Sharif Digital Repository

In this paper, the effect of silica nanoparticles on oil production due to the spontaneous imbibition of brine into oil-wet sandstones has been studied. The imbibed fluids were NaCl 3 wt. % solutions containing various concentrations of nanoparticles and the recovered oil for each solution was compared. The results revealed that nanoparticles yielded more oil recovery. Nanofluid was used after brine imbibition, and the oil recovery increased from 17.8% to 40% while in the case of using the same nanofluid as the first imbibed fluid the oil recovery was 53%. Also, the results indicated that the oil recovery depends on nanoparticle concentrations. © 2019, © 2019 Taylor & Francis Group, LLC  

The potential for using Thermophotovoltaic (1TPV) generators as an alternative for recovering energy losses in steel production industry is assessed. A mathematical model for the assessment of the performance of TPV application in the iron and steel industry has been developed. In order to support the mathematical model, a sample TPV apparatus in laboratory scale based on an IR emitter has been designed and assembled. The key modeling parameters of TPV generator include: the open circuit voltage, the short circuit current density and fill factor of the TPV cell. These parameters have been considered in the model as functions of several variables such as: the emitter (hot steel slab)... 

Optical tweezers are proven indispensable single-cell micro-manipulation and mechanical phenotyping tools. In this study, we have used optical tweezers for measuring the viscoelastic properties of human red blood cells (RBCs). Comparison of the viscoelastic features of the healthy fresh and atorvastatin treated cells revealed that the drug softens the cells. Using a simple modeling approach, we proposed a molecular model that explains the drug-induced softening of the RBC membrane. Our results suggest that direct interactions between the drug and cytoskeletal components underlie the drug-induced softening of the cells. © 2018 Optical Society of America  

This review aims to propose the integrative implementation of microfluidic devices, biomaterials, and computational methods that can lead to a significant progress in tissue engineering and regenerative medicine researches. Simultaneous implementation of multiple techniques can be very helpful in addressing biological processes. Providing controllable biochemical and biomechanical cues within artificial extracellular matrix similar to in vivo conditions is crucial in tissue engineering and regenerative medicine researches. Microfluidic devices provide precise spatial and temporal control over cell microenvironment. Moreover, generation of accurate and controllable spatial and temporal... 

The objective of this study is to design a novel and efficient portable lab-on-a-CD (LOCD) microfluidic device for separation of specific cells (target cells) using magnetic beads. In this study the results are shown for neutrophils as target cells. However, other kinds of target cells can be separated in a similar approach. The designed microfluidics can be utilized as a point of care system for neutrophil detection. This microfluidic system employs centrifugal and magnetic forces for separation. After model validation by the experimental data in the literature (that may be used as a design tool for developing centrifugo-magnetophoretic devices), two models are presented for separation of... 

Upon incubation of nanoparticles in biological fluids, a new layer called the protein corona is formed on their surface affecting the interactions between nanoparticles and targeted cells during the endocytosis process. In the present study, a mathematical model based on the diffusion of membrane mobile receptors is proposed. Opposing the endocytosis proceeding, membrane bending and tension energies are named as resistant energy. Also, the binding energy and free-energy associated with the configurational entropy are collectively termed promoter energy. Utilizing this model, endocytosis of gold nanoparticle (GNP) is simulated to explore the biological media effect. The results reveal that... 

In this study, a multi-scale model is proposed to assess softening kinetics and microstructural changes during isothermal annealing within an aluminum alloy. In the first stage, an elastic-plastic finite element analysis is performed for computing the distributions of effective plastic strain and stress while the stored energy after cold rolling is defined based on the predicted data and then utilized for generation of the initial conditions in the microstructural analysis. In the next stage, an algorithm based on cellular automata coupled with a first order rate equation is used to determine the progress of softening behavior at elevated temperatures while both recrystallization and... 

Biological cell injection is a sensitive and important work which is implemented in injection of foreign materials into individual cells. Microinjection is significantly developed in the field of drug discovery and genetics so predicting the behavior of cell in microinjection is remarkably important because a tiny excessive manipulation force can destroy the tissue of the biological cell. There are a few analytical methods available to simulate the cell injection, hence the numerical methods such as FEM are suitable to be used to model the microinjection. In this study, a new spherical super element is presented to model the biological cells and deformation of a specific cell under an... 

Biological cell injection is a sensitive and important work which is implemented in injection of foreign materials into individual cells. Microinjection is significantly developed in the field of drug discovery and genetics so predicting the behavior of cell in microinjection is remarkably important because a tiny excessive manipulation force can destroy the tissue of the biological cell. There are a few analytical methods available to simulate the cell injection, hence the numerical methods such as FEM are suitable to be used to model the microinjection. In this study, a new spherical super element is presented to model the biological cells and deformation of a specific cell under an... 

The graphene-based materials with unique, versatile, and tunable properties have brought new opportunities for the leading edge of advanced nanobiotechnology. In this regard, the use of graphene in gene delivery applications is still at early stages. In this study, we successfully designed a new complex of carboxylated-graphene (G-COOH) with ethidium bromide (EtBr) and used it as a nanovector for efficient gene delivery into the AGS cells. G-COOH, with carboxyl functions on its surface, in the presence of EtBr, formaldehyde, and cyclohexylisocyanide were participated in Ugi four component reaction to fabricate a stable amphiphilic graphene-EtBr (AG-EtBr) composite. The coupling reaction was... 

Several evidences support the idea that a small population of tumour cells representing self-renewal potential are involved in initiation, maintenance, metastasis, and outcomes of cancer therapy. Elucidation of microRNAs/genes regulatory networks activated in cancer stem cells (CSCs) is necessary for the identification of new targets for cancer therapy. The aim of the present study was to predict the miRNAs pattern, which can target both metastasis and self-renewal pathways using integration of literature and data mining. For this purpose, mammospheres derived from MCF-7, MDA-MB231, and MDA-MB468 were used as breast CSCs model. They had higher migration, invasion, and colony formation... 

Herein, the NH2-UiO-66 metal organic framework (MOF) has been green synthesized with the assistance of high gravity to provide a suitable and safe platform for drug loading. The NH2-UiO-66 MOF was characterized using a field-emission scanning electron microscope, transmission electron microscope (TEM), X-ray diffraction, and zeta potential analysis. Doxorubicin was then encapsulated physically on the porosity of the green MOF. Two different stimulus polymers, p(HEMA) and p(NIPAM), were used as the coating agents of the MOFs. Doxorubicin was loaded onto the polymer-coated MOFs as well, and a drug payload of more than 51% was obtained, which is a record by itself. In the next step, pCRISPR was... 

With large amounts of experimental data, modern molecular biology needs appropriate methods to deal with biological sequences. In this work, we apply a statistical method (Pearson's chi-square test) to recognize the signals appear in the whole genome of the Escherichia coli. To show the effectiveness of the method, we compare the Pearson's chi-square test with linguistic complexity on the complete genome of E. coli. The results suggest that Pearson's chi-square test is an efficient method for distinguishing genes (coding regions) form pseudogenes (noncoding regions). On the other hand, the performance of the linguistic complexity is much lower than the chi-square test method. We also use the... 

The separation of cancer cells from a heterogeneous biological sample such as blood plays a vital role in cancer study and future treatments. In this paper, we designed and investigated two microfluidic devices for cancer cell separation, including a serpentine inertial device and an integrated inertial-magnetophoretic device. Firstly, numerical modeling was carried out to study the fluid flow, particles’ trajectories in the inertial device. Then the device was fabricated using soft photolithography and suspension of two types of microparticles with the size of 10 and 15 µm were injected into the microchannel separately to investigate the particles’ trajectories and focusing behavior at... 

Multiple sequence alignment (MSA) is one of the basic and important problems in molecular biology. MSA can be used for different purposes including finding the conserved motifs and structurally important regions in protein sequences and determine evolutionary distance between sequences. Aligning several sequences cannot be done in polynomial time and therefore heuristic methods such as genetic algorithms can be used to find approximate solutions of MSA problems. Several algorithms based on genetic algorithms have been developed for this problem in recent years. Most of these algorithms use very complicated, problem specific and time consuming mutation operators. In this paper, we propose a... 

Abstract: A novel simple synthetic procedure for improving cell efficiency and reducing the production cost of TiO2 dye-sensitized solar cells (DSSCs) by modification and optimization of homemade formulated paste is reported. This is achieved in terms of morphological manipulation of deposited monolayer TiO2 films by controlling three processing parameters of paste formulation. These parameters are tailored to obtain a paste with proper viscosity suitable for spin-coating technique and to achieve uniform, homogeneous, and crack-free films with good connections between TiO2 grains and porous structure. Photovoltaic measurements show that TiO2... 

Cascaded split-source inverter (CSSI) is a new single-stage modular multilevel topology. Each cell of this converter converts DC to AC power in the buck or boost operation mode without any additional power switch. This paper develops a design method based on a detailed model for CSSI. This model shows that energy storage elements experience double-fundamental frequency ripples besides high-frequency ones. It accurately calculates voltage gains and capacitor voltage and inductor current ripples. On the other hand, common carrier-based multilevel modulations have been modified in terms of both reference and carrier signals to control the inverter under symmetric and asymmetric conditions. With... 

In this study, a general 3D distributed modeling of Trolling-Mode AFM (TR-AFM) as a nanorobot is presented to analyze the 2D manipulation process of a spherical cell. To this aim, the analysis is categorized into 3 sections. In the first section, 6 deformations of TR-AFM are taken into account, and the standard model of the system is obtained. Moreover, the system is simulated in ANSYS Workbench. The results of modal and transient analyses of the system from both analytical and software methods reveal high agreement, which confirms the accuracy of the presented analytical model. In the second section, by utilizing the 3D derived model, displacement of a spherical yeast single cell (W303)... 

Protein fibrillation process (e.g., from amyloid beta (Aβ) and α-synuclein) is the main cause of several catastrophic neurodegenerative diseases such as Alzheimer's and Parkinson diseases. During the past few decades, nanoparticles (NPs) were recognized as one of the most promising tools for inhibiting the progress of the disease by controlling the fibrillation kinetic process; for instance, gold NPs have a strong capability to inhibit Aβ fibrillations. It is now well understood that a layer of biomolecules would cover the surface of NPs (so called "protein corona") upon the interaction of NPs with protein sources. Due to the fact that the biological species (e.g., cells and amyloidal...