Search results for: molecular dynamic simulations

Authors: Exa Heydemans, Jessica Sjah, Dwinanti Rika Marthanty

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This paper presents numerical simulations using an open boundary algorithm with modified dynamic boundary condition (mDBC) for weakly compressible smoothed particle hydrodynamics models from particle-based code Dualsphysics. The problems of piping erosion in dams and dikes are aimed for studying the algorithm. The case 2D model of unsteady fluid flow past around a fixed cylinder is simulated, where various values of Reynold’s numbers (Re40, Re60, Re80, and Re100) and different model’s resolution are considered. A constant velocity with different values of viscosity for generating various Reynold’s numbers and different numbers of particles over a cylinder for the resolution are modeled. The interaction between solid particles of the cylinder and fluid particles is concerned. The cylinder is affected by the hydrodynamics force caused by the flow of fluid particles. The solid particles of the cylinder are the observation points to obtain force and pressure due to the hydrodynamics forces. As results of the simulation, which is to show the capability to model 2D unsteady with various Reynold’s numbers, the pressure coefficient, drag coefficient, lift coefficient, and Strouhal number are compared to the previous work from literature.

Keywords: hydrodynamics, internal erosion, dualsphysics, viscous fluid flow

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Authors: L. P. Gomes, G. F. Araújo, Y. M. L. Cordeiro, C. T. Andrade, E. M. Del Aguila, V. M. F. Paschoalin

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The application of nanoscale materials and nanostructures is an emerging area, these since materials may provide solutions to technological and environmental challenges in order to preserve the environment and natural resources. To reach this goal, the increasing demand must be accompanied by 'green' synthesis methods. Chitosan is a natural, nontoxic, biopolymer derived by the deacetylation of chitin and has great potential for a wide range of applications in the biological and biomedical areas, due to its biodegradability, biocompatibility, non-toxicity and versatile chemical and physical properties. Chitosan also presents high antimicrobial activities against a wide variety of pathogenic and spoilage microorganisms. Ultrasonication is a common tool for the preparation and processing of polymer nanoparticles. It is particularly effective in breaking up aggregates and in reducing the size and polydispersity of nanoparticles. High-intensity ultrasonication has the potential to modify chitosan molecular weight and, thus, alter or improve chitosan functional properties. The aim of this study was to evaluate the influence of sonication intensity and time on the changes of commercial chitosan characteristics, such as molecular weight and its potential antibacterial activity against Gram-negative bacteria. The nanoparticles (NPs) were produced from two commercial chitosans, of medium molecular weight (CS-MMW) and low molecular weight (CS-LMW) from Sigma-Aldrich®. These samples (2%) were solubilized in 100 mM sodium acetate pH 4.0, placed on ice and irradiated with an ultrasound SONIC ultrasonic probe (model 750 W), equipped with a 1/2" microtip during 30 min at 4°C. It was used on constant duty cycle and 40% amplitude with 1/1s intervals. The ultrasonic degradation of CS-MMW and CS-LMW were followed up by means of ζ-potential (Brookhaven Instruments, model 90Plus) and dynamic light scattering (DLS) measurements. After sonication, the concentrated samples were diluted 100 times and placed in fluorescence quartz cuvettes (Hellma 111-QS, 10 mm light path). The distributions of the colloidal particles were calculated from the DLS and ζ-potential are measurements taken for the CS-MMW and CS-LMW solutions before and after (CS-MMW30 and CS-LMW30) sonication for 30 min. Regarding the results for the chitosan sample, the major bands can be distinguished centered at Radius hydrodynamic (Rh), showed different distributions for CS-MMW (Rh=690.0 nm, ζ=26.52±2.4), CS-LMW (Rh=607.4 and 2805.4 nm, ζ=24.51±1.29), CS-MMW30 (Rh=201.5 and 1064.1 nm, ζ=24.78±2.4) and CS-LMW30 (Rh=492.5, ζ=26.12±0.85). The minimal inhibitory concentration (MIC) was determined using different chitosan samples concentrations. MIC values were determined against to E. coli (106 cells) harvested from an LB medium (Luria-Bertani BD™) after 18h growth at 37 ºC. Subsequently, the cell suspension was serially diluted in saline solution (0.8% NaCl) and plated on solid LB at 37°C for 18 h. Colony-forming units were counted. The samples showed different MICs against E. coli for CS-LMW (1.5mg), CS-MMW30 (1.5 mg/mL) and CS-LMW30 (1.0 mg/mL). The results demonstrate that the production of nanoparticles by modification of their molecular weight by ultrasonication is simple to be performed and dispense acid solvent addition. Molecular weight modifications are enough to provoke changes in the antimicrobial potential of the nanoparticles produced in this way.

Keywords: antimicrobial agent, chitosan, green production, nanoparticles

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Authors: Sourav Ray, Christoph Stein, Marcus Weber

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A new class of drug candidates, initially derived from mathematical modeling of ligand-receptor interactions, activate the μ-opioid receptor (MOR) preferentially at acidic extracellular pH-levels, as present in injured tissues. This is of commercial interest because it may preclude the adverse effects of conventional MOR agonists like fentanyl, which include but are not limited to addiction, constipation, sedation, and apnea. Animal studies indicate the importance of taking the pH value of the chemical environment of MOR into account when designing new drugs. Hydrogen bonds (HBs) play a crucial role in stabilizing protein secondary structure and molecular interaction, such as ligand-protein interaction. These bonds may depend on the pH value of the chemical environment. For the MOR, antagonist naloxone and agonist [D-Ala2,N-Me-Phe4,Gly5-ol]-enkephalin (DAMGO) form HBs with ionizable residue HIS 297 at physiological pH to modulate signaling. However, such interactions were markedly reduced at acidic pH. Although fentanyl-induced signaling is also diminished at acidic pH, HBs with HIS 297 residue are not observed at either acidic or physiological pH for this strong agonist of the MOR. Molecular dynamics (MD) simulations can provide greater insight into the interaction between the ligand of interest and the HIS 297 residue. Amino acid protonation states are adjusted to the model difference in system acidity. Unbiased and unrestrained MD simulations were performed, with the ligand in the proximity of the HIS 297 residue. Ligand-receptor complexes were embedded in 1-palmitoyl-2-oleoyl-sn glycero-3-phosphatidylcholine (POPC) bilayer to mimic the membrane environment. The occurrence of HBs between the different ligands and the HIS 297 residue of MOR at acidic and physiological pH values were tracked across the various simulation trajectories. No HB formation was observed between fentanyl and HIS 297 residue at either acidic or physiological pH. Naloxone formed some HBs with HIS 297 at pH 5, but no such HBs were noted at pH 7. Interestingly, DAMGO displayed an opposite yet more pronounced HB formation trend compared to naloxone. Whereas a marginal number of HBs could be observed at even pH 5, HBs with HIS 297 were more stable and widely present at pH 7. The HB formation plays no and marginal role in the interaction of fentanyl and naloxone, respectively, with the HIS 297 residue of MOR. However, HBs play a significant role in the DAMGO and HIS 297 interaction. Post DAMGO administration, these HBs might be crucial for the remediation of opioid tolerance and restoration of opioid sensitivity. Although experimental studies concur with our observations regarding the influence of HB formation on the fentanyl and DAMGO interaction with HIS 297, the same could not be conclusively stated for naloxone. Therefore, some other supplementary interactions might be responsible for the modulation of the MOR activity by naloxone binding at pH 7 but not at pH 5. Further elucidation of the mechanism of naloxone action on the MOR could assist in the formulation of cost-effective naloxone-based treatment of opioid overdose or opioid-induced side effects.

Keywords: effect of system acidity, hydrogen bond formation, opioid action, receptor activation

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Authors: Ashok Kumar, Sarita Sahu, H. N. Bar

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Low cycle fatigue behavior of a ferritic, martensitic pressure vessel steel at dynamic strain ageing regime of 250°C to 280°C has been investigated. Dynamic strain ageing is a mechanism that has attracted interests of researchers due to its fascinating inexplicable repetitive nature for quite a long time. The interaction of dynamic strain ageing and cyclic plasticity has been studied from the mechanistic point of view. Dynamic strain ageing gives rise to identical serrated flow behavior in tensile and compressive halves of hysteresis loops and this has been found to gives rise to initial cyclic hardening followed by softening behavior, where as in non-DSA regime continuous cyclic softening has been found to be the dominant mechanism. An appreciable sensitivity towards nature of serrations has been observed due to degree of hardening of stable loop. The increase in degree of hardening with strain amplitude in the regime where only A type serrations are present and it decreases with strain amplitude where A+B type of serrations are present. Masing type of locus has been found in the behavior of metal at 280°C. Cyclic Stress Strain curve and Master curve has been constructed to decipher among the fatigue strength and ductility coefficients. Fractographic examinations have also shown a competition between progression of striations and secondary cracking.

Keywords: dynamic strain ageing, hardening, low cycle fatigue, softening

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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: J. Y. Heo, H. G. Sung

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Numerical simulations have been performed for assessment of compressibility correction of two-equation turbulence models suitable for large scale separation flows perturbed by pintle strokes. In order to take into account pintle movement, a sliding mesh method was applied. The chamber pressure, mass flow rate, and thrust have been analyzed, and the response lag and sensitivity at the chamber and nozzle were estimated for a movable pintle. The nozzle performance for pintle reciprocating as its insertion and extraction processes, were analyzed to better understand the dynamic performance of the pintle nozzle.

Keywords: pintle, sliding mesh, turbulent model, compressibility correction

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Authors: Reza Dezvareh

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The aim of this study is to investigate the amount of wind turbulence on the aero hydrodynamic behavior of offshore wind turbines with a monopile holder platform. Since in the sea, the wind turbine structures are under water and structures interactions, the dynamic analysis has been conducted under combined wind and wave loading. The offshore wind turbines have been investigated undertow models of normal and severe wind turbulence, and the results of this study show that the amplitude of fluctuation of dynamic response of structures including thrust force and base shear force of structures is increased with increasing the amount of wind turbulence, and this increase is not necessarily observed in the mean values of responses. Therefore, conducting the dynamic analysis is inevitable in order to observe the effect of wind turbulence on the structures' response.

Keywords: offshore wind turbine, wind turbulence, structural vibration, aero-hydro dynamic

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Authors: Valentina Bonetti

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Exergy analysis successfully helps optimizing processes in various sectors. In the built environment, a second-law approach can enhance potential interactions between constructions and their surrounding environment and minimise fossil fuel requirements. Despite the research done in this field in the last decades, practical applications are hard to encounter, and few integrated exergy simulators are available for building designers. Undoubtedly, an obstacle for the diffusion of exergy methods is the strong dependency of results on the definition of its 'reference state', a highly controversial issue. Since exergy is the combination of energy and entropy by means of a reference state (also called "reference environment", or "dead state"), the reference choice is crucial. Compared to other classical applications, buildings present two challenging elements: They operate very near to the reference state, which means that small variations have relevant impacts, and their behaviour is dynamical in nature. Not surprisingly then, the reference state definition for the built environment is still debated, especially in the case of dynamic assessments. Among the several characteristics that need to be defined, a crucial decision for a dynamic analysis is between a fixed reference environment (constant in time) and a variable state, which fluctuations follow the local climate. Even if the latter selection is prevailing in research, and recommended by recent and widely-diffused guidelines, the fixed reference has been analytically demonstrated as the only choice which defines exergy as a proper function of the state in a fluctuating environment. This study investigates the impact of that crucial choice: Fixed or variable reference. The basic element of the building energy chain, the envelope, is chosen as the object of investigation as common to any building analysis. Exergy fluctuations in the building envelope of a case study (a typical house located in a Mediterranean climate) are confronted for each time-step of a significant summer day, when the building behaviour is highly dynamical. Exergy efficiencies and fluxes are not familiar numbers, and thus, the more easy-to-imagine concept of exergy storage is used to summarize the results. Trends obtained with a fixed and a variable reference (outside air) are compared, and their meaning is discussed under the light of the underpinning dynamical energy analysis. As a conclusion, a fixed reference state is considered the best choice for dynamic exergy analysis. Even if the fixed reference is generally only contemplated as a simpler selection, and the variable state is often stated as more accurate without explicit justifications, the analytical considerations supporting the adoption of a fixed reference are confirmed by the usefulness and clarity of interpretation of its results. Further discussion is needed to address the conflict between the evidence supporting a fixed reference state and the wide adoption of a fluctuating one. A more robust theoretical framework, including selection criteria of the reference state for dynamical simulations, could push the development of integrated dynamic tools and thus spread exergy analysis for the built environment across the common practice.

Keywords: exergy, reference state, dynamic, building

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Authors: Robson C. Santos, Christian N. Barreto, Gerson G. Cunha, Severino J. C. Neto

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This paper aims to project the construction of a prototype azimuthal thruster, mounted with materials of low cost and easy access, testing in a controlled environment to measure their performance, characteristics and feasibility of future projects. The construction of the simulation of dynamic positioning software, responsible for simulating a vessel and reposition it when necessary . Tests for partial and full validation of the model were conducted, operates independently of the control system and executes the commands and commands of the helix of rotation azimuth. The system provides an interface to the user and simulates the conditions unfavorable positioning of a vessel, accurately calculates the azimuth angle, the direction of rotation of the helix and the time that this should be turned on so that the vessel back to position original. There is a serial communication that connects the Simulation Dynamic Positioning System with Embedded System causing the user-generated data to simulate the DP system arrives in the form of control signals to the motors of the propellant. This article addresses issues in the marine industry employees.

Keywords: azimuthal thruster, dynamic positioning, embedded system, simulator dynamic positioning

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Authors: Muhammet Baldan, Emel Timuçin

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Generally, absorption and bioavailability increase if solubility increases; therefore, it is crucial to predict them in drug discovery applications. Molecular descriptors and Molecular properties are traditionally used for the prediction of water solubility. There are various key descriptors that are used for this purpose, namely Drogan Descriptors, Morgan Descriptors, Maccs keys, etc., and each has different prediction capabilities with differentiating successes between different data sets. Another source for the prediction of solubility is structural features; they are commonly used for the prediction of solubility. However, there are little to no studies that combine three or more properties or descriptors for prediction to produce a more powerful prediction model. Unlike available models, we used a combination of those features in a random forest machine learning model for improved solubility prediction to better predict and, therefore, contribute to drug discovery systems.

Keywords: solubility, random forest, molecular descriptors, maccs keys

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Authors: Rihab Hamdi, Amel Hadri Hamida, Ouafae Bennis, Sakina Zerouali

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This paper features a performance analysis and robustness assessment of a digitally controlled DC-DC three-cell buck converter associated in parallel, operating in continuous conduction mode (CCM), facing feeding parameters variation and loads disturbance. The control strategy relies on the continuous-time with an averaged modeling technique for high-frequency switching converter. The methodology is to modulate the complete design procedure, in regard to the existence of an instantaneous current operating point for designing the digital closed-loop, to the same continuous-time domain. Moreover, the adopted approach is to include a digital voltage control (DVC) technique, taking an account for digital control delays and sampling effects, which aims at improving efficiency and dynamic response and preventing generally undesired phenomena. The results obtained under load change, input change, and reference change clearly demonstrates an excellent dynamic response of the proposed technique, also as provide stability in any operating conditions, the effectiveness is fast with a smooth tracking of the specified output voltage. Simulations studies in MATLAB/Simulink environment are performed to verify the concept.

Keywords: continuous conduction mode, digital control, parallel multi-cells converter, performance analysis, power electronics

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Authors: Alaa Fezai, Anuj Sharma, Wolfgang Mueller-Hirsch, André Zimmermann

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Viscoelastic materials have been widely used in the automotive industry over the last few decades with different functionalities. Besides their main application as a simple and efficient surface damping treatment, they may ensure optimal operating conditions for on-board electronics as thermal interface or sealing layers. The dynamic behavior of viscoelastic materials is generally dependent on many environmental factors, the most important being temperature and strain rate or frequency. Prior to the reliability analysis of systems including viscoelastic layers, it is, therefore, crucial to accurately predict the dynamic and lifetime behavior of these materials. This includes the identification of the dynamic material parameters under critical temperature and frequency conditions along with a precise damage localization and identification methodology. The goal of this work is twofold. The first part aims at applying an inverse viscoelastic material-characterization approach for a wide frequency range and under different temperature conditions. For this sake, dynamic measurements are carried on a single lap joint specimen using an electrodynamic shaker and an environmental chamber. The specimen consists of aluminum beams assembled to adapter plates through a viscoelastic adhesive layer. The experimental setup is reproduced in finite element (FE) simulations, and frequency response functions (FRF) are calculated. The parameters of both the generalized Maxwell model and the fractional derivatives model are identified through an optimization algorithm minimizing the difference between the simulated and the measured FRFs. The second goal of the current work is to guarantee an on-line detection of the damage, i.e., delamination in the viscoelastic bonding of the described specimen during frequency monitored end-of-life testing. For this purpose, an inverse technique, which determines the damage location and size based on the modal frequency shift and on the change of the mode shapes, is presented. This includes a preliminary FE model-based study correlating the delamination location and size to the change in the modal parameters and a subsequent experimental validation achieved through dynamic measurements of specimen with different, pre-generated crack scenarios and comparing it to the virgin specimen. The main advantage of the inverse characterization approach presented in the first part resides in the ability of adequately identifying the material damping and stiffness behavior of soft viscoelastic materials over a wide frequency range and under critical temperature conditions. Classic forward characterization techniques such as dynamic mechanical analysis are usually linked to limitations under critical temperature and frequency conditions due to the material behavior of soft viscoelastic materials. Furthermore, the inverse damage detection described in the second part guarantees an accurate prediction of not only the damage size but also its location using a simple test setup and outlines; therefore, the significance of inverse numerical-experimental approaches in predicting the dynamic behavior of soft bonding layers applied in automotive electronics.

Keywords: damage detection, dynamic characterization, inverse approaches, vibration testing, viscoelastic layers

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Authors: Jia-Shiun Chen, Quoc-Viet Huynh

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This work develops a flexible-body dynamic model of an all-terrain vehicle (ATV), capable of recovering dynamic stresses while the ATV travels on random bumpy roads. The fatigue life of components is forecasted as well. While considering the interaction between dynamic forces and structure deformation, the proposed model achieves a highly accurate structure stress prediction and fatigue life prediction. During the simulation, stress time history of the ATV structure is retrieved for life prediction. Finally, the hot sports of the ATV frame are located, and the frame life for combined road conditions is forecasted, i.e. 25833.6 hr. If the usage of vehicle is eight hours daily, the total vehicle frame life is 8.847 years. Moreover, the reaction force and deformation due to the dynamic motion can be described more accurately by using flexible body dynamics than by using rigid-body dynamics. Based on recommendations made in the product design stage before mass production, the proposed model can significantly lower development and testing costs.

Keywords: flexible-body dynamics, veicle, dynamics, fatigue, durability

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Authors: Manoj Sarda, Abhishek Agarwal, Juhi Kaushik, Vatsal Sanjay, Arup Kumar Das

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Railways in India remain primary mode of transport having one of the largest networks in the world and catering to billions of transits yearly. Catastrophic economic damage and loss to life is encountered over the past few decades due to fire to locomotives. Study of fire dynamics and fire propagation plays an important role in evacuation planning and reducing losses. Simulation based study of propagation of fire and soot inside an air conditioned coach of Indian locomotive is done in this paper. Finite difference based solver, Fire Dynamic Simulator (FDS) version 6 has been used for analysis. A single air conditioned 3 tier coupe closed to ambient surroundings by glass windows having occupancy for 8 people is the basic unit of the domain. A system of three such coupes combined is taken to be fundamental unit for the entire study to resemble effect to an entire coach. Analysis of flame and soot contours and concentrations is done corresponding to variations in heat release rate per unit volume (HRRPUA) of fire source, variations in conditioned air velocity being circulated inside coupes by vents and an alternate fire initiation and propagation mechanism via ducts. Quantitative results of fractional area in top and front view of the three coupes under fire and smoke are obtained using MATLAB (IMT). Present simulations and its findings will be useful for organizations like Commission of Railway Safety and others in designing and implementing safety and evacuation measures.

Keywords: air conditioned coaches, fire propagation, flame contour, soot flow, train fire

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Authors: Ewelina Nowak, Anna Wisla-Swider, Krzysztof Danel

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Aqueous suspensions of DNA were illuminated with linearly polarized visible light and ultraviolet for 5, 15, 20 and 40 h. In order to check the nature of modification, DNA interactions were characterized by FTIR spectroscopy. For each illuminated sample, weight average molecular weight and hydrodynamic radius were measured by high pressure size exclusion chromatography. Resulting optical changes for illuminated DNA were investigated using UV-Vis spectra and photoluminescent. Optical properties show potential application in sensors based on modified DNA. Then selected DNA-surfactant complexes were illuminated with electromagnetic radiation for 5h. Molecular structure, optical characteristic were examinated for obtained complexes. Illumination led to changes of complexes physicochemical properties as compared with native DNA. Observed changes were induced by rearrangement of the molecular structure of DNA chains.

Keywords: biopolymers, deoxyribonucleic acid, ionic liquids, linearly polarized visible light, ultraviolet

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Authors: Kerkouri Abdelkadir

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Numerical calculations of turbulent flows are one of the most prominent modern interests in various engineering applications. Due to the difficulty of predicting, following up and studying this flow for computational fluid dynamic (CFD), in this paper, we simulated numerical study of a flow past in a staggered tube bundle, using CFD Code ANSYS FLUENT with several models of turbulence following: k-ε, k-ω and SST approaches. The flow is modeled based on the experimental studies. The predictions of mean velocities are in very good agreement with detailed LDA (Laser Doppler Anemometry) measurements performed in 8 stations along the depth of the array. The sizes of the recirculation zones behind the cylinders are also predicted. The simulations are conducted for Reynolds numbers of 12858. The Reynolds number is set to depend experimental results.

Keywords: flow, tube bundle, ANSYS Fluent, CFD, turbulence, LDA, RANS (k-ε, k-ω, SST)

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Authors: Deane Roehl, Roberto Quevedo

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Gas migration from pressurized formations is a problem reported in the oil and gas industry. This means increased risks for drilling, production, well integrity, and hydrocarbon escape. Different processes can contribute to the development of pressurized formations, particularly in High-Pressure–High-Temperature (HPHT) gas fields. Over geological time-scales, the different formations of those fields have maintained and/or developed abnormal pressures owing to low permeability and the presence of an impermeable seal. However, if this seal is broken, large volumes of gas could migrate into other less pressurized formations. Three main mechanisms for gas migration have been identified in the literature –molecular diffusion, continuous-phase flow, and continuous-phase flow coupled with mechanical effects. In relation to the latter, gas migration can occur as a consequence of the mechanical effects triggered by reservoir depletion. The compaction of the reservoir can redistribute the in-situ stresses sufficiently to induce deformations that may increase the permeability of rocks and lead to fracture processes or reactivate nearby faults. The understanding of gas flow through discontinuities is still under development. However, some models based on porosity changes and fracture aperture have been developed in order to obtain enhanced permeabilities in numerical simulations. In this work, a simple relationship to integrate fluid flow through rock matrix and discontinuities has been implemented in a fully thermo-hydro-mechanical simulator developed in-house. Numerical simulations of hydrocarbon production in an HPHT field were carried out. Results suggest that rock permeability can be considerably affected by the deformation of the field, creating preferential flow paths for the transport of large volumes of gas.

Keywords: gas migration, pressurized formations, fractured rocks, numerical modeling

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Authors: F. S. Irwansyah, I. Farida, Y. Maulana

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Studying chemistry requires the ability to understand three levels of understanding in the form of macroscopic, submicroscopic and symbolic, but the lack of emphasis on the submicroscopic level leads to the understanding of chemical concepts becoming incomplete, due to the limitations of the tools capable of providing visualization of submicroscopic concepts. The purpose of this study describes the stages of making augmented reality learning media on the concept of molecular geometry and analyze the feasibility test result of augmented reality learning media on the concept of molecular geometry. This research uses Research and Development (R & D) method which produces a product of AR learning media on molecular geometry concept and test the effectiveness of the product. Research stages include concept analysis and learning indicators, design development, validation, feasibility, and limited testing. The stages of validation and limited trial are aimed to get feedback in the form of assessment, suggestion and improvement on learning aspect, material substance aspect, visual communication aspect and software engineering aspects and media feasibility in terms of media creation purpose to be used in learning. The results of the overall feasibility test obtained r-calculation 0,7-0,9 with the interpretation of high feasibility value, whereas the result of limited trial got the percentage of eligibility with the average value equal to 70,83-92,5%. This percentage indicates that AR's learning media product on the concept of molecular geometry, deserves to be used as a learning resource.

Keywords: android, augmented reality, chemical learning, geometry

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Authors: Chinh Phuong Do

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Dynamic analysis of slope under seismic condition requires the elimination of spurious reflection at the bounded domain. This paper studies the performances of wave transmitting boundaries, including the standard viscous boundary and the viscoelastic boundary to the material point method (MPM) framework. First, analytical derivations of these non-reflecting conditions particularly to the implicit MPM are presented. Then, a number of benchmark and geotechnical examples will be shown. Overall, the results agree well with analytical solutions, indicating the ability to accurately simulate the radiation at the bounded domain.

Keywords: dynamic analysis, implicit, MPM, non-reflecting boundary

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Authors: Abdul Majid, Alia Jabeen, Nimra Zulifqar

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The inorganic molecular crystal (IMCs) due to their unusual structure has grabbed a lot of attention due to anisotropy in crystal structure. The IMCs consist of the molecular structures joined together via weak forces. Therefore, a difference between the bonding between the inter-cage and intra-cage interactions exists. To look closely at the bonding and interactions, we investigated interactions between two cages of Sb2O3 structure. The interactions were characterized via Extended Transition State-Natural Orbital for Chemical Valence-method (ETS-NOCV), Natural Bond Orbitals (NBO) and Quantum Theory of Atoms in Molecules (QTAIM). The results revealed strong intra-cage covalent bonding while weak van der Waals (vdWs) interactions along inter-cages exits. This structure cannot be termed as layered material although they have anisotropy in bonding and presence of weak vdWs interactions but its bulk is termed as inorganic layered clusters. This is due to the fact that the free standing sheet/films with these materials are not possible. This type of structures may be the most feasible to be used for the system to deal with high pressures and stress bearing materials.

Keywords: inorganic molecular crystals, density functional theory, cages, interactions

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Authors: Vagolu S. Krishna, Shan Zheng, Estharla M. Rekha, Luke W. Guddat, Dharmarajan Sriram

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Tuberculosis (TB) remains a major threat to human health. This due to the fact that current drug treatments are less than optimal as well as the rising occurrence of multi drug-resistant and extensively drug-resistant strains of the etiological agent, Mycobacterium tuberculosis (Mt). Given the wide-spread significance of this disease, we have undertaken a design and evaluation program to discover new anti-TB drug leads. Here, our attention is focused on ketol-acid reductoisomerase (KARI), the second enzyme in the branched-chain amino acid biosynthesis pathway. Importantly, this enzyme is present in bacteria but not in humans, making it an attractive proposition for drug discovery. In the present work, we used high-throughput virtual screening to identify seventeen potential inhibitors of KARI using the Birla Institute of Technology and Science in-house database. Compounds were selected based on high docking scores, which were assigned as the result of favourable interactions between the compound and the active site of KARI. The Ki values for two leads, compounds 14 and 16 are 3.71 and 3.06 µM, respectively for Mt KARI. To assess the mode of binding, 100 ns molecular dynamics simulations for these two compounds in association with Mt KARI were performed and showed that the complex was stable with an average RMSD of less than 2.5 Å for all atoms. Compound 16 showed an MIC of 2.06 ± 0.91 µM and a 1.9 fold logarithmic reduction in the growth of Mt in an infected macrophage model. The two compounds exhibited low toxicity against murine macrophage RAW 264.7 cell lines. Thus, both compounds are promising candidates for development as an anti-TB drug leads.

Keywords: ketol-acid reductoisomerase, macrophage, molecular docking and dynamics, tuberculosis

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Authors: Shelley Harrington

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As a result of increasingly dynamic business environments, the creation and fostering of dynamic capabilities, [those capabilities that enable sustained competitive success despite of dynamism through the awareness and reconfiguration of internal and external competencies], supported by organisational learning [a dynamic capability] has gained increased and prevalent momentum in the research arena. Presenting findings funded by the Economic Social Research Council, this paper investigates the extent to which Senior Management Team (SMT) personality (at the trait and facet level) is associated with the creation of dynamic managerial capabilities at the team level, and effective organisational learning/knowledge sharing within the firm. In doing so, this research highlights the importance of micro-foundations in organisational psychology and specifically dynamic capabilities, a field which to date has largely ignored the importance of psychology in understanding these important and necessary capabilities. Using a direct measure of personality (NEO PI-3) at the trait and facet level across 32 high technology and finance firms in the UK, their CEOs (N=32) and their complete SMTs [N=212], a new measure of dynamic managerial capabilities at the team level was created and statistically validated for use within the work. A quantitative methodology was employed with regression and gap analysis being used to show the empirical foundations of personality being positioned as a micro-foundation of dynamic capabilities. The results of this study found that personality homogeneity within the SMT was required to strengthen the dynamic managerial capabilities of sensing, seizing and transforming, something which was required to reflect strong organisational learning at middle management level [N=533]. In particular, it was found that the greater the difference [t-score gaps] between the personality profiles of a Chief Executive Officer (CEO) and their complete, collective SMT, the lower the resulting self-reported nature of dynamic managerial capabilities. For example; the larger the difference between a CEOs level of dutifulness, a facet contributing to the definition of conscientiousness, and their SMT’s level of dutifulness, the lower the reported level of transforming, a capability fundamental to strategic change in a dynamic business environment. This in turn directly questions recent trends, particularly in upper echelons research highlighting the need for heterogeneity within teams. In doing so, it successfully positions personality as a micro-foundation of dynamic capabilities, thus contributing to recent discussions from within the strategic management field calling for the need to empirically explore dynamic capabilities at such a level.

Keywords: dynamic managerial capabilities, senior management teams, personality, dynamism

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Authors: Jungkyun Im

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Nonsteroidal anti-inflammatory drugs (NSAIDs) are effective for relieving pain and reducing inflammation. They are nonselective inhibitors of two isoforms of COX, cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2), and thereby inhibiting the production of hormone-like lipid compounds such as, prostaglandins and thromboxanes which cause inflammation, pain, fever, platelet aggregation, etc. In addition, recently there are many research articles reporting the neuroprotective effect of NSAIDs in neurodegenerative diseases, such as Alzheimer’s disease (AD) and Parkinson’s disease (PD). However, the clinical use of NSAIDs in these diseases is limited by low brain distribution. Therefore, in order to assist the in-depth investigation on the pharmaceutical mechanism of flurbiprofen in neuroprotection and to make flurbiprofen a more potent drug to prevent or alleviate neurodegenerative diseases, delivery of flurbiprofen to brain should be effective and sufficient amount of flurbiprofen must penetrate the BBB thus gaining access into the patient’s brain. We have recently developed several types of guanidine-rich molecular carriers with high molecular weights and good water solubility that readily cross the blood-brain barrier (BBB) and display efficient distributions in the mouse brain. The G8 (having eight guanidine groups) molecular carrier based on D-sorbitol was found to be very effective in delivering anticancer drugs to a mouse brain. In the present study, employing the same molecular carrier, we prepared the flurbiprofen conjugate and studied its BBB permeation by mouse tissue distribution study. Flurbiprofen was attached to a molecular carrier with a fluorescein probe and multiple terminal guanidiniums. The conjugate was found to internalize into live cells and readily cross the BBB to enter the mouse brain. Our novel synthetic flurbiprofen conjugate will hopefully delivery NSAIDs into brain, and is therefore applicable to the neurodegenerative diseases treatment or prevention.

Keywords: flurbiprofen, drug delivery, molecular carrier, organic synthesis

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Authors: Tsu-Hsu Yen

Abstract:

The interfacial gas adsorption presents a frequent challenge and opportunity for micro-/nano-fluidic operation. In this study, we investigate the wettability, gas accumulation, and nanobubble formation on various homogeneous surface conditions by using MD simulation, including a series of 3D and quasi-2D argon-water-solid systems simulation. To precisely determine the wettability on various substrates, several indicators were calculated. Among these wettability indicators, the water PMF (potential of mean force) has the most correlation tendency with interfacial water molecular orientation than depletion layer width and droplet contact angle. The results reveal that the aggregation of argon molecules on substrates not only depending on the level of hydrophobicity but also determined by the competition between gas-solid and water-solid interaction as well as water molecular structure near the surface. In addition, the surface nanobubble is always observed coexisted with the gas enrichment layer. The water structure adjacent to water-gas and water-solid interfaces also plays an important factor in gas out-flux and gas aggregation, respectively. The quasi-2D simulation shows that only a slight difference in the curved argon-water interface from the plane interface which suggests no noticeable obstructing effect on gas outflux from the gas-water interfacial water networks.

Keywords: gas aggregation, interfacial nanobubble, molecular dynamics simulation, wettability

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Authors: Ibrahim Gomaa, Hoda M. O. Mokhtar

Abstract:

Although most of the existing skyline queries algorithms focused basically on querying static points through static databases; with the expanding number of sensors, wireless communications and mobile applications, the demand for continuous skyline queries has increased. Unlike traditional skyline queries which only consider static attributes, continuous skyline queries include dynamic attributes, as well as the static ones. However, as skyline queries computation is based on checking the domination of skyline points over all dimensions, considering both the static and dynamic attributes without separation is required. In this paper, we present an efficient algorithm for computing continuous skyline queries without discriminating between static and dynamic attributes. Our algorithm in brief proceeds as follows: First, it excludes the points which will not be in the initial skyline result; this pruning phase reduces the required number of comparisons. Second, the association between the spatial positions of data points is examined; this phase gives an idea of where changes in the result might occur and consequently enables us to efficiently update the skyline result (continuous update) rather than computing the skyline from scratch. Finally, experimental evaluation is provided which demonstrates the accuracy, performance and efficiency of our algorithm over other existing approaches.

Keywords: continuous query processing, dynamic database, moving object, skyline queries

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Authors: Irlana C. do Mar, Thayna A. Ferreira, Dayane S. Rezende, Bruno A. M. Figueira, José M. R. Mercury

Abstract:

This work presents a low-cost Mn starting material to synthesis manganese oxide octahedral molecular sieve with Mg²⁺ in the tunnel (Mg-OMS-1), based on the Mn residues from Carajás Mineral Province (Amazon, Brazil). After hydrothermal and cation exchange procedures, the Mn residues transformed to a single phase, Mg-OMS-1. The raw material and the synthesis processes were analyzed by means of X-ray diffraction (XRD), Scanning electron microscopy (SEM) and Infrared spectroscopy (FTIR). The tunnel structure was synthesized hydrothermally at 180 °C for three days without impurities. According to the XRD analysis, the formation of crystalline Mg-OMS-1 was identified through reflections at 9.8º, 12º and 18º (2θ), as well as a thermal stability around 300 ºC. The SEM analysis indicated that the final product presents good crystallinity with a homogeneous size. In addition, an intense and diagnostic FTIR band was identified at 515 cm⁻¹ related to the MnO₆ octahedral stretching vibrations.

Keywords: Mn residues , Octahedral Molecular Sieve, Synthesis, Characterization

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Authors: Odón R. Sánchez-Ccoyllo, Elizabeth Ayma-Choque, Alan Llacza

Abstract:

Sulphur dioxide (SO₂) and surface-ozone (O₃) concentrations are associated with diseases. The objective of this research is to evaluate the effectiveness of the air-quality-WRF-Chem model with a horizontal resolution of 5 km x 5 km. For this purpose, the measurements of the hourly SO₂ and O₃ concentrations available in three air quality monitoring stations in Lima, Peru were used for the purpose of validating the simulations of the SO₂ and O₃ concentrations obtained with the WRF-Chem model in February 2018. For the quantitative evaluation of the simulations of these gases, statistical techniques were implemented, such as the average of the simulations; the average of the measurements; the Mean Bias (MeB); the Mean Error (MeE); and the Root Mean Square Error (RMSE). The results of these statistical metrics indicated that the simulated SO₂ and O₃ values over-predicted the SO₂ and O₃ measurements. For the SO₂ concentration, the MeB values varied from 0.58 to 26.35 µg/m³; the MeE values varied from 8.75 to 26.5 µg/m³; the RMSE values varied from 13.3 to 31.79 µg/m³; while for O₃ concentrations the statistical values of the MeB varied from 37.52 to 56.29 µg/m³; the MeE values varied from 37.54 to 56.70 µg/m³; the RMSE values varied from 43.05 to 69.56 µg/m³.

Keywords: ground-ozone, lima, sulphur dioxide, WRF-chem

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Authors: Monika Kallubai, Shreya Dubey, Rajagopal Subramanyam

Abstract:

Our study is all about the biological interactions of synthesized 5β-dihydrocortisol (Dhc) and 5β-dihydrocortisol acetate (DhcA) molecules with carrier protein Human Serum Albumin (HSA). The cytotoxic study was performed on breast cancer cell line (MCF-7) normal human embryonic kidney cell line (HEK293), the IC50 values for MCF-7 cells were 28 and 25 µM, respectively, whereas no toxicity in terms of cell viability was observed with HEK293 cell line. The further experiment proved that Dhc and DhcA induced 35.6% and 37.7% early apoptotic cells and 2.5%, 2.9% late apoptotic cells respectively. Morphological observation of cell death through TUNEL assay revealed that Dhc and DhcA induced apoptosis in MCF-7 cells. The complexes of HSA–Dhc and HSA–DhcA were observed as static quenching, and the binding constants (K) was 4.7±0.03×104 M-1 and 3.9±0.05×104 M-1, and their binding free energies were found to be -6.4 and -6.16 kcal/mol, respectively. The displacement studies confirmed that lidocaine 1.4±0.05×104 M-1 replaced Dhc, and phenylbutazone 1.5±0.05×104 M-1 replaced by DhcA, which explains domain I and domain II are the binding sites for Dhc and DhcA. Further, CD results revealed that the secondary structure of HSA was altered in the presence of Dhc and DhcA. Furthermore, the atomic force microscopy and transmission electron microscopy showed that the dimensions like height and molecular sizes of the HSA–Dhc and HSA–DhcA complex were larger compared to HSA alone. Detailed analysis through molecular dynamics simulations also supported the greater stability of HSA–Dhc and HSA–DhcA complexes, and root-mean-square-fluctuation interpreted the binding site of Dhc as domain IB and domain IIA for DhcA. This information is valuable for the further development of steroid derivatives with improved pharmacological significance as novel anti-cancer drugs.

Keywords: apoptosis, dihydrocortisol, fluorescence quenching, protein conformations

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Authors: Mirvat Shamseddine, Issam Lakkis

Abstract:

We present an efficient, three-dimensional parallel multi-scale Direct Simulation Monte Carlo (DSMC) algorithm for the simulation of unsteady rarefied gas flows in micro/nanosystems. The algorithm employs a novel spatiotemporal adaptivity scheme. The scheme performs a fully dynamic multi-level grid adaption based on the gradients of flow macro-parameters and an automatic temporal adaptation. The computational domain consists of a hierarchical octree-based Cartesian grid representation of the flow domain and a triangular mesh for the solid object surfaces. The hybrid mesh, combined with the spatiotemporal adaptivity scheme, allows for increased flexibility and efficient data management, rendering the framework suitable for efficient particle-tracing and dynamic grid refinement and coarsening. The parallel algorithm is optimized to run DSMC simulations of strongly unsteady, non-equilibrium flows over multiple cores. The presented method is validated by comparing with benchmark studies and then employed to improve the design of micro-scale hotwire thermal sensors in rarefied gas flows.

Keywords: DSMC, oct-tree hierarchical grid, ray tracing, spatial-temporal adaptivity scheme, unsteady rarefied gas flows

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Authors: Riccardo Zanni, Maria Galvez-Llompart, Ramon Garcia-Domenech, Jorge Galvez

Abstract:

Biopesticides, such as naturally occurring chemicals, pheromones, fungi, bacteria and insect predators are often a winning choice in crop protection because of their environmental friendly profile. They are considered to have lower toxicity than traditional pesticides. After almost a century of pesticides use, resistances to traditional insecticides are wide spread, while those to bioinsecticides have raised less attention, and resistance management is frequently neglected. This seems to be a crucial mistake since resistances have already occurred for many marketed biopesticides. With an eye to the future, we present here a selection of new natural occurring chemicals as potential bioinsecticides. The molecules were selected using a consolidated mathematical paradigm called molecular topology. Several QSAR equations were depicted and subsequently applied for the virtual screening of hundred thousands molecules of natural origin, which resulted in the selection of new potential bioinsecticides. The most innovative aspect of this work does not only reside in the importance of the identification of new molecules overcoming biopesticides’ resistances, but on the possibility to promote shared knowledge in the field of green chemistry through this unique in silico discipline named molecular topology.

Keywords: green chemistry, QSAR, molecular topology, biopesticide

Procedia PDF Downloads 309