Analysis and modelling of immune cell behaviour in lymph nodes based on multi-photon imaging

This thesis presents quantitative studies of T cell and dendritic cell (DC) behaviour in mouse lymph nodes (LNs) in the naive state and following immunisation. These processes are of importance and interest in basic immunology, and better understanding could improve both diagnostic capacity and therapeutic manipulations, potentially helping in producing more effective vaccines or developing treatments for autoimmune diseases. The problem is also interesting conceptually as it is relevant to other fields where 3D movement of objects is tracked with a discrete scanning interval. A general immunology introduction is presented in chapter 1. In chapter 2, I apply quantitative methods to multi-photon imaging data to measure how T cells and DCs are spatially arranged in LNs. This has been previously studied to describe differences between the naive and immunised state and as an indicator of the magnitude of the immune response in LNs, but previous analyses have been generally descriptive. The quantitative analysis shows that some of the previous conclusions may have been premature. In chapter 3, I use Bayesian state-space models to test some hypotheses about the mode of T cell search for DCs. A two-state mode of movement where T cells can be classified as either interacting to a DC or freely migrating is supported over a model where T cells would home in on DCs at distance through for example the action of chemokines. In chapter 4, I study whether T cell migration is linked to the geometric structure of the fibroblast reticular network (FRC). I find support for the hypothesis that the movement is constrained to the fibroblast reticular cell (FRC) network over an alternative 'random walk with persistence time' model where cells would move randomly, with a short-term persistence driven by a hypothetical T cell intrinsic 'clock'. I also present unexpected results on the FRC network geometry. Finally, a quantitative method is presented for addressing some measurement biases inherent to multi-photon imaging. In all three chapters, novel findings are made, and the methods developed have the potential for further use to address important problems in the field. In chapter 5, I present a summary and synthesis of results from chapters 3-4 and a more speculative discussion of these results and potential future directions.

Generation of extended light-sheets for single and multi-photon fluorescence microscopy

We theoretically propose and computationally demonstrate the generation of extended light-sheet for fluorescence microscopy. This is made possible by the introduction of a specially designed double-window spatial filter that allows the light to pass through the periphery and center of a cylindrical lens. When illuminated with a plane wave, the proposed filter results in an extended depth-of-focus along with side-lobes which are due to other interferences in the transverse focal plane. Computational studies show a maximum extension of light-sheet by 3.38 times for single photon excitation and 3.68 times for multiphoton excitation as compared to state-of-art single plane illumination microscopy system. This technique may facilitate the study of large biological specimens (such as Zebrafish embryo and tissue) with high spatial resolution and reduced photobleaching. (C) 2013 AIP Publishing LLC.

Spatial filtering nearly eliminates the side-lobes in single- and multi-photon 4pi-type-C super-resolution fluorescence microscopy

Super-resolution microscopy has tremendously progressed our understanding of cellular biophysics and biochemistry. Specifically, 4pi fluorescence microscopy technique stands out because of its axial super-resolution capability. All types of 4pi-microscopy techniques work well in conjugation with deconvolution techniques to get rid of artifacts due to side-lobes. In this regard, we propose a technique based on spatial filter in a 4pi-type-C confocal setup to get rid of these artifacts. Using a special spatial filter, we have reduced the depth-of-focus. Interference of two similar depth-of-focus beams in a 4 pi geometry result in substantial reduction of side-lobes. Studies show a reduction of side-lobes by 46% and 76% for single and two photon variant compared to 4pi - type - C confocal system. This is incredible considering the resolving capability of the existing 4pi - type - C confocal microscopy. Moreover, the main lobe is found to be 150 nm for the proposed spatial filtering technique as compared to 690 nm of the state-of-art confocal system. Reconstruction of experimentally obtained 2PE - 4pi data of green fluorescent protein (GFP)-tagged mitocondrial network shows near elimination of artifacts arising out of side-lobes. Proposed technique may find interesting application in fluorescence microscopy, nano-lithography, and cell biology. (C) 2013 AIP Publishing LLC.

Multi-electron processes in 4.15-11.08 keV/u(13)C(6+) on argon collisions

The relative partial cross sections for C-13(6+)-Ar collisions at 4.15-11.08 keV/u incident energy are measured. The cross-section ratios sigma(2E)/sigma(SC), sigma(3E)/sigma(SC), sigma(4E)/sigma(SC) and sigma(5E)/sigma(SC) are approximately the constants of 0.51 +/- 0.05, 0.20 +/- 0.03, 0.06 +/- 0.03 and 0.02 +/- 0.01 in this region. The significance of the multi-electron process in highly charged ions (HCIs) with argon collisions is demonstrated (sigma(ME)/sigma(SC) as high as 0.79 +/- 0.06). In multi-electron processes, it is shown that transfer ionization is dominant while pure electron capture is weak and negligible. For all reaction channels, the cross-sections are independent of the incident energy in the present energy region, which is in agreement with the static characteristic of classic models, i.e. the molecular Coulomb over-the-barrier model (MCBM), the extended classical over-the-barrier (ECBM) and the semiempirical scaling laws (SL). The result is compared with these classical models and with our previous work of C-13(6+)-Ne collisions

High-order harmonic generation and multi-photon ionization of Na-2 in laser fields

In this paper high-order harmonic generation (HHG) spectra and the ionization probabilities of various charge states of small cluster Na-2 in the multiphoton regimes are calculated by using time-dependent local density approximation (TDLDA) for one-colour (1064 nm) and two-colour (1064 nm and 532 nm) ultrashort (25 fs) laser pulses. HHG spectra of Na2 have not the large extent of plateaus due to pronounced collective effects of electron dynamics. In addition, the two-colour laser field can result in the breaking of the symmetry and generation of the even order harmonic such as the second order harmonic. The results of ionization probabilities show that a two-colour laser field can increase the ionization probability of higher charge state.

Multi-electron processes in C-13(6+) ions with neon collisions in energy region 4.15-11.08 keV/u

The cross-section ratios of double-, triple-, quadruple-, and the total multi-electron processes to the single electron capture process sigma(DE)/sigma(SC), sigma(TE)/sigma(SC), sigma(QE)/sigma(SC) and sigma(ME)/sigma(SC)) as well as the relative ratios among reaction channels in double-electron active, triple-electron active and quadruple- electron active are measured in C-13(6+) -Ne collision in the energy region of 4.15-11.08 keV/u by employing position-sensitive and time-of-flight coincident techniques. It is determined that the cross-section ratios sigma(DE)/sigma(SC), sigma(TE)/sigma(SC), sigma(QE)/sigma(SC) and sigma(ME)/sigma(SC) are approximately the constants of 0.20 +/- 0.03, 0.16 +/- 0.04, 0.06 +/- 0.02 and 0.42 +/- 0.05. These values are obviously smaller than the predictions of the molecular Coulomb over-the-barrier model (MCBM) [J. Phys. B 23 (1990) 4293], the extended classical over-the-barrier model (ECBM) [J. Phys. B 19 (1986) 2925] and the semiempirical scaling laws (SL) [Phys. Rev. A 54 (1996) 4127]. However, the relative ratios among partial processes of DE, TE and QE are found to depend on collision energy, which suggests that the collision dynamics depends on the collision velocity. The limitation of velocity-independent character of ECBM, MCBM and SL is undoubtedly shown.

Computational modelling of multi-physics processes on high performance parallel computer systems

The demands of the process of engineering design, particularly for structural integrity, have exploited computational modelling techniques and software tools for decades. Frequently, the shape of structural components or assemblies is determined to optimise the flow distribution or heat transfer characteristics, and to ensure that the structural performance in service is adequate. From the perspective of computational modelling these activities are typically separated into: • fluid flow and the associated heat transfer analysis (possibly with chemical reactions), based upon Computational Fluid Dynamics (CFD) technology • structural analysis again possibly with heat transfer, based upon finite element analysis (FEA) techniques.

Computational modelling of multi-physics and multi-scale processes in parallel

This paper provides an overview of the developing needs for simulation software technologies for the computational modelling of problems that involve combinations of interactions amongst varying physical phenomena over a variety of time and space scales. Computational modelling of such problems requires software tech1nologies that enable the mathematical description of the interacting physical phenomena together with the solution of the resulting suites of equations in a numerically consistent and compatible manner. This functionality requires the structuring of simulation modules for specific physical phenomena so that the coupling can be effectively represented. These multi-physics and multi-scale computations are very compute intensive and the simulation software must operate effectively in parallel if it is to be used in this context. An approach to these classes of multi-disciplinary simulation in parallel is described, with some key examples of application to2 challenging engineering problems.

Resonantly Enhanced Multi-Photon Ionization Spectrum of the Neutral Green Fluorescent Protein Chromophore

The photophysics of the green fluorescent protein is governed by the electronic structure of the chromophore at the heart of its β-barrel protein structure. We present the first two-color, resonance-enhanced, multiphoton ionization spectrum of the isolated neutral chromophore in vacuo with supporting electronic structure calculations. We find the absorption maximum to be 3.65 ± 0.05 eV (340 ± 5 nm), which is blue-shifted by 0.5 eV (55 nm) from the absorption maximum of the protein in its neutral form. Our results show that interactions between the chromophore and the protein have a significant influence on the electronic structure of the neutral chromophore during photoabsorption and provide a benchmark for the rational design of novel chromophores as fluorescent markers or photomanipulators.

Assessment of epidermal cell viability by near infrared multi-photon microscopy following ballistic delivery of gold micro-particles

The use of gene guns in ballistically delivering DNA vaccine coated gold micro-particles to skin can potentially damage targeted cells, therefore influencing transfection efficiencies. In this paper, we assess cell death in the viable epidermis by non-invasive near infrared two-photon microscopy following micro-particle bombardment of murine skin. We show that the ballistic delivery of micro-particles to the viable epidermis can result in localised cell death. Furthermore, experimental results show the degree of cell death is dependant on the number of micro-particles delivered per unit of tissue surface area. Micro-particles densities of 0.16 +/- 0.27 (mean +/- S.D.), 1.35 +/- 0.285 and 2.72 +/- 0.47 per 1000 mu m(2) resulted in percent deaths of 3.96 +/- 5.22, 45.91 +/- 10.89, 90.52 +/- 12.28, respectively. These results suggest that optimization of transfection by genes administered with gene guns is - among other effects - a compromise of micro-particle payload and cell death. (c) 2005 Elsevier Ltd. All rights reserved.

Discontinuous control of multi-variable processes

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