Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 33163

Search results for: structure based drug design (SBDD)

33163 An In-silico Pharmacophore-Based Anti-Viral Drug Development for Hepatitis C Virus

Authors: Romasa Qasim, G. M. Sayedur Rahman, Nahid Hasan, M. Shazzad Hosain


Millions of people worldwide suffer from Hepatitis C, one of the fatal diseases. Interferon (IFN) and ribavirin are the available treatments for patients with Hepatitis C, but these treatments have their own side-effects. Our research focused on the development of an orally taken small molecule drug targeting the proteins in Hepatitis C Virus (HCV), which has lesser side effects. Our current study aims to the Pharmacophore based drug development of a specific small molecule anti-viral drug for Hepatitis C Virus (HCV). Drug designing using lab experimentation is not only costly but also it takes a lot of time to conduct such experimentation. Instead in this in silico study, we have used computer-aided techniques to propose a Pharmacophore-based anti-viral drug specific for the protein domains of the polyprotein present in the Hepatitis C Virus. This study has used homology modeling and ab initio modeling for protein 3D structure generation followed by pocket identification in the proteins. Drug-able ligands for the pockets were designed using de novo drug design method. For ligand design, pocket geometry is taken into account. Out of several generated ligands, a new Pharmacophore is proposed, specific for each of the protein domains of HCV.

Keywords: pharmacophore-based drug design, anti-viral drug, in-silico drug design, Hepatitis C virus (HCV)

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33162 Research on Architectural Steel Structure Design Based on BIM

Authors: Tianyu Gao


Digital architectures use computer-aided design, programming, simulation, and imaging to create virtual forms and physical structures. Today's customers want to know more about their buildings. They want an automatic thermostat to learn their behavior and contact them, such as the doors and windows they want to open with a mobile app. Therefore, the architectural display form is more closely related to the customer's experience. Based on the purpose of building informationization, this paper studies the steel structure design based on BIM. Taking the Zigan office building in Hangzhou as an example, it is divided into four parts, namely, the digital design modulus of the steel structure, the node analysis of the steel structure, the digital production and construction of the steel structure. Through the application of BIM software, the architectural design can be synergized, and the building components can be informationized. Not only can the architectural design be feedback in the early stage, but also the stability of the construction can be guaranteed. In this way, the monitoring of the entire life cycle of the building and the meeting of customer needs can be realized.

Keywords: digital architectures, BIM, steel structure, architectural design

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33161 In Silico Studies on Selected Drug Targets for Combating Drug Resistance in Plasmodium Falcifarum

Authors: Deepika Bhaskar, Neena Wadehra, Megha Gulati, Aruna Narula, R. Vishnu, Gunjan Katyal


With drug resistance becoming widespread in Plasmodium falciparum infections, development of the alternative drugs is the desired strategy for prevention and cure of malaria. Three drug targets were selected to screen promising drug molecules from the GSK library of around 14000 molecules. Using an in silico structure-based drug designing approach, the differences in binding energies of the substrate and inhibitor were exploited between target sites of parasite and human to design a drug molecule against Plasmodium. The docking studies have shown several promising molecules from GSK library with more effective binding as compared to the already known inhibitors for the drug targets. Though stronger interaction has been shown by several molecules as compare to reference, few molecules have shown the potential as drug candidates though in vitro studies are required to validate the results.

Keywords: plasmodium, malaria, drug targets, in silico studies

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33160 Improved Whale Algorithm Based on Information Entropy and Its Application in Truss Structure Optimization Design

Authors: Serges Mendomo Meye, Li Guowei, Shen Zhenzhong, Gan Lei, Xu Liqun


Given the limitations of the original whale optimization algorithm (WAO) in local optimum and low convergence accuracy in truss structure optimization problems, based on the fundamental whale algorithm, an improved whale optimization algorithm (SWAO) based on information entropy is proposed. The information entropy itself is an uncertain measure. It is used to control the range of whale searches in path selection. It can overcome the shortcomings of the basic whale optimization algorithm (WAO) and can improve the global convergence speed of the algorithm. Taking truss structure as the optimization research object, the mathematical model of truss structure optimization is established; the cross-sectional area of truss is taken as the design variable; the objective function is the weight of truss structure; and an improved whale optimization algorithm (SWAO) is used for optimization design, which provides a new idea and means for its application in large and complex engineering structure optimization design.

Keywords: information entropy, structural optimization, truss structure, whale algorithm

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33159 Design and Synthesis of Some Pyrimidine Derivatives as Bruton’s Tyrosine Kinase Inhibitors for Hematologic Malignancies

Authors: Ibrahim M. Labouta, Gina N. Tageldin, Salwa M. Fahmy, Hayam M. Ashour, Mounir A. Khalil, Tamer M. Ibrahim, Nefertiti A. El-Nikhely


Bruton’s tyrosine kinase (BTK) is a critical effector molecule in B cell antigen receptor (BCR) signaling transduction. It regulates B cell proliferation, development and survival. Since BTK is widely expressed in many B cell leukaemias and lymphomas, targeting BTK by small molecules inhibitors became an attractive idea as new treatment modalities for B cell mediated hematologic malignancies. Ibrutinib is the 1st generation BTK inhibitor, approved by FDA for treatment of relapsed mantle cell lymphoma (MCL) and chronic lymphocytic leukemia (CLL). It binds irreversibly to the unique cysteine (Cys481) within the ATP-binding pocket of BTK. Besides ibrutinib, many irreversible covalent BTK inhibitors comprising pyrimidine nucleus such as spebrutinib (phase IIb) showed high selectivity and potency when compared to it. In this study, the designed compounds were based on 5-cyano-2-methylsulfanyl pyrimidine core and decorated with electrophilic warheads which are essential for the optimal activity for targeted covalent inhibition (TCI). However, modifications at pyrimidine C4 or C6 were made by introduction of substituted amines which are provided to behave differently. The synthesized derivatives were evaluated for their anticancer activity in leukemia cell lines (e.g. THP-1). Results showed that, some derivatives exhibited antiproliferative activity with IC50 ranged from 5-50 μM, The in vitro enzymatic inhibitory assay for these compounds against BTK is still under investigation. Nevertheless, we could conclude from the initial biological screening that, the synthesized 4 or 6-subsitituted aminopyrimidines represent promising and novel antileukemic agents. Meanwhile, further studies are still needed to attribute this activity through targeting BTK enzyme and inhibition of BCR signaling pathway.

Keywords: BTK inhibitors, hematologic malignancies, structure based drug design (SBDD), targeted covalent inhibitors (TCI)

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33158 Structure-Based Drug Design of Daptomycin, Antimicrobial lipopeptide

Authors: Satya Eswari Jujjavarapu, Swast Dhagat


Contagious diseases enact severe public health problems and have upsetting consequences. The cyclic lipopeptides explained by bacteria Bacillus, Paenibacillus, Pseudomonas, Streptomyces, Serratia, Propionibacterium and fungus Fusarium are very critical in confining the pathogens. As the degree of drug resistance upsurges in unparalleled manner, the perseverance of searching novel cyclic lipopeptides is being professed. The intense study has shown the implication of these bioactive compounds extending beyond antibacterial and antifungal. Lipopeptides, composed of single units of peptide and fatty acyl moiety, show broad spectrum antimicrobial effects. Among the surplus of cyclic lipopeptides, only few have materialized as strong antibiotics. For their functional vigor, polymyxin, daptomycin, surfactin, iturin and bacillomycin have been integrated in mainstream healthcare. In our work daptomycin has been a major part of antimicrobial resource since the past decade. Daptomycin, a cyclic lipopeptide consists of 13-member amino acid with a decanoyl side-chain. This structure of daptomycin confers it the mechanism of action through which it forms pore in the bacterial cell membrane resulting in the death of cell. Daptomycin is produced by Streptococccus roseoporus and acts against Streptococcus pneumonia (PSRP), methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). The PDB structure and ligands of daptomycin are available online. The molecular docking studies of these ligands with the lipopeptides were performed and their docking score and glide energy were recorded.

Keywords: daptomycin, molecular docking, structure-based drug design, lipopeptide

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33157 Microwave Synthesis and Molecular Docking Studies of Azetidinone Analogous Bearing Diphenyl Ether Nucleus as a Potent Antimycobacterial and Antiprotozoal Agent

Authors: Vatsal M. Patel, Navin B. Patel


The present studies deal with the developing a series bearing a diphenyl ethers nucleus using structure-based drug design concept. A newer series of diphenyl ether based azetidinone namely N-(3-chloro-2-oxo-4-(3-phenoxyphenyl)azetidin-1-yl)-2-(substituted amino)acetamide (2a-j) have been synthesized by condensation of m-phenoxybenzaldehyde with 2-(substituted-phenylamino)acetohydrazide followed by the cyclisation of resulting Schiff base (1a-j) by conventional method as well as microwave heating approach as a part of an environmentally benign synthetic protocol. All the synthesized compounds were characterized by spectral analysis and were screened for in vitro antimicrobial, antitubercular and antiprotozoal activity. The compound 2f was found to be most active M. tuberculosis (6.25 µM) MIC value in the primary screening as well as this same derivative has been found potency against L. mexicana and T. cruzi with MIC value 2.09 and 6.69 µM comparable to the reference drug Miltefosina and Nifurtimox. To provide understandable evidence to predict binding mode and approximate binding energy of a compound to a target in the terms of ligand-protein interaction, all synthesized compounds were docked against an enoyl-[acyl-carrier-protein] reductase of M. tuberculosis (PDB ID: 4u0j). The computational studies revealed that azetidinone derivatives have a high affinity for the active site of enzyme which provides a strong platform for new structure-based design efforts. The Lipinski’s parameters showed good drug-like properties and can be developed as an oral drug candidate.

Keywords: antimycobacterial, antiprotozoal, azetidinone, diphenylether, docking, microwave

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33156 Direct Displacement-Based Design Procedure for Performance-Based Seismic Design of Structures

Authors: Haleh Hamidpour


Since the seismic damageability of structures is controlled by the inelastic deformation capacities of structural elements, seismic design of structure based on force analogy methods is not appropriate. In recent year, the basic approach of design codes have been changed from force-based approach to displacement-based. In this regard, a Direct Displacement-Based Design (DDBD) and a Performance-Based Plastic Design (PBPD) method are proposed. In this study, the efficiency of these two methods on seismic performance of structures is evaluated through a sample 12-story reinforced concrete moment frame. The building is designed separately based on the DDBD and the PBPD methods. Once again the structure is designed by the traditional force analogy method according to the FEMA P695 regulation. Different design method results in different structural elements. Seismic performance of these three structures is evaluated through nonlinear static and nonlinear dynamic analysis. The results show that the displacement-based design methods accommodate the intended performance objectives better than the traditional force analogy method.

Keywords: direct performance-based design, ductility demands, inelastic seismic performance, yield mechanism

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33155 In-silico Design of Riboswitch Based Potent Inhibitors for Vibrio cholera

Authors: Somdutt Mujwar, Kamal Raj Pardasani


Cholera pandemics are caused by facultative pathogenic Vibrio cholera bacteria persisting in the countries having warmer climatic conditions as well as the presence of large water bodies with huge amount of organic matter, it is responsible for the millions of deaths annually. Presently the available therapy for cholera is Oral Rehydration Therapy (ORT) with an antibiotic drug. Excessive utilization of life saving antibiotics drugs leads to the development of resistance by the infectious micro-organism against the antibiotic drugs resulting in loss of effectiveness of these drugs. Also, many side effects are also associated with the use of these antibiotic drugs. This riboswitch is explored as an alternative drug target for Vibrio cholera bacteria to overcome the problem of drug resistance as well as side effects associated with the antibiotics drugs. The bacterial riboswitch is virtually screened with 24407 legends to get possible drug candidates. The 10 ligands showing best binding with the riboswitch are selected to design a pharmacophore, which can be utilized to design lead molecules by using the phenomenon of bioisosterism.

Keywords: cholera, drug design, ligand, riboswitch, pharmacophore

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33154 Drug Delivery to Solid Tumor: Effect of Dynamic Capillary Network Induced by Tumor

Authors: Mostafa Sefidgar, Kaamran Raahemifar, Hossein Bazmara, Madjid Soltani


The computational methods provide condition for investigation related to the process of drug delivery, such as convection and diffusion of drug in extracellular matrices, and drug extravasation from microvascular. The information of this process clarifies the mechanisms of drug delivery from the injection site to absorption by a solid tumor. In this study, an advanced numerical method is used to solve fluid flow and solute transport equations simultaneously to show how capillary network structure induced by tumor affects drug delivery. The effect of heterogeneous capillary network induced by tumor on interstitial fluid flow and drug delivery is investigated by this multi scale method. The sprouting angiogenesis model is used for generating capillary network induced by tumor. Fluid flow governing equations are implemented to calculate blood flow through the tumor-induced capillary network and fluid flow in normal and tumor tissues. The Starling’s law is used for closing this system of equations and coupling the intravascular and extravascular flows. Finally, convection-diffusion-reaction equation is used to simulate drug delivery. The dynamic approach which changes the capillary network structure based on signals sent by hemodynamic and metabolic stimuli is used in this study for more realistic assumption. The study indicates that drug delivery to solid tumors depends on the tumor induced capillary network structure. The dynamic approach generates the irregular capillary network around the tumor and predicts a higher interstitial pressure in the tumor region. This elevated interstitial pressure with irregular capillary network leads to a heterogeneous distribution of drug in the tumor region similar to in vivo observations. The investigation indicates that the drug transport properties have a significant role against the physiological barrier of drug delivery to a solid tumor.

Keywords: solid tumor, physiological barriers to drug delivery, angiogenesis, microvascular network, solute transport

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33153 A High Quality Factor Filter Based on Quasi- Periodic Photonic Structure

Authors: Hamed Alipour-Banaei, Farhad Mehdizadeh


We report the design and characterization of ultra high quality factor filter based on one-dimensional photonic-crystal Thue-Morse sequence structure. The behavior of aperiodic array of photonic crystal structure is numerically investigated and we show that by changing the angle of incident wave, desired wavelengths could be tuned and a tunable filter is realized. Also it is shown that high quality factor filter be achieved in the telecommunication window around 1550 nm, with a device based on Thue-Morse structure. Simulation results show that the proposed structure has a quality factor more than 100000 and it is suitable for DWDM communication applications.

Keywords: Thue-Morse, filter, quality factor, photonic

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33152 Identifying Dynamic Structural Parameters of Soil-Structure System Based on Data Recorded during Strong Earthquakes

Authors: Vahidreza Mahmoudabadi, Omid Bahar, Mohammad Kazem Jafari


In many applied engineering problems, structural analysis is usually conducted by assuming a rigid bed, while imposing the effect of structure bed flexibility can affect significantly on the structure response. This article focuses on investigation and evaluation of the effects arising from considering a soil-structure system in evaluation of dynamic characteristics of a steel structure with respect to elastic and inelastic behaviors. The recorded structure acceleration during Taiwan’s strong Chi-Chi earthquake on different floors of the structure was our evaluation criteria. The respective structure is an eight-story steel bending frame structure designed using a displacement-based direct method assuring weak beam - strong column function. The results indicated that different identification methods i.e. reverse Fourier transform or transfer functions, is capable to determine some of the dynamic parameters of the structure precisely, rather than evaluating all of them at once (mode frequencies, mode shapes, structure damping, structure rigidity, etc.). Response evaluation based on the input and output data elucidated that the structure first mode is not significantly affected, even considering the soil-structure interaction effect, but the upper modes have been changed. Also, it was found that the response transfer function of the different stories, in which plastic hinges have occurred in the structure components, provides similar results.

Keywords: bending steel frame structure, dynamic characteristics, displacement-based design, soil-structure system, system identification

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33151 A Study on Performance-Based Design Analysis for Vertical Extension of Apartment Units

Authors: Minsun Kim, Ki-Sun Choi, Hyun-Jee Lee, Young-Chan You


There is no reinforcement example for the renovation of the vertical and horizontal extension to existing building structures which is a shear wall type in apartment units in Korea. Among these existing structures, the structures which are shear wall type are rare overseas, while Korea has many shear wall apartment units. Recently, in Korea, a few researchers are trying to confirm the possibility of the vertical extension in existing building with shear walls. This study evaluates the possibility of the renovation by applying performance-based seismic design to existing buildings with shear walls in the analysis phase of the structure. In addition, force-based seismic design, used by general structural engineers in Korea, is carried out to compare the amount of reinforcement of walls, which is a main component of wall structure. As a result, we suggest that performance-based design obtains more economical advantages than force-based seismic design.

Keywords: design for extension, performance-based design, remodeling, shear wall frame, structural analysis

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33150 Insight into the Binding Theme of CA-074Me to Cathepsin B: Molecular Dynamics Simulations and Scaffold Hopping to Identify Potential Analogues as Anti-Neurodegenerative Diseases

Authors: Tivani Phosa Mashamba-Thompson, Mahmoud E. S. Soliman


To date, the cause of neurodegeneration is not well understood and diseases that stem from neurodegeneration currently have no known cures. Cathepsin B (CB) enzyme is known to be involved in the production of peptide neurotransmitters and toxic peptides in neurodegenerative diseases (NDs). CA-074Me is a membrane-permeable irreversible selective cathepsin B (CB) inhibitor as confirmed by in vivo studies. Due to the lack of the crystal structure, the binding mode of CA-074Me with the human CB at molecular level has not been previously reported. The main aim of this study is to gain an insight into the binding mode of CB CA-074Me to human CB using various computational tools. Herein, molecular dynamics simulations, binding free energy calculations and per-residue energy decomposition analysis were employed to accomplish the aim of the study. Another objective was to identify novel CB inhibitors based on the structure of CA-074Me using fragment based drug design using scaffold hoping drug design approach. Results showed that two of the designed ligands (hit 1 and hit 2) were found to have better binding affinities than the prototype inhibitor, CA-074Me, by ~2-3 kcal/mol. Per-residue energy decomposition showed that amino acid residues Cys29, Gly196, His197 and Val174 contributed the most towards the binding. The Van der Waals binding forces were found to be the major component of the binding interactions. The findings of this study should assist medicinal chemist towards the design of potential irreversible CB inhibitors.

Keywords: cathepsin B, scaffold hopping, docking, molecular dynamics, binding-free energy, neurodegerative diseases

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33149 Design, Development and Characterization of Pioglitazone Transdermal Drug Delivery System

Authors: Dwarakanadha Reddy Peram, D. Swarnalatha, C. Gopinath


The main aim of this research work was to design and development characterization of Pioglitazone transdermal drug delivery system by using various polymers such as Olibanum with different concentration by solvent evaporation technique. The prepared formulations were evaluated for different physicochemical characteristics like thickness, folding endurance, drug content, percentage moisture absorption, percentage moisture loss, percentage elongation break test and weight uniformity. The diffusion studies were performed by using modified Franz diffusion cells. The result of dissolution studies shows that formulation, F3 (Olibanum with 50 mg) showed maximum release of 99.95 % in 12hrs, whereas F1 (Olibanum and EC backing membrane) showed minimum release of 93.65% in 12 hr. Based on the drug release and physicochemical values obtained the formulation F3 is considered as an optimized formulation which shows higher percentage of drug release of 99.95 % in 12 hr. The developed transdermal patches increase the therapeutic efficacy and reduced toxic effect of pioglitazone.

Keywords: pioglitazone, olibanum, transdermal drug delivery system, drug release percantage

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33148 Preparation of Bead-On-String Alginate/Soy Protein Isolated Nanofibers via Water-Based Electrospinning and Its Application for Drug Loading

Authors: Patcharakamon Nooeaid, Piyachat Chuysrinuan


Electrospun natural polymers-based nanofibers are one of the most interesting materials used in tissue engineering and drug delivery applications. Bead-on-string nanofibers have gained considerable interest for sustained drug release. Vancomycin was used as the model drug and sodium alginate (SA)/soy protein isolated (SPI) as the polymer blend to fabricate the bead-on-string nanofibers by aqueous-based electrospinning. The bead-on-string SA/SPI nanofibers were successfully fabricated by the addition of poly(ethylene oxide) (PEO) as a co-blending polymer. SA-PEO with mass ratio of 70/30 showed the best spinnability with continuous nanofibers without the occurrence of beads. Bead structure formed with the addition of SPI and bead number increased with increasing SPI content. The electrospinning of 80/20 SA-PEO/SPI was obtained as a great promising bead-on-string nanofibers for drug loading, while the solution of 50/50 was not able to obtain continuous fibers. In vitro release tests showed that a more sustainable release profile up to 14 days with less initial burst release on day 1 could be obtained from the bead-on-string fibers than from smooth fibers with uniform diameter. In addition, vancomycin-loaded beaded fibers inhibited the growth of Staphylococcus aureus (S. aureus) bacteria. Therefore, the SA-PEO/SPI nanofibers showed the potential to be used as biomaterials for tissue engineering and drug delivery.

Keywords: bead-on-string fibers, electrospinning, drug delivery, tissue engineering

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33147 Non-Linear Static Pushover Analysis of 15 Storied Reinforced Concrete Building Structure with Shear Wall

Authors: Hamid Nikzad, Shinta Yoshitomi


In this paper, nonlinear static pushover analysis is performed on 15 storied RC building structure with a shear wall to evaluate the seismic performance of the building. Section sizes of the members are obtained based on structural optimization method utilizing MATLAB frame optimizer, then the structure is simulated and designed in ETABS program conforming ACI 318-14 design code. The pushover curve has been generated by pushing the top node of the structure to the limited target displacement. Members failure due to the formation of plastic hinges, considering shear wall-frame structure was observed and the result of this study is presented based on current regulation of FEMA356, ASCE7-10, and ACI 318-14 design criteria

Keywords: structural optimization, linear static analysis, ETABS, MATLAB, RC moment frame, RC shear wall structures

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33146 Pharmaceutical Science and Development in Drug Research

Authors: Adegoke Yinka Adebayo


An understanding of the critical product attributes that impact on in vivo performance is key to the production of safe and effective medicines. Thus, a key driver for our research is the development of new basic science and technology underpinning the development of new pharmaceutical products. Research includes the structure and properties of drugs and excipients, biopharmaceutical characterisation, pharmaceutical processing and technology and formulation and analysis.

Keywords: drug discovery, drug development, drug delivery

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33145 Spatial Relationship of Drug Smuggling Based on Geographic Information System Knowledge Discovery Using Decision Tree Algorithm

Authors: S. Niamkaeo, O. Robert, O. Chaowalit


In this investigation, we focus on discovering spatial relationship of drug smuggling along the northern border of Thailand. Thailand is no longer a drug production site, but Thailand is still one of the major drug trafficking hubs due to its topographic characteristics facilitating drug smuggling from neighboring countries. Our study areas cover three districts (Mae-jan, Mae-fahluang, and Mae-sai) in Chiangrai city and four districts (Chiangdao, Mae-eye, Chaiprakarn, and Wienghang) in Chiangmai city where drug smuggling of methamphetamine crystal and amphetamine occurs mostly. The data on drug smuggling incidents from 2011 to 2017 was collected from several national and local published news. Geo-spatial drug smuggling database was prepared. Decision tree algorithm was applied in order to discover the spatial relationship of factors related to drug smuggling, which was converted into rules using rule-based system. The factors including land use type, smuggling route, season and distance within 500 meters from check points were found that they were related to drug smuggling in terms of rules-based relationship. It was illustrated that drug smuggling was occurred mostly in forest area in winter. Drug smuggling exhibited was discovered mainly along topographic road where check points were not reachable. This spatial relationship of drug smuggling could support the Thai Office of Narcotics Control Board in surveillance drug smuggling.

Keywords: decision tree, drug smuggling, Geographic Information System, GIS knowledge discovery, rule-based system

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33144 Performance Based Design of Masonry Infilled Reinforced Concrete Frames for Near-Field Earthquakes Using Energy Methods

Authors: Alok Madan, Arshad K. Hashmi


Performance based design (PBD) is an iterative exercise in which a preliminary trial design of the building structure is selected and if the selected trial design of the building structure does not conform to the desired performance objective, the trial design is revised. In this context, development of a fundamental approach for performance based seismic design of masonry infilled frames with minimum number of trials is an important objective. The paper presents a plastic design procedure based on the energy balance concept for PBD of multi-story multi-bay masonry infilled reinforced concrete (R/C) frames subjected to near-field earthquakes. The proposed energy based plastic design procedure was implemented for trial performance based seismic design of representative masonry infilled reinforced concrete frames with various practically relevant distributions of masonry infill panels over the frame elevation. Non-linear dynamic analyses of the trial PBD of masonry infilled R/C frames was performed under the action of near-field earthquake ground motions. The results of non-linear dynamic analyses demonstrate that the proposed energy method is effective for performance based design of masonry infilled R/C frames under near-field as well as far-field earthquakes.

Keywords: masonry infilled frame, energy methods, near-fault ground motions, pushover analysis, nonlinear dynamic analysis, seismic demand

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33143 Using Bamboo Structures for Protecting Mangrove Ecosystems: A Nature-Based Approach

Authors: Sourabh Harihar, Henk Jan Verhagen


The nurturing of a mangrove ecosystem requires a protected coastal environment with adequate drainage of the soil substratum. In a conceptual design undertaken for a mangrove rejuvenation project along the eastern coast of Mumbai (India), various engineering alternatives have been thought of as a protective coastal structure and drainage system. One such design uses bamboo-pile walls in creating shielded compartments in the form of various layouts, coupled with bamboo drains. The bamboo-based design is found to be environmentally and economically advantageous over other designs like sand-dikes which are multiple times more expensive. Moreover, employing a natural material such as bamboo helps the structure naturally blend with the developing mangrove habitat, allaying concerns about dismantling the structure post mangrove growth. A cost-minimising and eco-friendly bamboo structure, therefore, promises to pave the way for large rehabilitation projects in future. As mangrove ecosystems in many parts of the world increasingly face the threat of destruction due to urban development and climate change, protective nature-based designs that can be built in a short duration are the need of the hour.

Keywords: bamboo, environment, mangrove, rehabilitation

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33142 Displacement Based Design of a Dual Structural System

Authors: Romel Cordova Shedan


The traditional seismic design is the methodology of Forced Based Design (FBD). The Displacement Based Design (DBD) is a seismic design that considers structural damage to achieve a failure mechanism of the structure before the collapse. It is easier to quantify damage of a structure with displacements rather than forces. Therefore, a structure to achieve an inelastic displacement design with good ductility, it is necessary to be damaged. The first part of this investigation is about differences between the methodologies of DBD and FBD with some DBD advantages. In the second part, there is a study case about a dual building 5-story, which is regular in plan and elevation. The building is located in a seismic zone, which acceleration in firm soil is 45% of the acceleration of gravity. Then it is applied both methodologies into the study case to compare its displacements, shear forces and overturning moments. In the third part, the Dynamic Time History Analysis (DTHA) is done, to compare displacements with DBD and FBD methodologies. Three accelerograms were used and the magnitude of the acceleration scaled to be spectrum compatible with design spectrum. Then, using ASCE 41-13 guidelines, the hinge plastics were assigned to structure. Finally, both methodologies results about study case are compared. It is important to take into account that the seismic performance level of the building for DBD is greater than FBD method. This is due to drifts of DBD are in the order of 2.0% and 2.5% comparing with FBD drifts of 0.7%. Therefore, displacements of DBD is greater than the FBD method. Shear forces of DBD result greater than FBD methodology. These strengths of DBD method ensures that structure achieves design inelastic displacements, because those strengths were obtained due to a displacement spectrum reduction factor which depends on damping and ductility of the dual system. Also, the displacements for the study case for DBD results to be greater than FBD and DTHA. In that way, it proves that the seismic performance level of the building for DBD is greater than FBD method. Due to drifts of DBD which are in the order of 2.0% and 2.5% compared with little FBD drifts of 0.7%.

Keywords: displacement-based design, displacement spectrum reduction factor, dynamic time history analysis, forced based design

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33141 Study on Optimization Design of Pressure Hull for Underwater Vehicle

Authors: Qasim Idrees, Gao Liangtian, Liu Bo, Miao Yiran


In order to improve the efficiency and accuracy of the pressure hull structure, optimization of underwater vehicle based on response surface methodology, a method for optimizing the design of pressure hull structure was studied. To determine the pressure shell of five dimensions as a design variable, the application of thin shell theory and the Chinese Classification Society (CCS) specification was carried on the preliminary design. In order to optimize variables of the feasible region, different methods were studied and implemented such as Opt LHD method (to determine the design test sample points in the feasible domain space), parametric ABAQUS solution for each sample point response, and the two-order polynomial response for the surface model of the limit load of structures. Based on the ultimate load of the structure and the quality of the shell, the two-generation genetic algorithm was used to solve the response surface, and the Pareto optimal solution set was obtained. The final optimization result was 41.68% higher than that of the initial design, and the shell quality was reduced by about 27.26%. The parametric method can ensure the accuracy of the test and improve the efficiency of optimization.

Keywords: parameterization, response surface, structure optimization, pressure hull

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33140 Design Application Procedures of 15 Storied 3D Reinforced Concrete Shear Wall-Frame Structure

Authors: H. Nikzad, S. Yoshitomi


This paper presents the design application and reinforcement detailing of 15 storied reinforced concrete shear wall-frame structure based on linear static analysis. Databases are generated for section sizes based on automated structural optimization method utilizing Active-set Algorithm in MATLAB platform. The design constraints of allowable section sizes, capacity criteria and seismic provisions for static loads, combination of gravity and lateral loads are checked and determined based on ASCE 7-10 documents and ACI 318-14 design provision. The result of this study illustrates the efficiency of proposed method, and is expected to provide a useful reference in designing of RC shear wall-frame structures.

Keywords: design constraints, ETABS, linear static analysis, MATLAB, RC shear wall-frame structures, structural optimization

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33139 CompPSA: A Component-Based Pairwise RNA Secondary Structure Alignment Algorithm

Authors: Ghada Badr, Arwa Alturki


The biological function of an RNA molecule depends on its structure. The objective of the alignment is finding the homology between two or more RNA secondary structures. Knowing the common functionalities between two RNA structures allows a better understanding and a discovery of other relationships between them. Besides, identifying non-coding RNAs -that is not translated into a protein- is a popular application in which RNA structural alignment is the first step A few methods for RNA structure-to-structure alignment have been developed. Most of these methods are partial structure-to-structure, sequence-to-structure, or structure-to-sequence alignment. Less attention is given in the literature to the use of efficient RNA structure representation and the structure-to-structure alignment methods are lacking. In this paper, we introduce an O(N2) Component-based Pairwise RNA Structure Alignment (CompPSA) algorithm, where structures are given as a component-based representation and where N is the maximum number of components in the two structures. The proposed algorithm compares the two RNA secondary structures based on their weighted component features rather than on their base-pair details. Extensive experiments are conducted illustrating the efficiency of the CompPSA algorithm when compared to other approaches and on different real and simulated datasets. The CompPSA algorithm shows an accurate similarity measure between components. The algorithm gives the flexibility for the user to align the two RNA structures based on their weighted features (position, full length, and/or stem length). Moreover, the algorithm proves scalability and efficiency in time and memory performance.

Keywords: alignment, RNA secondary structure, pairwise, component-based, data mining

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33138 Determine of Design Variables and Target Reliability Indexes of Underground Structure

Authors: Yo-Seph Byun, Gyu-Phil Lee, Young-Bin Park, Gye-Chun Cho, Seong-Won Lee


In Korea, a study on Limit State Design (LSD) for underground structures is being conducted in order to perform more effective design. In this study, as a result of MCS (Monte-Carlo Simulation) technique, failure probabilities of the structure during normal and earthquake are estimated in reliability analysis. Target reliability indexes are determined depending on load combinations for underground structure, and then, design variables such as load and material factors in LSD are decided. As a result, through the research in order to determine more reliable design variables, a specification of LSD for underground structures is able to be developed.

Keywords: design variable, limit state design, target reliability index, underground structure

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33137 Design and Production of Thin-Walled UHPFRC Footbridge

Authors: P. Tej, P. Kněž, M. Blank


The paper presents design and production of thin-walled U-profile footbridge made of UHPFRC. The main structure of the bridge is one prefabricated shell structure made of UHPFRC with dispersed steel fibers without any conventional reinforcement. The span of the bridge structure is 10 m and the clear width of 1.5 m. The thickness of the UHPFRC shell structure oscillated in an interval of 30-45 mm. Several calculations were made during the bridge design and compared with the experiments. For the purpose of verifying the calculations, a segment of 1.5 m was first produced, followed by the whole footbridge for testing. After the load tests were done, the design was optimized to cast the final footbridge.

Keywords: footbridge, non-linear analysis, shell structure, UHPFRC, Ultra-High Performance Fibre Reinforced Concrete

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33136 Dynamics Analyses of Swing Structure Subject to Rotational Forces

Authors: Buntheng Chhorn, WooYoung Jung


Large-scale swing has been used in entertainment and performance, especially in circus, for a very long time. To increase the safety of this type of structure, a thorough analysis for displacement and bearing stress was performed for an extreme condition where a full cycle swing occurs. Different masses, ranging from 40 kg to 220 kg, and velocities were applied on the swing. Then, based on the solution of differential dynamics equation, swing velocity response to harmonic force was obtained. Moreover, the resistance capacity was estimated based on ACI steel structure design guide. Subsequently, numerical analysis was performed in ABAQUS to obtain the stress on each frame of the swing. Finally, the analysis shows that the expansion of swing structure frame section was required for mass bigger than 150kg.

Keywords: swing structure, displacement, bearing stress, dynamic loads response, finite element analysis

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33135 Structure-Based Virtual Screening and in Silico Toxicity Test of Compounds against Mycobacterium tuberculosis 7,8-Diaminopelargonic Acid Aminotransferase (MtbBioA)

Authors: Junie B. Billones, Maria Constancia O. Carrillo, Voltaire G. Organo, Stephani Joy Y. Macalino, Inno A. Emnacen, Jamie Bernadette A. Sy


One of the major interferences in the Philippines’ tuberculosis control program is the widespread prevalence of Mtb strains that are resistant to known drugs, such as the MDR-TB (Multi Drug Resistant Tuberculosis) and XDR-TB (Extensively Drug Resistant Tuberculosis). Therefore, there is a pressing need to search for novel Mtb drug targets in order to be able to combat these drug resistant strains. The enzyme 7,8-diaminopelargonic acid aminotransferase enzyme, or more commonly known as BioA, is one such ideal target, as it is known that humans do not possess this enzyme. BioA primarily plays a key role in Mtb’s lipid biosynthesis pathway; more specifically in the synthesis of the enzyme cofactor biotin. In this study, structure-based pharmacophore screening, docking, and ADMET evaluation of compounds obtained from the DrugBank chemical database were performed against the MtbBioA enzyme. Results of the screening, docking, ADMET, and TOPKAT calculations revealed that out of the 6,516 compounds in the library, only 7 compounds indicated more favorable binding energies as compared to the enzyme’s known inhibitor, amiclenomycin (ACM), as well as good solubility and toxicity properties. Moreover, out of these 7 compounds, Molecule 6 exhibited the best solubility and toxicity properties. In the future, these lead compounds may then be subjected to bioactivity assays in vitro or in vivo for further evaluation of its therapeutic efficacy.

Keywords: 7, 8-diaminopelargonic acid aminotransferase, BioA, pharmacophore, molecular docking, ADMET, TOPKAT

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33134 A Systematic Literature Review of the Influence of New Media-Based Interventions on Drug Abuse

Authors: Wen Huei Chou, Te Lung Pan, Tsu Wen Yeh


New media have recently received increasing attention as a new communication form. The COVID-19 outbreak has pushed people’s lifestyles into the digital age, and the drug market has infiltrated formal e-commerce platforms. The self-media boom has fostered growth in online drug myths. To set the record straight, it is imperative to develop new media-based interventions. However, the usefulness of new media on this issue has not yet been fully examined. This study selected 13 articles on the development of new media-based interventions to prevent drug abuse from Airiti Library and Pub-Med as of October 3, 2021. The key conclusions are that (1) new media have a significantly positive influence on skills, self-efficacy, and behavior; (2) most interventions package traditional course learning into new media formats; and (3) new media can create a covert, interactive environment that cannot be replicated offline, which may merit attention in future research.

Keywords: drug abuse, interventions, new media, systematic review

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