Search results for: homology modelling

Authors: Mohammadamin Hashemi, Mohammadreza Kashizadeh

Abstract:

Droughts pose a significant threat to sustainable water resource management, agriculture, and socioeconomic sectors, particularly in the field of climate change. This study investigates drought simulation using rainfall-runoff modelling in the Cuneo district, Italy, over the past 60-year period. The study leverages the TUW model, a lumped conceptual rainfall-runoff model with a semi-distributed operation capability. Similar in structure to the widely used Hydrologiska Byråns Vattenbalansavdelning (HBV) model, the TUW model operates on daily timesteps for input and output data specific to each catchment. It incorporates essential routines for snow accumulation and melting, soil moisture storage, and streamflow generation. Multiple catchments' discharge data within the Cuneo district form the basis for thorough model calibration employing the Kling-Gupta Efficiency (KGE) metric. A crucial metric for reliable drought analysis is one that can accurately represent low-flow events during drought periods. This ensures that the model provides a realistic picture of water availability during these critical times. Subsequent validation of monthly discharge simulations thoroughly evaluates overall model performance. Beyond model development, the investigation delves into drought analysis using the robust Standardized Runoff Index (SRI). This index allows for precise characterization of drought occurrences within the study area. A meticulous comparison of observed and simulated discharge data is conducted, with particular focus on low-flow events that characterize droughts. Additionally, the study explores the complex interplay between land characteristics (e.g., soil type, vegetation cover) and climate variables (e.g., precipitation, temperature) that influence the severity and duration of hydrological droughts. The study's findings demonstrate successful calibration of the TUW model across most catchments, achieving commendable model efficiency. Comparative analysis between simulated and observed discharge data reveals significant agreement, especially during critical low-flow periods. This agreement is further supported by the Pareto coefficient, a statistical measure of goodness-of-fit. The drought analysis provides critical insights into the duration, intensity, and severity of drought events within the Cuneo district. This newfound understanding of spatial and temporal drought dynamics offers valuable information for water resource management strategies and drought mitigation efforts. This research deepens our understanding of drought dynamics in the Cuneo region. Future research directions include refining hydrological modelling techniques and exploring future drought projections under various climate change scenarios.

Keywords: hydrologic extremes, hydrological drought, hydrological modelling, machine learning, rainfall-runoff modelling

Procedia PDF Downloads 41

Authors: Afaque Manzoor Soomro, Faheem Ahmed, Fida Hussain Memon, Kyung Hyun Choi

Abstract:

This paper proposes the bioinspired soft frog robot. All printing technology was used for the fabrication of the robot. Polyjet printing was used to print the front and back limbs, while ultrathin filament was used to print the body of the robot, which makes it a complete soft swimming robot. The dual thrust generation approach has been proposed by embedding the main muscle and antagonistic muscle in all the limbs, which enables it to attain high speed (18 mm/s), and significant control of swimming in dual modes (synchronous and asynchronous modes). To achieve the swimming motion of the frog, the design, motivated by the rigorous modelling and real frog dynamics analysis, enabled the as-developed frog robot (FROBOT) to swim at a significant level of consistency with the real frog. The FROBOT (weighing 65 g) can swim at different controllable frequencies (0.5–2Hz) and can turn in any direction by following custom-made LabVIEW software’s commands which enables it to swim at speed up to 18 mm/s on the surface of deep water (100 cm) with excellent weight balance.

Keywords: soft robotics, soft actuator, frog robot, 3D printing

Procedia PDF Downloads 101

Authors: Jahedul Islam Chowdhury, Bao Kha Nguyen, David Thornhill, Roy Douglas, Stephen Glover

Abstract:

Organic Rankine Cycle (ORC) is the most commonly used method for recovering energy from small sources of heat. The investigation of the ORC in supercritical condition is a new research area as it has a potential to generate high power and thermal efficiency in a waste heat recovery system. This paper presents a steady state ORC model in supercritical condition and its simulations with a real engine’s exhaust data. The key component of ORC, evaporator, is modelled using finite volume method, modelling of all other components of the waste heat recovery system such as pump, expander and condenser are also presented. The aim of this paper is to investigate the effects of mass flow rate and evaporator outlet temperature on the efficiency of the waste heat recovery process. Additionally, the necessity of maintaining an optimum evaporator outlet temperature is also investigated. Simulation results show that modification of mass flow rate is the key to changing the operating temperature at the evaporator outlet.

Keywords: Organic Rankine cycle, supercritical condition, steady state model, waste heat recovery

Procedia PDF Downloads 405

Authors: Adel Francis

Abstract:

Most of scheduling methods and software apply the critical path logic. This logic schedule activities, apply constraints between these activities and try to optimize and level the allocated resources. The extensive use of this logic produces a complex an erroneous network hard to present, follow and update. Planning and management building projects should tackle the coordination of works and the management of limited spaces, traffic, and supplies. Activities cannot be performed without the resources available and resources cannot be used beyond the capacity of workplaces. Otherwise, workspace congestion will negatively affect the flow of works. The objective of the space planning is to link the spatial and temporal aspects, promote efficient use of the site, define optimal site occupancy rates, and ensures suitable rotation of the workforce in the different spaces. The Chronographic scheduling modelling belongs to this category and models construction operations as well as their processes, logical constraints, association and organizational models, which help to better illustrate the schedule information using multiple flexible approaches. The model defined three categories of areas (punctual, surface and linear) and four different layers (space creation, systems, closing off space, finishing, and reduction of space). The Chronographical modelling is a more complete communication method, having the ability to alternate from one visual approach to another by manipulation of graphics via a set of parameters and their associated values. Each individual approach can help to schedule a certain project type or specialty. Visual communication can also be improved through layering, sheeting, juxtaposition, alterations, and permutations, allowing for groupings, hierarchies, and classification of project information. In this way, graphic representation becomes a living, transformable image, showing valuable information in a clear and comprehensible manner, simplifying the site management while simultaneously utilizing the visual space as efficiently as possible.

Keywords: building projects, chronographic modelling, CPM, critical path, precedence diagram, scheduling

Procedia PDF Downloads 155

Authors: Alexander V. Spirov, David M. Holloway, Ekaterina M. Myasnikova

Abstract:

Segmentation of the early Drosophila embryo results from the dynamic establishment of spatial gene expression patterns. Patterning occurs on an embryo geometry which is a 'deformed' prolate ellipsoid, with anteroposterior and dorsal-ventral major and minor axes, respectively. Patterning is largely independent along each axis, but some interaction can be seen in the 'bending' of the segmental expression stripes. This interaction is not well understood. In this report, we investigate how 3D geometrical features of the early embryo affect the segmental expression patterning. Specifically, we study the effect of geometry on formation of the Bicoid primary morphogenetic gradient. Our computational results demonstrate that embryos with a much longer ventral than dorsal surface ('bellied') can produce curved Bicoid concentration contours which could activate curved stripes in the downstream pair-rule segmentation genes. In addition, we show that having an extended source for Bicoid in the anterior of the embryo may be necessary for producing the observed exponential form of the Bicoid gradient along the anteroposterior axis.

Keywords: Drosophila embryo, bicoid morphogenetic gradient, exponential expression profile, expression surface form, segmentation genes, 3D modelling

Procedia PDF Downloads 274

Authors: Kyle Phillips, Ndiko Ludidi

Abstract:

Global climate change has resulted in altered rainfall patterns, which has resulted in annual losses in maize crop yields due to drought. Therefore it is important to produce maize cultivars that are more drought-tolerant, which is not an easily accomplished task as plants have a plethora of physical and biochemical adaptation methods. One such mechanism is the drought-induced expression of enzymatic and non-enzymatic proteins which assist plants to resist the effects of drought on their growth and development. One of these proteins is AtRD22 which has been identified in Arabidopsis thaliana. Using an in silico approach, a maize protein with 48% sequence homology to AtRD22 has been identified. This protein appears to be localized in the extracellular matrix, similarly to AtRD22. Promoter analysis of the encoding gene reveals cis-acting elements suggestive of induction of the gene’s expression by abscisic acid (ABA). Semi-quantitative transcriptomic analysis of the putative maize RD22 has revealed an increase in transcript levels after the exposure to drought. Current work elucidates the effect of up-regulation and silencing of the maize RD22 gene on the tolerance of maize to drought. The potential role of the maize RD22 gene in maize drought tolerance can be used as a tool to improve food security.

Keywords: abscisic acid, drought-responsive cis-acting elements, maize drought tolerance, RD22

Procedia PDF Downloads 464

Authors: Mohamed Elhakeem, A. N. Thanos Papanicolaou, Christopher Wilson, Yi-Jia Chang

Abstract:

In this study, a physically-based, modelling framework was developed to predict saturated hydraulic conductivity (KSAT) dynamics in the Clear Creek Watershed (CCW), Iowa. The modelling framework integrated selected pedotransfer functions and watershed models with geospatial tools. A number of pedotransfer functions and agricultural watershed models were examined to select the appropriate models that represent the study site conditions. Models selection was based on statistical measures of the models’ errors compared to the KSAT field measurements conducted in the CCW under different soil, climate and land use conditions. The study has shown that the predictions of the combined pedotransfer function of Rosetta and the Water Erosion Prediction Project (WEPP) provided the best agreement to the measured KSAT values in the CCW compared to the other tested models. Therefore, Rosetta and WEPP were integrated with the Geographic Information System (GIS) tools for visualization of the data in forms of geospatial maps and prediction of KSAT variability in CCW due to the seasonal changes in climate and land use activities.

Keywords: saturated hydraulic conductivity, pedotransfer functions, watershed models, geospatial tools

Procedia PDF Downloads 260

Authors: Ravi R. Patel, Vasudev R. Thakkar

Abstract:

Use of plant growth-promoting rhizobacteria (PGPR) to increase the production and decrees disease occurrence is a recent method in agriculture. An RA2 rhizospheric culture was isolated from peanut rhizosphere from Junagadh region of Gujarat, India and showed different direct and indirect plant growth promoting activity like indole acetic acid, gibberellic acid, siderophore, hydrogen cyanide, Ammonia and (1-Aminocyclopropane-1-Carboxylate) deaminase production, N2 fixation, phosphate and potassium solubilization in vitro. RA2 was able to protect peanut germinating seedling from A. niger infection and reduce collar rot disease incidence 60-35% to 72-41% and increase germination percentage from 70-82% to 75-97% in two varieties GG20 and GG2 of peanut. RA2 was found to induce resistance in A. hypogaea L. seedlings via induction of different defense-related enzymes like phenylalanine ammonia lyase, peroxidase, polyphenol oxidase, lipoxygenase and pathogenesis related protein like chitinase, ß – 1,3- glucanase. Jasmonic acid one of the major signaling molecules of inducing systemic resistance was also found to induced due to RA2 treatments. RA2 bacterium was also promoting peanut growth and reduce A. niger infection in pot studies. 16S rDNA sequence of RA2 showed 99 % homology to Azotobacter species.

Keywords: plant growth promoting rhizobacteria, peanut, aspergillus niger, induce systemic resistance

Procedia PDF Downloads 242

Authors: Sanja Podunavac-Kuzmanović, Strahinja Kovačević, Lidija Jevrić, Evgenija Djurendić, Jovana Ajduković

Abstract:

In the present study, the molecular modeling of a series of 24 17-picolyl and 17-picolinylidene androstane derivatives whit significant anticancer activity was carried out. Modelling of studied compounds was performed by CS ChemBioDraw Ultra v12.0 program for drawing 2D molecular structures and CS ChemBio3D Ultra v12.0 for 3D molecular modelling. The obtained 3D structures were subjected to energy minimization using molecular mechanics force field method (MM2). The cutoff for structure optimization was set at a gradient of 0.1 kcal/Åmol. Full geometry optimization was done by the Austin Model 1 (AM1) until the root mean square (RMS) gradient reached a value smaller than 0.0001 kcal/Åmol using Molecular Orbital Package (MOPAC) program. The obtained physicochemical, lipophilicity and topological descriptors were used for analysis of molecular similarities and dissimilarities applying suitable chemometric methods (principal component analysis and cluster analysis). These results are the part of the project No. 114-451-347/2015-02, financially supported by the Provincial Secretariat for Science and Technological Development of Vojvodina and CMST COST Action CM1306.

Keywords: androstane derivatives, anticancer activity, chemometrics, molecular descriptors

Procedia PDF Downloads 361

Authors: Leo Laine, Morgan Johansson

Abstract:

To meet the civilizations future needs for safe living and low environmental footprint, the engineers designing the complex systems of tomorrow will need efficient ways to model and optimize these systems for their intended purpose. For example, a civil defence shelter and its subsystem components needs to withstand, e.g. airblast and ground shock from decided design level explosion which detonates with a certain distance from the structure. In addition, the complex civil defence shelter needs to have functioning air filter systems to protect from toxic gases and provide clean air, clean water, heat, and electricity needs to also be available through shock and vibration safe fixtures and connections. Similar complex building systems can be found in any concentrated living or office area. In this paper, the authors use a multidomain modelling language called Modelica to model a concrete wall as a single degree of freedom (SDOF) system with elastoplastic properties with the implemented option of plastic hardening. The elastoplastic model was developed and implemented in the open source tool OpenModelica. The simulation model was tested on the case with a transient equivalent reflected pressure time history representing an airblast from 100 kg TNT detonating 15 meters from the wall. The concrete wall is approximately regarded as a concrete strip of 1.0 m width. This load represents a realistic threat on any building in a city like area. The OpenModelica model results were compared with an Excel implementation of a SDOF model with an elastic-plastic spring using simple fixed timestep central difference solver. The structural displacement results agreed very well with each other when it comes to plastic displacement magnitude, elastic oscillation displacement, and response times.

Keywords: airblast from explosives, elastoplastic spring model, Modelica modelling language, SDOF, structural response of concrete structure

Procedia PDF Downloads 130

Authors: B. Umaru Mohammed, Faris A. Al-Maziad, Mohammad Y. Numan

Abstract:

One of the most important factors affecting the energy performance within a building is a carefully and efficiently designed facade. The primary aim of this research was to identify and present the potentiality of utilising Double-Skin Facade (DSF) construction and critically examine its effect on the energy consumption of an office building located within a maritime desert climate as to the conventional single-skin curtain wall system. A comparative analysis of the effect on the overall energy consumption within an office building was investigated in which a combination of various Double-Skin Facade configurations, systems, and cavity depths, glazing types and orientations were utilised. A computer dynamic modelling was utilised in order to ensure accurate calculations and efficient simulations of the various DSF systems due to the complex nature of the various functions within the Facade cavity. Through the use of the dynamic thermal modelling simulations, the best cavity size glazed type and orientation were determined to lead to a detailed analysis of the efficiency of each respective combination of Double-Skin Facade construction. As such the optimal facade combination for use within an office building located in a maritime desert climate was identified. Results demonstrated that a multi-story Facade, depending on its configuration, save up to 5% on annual cooling loads respect to a Corridor Facade and while vented can save unto 12% when compared to the single skin façade, on annual cooling load in the maritime desert climate. The selected configuration of the DSF from SSF saves an overall annual cooling load of 32%.A comparative analysis of the effect on the overall energy consumption within an office building was investigated in which a combination of various Double-Skin Facade configurations, systems, and cavity depths, glazing types and orientations were utilized. A computer dynamic modelling was utilized in order to ensure accurate calculations and efficient simulations of the various DSF systems due to the complex nature of the various functions within the Facade cavity. Through the use of the dynamic thermal modelling simulations, the best cavity size glazed type and orientation were determined to lead to a detailed analysis of the efficiency of each respective combination of Double-Skin Facade construction. As such the optimal facade combination for use within an office building located in a maritime desert climate was identified. Results demonstrated that a multi-story Facade, depending on its configuration, save up to 5% on annual cooling loads respect to a Corridor Facade and while vented can save unto 12% when compared to the single skin facade, on annual cooling load in the maritime desert climate. The selected configuration of the DSF from SSF saves an overall annual cooling load of 32%.

Keywords: computer dynamics modelling, comparative analysis, energy computation, double skin facade, single skin curtain wall, maritime desert climate

Procedia PDF Downloads 342

Authors: Monika Rawat, Rahul Kumar

Abstract:

Input output Buffer Information Specification (IBIS) models are used for describing the analog behavior of the Input Output (I/O) buffers of a digital device. They are widely used to perform signal integrity analysis. Advantages of using IBIS models include simple structure, IP protection and fast simulation time with reasonable accuracy. As design complexity of driver and receiver increases, capturing exact behavior from transistor level model into IBIS model becomes an essential task to achieve better accuracy. In this paper, an improvement in existing methodology of generating IBIS model for complex I/O interfaces such as Inter-Integrated Circuit (I2C) and Low Voltage Differential Signaling (LVDS) is proposed. Furthermore, the accuracy and computational performance of standard method and proposed approach with respect to SPICE are presented. The investigations will be useful to further improve the accuracy of IBIS models and to enhance their wider acceptance.

Keywords: IBIS, signal integrity, open-drain buffer, low voltage differential signaling, behavior modelling, transient simulation

Procedia PDF Downloads 196

Authors: Urbánek Jiří J., Krahulec Josef, Urbánek Jiří F., Johanidesová Jitka

Abstract:

These Computational assistance for the research and modelling of critical infrastructure subjects continuity deal with this paper. It enables us the using of prevailing operation system MS Office (SmartArt...) for mathematical models, using DYVELOP (Dynamic Vector Logistics of Processes) method. It serves for crisis situations investigation and modelling within the organizations of critical infrastructure. In the first part of the paper, it will be introduced entities, operators and actors of DYVELOP method. It uses just three operators of Boolean algebra and four types of the entities: the Environments, the Process Systems, the Cases and the Controlling. The Process Systems (PrS) have five “brothers”: Management PrS, Transformation PrS, Logistic PrS, Event PrS and Operation PrS. The Cases have three “sisters”: Process Cell Case, Use Case and Activity Case. They all need for the controlling of their functions special Ctrl actors, except ENV – it can do without Ctrl. Model´s maps are named the Blazons and they are able mathematically - graphically express the relationships among entities, actors and processes. In the second part of this paper, the rich blazons of DYVELOP method will be used for the discovering and modelling of the cycling cases and their phases. The blazons need live PowerPoint presentation for better comprehension of this paper mission. The crisis management of energetic crisis infrastructure organization is obliged to use the cycles for successful coping of crisis situations. Several times cycling of these cases is a necessary condition for the encompassment of the both the emergency event and the mitigation of organization´s damages. Uninterrupted and continuous cycling process bring for crisis management fruitfulness and it is a good indicator and controlling actor of organizational continuity and its sustainable development advanced possibilities. The research reliable rules are derived for the safety and reliable continuity of energetic critical infrastructure organization in the crisis situation.

Keywords: blazons, computational assistance, DYVELOP method, critical infrastructure

Procedia PDF Downloads 382

Authors: Yunus Onur Yildiz, Mesut Kirca

Abstract:

In this study, mechanical properties of a nanoporous metal coated with a different metallic material are studied through a new atomistic modelling technique and molecular dynamics (MD) simulations. This new atomistic modelling technique is based on the Voronoi tessellation method for the purpose of geometric representation of the ligaments. With the proposed technique, atomistic models of nanoporous metals which have randomly oriented ligaments with non-uniform mass distribution along the ligament axis can be generated by enabling researchers to control both ligament length and diameter. Furthermore, by the utilization of this technique, atomistic models of coated nanoporous materials can be numerically obtained for further mechanical or thermal characterization. In general, this study consists of two stages. At the first stage, we use algorithms developed for generating atomic coordinates of the coated nanoporous material. In this regard, coordinates of randomly distributed points are determined in a controlled way to be employed in the establishment of the Voronoi tessellation, which results in randomly oriented and intersected line segments. Then, line segment representation of the Voronoi tessellation is transformed to atomic structure by a special process. This special process includes generation of non-uniform volumetric core region in which atoms can be generated based on a specific crystal structure. As an extension, this technique can be used for coating of nanoporous structures by creating another volumetric region encapsulating the core region in which atoms for the coating material are generated. The ultimate goal of the study at this stage is to generate atomic coordinates that can be employed in the MD simulations of randomly organized coated nanoporous structures. At the second stage of the study, mechanical behavior of the coated nanoporous models is investigated by examining deformation mechanisms through MD simulations. In this way, the effect of coating on the mechanical behavior of the selected material couple is investigated.

Keywords: atomistic modelling, molecular dynamic, nanoporous metals, voronoi tessellation

Procedia PDF Downloads 277

Authors: Pavel Shcherban, Vlad Golovanov

Abstract:

Nowadays, the depletion of hydrocarbon deposits on the land of the Kaliningrad region leads to active geological exploration and development of oil and natural gas reserves in the southeastern part of the Baltic Sea. LLC 'Lukoil-Kaliningradmorneft' implements a comprehensive program for the development of the region's shelf in 2014-2023. Due to heterogeneity of reservoir rocks in various open fields, as well as with ambiguous conclusions on the contours of deposits, additional geological prospecting and refinement of the recoverable oil reserves are carried out. The key element is use of an effective technique of computer stock modeling at the first stage of processing of the received data. The following step uses information for the cluster analysis, which makes it possible to optimize the field development approaches. The article analyzes the effectiveness of various methods for reserves' calculation and computer modelling methods of the offshore hydrocarbon fields. Cluster analysis allows to measure influence of the obtained data on the development of a technical and economic model for mining deposits. The relationship between the accuracy of the calculation of recoverable reserves and the need of modernization of existing mining infrastructure, as well as the optimization of the scheme of opening and development of oil deposits, is observed.

Keywords: cluster analysis, computer modelling of deposits, correction of the feasibility study, offshore hydrocarbon fields

Procedia PDF Downloads 166

Authors: Congping Lin

Abstract:

Intracellular transport in fungi has a number of important roles in, e.g., filamentous fungal growth and cellular metabolism. Two basic mechanisms for intracellular transport are motor-driven trafficking along microtubules (MTs) and diffusion. Mathematical modelling has been actively developed to understand such intracellular transport and provide unique insight into cellular complexity. Based on live-cell imaging data in Ustilago hyphal cells, probabilistic models have been developed to study mechanism underlying spatial organization of molecular motors and organelles. In particular, anther mechanism - stochastic motility of dynein motors along MTs has been found to contribute to half of its accumulation at hyphal tip in order to support early endosome (EE) recycling. The EE trafficking not only facilitates the directed motion of peroxisomes but also enhances their diffusive motion. Considering the importance of spatial organization of early endosomes in supporting peroxisome movement, computational and experimental approaches have been combined to a whole-cell level. Results from this interdisciplinary study promise insights into requirements for other membrane trafficking systems (e.g., in neurons), but also may inform future 'synthetic biology' studies.

Keywords: intracellular transport, stochastic process, molecular motors, spatial organization

Procedia PDF Downloads 133

Authors: Abdul Musaweer Habib, Habibul Hasan Mazumder, Saiful Islam, Sohel Sikder, Omar Faruk Sikder

Abstract:

The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1499 proteins of Fusobacterium nucleatum, which has no homolog in human genome. These proteins were subjected to screening further by using the Database of Essential Genes (DEG) that resulted in the identification of 32 vitally important proteins for the bacterium. Subsequent analysis of the identified pivotal proteins, using the KEGG Automated Annotation Server (KAAS) resulted in sorting 3 key enzymes of F. nucleatum that may be good candidates as potential drug targets, since they are unique for the bacterium and absent in humans. In addition, we have demonstrated the 3-D structure of these three proteins. Finally, determination of ligand binding sites of the key proteins as well as screening for functional inhibitors that best fitted with the ligands sites were conducted to discover effective novel therapeutic compounds against Fusobacterium nucleatum.

Keywords: colorectal cancer, drug target, Fusobacterium nucleatum, homology modeling, ligands

Procedia PDF Downloads 388

Authors: Olivia A. Wilson, Hannah E. Power, Murray Kendall

Abstract:

Sydney Harbour is an iconic location with a dense population and low-lying development. On the east coast of Australia, facing the Pacific Ocean, it is exposed to several tsunamigenic trenches. This paper presents a component of the most detailed assessment of the potential for earthquake-generated tsunami impact on Sydney Harbour to date. Models in this study use dynamic tides to account for tide-tsunami interaction. Sydney Harbour’s tidal range is 1.5 m, and the spring tides from January 2015 that are used in the modelling for this study are close to the full tidal range. The tsunami wave trains modelled include hypothetical tsunami generated from earthquakes of magnitude 7.5, 8.0, 8.5, and 9.0 M_W from the Puysegur and New Hebrides trenches as well as representations of the historical 1960 Chilean and 2011 Tohoku events. All wave trains are modelled for the peak wave to coincide with both a low tide and a high tide. A single wave train, representing a 9.0 M_W earthquake at the Puysegur trench, is modelled for peak waves to coincide with every hour across a 12-hour tidal phase. Using the hydrodynamic model ANUGA, results are compared according to the impact parameters of inundation area, depth variation and current speeds. Results show that both maximum inundation area and depth variation are tide dependent. Maximum inundation area increases when coincident with a higher tide, however, hazardous inundation is only observed for the larger waves modelled: NH90high and P90high. The maximum and minimum depths are deeper on higher tides and shallower on lower tides. The difference between maximum and minimum depths varies across different tidal phases although the differences are slight. Maximum current speeds are shown to be a significant hazard for Sydney Harbour; however, they do not show consistent patterns according to tide-tsunami phasing. The maximum current speed hazard is shown to be greater in specific locations such as Spit Bridge, a narrow channel with extensive marine infrastructure. The results presented for Sydney Harbour are novel, and the conclusions are consistent with previous modelling efforts in the greater area. It is shown that tide must be a consideration for both tsunami modelling and emergency management planning. Modelling with peak tsunami waves coinciding with a high tide would be a conservative approach; however, it must be considered that maximum current speeds may be higher on other tides.

Keywords: emergency management, sydney, tide-tsunami interaction, tsunami impact

Procedia PDF Downloads 242

Authors: Eric Dede, Marcus Tindall, John W. Cherrie, Steve Hankin, Christopher Collins

Abstract:

Current exposure models used in contaminated land risk assessment are highly conservative. Use of these models may lead to over-estimation of actual exposures, possibly resulting in negative financial implications due to un-necessary remediation. Thus, we are carrying out a study seeking to improve our understanding of human exposure to selected toxic elements in soil: arsenic (As), cadmium (Cd), chromium (Cr), nickel (Ni), and lead (Pb) resulting from allotment land-use. The study employs biomonitoring and physiologically-based pharmacokinetic (PBPK) modelling to quantify human exposure to these elements. We recruited 37 allotment users (adults > 18 years old) in Scotland, UK, to participate in the study. Concentrations of the elements (and their bioaccessibility) were measured in allotment samples (soil and allotment produce). Amount of produce consumed by the participants and participants’ biological samples (urine and blood) were collected for up to 12 consecutive months. Ethical approval was granted by the University of Reading Research Ethics Committee. PBPK models (coded in MATLAB) were used to estimate the distribution and accumulation of the elements in key body compartments, thus indicating the internal body burden. Simulating low element intake (based on estimated ‘doses’ from produce consumption records), predictive models suggested that detection of these elements in urine and blood was possible within a given period of time following exposure. This information was used in planning biomonitoring, and is currently being used in the interpretation of test results from biological samples. Evaluation of the models is being carried out using biomonitoring data, by comparing model predicted concentrations and measured biomarker concentrations. The PBPK models will be used to generate bioavailability values, which could be incorporated in contaminated land exposure models. Thus, the findings from this study will promote a more sustainable approach to contaminated land management.

Keywords: biomonitoring, exposure, PBPK modelling, toxic elements

Procedia PDF Downloads 319

Authors: Hamid Mustafa, Adeela Ajmal, Kim EuiSoo, Noor-ul-Ain

Abstract:

World wild, buffalo production is considered as most important component of food industry. Efficient buffalo production is related with reproductive performance of this species. Lack of knowledge of reproductive efficiency and its related genes in buffalo species is a major constraint for sustainable buffalo production. In this study, we performed some bioinformatics analysis on Follicle Stimulating Hormone Receptor (FSHR) gene and explored the possible relationship of this gene among different buffalo breeds and with other farm animals. We also found the evolution pattern for this gene among these species. We investigate CDS lengths, Stop codon variation, homology search, signal peptide, isoelectic point, tertiary structure, motifs and phylogenetic tree. The results of this study indicate 4 different motif in this gene, which are Activin-recp, GS motif, STYKc Protein kinase and transmembrane. The results also indicate that this gene has very close relationship with cattle, bison, sheep and goat. Multiple alignment (MA) showed high conservation of motif which indicates constancy of this gene during evolution. The results of this study can be used and applied for better understanding of this gene for better characterization of Follicle Stimulating Hormone Receptor (FSHR) gene structure in different farm animals, which would be helpful for efficient breeding plans for animal’s production.

Keywords: buffalo, FSHR gene, bioinformatics, production

Procedia PDF Downloads 532

Authors: Mohammed Seyam, Faridah Othman, Ahmed El-Shafie

Abstract:

The early warning of high stream flow events (HSF) and floods is an important aspect in the management of surface water and rivers systems. This process can be performed using either process-based models or data driven-based models such as artificial intelligence (AI) techniques. The main goal of this study is to develop efficient AI-based model for predicting the real-time hourly stream flow (Q) and apply it as early warning tool of HSF and floods in the downstream area of the Selangor River basin, taken here as a paradigm of humid tropical rivers in Southeast Asia. The performance of AI-based models has been improved through the integration of the lag time (Lt) estimation in the modelling process. A total of 8753 patterns of Q, water level, and rainfall hourly records representing one-year period (2011) were utilized in the modelling process. Six hydrological scenarios have been arranged through hypothetical cases of input variables to investigate how the changes in RF intensity in upstream stations can lead formation of floods. The initial SF was changed for each scenario in order to include wide range of hydrological situations in this study. The performance evaluation of the developed AI-based model shows that high correlation coefficient (R) between the observed and predicted Q is achieved. The AI-based model has been successfully employed in early warning throughout the advance detection of the hydrological conditions that could lead to formations of floods and HSF, where represented by three levels of severity (i.e., alert, warning, and danger). Based on the results of the scenarios, reaching the danger level in the downstream area required high RF intensity in at least two upstream areas. According to results of applications, it can be concluded that AI-based models are beneficial tools to the local authorities for flood control and awareness.

Keywords: floods, stream flow, hydrological modelling, hydrology, artificial intelligence

Procedia PDF Downloads 248

Authors: Tofigh Hamidavi, Sepehr Abrishami, Pasquale Ponterosso, David Begg

Abstract:

Structural design and analysis is an important and time-consuming process, particularly at the conceptual design stage. Decisions made at this stage can have an enormous effect on the entire project, as it becomes ever costlier and more difficult to alter the choices made early on in the construction process. Hence, optimisation of the early stages of structural design can provide important efficiencies in terms of cost and time. This paper suggests a structural design optimisation (SDO) framework in which Genetic Algorithms (GAs) may be used to semi-automate the production and optimisation of early structural design alternatives. This framework has the potential to leverage conceptual structural design innovation in Architecture, Engineering and Construction (AEC) projects. Moreover, this framework improves the collaboration between the architectural stage and the structural stage. It will be shown that this SDO framework can make this achievable by generating the structural model based on the extracted data from the architectural model. At the moment, the proposed SDO framework is in the process of validation, involving the distribution of an online questionnaire among structural engineers in the UK.

Keywords: building information, modelling, BIM, genetic algorithm, GA, architecture-engineering-construction, AEC, optimisation, structure, design, population, generation, selection, mutation, crossover, offspring

Procedia PDF Downloads 241

Authors: Bojana Horvat, Barbara Karleusa, Goran Volf, Nevenka Ozanic, Ivica Kisic

Abstract:

Forest fire is a major threat in many regions in Croatia, especially in coastal areas. Although they are often caused by natural processes, the most common cause is the human factor, intentional or unintentional. Forest fires drastically transform landscapes and influence natural processes. The main goal of the presented research is to analyse and quantify the impact of the forest fire on hydrological processes and propose the model that best describes changes in hydrological patterns in the analysed catchments. Keeping in mind the spatial component of the processes, geospatial analysis is performed to gain better insight into the spatial variability of the hydrological response to disastrous events. In that respect, two catchments that experienced severe forest fire were delineated, and various hydrological and meteorological data were collected both attribute and spatial. The major drawback is certainly the lack of hydrological data, common in small torrential karstic streams; hence modelling results should be validated with the data collected in the catchment that has similar characteristics and established hydrological monitoring. The event chosen for the modelling is the forest fire that occurred in July 2019 and burned nearly 10% of the analysed area. Surface (land use/land cover) conditions before and after the event were derived from the two Sentinel-2 images. The mapping of the burnt area is based on a comparison of the Normalized Burn Index (NBR) computed from both images. To estimate and compare hydrological behaviour before and after the event, curve number (CN) values are assigned to the land use/land cover classes derived from the satellite images. Hydrological modelling resulted in surface runoff generation and hence prediction of hydrological responses in the catchments to a forest fire event. The research was supported by the Croatian Science Foundation through the project 'Influence of Open Fires on Water and Soil Quality' (IP-2018-01-1645).

Keywords: Croatia, forest fire, geospatial analysis, hydrological response

Procedia PDF Downloads 136

Authors: Omar Qaftan

Abstract:

Earthquakes can cause tremendous loss of human life and can result in severe damage to a several of civil engineering structures especially the tall buildings. The response of a multistory structure subjected to earthquake loading is a complex task, and it requires to be studied by physical and numerical modelling. For many circumstances, the scale models on shaking table may be a more economical option than the similar full-scale tests. A shaking table apparatus is a powerful tool that offers a possibility of understanding the actual behaviour of structural systems under earthquake loading. It is required to use a set of scaling relations to predict the behaviour of the full-scale structure. Selecting the scale factors is the most important steps in the simulation of the prototype into the scaled model. In this paper, the principles of scaling modelling procedure are explained in details, and the simulation of scaled multi-storey concrete structure for dynamic studies is investigated. A procedure for a complete dynamic simulation analysis is investigated experimentally and numerically with a scale factor of 1/50. The frequency domain accounting and lateral displacement for both numerical and experimental scaled models are determined. The procedure allows accounting for the actual dynamic behave of actual size porotype structure and scaled model. The procedure is adapted to determine the effects of the tall multi-storey structure on a raft foundation. Four generated accelerograms were used as inputs for the time history motions which are in complying with EC8. The output results of experimental works expressed regarding displacements and accelerations are compared with those obtained from a conventional fixed-base numerical model. Four-time history was applied in both experimental and numerical models, and they concluded that the experimental has an acceptable output accuracy in compare with the numerical model output. Therefore this modelling methodology is valid and qualified for different shaking table experiments tests.

Keywords: structure, raft, soil, interaction

Procedia PDF Downloads 136

Authors: Victoria Goodall, Paul Fatti, Norman Owen-Smith

Abstract:

Hidden Markov Models have become popular for the analysis of animal tracking data. These models are being used to model the movements of a variety of species in many areas around the world. A common assumption of the model is that the observations need to have regular time steps. In many ecological studies, this will not be the case. The objective of the research is to modify the movement model to allow for irregularly spaced locations and investigate the effect on the inferences which can be made about the latent states. A modification of the likelihood function to allow for these irregular spaced locations is investigated, without using interpolation or averaging the movement rate. The suitability of the modification is investigated using GPS tracking data for lion (Panthera leo) in South Africa, with many observations obtained during the night, and few observations during the day. Many nocturnal predator tracking studies are set up in this way, to obtain many locations at night when the animal is most active and is difficult to observe. Few observations are obtained during the day, when the animal is expected to rest and is potentially easier to observe. Modifying the likelihood function allows the popular Hidden Markov Model framework to be used to model these irregular spaced locations, making use of all the observed data.

Keywords: hidden Markov Models, irregular observations, animal movement modelling, nocturnal predator

Procedia PDF Downloads 244

Authors: Jiun-Horng Tsai, Shi-Jie, Nieh

Abstract:

Fine particulate matter (PM₂.₅) has become an important issue all over the world over the last decade. Annual mean PM₂.₅ concentration has been over the ambient air quality standard of PM₂.₅ (annual average concentration as 15μg/m³) which adapted by Taiwan Environmental Protection Administration (TEPA). TEPA, therefore, has developed a number of air pollution control measures to improve the ambient concentration by reducing the emissions of primary fine particulate matter and the precursors of secondary PM₂.₅. This study investigated the potential improvement of ambient PM₂.₅ concentration by the TEPA program and the other scenario for further emission reduction on various sources. Four scenarios had been evaluated in this study, including a basic case and three reduction scenarios (A to C). The ambient PM₂.₅ concentration was evaluated by Community Multi-scale Air Quality modelling system (CMAQ) ver. 4.7.1 along with the Weather Research and Forecasting Model (WRF) ver. 3.4.1. The grid resolutions in the modelling work are 81 km × 81 km for domain 1 (covers East Asia), 27 km × 27 km for domain 2 (covers Southeast China and Taiwan), and 9 km × 9 km for domain 3 (covers Taiwan). The result of PM₂.₅ concentration simulation in different regions of Taiwan shows that the annual average concentration of basic case is 24.9 μg/m³, and are 22.6, 18.8, and 11.3 μg/m³, respectively, for scenarios A to C. The annual average concentration of PM₂.₅ would be reduced by 9-55 % for those control scenarios. The result of scenario C (the emissions of precursors reduce to allowance levels) could improve effectively the airborne PM₂.₅ concentration to attain the air quality standard. According to the results of unit precursor reduction contribution, the allowance emissions of PM₂.₅, SOₓ, and NOₓ are 16.8, 39, and 62 thousand tons per year, respectively. In the Kao-Ping air basin, the priority for reducing precursor emissions is PM₂.₅ > NOₓ > SOₓ, whereas the priority for reducing precursor emissions is PM₂.₅ > SOₓ > NOₓ in others area. The result indicates that the target pollutants that need to be reduced in different air basin are different, and the control measures need to be adapted to local conditions.

Keywords: airborne PM₂.₅, community multi-scale air quality modelling system, control measures, weather research and forecasting model

Procedia PDF Downloads 139

Authors: Wassana Naiyapo, Atichat Sangtong

Abstract:

The processes in software development by Object Oriented methodology have many stages those take time and high cost. The inconceivable error in system analysis process will affect to the design and the implementation process. The unexpected output causes the reason why we need to revise the previous process. The more rollback of each process takes more expense and delayed time. Therefore, the good test process from the early phase, the implemented software is efficient, reliable and also meet the user’s requirement. Unified Modelling Language (UML) is the tool which uses symbols to describe the work process in Object Oriented Analysis (OOA). This paper presents the approach for automatically generated UML use case diagram and test cases. UML use case diagram is generated from the event table and test cases are generated from use case specifications and Graphic User Interfaces (GUI). Test cases are derived from the Classification Tree Method (CTM) that classify data to a node present in the hierarchy structure. Moreover, this paper refers to the program that generates use case diagram and test cases. As the result, it can reduce work time and increase efficiency work.

Keywords: classification tree method, test case, UML use case diagram, use case specification

Procedia PDF Downloads 162

Authors: Mohammed Salahat, Steve Wade

Abstract:

This paper presents and compares the SSDDD “Systematic Soft Domain Driven Design Framework” to DDD “Domain Driven Design Framework” as a soft system approach of information systems development. The framework use SSM as a guiding methodology within which we have embedded a sequence of design tasks based on the UML leading to the implementation of a software system using the Naked Objects framework. This framework has been used in action research projects that have involved the investigation and modelling of business processes using object-oriented domain models and the implementation of software systems based on those domain models. Within this framework, Soft Systems Methodology (SSM) is used as a guiding methodology to explore the problem situation and to develop the domain model using UML for the given business domain. The framework is proposed and evaluated in our previous works, a comparison between SSDDD and DDD is presented in this paper, to show how SSDDD improved DDD as an approach to modelling and implementing business domain perspectives for Information Systems Development. The comparison process, the results, and the improvements are presented in the following sections of this paper.

Keywords: domain-driven design, soft domain-driven design, naked objects, soft language

Procedia PDF Downloads 298

Authors: Ashish Kumar Agrahari, Amit Kumar

Abstract:

Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired clonal blood disorder that manifests with hemolytic anemia, thrombosis, and peripheral blood cytopenias. The disease is caused by the deficiency of two glycosylphosphatidylinositols (GPI)-anchored proteins (CD55 and CD59) in the hemopoietic stem cells. The deficiency of GPI-anchored proteins has been associated with the somatic mutations in phosphatidylinositol glycan class A (PIGA). However, the mutations that do not cause PNH is associated with the multiple congenital anomalies-hypotonia-seizures syndrome 2 (MCAHS2). To best of our knowledge, no computational study has been performed to explore the atomistic level impact of PIGA mutations on the structure and dynamics of the protein. In the current work, we are mainly interested to get insights into the molecular mechanism of PIGA mutations. In the initial step, we screened the most pathogenic mutations from the pool of publicly available mutations. Further, to get a better understanding, pathogenic mutations were mapped to the modeled structure and subjected to 50ns molecular dynamics simulation. Our computational study suggests that four mutations are highly vulnerable to altering the structural conformation and stability of the PIGA protein, which illustrates its association with PNH and MCAHS2 phenotype.

Keywords: homology modeling, molecular dynamics simulation, missense mutations PNH, MCAHS2, PIGA

Procedia PDF Downloads 145

Authors: Cheng Zhang, James Marco, Walid Allafi, Truong Q. Dinh, W. D. Widanage

Abstract:

Equivalent circuit models (ECMs) are widely used in battery management systems in electric vehicles and other battery energy storage systems. The battery dynamics and the model parameters vary under different working conditions, such as different temperature and state of charge (SOC) levels, and therefore online parameter identification can improve the modelling accuracy. This paper presents a way of online ECM parameter identification using a continuous time (CT) estimation method. The CT estimation method has several advantages over discrete time (DT) estimation methods for ECM parameter identification due to the widely separated battery dynamic modes and fast sampling. The presented method can be used for online SOC estimation. Test data are collected using a lithium ion cell, and the experimental results show that the presented CT method achieves better modelling accuracy compared with the conventional DT recursive least square method. The effectiveness of the presented method for online SOC estimation is also verified on test data.

Keywords: electric circuit model, continuous time domain estimation, linear integral filter method, parameter and SOC estimation, recursive least square

Procedia PDF Downloads 383