Search results for: molecular dynamic simulations

Authors: Ali Kadir, O. Anwar Beg

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Thermal barrier coatings are among the most popular methods for providing corrosion protection in high temperature applications including aircraft engine systems, external spacecraft structures, rocket chambers etc. Many different materials are available for such coatings, of which ceramics generally perform the best. Motivated by these applications, the current investigation presents detailed finite element simulations of coating stress analysis for a 3- dimensional, 3-layered model of a test sample representing a typical gas turbine component scenario. Structural steel is selected for the main inner layer, Titanium (Ti) alloy for the middle layer and Silicon Carbide (SiC) for the outermost layer. The model dimensions are 20 mm (width), 10 mm (height) and three 1mm deep layers. ANSYS software is employed to conduct three types of analysis- static structural, thermal stress analysis and also computational fluid dynamic erosion/corrosion analysis (via ANSYS FLUENT). The specified geometry which corresponds to corrosion test samples exactly is discretized using a body-sizing meshing approach, comprising mainly of tetrahedron cells. Refinements were concentrated at the connection points between the layers to shift the focus towards the static effects dissipated between them. A detailed grid independence study is conducted to confirm the accuracy of the selected mesh densities. To recreate gas turbine scenarios; in the stress analysis simulations, static loading and thermal environment conditions of up to 1000 N and 1000 degrees Kelvin are imposed. The default solver was used to set the controls for the simulation with the fixed support being set as one side of the model while subjecting the opposite side to a tabular force of 500 and 1000 Newtons. Equivalent elastic strain, total deformation, equivalent stress and strain energy were computed for all cases. Each analysis was duplicated twice to remove one of the layers each time, to allow testing of the static and thermal effects with each of the coatings. ANSYS FLUENT simulation was conducted to study the effect of corrosion on the model under similar thermal conditions. The momentum and energy equations were solved and the viscous heating option was applied to represent improved thermal physics of heat transfer between the layers of the structures. A Discrete Phase Model (DPM) in ANSYS FLUENT was employed which allows for the injection of continuous uniform air particles onto the model, thereby enabling an option for calculating the corrosion factor caused by hot air injection (particles prescribed 5 m/s velocity and 1273.15 K). Extensive visualization of results is provided. The simulations reveal interesting features associated with coating response to realistic gas turbine loading conditions including significantly different stress concentrations with different coatings.

Keywords: thermal coating, corrosion, ANSYS FEA, CFD

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Authors: Sergio Alejandro Cuevas, Catherine Etchebest, Fernando Luis Barroso Da Silva

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The flavivirus genus has several organisms responsible for generating various diseases in humans. Special in Brazil, Zika (ZIKV), Dengue (DENV) and Yellow Fever (YFV) viruses have raised great health concerns due to the high number of cases affecting the area during the last years. Diagnostic is still a difficult issue since the clinical symptoms are highly similar. The understanding of their common structural/dynamical and biomolecular interactions features and differences might suggest alternative strategies towards differential serological diagnostics and therapeutic intervention. Due to their immunogenicity, the primary focus of this study was on the ZIKV, DENV and YFV non-structural proteins 1 (NS1) protein. By means of computational studies, we calculated the main physical chemical properties of this protein from different strains that are directly responsible for the biomolecular interactions and, therefore, can be related to the differential infectivity of the strains. We also mapped the electrostatic differences at both the sequence and structural levels for the strains from Uganda to Brazil that could suggest possible molecular mechanisms for the increase of the virulence of ZIKV. It is interesting to note that despite the small changes in the protein sequence due to the high sequence identity among the studied strains, the electrostatic properties are strongly impacted by the pH which also impact on their biomolecular interactions with partners and, consequently, the molecular viral biology. African and Asian strains are distinguishable. Exploring the interfaces used by NS1 to self-associate in different oligomeric states, and to interact with membranes and the antibody, we could map the strategy used by the ZIKV during its evolutionary process. This indicates possible molecular mechanisms that can explain the different immunological response. By the comparison with the known antibody structure available for the West Nile virus, we demonstrated that the antibody would have difficulties to neutralize the NS1 from the Brazilian strain. The present study also opens up perspectives to computationally design high specificity antibodies.

Keywords: zika, biomolecular interactions, electrostatic interactions, molecular mechanisms

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Authors: Shrawan Baghel, Helen Cathcart, Biall J. O'Reilly

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Amorphous drug formulations have great potential to enhance solubility and thus bioavailability of BCS class II drugs. However, the higher free energy and molecular mobility of the amorphous form lowers the activation energy barrier for crystallization and thermodynamically drives it towards the crystalline state which makes them unstable. Accurate determination of the crystallization tendency/kinetics is the key to the successful design and development of such systems. In this study, dipyridamole (DPM) and cinnarizine (CNZ) has been selected as model compounds. Thermodynamic fragility (m_T) is measured from the heat capacity change at the glass transition temperature (Tg) whereas dynamic fragility (m_D) is evaluated using methods based on extrapolation of configurational entropy to zero 〖(m〗_(D_CE )), and heating rate dependence of Tg 〖(m〗_(D_Tg)). The mean relaxation time of amorphous drugs was calculated from Vogel-Tammann-Fulcher (VTF) equation. Furthermore, the correlation between fragility and glass forming ability (GFA) of model drugs has been established and the relevance of these parameters to crystallization of amorphous drugs is also assessed. Moreover, the crystallization kinetics of model drugs under isothermal conditions has been studied using Johnson-Mehl-Avrami (JMA) approach to determine the Avrami constant ‘n’ which provides an insight into the mechanism of crystallization. To further probe into the crystallization mechanism, the non-isothermal crystallization kinetics of model systems was also analysed by statistically fitting the crystallization data to 15 different kinetic models and the relevance of model-free kinetic approach has been established. In addition, the crystallization mechanism for DPM and CNZ at each extent of transformation has been predicted. The calculated fragility, glass forming ability (GFA) and crystallization kinetics is found to be in good correlation with the stability prediction of amorphous solid dispersions. Thus, this research work involves a multidisciplinary approach to establish fragility, GFA and crystallization kinetics as stability predictors for amorphous drug formulations.

Keywords: amorphous, fragility, glass forming ability, molecular mobility, mean relaxation time, crystallization kinetics, stability

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Authors: Changgil Lee, Seunghee Park

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Although vehicle driving test for the development of BWIM system is necessary, but it needs much cost and time in addition application of various driving condition. Thus, we need the numerical-simulation method resolving the cost and time problems of vehicle driving test and the way of measuring response of bridge according to the various driving condition. Using the precision analysis model reflecting the dynamic characteristic is contributed to increase accuracy in numerical simulation. In this paper, we conduct a numerical simulation to apply precision analysis model, which reflects the dynamic characteristic of bridge using Bridge Weigh-in-Motion technique and suggest overload vehicle enforcement technology using precision analysis model.

Keywords: bridge weigh-in-motion(BWIM) system, precision analysis model, dynamic characteristic of bridge, numerical simulation

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Authors: Surbhi Rani, Sunita Gakkhar

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The four-dimensional food web system consisting of two prey species for a generalist middle predator and a top predator is proposed and investigated. The middle predator is predating both the prey species with a modified Holling type-II functional response. The food web model is found to be well-posed, bounded, and dissipative. The proposed model's essential dynamical features are studied in terms of local stability. The four species' survival is explored, and persistence conditions are established. The numerical simulations reveal the persistence in the form of a chaotic attractor or stable focus. The conclusion is that providing additional food to the middle predator may help to control the food chain's chaos.

Keywords: predator-prey model, existence of equilibrium points, local stability, chaos, numerical simulations

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Authors: Maik Kschischo, Dominik Kahl, Philipp Wendland, Andreas Weber

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Understanding and modelling of real-world complex dynamic systems in biology, engineering and other fields is often made difficult by incomplete knowledge about the interactions between systems states and by unknown disturbances to the system. In fact, most real-world dynamic networks are open systems receiving unknown inputs from their environment. To understand a system and to estimate the state dynamics, these inputs need to be reconstructed from output measurements. Reconstructing the input of a dynamic system from its measured outputs is an ill-posed problem if only a limited number of states is directly measurable. A first requirement for solving this problem is the invertibility of the input-output map. In our work, we exploit the fact that invertibility of a dynamic system is a structural property, which depends only on the network topology. Therefore, it is possible to check for invertibility using a structural invertibility algorithm which counts the number of node disjoint paths linking inputs and outputs. The algorithm is efficient enough, even for large networks up to a million nodes. To understand structural features influencing the invertibility of a complex dynamic network, we analyze synthetic and real networks using the structural invertibility algorithm. We find that invertibility largely depends on the degree distribution and that dense random networks are easier to invert than sparse inhomogeneous networks. We show that real networks are often very difficult to invert unless the sensor nodes are carefully chosen. To overcome this problem, we present a sensor node placement algorithm to achieve invertibility with a minimum set of measured states. This greedy algorithm is very fast and also guaranteed to find an optimal sensor node-set if it exists. Our results provide a practical approach to experimental design for open, dynamic systems. Since invertibility is a necessary condition for unknown input observers and data assimilation filters to work, it can be used as a preprocessing step to check, whether these input reconstruction algorithms can be successful. If not, we can suggest additional measurements providing sufficient information for input reconstruction. Invertibility is also important for systems design and model building. Dynamic models are always incomplete, and synthetic systems act in an environment, where they receive inputs or even attack signals from their exterior. Being able to monitor these inputs is an important design requirement, which can be achieved by our algorithms for invertibility analysis and sensor node placement.

Keywords: data-driven dynamic systems, inversion of dynamic systems, observability, experimental design, sensor node placement

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Authors: Radoslav Stojchevski, Leonid Poretsky, Dimiter Avtanski

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Proinflammatory cytokines play an important role in cancer initiation and progression by mediating the intracellular communication between the cancer cells and tumor microenvironment. Increased tumor growth causing reduced oxygen concentration and oxygen pressure commonly result in hypoxia. Mechanistically, hypoxia is characterized by stabilization and nuclear translocation of hypoxia-inducible factor 1 alpha (HIF-1α) followed by propagation of molecular pathway cascade involving multiple downstream targets. Cobalt(II) chloride (CoCl₂) is commonly used to mimic hypoxia in experimental conditions since it directly induces the expression of HIF-1α. The aim of the present study was to investigate the in vitro effects and the molecular mechanisms by which hypoxia regulates the cytokine secretory profile of breast cancer cells. As a model for this study, we used several breast cancer cell lines bearing various molecular characteristics and metastatic potential (MDA-MB-231 (clauding low, ER-/PR-/HER²⁻), MCF-7 (luminal A, ER⁺/PR⁺/HER²⁻), and BT-474 (liminal B, ER⁺/PR⁺/HER²⁺)). We demonstrated that breast cancer cells secrete numerous cytokines and cytokine ligands, including interleukins, chemokines, and growth factors. Treatment with CoCl₂significantly modulated the breast cancer cells' cytokine expression in a concentration- and time-dependent manner. These effects were mediated via activation of several signaling pathways (JNK/SAPK1, NF-κB, STAT5A/B, and Erk/MAPK1/2). Taken together, the present data define some of the molecular mechanisms by which hypoxia affects the breast cancer cells' cytokine secretory profile, thus contributing to the development of novel therapies for metastatic breast cancer.

Keywords: breast cancer, cytokines, cobalt(II) chloride (CoCl₂), hypoxia

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Authors: Ž. Nikolić, H. Smoljanović, N. Živaljić

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This paper presents numerical model based on finite-discrete element method for analysis of the structural response of dry stone masonry structures under static and dynamic loads. More precisely, each discrete stone block is discretized by finite elements. Material non-linearity including fracture and fragmentation of discrete elements as well as cyclic behavior during dynamic load are considered through contact elements which are implemented within a finite element mesh. The application of the model was conducted on several examples of these structures. The performed analysis shows high accuracy of the numerical results in comparison with the experimental ones and demonstrates the potential of the finite-discrete element method for modelling of the response of dry stone masonry structures.

Keywords: dry stone masonry structures, dynamic load, finite-discrete element method, static load

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Authors: Hamed Sanei, Mohammad Bagher Ayani

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Optimizations of Plate Heat Exchangers (PHS) have received great attention in the past decade. In this study, heat transfer and pressure drop coefficients are compared for rectangular and circular PHS employing numerical simulations. Plates are designed to have equivalent areas. Simulations were implemented to investigate the efficiency of PHSs considering heat transfer, friction factor and pressure drop. Amount of heat transfer and pressure drop was obtained for different range of Reynolds numbers. These two parameters were compared with aim of F "weighting factor correlation". In this comparison, the minimum amount of F indicates higher efficiency. Results reveal that the F value for rectangular shape is less than circular plate, and hence using rectangular shape of PHS is more efficient than circular one. It was observed that, the amount of friction factor is correlated to the Reynolds numbers, such that friction factor decreased in both rectangular and circular plates with an increase in Reynolds number. Furthermore, such simulations revealed that the amount of heat transfer in rectangular plate is more than circular plate for different range of Reynolds numbers. The difference is more distinct for higher Reynolds number. However, amount of pressure drop in circular plate is less than rectangular plate for the same range of Reynolds numbers which is considered as a negative point for rectangular plate efficiency. It can be concluded that, while rectangular PHSs occupy more space than circular plate, the efficiency of rectangular plate is higher.

Keywords: Chevron corrugated plate heat exchanger, heat transfer, friction factor, Reynolds numbers

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Authors: A. W. J. Wong, I. H. Ibrahim

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Increasing urbanisation has driven building designers to incorporate natural ventilation in the designs of sustainable buildings. This project utilises Computational Fluid Dynamics (CFD) to investigate the natural ventilation of an academic building, SIT@SP, using an assessment criterion based on daily mean temperature and mean velocity. The areas of interest are the pedestrian level of first and fourth levels of the building. A reference case recommended by the Architectural Institute of Japan was used to validate the simulation model. The validated simulation model was then used for coupled simulations on SIT@SP and neighbouring geometries, under two wind speeds. Both steady and transient simulations were used to identify differences in results. Steady and transient results are agreeable with the transient simulation identifying peak velocities during flow development. Under a lower wind speed, the first level was sufficiently ventilated while the fourth level was not. The first level has excessive wind velocities in the higher wind speed and the fourth level was adequately ventilated. Fourth level flow velocity was consistently lower than those of the first level. This is attributed to either simulation model error or poor building design. SIT@SP is concluded to have a sufficiently ventilated first level and insufficiently ventilated fourth level. Future works for this project extend to modifying the urban geometry, simulation model improvements, evaluation using other assessment metrics and extending the area of interest to the entire building.

Keywords: buildings, CFD Simulations, natural ventilation, urban airflow

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Authors: V. Radulescu, S. Dumitru

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Introduction: Determination of the temperature field inside a fluid in motion has many practical issues, especially in the case of turbulent flow. The phenomenon is greater when the solid walls have a different temperature than the fluid. The turbulent heat and mass transfer have an essential role in case of the thermal pollution, as it was the recorded during the damage of the Thermoelectric Power-plant Oradea (closed even today). Basic Methods: Solving the theoretical turbulent thermal pollution represents a particularly difficult problem. By using the semi-empirical theories or by simplifying the made assumptions, based on the experimental measurements may be assured the elaboration of the mathematical model for further numerical simulations. The three zones of flow are analyzed separately: the vicinity of the solid wall, the turbulent transition zone, and the turbulent core. For each area are determined the distribution law of temperature. It is determined the dependence of between the Stanton and Prandtl numbers with correction factors, based on measurements experimental. Major Findings/Results: The limitation of the laminar thermal substrate was determined based on the theory of Landau and Levice, using the assumption that the longitudinal component of the velocity pulsation and the pulsation’s frequency varies proportionally with the distance to the wall. For the calculation of the average temperature, the formula is used a similar solution as for the velocity, by an analogous mediation. On these assumptions, the numerical modeling was performed with a gradient of temperature for the turbulent flow in pipes (intact or damaged, with cracks) having 4 different diameters, between 200-500 mm, as there were in the Thermoelectric Power-plant Oradea. Conclusions: It was made a superposition between the molecular viscosity and the turbulent one, followed by addition between the molecular and the turbulent transfer coefficients, necessary to elaborate the theoretical and the numerical modeling. The concept of laminar boundary layer has a different thickness when it is compared the flow with heat transfer and that one without a temperature gradient. The obtained results are within the margin of error of 5%, between the semi-empirical classical theories and the developed model, based on the experimental data. Finally, it is obtained a general correlation between the Stanton number and the Prandtl number, for a specific flow (with associated Reynolds number).

Keywords: experimental measurements, numerical correlations, thermal pollution through pipelines, turbulent thermal flow

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Authors: Azza T. Tahera, Eman M. Ahmeda, Nadia A. Khalila, Yassin M. Nissanb

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New 3-(pyridin-4-yl)-[1,2,4] triazolo [4,3-b] pyridazine derivatives 2a-i, 4a,b and 6a,b were designed, synthesized and evaluated as cytotoxic agents. All compounds were investigated for their in vitro cytotoxicity at a single dose 10-5M concentration towards 60 cancer cell lines according to USA NCI protocol. The preliminary screening results showed that the majority of tested compounds exhibited remarkable activity against SR (leukemia) cell panel. Molecular docking for all synthesized compounds was performed on the active site of c-Met kinase. The most active compounds, 2f and 4a were further evaluated at a seven dose level screening and their IC50 as a c-Met kinase inhibitors were determined in vitro.

Keywords: triazolopyridazines, pyridazines, cytotoxic activity, cell panel

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Authors: Richard Tanaka, Ying Zhu

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This paper studies a few randomized algorithms in application-layer peer-to-peer networks. The significant gain in scalability and resilience that peer-to-peer networks provide has made them widely used and adopted in many real-world distributed systems and applications. The unique properties of peer-to-peer networks make them particularly suitable for randomized algorithms such as random walks and gossip algorithms. Instead of simulations of peer-to-peer networks, we leverage the Docker virtual container technology to develop implementations of the peer-to-peer networks and these distributed randomized algorithms running on top of them. We can thus analyze their behaviour and performance in realistic settings. We further consider the problem of identifying high-risk bottleneck links in the network with the objective of improving the resilience and reliability of peer-to-peer networks. We propose a randomized algorithm to solve this problem and evaluate its performance by simulations.

Keywords: distributed randomized algorithms, peer-to-peer networks, virtual container technology, resilient networks

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Authors: Daniel Micallef, Damien Bounaudet, Robert N. Farrugia, Simon P. Borg, Vincent Buhagiar, Tonio Sant

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The physical effects of upstream flow obstructions such as vegetation on cross-ventilation phenomena of a building are important for issues such as indoor thermal comfort. Modelling such effects in Computational Fluid Dynamics simulations may also be challenging. The aim of this work is to establish the cross-ventilation jet behaviour in such complex terrain conditions as well as to provide guidelines on the implementation of CFD numerical simulations in order to model complex terrain features such as vegetation in an efficient manner. The methodology consists of onsite measurements on a test cell coupled with numerical simulations. It was found that the cross-ventilation flow is highly turbulent despite the very low velocities encountered internally within the test cells. While no direct measurement of the jet direction was made, the measurements indicate that flow tends to be reversed from the leeward to the windward side. Modelling such a phenomenon proves challenging and is strongly influenced by how vegetation is modelled. A solid vegetation tends to predict better the direction and magnitude of the flow than a porous vegetation approach. A simplified terrain model was also shown to provide good comparisons with observation. The findings have important implications on the study of cross-ventilation in complex terrain conditions since the flow direction does not remain trivial, as with the traditional isolated building case.

Keywords: complex terrain, cross-ventilation, wind driven ventilation, wind resource, computational fluid dynamics, CFD

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Authors: Pyar S. Jassal, Sonal Gupta, Neema Chand, Rajni Johar

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In present study, Low molecular weight chitosan naoparticles (LMWCNP) were synthesized by using low molecular weight chitosan (LMWC) and sodium tripolyphosphate for the adsorption of anthraquinone dyes from waste water. The ionic-gel technique was used for this purpose. Size of nanoparticles was determined by “Scherrer equation”. The absorbance was carried out with UV-visible spectrophotometer for Acid Green 25 (AG25) and Reactive Blue 4 (RB4) dyes solutions at λmax 644 and λmax 598 nm respectively. The removal of dyes was dependent on the pH and the optimum adsorption was between pH 2 to 9. The extraction of dyes was linearly dependent on temperature. The equilibrium parameters, RL was calculated by using the Langmuir isotherm and shows that adsorption of dyes is favorable on the LMWCNP. The XRD images of LMWC show a crystalline nature whereas LMWCNP is amorphous one. The thermo gravimetric analysis (TGA) shows that LMWCNP thermally more stable than LMWC. As the contact time increases, percentage removal of Acid Green 25 and Reactive Blue 4 dyes also increases. TEM images reveal the size of the LMWCNP were in the range of 45-50 nm. The capacity of AG25 dye on LMWC was 5.23 mg/g, it compared with LMWCNP capacity which was 6.83 mg/g respectively. The capacity of RB4 dye on LMWC was 2.30 mg/g and 2.34 mg/g was on LMWCNP.

Keywords: low molecular weight chitosan nanoparticles, anthraquinone dye, removal efficiency, adsorption isotherm

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Authors: Haw-Long Lee, Win-Jin Chang, Yu-Ching Yang

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In the paper, the coupled equation of motion for the dynamic displacement of a fullerene moving in a (10,10) single-walled carbon nanotube (SWCNT) is derived using nonlocal Timoshenko beam theory, including the effects of rotary inertia and shear deformation. The effects of confined stiffness between the fullerene and nanotube, foundation stiffness, and nonlocal parameter on the dynamic behavior are analyzed using the Runge-Kutta Method. The numerical solution is in agreement with the analytical result for the special case. The numerical results show that increasing the confined stiffness and foundation stiffness decrease the dynamic displacement of SWCNT. However, the dynamic displacement increases with increasing the nonlocal parameter. In addition, result using the Euler beam theory and the Timoshenko beam theory are compared. It can be found that ignoring the effects of rotary inertia and shear deformation leads to an underestimation of the displacement.

Keywords: single-walled carbon nanotube, nanoparticle delivery, Nonlocal Timoshenko beam theory, Runge-Kutta Method, Van der Waals force

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Authors: Anna Dziubinska

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The article presents the results of numerical simulations of the new forging process of the automotive connector forging from cast preform. The high-strength ZK60 alloy (belonging to the Mg-Zn-Zr group of Mg alloys) was selected for numerical tests. Currently, this part of the industry is produced by multi-stage forging consisting of operations: bending, preforming, and finishing. The use of the cast preform would enable forging this component in one operation. However, obtaining specific mechanical properties requires inducing a certain level of strain within the forged part. Therefore, the design of the preform, its shape, and volume are of paramount importance. In work presented in this article, preforms of different shapes were designed and assessed using Finite Element (FE) analysis. The research was funded by the Polish National Agency for Academic Exchange within the framework of the Bekker programme.

Keywords: automotive connector, forging, magnesium alloy, numerical simulation, preform, ZK60

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Authors: Amir Reza Radmanesh, Sina Farajzadeh Khosroshahi, Hani Sadr

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The transient catalytic converter performance is governed by complex interactions between exhaust gas flow and the monolithic structure of the catalytic converter. Stringent emission regulations around the world necessitate the use of highly-efficient catalytic converters in vehicle exhaust systems. Computational fluid dynamics (CFD) is a powerful tool for calculating the flow field inside the catalytic converter. Radial velocity profiles, obtained by a commercial CFD code, present very good agreement with respective experimental results published in the literature. However the applicability of CFD for transient simulations is limited by the high CPU demands. In the present work, Geometric modeling ceramic monolith substrate is done with square shaped channel type of Catalytic converter and it is coated platinum and palladium. This example illustrates the effect of flow distribution on thermal response of a catalytic converter and different gas flow velocities, during the critical phase of catalytic converter warm up.

Keywords: catalytic converter, computational fluid dynamic, porous media, velocity distribution

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Authors: Sudhir Kumar Sharma, Ramesh Jagannathan

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The interaction of organic and inorganic matrices of biological origin resulting in self-assembled structures with unique properties is well established. The development of such self-assembled nanostructures by synthetic and bio-inspired techniques is an established field of active research. Among bio-materials, nacre, a laminar stack of calcium carbonate nanosheets, which are interleaved with organic material, has long been focused research due to its unique mechanical properties. In this paper, we present the development of nacre-like lamellar structures made up of calcium carbonate via a wet chemical route. We used the binding affinity of carboxylate anions and calcium cations using poly (acrylic) acid (PAA) to lead CaCO₃ crystallization. In these experiments, we selected calcium acetate as the precursor molecule along with PAA (Mw ~ 8000 Da). We found that Ca⁺²/COO⁻ ratio provided a tunable control for the morphology and growth of CaCO₃ nanostructures. Drop casting one such formulation on a silicon substrate followed by calcination resulted in co-planner, molecular sheets of CaCO₃, separated by a spacer layer of carbon. The scope of our process could be expanded to produce unit cell thick molecular sheets of other important inorganic materials.

Keywords: self-assembled structures, bio-inspired materials, calcium carbonate, wet chemical route

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Authors: Alireza Jalalvand, Maryam Saleh, Somayeh Behjat Khatouni, Zahra Bahri Najafi, Foroozan Fatahinia, Narges Ismailzadeh, Behrokh Farahmand

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Object: In the last two decades, the recent outbreak of Coronavirus (SARS-CoV-2) imposed a global pandemic in the world. Despite the increasing prevalence of the disease, there are no effective drugs to treat it. A suitable and rapid way to afford an effective drug and treat the global pandemic is a computational drug study. This study used molecular docking methods to examine the potential inhibition of over 50 antiviral drugs against three fundamental proteins of SARS-CoV-2. METHODS: Through a literature review, three important proteins (a key protease, RNA-dependent RNA polymerase (RdRp), and spike) were selected as drug targets. Three-dimensional (3D) structures of protease, spike, and RdRP proteins were obtained from the Protein Data Bank. Protein had minimal energy. Over 50 antiviral drugs were considered candidates for protein inhibition and their 3D structures were obtained from drug banks. The Autodock 4.2 software was used to define the molecular docking settings and run the algorithm. RESULTS: Five drugs, including indinavir, lopinavir, saquinavir, nelfinavir, and remdesivir, exhibited the highest inhibitory potency against all three proteins based on the binding energies and drug binding positions deduced from docking and hydrogen-bonding analysis. Conclusions: According to the results, among the drugs mentioned, saquinavir and lopinavir showed the highest inhibitory potency against all three proteins compared to other drugs. It may enter laboratory phase studies as a dual-drug treatment to inhibit SARS-CoV-2.

Keywords: covid-19, drug repositioning, molecular docking, lopinavir, saquinavir

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Authors: Ashiq Rahman, Sunil Thapa, Shunyao Fan, Niloy K. Dutta

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A 20-GHz and a 50-GHz pulse train are generated using a fiber ring laser setup that incorporates Rational Harmonic Mode Locking. Two separate experiments were carried out using charcoal nanoparticles and graphene nanoparticles acting as saturable absorbers to reduce the pulse width generated from rational harmonic mode-locking (RHML). Autocorrelator trace shows that the pulse width is reduced from 5.6-ps to 3.2-ps using charcoal at 20-GHz, and to 2.7-ps using graphene at 50-GHz repetition rates, which agrees with the simulation findings. Numerical simulations have been carried out to study the effect of varying the linear and nonlinear absorbance parameters of both absorbers on output pulse widths. Experiments closely agree with the simulations.

Keywords: fiber optics, fiber lasers, mode locking, saturable absorbers

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Authors: Meghdad Payan, Kostas Senetakis, Arman Khoshghalb, Nasser Khalili

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Dynamic properties of soils, especially at the range of very small strains, are of particular interest in geotechnical engineering practice for characterization of the behavior of geo-structures subjected to a variety of stress states. This study reports on the small-strain dynamic properties of sand-silt mixtures with particular emphasis on the effect of non-plastic fines content on the small strain shear modulus (Gmax), Young’s Modulus (Emax), material damping (Ds,min) and Poisson’s Ratio (v). Several clean sands with a wide range of grain size characteristics and particle shape are mixed with variable percentages of a silica non-plastic silt as fines content. Prepared specimens of sand-silt mixtures at different initial void ratios are subjected to sequential torsional and flexural resonant column tests with elastic dynamic properties measured along an isotropic stress path up to 800 kPa. It is shown that while at low percentages of fines content, there is a significant difference between the dynamic properties of the various samples due to the different characteristics of the sand portion of the mixtures, this variance diminishes as the fines content increases and the soil behavior becomes mainly silt-dominant, rendering no significant influence of sand properties on the elastic dynamic parameters. Indeed, beyond a specific portion of fines content, around 20% to 30% typically denoted as threshold fines content, silt is controlling the behavior of the mixture. Using the experimental results, new expressions for the prediction of small-strain dynamic properties of sand-silt mixtures are developed accounting for the percentage of silt and the characteristics of the sand portion. These expressions are general in nature and are capable of evaluating the elastic dynamic properties of sand-silt mixtures with any types of parent sand in the whole range of silt percentage. The inefficiency of skeleton void ratio concept in the estimation of small-strain stiffness of sand-silt mixtures is also illustrated.

Keywords: damping ratio, Poisson’s ratio, resonant column, sand-silt mixture, shear modulus, Young’s modulus

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Authors: Haijie Li, Xuping Zhang

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This paper presents a computationally efficient method for the modeling of robot manipulators with flexible links and joints. This approach combines the Discrete Time Transfer Matrix Method with the Finite Segment Method, in which the flexible links are discretized by a number of rigid segments connected by torsion springs; and the flexibility of joints are modeled by torsion springs. The proposed method avoids the global dynamics and has the advantage of modeling non-uniform manipulators. Experiments and simulations of a single-link flexible manipulator are conducted for verifying the proposed methodologies. The simulations of a three-link robot arm with links and joints flexibility are also performed.

Keywords: flexible manipulator, transfer matrix method, linearization, finite segment method

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Authors: Zainal Arifin, Avanti Fontana

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Considering that TOE framework is the most useful instrument for studying technology adoption in firm context, this paper will analyze the influence of technological, organizational and environmental (TOE) factors to the Dynamic capabilities (DCs) associated with technology adoption strategy for improving the firm’s performance. Focusing on the determinant factors of technology adoption at the firm level, the study will contribute to the broader study of resource base view (RBV) and dynamic capability (DC). There is no study connecting directly the TOE factors to the DCs, this paper proposes technology adoption as a functional competence/capability which mediates a relationship between technology adoptions with firm’s performance. The study wants to show a conceptual model of the indirect effects of DCs at the firm level, which can be key predictors of firm performance in dynamic business environment. The results of this research is mostly relevant to top corporate executives (BOD) or top management team (TMT) who seek to provide some supporting ‘hardware’ content and condition such as technological factors, organizational factors, environmental factors, and to improve firm's ‘software ‘ ability such as adaptive capability, absorptive capability and innovative capability, in order to achieve a successful technology adoption in organization. There are also mediating factors which are elaborated at this paper; timing and external network. A further research for showing its empirical results is highly recommended.

Keywords: technology adoption, TOE framework, dynamic capability, resources based view

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Authors: Xuhui Lin, Qiuchen Lu, Yi An, Tao Yang

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As global climate change intensifies, extreme weather events such as floods increasingly threaten urban infrastructure, making the vulnerability of urban road networks a pressing issue. Existing static repair strategies fail to adapt to the rapid changes in road network conditions during flood events, leading to inefficient resource allocation and suboptimal recovery. The main research gap lies in the lack of repair strategies that consider both the dynamic characteristics of networks and the progression of flood propagation. This paper proposes a topology-based dynamic repair strategy that adjusts repair priorities based on real-time changes in flood propagation and traffic demand. Specifically, a novel method is developed to assess and enhance the resilience of urban road networks during flood events. The method combines road network topological analysis, flood propagation modelling, and traffic flow simulation, introducing a local importance metric to dynamically evaluate the significance of road segments across different spatial and temporal scales. Using London's road network and rainfall data as a case study, the effectiveness of this dynamic strategy is compared to traditional and Transport for London (TFL) strategies. The most significant highlight of the research is that the dynamic strategy substantially reduced the number of stranded vehicles across different traffic demand periods, improving efficiency by up to 35.2%. The advantage of this method lies in its ability to adapt in real-time to changes in network conditions, enabling more precise resource allocation and more efficient repair processes. This dynamic strategy offers significant value to urban planners, traffic management departments, and emergency response teams, helping them better respond to extreme weather events like floods, enhance overall urban resilience, and reduce economic losses and social impacts.

Keywords: Urban resilience, road networks, flood response, dynamic repair strategy, topological analysis

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Authors: G. V. Novikov, V. S. Sivozhelezov, S. S. Kolesnikov, K. V. Shaitan

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The study reports about the influence of binding of orthosteric ligands as well as point mutations on the conformational dynamics of β-2-adrenoreceptor. Using molecular dynamics simulation we found that there was a little fraction of active states of the receptor in its apo (ligand free) ensemble corresponded to its constitutive activity. Analysis of MD trajectories indicated that such spontaneous activation of the receptor is accompanied by the motion in intracellular part of its alpha-helices. Thus receptor’s constitutive activity directly results from its conformational dynamics. On the other hand the binding of a full agonist resulted in a significant shift of the initial equilibrium towards its active state. Finally, the binding of the inverse agonist stabilized the receptor in its inactive state. It is likely that the binding of inverse agonists might be a universal way of constitutive activity inhibition in vivo. Our results indicate that ligand binding redistribute pre-existing conformational degrees of freedom (in accordance to the Monod-Wyman-Changeux-Model) of the receptor rather than cause induced fit in it. Therefore, the ensemble of biologically relevant receptor conformations is encoded in its spatial structure, and individual conformations from that ensemble might be used by the cell in conformity with the physiological behaviour.

Keywords: seven-transmembrane receptors, constitutive activity, activation, x-ray crystallography, principal component analysis, molecular dynamics simulation

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Authors: B. Kishore Kumar, Rakesh Pogula, T. Kishore Kumar

Abstract:

The steepness of an audio signal which is produced by the musical instruments, specifically percussive instruments is the perception of how high tone or low tone which can be considered as a frequency closely related to the fundamental frequency. This paper presents a novel method for silence removal and segmentation of music signals produced by the percussive instruments and the performance of proposed method is studied with the help of MATLAB simulations. This method is based on two simple features, namely the signal energy and the spectral centroid. As long as the feature sequences are extracted, a simple thresholding criterion is applied in order to remove the silence areas in the sound signal. The simulations were carried on various instruments like drum, flute and guitar and results of the proposed method were analyzed.

Keywords: percussive instruments, spectral energy, spectral centroid, silence removal

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Authors: Leonardo Herrera, Shield B. Lin, Stephen J. Montgomery-Smith, Ziraguen O. Williams

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A one-directional dynamic model of a Stewart Platform was developed to assist NASA in analyzing the dynamic response in spacecraft docking operations. A simplified mechanical drawing was created, capturing the physical structure's main features. A simplified schematic diagram was developed into a lumped mass model from the mechanical drawing. Three differential equations were derived according to the schematic diagram. A Simulink diagram was created using MATLAB to represent the three equations. System parameters, including spring constants and masses, are derived in detail from the physical system. The model can be used for further analysis via computer simulation in predicting dynamic response in its main docking direction, i.e., up-and-down motion.

Keywords: stewart platform, docking operation, spacecraft, spring constant

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Authors: Yi Tse Wang, Che Hsiu Chen, Zih Jian Huang, Hon Wen Cheng

Abstract:

Stretching treatments enhanced flexibility. On the other hand, decreases in hamstrings strength have been reported after stretching, especially with static stretching or passive stretching. Stretching has been shown to be more effective than static stretching to improve muscle performance, but a clear consensus for the effect of dynamic stretching on muscle performance has not been achieved. The purpose of this study was to compare the acute effect of a dynamic stretching, static stretching and eccentric exercise protocol on hamstrings stiffness, flexibility and muscle strength. Forty-five healthy active men (height 179.9 cm; weight 71.5 kg; age 22.5 years) were participated in 3 randomly ordered testing sessions: dynamic stretching (DS), active static stretching (ASS), and passive static stretching (PSS). All the stretch were performed 30 seconds and repeated 6 times. There was a 30-second interval between repetitions. The outcome measures were isokinetic concentric contraction (60°/s), eccentric contraction (30°/s) peak torque, muscle flexibility after stretching. The results showed that the muscle flexibility (3.6%, 3.9% and 1.59%, respectively) increased significantly after DS, PSS and ASS. Hamstring isokinetic concentric peak torque (-6.4%, -8.0% and -5.8%, respectively) and eccentric peak torque (-5.8%, -4.5% and -5.4%, respectively) decreased significantly after DS, PSS and ASS. Hence, although the stretching protocols improve hamstrings flexibility immediately, reduced hamstring muscle eccentric and concentric peak torque.

Keywords: hamstrings injury, warm-up, muscle performance, muscle stretching

Procedia PDF Downloads 378

Authors: Maria Sciammarella, Uttam M. Shrestha, Youngho Seo, Grant T. Gullberg, Elias H. Botvinick

Abstract:

Background: Myocardial perfusion imaging (MPI) is typically performed with static imaging protocols and visually assessed for perfusion defects based on the relative intensity distribution. Dynamic cardiac SPECT, on the other hand, is a new imaging technique that is based on time varying information of radiotracer distribution, which permits quantification of myocardial blood flow (MBF). In this abstract, we report a progress and current status of dynamic cardiac SPECT using conventional gamma camera (Infinia Hawkeye 4, GE Healthcare) for estimation of myocardial blood flow and coronary flow reserve. Methods: A group of patients who had high risk of coronary artery disease was enrolled to evaluate our methodology. A low-dose/high-dose rest/pharmacologic-induced-stress protocol was implemented. A standard rest and a standard stress radionuclide dose of ⁹⁹ᵐTc-tetrofosmin (140 keV) was administered. The dynamic SPECT data for each patient were reconstructed using the standard 4-dimensional maximum likelihood expectation maximization (ML-EM) algorithm. Acquired data were used to estimate the myocardial blood flow (MBF). The correspondence between flow values in the main coronary vasculature with myocardial segments defined by the standardized myocardial segmentation and nomenclature were derived. The coronary flow reserve, CFR, was defined as the ratio of stress to rest MBF values. CFR values estimated with SPECT were also validated with dynamic PET. Results: The range of territorial MBF in LAD, RCA, and LCX was 0.44 ml/min/g to 3.81 ml/min/g. The MBF between estimated with PET and SPECT in the group of independent cohort of 7 patients showed statistically significant correlation, r = 0.71 (p < 0.001). But the corresponding CFR correlation was moderate r = 0.39 yet statistically significant (p = 0.037). The mean stress MBF value was significantly lower for angiographically abnormal than that for the normal (Normal Mean MBF = 2.49 ± 0.61, Abnormal Mean MBF = 1.43 ± 0. 0.62, P < .001). Conclusions: The visually assessed image findings in clinical SPECT are subjective, and may not reflect direct physiologic measures of coronary lesion. The MBF and CFR measured with dynamic SPECT are fully objective and available only with the data generated from the dynamic SPECT method. A quantitative approach such as measuring CFR using dynamic SPECT imaging is a better mode of diagnosing CAD than visual assessment of stress and rest images from static SPECT images Coronary Flow Reserve.

Keywords: dynamic SPECT, clinical SPECT/CT, selective coronary angiograph, ⁹⁹ᵐTc-Tetrofosmin

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