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Open Access Article
1 - The Molecular Docking and Molecular Dynamics Simulation of Some HIV-1 protease Inhibitors For the treatment of Coronavirus Disease-19
ghasem ghasemi babak motahary robabe Sayadikordabadi Asghar Alizadehdakhel -
Open Access Article
2 - Molecular dynamics simulation of interaction of Melittin and DMPC bilayer: Temperature dependence
F. Kaveh H. Pasdar -
Open Access Article
3 - Gyration Radius and Energy Study at Different Temperatures for Acetylcholine Receptor Protein in Gas Phase by Monte Carlo, Molecular and Langevin Dynamics Simulations
M. Monajjemi A. R. Oliaey -
Open Access Article
4 - Modifications of Internal Molecular Structures of Asphalt Components Due to Physical Aging
Iffat R. Arisa -
Open Access Article
5 - QSAR studies, docking and molecular dynamics simulation of a number of heterocyclic compounds including nitrogen oxide as new anti-tuberculosis agents
Ghasem Ghasemi Babak Motahary Robabe SayadikordAbadiObjectiv: Mycobacterium tuberculosis (Mtb), is agent of tuberculosis. A series of novel N‑Oxide-Containing Heterocycles have been reported as selective Mycobacterium tuberculosis inhibitors. QSAR, Docking, and Molecular Dynamics Simulation studies were investigated.Mate MoreObjectiv: Mycobacterium tuberculosis (Mtb), is agent of tuberculosis. A series of novel N‑Oxide-Containing Heterocycles have been reported as selective Mycobacterium tuberculosis inhibitors. QSAR, Docking, and Molecular Dynamics Simulation studies were investigated.Materials and Methods: Imperialist Competitive Algorithm (ICA), Partial least squares (PLS), Principle Component Regression (PCR), Least Absolute Shrinkage, Selection Operator (LASSO), and Monte-Carlo simulation were used to create QSAR models. The molecular docking and molecular dynamics simulation were carried out on Mycobacterium tuberculosis (Mtb) strain H37Rv (PDB: 4XGQ).Findings: Atomic masses, atomic sanderson electronegativities, Ghose–Viswanadhan-Wendoloski antiinfective-like index and Ghose –Viswanadhan-Wendoloski hyptonic-like index were important in our study. The SMILES files have been used with coralsea software. The root-mean square errors of the training set, and the test set for ICA model, were 0.2970, 0.1395 respectively. The results of the Monte-Carlo method were the following: n=7, R²=0.9931, Q²=0.9857, MAE=0.039 (Training set); n=6, R²=0.9413, Q²=0.9107, MAE=0.367 (Test set).Conclusion: Molecules 10 and 11 were presented as the most stable ones that may be introduced for further investigations, including clinical experiments. Manuscript profile -
Open Access Article
6 - A DFT and Molecular Dynamics Study on Inhibitory Action of Three Amine Derivatives on Corrosion of Carbon Steel
Mohammad Hossein Ghorbani Maryam Dehdab -
Open Access Article
7 - Temperature Effect on Mechanical Properties of Top Neck Mollusk Shells Nano-Composite by Molecular Dynamics Simulations and Nano-Indentation Experiments
A Nouroozi Masir A Darvizeh A Zajkani -
Open Access Article
8 - Influences of Small-Scale Effect and Boundary Conditions on the Free Vibration of Nano-Plates: A Molecular Dynamics Simulation
S.F Asbaghian Namin R Pilafkan -
Open Access Article
9 - Molecular dynamics simulation study on the drug discovery in covid-19 disease
Pejman Shir Ali Poor Elham Tazikeh-Lemeski -
Open Access Article
10 - Investigation the effect of diameter and temperature on mechanical properties of single-walled boron nitride nanotubes by molecular dynamics simulation
Mohammad reza Mostafaei Abdolhosein Fereidoon Masoud Darvish ganjiThe molecular dynamics (MD) simulation is used to calculate the mechanical properties of single-walled BNNTs (SWBNNT). The effects of diameter, chirality and temperature on the mechanical properties of respected systems have been investigated. The results showed that, z MoreThe molecular dynamics (MD) simulation is used to calculate the mechanical properties of single-walled BNNTs (SWBNNT). The effects of diameter, chirality and temperature on the mechanical properties of respected systems have been investigated. The results showed that, zigzag BNNTs are stiffer than armchair ones with nearly the same diameter. Also the Young’s modulus of both type of SWBNNTs increase when the tube diameter increases till the specific diameter and then decrease slightly. We found that diameter changes have no significant influence on the failure stress and strain of zigzag BNNTs. In addition, the results confirmed that all measured mechanical properties decrease with increasing temperature. Our simulation findings afford not only a molecular level understanding of the BNNTs but also may be instructive to mechanical engineers and scientists who attempt to develop effective mechanical properties. Manuscript profile -
Open Access Article
11 - Atomistic simulations on the influence of diameter, number of walls, interlayer distance and temperature on the mechanical properties of MWBNNTs
mohammad reza mostafaei Abdolhosein Fereidoon Masoud Darvish ganjiBy using molecular dynamics (MD) simulation the mechanical properties of single, double and triple walled BNNTs (SWBNNT, DWBNNT and TWBNNT) is investigated. The effects of diameter, chirality, interlayer distance and temperature on the mechanical properties of respected MoreBy using molecular dynamics (MD) simulation the mechanical properties of single, double and triple walled BNNTs (SWBNNT, DWBNNT and TWBNNT) is investigated. The effects of diameter, chirality, interlayer distance and temperature on the mechanical properties of respected systems have been investigated. The results showed that, zigzag BNNTs are stiffer than armchair ones with nearly the same diameter. Also, the Young’s modulus of both type of DWBNNTs and TWBNNT increase when the tube diameter increases. In addition, the results confirmed that all measured mechanical properties decrease with increasing temperature. Furthermore, the Young’s modulus of DWBNNTs are smaller than TWBNNTs and larger than SWBNNT. We showed that the Young’s modulus of DWCNTs with various interlayer distances increase when separation wall distances were decreased. Our simulation findings afford not only a molecular level understanding of the BNNTs but also may be instructive to mechanical engineers and scientists who attempt to develop effective mechanical properties. Manuscript profile -
Open Access Article
12 - Molecular dynamic simulation for investigation of temperature, neck length and sheet size influence on mechanical properties of graphene nanobud
marjan khorasani Abdolhosein FereidonCarbon has several allotropes. One of the newest carbon allotrope is graphene nanobud. It isn’t available in laboratory. Graphene nanobud is formed by connecting fullerene and graphene sheet. Molecular dynamic simulation is used for calculating mechanical properti MoreCarbon has several allotropes. One of the newest carbon allotrope is graphene nanobud. It isn’t available in laboratory. Graphene nanobud is formed by connecting fullerene and graphene sheet. Molecular dynamic simulation is used for calculating mechanical properties of graphene nanobuds. Influence of temperature, neck length and size of graphene sheet are estimated in this study. The results shows that Young’s modulus has a little changes with temperature arrises. In another word, with increasing temperature the Young’s modulus doesn’t change very much and just alittle decrease. Also seen that in constant temperature with increasing the size of graphene sheet, the Young’s modulus arises. Our simulation findings afford not only a molecular level understanding of graphene nanobud but also may be instructive to mechanical engineers and scientists who attempt to develop effective mechanical properties. Manuscript profile -
Open Access Article
13 - In silico study to Identify New Inhibitors of Staphylococcus aureus (S. aureus) Sortase A
hassan sahebjamee Mehr Ali Mahmood JanlouIntroduction: Inhibition of key enzymes in bacteria that exert low evolutionary pressure can be a drug development strategy for bacterial antibiotic resistance. Sortase A (Srt A) is a transpeptidase that is widely used in site-specific protein modification. This enzyme MoreIntroduction: Inhibition of key enzymes in bacteria that exert low evolutionary pressure can be a drug development strategy for bacterial antibiotic resistance. Sortase A (Srt A) is a transpeptidase that is widely used in site-specific protein modification. This enzyme has a key function in the interactions between Staphylococcus aureus and the host and has been considered a promising target for the drug development of resistant bacteria. To date, some Srt A inhibitors have been discovered most of them are derived from flavonoid compounds, like myricetin. Aim: Since computational methods for monitoring the behavior of biomolecules at the microscopic level are more accurate and cost-effective, therefore, in this research, our goal is to use computational methods to find similar molecules but with higher binding and inhibitory effect than myricetin. Materials and Methods: In this study, we used computational methods such as structure-based virtual screening, molecular docking, MM-PBSA approach, and MD simulation. A molecular docking approach was used to understand protein-ligand interactions and inhibition constants in terms of affinity. MD simulation technique was used to monitor the conformational changes of Srt A enzyme. After the MD simulation studies, the MM-PBSA approach was used to interpret the binding free energy. Results: First, Chemspider's chemical library was screened by the "Similarity search" method, in which myricetin was placed as a reference molecule. The second stage of screening was done using PyRx software, so that the top 10 compounds were carefully selected based on their inhibitory potential from the set of ligands obtained from the previous stage. These compounds were subjected to Autodock4.2 for molecular docking. As a result, it was observed that compound-73945561 has a higher inhibitory effect than myrsteine. To investigate the stability and efficiency of ligand binding mode, free Srt A, its complexes with myrsteine and the best selected compound were subjected to 50s molecular dynamics simulation. MD simulation results showed that compound-73945561 had better binding profiles and interactions than myrsteine as a reference inhibitor, and steadily unstable behavior was observed in the docking complex. Conclusion: Overall, compound-73945561 may serve as a new inhibitor or provide a scaffold for further optimization toward the design of more potent SortA inhibitors. The development of such inhibitors would be an essential strategy against resistant bacteria. Manuscript profile -
Open Access Article
14 - QSAR, Molecular docking and Molecular dynamics studies simulation of Epigenetic inhibitors
ghasem ghasemi babak motahary Robabe SayadikordAbadi omid alizadehDevelopment of QSAR and molecular docking is a key to the elucidation of pathomechanisms of epigenetic diseases. Quantitative structure- activity relationship (QSAR), Molecular docking and molecular dynamics simulation were carried out for some modulators of modified ch MoreDevelopment of QSAR and molecular docking is a key to the elucidation of pathomechanisms of epigenetic diseases. Quantitative structure- activity relationship (QSAR), Molecular docking and molecular dynamics simulation were carried out for some modulators of modified chromatin proteins as anticancer agents. The Imperialist Competitive Algorithm (ICA), partial least squares (PLS), Principle component regression(PCR), Coralsea,and Multiple Linear Regression (MLR) were used to achieve the QSAR models. Suitable descriptors were selected which includes features such as atomic mass, Van der waals volume, shape and geometrical structure of compounds. Then, molecular docking studies were performed using Autodock Vina software which had a high throughput accuracy. Based on features such as number of hydrogen bonds, bonding length, binding affinity, and also root-mean-square deviation (RMSD), the best complex were selected. In general, QSAR, molecular docking and molecular dynamics simulation illustrated that compounds 9 and 14 were selected as suitable agents for the design of anticancer drugs. Drug-likeness descriptors of compounds calculated by DruLiTo. In the molecular docking study, the maximum binding affinity of -9 kcal/mol was obtained between each of enzyme systems (PDB: 3MXF) and the geometric-optimized molecules, representing a strong interaction. Manuscript profile -
Open Access Article
15 - Simulation of Fabrication toward High Quality Thin Films for Robotic Applications by Ionized Cluster Beam Deposition
Esmaeil Zaminpayma -
Open Access Article
16 - Molecular Dynamics Investigation of The Elastic Constants and Moduli of Single Walled Carbon Nanotubes
Mohammad Mahdi Zaeri Saeed Ziaei-Rad -
Open Access Article
17 - Effects of Colliding Particle Size and Velocity on Mechanical Properties of AZ31 after Surface Mechanical Attrition Treatment: Molecular Dynamics Simulation
Ali Kazemi Ali Heidari Kamran Amini Farshid Aghadavoudi Mohsen Loh-Mousavi -
Open Access Article
18 - Investigating the Effect of Poly (D L-Lactic Acid) Molecular Weight on the Shape Memory Parameters: A Molecular Dynamics Study
Mohammad Amini Abbas MontazeriShape memory polymers are a subset of smart materials that can regain their original shape after a temporary deformation. In recent years, these polymers have been vastly utilized in many industries (especially biomedical). The main purpose of this study was to find the MoreShape memory polymers are a subset of smart materials that can regain their original shape after a temporary deformation. In recent years, these polymers have been vastly utilized in many industries (especially biomedical). The main purpose of this study was to find the influence of the polymer molecular weight on the various shape memory parameters. Additionally, the mechanisms governing the shape memory behavior of polymers are thoroughly studied. Calculating the glass transition temperature and exploring its role on the shape memory behavior of polymeric materials are the other objectives of the current research. In this study, all models were built via Materials Studio and all the simulations were carried out using LAMMPS software. Based on the obtained results, the glass transition temperature of polymer increases with increasing the degree of polymerization. The attempts made to achieve an optimal microstructure revealed that the shape fixity parameter increases from 90% to 94% with increasing the molecular weight from 36000 g/mol to 108000 g/mol. In contrast to the shape fixity, the shape recovery parameter follows a descending trend with increasing the molecular weight. This is attributed to an increase in the ratio of the fixed phase to its reversible counterpart. Manuscript profile -
Open Access Article
19 - تاثیر هندسه زبری دیواره نانوکانال در رفتار جریان پوازیه نانوسیال آب-مس
محمد میثم امراللهی پورشیرازی داود طغرایی احمدرضا عظیمیانرفتار جریان داخل نانوکانال­ها با توجه به گسترده شدن کاربردهای آنها در سیستم­های نوین از اهمیت زیادی برخوردار است. با توجه به نتایج بدست آمده در این تحقیق شرط عدم لغزش روی دیواره نانوکانال، شرط قابل قبولی نیست زیرا لغزش در این ابعاد به پارامترهای متفاوتی از جمله Moreرفتار جریان داخل نانوکانال­ها با توجه به گسترده شدن کاربردهای آنها در سیستم­های نوین از اهمیت زیادی برخوردار است. با توجه به نتایج بدست آمده در این تحقیق شرط عدم لغزش روی دیواره نانوکانال، شرط قابل قبولی نیست زیرا لغزش در این ابعاد به پارامترهای متفاوتی از جمله زبری سطح دارد. در این تحقیق با ثابت نگه داشتن مساحت جانبی زبری ، اثر تغییر شکل آن بر روی رفتار جریان سیال بررسی شده است. مدلسازی به کمک نرم­افزار متن باز لمس با روش شبیه­سازی دینامیک مولکولی تعادلی انجام شده است. برخلاف تحقیقات گذشته، از نانوسیال موجود در شرایط آزمایشگاهی مانند آب-مس استفاده شده است. نتایج بدست آمده نشان از بیشترین تاثیر گذاری زبری مستطیلی و کمترین تاثیر گذاری زبری مثلثی بر رفتار جریان دارد و در نتیجه لغزش در نانوکانال با زبری مثلثی با شدت بیشتری رخ می­دهد. وجود زبری روی سطح باعث افزایش تعداد نوسانات در لایه های سیال می­شود ولی دامنه نوسان در نزدیکی دیواره صاف نسبت به زبر افزایش یافته است. حضور نانوذرات نیز باعث افزایش این اثرگذاری بر خواص جریان می­شود. Manuscript profile
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