Miracle-dz/UniFAR-FTUs huggingface dataset:
Valence shell structures in the distributions of the Laplacian of the electron density and the one-electron potential for diatomic molecules

The valence shell charge concentration, VSCC, in an atom is defined by Bader as the outermost spherical region for which ∇2ρ(r)<0. We compare and contrast an alternate definition of the VSCC as the outermost spherical region for which ∇2ρ(r)/2ρ(r)<0. The quantity ∇2ρ(r)/2ρ(r), termed the one-electron potential (OEP), is implicit in the (exact) one-electron Schrodinger equation. In a homonuclear diatomic bound by shared interaction, the VSCCs of the atoms are merged. Provided that the merged VSCCs persist, the diatomic is enclosed by an outermost zero-valued surface encompassing the VSCC of the molecule. The outermost ∇2ρ(r)=0 surface is termed the reactive surface while the outermost OEP=0 surface is termed the molecular envelope. In cases where the VSCCs are not revealed in the atoms, the reactive surfaces and molecular envelopes are incomplete or absent in the diatomics. We show that in many diatomics the molecular envelope is present although the reactive surface is missing. In an ionic diatomic bound .
Using Stakeholder Mapping and Analysis With a Mental Models Approach for Biosecurity Risk Communication With Peri-Urban Communities

The study found that the size of landholdings was not an important factor associated with knowledge and behaviour about biosecurity issues. Between 80 and 100% of people were aware of the main vectors and pathways for both weeds and animal diseases. Similarly high percentages of respondents employ appropriate risk management practices. There were lower levels of awareness of animal diseases than of weeds. The term „biosecurity‟ was not widely understood.
Application of ion chromatography and energy dispersive x-ray fluorescence spectrometry for examination of chemical composition of mineral fertilizers

Abstract: Product quality tests require accurate and precise analytical techniques. Fertilizers belong to a group of products whose chemical composition is of great importance due to health, environmental and economic reasons. The following paper presents the results of the research into the content of selected substances in several mineral fertilizers manufactured in Poland. Ion chromatography (IC) was employed to determine selected inorganic anions and cations, whereas energy dispersive X-ray fluorescence spectrometry (EDXRF) was used to determine the content of selected elements.
Loi de comportement viscoélastique pour les polymères fondus linéaires polymoléculaires, validation rhéométrique et par mesures de champs d'écoulement

On etudie le modele de Ianniruberto et Marrucci (2003), base sur la theorie de la reptation et le modele du tube incluant : «constraint release» (thermique et convectif), retraction partielle et extensibilite finie. Ce modele est applique a un polystyrene en cisaillement (rheometrie capillaire), elongation uniaxiale (rheometre extensionnel) et elongation plane (mesures de champ dans une contraction) pour differentes plages de taux de deformations. On montre que le modele est capable de rendre compte des differents resultats experimentaux uniquement pour des valeurs irrealistes des parametres moleculaires regissant les phenomenes de retraction et d’extensibilite finie, des valeurs realistes surestimant fortement la reponse en contraintes. Ces resultats sont consistants avec la theorie de Marrucci et Ianniruberto [Macromol. , 37, 3934-3942, 2004] qui propose qu’un phenomene de relaxation supplementaire (« interchain pressure effect ») regit la dynamique du diametre du tube.
Structural Study of TeO2 and LiCl-Li2O-TeO2 Glasses by Raman and 125Te MAS NMR Spectroscopies

The structures of TeO2 and Li2O-LiCl-TeO2 glasses have been investigated by means of Raman and 125Te MAS NMR spectroscopy. Extremely large isotropic chemical shifts of 1500–1700 ppm and linewidths of 160–230 kHz were observed in the 125Te MAS NMR spectra of both TeO2 crystals and TeO2-based glasses, indicating that Te atoms in TeO4 or TeO3+1 polyhedra in oxide crystals and glasses have very low symmetry mainly due to the presence of a lone pair of electrons. The Raman spectra revealed that pure TeO2 glass has a network structure similar to that of α-TeO2 rather than β-TeO2. The present Raman and 125Te MAS NMR spectra also confirmed that not only Li2O but also LiCl modifies the TeO2 glass network, forming TeO3, trigonal pyramid.
Proton Reactivity and Electronic Structure of Phenoxyl Radicals in Water

Application of proton reactivity in modeling the electronic structure of reactive chemical intermediates, interpreting their resonance Raman spectra in aqueous solution, and testing theoretical procedures has been demonstrated. The case of phenoxyl radicals (p-XC6H4O•), for which there has been persistent disagreement between the structural models derived from purely spectroscopic arguments and ab initio MO calculations, is discussed. It has been shown that the neutral p-aminophenoxyl (X = NH2) radical deprotonates in basic aqueous solutions (pKa = 14.5), implying a highly zwitterionic structure with formal positive charge on amine nitrogen, an amide-like CN bond (⩽1.33 A), and near planarity of the molecular geometry. The radical protonates at oxygen, rather than nitrogen, the proton dissociation constant (pKa = 2.2) corresponding to ∼36% negative electronic charge on the O atom and a CO bond length of ∼1.267 A. This chemical model of the radical structure contrasts with the ab initio UNO-CAS/6-31G* (pyr.
Simultaneous Gas Chromatographic Analysis of Ethanol and Acetic Acid in Vinegar

A method is developed for simultaneously determining ethanol and acetic acid in vinegars by quantitative packed-column gas chromatography. Vinegars were filtrated and directly chromatographed on a stainless steel column packed with Tenax-GC, 80/100. Ethanol, isopropy alcohol as an internal standard, and acetic acid were completely separated within 20 min of running time without any interfering peaks. The accuracy of packed column gas solid chromatography (PCGSC) was discussed compared to the analytical data by titration, high performance liquid chromatography and capillary column gas liquid chromatography (CCGLC).
Beyond the gap of pressure : XPS studies of interfaces at near ambient pressures

In many processes or technological objects, such as coating deposition, advanced material processing for electronics, magnetic or optical devices, electrochemical processes at an electrode, sensors and catalysis, etc. the interface between a surface of a solid and a liquid or a gas phase, plays a prominent role. Analogously, environmental sciences and sciences of the Living integrate into their models chemical reactions taking place at solid/liquid or liquid/gas interfaces.XPS is a powerful technique for interface analysis and has been widely use in the case of solid surface. The main advantage of XPS is its sensitivity to the material surface. Indeed, due to the low electron mean free path of electrons in a solid, only the photoelectrons at the extreme outer surface (1-10 nm) can escape the sample. However, XPS has traditionally been conducted under ultra-high vacuum (UHV) conditions. UHV conditions are utilized for two reasons. First, the analyzers are designed to work under UHV conditions. Second, the electrons must reach the detector and their mean free path is short at high pressures. For example at a pressure of 1 mbar, 100 eV electrons will travel 1 mm while under UHV conditions, the mean free path increases to 105 m. UHV chambers (10-10 mbar) help maximize the mean free path so that a high number of electrons will reach the detector/analyzer and the signal/noise ratio will increase making it possible to analyze the spectrum produced. This constraint makes UHV the standard environment of X-ray Photoelectron Spectroscopy (XPS) experiments.In order to make possible the use of XPS on a larger pressure range, a few groups around the world have designed photoemission equipment that can be operated under ambient pressure (up to 5 mbar). The Berkeley group (M. Salmeron LBNL-Materials Sciences Division, H. Bluhm LBNL-Chemical Sciences Division), who pioneered this field, has two such setups installed at the Advanced Light Source. The Fritz Haber Institute has built a high pressure XPS based on the Berkeley prototype, installed at BESSY synchrotron (Berlin), since 2002. The building of Ambient Pressure XPS (APXPS) analyzers of the Berkeley type, able to be operated at pressures in the range of 1 mbar, about 7 orders of magnitude higher than the pressure limit of conventional UHV equipment is both a technological and conceptual breakthrough. Differential pumping stages allow the sample to remain at environmental pressures, while maximizing the mean free path of emitted electrons, so they can reach the detector. Additionally, voltages are applied to electrostatic lenses in the unit to accelerate and focus the electrons onto the focal plane of the electron energy analyzer. A similar system Near-Ambient Pressure XPS, NAP-XPS), described in details in chapter 1, was delivered in December 2012 and installed at TEMPO beamline in February 2013. The first beamtime occurred in May 2013. During my thesis that started in October 2011 two different projects were developed, both related to interface analysis using the NAP-XPS instrument.
Planar Chirality of Imidazole-Containing Macrocycles - Understanding and Tuning Atropisomerism

The synthesis and characterization of imidazole-containing macrocycles displaying planar chirality has been achieved. HLPC and NMR studies revealed the crucial role of the alicyclic chain length in determining the rate of stereoisomerisation: 15- and 16-membered cyclic compounds are chiral whereas their larger-ringed analogues equilibrate rapidly at room temperature. Computational calculations are in good agreement with experimental observations and allow us to understand the mechanism and the interactions involved in the conformational equilibrium between the two atropisomers. Separation of the two enantiomers of the 15-membered macrocycle by semipreparative chiral HPLC allowed us to investigate the influence of chirality on its biological activity.
Characterization of plasma electrolytic oxidation coatings formed on Mg–Li alloy in an alkaline silicate electrolyte containing silica sol

We investigate the influence of silica sol addition on the ceramic coatings of Mg–Li alloy by plasma electrolytic oxidation (PEO) in an alkaline silicate electrolyte. Scanning electron microscopy, X‐ray diffraction, X‐ray photoelectron spectroscopy, and energy dispersive spectroscopy are employed to characterize the microstructure and composition of the ceramic coatings. The anti‐corrosion behavior of the ceramic coatings is evaluated by potentiodynamic polarization measurements in conjunction with electrochemical impedance analysis. The ceramic coating formed in the electrolyte containing silica sol contains SiO2 and Mg2SiO4 phase and has more uniform morphology and higher corrosion resistance than that formed in the electrolyte without addition of silica sol.
Small Molecule Investigation of KCNQ Potassium Channels: A Dissertation

Voltage-gated K channels associate with multiple regulatory proteins to form complexes with diverse gating properties and pharmacological sensitivities. Small molecules which activate or inhibit channel function are valuable tools for dissecting the assembly and function of these macromolecular complexes. My thesis focuses on the discovery and use of small molecules to probe the structure and function of the KCNQ family of voltage-gated K channels. One protein that obligatorily assembles with KCNQ channels to mediate proper assembly, trafficking, and gating is the calcium sensor, calmodulin. Although resolution of the crystal structures of calmodulin associated with isolated peptide fragments from other ion channels has provided some insight into how calmodulin interacts with and modulates KCNQ channels, structural information for calmodulin bound to a fully folded ion channel in the membrane is unknown. In Chapter II, I developed an intracellular tethered blocker approach to determine the location of calmodulin binding with respect to the KCNQ ion-conducting pathway. Using distance restraints from a panel of these intracellular tethered blockers we then generated models of the KCNQ-calmodulin complex. Our model places calmodulin close to the gate of KCNQ channels, providing structural insight into how CaM is able to communicate changes in intracellular calcium levels to KCNQ channel complexes. In addition to pore blockers, chemical modification of ion channels has been used to probe ion channel function. During my initial attempt to chemically activate KCNQ channels, I discovered that some boronates modulate KCNQ complexes. In Chapter III,
Fostering Inclusive Activities in Mixed-visual Abilities Classrooms using Social Robots

Visually impaired children are increasingly educated in mainstream schools following an inclusive educational approach. However, even though visually impaired (VI) and sighted peers are side by side in the classroom, previous research showed a lack of participation of VI children in classroom dynamics and group activities. That leads to a reduced engagement between VI children and their sighted peers and a missed opportunity to value and explore class members' differences. Robots due to their physicality, and ability to perceive the world, socially-behave and act in a wide range of interactive modalities, can leverage mixed-visual ability children access to group activities while fostering their mutual understanding and social engagement. With this work, we aim to use social robots, as facilitators, to booster inclusive activities in mixed-visual abilities classroom.
A lysimeter study using nitrogen-15 on the uptake of fertilizer nitrogen by perennial ryegrass swards and losses by leaching.

Summary Perennial ryegrass growing in monolith lysimeters and treated with 400 kg N ha-1 as calcium nitrate labelled with nitrogen-15 (10.5 atoms per cent), during one growing season recovered between 43 and 54 per cent of the fertilizer nitrogen. In the following year without further nitrogen additions 4.6–9.5 per cent was taken up, whilst in the fifth year the recovery was less than 1 per cent. The contribution of non-fertilizer sources of nitrogen to the total nitrogen taken up by the plants during the season that nitrogen was applied was estimated using tracer methods to be about 13–14 g N m-2 year-1. The estimate from measuring the nitrogen content of an unfertilized sward was 7 g N m-2 year-1. The residual effects of a fertilizer application are likely to be detectable for a period of between 6 and 9 years. Losses of nitrogen to drainage in the winter after application represented 2–5 per cent of the fertilizer applied, whilst in subsequent years the amounts did not exceed 0.1 per cent. Mean concentrations of nitrate ranged between 4 and 16 mg N I-1. Fertilizer contributed about 60–70 per cent of the total nitrogen lost in the first winter after nitrogen application and 45–60 per cent averaged over three winters.
Surface property directed microchannel flows in biosensors

It is known that rapid mixing in biosensors is required; however, these sensors may use reagents having small diffusion coefficients and whose mixing time scale is longer than the chemical reaction or molecular event time scale. Thus, it is necessary to overcome the inherent diffusion limited mixing of laminar flow. Many techniques to enhance microfluidic mixing are under development such as slanted wells, shallow grooves, electrokinetic instability mixing and surface layers. In this work, enhanced mixing is explored using lattice Boltzmann simulation techniques of two and three dimensional microfluidic channels at low Reynolds numbers. Surface temperature variations and flow field slip and no-slip boundary conditions emulating hydrophobic and hydrophilic surfaces were applied. The combined effect of wall temperature and surface property distributions presents a new way to manipulate microchannel flow fields. The momentum and thermal lattice Boltzmann equations were coupled via a body force term in the momentum equation. Also, a two dimensional, binary fluid model was incorporated. The results show how various wall temperature distributions, subjected to various velocity wall boundary conditions, can be either beneficial or counter productive to obtain uniform flow temperature profiles in, for example, PCR applications. The addition of the binary fluid model demonstrates the effects of both wall temperature and wall velocity boundary conditions.
Assessing Impacts of Changes in External Nutrient Loadings on a Temperate Chinese Drinking Water Reservoir

The safety of drinking water is constantly being evaluated. In the last few decades, however, many drinking waters sources in the world, including in China, have undergone serious eutrophication and consequently water quality deterioration due to anthropogenic induced stressors such as elevated external nutrient inputs. In this study, we used the state-of-the-art complex, dynamic, mechanistic model GOTM-FABM-PCLake (a coupled one-dimensional hydrodynamic-lake ecosystem model) to quantitatively assess the impacts of external nutrient loading on the temperate Jihongtan reservoir in Shandong Province, China. Simulated values of all variables targeted in calibration (water temperature, dissolved oxygen, total nitrogen, total phosphorus, and chlorophyll a) agreed well with observations throughout the entire calibration and validation period and generally mimicked seasonal dynamics and inter-annual variations as found in the monitoring data. A series of scenarios, representing changed external nutrient loadings (both increasing and decreasing compared to the current nutrient load), were set up to quantify the effects on the reservoir water quality. Changes relative to the current external nutrient load had a significant effect on the simulated TN and TP concentrations in the reservoir. Our impact assessment indicate that TN will meet the Chinese water quality requirements of the water source (Class III) when the external nitrogen load is reduced by 70%, whereas TP will meet the requirements even if the external phosphorus load is increased by 100% relative to current loads. The model predicts progressively higher summer and autumn phytoplankton biomasses in the scenarios with increasing external phosphorus loading and potential toxic cyanobacteria will become more dominant at the expense of diatoms and other algae. Strict control of the external nutrient loading is therefore needed to maintain good drinking water quality in the reservoir.
Correlated ab initio molecular dynamics simulations of the acetone–carbon dioxide complex: implications for solubility in supercritical CO2

Ab initio molecular dynamics simulations of the acetone–CO2 complex (MP2/6-31G(d) level) were performed to investigate the effect of dynamics at finite temperature on the weak electron donor–acceptor intermolecular interactions. In addition, we carried out a study of the free energy of formation of the complex by means of umbrella sampling technique at the MP2 level with a perturbative CCSD(T) correction. The potential of mean force was obtained along a reaction coordinate describing the acetone–CO2 interaction. The results obtained here support some hypothesis that we already explored in past works using static electronic calculations. In particular, when interacting with a molecule having a carbonyl function, carbon dioxide displays both Lewis acid and Lewis base behaviour. This property can be exploited to design molecular systems that are easily solubilised in supercritical CO2.
Dysregulation of MicroRNAs and PIWI-Interacting RNAs in a Caenorhabditis elegans Parkinson’s Disease Model Overexpressing Human α-Synuclein and Influence of tdp-1

MicroRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs) regulate gene expression and biological processes through specific genetic and epigenetic mechanisms. Recent studies have described a dysregulation of small non-coding RNAs in Parkinson’s disease (PD) tissues but have been limited in scope. Here, we extend these studies by comparing the dysregulation of both miRNAs and piRNAs from transgenic Caenorhabditis elegans (C. elegans) nematodes overexpressing pan-neuronally human α-synuclein wild-type (WT) (HASNWT OX) or mutant (HASNA53T OX). We observed 32 miRNAs and 112 piRNAs dysregulated in HASNA53T OX compared with WT. Genetic crosses of HASNA53T OX PD animal models with tdp-1 null mutants, the C. elegans ortholog of TDP-43, an RNA-binding protein aggregated in frontal temporal lobar degeneration, improved their behavioral deficits and changed the number of dysregulated miRNAs to 11 and piRNAs to none. Neuronal function-related genes T28F4.5, C34F6.1, C05C10.3, camt-1, and F54D10.3 were predicted to be targeted by cel-miR-1018, cel-miR-355-5p (C34F6.1 and C05C10.3), cel-miR-800-3p, and 21ur-1581 accordingly. This study provides a molecular landscape of small non-coding RNA dysregulation in an animal model that provides insight into the epigenetic changes, molecular processes, and interactions that occur during PD-associated neurodegenerative disorders.
Failure Handling of Robotic Pick and Place Tasks With Multimodal Cues Under Partial Object Occlusion

The success of a robotic pick and place task depends on the success of the entire procedure: from the grasp planning phase, to the grasp establishment phase, then the lifting and moving phase, and finally the releasing and placing phase. Being able to detect and recover from grasping failures throughout the entire process is therefore a critical requirement for both the robotic manipulator and the gripper, especially when considering the almost inevitable object occlusion by the gripper itself during the robotic pick and place task. With the rapid rising of soft grippers, which rely heavily on their under-actuated body and compliant, open-loop control, less information is available from the gripper for effective overall system control. Tackling on the effectiveness of robotic grasping, this work proposes a hybrid policy by combining visual cues and proprioception of our gripper for the effective failure detection and recovery in grasping, especially using a proprioceptive self-developed soft robotic gripper that is capable of contact sensing. We solved failure handling of robotic pick and place tasks and proposed (1) more accurate pose estimation of a known object by considering the edge-based cost besides the image-based cost; (2) robust object tracking techniques that work even when the object is partially occluded in the system and achieve mean overlap precision up to 80%; (3) contact and contact loss detection between the object and the gripper by analyzing internal pressure signals of our gripper; (4) robust failure handling with the combination of visual cues under partial occlusion and proprioceptive cues from our soft gripper to effectively detect and recover from different accidental grasping failures. The proposed system was experimentally validated with the proprioceptive soft robotic gripper mounted on a collaborative robotic manipulator, and a consumer-grade RGB camera, showing that combining visual cues and proprioception from our soft actuator robotic gripper was effective in improving the detection and recovery from the major grasping failures in different stages for the compliant and robust grasping.