Search results for: molecular states

Authors: L. Heidari, M. Jalili Ghazizade

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In recent years, different petrochemical complexes have been established to produce aromatic compounds. Among them, Nouri Petrochemical Complex (NPC) is the largest producer of aromatic raw materials in the world, and is located in south of Iran. Environmental concerns have been raised in this region due to generation of different types of solid waste generated in the process of aromatics production, and subsequently, industrial waste characterization has been thoroughly considered. The aim of this study is qualitative and quantitative characterization of industrial waste generated in the aromatics production process and determination of the best method for industrial waste management. For this purpose, all generated industrial waste during the production process was determined using a checklist. Four main industrial wastes were identified as follows: spent industrial soil, spent catalyst, spent molecular sieves and spent N-formyl morpholine (NFM) solvent. The amount of heavy metals and organic compounds in these wastes were further measured in order to identify the nature and toxicity of such a dangerous compound. Then industrial wastes were classified based on lab analysis results as well as using different international lists of hazardous waste identification such as EPA, UNEP and Basel Convention. Finally, the best method of waste disposal is selected based on environmental, economic and technical aspects. 

Keywords: aromatic compounds, industrial soil, molecular sieve, normal formyl morpholine solvent

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Authors: Dinesh Kumar Maurya, Sapan Mohan Saini

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A theoretical formalism to calculate the structural, electronic and optical properties of orthorhombic crystals from first principle calculations is described. This is applied first time to new YNi4Si-type DyNi4Si compound. Calculations are performed using full-potential augmented plane wave (FPLAPW) method in the framework of density functional theory (DFT). The Coulomb corrected local-spin density approximation (LSDA+U) in the self-interaction correction (SIC) has been used for exchange-correlation potential. Our optimized results of lattice parameters show good agreement to the previously reported experimental study. Analysis of the calculated band structure of DyNi4Si compound demonstrates their metallic character. We found Ni-3d states mainly contribute to density of states from -5.0 eV to the Fermi level while the Dy-f states peak stands tall in comparison to the small contributions made by the Ni-d and R-d states above Fermi level, which is consistent with experiment, in DNi4Si compound. Our calculated optical conductivity compares well with the experimental data and the results are analyzed in the light of band-to-band transitions. We also report the frequency-dependent refractive index n(ω) and the extinction coefficient k(ω) of the compound.

Keywords: band structure, density of states, optical properties, LSDA+U approximation, YNi4Si- type DyNi4Si compound

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Authors: Sinethemba Yakobi, Lindiwe Zuma, Ofentse Pooe

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Gonococcal infections present a notable public health issue, and the major approach for treatment involves using β-lactam antibiotics that specifically target penicillin-binding protein 2 (PBP2) in Neisseria gonorrhoeae. This study examines the influence of flavonoids, namely rutin, on the structural changes of PBP2 in both penicillin-resistant (FA6140) and penicillin-susceptible (FA19) strains. The research clarifies the structural effects of particular mutations, such as inserting an aspartate residue at position 345 (Asp-345a) in the PBP2 protein. The strain FA6140, which is resistant to penicillin, shows specific changes that lead to a decrease in penicillin binding. These mutations, namely P551S and F504L, significantly impact the pace at which acylation occurs and the stability of the strain under high temperatures. Molecular docking analyses investigate the antibacterial activities of rutin and other phytocompounds, emphasizing its exceptional binding affinity and potential as an inhibitor of PBP2. Quercetin and protocatechuic acid have encouraging antibacterial effectiveness, with quercetin displaying characteristics similar to those of drugs. Molecular dynamics simulations offer a detailed comprehension of the interactions between flavonoids and PBP2, highlighting rutin's exceptional antioxidant effects and strong affinity for the substrate binding site. The study's wider ramifications pertain to the pressing requirement for antiviral treatments in the context of the ongoing COVID-19 epidemic. Flavonoids have a strong affinity for binding to PBP2, indicating their potential as inhibitors to impair cell wall formation in N. gonorrhoeae. Ultimately, this study provides extensive knowledge on the interactions between proteins and ligands, the dynamics of the structure, and the ability of flavonoids to combat penicillin-resistant N. gonorrhoeae bacteria. The verified simulation outcomes establish a basis for creating potent inhibitors and medicinal therapies to combat infectious illnesses.

Keywords: phytochemicals, penicillin-binding protein 2, gonococcal infection, ligand-protein interaction, binding energy, neisseria gonorrhoeae FA19, neisseria gonorrhoeae FA6140, flavonoids

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Authors: Janneth Gonzalez, Marco Avila, George Barreto

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GRP78 participates in multiple functions in the cell during normal and pathological conditions, controlling calcium homeostasis, protein folding and unfolded protein response. GRP78 is located in the endoplasmic reticulum, but it can change its location under stress, hypoxic and apoptotic conditions. NF-κB represents the keystone of the inflammatory process and regulates the transcription of several genes related with apoptosis, differentiation, and cell growth. The possible relationship between GRP78-NF-κB could support and explain several mechanisms that may regulate a variety of cell functions, especially following brain injuries. Although several reports show interactions between NF-κB and heat shock proteins family members, there is a lack of information on how GRP78 may be interacting with NF-κB, and possibly regulating its downstream activation. Therefore, we assessed the computational predictions of the GRP78 (Chain A) and NF-κB complex (IkB alpha and p65) protein-protein interactions. The interaction interface of the docking model showed that the amino acids ASN 47, GLU 215, GLY 403 of GRP78 and THR 54, ASN 182 and HIS 184 of NF-κB are key residues involved in the docking. The electrostatic field between GRP78-NF-κB interfaces and molecular dynamic simulations support the possible interaction between the proteins. In conclusion, this work shed some light in the possible GRP78-NF-κB complex indicating key residues in this crosstalk, which may be used as an input for better drug design strategy targeting NF-κB downstream signaling as a new therapeutic approach following brain injuries.

Keywords: computational biology, protein interactions, Grp78, bioinformatics, molecular dynamics

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Authors: I. Benkaddour, Y. Benkaddour, A. Benk Addour

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The structural, elastic, Thermal, electronic, and magnetic properties of intermetallic RMn₂Ge₂ (R= Ca, Y, Nd) are investigated by density functional theory (DFT), using the full potential –linearised augmented plane wave method (FP-LAPW). In this approach, the local-density approximation (LDA) is used for the exchange-correlation (XC) potential. The equilibrium lattice constant and magnetic moment agree well with the experiment. The density of states shows that these phases are conductors, with contribution predominantly from the R and Mn d states. We have determined the elastic constants C₁₁, C₁₂, C₁₃, C₄₄, C₃₃, andC₆₆ at ambient conditions in, which have not been established neither experimentally nor theoretically. Thermal properties, including the relative expansion coefficients and the heat capacity, have been estimated using a quasi-harmonic Debye model.

Keywords: RMn₂Ge₂, intermetallic, first-principles, density of states, mechanical properties

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Authors: Takahiro Ishizaki, Shutaro Hisada, Oi Lun Li

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Control of surface wettability is very important in various industrial fields. Thus, contact angle hysteresis which is defined as the difference between advancing and receding water contact angles has been paid attention because the surface having low contact angle hysteresis can control wetting behavior of water droplet. Self-assembled monolayer (SAM) formed using organic silane molecules has been used to control surface wettability, in particular, static contact angles, however, the effect of alkyl-chain length in organic silane molecules on the contact angle hysteresis has not yet clarified. In this study, we aimed to investigate the effect of alkyl-chain length (C1-C18) in organic silane molecules on the contact angle hysteresis. SAMs were formed on Si wafer by thermal CVD method using silane coupling agents having different alkyl-chain length. The static water contact angles increased with an increase in the alkyl-chain length. On the other hand, although the water contact angle hysteresis tended to decrease with an increase in the alkyl-chain length, in case of the alkyl-chain length of more than C16 the contact angle hysteresis increased. This could be due to the decrease in the molecular mobility because of the increase in the molecular packing density in chemisorbed silane molecules.

Keywords: alkyl-chain length, self-assembled monolayer, silane coupling agent, surface wettability

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Authors: Amanda C. Evans

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Enabling technologies such as continuous processing (CP) approaches can provide the tools needed to control and manipulate reactivities and transform chemical reactions into micro-controlled in-flow processes. Traditional synthetic approaches can be radically transformed by the application of CP, facilitating the pairing of chemical methodologies with technologies from other disciplines. CP supports sustainable processes that controllably generate reaction specificity utilizing supramolecular interactions. Continuous photochemical processing is an emerging field of investigation. The use of light to drive chemical reactivity is not novel, but the controlled use of specific and tunable wavelengths of light to selectively generate molecular structure under continuous processing conditions is an innovative approach towards chemical synthesis. This investigation focuses on the use of circularly polarized (cp) light as a sustainable catalyst for the CP generation of asymmetric molecules. Chiral photolysis has already been achieved under batch, solid-phase conditions: using synchrotron-sourced cp light, asymmetric photolytic selectivities of up to 4.2% enantiomeric excess (e.e.) have been reported. In order to determine the optimal wavelengths to use for irradiation with cp light for any given molecular building block, CD and anisotropy spectra for each building block of interest have been generated in two different solvents (water, hexafluoroisopropanol) across a range of wavelengths (130-400 nm). These spectra are being used to support a series of CP experiments using cp light to generate enantioselectivity.

Keywords: anisotropy, asymmetry, flow chemistry, active pharmaceutical ingredients

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Authors: Avinash Kishore, Suman Chakrabarti

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In September 2013, the parliament of India enacted the National Food Security Act (NFSA) which entitles two-thirds of India’s population to five kilograms of rice, wheat or coarse cereals per person per month at one to three rupees per kilogram. Five states in India—Andhra Pradesh, Chhattisgarh, Tamil Nadu, Odisha and West Bengal—had already implemented somewhat similar changes in the TPDS a few years earlier using their own budgetary resources. They made rice—coincidentally, all five states are predominantly rice-eating—available in fair price shops to a majority of their population at very low prices (less than Rs.3/kg). This paper tries to account for the changes in household consumption patterns associated with the change in TPDS policy in these states using data from household consumption surveys by the National Sample Survey Organization (NSSO). NSS data show improvement in the coverage of TPDS and average off-take of grains from fair price shops between 2004-05 and 2009-10 across all states of India. However, the increase in coverage and off-take was significantly higher in four out of these five states than in the rest of India. An average household in these states purchased three kilos more rice per month from fair price shops than its counterpart in non-treated states as a result of more generous TPDS policies backed by administrative reforms. The increase in consumption of PDS rice was the highest in Chhattisgarh, the poster state of PDS reforms. Households in Chhattisgarh used money saved on rice to spend more on pulses, edible oil, vegetables and sugar and other non-food items. We also find evidence that making TPDS more inclusive and more generous is not enough unless it is supported by administrative reforms to improve grain delivery and control diversion to open markets.

Keywords: public distribution system, social safety-net, national food security act, diet quality, Chhattisgarh

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Authors: Sumachaya Harnsukworapanich, Tetsuo Ichimori

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The apportionment method is used by many countries, to calculate the distribution of seats in political bodies. For example, this method is used in the United States (U.S.) to distribute house seats proportionally based on the population of the electoral district. Famous apportionment methods include the divisor methods called the Adams Method, Dean Method, Hill Method, Jefferson Method and Webster Method. Sometimes the results from the implementation of these divisor methods are unfair and include errors. Therefore, it is important to examine the optimization of this method by using a bias measurement to figure out precise and fair results. In this research we investigate the bias of divisor methods in the U.S. Houses of Representatives toward large and small states by applying the Stolarsky Mean Method. We compare the bias of the apportionment method by using two famous bias measurements: The Balinski and Young measurement and the Ernst measurement. Both measurements have a formula for large and small states. The Third measurement however, which was created by the researchers, did not factor in the element of large and small states into the formula. All three measurements are compared and the results show that our measurement produces similar results to the other two famous measurements.

Keywords: apportionment, bias, divisor, fair, measurement

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Authors: Nigatu Tadesse, Ying Liu, Juan Li, Hong Ming Liu

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Gastric carcinogenesis is a lengthy process of histopathological transition from normal to atrophic gastritis (AG) to intestinal metaplasia (GIM), dysplasia toward gastric cancer (GC). The stage of GIM identified as precancerous lesions with resistance to H-pylori eradication and recurrence after endoscopic surgical resection therapies. GIM divided in to two morphologically distinct phenotypes such as complete GIM bearing intestinal type morphology whereas the incomplete type has colonic type morphology. The incomplete type GIM considered to be the greatest risk factor for the development of GC. Studies indicated the expression of the caudal type homeobox 2 (CDX2) gene is responsible for the development of complete GIM but its progressive downregulation from incomplete metaplasia toward advanced GC identified as the risk for IM progression and neoplastic transformation. The downregulation of CDX2 gene have promoted cell growth and proliferation in gastric and colon cancers and ascribed in chemo-treatment inefficacies. CDX2 downregulated through promoter region hypermethylation in which the methylation frequency positively correlated with the dietary history of the patients, suggesting the role of diet as methyl carbon donor sources such as methionine. However, the metabolism of exogenous methionine is yet unclear. Targeting exogenous methionine metabolism has become a promising approach to limits tumor cell growth, proliferation and progression and increase treatment outcome. This review article discusses molecular alterations that could shed light on the potential of exogenous methionine metabolisms, such as gut microbiota alteration as sources of methionine to host cells, metabolic pathway signaling via PI3K/AKt/mTORC1-c-MYC to rewire exogenous methionine and signature of increased gene methylation index, cell growth and proliferation in GIM, with insights to new treatment avenue via targeting methionine metabolism, and the need for future integrated studies on molecular alterations and metabolomics to uncover altered methionine metabolism and characterization of CDX2 methylation in gastric intestinal metaplasia for potential therapeutic exploitation.

Keywords: altered methionine metabolism, Intestinal metaplesia, CDX2 gene, gastric cancer

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Authors: Geetakshi Arora, Danish Malhotra

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Diabetic wounds are serious health issues and often fail to heal, leading to limb amputation that makes the life of the patient miserable. Delayed wound healing has been characterized by an increase in matrix metalloproteinase-9 (MMP-9). Thus research throughout the world has been going on to develop selective MMP-9 inhibitors for aiding diabetic wound healing. Bioactive constituents from natural sources always served as potential leads in drug development with high rates of success. Considering the need for novel selective MMP-9 inhibitors and the importance of natural bioactive compounds in drug development, we have screened a library of bioactive constituents from plant sources that were effective in diabetic wound healing on human MMP-9 (hMMP-9) using molecular docking studies. Screened constituents are ranked according to their dock score, ∆G value (binding affinity), and Ligand efficiency evaluated from FleXX docking and Hyde scoring modules available with drug designing platform LeadIT. Rhamnocitrin showed the highest correlation between dock score, ∆G value (binding affinity), and Ligand efficiency was further explored for binding interactions with hMMP-9. The overall study suggest that Rhamnocitrin is sufficiently decorated with both hydrophilic and hydrophobic substitutions that perfectly block hMMP-9 and act as a potential lead in the design and development of selective hMMP-9 inhibitors.

Keywords: MMP-9, diabetic wound, molecular docking, phytoconstituents

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Authors: Rajendra Singh, Krishna Mondal, Chandranath Chatterjee

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The water, energy, and food (WEF) nexus describes the interconnectedness of these three essential elements of human life. Each of these three sectors depends on the others. India's expanding population, urbanization, and industrialization make WEF nexus management difficult. Coupling and coordination degrees can be used as indicators of a complex system's level of sustainable development. Thus, coupling and coordination of WEF sectors in India are essential for achieving Sustainable Development Goals (SDGs) 2 (zero hunger), 6 (clean water and sanitation), and 7 (affordable and clean energy). This study used a newly developed WEF nexus model and the concept of coupling coordination degree model to examine the coupling and coordination degrees of the WEF nexus at India's sub-national scale (States/Union Territories (UTs)) for the years 2011 and 2021. Results indicate that the WEF nexus coupling degree was reasonably stable among the Indian States/UTs in both years, with all having a coupling degree above 0.90, indicating high-quality coupling. However, the degree of coordination varied spatially and temporally from ‘primary development’ to ‘quality development’ for the Indian States/UTs. In 2021, it went from 53% to 14% intermediate development and 44% to 83% good development compared to 2011. Most Indian States/UTs developed SDG2 more than SDG6 and SDG7. This study also suggests that most States/UTs must implement WEF-related policies and programmes effectively to achieve quality coordinated WEF nexus development. This study may help administrators and policymakers identify States/UTs that need more attention to implement existing or new policies for achieving SDGs 2, 6, and 7.

Keywords: WEF nexus model, Pardee-RAND WEF nexus, sustainable development, policy

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Authors: Renata Silva-Mann, Sheila Valéria Álvares Carvalho, Robério Anastácio Ferreira, Laura Jane Gomes

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There is growing interest in defining indicators of sustainability, which are important for monitoring the conservation of native forests, particularly in areas of permanent protection. These indicators are references for assessing the state of the forest and the status of the depredated area and its ability to maintain species populations. The aim of the present study was to select genetic parameters as indicators of sustainability for Schinus terebinthifolius Raddi. Fragments located in riparian areas between the Sergipe and Alagoas States in Brazil. This species has been exploited for traditional communities, which represent 20% of the incoming. This study was carried out using the indicators suggested by the Organization for Economic Cooperation and Development, which were identified as Driving-Pressure-State-Impact-Response (DPSIR) factors. The genetic parameters were obtained in five populations located on the shores and islands of the São Francisco River, one of the most important rivers in Brazil. The framework for Schinus conservation suggests seventeen indicators of sustainability. In accordance with genetic parameters, the populations are isolated, and these genetic parameters can be used to monitor the sustainability of those populations in riparian area with the aim of defining strategies for forest restoration.

Keywords: alleles, molecular markers, genetic diversity, biodiversity

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Authors: Jarek Krajewski, David Daxberger, Luzi Beyer

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Finding objective and non-intrusive measurements of emotional and psychopathological states (e.g., post-traumatic stress disorder, PTSD) is an important challenge. Thus, the proposed approach here uses Photoplethysmographic imaging (PPGI) applying facial RGB Cam videos to estimate heart rate levels. A pipeline for the signal processing of the raw image has been proposed containing different preprocessing approaches, e.g., Independent Component Analysis, Non-negative Matrix factorization, and various other artefact correction approaches. Under resting and constant light conditions, we reached a sensitivity of 84% for pulse peak detection. The results indicate that PPGI can be a suitable solution for providing heart rate data derived from these indirectly post-traumatic stress states.

Keywords: heart rate, PTSD, PPGI, stress, preprocessing

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Authors: Jiajia Yao, Guanlin Wu, Fang Liu, Junshuai Xue, Yue Hao

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This study reports on the epitaxial growth of a GaN-based resonant tunneling diode (RTD) structure with stable and repeatable double negative differential resistance (NDR) characteristics at room temperature on a c-plane GaN-on-sapphire template using plasma-assisted molecular beam epitaxy (PA-MBE) technology. In this structure, two independent AlN/GaN RTDs are epitaxially connected in series in the vertical growth direction through a silicon-doped GaN layer. As the collector electrode bias voltage increases, the two RTDs respectively align the ground state energy level in the quantum well with the 2DEG energy level in the emitter accumulation well to achieve quantum resonant tunneling and then reach the negative differential resistance (NDR) region. The two NDR regions exhibit similar peak current densities and peak-to-valley current ratios, which are 230 kA/cm² and 249 kA/cm², 1.33 and 1.38, respectively, for a device with a collector electrode mesa diameter of 1 µm. The consistency of the NDR is much higher than the results of on-chip discrete RTD device interconnection, resulting from the smaller chip area, fewer interconnect parasitic parameters, and less process complexity. The methods and results presented in this paper show the brilliant prospects of GaN RTDs in the development of multi-value logic digital circuits.

Keywords: MBE, AlN/GaN, RTDs, double NDR

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Authors: Mohammad Anvari, Helen S. Joyner (Melito)

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Camelina sativa (L.) Crantz is an oilseed crop currently used for the production of biofuels. However, the low price of diesel and gasoline has made camelina an unprofitable crop for farmers, leading to declining camelina production in the US. Hence, the ability to utilize camelina byproduct (defatted meal) after oil extraction would be a pivotal factor for promoting the economic value of the plant. Camelina defatted meal is rich in proteins and polysaccharides. The great diversity in the polysaccharide structural features provides a unique opportunity for use in food formulations as thickeners, gelling agents, emulsifiers, and stabilizers. There is currently a great degree of interest in the study of novel plant polysaccharides, as they can be derived from readily accessible sources and have potential application in a wide range of food formulations. However, there are no published studies on the polysaccharide extracted from camelina meal, and its potential industrial applications remain largely underexploited. Rheological properties are a key functional feature of polysaccharides and are highly dependent on the material composition and molecular structure. Therefore, the objective of this study was to evaluate the rheological properties of the polysaccharide extracted from camelina meal at different conditions to obtain insight on the molecular characteristics of the polysaccharide. Flow and dynamic mechanical behaviors were determined under different temperatures (5-50°C) and concentrations (1-6% w/v). Additionally, the zeta potential of the polysaccharide dispersion was measured at different pHs (2-11) and a biopolymer concentration of 0.05% (w/v). Shear rate sweep data revealed that the camelina polysaccharide displayed shear thinning (pseudoplastic) behavior, which is typical of polymer systems. The polysaccharide dispersion (1% w/v) showed no significant changes in viscosity with temperature, which makes it a promising ingredient in products requiring texture stability over a range of temperatures. However, the viscosity increased significantly with increased concentration, indicating that camelina polysaccharide can be used in food products at different concentrations to produce a range of textures. Dynamic mechanical spectra showed similar trends. The temperature had little effect on viscoelastic moduli. However, moduli were strongly affected by concentration: samples exhibited concentrated solution behavior at low concentrations (1-2% w/v) and weak gel behavior at higher concentrations (4-6% w/v). These rheological properties can be used for designing and modeling of liquid and semisolid products. Zeta potential affects the intensity of molecular interactions and molecular conformation and can alter solubility, stability, and eventually, the functionality of the materials as their environment changes. In this study, the zeta potential value significantly decreased from 0.0 to -62.5 as pH increased from 2 to 11, indicating that pH may affect the functional properties of the polysaccharide. The results obtained in the current study showed that camelina polysaccharide has significant potential for application in various food systems and can be introduced as a novel anionic thickening agent with unique properties.

Keywords: Camelina meal, polysaccharide, rheology, zeta potential

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Authors: Nana Kwasi Amoateng

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The paper uses secondary information to investigate some longstanding limitations in International Relations (IR) theory. Specifically, the analysis highlights IR theory through the lens of J. C. Sharman’s brilliant concept of outside-in state-building logic in which some states, particularly those in Africa, have relied mainly on foreign resources to address local threats. The key findings are that IR theory has been largely understood from the perspective of an inside-out state-building logic, whereby Western and other advanced states have heavily relied on local resources to address foreign threats. In this vein, IR theorists, including Critical Theorists, have not been able to fully grasp African states and states elsewhere that have generally relied on an outside-in logic of state-building. The paper helps to fill a major gap in IR theory, which has mainly addressed criticisms of being Euro- or Western-centric or failing to include the unique experiences of states and other actors in the Global South by developing critical theories such as post-colonial theory and neo-colonialism. Although this has helped to understand some experiences of actors in the Global South, the fundamental difference between state-building in the West and the Global South, particularly Africa, has not been adequately explored to fully comprehend why, despite the works of Critical Theorists, IR theory still fails to capture many political and socioeconomic realities in Africa and elsewhere.

Keywords: international relations theory, outside-in state-building logic, inside-out state-building logic, Africa

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Authors: Lotanna Ezeonu, Jason P. Robbins, Ziyu Tang, Xiaofang Yang, Bruce E. Koel, Simon G. Podkolzin

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The interaction of organic molecules with metal surfaces is of interest in numerous technological applications, such as catalysis, bone replacement, and biosensors. Acetic acid is one of the main products of bio-oils produced from the pyrolysis of hemicellulosic feedstocks. However, their high oxygen content makes them unsuitable for use as fuels. Hydrodeoxygenation is a proven technique for catalytic deoxygenation of bio-oils. An understanding of the energetics and control of the bond-breaking sequences of biomass-derived oxygenates on metal surfaces will enable a guided optimization of existing catalysts and the development of more active/selective processes for biomass transformations to fuels. Such investigations have been carried out with the aid of ultrahigh vacuum and its concomitant techniques. The high catalytic activity of platinum in biomass-derived oxygenate transformations has sparked a lot of interest. We herein exploit infrared reflection absorption spectroscopy(IRAS), temperature-programmed desorption(TPD), and density functional theory(DFT) to study the adsorption and decomposition of acetic acid on a Pt(111) surface, which was then compared with Ni(111), a model non-noble metal. We found that acetic acid adsorbs molecularly on the Pt(111) surface, interacting through the lone pair of electrons of one oxygen atomat 90 K. At 140 K, the molecular form is still predominant, with some dissociative adsorption (in the form of acetate and hydrogen). Annealing to 193 K led to complete dehydrogenation of molecular acetic acid species leaving adsorbed acetate. At 440 K, decomposition of the acetate species occurs via decarbonylation and decarboxylation as evidenced by desorption peaks for H₂,CO, CO₂ and CHX fragments (x=1, 2) in theTPD.The assignments for the experimental IR peaks were made using visualization of the DFT-calculated vibrational modes. The results showed that acetate adsorbs in a bridged bidentate (μ²η²(O,O)) configuration. The coexistence of linear and bridge bonded CO was also predicted by the DFT results. Similar molecular acid adsorption energy was predicted in the case of Ni(111) whereas a significant difference was found for acetate adsorption.

Keywords: acetic acid, platinum, nickel, infared-absorption spectrocopy, temperature programmed desorption, density functional theory

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Authors: Ergun Sakalar, Kubra Bilgic

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In the last decades, real-time PCR has become a reliable tool preferred to use in many laboratories for pathogen detection. This technique allows for monitoring target amplification via fluorescent molecules besides admit of quantitative analysis by enabling of convert outcomes of thermal cycling to digital data. Sensitivity and traceability of real-time PCR are based on measuring of fluorescence that appears only when fluorescent reporter dye bound to specific target DNA.The fluorescent reporter systems developed for this purpose are divided into two groups. The first group consists of intercalator fluorescence dyes such as SYBR Green, EvaGreen which binds to double-stranded DNA. On the other hand, the second group includes fluorophore-labeled oligonucleotide probes that are separated into three subgroups due to differences in mechanism of action; initial primer-probes such as Cyclicons, Angler®, Amplifluor®, LUX™, Scorpions, and the second one hydrolysis probes like TaqMan, Snake assay, finally hybridization probes, for instance, Molecular Beacons, Hybprobe/FRET, HyBeacon™, MGB-Eclipse, ResonSense®, Yin-Yang, MGB-Pleiades. In addition nucleic acid analogues, an increase of probe affinity to target site is also employed with fluorescence-labeled probes. Consequently, abundant real-time PCR detection chemistries are chosen by researcher according to the field of application, mechanism of action, advantages, and proper structures of primer/probes.

Keywords: fluorescent dye, food safety, molecular probes, nucleic acid analogues

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Authors: Debamitra Chakravorty, Pratap K. Parida

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Cold-adapted proteases enhance wash performance in low-temperature laundry resulting in a reduction in energy consumption and wear of textiles and are also used in the dehairing process in leather industries. Unfortunately, the possible drawbacks of using cold-adapted proteases are their instability at higher temperatures. Therefore, proteases with broad temperature stability are required. Unfortunately, wild-type cold-adapted proteases exhibit instability at higher temperatures and thus have low shelf lives. Therefore, attempts to engineer cold-adapted proteases by protein engineering were made previously by directed evolution and random mutagenesis. The lacuna is the time, capital, and labour involved to obtain these variants are very demanding and challenging. Therefore, rational engineering for cold stability without compromising an enzyme's optimum pH and temperature for activity is the current requirement. In this work, mutations were rationally designed with the aid of high throughput computational methodology of network analysis, evolutionary conservation scores, and molecular dynamics simulations for Savinase from Bacillus lentus with the intention of rendering the mutants cold stable without affecting their temperature and pH optimum for activity. Further, an attempt was made to incorporate a mutation in the most stable mutant rationally obtained by this method to introduce oxidative stability in the mutant. Such enzymes are desired in detergents with bleaching agents. In silico analysis by performing 300 ns molecular dynamics simulations at 5 different temperatures revealed that these three mutants were found to be better in cold stability compared to the wild type Savinase from Bacillus lentus. Conclusively, this work shows that cold adaptation without losing optimum temperature and pH stability and additionally stability from oxidative damage can be rationally designed by in silico enzyme engineering. The key findings of this work were first, the in silico data of H5 (cold stable savinase) used as a control in this work, corroborated with its reported wet lab temperature stability data. Secondly, three cold stable mutants of Savinase from Bacillus lentus were rationally identified. Lastly, a mutation which will stabilize savinase against oxidative damage was additionally identified.

Keywords: cold stability, molecular dynamics simulations, protein engineering, rational design

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Authors: Shubham Dwivedi, Raghavender Medishetti, Rita Rani, Aarti Sevilimedu, Pushkar Kulkarni, Yogeeswari Perumal

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Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder of early onset, characterized by impaired sociability, cognitive function and stereotypies. There is a significant urge to develop and establish new animal models with ASD-like characteristics for better understanding of underlying mechanisms. The aim of the present study was to develop a cost and time effective zebrafish model with quantifiable parameters to facilitate mechanistic studies as well as high-throughput screening of new molecules for autism. Zebrafish embryos were treated with valproic acid and a battery of behavioral tests (anxiety, inattentive behavior, irritability and social impairment) was performed on larvae at 7th day post fertilization, followed by study of molecular markers of autism. This model shows a significant behavioural impairment in valproic acid treated larvae in comparison to control which was again supported by alteration in few marker genes and proteins of autism. The model also shows a rescue of behavioural despair with positive control drugs. The model shows robust parameters to study behavior, molecular mechanism and drug screening approach in a single frame. Thus we postulate that our 7 days zebrafish larval model for autism can help in high throughput screening of new molecules on autism.

Keywords: autism, zebrafish, valproic acid, neurodevelopment, behavioral assay

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Authors: William Abiodun Duyile

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It is common knowledge that marine food has always been found from the sea, energy can also be found underneath and, to a growing extent; other mineral resources have come from the sea spaces. It is the importance of the sea and the sea lines of communication to littoral nations that has made concepts such as sea power, naval power, etc., significant to them. The study relied on documentary data. The documentary data were sourced from government annual departmental reports, newspapers and correspondence. The secondary sources used were subjected to internal and external criticism for authentication, and then to textual and contextual analyses. The study found that the differential level of seamanship amongst states defined their relationship. It was sea power that gave some states an edge over the others. The study proves that over the ages sea power has been core to the development of States or Empires. The study found that the Nigerian Navy was centre to Nigeria’s conquest of the littoral areas of Biafra, like Bonny, Port-Harcourt, and Calabar; it was also an important turning point of the Nigerian civil war since by it Biafra became landlocked. The research was able to identify succinctly the Nigerian Navy’s contribution to the security and development of the Nigerian State.

Keywords: sea power, naval power, land locked states, warship

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Authors: A. E. Kobryn

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We present both descriptive and predictive modeling of structural properties of blends of PCBM or organic-inorganic hybrid perovskites of the type CH3NH3PbX3 (X=Cl, Br, I) with P3HT, P3BT or squaraine SQ2 dye sensitizer, including adsorption on TiO2 clusters having rutile (110) surface. In our study, we use a methodology that allows computing the microscopic structure of blends on the nanometer scale and getting insight on miscibility of its components at various thermodynamic conditions. The methodology is based on the integral equation theory of molecular liquids in the reference interaction site representation/model (RISM) and uses the universal force field. Input parameters for RISM, such as optimized molecular geometries and charge distribution of interaction sites, are derived with the use of the density functional theory methods. To compare the diffusivity of the PCBM in binary blends with P3HT and P3BT, respectively, the study is complemented with MD simulation. A very good agreement with experiment and the reports of alternative modeling or simulation is observed for PCBM in P3HT system. The performance of P3BT with perovskites, however, seems as expected. The calculated nanoscale morphologies of blends of P3HT, P3BT or SQ2 with perovskites, including adsorption on TiO2, are all new and serve as an instrument in rational design of organic/hybrid photovoltaics. They are used in collaboration with experts who actually make prototypes or devices for practical applications.

Keywords: multiscale theory and modeling, nanoscale morphology, organic-inorganic halide perovskites, three dimensional distribution

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Authors: M. Moaeen-ud-Din, G. Bilal, M. Yaqoob

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Identification of genes of importance regarding production traits in buffalo is impaired by a paucity of genomic resources. Choice to fill this gap is to exploit data available for cow. The cross-species application of comparative genomics tools is potential gear to investigate the buffalo genome. However, this is dependent on nucleotide sequences similarity. In this study gene diversity between buffalo and cattle was determined by using 86 gene orthologues. There was about 3% difference in all genes in term of nucleotide diversity; and 0.267±0.134 in amino acids indicating the possibility for successfully using cross-species strategies for genomic studies. There were significantly higher non synonymous substitutions both in cattle and buffalo however, there was similar difference in term of dN – dS (4.414 vs 4.745) in buffalo and cattle respectively. Higher rate of non-synonymous substitutions at similar level in buffalo and cattle indicated a similar positive selection pressure. Results for relative rate test were assessed with the chi-squared test. There was no significance difference on unique mutations between cattle and buffalo lineages at synonymous sites. However, there was a significance difference on unique mutations for non synonymous sites indicating ongoing mutagenic process that generates substitutional mutation at approximately the same rate at silent sites. Moreover, despite of common ancestry, our results indicate a different divergent time among genes of cattle and buffalo. This is the first demonstration that variable rates of molecular evolution may be present within the family Bovidae.

Keywords: buffalo, cattle, gene diversity, molecular evolution

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Authors: Moustafa Osman Mohammed

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This paper introduces Luhmann’s autopoietic social systems starting with the original concept of autopoiesis by biologists and scientists, including the modification of general systems based on socialized medicine. A specific type of autopoietic system is explained in the three existing groups of the ecological phenomena: interaction, social and medical sciences. This hypothesis model, nevertheless, has a nonlinear interaction with its natural environment ‘interactional cycle’ for the exchange of photon energy with molecular without any changes in topology. The external forces in the systems environment might be concomitant with the natural fluctuations’ influence (e.g. radioactive radiation, electromagnetic waves). The cantilever sensor deploys insights to the future chip processor for prevention of social metabolic systems. Thus, the circuits with resonant electric and optical properties are prototyped on board as an intra–chip inter–chip transmission for producing electromagnetic energy approximately ranges from 1.7 mA at 3.3 V to service the detection in locomotion with the least significant power losses. Nowadays, therapeutic systems are assimilated materials from embryonic stem cells to aggregate multiple functions of the vessels nature de-cellular structure for replenishment. While, the interior actuators deploy base-pair complementarity of nucleotides for the symmetric arrangement in particular bacterial nanonetworks of the sequence cycle creating double-stranded DNA strings. The DNA strands must be sequenced, assembled, and decoded in order to reconstruct the original source reliably. The design of exterior actuators have the ability in sensing different variations in the corresponding patterns regarding beat-to-beat heart rate variability (HRV) for spatial autocorrelation of molecular communication, which consists of human electromagnetic, piezoelectric, electrostatic and electrothermal energy to monitor and transfer the dynamic changes of all the cantilevers simultaneously in real-time workspace with high precision. A prototype-enabled dynamic energy sensor has been investigated in the laboratory for inclusion of nanoscale devices in the architecture with a fuzzy logic control for detection of thermal and electrostatic changes with optoelectronic devices to interpret uncertainty associated with signal interference. Ultimately, the controversial aspect of molecular frictional properties is adjusted to each other and forms its unique spatial structure modules for providing the environment mutual contribution in the investigation of mass temperature changes due to pathogenic archival architecture of clusters.

Keywords: autopoiesis, nanoparticles, quantum photonics, portable energy, photonic structure, photodynamic therapeutic system

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Authors: Hiroyuki Aoki

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Polymeric materials are often used in a form of thin film such as food wrap and surface coating. In such the applications, polymer films thinner than 100 nm have been often used. The thickness of such the ultra-thin film is less than the unperturbed size of a polymer chain; therefore, the polymer chain in an ultra-thin film is strongly constrained. However, the details on the constrained dynamics of polymer molecules in ultra-thin films are still unclear. In the current study, the segmental dynamics of single polymer chain was directly investigated by fluorescence microscopy. The individual chains of poly(alkyl methacrylate) labeled by a perylenediimide dye molecule were observed by a highly sensitive fluorescence microscope in a defocus condition. The translational and rotational diffusion of the center segment in a single polymer chain was directly analyzed. The segmental motion in a thin film with a thickness of 10 nm was found to be suppressed compared to that in a bulk state. The detailed analysis of the molecular motion revealed that the diffusion rate of the in-plane rotation was similar to the thin film and the bulk; on the other hand, the out-of-plane motion was restricted in a thin film. This result indicates that the spatial restriction in an ultra-thin film thinner than the unperturbed chain dimension alters the dynamics of individual molecules in a polymer system.

Keywords: polymer materials, single molecule, molecular motion, fluorescence microscopy, super-resolution techniques

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Authors: Ece A. Irmak, Amdulla O. Mekhrabov, M. Vedat Akdeniz

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There is a growing interest in the modeling and simulation of magnetic nanoalloys by various computational methods. Magnetic crystalline/amorphous nanoparticles (NP) are interesting materials from both the applied and fundamental points of view, as their properties differ from those of bulk materials and are essential for advanced applications such as high-performance permanent magnets, high-density magnetic recording media, drug carriers, sensors in biomedical technology, etc. As an important magnetic material, Fe-Ni based nanoalloys have promising applications in the chemical industry (catalysis, battery), aerospace and stealth industry (radar absorbing material, jet engine alloys), magnetic biomedical applications (drug delivery, magnetic resonance imaging, biosensor) and computer hardware industry (data storage). The physical and chemical properties of the nanoalloys depend not only on the particle or crystallite size but also on composition and atomic ordering. Therefore, computer modeling is an essential tool to predict structural, electronic, magnetic and optical behavior at atomistic levels and consequently reduce the time for designing and development of new materials with novel/enhanced properties. Although first-principles quantum mechanical methods provide the most accurate results, they require huge computational effort to solve the Schrodinger equation for only a few tens of atoms. On the other hand, molecular dynamics method with appropriate empirical or semi-empirical inter-atomic potentials can give accurate results for the static and dynamic properties of larger systems in a short span of time. In this study, structural evolutions, magnetic and electronic properties of Fe-Ni based nanoalloys have been studied by using molecular dynamics (MD) method in Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) and Density Functional Theory (DFT) in the Vienna Ab initio Simulation Package (VASP). The effects of particle size (in 2-10 nm particle size range) and temperature (300-1500 K) on stability and structural evolutions of amorphous and crystalline Fe-Ni bulk/nanoalloys have been investigated by combining molecular dynamic (MD) simulation method with Embedded Atom Model (EAM). EAM is applicable for the Fe-Ni based bimetallic systems because it considers both the pairwise interatomic interaction potentials and electron densities. Structural evolution of Fe-Ni bulk and nanoparticles (NPs) have been studied by calculation of radial distribution functions (RDF), interatomic distances, coordination number, core-to-surface concentration profiles as well as Voronoi analysis and surface energy dependences on temperature and particle size. Moreover, spin-polarized DFT calculations were performed by using a plane-wave basis set with generalized gradient approximation (GGA) exchange and correlation effects in the VASP-MedeA package to predict magnetic and electronic properties of the Fe-Ni based alloys in bulk and nanostructured phases. The result of theoretical modeling and simulations for the structural evolutions, magnetic and electronic properties of Fe-Ni based nanostructured alloys were compared with experimental and other theoretical results published in the literature.

Keywords: density functional theory, embedded atom model, Fe-Ni systems, molecular dynamics, nanoalloys

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Authors: Rim Frikha, Nouha Bouayed, Afifa Sellami, Nozha Chakroun, Salima Daoud, Leila Keskes, Tarek Rebai

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Introduction: Recurrent pregnancy loss (RPL) defined as two or more pregnancy losses, is a serious clinical problem. Methylene-tetrahydro-folate-reductase (MTHFR) polymorphisms, commonly the variant C677T is recognized as an inherited thrombophilia which might affect embryonic development and pregnancy success and cause pregnancy complications as RPL. Material and Methods DNA was extracted from peripheral blood samples and PCR-RFLP was performed for the molecular diagnosis of the C677T MTHFR polymorphism among 70 patients (35 couples) with more than 2 fetal losses. Aims and Objective: The aim of this study is to determine the frequency of MTHFR C677T among Tunisian couples with RPL and to critically analyze the available literature on the importance of MTHFR polymorphism testing in the management of RPL. Result and comments: No C677T mutation was detected in the carriers of RPL. This result would be related to sample size and to different criteria (number of abortion), - The association between MTHFR polymorphisms and pregnancy complications has been reported but with controversial results. - A lack of evidence for MTHFR polymorphism testing previously recommended by ACMG (American College of Medical medicine). Our study highlights the importance of screening of MTHFR polymorphism since the real impact of such thrombotic molecular defect on the pregnancy outcome is evident. - Folic supplementation of these patients during pregnancy can prevent such complications and lead to a successful pregnancy outcome.

Keywords: methylenetetrahydrofolate reductase, C677T, recurrent pregnancy loss, genetic testing

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Authors: Peter O. Osifo, Hein W. J. P. Neomagus, Hein V. D. Merwe

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Chitosan materials from different sources of raw materials were characterized in order to determine optimal preparation conditions and parameters for membrane production. The membrane parameters such as molecular weight, viscosity, and degree of deacetylation were used to evaluate the membrane performance for zinc ion adsorption. The molecular weight of the chitosan was found to influence the viscosity of the chitosan/acetic acid solution. An increase in molecular weight (60000-400000 kg.kmol-1) of the chitosan resulted in a higher viscosity (0.05-0.65 Pa.s) of the chitosan/acetic acid solution. The effect of the degree of deacetylation on the viscosity is not significant. The effect of the membrane production parameters (chitosan- and acetic acid concentration) on the viscosity is mainly determined by the chitosan concentration. For higher chitosan concentrations, a membrane with a better adsorption capacity was obtained. The membrane adsorption capacity increases from 20-130 mg Zn per gram of wet membrane for an increase in chitosan concentration from 2-7 mass %. Chitosan concentrations below 2 and above 7.5 mass % produced membranes that lack good mechanical properties. The optimum manufacturing conditions including chitosan concentration, acetic acid concentration, sodium hydroxide concentration and crosslinking for chitosan membranes within the workable range were defined by the criteria of adsorption capacity and flux. The adsorption increases (50-120 mg.g-1) as the acetic acid concentration increases (1-7 mass %). The sodium hydroxide concentration seems not to have a large effect on the adsorption characteristics of the membrane however, a maximum was reached at a concentration of 5 mass %. The adsorption capacity per gram of wet membrane strongly increases with the chitosan concentration in the acetic acid solution but remains constant per gram of dry chitosan. The optimum solution for membrane production consists of 7 mass % chitosan and 4 mass % acetic acid in de-ionised water. The sodium hydroxide concentration for phase inversion is at optimum at 5 mass %. The optimum cross-linking time was determined to be 6 hours (Percentage crosslinking of 18%). As the cross-linking time increases the adsorption of the zinc decreases (150-50 mg.g-1) in the time range of 0 to 12 hours. After a crosslinking time of 12 hours, the adsorption capacity remains constant. This trend is comparable to the effect on flux through the membrane. The flux decreases (10-3 L.m-2.hr-1) with an increase in crosslinking time range of 0 to 12 hours and reaches a constant minimum after 12 hours.

Keywords: chitosan, membrane, waste water, heavy metal ions, adsorption

Procedia PDF Downloads 379

Authors: M. Al Huwayz, A. Salhi, S. Alhassan, S. Alotaibi, A. Almalki, M.Almunyif, A. Alhassni, M. Henini

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Recently, there has been much research carried out to investigate quantum dots (QDs) lasers with the aim to increase the gain of quantum well lasers. However, one of the difficulties with these structures is that electrically active defects can lead to serious issues in the performance of these devices. It is therefore essential to fully understand the types of defects introduced during the growth and/or the fabrication process. In this study, the effects of Gamma radiation on the electrically active defects in p-i-n InAs/InGaAsQDs laser structures grown by Molecular Beam Epitaxy (MBE) technique on GaAs substrates were investigated. Deep Level Transient Spectroscopy (DLTS), current-voltage (I-V), and capacitance-voltage (C-V) measurements were performed to explore these effects on the electrical properties of these QDs lasers. I-V measurements showed that as-grown sample had better electrical properties than the irradiated sample. However, DLTS and Laplace DLTS measurements at different reverse biases revealed that the defects in the-region of the p-i-n structures were decreased in the irradiated sample. In both samples, a trap with an activation energy of ~ 0.21 eV was assigned to the well-known defect M1 in GaAs layers

Keywords: quantum dots laser structures, gamma radiation, DLTS, defects, nAs/IngaAs

Procedia PDF Downloads 182