Search results for: computational biophysics

Authors: Sabyasachi Mukhopadhyay, Joseph Ogutu, Hans-Peter Piepho

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We aim to model dynamics of wildlife or pastoral livestock population for understanding of their population change and hence for wildlife conservation and promoting human welfare. The study is motivated by an age-sex structured population counts in different regions of Serengeti-Mara during the period 1989-2003. Developing reliable and realistic models for population dynamics of large herbivore population can be a very complex and challenging exercise. However, the Bayesian statistical domain offers some flexible computational methods that enable the development and efficient implementation of complex population dynamics models. In this work, we have used a novel Bayesian state-space model to analyse the dynamics of topi and hartebeest populations in the Serengeti-Mara Ecosystem of East Africa. The state-space model involves survival probabilities of the animals which further depend on various factors like monthly rainfall, size of habitat, etc. that cause recent declines in numbers of the herbivore populations and potentially threaten their future population viability in the ecosystem. Our study shows that seasonal rainfall is the most important factors shaping the population size of animals and indicates the age-class which most severely affected by any change in weather conditions.

Keywords: bayesian state-space model, Markov Chain Monte Carlo, population dynamics, conservation

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Authors: Sai Hung Cheung, Zhe Shao

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Recent earthquake-induced tsunamis in Padang, 2004 and Tohoku, 2011 brought huge losses of lives and properties. Maintaining vertical evacuation systems is the most crucial strategy to effectively reduce casualty during the tsunami event. Thus, it is of our great interest to quantify the risk to structural dynamic systems due to earthquake-induced tsunamis. Despite continuous advancement in computational simulation of the tsunami and wave-structure interaction modeling, it still remains computationally challenging to evaluate the reliability (or its complement failure probability) of a structural dynamic system when uncertainties related to the system and its modeling are taken into account. The failure of the structure in a tsunami-wave-structural system is defined as any response quantities of the system exceeding specified thresholds during the time when the structure is subjected to dynamic wave impact due to earthquake-induced tsunamis. In this paper, an approach based on a novel integration of the Subset Simulation algorithm and a recently proposed moving least squares response surface approach for stochastic sampling is proposed. The effectiveness of the proposed approach is discussed by comparing its results with those obtained from the Subset Simulation algorithm without using the response surface approach.

Keywords: response surface model, subset simulation, structural reliability, Tsunami risk

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Authors: Amr Ali Bayoumi, Ola Ali Bayoumi

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The aim of this research is enhancing one of the main aspects (Social Aspect) for developing an eco-lodge in Siwa oasis in Egyptian Western Desert. According to credible weightings built in this research through formal and informal questionnaires, the researcher detected one of the highest credible aspects, 'Social Aspect': through which it carries the maximum priorities among the total environmental and economic categories. From here, the researcher suggested the usage of ethnographic design approach and Space Syntax as observational and computational methods for developing future Eco-lodge in Siwa Oasis. These methods are used to study social spaces of Babenshal eco-lodge as a case study. This hybrid method is considered as a beginning of building Social Assessment Tool (SAT) for ecological tourism buildings located in Siwa as a case of Egyptian Western desert community. Towards livable social spaces, the proposed SAT was planned to be the optimum measurable weightings for social aspect's priorities of future Siwan eco-lodge(s). Finally, recommendations are proposed for enhancing SAT to be more correlated with sensitive desert biome (Siwa Oasis) to be adapted with the continuous social and environmental changes of the oasis.

Keywords: ecolodge, social aspect, space syntax, Siwa Oasis

Procedia PDF Downloads 111

Authors: M. Ezkurra, J. A. Esnaola, M. Martinez-Agirre, U. Etxeberria, U. Lertxundi, L. Colomo, M. Begiristain, I. Zurutuza

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Butterfly valves are widely used industrial piping components as on-off and flow controlling devices. The main challenge in the design process of this type of valves is the correct dimensioning to ensure proper mechanical performance as well as to minimise flow losses that affect the efficiency of the system. Butterfly valves are typically dimensioned in a closed position based on mechanical approaches considering uniform hydrostatic pressure, whereas the flow losses are analysed by means of CFD simulations. The main limitation of these approaches is that they do not consider either the influence of the dynamics of the manoeuvring stage or coupled phenomena. Recent works have included the influence of the flow on the mechanical behaviour for different opening angles by means of one-way FSI approach. However, these works consider steady-state flow for the selected angles, not capturing the effect of the transient flow evolution during the manoeuvring stage. Two-way FSI modelling approach could allow overcoming such limitations providing more accurate results. Nevertheless, the use of this technique is limited due to the increase in the computational cost. In the present work, the applicability of FSI one-way and two-way approaches is evaluated for the analysis of butterfly valves, showing that not considering fluid-structure coupling involves not capturing the most critical situation for the valve disc.

Keywords: butterfly valves, fluid-structure interaction, one-way approach, two-way approach

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Authors: Songul Cinaroglu

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Background: Random Forest is an efficient, multi-class machine learning method using for classification, regression and other tasks. This method is operating by constructing each tree using different bootstrap sample of the data. Determining the number of trees in random forests is an open question in the literature for studies about improving classification performance of random forests. Aim: The aim of this study is to analyze whether there is an optimal number of trees in Random Forests and how performance of Random Forests differ according to increase in number of trees using sample health data sets in R programme. Method: In this study we analyzed the performance of Random Forests as the number of trees grows and doubling the number of trees at every iteration using “random forest” package in R programme. For determining minimum and optimal number of trees we performed Mc Nemar test and Area Under ROC Curve respectively. Results: At the end of the analysis it was found that as the number of trees grows, it does not always means that the performance of the forest is better than forests which have fever trees. In other words larger number of trees only increases computational costs but not increases performance results. Conclusion: Despite general practice in using random forests is to generate large number of trees for having high performance results, this study shows that increasing number of trees doesn’t always improves performance. Future studies can compare different kinds of data sets and different performance measures to test whether Random Forest performance results change as number of trees increase or not.

Keywords: classification methods, decision trees, number of trees, random forest

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Authors: Tolga Arda Eraslan

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The quality of the indoor environment is significant to occupants’ health, comfort, and productivity, as Covid-19 spread throughout the world, people started spending most of their time indoors. Since buildings are getting bigger, mechanical ventilation systems are widely used where natural ventilation is insufficient. Four primary tasks of a ventilation system have been identified indoor air quality, comfort, contamination control, and energy performance. To fulfill such requirements, air diffusers, which are a part of the ventilation system, have begun to enter our lives in different airflow distribution systems. Detailed observations are needed to assure that such devices provide high levels of comfort effectiveness and energy efficiency. This study addresses these needs. The objective of this article is to observe air characterizations of different air diffusers at different angles and their effect on people by the thermal comfort model in CFD simulation and to validate the outputs with the help of data results based on a simulated office room. Office room created to provide validation; Equipped with many thermal sensors, including head height, tabletop, and foot level. In addition, CFD simulations were carried out by measuring the temperature and velocity of the air coming out of the supply diffuser. The results considering the flow interaction between diffusers and surroundings showed good visual illustration.

Keywords: computational fluid dynamics, fanger’s model, predicted mean vote, thermal comfort

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Authors: Samantha Shallop, Hakinya Karra, Tytus Bernas, Gladys Shaw, Gretchen Neigh, Jeffrey Dupree, Mathula Thangarajh

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Abnormal neuronal homeostasis is considered a structural correlate of cognitive deficits in Duchenne Muscular Dystrophy. Neurons are highly polarized cells with multiple dendrites but a single axon. Trafficking of cellular organelles are highly regulated, with the cargo in the somatodendritic region of the neuron not permitted to enter the axonal compartment. We investigated the molecular mechanisms that regular organelle trafficking in neurons using a multimodal approach, including high-resolution structural illumination, proteomics, immunohistochemistry, and computational modeling. We investigated the expression of ankyrin-G, the master regulator controlling neuronal polarity. The expression of ankyrin G and the morphology of the axon initial segment was profoundly abnormal in the CA1 hippocampal neurons in the mdx52 animal model of DMD. Ankyrin-G colocalized with kinesin KIF5a, the anterograde protein transporter, with higher levels in older mdx52 mice than younger mdx52 mice. These results suggest that the functional trafficking from the somatodendritic compartment is abnormal. Our data suggests that dystrophin deficiency compromised neuronal homeostasis via ankyrin-G-based mechanisms.

Keywords: neurons, axonal transport, duchenne muscular dystrophy, organelle transport

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Authors: Bhavesh Dadhich, Fenil Bamnoliya, Akshita Swaminathan

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This project aims to design a system to generate energy from flowing wind due to the motion of a vehicle on the road or from the flow of wind in compact areas to utilize the wasteful energy into a useful one. It is envisaged through a design and aerodynamic performance improvement of a Savonius vertical axis wind turbine rotor and used in an integrated system with a Triboelectric Nanogenerator (TENG) that can generate a good amount of electrical energy. Aerodynamic calculations are performed numerically using Computational Fluid Dynamics software, and TENG's performance is evaluated analytically. The Turbine's coefficient of power is validated with published results for an inlet velocity of 7 m/s with a Tip Speed Ratio of 0.75 and found to reasonably agree with that of experiment results. The baseline design is modified with a new blade arc angle and rotor position angle based on the recommended parameter ranges suggested by previous researchers. Simulations have been performed for different T.S.R. values ranging from 0.25 to 1.5 with an interval of 0.25 with two applicable free stream velocities of 5 m/s and 7m/s. Finally, the newly designed VAWT CFD performance results are used as input for the analytical performance prediction of the triboelectric nanogenerator. The results show that this approach could be feasible and useful for small power source applications.

Keywords: savonius turbine, power, overlap ratio, tip speed ratio, TENG

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Authors: Ataollah Rabiee1, Amir Hossein Kamalinia, Alireza Atf

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One of the most important issues in the design of nuclear fusion power plants is the heat removal from the hottest region at the diverter. Various methods could be employed in order to improve the heat transfer efficiency, such as generating turbulent flow and injection of nanoparticles in the host fluid. In the current study, Water/AL₂O₃ nanofluid forced swirl flow boiling has been investigated by using a homogeneous thermophysical model within the Eulerian-Eulerian framework through a twisted tape tube, and the boiling phenomenon was modeled using the Rensselaer Polytechnic Institute (RPI) approach. In addition to comparing the results with the experimental data and their reasonable agreement, it was evidenced that higher flow mixing results in more uniform bulk temperature and lower wall temperature along the twisted tape tube. The presence of AL₂O₃ nanoparticles in the boiling flow field showed that increasing the nanoparticle concentration leads to a reduced vapor volume fraction and wall temperature. The Computational fluid dynamics (CFD) results show that the average heat transfer coefficient in the tube increases both by increasing the nanoparticle concentration and the insertion of twisted tape, which significantly affects the thermal field of the boiling flow.

Keywords: nanoparticle, boiling, CFD, two phase flow, alumina, ITER

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Authors: Saroj Poudel, Joshua Mancini, Douglas Pike, Jennifer Timm, Alexei Tyryshkin, Vikas Nanda, Paul Falkowski

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On the early Earth, protein-metal complexes likely harvested energy from a reduced environment. These complexes would have been precursors to the metabolic enzymes of ancient organisms. Hydrogenase is an essential enzyme in most anaerobic organisms for the reduction and oxidation of hydrogen in the environment and is likely one of the earliest evolved enzymes. To attempt to reinvent a precursor to modern hydrogenase, we computationally designed a short thirteen amino acid peptide that binds the often-required catalytic transition metal Nickel in hydrogenase. This simple complex can achieve hundreds of hydrogen evolution cycles using light energy in a broad range of temperature and pH. Biophysical and structural investigations strongly indicate the peptide forms a di-nickel active site analogous to Acetyl-CoA synthase, an ancient protein central to carbon reduction in the Wood-Ljungdahl pathway and capable of hydrogen evolution. This work demonstrates that prior to the complex evolution of multidomain enzymes, early peptide-metal complexes could have catalyzed energy transfer from the environment on the early Earth and enabled the evolution of modern metabolism

Keywords: hydrogenase, prebiotic enzyme, metalloenzyme, computational design

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Authors: Fatéma Zahra Benchara, Mohamed Youssfi, Omar Bouattane, Hassan Ouajji, Mohamed Ouadi Bensalah

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The aim of this paper is to present a distributed implementation of the Type-2 Fuzzy algorithm in a parallel and distributed computing environment based on mobile agents. The proposed algorithm is assigned to be implemented on a SPMD (Single Program Multiple Data) architecture which is based on cooperative mobile agents as AVPE (Agent Virtual Processing Element) model in order to improve the processing resources needed for performing the big data image segmentation. In this work we focused on the application of this algorithm in order to process the big data MRI (Magnetic Resonance Images) image of size (n x m). It is encapsulated on the Mobile agent team leader in order to be split into (m x n) pixels one per AVPE. Each AVPE perform and exchange the segmentation results and maintain asynchronous communication with their team leader until the convergence of this algorithm. Some interesting experimental results are obtained in terms of accuracy and efficiency analysis of the proposed implementation, thanks to the mobile agents several interesting skills introduced in this distributed computational model.

Keywords: distributed type-2 fuzzy algorithm, image processing, mobile agents, parallel and distributed computing

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Authors: Anders Schou Simonsen, Thomas Condra, Kim Sørensen

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Various processes are modelled using a discrete phase, where particles are seeded from a source. Such particles can represent liquid water droplets, which are affecting the continuous phase by exchanging thermal energy, momentum, species etc. Discrete phases are typically modelled using parcel, which represents a collection of particles, which share properties such as temperature, velocity etc. When coupling the phases, the exchange rates are integrated over the cell, in which the parcel is located. This can cause spikes and fluctuating exchange rates. This paper presents an alternative method of coupling a discrete and a continuous plug flow phase. This is done using triangular parcels, which span between nodes following the dynamics of single droplets. Thus, the triangular parcels are propagated using the corner nodes. At each time step, the exchange rates are spatially integrated over the surface of the triangular parcels, which yields a smooth continuous exchange rate to the continuous phase. The results shows that the method is more stable, converges slightly faster and yields smooth exchange rates compared with the steam tube approach. However, the computational requirements are about five times greater, so the applicability of the alternative method should be limited to processes, where the exchange rates are important. The overall balances of the exchanged properties did not change significantly using the new approach.

Keywords: CFD, coupling, discrete phase, parcel

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Authors: Reza Ferdousi, Reza Safdari, Yadollah Omidi

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Drug-drug interactions (DDIs) are main cause of the adverse drug reactions and nature of the functional and molecular complexity of drugs behavior in human body make them hard to prevent and treat. With the aid of new technologies derived from mathematical and computational science the DDIs problems can be addressed with minimum cost and efforts. Market basket analysis is known as powerful method to identify co-occurrence of thing to discover patterns and frequency of the elements. In this research, we used market basket analysis to identify important bio-elements in DDIs occurrence. For this, we collected all known DDIs from DrugBank. The obtained data were analyzed by market basket analysis method. We investigated all drug-enzyme, drug-carrier, drug-transporter and drug-target associations. To determine the importance of the extracted bio-elements, extracted rules were evaluated in terms of confidence and support. Market basket analysis of the over 45,000 known DDIs reveals more than 300 important rules that can be used to identify DDIs, CYP 450 family were the most frequent shared bio-elements. We applied extracted rules over 2,000,000 unknown drug pairs that lead to discovery of more than 200,000 potential DDIs. Analysis of the underlying reason behind the DDI phenomena can help to predict and prevent DDI occurrence. Ranking of the extracted rules based on strangeness of them can be a supportive tool to predict the outcome of an unknown DDI.

Keywords: drug-drug interaction, market basket analysis, rule discovery, important bio-elements

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Authors: Imran Hashmi, Sipkaduwa Arachchige Sashika Sureni Wickramasooriya

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Gene-drive technology has emerged as a promising tool for disease control by influencing the population dynamics of disease-carrying organisms. Various gene drive mechanisms, derived from global laboratory experiments, aim to strategically manage and prevent the spread of targeted diseases. One prominent strategy involves population replacement, wherein genetically modified mosquitoes are introduced to replace the existing local wild population. To enhance our understanding and aid in the design of effective release strategies, we employ a comprehensive mathematical model. The utilized approach employs agent-based modeling, enabling the consideration of individual mosquito attributes and flexibility in parameter manipulation. Through the integration of an agent-based model and a meta-population spatial approach, the dynamics of gene drive mosquito spreading in a released site are simulated. The model's outcomes offer valuable insights into future population dynamics, providing guidance for the development of informed release strategies. This research significantly contributes to the ongoing discourse on the responsible and effective implementation of gene drive technology for disease vector control.

Keywords: gene drive, agent-based modeling, disease-carrying organisms, malaria

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Authors: Rômulo Eustáquio Martins de Souza, Paulo Alexandre Rodrigues de Vasconcelos Figueiredo

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In recent years, there has been a surge in interest in applying artificial intelligence techniques, particularly machine learning algorithms. Machine learning is a data-analysis technique that automates the creation of analytical models, making it especially useful for designing complex situations. As a result, this technology aids in reducing human intervention while producing accurate results. This methodology is also extensively used in aerospace engineering since this is a field that encompasses several high-complexity operations, such as rocket propulsion. Rocket propulsion is a high-risk operation in which engine failure could result in the loss of life. As a result, it is critical to use computational methods capable of precisely representing the spacecraft's analytical model to guarantee its security and operation. Thus, this paper describes the use of machine learning algorithms for rocket propulsion to aid the realization that this technique is an efficient way to deal with challenging and restrictive aerospace engineering activities. The paper focuses on three machine-learning-aided rocket propulsion applications: set-point control of an expander-bleed rocket engine, supersonic retro-propulsion of a small-scale rocket, and leak detection and isolation on rocket engine data. This paper describes the data-driven methods used for each implementation in depth and presents the obtained results.

Keywords: data analysis, modeling, machine learning, aerospace, rocket propulsion

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Authors: Hassan Mohammadi Khujin

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Tissue engineering is the science of tissues and complex organs creation using scaffolds, cells and biologically active components. Most cells require scaffolds to grow and proliferate. These temporary support structures for tissue regeneration are later replaced with extracellular matrix produced inside the body. Recent advances in additive manufacturing methods allow production of highly porous, complex three dimensional scaffolds suitable for cell growth and proliferation. The current paper investigates the mechanical properties, including elastic modulus and compressive strength, as well as fluid flow dynamics, including permeability and flow-induced shear stress of scaffolds with four triply periodic minimal surface (TPMS) configurations, namely the Schwarz primitive, the Schwarz diamond, the gyroid, and the Neovius structures. Higher porosity in all scaffold types resulted in lower mechanical properties. The permeability of the scaffolds was determined using Darcy's law with reference to geometrical parameters and the pressure drop derived from the computational fluid dynamics (CFD) analysis. Higher porosity enhanced permeability and reduced wall shear stress in all scaffold designs.

Keywords: highly porous scaffolds, tissue engineering, finite elements analysis, CFD analysis

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Authors: Hassan Athari, Abdurrahim Bolukbasi, Dogan Ciloglu

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This study represented the respiratory alveoli system, and determined the trajectory of inhaled particles more accurately using the modified three-dimensional model with deformable walls of alveoli. The study also considered the tissue tension in the model to demonstrate the effect of lung. Tissue tensions are transferred by the lung parenchyma and produce the pressure gradient. This load expands the alveoli and establishes a sub-ambient (vacuum) pressure within the lungs. Thus, at the alveolar level, the flow field and movement of alveoli wall lead to an integrated effect. In this research, we assume that the three-dimensional alveolus has a visco-elastic tissue (walls). For accurate investigation of pulmonary tissue mechanical properties on particle transport and alveolar flow field, the actual relevance between tissue movement and airflow is solved by two-way FSI (Fluid Structure Interaction) simulation technique in the alveolus. Therefore, the essence of real simulation of pulmonary breathing mechanics can be achieved by developing a coupled FSI computational model. We, therefore conduct a series of FSI simulations over a range of tissue models and breathing rates. As a result, the fluid flows and streamlines have changed during present flexible model against the rigid models and also the two-way coupling particle trajectories have changed against the one-way particle coupling.

Keywords: FSI, two-way particle coupling, alveoli, CDF

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Authors: Ana Rahma Yuniarti, Ki Moo Lim

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Slowed myocardial conduction velocity (CV) and shortened action potential duration (APD) due to some reason are associated with an increased risk of re-entrant excitation, predisposing to cardiac arrhythmia. That is because both of CV reduction and APD shortening induces shortening of wavelength. In this study, we investigated quantitatively the cardiac mechanical responses under various CV and APD using multi-scale computational model of the heart. The model consisted of electrical model coupled with the mechanical contraction model together with a lumped model of the circulatory system. The electrical model consisted of 149.344 numbers of nodes and 183.993 numbers of elements of tetrahedral mesh, whereas the mechanical model consisted of 356 numbers of nodes and 172 numbers of elements of hexahedral mesh with hermite basis. We performed the electrical simulation with two scenarios: 1) by varying the CV values with constant APD and 2) by varying the APD values with constant CV. Then, we compared the electrical and mechanical responses for both scenarios. Our simulation showed that faster CV and longer APD induced largest resultants wavelength and generated better cardiac pumping efficacy by increasing the cardiac output and consuming less energy. This is due to the long wave propagation and faster conduction generated more synchronous contraction of whole ventricle.

Keywords: conduction velocity, action potential duration, mechanical contraction model, circulatory model

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Authors: Nusrat T. Chowdhury, M. F. Baki, A. Azab

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The production planning problem is concerned with specifying the optimal quantities to produce in order to meet the demand for a prespecified planning horizon with the least possible expenditure. Making the right decisions in production planning will affect directly the performance and productivity of a manufacturing firm, which is important for its ability to compete in the market. Therefore, developing and improving solution procedures for production planning problems is very significant. In this paper, we develop a Dantzig-Wolfe decomposition of a multi-item hierarchical production planning problem with capacity constraint and present a column generation approach to solve the problem. The original Mixed Integer Linear Programming model of the problem is decomposed item by item into a master problem and a number of subproblems. The capacity constraint is considered as the linking constraint between the master problem and the subproblems. The subproblems are solved using the dynamic programming approach. We also propose a multi-step iterative capacity allocation heuristic procedure to handle any kind of infeasibility that arises while solving the problem. We compare the computational performance of the developed solution approach against the state-of-the-art heuristic procedure available in the literature. The results show that the proposed heuristic-based decomposition approach improves the solution quality by 20% as compared to the literature.

Keywords: inventory, multi-level capacitated lot-sizing, emission control, setup carryover

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Authors: Chih-Hua Wu, Bang-Fuh Chen, Keryea Soong

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Midges can move on the surface of the water at speeds of approximately 340 body-lengths/s and can move continuously for >90 min. Their wings periodically scull the sea surface to push water backward and thus generate thrust; their other body parts, including their three pairs of legs, touch the water only occasionally. The aim of this study was to investigate the locomotion mechanism of marine midges with a size of 2 mm and living in shallow reefs in Wanliton, southern Taiwan. We assumed that midges generate lift through two mechanisms: by sculling the surface of seawater to leverage the generated tension for thrust and by retracting their wings to generate aerodynamic lift at a suitable angle of attack. We performed computational fluid dynamic simulations to determine the mechanism of midge locomotion above the surface of the water. The simulations indicated that ground effects are essential and that both the midge trunk and wing tips must be very close to the water surface to produce sufficient lift to keep the midge airborne. Furthermore, a high wing-beat frequency is crucial for the midge to produce sufficient lift during wing retraction. Accordingly, ground effects, forward speed, and high wing-beat frequency are major factors influencing the ability of midges to generate sufficient lift and remain airborne above the water surface.

Keywords: ground effect, water locomotion, CFD, aerodynamic lift

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Authors: Chen T. Chen, Hui L. Cheng

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Due to the different knowledge, experience and expertise of experts, they usually provide the different opinions in the group decision-making process. Therefore, it is an important issue to reach the group consensus of opinions of experts in group multiple-criteria decision-making (GMCDM) process. Because the subjective opinions of experts always are fuzziness and uncertainties, it is difficult to use crisp values to describe the real opinions of experts or decision-makers. It is reasonable for experts to use the linguistic variables to express their opinions. The hesitant fuzzy set are extended from the concept of fuzzy sets. Experts use the hesitant fuzzy sets can be flexible to describe their subjective opinions. In order to aggregate the hesitant fuzzy linguistic variables of all experts effectively, an adjustment method based on distance function will be presented in this paper. Based on the opinions adjustment method, this paper will present an effective approach to adjust the hesitant fuzzy linguistic variables of all experts to reach the group consensus. Then, a new hesitant linguistic GMCDM method will be presented based on the group consensus of hesitant fuzzy linguistic variables. Finally, an example will be implemented to illustrate the computational process to enhance the practical value of the proposed model.

Keywords: group multi-criteria decision-making, linguistic variables, hesitant fuzzy linguistic variables, distance function, group consensus

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Authors: Nan Deng, Zhenqiu Liu

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Thousands of patients with metastatic tumors were diagnosed with cancers of unknown primary sites each year. The inability to identify the primary cancer site may lead to inappropriate treatment and unexpected prognosis. Nowadays, a large amount of genomics and transcriptomics cancer data has been generated by next-generation sequencing (NGS) technologies, and The Cancer Genome Atlas (TCGA) database has accrued thousands of human cancer tumors and healthy controls, which provides an abundance of resource to differentiate cancer types. Meanwhile, deep convolutional neural networks (CNNs) have shown high accuracy on classification among a large number of image object categories. Here, we utilize 25 cancer primary tumors and 3 normal tissues from TCGA and convert their RNA-Seq gene expression profiling to color images; train, validate and test a CNN classifier directly from these images. The performance result shows that our CNN classifier can archive >80% test accuracy on most of the tumors and normal tissues. Since the gene expression pattern of distant metastases is similar to their primary tumors, the CNN classifier may provide a potential computational strategy on identifying the unknown primary origin of metastatic cancer in order to plan appropriate treatment for patients.

Keywords: bioinformatics, cancer, convolutional neural network, deep leaning, gene expression pattern

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Authors: Masoud Shahmanzari

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The aim of this paper is to present a Variable Neighborhood Search (VNS) with Tabu Search (TS) conditions for the Roaming Salesman Problem (RSP). The RSP is a special case of the well-known traveling salesman problem (TSP) where a set of cities with time-dependent rewards and a set of campaign days are given. Each city can be visited on any day and a subset of cities can be visited multiple times. The goal is to determine an optimal campaign schedule consist of daily open/closed tours that visit some cities and maximizes the total net benefit while respecting daily maximum tour duration constraints and the necessity to return campaign base frequently. This problem arises in several real-life applications and particularly in election logistics where depots are not fixed. We formulate the problem as a mixed integer linear programming (MILP), in which we capture as many real-world aspects of the RSP as possible. We also present a hybrid metaheuristic algorithm based on a VNS with TS conditions. The initial feasible solution is constructed via a new matheuristc approach based on the decomposition of the original problem. Next, this solution is improved in terms of the collected rewards using the proposed local search procedure. We consider a set of 81 cities in Turkey and a campaign of 30 days as our largest instance. Computational results on real-world instances show that the developed algorithm could find near-optimal solutions effectively.

Keywords: optimization, routing, election logistics, heuristics

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Authors: Ramin Mansouri

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The manhole is one of the types of structures that are installed at the site of change direction or change in the pipe diameter or sewage pipes as well as in step slope areas to reduce the flow velocity. In this study, the flow characteristics of hydraulic structures in a manhole structure have been investigated with a numerical model. In this research, the types of computational grid coarse, medium, and fines have been used for simulation. In order to simulate flow, k-ε model (standard, RNG, Realizable) and k-w model (standard SST) are used. Also, in order to find the best wall conditions, two types of standard and non-equilibrium wall functions were investigated. The turbulent model k-ε has the highest correlation with experimental results or all models. In terms of boundary conditions, constant speed is set for the flow input boundary, the output pressure is set in the boundaries which are in contact with the air, and the standard wall function is used for the effect of the wall function. In the numerical model, the depth at the output of the second manhole is estimated to be less than that of the laboratory and the output jet from the span. In the second regime, the jet flow collides with the manhole wall and divides into two parts, so hydraulic characteristics are the same as large vertical shaft hydraulic characteristics. In this situation, the turbulence is in a high range since it can be seen more energy loss in it. According to the results, energy loss in numerical is estimated at 9.359%, which is more than experimental data.

Keywords: manhole, energy, depreciation, turbulence model, wall function, flow

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Authors: Shreya Banerjee, Roshmi Sen, Subrata Chattopadhyay

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Urbanization during the second half of the last century has created many serious environment related issues leading to global warming and climate change. India is not an exception as the country is also facing the problems of global warming and urban heat islands (UHI) in all the major metropolises. This paper discusses the effect of different housing cluster layouts, site geometry, and geometry of urban street canyons on the urban heat island profile. The study is carried out using the three dimensional microclimatic computational fluid dynamics model ENVI-met version 3.1. Simulation models are done for a typical summer day of 21st June, 2015 in four different residential neighborhoods in the city of Kolkata which predominantly belongs to Warm-Humid Monsoon Climate. The results show the changing pattern of urban heat island profile with respect to different clustering layouts, geometry, and morphology of urban street canyons. The comparison between the four neighborhoods shows that different microclimatic variables are strongly dependant on the neighborhood layout pattern and geometry. The inferences obtained from this study can be indicative towards the formulation of neighborhood design by-laws that will attenuate the urban heat island effect.

Keywords: urban heat island, neighborhood morphology, site microclimate, ENVI-met, numerical analysis

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Authors: Rims Janeliukstis, Deniss Mironovs, Andrejs Kovalovs

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Operational Modal Analysis (OMA) is widely applied as a method for Structural Health Monitoring for structural damage identification and assessment by tracking the changes of the identified modal parameters over time. Unfortunately, modal parameters also depend on such external factors as temperature and loads. Any structural condition assessment using modal parameters should be done taking into consideration those external factors, otherwise there is a high chance of false positives. A method of structural reliability assessment based on anomaly detection technique called Machalanobis Squared Distance (MSD) is proposed. It requires a set of reference conditions to learn healthy state of a structure, which all future parameters are compared to. In this study, structural modal parameters (natural frequency and mode shape), as well as ambient temperature and loads acting on the structure are used as features. Numerical tests were performed on a finite element model of a carbon fibre reinforced polymer composite beam with delamination damage at various locations and of various severities. The advantages of the demonstrated approach include relatively few computational steps, ability to distinguish between healthy and damaged conditions and discriminate between different damage severities. It is anticipated to be promising in reliability assessment of massively produced structural parts.

Keywords: operational modal analysis, reliability assessment, anomaly detection, damage, mahalanobis squared distance

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Authors: Fahad Alhussein, Huaping Liu

Abstract:

This paper compares the multipath mitigation performance of code correlation reference waveform receivers with variable and fixed window width, for binary offset carrier and multiplexed binary offset carrier signals typically used in global navigation satellite systems. In the variable window width method, such width is iteratively reduced until the distortion on the discriminator with multipath is eliminated. This distortion is measured as the Euclidean distance between the actual discriminator (obtained with the incoming signal), and the local discriminator (generated with a local copy of the signal). The variable window width have shown better performance compared to the fixed window width. In particular, the former yields zero error for all delays for the BOC and MBOC signals considered, while the latter gives rather large nonzero errors for small delays in all cases. Due to its computational simplicity, the variable window width method is perfectly suitable for implementation in low-cost receivers.

Keywords: correlation reference waveform receivers, binary offset carrier, multiplexed binary offset carrier, global navigation satellite systems

Procedia PDF Downloads 119

Authors: Evgeniia V. Mekhonoshina, Vladimir Ya. Modorskii, Vasilii Yu. Petrov

Abstract:

At present, vibrations of rotors of gas transmittal unit evade sustainable forecasting. This paper describes elastic oscillation modes in resilient supports and rotor impellers modeled during computational experiments with regard to interference in the system of gas-dynamic flow and compressor rotor. Verification of aeroelastic approach was done on model problem of interaction between supersonic jet in shock tube with deformed plate. ANSYS 15.0 engineering analysis system was used as a modeling tool of numerical simulation in this paper. Finite volume method for gas dynamics and finite elements method for assessment of the strain stress state (SSS) components were used as research methods. Rotation speed and material’s elasticity modulus varied during calculations, and SSS components and gas-dynamic parameters in the dynamic system of gas-dynamic flow and compressor rotor were evaluated. The analysis of time dependence demonstrated that gas-dynamic parameters near the rotor blades oscillate at 200 Hz, and SSS parameters at the upper blade edge oscillate four times higher, i.e. with blade frequency. It has been detected that vibration amplitudes correction in the test points at magnetic bearings by aeroelasticity may correspond up to 50%, and about -π/4 for phases.

Keywords: Centrifugal compressor, aeroelasticity, interdisciplinary calculation, oscillation phase displacement, vibration, nonstationarity

Procedia PDF Downloads 246

Authors: Lucas Viani, Benedetta Mennucci, Soo Young Park, Johannes Gierschner

Abstract:

Organic semiconductors have attracted the attention of the scientific community in the past decades due to their unique physicochemical properties, allowing new designs and alternative device fabrication methods. Until today, organic electronic devices are largely based on conjugated polymers mainly due to their easy processability. In the recent years, due to moderate ET and CT efficiencies and the ill-defined nature of polymeric systems the focus has been shifting to small conjugated molecules with well-defined chemical structure, easier control of intermolecular packing, and enhanced CT and ET properties. It has led to the synthesis of new small molecules, followed by the growth of their crystalline structure and ultimately by the device preparation. This workflow is commonly followed without a clear knowledge of the ET and CT properties related mainly to the macroscopic systems, which may lead to financial and time losses, since not all materials will deliver the properties and efficiencies demanded by the current standards. In this work, we present a theoretical workflow designed to predict the key properties of ET of these new materials prior synthesis, thus speeding up the discovery of new promising materials. It is based on quantum mechanical, hybrid, and classical methodologies, starting from a single molecule structure, finishing with the prediction of its packing structure, and prediction of properties of interest such as static and averaged excitonic couplings, and exciton diffusion length.

Keywords: organic semiconductor, organic crystals, energy transport, excitonic couplings

Procedia PDF Downloads 242

Authors: Nanjiang Chen

Abstract:

In the backdrop of expanding urban landscapes, accurately assessing spatial openness is critical. Traditional visibility analysis methods grapple with discretization errors and inefficiencies, creating a gap in truly capturing the human experi-ence of space. Addressing these gaps, this paper introduces a distinct continuous visibility algorithm, a leap in measuring urban spaces from a human-centric per-spective. This study presents a methodological breakthrough by applying this algorithm to urban visibility analysis. Unlike conventional approaches, this tech-nique allows for a continuous range of visibility assessment, closely mirroring hu-man visual perception. By eliminating the need for predefined subdivisions in ray casting, it offers a more accurate and efficient tool for urban planners and architects. The proposed algorithm not only reduces computational errors but also demonstrates faster processing capabilities, validated through a case study in Bei-jing's urban setting. Its key distinction lies in its potential to benefit a broad spec-trum of stakeholders, ranging from urban developers to public policymakers, aid-ing in the creation of urban spaces that prioritize visual openness and quality of life. This advancement in urban analysis methods could lead to more inclusive, comfortable, and well-integrated urban environments, enhancing the spatial experience for communities worldwide.

Keywords: visual openness, spatial continuity, ray-tracing algorithms, urban computation

Procedia PDF Downloads 19