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Aluminum nano-films are one of the functional elements that have various applications in different fields such as strengthening cement base materials, improving the performance and efficiency of concrete, and enhancing the mechanical and volumetric properties of clay. In this study, the mechanical responses of aluminum nano-film are investigated under uniaxial tensile and compressive tests using the molecular dynamics (MD) method. The initial configuration of the nano-film is constructed based on a 3D aluminum core—alumina shell model that provides a suitable description of surface oxidation in the nano-film. This model is useful to determine the influence of surface oxidation on the mechanical behavior of nan-film. Because of the accuracy and competency, the inter-atomic interactions are evaluated using the EAM+CTI potential, which is a hybrid potential consisting of two components, i.e., EAM and CTI potential, such that it can also take into account the electrostatic interactions between the atoms. After establishing the initial configuration, the energy minimization process is performed on the nano-film, and then its temperature and pressure are adapted to the environmental conditions through the relaxation process. The MD analysis is accomplished by the open-source LAMMPS software, and the visualization of outputs is performed by the open-source OVITO software. The periodic boundary condition is imposed on the lateral sides of the nano-film to eliminate the free surface effect of the atomistic analysis. The tensile and compressive tests are applied to the nano-film in accordance with the experimental tests, and the stress—strain curves are determined. The concept of Virial stress is employed to calculate the stress of the atomic model, which is equivalent to the conventional Cauchy stress in classical mechanics. In order to diminish the dynamic effects, deformation is incrementally applied to the nano-film, such that at each increment, a small strain is gently imposed, then the nano-film is relaxed under the deformed conditions, and finally the stress and strains are evaluated. The numerical simulations are verified by comparing them with experimental data, which demonstrates the acceptable accuracy of the obtained numerical results. The influence of various parameters such as the thickness and the percentages of oxide layers are investigated on the mechanical response and stress-strain curve of aluminum nano-film under the uniaxial tests. It is demonstrated that the thickness of the oxide layer significantly impacts the mechanical behavior, such that the hardness and energy absorption capacity of the nano-film is increased considerably by increasing the percentage of the oxide layer thickness. However, increasing the total thickness of the nano-film leads to a decrease in the Young’s modulus and elastic limit of the specimen. It is because of the decrease in the percentage of oxide layer thickness by increasing the total thickness of the nano-film. Point defects are one of the important imperfections in the crystal structures of atomic configuration that have a significant effect on the mechanical behavior of materials. In order to investigate the influence of point defects, different percentages of voids are generated by randomly omitting some atoms in the nano-film domain. The generated specimens are analyzed under the uniaxial tests, and their mechanical characteristics are evaluated. The numerical simulations demonstrate that the hardness of the nano-film is significantly reduced by increasing the point defects.
 

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Nowadays, investigating and researching on energetic polymers in order to increase mechanical, thermodynamic, and detonational properties of them have been highly regarded. One of these energetic polymers is GAP. In this paper, molecular dynamics simulation has been used to compare the properties of GAP and GTP energetic polymers. GTP, in principle is the modified form of GAP, in which functional group of triazolium methyl nitrate has been added instead of azide. The mechanical properties of GAP is a challenging topic in the field of energetic materials. Due to the attributes of the 3 azoliom methyl nitrate ring, the mechanical and thermodynamic properties of GTP are expected to be higher than GAP. The results obtained by molecular dynamics simulation showed that GTP is a stable material and its mechanical properties such as Young, and shear modulus compared to GTP have been decreased 27% and 32% respectively, and bulk modulus, Poisson coefficient, and K/G ratio compared to GTPhave been increased 17%, 42%, and 71% respectively. It was also found that the detonation speed, detonation pressure, and oxygen balance of energetic polymer compared to GAP, have been increased 5%, 14%, and 21% respectively. As a result, usage of GTP will increase as a modified GAP material in applications such as clean and chlorine-free propellants for the solid propellant rockets and also safety systems of automobiles.

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Research subject: Poly (2-oxazoline) (PEOX) polymers are a family of synthetic macromolecules with biodegradable and biocompatible features. They resemble polypeptides in structure and therefore, have recently taken put to use in drug delivery. Nonetheless, these polymers suffer from relatively low thermal and mechanical performance and thus are reinforced with nanoparticles as nanocomposites. The molecular details of the reinforcement mechanism of PEOX have not yet been elucidated.
Research approach: This research work was done to reach an understanding on interaction of 2-oxazoline-based polymers with 2D nanoscale reinforcements and to shed light on the mechanism of reinforcing the respective nanocomposites. To this end, conformation and dynamics of poly (2-ethyl-2-oxazoline), as a known representative member of this family, near a functionalized graphene nanosheet were studied via classical molecular dynamics for a period of 10 ns. The effects of various temperatures and polymer chain lengths on polymer conformation and dynamics were assessed.
Main results: Molecular dynamics snapshots exhibited effective interaction of the polymer chain with the graphene nanosheet leading to adsorption, whereby conformation and dynamics of the chain underwent transition. The adsorbed polymer chain adopted a flat, folded arrangement parallel with the graphene plane. Also, the gyration radius was found to increase, when the polymer chain approached the graphene nanosheet. Pair correlation function curves revealed that the adsorption correlation length was on the order of the repeating unit end-to-end distance. Mean-square-displacement of the polymer chain decreased as it moved towards graphene. An increase in temperature led to a change in structure and dynamics of the adsorbed polymer chain.
 

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Bacteriorhodopsin (bR) is a membrane protein that acts as a light-driven proton pump in Halobacterium salinarum. This protein contains seven transmembrane α-helical subunits, helices A–G, one beta-sheet and a retinal chromophore. Studies show that bR have the property of absorbing the microwave. Among several methods molecular dynamics simulation (MD) is the most systemic approach. With this method we can study structural changes and dynamic of macromolecules. In this project, we use modeling and molecular dynamic simulation. To obtain more accurate structures after the equilibration a 15 ns MD simulation was done. After that, in order to find the effective sites of microwave absorption on bR a production run was performed with applying electric field in the time intervals of 786 ps that is equal to one sinusoidal frequency at microwave spectrum. At last, conformational changes under effect of sinusoidal wave has been assigned the effective sites of microwave absorption in the protein. Our study shows that microwave in the frequency of 8 GHZ and the time interval that mentioned above, cannot make significant changes on the protein. In the other hand, we have seen some reversible changes in Beta-sheet and D, C, B helices.

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Aims: Today, due to the advent of drug resistance in cancer cells against conventional drugs, attention has been paid to the development of anti-cancer drugs with new mechanisms. Pardaxin is an amphipathic polypeptide neurotoxin.The aim of this study was to investigate the interaction of antimicrobial peptide pardaxin with DPPC (composed of 1, 2-dipalmitoyl-sn-glycero-3-phosphocholine) bilayers by molecular dynamics simulation.
Materials & Methods: In the present study, simulations for different membrane environments were designed under neutral pH conditions. At first, the Linux system was used to install the VMD 1.8.6 (Visual Molecular Dynamics) software; then, Gromacs 4.5.5 software was used to perform all the simulations. The pdb peptide structure (1XC0) was prepared from the Protein Data Bank and DPPC lipid bilayer was used for lipid-peptide simulation.
Findings: During the 500 nanoseconds of simulation, the peptide was infiltrated into the membrane. In the DPPC system, at first, the number of hydrogen bonds between the peptide and the lipid bilayer were increased and, then, remained almost constant until the end of the simulation and decreased over time with the number of hydrogen bonds between peptides and water. Pardaxin contacted with the membrane surface and entered into the membrane. In the presence of the peptide, the thickness of the membrane and the range of each lipid decreased and the membrane penetration increased.
Conclusion: The mechanism of Pardaxin is dependent on the bilayer composition, so that the pardaxin peptide contacts with DPPC lipid membrane surface and enters into it.

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Aims: Molecular insights into the analyte-bioreceptor interactions play a vital role in the efficacy of designing biosensors. Biosensors that utilize aptamers as bioreceptors are highly efficient with high specificity and reusability. Aptasensors can be used in a variety of conditions of in vivo or in vitro. The aim of this study was to study the changes in the solvent conditions of the binding of MUC1-G peptide and the anti-MUC1 aptamer.
Materials and Methods: The molecular dynamics simulation method has been used to investigate the change of molecular interactions due to selective variations in solvent conditions. The results can be used to reflect a variety of environments, in which the aptasensor utilizes anti-MUC1 S2.2 aptamer as a bioreceptor and MUC1–G peptide as a biomarker.
Findings: Based on the calculated binding energies, the medium containing 0.10M NaCl and anti-MUC1 S2.2 aptamer demonstrates the highest affinity toward the MUC1-G peptide among the studied concentrations of NaCl, and the arginine amino acid has a key role in the aptamer–peptide binding. Conclusion: The results of MD simulation indicated that the increase in the concentration of NaCl in the interaction environment leads to a decrease in binding energies; therefore, the binding affinity of the anti-MUC1 aptamer to MUC1-G peptide decreases. Insights from present modeling demonstrate the selectiveness and sensitivity to solvent conditions, which should be considered in the development of biosensors.

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The interactions between carbon nanotubes (CNTs) and proteins were considered much attention. Advanced CNT applied biomolecules require mutual understanding of their interactions with biological molecules. Enhanced biomedical applications of CNTs have necessitated the need for the understanding their interaction with biomolecules. Non-covalent interactions of blood peptides, such as hepcidin, with carbon nanotubes, have important effects in a wide range of biological applications that are detected by analyzing the thermodynamic parameters of the interaction between CNTs and peptides. In addition, the effects of different parameters in order to evaluate how the interaction of CNTs with peptide affects and structural changes and stability of peptides were studied. In this study, based on molecular dynamics (MD) simulation, the structural changes of hepcidin 20 in interaction with multi walled carbon nanotubes (MWCNTs-COOH ) were investigated. The simulation results revealed that carbon nanotubes cause to loose the hepcidin structure and make structural changes in this peptide. On the other hand, the loose of the hepcidin structure may lead to a change in its activity. The results indicated that significant changes were made in the structure of hepcidin 20 in the presence of carbon nanotubes. The difference of parameter amounts calculated in heptidine 20 is related to their N-terminal, and loop regions.  

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Integrin inhibitors may change conformational and dynamical properties of integrin, but its molecular properties in this process is not clearly understood. Tumstatin is an anti-angiogenesis protein derived from collagen XVIII, but little is known about how tumstatin applies its antiangiogenic and antitumor effects. It has been reported that 18 amino acids fragment of tumstatin has anti-tumor activities similar to tumstatin. We used molecular docking and molecular dynamic simulations to describe inhibitor activity of peptide in molecular level. We described the binding of this peptide to Hybrid/EGF-4 interface and that these interactions might contribute to improved hydrophobic interactions at these regions and also fixed the mobile domains of integrin. In the complex, we recognized a novel binding site on integrin for integrin inhibitors that may have critical role in integrin inhibition. These results support the idea that hydrophobic interactions between Hybrid/EGF-4 domain and peptide-anti tumor might contribute to stability of bended state and therefore inhibit integrin activation.  Our finding can be applied to understand the mechanism of out-in pathway integrin signaling and development of integrin targeted drug.

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Glucoamylase, is an important economic enzyme due to its ability to hydrolyze starch and β-D-glucose polymers. Understanding of factors affecting the thermal stability of the glucoamylase enzyme is critical in the production of isoenzymes with high heat or cold stability.  In this study, the effect of temperature on the structure and properties of each of the isoenzymes of the mesophilic, thermophilic and psychrophilic glucoamylase were studied. For this purpose, molecular dynamics simulation was used to assess these factors and structural differences. 240 nanosecond of MD simulation was done for three isoenzymes of glucoamylase in four temperatures at 300, 350, 400 and 450 K. The variations of each of these parameters were compared for three isoenzymes, and it was found that among the computable factors in molecular dynamics simulation, electrostatic energy of protein with water, van der Waals energy between proteins and water, free energy solubility (∆G_solvation), instability parameter, nonpolar solvent accessible surface, and total solvent accessible surface can be used to predict thermal stability of a protein during increase of temperature.
 

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Transforming growth factor beta (TGF-β), is a small homodimeric signaling protein. The TGF-β isoforms (TGFβ1, β2 and β3) are involved in many cellular processes including growth inhibition, extracellular matrix remodeling, tissue development, cell migration, invasion and immune regulation. For research aims, TGFβs are overexpressed using recombinant eukaryotic cell or bacterial expression systems. For achieving an efficient purification of TGF-β by immobilized metal ion affinity chromatography (IMAC), a histidine tag was placed either at the C-terminal (C-TGFβ) or N-terminal (N-TGFβ) region of the sequence and the effect of His-tag on TGF-β structure has been studied by computational tools. Proteins 3D structures were modeled using MODELLER software and molecular dynamics simulation of native TGF-β and modelled proteins, N-TGFβ and C-TGFβ were studied in water by GROMACS package. Protein dynamics modeling indicated that the His-tag attached at the C-terminus but not at the N-terminus of the TGF-β can affect the fluctuations of amino acids and protein structure. It is concluded that the C-terminal tagging may cause distortion and misfolding in the structure.

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Molecular dynamics simulations have been performed to study the mechanical properties of hydrogen functionalized graphene. We find out that Young’s modulus and tensile strength of pristine graphene are in good agreement with experimental results. It is shown that hydrogen functionalization can considerably modify the mechanical properties of graphene. It is also found that the patterned orrandom hydrogen coverage have different effects on the mechanical properties of graphene. Using molecular dynamics simulation, we study the mechanical properties of hydrogen functionalized graphene under tension and shear deformations at constant room temperature. Young’s modulus and shear modulus, tensile and shear strengths and tensile and shear fracture strains are mechanical parameters that are calculated in order to investigate the mechanical properties of hydrogen functionalized graphene. Results show that in some cases, hydrogen coverage pattern is important independent of its coverage percentage. The underlying mechanisms were explained considering the difference between sp^2 and sp^3 hybridization.

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Designing new drug delivery systems is important; therefore, in the present study the interaction between an anti-cancer drug, bicalutamide, and an amide/acid hydrogel was studied. Analyzing was done by using docking and molecular dynamics simulation methods. Molecular dynamics simulations were performed at 37 and 42 °C. The results showed that the binding free energies of the drug to the hydrogel system at two temperatures were similar, and altering the temperature did not affect the stability of the system. The van der Waals interaction is the most crucial interaction between the drug and the hydrogel, which depends on the distance between the drug and hydrogel. Intra- and intermolecular hydrogen bonds and van der Waals interactions, are the major factors in the stability of the hydrogel system. Due to the stability of the studied system, it can be used as a drug carrier.
 

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Vitamins D and E are two common medicines for diabetes treatment. Among the main issues in this field is the release of insulin into the circulatory system. Increasing the stability of insulin hexamer is an evolving strategy in improving insulin secretion efficiency. Insulin protein is commonly found in three forms: monomer, dimer, and hexamer. In this study, for the first time, computational approaches were used to investigate the effect of vitamins D3 and E on the stability of insulin hexamer. The molecular docking results indicate six specific binding sites for these vitamins. These bind to the hydrophobic sites of insulin subunits due to their structural rings and hydrophobic properties. The G-mmpbsa analysis indicates the stabilizing role of both vitamins. The binding of these vitamins to the hexamer has significantly increased the binding energy between insulin subunits. Also, the number of hydrogen bonds between monomeric subunits of each insulin homodimer increased in the presence of the vitamins. It also significantly increases the number of internal hydrogen bonds of hexamer protein. Accordingly, vitamins D3 and E bind to and stabilize the insulin hexamer, resulting in a slower and more balanced insulin release as well as a longer half-life for the dimer in the bloodstream. These findings will pave the way to design a new strategy to regulate insulin release and increase its half-life in the blood for type II diabetes treatment. Besides, hexamer stabilization can be an effective treatment strategy for type I diabetes through slow release from an implanted biosensor system.

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In the present paper, Molecular Dynamics Simulation (MDS) is performed for Poiseuille flow of liquid Argon in a nanochannel by embedding the fluid particles in an external force with different potential functions. Three types of Lennard-Jones (LJ) potentials are used as interatomistic or molecular models for evaluations of interactions and density, velocity profiles across the channel are investigated. The interatomic potentials are LJ 12-6 potential, LJ 9-6 potential and LJ-Smooth potential. Density and velocity profiles across the channel are investigated. Obtained results show that hydrodynamic characteristics and behavior of flow depends on the type of interaction potential. It is shown that the LJ 9-6 predictions for velocity and temperature are larger than those of LJ12-6 and LJ-Smooth potentials. Also, applying LJ 9-6 results in further calculations time. The results show the effect of interaction force model on the understanding and analyzing of nanoscale flows.

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Metals have a crystalline structure and the plastic flow in these materials occurred in the special crystalline planes and special crystalline directs that occurs in the planes. This mechanism is related to metals plastic deformation in the microscopic level. In this mechanism, non homogenous microstructure and the effect of crystalline direction play a major rule in the material behavior. Crystal plasticity constitutive equations are used for investigation of the crystalline direction effect and material texture. Voronoi method is used for simulating the non homogenous microstructure in plastic deformation. In this study, the elastic modulus parameters obtained by molecular dynamic simulations. Finally, the plastic deformation of Fe metal is simulated with finite element method that good agreement was observed with the experimental data.

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The main purpose of the present research is analytical and numerical analyses of graphene/epoxy nanocomposites with a random distribution of nanoparticles. For this purpose, by combining the molecular dynamics and micromechanics methods, a new approach is presented. The molecular dynamics method is used to model the stiffness of the graphene/epoxy nanocomposites containing one layer of nano graphene embedded in epoxy resin. A multi-scale modeling strategy from macro to meso, then from meso to micro and finally from micro to nano scales is introduced. A representative volume element (RVE) is selected and for a nanocomposite having a single monolayer graphene embedded in epoxy resin, the longitudinal (E11), transverse (E22) and normal (E33) stiffnesses for three RVEs with arbitary graphene size are simulated. The best curve is fitted to each stiffness diagram and stiffnesses of the RVE in three directions with true graphene size are investigated. In order to consider the effect of randomly graphene sheets distribution in epoxy resin, micromechanical approach is used. Finally, the stiffness of the nanocomposites with randomly distributed graphene is calculated. For evaluation of the present approach in this research an experimental program is conducted. The result of the modeling is well agreed with the experimental data.

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Aim: Follistatin-like protein 1 (FSTL1) is a secreted glycoprotein that plays an important role in regulating cell survival, proliferation, differentiation, migration, inflammation, and modulating the immune system. The FK domain in FSTL1 has 10 conserved cysteine residues that form 5 disulfide bonds. Despite extensive studies on the function of FSTL1, limited structural information is available about this biologically important molecule.
Materials and Methods:Using the SWISS-MODEL server and using the crystal structure of the FK domain of the mouse FSTL1 protein with the code (PDB: 6jzw) as a template, structural models of the FK domain of the human FSTL1 protein were prepared. In the next step, the resulting structures were checked using Swiss-PDB Viewer 4.10, Chimera 1.12 software, Ramachandaran diagram and PDBSUM server, in terms of the distance between two cysteine residues, the modeling error range, and the formation of disulfide bonds. Molecular dynamics simulations were performed using the AMBER software package with the ff14SB force field.
Results: The results showed that the FK domain without disulfide bond has root mean square deviations (RMSD) and root mean square fluctuations (RMSF), higher than the native FK domain. In addition, the radius of gyration in domain without disulfide bonds is significantly lower than that of native FK domain. The results show that the disulfide bonds of the FK domain play a role in the stability of the structural folding of the FK domain and the removal of these bonds increases the structural flexibility of this domain.
 

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Recently, great attention has been focused on epoxy polymers in different industrial and scientific activities, owing to superior mechanical properties and their stability in different environmental conditions. In this study, the molecular dynamics method was used to study the structure of cross-linked epoxy polymers and predict glass their transition temperature (Tg). The epoxy polymer with a certain degree of cross linking was constructed through the previously proposed cross linking procedure. A temperature cycle (300-600 K) with a constant rate was then applied to the cross-linked epoxy, and a rough estimate of the glass transition region was obtained through mean squared displacement curves. Thereafter, variation of density in terms of temperature was utilized to precisely calculate Tg. The estimated Tg was found to be in good agreement with experimental observations. Radial distribution function was finally used to investigate the effects of temperature and cross linking on the local structure of simulated polymer.