Modelling of Complex Plasmas

Nowadays plasmas are used for various applications such as the fabrication of silicon solar cells, integrated circuits, coatings and dental cleaning. In the case of a processing plasma, e.g. for the fabrication of amorphous silicon solar cells, a mixture of silane and hydrogen gas is injected in a reactor. These gases are decomposed by making a plasma. A plasma with a low degree of ionization (typically 10_5) is usually made in a reactor containing two electrodes driven by a radio-frequency (RF) power source in the megahertz range. Under the right circumstances the radicals, neutrals and ions can react further to produce nanometer sized dust particles. The particles can stick to the surface and thereby contribute to a higher deposition rate. Another possibility is that the nanometer sized particles coagulate and form larger micron sized particles. These particles obtain a high negative charge, due to their large radius and are usually trapped in a radiofrequency plasma. The electric field present in the discharge sheaths causes the entrapment. Such plasmas are called dusty or complex plasmas. In this thesis numerical models are presented which describe dusty plasmas in reactive and nonreactive plasmas. We started first with the development of a simple one-dimensional silane fluid model where a dusty radio-frequency silane/hydrogen discharge is simulated. In the model, discharge quantities like the fluxes, densities and electric field are calculated self-consistently. A radius and an initial density profile for the spherical dust particles are given and the charge and the density of the dust are calculated with an iterative method. During the transport of the dust, its charge is kept constant in time. The dust influences the electric field distribution through its charge and the density of the plasma through recombination of positive ions and electrons at its surface. In the model this process gives an extra production of silane radicals, since the growth of dust is not included. Results are presented for situations in which the dust signi_cantly changes the discharge characteristics, both by a strong reduction of the electron density and by altering the electric field by its charge. Simulations for dust with a radius of 2 mu-m show that the stationary solution of the dust density and the average electric field depend on the total amount of the dust. The presence of dust enhances the deposition rate of amorphous silicon 2 at the electrodes because of the rise in the average electron energy associated with the decrease of the electron density and the constraint of a constant power input. This increase of deposition rate has also been observed in experiments by others. To study the behavior of dust in a less complicated environment, experiments in non-reactive plasmas have been carried out by a number of research groups. In these experiments the dust particles are injected through the electrodes in an argon discharge. These experiments have shown very interesting phenomena. Dust particles start to interact with each other in the discharge and form two-dimensional Coulomb clusters. These experiments often show an appearance of a void, a dustfree region in the discharge. Similar experiments have also been carried out under microgravity. These experiments have shown three-dimensional Coulomb clusters of dust particles also with the appearance of a void. Also rotating dust clouds (vortices) near the edges of the electrodes have been observed, that tend to rotate as long as the plasmas is on. To understand the behavior of the particles, we have developed a two-dimensional fluid model for a dusty argon plasma in which the plasma and dust parameters are solved self-consistently to study the behavior of dust particles. Simulations for dust with a radius of 7.5 mu-m show that a double space charge layer is created around the sharp boundary of the dust crystal. The inter-particle interaction is taken into account by means of an equation of state for the dust. A central dust-free region (void) is created by the ion drag force. The contribution of the thermophoretic force, driven by the temperature gradient induced by gas heating from ion-neutral collisions and heating of the dust particle material by the recombining ions and electrons, can be neglected in the quasi-neutral center of the plasma. Inside this void a strong increase of the production of argon meta-stables is found. This phenomenon is in agreement with experimental observations, where an enhanced light emission is seen inside the void

Knowledge and practice related to compliance with mass drug administration during the Egyptian national filariasis elimination program

Lymphatic filariasis (LF) has been targeted for global elimination by 2020. The primary tool for the program is mass drug administration (MDA) with antifilarial medications to reduce the source of microfilariae required for mosquito transmission of the parasite. This strategy requires high MDA compliance rates. Egypt initiated a national filariasis elimination program in 2000 that targeted approximately 2.7 million persons in 181 disease-endemic localities. This study assessed factors associated with MDA compliance in year three of the Egyptian LF elimination program. 2,859 subjects were interviewed in six villages. The surveyed compliance rate for MDA in these villages was 85.3% (95% confidence interval = 83.9–86.5%). Compliance with MDA was positively associated with LF knowledge scores, male sex, and older age. Adverse events reported by 18.4% of participants were mild and more common in females. This study has provided new information on factors associated with MDA compliance during Egypt's successful LF elimination program

A critical appraisal of molecular xenomonitoring as a tool for assessing progress toward elimination of lymphatic filariasis

We used molecular xenomonitoring (MX, detection of filarial DNA in mosquitoes) to evaluate the impact of mass drug administration (MDA) in sentinel locations in Egypt with high (11.5%) and low (4.1%) baseline microfilaria prevalence rates. Blood-fed Culex pipiens were pooled by household and tested for Wuchereria bancrofti DNA by PCR. There was no significant relationship between the infection status of household residents and parasite DNA status of mosquitoes from the same houses. After 5 MDA rounds, parasite DNA rates in mosquitoes in high- and low-prevalence areas were reduced by 93.8% and 100% to 0.19% (95% CI: 0.076–0.382%) and 0% (95% CI: 0–0.045%), respectively. These changes were consistent with decreases in microfilaria prevalence rates in these sites; they provide insight regarding the minimal mosquito DNA rates necessary for sustained transmission of filariasis in Egypt. We conclude that MX is a powerful tool for monitoring the impact of MDA on filariasis endemicity and transmission

A Reverse Transcriptase-PCR Assay for Detecting Filarial Infective Larvae in Mosquitoes

Background: Existing molecular assays for filarial parasite DNA in mosquitoes cannot distinguish between infected mosquitoes that contain any stage of the parasite and infective mosquitoes that harbor third stage larvae (L3) capable of establishing new infections in humans. We now report development of a molecular L3-detection assay for Brugia malayi in vectors based on RT-PCR detection of an L3-activated gene transcript. Methodology/Principal Findings: Candidate genes identified by bioinformatics analysis of EST datasets across the B. malayilife cycle were initially screened by PCR using cDNA libraries as templates. Stage-specificity was confirmed using RNA isolated from infected mosquitoes. Mosquitoes were collected daily for 14 days after feeding on microfilaremic cat blood. RT-PCR was performed with primer sets that were specific for individual candidate genes. Many promising candidates with strong expression in the L3 stage were excluded because of low-level transcription in less mature larvae. One transcript (TC8100, which encodes a particular form of collagen) was only detected in mosquitoes that contained L3 larvae. This assay detects a single L3 in a pool of 25 mosquitoes. Conclusions/Significance: This L3-activated gene transcript, combined with a control transcript (tph-1, accession # U80971) that is constitutively expressed by all vector-stage filarial larvae, can be used to detect filarial infectivity in pools of mosquito vectors. This general approach (detection of stage-specific gene transcripts from eukaryotic pathogens) may also be useful for detecting infective stages of other vector-borne parasites

The effect of compliance on the impact of mass drug administration for elimination of lymphatic filariasis in Egypt

We studied effects of compliance on the impact of mass drug administration (MDA) with diethylcarbamazine and albendazole for lymphatic filariasis (LF) in an Egyptian village. Baseline microfilaremia (mf) and filarial antigenemia rates were 11.5% and 19.0%, respectively. The MDA compliance rates were excellent (> 85%). However, individual compliance was highly variable; 7.4% of those surveyed after five rounds of MDA denied having ever taken the medications and 52.4% reported that they had taken all five doses. The mf and antigenemia rates were 0.2% and 2.7% in those who reported five doses of MDA and 8.3% and 13.8% in those who reported zero doses. There was no significant difference in residual infection rates among those who had taken two or more doses. These results underscore the importance of compliance for LF elimination programs based on MDA and suggest that two ingested doses of MDA are as effective as five doses for reducing filariasis infection rates

A real-time PCR-based assay for detection of Wuchereria bancrofti DNA in blood and mosquitoes

We developed and evaluated real-time polymerase chain reaction (PCR) assays for detecting Wuchereria bancrofti DNA in human blood and in mosquitoes. An assay based on detection of the W. bancrofti “LDR” repeat DNA sequence was more sensitive than an assay for Wolbachia 16S rDNA. The LDR-based assay was sensitive for detecting microfilarial DNA on dried membrane filters or on filter paper. We also compared real-time PCR with conventional PCR (C-PCR) for detecting W. bancrofti DNA in mosquito samples collected in endemic areas in Egypt and Papua New Guinea. Although the two methods had comparable sensitivity for detecting filarial DNA in reference samples, real-time PCR was more sensitive than C-PCR in practice with field samples. Other advantages of real-time PCR include its high-throughput capacity and decreased risk of cross-contamination between test samples. We believe that real-time PCR has great potential as a tool for monitoring progress in large-scale filariasis elimination programs

Particulate matter from both heavy fuel oil and diesel fuel shipping emissions show strong biological effects on human lung cells at realistic and comparable in vitro exposure conditions

Background: Ship engine emissions are important with regard to lung and cardiovascular diseases especially in coastal regions worldwide. Known cellular responses to combustion particles include oxidative stress and inflammatory signalling. Objectives: To provide a molecular link between the chemical and physical characteristics of ship emission particles and the cellular responses they elicit and to identify potentially harmful fractions in shipping emission aerosols. Methods: Through an air-liquid interface exposure system, we exposed human lung cells under realistic in vitro conditions to exhaust fumes from a ship engine running on either common heavy fuel oil (HFO) or cleaner-burning diesel fuel (DF). Advanced chemical analyses of the exhaust aerosols were combined with transcriptional, proteomic and metabolomic profiling including isotope labelling methods to characterise the lung cell responses. Results: The HFO emissions contained high concentrations of toxic compounds such as metals and polycyclic aromatic hydrocarbon, and were higher in particle mass. These compounds were lower in DF emissions, which in turn had higher concentrations of elemental carbon (“soot”). Common cellular reactions included cellular stress responses and endocytosis. Reactions to HFO emissions were dominated by oxidative stress and inflammatory responses, whereas DF emissions induced generally a broader biological response than HFO emissions and affected essential cellular pathways such as energy metabolism, protein synthesis, and chromatin modification. Conclusions: Despite a lower content of known toxic compounds, combustion particles from the clean shipping fuel DF influenced several essential pathways of lung cell metabolism more strongly than particles from the unrefined fuel HFO. This might be attributable to a higher soot content in DF. Thus the role of diesel soot, which is a known carcinogen in acute air pollution-induced health effects should be further investigated. For the use of HFO and DF we recommend a reduction of carbonaceous soot in the ship emissions by implementation of filtration devices