Sharif Digital Repository

The discrete fracture network (DFN) and Multiple-Continua concept are among the most widely used methods to model naturally fractured reservoirs. Each faces specific limitations. The recently introduced recovery curve method (RCM) is believed to be a compromise between these two current methods. In this method the recovery curves are used to determine the amount of mass exchanges between the matrix and fracture mediums. Two recovery curves are assigned for each simulation cell, one curve for gas displacement in the presence of the gravity drainage mechanism, and another for water displacement in the case of the occurrence of the imbibition mechanism. These curves describe matrix-fracture... 

Intracellular production of recombinant proteins in prokaryotes necessitates subsequent disruption of cells for protein recovery. Since the cell disruption and subsequent purification steps largely contribute to the total production cost, scalable tools for protein release into the extracellular space is of utmost importance. Although there are several ways for enhancing protein release, changing culture conditions is rather a simple and scalable approach compared to, for example, molecular cell design. This contribution aimed at quantitatively studying process technological means to boost protein release of a periplasmatic recombinant protein (alkaline phosphatase) from E. coli.... 

Natural aging behavior of the aluminum 6061 alloy after a novel Severe Plastic Deformation process called Tube Channel Pressing (TCP) was studied. For this purpose, Vickers microhardness test was used to investigate the changes of mechanical properties while TEM and XRD observations were utilized in order to characterize microstructural evolution during natural aging. Results show that Si-enriched precipitates appear and coarsen rapidly in the first few days of natural aging of TCPed aluminum 6061 alloy which causes consecutive increase and decrease of Vickers microhardness, respectively. Similarly, other alloying elements such as Cu and Fe lead to formation of coarse precipitates during... 

Upon incorporation of nanoparticles (NPs) into the body, they are exposed to biological fluids, and their interaction with the dissolved biomolecules leads to the formation of the so-called protein corona on the surface of the NPs. The composition of the corona plays a crucial role in the biological fate of the NPs. While the effects of various physicochemical parameters on the composition of the corona have been explored in depth, the role of temperature upon its formation has received much less attention. In this work, we have probed the effect of temperature on the protein composition on the surface of a set of NPs with various surface chemistries and electric charges. Our results... 

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... 

Nano-micro grippers are able to pick-transport-place the micro or nanometer -sized materials, such as manipulation of biological cells or DNA molecules in a liquid medium. This paper proposes a novel monolithic nano-micro gripper structure with two axis piezoresistive force sensor which its resolution is under nanoNewton. The results of the study have been obtained by the simulation of the proposed gripper structure in Matlab software. Motion of the gripper arm is produced by a voice coil actuator. The behavior of the cell has been derived using the assumptions in the literatures. Moreover, two simple PID controllers, one for control of the gripper motion and another for control of the force... 

In this study, neural network models have been used to predict the mechanical behaviors of mouse embryos. In addition, sensitivity analysis has been carried out to investigate the influence of the significance of input parameters on the mechanical behavior of mouse embryos. In order to reach these purposes two neural network models have been implemented. Experimental data earlier deduced-by [Flückiger, M. (2004). Cell Membrane Mechanical Modeling for Microrobotic Cell Manipulation. Diploma Thesis, ETHZ Swiss Federal Institute of Technology, Zurich, WS03/04]-were collected to obtain training and test data for the neural network. The results of these investigations show that the correlation... 

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 present study investigated the biological treatment of produced water in a microbial electrochemical cell (MXC). The main objectives were to develop a novel spiral microbial electrochemical cell (SMXC) and test its performance for produced water treatment under highly saline conditions (salinity > 200000 ppm). The bioelectrochemical performance of the system was also evaluated in terms of power and hydrogen production over time. The comparatively inexpensive material and ease of application increased the feasibility of the SMXC configuration for produced water treatment. Optimal SMXC performance as a microbial fuel cell was achieved at a maximum open circuit potential of 330 mV, maximum... 

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... 

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... 

The discrete fracture network (DFN) and Multiple-Continua concept are among the most widely used methods to model naturally fractured reservoirs. Each faces specific limitations. The recently introduced recovery curve method (RCM) is believed to be a compromise between these two current methods. In this method the recovery curves are used to determine the amount of mass exchanges between the matrix and fracture mediums. Two recovery curves are assigned for each simulation cell, one curve for gas displacement in the presence of the gravity drainage mechanism, and another for water displacement in the case of the occurrence of the imbibition mechanism. These curves describe matrix-fracture... 

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... 

Developments of sensitive, rapid, and cheap systems for identification of a wide range of biomolecules have been recognized as a critical need in the biology field. Here, we introduce a simple colorimetric sensor array for detection of biological thiols, based on aggregation of three types of surface engineered gold nanoparticles (AuNPs). The low-molecular-weight biological thiols show high affinity to the surface of AuNPs; this causes replacement of AuNPs' shells with thiol containing target molecules leading to the aggregation of the AuNPs through intermolecular electrostatic interaction or hydrogen-bonding. As a result of the predetermined aggregation, color and UV-vis spectra of AuNPs... 

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)... 

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... 

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... 

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...