Search results for: inorganic molecular crystals

Authors: Eunae Lee, Oh-Kuen Kwon, Ki-Sub Kim, Jeong Won Kang

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We investigated the dynamic properties of graphene-nanoribbon (GNR) memory encapsulating graphene-nanoflake (GNF) shuttle in the potential to be applicable as a non-volatile random access memory via molecular dynamics simulations. This work explicitly demonstrates that the GNR encapsulating the GNF shuttle can be applied to nonvolatile memory. The potential well was originated by the increase of the attractive vdW energy between the GNRs when the GNF approached the edges of the GNRs. So the bistable positions were located near the edges of the GNRs. Such a nanoelectromechanical non-volatile memory based on graphene is also applicable to the development of switches, sensors, and quantum computing.

Keywords: graphene nanoribbon, graphene nanoflake, shuttle memory, molecular dynamics

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Authors: Eman M. Sarhan, Doaa A. Ghareeb, Gabriella Ortore, Amr A. Amara, Mohamed M. El-Sayed

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Drug salting and nanoparticle-based drug delivery formulations are considered to be an effective means for rendering the hydrophobic drugs’ nano-scale dispersion in aqueous media, and thus circumventing the pitfalls of their poor solubility as well as enhancing their membrane permeability. The current study aims to increase the bioavailability of quaternary ammonium berberine through acid salting and biodegradable bovine serum albumin (BSA)-based nanoparticulate drug formulation. Berberine hydroxide (BBR-OH) that was chemically synthesized by alkalization of the commercially available berberine hydrochloride (BBR-HCl) was then acidified to get Di-berberine sulfate (BBR)₂SO₄. The purified crystals were spectrally characterized. The desolvation technique was optimized for the preparation of size-controlled BSA-BBR-HCl, BSA-BBR-OH, and BSA-(BBR)₂SO₄ nanoparticles. Particle size, zeta potential, drug release, encapsulation efficiency, Fourier transform infrared spectroscopy (FTIR), tandem MS-MS spectroscopy, energy-dispersive X-ray spectroscopy (EDX), scanning and transmitting electron microscopic examination (SEM, TEM), in vitro bioactivity, and in silico drug-polymer interaction were determined. BSA (PDB ID; 4OR0) protonation state at different pH values was predicted using Amber12 molecular dynamic simulation. Then blind docking was performed using Lamarkian genetic algorithm (LGA) through AutoDock4.2 software. Results proved the purity and the size-controlled synthesis of berberine-BSA-nanoparticles. The possible binding poses, hydrophobic and hydrophilic interactions of berberine on BSA at different pH values were predicted. Antioxidant, anti-hemolytic, and cell differentiated ability of tested drugs and their nano-formulations were evaluated. Thus, drug salting and the potentially effective albumin berberine nanoparticle formulations can be successfully developed using a well-optimized desolvation technique and exhibiting better in vitro cellular bioavailability.

Keywords: berberine, BSA, BBR-OH, BBR-HCl, BSA-BBR-HCl, BSA-BBR-OH, (BBR)₂SO₄, BSA-(BBR)₂SO₄, FTIR, AutoDock4.2 Software, Lamarkian genetic algorithm, SEM, TEM, EDX

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Authors: Chris J. Boreham, Dianne S. Edwards, Amber Jarrett, Justin Davies, Robert Poreda, Alex Sessions, John Eiler

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The origins of natural gases in the Amadeus Basin have been assessed using molecular and stable isotope (C, H, N, He) systematics. A dominant end-member thermogenic, oil-associated gas is considered for the Ordovician Pacoota−Stairway sandstones of the Mereenie gas and oil field. In addition, an abiogenic end-member is identified in the latest Proterozoic lower Arumbera Sandstone of the Dingo gasfield, being most likely associated with radiolysis of methane with polymerisation to wet gases. The latter source assignment is based on a similar geochemical fingerprint derived from the laboratory gamma irradiation experiments on methane. A mixed gas source is considered for the Palm Valley gasfield in the Ordovician Pacoota Sandstone. Gas wetness (%∑C₂−C₅/∑C₁−C₅) decreases in the order Mereenie (19.1%) > Palm Valley (9.4%) > Dingo (4.1%). Non-produced gases at Magee-1 (23.5%; Late Proterozoic Heavitree Quartzite) and Mount Kitty-1 (18.9%; Paleo-Mesoproterozoic fractured granitoid basement) are very wet. Methane thermometry based on clumped isotopes of methane (¹³CDH₃) is consistent with the abiogenic origin for the Dingo gas field with methane formation temperature of 254ᵒC. However, the low methane formation temperature of 57°C for the Mereenie gas suggests either a mixed thermogenic-biogenic methane source or there is no thermodynamic equilibrium between the methane isotopomers. The shallow reservoir depth and present-day formation temperature below 80ᵒC would support microbial methanogenesis, but there is no accompanying alteration of the C- and H-isotopes of the wet gases and CO₂ that is typically associated with biodegradation. The Amadeus Basin gases show low to extremely high inorganic gas contents. Carbon dioxide is low in abundance (< 1% CO₂) and becomes increasing depleted in ¹³C from the Palm Valley (av. δ¹³C 0‰) to the Mereenie (av. δ¹³C -6.6‰) and Dingo (av. δ¹³C -14.3‰) gas fields. Although the wide range in carbon isotopes for CO₂ is consistent with multiple origins from inorganic to organic inputs, the most likely process is fluid-rock alteration with enrichment in ¹²C in the residual gaseous CO₂ accompanying progressive carbonate precipitation within the reservoir. Nitrogen ranges from low−moderate (1.7−9.9% N₂) abundance (Palm Valley av. 1.8%; Mereenie av. 9.1%; Dingo av. 9.4%) to extremely high abundance in Magee-1 (43.6%) and Mount Kitty-1 (61.0%). The nitrogen isotopes for the production gases have δ¹⁵N = -3.0‰ for Mereenie, -3.0‰ for Palm Valley and -7.1‰ for Dingo, suggest all being mixed inorganic and thermogenic nitrogen sources. Helium (He) abundance varies over a wide range from a low of 0.17% to one of the world’s highest at 9% (Mereenie av. 0.23%; Palm Valley av. 0.48%, Dingo av. 0.18%, Magee-1 6.2%; Mount Kitty-1 9.0%). Complementary helium isotopes (R/Ra = ³He/⁴Hesample / ³He/⁴Heair) range from 0.013 to 0.031 R/Ra, indicating a dominant crustal origin for helium with a sustained input of radiogenic 4He from the decomposition of U- and Th-bearing minerals, effectively diluting any original mantle helium input. The high helium content in the non-produced gases compared to the shallower producing wells most likely reflects their stratigraphic position relative to the Tonian Bitter Springs Group with the former below and the latter above an effective carbonate-salt seal.

Keywords: amadeus gas, thermogenic, abiogenic, C, H, N, He isotopes

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Authors: Minas Balyan

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In the third-order nonlinear Takagi’s equations for monochromatic waves and in the third-order nonlinear time-dependent dynamical diffraction equations for X-ray pulses for forbidden reflections the Fourier-coefficients of the linear and the third order nonlinear susceptibilities are zero. The dynamical diffraction in the nonlinear case is related to the presence in the nonlinear equations the terms proportional to the zero order and the second order nonzero Fourier coefficients of the third order nonlinear susceptibility. Thus in the third order nonlinear Bragg diffraction case a nonlinear analogue of the well known Renninger effect takes place. In this work, the ‘third order nonlinear Renninger effect’ is considered theoretically and numerically. If the reflection exactly is forbidden the diffracted wave’s amplitude is zero both in Laue and Bragg cases since the boundary conditions and dynamical diffraction equations are compatible with zero solution. But in real crystals due to some percent of dislocations and other localized defects, the atoms are displaced with respect to their equilibrium positions. Thus in real crystals susceptibilities of forbidden reflection are by some order small than for usual not forbidden reflections but are not exactly equal to zero. The numerical calculations for susceptibilities two order less than for not forbidden reflection show that in Bragg geometry case the nonlinear reflection curve’s behavior is the same as for not forbidden reflection, but for forbidden reflection the rocking curves’ width, center and boundaries are two order sensitive on the input intensity value. This gives an opportunity to investigate third order nonlinear X-ray dynamical diffraction for not intense beams – 0.001 in the units of critical intensity.

Keywords: third order nonlinearity, Bragg diffraction, nonlinear Renninger effect, rocking curves

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Authors: T. Rajamäki

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In clean room environment molecular contamination in very small concentrations can cause significant harm for the components and processes. This is commonly referred as airborne molecular contamination (AMC). There is a shortage of high sensitivity continuous measurement data for existence and behavior of several of these contaminants. Accordingly, in most cases correlation between concentration of harmful molecules and their effect on processes is not known. In addition, the formation and distribution of contaminating molecules are unclear. In this work sensitive optical techniques are applied in clean room facilities for investigation of concentrations, forming mechanisms and effects of contaminating molecules. Special emphasis is on reactive acid and base gases ammonia (NH3) and hydrogen fluoride (HF). They are the key chemicals in several operations taking place in clean room processes.

Keywords: AMC, clean room, concentration, reactive gas

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Authors: Mosaab A. Omara, Layla O. Elmajdoubb, Mohammad Saleh Al-Aboodyc, Ahmed ElSifyd, Ahmed O. Elkhtamd

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The aim of this study is to present the molecular characterization of cysticercus tenuicolis of Taenia hydatigena from livestock isolates in Egypt, using the amplification of sequencing of the mt-CO1 gene. We introduce a detailed image of the Cysticercus tenuicolis infection in ruminant animals in Upper Egypt. Cysticercus tenuicolis inhabits such organs in ruminants as the omentum, viscera, and liver. In the present study, the infection rate of Cysticercus tenuicolis was found to be 16% and 19% in sheep and goat sample respectively. Firstly we report one larval stage of Taenia hydatigena detected in the camel liver in Egypt. Cysticercus tenuicolis infection manifested a higher prevalence in females than in males. Those above 2 years of age manifested a higher infection rate than younger animals. The preferred site for the infection was the omentum: a 70% preference in sheep and a 68% preference in goat samples. The molecular characterization using the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene of isolates from sheep, goats and camels corresponded to T. hydatigena. For this study, molecular characterizations of T. hydatigena were done for the first time in Egypt. Molecular tools are of great assistance in characterizing the Cysticercus tenuicolis parasite especially when the morphological character cannot be detected because the metacestodes are frequently confused with infection by the Hydatid cyst, especially when these occur in the visceral organs. In the present study, Cysticercus tenuicolis manifested high identity in the goat and sheep samples, while differences were found more frequently in the camel samples (10 pairbase). Clearly molecular diagnosis for Cysticercus tenuicolis infection significantly helps to differentiate it from such other metacestodes.

Keywords: cysticercus tenuicolis, its2, genetic, qena, molecular and taenia hydatigena

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Authors: Somayeh Akrami, Vali-Allah Mozaffarian, Habib Onsori

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The studied region in this research, watershed Kuhkamar river, is about 112.66 square kilometers, it is located between 45º 48' 9" to 45º 2' 20" N and 38º 34' 15" to 38º 40' 28" E. The gained results of the studies on flora combinations, proved 287 plant species in 190 genera and 51 families. Asteracea with 49 and Lamiaceae with 27 plant species are the major plant families. Among collected species one interesting plant was found and determined as a new record Anemone narcissiflora L. for flora of Iran. This plant is known as a complex species that shows intraspecific speciation and is classified into about 12 subspecies and 10 varieties in world. To identify the infraspecies taxons of this species, in addition to morphological characteristics, the use of appropriate molecular markers for the better isolation of the individuals were needed.

Keywords: Anemone narcissiflora, floristic Study, kuhkamar, molecular marker

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Authors: Ewon Kaliyadasa, U. L. B. Jayasinghe, S. E. Peiris

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Ashwagandha (Withania sominifera Duanal) is an important medicinal herb belongs to family Solanaceae. This plant has raised its popularity after discovering anti stress and sex stimulating properties that mainly due to the presence of biologically active alkaloid compounds. Therefore it is vital to adapt to a proper agro technological package that ensure optimum growth of ashwagandha to obtain the finest quality without degrading pharmacologically active constituents. Organic and inorganic fertilizer mixtures were combined with direct seeding and transplanting as four different treatments in this study. Tuber fresh and dry weights were recorded up to twelve months starting from two months after sowing (MAS) while shoot height, root length, number of leaves, shoot fresh and dry weights and root: shoot ratio up to 6MAS. Results revealed that growth of ashwagandha was not affected significantly by method of planting or type of fertilizer or its combinations during most of the harvests. However, tubers harvested at 6MAS recorded the highest dry tuber weight per plant in all four treatments compared to early harvests where two direct seeded treatments are the best. Chemical comparison of these two treatments, direct seeding coupled with organic and inorganic fertilizer shown that direct seeding with organic treatment recorded the highest values for alkaloid and withaferine A content with lower percentage of fiber. Further these values are in concurring with the values of commercially available tuber samples. Having considered all facts, 6MAS can be recommended as the best harvesting stage to obtain high quality tubers of ashwagandha under local conditions.

Keywords: alkaloids, direct seeding, dry tuber weight, inorganic fertilizer, organic fertilizer, transplanting, withaferine a

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Authors: Son Nguyen, Thanh Van, Ly Le

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Ca2+ - dependent calmodulin kinase IIa (CaMKIIa) has recently been found to associate with protein tau missorting and polymerization in Alzheimer’s Disease (AD). However, there has yet inhibitors targeting CaMKIIa to investigate the correlation between CaMKIIa activity and protein tau polymer formation. Combining virtual screening and our statistics in binding contribution scoring function (BCSF), we rationally identified potential compounds that bind to specific CaMKIIa active site and specificity-affinity distribution of the ligand within the active site. Using molecular dynamics simulation, we identified structural stability of CaMKIIa and potent inhibitors, and site-directed bonding, separating non-specific and specific molecular interaction features. Despite of variation in confirmation of simulation time, interactions of the potent inhibitors were found to be strongly associated with the unique chemical features extracted from molecular binding poses. In addition, competitive inhibitors within CaMKIIa showed an important molecular recognition pattern toward specific ligand features. Our approach combining virtual screening with BCSF may provide an universally applicable method for precise identification in the discovery of compounds.

Keywords: Alzheimer’s disease, Ca 2+ -dependent calmodulin kinase IIa, protein tau, molecular docking

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Authors: Uchechukwu Vincent Okpala

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Under the Sun, energy is a key factor for the sustenance of life and its environment. The need to protect the environment as energy is generated and consumed has called for renewable and green energy sources. To be part of this green revolution, we synthesized and characterized undoped and velvet tamarind doped zinc sulfide (ZnS) crystals using sol-gel methods. Velvet tamarind was whittled down using the top-down approach of nanotechnology. Sodium silicate, tartaric acid, zinc nitrate, and thiourea were used as precursors. The grown samples were annealed at 105°C. Structural, optical, and compositional analyses of the grown samples revealed crystalline structures with varied crystallite sizes influenced by doping. Energy-dispersive X-ray spectroscopy confirmed elemental compositions of Zn, S, C and O in the films. Atomic percentages of the elements varied with VT doping. FT-IR analysis indicated the presence of functional groups like O-H stretching (alcohol), C=C=C stretching (alkene group), C=C bending, C-H stretching (alkane), N-H stretching (aliphatic primary amine) and N=C=S stretching (isothiocyanate) constituent in the film. The transmittance of the samples increased from the visible region to the infrared region making the samples good for poultry and solar energy applications. The bandgap energy of the films decreased as the number of VT drops increased, from 2.4 to 2.2. They were wide band gap materials and were good for optoelectronic, photo-thermal, high temperature, high power and solar cell applications.

Keywords: doping, sol-gel, velvet tamarind, ZnS.

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Authors: Fathi Soliman

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With the ultimate goal of developing the separation of n-paraffin as phase change material (PCM) by means of molecular dynamic simulations, we attempt to predict the solubility of aromatic n-paraffin in two organic solvents: Butyl Acetate (BA) and Methyl Iso Butyl Ketone (MIBK). A simple model of aromatic paraffin: 2-hexadecylantharacene with amorphous molecular structure and periodic boundary conditions was constructed. The results showed that MIBK is the best solvent to separate ultra-pure phase change materials and this data was compatible with experimental data done to separate ultra-pure n-paraffin from waste petroleum aromatic paraffin wax, the separated n-paraffin was characterized by XRD, TGA, GC and DSC, moreover; data revealed that the n-paraffin separated by using MIBK is better as PCM than that separated using BA.

Keywords: molecular dynamics simulation, n-paraffin, organic solvents, phase change materials, solvent extraction

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Authors: Muchun Yu, Xue Gao, Qian Chen

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As a novel passive vibration isolation technology, molecular spring isolator (MSI) is investigated in this paper. An MSI consists of water and hydrophobic zeolites as working medium. Under periodic excitation, water molecules intrude into hydrophobic pores of zeolites when the pressure rises and water molecules extrude from hydrophobic pores when pressure drops. At the same time, energy is stored, released and dissipated. An MSI of piston-cylinder structure was designed in this work. Experiments were conducted to investigate the stiffness properties of MSI. The results show that MSI exhibits high-static-low dynamic (HSLD) stiffness. Furthermore, factors such as the quantity of zeolites, temperature, and ions in water are proved to have an influence on the stiffness properties of MSI.

Keywords: hydrophobic zeolites, molecular spring, stiffness, vibration isolation

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Authors: Sylwia Orzechowska, Andrzej Wróbel, Eugeniusz Rokita

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The mineralization is a curious problem of connective tissues. Factors which may play a decisive role in the regulation of the yellow ligaments (YL) mineralization are still open questions. The aim of the studies was a detailed description of the chemical composition and morphology of mineral deposits in the human yellow ligaments. Investigations of the structural features of deposits were used to explain the impact of various factors on mineralization process. The studies were carried out on 24 YL samples, surgically removed from patients suffer from spinal canal stenosis and the patients who sustained a trauma. The micro-computed tomography was used to describe the morphology of mineral deposits. The X-ray fluorescence method and Fourier transform infrared spectroscopy were applied to determine the chemical composition of the samples. In order to eliminate the effect of blur in microtomographic images, the correction method of partial volume effect was used. The mineral deposits appear in 60% of YL samples, both in patients with a stenosis and following injury. The mineral deposits have a heterogeneous structure and they are a mixture of the tissue and mineral grains. The volume of mineral grains amounts to (1.9 ± 3.4)*10-3 mm3 while the density distribution of grains occurs in two distinct ranges (1.75 - 2.15 and 2.15-2.5) g/cm3. Application of the partial volume effect correction allows accurate calculations by eliminating the averaging effect of gray levels in tomographic images. The B-type carbonate-containing hydroxyapatite constitutes the mineral phase of majority YLs. The main phase of two samples was calcium pyrophosphate dihydrate (CPPD). The elemental composition of minerals in all samples is almost identical. This pathology may be independent on the spine diseases and it does not evoke canal stenosis. The two ranges of grains density indicate two stages of grains growth and the degree of maturity. The presence of CPPD crystals may coexist with other pathologies.

Keywords: FTIR, micro-tomography, mineralization, spinal ligaments

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Authors: Milica Karadžić, Lidija Jevrić, Sanja Podunavac-Kuzmanović, Strahinja Kovačević, Anamarija Mandić, Aleksandar Oklješa, Andrea Nikolić, Marija Sakač, Katarina Penov Gaši

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Using chemometric approach, the relationships between the chromatographic lipophilicity and in silico molecular descriptors for twenty-nine selected steroid derivatives were studied. The chromatographic lipophilicity was predicted using artificial neural networks (ANNs) method. The most important in silico molecular descriptors were selected applying stepwise selection (SS) paired with partial least squares (PLS) method. Molecular descriptors with satisfactory variable importance in projection (VIP) values were selected for ANN modeling. The usefulness of generated models was confirmed by detailed statistical validation. High agreement between experimental and predicted values indicated that obtained models have good quality and high predictive ability. Global sensitivity analysis (GSA) confirmed the importance of each molecular descriptor used as an input variable. High-quality networks indicate a strong non-linear relationship between chromatographic lipophilicity and used in silico molecular descriptors. Applying selected molecular descriptors and generated ANNs the good prediction of chromatographic lipophilicity of the studied steroid derivatives can be obtained. This article is based upon work from COST Actions (CM1306 and CA15222), supported by COST (European Cooperation and Science and Technology).

Keywords: artificial neural networks, chemometrics, global sensitivity analysis, liquid chromatography, steroids

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Authors: Mahmoud A. Abdulhamid

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Poly(ether-ether-ketone) (PEEK) has received increased attention due to its outstanding performance in different membrane applications including gas and liquid separation. However, it suffers from a semi-crystalline morphology, bad solubility and low porosity. To fabricate membranes from PEEK, the usage of harsh acid such as sulfuric acid is essential, regardless its hazardous properties. In this work, we report the molecular design of poly(ether-ether-ketones) (iPEEKs) with intrinsic porosity character, by incorporating kinked units into PEEK backbone such as spirobisindane, Tröger's base, and triptycene. The porous polymers were used to fabricate stable membranes for organic solvent nanofiltration application. To better understand the mechanism, we conducted molecular dynamics simulations to evaluate the possible interactions between the polymers and the solvents. Notable enhancement in separation performance was observed confirming the importance of molecular engineering of high-performance polymers. The iPEEKs demonstrated good solubility in polar aprotic solvents, a high surface area of 205–250 m² g⁻¹, and excellent thermal stability. Mechanically flexible nanofiltration membranes were prepared from N-methyl-2-pyrrolidone dope solution at iPEEK concentrations of 19–35 wt%. The molecular weight cutoff of the membranes was fine-tuned in the range of 450–845 g mol⁻¹ displaying 2–6 fold higher permeance (3.57–11.09 L m⁻² h⁻¹ bar⁻¹) than previous reports. The long-term stabilities were demonstrated by a 7 day continuous cross-flow filtration.

Keywords: molecular engineering, polymer synthesis, membrane fabrication, liquid separation

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Authors: Saleem Rao, Mohammed Al-Ghadeer, Archan Banerjee, Hossein Fariborzi

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Materials imperfection, particularly two-level-system (TLS) defects in planer superconducting quantum circuits, contributes significantly to decoherence, ultimately limiting the performance of quantum computation and sensing. Oxides at air interfaces are among the host of TLS, and different material has been used to reduce TLS losses. Passivation with an inorganic layer is not an option to reduce these interface oxides; however, they can be etched away, but their regrowth remains a problem. Here, we report the chemisorption of molecular self-assembled monolayers (SAMs) at air interfaces of superconducting co-planer waveguide (CPW) resonators that suppress the regrowth of oxides and also modify the dielectric constant of the interface. With SAMs, we observed sustained order of magnitude improvement in quality factor -better than oxide etched interfaces. Quality factor measurements at millikelvin temperature and at single photon, XPS data, and TEM images of SAM passivated air interface sustenance our claim. Compatibility of SAM with micro-/nano-fabrication processes opens new ways to improve the coherence time in cQED.

Keywords: superconducting circuits, quality-factor, self-assembled monolayer, coherence

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Authors: Tomasz Łęga, Marta Sosnowska, Mirosława Panasiuk, Lilit Hovhannisyan, Beata Gromadzka, Marcin Olszewski, Sabina Zoledowska, Dawid Nidzworski

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Toxic heavy metal ion contamination of industrial wastewater has recently become a significant environmental concern in many regions of the world. Although the majority of heavy metals are naturally occurring elements found on the earth's surface, anthropogenic activities such as mining and smelting, industrial production, and agricultural use of metals and metal-containing compounds are responsible for the majority of environmental contamination and human exposure. The permissible limits (ppm) for heavy metals in food, water and soil are frequently exceeded and considered hazardous to humans, other organisms, and the environment as a whole. Human exposure to highly nickel-polluted environments causes a variety of pathologic effects. In 2008, nickel received the shameful name of “Allergen of the Year” (GILLETTE 2008). According to the dermatologist, the frequency of nickel allergy is still growing, and it can’t be explained only by fashionable piercing and nickel devices used in medicine (like coronary stents and endoprostheses). Effective remediation methods for removing heavy metal ions from soil and water are becoming increasingly important. Among others, methods such as chemical precipitation, micro- and nanofiltration, membrane separation, conventional coagulation, electrodialysis, ion exchange, reverse and forward osmosis, photocatalysis and polymer or carbon nanocomposite absorbents have all been investigated so far. The importance of environmentally sustainable industrial production processes and the conservation of dwindling natural resources has highlighted the need for affordable, innovative biosorptive materials capable of recovering specific chemical elements from dilute aqueous solutions. The use of combinatorial phage display techniques for selecting and recognizing material-binding peptides with a selective affinity for any target, particularly inorganic materials, has gained considerable interest in the development of advanced bio- or nano-materials. However, due to the limitations of phage display libraries and the biopanning process, the accuracy of molecular recognition for inorganic materials remains a challenge. This study presents the isolation, identification and characterisation of metal binding phage clones that preferentially recover nickel.

Keywords: Heavy metal recovery, cleaning water, phage display, nickel

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Authors: M. R. Ghasemi, R. Ghiasi, H. Varaee

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Model updating method has received increasing attention in damage detection structures based on measured modal parameters. Therefore, a probability-based damage detection (PBDD) procedure based on a model updating procedure is presented in this paper, in which a one-stage model-based damage identification technique based on the dynamic features of a structure is investigated. The presented framework uses a finite element updating method with a Monte Carlo simulation that considers the uncertainty caused by measurement noise. Enhanced ideal gas molecular movement (EIGMM) is used as the main algorithm for model updating. Ideal gas molecular movement (IGMM) is a multiagent algorithm based on the ideal gas molecular movement. Ideal gas molecules disperse rapidly in different directions and cover all the space inside. This is embedded in the high speed of molecules, collisions between them and with the surrounding barriers. In IGMM algorithm to accomplish the optimal solutions, the initial population of gas molecules is randomly generated and the governing equations related to the velocity of gas molecules and collisions between those are utilized. In this paper, an enhanced version of IGMM, which removes unchanged variables after specified iterations, is developed. The proposed method is implemented on two numerical examples in the field of structural damage detection. The results show that the proposed method can perform well and competitive in PBDD of structures.

Keywords: enhanced ideal gas molecular movement (EIGMM), ideal gas molecular movement (IGMM), model updating method, probability-based damage detection (PBDD), uncertainty quantification

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Authors: Christy Rosaline, Rathankar Roa, Waheeta Hopper

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Persistence of tuberculosis, emergence of multidrug-resistance and extensively drug-resistant forms of the disease, has increased the interest in developing new antitubercular drugs. Developing inhibitors for 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis (MtbDAH7Ps), an enzyme involved in shikimate pathway, gives a selective target for antitubercular agents. MtbDAH7Ps was screened against ZINC database, and shortlisted compounds were subjected to induce fit docking. Prime/Molecular Mechanics Generalized Born Surface Area calculation was used to validate the binding energy of ligand-protein complex. Molecular Dynamics analysis for of the lead compounds–MtbDAH7Ps complexes showed that the backbone of MtbDAH7Ps in their complexes were stable. These results suggest that the shortlisted lead compounds ZINC04097114, ZINC15163225, ZINC16857013, ZINC06275603, and ZINC05331260 could be developed into novel drug leads to inhibit DAH7Ps in Mycobacterium tuberculosis.

Keywords: MtbDAH7Ps, Mycobacterium tuberculosis, HTVS, molecular dynamics

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Authors: Nikhil Agrawal, Adam A. Skelton

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Alzheimer’s disease (AD) is one of the most common forms of dementia, which is caused by misfolding and aggregation of amyloid beta (Aβ) peptides into amyloid-β fibrils (Aβ fibrils). To disrupt the remodeling of Aβ fibrils, a number of candidate molecules have been proposed. To study the molecular mechanisms of Aβ fibrils remodeling we performed a series of all-atom molecular dynamics simulations, a total time of 3µs, in explicit solvent. Several previously undiscovered candidate molecule-Aβ fibrils binding modes are unraveled; one of which shows the direct conformational change of the Aβ fibril by understanding the physicochemical factors responsible for binding and subsequent remodeling of Aβ fibrils by the candidate molecule, open avenues into structure-based drug design for AD can be opened.

Keywords: alzheimer’s disease, amyloid, MD simulations, misfolded protein

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Authors: Micheale Yifter Weldemichael

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Sesame (Sesamum indicum L.) is among the most important oilseed crops for its high edible oil quality and quantity. Sesame is grown for food, medicinal, pharmaceutical, and industrial uses. Sesame is also cultivated as a main cash crop in Asia and Africa by smallholder farmers. Despite the global exponential increase in sesame cultivation area, its production and productivity remain low, mainly due to biotic and abiotic constraints. Notwithstanding the efforts to solve these problems, a low level of genetic variation and inadequate genomic resources hinder the progress of sesame improvement. The objective of this paper is, therefore, to review recent advances in the area of molecular breeding and transformation to overcome major production constraints and could result in enhanced and sustained sesame production. This paper reviews various researches conducted to date on molecular breeding and genetic transformation in sesame focusing on molecular markers used in assessing the available online database resources, genes responsible for key agronomic traits as well as transgenic technology and genome editing. The review concentrates on quantitative and semi-quantitative studies on molecular breeding for key agronomic traits such as improvement of yield components, oil and oil-related traits, disease and insect/pest resistance, and drought, waterlogging and salt tolerance, as well as sesame genetic transformation and genome editing techniques. Pitfalls and limitations of existing studies and methodologies used so far are identified and some priorities for future research directions in sesame genetic improvement are identified in this review.

Keywords: abiotic stress, biotic stress, improvement, molecular breeding, oil, sesame, shattering

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Authors: Ngozi Nwogu, Godson Osueke, Mamdud Hossain, Edward Gobina

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An unconventional composite inorganic ceramic membrane capable in carbon dioxide emission decline was fabricated and tested at laboratory scale to develop in conformism to various environmental guidelines to mitigate the effect of global warming. A review of the existing membrane technologies for carbon capture including the relevant gas transport mechanisms are presented and discussed. Single gas separation experiments using silica modified ceramic membrane with internal diameter 20mm, outside diameter 25mm and length of 368mm deposited on a macro porous supported reactor.was carried out to investigate individual gas permeation behaviours at different pressures and membrane efficiency after a dip coating method. Nitrogen, Carbon dioxide, Argon, Oxygen and Methane pure gases were used to investigate their individual permeation rates at various pressures. Results show that the gas flow rate increases with pressure drop. However at above a pressure of 3bar, CO2 permeability ratio to than the other gases indicated control of a more selective surface adsorptive transport mechanism.

Keywords: carbon dioxide, composite membranes, permeability, transport mechanisms

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Authors: Nikolaus Wilke, Boaz Paz

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Museum staff, conservators, restorers, curators, registrars, art handlers but potentially also museum visitors are often exposed to the harmful effects of biocides, which have been applied to collections in the past for the protection and preservation of cultural heritage. Due to stable light, moisture, and temperature conditions, the biocidal active ingredients were preserved for much longer than originally assumed by chemists, pest controllers, and museum scientists. Given the requirements to minimize the use and handling of toxic substances and the obligations of employers regarding safe working environments for their employees, but also for visitors, the museum sector worldwide needs adequate decontamination solutions. Today there are millions of contaminated objects in museums. This paper introduces the results of a systematic investigation into the reduction rate of biocide contamination in various organic materials that were treated with the humidity and temperature controlled ICM (Integrated Contamination Management) method. In the past, collections were treated with a wide range, at times even with a combination of toxins, either preventively or to eliminate active insect or fungi infestations. It was only later that most of those toxins were recognized as CMR (cancerogenic mutagen reprotoxic) substances. Among them were numerous chemical substances that are banned today because of their toxicity. While the biocidal effect of inorganic salts such as arsenic (arsenic(III) oxide), sublimate (mercury(II) chloride), copper oxychloride (basic copper chloride) and zinc chloride was known very early on, organic tar distillates such as paradichlorobenzene, carbolineum, creosote and naphthalene were increasingly used from the 19th century onwards, especially as wood preservatives. With the rapid development of organic synthesis chemistry in the 20th century and the development of highly effective warfare agents, pesticides and fungicides, these substances were replaced by chlorogenic compounds (e.g. γ-hexachlorocyclohexane (lindane), dichlorodiphenyltrichloroethane (DDT), pentachlorophenol (PCP), hormone-like derivatives such as synthetic pyrethroids (e.g., permethrin, deltamethrin, cyfluthrin) and phosphoric acid esters (e.g., dichlorvos, chlorpyrifos). Today we know that textile artifacts (costumes, uniforms, carpets, tapestries), wooden objects, herbaria, libraries, archives and historical wall decorations made of fabric, paper and leather were also widely treated with toxic inorganic and organic substances. The migration (emission) of pollutants from the contaminated objects leads to continuous (secondary) contamination and accumulation in the indoor air and dust. It is important to note that many of mentioned toxic substances are also material-damaging; they cause discoloration and corrosion. Some, such as DDT, form crystals, which in turn can cause micro tectonic, destructive shifting, for example, in paint layers. Museums must integrate sustainable solutions to address the residual biocide problems already in the planning phase. Gas and dust phase measurements and analysis must become standard as well as methods of decontamination.

Keywords: biocides, decontamination, museum collections, toxic substances in museums

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Authors: Milica Ž. Karadžić, Lidija R. Jevrić, Sanja Podunavac-Kuzmanović, Strahinja Z. Kovačević, Anamarija I. Mandić, Katarina Penov-Gaši, Andrea R. Nikolić, Aleksandar M. Oklješa

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This study considered selection of the in silico molecular descriptors and the models for newly synthesized steroid derivatives description and their characterization using chemometric techniques. Multiple linear regression (MLR) models were established and gave the best molecular descriptors for quantitative structure-retention relationship (QSRR) modeling of the retention of the investigated molecules. MLR models were without multicollinearity among the selected molecular descriptors according to the variance inflation factor (VIF) values. Used molecular descriptors were ranked using generalized pair correlation method (GPCM). In this method, the significant difference between independent variables can be noticed regardless almost equal correlation between dependent variable. Generated MLR models were statistically and cross-validated and the best models were kept. Models were ranked using sum of ranking differences (SRD) method. According to this method, the most consistent QSRR model can be found and similarity or dissimilarity between the models could be noticed. In this study, SRD was performed using average values of experimentally observed data as a golden standard. Chemometric analysis was conducted in order to characterize newly synthesized steroid derivatives for further investigation regarding their potential biological activity and further synthesis. This article is based upon work from COST Action (CM1105), supported by COST (European Cooperation in Science and Technology).

Keywords: generalized pair correlation method, molecular descriptors, regression analysis, steroids, sum of ranking differences

Procedia PDF Downloads 347

Authors: Salah Belaidi

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We have carried out extensive and in-depth research to search for bioactive compounds based on Algerian plants. A selection of 50 ligands from Algerian medicinal plants. Several compounds used in herbal medicine have been drawn using Marvin Sketch software. We determined the three-dimensional structures of the ligands with the MMFF94 force field in order to prepare these ligands for molecular docking. The 3D protein structure of the SARS-CoV-2 main protease was taken from the Protein Data Bank. We used AutoDockVina software to apply molecular docking. The hydrogen atoms were added during the molecular docking process, and all the twist bonds of the ligands were added using the (ligand) module in the AutoDock software. The COVID-19 main protease (Mpro) is a key enzyme that plays a vital role in viral transcription and mediating replication, so it is a very attractive drug target for SARS-CoV-2. In this work, an evaluation was carried out on the biologically active compounds present in these selected medicinal plants as effective inhibitors of the protease enzyme of COVID-19, with an in-depth computational calculation of the molecular docking using the Autodock Vina software. The top 7 ligands: Phloroglucinol, Afzelin, Myricetin-3-O- rutinosidTricin 7-neohesperidoside, Silybin, Silychristinthat and Kaempferol are selected among the 50 molecules studied which are Algerian medicinal plants, whose selection is based on the best binding energy which is relatively low compared to the reference molecule with binding affinities of -9.3, -9.3, -9, -8.9, -8 .5, 8.3 and -8.3 kcal mol-1 respectively. Then, we analyzed the ADME properties of the best7 ligands using the web server SwissADME. Two ligands (Silybin, Silychristin) were found to be potential candidates for the discovery and design of novel drug inhibitors of the protease enzyme of SARS-CoV-2. The stability of the two ligands in complexing with the Mpro protease was validated by molecular dynamics simulation; they revealed a stable trajectory in both techniques, RMSD and RMSF, by showing molecular properties with coherent interactions in molecular dynamics simulations. Finally, we conclude that the Silybin ligand forms a more stable complex with the Mpro protease compared to the Silychristin ligand.

Keywords: COVID-19, medicinal plants, molecular docking, ADME properties, molecular dynamics

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Authors: Ambrish Singh

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The corrosion inhibition performance of pyran derivatives (AP) on mild steel in 15% HCl was investigated by electrochemical impedance spectroscopy (EIS), potentiodynamic polarization, weight loss, contact angle, and scanning electron microscopy (SEM) measurements, DFT and molecular dynamic simulation. The adsorption of APs on the surface of mild steel obeyed Langmuir isotherm. The potentiodynamic polarization study confirmed that inhibitors are mixed type with cathodic predominance. Molecular dynamic simulation was applied to search for the most stable configuration and adsorption energies for the interaction of the inhibitors with Fe (110) surface. The theoretical data obtained are, in most cases, in agreement with experimental results.

Keywords: acidizing inhibitor, pyran derivatives, DFT, molecular simulation, mild steel, EIS

Procedia PDF Downloads 195

Authors: Danish Idrees, Vijay Kumar, Samudrala Gourinath

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Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease caused by misfolding and aggregation of Cu, Zn superoxide dismutase (SOD1). The use of small molecules has been shown to stabilize the SOD1 dimer and preventing its dissociation and aggregation. In this study, we employed molecular docking, molecular dynamics simulation and surface plasmon resonance (SPR) to study the interactions between SOD1 and natural polyphenolic compounds. In order to explore the noncovalent interaction between SOD1 and natural polyphenolic compounds, molecular docking and molecular dynamic (MD) simulations were employed to gain insights into the binding modes and free energies of SOD1-polyphenolic compounds. MM/PBSA methods were used to calculate free energies from obtained MD trajectories. The compounds, Hesperidin, Ergosterol, and Rutin showed the excellent binding affinity in micromolar range with SOD1. Ergosterol and Hesperidin have the strongest binding affinity to SOD1 and was subjected to further characterization. Biophysical experiments using Circular Dichroism and Thioflavin T fluorescence spectroscopy results show that the binding of these two compounds can stabilize SOD1 dimer and inhibit the aggregation of SOD1. Molecular simulation results also suggest that these compounds reduce the dissociation of SOD1 dimers through direct interaction with the dimer interface. This study will be helpful to develop other drug-like molecules which may have the effect to reduce the aggregation of SOD1.

Keywords: amyotrophic lateral sclerosis, molecular dynamics simulation, surface plasmon resonance, superoxide dismutase

Procedia PDF Downloads 138

Authors: Edvard Kokanyan, Narine Babajanyan, Ninel Kokanyan, Marco Bazzan

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Lithium niobate (LN) crystals, renowned for their exceptional nonlinear optical, electro-optical, piezoelectric, and photorefractive properties, stand as foundational materials in diverse fields of study and application. While they have long been utilized in frequency converters of laser radiation, electro-optical modulators, and holographic information recording media, LN crystals doped with rare earth ions represent a compelling frontier for modern compact devices. These materials exhibit immense potential as key components in infrared lasers, optical sensors, self-cooling systems, and radiation balanced laser setups. In this study, we present the successful synthesis of Ho-doped lithium niobate (LN:Ho) thin films on sapphire substrates employing the Sol-Gel technique. The films exhibit a strong crystallographic orientation along the perpendicular direction to the substrate surface, with X-ray diffraction analysis confirming the predominant alignment of the film's "c" axis, notably evidenced by the intense (006) reflection peak. Further characterization through Raman spectroscopy, employing a confocal Raman microscope (LabRAM HR Evolution) with exciting wavelengths of 532 nm and 785 nm, unraveled intriguing insights. Under excitation with a 785 nm laser, Raman scattering obeyed selection rules, while employing a 532 nm laser unveiled additional forbidden lines reminiscent of behaviors observed in bulk LN:Ho crystals. These supplementary lines were attributed to luminescence induced by excitation at 532 nm. Leveraging data from anti-Stokes Raman lines facilitated the disentanglement of luminescence spectra from the investigated samples. Surface scanning affirmed the uniformity of both structure and luminescence across the thin films. Notably, despite the robust orientation of the "c" axis perpendicular to the substrate surface, Raman signals indicated a stochastic distribution of "a" and "b" axes, validating the mosaic structure of the films along the mentioned axis. This study offers valuable insights into the structural properties of Ho-doped lithium niobate thin films, with the observed luminescence behavior holding significant promise for potential applications in optoelectronic devices.

Keywords: lithium niobate, Sol-Gel, luminescence, Raman spectroscopy

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Authors: Salma M. Wakil

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Advances in the field of genetics overwhelmed detecting large number of inherited disorders at the molecular level and directed to the development of innovative technologies. These innovations have led to gene sequencing, prenatal mutation detection, pre-implantation genetic diagnosis; population based carrier screening and genome wide analyses using microarrays. Microarrays are widely used in establishing clinical and diagnostic setup for genetic anomalies at a massive level, with the advent of cytoscan molecular karyotyping as a clinical utility card for detecting chromosomal aberrations with high coverage across the entire human genome. Unlike a regular karyotype that relies on the microscopic inspection of chromosomes, molecular karyotyping with cytoscan constructs virtual chromosomes based on the copy number analysis of DNA which improves its resolution by 100-fold. We have been investigating a large number of patients with Developmental Delay and Intellectual disability with this platform for establishing micro syndrome deletions and have detected number of novel CNV’s in the Arabian population with the clinical relevance.

Keywords: microarrays, molecular karyotyping, developmental delay, genetics

Procedia PDF Downloads 456

Authors: Sajjad Seifoori

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Impact behavior of striker on graphene sheet and carbon nanotube is investigated based on molecular dynamics (MD) simulations. A MD simulation is conducted to obtain the maximum dynamic deflections of a square and rectangular single-layered graphene sheets (SLGSs) with various values of side-length and striker parameter. Effect of (i) chirality, (ii) graphene side-length and nanotube length, (iii) striker mass on the maximum dynamic deflections of graphene and nanotube are investigated. The effect of different types of boundary condition on the maximum dynamic deflections is studied for zigzag and armchair SWCNTs with various aspect ratios (Length/Diameter).

Keywords: impact, molecular dynamic, graphene, spring mass

Procedia PDF Downloads 329