Dissertations / Theses on the topic 'Mean square displacement'

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.

One of the characteristics that distinguishes living things from non-living things is motility. On the cellular level, the motility or non-motility of different types of cells can be life building, life-saving or life-threatening. A thorough study of cell motion is needed to help understand the underlying mechanisms that enhance or prohibit cell motion. We introduce a discrete centroid model of cell motion in the context of a generalized random walk. We find an approximation for the theoretical mean square displacement (MSD) that uses a subset of the state space to estimate the MSD for the entire space. We give some intuition as to why this is an unexpectedly good estimate. A lower and upper bound for the MSD is also given. We extend the centroid model to an ODE model and use it to analyze the distribution of focal adhesion (FA) lifetimes gathered from experimental data. We found that in all but one case a unimodal, non-symmetric gamma distribution is a good match for the experimental data. We use a detach-rate function in the ODE model to determine how long a FA will persist before it detaches. A detach-rate function that is dependent on both force and time produces distributions with a best fit gamma curve that closely matches the data. Using the data gathered from the matching simulations, we calculate both the cell speed and mean FA lifetime and compare them. Where available, we also compare this relationship to that of the experimental data and find that the simulation reasonably matches it in most cases. In both the simulations and experimental data, the cell speed and mean FA lifetime are related, with longer mean lifetimes being indicative of slower speeds. We suspect that one of the main predictors of cell speed for migrating cells is the distribution of the FA lifetimes.

The mean-square displacement amplitudes (MSDA) of the tetrahedral cations Si and Al are compared to the MSDA of their coordinated O atoms in framework silica polymorphs and aluminosilicate structures. Criteria are established which indicate order, structural disorder or substitutional disorder in a framework crystal.

Master of Science

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 . Applying different bias amplitudes on several regular Sierpinski carpets we obtain maximal drift velocities for weak field strengths. According to ~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 zu bestimmen. Wir wenden unterschiedliche Feldstärken bei verschiedenen regelmäßigen Sierpinski-Teppichen an und erhalten maximale Driftgeschwindigkeiten für schwache Feldstärken. Über ~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.

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

Interprétation de données vibrationnelles obtenues sur les aluminés béta par des calculs de champ de force. Calcul des déplacements quadratiques moyens dans les aluminés béta. Les mécanismes de conduction ont été utilisés par diffusion quasi élastique de neutrons et calorimétrie adiabatique. Le calcul des intensités raman sur un cristal de ga::(2)o::(3) est en bon accord avec l'experience

In dieser Arbeit betrachten wir das Strömungs-Diffusions-(Reaktions)-Problem für passive Markerteilchen, die in zweidimensionalen laminaren Strömungsmustern mit geringem thermischem Rauschen gelöst sind. Der deterministische Fluss umfasst Zellen in Form von Quadraten oder Katzenaugen. In ihnen tritt Rotationsbewegung auf. Einige der Strömungen bestehen aus wellenförmigen Bereichen mit gerader Vorwärtsbewegung. Alle Systeme sind entweder periodisch oder durch Wände begrenzt. Eine untersuchte Familie von Strömungen interpoliert kontinuierlich zwischen Reihen von Wirbeln und Scherflüssen. Wir analysieren zahlreiche numerische Simulationen, die bisherige theoretische Vorhersagen bestätigen und neue Phänomene offenbaren. Ohne Rauschen sind die Teilchen in einzelnen Bestandteilen des Flusses für immer gefangen. Durch Hinzufügen von schwachem thermischen Rauschen wird die normale Diffusion für lange Zeiten stark verstärkt und führt zu verschiedenen Diffusionsarten für mittlere Zeiten. Mit Continuous-Time-Random-Walk-Modellen leiten wir analytische Ausdrücke in Übereinstimmung mit den numerischen Ergebnissen her, die je nach Parametern, Anfangsbedingungen und Alterungszeiten von subdiffusiver bis superballistischer anomaler Diffusion für mittlere Zeiten reichen. Wir sehen deutlich, dass einige der früheren Vorhersagen nur für Teilchen gelten, die an der Separatrix des Flusses starten - der einzige Fall, der in der Vergangenheit ausführlich betrachtet wurde - und dass das System zu vollkommen anderem Verhalten in anderen Situationen führen kann, einschließlich einem Schwingenden beim Start im Zentrum einesWirbels nach einer gewissen Alterungszeit. Darüber hinaus enthüllen die Simulationen, dass Teilchenreaktionen dort häufiger auftreten, wo sich die Geschwindigkeit der Strömung stark ändert, was dazu führt, dass langsame Teilchen von schnelleren getroffen werden, die ihnen folgen. Die umfangreichen numerischen Simulationen, die für diese Arbeit durchgeführt wurden, mussten jetzt durchgeführt werden, da wir die Rechenleistung dafür besitzen.
In this thesis, we consider the advection-diffusion-(reaction) problem for passive tracer particles suspended in two-dimensional laminar flow patterns with small thermal noise. The deterministic flow comprises cells in the shape of either squares or cat’s eyes. Rotational motion occurs inside them. Some of the flows consist of sinusoidal regions of straight forward motion. All systems are either periodic or are bounded by walls. One examined family of flows continuously interpolates between arrays of eddies and shear flows. We analyse extensive numerical simulations, which confirm previous theoretical predictions as well as reveal new phenomena. Without noise, particles are trapped forever in single building blocks of the flow. Adding small thermal noise, leads to largely enhanced normal diffusion for long times and several kinds of diffusion for intermediate times. Using continuous time random walk models, we derive analytical expressions in accordance with numerical results, ranging from subdiffusive to superballistic anomalous diffusion for intermediate times depending on parameters, initial conditions and aging time. We clearly see, that some of the previous predictions are only true for particles starting at the separatrix of the flow - the only case considered in depth in the past - and that the system might show a vastly different behavior in other situations, including an oscillatory one, when starting in the center of an eddy after a certain aging time. Furthermore, simulations reveal that particle reactions occur more frequently at positions where the velocity of the flow changes the most, resulting in slow particles being hit by faster ones following them. The extensive numerical simulations performed for this thesis had to be done now that we have the computational means to do so. Machines are powerful tools in order to gain a deeper and more detailed insight into the dynamics of many complicated dynamical and stochastic systems.

A new method of adaptive impulse control is developed to precisely and quickly control the position of machine components subject to friction. Friction dominates the forces affecting fine positioning dynamics. Friction can depend on payload, velocity, step size, path, initial position, temperature, and other variables. Control problems such as steady-state error and limit cycles often arise when applying conventional control techniques to the position control problem. Studies in the last few decades have shown that impulsive control can produce repeatable displacements as small as ten nanometers without limit cycles or steady-state error in machines subject to dry sliding friction. These displacements are achieved through the application of short duration, high intensity pulses. The relationship between pulse duration and displacement is seldom a simple function. The most dependable practical methods for control are self-tuning; they learn from online experience by adapting an internal control parameter until precise position control is achieved. To date, the best known adaptive pulse control methods adapt a single control parameter. While effective, the single parameter methods suffer from sub-optimal settling times and poor parameter convergence. To improve performance while maintaining the capacity for ultimate precision, a new control method referred to as Adaptive Impulse Control (AIC) has been developed. To better fit the nonlinear relationship between pulses and displacements, AIC adaptively tunes a set of parameters. Each parameter affects a different range of displacements. Online updates depend on the residual control error following each pulse, an estimate of pulse sensitivity, and a learning gain. After an update is calculated, it is distributed among the parameters that were used to calculate the most recent pulse. As the stored relationship converges to the actual relationship of the machine, pulses become more accurate and fewer pulses are needed to reach each desired destination. When fewer pulses are needed, settling time improves and efficiency increases. AIC is experimentally compared to conventional PID control and other adaptive pulse control methods on a rotary system with a position measurement resolution of 16000 encoder counts per revolution of the load wheel. The friction in the test system is nonlinear and irregular with a position dependent break-away torque that varies by a factor of more than 1.8 to 1. AIC is shown to improve settling times by as much as a factor of two when compared to other adaptive pulse control methods while maintaining precise control tolerances.

In the present thesis we compare the mean square displacement (MSD) values obtained on dry and hydrated (H2O and D2O) lysozyme samples by using two spectrometers, IN13 and IN10 at the Institute Laue Langevin (Grenoble, France), working at the energy resolution value of 8μeV, corresponding to an elastic time resolution of 516 ps, and at the energy resolution value of 1μeV, corresponding to an elastic time resolution of 4136 ps. In particular the comparison is performed when only vibrational motions occur, i.e. when the system MSD can be considered almost constant 〈r^2 〉(t)→〈r^2 〉^V. Such a condition is approximately satisfled in the low temperature range up to T=40K. The analysis furnish values that agree very well with data reported in literature while comparison between the measured MSDs shows the role played by the instrumental energy resolution.

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

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 . Applying different bias amplitudes on several regular Sierpinski carpets we obtain maximal drift velocities for weak field strengths. According to ~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 zu bestimmen. Wir wenden unterschiedliche Feldstärken bei verschiedenen regelmäßigen Sierpinski-Teppichen an und erhalten maximale Driftgeschwindigkeiten für schwache Feldstärken. Über ~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.