Interactive Visualization of Molecular Dynamics Simulation Data

Molecular Dynamics Simulations (MD) plays an essential role in the field of computational biology. The simulations produce extensive high-dimensional, spatio-temporal data describ-ing the motion of atoms and molecules. A central challenge in the field is the extraction and visualization of useful behavioral patterns from these simulations. Throughout this thesis, I collaborated with a computational biologist who works on Molecular Dynamics (MD) Simu-lation data. For the sake of exploration, I was provided with a large and complex membrane simulation. I contributed solutions to his data challenges by developing a set of novel visual-ization tools to help him get a better understanding of his simulation data. I employed both scientific and information visualization, and applied concepts of abstraction and dimensions projection in the proposed solutions. The first solution enables the user to interactively fil-ter and highlight dynamic and complex trajectory constituted by motions of molecules. The molecular dynamic trajectories are identified based on path length, edge length, curvature, and normalized curvature, and their combinations. The tool exploits new interactive visual-ization techniques and provides a combination of 2D-3D path rendering in a dual dimension representation to highlight differences arising from the 2D projection on a plane. The sec-ond solution introduces a novel abstract interaction space for Protein-Lipid interaction. The proposed solution addresses the challenge of visualizing complex, time-dependent interactions between protein and lipid molecules. It also proposes a fast GPU-based implementation that maps lipid-constituents involved in the interaction onto the abstract protein interaction space. I also introduced two abstract level-of-detail (LoD) representations with six levels of detail for lipid molecules and protein interaction. Finally, I proposed a novel framework consisting of four linked views: A time-dependent 3D view, a novel hybrid view, a clustering timeline, and a details-on-demand window. The framework exploits abstraction and projection to enable the user to study the molecular interaction and the behavior of the protein-protein interaction and clusters. I introduced a selection of visual designs to convey the behavior of protein-lipid interaction and protein-protein interaction through a unified coordinate system. Abstraction is used to present proteins in hybrid 2D space, and a projected tiled space is used to present both Protein-Lipid Interaction (PLI) and Protein-Protein Interaction (PPI) at the particle level in a heat-map style visual design. Glyphs are used to represent PPI at the molecular level. I coupled visually separable visual designs in a unified coordinate space. The result lets the user study both PLI and PPI separately, or together in a unified visual analysis framework

Novel enhancement of HVOF thermal sprayed nanostructured WC-12Co / inconel-625 coatings for tribocorrosion applications

The HVOF thermal spray process is gradually becoming one of the leading coating techniques taking over traditional electrolytic chrome plating (EHC) due to EHCs harmful effects on the human body. Despite the high quality coatings produced by the HVOF thermal spray system, its role has yet to be validated in the replacement of other traditional coating techniques where specific surface properties are required in particular service operation. Obstacles associated with high-velocity oxy-fuel (HVOF) thermal spray significantly affect coating performance, especially in erosion and corrosion preventive applications. The coating layer therefore must be enhanced with a view to reducing microstructural defects and thereby prolonging the coating’s service life. This research is aimed at examining the effect of using a CO2 laser system as a post-heat treatment and enhancement procedure applied to two coatings types investigated in this research that were deposited by an HVOF thermally sprayed process onto carbon steel 4041 substrates: firstly, 100% tungsten carbide cobalt (nano-structured) WC-12Co (InfralloyTM S7412) and secondly, WC-12Co nanostructured powder mixed with a nickel chromium alloy (Diamalloy 1005- Inconel 625) at an optimised weight percentage composition of 75% and 25% respectively. The work was carried out through the introduction of experimentally based mathematical models developed by applying response surface methodology (RSM) through Box-Behnken design (BBD), based on three levels of each factor selected, namely laser power, scanning speed and focal position/beam size, using Design of Expert software related to the coating’s erosion resistance, melt-pool geometry, mechanical properties and operating cost of the laser treatment. Furthermore, the desirability optimisation approach, based on two criteria (quality and cost), was used for both coatings in conjunction with RSM to determine the optimal combination of the laser parameters to achieve the required laser-treated coating desirability. Different outcomes of surface properties were achieved by varying the laser-processing parameters. The results demonstrate that significant improvement in coating erosion wear (dry and slurry erosion) and mechanical properties (bending strength, surface roughness and microhardness), compared to as-sprayed coating, was achieved after laser treatment in both coating types, especially the singular nanostructured WC-12Co coating. The optimal laser settings found in the quality criteria are 350 W, 37.24 mm and 150.00 mm/min for laser power, focal position and scanning speed, respectively, for the monomial nWC-12Co coating and 350 W, 45 mm and 300 mm/min for the cost criteria. To the same extent, the optimal setting for the mixed coating for the quality criteria are 169 W, 35 mm and 257.4 mm/min and 250 W, 45 mm and 300 mm/min for the cost criterion. The optimal laser setting mentioned in the quality criteria for the erosive wear, for example, saw an approximately five- to seven-fold reduction in mass loss for dry and slurry erosion in comparison to the untreated monomial nWC-12Co coating. The latter setting created an approximately 7-fold reduction in mass losses for the dry erosion and a 27% reduction in mass losses for slurry erosion compared to their untreated counterparts. This can mainly be ascribed to the elimination of the discrete splat structure, porosity and microcrevice, as well as the enhanced homogeneity of the nano-scale WC hard ceramic distribution across the metal matrix. Less improvement was seen for the mixed coating as a result of high energy fluence (J/mm2); the coating surface became rough and gas pockets started forming within the melted zones, creating a porous coating layer that had a negative impact on coating bending strength and erosion performance. Moreover, the results indicate a strong correlation between irradiance and residence time of the laser processing, along with coating composition, with respect to the melt-pool dimensions. Finally, based on the enhancement achieved in the coating properties under the optimal laser settings for both coatings, compared to the untreated ones, the results prove that laser post processing is a cost-effective procedure (approximately 17% or less of that of HVOF) and therefore will markedly extend the service life of both coatings, saving a lot of money that would be wasted in the case of the untreated ones

A numerical investigation into natural ventilation of double skin façades and the improvement of energy efficiency in high rise buildings

Buildings consume a large amount of energy, around 40% of global energy use. Under keeping comfortable environments for building occupants, reduction of buildings’ energy use is significant and also challenging. Passive techniques, such as natural ventilation, are promoted in certain climates to provide low energy cooling and ventilation. However, controlling natural ventilation in an effective manner to maintain occupant comfort can be a difficult task, particularly during warm periods. One of the passive techniques is carefully designing building façade, e.g., ‘double-skin faҫade’, one of the best options in managing the interaction between the outdoor and internal spaces. Double-skin façade (DSF) building is one of the energy conservation opportunities available through recent intelligent buildings. Not only does the façade constitute the architectural aesthetics of the building, but it is also of great importance due to its impact on energy performance and interior function. Therefore, the development of innovative façade technology continues to be one of the most active research areas for the built environment. In this work, an investigation into the optimal application of a double-skin façade (DSF) for high-rise buildings is presented using computational fluid dynamics (CFD) approaches. The work firstly reviewed state-of-the-art research, technologies and applications for double-skin façades. Based on the review, the author then proposed some new and innovative forms of double-skin faҫade which are particularly applicable to high-rise buildings. These façades offer natural ventilations for tall office buildings. The forces driving the ventilations, i.e., buoyancies, are produced from the solar energy. As CFD is applied, the effects of the wind and buoyancy are then investigated separately or in combination. The overall objectives of the investigations are to determine whether the magnitude of airflow rates and the desired flow pattern through openings can be achieved over a range of specified conditions. Potential conditions where the design goals may not be ensured are identified. It is supposed that a seasonal control could be developed to provide the optimum desired flow pattern, sufficient flow rates for ventilated cooling and uniform airflow rates across floors. Segmented and non-segmented DSF cavity patterns with ventilated double façades are adopted as the main building configurations for coping with the potential magnitude of wind at high levels. The ducts between cavities are designed to control the natural ventilations in tall office buildings. Steady state condition approaches are adopted for investigating these cases. The results show that segmentation has tends to create relatively uniform air pressure, airflow and temperature at various elevations within the building, and therefore has the best performance. In order to quantitatively assess the performance of the proposed double-skin faҫades, various CFD models were developed. These models are involved in turbulence calculations with kappa-epsilon model heat transfer. Various validations of the CFD models show that the models are able to produce precise results. Ultimately, the CFD, CFX5 codes were applied to estimate and investigate the performance of the proposed DSFs and produce the optimal application of double-skin façades for high-rise buildings

Indirect three dimensional printing of Apatite-Wollastonite structures for biomedical applications

PhD ThesisThe main goal of the current study was to investigate the capabilities of the indirect three-dimensional printing (3DP) process when used in combination with bioceramic Apatite-Wollastonite (A-W) powders and to evaluate the mechanical properties of the printed parts. A-W glass ceramic is a bioactive material that is used clinically for bone substitutes due to its suitable mechanical properties. Additive manufacturing approaches, especially 3DP, have been shown to produce 3D complex structures via computer aided design. A-W with weight % of 4.6 MgO, 44.7 CaO, 34 SiO2, 16.2 P2O5 and 0.5 CaF2 was used in the present study. The approach taken to indirect 3DP was: (i) blending of the A-W with maltodextrin (MD) powder; (ii) using a Z Corp Z310plus 3D printer to selectively print binder into sequentially deposited thin layers of the blended powders in order to build up a 3D structure; (iii) heat treating the 3D printed parts to 1150°C to burn off the MD and sinter the A-W to create a consolidated 3D structure. Phosphate glass infiltration was used to fill the porosities and increase the mechanical strength of the sintered parts. Bioactive phosphate glass with weight % of 6.22 Na2O, 71.29 P2O5, and 22.49 CaO was used because it can dissolve faster than A-W. The flexural strength, Young’s modulus, porosity and shrinkage were measured on various samples printed from the seven powder blends (PBs). PBs with 30% MD and zb®60 binder were required for the parts to develop sufficient strength. PBs 1, 4, and 5 develop the highest strength after sintering. PB1 contains A-W particle sizes in the range of 53-90 μm, PB4 contains A-W particle sizes in the range of 0-53 μm and PB5 contains mixed particle size ranges (78.5% in the range of 53-90 μm with 21.5% in the range of 0-53 μm). Average flexural strengths of 23.65 MPa, 35.64 MPa, and 25.68 MPa were achieved for PB1, PB4, and PB5, respectively. The average strength of PB5 increased to 31.34 MPa after glass infiltration. In all cases, the increase in strength is a result of the increased consolidation during sintering, as indicated by the observed reduced porosity. Indirect 3D printing of A-W structures can be used to create strong, highly porous structures, but care must be taken to appropriately select binder and processing parameters. Moreover, this is a promising approach for fabrication in bone tissue engineering.Saudi Interior Ministry and Border Guard

Synthesis of new high-pressure A-site manganite perovskites and investigation of their magnetic properties

Perovskites, with the general formula, ABO3, have been extensively studied due to their large variety of intriguing electronic and magnetic properties, which can be achieved via a number of possible chemical compositions. The use of A and B site cations of various sizes and charges induce cation order, giving rise to A2BB’O6 and AA’B2O6 double perovskites (DPv), while, the combination of cation order into both sublattices in an AA’BB’O6 double double perovskite (DDPv) is uncommon. However, the well-known DDPv arrangement in A and B-sites is a layered arrangement of A and A’, which coexists with the rock-salt motif of B and B’. The A-site is usually occupied by a large cation with 12-fold coordination, but it can host smaller cations comparable in size to B-site cations as it becomes distorted (e.g. larger tilt angles). The smaller the ionic radius of A, the higher the distortion, and higher pressure is required to stabilise the structure. Employing the formula A= Mn2+ demonstrates some significant structural features and magnetic properties. An attempt has been made to synthesise new DPv and DDPv materials, which contain Mn2+, into the A-site to enhance the physical properties of the material. Three different compounds were successfully synthesised: Mn2NiReO6, CaMnCrSbO6 and CaMnMnWO6. Firstly, Mn2NiReO6 is a new member of the ´all transition metal’ (ATM) double perovskite family and is obtained under high pressure (8 GPa) and high temperature (1573 K) conditions. The crystal structure was confirmed by PXRD and NPD, with monoclinic P21/n symmetry, which shows fully ordered Ni2+ and Re6+ within the octahedral sites in a rock-salt motif and a large distortion, with the greatest tilt angles observed to date, in A-site manganite double perovskite oxides. Magnetic structure refinement indicates that all moments are ordered antiferromagnetically below TM1 = 80 K. However, the unusual continuous spin rotation of Mn spins occur down to a second transition (TM2 = 42 K). This effect has not been reported in any of the previous Mn2BB’O6 compounds. Secondly, CaMnCrSbO6 was synthesised under high pressure (10 GPa) and high temperature (1373 K) conditions. The compound crystallises via PXRD and NPD with a DDPv structure, which combines columnar order in the A-site cations (Ca and Mn) and rock-salt order of the B-site cations (Cr and Sb). The Mn in the A and A` sites show alternating square planar and tetrahedral coordination. CaMnCrSbO6 has a single magnetic transition at 49 K, where Mn2+ and Cr3+ spin order into antiparallel FM sublattices. Finally, CaMnMnWO6 crystallises via PXRD and NPD at 10 GPa with the monoclinic P21/n space group in a DPv structure with rock-salt order of the B sites at a high temperature (1573 K). While at a lower temperature (1273 K), a DDPv structure with the P42/n space group is observed with A-site cations ordered in the columnar order and B-site cations in the rock salt environment. The magnetic refinement reveals a spin glass behaviour for the DPv structure, whereas, the DDPv magnetic structure shows antiferromagnetic coupling between ferromagnetic sublattices at TC = 45 K

Two-Dimensional Materials for Terahertz Emission

The demand for ultrahigh-speed, lightweight, low-cost, and defect-tolerant electronic devices drives the industry to switch to terahertz (THz) technologies. The use of two-dimensional (2D) materials has massively increased in THz applications due to their appealing electronic and optoelectronic properties, including tunable bandgap, high carrier mobility, wideband optical absorption, and relatively short carrier lifetime. Several 2D-material-based emitters, modulators, and detectors have been fabricated and examined. In this context, considerable research has been going on for 2D-material-based THz emitting sources, including materials and device structure to understand the electronics and optoelectronics mechanisms occurring in the THz region. This chapter focuses on the 2D-material-based emitters with insights into the background, the physical principle of photoconductive THz emitters, the 2D materials’ properties, and the research trends in the fabrication and characterization of the THz sources based upon 2D materials

Modeling the time-dependent characteristics of perovskite solar cells

We proposed two different time-dependent modeling approaches for variation of device characteristics of perovskite solar cells under stress conditions. The first approach follows Sah-Noyce-Shockley (SNS) model based on Shockley–Read–Hall recombination/generation across the depletion width of pn junction and the second approach is based on thermionic emission model for Schottky diodes. The connecting point of these approaches to time variation is the time-dependent defect generation in depletion width (W) of the junction. We have fitted the two models with experimental data reported in the literature to perovskite solar cell and found out that each model has a superior explanation for degradation of device metrics e.g. current density and efficiency by time under stress conditions. Nevertheless, the Sah-Noyce-Shockley model is more reliable than thermionic emission at least for solar cells

Orientation management in organization as a tool to increase the employee productivity

Orientation programs are prudent for the employees in a new environment for undergo plan and strategic orientation to speed up their acceptance into the organization’s system. Organizations with policies and guidelines on orientation program remain more relevant and competitive in their business fields because they equip the employees with relevant knowledge, competence, and skills necessary for the modern work place. This study is one of the most important management skills that a human resource manager must possess to give the employees the opportunity to understand the environment where they intend to work. This paper will seek to find answers to three research questions: (i) what is the importance of orientation management to the employee and organization? (ii) What the best ways of managing orientation in an organization?, and (iii) Who is responsible for managing the orientation program in an organization? Research studies involve the process of relevant collective data that would help the researcher to arrive at the right conclusion about the findings. Many research studies have linked the success of the organization to the organization’s ability to organize successful orientation programs for the employees. Thus, orientation remains one of the most effective methods of improving productivity in organizations. Keywords: Orientation Program, Productivity, Competence, Strategic orientation, Socialization Process DOI: 10.7176/JMCR/62-06 Publication date: November 30th 201

Modeling the time-dependent characteristics of perovskite solar cells

We proposed two different time-dependent modeling approaches for variation of device characteristics of perovskite solar cells under stress conditions. The first approach follows Sah-Noyce-Shockley (SNS) model based on Shockley–Read–Hall recombination/generation across the depletion width of pn junction and the second approach is based on thermionic emission model for Schottky diodes. The connecting point of these approaches to time variation is the time-dependent defect generation in depletion width (W) of the junction. We have fitted the two models with experimental data reported in the literature to perovskite solar cell and found out that each model has a superior explanation for degradation of device metrics e.g. current density and efficiency by time under stress conditions. Nevertheless, the Sah-Noyce-Shockley model is more reliable than thermionic emission at least for solar cells

Squint Among Adult Population in Hail City, Saudi Arabia

Background: Strabismus, also known as crossed eyes, is a condition in which the eyes do not properly align with each other when looking at an object. If present during a large part of childhood, it may result in amblyopia. If onset is during adulthood, it is more likely to result in double vision. Objective: The aim of the study was to estimate the prevalence of squint, types and treatment characteristics in the studied adults in Hail city, Saudi Arabia. Methods: A cross-sectional study conducted in Hail city, Saudi Arabia. The study included 294 participants; 95 male and 199 female adults aged >20 years. The study period was from 1 January to 30 April 2018. Data collected by personal interview using a pre-designed questionnaire, which distributed among the participants to be self-reported. Results: The prevalence of squint among the studied population was 9.9%. it was more common in females than males. Squint was right sided in 24.1% of the cases, left sided in 51.7% and in both eyes in 24.1% of the studied cases. About half (44.8%) of cases had inward squint (esotropia) and 10.3% outward squint (exsotropia), 24.1% of the cases had Intermittent squint and 6.9% had permanent squint. Most (55.2%) of squint cases use glasses and 34.5% of cases squint affected their visual acuity. In 6.9%, squint causes psychological troubles. As regards treatment, 20.7% received medical treatment and 17.2% received surgical treatment but 62.1% do not seek medical care. Only 10.3% of cases completely cured and 13.8% had recurrence. There was insignificant relation with age, sex, education, squint in parents, chronic diseases, consanguinity or hereditary diseases (P>0.05). Conclusion: in this study, the prevalence of squint in the adult participants in Hail city, Saudi Arabia was 9.9% but 62.1% do not seek medical care. After treatment, only 10.3% of cases completely cured and 13.8% had recurrence. Health education of the public about importance of early treatment is highly recommended. Keywords: Squint; strabismus; adult population; prevalence; types; Hail; Saudi Arabia