Sharif Digital Repository

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... 

In this study, numerical simulation of collective cell migration is presented in order to mimic the group migration of endothelial cells subjected to the concentration gradients of a biochemical factor. The developed 2D model incorporates basic elements of the cell, including both the cell membrane and the cell cytoskeleton, based on a viscoelastic cell mechanic model. Various cell processes - including cell random walk, cell-cell interactions, cell chemotaxis, and cellular cytoskeleton rearrangements - are considered and analyzed in our developed model. After validating the model by using available experimental data, the model is used to investigate various important parameters during... 

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... 

Mixing is an essential operation in many microfluidic devices. Droplet-based micromixers utilize droplets for mixing enhancement. In the present study, a novel three-dimensional simulation is conducted which has the ability to capture not only the mixing process, but also the chemical reactions inside liquid droplets. This two-phase model is used for simulating the reacting flow inside a serpentine microchannel and explores the effects of droplet size and reaction rate on the production and consumption of species in droplets. It is observed that the chemical reaction in each droplet, begins from its front area. Furthermore, it is shown that the production of species does not depend on water... 

Finding the optimal flow pattern in bipolar plates of a proton exchange membrane is a crucial step for enhancing the performance of the device. This design plays a critical role in fluid mass transport through microporous layers, charge transfer through conductive media, management of the liquid water produced in microchannels, and microporous layers and heat management in fuel cells. This article investigates different types of common flow patterns in bipolar plates while considering a uniform pressure and velocity distribution as well as a uniform distribution of reactants through all the surfaces of the catalyst layer as the design criteria so that there would be a consistent electron... 

Obstruction of left anterior descending artery (LAD) due to the thrombosis or atherosclerotic plaques is the leading cause of death worldwide. Targeted delivery of drugs through micro- and nanoparticles is a very promising approach for developing new strategies in clot-busting or treating restenosis. In this work, we modelled the blood flow characteristics in a patient-specific reconstructed LAD artery by the fluid–solid interaction method and based on physiological boundary conditions. Next, we provided a Lagrangian description of micro- and nanoparticles dynamics in the blood flow considering their Brownian motion and the particle–particle interactions. Our results state that the number of... 

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... 

This paper presents a three-dimensional micromechanical model of brain white matter tissue as a transversely isotropic soft composite described by the generalized Ogden hyperelastic model. The embedded element technique, with corrected stiffness redundancy in large deformations, was used for the embedment of a histology-informed probabilistic distribution of the axonal fibers in the extracellular matrix. The model was linked to a multi-objective, multi-parametric optimization algorithm, using the response surface methodology, for characterization of material properties of the axonal fibers and extracellular matrix in an inverse finite element analysis. The optimum hyperelastic... 

Recent advances in the field of microfabrication have made the application of high-throughput microfluidics feasible. Mixing which is an essential part of any miniaturized standalone system remains the key challenge. This paper proposes a geometrically simple micromixer for efficient mixing for high-throughput microfluidic devices. The proposed micromixer utilizes a curved microchannel (spiral microchannel) to induce chaotic advection and enhance the mixing process. It is shown that the spiral microchannel is more efficient in comparison to a straight microchannel, mixing wise. The pressure drop in the spiral microchannel is only slightly higher than that in the straight microchannel. It is... 

Obstruction of left anterior descending artery (LAD) due to the thrombosis or atherosclerotic plaques is the leading cause of death worldwide. Targeted delivery of drugs through micro- and nanoparticles is a very promising approach for developing new strategies in clot-busting or treating restenosis. In this work, we modelled the blood flow characteristics in a patient-specific reconstructed LAD artery by the fluid–solid interaction method and based on physiological boundary conditions. Next, we provided a Lagrangian description of micro- and nanoparticles dynamics in the blood flow considering their Brownian motion and the particle–particle interactions. Our results state that the number of... 

This paper aims to give a comprehensive atomistic modeling of the nanomechanical behavior of actin monomer. Actin is a ubiquitous and essential component of cytoskeleton which forms many different cellular structures. Despite for several years great effort has been devoted to the investigation of mechanical properties of the actin filament, studies on the nanomechanical behavior of actin monomer are still lacking. These scales are, however, important for a complete understanding of the role of actin as an important component in the cytoskeleton structure. Based on the accuracy of atomistic modeling methods such as molecular dynamics simulations, steered molecular dynamics method is performed... 

A transverse-plane hyperelastic micromechanical model of brain white matter tissue was developed using the embedded element technique (EET). The model consisted of a histology-informed probabilistic distribution of axonal fibers embedded within an extracellular matrix, both described using the generalized Ogden hyperelastic material model. A correcting method, based on the strain energy density function, was formulated to resolve the stiffness redundancy problem of the EET in large deformation regime. The model was then used to predict the homogenized tissue behavior and the associated localized responses of the axonal fibers under quasi-static, transverse, large deformations. Results... 

This paper presents a comprehensive 3D numerical simulation of reacting flows in micro scale dimension through centrifugal, or Lab-On-a-CD (LOCD), and pressure-driven, or Lab-On-a-Chip (LOC) devices. Three different serpentine channel configurations (rectangular, triangular and sinusoidal) are investigated. In these configurations, two chemical species enter from two inlets and according to an irreversible chemical reaction, start yielding other species. Both Newtonian and generalized Newtonian fluids are considered in the simulations and the results are compared for both LOC and LOCD devices. Besides, the effects of different parameters such as the aspect ratio of channels’ cross section,... 

Gene proliferation is vital for infectious and genetic diseases diagnosis from a blood sample, even before birth. In addition, DNA sequencing, genetic finger-print analyzing, and genetic mutation detecting can be mentioned as other procedures requiring gene reproduction. Polymerase chain reaction, briefly known as PCR, is a convenient and effective way to accomplish this task; where the DNA containing sample faces three temperature phases alternatively. These phases are known as denaturation, annealing, and elongation/extension which in this study -regarding the type of the primers and the target DNA sequence- are set to occur at 95, 58, and 72 degrees of Celsius. In this study, a PCR device... 

Zinc binding to β-amyloid structure could promote amyloid-β aggregation, as well as reactive oxygen species (ROS) production, as suggested in many experimental and theoretical studies. Therefore, the introduction of multifunctional drugs capable of chelating zinc metal ion and inhibiting Aβ aggregation is a promising strategy in the development of AD treatment. The present study has evaluated the efficacy of a new bifunctional peptide drug using molecular docking and molecular dynamics (MD) simulations. This drug comprises two different domains, an inhibitor domain, obtained from the C-terminal hydrophobic region of Aβ, and a Zn2+ chelating domain, derived from rapeseed meal, merge with a... 

In this study, using fluid-structure interaction (FSI), 3-dimensional blood flow in an aneurysm in the circle of Willis-which is located in the middle cerebral artery (MCA)-has been simulated. The purpose of this study is to evaluate the effect of a partly blocked vessel on an aneurysm. To achieve this purpose, two cases have been investigated using the FSI method: in the first case, an ideal geometry of aneurysm in the MCA has been simulated; in the second case, modeling is performed for an ideal geometry of the aneurysm in the MCA with a partly blocked vessel. All boundary conditions, properties and modeling methods were considered the same for both cases. The only difference between the... 

Inertial microfluidics is utilized as a powerful passive method for particle and cell manipulation, which uses the hydrodynamic forces of the fluid in the channel to focus particles in specific equilibrium positions in the cross section of the channel. To achieve high performance manipulation, knowledge of focusing pattern of particles in the cross section of channel is essential. In this paper, we propose a method to address this important issue. To this end, firstly inertial microfluidics is analyzed in rectangular cross section channels. The results indicate that fluid flow velocity and channel's cross-sectional profiles have great impacts on the forces exerted on particles. Next, these... 

Polymerase Chain Reaction (PCR) is an important and prevalent technique in biotechnology because of its crucial role in cloning DNA fragments and diagnostic applications. In the present study, a high-throughput two-phase PCR device is designed and fabricated which utilizes a serpentine microchannel together with a spiral structure. The former is for the droplet-generation and mixing and the latter is for the thermal cycling process. Moreover, the effect of diamond nanoparticles (diamondNP) on the performance of PCR is also investigated while using commercial PCR devices and the fabricated PCR device designed in this study. Using numerical simulation, it is shown that within the simple and... 

Nucleic acid amplification via polymerase chain reaction (PCR) is one of the essential and powerful methods used in a myriad of bio-assays in clinical laboratories. Application of microfluidic devices in biologically-related processes like PCR can result in the usage of less volume of reactant samples and reduce the processing time. By implementing PCR systems on centrifugal microfluidic platforms, automation and portability can be easily achieved. Although several methods have been developed, most of them are still dealing with challenges of the required high processing time. This study presents the numerical simulation of a fully automated PCR system with the goal of enhancing the mixing... 

Small diameter vascular grafts (<6 mm) are highly demanded for patients suffering from severe occluded arteries to be used as a bypass or substituted conduit. Fabricating a graft with appropriate structural, mechanical and cell growth properties which has simultaneously anti-thrombogenic trait is a challenge nowadays. Here, we proposed a bilayer heparinized vascular graft that can mimic the structural and mechanical characteristics close to those of the native coronary artery by combining electrospinning and freeze drying methods. In this study, the inner layer was made by co-electrospinning of synthetic polymer, poly-caprolactone (PCL) and the natural polymer, gelatin (Gel). Also, heparin...