In this study, molecular dynamics (MD) simulations was employed to investigate (5,5), (10,10) single-walled nanocoils and (5,5)@(10,10) double-walled carbon nanocoils. The study can be arranged into two parts¡G In part I: Investigate the mechanical properties of (5,5), (10,10) single-walled nanocoils and (5,5)@(10,10) double-walled carbon nanocoils. The second reactive empirical bond order (REBO) potential was employed to model the interaction between carbon atoms. The contours of atomic slip vector and sequential slip vector were used to investigate the structural variations at different strains during the tension process. The yielding stress, maximum tensile strength, and Young¡¦s modulus were determined from the tensile stress-strain profiles. The results show that the nanocoils have superelastic characteristics to the carbon nanotube in the same tube diameter. In part II: Investigate the diffusion behavior of water molecules confined inside narrow (5,5) and (10,10) carbon nanocoils under different tensile strains. The condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) potential was employed to model the interaction between carbon-carbon atoms¡Acarbon atoms-water molecules and water-water molecules. To analysis the kinetic behavior of water molecules in two carbon nanocoils, the diffusion coefficients, square displacement (SD) and mean square displacement (MSD) of water molecules were calculated. The results show that diffusion coefficient of water will increase with the strains of carbon nanocoils. However, the diffusion coefficient has a significant decrease in a large strain due to the structural deformation of carbon nanocoils. The diffusion behaviors of water inside the (5,5) and (10,10) carbon nanotubes were also investigated to compare the results in (5,5) and (10,10) carbon nanotubes. Our results indicate that two carbon nanocoils have a lower diffusion coefficient of water than that of carbon nanotubes because the geometry of carbon nanocoil is easily to block up the diffusion of water molecules.

Despite the importance of single particle motion in biological systems, systematic inference approaches to analyze particle trajectories and evaluate competing motion models are lacking. An automated approach for robust evaluation of motion models that does not require manual intervention is highly desirable to enable analysis of datasets from high-throughput imaging technologies that contain hundreds or thousands of trajectories of biological particles, such as membrane receptors, vesicles, chromosomes or kinetochores, mRNA particles, or whole cells in developing embryos. Bayesian inference is a general theoretical framework for performing such model comparisons that has proven successful in handling noise and experimental limitations in other biological applications. The inherent Bayesian penalty on model complexity, which avoids overfitting, is particularly important for particle trajectory analysis given the highly stochastic nature of particle diffusion. This thesis presents two complementary approaches for analyzing particle motion using Bayesian inference. The first method, MSD-Bayes, discriminates a wide range of motion models--including diffusion, directed motion, anomalous and confined diffusion--based on mean- square displacement analysis of a set of particle trajectories, while the second method, HMM-Bayes, identifies dynamic switching between diffusive and directed motion along individual trajectories using hidden Markov models. These approaches are validated on biological particle trajectory datasets from a wide range of experimental systems, demonstrating their broad applicability to research in cell biology.

As part of this project and in preparation for future experimental studies of gas-phase ion-molecule reactions, extensive modification and characterization of the crossed molecular beam machine in the Department of Chemistry, University of Canterbury has been carried out. This instrument has been configured and some preliminary testing completed to enable the future study of gas-phase ion-molecule collisions of H⁺₃ and Y⁻ (Y = F, Cl, Br) with dipole-oriented CZ₃X (Z = H, F and X = F, Cl, Br). Theoretical calculations (ab initio and density functional theory) are reported on previously experimentally characterized Na + CH₃NO₂, Na + CH₃NC, and K + CH₃NC systems, and several other systems of relevance. All gas-phase experimental and theoretical studies have the common theme of studying collision orientation dependence of reaction under singlecollision conditions. Experimental measurements, theoretical simulations and calculations are also reported on some selected ferrous (Fe²⁺) high-spin (S=2) crystals, in an attempt to resolve microscopic contributions of two fundamental macroscopic tensor properties: the electric-field gradient (efg); and the mean square displacement (msd) in the case when more than one symmetry related site of low local point-group symmetry contributes to the same quadrupole doublet. These determinations have been made using the nuclear spectroscopic technique of Mössbauer spectroscopy, and complemented with X-ray crystallographic measurements.

We study anomalous diffusion on fractals with a static external field applied. We utilise the master equation to calculate particle distributions and from that important quantities as for example the mean square displacement <r^2(t)>. Applying different bias amplitudes on several regular Sierpinski carpets we obtain maximal drift velocities for weak field strengths. According to <r^2(t)>~t^(2/d_w), we determine random walk dimensions of d_w<2 for applied external fields. These d_w corresponds to superdiffusion, although diffusion is hindered by the structure of the carpet, containing dangling ends. This seems to result from two competing effects arising within an external field. Though the particles prefer to move along the biased direction, some particles get trapped by dangling ends. To escape from there they have to move against the field direction. Due to the by the bias accelerated particles and the trapped ones the probability distribution gets wider and thus d_w<2. / In dieser Arbeit untersuchen wir anomale Diffusion auf Fraktalen unter Einwirkung eines statisches äußeres Feldes. Wir benutzen die Mastergleichung, um die Wahrscheinlichkeitsverteilung der Teilchen zu berechnen, um daraus wichtige Größen wie das mittlere Abstandsquadrat <r^2(t)> zu bestimmen. Wir wenden unterschiedliche Feldstärken bei verschiedenen regelmäßigen Sierpinski-Teppichen an und erhalten maximale Driftgeschwindigkeiten für schwache Feldstärken. Über <r^2(t)>~t^{2/d_w} bestimmen wir die Random-Walk-Dimension d_w als d_w<2. Dieser Wert für d_w entspricht der Superdiffusion, obwohl der Diffusionsprozess durch Strukturen des Teppichs, wie Sackgassen, behindert wird. Es schient, dass dies das Ergebnis zweier konkurrierender Effekte ist, die durch das Anlegen eines äußeren Feldes entstehen. Einerseits bewegen sich die Teilchen bevorzugt entlang der Feldrichtung. Andererseits gelangen einige Teilchen in Sackgassen. Um die Sackgassen, die in Feldrichtung liegen, zu verlassen, müssen sich die Teilchen entgegen der Feldrichtung bewegen. Somit sind die Teilchen eine gewisse Zeit in der Sackgasse gefangen. Infolge der durch das äußere Feld beschleunigten und der gefangenen Teilchen, verbreitert sich die Wahrscheinlichkeitsverteilung der Teilchen und somit ist d_w<2.

No description available.

Single-particle tracking (SPT) is a method used to study the diffusion of various molecules within the cell. SPT involves tagging proteins with optical labels and observing their individual two-dimensional trajectories with a microscope. The analysis of this data provides important information about protein movement and mechanism, and is used to create multistate biological models. One of the challenges in SPT analysis is the variety of complex environments that contribute to heterogeneity within movement paths. In this thesis, we explore the limitations of current methods used to analyze molecular movement, and adapt analytical methods used in animal movement analysis, such as correlated random walks and first-passage time variance, to SPT data of leukocyte function-associated antigen-1 (LFA-1) integral membrane proteins. We discuss the consequences of these methods in understanding different types of heterogeneity in protein movement behaviour, and provide support to results from current experimental work. / Applied Mathematics

La diffusion multiple de la lumière(DWS) est une technique qui permet de sonder la dynamique interne de milieux opaques et concentrés à des fréquences élevées. Elle a été utilisée pour déterminer les propriétés viscoélastiques de ces milieux. Elle a l'avantage d'être non destructive, rapide et sensible. Ce travail a pour objectif l'étude des tissus biologiques mous par DWS. La première étape est la mise en place du dispositif expérimental. Afin d'évaluer les limites de la technique, des études successives ont été réalisées sur des matériaux de complexité croissante (une suspension, le lait et une mousse) tendant vers la complexité structurale des tissus biologiques. Pour la suspension et le lait, la théorie de DWS peut s'appliquer et permet de mesurer avec une bonne précision leur viscosité. Les limites de DWS pour évaluer la viscosité sont atteintes avec la mousse dont la structure complexe est proche de celle des tissus biologiques. Enfin, le cortex rénal, le parenchyme hépatique et le cerveau de porc ont été étudiés. La théorie appliquée pour les milieux précédents ne permet pas de remonter à leur viscosité. Mais la DWS a permis de suivre leur microstructure au cours de la déshydratation et de la dégénérescence. Pour tous ces milieux la répétabilité, la reproductibilité, la variabilité et l'effet des conditions expérimentales ont été évalués. La DWS pourrait être utilisée pour étudier l'effet de la température et de la congélation sur le spectre de DWS des tissus biologiques ou combinée à la rhéologie pour suivre l'évolution des spectres de DWS au cours d'un cisaillement / Diffusing Wave Spectroscopy (DWS) is a technique that allows to probe the internal dynamics of opaque media and concentrated at high frequencies. It has been used to determine the viscoelastic properties of these media. It has the advantage of being nondestructive, rapid and sensitive. This work aims to study soft biological materials by DWS. The first step is setting up of the experimental device. To evaluate the limits of the art, successive studies were conducted on materials of increasing complexity (a suspension, milk and a foam) tending to the structural complexity of biological tissues. Concerning the suspension and milk, two concentrated media, and mono-dispersed in which the particles are in Brownian motion, DWS allowed to measure with good precision their viscosity. The limits of DWS to evaluate the viscosity of the medium are achieved with the foam which the complex structure is similar to that of soft biological tissues. Finally, the renal cortex, the hepatic parenchyma and porcine brain were studied. The theory applied to previous media does not allow to calculate viscosity. But the DWS allowed us to follow their microstructure during dehydration and degeneration. For all these media, repeatability, reproducibility, variability and effect of experimental conditions were evaluated. The DWS could be used to study the effect of temperature and freezing on the DWS spectrum of biological tissues, or combined with rheology to monitor the evolution spectra DWS during shear

We study anomalous diffusion on fractals with a static external field applied. We utilise the master equation to calculate particle distributions and from that important quantities as for example the mean square displacement <r^2(t)>. Applying different bias amplitudes on several regular Sierpinski carpets we obtain maximal drift velocities for weak field strengths. According to <r^2(t)>~t^(2/d_w), we determine random walk dimensions of d_w<2 for applied external fields. These d_w corresponds to superdiffusion, although diffusion is hindered by the structure of the carpet, containing dangling ends. This seems to result from two competing effects arising within an external field. Though the particles prefer to move along the biased direction, some particles get trapped by dangling ends. To escape from there they have to move against the field direction. Due to the by the bias accelerated particles and the trapped ones the probability distribution gets wider and thus d_w<2. / In dieser Arbeit untersuchen wir anomale Diffusion auf Fraktalen unter Einwirkung eines statisches äußeres Feldes. Wir benutzen die Mastergleichung, um die Wahrscheinlichkeitsverteilung der Teilchen zu berechnen, um daraus wichtige Größen wie das mittlere Abstandsquadrat <r^2(t)> zu bestimmen. Wir wenden unterschiedliche Feldstärken bei verschiedenen regelmäßigen Sierpinski-Teppichen an und erhalten maximale Driftgeschwindigkeiten für schwache Feldstärken. Über <r^2(t)>~t^{2/d_w} bestimmen wir die Random-Walk-Dimension d_w als d_w<2. Dieser Wert für d_w entspricht der Superdiffusion, obwohl der Diffusionsprozess durch Strukturen des Teppichs, wie Sackgassen, behindert wird. Es schient, dass dies das Ergebnis zweier konkurrierender Effekte ist, die durch das Anlegen eines äußeren Feldes entstehen. Einerseits bewegen sich die Teilchen bevorzugt entlang der Feldrichtung. Andererseits gelangen einige Teilchen in Sackgassen. Um die Sackgassen, die in Feldrichtung liegen, zu verlassen, müssen sich die Teilchen entgegen der Feldrichtung bewegen. Somit sind die Teilchen eine gewisse Zeit in der Sackgasse gefangen. Infolge der durch das äußere Feld beschleunigten und der gefangenen Teilchen, verbreitert sich die Wahrscheinlichkeitsverteilung der Teilchen und somit ist d_w<2.

We employ the empirical potential function Airebo to computationally model free-standing Carbon-12 graphene in a classical setting. Our objective is to measure the mean square displacement (MSD) of atoms in the system for different average temperatures and Carbon-13 isotope concentrations. From results of the MSD we aim to develop a technique that employs Transmission Electron Microscopy (TEM), using high-angle annular dark filed (HAADF) detection, to obtain atomic-resolution images. From the thermally diffusive images, produced by the vibrations of atoms, we intent to resolve isotopes types in graphene. For this, we establish a relationship between the full width half maximum (FWHM) of real-space intensity images and MSD for temperature and isotope concentration changes. For the case of changes in the temperature of the system, simulation results show a linear relationship between the MSD as a function of increased temperature in the system, with a slope of 7.858×10-6 Å2/K. We also note a power dependency for the MSD in units of [Å2] with respect to the FWHM in units of [Å] given by FWHM(MSD)=0.20MSD0.53+0.67. For the case of increasing isotope concentration, no statistically significant changes to the MSD of 12C and 13C are noted for graphene systems with 2,000 atoms or more. We note that for the experimental replication of results, noticeable differences in the MSD for systems with approximately 320,000 atoms must be observable. For this, we conclude that isotopes in free-standing graphene cannot be distinguished using TEM.

Thesis (M.Sc. (Physics)) -- University of Limpopo, 2022 / The gas sensing performance of two-dimensional (2D) hexagonal boron nitride nanosheets (h-BNNSs) has being studied by means of computational and experimental methods. The structural, stability and vacancies properties of both defect free and defected 2D h-BNNSs were studied using the classical molecular dynamics (MD) approach. The calculations were performed in the NVT Evans and NPT hoover ensembles using the Tersoff potentials with the Verlet leapfrog algorithm to obtain reliable structural properties and energies for defect free, boron (B) and nitrogen (N) vacancies. B and N defect energies were calculated relative to the bulk defect free total energies, and the results suggest that N vacancy is the most stable vacancy as compared to the B vacancy. The radial distribution functions and structure factors were used to predict the most probable structural form. Mean square displacements suggests the mobility of B and N atoms in the system is increasing with an increase in the surface area of the nanosheets. Results obtained are compared with the bulk defect free h-BNNSs. Experimentally, 2D h-BNNSs were synthesised using the wet chemical reaction method through chemical vapour deposition (CVD) catalyst free approach. The X-Ray Diffraction (XRD), Transmission Electron Microscopy (TEM), Fourier Transform Infrared Spectroscopy (FTIR), Raman Spectroscopy (RM), UV-visible Spectroscopy (UV-VIS), dynamic light scattering (DLS), Energy Dispersion Spectroscopy (EDS) and Brunauer-Emmett Teller (BET) were adopted to attain the structural properties of the nanosheets. Each spectroscopic technique affirmed unique features about the surface morphology of h BNNSs. The crystallinity of the nanosheets with the stacking of the B and N vii honeycomb lattice was validated by the XRD, while the TEM disclosed the specimen orientations and chemical compositions of phases with the number of layers of a planar honeycomb BN sheet, the EDS express the atoms present in the samples and BET validated the surface area of the materials. The FTIR, RM, DLS and the UV-vis expressed the formation of the in-plane, out-of-plane h-BN vibrations and, the nature of the surface with the thickness, particles stability together with the optical properties of the nanosheets. From TEM, FTIR, RS and BET the material fabricated at 800°C showed different morphologies, large number of disordering together with high surface area, which enhances the sensing properties of the nanosheets. However, with an increase in temperature the sensitivity of the nanosheets was found to decrease. Additionally, the UV-vis results, confirmed a lower energy band gap of 4.79, 4.55 and 4.70 eV for materials fabricated at 800, 900 and 1000 °C, that improved the semiconducting properties of the materials, which in return enhanced the sensing properties of the nanosheets. The gas sensing properties of the 2D h BNNSs were also investigated on hydrogen sulphide (H2S) and carbon monoxide (CO). The fabricated sensor based on 800 – 900 °C h-BNNSs showed good sensitivity towards ppm of H2S at 250 °C. The excellent gas sensing properties could be attributed to high surface area, small crystallite size, defect/disordering of h BNNSs. Overall, the h-BNNSs were found to be more sensitive to H2S over CO. / University of Limpopo (UL) Mintek Council for Scientific and Industrial Research (CSIR) Center for High Performance Computing (CHPC)