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Journal of the Serbian Society for Computational Mechanics最新文献

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THE INTERACTION OF PROTONATED OCTOPAMINE AND NOREPINEPHRINE WITH Β1-ADRENERGIC RECEPTOR: MOLECULAR DOCKING AND DYNAMICAL SIMULATION 质子化章鱼胺和去甲肾上腺素与Β1-adrenergic受体的相互作用:分子对接和动力学模拟
IF 0.4
Journal of the Serbian Society for Computational Mechanics Pub Date : 2020-06-01 DOI: 10.24874/JSSCM.2020.01.02
Žiko B. Milanović, D. Dimić, J. M. Markovic, Marijana Stanojević-Pirković, Edina H. Avdović, Z. Marković
{"title":"THE INTERACTION OF PROTONATED OCTOPAMINE AND NOREPINEPHRINE WITH Β1-ADRENERGIC RECEPTOR: MOLECULAR DOCKING AND DYNAMICAL SIMULATION","authors":"Žiko B. Milanović, D. Dimić, J. M. Markovic, Marijana Stanojević-Pirković, Edina H. Avdović, Z. Marković","doi":"10.24874/JSSCM.2020.01.02","DOIUrl":"https://doi.org/10.24874/JSSCM.2020.01.02","url":null,"abstract":"In the current study, the interaction mechanisms between protonated neurotransmitters: octopamine (4-(2-amino-1-hydroxyethyl)phenol) and norepinephrine (4-[(1R)-2-amino-1-hydroxyethyl]benzene-1,2-diol) with the β-1 adrenergic receptor (β1AR) were examined by molecular docking, molecular dynamics (MD) simulations and MM/PBSA free energy calculations. The investigated receptor belongs to the G-protein coupled receptor group. The investigation was carried out at physiological pH=7.4. It was estimated that both compounds exist in the protonated form in the water at physiological pH. It was found that both protonated neurotransmitters established similar interactions with amino acid residues of the receptor, such as salt bridges, conventional hydrogen bonds, π-σ, and T-shaped π-π interactions, as shown by molecular docking simulations. As the initial structures for MD simulation with a total time of 10ns the most stable docking structures were used. The presented results are expected to provide some useful information for the design of specific β1AR agonists.","PeriodicalId":42945,"journal":{"name":"Journal of the Serbian Society for Computational Mechanics","volume":" ","pages":""},"PeriodicalIF":0.4,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42284018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
AN EXPERIMENTAL AND THEORETICAL STUDY OF THE REACTIVITY OF SELECTED CATECHOLAMINES AND THEIR PRECURSORS TOWARDS ASCORBYL RADICAL 选定的儿茶酚胺及其前体对抗坏血酸自由基反应性的实验和理论研究
IF 0.4
Journal of the Serbian Society for Computational Mechanics Pub Date : 2020-06-01 DOI: 10.24874/JSSCM.2020.01.01
D. Dimić, Đura Nakarada, M. Mojović, J. M. Markovic
{"title":"AN EXPERIMENTAL AND THEORETICAL STUDY OF THE REACTIVITY OF SELECTED CATECHOLAMINES AND THEIR PRECURSORS TOWARDS ASCORBYL RADICAL","authors":"D. Dimić, Đura Nakarada, M. Mojović, J. M. Markovic","doi":"10.24874/JSSCM.2020.01.01","DOIUrl":"https://doi.org/10.24874/JSSCM.2020.01.01","url":null,"abstract":"Ascorbyl radical is often used as a biomarker of oxidative stress in human organism. It is a product of the antioxidant activity of ascorbic acid and it is not expected to react further with biologically important molecules. For the first time, the reactivity of catecholamines and their precursors was investigated theoretically and experimentally towards ascorbyl radical and the main structural parameters governing activity were analyzed. It was shown that catechol moiety plays an important role, which classifies norepinephrine and 3,4-dihydroxyphenylacetic acid as the most reactive when compared to homovanillic acid, vanillylmandelic acid, and octopamine. DFT methods have been employed to determine the most probable mechanism of the reaction. Based on the change in reaction enthalpy it was concluded that Hydrogen Atom Transfer (HAT) is a preferred mechanism both in water and pentyl ethanoate. The stabilization interactions in ascorbic acid, its anion and radical are carefully analyzed in order to understand the preferability of the mentioned mechanism. The stability of the ascorbyl radical is explained in detail. The results prove that ascorbyl radical is not just a product of antioxidant activity, but also a potentially harmful species in an organism.","PeriodicalId":42945,"journal":{"name":"Journal of the Serbian Society for Computational Mechanics","volume":" ","pages":""},"PeriodicalIF":0.4,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43414804","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
DO EQUOL’S C-RING HYDROGENS CONTRIBUTE TO FREE RADICAL SCAVENGING? 马酚的c环氢有助于清除自由基吗?
IF 0.4
Journal of the Serbian Society for Computational Mechanics Pub Date : 2020-06-01 DOI: 10.24874/JSSCM.2020.01.05
Ana D. Amic, D. Milenković, J. M. Markovic, Z. Marković
{"title":"DO EQUOL’S C-RING HYDROGENS CONTRIBUTE TO FREE RADICAL SCAVENGING?","authors":"Ana D. Amic, D. Milenković, J. M. Markovic, Z. Marković","doi":"10.24874/JSSCM.2020.01.05","DOIUrl":"https://doi.org/10.24874/JSSCM.2020.01.05","url":null,"abstract":"Free radical scavenging potency of physiologically active equol molecule, derived by gut microbiota from soy isoflavone daidzein, was investigated by using M06-2X/6-311++G(d,p) level of theory, accompanied with the TST and Eckart tunneling corrections for the estimation of rate constants. Phenolic hydrogens of equol are recognized as much more abstractable than C-ring hydrogens. This finding is opposite to the one very recently suggested, but in accordance with well-known facts related to the flavonoid chemistry and phenolic O−H vs C−H reactivity.","PeriodicalId":42945,"journal":{"name":"Journal of the Serbian Society for Computational Mechanics","volume":" ","pages":""},"PeriodicalIF":0.4,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45163133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
RESOLVENT ENERGY AND ESTRADA INDEX OF BENZENOID HYDROCARBONS 苯类烃的分解能和estada指数
IF 0.4
Journal of the Serbian Society for Computational Mechanics Pub Date : 2020-06-01 DOI: 10.24874/JSSCM.2020.01.04
Izudin Redžepović, Boris Furtula
{"title":"RESOLVENT ENERGY AND ESTRADA INDEX OF BENZENOID HYDROCARBONS","authors":"Izudin Redžepović, Boris Furtula","doi":"10.24874/JSSCM.2020.01.04","DOIUrl":"https://doi.org/10.24874/JSSCM.2020.01.04","url":null,"abstract":"The relationship between the resolvent and Estrada indices for the alkanes has been recently demonstrated. That relationship involved the first Zagreb index besides these two eigenvalue-based molecular descriptors. In this paper, the quality of the correlation is tested in the case of isomeric benzenoid hydrocarbons, where the first Zagreb index is constant. Extraordinary linear correlations are identified for all studied groups of isomeric benzenoid hydrocarbons. Additionally, the relationship of these indices with the boiling points of a set of benzenoid hydrocarbons is presented.","PeriodicalId":42945,"journal":{"name":"Journal of the Serbian Society for Computational Mechanics","volume":" ","pages":""},"PeriodicalIF":0.4,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46835096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
ANTIOXIDATIVE AND INHIBITION POTENCY OF CYNODONTIN 犬牙草素的抗氧化和抑制作用
IF 0.4
Journal of the Serbian Society for Computational Mechanics Pub Date : 2020-06-01 DOI: 10.24874/JSSCM.2020.01.06
J. Đorović, M. Antonijević, Z. Marković
{"title":"ANTIOXIDATIVE AND INHIBITION POTENCY OF CYNODONTIN","authors":"J. Đorović, M. Antonijević, Z. Marković","doi":"10.24874/JSSCM.2020.01.06","DOIUrl":"https://doi.org/10.24874/JSSCM.2020.01.06","url":null,"abstract":"The antioxidant activity of cynodontin was studied in the absence and the presence of free radical species. This in silico study was performed in water and benzene, with the aim to simulate polar and non-polar environment. To determine the most probable mechanism of antioxidant action, density functional theory (DFT) was employed. The change in reaction enthalpy of cynodontin with three different free radicals (hydroxyl, hydroperoxyl, and methyl peroxyl radical) were examined and presented. SET-PT (Single Electron Transfer – Proton Transfer) mechanism is not an operative mechanism of antioxidant action. The obtained results imply that the possible mechanism of antioxidant action in water is SPLET (Sequential Proton Loss Electron Transfer), while in benzene HAT (Hydrogen atom transfer) and SPLET are competitive mechanisms. The molecular docking study was performed in order to estimate the inhibition potency of the investigated compound toward human leukocyte elastase (HLE). The obtained results indicate that numerous interactions determine the inhibition activity towards the investigated protein.","PeriodicalId":42945,"journal":{"name":"Journal of the Serbian Society for Computational Mechanics","volume":" ","pages":""},"PeriodicalIF":0.4,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46257761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
VISCOSITY VARIATION EFFECT ON THE MAGNETIC FLUID LUBRICATION OF A SHORT BEARING 粘度变化对短轴承磁流体润滑的影响
IF 0.4
Journal of the Serbian Society for Computational Mechanics Pub Date : 2019-12-01 DOI: 10.24874/jsscm.2019.13.02.05
J. Patel, G. Deheri
{"title":"VISCOSITY VARIATION EFFECT ON THE MAGNETIC FLUID LUBRICATION OF A SHORT BEARING","authors":"J. Patel, G. Deheri","doi":"10.24874/jsscm.2019.13.02.05","DOIUrl":"https://doi.org/10.24874/jsscm.2019.13.02.05","url":null,"abstract":"The performance of a magnetic fluid based short bearing is examined with the effect of viscosity variation. The pressure temperature relation of Tipei (1962) concerning viscosity variation is adopted here. The Neuringer-Rosensweig’s model has been considered for the magnetic fluid flow. The related modified Reynolds type equation is solved for the calculation of pressure distribution leading to the computation of load bearing capacity. The graphical representations indicate that the positive effect of viscosity variation gets aided considerably by the ferrofluid lubrication.","PeriodicalId":42945,"journal":{"name":"Journal of the Serbian Society for Computational Mechanics","volume":" ","pages":""},"PeriodicalIF":0.4,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45689836","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
A Proposed Method for Determining Propulsion Coefficient Based on Testing Motor Freighters on Danube Waterway Network 一种基于多瑙河航道网机动货运试验确定推进系数的方法
IF 0.4
Journal of the Serbian Society for Computational Mechanics Pub Date : 2019-09-30 DOI: 10.24874/jsscm.2019.13.01.09
R. Rajković, D. Mitic, A. Lebl, S. Rajković
{"title":"A Proposed Method for Determining Propulsion Coefficient Based on Testing Motor Freighters on Danube Waterway Network","authors":"R. Rajković, D. Mitic, A. Lebl, S. Rajković","doi":"10.24874/jsscm.2019.13.01.09","DOIUrl":"https://doi.org/10.24874/jsscm.2019.13.01.09","url":null,"abstract":"The paper presents a proposal of mathematical models for the determination of propulsion coefficient, ηpp, intended for the analysis of motor freighters applied on the river watercourses. As the main paper contribution three different model types are developed, depending on the variable which contributes to ηpp value. These variables are: 1. the freighter sailing velocity, (v); 2. the installed capacity of the main drive motor of outboard unit, (Ninst); 3. the combination of these two variables, (Ninst,v). The models are verified on the examples of several motor freighters which are applied at Danube river. The special attention is paid to the determination of the optimum approximation function in each case. In all three cases it is a quadratic function. The correlation coefficient for the comparison in all analyzed examples is higher than 0.87, being even higher than 0.99 for the first model.","PeriodicalId":42945,"journal":{"name":"Journal of the Serbian Society for Computational Mechanics","volume":" ","pages":""},"PeriodicalIF":0.4,"publicationDate":"2019-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49660540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
1D and 3D Modeling of Modern Automotive Exhaust Manifold 现代汽车排气歧管的1D和3D建模
IF 0.4
Journal of the Serbian Society for Computational Mechanics Pub Date : 2019-09-01 DOI: 10.24874/jsscm.2019.13.01.05
Barhm Mohamad, A. Zelentsov
{"title":"1D and 3D Modeling of Modern Automotive Exhaust Manifold","authors":"Barhm Mohamad, A. Zelentsov","doi":"10.24874/jsscm.2019.13.01.05","DOIUrl":"https://doi.org/10.24874/jsscm.2019.13.01.05","url":null,"abstract":"This paper presents the simulation of the multi-cylinder 4-stroke cycle spark-ignition engine using a commercial simulation tool, AVL BOOST and Fire. Various models were examined to select the appropriate models that would best serve to analyze the main components of the exhaust systems: the plenum chamber, the muffler and the exhaust manifold branch junction. For the plenum chamber and the muffler, the whole duct model was tested. In order to analyze the exhaust manifold branch junction, a complicated model which reflects the actual shape and involves pressure drops, velocity magnitude and sound pressure was compared to a simplified one. However, the results from 1D and 3D model calculations compared with Honda K20B Engine experimental data also show that both models are applicable with satisfying accuracy for exhaust manifold branch junction. The simplified 1D model is recommended in regard to convenience in modeling and efficiency in calculation.","PeriodicalId":42945,"journal":{"name":"Journal of the Serbian Society for Computational Mechanics","volume":"1 1","pages":""},"PeriodicalIF":0.4,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41400425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
Aerodynamic performances improvement of NACA 4415 profile by passive flow control using vortex generators 采用涡流发生器的被动流动控制改善NACA 4415型面的气动性能
IF 0.4
Journal of the Serbian Society for Computational Mechanics Pub Date : 2019-09-01 DOI: 10.24874/jsscm.2019.13.01.02
Hocine Hares, G. Mebarki, M. Brioua, M. Naoun
{"title":"Aerodynamic performances improvement of NACA 4415 profile by passive flow control using vortex generators","authors":"Hocine Hares, G. Mebarki, M. Brioua, M. Naoun","doi":"10.24874/jsscm.2019.13.01.02","DOIUrl":"https://doi.org/10.24874/jsscm.2019.13.01.02","url":null,"abstract":"Improvement of the airfoil NACA 4415 aerodynamic performances by flow control using a passive technique was achieved in this study. Gothic-shaped vortex generators were added at the profile upper surface. Vortex Generators (VG) were used to avoid boundary layer separation at the profile trailing edge, thus reducing the drag force and improving aerodynamic performances. A numerical simulation with fluent code was performed. A parametric study was carried out to determine optimal disposition and dimensions of the VG. Six VG parameters were tested; thickness (E), height (H), length (L), aspect ratio (r), incidence angle (α) and the VG position relative to the chord of the profile (XVG). The results show an increase in the lift coefficient for the profile with vortex generators in the range of high attack angles. Optimal dimensions and positions of the VG were obtained.","PeriodicalId":42945,"journal":{"name":"Journal of the Serbian Society for Computational Mechanics","volume":" ","pages":""},"PeriodicalIF":0.4,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45651723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
Computational Analysis of Hip Implant Surfaces 髋关节植入物表面的计算分析
IF 0.4
Journal of the Serbian Society for Computational Mechanics Pub Date : 2019-09-01 DOI: 10.24874/jsscm.2019.13.01.07
Aleksandra Vulovic, N. Filipovic
{"title":"Computational Analysis of Hip Implant Surfaces","authors":"Aleksandra Vulovic, N. Filipovic","doi":"10.24874/jsscm.2019.13.01.07","DOIUrl":"https://doi.org/10.24874/jsscm.2019.13.01.07","url":null,"abstract":"","PeriodicalId":42945,"journal":{"name":"Journal of the Serbian Society for Computational Mechanics","volume":" ","pages":""},"PeriodicalIF":0.4,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42587177","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 11
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