Search results for: molecular docking and simulation

Authors: Somayeh Akrami, Vali-Allah Mozaffarian, Habib Onsori

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The studied region in this research, watershed Kuhkamar river, is about 112.66 square kilometers, it is located between 45º 48' 9" to 45º 2' 20" N and 38º 34' 15" to 38º 40' 28" E. The gained results of the studies on flora combinations, proved 287 plant species in 190 genera and 51 families. Asteracea with 49 and Lamiaceae with 27 plant species are the major plant families. Among collected species one interesting plant was found and determined as a new record Anemone narcissiflora L. for flora of Iran. This plant is known as a complex species that shows intraspecific speciation and is classified into about 12 subspecies and 10 varieties in world. To identify the infraspecies taxons of this species, in addition to morphological characteristics, the use of appropriate molecular markers for the better isolation of the individuals were needed.

Keywords: Anemone narcissiflora, floristic Study, kuhkamar, molecular marker

Procedia PDF Downloads 461

Authors: M. Gregušová, V. Schindlerová, I. Šajdlerová, P. Mohyla, J. Kedroň

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Company managers are always looking for more and more opportunities to succeed in today's fiercely competitive market. Maintain your place among the successful companies on the market today or come up with a revolutionary business idea; it is much more difficult than before. Each new or improved method, tools, or the approach that can improve the functioning of business processes or even the entire system is worth checking and verification. The use of simulation in the design of manufacturing systems and their management in practice is one of the ways without increased risk to find the optimal parameters of manufacturing processes and systems. The paper presents an example of using simulation to solve the bottleneck problem in concrete company.

Keywords: practical applications, business processes, systems, simulation

Procedia PDF Downloads 618

Authors: Boukais Meriem, B. Dennai, A. Ould-Abbas

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The efficiency of SiGe solar cells might be improved by a wide-band-gap window layer. In this work we were simulated using the one dimensional simulation program called analysis of microelectronic and photonic structures (AMPS-1D). In the simulation, the thickness of silicon window was varied from 80 to 150 nm. The rest of layer’s thicknesses were kept constant, by varying thickness of window layer the simulated device performance was demonstrate in the form of current-voltage (I-V) characteristics and quantum efficiency (QE).

Keywords: SiGe, AMPS-1D, simulation, conversion, efficiency, quantum efficiency

Procedia PDF Downloads 775

Authors: Ricardo Merlo

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The use of simulation as a digital didactic tool allowed students to reproduce the laws of Physics in order to improve their academic performance. The didactic resource of simulation also favored the motivation of most of the young people, depending on the subject of Physics to be developed in the classroom and in that sense, it was significant to know the favorable or unfavorable attitude that the students presented about the use of simulation resources to maximize the anchorage of the contents planned for the different classes developed in the classroom. The different real-time simulation applications that were offered free of charge through the Internet were not presented as a specific resource that could be used in a didactic model, and in that framework, the teachers of Physics at the university level did not apply these resources in a systematic way with the knowledge of the favorable or unfavorable attitude of the students towards these didactic resources. For this reason, this work proposed the design and application of attitude questionnaires to enhance the use of those simulation resources that allowed for improving the quality of the class and the academic performance of the students.

Keywords: physics teaching, attitude, motivation, didactic resources

Procedia PDF Downloads 41

Authors: Rauan Sakenov, Peter Bukovics, Peter Gaszler, Veronika Tokacs-Kollar, Beata Bugyi

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FH2 (formin homology-2) domains of several proteins, collectively known as formins, including DAAM, DAAM1 and mDia1, promote G-actin nucleation and elongation. FH2 domains of these formins exist as oligomers. Chain dimerization by ring structure formation serves as a structural basis for actin polymerization function of FH2 domain. Proper single chain configuration and specific interactions between its various regions are necessary for individual chains to form a dimer functional in G-actin nucleation and elongation. FH1 and WH2 domain-containing formins were shown to behave as intrinsically disordered proteins. Thus, the aim of this research was to study structural dynamics of FH2 domain of DAAM. To investigate structural features of FH2 domain of DAAM, molecular dynamics simulation of chain A of FH2 domain of DAAM solvated in water box in 50 mM NaCl was conducted at temperatures from 293.15 to 353.15K, with VMD 1.9.2, NAMD 2.14 and Amber Tools 21 using 2z6e and 1v9d PDB structures of DAAM was obtained on I-TASSER webserver. Calcium and ATP bound G-actin 3hbt PDB structure was used as a reference protein with well-described structural dynamics of denaturation. Topology and parameter information of CHARMM 2012 additive all-atom force fields for proteins, carbohydrate derivatives, water and ions were used in NAMD 2.14 and ff19SB force field for proteins in Amber Tools 21. The systems were energy minimized for the first 1000 steps, equilibrated and produced in NPT ensemble for 1ns using stochastic Langevin dynamics and the particle mesh Ewald method. Our root-mean square deviation (RMSD) analysis of molecular dynamics of chain A of FH2 domains of DAAM revealed similar insignificant changes of total molecular average RMSD values of FH2 domain of these formins at temperatures from 293.15 to 353.15K. In contrast, total molecular average RMSD values of G-actin showed considerable increase at 328K, which corresponds to the denaturation of G-actin molecule at this temperature and its transition from native, ordered, to denatured, disordered, state which is well-described in the literature. RMSD values of lasso and tail regions of chain A of FH2 domain of DAAM exhibited higher than total molecular average RMSD at temperatures from 293.15 to 353.15K. These regions are functional in intra- and interchain interactions and contain highly conserved tryptophan residues of lasso region, highly conserved GNYMN sequence of post region and amino acids of the shell of hydrophobic pocket of the salt bridge between Arg171 and Asp321, which are important for structural stability and ordered state of FH2 domain of DAAM and its functions in FH2 domain dimerization. In conclusion, higher than total molecular average RMSD values of lasso and post regions of chain A of FH2 domain of DAAM may explain disordered state of FH2 domain of DAAM at temperatures from 293.15 to 353.15K. Finally, absence of marked transition, in terms of significant changes in average molecular RMSD values between native and denatured states of FH2 domain of DAAM at temperatures from 293.15 to 353.15K, can make it possible to attribute these formins to the group of intrinsically disordered proteins rather than to the group of intrinsically ordered proteins such as G-actin.

Keywords: FH2 domain, DAAM, formins, molecular modelling, computational biophysics

Procedia PDF Downloads 115

Authors: Muchun Yu, Xue Gao, Qian Chen

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As a novel passive vibration isolation technology, molecular spring isolator (MSI) is investigated in this paper. An MSI consists of water and hydrophobic zeolites as working medium. Under periodic excitation, water molecules intrude into hydrophobic pores of zeolites when the pressure rises and water molecules extrude from hydrophobic pores when pressure drops. At the same time, energy is stored, released and dissipated. An MSI of piston-cylinder structure was designed in this work. Experiments were conducted to investigate the stiffness properties of MSI. The results show that MSI exhibits high-static-low dynamic (HSLD) stiffness. Furthermore, factors such as the quantity of zeolites, temperature, and ions in water are proved to have an influence on the stiffness properties of MSI.

Keywords: hydrophobic zeolites, molecular spring, stiffness, vibration isolation

Procedia PDF Downloads 449

Authors: Milica Karadžić, Lidija Jevrić, Sanja Podunavac-Kuzmanović, Strahinja Kovačević, Anamarija Mandić, Aleksandar Oklješa, Andrea Nikolić, Marija Sakač, Katarina Penov Gaši

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Using chemometric approach, the relationships between the chromatographic lipophilicity and in silico molecular descriptors for twenty-nine selected steroid derivatives were studied. The chromatographic lipophilicity was predicted using artificial neural networks (ANNs) method. The most important in silico molecular descriptors were selected applying stepwise selection (SS) paired with partial least squares (PLS) method. Molecular descriptors with satisfactory variable importance in projection (VIP) values were selected for ANN modeling. The usefulness of generated models was confirmed by detailed statistical validation. High agreement between experimental and predicted values indicated that obtained models have good quality and high predictive ability. Global sensitivity analysis (GSA) confirmed the importance of each molecular descriptor used as an input variable. High-quality networks indicate a strong non-linear relationship between chromatographic lipophilicity and used in silico molecular descriptors. Applying selected molecular descriptors and generated ANNs the good prediction of chromatographic lipophilicity of the studied steroid derivatives can be obtained. This article is based upon work from COST Actions (CM1306 and CA15222), supported by COST (European Cooperation and Science and Technology).

Keywords: artificial neural networks, chemometrics, global sensitivity analysis, liquid chromatography, steroids

Procedia PDF Downloads 318

Authors: A. Nuchitprasittichai, N. Lerdritsirikoon, T. Khamsing

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Simulation modeling can be used to solve real world problems. It provides an understanding of a complex system. To develop a simplified model of process simulation, a suitable experimental design is required to be able to capture surface characteristics. This paper presents the experimental design and algorithm used to model the process simulation for optimization problem. The CO₂ liquefaction based on external refrigeration with two refrigeration circuits was used as a simulation case study. Latin Hypercube Sampling (LHS) was purposed to combine with existing Central Composite Design (CCD) samples to improve the performance of CCD in generating the second order model of the system. The second order model was then used as the objective function of the optimization problem. The results showed that adding LHS samples to CCD samples can help capture surface curvature characteristics. Suitable number of LHS sample points should be considered in order to get an accurate nonlinear model with minimum number of simulation experiments.

Keywords: central composite design, CO2 liquefaction, latin hypercube sampling, simulation-based optimization

Procedia PDF Downloads 143

Authors: Mahmoud A. Abdulhamid

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Poly(ether-ether-ketone) (PEEK) has received increased attention due to its outstanding performance in different membrane applications including gas and liquid separation. However, it suffers from a semi-crystalline morphology, bad solubility and low porosity. To fabricate membranes from PEEK, the usage of harsh acid such as sulfuric acid is essential, regardless its hazardous properties. In this work, we report the molecular design of poly(ether-ether-ketones) (iPEEKs) with intrinsic porosity character, by incorporating kinked units into PEEK backbone such as spirobisindane, Tröger's base, and triptycene. The porous polymers were used to fabricate stable membranes for organic solvent nanofiltration application. To better understand the mechanism, we conducted molecular dynamics simulations to evaluate the possible interactions between the polymers and the solvents. Notable enhancement in separation performance was observed confirming the importance of molecular engineering of high-performance polymers. The iPEEKs demonstrated good solubility in polar aprotic solvents, a high surface area of 205–250 m² g⁻¹, and excellent thermal stability. Mechanically flexible nanofiltration membranes were prepared from N-methyl-2-pyrrolidone dope solution at iPEEK concentrations of 19–35 wt%. The molecular weight cutoff of the membranes was fine-tuned in the range of 450–845 g mol⁻¹ displaying 2–6 fold higher permeance (3.57–11.09 L m⁻² h⁻¹ bar⁻¹) than previous reports. The long-term stabilities were demonstrated by a 7 day continuous cross-flow filtration.

Keywords: molecular engineering, polymer synthesis, membrane fabrication, liquid separation

Procedia PDF Downloads 79

Authors: Mehdi Homayouni, Karim Adinehvand, Bakhtiar Azadbakht

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In this study, we used Monte Carlo code (MCNP4C) that is a general method, for simulation, electron source and electric field, a disc source with 0.05 cm radius in direct of anode are used, radius of disc source show focal spot of X-ray tube that here is 0.05 cm. In this simulation, the anode is from tungsten with 18.9 g/cm3 density and angle of the anode is 18°. We simulated X-ray tube for 140 kv. For increasing of speed data acquisition, we use F5 tally. With determination the exact position of F5 tally in the program, outputs are acquired. In this spectrum the start point is about 0.02 Mev, the absorption edges are about 0.06 Mev and 0.07 Mev, and average energy is about 0.05 Mev.

Keywords: X-spectrum, simulation, Monte Carlo, tube

Procedia PDF Downloads 703

Authors: Jiahui Song

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In order to predict or explain a complicated biological process, it is important first to construct mathematical models that can be used to yield analytical solutions. Through numerical simulation, mathematical model results can be used to test scenarios that might not be easily attained in a laboratory experiment, or to predict parameters or phenomena. High-intensity, nanosecond pulse electroporation has been a recent development in bioelectrics. The dynamic pore model can be achieved by including a dynamic aspect and a dependence on the pore population density into pore formation energy equation to analyze and predict such electroporation effects. For greater accuracy, with inclusion of atomistic details, molecular dynamics (MD) simulations were also carried out during this study. Besides inducing pores in cells, external voltages could also be used in principle to modulate action potential generation in nerves. This could have an application in electrically controlled ‘pain management’. Also a simple model-based rate equation treatment of the various cellular bio-chemical processes has been used to predict the pulse number dependent cell survival trends.

Keywords: model, high-intensity, nanosecond, bioelectrics

Procedia PDF Downloads 206

Authors: Yoshinori Matsuura, Saori Iwanaga

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The Great East Japan Earthquake occurred at 14:46 on Friday, March 11, 2011. It was the most powerful known earthquake to have hit Japan. The earthquake triggered extremely destructive tsunami waves of up to 40.5 meters in height. We focus on the ship’s evacuation from tsunami. Then we analyze about ships evacuation from tsunami using multi-agent simulation and we want to prepare for a coming earthquake. We developed a simulation model of ships that set sail from the port in order to evacuate from the tsunami considering the ship carrying dangerous goods.

Keywords: Ship’s evacuation, multi-agent simulation, tsunami

Procedia PDF Downloads 438

Authors: Martin Kendra, Tomas Skrucany, Jozef Gnap, Jan Ponicky

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Paper deals with the modeling and simulation of energy consumption and GHG production of two different modes of regional passenger transport – road and railway. These two transport modes use the same type of fuel – diesel. Modeling and simulation of the energy consumption in transport is often used due to calculation satisfactory accuracy and cost efficiency. Paper deals with the calculation based on EN standards and information collected from technical information from vehicle producers and characteristics of tracks. Calculation included maximal theoretical capacity of bus and train and real passenger’s measurement from operation. Final energy consumption and GHG production is calculated by using software simulation. In evaluation of the simulation is used system ‘well to wheel’.

Keywords: bus, consumption energy, GHG, production, simulation, train

Procedia PDF Downloads 419

Authors: Amin Sahebnasagh, Karim Adinehvand, Bakhtiar Azadbakht

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In this study, we used Monte Carlo code (MCNP4C) that is a general method, for simulation, electron source and electric field, a disc source with 0.05 cm radius in direct of anode are used, radius of disc source show focal spot of x-ray tube that here is 0.05 cm. In this simulation, anode is from tungsten with 18.9 g/cm3 density and angle of anode is 180. we simulated x-ray tube for 140 kv. For increasing of speed data acquisition we use F5 tally. With determination the exact position of F5 tally in program, outputs are acquired. In this spectrum the start point is about 0.02 Mev, the absorption edges are about 0.06 Mev and 0.07 Mev and average energy is about 0.05 Mev.

Keywords: x-spectrum, simulation, Monte Carlo, MCNP4C code

Procedia PDF Downloads 627

Authors: Micheale Yifter Weldemichael, Stefaan Werbrouck, Hailay Mehari Gebremedhn

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Sesame (Sesamum indicum L.) is among the most important oilseed crops for its high edible oil quality and quantity. Sesame is grown for food, medicinal, pharmaceutical, and industrial uses. Sesame is also cultivated as a main cash crop in Asia and Africa by smallholder farmers. Despite the global exponential increase in sesame cultivation area, its production and productivity remain low, mainly due to biotic and abiotic constraints. Notwithstanding the efforts to solve these problems, a low level of genetic variation and inadequate genomic resources hinder the progress of sesame improvement. The objective of this paper is, therefore, to review recent advances in the area of molecular breeding and transformation to overcome major production constraints and could result in enhanced and sustained sesame production. This paper reviews various researches conducted to date on molecular breeding and genetic transformation in sesame focusing on molecular markers used in assessing the available online database resources, genes responsible for key agronomic traits as well as transgenic technology and genome editing. The review concentrates on quantitative and semi-quantitative studies on molecular breeding for key agronomic traits such as improvement of yield components, oil and oil-related traits, disease and insect/pest resistance, and drought, waterlogging and salt tolerance, as well as sesame genetic transformation and genome editing techniques. Pitfalls and limitations of existing studies and methodologies used so far are identified and some priorities for future research directions in sesame genetic improvement are identified in this review.

Keywords: molecular breeding, oil, sesame, shattering

Procedia PDF Downloads 51

Authors: Nikhil Agrawal, Adam A. Skelton

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Alzheimer’s disease (AD) is one of the most common forms of dementia, which is caused by misfolding and aggregation of amyloid beta (Aβ) peptides into amyloid-β fibrils (Aβ fibrils). To disrupt the remodeling of Aβ fibrils, a number of candidate molecules have been proposed. To study the molecular mechanisms of Aβ fibrils remodeling we performed a series of all-atom molecular dynamics simulations, a total time of 3µs, in explicit solvent. Several previously undiscovered candidate molecule-Aβ fibrils binding modes are unraveled; one of which shows the direct conformational change of the Aβ fibril by understanding the physicochemical factors responsible for binding and subsequent remodeling of Aβ fibrils by the candidate molecule, open avenues into structure-based drug design for AD can be opened.

Keywords: alzheimer’s disease, amyloid, MD simulations, misfolded protein

Procedia PDF Downloads 321

Authors: Hamzeh Alipour, Masoumeh Bagheri, Abbasali Raz, Javad Dadgar Pakdel, Kourosh Azizi, Aboozar Soltani, Mohammad Djaefar Moemenbellah-Fard

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Background: Maggot debridement therapy is an appropriate, effective, and controlled method using sterilized larvae of Luciliasericata (L.sericata) to treat wounds. Netrin-A is an enzyme in the Laminins family which secreted from salivary gland of L.sericata with a central role in neural regeneration and angiogenesis. This study aimed to production of new recombinant Netrin-A protein of Luciliasericata larvae by baculovirus expression vector system (BEVS) in SF9. Material and methods: In the first step, gene structure was subjected to the in silico studies, which were include determination of Antibacterial activity, Prion formation risk, homology modeling, Molecular docking analysis, and Optimization of recombinant protein. In the second step, the Netrin-A gene was cloned and amplified in pTG19 vector. After digestion with BamH1 and EcoR1 restriction enzymes, it was cloned in pFastBac HTA vector. It was then transformed into DH10Bac competent cells, and the recombinant Bacmid was subsequently transfected into insect Sf9 cells. The expressed recombinant Netrin-A was thus purified in the Ni-NTA agarose. This protein evaluation was done using SDS-PAGE and western blot, respectively. Finally, its concentration was calculated with the Bradford assay method. Results: The Bacmid vector structure with Netrin-A was successfully constructed and then expressed as Netrin-A protein in the Sf9 cell lane. The molecular weight of this protein was 52 kDa with 404 amino acids. In the in silico studies, fortunately, we predicted that recombinant LSNetrin-A have Antibacterial activity and without any prion formation risk.This molecule hasa high binding affinity to the Neogenin and a lower affinity to the DCC-specific receptors. Signal peptide located between amino acids 24 and 25. The concentration of Netrin-A recombinant protein was calculated to be 48.8 μg/ml. it was confirmed that the characterized gene in our previous study codes L. sericata Netrin-A enzyme. Conclusions: Successful generation of the recombinant Netrin-A, a secreted protein in L.sericata salivary glands, and because Luciliasericata larvae are used in larval therapy. Therefore, the findings of the present study could be useful to researchers in future studies on wound healing.

Keywords: blowfly, BEVS, gene, immature insect, recombinant protein, Sf9

Procedia PDF Downloads 69

Authors: Milica Ž. Karadžić, Lidija R. Jevrić, Sanja Podunavac-Kuzmanović, Strahinja Z. Kovačević, Anamarija I. Mandić, Katarina Penov-Gaši, Andrea R. Nikolić, Aleksandar M. Oklješa

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This study considered selection of the in silico molecular descriptors and the models for newly synthesized steroid derivatives description and their characterization using chemometric techniques. Multiple linear regression (MLR) models were established and gave the best molecular descriptors for quantitative structure-retention relationship (QSRR) modeling of the retention of the investigated molecules. MLR models were without multicollinearity among the selected molecular descriptors according to the variance inflation factor (VIF) values. Used molecular descriptors were ranked using generalized pair correlation method (GPCM). In this method, the significant difference between independent variables can be noticed regardless almost equal correlation between dependent variable. Generated MLR models were statistically and cross-validated and the best models were kept. Models were ranked using sum of ranking differences (SRD) method. According to this method, the most consistent QSRR model can be found and similarity or dissimilarity between the models could be noticed. In this study, SRD was performed using average values of experimentally observed data as a golden standard. Chemometric analysis was conducted in order to characterize newly synthesized steroid derivatives for further investigation regarding their potential biological activity and further synthesis. This article is based upon work from COST Action (CM1105), supported by COST (European Cooperation in Science and Technology).

Keywords: generalized pair correlation method, molecular descriptors, regression analysis, steroids, sum of ranking differences

Procedia PDF Downloads 328

Authors: Apisaraporn Baicharoen, Prapasiri Pongprayoon

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Betaine aldehyde dehydrogenase 2 (BADH2) is an enzyme that inhibits the accumulation of 2-acetyl-1-pyrroline (2AP), a potent flavor compound in rice fragrance. BADH2 contains three domains (NAD-binding, substrate-binding, and oligomerization domains). It catalyzes the oxidation of amino aldehydes. The lack of BADH2 results in the formation of 2AP and consequently an increase in rice fragrance. To date, inadequate data on BADH2 structure and function are available. An insight into the nature of BADH2 can serve as one of key starting points for the production of high quality fragrant rice. In this study, we therefore constructed the homology model of BADH2 and employed 500-ns Molecular Dynamics simulations (MD) to primarily understand the structural and dynamic properties of BADH2. Initially, Ramachandran plot confirms the good quality of modeled protein structure. Principle Component Analysis (PCA) was also calculated to capture the protein dynamics. Among 3 domains, the results show that NAD binding site is found to be more flexible. Moreover, interactions from key amino acids (N162, E260, C294, and Y419) that are crucial for function are investigated.

Keywords: betaine aldehyde dehydrogenase 2, fragrant rice, homology modeling, molecular dynamics simulations

Procedia PDF Downloads 190

Authors: B. A. A. Paixão, J. V. B. Gomide

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This work aims to analyze the locative structure used by the locative games of the company Niantic. To fulfill this objective, a literature review on the representation and simulation of cities was developed; interviews with Ingress players and playing Ingress. Relating these data, it was possible to deepen the relationship between the virtual and the real to create the simulation of cities and their cultural objects in locative games. Cities representation associates geo-location provided by the Global Positioning System (GPS), with augmented reality and digital image, and provides a new paradigm in the city interaction with its parts and real and virtual world elements, homeomorphic to real world. Bibliographic review of papers related to the representation and simulation study and their application in locative games was carried out and is presented in the present paper. The cities representation and simulation concepts in locative games, and how this setting enables the flow and immersion in urban space, are analyzed. Some examples of games are discussed for this new setting development, which is a mix of real and virtual world. Finally, it was proposed a Locative Structure for electronic games using the concepts of heterotrophic representations and isotropic representations conjoined with immediacy and hypermediacy.

Keywords: cities representation, cities simulation, games simulation, immersion, locative games

Procedia PDF Downloads 183

Authors: Salma M. Wakil

Abstract:

Advances in the field of genetics overwhelmed detecting large number of inherited disorders at the molecular level and directed to the development of innovative technologies. These innovations have led to gene sequencing, prenatal mutation detection, pre-implantation genetic diagnosis; population based carrier screening and genome wide analyses using microarrays. Microarrays are widely used in establishing clinical and diagnostic setup for genetic anomalies at a massive level, with the advent of cytoscan molecular karyotyping as a clinical utility card for detecting chromosomal aberrations with high coverage across the entire human genome. Unlike a regular karyotype that relies on the microscopic inspection of chromosomes, molecular karyotyping with cytoscan constructs virtual chromosomes based on the copy number analysis of DNA which improves its resolution by 100-fold. We have been investigating a large number of patients with Developmental Delay and Intellectual disability with this platform for establishing micro syndrome deletions and have detected number of novel CNV’s in the Arabian population with the clinical relevance.

Keywords: microarrays, molecular karyotyping, developmental delay, genetics

Procedia PDF Downloads 430

Authors: Markéta Gregušová, Vladimíra Schindlerová, Ivana Šajdlerová, Petr Mohyla, Jan Kedroň

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Company managers are always looking for more and more opportunities to succeed in today's fiercely competitive market. To maintain your place among the successful companies on the market today or to come up with a revolutionary business idea is much more difficult than before. Each new or improved method, tool, or approach that can improve the functioning of business processes or even of the entire system is worth checking and verification. The use of simulation in the design of manufacturing systems and their management in practice is one of the ways without increased risk, which makes it possible to find the optimal parameters of manufacturing processes and systems. The paper presents an example of use of simulation for solution of the bottleneck problem in the concrete company.

Keywords: practical applications, business processes, systems, simulation

Procedia PDF Downloads 524

Authors: U. P. L. Wijayarathne, K. C. Wasalathilake

Abstract:

This work presents the modelling and simulation of saponification of ethyl acetate in the presence of sodium hydroxide in a plug flow reactor using Aspen Plus simulation software. Plug flow reactors are widely used in the industry due to the non-mixing property. The use of plug flow reactors becomes significant when there is a need for continuous large scale reaction or fast reaction. Plug flow reactors have a high volumetric unit conversion as the occurrence for side reactions is minimum. In this research Aspen Plus V8.0 has been successfully used to simulate the plug flow reactor. In order to simulate the process as accurately as possible HYSYS Peng-Robinson EOS package was used as the property method. The results obtained from the simulation were verified by the experiment carried out in the EDIBON plug flow reactor module. The correlation coefficient (r2) was 0.98 and it proved that simulation results satisfactorily fit for the experimental model. The developed model can be used as a guide for understanding the reaction kinetics of a plug flow reactor.

Keywords: aspen plus, modelling, plug flow reactor, simulation

Procedia PDF Downloads 577

Authors: Thomas Trouton, Sebastian Tanner, Manvir Sandher

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The use of simulation in undergraduate and postgraduate medical curricula is ever-growing, is a useful addition to the traditional apprenticeship model of learning within medical education, and better prepares graduates for the team-based approach to healthcare seen in real-life clinical practice. As a learning tool, however, undergraduate medical students often have little understanding of the theory behind the use of medical simulation and have little experience in planning and delivering their own simulated teaching sessions. We designed and implemented a student-selected component (SSC) as part of the undergraduate medical curriculum at the University of Buckingham Medical School to introduce students to the concepts behind the use of medical simulation in education and allow them to plan and deliver their own simulated medical scenario to their peers. The SSC took place over a 2-week period in the 3rd year of the undergraduate course. There was a mix of lectures, seminars and interactive group work sessions, as well as hands-on experience in the simulation suite, to introduce key concepts related to medical simulation, including technical considerations in simulation, human factors, debriefing and troubleshooting scenarios. We evaluated the success of our SSC using “Net Promotor Scores” (NPS) to assess students’ confidence in planning and facilitating a simulation-based teaching session, as well as leading a debrief session. In all three domains, we showed an increase in the confidence of the students. We also showed an increase in confidence in the management of common medical emergencies as a result of the SSC. Overall, the students who chose our SSC had the opportunity to learn new skills in medical education, with a particular focus on the use of simulation-based teaching, and feedback highlighted that a number of students would take these skills forward in their own practice. We demonstrated an increase in confidence in several domains related to the use of medical simulation in education and have hopefully inspired a new generation of medical educators.

Keywords: simulation, SSC, teaching, medical students

Procedia PDF Downloads 101

Authors: Walid Hassairi, Moncef Bousselmi, Mohamed Abid

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Functional verification is a major part of today’s system design task. Several approaches are available for verification on a high abstraction level, where designs are often modeled using MATLAB/Simulink. However, different approaches are a barrier to a unified verification flow. In this paper, we propose a co-simulation interface between SystemC and MATLAB and Simulink to enable functional verification of multi-abstraction levels designs. The resulting verification flow is tested on JPEG compression algorithm. The required synchronization of both simulation environments, as well as data type conversion is solved using the proposed co-simulation flow. We divided into two encoder jpeg parts. First implemented in SystemC which is the DCT is representing the HW part. Second, consisted of quantization and entropy encoding which is implemented in Matlab is the SW part. For communication and synchronization between these two parts we use S-Function and engine in Simulink matlab. With this research premise, this study introduces a new implementation of a Hardware SystemC of DCT. We compare the result of our simulation compared to SW / SW. We observe a reduction in simulation time you have 88.15% in JPEG and the design efficiency of the supply design is 90% in SDR.

Keywords: hardware/software, co-design, co-simulation, systemc, matlab, s-function, communication, synchronization

Procedia PDF Downloads 375

Authors: He Chao, Zhang Lei, Liu Ran, Li Ang

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Temperature regulating system by gaseous nitrogen is of importance to the space environment simulator, which keep the shrouds in the temperature range from -150℃ to +150℃. Liquid nitrogen spray equipment is one of the most critical parts in the temperature regulating system by gaseous nitrogen. Y type jet atomizer and internal mixing atomizer of the liquid nitrogen spray equipment are studied in this paper, 2D/3D atomizer model was established and grid division was conducted respectively by the software of Catia and ICEM. Based on the above preparation, numerical simulation on the spraying process of the atomizer by FLUENT is performed. Using air and water as the medium, comparison between the tests and numerical simulation was conducted and the results of two ways match well. Hence, it can be conclude that this atomizer model can be applied in the numerical simulation of liquid nitrogen spray equipment.

Keywords: space environmental simulator, liquid nitrogen spray, Y type jet atomizer, internal mixing atomizer, numerical simulation, fluent

Procedia PDF Downloads 383

Authors: Oleg Reva, Ilya Korotetskiy, Marina Lankina, Murat Kulmanov, Aleksandr Ilin

Abstract:

Molecular docking approaches are widely used for design of new antibiotics and modeling of antibacterial activities of numerous ligands which bind specifically to active centers of indispensable enzymes and/or key signaling proteins of pathogens. Widespread drug resistance among pathogenic microorganisms calls for development of new antibiotics specifically targeting important metabolic and information pathways. A generally recognized problem is that almost all molecular targets have been identified already and it is getting more and more difficult to design innovative antibacterial compounds to combat the drug resistance. A promising way to overcome the drug resistance problem is an induction of reversion of drug resistance by supplementary medicines to improve the efficacy of the conventional antibiotics. In contrast to well established computer-based drug design, modeling of drug resistance reversion still is in its infancy. In this work, we proposed an approach to identification of compensatory genetic variants reducing the fitness cost associated with the acquisition of drug resistance by pathogenic bacteria. The approach was based on an analysis of the population genetic of Mycobacterium tuberculosis and on results of experimental modeling of the drug resistance reversion induced by a new anti-tuberculosis drug FS-1. The latter drug is an iodine-containing nanomolecular complex that passed clinical trials and was admitted as a new medicine against MDR-TB in Kazakhstan. Isolates of M. tuberculosis obtained on different stages of the clinical trials and also from laboratory animals infected with MDR-TB strain were characterized by antibiotic resistance, and their genomes were sequenced by the paired-end Illumina HiSeq 2000 technology. A steady increase in sensitivity to conventional anti-tuberculosis antibiotics in series of isolated treated with FS-1 was registered despite the fact that the canonical drug resistance mutations identified in the genomes of these isolates remained intact. It was hypothesized that the drug resistance phenotype in M. tuberculosis requires an adjustment of activities of many genes to compensate the fitness cost of the drug resistance mutations. FS-1 cased an aggravation of the fitness cost and removal of the drug-resistant variants of M. tuberculosis from the population. This process caused a significant increase in genetic heterogeneity of the Mtb population that was not observed in the positive and negative controls (infected laboratory animals left untreated and treated solely with the antibiotics). A large-scale search for linkage disequilibrium associations between the drug resistance mutations and genetic variants in other genomic loci allowed identification of target proteins, which could be influenced by supplementary drugs to increase the fitness cost of the drug resistance and deprive the drug-resistant bacterial variants of their competitiveness in the population. The approach will be used to improve the efficacy of FS-1 and also for computer-based design of new drugs to combat drug-resistant infections.

Keywords: complete genome sequencing, computational modeling, drug resistance reversion, Mycobacterium tuberculosis

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Authors: Elena K. Schneider, Johnny X. Huang, Vincenzo Carbone, Mark Baker, Mohammad A. K. Azad, Matthew A. Cooper, Jian Li, Tony Velkov

Abstract:

Ivacaftor is a novel CF trans-membrane conductance regulator (CFTR) potentiator that improves the pulmonary function for cystic fibrosis patients bearing a G551D CFTR-protein mutation. Because ivacaftor is highly bound (>97%) to plasma proteins, there is the strong possibility that co-administered CF drugs that compete for the same plasma protein binding sites and impact the free drug concentration. This in turn could lead to drastic changes in the in vivo efficacy of ivacaftor and therapeutic outcomes. This study compares the binding affinity of ivacaftor and co-administered CF drugs for human serum albumin (HSA) and α1-acid glycoprotein (AGP) using surface plasmon resonance and fluorimetric binding assays that measure the displacement of site selective probes. Due to their high plasma protein binding affinities, drug-drug interactions between ivacaftor are to be expected with ducosate, montelukast, ibuprofen, dicloxacillin, omeprazole and loratadine. The significance of these drug-drug interactions is interpreted in terms of the pharmacodynamic/pharmacokinetic parameters and molecular docking simulations. The translational outcomes of the data are presented as recommendations for a staggered treatment regimen for future clinical trials which aims to maximize the effective free drug concentration and clinical efficacy of ivacaftor.

Keywords: human α-1-acid glycoprotein, binding affinity, human serum albumin, ivacaftor, cystic fibrosis

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Authors: Galu Papy Yuma

Abstract:

This paper presents a new dynamic simulation of a power system consisting of four machines equipped with the Generalized Unified Power Flow Controller (GUPFC) to improve power system stability. The dynamic simulation of the GUPFC consists of one shunt converter and two series converters based on voltage source converter, and DC link capacitor installed in the power system. MATLAB/Simulink is used to arrange the dynamic simulation of the GUPFC, where the power system is simulated in order to investigate the impact of the controller on power system oscillation damping and to show the simulation program reliability. The Improved Chaotic- Harmony Search (IC-HS) Algorithm is used to provide the parameter controller in order to lead-lag compensation design. The results obtained by simulation show that the power system with four machines is suitable for stability analysis. The use of GUPFC and IC-HS Algorithm provides the excellent capability in fast damping of power system oscillations and improve greatly the dynamic stability of the power system.

Keywords: GUPFC, IC-HS algorithm, Matlab/Simulink, damping oscillation

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Authors: Md. Samsuddin Ansari, Ashish Arora

Abstract:

Every year 10 million people fall ill with one of the oldest diseases known as tuberculosis, caused by Mycobacterium tuberculosis. The success of M. tuberculosis as a pathogen is because of its ability to persist in host tissues. Multidrug resistance (MDR) mycobacteria cases increase every day, which is associated with efflux pumps controlled at the level of transcription. The transcription regulators of MDR transporters in bacteria belong to one of the following four regulatory protein families: AraC, MarR, MerR, and TetR. Phenolic acid decarboxylase repressor (PadR), like a family of transcription regulators, is closely related to the MarR family. Phenolic acid decarboxylase repressor (PadR) was first identified as a transcription factor involved in the regulation of phenolic acid stress response in various microorganisms (including Mycobacterium tuberculosis H37Rv). Recently research has shown that the PadR family transcription factors are global, multifunction transcription regulators. Rv0047c is a PadR subfamily-1 protein. We are exploring the biophysical and structural characterization of Rv0047c. The Rv0047 gene was amplified by PCR using the primers containing EcoRI and HindIII restriction enzyme sites cloned in pET-NH6 vector and overexpressed in DH5α and BL21 (λDE3) cells of E. coli following purification with Ni2+-NTA column and size exclusion chromatography. We did DSC to know the thermal stability; the Tm (transition temperature) of protein is 55.29ºC, and ΔH (enthalpy change) of 6.92 kcal/mol. Circular dichroism to know the secondary structure and conformation and fluorescence spectroscopy for tertiary structure study of protein. To understand the effect of pH on the structure, function, and stability of Rv0047c we employed spectroscopy techniques such as circular dichroism, fluorescence, and absorbance measurements in a wide range of pH (from pH-2.0 to pH-12). At low and high pH, it shows drastic changes in the secondary and tertiary structure of the protein. EMSA studies showed the specific binding of Rv0047c with its own 30-bp promoter region. To determine the effect of complex formation on the secondary structure of Rv0047c, we examined the CD spectra of the complex of Rv0047c with promoter DNA of rv0047. The functional role of Rv0047c was characterized by over-expressing the Rv0047c gene under the control of hsp60 promoter in Mycobacterium tuberculosis H37Rv. We have predicted the three-dimensional structure of Rv0047c using the Swiss Model and Modeller, with validity checked by the Ramachandra plot. We did molecular docking of Rv0047c with dnaA, through PatchDock following refinement through FireDock. Through this, it is possible to easily identify the binding hot-stop of the receptor molecule with that of the ligand, the nature of the interface itself, and the conformational change undergone by the protein pattern. We are using X-crystallography to unravel the structure of Rv0047c. Overall the studies show that Rv0047c may have transcription regulation along with providing an insight into the activity of Rv0047c in the pH range of subcellular environment and helps to understand the protein-protein interaction, a novel target to kill dormant bacteria and potential strategy for tuberculosis control.

Keywords: mycobacterium tuberculosis, phenolic acid decarboxylase repressor, Rv0047c, Circular dichroism, fluorescence spectroscopy, docking, protein-protein interaction

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