Sharif Digital Repository

A combination of molecular dynamics (MD), continuum elasticity and FEM is used to predict the effect of CNT orientation on the shear modulus of SWCNT-polymer nanocomposites. We first develop a transverse-isotropic elastic model of SWCNTs based on the continuum elasticity and MD to compute the transverse-isotropic elastic constants of SWCNTs. These constants are then used in an FEM-based simulation to investigate the effect of SWCNT alignment on the shear modulus of nanocomposites. Furthermore, shear stress distributions along the nanotube axis and over its cross-sectional area are investigated to study the effect of CNT orientation on the shear load transfer  

The Poiseuille flow through slit-like nanochannels is investigated using the nonequilibrium molecular dynamics simulations. To drive a dense flow through the channel, we use two self-adjusting vertical plates strategy. These plates force the liquid to flow through the nanochannel under adjustable inlet and outlet boundary conditions. Comparing with the dual-control-volume grand-canonical molecular dynamics method, the current strategy provides many advantages. The current strategy does not need particle insertion and deletion, therefore, the system dynamics would not be affected at all. Moreover, the number of particles in the simulation system is fixed due to inserting the two... 

Metallic nanoparticles are interesting because of their use in catalysis and sensors. The surface energy of the FCC platinum nanoparticles are investigated via molecular dynamics simulation using Quantum Sutton-Chen (QSC) potential. We have calculated the Gibbs free energy for the FCC platinum bulk and also for its nanoparticle. All calculations have been carried out at zero pressure. We have used the thermodynamic integration method to obtain the Gibbs free energy. The total Gibbs free energy is taken as the sum of its central bulk and its surface free energy. We have calculated the free energy of a platinum nanoparticle as a function of temperature  

Molecular dynamics simulation was used to study of mechanical properties of NiTi/Cu bilayer by nanoindentation and tensile testing. A comparison has been made among mechanical properties measured and plastic deformation process at different copper thickness during nanoindnetation and tensile test of the samples. Embedded atom method potentials for describing of inter-Atomic interaction and Nose-Hoover thermostat and barostat are employed in the simulation at 400 K. The results showed that as the copper film thickness decreased, the maximum load and hardness values increased during nanoindetation. Saha and Nix model is used to describe reduced young's modulus behaviour of the bilayer system... 

The effect of temperature on the short-range order (SRO) structures, deformation mechanisms and failure modes of metallic glasses (MGs) is of fundamental importance for their practical applications. However, due to lack of direct structural information at the atomistic level from experiments and the absence of previous molecular dynamics (MD) simulations to reproduce experimental observations over a wide range of temperature, this issue has not been well understood. Here, by carefully constructing the atomistic models of Cu64Zr36 and Fe80W20 MGs, we are able to reproduce the major deformation modes observed experimentally, i.e. single shear banding (SB) at low temperatures, multiple... 

Classical molecular dynamics simulations are used to compute the solvation free energy of two pharmaceutical solids, namely ibuprofen and acetaminophen in carbon dioxide (CO2), over the density range of interest in supercritical processes. In order to examine the influence of the solvent model on the resulting free energies, three popular CO2 models (Zhang, EPM2, and TraPPE) are studied. Relatively large discrepancies for the solvation free energy exist between these CO2 models, suggesting that the former is sensitive to the different balances between dispersive and electrostatic forces used in these models. In particular, for the solvation of the highly polar (dipole moment of ∼5.2 Debye)... 

The local buckling behavior of perfect/defective and single/multi-walled carbon nanotubes (CNTs) under axial compressive forces has been investigated by the molecular dynamics approach. Effects of different types of defects including vacancy and Stone-Wales (SW) defects and their configurations on CNTs with different chiralities at room temperature are studied. Results show that defects largely reduce the buckling stress and the ratio of immediate reduction in buckling compressive stress of the defective CNT to the perfect one, but have little influence on their compressive elastic modulus. SW defects usually reduce the mechanical properties more than vacancy defects, and zigzag CNTs are... 

If an ideal membrane for gas separation is to be obtained, the following three characteristics should be considered: the membrane should be as thin as possible, be mechanically robust, and have welldefined pore sizes. These features will maximize its solvent flux, preserve it from fracture, and guarantee its selectivity. Graphene is made up of a hexagonal honeycomb lattice of carbon atoms with sp2 hybridization state forming a one-atom-thick sheet of graphite. Following conversion of the honeycomb lattices into nanopores with a specific geometry and size, a nanoporous graphene membrane that offers high efficiency as a separation membrane because of the ultrafast molecular permeation rate as... 

Interactions between P-selectin, expressed on activated endothelium, and its counterpart P-selectin glycoprotein ligand-1 (PSGL-1), expressed on leukocytes, play a pivotal role in adhesive events that recruit circulating leukocytes toward inflamed or injured tissues. Atomistic understanding of the association and dissociation of these bonds under blood flow is necessary to define the underlying mechanism. In this study, steered molecular dynamics (SMD) simulations were applied to investigate the conformational changes of P-LE/SGP-3 construct (an effective binding unit of the P-selectin/PSGL-1 complex) under stretching with constant velocity. In the present simulations, a self-built force... 

Molecular dynamics (MD) simulation was used to study of thermal properties of NiTi/Cu. Embedded atom method (EAM) potentials for describing of inter-atomic interaction and Nose-Hoover thermostat and barostat are employed. The melting of the bi-layers was considered by studying the temperature dependence of the cohesive energy and mean square displacement. To highlight the differences between bi-layers with various copper layer thickness, the effect of copper film thickness on thermal properties containing the cohesive energy, melting point, isobaric heat capacity and latent heat of fusion was estimated. The results show that thermal properties of bi-layer systems are higher than that of... 

According to the Amyloid hypothesis, as the foremost scientific explanation for Alzheimer Disease (AD), the neuropathology of AD is related to toxic fragments of amyloid beta (Aβ) protein. Based on this hypothesis, an attractive therapeutic approach was demonstrated to identify multifunctional peptides able to modulate Aβ pathologies as the source of AD. On this premise, a bifunctional polypeptide based on the iAβ5p lead compound, was designed to inhibit Aβ aggregation and free metal ions. Herein, the efficacy of this novel drug in Zn2+ and Cd2+ ion chelation was examined through an integrated technique comprising combined Docking, QM, and MD simulations. MD relaxation of a set of probable... 

Metallic nanoclusters are interesting because of their utility in catalysis and sensors. The thermal and physical characteristics of metallic Pt nanoclusters with different sizes were investigated via molecular-dynamics simulations using Quantum Sutton-Chen (QSC) potential. This force field accurately predicts solid and liquid states properties as well as melting of the bulk platinum. Molecular dynamic simulations of Pt nanoclusters with 256, 456, 500, 864, 1372, 2048, 2916, 4000, 5324, 6912, 8788 atoms have been carried out at various temperatures. The Pt-Pt radial distribution function, internal energy, heat capacity, enthalpy, entropy of the nanoclusters were calculated at some... 

In this research, nanoparticle translocation through cell membrane has been studied and simulated. To this end, gold nanoparticles have been selected as the main carrier of the drug and have been functionalized with some selected ligands. The partial charges of the ligands have been calculated using quantum mechanics based on HF technique with 6-31Gd basis set. To achieve the realistic shape of a drug, the number and arrangement of ligands loaded on the gold nanoparticle have been optimized. After determining the properties such as diffusion coefficient and validating the results with experimental data, a MARTINI coarse-grained mapping of the drugs is created. The coarse-grained model of the... 

In this research, nanoparticle translocation through cell membrane has been studied and simulated. To this end, gold nanoparticles have been selected as the main carrier of the drug and have been functionalized with some selected ligands. The partial charges of the ligands have been calculated using quantum mechanics based on HF technique with 6-31Gd basis set. To achieve the realistic shape of a drug, the number and arrangement of ligands loaded on the gold nanoparticle have been optimized. After determining the properties such as diffusion coefficient and validating the results with experimental data, a MARTINI coarse-grained mapping of the drugs is created. The coarse-grained model of the... 

The designability of structures in a two-dimensional hydrophobic-polar (HP) pair contact lattice model in a wide range of intermonomer interaction parameters was studied by considering HP constraints. The designability of all structures was clarified by enumerating all sequences of length 20. Results confirm that changing the intermolecular interactions affects the structure designability and also chooses the search space of the native state but the set of HDSs is invariant