Gene therapy has the potential to treat a wide variety of diseases. Delivering nucleic acids, such as DNA and mRNA, allows for the production of an aberrant or absent protein that is causing the disease. Delivery of genes via viruses is very efficient but falls short because of other issues. Nonviral delivery, on the other hand, struggles with efficiency but has advantages in terms of lack of immunogenicity, ease in production, and carrying capacity. DNA is much more stable than mRNA, and the protein production from DNA persists for a longer time. However, DNA delivered to cells must pass through the nuclear envelope to produce protein. Nuclear penetration with nonviral DNA delivery in vivo has not yet been accomplished. mRNA only needs to be delivered to the cytoplasm. Recent interest in nonviral delivery of mRNA has surged upward because delivery of mRNA to various cells in vivo has proven successful. Yet mRNA still struggles with nuclease stability, which is a major impediment toward efficient expression. A polyacridine PEG-peptide (PEG-peptide) has been previously used to stabilize DNA against nuclease hydrolysis by binding through ionic and intercalative interactions. Binding of PEG-peptide to DNA results in a PEGylated nanoparticle, or polyplex, and which protects the DNA. The same PEG-peptide was applied to mRNA. To increase the ability of PEG-peptide to bind through intercalation, a reverse complementary strand was hybridized to the mRNA, forming double stranded mRNA (dsmRNA). In a similar manner to DNA, complexing dsmRNA or single stranded mRNA (ssmRNA) with PEG-peptide resulted in formation of PEG-peptide polyplexes. A dsmRNA polyplex was much more resistant to ribonuclease challenge in vitro than a ssmRNA polyplex. The mRNA constructs were tested in vivo by hydrodynamic dosing. dsmRNA was found to be translationally competent by producing a high level of luciferase reporter enzyme in the liver of mice. When the reverse strand length was modified such that it hybridized with only the coding region, leaving the untranslated regions (UTRs) and poly(A) tail single stranded, the in vivo translatability (level of expression) and persistence (duration of expression) of dsmRNA was equivalent to that of ssmRNA. Full hybridization of the reverse strand with the coding region, the UTRs, and poly(A) tail resulted in a decrease of in vivo translatability. However, the circulatory stability (an in vivo measure of resistance to degradation in blood) was greatly increased when the reverse strand was fully hybridized. The persistence of expression of exogenously delivered mRNA is poor in comparison to DNA. The first step in mRNA decay in the cytoplasm is predominantly poly(A) tail shortening, or deadenylation. To address the persistence issue, mRNA with nonadenosine extensions at the 3’ end of the poly(A) tail was synthesized to inhibit deadenylation-dependent mRNA decay. However, increase of the length of tail extension resulted in a concomitant overall decrease in translatability and no increase in persistence. Hybridization of a DNA oligo to the origin of the tail extension activated endogenous RNase H, cleaving the tail extension, exposing the poly(A) tail, and reactivating the mRNA for high level translation, although no increase in persistence was seen with this strategy. A structured tail extension consisting of two human β-globin 3’UTR sequences increased persistence but also decreased overall translatability. Enzymatic poly(A) tailing of this structured tail extension brought back the translatability but simultaneously lost the persistence gain. While this study on poly(A) tail extension mRNA did not produce a highly active mRNA that had increased persistence, its results may be applicable toward other gene therapy applications. Other efforts to increase the metabolic stability or persistence of mRNA were pursued. Scavenger receptors on resident liver macrophages remove polyplexes from the blood by phagocytosis. Saturation of the scavenger receptors by coadministration of a scavenger receptor inhibitor resulted in increased circulatory stability of dsmRNA. However the scavenger receptor inhibitor was toxic in mice. Another effort to increase the persistence of gene expression in vivo was utilizing an autogene. Autogenes are able to drive the expression of a DNA-based gene outside of the nucleus. In its final form, the autogene did not produce expression. It is an exciting time to be in the field of mRNA gene therapy. Hopefully the research presented in this thesis will factor in to the knowledge base that can treat and cure human diseases.

L'utilisation des lasers de puissance permet l'étude des propriétés de la matière dans des conditions extrêmes de température et de densité. En effet, l'interaction d'un laser de puissance sur une cible créée un plasma dont la température est suffisamment grande pour atteindre des degrés d'ionisation élevés. Ces conditions peuvent permettre, via divers processus, d'exciter le noyau dans un état nucléaire et notamment dans un état isomère. Un noyau d'intérêt pour étudier ces phénomènes est le 201 Hg. Ce travail de thèse s'inscrit dans le cadre du dimensionnement d'une expérience visant la mise en évidence de l'excitation du 201 Hg dans un plasma laser.La première partie de ce manuscrit présente la détermination des taux d'excitation nucléaire dans les plasmas. Depuis une dizaine d'années les taux d'excitation sont déterminés en utilisant le modèle de l'atome moyen. Afin de valider ce modèle, un code, appelé ADAM (Au-Delà de l'Atome Moyen), a été développé afin de calculer le taux d'excitation nucléaire en DCA (Detailed Conguration Accounting). Il nous permettra d'en déduire un domaine thermodynamique en température et densité où les taux d'excitation déterminés avec le modèle de l'atome moyen sont pertinents.La deuxième partie présente le couplage des taux d'excitation nucléaire avec un code hydrodynamique afin d'en déduire, pour différentes intensités laser, le nombre de noyaux qu'il serait possible d'exciter par tir laser. Enfin, dans une dernière partie,les premières approches expérimentales qui serviront au dimensionnement d'une expérience sur une installation laser sont présentées. Ces approches sont basées sur la détection et la détermination de la quantité d'ions multichargés obtenue loin de la cible (~80 cm). Pour cela, un déviateur électrostatique a été utilisé. / The use of high power lasers allows the study of the properties of matter in extremeconditions of temperature and density. Indeed, the interaction of a power laser and atarget creates a plasma in which the temperature is high enough to reach important degrees of ionization. These conditions can allow the excitation of the nucleus. Anucleus of interest to study the processes of nuclear excitation is the 201 Hg. Thiswork aims to design an experiment where the 201 Hg excitation will be observed in aplasma produced by a high power laser. The first part of this manuscript presents the calculation of the expected nuclear excitation rates in the plasma. For about ten years, nuclear excitation rates have been calculated using the average atom model. To validate this model a code named ADAM (french acronym for Beyond The Average Atom Model) was developed to calculate the nuclear excitation rates under the DCA (Detailed Configuration Accounting) hypothesis. ADAM allows us to deduce the thermo dynamical domain where the nuclear excitation rates determined with the average atom model are relevant. The second part of this manuscript presents the coupling of the excitation rate calculation with a hydrodynamic code to calculate the number of excited nuclei produced in one laser shot for different laser intensity. Finally, in the last part, first experimental approaches which will be used to design an experiment on a laser installation are presented. These approaches are based on the detection and determination of the amount of multicharged ions obtained far from the target (~80 cm). For this purpose, an electrostatic analyzer was used.

Numerical modeling systems are very important tools to study tidal inlets. In order to test its capability and accuracy of solving multi-inlet system problems, this study selected two widely used numerical modeling systems: Coastal Modeling System (CMS) and Delft3D Modeling Package. The hydrodynamics modules of the two modeling systems were tested at John's Pass and Blind Pass, Florida, a dual-inlets system, based on a similar modeling scheme. Detailed bathymetric surveys and hydraulic measurements were conducted to collect water depths, tide conditions, wave and current velocities as the input data as well as verification data for the models. A comparison study was conducted by comparing computed hydrodynamic results from both models with the extensive field measurement data. Results show that both of the modeling systems yield better prediction for water levels than for current velocity. Furthermore, under the similar modeling scheme, Delft3D was able to capture the measured tidal phase lag between the ocean boundary and the coastal inlet, therefore gave better water level prediction than the CMS model. However, the CMS yielded current velocities that are closer to the measured values than the DELFT3D model. CMS has a more user-friendly Graphic User's Interface (GUI) for input data preprocessing and plotting and visualization of output data. Delft3D has faster calculation speed.

<p>This thesis represents an attempt to reveal and explain the mysterious excitation sources which cause global wave induced vibrations of ships. The wave induced vibrations of the hull girder are referred to as springing when they are associated with a resonance phenomenon, and whipping when they are caused by a transient impact loading. Both phenomena excite the governing vertical 2-node mode and possibly higher order modes, and consequently increase the fatigue and extreme loading of the hull girder. These effects are currently disregarded in conventional ship design. The thesis focuses on the additional fatigue damage on large blunt ships.</p><p>The study was initiated by conducting an extensive literature study and by organizing an international workshop. The literature indicated that wave induced vibrations should be expected on any ship type, but full scale documentation (and model tests) was mainly related to blunt ships. While the theoretical investigation of whipping mostly focused on slender vessels with pronounced bow flare, full scale measurements indicated that whipping could be just as important for blunt as for slender ships. Moreover, all estimates dealing with the fatigue damage due to wave induced vibration based on full scale measurements before the year of 2000 were nonconservative due to crude simplifications. The literature on the actual importance of the additional fatigue contribution is therefore scarce.</p><p>The workshop was devoted to the wave induced vibrations measured onboard a 300m iron ore carrier. Full scale measurements in ballast condition were compared with numerical predictions from four state-of-the-art hydroelastic programs. The predicted response was unreliable, and the programs in general underestimated the vibration level. The excitation source was either inaccurately described or lacking. The prediction of sea state parameters and high frequency tail behavior of the wave spectra based on wave radars without proper setting and calibration was also questioned. The measurements showed that vibrations in ballast condition were larger than in the cargo condition, the vibration was more correlated with wind speed than wave height, head seas caused higher vibration levels than following seas, the vibration level towards beam seas decayed only slightly, and the damping ratio was apparently linear and about 0.5%. The additional vibration damage constituted 44% of the total measured fatigue loading in deck amidships in the North Atlantic iron ore trade, with prevailing head seas encountered in ballast condition.</p><p>Four hypotheses, which may contribute to explain the high vibration levels, were formulated. They include the effect of the steady wave field and the interaction with the unsteady wave field, amplification of short incident waves due to bow reflection, bow impacts including the exit phase and sum frequency excitation due to the bow reflection. The first three features were included in a simplified program to get an idea of the relative importance. The estimates indicated that the stem flare whipping was insignificant in ballast condition, but contributed in cargo condition. The whipping was found to be sensitive to speed. Simplified theory was employed to predict the speed reduction, which was about 5kn in 5m significant wave height. The estimated speed reduction was in fair agreement with full scale measurements of the iron ore carrier.</p><p>Extensive model tests of a large 4-segmented model of an iron ore carrier were carried out. Two loading conditions with three bow shapes were considered in regular and irregular waves at different speeds. By increasing the forward trim, the increased stem flare whipping was again confirmed to be of less importance than the reduced bottom forces in ballast condition. The bow reflection, causing sum frequency excitation, was confirmed to be important both in ballast and cargo condition. It was less sensitive to speed than linear springing. The second order transfer function amplitude displayed a bichromatic sum frequency springing (at resonance), which was almost constant independent of the frequency difference. The nondimensional monochromatic sum frequency springing response was even higher. The sum frequency pressure was mainly confined to the bow area. Surprisingly, for the sharp triangular bow with vertical stem designed to remove the sum frequency effect, the effect was still pronounced, although smaller. The reflection of incident waves did still occur.</p><p>In irregular head sea states in ballast condition whipping occurred often due to bottom bilge (flare) impacts, starting with the first vibration cycle in hogging. This was also observed in cargo condition, and evident in full scale. This confirmed that the exit phase, which was often inaccurately represented or lacking in numerical codes, was rather important. Flat bottom slamming was observed at realistic speeds, but the vibratory response was not significantly increased. Stern slamming did not give any significant vibration at realistic forward speeds.</p><p>The fatigue assessment showed that the relative importance of the vibration damage was reduced for increasing peak period, and secondly that it increased for increasing wave heights due to nonlinearities. All three bows displayed a similar behavior. For the sharp bow, the additional fatigue damage was reduced significantly in steep and moderate to small sea states, but the long term vibration damage was less affected. The effect of the bulb appeared to be small. The contribution of the vibration damage was reduced significantly with speed. For a representative North Atlantic iron ore trade with head sea in ballast and following sea in cargo condition the vibration damage reduced from 51% at full speed to 19% at realistic speeds. This was less than measured in full scale, but the damping ratio of 1-3.5% in model tests was too high, and the wave damage in following seas in cargo condition was represented by head sea states (to high wave damage due to too high encounter frequency). Furthermore, the contribution from vibration damage was observed to increase in less harsh environment from 19% in the North Atlantic to 26% in similarWorld Wide trade. This may also be representative for the effect of routing. The dominating wave and vibration damage came from sea states with a significant wave height of 5m. This was in agreement with full scale results. In ballast condition, the nonlinear sum frequency springing appeared to be more important than the linear springing, and the total springing seemed to be of equivalent importance as the whipping process, which was mainly caused by bottom bilge (flare) impacts. All three effects should be incorporated in numerical tools.</p><p>In full scale, the vibration response reached an apparently constant level as a function of wave height in both ballast and cargo condition in head seas. This behaviour could be explained by the speed reduction in higher sea states. The vibration level in cargo condition was 60-70% of the level in ballast condition. Although common knowledge implies that larger ships may experience higher springing levels due to a lower eigenfrequency, a slightly smaller ore carrier displayed a higher contribution from the vibration damage (57%) in the same trade, explained by about 1m smaller draft. Moreover, the strengthening of the larger ship resulted in a 10% increase of the 2-node eigenfrequency. The subsequent measurements confirmed that an increased hull girder stiffness was not an effective means to reduce the relative importance of the vibration damage.</p><p>The relative importance of the excitation sources causing wave induced vibration may differ considerably for a slender compared to a blunt vessel. Therefore, full scale measurements on a 300m container vessel were briefly evaluated. The damping ratio was almost twice as high as for several blunt ships, possibly due to significant contribution from the container stacks. The reduced relative importance of the vibration damage with increasing wave height for the iron ore carrier in full scale was opposite to the trend obtained for the container vessel. Less speed reduction in higher sea states was confirmed, and the whipping process was apparently relatively more important for the container vessel. Both for the blunt and slender ship of roughly 300m length, the total fatigue damage due to vibration was of similar importance as the conventional wave frequency damage. The contribution to fatigue damage from wave induced vibrations should be accounted for, for ships operating in harsh environment with limited effect of routing, especially when they are optimized with respect to minium steel weight.</p><p>The four hypotheses were all relevant in relation to wave induced vibrations on blunt ships. Further numerical investigation should focus on the sum frequency springing caused by bow reflection and the whipping impacts at the bow quarter. The wave amplification, steady wave elevation and the exit phase must be properly incorporated. When it comes to design by testing, an optimized model size must be selected (wall interaction versus short wave quality). The speed must be selected in combination with sea state. The wave quality must be monitored, and a realistic damping ratio should be confirmed prior to testing. For the purpose of investigating sum frequency excitation, a large restrained bow model tested in higher waves may be utilized to reduce uncertainties in the small measured pressures.</p>

La faisabilite de la fusion magnetique est dependante de notre capacite a confiner l'energie des particules supra-thermiques liberees a haute energie par les reactions de fusion, dans les meilleures conditions de securite et d'efficacite. Dans ce but, il est necessaire de comprendre l'interaction entre les particules energetiques et le plasma thermo-nucleaire qui constitue l'environnement des reactions de fusion, afin de la controler. La these que nous presentons ici s'inscrit dans cet effort. Le coeur du travail mene est l'etude d'un type d'instabilite, le Beta Alfven Eigenmode (BAE), que peuvent exciter les particules energetiques, et dont on peut craindre qu'il degrade fortement non seulement le confinement des particules energetiques mais aussi le confinement du plasma dans sa globalite. Dans un premier temps, nous nous attacherons a decrire les caracteristiques de ce mode et nous deriverons sa relation de dispersion ainsi que sa structure. Dans une seconde partie, nous effectuerons l'etude de la stabilite lineaire de ce mode en presence de particules energetiques. Cette etude nous a permis de definir un critere analytique rendant compte de la capacite des particules energetiques a exciter le BAE. Ce critere sera discute et confronte aux resultats d'experiences menees durant la these. Cette etude lineaire presentant cependant quelques limites, il nous est apparu important de nous poser la question de la possibilite d'une modication de la stabilite du BAE liee a l'utilisation d'une description non-lineaire. Nous suggererons dans cette presentation un processus, verifie analytiquement et numeriquement, dont peut resulter l'existence d'etats meta-stables pour le BAE.

We present predictions for the statistical error due to finite sampling in the presence of thermal fluctuations in molecular simulation algorithms. Specifically, we present predictions for the error dependence on hydrodynamic parameters and the number of samples taken. Expressions for the common hydrodynamic variables of interest such as flow velocity, temperature, density, pressure, shear stress and heat flux are derived using equilibrium statistical mechanics. Both volume-averaged and surface-averaged quantities are considered. Comparisons between theory and computations using direct simulation Monte Carlo for dilute gases, and molecular dynamics for dense fluids, show that the use of equilibrium theory provides accurate results. / Singapore-MIT Alliance (SMA)

Thesis (M.Sc. (Physics))--North-West University, Potchefstroom Campus, 2008.

Understanding the mechanism of bubble-particle interactions plays a critical role in advancing flotation technology. In this study, submicron size bubbles with an average diameter less than 1 μm and a life time of at least several hours were generated using a novel hydrodynamic cavitation method. Effect of mechanical force and water chemistry on generation and stability of submicron size bubbles is investigated. With recent development in measuring zeta potential distributions of colloidal systems, interactions of bubbles and fine solid particles in various electrolyte, surfactant and frother solutions as well as in industrial process water were studied using the stable submicron size bubbles generated by hydrodynamic cavitation. The outcome of this study provides not only a better understanding of bubble-particle attachment mechanism and its role in flotation, but also a direct evidence of armour-coating of bubbles and enhanced bubble-particle interactions by in situ gas nucleation. / Chemical Engineering

State of the art research in hydrodynamic stability analysis has moved from classic one-dimensional methods such as the local nonparallel approach and the parabolized stability equations to two-dimensional, biglobal, methods. The paradigm shift toward two dimensional techniques with the ability to accommodate fully three-dimensional base flows is a necessary step toward modeling complex, multidimensional flowfields in modern propulsive applications. Here, we employ a two-dimensional spatial waveform with sinusoidal temporal dependence to reduce the three-dimensional linearized Navier-Stokes equations to their biglobal form. Addressing hydrodynamic stability in this way circumvents the restrictive parallel-flow assumption and admits boundary conditions in the streamwise direction. Furthermore, the following work employs a full momentum formulation, rather than the reduced streamfunction form, accounting for a nonzero tangential mean flow velocity. This approach adds significant complexity in both formulation and implementation but renders a more general methodology applicable to a broader spectrum of mean flows. Specifically, we consider the stability of three models for bidirectional vortex flow. While a complete parametric study ensues, the stabilizing effect of the swirl velocity is evident as the injection parameter, kappa, is closely examined.

The production of chlorate, chlorine and sodium hydroxiderelies heavily on electrical energy, so that savings in thisarea are always a pertinent issue. This can be brought aboutthrough increased mass transfer of reacting species to therespective electrodes, and through increased catalytic activityand uniformity of current density distribution at theseelectrodes. This thesis will present studies involvingmathematical modelling and experimental investigations of theseprocesses. They will show the effect that hydrodynamicbehaviour has on the total current density and cell voltages,along with the effects on current density distributions andindividual overpotentials atthe respective electrodes. Primary, secondary and psuedo-tertiary current densitydistribution models of a chlor-alkali anode are presented anddiscussed. It is shown that the secondary model presentsresults rather similar to the pseudo-tertiary model, when thecurrent density distribution is investigated, although thepotential distribution differs rather markedly. Furthermore, itis seen that an adequate description of the hydrodynamicsaround the anode is required if the potential distribution, andthereby the prevalence of side-reactions, is to be reasonablepredicted. A rigorous tertiary current density distribution model ofthe chlorate cell is also presented, which takes into accountthe developing hydrodynamic behaviour along the height of thecell. This shows that an increased flowrate gives more uniformcurrent density distributions. This is due to the fact that theincreased vertical flowrate of electrolyte replenishes ioncontent at the electrode surfaces, thus reducing concentrationoverpotentials. Furthermore, results from the model lead to theconclusion that it is the hypochlorite ion that partakes in themajor oxygen producing side-reaction. A real-scale cross-section of a segmented anode-cathode pairfrom a chlorate cell was designed and built in order to studythe current density distribution in industrial conditions.These experiments showed that increased flowrate brought aboutmore even current density distributions, reduced cell voltageand increased the total current density. An investigation ofthe hydrodynamic effects on the respective electrodeoverpotentials shows the anode reactions being more favoured byincreased flowrate. This leads to the conclusion that theuniform current density distribution, caused by increasedflowrate, occurs primarily through decreasing the concentrationoverpotential at the anode rather than by decreasing thebubble-induced ohmic drop at the cathode. Finally, results from experiments investigating thebubble-induced free convection from a small electrochemicalcell are presented. These experiments show that Laser DopplerVelocimetry is the most effective instrument for investigatingthe velocity profiles in bubble-containing electrochemicalsystems. The results also show that the flow can transform fromlaminar to turbulent behaviour on both the vertical andhorizontal planes, in electrochemical systems where bubbles areevolved.