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 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... 

Since physiological and pathological processes occur at nano-environments, nanotechnology has considered as an efficient tool for designing of next generation specific biomolecules with enhanced pharmacodynamic and pharmacodynamic properties. In the current investigation, by control of the size and hydrodynamic volume at the nanoscale, for the first time, physicochemical and pharmacokinetic properties of an anti-VEGFA nanobody was remarkably improved by attachment of a Proline-Alanine-Serine (PAS) rich sequence. The results elucidated unexpected impressive effects of PAS sequence on physicochemical properties especially on size, hydrodynamics radius, and even solubility of nanobody. CD... 

Since physiological and pathological processes occur at nano-environments, nanotechnology has considered as an efficient tool for designing of next generation specific biomolecules with enhanced pharmacodynamic and pharmacodynamic properties. In the current investigation, by control of the size and hydrodynamic volume at the nanoscale, for the first time, physicochemical and pharmacokinetic properties of an anti-VEGFA nanobody was remarkably improved by attachment of a Proline-Alanine-Serine (PAS) rich sequence. The results elucidated unexpected impressive effects of PAS sequence on physicochemical properties especially on size, hydrodynamics radius, and even solubility of nanobody. CD... 

Motif discovery is a challenging problem in molecular biology and has been attracting researcher's attention for years. Different kind of data and computational methods have been used to unravel this problem, but there is still room for improvement. In this study, our goal was to develop a method with the ability to identify all the TFBS signals, including known and unknown, inside the input set of sequences. We developed a clustering method specialized as part of our algorithm which outperforms other existing clustering methods such as DNACLUST and CD-HIT-EST in clustering short sequences. A scoring system was needed to determine how much a cluster is close to being a real motif. Multiple... 

Haplotype information has become increasingly important in analyzing fine-scale molecular genetics data, Due to the mutated form in human genome; SNPs (Single Nucleotide Polymorphism) are responsible for some genetic diseases. As a consequence, obtaining all SNPs from human populations is one of the primary goals of studies in human genomics. In this paper, a data fusion method based on multiple parallel classifiers for reconstruction of haplotypes from a given sample Single Nucleotide Polymorphism (SNP) is proposed. First, we design a single greedy algorithm for solving haplotype reconstructions. [2] is used as an efficient approach to be combined with first classification method. The... 

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 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... 

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... 

Breast cancer incidence has increased in recent decades. In the present study, an optimum formulation of chitosan (CS)-adorned niosome-based nanocarriers for co-delivery of doxorubicin (DOX) and vincristine (VIN) was developed for the treatment of breast cancer to reduce drug doses and overcome multidrug resistance. The three-level Box-Behnken method was utilized to optimize the particles in terms of size, polydispersity index (PDI), entrapment efficacy (EE (%)), and percent of drug release (%). The release rate of two drugs from CS-adorned nanoparticles (DOX+VIN/Nio/CS) in acidic and physiological pH is less than uncoated niosome (DOX+VIN/Nio). In addition, acidic pH increases the release... 

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... 

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...