Search results for: computational imaging
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 3266

Search results for: computational imaging

806 Numerical Simulation of the Effect of Single and Dual Synthetic Jet on Stall Phenomenon On NACA (National Advisory Committee for Aeronautics) GA(W)-2 Airfoil

Authors: Abbasali Abouei Mehrizi, Hamid Hassanzadeh Afrouzi

Abstract:

Reducing the drag force increases the efficiency of the aircraft and its better performance. Flow control methods delay the phenomenon of flow separation and consequently reduce the reversed flow phenomenon in the separation region and enhance the performance of the lift force while decreasing the drag force and thus improving the aircraft efficiency. Flow control methods can be divided into active and passive types. The use of synthetic jets actuator (SJA) used in this study for NACA GA (W) -2 airfoil is one of the active flow control methods to prevent stall phenomenon on the airfoil. In this research, the relevant airfoil in different angles of attack with and without jets has been compared by OpenFOAM. Also, after achieving the proper SJA position on the airfoil suction surface, the simultaneous effect of two SJAs has been discussed. It was found to have the best effect at 12% chord (C), close to the airfoil’s leading edge (LE). At 12% chord, SJA decreases the drag significantly with increasing lift, and also, the average lift increase was higher than other situations and was equal to 10.4%. The highest drag reduction was about 5% in SJA=0.25C. Then, due to the positive effects of SJA in the 12% and 25% chord regions, these regions were considered for applying dual jets in two post-stall angles of attack, i.e., 16° and 22°.

Keywords: active and passive flow control methods, computational fluid dynamics, flow separation, synthetic jet

Procedia PDF Downloads 83
805 Automatic Fluid-Structure Interaction Modeling and Analysis of Butterfly Valve Using Python Script

Authors: N. Guru Prasath, Sangjin Ma, Chang-Wan Kim

Abstract:

A butterfly valve is a quarter turn valve which is used to control the flow of a fluid through a section of pipe. Generally, butterfly valve is used in wide range of applications such as water distribution, sewage, oil and gas plants. In particular, butterfly valve with larger diameter finds its immense applications in hydro power plants to control the fluid flow. In-lieu with the constraints in cost and size to run laboratory setup, analysis of large diameter values will be mostly studied by computational method which is the best and inexpensive solution. For fluid and structural analysis, CFD and FEM software is used to perform large scale valve analyses, respectively. In order to perform above analysis in butterfly valve, the CAD model has to recreate and perform mesh in conventional software’s for various dimensions of valve. Therefore, its limitation is time consuming process. In-order to overcome that issue, python code was created to outcome complete pre-processing setup automatically in Salome software. Applying dimensions of the model clearly in the python code makes the running time comparatively lower and easier way to perform analysis of the valve. Hence, in this paper, an attempt was made to study the fluid-structure interaction (FSI) of butterfly valves by varying the valve angles and dimensions using python code in pre-processing software, and results are produced.

Keywords: butterfly valve, flow coefficient, automatic CFD analysis, FSI analysis

Procedia PDF Downloads 241
804 Remote Sensing-Based Prediction of Asymptomatic Rice Blast Disease Using Hyperspectral Spectroradiometry and Spectral Sensitivity Analysis

Authors: Selvaprakash Ramalingam, Rabi N. Sahoo, Dharmendra Saraswat, A. Kumar, Rajeev Ranjan, Joydeep Mukerjee, Viswanathan Chinnasamy, K. K. Chaturvedi, Sanjeev Kumar

Abstract:

Rice is one of the most important staple food crops in the world. Among the various diseases that affect rice crops, rice blast is particularly significant, causing crop yield and economic losses. While the plant has defense mechanisms in place, such as chemical indicators (proteins, salicylic acid, jasmonic acid, ethylene, and azelaic acid) and resistance genes in certain varieties that can protect against diseases, susceptible varieties remain vulnerable to these fungal diseases. Early prediction of rice blast (RB) disease is crucial, but conventional techniques for early prediction are time-consuming and labor-intensive. Hyperspectral remote sensing techniques hold the potential to predict RB disease at its asymptomatic stage. In this study, we aimed to demonstrate the prediction of RB disease at the asymptomatic stage using non-imaging hyperspectral ASD spectroradiometer under controlled laboratory conditions. We applied statistical spectral discrimination theory to identify unknown spectra of M. Oryzae, the fungus responsible for rice blast disease. The infrared (IR) region was found to be significantly affected by RB disease. These changes may result in alterations in the absorption, reflection, or emission of infrared radiation by the affected plant tissues. Our research revealed that the protein spectrum in the IR region is impacted by RB disease. In our study, we identified strong correlations in the region (Amide group - I) around X 1064 nm and Y 1300 nm with the Lambda / Lambda derived spectra methods for protein detection. During the stages when the disease is developing, typically from day 3 to day 5, the plant's defense mechanisms are not as effective. This is especially true for the PB-1 variety of rice, which is highly susceptible to rice blast disease. Consequently, the proteins in the plant are adversely affected during this critical time. The spectral contour plot reveals the highly correlated spectral regions 1064 nm and Y 1300 nm associated with RB disease infection. Based on these spectral sensitivities, we developed new spectral disease indices for predicting different stages of disease emergence. The goal of this research is to lay the foundation for future UAV and satellite-based studies aimed at long-term monitoring of RB disease.

Keywords: rice blast, asymptomatic stage, spectral sensitivity, IR

Procedia PDF Downloads 86
803 Structural Performance Evaluation of Electronic Road Sign Panels Reflecting Damage Scenarios

Authors: Junwon Seo, Bipin Adhikari, Euiseok Jeong

Abstract:

This paper is intended to evaluate the structural performance of welded electronic road signs under various damage scenarios (DSs) using a finite element (FE) model calibrated with full-scale ultimate load testing results. The tested electronic road sign specimen was built with a back skin made of 5052 aluminum and two channels and a frame made of 6061 aluminum, where the back skin was connected to the frame by welding. The size of the tested specimen was 1.52 m long, 1.43 m wide, and 0.28 m deep. An actuator applied vertical loads at the center of the back skin of the specimen, resulting in a displacement of 158.7 mm and an ultimate load of 153.46 kN. Using these testing data, generation and calibration of a FE model of the tested specimen were executed in ABAQUS, indicating that the difference in the ultimate load between the calibrated model simulation and full-scale testing was only 3.32%. Then, six different DSs were simulated where the areas of the welded connection in the calibrated model were diminished for the DSs. It was found that the corners at the back skin-frame joint were prone to connection failure for all the DSs, and failure of the back skin-frame connection occurred remarkably from the distant edges.

Keywords: computational analysis, damage scenarios, electronic road signs, finite element, welded connections

Procedia PDF Downloads 92
802 Iris Feature Extraction and Recognition Based on Two-Dimensional Gabor Wavelength Transform

Authors: Bamidele Samson Alobalorun, Ifedotun Roseline Idowu

Abstract:

Biometrics technologies apply the human body parts for their unique and reliable identification based on physiological traits. The iris recognition system is a biometric–based method for identification. The human iris has some discriminating characteristics which provide efficiency to the method. In order to achieve this efficiency, there is a need for feature extraction of the distinct features from the human iris in order to generate accurate authentication of persons. In this study, an approach for an iris recognition system using 2D Gabor for feature extraction is applied to iris templates. The 2D Gabor filter formulated the patterns that were used for training and equally sent to the hamming distance matching technique for recognition. A comparison of results is presented using two iris image subjects of different matching indices of 1,2,3,4,5 filter based on the CASIA iris image database. By comparing the two subject results, the actual computational time of the developed models, which is measured in terms of training and average testing time in processing the hamming distance classifier, is found with best recognition accuracy of 96.11% after capturing the iris localization or segmentation using the Daughman’s Integro-differential, the normalization is confined to the Daugman’s rubber sheet model.

Keywords: Daugman rubber sheet, feature extraction, Hamming distance, iris recognition system, 2D Gabor wavelet transform

Procedia PDF Downloads 65
801 An Interesting Case of Management of Life Threatening Calcium Disequilibrium in a Patient with Parathyroid Tumor

Authors: Rajish Shil, Mohammad Ali Houri, Mohammad Milad Ismail, Fatimah Al Kaabi

Abstract:

The clinical presentation of Primary hyperparathyroidism can vary from simple asymptomatic hypercalcemia to severe life-threatening hypercalcemic crisis with multi-organ dysfunction, which can be due to parathyroid adenoma or sometimes with malignant cancer. This cascade of clinical presentation can lead to a diagnostic and therapeutic challenge for treating the disease. We are presenting a case of severe hypercalcemic crisis due to parathyroid adenoma with an emphasis on early management, diagnosis, and interventions to prevent any lifelong complications and any permanent organ dysfunction. A 30 years old female with a history of primary Infertility, admitted to Al Ain Hospital critical care unit with Acute Severe Necrotizing Pancreatitis. She initially had a 1-month history of abdominal pain on and off, for which she was treated conservatively with no much improvement, and later on, she developed life-threatening severe pancreatitis, which required her to be admitted to the critical care unit. She was transferred from a private healthcare facility, where she was found to have a very high level of calcium up to 15mmol/L. She received systemic Zoledronic Acid, which lowered her calcium level transiently and later was increased again. She went on to develop multiple end-organ damages along with multiple electrolytes disturbances. She was found to have high levels of Parathyroid hormone, which was correlated with a parathyroid mass on the neck via radiological imaging. After a long course of medical treatment to lower the calcium to a near-normal level, parathyroidectomy was done, which showed parathyroid adenoma on histology. She developed hungry bone syndrome after the surgery and pancreatic pseudocyst after resolving of pancreatitis. She required aggressive treatment with Intravenous calcium for her hypocalcemia as she received zoledronic acid at the beginning of the disease. Later on, she was discharged on long term calcium and other electrolytes supplements. In patients presenting with hypercalcemia, it is prudent to investigate and start treatment early to prevent complications and end-organ damage from hypercalcemia and also to treat the primary cause of the hypercalcemia, with conscious follow up to prevent hypocalcemic complications after treatment. It is important to follow up patients with parathyroid adenomas for a long period in order to detect any recurrence of the tumor or to make sure if the primary tumor is either benign or malignant.

Keywords: hypercalcemia, pancreatitis, hypocalcemia, hyperparathyroidism

Procedia PDF Downloads 123
800 Control of Doxorubicin Release Rate from Magnetic PLGA Nanoparticles Using a Non-Permanent Magnetic Field

Authors: Inês N. Peça , A. Bicho, Rui Gardner, M. Margarida Cardoso

Abstract:

Inorganic/organic nanocomplexes offer tremendous scope for future biomedical applications, including imaging, disease diagnosis and drug delivery. The combination of Fe3O4 with biocompatible polymers to produce smart drug delivery systems for use in pharmaceutical formulation present a powerful tool to target anti-cancer drugs to specific tumor sites through the application of an external magnetic field. In the present study, we focused on the evaluation of the effect of the magnetic field application time on the rate of drug release from iron oxide polymeric nanoparticles. Doxorubicin, an anticancer drug, was selected as the model drug loaded into the nanoparticles. Nanoparticles composed of poly(d-lactide-co-glycolide (PLGA), a biocompatible polymer already approved by FDA, containing iron oxide nanoparticles (MNP) for magnetic targeting and doxorubicin (DOX) were synthesized by the o/w solvent extraction/evaporation method and characterized by scanning electron microscopy (SEM), by dynamic light scattering (DLS), by inductively coupled plasma-atomic emission spectrometry and by Fourier transformed infrared spectroscopy. The produced particles yielded smooth surfaces and spherical shapes exhibiting a size between 400 and 600 nm. The effect of the magnetic doxorubicin loaded PLGA nanoparticles produced on cell viability was investigated in mammalian CHO cell cultures. The results showed that unloaded magnetic PLGA nanoparticles were nontoxic while the magnetic particles without polymeric coating show a high level of toxicity. Concerning the therapeutic activity doxorubicin loaded magnetic particles cause a remarkable enhancement of the cell inhibition rates compared to their non-magnetic counterpart. In vitro drug release studies performed under a non-permanent magnetic field show that the application time and the on/off cycle duration have a great influence with respect to the final amount and to the rate of drug release. In order to determine the mechanism of drug release, the data obtained from the release curves were fitted to the semi-empirical equation of the the Korsmeyer-Peppas model that may be used to describe the Fickian and non-Fickian release behaviour. Doxorubicin release mechanism has shown to be governed mainly by Fickian diffusion. The results obtained show that the rate of drug release from the produced magnetic nanoparticles can be modulated through the magnetic field time application.

Keywords: drug delivery, magnetic nanoparticles, PLGA nanoparticles, controlled release rate

Procedia PDF Downloads 259
799 Molecular Interactions Driving RNA Binding to hnRNPA1 Implicated in Neurodegeneration

Authors: Sakina Fatima, Joseph-Patrick W. E. Clarke, Patricia A. Thibault, Subha Kalyaanamoorthy, Michael Levin, Aravindhan Ganesan

Abstract:

Heteronuclear ribonucleoprotein (hnRNPA1 or A1) is associated with the pathology of different diseases, including neurological disorders and cancers. In particular, the aggregation and dysfunction of A1 have been identified as a critical driver for neurodegeneration (NDG) in Multiple Sclerosis (MS). Structurally, A1 includes a low-complexity domain (LCD) and two RNA-recognition motifs (RRMs), and their interdomain coordination may play a crucial role in A1 aggregation. Previous studies propose that RNA-inhibitors or nucleoside analogs that bind to RRMs can potentially prevent A1 self-association. Therefore, molecular-level understanding of the structures, dynamics, and nucleotide interactions with A1 RRMs can be useful for developing therapeutics for NDG in MS. In this work, a combination of computational modelling and biochemical experiments were employed to analyze a set of RNA-A1 RRM complexes. Initially, the atomistic models of RNA-RRM complexes were constructed by modifying known crystal structures (e.g., PDBs: 4YOE and 5MPG), and through molecular docking calculations. The complexes were optimized using molecular dynamics simulations (200-400 ns), and their binding free energies were computed. The binding affinities of the selected complexes were validated using a thermal shift assay. Further, the most important molecular interactions that contributed to the overall stability of the RNA-A1 RRM complexes were deduced. The results highlight that adenine and guanine are the most suitable nucleotides for high-affinity binding with A1. These insights will be useful in the rational design of nucleotide-analogs for targeting A1 RRMs.

Keywords: hnRNPA1, molecular docking, molecular dynamics, RNA-binding proteins

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798 A Finite Element Based Predictive Stone Lofting Simulation Methodology for Automotive Vehicles

Authors: Gaurav Bisht, Rahul Rathnakumar, Ravikumar Duggirala

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Predictive simulations are one of the key focus areas in safety-critical industries such as aerospace and high-performance automotive engineering. The stone-chipping study is one such effort taken up by the industry to predict and evaluate the damage caused due to gravel impact on vehicles. This paper describes a finite elements based method that can simulate the ejection of gravel chips from a vehicle tire. The FE simulations were used to obtain the initial ejection velocity of the stones for various driving conditions using a computational contact mechanics approach. To verify the accuracy of the tire model, several parametric studies were conducted. The FE simulations resulted in stone loft velocities ranging from 0–8 m/s, regardless of tire speed. The stress on the tire at the instant of initial contact with the stone increased linearly with vehicle speed. Mesh convergence studies indicated that a highly resolved tire mesh tends to result in better momentum transfer between the tire and the stone. A fine tire mesh also showed a linearly increasing relationship between the tire forward speed and stone lofting speed, which was not observed in coarser meshes. However, it also highlighted a potential challenge, in that the ejection velocity vector of the stone seemed to be sensitive to the mesh, owing to the FE-based contact mechanical formulation of the problem.

Keywords: abaqus, contact mechanics, foreign object debris, stone chipping

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797 The Role of High-Intensity Focused Ultrasound (HIFU) in the Treatment of Fibroadenomas: A Systematic Review

Authors: Ahmed Gonnah, Omar Masoud, Mohamed Abdel-Wahab, Ahmed ElMosalamy, Abdulrahman Al-Naseem

Abstract:

Introduction: Fibroadenomas are solid, mobile, and non-tender benign breast lumps, with the highest prevalence amongst young women aged between 15 and 35. Symptoms can include discomfort, and they can become problematic, particularly when they enlarge, resulting in many referrals for biopsies, with fibroadenomas accounting for 30-75% of the cases. Diagnosis is based on triple assessment that involves a clinical examination, ultrasound imaging and mammography, as well as core needle biopsies. Current management includes observation for 6-12 months, with the indication of definitive surgery, in cases that are older than 35 years or with fibroadenoma persistence. Serious adverse effects of surgery might include nipple-areolar distortion, scarring and damage to the breast tissue, as well as the risks associated with surgery and anesthesia, making it a non-feasible option. Methods: A literature search was performed on the databases EMBASE. MEDLINE/PubMed, Google scholar and Ovid, for English language papers published between 1st of January 2000 and 17th of March 2021. A structured protocol was employed to devise a comprehensive search strategy with keywords and Boolean operators defined by the research question. The keywords used for the search were ‘HIFU’, ‘High-Intensity Focused Ultrasound’, ‘Fibroadenoma’, ‘Breast’, ‘Lesion’. This review was carried out in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Results: Recently, a thermal ablative technique, High Intensity Focused Ultrasound (HIFU), was found to be a safe, non-invasive, and technically successful alternative, having displayed promising outcomes in reducing the volume of fibroadenomas, pain experienced by patients, and the length of hospitalization. Quality of life improvement was also evidenced, exhibited by the disappearance of symptoms, and enhanced physical activity post-intervention, in addition to patients’ satisfaction with the cosmetic results and future recommendation of the procedure to other patients. Conclusion: Overall, HIFU is a well-tolerated treatment associated with a low risk of complications that can potentially include erythema, skin discoloration and bruising, with the majority of this self-resolving shortly after the procedure.

Keywords: ultrasound, HIFU, breast, efficacy, side effects, fibroadenoma

Procedia PDF Downloads 225
796 Assessment of the Effect of Building Materials on Energy Demand of Buildings in Jos: An Experimental and Numerical Approach

Authors: Zwalnan Selfa Johnson, Caleb Nanchen Nimyel, Gideon Duvuna Ayuba

Abstract:

Air conditioning accounts for a significant share of the overall energy consumed in residential buildings. Solar thermal gains in buildings account for a significant component of the air conditioning load in buildings. This study compares the solar thermal gain and air conditioning load of a proposed building design with a typical conventional building in the climatic conditions of Jos, Nigeria, using a combined experimental and computational method using TRNSYS software. According to the findings of this study, the proposed design building's annual average solar thermal gains are lower compared to the reference building's average solar heat gains. The study case building's decreased solar heat gain is mostly attributable to the lower temperature of the building zones because of the greater building volume and lower fenestration ratio (ratio external opening area to the area of the external walls). This result shows that the proposed building design adjusts to the local climate better than the standard conventional construction in Jos to maintain a suitable temperature within the building. This finding means that the air-conditioning electrical energy consumption per volume of the proposed building design will be lower than that of a conventional building design.

Keywords: solar heat gain, building zone, cooling energy, air conditioning, zone temperature

Procedia PDF Downloads 93
795 Movie Genre Preference Prediction Using Machine Learning for Customer-Based Information

Authors: Haifeng Wang, Haili Zhang

Abstract:

Most movie recommendation systems have been developed for customers to find items of interest. This work introduces a predictive model usable by small and medium-sized enterprises (SMEs) who are in need of a data-based and analytical approach to stock proper movies for local audiences and retain more customers. We used classification models to extract features from thousands of customers’ demographic, behavioral and social information to predict their movie genre preference. In the implementation, a Gaussian kernel support vector machine (SVM) classification model and a logistic regression model were established to extract features from sample data and their test error-in-sample were compared. Comparison of error-out-sample was also made under different Vapnik–Chervonenkis (VC) dimensions in the machine learning algorithm to find and prevent overfitting. Gaussian kernel SVM prediction model can correctly predict movie genre preferences in 85% of positive cases. The accuracy of the algorithm increased to 93% with a smaller VC dimension and less overfitting. These findings advance our understanding of how to use machine learning approach to predict customers’ preferences with a small data set and design prediction tools for these enterprises.

Keywords: computational social science, movie preference, machine learning, SVM

Procedia PDF Downloads 260
794 Polypeptide Modified Carbon Nanotubes – Mediated GFP Gene Transfection for H1299 Cells and Toxicity Assessment

Authors: Pei-Ying Lo, Jing-Hao Ciou, Kai-Cheng Yang, Jia-Huei Zheng, Shih-Hsiang Huang, Kuen-Chan Lee, Er-Chieh Cho

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As-produced CNTs are insoluble in all organic solvents and aqueous solutions have imposed limitations to the use of CNTs. Therefore, how to debundle carbon nanotubes and to modify them for further uses is an important issue. There are several methods for the dispersion of CNTs in water using covalent attachment of hydrophilic groups to the surface of tubes. These methods, however, alter the electronic structure of the nanotubes by disrupting the network of sp2 hybridized carbons. In order to keep the nanotubes’ intrinsic mechanical and electrical properties intact, non-covalent interactions are increasingly being explored as an alternative route for dispersion. Apart from conventional surfactants such as sodium dodecylsulfate (SDS) or sodium dodecylbenzenesulfonate (SDBS) which are highly effective in dispersing CNTs, biopolymers have received much attention as dispersing agents due to the anticipated biocompatibility of the dispersed CNTs. Also, The pyrenyl group is known to interact strongly with the basal plane of graphene via π-stacking. In this study, a highly re-dispersible biopolymer is reported for the synthesis of pyrene-modified poly-L-lysine (PBPL) and poly(D-Glu, D-Lys) (PGLP). To provide the evidence of the safety of the PBPL/CNT & PGLP/CNT materials we use in this study, H1299 and HCT116 cells were incubated with PBPL/CNT & PGLP/CNT materials for toxicity analysis, MTS assays. The results from MTS assays indicated that no significant cellular toxicity was shown in H1299 and HCT116 cells. Furthermore, the fluorescence marker fluorescein isothiocyanate (FITC) was added to PBPL & PGLP dispersions. From the fluorescent measurements showed that the chemical functionalisation of the PBPL/CNT & PGLP/CNT conjugates with the fluorescence marker were successful. The fluorescent PBPL/CNT & PGLP/CNT conjugates could find application in medical imaging. In the next step, the GFP gene is immobilized onto PBPL/CNT conjugates by introducing electrostatic interaction. GFP-transfected cells that emitted fluorescence were imaged and counted under a fluorescence microscope. Due to the unique biocompatibility of PBPL modified CNTs, the GFP gene could be transported into H1299 cells without using antibodies. The applicability of such soluble and chemically functionalised polypeptide/CNT conjugates in biomedicine is currently investigated. We expect that this polypeptide/CNT system will be a safe and multi-functional nanomedical delivery platform and contribute to future medical therapy.

Keywords: carbon nanotube, nanotoxicology, GFP transfection, polypeptide/CNT hybrids

Procedia PDF Downloads 339
793 Impacts on the Modification of a Two-Blade Mobile on the Agitation of Newtonian Fluids

Authors: Abderrahim Sidi Mohammed Nekrouf, Sarra Youcefi

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Fluid mixing plays a crucial role in numerous industries as it has a significant impact on the final product quality and performance. In certain cases, the circulation of viscous fluids presents challenges, leading to the formation of stagnant zones. To overcome this issue, stirring devices are employed for fluid mixing. This study focuses on a numerical analysis aimed at understanding the behavior of Newtonian fluids when agitated by a two-blade agitator in a cylindrical vessel. We investigate the influence of the agitator shape on fluid motion. Bi-blade agitators of this type are commonly used in the food, cosmetic, and chemical industries to agitate both viscous and non-viscous liquids. Numerical simulations were conducted using Computational Fluid Dynamics (CFD) software to obtain velocity profiles, streamlines, velocity contours, and the associated power number. The obtained results were compared with experimental data available in the literature, validating the accuracy of our numerical approach. The results clearly demonstrate that modifying the agitator shape has a significant impact on fluid motion. This modification generates an axial flow that enhances the efficiency of the fluid flow. The various velocity results convincingly reveal that the fluid is more uniformly agitated with this modification, resulting in improved circulation and a substantial reduction in stagnant zones.

Keywords: Newtonian fluids, numerical modeling, two blade., CFD

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792 A Posteriori Trading-Inspired Model-Free Time Series Segmentation

Authors: Plessen Mogens Graf

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Within the context of multivariate time series segmentation, this paper proposes a method inspired by a posteriori optimal trading. After a normalization step, time series are treated channelwise as surrogate stock prices that can be traded optimally a posteriori in a virtual portfolio holding either stock or cash. Linear transaction costs are interpreted as hyperparameters for noise filtering. Trading signals, as well as trading signals obtained on the reversed time series, are used for unsupervised channelwise labeling before a consensus over all channels is reached that determines the final segmentation time instants. The method is model-free such that no model prescriptions for segments are made. Benefits of proposed approach include simplicity, computational efficiency, and adaptability to a wide range of different shapes of time series. Performance is demonstrated on synthetic and real-world data, including a large-scale dataset comprising a multivariate time series of dimension 1000 and length 2709. Proposed method is compared to a popular model-based bottom-up approach fitting piecewise affine models and to a recent model-based top-down approach fitting Gaussian models and found to be consistently faster while producing more intuitive results in the sense of segmenting time series at peaks and valleys.

Keywords: time series segmentation, model-free, trading-inspired, multivariate data

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791 Antidiabetic and Admet Pharmacokinetic Properties of Grewia Lasiocarpa E. Mey. Ex Harv. Stem Bark Extracts: An in Vitro and in Silico Study

Authors: Akwu N. A., Naidoo Y., Salau V. F., Olofinsan K. A.

Abstract:

Grewia lasiocarpa E. Mey. ex Harv. (Malvaceae) is a Southern African medicinal plant indigenously used with other plants for birthing problems. The anti-diabetic properties of the hexane, chloroform, and methanol extracts of Grewia lasiocarpa stem bark were assessed using in vitro α-glucosidase enzyme inhibition assay. The predictive in silico drug-likeness and toxicity properties of the phytocompounds were conducted using the pKCSM, ADMElab, and SwissADME computer-aided online tools. The highest α-glucosidase percentage inhibition was observed in the hexane extract (86.76%, IC50= 0.24 mg/mL), followed by chloroform (63.08%, IC50= 4.87 mg/mL) and methanol (53.22%, IC50= 9.41 mg/mL); while acarbose, the standard anti-diabetic drug was (84.54%, IC50= 1.96 mg/mL). The α-glucosidase assay revealed that the hexane extract exhibited the strongest carbohydrate inhibiting capacity and is a better inhibitor than the standard reference drug-acarbose. The computational studies also affirm the results observed in the in vitroα-glucosidaseassay. Thus, the extracts of G. lasiocarpa may be considered a potential plant-sourced compound for treating type 2 diabetes mellitus. This is the first study on the anti-diabetic properties of Grewia lasiocarpa hexane, chloroform, and methanol extracts using in vitro and in silico models.

Keywords: grewia lasiocarpa, α-glucosidase inhibition, anti-diabetes, ADMET

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790 Automatic Tuning for a Systemic Model of Banking Originated Losses (SYMBOL) Tool on Multicore

Authors: Ronal Muresano, Andrea Pagano

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Nowadays, the mathematical/statistical applications are developed with more complexity and accuracy. However, these precisions and complexities have brought as result that applications need more computational power in order to be executed faster. In this sense, the multicore environments are playing an important role to improve and to optimize the execution time of these applications. These environments allow us the inclusion of more parallelism inside the node. However, to take advantage of this parallelism is not an easy task, because we have to deal with some problems such as: cores communications, data locality, memory sizes (cache and RAM), synchronizations, data dependencies on the model, etc. These issues are becoming more important when we wish to improve the application’s performance and scalability. Hence, this paper describes an optimization method developed for Systemic Model of Banking Originated Losses (SYMBOL) tool developed by the European Commission, which is based on analyzing the application's weakness in order to exploit the advantages of the multicore. All these improvements are done in an automatic and transparent manner with the aim of improving the performance metrics of our tool. Finally, experimental evaluations show the effectiveness of our new optimized version, in which we have achieved a considerable improvement on the execution time. The time has been reduced around 96% for the best case tested, between the original serial version and the automatic parallel version.

Keywords: algorithm optimization, bank failures, OpenMP, parallel techniques, statistical tool

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789 Relationship between Pushing Behavior and Subcortical White Matter Lesion in the Acute Phase after Stroke

Authors: Yuji Fujino, Kazu Amimoto, Kazuhiro Fukata, Masahide Inoue, Hidetoshi Takahashi, Shigeru Makita

Abstract:

Aim: Pusher behavior (PB) is a disorder in which stroke patients shift their body weight toward the affected side of the body (the hemiparetic side) and push away from the non-hemiparetic side. These patients often use further pushing to resist any attempts to correct their position to upright. It is known that the subcortical white matter lesion (SWML) usually correlates of gait or balance function in stroke patients. However, it is unclear whether the SWML influences PB. The purpose of this study was to investigate if the damage of SWML affects the severity of PB on acute stroke patients. Methods: Fourteen PB patients without thalamic or cortical lesions (mean age 73.4 years, 17.5 days from onset) participated in this study. Evaluation of PB was performed according to the Scale for Contraversive Pushing (SCP) for sitting and/or standing. We used modified criteria wherein the SCP subscale scores in each section of the scale were >0. As a clinical measurement, patients were evaluated by the Stroke Impairment Assessment Set (SIAS). For the depiction of SWML, we used T2-weighted fluid-attenuated inversion-recovery imaging. The degree of damage on SWML was assessed using the Fazekas scale. Patients were divided into two groups in the presence of SWML (SWML+ group; Fazekas scale grade 1-3, SWML- group; Fazekas scale grade 0). The independent t-test was used to compare the SCP and SIAS. This retrospective study was approved by the Ethics Committee. Results: In SWML+ group, the SCP was 3.7±1.0 points (mean±SD), the SIAS was 28.0 points (median). In SWML- group, the SCP was 2.0±0.2 points, and the SIAS was 31.5 points. The SCP was significantly higher in SWML+ group than in SWML- group (p<0.05). The SIAS was not significant in both groups (p>0.05). Discussion: It has been considered that the posterior thalamus is the neural structures that process the afferent sensory signals mediating graviceptive information about upright body orientation in humans. Therefore, many studies reported that PB was typically associated with unilateral lesions of the posterior thalamus. However, the result indicates that these extra-thalamic brain areas also contribute to the network controlling upright body posture. Therefore, SMWL might induce dysfunction through malperfusion in distant thalamic or other structurally intact neural structures. This study had a small sample size. Therefore, future studies should be performed with a large number of PB patients. Conclusion: The present study suggests that SWML can be definitely associated with PB. The patients with SWML may be severely incapacitating.

Keywords: pushing behavior, subcortical white matter lesion, acute phase, stroke

Procedia PDF Downloads 245
788 Off-Policy Q-learning Technique for Intrusion Response in Network Security

Authors: Zheni S. Stefanova, Kandethody M. Ramachandran

Abstract:

With the increasing dependency on our computer devices, we face the necessity of adequate, efficient and effective mechanisms, for protecting our network. There are two main problems that Intrusion Detection Systems (IDS) attempt to solve. 1) To detect the attack, by analyzing the incoming traffic and inspect the network (intrusion detection). 2) To produce a prompt response when the attack occurs (intrusion prevention). It is critical creating an Intrusion detection model that will detect a breach in the system on time and also challenging making it provide an automatic and with an acceptable delay response at every single stage of the monitoring process. We cannot afford to adopt security measures with a high exploiting computational power, and we are not able to accept a mechanism that will react with a delay. In this paper, we will propose an intrusion response mechanism that is based on artificial intelligence, and more precisely, reinforcement learning techniques (RLT). The RLT will help us to create a decision agent, who will control the process of interacting with the undetermined environment. The goal is to find an optimal policy, which will represent the intrusion response, therefore, to solve the Reinforcement learning problem, using a Q-learning approach. Our agent will produce an optimal immediate response, in the process of evaluating the network traffic.This Q-learning approach will establish the balance between exploration and exploitation and provide a unique, self-learning and strategic artificial intelligence response mechanism for IDS.

Keywords: cyber security, intrusion prevention, optimal policy, Q-learning

Procedia PDF Downloads 236
787 Axillary Evaluation with Targeted Axillary Dissection Using Ultrasound-Visible Clips after Neoadjuvant Chemotherapy for Patients with Node-Positive Breast Cancer

Authors: Naomi Sakamoto, Eisuke Fukuma, Mika Nashimoto, Yoshitomo Koshida

Abstract:

Background: Selective localization of the metastatic lymph node with clip and removal of clipped nodes with sentinel lymph node (SLN), known as targeted axillary dissection (TAD), reduced false-negative rates (FNR) of SLN biopsy (SLNB) after neoadjuvant chemotherapy (NAC). For the patients who achieved nodal pathologic complete response (pCR), accurate staging of axilla by TAD lead to omit axillary lymph node dissection (ALND), decreasing postoperative arm morbidity without a negative effect on overall survival. This study aimed to investigate the ultrasound (US) identification rate and success removal rate of two kinds of ultrasound-visible clips placed in metastatic lymph nodes during TAD procedure. Methods: This prospective study was conducted using patients with clinically T1-3, N1, 2, M0 breast cancer undergoing NAC followed by surgery. A US-visible clip was placed in the suspicious lymph node under US guidance before neoadjuvant chemotherapy. Before surgery, US examination was performed to evaluate the detection rate of clipped node. During the surgery, the clipped node was removed using several localization techniques, including hook-wire localization, dye-injection, or fluorescence technique, followed by a dual-technique SLNB and resection of palpable nodes if present. For the fluorescence technique, after injection of 0.1-0.2 mL of indocyanine green dye (ICG) into the clipped node, ICG fluorescent imaging was performed using the Photodynamic Eye infrared camera (Hamamatsu Photonics k. k., Shizuoka, Japan). For the dye injection method, 0.1-0.2 mL of pyoktanin blue dye was injected into the clipped node. Results: A total of 29 patients were enrolled. Hydromark™ breast biopsy site markers (Hydromark, T3 shape; Devicor Medical Japan, Tokyo, Japan) was used in 15patients, whereas a UltraCor™ Twirl™ breast marker (Twirl; C.R. Bard, Inc, NJ, USA) was placed in 14 patients. US identified the clipped node marked with the UltraCore Twirl in 100% (14/14) and with the Hydromark in 93.3% (14/15, p = ns). Success removal of clipped node marked with the UltraCore Twirl was achieved in 100% (14/14), whereas the node marked with the Hydromark was removed in 80% (12/15) (p = ns). Conclusions: The ultrasound identification rate differed between the two types of ultrasound-visible clips, which also affected the success removal rate of clipped nodes. Labelling the positive node with a US-highly-visible clip allowed successful TAD.

Keywords: breast cancer, neoadjuvant chemotherapy, targeted axillary dissection, breast tissue marker, clip

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786 Power Allocation Algorithm for Orthogonal Frequency Division Multiplexing Based Cognitive Radio Networks

Authors: Bircan Demiral

Abstract:

Cognitive radio (CR) is the promising technology that addresses the spectrum scarcity problem for future wireless communications. Orthogonal Frequency Division Multiplexing (OFDM) technology provides more power band ratios for cognitive radio networks (CRNs). While CR is a solution to the spectrum scarcity, it also brings up the capacity problem. In this paper, a novel power allocation algorithm that aims at maximizing the sum capacity in the OFDM based cognitive radio networks is proposed. Proposed allocation algorithm is based on the previously developed water-filling algorithm. To reduce the computational complexity calculating in water filling algorithm, proposed algorithm allocates the total power according to each subcarrier. The power allocated to the subcarriers increases sum capacity. To see this increase, Matlab program was used, and the proposed power allocation was compared with average power allocation, water filling and general power allocation algorithms. The water filling algorithm performed worse than the proposed algorithm while it performed better than the other two algorithms. The proposed algorithm is better than other algorithms in terms of capacity increase. In addition the effect of the change in the number of subcarriers on capacity was discussed. Simulation results show that the increase in the number of subcarrier increases the capacity.

Keywords: cognitive radio network, OFDM, power allocation, water filling

Procedia PDF Downloads 137
785 Gray’s Anatomy for Students: First South Asia Edition Highlights

Authors: Raveendranath Veeramani, Sunil Jonathan Holla, Parkash Chand, Sunil Chumber

Abstract:

Gray’s Anatomy for Students has been a well-appreciated book among undergraduate students of anatomy in Asia. However, the current curricular requirements of anatomy require a more focused and organized approach. The editors of the first South Asia edition of Gray’s Anatomy for Students hereby highlight the modifications and importance of this edition. There is an emphasis on active learning by making the clinical relevance of anatomy explicit. Learning anatomy in context has been fostered by the association between anatomists and clinicians in keeping with the emerging integrated curriculum of the 21st century. The language has been simplified to aid students who have studied in the vernacular. The original illustrations have been retained, and few illustrations have been added. There are more figure numbers mentioned in the text to encourage students to refer to the illustrations while learning. The text has been made more student-friendly by adding generalizations, classifications and summaries. There are useful review materials at the beginning of the chapters which include digital resources for self-study. There are updates on imaging techniques to encourage students to appreciate the importance of essential knowledge of the relevant anatomy to interpret images, due emphasis has been laid on dissection. Additional importance has been given to the cranial nerves, by describing their relevant details with several additional illustrations and flowcharts. This new edition includes innovative features such as set inductions, outlines for subchapters and flowcharts to facilitate learning. Set inductions are mostly clinical scenarios to create interest in the need to study anatomy for healthcare professions. The outlines are a modern multimodal facilitating approach towards various topics to empower students to explore content and direct their learning and include learning objectives and material for review. The components of the outline encourage the student to be aware of the need to create solutions to clinical problems. The outlines help students direct their learning to recall facts, demonstrate and analyze relationships, use reason to explain concepts, appreciate the significance of structures and their relationships and apply anatomical knowledge. The 'structures to be identified in a dissection' are given as Level I, II and III which represent the 'must know, desirable to know and nice to know' content respectively. The flowcharts have been added to get an overview of the course of a structure, recapitulate important details about structures, and as an aid to recall. There has been a great effort to balance the need to have content that would enable students to understand concepts as well as get the basic material for the current condensed curriculum.

Keywords: Grays anatomy, South Asia, human anatomy, students anatomy

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784 Object-Based Flow Physics for Aerodynamic Modelling in Real-Time Environments

Authors: William J. Crowther, Conor Marsh

Abstract:

Object-based flow simulation allows fast computation of arbitrarily complex aerodynamic models made up of simple objects with limited flow interactions. The proposed approach is universally applicable to objects made from arbitrarily scaled ellipsoid primitives at arbitrary aerodynamic attitude and angular rate. The use of a component-based aerodynamic modelling approach increases efficiency by allowing selective inclusion of different physics models at run-time and allows extensibility through the development of new models. Insight into the numerical stability of the model under first order fixed-time step integration schemes is provided by stability analysis of the drag component. The compute cost of model components and functions is evaluated and compared against numerical benchmarks. Model static outputs are verified against theoretical expectations and dynamic behaviour using falling plate data from the literature. The model is applied to a range of case studies to demonstrate the efficacy of its application in extensibility, ease of use, and low computational cost. Dynamically complex multi-body systems can be implemented in a transparent and efficient manner, and we successfully demonstrate large scenes with hundreds of objects interacting with diverse flow fields.

Keywords: aerodynamics, real-time simulation, low-order model, flight dynamics

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783 Experimental and Computational Analysis of Glass Fiber Reinforced Plastic Beams with Piezoelectric Fibers

Authors: Selin Kunc, Srinivas Koushik Gundimeda, John A. Gallagher, Roselita Fragoudakis

Abstract:

This study investigates the behavior of Glass Fiber Reinforced Plastic (GFRP) laminated beams additionally reinforced with piezoelectric fibers. The electromechanical behavior of piezoelectric materials coupled with high strength/low weight GFRP laminated beams can have significant application in a wide range of industries. Energy scavenging through mechanical vibrations is the focus of this study, and possible applications can be seen in the automotive industry. This study examines the behavior of such composite laminates using Classical Lamination Theory (CLT) under three-point bending conditions. Fiber orientation is optimized for the desired stiffness and deflection that yield maximum energy output. Finite element models using ABAQUS/CAE are verified through experimental testing. The optimum stacking sequences examined are [0o]s, [ 0/45o]s, and [45/-45o]s. Results show the superiority of the stacking sequence [0/45o]s, providing higher strength at a lower weight, and maximum energy output. Furthermore, laminated GFRP beams additionally reinforced with piezoelectric fibers can be used under bending to not only replace metallic component while providing similar strength at a lower weight but also provide an energy output.

Keywords: classical lamination theory (CLT), energy scavenging, glass fiber reinforced plastics (GFRP), piezoelectric fibers

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782 Modified Model for UV-Laser Corneal Ablation

Authors: Salah Hassab Elnaby, Omnia Hamdy, Aziza Ahmed Hassan, Salwa Abdelkawi, Ibrahim Abdelhalim

Abstract:

Laser corneal reshaping has been proposed as a successful treatment of many refraction disorders. However, some physical and chemical demonstrations of the laser effect upon interaction with the corneal tissue are still not fully explained. Therefore, different computational and mathematical models have been implemented to predict the depth of the ablated channel and calculate the ablation threshold and the local temperature rise. In the current paper, we present a modified model that aims to answer some of the open questions about the ablation threshold, the ablation rate, and the physical and chemical mechanisms of that action. The proposed model consists of three parts. The first part deals with possible photochemical reactions between the incident photons and various components of the cornea (collagen, water, etc.). Such photochemical reactions may end by photo-ablation or just the electronic excitation of molecules. Then a chemical reaction is responsible for the ablation threshold. Finally, another chemical reaction produces fragments that can be cleared out. The model takes into account all processes at the same time with different probabilities. Moreover, the effect of applying different laser wavelengths that have been studied before, namely the common excimer laser (193-nm) and the solid state lasers (213-nm & 266-nm), has been investigated. Despite the success and ubiquity of the ArF laser, the presented results reveal that a carefully designed 213-nm laser gives the same results with lower operational drawbacks. Moreover, the use of mode locked laser could also decrease the risk of heat generation and diffusion.

Keywords: UV lasers, mathematical model, corneal ablation, photochemical ablation

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781 Effects of Inlet Distorted Flows on the Performance of an Axial Compressor

Authors: Asad Islam, Khalid Parvez

Abstract:

Compressor fans in modern aircraft engines are of considerate importance, as they provide majority of thrust required by the aircraft. Their challenging environment is frequently subjected to non-uniform inflow conditions. These conditions could be either due to the flight operating requirements such as take-off and landing, wake interference from aircraft fuselage or cross-flow wind conditions. So, in highly maneuverable flights regimes of fighter aircrafts affects the overall performance of an engine. Since the flow in compressor of an aircraft application is highly sensitive because of adverse pressure gradient due to different flow orientations of the aircraft. Therefore, it is prone to unstable operations. This paper presents the study that focuses on axial compressor response to inlet flow orientations for the range of angles as 0 to 15 degrees. For this purpose, NASA Rotor-37 was taken and CFD mesh was developed. The compressor characteristics map was generated for the design conditions of pressure ratio of 2.106 with the rotor operating at rotational velocity of 17188.7 rpm using CFD simulating environment of ANSYS-CFX®. The grid study was done to see the effects of mesh upon computational solution. Then, the mesh giving the best results, (when validated with the available experimental NASA’s results); was used for further distortion analysis. The flow in the inlet nozzle was given angle orientations ranging from 0 to 15 degrees. The CFD results are analyzed and discussed with respect to stall margin and flow separations due to induced distortions.

Keywords: axial compressor, distortions, angle, CFD, ANSYS-CFX®, bladegen®

Procedia PDF Downloads 456
780 Intelligent Agent-Based Model for the 5G mmWave O2I Technology Adoption

Authors: Robert Joseph M. Licup

Abstract:

The deployment of the fifth-generation (5G) mobile system through mmWave frequencies is the new solution in the requirement to provide higher bandwidth readily available for all users. The usage pattern of the mobile users has moved towards either the work from home or online classes set-up because of the pandemic. Previous mobile technologies can no longer meet the high speed, and bandwidth requirement needed, given the drastic shift of transactions to the home. The millimeter-wave (mmWave) underutilized frequency is utilized by the fifth-generation (5G) cellular networks that support multi-gigabit-per-second (Gbps) transmission. However, due to its short wavelengths, high path loss, directivity, blockage sensitivity, and narrow beamwidth are some of the technical challenges that need to be addressed. Different tools, technologies, and scenarios are explored to support network design, accurate channel modeling, implementation, and deployment effectively. However, there is a big challenge on how the consumer will adopt this solution and maximize the benefits offered by the 5G Technology. This research proposes to study the intricacies of technology diffusion, individual attitude, behaviors, and how technology adoption will be attained. The agent based simulation model shaped by the actual applications, technology solution, and related literature was used to arrive at a computational model. The research examines the different attributes, factors, and intricacies that can affect each identified agent towards technology adoption.

Keywords: agent-based model, AnyLogic, 5G O21, 5G mmWave solutions, technology adoption

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779 Acoustic Radiation Pressure Detaches Myoblast from Culture Substrate by Assistance of Serum-Free Medium

Authors: Yuta Kurashina, Chikahiro Imashiro, Kiyoshi Ohnuma, Kenjiro Takemura

Abstract:

Research objectives and goals: To realize clinical applications of regenerative medicine, a mass cell culture is highly required. In a conventional cell culture, trypsinization was employed for cell detachment. However, trypsinization causes proliferation decrease due to injury of cell membrane. In order to detach cells using an enzyme-free method, therefore, this study proposes a novel cell detachment method capable of detaching adherent cells using acoustic radiation pressure exposed to the dish by the assistance of serum-free medium with ITS liquid medium supplement. Methods used In order to generate acoustic radiation pressure, a piezoelectric ceramic plate was glued on a glass plate to configure an ultrasonic transducer. The glass plate and a chamber wall compose a chamber in which a culture dish is placed in glycerol. Glycerol transmits acoustic radiation pressure to adhered cells on the culture dish. To excite a resonance vibration of transducer, AC signal with 29-31 kHz (swept) and 150, 300, and 450 V was input to the transducer for 5 min. As a pretreatment to reduce cell adhesivity, serum-free medium with ITS liquid medium supplement was spread to the culture dish before exposed to acoustic radiation pressure. To evaluate the proposed cell detachment method, C2C12 myoblast cells (8.0 × 104 cells) were cultured on a ø35 culture dish for 48 hr, and then the medium was replaced with the serum-free medium with ITS liquid medium supplement for 24 hr. We replaced the medium with phosphate buffered saline and incubated cells for 10 min. After that, cells were exposed to the acoustic radiation pressure for 5 min. We also collected cells by using trypsinization as control. Cells collected by the proposed method and trypsinization were respectively reseeded in ø60 culture dishes and cultured for 24 hr. Then, the number of proliferated cells was counted. Results achieved: By a phase contrast microscope imaging, shrink of lamellipodia was observed before exposed to acoustic radiation pressure, and no cells remained on the culture dish after the exposed of acoustic radiation pressure. This result suggests that serum-free medium with ITS liquid inhibits adhesivity of cells and acoustic radiation pressure detaches cells from the dish. Moreover, the number of proliferated cells 24 hr after collected by the proposed method with 150 and 300 V is the same or more than that by trypsinization, i.e., cells were proliferated 15% higher with the proposed method using acoustic radiation pressure than with the traditional cell collecting method of trypsinization. These results proved that cells were able to be collected by using the appropriate exposure of acoustic radiation pressure. Conclusions: This study proposed a cell detachment method using acoustic radiation pressure by the assistance of serum-free medium. The proposed method provides an enzyme-free cell detachment method so that it may be used in future clinical applications instead of trypsinization.

Keywords: acoustic radiation pressure, cell detachment, enzyme free, ultrasonic transducer

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778 Computer Simulation to Investigate Magnetic and Wave-Absorbing Properties of Iron Nanoparticles

Authors: Chuan-Wen Liu, Min-Hsien Liu, Chung-Chieh Tai, Bing-Cheng Kuo, Cheng-Lung Chen, Huazhen Shen

Abstract:

A recent surge in research on magnetic radar absorbing materials (RAMs) has presented researchers with new opportunities and challenges. This study was performed to gain a better understanding of the wave-absorbing phenomenon of magnetic RAMs. First, we hypothesized that the absorbing phenomenon is dependent on the particle shape. Using the Material Studio program and the micro-dot magnetic dipoles (MDMD) method, we obtained results from magnetic RAMs to support this hypothesis. The total MDMD energy of disk-like iron particles was greater than that of spherical iron particles. In addition, the particulate aggregation phenomenon decreases the wave-absorbance, according to both experiments and computational data. To conclude, this study may be of importance in terms of explaining the wave- absorbing characteristic of magnetic RAMs. Combining molecular dynamics simulation results and the theory of magnetization of magnetic dots, we investigated the magnetic properties of iron materials with different particle shapes and degrees of aggregation under external magnetic fields. The MDMD of the materials under magnetic fields of various strengths were simulated. Our results suggested that disk-like iron particles had a better magnetization than spherical iron particles. This result could be correlated with the magnetic wave- absorbing property of iron material.

Keywords: wave-absorbing property, magnetic material, micro-dot magnetic dipole, particulate aggregation

Procedia PDF Downloads 490
777 Accelerated Molecular Simulation: A Convolution Approach

Authors: Jannes Quer, Amir Niknejad, Marcus Weber

Abstract:

Computational Drug Design is often based on Molecular Dynamics simulations of molecular systems. Molecular Dynamics can be used to simulate, e.g., the binding and unbinding event of a small drug-like molecule with regard to the active site of an enzyme or a receptor. However, the time-scale of the overall binding event is many orders of magnitude longer than the time-scale of simulation. Thus, there is a need to speed-up molecular simulations. In order to speed up simulations, the molecular dynamics trajectories have to be ”steared” out of local minimizers of the potential energy surface – the so-called metastabilities – of the molecular system. Increasing the kinetic energy (temperature) is one possibility to accelerate simulated processes. However, with temperature the entropy of the molecular system increases, too. But this kind ”stearing” is not directed enough to stear the molecule out of the minimum toward the saddle point. In this article, we give a new mathematical idea, how a potential energy surface can be changed in such a way, that entropy is kept under control while the trajectories are still steared out of the metastabilities. In order to compute the unsteared transition behaviour based on a steared simulation, we propose to use extrapolation methods. In the end we mathematically show, that our method accelerates the simulations along the direction, in which the curvature of the potential energy surface changes the most, i.e., from local minimizers towards saddle points.

Keywords: extrapolation, Eyring-Kramers, metastability, multilevel sampling

Procedia PDF Downloads 328