Sharif Digital Repository

Microfluidic devices are beneficial in miniaturizing and multiplexing various cellular assays in a single platform. Chondrogenesis is known to pertain to chemical, topographical, and mechanical cues in the microenvironment. Mechanical cues themselves have numerous parameters such as strain magnitude, frequency, and stimulation time. Effects of different strain magnitudes on the chondrogenic differentiation of adult stem cells have not been explored thoroughly. Here, a new multilayer microdevice is presented for the unidirectional compressive stimulation of cells in a three-dimensional cell culture. Numerical simulations were performed to evaluate and optimize the design. Results showed a... 

Endothelial cell migration is a crucial step in the process of new blood vessel formation - a necessary process to maintain cell viability inside thick tissue constructs. Here, we report a new method for maintaining cell viability and inducing cell migration using a perfused microfluidic platform based on collagen gel and a gradient hydrogel sheet. Due to the helpful role of the extracellular matrix components in cell viability, we developed a hydrogel sheet from decellularized tissue (DT) of the bovine heart and chitosan (CS). The results showed that hydrogel sheets with an optimum weight ratio of CS/DT = 2 possess a porosity of around 75%, a mechanical strength of 23 kPa, and display cell... 

Stepped planing hulls enable the feasibility of running at relatively low Drag-Lift ratio by means of achieving more optimal trim angle at high speeds. Currently, there is no precise method to analyze these hulls over the full range of operating speeds. In this study, a three-dimensional computational fluid dynamics (CFD) model using volume of fluid (VOF) approach is presented for examining the characteristics of a planing hull having one transverse step. A procedure is presented to transform a series of fixed-position simulations into a free to heave and pitch simulation. Resistance, lift, running draft, dynamic trim angle, and wetted area are compared with available experimental data and... 

Particle separation has a variety of applications in biology, chemistry and industry. Among them, circulating tumor cells (CTCs) separation has drawn significant attention to itself due to its high impact on both cancer diagnosis and therapeutics. In recent years, there has been growing interest in using inertial microfluidics to separate micro/nano particles based on their sizes. This technique offers label-free, high-throughput and efficient separation and can be easily fabricated. However, further improvements are needed for potential clinical applications. In this study, a novel inertial separation technique using spiral microchannel having stair-like cross section is introduced. The... 

The lipid membranes of living cells form an integral part of biological systems, and the mechanical properties of these membranes play an important role in biophysical investigations. One interesting problem to be evaluated is the effect of protein insertion in one leaflet of a bilayer on the physical properties of lipid membrane. In the present study, an all atom (fine-grained) molecular dynamics simulation is used to investigate the binding of cytotoxin A3 (CTX A3), a cytotoxin from snake venom, to a phosphatidylcholine lipid bilayer. Then, a 5 ms coarse-grained molecular dynamics simulation is carried out to compute the pressure tensor, lateral pressure, surface tension, and first moment... 

Molecular dynamics simulations of four ionic liquids (ILs) based on the [Tf2N] bis(trifluoromethanesulfonyl)imide anion, and imidazolium cations with different alkyl side chains have been performed. These simulations investigate the influence of butyl side chain elimination, tail amine functional addition, and C2 methylation on the dynamics and transport properties of this family of ionic liquids at 400 K. In our earlier work (J. Chem. Eng. Data, 2014, 59, 2834-2849), a suite of thermodynamic quantities and microscopic structures of these ILs were studied by classical molecular dynamics simulations and ab initio calculations. In this work, the dynamics of the ILs are studied by calculating... 

One of the most important biological components is lipid nanobio membrane. The lipid membranes of alive cells and their mechanical properties play an important role in biophysical investigations. Some proteins affect the shape and properties of the nanobio membrane while interacting with it. In this study a multiscale approach is experienced: first a 100ns all atom (fine-grained) molecular dynamics simulation is done to investigate the binding of CTX A3, a protein from snake venom, to a phosphatidylcholine lipid bilayer, second, a 5 micro seconds coarse-grained molecular dynamics simulation is carried out to compute the pressure tensor, lateral pressure, surface tension, and first moment of... 

In this study, the feasibility of producing power and hydrogen from the waste heat of different City Gate Stations (CGSs) is investigated to select the optimal working conditions. A thermodynamic model is developed for a proposed system combined of the CGS station, the Rankin cycle and the extended hydrogen production cycle. Initially, six CGS stations are simulated based on energy, exergy-economic and environmental analysis and then a comparative study is conducted between different stations. The results of numerical modeling show that the Mashhad-old station with 5315 kW and 31.062 ton/year has the highest amount of power and hydrogen production among other stations, respectively. It is... 

A very important part of the living cells of biological systems is the lipid membrane. The mechanical properties of this membrane play an important role in biophysical studies. Investigation as to how the insertion of additional phospholipids in one leaflet of a bilayer affects the physical properties of the obtained asymmetric lipid membrane is of recent practical interest. In this work a coarse-grained molecular dynamics simulation was carried out in order to compute the pressure tensor, the lateral pressure, the surface tension and the first moment of lateral pressure in each leaflet of such a bilayer. Our simulations indicate that adding more phospholipids into one monolayer results in... 

Uranium (VI) sorption using an anionic exchanger resin, namely Amberlite IRA910, in the presence of sulfate anions was the subject of current study. Batch sorption experiments were carried out to evaluate the influence of operational parameters such as pH, contact time, initial concentration and existence of various anions (including phosphate, sulfate, chloride, fluoride, and nitrate) in the solution on Amberlite IRA910 sorption behavior. Experiments revealed that uranium adsorption was fulfiled at pH>3 and 50 min to amount of 80%. Kinetics study revealed that the pseudo-second-order model showed better curve-fitting regression of the experimental data than the pseudo-first-order one.... 

Modeling and analysis of information system vulnerabilities helps us to predict possible attacks to networks using the network configuration and vulnerabilities information. As a fact, exploiting most of vulnerabilities result in access rights alteration. In this paper, we propose a new vulnerability analysis method based on the Take-Grant protection model. We extend the initial Take-Grant model to address the notion of vulnerabilities and introduce the vulnerabilities rewriting rules to specify how the protection state of the system can be changed by exploiting vulnerabilities. Our analysis is based on a bounded polynomial algorithm, which generates the closure of the Take-Grant graph... 

We study the translocation of stiff polymers through a nanopore, driven by the chemical-potential gradient exerted by binding proteins (chaperones) on the trans side of the pore. Bound chaperones prevent backsliding through the pore and, therefore, partially rectify the polymer passage. We show that the sequence of chain monomers with different binding affinity for the chaperones significantly affects the translocation dynamics. In particular, we investigate the effect of the nearest-neighbor adjacency probability of the two monomer types. Depending on the magnitude of the involved binding energies, the translocation speed may either increase or decrease with the adjacency probability. We... 

Combining the advection-diffusion equation approach with Monte Carlo simulations we study chaperone driven polymer translocation of a stiff polymer through a nanopore. We demonstrate that the probability density function of first passage times across the pore depends solely on the Péclet number, a dimensionless parameter comparing drift strength and diffusivity. Moreover it is shown that the characteristic exponent in the power-law dependence of the translocation time on the chain length, a function of the chaperone-polymer binding energy, the chaperone concentration, and the chain length, is also effectively determined by the Péclet number. We investigate the effect of the chaperone size on... 

The amount of rippling in graphene sheets is related to the interactions with the substrate or with the suspending structure. Here, we report on an irreversibility in the response to forces that act on suspended graphene sheets. This may explain why one always observes a ripple structure on suspended graphene. We show that a compression-relaxation mechanism produces static ripples on graphene sheets and determine a peculiar temperature Tc, such that for T