Search results for: homology modeling

Authors: Fatemeh Mohammadi Aghjeh Mashhad

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In this paper, we give several ways for computing generalized local homology modules by using Gorenstein flat resolutions. Also, we find some bounds for vanishing of generalized local homology modules.

Keywords: a-adic completion functor, generalized local homology modules, Gorenstein flat modules

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Authors: Zuhier Altawallbeh

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In this paper, an explicit homotopic function is constructed to compute the Hochschild homology of a finite dimensional free k-module V. Because the polynomial algebra is of course fundamental in the computation of the Hochschild homology HH and the cyclic homology CH of commutative algebras, we concentrate our work to compute HH of the polynomial algebra.by providing certain homotopic function.

Keywords: hochschild homology, homotopic function, free and projective modules, free resolution, exterior algebra, symmetric algebra

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Authors: Y. Ruchi, A. Prerna, S. Deepshikha

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Amyotrophic lateral sclerosis (ALS), also known as “Lou Gehrig’s disease”. It is a neurodegenerative disease associated with degeneration of motor neurons in the cerebral cortex, brain stem, and spinal cord characterized by distal muscle weakness, atrophy, normal sensation, pyramidal signs and progressive muscular paralysis reflecting. ALS2 is a juvenile autosomal recessive disorder, slowly progressive, that maps to chromosome 2q33 and is associated with mutations in the alsin gene, a putative GTPase regulator. In this paper we have done homology modeling of alsin2 protein using multiple templates (3KCI_A, 4LIM_A, 402W_A, 4D9S_A, and 4DNV_A) designed using the Prime program in Schrödinger software. Further modeled structure is used to identify effective binding sites on the basis of structural and physical properties using sitemap program in Schrödinger software, structural and function analysis is done by using Prosite and ExPASy server that gives insight into conserved domains and motifs that can be used for protein classification. This paper summarizes the structural, functional and binding site property of alsin2 protein. These binding sites can be potential drug target sites and can be used for docking studies.

Keywords: ALS, binding site, homology modeling, neuronal degeneration

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Authors: Ravinder Singh, Ankita Gurao, Saroj Bandhan, Sudhir Kumar Kashyap

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The Bos taurus Beta defensin 3 is a defensin peptide secreted by neutrophils and epithelial that exhibits anti-microbial activity. It is one of the crucial components forming an innate defense against intra mammary infections in livestock. The beta defensin 3 by virtue of its anti-microbial activity inhibits major mastitis pathogens including Staphylococcus aureus and Pseudomonas aeruginosa etc, which are also responsible for biofilm formation leading to antibiotic resistance phenomenon. Therefore, the defensin may prove as a non-conventional option to treat mastitis. In this study, computational analysis has been performed including sequence comparison among species and homology modeling of Bos taurus beta defensin 3 protein. The assessments of protein structure were done using the protein structure and model assessment tools integrated in Swiss Model server, which employs various local and global quality evaluation parameters. Further, molecular docking was also carried out between the defensin peptide and the components of biofilm to gain insight into various interactions and structural differences crucial for functionality of this protein.

Keywords: beta defensin 3, bos taurus, docking, homology modeling

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Authors: Minh Quang Le, Dane Taylor

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Convection is a well-studied topic in fluid dynamics, yet it is less understood in the context of networks flows. Here, we incorporate techniques from topological data analysis (namely, persistent homology) to automate the detection and characterization of convective/cyclic/chiral flows over networks, particularly those that arise for irreversible Markov chains (MCs). As two applications, we study convection cycles arising under the PageRank algorithm, and we investigate chiral edges flows for a stochastic model of a bi-monomer's configuration dynamics. Our experiments highlight how system parameters---e.g., the teleportation rate for PageRank and the transition rates of external and internal state changes for a monomer---can act as homology regularizers of convection, which we summarize with persistence barcodes and homological bifurcation diagrams. Our approach establishes a new connection between the study of convection cycles and homology, the branch of mathematics that formally studies cycles, which has diverse potential applications throughout the sciences and engineering.

Keywords: homology, persistent homolgy, markov chains, convection cycles, filtration

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Authors: Bin Liu

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Protein remote homology detection and fold recognition are two most important tasks in protein sequence analysis, which is critical for protein structure and function studies. In this study, we combined the profile-based features with various string kernels, and constructed several computational predictors for protein remote homology detection and fold recognition. Experimental results on two widely used benchmark datasets showed that these methods outperformed the competing methods, indicating that these predictors are useful computational tools for protein sequence analysis. By analyzing the discriminative features of the training models, some interesting patterns were discovered, reflecting the characteristics of protein superfamilies and folds, which are important for the researchers who are interested in finding the patterns of protein folds.

Keywords: protein remote homology detection, protein fold recognition, profile-based features, Support Vector Machines (SVMs)

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Authors: Eashwar V. Somasundaram, Raoul R. Wadhwa, Jacob G. Scott

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The use of radiomics in measuring geometric properties of tumor images such as size, surface area, and volume has been invaluable in assessing cancer diagnosis, treatment, and prognosis. In addition to analyzing geometric properties, radiomics would benefit from measuring topological properties using persistent homology. Intuitively, features uncovered by persistent homology may correlate to tumor structural features. One example is necrotic cavities (corresponding to 2D topological features), which are markers of very aggressive tumors. We develop a data pipeline in R that clusters tumors images based on persistent homology is used to identify meaningful clinical distinctions between tumors and possibly new relationships not captured by established clinical categorizations. A preliminary analysis was performed on 16 Magnetic Resonance Imaging (MRI) breast tissue segments downloaded from the 'Investigation of Serial Studies to Predict Your Therapeutic Response with Imaging and Molecular Analysis' (I-SPY TRIAL or ISPY1) collection in The Cancer Imaging Archive. Each segment represents a patient’s breast tumor prior to treatment. The ISPY1 dataset also provided the estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) status data. A persistent homology matrix up to 2-dimensional features was calculated for each of the MRI segmentation. Wasserstein distances were then calculated between all pairwise tumor image persistent homology matrices to create a distance matrix for each feature dimension. Since Wasserstein distances were calculated for 0, 1, and 2-dimensional features, three hierarchal clusters were constructed. The adjusted Rand Index was used to see how well the clusters corresponded to the ER/PR/HER2 status of the tumors. Triple-negative cancers (negative status for all three receptors) significantly clustered together in the 2-dimensional features dendrogram (Adjusted Rand Index of .35, p = .031). It is known that having a triple-negative breast tumor is associated with aggressive tumor growth and poor prognosis when compared to non-triple negative breast tumors. The aggressive tumor growth associated with triple-negative tumors may have a unique structure in an MRI segmentation, which persistent homology is able to identify. This preliminary analysis shows promising results in the use of persistent homology on tumor imaging to assess the severity of breast tumors. The next step is to apply this pipeline to other tumor segment images from The Cancer Imaging Archive at different sites such as the lung, kidney, and brain. In addition, whether other clinical parameters, such as overall survival, tumor stage, and tumor genotype data are captured well in persistent homology clusters will be assessed. If analyzing tumor MRI segments using persistent homology consistently identifies clinical relationships, this could enable clinicians to use persistent homology data as a noninvasive way to inform clinical decision making in oncology.

Keywords: cancer biology, oncology, persistent homology, radiomics, topological data analysis, tumor imaging

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Authors: Bin Liu

Abstract:

As one of the most important tasks in protein sequence analysis, protein remote homology detection has been studied for decades. Currently, the profile-based methods show state-of-the-art performance. Position-Specific Frequency Matrix (PSFM) is widely used profile. However, there exists noise information in the profiles introduced by the amino acids with low frequencies. In this study, we propose a method to remove the noise information in the PSFM by removing the amino acids with low frequencies called Top frequency profile (TFP). Three new matrix transformation methods, including Autocross covariance (ACC) transformation, Tri-gram, and K-separated bigram (KSB), are performed on these profiles to convert them into fixed length feature vectors. Combined with Support Vector Machines (SVMs), the predictors are constructed. Evaluated on two benchmark datasets, and experimental results show that these proposed methods outperform other state-of-the-art predictors.

Keywords: protein remote homology detection, protein fold recognition, top frequency profile, support vector machines

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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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Authors: Chinmayee Choudhury

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Human Melanocortin 4 Receptor (HMC4R) is one of the most potential drug targets for the treatment of obesity which controls the appetite. A deletion of the residues 88-92 in HMC4R is sometimes the cause of severe obesity in the humans. In this study, two homology models are constructed for the normal as well as mutated HMC4Rs and some phytochemicals present in Green Tea, Honey and Cinnamon have been docked to them to study their differential binding to the normal and mutated HMC4R as compared to the natural agonist α- MSH. Two homology models have been constructed for the normal as well as mutated HMC4Rs using the Modeller9v7. Some of the phytochemicals present in Green Tea, Honey, and Cinnamon, which have appetite suppressant activities are constructed, minimized and docked to these normal and mutated HMC4R models using ArgusLab 4.0.1. The mode of binding of the phytochemicals with the Normal and Mutated HMC4Rs have been compared. Further, the mode of binding of these phytochemicals with that of the natural agonist α- Melanocyte Stimulating Hormone(α-MSH) to both normal and mutated HMC4Rs have also been studied. It is observed that the phytochemicals Kaempherol, Epigallocatechin-3-gallate (EGCG) present in Green Tea and Honey, Isorhamnetin, Chlorogenic acid, Chrysin, Galangin, Pinocambrin present in Honey, Cinnamaldehyde, Cinnamyl acetate and Cinnamyl alcohol present in Cinnamon have capacity to form more stable complexes with the Mutated HMC4R as compared to α- MSH. So they may be potential agonists of HMC4R to suppress the appetite.

Keywords: HMC4R, α-MSH, docking, photochemical, appetite suppressant, homology modelling

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Authors: Muhammad Fadli Muslimin

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Negeri Para Bedebah is known as one of the works of Tere Liye, an Indonesia author. In the literary works, the fiction as always tries to reflect the reality of the society where the author or the social groups lived in. The essential or nature of society is generally a reality while literary work is fiction and both of them are social fact. Negeri Para Bedebah is a novel fiction which is a social fact and which holds an important role in reality. It is more likely as the representation of social, economy and politic aspects in Indonesia. The purpose of this study is to reveal the world view of Tere Liye throughout novel Negeri Para Bedebah. By analyzing the object using genetic structuralism Lucien Goldmann which chiefly focuses on world view, it is stated that the literary work is an structure and it has homology with the structure in society. The structure of literary work is not chiefly homolog to the structure of society but homolog to the world view which is growing and developing inside the society. The methodological research used in this paper is a dialectic method which focuses on the starting and ending points lied in the literary text by paying attention to the coherent meanings. The result of this study is that Tere Liye shows us his world view about the structure of the society where he is living in, but one is an imaginative form of the world and the homology to the reality itself.

Keywords: homology, literary work, society, structure, world view

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Authors: Muhammad A. Khan, Waseem Shahzad

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Analysis of protein sequences is carried out for the purpose to discover their structural and ancestry relationship. Sequence similarity determines similar protein structures, similar function, and homology detection. Biological sequences composed of amino acid residues or nucleotides provide significant information through sequence alignment. In this paper, we present a new similarity/dissimilarity measure to sequence alignment based on the primary structure of a protein. The approach finds the distance between the two given sequences using the novel sequence alignment algorithm and a mathematical model. The algorithm runs at a time complexity of O(n²). A distance matrix is generated to construct a phylogenetic tree of different species. The new similarity/dissimilarity measure outperforms other existing methods.

Keywords: alignment, distance, homology, mathematical model, phylogenetic tree

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Authors: Alok Shiomurti Tripathi, Ajay Kumar Timiri, Papiya Mitra Mazumder, Anil Chandewar

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The present study evaluates the possible drug interaction between glimepiride (GLIM) and sildenafil citrate (SIL) in streptozotocin (STZ) induced in diabetic nephropathic (DN) animals and also postulates the possible mechanism of interaction by molecular modeling studies. Diabetic nephropathy was induced by single dose of STZ (60 mg/kg, ip) and confirms it by assessing the blood and urine biochemical parameters on 28th day of its induction. Selected DN animals were used for the drug interaction between GLIM (0.5mg/kg, p.o.) and SIL (2.5 mg/kg, p.o.) after 29th and 70th day of protocol. Drug interaction were assessed by evaluating the plasma drug concentration using HPLC-UV and also determine the change in the biochemical parameter in blood and urine. Mechanism of the interaction was postulated by molecular modeling study using Maestro module of Schrodinger software. DN was confirmed as there was significant alteration in the blood and urine biochemical parameter in STZ treated groups. The concentration of SIL increased significantly (p<0.001) in rat plasma when co administered with GLIM after 70th day of protocol. Molecular modelling study revealed few important interactions with rat serum albumin and CYP2C9.GLIM has strong hydrophobic interaction with binding site residues of rat serum albumin compared to SIL. Whereas, for CYP2C9, GLIM has strong hydrogen bond with polar contacts and hydrophobic interactions than SIL. Present study concludes that bioavailability of SIL increases when co-administered chronically with GLIM in the management of DN animals and mechanism has been supported by molecular modeling studies.

Keywords: diabetic nephropathy, glimepiride, sildenafil citrate, pharmacokinetics, homology modeling, schrodinger

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Authors: Kalyan S. Ghosh, B. L. Dhananjaya

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Snake bite causes fatal injuries in multi-organs and even many deaths due to several adverse physiological effects of various phospholipases (PLA2s) present in snake venom. Though these PLA2s bear highly homologues sequences and also structure but exhibit a different extent of those pharmacological effects. In this study, we have explored the difference in the neurotoxicity of two PLA2 namely PLA2-V, PLA2-VIIIa present in the venom from Vipera russellii. Bioinformatics studies on sequences of these two proteins along with detailed structural comparison enable us to explore the differences unambiguously. The identification of the residues involved in neurotoxicity will further lead towards proper designing of inhibitors against such killing effects of the venom.

Keywords: electrostatic potential, homology modeling, hydrophobicity, neurotoxicity, Phospholipase A2

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Authors: Chil-Chyuan Kuo, Chen-Hsuan Tsai

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This study presents a cost-effective approach for rapid fabricating modeling platforms utilized in fused deposition modeling system. A small-batch production of modeling platforms about 20 pieces can be obtained economically through silicone rubber mold using vacuum casting without applying the plastic injection molding. The air venting systems is crucial for fabricating modeling platform using vacuum casting. Modeling platforms fabricated can be used for building rapid prototyping model after sandblasting. This study offers industrial value because it has both time-effectiveness and cost-effectiveness.

Keywords: vacuum casting, fused deposition modeling, modeling platform, sandblasting, surface roughness

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Authors: Seongsoo Lee

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IP reuse is an effective design methodology for modern SoC design to reduce effort and time. However, description and modeling methods of IP interfaces are different due to different IP designers. In this paper, standardized description and modeling methods of IP interfaces are proposed. It consists of 11 items such as IP information, model provision, data type, description level, interface information, port information, signal information, protocol information, modeling level, modeling information, and source file. The proposed description and modeling methods enables easy understanding, simulation, verification, and modification in IP reuse.

Keywords: interface, standardization, description, modeling, semiconductor IP

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Authors: Ayse Ozturk

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The study extends the prior research on modeling competencies by positioning students’ cognitive and language resources as the fundamentals for pursuing their own inquiry and expression lines through mathematical modeling. This strategy aims to answer the question that guides this study, “How do students’ group approaches to modeling tasks affect their modeling competencies over a unit of instruction?” Six bilingual tenth-grade students worked on open-ended modeling problems along with the content focused on quantities over six weeks. Each group was found to have a unique cognitive approach for solving these problems. Three different problem-solving strategies affected how the groups’ modeling competencies changed. The results provide evidence that the discussion around groups’ solutions, coupled with their reflections, advances group interpreting and validating competencies in the mathematical modeling process

Keywords: cognition, collective learning, mathematical modeling competencies, problem-solving

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Authors: Romasa Qasim, G. M. Sayedur Rahman, Nahid Hasan, M. Shazzad Hosain

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Millions of people worldwide suffer from Hepatitis C, one of the fatal diseases. Interferon (IFN) and ribavirin are the available treatments for patients with Hepatitis C, but these treatments have their own side-effects. Our research focused on the development of an orally taken small molecule drug targeting the proteins in Hepatitis C Virus (HCV), which has lesser side effects. Our current study aims to the Pharmacophore based drug development of a specific small molecule anti-viral drug for Hepatitis C Virus (HCV). Drug designing using lab experimentation is not only costly but also it takes a lot of time to conduct such experimentation. Instead in this in silico study, we have used computer-aided techniques to propose a Pharmacophore-based anti-viral drug specific for the protein domains of the polyprotein present in the Hepatitis C Virus. This study has used homology modeling and ab initio modeling for protein 3D structure generation followed by pocket identification in the proteins. Drug-able ligands for the pockets were designed using de novo drug design method. For ligand design, pocket geometry is taken into account. Out of several generated ligands, a new Pharmacophore is proposed, specific for each of the protein domains of HCV.

Keywords: pharmacophore-based drug design, anti-viral drug, in-silico drug design, Hepatitis C virus (HCV)

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Authors: Andi Aliah Hidayani, Asmi Citra Malina A. R. Tassakka, Andi Parenrengi

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Vanname Shrimp is one of the high yielding varieties that are more resistant to virus attacks. However, now this shrimp more death due to virus attack such as white spot disease caused by white spot syndrome virus (WSSV). Various efforts have done to prevent the disease, like immunostimulatory, probiotics, and vaccine. White spot syndrome virus (WSSV) envelope protein VP19 gene is important because of its involvement in the system infection of shrimp. This study aimed to isolate and characterize an envelope protein VP19 – encoding gene of WSSV using WSSV infected Vanname Shrimp sample from some areas in South Sulawesi (Pangkep, Barru and Pinrang). The genomic of DNA were isolated from shrimp muscle using DTAB-CTAB method. Isolation of gene encoding envelope protein VP19 WSSV ws successfully performed with the results of the length of DNA fragment was 387 bp. The results of homology analysis using BLASTn homology suggested that these isolates genes from Barru, Pangkep and Pinrang have closest relationship with isolates from Mexican.

Keywords: vanname, shrimp, WSSV, viral protein 19

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Authors: M. J. Norashirene, Y. Zakiah, S. Nurdiana, I. Nur Hilwani, M. H. Siti Khairiyah, M. J. Muhamad Arif

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In this study, six bacterial isolates of a slightly thermophilic organism from the Sg. Klah hot spring, Malaysia were successfully isolated and designated as M7T55D1, M7T55D2, M7T55D3, M7T53D1, M7T53D2 and M7T53D3 respectively. The bacterial isolates were screened for their cellulose hydrolytic ability on Carboxymethlycellulose agar medium. The isolated bacterial strains were identified morphologically, biochemically and molecularly with the aid of 16S rDNA sequencing. All of the bacteria showed their optimum growth at a slightly alkaline pH of 7.5 with a temperature of 55°C. All strains were Gram-negative, non-spore forming type, strictly aerobic, catalase-positive and oxidase-positive with the ability to produce thermostable cellulase. Based on BLASTn results, bacterial isolates of M7T55D2 and M7T53D1 gave the highest homology (97%) with similarity to Tepidimonas ignava while isolates M7T55D1, M7T55D3, M7T53D2 and M7T53D3 showed their closest homology (97%-98%) with Tepidimonas thermarum. These cellulolytic thermophiles might have a commercial potential to produce valuable thermostable cellulase.

Keywords: cellulase, cellulolytic, thermophiles, 16S rDNA gene

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Authors: Katalina Grigorova, Kaloyan Mironov

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The paper focuses on the benefits of business process modeling. Although this discipline is developing for many years, there is still necessity of creating new opportunities to meet the ever-increasing users’ needs. Because one of these needs is related to the conversion of business process models from one standard to another, the authors have developed a converter between BPMN and EPC standards using workflow patterns as intermediate tool. Nowadays there are too many systems for business process modeling. The variety of output formats is almost the same as the systems themselves. This diversity additionally hampers the conversion of the models. The presented study is aimed at discussing problems due to differences in the output formats of various modeling environments.

Keywords: business process modeling, business process modeling standards, workflow patterns, converting models

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Authors: Jay Xiong, Li Lin

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Existing software modeling and visualization approaches using UML are outdated, which are outcomes of reductionism and the superposition principle that the whole of a system is the sum of its parts, so that with them all tasks of software modeling and visualization are performed linearly, partially, and locally. This paper introduces revolutionary solutions for modeling and visualization of complex software systems, which make complex software systems much easy to understand, test, and maintain. The solutions are based on complexity science, offering holistic, automatic, dynamic, virtual, and executable approaches about thousand times more efficient than the traditional ones.

Keywords: complex systems, software maintenance, software modeling, software visualization

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Authors: S. A. Che Osmi, W. M. F. W. Ishak, S. F. Che Osmi

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Nowadays the issues of water quality and water pollution have been a major problem across the country. A lot of management attempt to develop their own TMDL database in order to control the river pollution. Over the past decade, the mathematical modeling has been used as the tool for the development of TMDL. This paper presents the application of water quality modeling to develop the total maximum daily load (TMDL) information. To obtain the reliable database of TMDL, the appropriate water quality modeling should choose based on the available data provided. This paper will discuss on the use of several water quality modeling such as QUAL2E, QUAL2K, and EFDC to develop TMDL. The attempts to integrate several modeling are also being discussed in this paper. Based on this paper, the differences in the application of water quality modeling based on their properties such as one, two or three dimensional are showing their ability to develop the modeling of TMDL database.

Keywords: TMDL, water quality modeling, QUAL2E, EFDC

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Authors: Natália Maria Rego

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ALeibnizn-algebraGis aK-vector space endowed whit a n-linearbracket operation [-,…-] : GG … G→ Gsatisfying the fundamental identity, which can be expressed saying that the right multiplication map Ry2, …, ᵧₙ: Gn→ G, Rᵧ₂, …, ᵧₙn(ˣ¹, …, ₓₙ) = [[ˣ¹, …, ₓₙ], ᵧ₂, …, ᵧₙ], is a derivation. This structure, together with its skew-symmetric version, named as Lie n-algebra or Filippov algebra, arose in the setting of Nambumechanics, an n-ary generalization of the Hamiltonian mechanics. Thefirst goal of this work is to provide a characterization of various classes of central extensions of Leibniz n-algebras in terms of homological properties. Namely, Commutator extension, Quasi-commutator extension, Stem extension, and Stem cover. These kind of central extensions are characterized by means of the character of the map *(E): nHL1(G) → M provided by the five-term exact sequence in homology with trivial coefficients of Leibniz n-algebras associated to an extension E : 0 → M → K → G → 0. For a free presentation 0 →R→ F →G→ 0of a Leibniz n-algebra G,the term M(G) = (R[F,…n.., F])/[R, F,..n-1..,F] is called the Schur multiplier of G, which is a Baer invariant, i.e., it does not depend on the chosen free presentation, and it is isomorphic to the first Leibniz n-algebras homology with trivial coefficients of G. A central extension of Leibniz n-algebras is a short exact sequenceE : 0 →M→K→G→ 0such that [M, K,.. ⁿ⁻¹.., K]=0. It is said to be a stem extension if M⊆[G, .. n.., G]. Additionally, if the induced map M(K) → M(G) is the zero map, then the stem extension Eis said to be a stem cover. The second aim of this work is to analyze the interplay between stem covers of Leibniz n-algebras and the Schur multiplier. Concretely, in the case of finite-dimensional Leibniz n-algebras, we show the existence of coverings, and we prove that all stem covers with finite-dimensional Schur multiplier are isoclinic. Additionally, we characterize stem covers of perfect Leibniz n-algebras.

Keywords: leibniz n-algebras, central extensions, Schur multiplier, stem cover

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Authors: Ncoza Dlova, Tivani Mashamba-Thompson

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Garcinia livingstonei (Clusiaceae) extracts, morelloflavone- 7″- sulphate and sargaol were shown to be effective against hyper-pigmentation through inhibition of tyrosinase enzyme, in vitro . The aim of this study is to elucidate the structural mechanism through which morelloflavone- 7″- sulphate and sargaol binds human tyrosinase. Implementing a homology model to construct a tyrosinase model using the crystal structure of a functional unit from Octopus hemocyanin (PDB: 1JS8) as a reference template enabled us to create a human tyrosinase model. Molecular dynamics and binding free energy calculations were optimized to enable molecular dynamics simulation of the copper dependent inhibitors. Results show the importance of the hydrogen bond formation morelloflavone- 7″- sulphate and sargaol between compound and active site residues. Both complexes demonstrated the metallic coordination between compound and arginine residue as well as copper ions within the active site. The comprehensive molecular insight gained from this study should be vital in understanding the binding mechanism morelloflavone- 7″- sulphate and sargaol. Moreover, these results will assist in the design of novel of metal ion dependent enzyme inhibitors as potential anti-hyper-pigmentation disorder therapies.

Keywords: hyper-pigmentation disorders, dyschromia African skin, morelloflavone- 7″- sulphate, sagoal

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Authors: Zoltan Theisz, Gergely Mezei

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Modern industrial automation relies on service oriented concepts of Internet of Things (IoT) device modeling in order to provide a flexible and extendable environment for service meta-repository. However, state-of-the-art meta-modeling techniques prefer design-time modeling, which results in a heavy usage of class sometimes unnecessary static subtyping. Although this approach benefits from clear-cut object-oriented design principles, it also seals the model repository for further dynamic extensions. In this paper, a dynamic multi-level modeling approach is introduced that enables dynamic subtyping through a more relaxed partial instantiation mechanism. The approach is demonstrated on a simple sensor network example.

Keywords: meta-modeling, dynamic subtyping, DMLA, industrial automation, arrowhead

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Authors: Selisha A. Sooklal, Phelelani Mpangase, Shaun Aron, Karl Rumbold

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Organically bound fluorine (C-F bond) is extremely rare in nature. Despite this, the first fluorinated secondary metabolite, fluoroacetate, was isolated from the plant Dichapetalum cymosum (commonly known as Gifblaar). However, the enzyme responsible for fluorination (fluorinase) in Gifblaar was never isolated and very little progress has been achieved in understanding this process in higher plants. Fluorinated compounds have vast applications in the pharmaceutical, agrochemical and fine chemicals industries. Consequently, an enzyme capable of catalysing a C-F bond has great potential as a biocatalyst in the industry considering that the field of fluorination is virtually synthetic. As with any biocatalyst, a range of these enzymes are required. Therefore, it is imperative to expand the exploration for novel fluorinases. This study aimed to gain molecular insights into secondary metabolite biosynthesis in Gifblaar using a high-throughput sequencing-based approach. Mechanical wounding studies were performed using Gifblaar leaf tissue in order to induce expression of the fluorinase. The transcriptome of the wounded and unwounded plant was then sequenced on the Illumina HiSeq platform. A total of 26.4 million short sequence reads were assembled into 77 845 transcripts using Trinity. Overall, 68.6 % of transcripts were annotated with gene identities using public databases (SwissProt, TrEMBL, GO, COG, Pfam, EC) with an E-value threshold of 1E-05. Sequences exhibited the greatest homology to the model plant, Arabidopsis thaliana (27 %). A total of 244 annotated transcripts were found to be differentially expressed between the wounded and unwounded plant. In addition, secondary metabolic pathways present in Gifblaar were successfully reconstructed using Pathway tools. Due to lack of genetic information for plant fluorinases, a transcript failed to be annotated as a fluorinating enzyme. Thus, a local database containing the 5 existing bacterial fluorinases was created. Fifteen transcripts having homology to partial regions of existing fluorinases were found. In efforts to obtain the full coding sequence of the Gifblaar fluorinase, primers were designed targeting the regions of homology and genome walking will be performed to amplify the unknown regions. This is the first genetic data available for Gifblaar. It has provided novel insights into the mechanisms of metabolite biosynthesis and will allow for the discovery of the first eukaryotic fluorinase.

Keywords: biocatalyst, fluorinase, gifblaar, transcriptome

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Authors: Amanbek Jainakov, Abdikerim Kurbanaliev

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The work presents the results of mathematical modeling of large-scale flows in areas with a complex topographic relief. The Reynolds-averaged Navier—Stokes equations constitute the basis of the three-dimensional unsteady modeling. The well-known Volume of Fluid method implemented in the solver interFoam of the open package OpenFOAM 2.3 is used to track the free-boundary location. The mathematical model adequacy is checked by comparing with experimental data. The efficiency of the applied technology is illustrated by the example of modeling the breakthrough of the dams of the Andijan (Uzbekistan) and Papan (near the Osh town, Kyrgyzstan) reservoir.

Keywords: three-dimensional modeling, free boundary, the volume-of-fluid method, dam break, flood, OpenFOAM

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Authors: Himanshu Payal, Sachin Maheshwari, Pushpendra S. Bharti

Abstract:

Electrical discharge machining (EDM), a non-conventional machining process, finds wide applications for shaping difficult-to-cut alloys. Process modeling of EDM is required to exploit the process to the fullest. Process modeling of EDM is a challenging task owing to involvement of so many electrical and non-electrical parameters. This work is an attempt to model the EDM process using artificial neural network (ANN). Experiments were carried out on die-sinking EDM taking Inconel 825 as work material. ANN modeling has been performed using experimental data. The prediction ability of trained network has been verified experimentally. Results indicate that ANN can predict the values of performance measures of EDM satisfactorily.

Keywords: artificial neural network, EDM, metal removal rate, modeling, surface roughness

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Authors: Hycham Aboutaleb, Bruno Monsuez

Abstract:

Current systems complexity has reached a degree that requires addressing conception and design issues while taking into account all the necessary aspects. Therefore, one of the main challenges is the way complex systems are specified and designed. The exponential growing effort, cost and time investment of complex systems in modeling phase emphasize the need for a paradigm, a framework and a environment to handle the system model complexity. For that, it is necessary to understand the expectations of the human user of the model and his limits. This paper presents a generic framework for designing complex systems, highlights the requirements a system model needs to fulfill to meet human user expectations, and defines the refined functional as well as non functional requirements modeling tools needs to meet to be useful in model-based system engineering.

Keywords: system modeling, modeling language, modeling requirements, framework

Procedia PDF Downloads 503