Search results for: first-principle molecular dynamics simulation of multiscale shock technique

Authors: Juan Antonio Mondragon Sanchez, Ruben Santamaria

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The DNA G-quadruplex is a four-stranded DNA structure formed by stacked planes of four base paired guanines (G-quartet). Guanine rich DNA sequences appear in many sites of genomic DNA and can potential form G-quadruplexes, such as those occurring at 3'-terminus of the human telomeric DNA. The formation and stabilization of a G-quadruplex by small ligands at the telomeric region can inhibit the telomerase activity. In turn, the ligands can be used to down regulate oncogene expression making G-quadruplex an attractive target for anticancer therapy. Many G-quadruplex ligands have been proposed with a planar core to facilitate the pi–pi stacking and electrostatic interactions with the G-quartets. However, many drug candidates are impossibilitated to discriminate a G-quadruplex from a double helix DNA structure. In this context, it is important to investigate the site topology for the interaction of a G-quadruplex with a ligand. In this work, we determine the free energy surface of a G-quadruplex-ligand to study the binding modes of the G-quadruplex (TG4T) with the daunomycin (DM) drug. The complex TG4T-DM is studied using classical molecular dynamics in combination with metadynamics simulations. The metadynamics simulations permit an enhanced sampling of the conformational space with a modest computational cost and obtain free energy surfaces in terms of the collective variables (CV). The free energy surfaces of TG4T-DM exhibit other local minima, indicating the presence of additional binding modes of daunomycin that are not observed in short MD simulations without the metadynamics approach. The results are compared with similar calculations on a different structure (the mutated mu-G4T-DM where the 5' thymines on TG4T-DM have been deleted). The results should be of help to design new G-quadruplex drugs, and understand the differences in the recognition topology sites of the duplex and quadruplex DNA structures in their interaction with ligands.

Keywords: g-quadruplex, cancer, molecular dynamics, metadynamics

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Authors: Virany Diana, Martono Tri Utomo, Risa Etika

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Background: Shock is one severe condition that can be a major cause of morbidity and mortality in the Neonatal Intensive Care Unit. Preterm infants are very susceptible to shock caused by many complications such as asphyxia, patent ductus arteriosus, intra ventricle haemorrhage, necrotizing enterocolitis, persistent pulmonal hypertension of the newborn, and septicaemia. Limited hemodynamic monitoring for early detection of shock causes delayed intervention and comprises the outcomes. Clinical parameters still used in neonatal shock detection, such as Capillary Refill Time, heart rate, cold extremity, and urine production. Blood pressure is most frequently used to evaluate preterm's circulation, but hypotension indicates uncompensated shock. Near-infrared spectroscopy (NIRS) is known as a noninvasive tool for monitoring and detecting the state of inadequate tissue perfusion. Muscle oxygen saturation shows decreased cardiac output earlier than systemic parameters of tissue oxygenation when cerebral regional oxygen saturation is still stabilized by autoregulation. However, to our best knowledge, until now, no study has analyzed the decrease of muscle oxygen regional saturation (mRSO₂) and the ratio of muscle and cerebral oxygen regional saturation (mRSO₂/cRSO₂) by NIRS in preterm with shock. Purpose: The purpose of this study is to analyze the decrease of mRSO₂ and ratio of muscle to cerebral oxygen regional saturation (mRSO₂/cRSO₂) by NIRS in preterm with shock. Patients and Methods: This cross-sectional study was conducted on preterm infants with 28-34 weeks gestational age, admitted to the NICU of Dr. Soetomo Hospital from November to January 2022. Patients were classified into two groups: shock and non-shock. The diagnosis of shock is based on clinical criteria (tachycardia, prolonged CRT, cold extremity, decreased urine production, and MAP Blood Pressure less than GA in weeks). Measurement of mRSO₂ and cRSO₂ by NIRS was performed by the doctor in charge when the patient came to NICU. Results: We enrolled 40 preterm infants. The initial conventional hemodynamic parameter as the basic diagnosis of shock showed significant differences in all variables. Preterm with shock had higher mean HR (186.45±1.5), lower MAP (29.8±2.1), and lower SBP (45.1±4.28) than non-shock children, and most had a prolonged CRT. The patients’ outcome was not a significant difference between shock and non-shock patients. The mean mRSO₂ in the shock and non-shock groups were 33,65 ± 11,32 vs. 69,15 ± 3,96 (p=0.001), and the mean ratio mRSO₂/cRSO₂ 0,45 ± 0,12 vs. 0,84 ± 0,43 (p=0,001), were significantly different. The mean cRSO₂ in the shock and non-shock groups were 71,60 ± 4,90 vs. 81,85 ± 7,85 (p 0.082), not significantly different. Conclusion: The decrease of mRSO₂ and ratio of mRSO₂/cRSO₂ can differentiate between shock and non-shock in the preterm infant when cRSO₂ is still normal.

Keywords: preterm infant, regional muscle oxygen saturation, regional cerebral oxygen saturation, NIRS, shock

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Authors: Agnieszka S. Dzielendziak, Lindsay-Marie Armstrong, Matthew E. Potter, Robert Raja, Pier J. A. Sazio

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Reducing carbon dioxide, CO₂, is one of the greatest global challenges. Conversion of CO₂ for utilisation across synthetic fuel, pharmaceutical, and agrochemical industries offers a promising option, yet requires significant research to understanding the complex multiscale processes involved. To experimentally understand and optimize such processes at that catalytic sites and exploring the impact of the process at reactor scale, is too expensive. Computational methods offer significant insight and flexibility but require a more detailed multi-scale approach which is a significant challenge in itself. This work introduces a computational approach which incorporates detailed catalytic models, taken from experimental investigations, into a larger-scale computational flow dynamics framework. The reactor-scale species transport approach is modified near the catalytic walls to determine the influence of catalytic clustering regions. This coupling approach enables more accurate modelling of velocity, pressures, temperatures, species concentrations and near-wall surface characteristics which will ultimately enable the impact of overall reactor design on chemical conversion performance.

Keywords: catalysis, CCU, CO₂, multi-scale model

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Authors: H. Masaeli, R. Ziaei, F. Khoshnoudian

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Shock response analysis of the soil–structure systems induced by near–fault pulses is investigated. Vibration transmissibility of the soil–structure systems is evaluated by Shock Response Spectra (SRS). Medium–to–high rise buildings with different aspect ratios located on different soil types as well as different foundations with respect to vertical load bearing safety factors are studied. Two types of mathematical near–fault pulses, i.e. forward directivity and fling step, with different pulse periods as well as pulse amplitudes are selected as incident ground shock. Linear versus nonlinear Soil–Structure Interaction (SSI) condition are considered alternatively and the corresponding results are compared. The results show that nonlinear SSI is likely to amplify the acceleration responses when subjected to long–period incident pulses with normalized period exceeding a threshold. It is also shown that this threshold correlates with soil type, so that increased shear–wave velocity of the underlying soil makes the threshold period decrease.

Keywords: nonlinear soil–structure interaction, shock response spectrum, near–fault ground shock, rocking isolation

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Authors: Ferdinando Montemari, Antonio Vitale, Nicola Genito, Giovanni Cuciniello

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The introduction of tilt-rotor aircraft into the existing civilian air transportation system will provide beneficial effects due to tilt-rotor capability to combine the characteristics of a helicopter and a fixed-wing aircraft into one vehicle. The disposability of reliable tilt-rotor simulation models supports the development of such vehicle. Indeed, simulation models are required to design automatic control systems that increase safety, reduce pilot's workload and stress, and ensure the optimal aircraft configuration with respect to flight envelope limits, especially during the most critical flight phases such as conversion from helicopter to aircraft mode and vice versa. This article presents a process to build a simplified tilt-rotor simulation model, derived from the analysis of flight data. The model aims to reproduce the complex dynamics of tilt-rotor during the in-flight conversion phase. It uses a set of scheduled linear transfer functions to relate the autopilot reference inputs to the most relevant rigid body state variables. The model also computes information about the rotor flapping dynamics, which are useful to evaluate the aircraft control margin in terms of rotor collective and cyclic commands. The rotor flapping model is derived through a mixed theoretical-empirical approach, which includes physical analytical equations (applicable to helicopter configuration) and parametric corrective functions. The latter are introduced to best fit the actual rotor behavior and balance the differences existing between helicopter and tilt-rotor during flight. Time-domain system identification from flight data is exploited to optimize the model structure and to estimate the model parameters. The presented model-building process was applied to simulated flight data of the ERICA Tilt-Rotor, generated by using a high fidelity simulation model implemented in FlightLab environment. The validation of the obtained model was very satisfying, confirming the validity of the proposed approach.

Keywords: flapping dynamics, flight dynamics, system identification, tilt-rotor modeling and simulation

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Authors: A. Rezaei, M. Huisman, W. Van Paepegem

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Atomic interactions in molecular systems are mainly studied by particle mechanics. Nevertheless, researches have also put on considerable effort to simulate them using continuum methods. In early 2000, simple equivalent finite element models have been developed to study the mechanical properties of carbon nanotubes and graphene in composite materials. Afterward, many researchers have employed similar structural simulation approaches to obtain mechanical properties of nanostructured materials, to simplify interface behavior of fiber-reinforced composites, and to simulate defects in carbon nanotubes or graphene sheets, etc. These structural approaches, however, are limited to small deformations due to complicated local rotational coordinates. This article proposes a method for the finite element simulation of molecular mechanics. For ease in addressing the approach, here it is called Structural Finite Element Molecular Modeling (SFEMM). SFEMM method improves the available structural approaches for large deformations, without using any rotational degrees of freedom. Moreover, the method simulates molecular conformation, which is a big advantage over the previous approaches. Technically, this method uses nonlinear multipoint constraints to simulate kinematics of the atomic multibody interactions. Only truss elements are employed, and the bond potentials are implemented through constitutive material models. Because the equilibrium bond- length, bond angles, and bond-torsion potential energies are intrinsic material parameters, the model is independent of initial strains or stresses. In this paper, the SFEMM method has been implemented in ABAQUS finite element software. The constraints and material behaviors are modeled through two Fortran subroutines. The method is verified for the bond-stretch, bond-angle and bond-torsion of carbon atoms. Furthermore, the capability of the method in the conformation simulation of molecular structures is demonstrated via a case study of a graphene sheet. Briefly, SFEMM builds up a framework that offers more flexible features over the conventional molecular finite element models, serving the structural relaxation modeling and large deformations without incorporating local rotational degrees of freedom. Potentially, the method is a big step towards comprehensive molecular modeling with finite element technique, and thereby concurrently coupling an atomistic domain to a solid continuum domain within a single finite element platform.

Keywords: finite element, large deformation, molecular mechanics, structural method

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Authors: Sakiru Badmos, David R. Cole, Alberto Striolo

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It is known that confinement in nm-size pores affects many structural and transport properties of water and co-existing volatile species. Of particular interest for fluids in sub-surface systems, in catalysis, and in separations are reports that confinement can enhance the solubility of gases in water. Equilibrium molecular dynamics simulations were performed for aqueous H₂S confined in slit-shaped silica pores at 313K. The effect of pore width on the H₂S solubility in water was investigated. Other properties of interest include the molecular distribution of the various fluid molecules within the pores, the hydration structure for solvated H₂S molecules, and the dynamical properties of the confined fluids. The simulation results demonstrate that confinement reduces the H₂S solubility in water and that the solubility increases with pore size. Analysis of spatial distribution functions suggests that these results are due to perturbations on the coordination of water molecules around H₂S due to confinement. Confinement is found to dampen the dynamical properties of aqueous H₂S as well. Comparing the results obtained for aqueous H₂S to those reported elsewhere for aqueous CH₄, it can be concluded that H₂S permeates hydrated slit-shaped silica nano-pores faster than CH₄. In addition to contributing to better understanding the behavior of fluids in subsurface formations, these observations could also have important implications for developing new natural gas sweetening technologies.

Keywords: confinement, interfacial properties, molecular dynamic simulation, sub-surface formations

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Authors: Xiaoxin Ye, Guoyi Tang

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The effect of electropulsing ultrasonic shock (EUS) on the surface hardening and microstructure of Ti6Al4V alloy was studied. It was found that electropulsing improved the microhardness dramatically both in the influential depth and maximum value, compared with the only ultrasonic-shocked sample. It’s indicated that refined surface layer with nanocrystalline and improved microhardness were obtained on account of surface severe plastic deformation, dynamic recrystallization (DRX) and phase change, which was implemented at relative low temperature and high strain rate/capacity due to the coupling of the thermal and athermal effects of EUS. It’s different from conventional experiments and theory. It’s discussed that the positive contributions of EPT in the thermodynamics and kinetics of microstructure and properties change were attributed to the reduction of nucleation energy barrier and acceleration of atomic diffusion. Therefore, it’s supposed that EUS is an energy-saving and high-efficiency method of surface treatment technique with the help of high-energy electropulses, which is promising in cost reduction of the surface engineering and energy management.

Keywords: titanium alloys, electropulsing, ultrasonic shock, microhardness, nanocrystalline

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Authors: Johns Paul, Santhosh J. Nalluveettil, P. Purushothaman, M. Premdas

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Lunar landing is one of the most critical phases of lunar mission. The lander is provided with a soft landing system to prevent structural damage of lunar module by absorbing the landing shock and also assure stability during landing. Presently available software are not capable to simulate the rigid body dynamics coupled with contact simulation and elastic/plastic deformation analysis. Hence a separate mathematical model has been generated for studying the dynamics of a typical lunar soft lander. Parameters used in the analysis includes lunar surface slope, coefficient of friction, initial touchdown velocity (vertical and horizontal), mass and moment of inertia of lander, crushing force due to energy absorbing material in the legs, number of legs and geometry of lander. The mathematical model is capable to simulate plastic and elastic deformation of honey comb, frictional force between landing leg and lunar soil, surface contact simulation, lunar gravitational force, rigid body dynamics and linkage dynamics of inverted tripod landing gear. The non linear differential equations generated for studying the dynamics of lunar lander is solved by numerical method. Matlab programme has been used as a computer tool for solving the numerical equations. The position of each kinematic joint is defined by mathematical equations for the generation of equation of motion. All hinged locations are defined by position vectors with respect to body fixed coordinate. The vehicle rigid body rotations and motions about body coordinate are only due to the external forces and moments arise from footpad reaction force due to impact, footpad frictional force and weight of vehicle. All these force are mathematically simulated for the generation of equation of motion. The validation of mathematical model is done by two different phases. First phase is the validation of plastic deformation of crushable elements by employing conservation of energy principle. The second phase is the validation of rigid body dynamics of model by simulating a lander model in ADAMS software after replacing the crushable elements to elastic spring element. Simulation of plastic deformation along with rigid body dynamics and contact force cannot be modeled in ADAMS. Hence plastic element of primary strut is replaced with a spring element and analysis is carried out in ADAMS software. The same analysis is also carried out using the mathematical model where the simulation of honeycomb crushing is replaced by elastic spring deformation and compared the results with ADAMS analysis. The rotational motion of linkages and 6 degree of freedom motion of lunar Lander about its CG can be validated by ADAMS software by replacing crushing element to spring element. The model is also validated by the drop test results of 4 leg lunar lander. This paper presents the details of mathematical model generated and its validation.

Keywords: honeycomb, landing leg tripod, lunar lander, primary link, secondary link

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Authors: Samy Madbouly

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The relaxation behavior of biorenewable castor oil-based polyurethane-lignin thin films synthesized in homogenous waterborne dispersions was investigated as a function of concentration at different temperatures and frequencies using broadband dielectric relaxation spectroscopy (BDRS). The molecular dynamics of the glass relaxation process and the local relaxation process of the PU-LS thin films were studied over a wide range of temperatures (-70 to 30 ℃) and frequencies (5 × 10−2 to 0.5 × 107 Hz) for different lignin concentration. Four relaxation processes have been observed namely; ?-, β-, γ-relaxations and ionic conductivity for pure castor oil-based PU and castor oil-lignin-based PU thin films at different temperatures and frequencies ranges. The Vogel-Fulcher-Tammann equation was found to be well described the temperature dependence of the characteristic relaxation times of the ?-relaxation process. However, on the other hand, the molecular dynamics of both β- and γ-relaxation processes were given by the Arrhenius equation. The incorporation of lignin into the castor oil-based PU significantly increased the glass transition temperature and primitivity of the thin films. In addition, the broadness, intensity, and molecular dynamics of the only observed ?-relaxation process were found to be strongly dependent on lignin concentration.

Keywords: castor oil, lignin, polyurethane, dielectric, dispersions

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Authors: K. S. Agrawal

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The performance of jet ejector was studied in detail by different authors. Several authors have studied mass transfer characteristics like interfacial area, mass transfer coefficients etc. In this paper, we have made an attempt to develop PDE model by considering bubble properties and apply Lattice-Boltzmann technique for PDE model. We may present the results for the interfacial area which we have obtained from our numerical simulation. Later the results are compared with previous work.

Keywords: jet ejector, mass transfer characteristics, numerical simulation, Lattice-Boltzmann technique

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Authors: Fadi Al Khatib, Raouf Mbarki, Malek Adouni

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In various sport and recreational activities, the patellofemoral joint undergoes large forces and moments while accommodating the significant knee joint movement. In doing so, this joint is commonly the source of anterior knee pain related to instability in normal patellar tracking and excessive pressure syndrome. One well-observed explanation of the instability of the normal patellar tracking is the patellofemoral ligaments and patellar tendon damage. Improved knowledge of the damage mechanism mediating ligaments and tendon injuries can be a great help not only in rehabilitation and prevention procedures but also in the design of better reconstruction systems in the management of knee joint disorders. This damage mechanism, specifically due to excessive mechanical loading, has been linked to the micro level of the fibred structure precisely to the tropocollagen molecules and their connection density. We argue defining a clear frame starting from the bottom (micro level) to up (macro level) in the hierarchies of the soft tissue may elucidate the essential underpinning on the state of the ligaments damage. To do so, in this study a multiscale fibril reinforced hyper elastoplastic Finite Element model that accounts for the synergy between molecular and continuum syntheses was developed to determine the short-term stresses/strains patellofemoral ligaments and tendon response. The plasticity of the proposed model is associated only with the uniaxial deformation of the collagen fibril. The yield strength of the fibril is a function of the cross-link density between tropocollagen molecules, defined here by a density function. This function obtained through a Coarse-graining procedure linking nanoscale collagen features and the tissue level materials properties using molecular dynamics simulations. The hierarchies of the soft tissues were implemented using the rule of mixtures. Thereafter, the model was calibrated using a statistical calibration procedure. The model then implemented into a real structure of patellofemoral ligaments and patellar tendon (OpenKnee) and simulated under realistic loading conditions. With the calibrated material parameters the calculated axial stress lies well with the experimental measurement with a coefficient of determination (R2) equal to 0.91 and 0.92 for the patellofemoral ligaments and the patellar tendon respectively. The ‘best’ prediction of the yielding strength and strain as compared with the reported experimental data yielded when the cross-link density between the tropocollagen molecule of the fibril equal to 5.5 ± 0.5 (patellofemoral ligaments) and 12 (patellar tendon). Damage initiation of the patellofemoral ligaments was located at the femoral insertions while the damage of the patellar tendon happened in the middle of the structure. These predicted finding showed a meaningful correlation between the cross-link density of the tropocollagen molecules and the stiffness of the connective tissues of the extensor mechanism. Also, damage initiation and propagation were documented with this model, which were in satisfactory agreement with earlier observation. To the best of our knowledge, this is the first attempt to model ligaments from the bottom up, predicted depending to the tropocollagen cross-link density. This approach appears more meaningful towards a realistic simulation of a damaging process or repair attempt compared with certain published studies.

Keywords: tropocollagen, multiscale model, fibrils, knee ligaments

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Authors: Payam Haghparast, Mikhail V. Sorin, Hakim Nesreddine

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The complex oblique shock phenomenon can be simply assumed as a normal shock at the constant area section to simulate a sharp pressure increase and velocity decrease in 1-D thermodynamic models. The assumed normal shock location is one of the greatest sources of error in ejector thermodynamic models. Most researchers consider an arbitrary location without justifying it. Our study compares the effect of normal shock place on ejector dimensions in 1-D models. To this aim, two different ejector experimental test benches, a constant area-mixing ejector (CAM) and a constant pressure-mixing (CPM) are considered, with different known geometries, operating conditions and working fluids (R245fa, R141b). In the first step, in order to evaluate the real value of the efficiencies in the different ejector parts and critical back pressure, a CFD model was built and validated by experimental data for two types of ejectors. These reference data are then used as input to the 1D model to calculate the lengths and the diameters of the ejectors. Afterwards, the design output geometry calculated by the 1D model is compared directly with the corresponding experimental geometry. It was found that there is a good agreement between the ejector dimensions obtained by the 1D model, for both CAM and CPM, with experimental ejector data. Furthermore, it is shown that normal shock place affects only the constant area length as it is proven that the inlet normal shock assumption results in more accurate length. Taking into account previous 1D models, the results suggest the use of the assumed normal shock location at the inlet of the constant area duct to design the supersonic ejectors.

Keywords: 1D model, constant area-mixing, constant pressure-mixing, normal shock location, ejector dimensions

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Authors: Hiroyuki Aoki

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The physical properties of polymer materials are dependent on the conformation and molecular motion of a polymer chain. Therefore, the structure and dynamic behavior of the single polymer chain have been the most important concerns in the field of polymer physics. However, it has been impossible to directly observe the conformation of the single polymer chain in a bulk medium. In the current work, the novel techniques to study the conformation and dynamics of a single polymer chain are proposed. Since a fluorescence method is extremely sensitive, the fluorescence microscopy enables the direct detection of a single molecule. However, the structure of the polymer chain as large as 100 nm cannot be resolved by conventional fluorescence methods because of the diffraction limit of light. In order to observe the single chains, we developed the labeling method of polymer materials with a photo-switchable dye and the super-resolution microscopy. The real-space conformational analysis of single polymer chains with the spatial resolution of 15-20 nm was achieved. The super-resolution microscopy enables us to obtain the three-dimensional coordinates; therefore, we succeeded the conformational analysis in three dimensions. The direct observation by the nanometric optical microscopy would reveal the detailed information on the molecular processes in the various polymer systems.

Keywords: polymer materials, single molecule, super-resolution techniques, conformation

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Authors: M. S. Jouini, A. Al-Sumaiti, M. Tembely, K. Rahimov

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Characterizing rock properties of carbonate reservoirs is highly challenging because of rock heterogeneities revealed at several length scales. In the last two decades, the Digital Rock Physics (DRP) approach was implemented successfully in sandstone rocks reservoirs in order to understand rock properties behaviour at the pore scale. This approach uses 3D X-ray Microtomography images to characterize pore network and also simulate rock properties from these images. Even though, DRP is able to predict realistic rock properties results in sandstone reservoirs it is still suffering from a lack of clear workflow in carbonate rocks. The main challenge is the integration of properties simulated at different scales in order to obtain the effective rock property of core plugs. In this paper, we propose several approaches to characterize absolute permeability in some carbonate core plugs samples using multi-scale numerical simulation workflow. In this study, we propose a procedure to simulate porosity and absolute permeability of a carbonate rock sample using textures of Micro-Computed Tomography images. First, we discretize X-Ray Micro-CT image into a regular grid. Then, we use a textural parametric model to classify each cell of the grid using supervised classification. The main parameters are first and second order statistics such as mean, variance, range and autocorrelations computed from sub-bands obtained after wavelet decomposition. Furthermore, we fill permeability property in each cell using two strategies based on numerical simulation values obtained locally on subsets. Finally, we simulate numerically the effective permeability using Darcy’s law simulator. Results obtained for studied carbonate sample shows good agreement with the experimental property.

Keywords: multiscale modeling, permeability, texture, micro-tomography images

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Authors: Zhao Wang, Hong Yan

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In this paper, a unified-gas kinetic scheme (UGKS) for the gas-particle flow is constructed. UGKS is a direct modeling method for both continuum and rarefied flow computations. The dynamics of particle and gas are described as rarefied and continuum flow, respectively. Therefore, we use the Bhatnagar-Gross-Krook (BGK) equation for the particle distribution function. For the gas phase, the gas kinetic scheme for Navier-Stokes equation is solved. The momentum transfer between gas and particle is achieved by the acceleration term added to the BGK equation. The new scheme is tested by a 2cm-in-thickness dense bed comprised of glass particles with 1.5mm in diameter, and reasonable agreement is achieved.

Keywords: gas-particle flow, unified gas-kinetic scheme, momentum transfer, shock-induced fluidization

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Authors: Alok Khaware, Vinay Kumar Gupta, Jean Noel Pederzani

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Lifeboat launching from marine vessel or offshore platform is one of the important areas of research in offshore applications. With the advancement of computational fluid dynamic simulation (CFD) technology to solve fluid induced motions coupled with Six Degree of Freedom (6DOF), rigid body dynamics solver, it is now possible to predict the motion of the lifeboat precisely in different challenging conditions. Traditionally dynamic remeshing approach is used to solve this kind of problems, but remeshing approach has some bottlenecks to control good quality mesh in transient moving mesh cases. In the present study, an overset method with higher-order interpolation is used to simulate a lifeboat launched from an offshore platform into calm water, and volume of fluid (VOF) method is used to track free surface. Overset mesh consists of a set of overlapping component meshes, which allows complex geometries to be meshed with lesser effort. Good quality mesh with local refinement is generated at the beginning of the simulation and stay unchanged throughout the simulation. Overset mesh accuracy depends on the precise interpolation technique; the present study includes a robust and accurate least square interpolation method and results obtained with overset mesh shows good agreement with experiment.

Keywords: computational fluid dynamics, free surface flow, lifeboat launching, overset mesh, volume of fluid

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Authors: A. Kalaei, A. H. W. Ngan

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In this study, a mesoscopic continuum dislocation dynamics (CDD) approach is applied to simulate the intergranular slip transfer. The CDD scheme applies an efficient kinematics equation to model the evolution of the “all-dislocation density,” which is the line-length of dislocations of each character per unit volume. As the consideration of every dislocation line can be a limiter for the simulation of slip transfer in large scales with a large quantity of participating dislocations, a coarse-grained, extensive description of dislocations in terms of their density is utilized to resolve the effect of collective motion of dislocation lines. For dynamics closure, namely, to obtain the dislocation velocity from a velocity law involving the effective glide stress, mutual elastic interaction of dislocations is calculated using Mura’s equation after singularity removal at the core of dislocation lines. The developed scheme for slip transfer can therefore resolve the effects of the elastic interaction and pile-up of dislocations, which are important physics omitted in coarser models like crystal plasticity finite element methods (CPFEMs). Also, the length and timescales of the simulationareconsiderably larger than those in molecular dynamics (MD) and discrete dislocation dynamics (DDD) models. The present work successfully simulates that, as dislocation density piles up in front of a grain boundary, the elastic stress on the other side increases, leading to dislocation nucleation and stress relaxation when the local glide stress exceeds the operation stress of dislocation sources seeded on the other side of the grain boundary. More importantly, the simulation verifiesa phenomenological misorientation factor often used by experimentalists, namely, the ease of slip transfer increases with the product of the cosines of misorientation angles of slip-plane normals and slip directions on either side of the grain boundary. Furthermore, to investigate the effects of the critical stress-intensity factor of the grain boundary, dislocation density sources are seeded at different distances from the grain boundary, and the critical applied stress to make slip transfer happen is studied.

Keywords: grain boundary, dislocation dynamics, slip transfer, elastic stress

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Authors: Sumit Kumar, Sunil Kumar, Chandan Deep Singh

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This paper presents modeling and simulation of flexible robot in an underwater environment. The underwater environment completely contrasts with ground or space environment. The robot in an underwater situation is subjected to various dynamic forces like buoyancy forces, hydrostatic and hydrodynamic forces. The underwater robot is modeled as Rayleigh beam. The developed model further allows estimating the deflection of tip in two directions. The complete dynamics of the underwater robot is analyzed, which is the main focus of this investigation. The control of robot trajectory is not discussed in this paper. Simulation is performed using Symbol Shakti software.

Keywords: bond graph modeling, dynamics. modeling, rayleigh beam, underwater robot

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Authors: L. S. Godlevsky, N. V. Kresyun, V. P. Martsenyuk, K. S. Shakun, T. V. Tatarchuk, K. O. Prybolovets, L. F. Kalinichenko, M. Karpinski, T. Gancarczyk

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Structures of eye bottom were extracted using multiscale texture gradient method and color characteristics of macular zone and vessels were verified in CIELAB scale. The difference of average values of L*, a* and b* coordinates of CIE (International Commision of Illumination) scale in patients with diabetes and healthy volunteers was compared. The average value of L* in diabetic patients exceeded such one in the group of practically healthy persons by 2.71 times (P < 0.05), while the value of a* index was reduced by 3.8 times when compared with control one (P < 0.05). b* index exceeded such one in the control group by 12.4 times (P < 0.05). The integrated index on color difference (ΔE) exceeded control value by 2.87 times (P < 0.05). More pronounced differences with ΔE were followed by a shorter period of MA appearance with a correlation level at -0.56 (P < 0.05). The specificity of diagnostics raised by 2.17 times (P < 0.05) and negative prognostic index exceeded such one determined with the expert method by 2.26 times (P < 0.05).

Keywords: diabetic retinopathy, multiscale texture gradient, color spectrum analysis, medical diagnostics

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Authors: Ritesh K. Shukla

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Degradation of biological samples in terms of macromolecules (DNA, RNA, and protein) are the major challenges in the forensic investigation which misleads the result interpretation. Currently, there are no precise methods available to circumvent this problem. Therefore, at the preliminary level, some methods are urgently needed to solve this issue. In this order, Comet assay is one of the most versatile, rapid and sensitive molecular biology technique to assess the DNA degradation. This technique helps to assess DNA degradation even at very low amount of sample. Moreover, the expedient part of this method does not require any additional process of DNA extraction and isolation during DNA degradation assessment. Samples directly embedded on agarose pre-coated microscopic slide and electrophoresis perform on the same slide after lysis step. After electrophoresis microscopic slide stained by DNA binding dye and observed under fluorescent microscope equipped with Komet software. With the help of this technique extent of DNA degradation can be assessed which can help to screen the sample before DNA fingerprinting, whether it is appropriate for DNA analysis or not. This technique not only helps to assess degradation of DNA but many other challenges in forensic investigation such as time since deposition estimation of biological fluids, repair of genetic material from degraded biological sample and early time since death estimation could also be resolved. With the help of this study, an attempt was made to explore the application of well-known molecular biology technique that is Comet assay in the field of forensic science. This assay will open avenue in the field of forensic research and development.

Keywords: comet assay, DNA degradation, forensic, molecular biology

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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: Wayde Veldman, Ozlem T. Bishop, Igor Polikarpov

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In bacteria, mono and disaccharides are phosphorylated during uptake into the cell via the widely used phosphoenolpyruvate (PEP)-dependent phosphotransferase transport system. As an initial step in the phosphorylated disaccharide metabolism pathway, certain glycoside hydrolase family 1 (GH1) enzymes play a crucial role in releasing phosphorylated and non-phosphorylated monosaccharides. However, structural determinants for the specificity of these enzymes still need to be clarified. GH1 enzymes are known to have a wide array of functions. According to the CAZy database, there are twenty-one different enzymatic activities in the GH1 family. Here, the structure and substrate specificity of a GH1 enzyme from Bacillus licheniformis, hereafter known as BlBglH, was investigated. The sequence of the enzyme BlBglH was compared to the sequences of other characterized GH1 enzymes using sequence alignment, sequence identity calculations, phylogenetic analysis, and motif discovery. Through these various analyses, BlBglH was found to have sequence features characteristic of the 6-phospho-β-glucosidase activity enzymes. Additionally, motif and structure comparisons of the three most commonly studied GH1 enzyme-activities revealed a shared loop amongst the different structures that consist of different sequence motifs – this loop is thought to guide specific substrates (depending on activity) towards the active-site. To further affirm BlBglH enzyme activity, molecular docking and molecular dynamics simulations were performed. Docking was carried out using 6-phospho-β-glucosidase enzyme-activity positive (p-Nitrophenyl-beta-D-glucoside-6-phosphate) and negative (p-Nitrophenyl-beta-D-galactoside-6-phosphate) control ligands, followed by 400 ns molecular dynamics simulations. The positive-control ligand maintained favourable interactions within the active site until the end of the simulation. The negative-control ligand was observed exiting the enzyme at 287 ns. Binding free energy calculations showed that the positive-control complex had a substantially more favourable binding energy compared to the negative-control complex. Jointly, the findings of this study suggest that the BlBglH enzyme possesses 6-phospho-β-glucosidase enzymatic activity.

Keywords: 6-P-β-glucosidase, glycoside hydrolase 1, molecular dynamics, sequence analysis, substrate specificity

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Authors: Igor Velickovski, Aleksandar Stojkov, Ivana Rajkovic

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This paper investigates drivers of shock synchronization using quarterly data for 27 European countries over the period 1999-2013 and taking into account the difference between core (‘the euro area core locomotive’) and peripheral euro area and transition countries (‘the peripheral wagons’). Results from panel error-correction models suggest that core of the euro area has not been strong magnetizer of the shock convergence of periphery and transition countries since the euro inception as a result of the offsetting effects of the various factors that affected the shock convergence process. These findings challenge the endogeneity hypothesis in the optimum currency area framework and rather support the specialisation paradigm which is concerning evidence for the future stability of the euro area.

Keywords: dynamic panel models, shock synchronisation, trade, optimum currency area

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Authors: Mohammad Reza Ghaani, Niall English

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Hydrogen is looked upon as the next-generation clean-energy carrier; the search for an efficient material and method for storing hydrogen has been, and is, pursued relentlessly. Clathrate hydrates are inclusion compounds wherein guest gas molecules like hydrogen are trapped in a host water-lattice framework. These types of materials can be categorised as potentially attractive hosting environments for physical hydrogen storage (i.e., no chemical reaction upon storage). Non-equilibrium molecular dynamics (NEMD) simulations have been performed to investigate thermal-driven break-up of propane-hydrate interfaces with liquid water at 270-300 K, with the propane hydrate containing either one or no hydrogen molecule in each of its small cavities. In addition, two types of hydrate-surface water-lattice molecular termination were adopted, at the hydrate edge with water: a 001-direct surface cleavage and one with completed cages. The geometric hydrate-ice-liquid distinction criteria of Báez and Clancy were employed to distinguish between the hydrate, ice lattices, and liquid-phase. Consequently, the melting temperatures of interface were estimated, and dissociation rates were observed to be strongly dependent on temperature, with higher dissociation rates at larger over-temperatures vis-à-vis melting. The different hydrate-edge terminations for the hydrate-water interface led to statistically-significant differences in the observed melting point and dissociation profile: it was found that the clathrate with the planar interface melts at around 280 K, whilst the melting temperature of the cage-completed interface was determined to be circa 270 K.

Keywords: hydrogen storage, clathrate hydrate, molecular dynamics, thermal dissociation

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Authors: Shrikant Ghadage

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Study of shock waves generated in the Scramjet engine is typically restricted to pressure, temperature, density, entropy and Mach number variation across the shock wave. The present work discusses the impact of inlet shock wave angles on the specific impulse of the Scramjet engine. A mathematical analysis has done for the isentropic hypersonic flow of air flowing through a Scramjet with hydrogen fuel at an altitude of 30 km. Analysis has been done in order to get optimum shock wave angle to achieve maximum impulse. Since external drag has excluded from the analysis, the losses due to friction are not considered for the present analysis. When Mach number of the airflow at the entry of the nozzle reaches unity, then that flow is choked. This condition puts limitations on increasing the inlet shock wave angle. As inlet shock wave angle increases, speed of the flow entering into the nozzle decreases, which results in an increase in the specific impulse of the engine. When the speed of the flow at the entry of the nozzle reduces below sonic speed, then there is no further increase in the specific impulse of the engine. Here the Conclusion is the thrust and specific impulse of a scramjet engine, which increases gradually with an increase in inlet shock wave angle up to the condition when airflow speed reaches sonic velocity at the exit of the combustor. In addition to that, variation in drag force at the inlet of the scramjet and variation in hypersonic flow conditions at every stage of the scramjet also studied in order to understand variation on flow characteristics with respect to flow deflection angle. Essentially, it helps in designing inlet profile for the Scramjet engine to achieve optimum specific impulse.

Keywords: hypersonic flow, scramjet, shock waves, specific impulse, mathematical analysis

Procedia PDF Downloads 135

Authors: Doki Naomi Onyeje, Doki Gowon Ama

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The past 4 years have been traumatic for Nigerians, having to deal with a number of complex economic issues with dire consequences for the economy. Households have had to respond variously to some of these problems in peculiar ways, depending, of course, on the nature and character of a particular shock. The type, magnitude, intensity and duration of a particular shock might be the determinant of different household responses. While households’ responses to the Global Financial Crisis and Covid 19 Pandemic have been documented by researchers, other economic shocks have continued to emerge in Nigeria. The dramatic turn of events since coming on board of the new government on May 29th 2023, has introduced a new economic twist that households will have to adjust to. This study, therefore, sets out to examine household responses by disaggregating them by their livelihood sources. A survey of 420 households across North Central Nigeria will be done to generate information on the respective responses. A Multinomial logit regression analysis will be employed to test the hypothesis that livelihood source(s) influences household responses to economic shocks. Consequently, responses from public and private households will be examined. The expected results should be that household responses might have some similarities, but it is expected that some peculiar responses across groups will emerge and these differences will guide for group-specific interventions. The Theatre for Development (TfD) approach will be used to disseminate and propagate results from this study to and among stakeholders for effective policy frameworks.

Keywords: drama, dynamics, economic shocks, household responses, Nigeria

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Authors: Bao Liu, Maarten Vanierschot, Frank Buysschaert

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The present work examines the wake dynamics of a rim-driven thruster (RDT) with Computational Fluid Dynamics (CFD). Unsteady Reynolds-averaged Navier-Stokes (URANS) equations were solved in the commercial solver ANSYS Fluent in combination with the SST k-ω turbulence model. The application of the moving reference frame (MRF) and sliding mesh (SM) approach to handling the rotational movement of the propeller were compared in the transient simulations. Validation and verification of the numerical model was performed to ensure numerical accuracy. Two representative scenarios were considered, i.e., the bollard condition (J=0) and a very light loading condition(J=0.7), respectively. From the results, it’s confirmed that compared to the SM method, the MRF method is not suitable for resolving the unsteady flow features as it only gives the general mean flow but smooths out lots of characteristic details in the flow field. By evaluating the simulation results with the SM technique, the instantaneous wake flow field under both conditions is presented and analyzed, most notably the helical vortex structure. It’s observed from the results that the tip vortices, blade shed vortices, and hub vortices are present in the wake flow field and convect downstream in a highly non-linear way. The shear layer vortices shedding from the duct displayed a strong interaction with the distorted tip vortices in an irregularmanner.

Keywords: computational fluid dynamics, rim-driven thruster, sliding mesh, wake dynamics

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Authors: Ambrish Singh

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The corrosion inhibition performance of pyran (AP) and benzimidazole (BI) derivatives on J55 steel in 3.5% NaCl solution saturated with CO₂ was investigated by electrochemical, weight loss, surface characterization, and theoretical studies. The electrochemical studies included electrochemical impedance spectroscopy (EIS), potentiodynamic polarization (PDP), electrochemical frequency modulation (EFM), and electrochemical frequency modulation trend (EFMT). Surface characterization was done using contact angle, scanning electron microscopy (SEM), and atomic force microscopy (AFM) techniques. DFT and molecular dynamics (MD) studies were done using Gaussian and Materials Studio softwares. All the studies suggested the good inhibition by the synthesized inhibitors on J55 steel in 3.5% NaCl solution saturated with CO₂ due to the formation of a protective film on the surface. Molecular dynamic simulation was applied to search for the most stable configuration and adsorption energies for the interaction of the inhibitors with Fe (110) surface.

Keywords: corrosion, inhibitor, EFM, AFM, DFT, MD

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Authors: Prosper Kudzanai Mushauri

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Shock therapy has been used in persons living with depression and deeply depressed persons. It has been used in children also. Shock therapy has been also among its pros believed to improve the quality of life and an effective treatment of depression. The review of the literature on ECT papers have highlighted that benefits to users of ECT are elusive, and iatrogenic harm often occurs showing that the approach will always fall far in comporting to psychological ethics. On the contrary, ECT is known as shock therapy which is the administration of electric shock within the brain; it has been challenged on ethical grounds if it’s proper ethically. From this ethical aperture, it has emerged that relapse rates are approximately higher than 50%, it results in diencephalon disturbances and has also side effects related to cognitive function among other negative effects. It is from these reviewed studies that that ECT should not be viewed as an effective treatment of depression as it does not comport to the mores of psychological ethics.

Keywords: anterograde amnesia, depression, electroconvulsive therapy, ethics, retrograde amnesia

Procedia PDF Downloads 167