Molecular Dynamics Studies of Interactions of Phospholipid Membranes with Dehydroergosterol and Penetrating Peptides

We have performed molecular modeling of membrane and peptide systems by employing the classical molecular dynamics method and force field parameterizations. In this thesis, our main interest is the interaction of sterols as well as peptides with membranes. The thesis consists of three related projects. The first project focuses on cholesterol (CHOL) and dehydroergosterol (DHE) interacting with palmitoyl-oleoyl phosphatidylcholine (POPC) lipid bilayers. We study the effects of both sterols on the bilayer and compare them with each other. We first study the condensing and ordering effect of these sterols. Then, we study their orientations within the bilayer and relate them to their interactions with the bilayer.In the second project, we study the interaction of a cell-penetrating-peptide, namely transportan, with dipalmitoyl phosphatidylcholine (DPPC) lipid bilayers with the aim of understanding the physical mechanism of the penetration process. By analyzing 10 simulations, we shed light on the behavior of the peptide and membrane when they are associated with each other. We also analyze four simulations in which the peptide is directly inserted in the bilayer core so as to study the behavior of the peptide when it is deep in the bilayer. By using umbrella sampling method and performing 41 biased simulations, we also try to find the free energy profile of the system as a function of the distance between the peptide and the center of mass of the bilayer.In the third project, we study the interaction of another cell-penetrating peptide, namely penetratin, with DPPC lipid bilayers. In this research, the spontaneous binding of a penetratin peptide as well as the role of different residues in binding are investigated. The behavior of penetratin is then compared with that of transportan and important differences are highlighted

Determining the Reaction Rate of Electrochemical Process for Purification of Polluted Water

Abstract Aims: Turbidity in higher than standard levels, indicates failure in the water treatment plant. An electrochemical disinfection process takes place through electricity transition between two or more electrodes. This research aimed to determine the reaction rate of electrochemical process for purification of polluted water. Materials & Methods: This is a bench scale, experimental study performed in a batch system on synthetic wastewater. 1700ml of prepared synthetic wastewater was put in an electrolytic cell and constant 600mA current was flowed into the cell content through merged aluminum electrodes for 1 hour. Samples were taken from the batch in the beginning and every 10 minutes and were analyzed for, turbidity, Coliform bacteria (probably, confirmed and E. coli) and Heterotrophic Plat Count. Fisher exact test was used to analyze data. Findings: All the parameters of turbidity, HPC, total coliform, confirmed coliform and E. coli were decreased during the time. The electrochemical process reduced the average of turbidity below 3NTU after 50 minutes (91.05 removal). The HPC number reduced from 130n/ml to 2.4n/ml (98.15 removal) after 50 minutes. No coliforms were seen after 40 minutes of the electrochemical process. Conclusion: 40 minutes of electrochemical process in 600mA by aluminum electrodes is the optimum condition for removing the turbidity, Coliform bacteria (total, confirmed and E. coli) and HPC from polluted water

A new weighted distribution based on the mixture of asymmetric Laplace family with application in survival analysis

The generalization of asymmetric Laplace (AL) distribution has recently received considerable attention in dealing with skewed and long-tailed data. In this article, we introduce a new family of distributions based on the location mixture of asymmetric Laplace (LM-AL) distribution. Some properties of this family, such as expressions for mean, variance, skewness and kurtosis coefficients and characteristic function, are derived. We show that this family of distributions is quite flexible because it has wider ranges of skewness and kurtosis than the other skew distributions introduced in the literature. We also introduce a family of weighted distributions based on the survival function of the exponential distribution and will show that truncated LM-AL distribution in zero which can be used in survival analysis, belongs to this family. In order to compute the maximum likelihood (ML) estimation of the parameters in the location mixture of AL distribution, an EM-type algorithm is developed and the estimation of parameters of model in survival analysis performed using a maximization algorithm, due to the problem complexity. Finally, the performance and applicability of the truncated LM-AL model in survival analysis is illustrated through analyzing a simulation study and two real data set. This family of distributions represent a suitable alternative to existing models such as Weibull, log-normal, log-logistic, gamma and Lindley distributions

The cooperative behaviour of antimicrobial peptides in model membranes

A systematic analysis of the hypothesis of the antimicrobial peptides' (AMPs) cooperative action is performed by means of full atomistic molecular dynamics simulations accompanied by circular dichroism experiments. Several AMPs from the aurein family (2.5,2.6, 3.1), have a similar sequence in the first ten amino acids, are investigated in different environments including aqueous solution, trifluoroethanol (TFE), palmitoyloleoylphosphatidylethanolamine (POPE), and palmitoyloleoylphosphatidylglycerol (POPG) lipid bilayers. It is found that the cooperative effect is stronger in aqueous solution and weaker in TFE. Moreover, in the presence of membranes, the cooperative effect plays an important role in the peptide/lipid bilayer interaction. The action of AMPs is a competition of the hydrophobic interactions between the side chains of the peptides and the hydrophobic region of lipid molecules, as well as the intra peptide interaction. The aureins 2.5-COOH and 2.6-COOH form a hydrophobic aggregate to minimize the interaction between the hydrophobic group and the water. Once that the peptides reach the water/lipid interface the hydrophobic aggregate becomes smaller and the peptides start to penetrate into the membrane. In contrast, aurein 3.1-COOH forms only a transient aggregate which disintegrates once the peptides reached the membrane, and it shows no cooperativity in membrane penetratio

An interpretation of skew-elliptical distributions in terms of fuzzy events

AbstractIn this note, we introduce a fuzzy method for producing family of univariate and multivariate skew-elliptical distributions based on fuzzy conditional events. We illustrate special cases of interest, such as skew-normal distribution. Furthermore, we use the idea of fuzzy events for calculating tail conditional expectations for elliptical and skew-elliptical distributions

A Note on Moment Generating Function of a Linear Combination of Order Statistics from a Bivariate Laplace Distribution

. In this note we propose an extended skew-Laplace distribution. We obtain explicit expressions for moment generating function and the two first moments of this distribution. Next, we show that the distribution of a linear combination of order statistics from a bivariate Laplace distribution can be expressed as a mixture of extended skewLaplace distributions. This mixture representation enables us to derive moment generating function and moments of this linear combinatio

The effect of anionic charge reduction of deinked pulp in Physical Strengths Improvement

Wet tensile strength is very important in some cellulosic health products. When these products produced during the recycling process some of the characteristics in pulp suspension due to lack of stability of desirable quality properties is difficult to achieve. In this study, using a variety of different doses of cationic polymers with laboratory methods, at first reduced the anionic charge amount in pulp suspension gradually. Then the Poly (amine) amide epichlorohydrin and its stabilizer injected to the suspension. The pulp suspension and physical properties of handsheets were evaluated. The type and amount of cationic polymers have a significant effect on the reduction of anionic charge of pulp suspension and the resulting increase in wet tensile strength and other physical resistance of handsheets. The effect of polymers resulted that anionic charge of suspension improved from 237 µeq /L in control samples to32µeq/L in the best conditions. Physical properties of handsheets improved after chemical treatments with different amounts of variety of polymers. Wet tensile strength increased than13 N/m to 121N/m, dry tensile strength improved 2730 N/m to 2860 N/m the burst resistance increased than 146 KPa to 160KPa in superior treatment using 135 mg/L of Gfloc F10. Stepwise regression analysis showed the significant relationship of the anionic charge in the pulp suspension and the physical properties of handsheets. So using different cationic polymers can be reduced the anionic charge of the pulp suspension and improved the quality properties of paper base products

Physical and Mechanical Properties of Walnut Shell Flour-Filled Thermoplastic Starch Composites

The goal of this work was to evaluate the technical feasibility of walnut shell flour (WSF) as substitute for wood in walnut shell flour/thermoplastic starch (WSF/TPS) composites. The effects of walnut shell flour (WSF), thermoplastic starch (TPS), and nanoclay on the physical and mechanical properties of WSF/TPS composites were investigated. The composite samples were formed in a Colin extruder with four-chamber heat with temperatures. Then, test samples were made using injection molding. The addition of up to 40% WSF greatly improved the tensile strength, flexural strength, and elasticity modulus of the composite. Also, the composites made with higher WSF contents had increased thickness swelling and water absorption. The incorporation of nanoclay (0% to 5%), greatly improved the tensile properties. Soil burial degradation experiments showed that biodegradation was accelerated by the increase of starch in the composite mixtures. The study showed that WSF can be successfully utilized for the manufacture of composites with useful physical and mechanical properties