Sharif Digital Repository

The motion of a C60 molecule over a graphene sheet at finite temperature is investigated both theoretically and computationally. We show that a graphene sheet generates a van der Waals laterally periodic potential, which directly influences the motion of external objects in its proximity. The translational motion of a C60 molecule near a graphene sheet is found to be diffusive in the lateral directions, while in the perpendicular direction, the motion may be described as diffusion in an effective harmonic potential which is determined from the distribution function of the position of the C60 molecule. We also examine the rotational diffusion of C 60 and show that its motion over the graphene... 

Corrosion inhibition properties of some heterocyclic compounds (3-mercapto 1,2,4 triazole, benzotriazole, thiophene, and tetra hydro-thiophene) in Cu/H3PO4 medium were investigated theoretically and experimentally via cluster/polarized continuum and gravimetric approaches. Second-order Møller-Plesset perturbation and density functional theories were applied, and the electronic chemical potential, molecular softness, and extent of charge transfer were determined for inhibitor molecules at the metal/solution interface. Good correlations were observed for both theories between the calculated quantities and experimental data. To reveal the quality of metal-inhibitor interactions, comprehensive... 

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... 

Linear-dendritic ABA triblock copolymers containing poly(ethylene glycol) (PEG) as B block and hyperbranched poly(citric acid) (PCA) as A blocks were synthesized through polycondensation. The molecular self-assembly of synthesized PCA-PEG-PCA copolymers in water led to formation of nanoparticles and fibers in different sizes and shapes depending on the time and size of PCA blocks. Ten days after dissolving PCA-PEG-PCA copolymers in water, the size of fibers had reached several millimeters. Mixing a water solution of fluorescein as a small guest molecule and PCA-PEG-PCA copolymers led to the encapsulation of fluorescein by products of molecular self-assembly. To investigate their potential... 

In this article, the interaction of an arbitrary number of quantum dots behaving as artificial molecules with different energy levels and a multi-mode electromagnetic field is studied. We make the assumption that each quantum dot can be represented as an atom with zero kinetic energy, and that all excitonic effects except dipole-dipole interactions may be. disregarded. We use the. Jaynes-Cummings-Paul model with applications to quantum systems based on a time-dependent Hamiltonian and entangled states. We obtain a system of equations describing the interaction, and present a method to solve the equations analytically for a single mode fi,eld within the Rotating-Wave Approximation. As an... 

Magnetite (Fe3O4) nanostructures with different morphologies including uniform nanoparticles, magnetic beads and nanorods were synthesized via a co-precipitation method. The synthesis process was performed at various temperatures in the presence of polyvinyl alcohol (PVA) at different concentrations. It is shown that small amounts of PVA act as a template in hot water (70 °C), leading to the oriented growth of Fe3O4 nanorods, which was confirmed by selected area electron diffraction. Individually coated magnetite nanoparticles and magnetic beads were formed at a relatively lower temperature of 30 °C in the folded polymer molecules due to the thermo-physical properties of PVA. When a moderate... 

Bacterial outer membrane porins (Omp) that have robust β -barrel structures, show potential applications for nanomedicine devices in synthetic membranes and single molecule detection biosensors. Here, we explore the conformational dynamics of a set of 22 outer membrane porins, classified into five major groups: general porins, specific porins, transport Omps, poreless Omps and composed pores. Normal mode analysis, based on mechanical vibration theory and elastic network model, is performed to study the fluctuations of residues of aforementioned porins around their equilibrium positions. We find that a simple modification in this model considering weak interaction between protein and... 

A quantum modeling of the CO adsorption on illuminated anatase TiO2 (0 0 1) is presented. The calculated adsorption energy and geometries of illuminated case are compared with the ground state case. The calculations were achieved by using DFT formalism and the BH and HLYP. Upon photoexcitation, an electron-hole pair is generated. Comparing of natural population in the ground state and the exited state, shows that an electron is trapped in a Ti4+ ion and a hole is localized in an oxygen ion. The photoelectron helps generation of a CO2 molecule on the TiO2 surface. As shown by optimization of these systems, the CO molecule adsorbed vertically on the TiO2 (0 0 1) surface in the ground state... 

The effects of embedded proteins on the dynamical properties of lipid bilayer membranes are studied in shear flow. Coarse-grained molecular simulations are employed, in which lipids are modeled as short polymers consisting of hydrophilic head groups and hydrophobic tail monomers; similarly, transmembrane proteins are modeled as connected hydrophobic double- or triple-chain molecules with hydrophilic groups at both ends. In thermal equilibrium, rigid proteinlike molecules aggregate in a membrane of flexible lipids, while flexible proteins do not aggregate. In shear flow parallel to the membrane, the monolayers of lipid bilayer slide over each other. The presence of transmembrane proteins... 

Theoretical study of NH3(H2O) n=0,1,2,3 adsorption on (8, 0) carbon nanotube was performed at the X3LYP/6-31G* level of density functional theory (DFT). The tube-NH3 interaction was discussed in the terms of binding energy (EB), coupling energy (EC), charge density, molecular orbitals, and dipole moments. The results reveal that addition of water molecules to tube-NH3 system increases the interaction between tube and ammonia molecule  

In this paper, we try to explain the origin of the anomalous elastic behavior of nanometersized DNA molecules, which has been observed in all-atom molecular dynamic simulations [A.K. Mazur, Biophys. J. 2006]. It is shown that this anomalous behavior is a consequence of nonlocal interactions between DNA base pairs and the intrinsic curvature of DNA. A nonlocal harmonic elastic rod model is proposed, which can successfully describe the elastic behavior of short DNA molecules  

The influence of the addition of the nonionic surfactants C12DMPO, C14DMPO, C10OH, and C10EO5 at concentrations between 10-5 and 10-1 mmol/L to solutions of β-casein (BCS) and β-lactoglobulin (BLG) at a fixed concentration of 10-5 mmol/L on the dilational surface rheology is studied. A maximum in the viscoelasticity modulus |E| occurs at very low surfactant concentrations (10-4 to 10-3 mmol/L) for mixtures of BCS with C12DMPO and C14DMPO and for mixtures of BLG with C10EO5, while for mixture of BCS with C10EO5 the value of |E| only slightly increased. The |E| values... 

In radio channels modelings, the phases and amplitudes of the rays undergo some modifications when they are reflected from or transmitted through a particular material. These reflection and transmission coefficients make use of the electrical properties of the materials, thus, it is essential to know the values of the relative dielectric constant and of the conductivity or the loss tangent of the materials that appear in the propagation environments. In this paper, a theoretical model based on the inter-molecule interactions, has been developed and used to estimate the dielectric parameters of glass. ©2009 IEEE  

In this paper, we consider abnormality detection via diffusive molecular communications (MCs) for a network consisting of several sensors and a fusion center (FC). If a sensor detects an abnormality, it injects a number of molecules into the medium which is proportional to its sensing output. Two transmission schemes for releasing molecules into the medium are considered. In the first scheme, each sensor releases a different type of molecule (DTM), whereas in the second scheme, all sensors release the same type of molecule (STM). The molecules released by the sensors propagate through the MC channel and some may reach the FC where the final decision regarding whether or not an abnormality... 

The objective of this paper is to investigate dynamical pull-in behavior of an electrostatic actuated nano-device based on Eringen's nonlocal elasticity theory. The Euler–Bernoulli beam model is used to establish the dynamic equation of motion of the nano-device subjected to both electrostatic and intermolecular forces. The nanobeam is considered with axially immovable ends and the geometrically nonlinearity due to mid-plane stretching is incorporated to the model as well. A new intermolecular attractive force model based on the macroscopic interactions of a circular cross section nanobeam and a flat surface is presented for the carbon nanotube based nano-device. The nonlinear static... 

Perovskite solar cells (PSCs) use perovskites with an APbX3 structure, where A is a monovalent cation and X is a halide such as Cl, Br, and/or I. Currently, the cations for high-efficiency PSCs are Rb, Cs, methylammonium (MA), and/or formamidinium (FA). Molecules larger than FA, such as ethylammonium (EA), guanidinium (GA), and imidazolium (IA), are usually incompatible with photoactive “black”-phase perovskites. Here, novel molecular descriptors for larger molecular cations are introduced using a “globularity factor”, i.e., the discrepancy of the molecular shape and an ideal sphere. These cationic radii differ significantly from previous reports, showing that especially ethylammonium (EA)... 

The multielectron dissociative ionization of CH4 and CH2O molecules has been investigated using optimum convolution of different dual tailored short laser pulses. Based on three dimensional molecular dynamics simulations and TDDFT approach, the dissociation probability is enhanced by designing the dual chirped-chirped laser pulses and chirped-ordinary laser pulses for formaldehyde molecule. However, it is interesting to notice that the sensitivity of enhanced dissociation probability into different tailored laser pulses is not significant for methane molecule. In this presented modifications, time variation of bond length, velocity, time dependent electron localization function and evolution... 

Conformational diseases have been investigated extensively in recent years; as a result, a number of drug candidates have been introduced as amyloid inhibitors; however, no effective therapies have been put forward. RS-0406 with pyridazine as its core chemical structure has so far shown promising results in inhibiting amyloid formation. In the present work, using molecular dynamics, we undertook the investigation of RS-0406 interactions with U-shaped Aβ1−42 and Aβ1−40 pentamers, Aβ1−42 monomers, and double-horseshoe-like Aβ1−42. To set better parameters for the small molecule, experimental and computational log P values were obtained. In addition, an analogue of RS-0406 was also simulated... 

Diffusion weighted imaging is a non-invasive method for investigation of brain fiber bundles. In diffusion tensor imaging (DTI), the diffusion of water molecules is assumed Gaussian, therefore, it can just show a single fiber direction in a voxel. To overcome this limitation, a number of high angular resolution diffusion imaging methods have been proposed. One of these techniques is Q-ball imaging. Using this method, we can extract orientation distribution function (ODF) that shows the orientations of multiple fibers in a voxel. For extracting the fiber directions, the maxima of the ODFs are conventionally determined. However, the results of this approach are sensitive to noise. To improve... 

Highly sensitive flexible humidity sensors based on graphene quantum dots (GQDs) were developed. The GQDs were prepared using a facile hydrothermal method and characterized considering morphological, structural, and compositional experiments. Then, their humidity sensing properties in correlation with flexibility characteristics were investigated. Good selectivity and response (∼390 for a RH change of 99%), broad detection range (1-100% RH), rather short response and recovery times (12 and 43 s, respectively) as well as flexibility were obtained, demonstrating that the GQD sensors have potential for application in wearable electronics and RH monitoring. Detection of hydrogen (H2) gas by the...