Search results for: molecular motors
2102 Simple Rheological Method to Estimate the Branch Structures of Polyethylene under Reactive Modification
Authors: Mahdi Golriz
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The aim of this work is to estimate the change in molecular structure of linear low-density polyethylene (LLDPE) during peroxide modification can be detected by a simple rheological method. For this purpose a commercial grade LLDPE (Exxon MobileTM LL4004EL) was reacted with different doses of dicumyl peroxide (DCP). The samples were analyzed by size-exclusion chromatography coupled with a light scattering detector. The dynamic shear oscillatory measurements showed a deviation of the δ-׀G ׀٭curve from that of the linear LLDPE, which can be attributed to the presence of long-chain branching (LCB). By the use of a simple rheological method that utilizes melt rheology, transformations in molecular architecture induced on an originally linear low density polyethylene during the early stages of reactive modification were indicated. Reasonable and consistent estimates are obtained, concerning the degree of LCB, the volume fraction of the various molecular species produced in peroxide modification of LLDPE.Keywords: linear low-density polyethylene, peroxide modification, long-chain branching, rheological method
Procedia PDF Downloads 1482101 Computational Studies of the Reactivity Descriptors and the Optoelectronic Properties on the Efficiency Free-Base- and Zn-Porphyrin-Sensitized Solar Cells
Authors: Soraya Abtouche, Zeyneb Ghoualem, Syrine Daoudi, Lina Ouldmohamed, Xavier Assfeld
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This work reports density functional theory calculations of the optimized geometries, molecular reactivity, energy gap,and thermodynamic properties of the free base (H2P) and their Zn (II) metallated (ZnP), bearing one, two, or three carboxylic acid groups using the hybrid functional B3LYP, Cam-B3lYP, wb97xd with 6-31G(d,p) basis sets. When donating groups are attached to the molecular dye, the bond lengths are slightly decreased, which is important for the easy transfer of an electron from donating to the accepting group. For all dyes, the highest occupied molecular orbital/lowest occupied molecular orbital analysis results in positive outcomes upon electron injection to the semiconductor and subsequent dye regeneration by the electrolyte. The ionization potential increases with increasing conjugation; therefore, the compound dye attached to one carboxylic acid group has the highest ionization potential. The results show higher efficiencies of those sensitized with ZnP. These results have been explained, taking into account the electronic character of the metal ion, which acts as a mediator in the injection step, and, on the other hand, considering the number of anchoring groups to which it binds to the surface of TiO2.Keywords: DSSC, porphyrin, TD-DFT, electronic properties, donor-acceptor groups
Procedia PDF Downloads 712100 Computational Approach to Cyclin-Dependent Kinase 2 Inhibitors Design and Analysis: Merging Quantitative Structure-Activity Relationship, Absorption, Distribution, Metabolism, Excretion, and Toxicity, Molecular Docking, and Molecular Dynamics Simulations
Authors: Mohamed Moussaoui, Mouna Baassi, Soukayna Baammi, Hatim Soufi, Mohammed Salah, Rachid Daoud, Achraf EL Allali, Mohammed Elalaoui Belghiti, Said Belaaouad
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The present study aims to investigate the quantitative structure-activity relationship (QSAR) of a series of Thiazole derivatives reported as anticancer agents (hepatocellular carcinoma), using principally the electronic descriptors calculated by the density functional theory (DFT) method and by applying the multiple linear regression method. The developed model showed good statistical parameters (R²= 0.725, R²ₐ𝒹ⱼ= 0.653, MSE = 0.060, R²ₜₑₛₜ= 0.827, Q²𝒸ᵥ = 0.536). The energy of the highest occupied molecular orbital (EHOMO) orbital, electronic energy (TE), shape coefficient (I), number of rotatable bonds (NROT), and index of refraction (n) were revealed to be the main descriptors influencing the anti-cancer activity. Additional Thiazole derivatives were then designed and their activities and pharmacokinetic properties were predicted using the validated QSAR model. These designed molecules underwent evaluation through molecular docking (MD) and molecular dynamic (MD) simulations, with binding affinity calculated using the MMPBSA script according to a 100 ns simulation trajectory. This process aimed to study both their affinity and stability towards Cyclin-Dependent Kinase 2 (CDK2), a target protein for cancer disease treatment. The research concluded by identifying four CDK2 inhibitors - A1, A3, A5, and A6 - displaying satisfactory pharmacokinetic properties. MDs results indicated that the designed compound A5 remained stable in the active center of the CDK2 protein, suggesting its potential as an effective inhibitor for the treatment of hepatocellular carcinoma. The findings of this study could contribute significantly to the development of effective CDK2 inhibitors.Keywords: QSAR, ADMET, Thiazole, anticancer, molecular docking, molecular dynamic simulations, MMPBSA calculation
Procedia PDF Downloads 962099 Static Test Pad for Solid Rocket Motors
Authors: Svanik Garg
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Static Test Pads are stationary mechanisms that hold a solid rocket motor, measuring the different parameters of its operation including thrust and temperature to better calibrate it for launch. This paper outlines a specific STP designed to test high powered rocket motors with a thrust upwards of 4000N and limited to 6500N. The design includes a specific portable mechanism with cost an integral part of the design process to make it accessible to small scale rocket developers with limited resources. Using curved surfaces and an ergonomic design, the STP has a delicately engineered façade/case with a focus on stability and axial calibration of thrust. This paper describes the design, operation and working of the STP and its widescale uses given the growing market of aviation enthusiasts. Simulations on the CAD model in Fusion 360 provided promising results with a safety factor of 2 established and stress limited along with the load coefficient A PCB was also designed as part of the test pad design process to help obtain results, with visual output and various virtual terminals to collect data of different parameters. The circuitry was simulated using ‘proteus’ and a special virtual interface with auditory commands was also created for accessibility and wide-scale implementation. Along with this description of the design, the paper also emphasizes the design principle behind the STP including a description of its vertical orientation to maximize thrust accuracy along with a stable base to prevent micromovements. Given the rise of students and professionals alike building high powered rockets, the STP described in this paper is an appropriate option, with limited cost, portability, accuracy, and versatility. There are two types of STP’s vertical or horizontal, the one discussed in this paper is vertical to utilize the axial component of thrust.Keywords: static test pad, rocket motor, thrust, load, circuit, avionics, drag
Procedia PDF Downloads 3652098 Preparation of Melt Electrospun Polylactic Acid Nanofibers with Optimum Conditions
Authors: Amir Doustgani
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Melt electrospinning is a safe and simple technique for the production of micro and nanofibers which can be an alternative to conventional solvent electrospinning. The effects of various melt-electrospinning parameters, including molecular weight, electric field strength, flow rate and temperature on the morphology and fiber diameter of polylactic acid were studied. It was shown that molecular weight was the predominant factor in determining the obtainable fiber diameter of the collected fibers. An orthogonal design was used to examine process parameters. Results showed that molecular weight is the most effective parameter on the average fiber diameter of melt electrospun PLA nanofibers and the flow rate has the less important impact. Mean fiber diameter increased by increasing MW and flow rate, but decreased by increasing electric field strength and temperature. MFD of optimized fibers was below 100 nm and the result of software was in good agreement with the experimental condition.Keywords: fiber formation, processing, spinning, melt blowing
Procedia PDF Downloads 4362097 Exploring the Design of Prospective Human Immunodeficiency Virus Type 1 Reverse Transcriptase Inhibitors through a Comprehensive Approach of Quantitative Structure Activity Relationship Study, Molecular Docking, and Molecular Dynamics Simulations
Authors: Mouna Baassi, Mohamed Moussaoui, Sanchaita Rajkhowa, Hatim Soufi, Said Belaaouad
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The objective of this paper is to address the challenging task of targeting Human Immunodeficiency Virus type 1 Reverse Transcriptase (HIV-1 RT) in the treatment of AIDS. Reverse Transcriptase inhibitors (RTIs) have limitations due to the development of Reverse Transcriptase mutations that lead to treatment resistance. In this study, a combination of statistical analysis and bioinformatics tools was adopted to develop a mathematical model that relates the structure of compounds to their inhibitory activities against HIV-1 Reverse Transcriptase. Our approach was based on a series of compounds recognized for their HIV-1 RT enzymatic inhibitory activities. These compounds were designed via software, with their descriptors computed using multiple tools. The most statistically promising model was chosen, and its domain of application was ascertained. Furthermore, compounds exhibiting comparable biological activity to existing drugs were identified as potential inhibitors of HIV-1 RT. The compounds underwent evaluation based on their chemical absorption, distribution, metabolism, excretion, toxicity properties, and adherence to Lipinski's rule. Molecular docking techniques were employed to examine the interaction between the Reverse Transcriptase (Wild Type and Mutant Type) and the ligands, including a known drug available in the market. Molecular dynamics simulations were also conducted to assess the stability of the RT-ligand complexes. Our results reveal some of the new compounds as promising candidates for effectively inhibiting HIV-1 Reverse Transcriptase, matching the potency of the established drug. This necessitates further experimental validation. This study, beyond its immediate results, provides a methodological foundation for future endeavors aiming to discover and design new inhibitors targeting HIV-1 Reverse Transcriptase.Keywords: QSAR, ADMET properties, molecular docking, molecular dynamics simulation, reverse transcriptase inhibitors, HIV type 1
Procedia PDF Downloads 842096 Computational Prediction of the Effect of S477N Mutation on the RBD Binding Affinity and Structural Characteristic, A Molecular Dynamics Study
Authors: Mohammad Hossein Modarressi, Mozhgan Mondeali, Khabat Barkhordari, Ali Etemadi
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The COVID-19 pandemic, caused by SARS-CoV-2, has led to significant concerns worldwide due to its catastrophic effects on public health. The SARS-CoV-2 infection is initiated with the binding of the receptor-binding domain (RBD) in its spike protein to the ACE2 receptor in the host cell membrane. Due to the error-prone entity of the viral RNA-dependent polymerase complex, the virus genome, including the coding region for the RBD, acquires new mutations, leading to the appearance of multiple variants. These variants can potentially impact transmission, virulence, antigenicity and evasive immune properties. S477N mutation located in the RBD has been observed in the SARS-CoV-2 omicron (B.1.1. 529) variant. In this study, we investigated the consequences of S477N mutation at the molecular level using computational approaches such as molecular dynamics simulation, protein-protein interaction analysis, immunoinformatics and free energy computation. We showed that displacement of Ser with Asn increases the stability of the spike protein and its affinity to ACE2 and thus increases the transmission potential of the virus. This mutation changes the folding and secondary structure of the spike protein. Also, it reduces antibody neutralization, raising concern about re-infection, vaccine breakthrough and therapeutic values.Keywords: S477N, COVID-19, molecular dynamic, SARS-COV2 mutations
Procedia PDF Downloads 1662095 Energy Efficient Autonomous Lower Limb Exoskeleton for Human Motion Enhancement
Authors: Nazim Mir-Nasiri, Hudyjaya Siswoyo Jo
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The paper describes conceptual design, control strategies, and partial simulation for a new fully autonomous lower limb wearable exoskeleton system for human motion enhancement that can support its weight and increase strength and endurance. Various problems still remain to be solved where the most important is the creation of a power and cost efficient system that will allow an exoskeleton to operate for extended period without batteries being frequently recharged. The designed exoskeleton is enabling to decouple the weight/mass carrying function of the system from the forward motion function which reduces the power and size of propulsion motors and thus the overall weight, cost of the system. The decoupling takes place by blocking the motion at knee joint by placing passive air cylinder across the joint. The cylinder is actuated when the knee angle has reached the minimum allowed value to bend. The value of the minimum bending angle depends on usual walk style of the subject. The mechanism of the exoskeleton features a seat to rest the subject’s body weight at the moment of blocking the knee joint motion. The mechanical structure of each leg has six degrees of freedom: four at the hip, one at the knee, and one at the ankle. Exoskeleton legs are attached to subject legs by using flexible cuffs. The operation of all actuators depends on the amount of pressure felt by the feet pressure sensors and knee angle sensor. The sensor readings depend on actual posture of the subject and can be classified in three distinct cases: subject stands on one leg, subject stands still on both legs and subject stands on both legs but transit its weight from one leg to other. This exoskeleton is power efficient because electrical motors are smaller in size and did not participate in supporting the weight like in all other existing exoskeleton designs.Keywords: energy efficient system, exoskeleton, motion enhancement, robotics
Procedia PDF Downloads 3642094 Preparation and Study of Pluronic F127 Monolayers at Air-Water Interface
Authors: Neha Kanodia, M. Kamil
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Properties of mono layers of Pluronic F127 at air/water interface have been investigated by using Langmuir trough method. Pluronic F127 is a triblock copolymer of poly (ethyleneoxide) (PEO groups)– poly (propylene oxide) (PO groups)–poly(ethylene oxide) (PEO groups). Surface pressure versus mean molecular area isotherms is studied. The isotherm of the mono layer showed the characteristics of a pancake-to-brush transition upon compression of the mono layer. The effect of adding surfactant (SDS) to polymer and the effect of increasing loading on polymer was also studied. The effect of repeated compression and expansion cycle (or hysteresis curve) is investigated to know about stability of the film formed. Static elasticity of mono layer gives information about molecular arrangement, phase structure and phase transition.Keywords: surface-pressure, mean molecular area isotherms, hysteresis, static elasticity
Procedia PDF Downloads 4432093 Cannabis Sativa L as Natural Source of Promising Anti-Alzheimer Drug Candidates: A Comprehensive Computational Approach Including Molecular Docking, Molecular Dynamics, ADMET and MM-PBSA Studies
Authors: Hassan Nour, Nouh Mounadi, Oussama Abchir, Belaidi Salah, Samir Chtita
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Cholinesterase enzymes are biological catalysts essential for the transformation of acetylcholine, which is a neurotransmitter implicated in memory and learning, into acetic acid and choline, altering the neurotransmission process in Alzheimer’s disease patients. Therefore, inhibition of cholinesterase enzymes is a relevant strategy for the symptomatic treatment of Alzheimer’s disease. The current investigation aims to explore potential cholinesterase (ChE) inhibitors through a comprehensive computational approach. Forty-nine phytoconstituents extracted from Cannabis sativa L. were in-silico screened using molecular docking and pharmacokinetic and toxicological analysis to evaluate their possible inhibitory effect on the cholinesterase enzymes. Two phytoconstituents belonging to cannabinoid derivatives were revealed to be promising candidates for Alzheimer's therapy by acting as cholinesterase inhibitors. They have exhibited high binding affinities towards the cholinesterase enzymes and showed their ability to interact with key residues involved in cholinesterase enzymatic activity. In addition, they presented good ADMET profiles allowing them to be promising oral drug candidates. Furthermore, molecular dynamics (MD) simulations were executed to explore their interaction stability under mimetic biological conditions and thus support our findings. To corroborate the docking results, the binding free energy corresponding to the more stable ligand-ChE complexes was re-estimated by applying the MM-PBSA method. MD and MM-PBSA studies affirmed that the ligand-ChE recognition is a spontaneous reaction leading to stable complexes. The conducted investigations have led to great findings that would strongly guide the pharmaceutical industries toward the rational development of potent anti-Alzheimer agents.Keywords: Alzheimer’s disease, molecular docking, Cannabis sativa L., cholinesterase inhibitors, molecular dynamics, ADMET, MM-PBSA
Procedia PDF Downloads 742092 Robust Control of Traction Motors based Electric Vehicles by Means of High-Gain
Authors: H. Mekki, A. Djerioui, S. Zeghlache, L. Chrifi-Alaoui
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Induction motor (IM)Induction motor (IM) are nowadays widely used in industrial applications specially in electric vehicles (EVs) and traction locomotives, due to their high efficiency high speed and lifetime. However, since EV motors are easily influenced by un-certainties parameter variations and external load disturbance, both robust control techniques have received considerable attention during the past few decades. This paper present a robust controller design based sliding mode control (SMC) and high gain flux observer (HGO) for induction motor (IM) based Electric Vehicles (EV) drives. This control technique is obtained by the combination between the field oriented and the sliding mode control strategy and present remarkable dynamic performances just as a good robustness with respect to EV drives load torque. A high gain flux observer is also presented and associated in order to design sensorless control by estimating the rotor flux only using measurements of the stator voltages and currents. Simulations results are provided to evaluate the consistency and to show the effectiveness of the proposed SMC strategy also the performance of the HGO for Electric Vehicles system are nowadays widely used in industrial applications specially in electric vehicles (EVs) and traction locomotives, due to their high efficiency high speed and lifetime. However, since EV motors are easily influenced by un-certainties parameter variations and external load disturbance, both robust control techniques have received considerable attention during the past few decades. This paper present a robust controller design based sliding mode control (SMC) and high gain flux observer (HGO) for induction motor (IM) based Electric Vehicles (EV) drives. This control technique is obtained by the combination between the field oriented and the sliding mode control strategy and present remarkable dynamic performances just as a good robustness with respect to EV drives load torque. A high gain flux observer is also presented and associated in order to design sensorless control by estimating the rotor flux only using measurements of the stator voltages and currents. Simulations results are provided to evaluate the consistency and to show the effectiveness of the proposed SMC strategy also the performance of the HGO for Electric Vehicles system.Keywords: electric vehicles, sliding mode control, induction motor drive, high gain observer
Procedia PDF Downloads 692091 Computational Analysis of Potential Inhibitors Selected Based on Structural Similarity for the Src SH2 Domain
Authors: W. P. Hu, J. V. Kumar, Jeffrey J. P. Tsai
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The inhibition of SH2 domain regulated protein-protein interactions is an attractive target for developing an effective chemotherapeutic approach in the treatment of disease. Molecular simulation is a useful tool for developing new drugs and for studying molecular recognition. In this study, we searched potential drug compounds for the inhibition of SH2 domain by performing structural similarity search in PubChem Compound Database. A total of 37 compounds were screened from the database, and then we used the LibDock docking program to evaluate the inhibition effect. The best three compounds (AP22408, CID 71463546 and CID 9917321) were chosen for MD simulations after the LibDock docking. Our results show that the compound CID 9917321 can produce a more stable protein-ligand complex compared to other two currently known inhibitors of Src SH2 domain. The compound CID 9917321 may be useful for the inhibition of SH2 domain based on these computational results. Subsequently experiments are needed to verify the effect of compound CID 9917321 on the SH2 domain in the future studies.Keywords: nonpeptide inhibitor, Src SH2 domain, LibDock, molecular dynamics simulation
Procedia PDF Downloads 2622090 VHL, PBRM1, and SETD2 Genes in Kidney Cancer: A Molecular Investigation
Authors: Rozhgar A. Khailany, Mehri Igci, Emine Bayraktar, Sakip Erturhan, Metin Karakok, Ahmet Arslan
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Kidney cancer is the most lethal urological cancer accounting for 3% of adult malignancies. VHL, a tumor-suppressor gene, is best known to be associated with renal cell carcinoma (RCC). The VHL functions as negative regulator of hypoxia inducible factors. Recent sequencing efforts have identified several novel frequent mutations of histone modifying and chromatin remodeling genes in ccRCC (clear cell RCC) including PBRM1 and SETD2. The PBRM1 gene encodes the BAF180 protein, which involved in transcriptional activation and repression of selected genes. SETD2 encodes a histone methyltransferase, which may play a role in suppressing tumor development. In this study, RNAs of 30 paired tumor and normal samples that were grouped according to the types of kidney cancer and clinical characteristics of patients, including gender and average age were examined by RT-PCR, SSCP and sequencing techniques. VHL, PBRM1 and SETD2 expressions were relatively down-regulated. However, statistically no significance was found (Wilcoxon signed rank test, p > 0.05). Interestingly, no mutation was observed on the contrary of previous studies. Understanding the molecular mechanisms involved in the pathogenesis of RCC has aided the development of molecular-targeted drugs for kidney cancer. Further analysis is required to identify the responsible genes rather than VHL, PBRM1 and SETD2 in kidney cancer.Keywords: kidney cancer, molecular biomarker, expression analysis, mutation screening
Procedia PDF Downloads 4502089 Molecular Modeling a Tool for Postulating the Mechanism of Drug Interaction: Glimepiride Alters the Pharmacokinetics of Sildenafil Citrate in Diabetic Nephropathy Animals
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
Procedia PDF Downloads 3692088 Prevalence of Breast Cancer Molecular Subtypes at a Tertiary Cancer Institute
Authors: Nahush Modak, Meena Pangarkar, Anand Pathak, Ankita Tamhane
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Background: Breast cancer is the prominent cause of cancer and mortality among women. This study was done to show the statistical analysis of a cohort of over 250 patients detected with breast cancer diagnosed by oncologists using Immunohistochemistry (IHC). IHC was performed by using ER; PR; HER2; Ki-67 antibodies. Materials and methods: Formalin fixed Paraffin embedded tissue samples were obtained by surgical manner and standard protocol was followed for fixation, grossing, tissue processing, embedding, cutting and IHC. The Ventana Benchmark XT machine was used for automated IHC of the samples. Antibodies used were supplied by F. Hoffmann-La Roche Ltd. Statistical analysis was performed by using SPSS for windows. Statistical tests performed were chi-squared test and Correlation tests with p<.01. The raw data was collected and provided by National Cancer Insitute, Jamtha, India. Result: Luminal B was the most prevailing molecular subtype of Breast cancer at our institute. Chi squared test of homogeneity was performed to find equality in distribution and Luminal B was the most prevalent molecular subtype. The worse prognostic indicator for breast cancer depends upon expression of Ki-67 and her2 protein in cancerous cells. Our study was done at p <.01 and significant dependence was observed. There exists no dependence of age on molecular subtype of breast cancer. Similarly, age is an independent variable while considering Ki-67 expression. Chi square test performed on Human epidermal growth factor receptor 2 (HER2) statuses of patients and strong dependence was observed in percentage of Ki-67 expression and Her2 (+/-) character which shows that, value of Ki depends upon Her2 expression in cancerous cells (p<.01). Surprisingly, dependence was observed in case of Ki-67 and Pr, at p <.01. This shows that Progesterone receptor proteins (PR) are over-expressed when there is an elevation in expression of Ki-67 protein. Conclusion: We conclude from that Luminal B is the most prevalent molecular subtype at National Cancer Institute, Jamtha, India. There was found no significant correlation between age and Ki-67 expression in any molecular subtype. And no dependence or correlation exists between patients’ age and molecular subtype. We also found that, when the diagnosis is Luminal A, out of the cohort of 257 patients, no patient shows >14% Ki-67 value. Statistically, extremely significant values were observed for dependence of PR+Her2- and PR-Her2+ scores on Ki-67 expression. (p<.01). Her2 is an important prognostic factor in breast cancer. Chi squared test for Her2 and Ki-67 shows that the expression of Ki depends upon Her2 statuses. Moreover, Ki-67 cannot be used as a standalone prognostic factor for determining breast cancer.Keywords: breast cancer molecular subtypes , correlation, immunohistochemistry, Ki-67 and HR, statistical analysis
Procedia PDF Downloads 1172087 Molecular Basis for Amyloid Inhibition by L-Dopa: Implication towards Systemic Amyloidosis
Authors: Rizwan H. Khan, Saima Nusrat
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Despite the fact that amyloid associated neurodegenerative diseases and non-neuropathic systemic amyloidosis have allured the research endeavors, as no curative drugs have been proclaimed up till now except for symptomatic cure. Therapeutic compounds which can diminish or disaggregate such toxic oligomers and fibrillar species have been examined and more are on its way. In the present study, we had reported an extensive biophysical, microscopic and computational study, revealing that L-3, 4-dihydroxyphenylalanine (L-Dopa) possess undeniable potency to inhibit heat induced human lysozyme (HL) amyloid fibrillation and also retain the fibril disaggregating potential. L-Dopa interferes in the amyloid fibrillogenesis process by interacting hydrophobically and also by forming hydrogen bonds with the amino acid residues found in amyloid fibril forming prone region of HL as elucidated by molecular docking results. L-Dopa also disaggregates the mature amyloid fibrils into some unorganised species. Thus, L-Dopa and related compounds can work as a promising inhibitor for the therapeutic advancement prospective against systemic amyloidosis.Keywords: amyloids, disaggregation, human lysozyme, molecular docking
Procedia PDF Downloads 3202086 Some Conjectures and Programs about Computing the Detour Index of Molecular Graphs of Nanotubes
Authors: Shokofeh Ebrtahimi
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Let G be the chemical graph of a molecule. The matrix D = [dij ] is called the detour matrix of G, if dij is the length of longest path between atoms i and j. The sum of all entries above the main diagonal of D is called the detour index of G.Chemical graph theory is the topology branch of mathematical chemistry which applies graph theory to mathematical modelling of chemical phenomena.[1] The pioneers of the chemical graph theory are Alexandru Balaban, Ante Graovac, Ivan Gutman, Haruo Hosoya, Milan Randić and Nenad TrinajstićLet G be the chemical graph of a molecule. The matrix D = [dij ] is called the detour matrix of G, if dij is the length of longest path between atoms i and j. The sum of all entries above the main diagonal of D is called the detour index of G. In this paper, a new program for computing the detour index of molecular graphs of nanotubes by heptagons is determineded. Some Conjectures about detour index of Molecular graphs of nanotubes is included.Keywords: chemical graph, detour matrix, Detour index, carbon nanotube
Procedia PDF Downloads 2842085 Spectroscopic, Molecular Structure and Electrostatic Potential, Polarizability, Hyperpolarizability, and HOMO–LUMO Analysis of Monomeric and Dimeric Structures of N-(2-Methylphenyl)-2-Nitrobenzenesulfonamide
Authors: A. Didaoui, N. Benhalima, M. Elkeurti, A. Chouaih, F. Hamzaoui
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The monomer and dimer structures of the title molecule have been obtained from density functional theory (DFT) B3LYP method with 6-31G (d,p) as basis set calculations. The optimized geometrical parameters obtained by B3LYP/6-31G (d,p) method show good agreement with xperimental X-ray data. The polarizability and first order hyperpolarizabilty of the title molecule were calculated and interpreted. the intermolecular N–H•••O hydrogen bonds are discussed in dimer structure of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 03 set of quantum chemistry codes. The predicted frontier molecular orbital energies at B3LYP/6-31G(d,p) method set show that charge transfer occurs within the molecule. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the total static hyperpolarizability. The results also show that N-(2-Methylphenyl)-2-nitrobenzenesulfonamide molecule may have nonlinear optical (NLO) comportment with non-zero values.Keywords: DFT, Gaussian 03, NLO, N-(2-Methylphenyl)-2-nitrobenzenesulfonamide
Procedia PDF Downloads 5422084 The Spectroscopic, Molecular Structure and Electrostatic Potential, Polarizability Hyperpolarizability, and Homo–Lumo Analysis of Monomeric and Dimeric Structures of 2-Chloro-N-(2 Methylphenyl) Benzamide
Authors: N. Khelloul, N. Benhalima, A. Chouaih, F. Hamzaoui
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The monomer and dimer structures of the title molecule have been obtained from density functional theory (DFT) B3LYP method with 6-31G (d,p) as basis set calculations. The optimized geometrical parameters obtained by B3LYP/6-31G (d,p) method shows good agreement with experimental X-ray data. The polarizability and first order hyperpolarizabilty of the title molecule were calculated and interpreted. The intermolecular N–H•••O hydrogen bonds are discussed in dimer structure of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 09 set of quantum chemistry codes. The predicted frontier molecular orbital energies at B3LYP/6-31G(d,p) method set show that charge transfer occurs within the molecule. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the total static hyperpolarizability. The results also show that 2-Chloro-N-(2-methylphenyl) benzamide 2 molecule may have nonlinear optical (NLO) comportment with non-zero values.Keywords: DFT, HOMO, LUMO, NLO
Procedia PDF Downloads 3342083 Analysis of Non-Coding Genome in Streptococcus pneumoniae for Molecular Epidemiology Typing
Authors: Martynova Alina, Lyubov Buzoleva
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Streptococcus pneumoniae is the causative agent of pneumonias and meningitids throught all the world. Having high genetic diversity, this microorganism can cause different clinical forms of pneumococcal infections and microbiologically it is really difficult diagnosed by routine methods. Also, epidemiological surveillance requires more developed methods of molecular typing because the recent method of serotyping doesn't allow to distinguish invasive and non-invasive isolates properly. Non-coding genome of bacteria seems to be the interesting source for seeking of highly distinguishable markers to discriminate the subspecies of such a variable bacteria as Streptococcus pneumoniae. Technically, we proposed scheme of discrimination of S.pneumoniae strains with amplification of non-coding region (SP_1932) with the following restriction with 2 types of enzymes of Alu1 and Mn1. Aim: This research aimed to compare different methods of typing and their application for molecular epidemiology purposes. Methods: we analyzed population of 100 strains of S.pneumoniae isolated from different patients by different molecular epidemiology methods such as pulse-field gel electophoresis (PFGE), restriction polymorphism analysis (RFLP) and multilolocus sequence typing (MLST), and all of them were compared with classic typing method as serotyping. The discriminative power was estimated with Simpson Index (SI). Results: We revealed that the most discriminative typing method is RFLP (SI=0,97, there were distinguished 42 genotypes).PFGE was slightly less discriminative (SI=0,95, we identified 35 genotypes). MLST is still the best reference method (SI=1.0). Classic method of serotyping showed quite weak discriminative power (SI=0,93, 24 genotypes). In addition, sensivity of RFLP was 100%, specificity was 97,09%. Conclusion: the most appropriate method for routine epidemiology surveillance is RFLP with non-coding region of Streptococcsu pneumoniae, then PFGE, though in some cases these results should be obligatory confirmed by MLST.Keywords: molecular epidemiology typing, non-coding genome, Streptococcus pneumoniae, MLST
Procedia PDF Downloads 3912082 Comparison of Physicochemical Properties of DNA-Ionic Liquids Complexes
Authors: Ewelina Nowak, Anna Wisla-Swider, Gohar Khachatryan, Krzysztof Danel
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Complexes of ionic liquids with different heterocyclic-rings were synthesized by ion exchange reactions with pure salmon DNA. Ionic liquids (ILs) like 1-hexyl-3-methylimidazolium chloride, 1-butyl-4-methylpyridinium chloride and 1-ethyl-1-methylpyrrolidinium bromide were used. The ILs were built into helical state and confirmed by IR spectrometric techniques. Patterns of UV-Vis, photoluminescence, IR, and CD spectra indicated inclusion of small molecules into DNA structure. Molecular weight and radii of gyrations values of ILs-DNA complexes chains were established by HPSEC–MALLS–RI method. Modification DNA with 1-ethyl-1-methylpyrrolidinium bromide gives more uniform material and leads to elimination of high molecular weight chains. Thus, the incorporation DNA double helical structure with both 1-hexyl-3-methylimidazolium chloride and 1-butyl-4-methylpyridinium chloride exhibited higher molecular weight values. Scanning electron microscopy images indicate formation of nanofibre structures in all DNA complexes. Fluorescence depends strongly on the environment in which the chromophores are inserted and simultaneously on the molecular interactions with the biopolymer matrix. The most intensive emission was observed for DNA-imidazole ring complex. Decrease in intensity UV-Vis peak absorption is a consequence of a reduction in the spatial order of polynucleotide strands and provides different π–π stacking structure. Changes in optical properties confirmed by spectroscopy methods make DNA-ILs complexes potential biosensor applications.Keywords: biopolymers, biosensors, cationic surfactant, DNA, DNA-gels
Procedia PDF Downloads 1782081 Understanding Inhibitory Mechanism of the Selective Inhibitors of Cdk5/p25 Complex by Molecular Modeling Studies
Authors: Amir Zeb, Shailima Rampogu, Minky Son, Ayoung Baek, Sang H. Yoon, Keun W. Lee
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Neurotoxic insults activate calpain, which in turn produces truncated p25 from p35. p25 forms hyperactivated Cdk5/p25 complex, and thereby induces severe neuropathological aberrations including hyperphosphorylated tau, neuroinflammation, apoptosis, and neuronal death. Inhibition of Cdk5/p25 complex alleviates aberrant phosphorylation of tau to mitigate AD pathology. PHA-793887 and Roscovitine have been investigated as selective inhibitors of Cdk5/p25 with IC50 values 5nM and 160nM, respectively, but their mechanistic studies remain unknown. Herein, computational simulations have explored the binding mode and interaction mechanism of PHA-793887 and Roscovitine with Cdk5/p25. Docking results suggested that PHA-793887 and Rsocovitine have occupied the ATP-binding site of Cdk5 and obtained highest docking (GOLD) score of 66.54 and 84.03, respectively. Furthermore, molecular dynamics (MD) simulation demonstrated that PHA-793887 and Roscovitine established stable RMSD of 1.09 Å and 1.48 Å with Cdk5/p25, respectively. Profiling of polar interactions suggested that each inhibitor formed hydrogen bonds (H-bond) with catalytic residues of Cdk5 and could remain stable throughout the molecular dynamics simulation. Additionally, binding free energy calculation by molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA) suggested that PHA-793887 and Roscovitine had lowest binding free energies of -150.05 kJ/mol and -113.14 kJ/mol, respectively with Cdk5/p25. Free energy decomposition demonstrated that polar energy by H-bond between the Glu81 of Cdk5 and PHA-793887 is the essential factor to make PHA-793887 highly selective towards Cdk5/p25. Overall, this study provided substantial evidences to explore mechanistic interactions of the selective inhibitors of Cdk5/p25 and could be used as fundamental considerations in the development of structure-based selective inhibitors of Cdk5/p25.Keywords: Cdk5/p25 inhibition, molecular modeling of Cdk5/p25, PHA-793887 and roscovitine, selective inhibition of Cdk5/p25
Procedia PDF Downloads 1372080 Binding Studies of Complexes of Anticancer Drugs with DNA and Enzymes Involved in DNA Replication Using Molecular Docking and Cell Culture Techniques
Authors: Fouzia Perveen, Rumana Qureshi
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The presently studied twelve anticancer drugs are the cytotoxic agents which inhibit the replication of DNA and activity of enzymes involved in DNA replication namely topoisomerase-II, polymerase and helicase and have shown remarkable anticancer activity in clinical trials. In this study, we performed molecular docking studies of twelve antitumor drugs against DNA and DNA enzymes in the presence and absence of ascorbic acid (AA) and developed the quantitative structure-activity relationship (QSAR) model for anticancer activity screening. A number of electronic and steric descriptors were calculated using MOE software package. QSAR was established showing a correlation of binding strength with various physicochemical descriptors. Out of these twelve, eight cytotoxic drugs were tested on Non-Small Cell Lung Cancer cell lines (H-157 and H-1299) in the absence and presence of ascorbic acid and experimental IC50 values were calculated. From the docking studies, binding constants were calculated indicating the strength of drug-DNA and drug-enzyme complex formation and it was correlated to the IC50 values (both experimental and theoretical). These results can offer useful references for directing the molecular design of DNA enzyme inhibitor with improved anticancer activity.Keywords: ascorbic acid, binding constant, cytotoxic agents, cell culture, DNA, DNA enzymes, molecular docking
Procedia PDF Downloads 4192079 Aerodynamic Interference of Propellers Group with Adjustable Mutual Position
Authors: Michal Biały, Krzysztof Skiba, Zdzislaw Kaminski
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The research results of the influence of the adjustable mutual position of the propellers for getting optimal lift force on a specially designed bench. The bench consists of frame with electric motors and with attached propellers. Engines were arranged in a matrix of two columns and three rows. The distance between the columns averages from 0 to 20”, while the engine was placed at a height of 8”, 15.5” and 23.6”. By adjusting the tilt of an electric motor, an angle of the propeller in the range of 0° to 60°, by 15° was controlled. Propellers with a diameter of 8" and pitch of 4.5” were driven by brushless model engines Roxxy BL-Outrunner 2827/26 with a power of 110W (each). Rotational speed control of electric motors were realized parallel for all propellers. The speed adjustment was realized using an aggregate of radio-controlled regulators. Electric power supplied to the engines from zero to maximum power, by the setting for every 14W, was controlled by radio system. Measurement system was placed on a laboratory scale. The lift was measured and recorded by an electronic scale. The lift force for different configurations of propellers arrangement was recorded during the test. All propellers were driven in one rotational direction and in different directions when they were in the same pairs. Propellers were driven concurrently and contra-concurrently along one of the columns and along the selected rows. During the tests, except the lift, parameters such as: rotational speed of propellers, voltage and current to the electric engines were recorded. The main aim of the research was to show the influence of aerodynamic interference between the propellers to receive lift force depending on the drive configuration of individual propellers. The research has shown that, this interference exists. The increase of the lift force for a distance between columns above 26.6” was noticed during the driving propellers in different directions. The optimum tilt angle of the propeller was 45°. Furthermore there has been also approx. 12% increase of the lift for propellers driven alternately in column and contra-concurrently in relation to the contra-rotating drive in the row.Keywords: aerodynamic, interference, lift force, propeller, propulsion system
Procedia PDF Downloads 3392078 Polysaccharides as Pour Point Depressants
Authors: Ali M. EL-Soll
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Physical properties of Sarir waxy crude oil was investigated, pour-point was determined using ASTM D-79 procedure, paraffin content and carbon number distribution of the paraffin was determined using gas liquid Chromatography(GLC), polymeric additives were prepared and their structures were confirmed using IR spectrophotometer. The molecular weight and molecular weigh distribution of these additives were determined by gel permeation chromatography (GPC). the performance of the synthesized additives as pour-point depressants was evaluated, for the mentioned crude oil.Keywords: sarir, waxy, crude, pour point, depressants
Procedia PDF Downloads 4482077 The Spectroscopic, Molecular Structure and Electrostatic Potential, Polarizability, Hyperpolarizability, and HOMO–LUMO Analysis of Monomeric and Dimeric Structures of N-(2-Methylphenyl)-2-Nitrobenzenesulfonamide
Authors: A. Didaoui, N. Benhalima, M. Elkeurti, A. Chouaih, F. Hamzaoui
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The monomer and dimer structures of the title molecule have been obtained from density functional theory (DFT) B3LYP method with 6-31G(d,p) as basis set calculations. The optimized geometrical parameters obtained by B3LYP/6-31G(d,p) method show good agreement with experimental X-ray data. The polarizability and first order hyperpolarizability of the title molecule were calculated and interpreted. The intermolecular N–H•••O hydrogen bonds are discussed in dimer structure of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 03 set of quantum chemistry codes. The predicted frontier molecular orbital energies at B3LYP/6-31G(d,p) method set show that charge transfer occurs within the molecule. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the total static hyperpolarizability. The results also show that N-(2-Methylphenyl)-2-nitrobenzenesulfonamide molecule may have nonlinear optical (NLO) comportment with non-zero values.Keywords: DFT, Gaussian 03, NLO, N-(2-Methylphenyl)-2-nitrobenzenesulfonamide, polarizability
Procedia PDF Downloads 3172076 Education-based, Graphical User Interface Design for Analyzing Phase Winding Inter-Turn Faults in Permanent Magnet Synchronous Motors
Authors: Emir Alaca, Hasbi Apaydin, Rohullah Rahmatullah, Necibe Fusun Oyman Serteller
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In recent years, Permanent Magnet Synchronous Motors (PMSMs) have found extensive applications in various industrial sectors, including electric vehicles, wind turbines, and robotics, due to their high performance and low losses. Accurate mathematical modeling of PMSMs is crucial for advanced studies in electric machines. To enhance the effectiveness of graduate-level education, incorporating virtual or real experiments becomes essential to reinforce acquired knowledge. Virtual laboratories have gained popularity as cost-effective alternatives to physical testing, mitigating the risks associated with electrical machine experiments. This study presents a MATLAB-based Graphical User Interface (GUI) for PMSMs. The GUI offers a visual interface that allows users to observe variations in motor outputs corresponding to different input parameters. It enables users to explore healthy motor conditions and the effects of short-circuit faults in the one-phase winding. Additionally, the interface includes menus through which users can access equivalent circuits related to the motor and gain hands-on experience with the mathematical equations used in synchronous motor calculations. The primary objective of this paper is to enhance the learning experience of graduate and doctoral students by providing a GUI-based approach in laboratory studies. This interactive platform empowers students to examine and analyze motor outputs by manipulating input parameters, facilitating a deeper understanding of PMSM operation and control.Keywords: magnet synchronous motor, mathematical modelling, education tools, winding inter-turn fault
Procedia PDF Downloads 462075 Quantitative Structure-Activity Relationship Analysis of Binding Affinity of a Series of Anti-Prion Compounds to Human Prion Protein
Authors: Strahinja Kovačević, Sanja Podunavac-Kuzmanović, Lidija Jevrić, Milica Karadžić
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The present study is based on the quantitative structure-activity relationship (QSAR) analysis of eighteen compounds with anti-prion activity. The structures and anti-prion activities (expressed in response units, RU%) of the analyzed compounds are taken from CHEMBL database. In the first step of analysis 85 molecular descriptors were calculated and based on them the hierarchical cluster analysis (HCA) and principal component analysis (PCA) were carried out in order to detect potential significant similarities or dissimilarities among the studied compounds. The calculated molecular descriptors were physicochemical, lipophilicity and ADMET (absorption, distribution, metabolism, excretion and toxicity) descriptors. The first stage of the QSAR analysis was simple linear regression modeling. It resulted in one acceptable model that correlates Henry's law constant with RU% units. The obtained 2D-QSAR model was validated by cross-validation as an internal validation method. The validation procedure confirmed the model’s quality and therefore it can be used for prediction of anti-prion activity. The next stage of the analysis of anti-prion activity will include 3D-QSAR and molecular docking approaches in order to select the most promising compounds in treatment of prion diseases. These results are the part of the project No. 114-451-268/2016-02 financially supported by the Provincial Secretariat for Science and Technological Development of AP Vojvodina.Keywords: anti-prion activity, chemometrics, molecular modeling, QSAR
Procedia PDF Downloads 2952074 Molecular Characterization of Ardi Goat Assisted by Microsatellite Markers
Authors: M. F. Elzarei, A. M. Alseaf
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Hundred uncorrelated animal and thirty six markers were used in this study to study the molecular characterization of Saudi native Ardi goat (BM18189, ILSTS030, INRA005, OarFCB48, BM2113, ILSTS033, INRA023, RM088, CSRD247, ILSTS034, INRA063, SRCRSP1, ILSTS002, ILSTS044, INRA172, SRCRSP5, ILSTS005, ILSTS049, MAF70, SRCRSP8, ILSTS011, ILSTS058, OarAE54, SRCRSP9, ILSTS019, ILSTS059, OARCP34, TGLA53, ILSTS022, ILSTS082, OARE129, TGLA73, ILSTS029, ILSTS087, OARE193, and RM004). Ardi goat showed high variability. The mean number of alleles per locus ranged from 5 in SRCRSP1 locus to 13.5 in CSRD247 locus. Gene diversities varied within a wide range, from 0.53 in ILSTS002 locus to 0.86 in RM088 locus. Hardy-Weinberg equilibrium was tested in order to evaluate the significance of inbreeding occurring in each locus in Ardi population. Only SRCRSP9, INRA005, ILSTS030 loci showed significance in this way.Keywords: molecular characterization, microsatellite markers, Ardi goats, Hardy-Weinberg equilibrium
Procedia PDF Downloads 3242073 Evaluation of Hydrocarbons in Tissues of Bivalve Mollusks from the Red Sea Coast
Authors: Asma Ahmed Aljohani, Mohammed Orif
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The concentration of polycyclic aromatic hydrocarbons (PAH) in clam (A. glabrata) was examined in samples collected from Alseef Beach, 30 km south of Jeddah city. Gas chromatography-mass spectrometry (GC-MS) was used to analyse the 14 PAHs. The concentration of total PAHs was found to range from 11.521 to 40.149 ng/gdw with a mean concentration of 21.857 ng/gdw, which is lower compared to similar studies. The lower molecular weight PAHs with three rings comprised 18.14% of the total PAH concentrations in the clams, while the high molecular weight PAHs with four rings, five rings, and six rings account for 81.86%. Diagnostic ratios for PAH source distinction suggested pyrogenic or anthropogenic sources.Keywords: bivalves, biomonitoring, hydrocarbons, PAHs
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