Sharif Digital Repository

We investigate heat transfer between parallel plates separated by liquid argon using two-dimensional molecular dynamics (MD) simulations incorporating with 6-12 Lennard-Jones potential between molecule pairs. In molecular dynamics simulation of nanoscale flows through nanochannels, it is customary to fix the wall molecules. However, this approach cannot suitably model the heat transfer between the fluid molecules and wall molecules. Alternatively, we use thermal walls constructed from the oscillating molecules, which are connected to their original positions using linear spring forces. This approach is much more effective than the one which uses a fixed lattice wall modeling to simulate the... 

As the delay time and hence nuclei formation play a crucial role in the pathophysiology of sickle cell disease, MD simulation and molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) calculations have been performed on three systems of hemoglobin; namely dimer of hemoglobin with valine (Hb S), tryptophan (Hbβ6W), and phenylalanine (Hbβ6F) at β6 position. The structural changes due to these aromatic substitutions are investigated. It is shown that β subunits have significant impact on the differences between a dimer and other crystal structures. Transition from a dimer to polymer for Hb S system affects the donor molecule more than that of the acceptor. In the case of donor and... 

In this article, a multiscale modeling procedure is implemented to study the effect of interphase on the Young's modulus of CNT/polymer composites. For this purpose, a three-phase RVE is introduced which consists of three components, i.e., a carbon nanotube, an interphase layer, and an outer polymer matrix. The nanotube is modeled at the atomistic scale using molecular structural mechanics. Moreover, three-dimensional elements are employed to model the interphase layer and polymer matrix. The nanotube and polymer matrix are assumed to be bonded by van der Waals interactions based on the Lennard-Jones potential at the interface. Using this Molecular Structural Mechanics/Finite Element... 

In this paper, the hysteresis in the tipsample interaction force in noncontact force microscopy (NC-AFM) is measured with the aid of atomistic dynamics simulations. The observed hysteresis in the interaction force and displacement of the system atoms leads to the loss of energy during imaging of the sample surface. Using molecular dynamics simulations it is shown that the mechanism of the energy dissipation occurs due to bistabilities caused by atomic jumps of the surface and tip atoms in the contact region. The conducted simulations demonstrate that when a gold coated nano-probe is brought close to the Au(0 0 1) surface, the tip apex atom jumps to the surface, and instantaneously, four... 

The main focus of this study is to address the possibility of using molecular dynamics (MD) simulation, as a computational framework, coupled with experimental assays, to optimize composite structures of a particular electrospun scaffold. To this aim, first, MD simulations were performed to obtain an initial theoretical insight into the capability of heterogeneous surfaces for protein adsorption. The surfaces were composed of six different blends of PVA (polyvinyl alcohol) and PCL (polycaprolactone) with completely unlike hydrophobicity. Next, MTT assay was performed on the electrospun scaffolds made from the same percentages of polymers as in MD models to gain an understanding of the... 

Comprehensive structural/molecular simulations have been undertaken to study the poly(benzimidazoles) (PBI) membrane combined with four different nano-oxide materials (ZnO, Al2O3, SiO2 and TiO2) for purification and production of hydrogen from natural gases. Composite membranes were built with different amounts of nano-oxide materials to investigate the influence of nano-oxide content on the PBI membrane performance. Several structural characterizations such as FFV, WAXD and also a thermal one (glass transition temperature) were done to study the structural properties of all simulated membrane cells. Moreover, MSD and adsorption isotherms tasks were used to estimate the diffusivity and... 

A finite element-based hierarchical multiscale modeling scheme is presented and used for the analysis of nanotube-reinforced polymer composites. The scheme presented here consists of micro- and macroscale boundary value problems linked together using a computational homogenization scheme. Using the presented hierarchical multiscale scheme, we have studied nanotube-reinforced polymer composites, and the elastic properties are determined. Using different representative volume elements (RVEs) representing different volume fractions of aligned nanotubes, the effect of the nanotube volume fraction and the existence of an interphase layer on the effective elastic modulus of the nanocomposite are... 

It is of interest to explore transfer of fluid through nanopores because of widespread applications for such systems. Carbon Nanotubes (CNTs) with their exceptional properties are the best candidates as building blocks for nanostructures. Water transfer in lots of biological systems acts as an important role for keeping the tissue working properly. Peptide nanotube is one of the best biological channels which was proposed recently. While the mechanism of water permeation through channels is very complex, however, investigations such as effect of charge distributions and temperature on water permeation could shed light on the determinants of water and proton conduction rates in biol ogical... 

Connate water has been coexisting with oil and mineral for centuries within underground reservoirs. The oil recovery techniques, such as low salinity water injection, disturb this prolonged equilibrium state of oil/brine/rock system. However, a thorough understanding of this complex equilibrium in the reservoir is still lacking. In this study, we performed molecular dynamics simulations to provide quantitative comprehension of the thin brine film characteristics that wets carbonate reservoir rocks at molecular level. While an electric double layer is formed at the interface of calcite/low salinity water, the ions in the high saline water form several aggregates of ions. We found that these... 

Seawater, which has been frequently applied in cooling and injection water systems, imposes severe pitting corrosion to mild steel. Addition of green and sustainable inhibitors based on renewable sources is one of the promising methodologies for restricting metal corrosion in chloride-containing electrolytes. In this study, for the first time, from both theoretical and experimental faces, the role of Juglans regia green fruit shell (JRS) extract as a sustainable potent corrosion inhibitor for mild steel was studied. The chemical structure of the JRS extract was deliberated by Fourier transform infrared spectroscopy (FT-IR). By electrochemical techniques including polarization, EIS and... 

In this work, molecular dynamic simulation of the mixture of imidazolium based ionic liquids with alcohols is implemented in order to investigate mixing excess properties and some structural and physical properties of the mixture. Excess volumes and enthalpies are evaluated for 11 different mole fractions of ionic liquids at each 0.1, in the range of 0 to 1. Radial distribution function, cohesive energy density, potential of mean force, solvation energy, and diffusion coefficient are reported and analysed. The effects of the cationic alkyl chain length, in comparison with changes of the anions, on these properties are reported. Results reveal that the methanol molecule participates with its... 

In this research, the atomic scale local structures in (Zr0.5Cu0.5)100−xAlx (x = 0,2,4,6,8,10,12) bulk metallic glass was studied using molecular dynamics simulation method. The pair distribution function, Voronoi analysis and mean squared displacement (MSD) were adopted for investigation of the local structures. It was found that Cu- and Al-centered full icosahedra possess the most frequency accompanied by the most changes during the glass transition process in the supercooled liquid region temperature. Moreover, it was observed that the Al-centered full icosahedra (Al-FI) and Cu-centered full icosahedra (Cu-FI) clusters with 2.5% and 1.9% increase (relative to total atoms), respectively,... 

Interleukin 1 Receptor type I (IL-1RI) is a multi-domain transmembrane receptor that triggers the inflammatory response. Understanding its detailed mechanism of action is crucial for treating immune disorders. IL-1RI is activated upon formation of its functional assembly that occurs by binding of the IL-1 cytokine and the accessory protein (Il-1RAcP) to it. X-ray crystallography, small-Angle X-ray Scattering and molecular dynamics simulation studies showed that IL-1RI adopts two types of ‘compact’ and ‘extended’ conformational states in its dynamical pattern. Furthermore, glycosylation has shown to play a critical role in its activation process. Here, classical and accelerated atomistic... 

Gating of mechanosensitive (MS) channels is driven by a hierarchical cascade of movements and deformations of transmembrane helices in response to bilayer tension. Determining the intrinsic mechanical properties of the individual transmembrane helices is therefore central to understanding the intricacies of the gating mechanism of MS channels. We used a constant-force steered molecular dynamics (SMD) approach to perform unidirectional pulling tests on all the helices of MscL in M. tuberculosis and E. coli homologs. Using this method, we could overcome the issues encountered with the commonly used constant-velocity SMD simulations, such as low mechanical stability of the helix during... 

Endothelial inflammation as a prominent precursor to atherosclerosis elicits a distinct pathological surface expression of particular vascular proteins. To exhibit a site-specific behaviour, micro- and nanoparticles, as carriers of therapeutics or imaging agents, can distinguish and use these proteins as targeted docking sites. Here, a computational patient-specific model capturing the exclusive luminal qualities has been developed to study the transport and adsorption of particles decorated with proper antibodies over an atherosclerotic plaque located in the LAD artery of the patient. Particles, in nano- and micron sizes, have been decorated with Sialyl Lewisx (sLex), P-selectin aptamer... 

Protein aggregation, such as amyloid fibril formation, is molecular hallmark of many neurodegenerative disorders including Alzheimer's, Parkinson's, and Prion disease. Indole alkaloids are well-known as the compounds having the ability to inhibit protein fibrillation. In this study, we experimentally and computationally have investigated the anti-amyloid property of a derivative of a synthesized tetracyclic indole alkaloid (TCIA), possessing capable functional groups. The fibrillation reaction of Hen White Egg Lysozyme (HEWL) was performed in absence and presence of the indole alkaloid. For quantitative analysis, we used Thioflovin T binding assay which showed ~50% reduction in fibril...