Receptors

Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that mediate excitatory neurotransmission events in the central nervous system. All distinct classes of iGluRs (AMPA, NMDA, Kainate) are composed of an N-terminal domain (NTD) and a ligand-binding domain (LBD) in their extracellular domain, a transmembrane domain (TMD) and an intracellular carboxy-terminal domain (CTD). Ligand binding to the LBD facilitates ion channel activation. The NTDs modulate channel gating allosterically in NMDA receptors (NMDARs). A similar function of the NTD in AMPA receptors (AMPARs) is still a matter of debate. Taking advantage of recently resolved structures of the NTD and the intact AMPAR, the main focus of this dissertation is a comprehensive examination of iGluR NTD structural dynamics, ligand binding and allosteric potential of AMPARs. We use a multiscale, multi-dimensional approach using coarse-grained network models and all-atom simulations for structural analyses and information theoretic approaches for examination of evolutionary correlations. Our major contribution has been the characterization of the global motions favored by iGluR NTD architecture. These intrinsic motions favor ligand binding in NMDAR NTDs and are also shared by other iGluR NTDs. We also identified structural determinants of flexibility in AMPARs and confirmed their role through in silico mutants. The overall similarity in collective dynamics among iGluRs hints at a putative allosteric capacity of non-NMDARs and has propelled the elucidation of interdomain and intersubunit coupling in the intact AMPAR. To this end, we identified “effector” and “sensor” regions in AMPARs using a perturbation-response technique. We identified potentially functional residues that enable information propagation between effector regions and proposed an efficient mechanism of allosteric communication based on a combination of tools including network models, graph theoretical methods and sequence analyses. Finally, we assessed the “druggability” of iGluR NTDs using molecular dynamics simulations in the presence of probe molecules containing fragments shared by drug-like molecules. Based on our study, we offer key insights into the ligand-binding landscape of iGluR NTD monomers and dimers, and we also identify a novel ligand-binding site in AMPAR dimers. These findings open an avenue of searching for molecules able to bind to iGluR NTDs and allosterically modulate receptor activity.
Spatial Distribution of Pierce’s Disease in the Coachella Valley: Implications for Sampling

A three-year survey was conducted to characterize the spatial distribution patterns of Pierce’s disease (PD) of grapevines in the Coachella Valley (Riverside County, CA). Spatial structures of PD distributions were characterized with geostatistics and spatial analysis with distance indices (SADIE). The survey confirmed 97 diseased grapevines from seven vineyards in the valley, and the diseased vines were localized within the vineyards. Approximately 82% of diseased grapevines were found near two to six consecutive dead, missing, or replanted grapevines in a row. Six vineyards had low ( p
Chemical Composition of Some Pinus sylvestris L. Oleoresins from Southern Serbia, Bosnia and Makedonia. Two Entities of Scotch Pine Present on the Balkan Peninsula

Scotch pine (P. sylvestris L.) xylem oleoresins from different provenances in central and southern Yugoslavia were studied by means of gas chromatography. The differences in the chemical composition of resin acids and neutral diterpenes compared to samples from other provenances in Europe are in the normal range of variation. The composition of the monoterpene hydrocarbons, however, were variable.Two samples from authochtone stands in western Serbia and southern Makedonia contain levorotatory turpentine oils which are free from 3-carene. A sample from Bosnia yielded a dextrorotatory turpentine oil containing 8.6 per cent 3-carene among the mixture of monoterpenes. Obviously the Bosnian pine stand belongs to the northern Eurasian type of P. sylvestris while the two other provenances are of the Mediterranean entity.
Effects of isotopic composition, temperature, pressure, and dissolved gases on the density of liquid water

A review is made of measurements of the effect of temperature, pressure, isotopic composition, and dissolved atmospheric gases on the density of liquid water at temperatures to 100°C. The molar volume is expanded as a multiple power series in the variables, and the coefficients determined. A number of gaps become evident in our knowledge of properties that are within the capacity of current measurements. For example, there appears to be no measurement of the effect of oxygen isotopes on the compressibility. Data on the thermal expansion of D2O are strikingly inconsistent. The partial molar volumes of dissolved gases are only sketchily known. At O°C, equilibration with the oxygen, nitrogen, and argon of the atmosphere lowers the density about 3 p.p.m. , while atmospheric carbon dioxide raises it about 0.3 p.p.m. Appendix I discusses the care needed to obtain various degrees of precision in practical density measurements, and the effect of isotopic uncertainties on them. Appendix II treats the representation.
Constituents of essential oils of Cupressus arizonica Greene from Uttarakhand Himalaya (India)

Essential oils isolated from the branchlets of two populations of Cupressus arizonica Greene (Cupressaceae) growing in Uttarakhand Himalaya (India) were analyzed by GC and GC/MS in order to determine the variation in composition of their constituents. A total of 36 constituents representing 90.7–92.2% of the total composition have been identified in two locations. In the oils, monoterpenoids (90.0–90.7%) were the principal class of the components (oxygenated monoterpenes, 46.3–52.6%; monoterpene hydrocarbons, 37.4–44.4%), while sesquiterpene hydrocarbons found in lesser amounts (0.7–1.5%). Umbellulone was identified as the major constituent of the essential oils, which ranged from 20.9 to 30.6%. The other main constituents in the essential oils were found to be limonene (8.0–12.9%), α-pinene (7.1–8.1%), sabinene (6.6–7.0%), p-cymene (3.2–5.9%) and terpinen-4-ol (4.2–5.6%). In summary, the characteristic of C. arizonica essential oil from Uttarakhand Himalaya (India) is due to the presence of umbellulone and limonene in higher amounts.
A Flux‐Free Fusion Technique for Rapid Determination of Major and Trace Elements in Silicate Rocks by LA‐ICP‐MS

A simple flux‐free fusion technique was developed to analyse major and trace element compositions of silicate rocks. The sample powders were melted in a molybdenum capsule sealed in a graphite tube to make a homogenous glass in a temperature‐controlled one‐atmosphere furnace. The glass was then measured for both major and trace element concentrations by LA‐ICP‐MS using a calibration strategy of total metal‐oxide normalisation. The optimum conditions (i.e., temperature and duration) to make homogeneous glasses were obtained by performing melting experiments using a series of USGS reference materials including BCR‐2, BIR‐1, BHVO‐2, AGV‐1, AGV‐2, RGM‐1, W‐2 and GSP‐2 with SiO2 contents from 47 to 73% m/m. Analytical results of the USGS reference materials using our method were generally consistent with the recommended values within a discrepancy of 5–10% for most elements. The routine precision of our method was generally better than 5–10% RSD. Compared with previous methods of LA‐ICP‐MS whole‐rock analyses, our flux‐free fusion method is convenient and efficient in making silicate powder into homogeneous glass. Furthermore, it limits contamination and loss of volatile elements during heating. Therefore, our new method has great potential to provide reliable and rapid determinations of major and trace element compositions for silicate rocks.
The atomic and magnetic structure and dynamics of iron phosphate glasses

Iron phosphate glasses, xFe2O3. (100−x)P2O5 {hereinafter denoted xFe. (100−x)P}, are not only of potential commercial importance for the immobilisation of plutonium containing and other high level nuclear wastes but are also of great scientific interest in that, at low temperatures, they exhibit short range antiferromagnetic (speromagnetic) ordering, as demonstrated by an earlier neutron magnetic diffraction investigation and by magnetic susceptibility measurements. However, studies of this system are complicated by the fact that the glasses may contain a variable amount of Fe, depending on the preparation conditions. The crystallography of the FeO–Fe2O3–P2O5 system is also extremely complex, as may be seen from Table 1 of Ref. 5. In a previous paper, a subset of the authors presented neutron diffraction data for three samples, with nominal compositions 30Fe.70P, 40Fe.60P and 44Fe.56P, and compared the resulting real space total correlation functions, T(r), with two structural models, one, originally proposed for vitreous 44Fe.56P, comprising alternating FeO4 and PO4 tetrahedra (cf. quartz polymorphs of FePO4) plus O=PO3 units, where O represents a bridging oxygen atom, and the other, for vitreous 40Fe.60P, based on (Fe3O12) clusters, as found in crystalline Fe3(P2O7)2. It was concluded that the structure is much more compliThe atomic and magnetic structure and dynamics of iron phosphate glasses
EFFICIENCY OF MULTINUTRIENT EXTRACTANTS FOR THE DETERMINING OF AVAILABLE ZINC IN SOILS

The increasing use of the ICP-AES (inductively coupled plasma atomic emission spectrophotometry) as a multielement analytical technique has stressed the preference for the use of multinutrient extractants in routine soil analysis. However, few studies relating the extraction of zinc (Zn) from soil with such extractants and the absorption of the element by plants have been published. Two experiments under greenhouse conditions were carried out in order to determine the efficiency of some multinutrient extractants for the determination of available Zn in 44 soils from the State of São Paulo, Brazil, for corn and soybean. All soil samples were limed to increase the CEC's base saturation at pH 7 to 70%. Twenty-two soil samples with DTPA (diethylenetriaminepentaacetic acid) extractable Zn concentration lower than 0.6 mg dm−3 received either the application of B, Cu, Mn, Zn or of these micronutrients excluding Zn. The remaining 22 soil samples, with Zn concentration above 0.6 mg dm−3, received application of three micronutrients (B, Cu and Mn). Macronutrients were applied to all pots as needed for crop development. Zinc was extracted from the soils before each planting using the extracting solutions, DTPA, Mehlich 1 (M-1), Mehlich 3 (M-3) and AB-DTPA (ammonium bicarbonate-DTPA) and determined by ICP-AES. The results showed significant correlations between plant Zn concentration and soil Zn concentration. The correlation values between soil-Zn and plant-Zn were of 0.74 (M-3), 0.73 (DTPA), 0.62 (AB-DTPA) and 0.61 (M-1) for corn, and of 0.71 (DTPA), 0.63 (M-1), 0.58 (M-3) and 0.46 (AB-DTPA) for soybean. Thus, the DTPA solution was the most efficient extractant for the determination of bioavailable Zn when both crops are considered together.
The Optical Response of Strongly Coupled Quantum Dot- Metal Nanoparticle Hybrid Systems

Title of dissertation: The Optical Response of Strongly Coupled Quantum DotMetal Nanoparticle Hybrid Systems Ryan Domenick Artuso, Doctor of Philosophy, 2012 Dissertation directed by: Dr. Garnett W. Bryant National Institute of Standards and Technology In this thesis, we study, theoretically, hybrid systems composed of semiconducting quantum dots (SQDs) and metallic nanoparticles (MNPs) which are coupled by means of an applied optical field. Systems composed of SQDs and MNPs have recently been a very active area of research. Such structures are considered to be viable candidates for use in nanodevices in quantum information and nanoscale excitation transfer. The goal of this thesis is to investigate the interactions of the constituent particles and predict the hybrid response of SQD/MNP systems. We first study a single SQD coupled to a spherical MNP, and explore the relationship between the size of the constituents and the response of the system. We identify four distinct regimes of behavior in the strong field limit that each exhibit novel properties, namely, the Fano regime, exciton induced transparency, suppression and bistability. In chapter 3, we will explore these four regimes in detail and set bounds on each. In chapter 4, we then show that the response of the system can be tailored by engineering metal nanoparticle shape and the exciton resonance of SQDs to control the local-fields that couple the MNPs and SQDs. We identify regimes where dark modes and higher order multipolar modes can influence hybrid response. External fields do not directly drive MNP dark modes, so SQD/MNP coupling is dominated by the local induced coupling, providing a situation in which the induced self-interaction could be probed using near field techniques. Finally, we consider a system of two SQDs coupled to a MNP. In particular, we identify and address issues in modeling the system using a semiclassical approach, which can lead to unstable and chaotic behavior in a strong SQD-SQD coupling regime. When we model the system using a more quantum mechanical approach, this chaotic regime is absent. Finally, we compare the two models on a system with a strong plasmon-mediated interaction between the SQDs and a weak direct interaction between them. The Optical Response of Strongly Coupled Quantum DotMetal Nanoparticle Hybrid Systems
Fate and Transport of High Explosives in a Sandy Soil: Adsorption and Desorption

Several areas of the Massachusetts Military Reservation (MMR) have soils with significant levels of high explosives (HE) contamination because of a long history of training and range activities (such as open burning, open detonation, disposal, and artillery and mortar firing). Site-specific transport and attenuation mechanisms were assessed in sandy soils for three contaminants of concern: the nitramine hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), and the nitroaromatics 2,4-dinitrotolune (2,4-DNT) and 2,4,6-trinitrotoluene (TNT). For all three contaminants, linear distribution coefficients (Kd) were dependent on the fraction of organic carbon in soil. The nitroaromatics sorbed much more strongly than RDX in both soils. Over 120 hours, the desorption rate of RDX from field contaminated surface soil was much slower than its sorption rate, with the desorption Kd (1.5 L/kg) much higher than Kd for sorption (0.37 L/kg). Desorption of 2,4-DNT was negligible over 120 hours. Thus, applying sorption-derived Kd values for transport modeling may significantly overestimate the flux of explosives from MMR soils. Based on multiple component column transport tests, RDX will be the most mobile of these contaminants in MMR soils. In saturated columns packed with uncontaminated soil, RDX broke through rapidly, whereas the nitroaromatics were significantly attenuated by irreversible sorption or abiotic transformations.
“Green Star”: a holistic Green Chemistry metric for evaluation of teaching laboratory experiments

Abstract This paper presents a new semi-quantitative metric, Green Star (GS), for evaluation of the global greenness of chemical reactions used in teaching laboratories. Its purpose is to help choose the more acceptable reactions for implementing Green Chemistry (GC) and to identify suitable modifications of protocols to improve the greenness of the chemistry practiced by students. GS considers globally, in principle, all the Twelve Principles of GC. The metric consists in the evaluation of the greenness of the reaction for each principle by pre-defined criteria, followed by graphical representation of the results in an Excel radar chart – the fuller the chart, the higher degree of greenness. To illustrate the construction and the scope of the metric, a case study is presented – the iron(II) oxalate dihydrate synthesis performed under several sets of conditions to pursue the implementation of greenness.
Energy‐adjusted ab initio pseudopotentials for the first row transition elements

Nonrelativistic and quasirelativistic ab‐initio pseudopotentials representing the Ne‐like X(Z−10)+ cores (X=Sc–Zn) of the first row transition metals and optimized (8s7p6d1f )/[6s5p3d1f ]‐GTO valence basis sets for use in molecular calculations have been generated. Excitation and ionization energies of the low lying states of Sc through Zn from numerical HF‐ as well as SCF‐ and CI(SD)‐pseudopotential calculations using the derived basis sets differ by less than 0.1 eV from corresponding all‐electron results.
Dynamic behaviour of rotary lip seal

We report on the dynamic behavior of a rotary lip seal by considering the interaction between lip, film and shaft roughness assumed to have a periodic form. The nonlinearities of stiffness and viscosity of the film are taken into account in a mass-spring-dumper model. Using the harmonic balance method, analytical prediction of the lip displacement is obtained, the frequency response is provided and the effect of the shaft undulation on the amplitude jumps of the lip displacement and on the film thickness fluctuations are discussed. The results have direct applications in reducing leakage that may occur between a smooth lip seal and a rough shaft.
Isolation and Identification of Phenolic Compounds in the Fruit of Benincasa hispida by HSCCC

Abstract Separation of phenolic components from the fruit Benincasa hispida was conducted using high‐speed countercurrent chromatography (HSCCC) with two solvent systems, n‐hexane–n–butanol–methanol–water (10:16:5:20, v/v) and n‐hexane–ethyl acetate–methanol–water (1:1:1:1, v/v). Three compounds, astilbin (120 mg), catechin (103 mg), and naringenin (79 mg) were obtained from the separation of 2 g of crude phenolic component extract of the fruit. Chemical structures of these three compounds were confirmed by electrospray ionization ion trap multiple mass spectrometry (ESI‐MS) and NMR.
Limitation of Determination of Surface Fractal Dimension using N2 Adsorption Isotherms and Modified Frenkel-Halsey-Hill Theory

Surface fractal dimensions, DS, of smooth and corrugated bovine serum albumin particles were obtained from N2 adsorption isotherms using modified Frenkel−Halsey−Hill (FHH) theory. It was found that for different particles, the correct DS values depended on the number of adsorbed layers, n. For corrugated particles, when 1 ≤ n ≤ 10, the value of DS is equal to 2.39, which agrees with the value obtained from light scattering (2.39 ± 0.05). Unlike the corrugated particles, the adsorption isotherm for the smooth particles generated the correct value of DS (2.12) only for 1.0 ± 0.5 ≤ n ≤ 2.0 ± 0.5 (i.e., around monolayer coverage). Determination of DS in the multilayer region (n > 2) produced a higher value than the one obtained from monolayer coverage. This was because the smooth particles were in closer contact with each other; at higher coverage the gas molecules probed the surface of the aggregates instead of the single particles. As there were fewer contact points between the corrugated particles compared.
A thermodynamic theory of the Soret effect in a multicomponent liquid

A phenomenological theory of the Soret effect in a multicomponent mixture is presented. The theory is applicable to mixtures in which the Soret effect is determined mainly by the energetic interaction between the molecules, such as liquids and dense gases, and it is based on the assumption that the steady state has a maximum number of possible microstates. The equations derived for the separation enable the thermal diffusion factor αT of each component to be calculated using only an equation of state for the mixture and the standard state enthalpy. With a sufficiently accurate equation of state, the calculated αT values correspond well with the data on measured αT values of liquids and dense gases and show a better correspondence than Haase’s theory. The method presented may be applicable to other coupled transport phenomena in the steady state.
Gas hold-up and oxygen transfer in three-phase external-loop airlift bioreactors : Non-Newtonian fermentation broths

The effects of solids loading on gas hold-up and oxygen transfer in external-loop airlift bioreactors with non-Newtonian fermentation media are discussed. Experiments were performed in two model external-loop airlift bioreactors with aqueous solutions of carboxymethyl cellulose (CMC) and xanthan gum representing non-Newtonian flows. Low-density plastic particles of 1030 and 1300 kg m -3 were used and the solids loading was varied in the range 0-20% (v/v). For the inelastic non-Newtonian CMC aqueous solutions, the presence of low-density solid particles slightly increased the riser gas hold-up, Φ gr , but decreased the volumetric mass transfer coefficient, k L a. On the other hand, Φ gr decreased but k L a increased with solids loading in the viscoelastic non-Newtonian xanthan gum aqueous solution. The extent of these effects depended on non-Newtonian flow behavior. Theoretical models of riser gas hold-up and volumetric mass transfer coefficient have been developed. The capability of the proposed models was examined using the present experimental data obtained in the model external-loop airlift bioreactors and the available data in the literature. The data were successfully correlated by the proposed correlations except the results for k L a coefficient in the xanthan gum solution.
HIGH PRESSURE REDOX GEOCHEMISTRY OF TUNGSTEN IN METAL-SILICATE SYSTEMS: IMPLICATIONS FOR CORE FORMATION IN THE EARTH

Title of Document: HIGH PRESSURE REDOX GEOCHEMISTRY OF TUNGSTEN IN METAL–SILICATE SYSTEMS: IMPLICATIONS FOR CORE FORMATION IN THE EARTH Gregory Allen Shofner, Ph.D., 2011 Directed By: Adjunct Associate Professor, Andrew J. Campbell, Department of Geology Geochemical models of core formation are commonly based on core and mantle abundances of siderophile elements. Because of the affinity of these elements for metallic phases, they are thought to be highly concentrated in Earth's core. Tungsten is a moderately siderophile element that may provide constraints on the pressure, temperature, composition, and oxygen fugacity conditions, and on the timing of core formation in the Earth. Previous experimental studies suggest that pressure exerts little influence over tungsten metal/silicate partitioning up to 20 gigapascals (GPa). But, core formation models, based on W, predict metal–silicate equilibration pressures outside the available experimental pressure range, thus, requiring extrapolation. Therefore, higher pressure experimental data on tungsten were needed to constrain this important parameter. High pressure melting experiments were conducted to 50 GPa and 4400 K using a diamond anvil cell, and to 26 GPa and 2500 K using a multi-anvil press. Diamond anvil cell samples were sectioned using a focused ion beam instrument. The W-WO2 oxygen fugacity buffer was characterized to high pressure, also using diamond anvil cells and a multi-anvil press, combined with synchrotron x-ray diffraction. Combining the high pressure W-WO2 oxygen fugacity buffer and the database of metal/silicate partitioning data, a new approach was taken to model the Fe-W exchange reaction. Compared to the common linear method of parameterizing metalsilicate partitioning data, this approach captures the non-linear pressure dependence on oxygen fugacity, and allows for modeling of the excess Gibbs energy of mixing based on the activity ratios of Fe, FeO, W, and WO2. Applying this non-linear parameterization to the problem of core formation in the Earth, a pressure–temperature solution of 38 GPa and 3100 K in a peridotite silicate composition for a single-stage, magma ocean core formation model was determined that constrains equilibrium core formation conditions in the Earth. This solution was further constrained by Ni, Co, and Mo parameterizations from the literature. The pressure and temperature conditions of this solution represents a combination of the averaged effects of a deepening magma ocean through time and the "Moon-forming"