Search results for: molecular modeling

Authors: Jiun Jeon, Byung-Ju Yi

Abstract:

This paper investigates modeling and shape prediction of elastic kinematic chains such as colonoscopy. 2D and 3D models of elastic kinematic chains are suggested and their behaviors are demonstrated through simulation. To corroborate the effectiveness of those models, experimental work is performed using a magnetic sensor system.

Keywords: elastic kinematic chain, shape prediction, colonoscopy, modeling

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Authors: R. Mkahl, A. Nait-Sidi-Moh, M. Wack

Abstract:

Batteries of electric vehicles (BEV) are becoming more attractive with the advancement of new battery technologies and promotion of electric vehicles. BEV batteries are recharged on board vehicles using either the grid (G2V for Grid to Vehicle) or renewable energies in a stand-alone application (H2V for Home to Vehicle). This paper deals with the modeling, sizing and control of a photo voltaic stand-alone application that can charge the BEV at home. The modeling approach and developed mathematical models describing the system components are detailed. Simulation and experimental results are presented and commented.

Keywords: electric vehicles, photovoltaic energy, lead-acid batteries, charging process, modeling, simulation, experimental tests

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Authors: Titus A. Beu

Abstract:

Many modern gene-delivery protocols rely on condensed complexes of DNA with polycations to introduce the genetic payload into cells by endocytosis. In particular, polyethyleneimine (PEI) stands out by a high buffering capacity (enabling the efficient condensation of DNA) and relatively simple fabrication. Realistic computational studies can offer essential insights into the formation process of DNA-PEI polyplexes, providing hints on efficient designs and engineering routes. We present comprehensive computational investigations of solvated PEI and DNA-PEI polyplexes involving calculations at three levels: ab initio, all-atom (AA), and coarse-grained (CG) molecular mechanics. In the first stage, we developed a rigorous AA CHARMM (Chemistry at Harvard Macromolecular Mechanics) force field (FF) for PEI on the basis of accurate ab initio calculations on protonated model pentamers. We validated this atomistic FF by matching the results of extensive molecular dynamics (MD) simulations of structural and dynamical properties of PEI with experimental data. In a second stage, we developed a CG MARTINI FF for PEI by Boltzmann inversion techniques from bead-based probability distributions obtained from AA simulations and ensuring an optimal match between the AA and CG structural and dynamical properties. In a third stage, we combined the developed CG FF for PEI with the standard MARTINI FF for DNA and performed comprehensive CG simulations of DNA-PEI complex formation and condensation. Various technical aspects which are crucial for the realistic modeling of DNA-PEI polyplexes, such as options of treating electrostatics and the relevance of polarizable water models, are discussed in detail. Massive CG simulations (with up to 500 000 beads) shed light on the mechanism and provide time scales for DNA polyplex formation independence of PEI chain size and protonation pattern. The DNA-PEI condensation mechanism is shown to primarily rely on the formation of DNA bundles, rather than by changes of the DNA-strand curvature. The gained insights are expected to be of significant help for designing effective gene-delivery applications.

Keywords: DNA condensation, gene-delivery, polyethylene-imine, molecular dynamics.

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Authors: Mesbah Khaled, Bouraoui Ouissal, Benkiniouar Rachid, Belkhiri Lotfi

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Alstonia, which are tropical plants with a wide geographical distribution, have been divided into different sections by different authors based on previous studies of several species within the genus. Monachino divides Alstonia into 5 sections, while Pichon divides it into 3 sections. Several plants belonging to this genus, such as Alstonia brassii, have been used in traditional folk medicine to treat ailments such as fever, malaria and dysentery]. Previous studies focusing on the chemical composition of these plants have successfully identified indol alkaloids with cytotoxic, anti-diabetic and anti-inflammatory properties. The newly discovered monomers are structurally similar to the backbones of picralin, affinisin and macrolin. On the other hand, all recently isolated dimeric compounds have a macrolin moiety. In this study, a computational analysis was performed on a series of novel molecules, including both monomeric and dimeric compounds with different structural frameworks. This investigation represents the first computational study of these molecules using an in silico approach incorporating 2D-QSAR data. The analysis involved various computational techniques, including 2D-QSAR modelling, molecular docking studies and subsequent validation by molecular dynamics simulation and assessment of ADMET properties. The chemical composition was identified by 1D and 2D NMR. Eight new alkaloids were isolated, 5 monomers and 3 dimers. In this section, we focus on the biological activity of 4 new alkaloids belonging to two different skeletons, the affinisine skeleton.

Keywords: affinisine, talcarpine, macroline, cytotoxicity, alkaloids

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Authors: H. Ghodbane, A. A. Taleb, O. Kraa

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This paper presents geometric design of induction heating system. The objective of this design is to improve the temperature distribution in the load. The study of such a device requires the use of models or modeling representation, physical, mathematical, and numerical. This modeling is the basis of the understanding, the design, and optimization of these systems. The optimization technique is to find values of variables that maximize or minimize the objective function.

Keywords: optimization, modeling, geometric design system, temperature increase

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Authors: Ashkan Forootan, Reza Rashedi

Abstract:

Polyethylene has wide usage areas such as blow molding, pipe, film, cable insulation. However, regardless to its growing applications, it has some constraints such as the limited 70C operating temperature. Polyethylene thermo setting procedure whose molecules are knotted and 3D-molecular-network formed , is developed to conquer the above problem and to raise the applicable temperature of the polymer. This paper reports the cross-linking for two different molecular weight grades of LLDPE by adding 0.5, 1, and 2% of DCP (Dicumyl Peroxide). DCP was chosen for its prevalence among various cross-linking agents. Structural parameters such as molecular weight, melt flow index, comonomer, number of branches,etc. were obtained through the use of relative tests as Gel Permeation Chromatography and Fourier Transform Infra Red spectrometer. After calculating the percentage of gel content, properties of the pure and cross-linked samples were compared by thermal and mechanical analysis with DMTA and FTIR and the effects of cross-linking like viscous and elastic modulus were discussed by using various structural paprameters such as MFI, molecular weight, short chain branches, etc. Studies showed that cross-linked polymer, unlike the pure one, had a solid state with thermal mechanical properties in the range of 110 to 120C and this helped overcome the problem of using polyethylene in temperatures near the melting point.

Keywords: LLDPE, cross-link, structural parameters, DCP, DMTA, GPC

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Authors: Strahinja Z. Kovačević, Lidija R. Jevrić, Sanja O. Podunavac Kuzmanović

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The relationship between antibacterial activity of eighteen different substituted benzimidazole derivatives and their molecular characteristics was studied using chemometric QSAR (Quantitative Structure–Activity Relationships) approach. QSAR analysis has been carried out on inhibitory activity towards Staphylococcus aureus, by using molecular descriptors, as well as minimal inhibitory activity (MIC). Molecular descriptors were calculated from the optimized structures. Principal component analysis (PCA) followed by hierarchical cluster analysis (HCA) and multiple linear regression (MLR) was performed in order to select molecular descriptors that best describe the antibacterial behavior of the compounds investigated, and to determine the similarities between molecules. The HCA grouped the molecules in separated clusters which have the similar inhibitory activity. PCA showed very similar classification of molecules as the HCA, and displayed which descriptors contribute to that classification. MLR equations, that represent MIC as a function of the in silico molecular descriptors were established. The statistical significance of the estimated models was confirmed by standard statistical measures and cross-validation parameters (SD = 0.0816, F = 46.27, R = 0.9791, R2CV = 0.8266, R2adj = 0.9379, PRESS = 0.1116). These parameters indicate the possibility of application of the established chemometric models in prediction of the antibacterial behaviour of studied derivatives and structurally very similar compounds.

Keywords: antibacterial, benzimidazole, molecular descriptors, QSAR

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Authors: Vishwesh Kulkarni, Nikhil Bellarykar

Abstract:

Cellular complexity stems from the interactions among thousands of different molecular species. Thanks to the emerging fields of systems and synthetic biology, scientists are beginning to unravel these regulatory, signaling, and metabolic interactions and to understand their coordinated action. Reverse engineering of biological networks has has several benefits but a poor quality of data combined with the difficulty in reproducing it limits the applicability of these methods. A few years back, many of the commonly used predictive algorithms were tested on a network constructed in the yeast Saccharomyces cerevisiae (S. cerevisiae) to resolve this issue. The network was a synthetic network of five genes regulating each other for the so-called in vivo reverse-engineering and modeling assessment (IRMA). The network was constructed in S. cereviase since it is a simple and well characterized organism. The synthetic network included a variety of regulatory interactions, thus capturing the behaviour of larger eukaryotic gene networks on a smaller scale. We derive a new set of algorithms by solving a nonlinear optimization problem and show how these algorithms outperform other algorithms on these datasets.

Keywords: synthetic gene network, network identification, optimization, nonlinear modeling

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Authors: A. Torokhti

Abstract:

A new method of mathematical modeling of the distributed nonlinear system is developed. The system is represented by a combination of the set of spatially distributed sensors and the fusion center. Its mathematical model is obtained from the iterative procedure that converges to the model which is optimal in the sense of minimizing an associated cost function.

Keywords: mathematical modeling, non-linear system, spatially distributed sensors, fusion center

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Authors: Nidhi Chadha, A. K. Tiwari, Marilyn D. Milton, Anil K. Mishra

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Translocator protein (18 kDa) TSPO is highly expressed during microglia activation in neuroinflammation. Although a number of PET ligands have been developed for the visualization of activated microglia, one of the advantageous approaches is to develop potential optical imaging (OI) probe. Our study involves computational screening, synthesis and evaluation of TSPO ligand through various imaging modalities namely PET/SPECT/Optical. The initial computational screening involves pharmacophore modeling from the library designing having oxo-benzooxazol-3-yl-N-phenyl-acetamide groups and synthesis for visualization of efficacy of these compounds as multimodal imaging probes. Structure modeling of monomer, Ala147Thr mutated, parallel and anti-parallel TSPO dimers was performed and docking analysis was performed for distinct binding sites. Computational analysis showed pattern of variable binding profile of known diagnostic ligands and NBMP via interactions with conserved residues along with TSPO’s natural polymorphism of Ala147→Thr, which showed alteration in the binding affinity due to considerable changes in tertiary structure. Preliminary in vitro binding studies shows binding affinity in the range of 1-5 nm and selectivity was also certified by blocking studies. In summary, this skeleton was found to be potential probe for TSPO imaging due to ease in synthesis, appropriate lipophilicity and reach to specific region of brain.

Keywords: TSPO, molecular modeling, imaging, docking

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Authors: Zhanat Umarova

Abstract:

Until the present time, modeling of the pores form influence on the hydraulic resistance of membranes and their permeability has not been analyzed. The aim of the given work is the theoretical consideration of the issue on the productivity of polymer membranes with the profile pores and determination of the optimum form of pores.

Keywords: modeling, polymer membranes, permeability, pore’s density

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Authors: Yasmina Houda Bendahma, Tewfik Bouchaour, Meriem Merad, Ulrich Maschke

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The purpose of this work is to study retention of dye dissolved in distilled water, by an hydrophilic acrylic polymer network. The polymer network considered is Poly (2-hydroxyethyl methacrylate) (PHEMA): it is prepared by photo-polymerization under UV irradiation in the presence of a monomer (HEMA), initiator and an agent cross-linker. PHEMA polymer network obtained can be used in the retention of dye molecules present in the wastewater. The results obtained are interesting in the study of the kinetics of swelling and de-swelling of cross linked polymer networks PHEMA in colored aqueous solutions. The dyes used for retention by the PHEMA networks are eosin Y and Malachite Green, dissolved in distilled water. Theoretical conformational study by a simplified molecular model of system cross linked PHEMA / dye (eosin Y and Malachite Green), is used to simulate the retention phenomenon (or Docking) dye molecules in cavities in nano-domains included in the PHEMA polymer network.

Keywords: dye retention, molecular modeling, photochemically crosslinked polymer network, swelling deswelling, PHEMA, HEMA

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Authors: Aliyu Adamu, Fahrul Huyop, Roswanira Abdul Wahab, Mohd Shahir Shamsir

Abstract:

Halogenated organic compounds occur in huge amount in biosphere. This is attributable to the diverse use of halogen-based compounds in the synthesis of various industrially important products. Halogenated compound is toxic and may persist in the environment, thereby causing serious health and environmental pollution problems. L-2-haloacid dehalogenases (EC 3.8.1.2) catalyse the specific cleavage of carbon-halogen bond in L-isomers of halogenated compounds, which consequently reverse the effects of environmental halogen-associated pollution. To enhance the efficiency and utility of these enzymes, this study investigates the catalytic amino acid residues and the molecular functional mechanism of DehL, by classical molecular dynamic simulations, MM-PBSA and ab initio fragments molecular orbital (FMO) calculations. The results of the study will serve as the basis for the molecular engineering of the enzyme.

Keywords: DehL, Functional mechanism, Catalytic residues, L-2-haloacid dehalogenase

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Authors: Ridha Salhi, Mondher Labidi, Fethi Choubani

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Metamaterials have attracted much attention in recent years because of their electromagnetic exquisite proprieties. We will present, in this paper, the modeling of three metamaterial structures by equivalent circuit model. We begin by modeling the SRR (Split Ring Resonator), then we model the HIS (High Impedance Surfaces), and finally, we present the model of the CPW (Coplanar Wave Guide). In order to validate models, we compare the results obtained by an equivalent circuit models with numerical simulation.

Keywords: metamaterials, SRR, HIS, CPW, IDC

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Authors: Ainoa Guinart, Maria Korpidou, Daniel Doellerer, Cornelia Palivan, Ben L. Feringa

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Stimuli responsive systems arise from the need to meet unsolved needs of current molecular drugs. Our study presents the design of a delivery system with high spatiotemporal control and tuneable release profiles. We study the incorporation of a hydrophobic synthetic molecular motor into PDMS-b-PMOXA block copolymer vesicles to create a self-assembled system. We prove their successful incorporation and selective activation by low powered visible light (λ 430 nm, 6.9 mW). We trigger the release of a fluorescent dye with high release efficiencies over sequential cycles (up to 75%) with the ability to turn on and off the release behaviour on demand by light irradiation. Low concentrations of photo-responsive units are proven to trigger release down to 1 mol% of molecular motor. Finally, we test our system in relevant physiological conditions using a lung cancer cell line and the encapsulation of an approved drug. Similar levels of cell viability are observed compared to the free-given drugshowing the potential of our platform to deliver functional drugs on demand with the same efficiency and lower toxicity.

Keywords: molecular motor, polymer, drug delivery, light-responsive, cancer, selfassembly

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Authors: M. M. Wagh, V. V. Kulkarni

Abstract:

The rising economic activities, growing population and improving living standards of world have led to a steady growth in its appetite for quality and quantity of energy services. As the economy expands the electricity demand is going to grow further, increasing the challenges of the more generation and stresses on the utility grids. Appropriate energy model will help in proper utilization of the locally available renewable energy sources such as solar, wind, biomass, small hydro etc. to integrate in the available grid, reducing the investments in energy infrastructure. Further to these new technologies like smart grids, decentralized energy planning, energy management practices, energy efficiency are emerging. In this paper, the attempt has been made to study and review the recent energy planning models, energy forecasting models, and renewable energy integration models. In addition, various modeling techniques and tools are reviewed and discussed.

Keywords: energy modeling, integration of renewable energy, energy modeling tools, energy modeling techniques

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Authors: Kaining Zhang, Lang Chen, Danyang Liu, Jianying Lu, Kun Yang, Junying Wu

Abstract:

In order to solve the problem of a large amount of simulation and limited simulation scale in the first-principle molecular dynamics simulation of energetic material detonation reaction, we established an artificial intelligence model for analyzing and predicting the detonation reaction mechanism of CL-20 based on the first-principle molecular dynamics simulation of the multiscale shock technique (MSST). We employed principal component analysis to identify the dominant charge features governing molecular reactions. We adopted the K-means clustering algorithm to cluster the reaction paths and screen out the key reactions. We introduced the neural network algorithm to construct the mapping relationship between the charge characteristics of the molecular structure and the key reaction characteristics so as to establish a calculation method for predicting detonation reactions based on the charge characteristics of CL-20 and realize the rapid analysis of the reaction mechanism of energetic materials.

Keywords: energetic material detonation reaction, first-principle molecular dynamics simulation of multiscale shock technique, neural network, CL-20

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Authors: Abishek Rajkumar

Abstract:

Antibiotic resistance can occur naturally given the selective pressure placed on antibiotics. Within a large population of bacteria, there is a significant chance that some of those bacteria can develop resistance via mutations or genetic recombination. However, a growing public health concern has arisen over the fact that antibiotic resistance has increased significantly over the past few decades. This is because humans have been over-consuming and producing antibiotics, which has ultimately accelerated the antibiotic resistance seen in these bacteria. The product of all of this is an ongoing race between scientists and the bacteria as bacteria continue to develop resistance, which creates even more demand for an antibiotic that can still terminate the newly resistant strain of bacteria. This paper will focus on a myriad of aspects of antibiotic resistance in bacteria starting with how it occurs on a molecular level and then focusing on the antibiotic concentrations and how they affect the resistance and fitness seen in bacteria.

Keywords: antibiotic, molecular, mutation, resistance

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Authors: Ling Dai

Abstract:

Surface-sensing devices such as atomic force microscope have been widely used to characterize the surface structure and properties of nanoscale polymer films. However, using molecular dynamics simulations, we show that there is intrinsic and unavoidable inelastic deformation at polymer surfaces induced by the sensing tip. For linear chain polymers like perfluoropolyether, such tip-induced deformation derives from the differences in the atomic interactions which are atomic specie-based Van der Waals interactions, and resulting in atomic shuffling and causing inelastic alternation in both molecular structures and mechanical properties at the regions of the polymer surface. For those aromatic chain polymers like epoxy, the intrinsic deformation is depicted as the intra-chain rotation of aromatic rings and kinking of linear atomic connections. The present work highlights the need to reinterpret the data obtained from surface-sensing tests by considering this intrinsic inelastic deformation occurring at polymer surfaces.

Keywords: polymer, surface, nano, molecular dynamics

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Authors: Sumit Kumar, Sunil Kumar, Chandan Deep Singh

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This paper presents modeling and simulation of flexible robot in an underwater environment. The underwater environment completely contrasts with ground or space environment. The robot in an underwater situation is subjected to various dynamic forces like buoyancy forces, hydrostatic and hydrodynamic forces. The underwater robot is modeled as Rayleigh beam. The developed model further allows estimating the deflection of tip in two directions. The complete dynamics of the underwater robot is analyzed, which is the main focus of this investigation. The control of robot trajectory is not discussed in this paper. Simulation is performed using Symbol Shakti software.

Keywords: bond graph modeling, dynamics. modeling, rayleigh beam, underwater robot

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Authors: Abdulmannan Fadel

Abstract:

Arabinoxylan is a non-starch polysaccharide (NSP), which is one of the most important polysaccharides contained within cereal grains. Wheat endosperm pentosan and rice bran contain a significant amount of arabinoxylan (7% in rice bran and 10-12% in wheat endosperm pentosan). Several methods have been used for arabinoxylan extraction with varying degrees of success e.g. enzymatic and alkaline treatment. Yet, the use of extrusion alone as a pre-treatment to increase the yield and reduce the molecular weight in wheat endosperm pentosan and rice bran has not been investigated. The samples (wheat pentosan and rice bran) were extruded using a Twin-screw extruder at a range of screw speeds (80 and 160 rpm) and barrel temperatures range (80 to 140°C) with a throughput of 30 Kg hr-1 and moisture content of 25%. Arabinoxylans were extracted with water and the extraction yield and molecular weight was determined using size exclusion high-pressure liquid chromatography system. It was found that increasing screw speed from 80 rpm to 160 rpm, did not effect the extraction yield (p < 0.05) of arabinoxylan from either the wheat endosperm pentosan or the rice bran. However, the molecular weight of the extracted arabinoxylans from pentosan was found to decrease with increasing screw speed in wheat endosperm pentosan. These low molecular weight arabinoxylans have been suggested as immunomodulators.

Keywords: arabinoxylans, extrusion, wheat endosperm pentosan, rice bran

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Authors: Bin Wang, Yong Xu, Honggang Qu, Rongmei Liu, Zhenji Gao

Abstract:

Today's mining industry is advancing gradually toward digital and visual direction. The three dimensional visualization geological modeling of mine is the digital characterization of mineral deposit, and is one of the key technology of digital mine. The three-dimensional geological modeling is a technology that combines the geological spatial information management, geological interpretation, geological spatial analysis and prediction, geostatistical analysis, entity content analysis and graphic visualization in three-dimensional environment with computer technology, and is used in geological analysis. In this paper, the three-dimensional geological modeling of an iron mine through the use of Surpac is constructed, and the weight difference of the estimation methods between distance power inverse ratio method and ordinary kriging is studied, and the ore body volume and reserves are simulated and calculated by using these two methods. Compared with the actual mine reserves, its result is relatively accurate, so it provided scientific bases for mine resource assessment, reserve calculation, mining design and so on.

Keywords: three-dimensional geological modeling, geological database, geostatistics, block model

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Authors: N. S. Vassilieva-Vashakmadze, R. A. Gakhokidze, I. M. Khachatryan

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In the first part of the paper it is shown that both the depolarization of the cytoplasmic membrane of rods observed in invertebrates and hyperpolarization characteristic of vertebrates on the light may activate the functioning of ion (Na+) channels of cytoplasmic membrane of rods and thus provide the emergence of nerve impulse and its transfer to the neighboring neuron etc. In the second part, using the quantum mechanical program for modeling of the molecular processes, we got a clear picture demonstrating the effect of charged phosphate groups on the protein components of α-helical subunits of the visual rhodopsin receptor. The analysis shows that the phosphorylation of terminal amino acid of seventh α-helical subunits of the visual rhodopsin causes a redistribution of electron density on the atoms, i.e. polarization of subunits, also the changing the configuration of the nuclear subsystem, which corresponds to the deformation process in the molecule. Based on the use of models it can be concluded that this system has an internal relationship between polarization and deformation processes that indicates on the allosteric effect. The allosteric effect is based on quantum-mechanical principle of the self-consistency of the molecules.

Keywords: membrane potential, ion channels, visual rhodopsin, allosteric effect

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Authors: Shigeyuki Haruyama, Ken Kaminishi, Junji Kaneko, Tadayuki Kyoutani, Siti Ruhana Omar, Oke Oktavianty

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This study is used as a definition method to the value and function in manufacturing sector. In concurrence of discussion about present condition of modeling method, until now definition of 1D-CAE is ambiguity and not conceptual. Across all the physics fields, those methods are defined with the formulation of differential algebraic equation which only applied time derivation and simulation. At the same time, we propose semi-acausal modeling concept and differential algebraic equation method as a newly modeling method which the efficiency has been verified through the comparison of numerical analysis result between the semi-acausal modeling calculation and FEM theory calculation.

Keywords: system model, physical models, empirical models, conservation law, differential algebraic equation, object-oriented

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Authors: Elizabeth O. Odewale, Sachithra T. Wanasinghe, Aaron S. Rury

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Cavity polaritons form when molecular excitons strongly couple to photons in carefully constructed optical cavities. These polaritons, which are hybrid light-matter states possessing a unique combination of photonic and excitonic properties, present the opportunity to manipulate the properties of various semiconductor materials. The systematic manipulation of materials through polariton formation could potentially improve the functionalities of many optoelectronic devices such as lasers, light-emitting diodes, photon-based quantum computers, and solar cells. However, the prospects of leveraging polariton formation for novel devices and device operation depend on more complete connections between the properties of molecular chromophores, and the hybrid light-matter states they form, which remains an outstanding scientific goal. Specifically, for most optoelectronic applications, it is paramount to understand how polariton formation affects the spectra of light absorbed by molecules coupled strongly to cavity photons. An essential feature of a polariton state is its dispersive energy, which occurs due to the enhanced spatial delocalization of the polaritons relative to bare molecules. To leverage the spatial delocalization of cavity polaritons, angle-resolved photoluminescence excitation spectroscopy was employed in characterizing light emission from the polaritonic states. Using lasers of appropriate energies, the polariton branches were resonantly excited to understand how molecular light absorption changes under different strong light-matter coupling conditions. Since an excited state has a finite lifetime, the photon absorbed by the polariton decays non-radiatively into lower-lying molecular states, from which radiative relaxation to the ground state occurs. The resulting fluorescence is collected across several angles of excitation incidence. By modeling the behavior of the light emission observed from the lower-lying molecular state and combining this result with the output of angle-resolved transmission measurements, inferences are drawn about how the behavior of molecules changes when they form polaritons. These results show how the intrinsic properties of molecules, such as the excitonic lifetime, affect the rate at which the polaritonic states relax. While it is true that the lifetime of the photon mediates the rate of relaxation in a cavity, the results from this study provide evidence that the lifetime of the molecular exciton also limits the rate of polariton relaxation.

Keywords: flourescece, molecules in cavityies, optical cavity, photoluminescence excitation, spectroscopy, strong coupling

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Authors: Assem El-Ansary

Abstract:

This paper illustrates the event-oriented Behavioral Pattern Analysis (BPA) modeling approach using the Healthcare Multi-Agent System. The Event defined in BPA is a real-life conceptual entity that is unrelated to any implementation. The major contributions of this research are: The Behavioral Pattern Analysis (BPA) modeling methodology. The development of an interactive software tool (DECISION), which is based on a combination of the Analytic Hierarchy Process (AHP) and the ELECTRE Multi-Criteria Decision Making (MCDM) methods.

Keywords: analysis, modeling methodology, software modeling, event-oriented, behavioral pattern, use cases, Healthcare Multi-Agent System

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Authors: Assem El-Ansary

Abstract:

This paper illustrates the event-oriented Behavioral Pattern Analysis (BPA) modeling approach in developing an Intelligent Agent Reservation System (IARS). The Event defined in BPA is a real-life conceptual entity that is unrelated to any implementation. The major contributions of this research are developing the Behavioral Pattern Analysis (BPA) modeling methodology, and developing an interactive software tool (DECISION) which is based on a combination of the Analytic Hierarchy Process (AHP) and the ELECTRE Multi-Criteria Decision Making (MCDM) methods.

Keywords: analysis, intelligent agent, reservation system, modeling methodology, software modeling, event-oriented, behavioral pattern, use cases

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Authors: Honggang Qu, Yong Xu, Rongmei Liu, Zhenji Gao, Bin Wang

Abstract:

Today's mining industry is advancing gradually toward digital and visual direction. The three-dimensional visualization geological modeling of mine is the digital characterization of mineral deposits and is one of the key technology of digital mining. Three-dimensional geological modeling is a technology that combines geological spatial information management, geological interpretation, geological spatial analysis and prediction, geostatistical analysis, entity content analysis and graphic visualization in a three-dimensional environment with computer technology and is used in geological analysis. In this paper, the three-dimensional geological modeling of an iron mine through the use of Surpac is constructed, and the weight difference of the estimation methods between the distance power inverse ratio method and ordinary kriging is studied, and the ore body volume and reserves are simulated and calculated by using these two methods. Compared with the actual mine reserves, its result is relatively accurate, so it provides scientific bases for mine resource assessment, reserve calculation, mining design and so on.

Keywords: three-dimensional geological modeling, geological database, geostatistics, block model

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Authors: Ahmed Ferhati, Arezki Adjrad, Ratiba Mitiche-Kettab, Hakim Djafer Khodja

Abstract:

The porous media are omnipresent around us that they are natural as sand, clay, rocks, or manufactured like concretes, cement, and ceramics. The variety of porous environment indicates a wide material range which can be very different from each other. Their common point is to be made up of a solid matrix and a porous space. In our case of study, we made the modeling of the flows in porous environments through the massives as in the case of an earth dam. The computer code used (PLAXIS) offer the possibility of modeling of various structures, in particular, the works in lands because that it deals with the pore water pressure due to the underground flow and the calculation of the plastic deformations. To confirm results obtained by PLAXIS, GeoStudio SEEP/W code was used. This work treats modeling of flows and mechanical and hydraulic behavior of earth dam. A general framework which can fit the calculation of this kind of structures and the coupling of the soil consolidation and free surface flows was defined. In this study; we have confronted a real case modeling of an earth dam. It was shown, in particular, that it is possible to entirely lead the calculation of real dam and to get encouraging results from the hydraulic and mechanical point of view.

Keywords: analyzes, dam, flow, modeling, PLAXIS, seep/w, slope

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Authors: Apisaraporn Baicharoen, Prapasiri Pongprayoon

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

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

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