Sharif Digital Repository

We introduce a two-channel microfluidic atomic force microscopy (AFM) cantilever that combines the nanomechanical sensing functionality of an AFM cantilever with the ability to manipulate fluids of picolitres or smaller volumes through nanoscale apertures near the cantilever tip. Each channel is connected to a separate fluid reservoir, which can be independently controlled by pressure. Various systematic experiments with fluorescent liquids were done by either injecting the liquids from the on-chip reservoir or aspirating directly through the nanoscale apertures at the tip. A flow rate analysis of volume dosing, aspiration and concentration dosing inside the liquid medium was performed. To... 

The main focus of this study is to address the possibility of using molecular dynamics (MD) simulation, as a computational framework, coupled with experimental assays, to optimize composite structures of a particular electrospun scaffold. To this aim, first, MD simulations were performed to obtain an initial theoretical insight into the capability of heterogeneous surfaces for protein adsorption. The surfaces were composed of six different blends of PVA (polyvinyl alcohol) and PCL (polycaprolactone) with completely unlike hydrophobicity. Next, MTT assay was performed on the electrospun scaffolds made from the same percentages of polymers as in MD models to gain an understanding of the... 

Resection of the epilepsy foci is the best treatment for more than 15% of epileptic patients or 50% of patients who are refractory to all forms of medical treatment. Accurate mapping of the locations of epileptic neuronal networks can result in the complete resection of epileptic foci. Even though currently electroencephalography is the best technique for mapping the epileptic focus, it cannot define the boundary of epilepsy that accurately. Herein we put forward a new accurate brain mapping technique using superparamagnetic nanoparticles (SPMNs). The main hypothesis in this new approach is the creation of super-paramagnetic aggregates in the epileptic foci due to high electrical and... 

Stress sensitivity is a phenomenon that affects reservoir rock properties, such as permeability and therefore changes the well pressure transient behavior. This paper aims to study these behaviors in stress sensitive reservoirs and evaluate the pressure loss in such reservoirs during the process of hydrocarbon production. A power model is used to correlate the changes in permeability with pore pressure. A novel semi-implicit three-dimensional finite element method has been employed to numerically solve the flow problem. The numerical results have been validated by analytical results obtained in a non-sensitive reservoir. Pressure drawdown test for different scenarios has been studied. The... 

Axon is a filament in neuronal system and axonal microtubules are bundles in axons. In axons, microtubules are coated with microtubule-associated protein tau, a natively unfolded profuse filamentous protein in the central nervous system. These proteins are responsible for the cross-linked structure of the axonal microtubule bundles. Through complimentary dimerization with other tau proteins, bridges are formed to nearby microtubules to create bundles. The transverse reinforcement of microtubules by cross-linking to the cytoskeleton has been shown to enhance their ability to bear compressive loads. Though microtubules are conventionally regarded as bearing compressive loads, in certain... 

Skeletal muscle tissue engineering aims to fabricate tissue constructs to replace or restore diseased or injured skeletal muscle tissues in the body. Several biomaterials and microscale technologies have been used in muscle tissue engineering. However, it is still challenging to mimic the function and structure of the native muscle tissues. Three-dimensional (3D) bioprinting is a powerful tool to mimic the hierarchical structure of native tissues. Here, 3D bioprinting was used to fabricate tissue constructs using gelatin methacryloyl (GelMA)-alginate bioinks. Mechanical and rheological properties of GelMA-alginate hydrogels were characterized. C2C12 myoblasts at the density 8 × 106 cells/mL... 

The main goal of this study is to investigate the role of vascular graft thickness in wall stress gradient in anastomosis region. Atherosclerosis is a common heart disease causes high mortality rates every year. The gold standard treatment of atherosclerosis is replacing with autologous vein extracted from patient's body. Since proper autologous vein is limited, researchers have made efforts to achieve compliance engineered blood vessels. Mechanical stress has great effect on both smooth muscle cells and endothelial cells and it is considered as a stimulus in plaque formation. In this study, we evaluate the role of thickness in wall stress of anastomosis region. For this purpose, two... 

The main goal of this study is to investigate the role of vascular graft thickness in wall stress gradient in anastomosis region. Atherosclerosis is a common heart disease causes high mortality rates every year. The gold standard treatment of atherosclerosis is replacing with autologous vein extracted from patient's body. Since proper autologous vein is limited, researchers have made efforts to achieve compliance engineered blood vessels. Mechanical stress has great effect on both smooth muscle cells and endothelial cells and it is considered as a stimulus in plaque formation. In this study, we evaluate the role of thickness in wall stress of anastomosis region. For this purpose, two... 

In this paper, the eXtended Finite Element Method (X-FEM) is developed in pressure-sensitive plasticity of powder compaction process. In X-FEM, the need for mesh adaption to discontinuity interface is neglected and the process is accomplished by employing additional functions, which are added to approximate the displacement field of the elements located on the interface. The double-surface cap plasticity model is employed within the X-FEM framework in numerical simulation of powder material. The plasticity model includes a failure surface and an elliptical cap, which closes the open space between the failure surface and hydrostatic axis. The moving cap expands in the stress space according... 

A great amount of effort has been made in order to reach a more precise understanding of the adhesion phenomenon that happens as a vital component of several biological systems. Therefore, a firm understanding of the important factors that influence this phenomenon is of special importance in triggering the adhesive characteristics of different biological, bio-inspired and synthetic materials in fields such as tissue engineering. In this study the adhesive characteristics of a multi-material system consisting of the frequently used synthetic material, graphene, in the form of armchair-configuration sheets, and an important biological filament which is type 1 Collagen consisting of 3 alpha... 

Achieving high efficiency and throughput in droplet-based mixing over a small characteristic length, such as microfluidic channels, is one of the crucial parameters in Lab-on-a-Chip (LOC) applications. One solution to achieve efficient mixing is to use active mixers in which an external power source is utilized to mix two fluids. One of these active methods is magnetic micromixers using ferrofluid. In this technique, magnetic nanoparticles are used to make one phase responsive to magnetic force, and then by applying a magnetic field, two fluid phases, one of which is magneto-responsive, will sufficiently mix. In this study, we investigated the effect of the magnetic field’s characteristics... 

Since the beginning of the COVID-19 pandemic, nearly most confirmed cases develop respiratory syndromes. Using targeted drug delivery by microcarriers is one of the most important noteworthy methods for delivering drugs to the involved bronchi. This study aims to investigate the performance of a drug delivery that applies microcarriers to each branch of the lung under the influence of a magnetic field. The results show that by changing the inlet velocity from constant to pulsatile, the drug delivery performance to the lungs increases by ∼31%. For transferring the microcarriers to the right side branches (LUL and LLL), placing the magnet at zero height and ∼30° angle yields the best outcome.... 

Epilepsy is the most common neurological disorder that is known with uncontrolled seizure. Around 30% of patients with epilepsy resist to all forms of medical treatments and therefore, the removal of epileptic brain tissue is the only solution to get these patients free from chronical seizures. The precise detection of an epileptic zone is key to its treatment. In this paper, we propose a method of epilepsy detection using brain magnetic field. The possibility of superparamagnetic nanoparticle (SPMN) as sensors for the detection of the epileptic area inside the brain is investigated. The aggregation of nanoparticles in the weak magnetic field of epileptic brain is modeled using potential... 

In the recent years a great attention of research deals with different physical and biological aspects of the BBB structure, a robust shield that separates the blood and brain, a recent research held by the authors of this paper has focused on figuring out computing the diffusion coefficient of endothelial cell membrane. In this study, the major efforts have been concentrated on calculating a standardized measure for the amount of permeability and diffusion of this barrier. As a result, this work is dedicated to molecular dynamics (MD) simulation of calculating the interaction force between nano-particle and BBB membrane. data is recorded by using steered molecular dynamics simulation and... 

Paramecium or other ciliates have the potential to be utilized for minimally invasive surgery systems, making internal body organs accessible. Paramecium shows interesting responses to changes in the concentration of specific ions such as K+, Mg2+, and Ca2+ in the ambient fluid. Some specific responses are observed as, changes in beat pattern of cilia and swimming toward or apart from the ion source. Therefore developing a model for chemotactic motility of small organisms is necessary in order to control the directional movements of these microorganisms before testing them. In this article, we have developed a numerical model, investigating the effects of Ca2+ on swimming trajectory of... 

Chemical bioreactions are an important aspect of many recent microfluidic devices, and their applications in biomedical science have been growing worldwide. Droplet-based microreactors are among the attractive types of unit operations, which utilize droplets for enhancement in both mixing and chemical reactions. In the present study, a finite-volume-method (FVM) numerical investigation is conducted based on the volume-of-fluid (VOF) applying for the droplet-based flows. This multiphase computational modeling is used for the study of the chemical reaction and mixing phenomenon inside a serpentine microchannel and explores the effects of the aspect ratio (i.e., AR = height/width) of... 

Alzheimer’s disease (AD) is an irreversible neurological disorder that progresses gradually and can cause severe cognitive and behavioral impairments. This disease is currently considered a social and economic incurable issue due to its complicated and multifactorial characteristics. Despite decades of extensive research, we still lack definitive AD diagnostic and effective therapeutic tools. Consequently, one of the most challenging subjects in modern medicine is the need for the development of new strategies for the treatment of AD. A large body of evidence indicates that amyloid-β (Aβ) peptide fibrillation plays a key role in the onset and progression of AD. Recent studies have reported... 

The main goal of this study is to investigate the effects of plaque structure on its stress distribution. Rupture of plaque causes cerebrovascular diseases which lead to high mortality rates all over the world. Computers are powerful tools to understand the mechanism of plaque rupture. In this study, 3D fluid structure interaction simulation is constructed in ABAQUS 6.13 to clarify the relation between stress distribution of plaque and its structure. A model of common carotid artery with distributed stenosis was chosen for the simulation. To investigate the effects of plaque structure on stress distribution, thickness of fibrous cap and lipid core size were varied in the stenosis.... 

Atherosclerotic plaques and thrombosis are chronic inflammatory complications and the main manifestations of cardiovascular diseases (CVD), the leading cause of death globally. Achieving non/minimal-invasive therapeutic means for these implications in the coronary network is vital and has become an interdisciplinary concern. Accordingly, smart drug delivery systems, specifically based on micro- and nanoparticles, as a promising method to offer non/minimal-invasive therapeutic mechanisms are under active research. Notably, computational models enable us to study, design, and predict treatment strategies based on smart drug delivery systems with less time and cost compared with conventional... 

Microfluidic experiments have found wide applications in medical sciences and engineering, such as cell separation and focusing. In the present study, focusing and separation of particles with different sizes and densities were investigated by designing inertial microfluidic devices. The microfluidic channel is designed by analyzing the induced forces on the particles. In the designing process, the objective was to focus and separate the particles in the shortest length of the channel with the lowest possible cycles and high efficiency. The simulation is then used for analyzing the two proposed geometries to evaluate their particle separation and focusing ability, named convergent and...