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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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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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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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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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The COVID-19 pandemic has created a global health crisis, and developing effective treatments is essential to prevent the spread of the disease and save millions of lives. One of the key proteins involved in the replication cycle of SARS-CoV-2, the virus that causes COVID-19, is the main protease enzyme, 3CL^pro. Due to its high importance, this enzyme is the subject of molecular, structural, and clinical investigations, and efforts have been made to develop drugs that can inhibit its activity. One such drug is the chemical compound N3, which has been found to have a high inhibitory effect against 3CL^pro. However, traditional medicine perspectives on this issue have been less explored. In this research, molecular docking interaction simulation and all-atom molecular dynamics (MD) simulation were conducted to study the potential inhibitory capability of generally available 21 plant-extracted compounds against the 3CL^pro enzyme. Three compounds with the highest inhibition probability were selected from the molecular docking results and subjected to 100 ns of MD simulation to investigate their stability and structural-dynamic-energetic features. Beside the complexes stability, the results from the simulation demonstrated that, all our selected three compounds induce N3 comparable structural-dynamics characteristics to 3CL^pro and, therefore, are expected to have a similar inhibitory ability against this enzyme. Compound number 5 was found to have the most favorable binding energy and was proposed as the best plant substitute for N3. The results from this research can be directly used to design experimental research for 3CLpro enzyme inhibition, saving the time-financial cost.

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PFU DNA polymerse shows  the lowest error rate in Polymerase Chain Reaction (PCR) but it seperates from DNA  after about 20 nucleotides  add  to the end of primer strand. The research purpus is processivity improvement of PFU DNA polymerase by means of rational design and point mutation due to lowest enthropy and enthalpy costs. so DNA polymerases in B family with high processivity were selected and their structures and sequences were compared with PFU DNA polymerase then an optimized mutation was induced . Native form and mutant were simulated for 100 ns and the trajectories were analyzed. ΔG_binding was calculated by g_mmpbsa tool and proved that the mutant shows a robust affinity .

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Fluid flow through channels and ducts in nano scales is an important issue which needs numerical simulations for better analysis of fluid behavior because of the limitations of experimental methods. Hence, in the present study Molecular Dynamics simulation is used as a precise method for molecular scale problems to investigate fluid behavior. This method which is based on Newton’s second law, is applied to investigate liquid Argon flow in steady Couette flows through smooth and rough nanochannels. Using LAMMPS software, were performed simulation. In the present study, the fluid velocity and fluid slip in steady Couette flows were obtained to investigate various effects including: wall velocity, channel height, wall density, fluid-wall interaction, and surface roughness with different shapes such as rectangular and triangular in different dimensions. Based on the results, an increase in wall velocity increases the fluid slip velocity. For velocity constant values, an increase of channel height will decrease the fluid slip velocity. In steady Couette flow, decrease of wall density will result in decrease of fluid slip velocity. Reducing the energy parameter between fluid and wall will increase the fluid slip velocity and on the other hand, decreasing the fluid-wall length parameter will decrease the fluid slip velocity. The rectangular and triangular roughness at the bottom wall reduces the fluid slip velocity, and an increase of roughness height will further decrease the fluid slip velocity.

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Using molecular dynamics simulations, the structural properties and vibrational behavior of single- and double-walled carbon nanotubes (CNTs) under physical adsorption (functionalization) of Flavin Mononucleotide (FMN) biomolecule are analyzed and the effects of different boundary conditions, the weight percentage of FMN, radius and number of walls on the natural frequency are investigated. As the functionalized nanotubes mainly operate in aqueous environment, two different simulation environments, i.e. vacuum and aqueous environments, are considered. Considering the structural properties, increasing the weight percentage of FMN biomolecules results in linearly increasing the gyration radius. Also, it is observed that presence of water molecules expands the distribution of FMN molecules wrapped around CNTs compared to that of FMN molecules in vacuum. It is demonstrated that functionalization reduces the frequency of CNTs, depending on their boundary conditions in vacuum which is more considerable for fully clamped (CC) boundary conditions. Performing the simulations in aqueous environments demonstrates that, in the case of clamped-free (CF) boundary conditions, the frequency increases unlike that of CNTs with fully clamped and fully simply supported boundary conditions. The value of frequency shift increases by rising the weight percentage of FMN biomolecule. Moreover, it is observed that the frequency shifts of SWCNTs with bigger radius are more considerable, whereas the sensitivity of frequency shift to the weight percentage of FMN biomolecule reduces and this is more pronounced as the simulation environment is aqueous.

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In this study, the method of molecular dynamics simulation is performed to investigate the shockwave propagation in a solid. The simulation cell contains 51840 atoms at 5 K interacting by means of a pairwise potential. The shockwave is generated using the motion of a piston with different velocities in the solid and the resulted shockwave velocity is in good agreement with the experimental data and the Hugoniot curve. The piston hited the sample from one side of the simulation box, at speeds ranging from 1.2 to 1.3 times the speed of sound in solid argon at the chosen density. Some thermodynamics properties such as density, temperature and pressure are measured during propagation of shockwave. It is found that those thermodynamics properties (density, temperature and pressure) are remarkably and significantly increase when the shockwave passed through the solid. We also show that creating initial strain in the solid up to 6.5% can enhance the pressure increment in the solid up to 9%. The results can be useful in enhancing of the shockwave power by giving a detailed microscopic description of the process.

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Due to their accuracy and reliability, atomistic-based methods such as molecular dynamics (MD) simulations have played an essential role in the field of predictive modeling of single layered graphene sheets (SLGSs(. However, due to the computational costs, applications of these methods are limited to small systems. Additionally, according to the discrete nature of SLGSs, conventional continuum-based methods cannot be utilized to study the mechanical characteristics of them. To overcome these issues, here, a new Atomic-scale Finite Element Method (AFEM) based on the Tersoff-Brenner potential has been developed. Efficiency of the proposed method is evaluated through a numerical example analyzed by both of the proposed method and MD simulation. The results show that the computational cost is much reduced (~100 times), while the accuracy of MD simulation is kept. Furthermore, the effects of initial C-C bond length and number of atoms on the speed of the proposed method is investigated. To mimic the MD simulation completely, periodic boundary conditions have been implemented in the extended AFEM. It is demonstrated that there is a noticeable deviation from MD results without considering this type of boundary conditions.

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Polyvinylidene fluoride polymer poses unique properties such as piezoelectric and high mechanical, thermal, and chemical resistance due to the consisting of the most electronegative element, fluorine, in its combination. In this paper, molecular dynamics simulation of amorphous polyvinylidene fluoride polymer containing polarized monomers is utilized to study its mechanical properties. Firstly, by using tensile test, elastic modulus and ultimate stress are determined and their changes due to temperature and strain rate change are studied. Then, by using dynamic mechanical analysis, tensile and shear dynamic complex modulus are calculated and their changes are studied while strain rate changes. This is for the first time that dynamic mechanical analysis is simulated by molecular dynamics. In addition to determining the viscoelastic properties of the material, straight forward elimination of temperature disturbances due to the sinusoidal pattern of stress and strain functions in terms of time is one of the advantages of the dynamic mechanical analysis. Consistency between simulated and actual trends shows the efficiency of the proposed model.