Diffusion of Lipid and Protein Molecules in Cell Membranes

, Ph.D. Dissertation Sharif University of Technology Khoshnood, Atefeh (Author) ; Jalali, Abbas (Supervisor)

Abstract

Lipid membranes are fundamental constituents of cell membranes and are now used in lap-on-a-chip technology. Membranes in living cells contain a significant fraction of proteins, which undergo lateral random movements due to thermal fluctuations and shear forces imposed by the solvent fluid. Prominent natural and biotechnological systems where membranes are highly sheared include the plasma membrane of endothelial cells, and membranes used in biosensors for high throughput screening of drug candidates, and in water purification devices. In these systems membrane is in direct contact with the mainstream suspension flow, which is driven by pressure gradients. The efficiency and function of...

U-Shaped Assembly Line Rebalancing With Cost Minimization Objectives

, M.Sc. Thesis Sharif University of Technology Khoshnood, Sara (Author) ; Akbari, Javad (Supervisor)

Abstract

U-shaped assembly lines usually are more effective than straight lines. Therefore special attention has been paid to u-shaped line balancing problem in recent years. On the other hand most articles on the line balancing problems are investigated for the first time. However, within the lifetime of an ALB, the balancing problems do not occur only once prior to its construction, but rather continuously as rebalancing. For example whenever the demand structure or production technology changes or producing seasonal products, the ALB needs to be reconﬁgured. So many balancing issues in the real world are related to re-balancing of production lines.
Therefore in this study, U-shaped assembly...

Anomalous diffusion of proteins in sheared lipid membranes

, Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 88, Issue 3 , September , 2013 ; 15393755 (ISSN) Khoshnood, A ; Jalali, M. A ; Sharif University of Technology

2013

Abstract

We use coarse grained molecular dynamics simulations to investigate diffusion properties of sheared lipid membranes with embedded transmembrane proteins. In membranes without proteins, we find normal in-plane diffusion of lipids in all flow conditions. Protein embedded membranes behave quite differently: by imposing a simple shear flow and sliding the monolayers of the membrane over each other, the motion of protein clusters becomes strongly superdiffusive in the shear direction. In such a circumstance, the subdiffusion regime is predominant perpendicular to the flow. We show that superdiffusion is a result of accelerated chaotic motions of protein-lipid complexes within the membrane voids,...

Long-lived and unstable modes of Brownian suspensions in microchannels

, Article Journal of Fluid Mechanics ; Volume 701 , 2012 , Pages 407-418 ; 00221120 (ISSN) Khoshnood, A ; Jalali, M. A ; Sharif University of Technology

2012

Abstract

We investigate the stability of the pressure-driven, low-Reynolds-number flow of Brownian suspensions with spherical particles in microchannels. We find two general families of stable/unstable modes: (i) degenerate modes with symmetric and antisymmetric patterns; (ii) single modes that are either symmetric or antisymmetric. The concentration profiles of degenerate modes have strong peaks near the channel walls, while single modes diminish there. Once excited, both families would be detectable through high-speed imaging. We find that unstable modes occur in concentrated suspensions whose velocity profiles are sufficiently flattened near the channel centreline. The patterns of growing unstable...

Lipid membranes with transmembrane proteins in shear flow

, Article Journal of Chemical Physics ; Volume 132, Issue 2 , 2010 ; 00219606 (ISSN) Khoshnood, A ; Noguchi, H ; Gompper, G ; Sharif University of Technology

2010

Abstract

The effects of embedded proteins on the dynamical properties of lipid bilayer membranes are studied in shear flow. Coarse-grained molecular simulations are employed, in which lipids are modeled as short polymers consisting of hydrophilic head groups and hydrophobic tail monomers; similarly, transmembrane proteins are modeled as connected hydrophobic double- or triple-chain molecules with hydrophilic groups at both ends. In thermal equilibrium, rigid proteinlike molecules aggregate in a membrane of flexible lipids, while flexible proteins do not aggregate. In shear flow parallel to the membrane, the monolayers of lipid bilayer slide over each other. The presence of transmembrane proteins...

Assisted passive snake robots: Conception and dynamic modeling using kane's method

, Article 2005 ASME International Mechanical Engineering Congress and Exposition, IMECE 2005, Orlando, FL, 5 November 2005 through 11 November 2005 ; Volume 74 DSC, Issue 2 PART B , 2005 , Pages 1475-1482 ; 0791842169 (ISBN); 9780791842164 (ISBN) Pendar, H ; Vossoughi, G ; Khoshnood, A ; Poursamad, A ; Sharif University of Technology

2005

Abstract

In this paper conception and dynamic modeling of a snake-like robot with passive wheels and compliant joints is investigated. The proposed robot has the ability to follow a socalled Serpenoid curve passively by using an appropriate set of initial conditions. Introduction of a unique structure at each joint enables the robot to achieve passive motion. A torsional spring is used in series with an actuator between each two consecutive links. Using wheels at the middle of each link imposes many non-holonomic constraints to the system. These constraints reduce the degrees of freedom of the system to only two. Due to the existence of these non-holonomic constraints, dynamic equations governing the...

Dynamics of Protein-Embedded Vesicles in Simple Shear Flow

, M.Sc. Thesis Sharif University of Technology Hoore, Masoud (Author) ; Jalali, Mir Abbas (Supervisor) ; Khoshnood, Atefeh (Co-Advisor)

Abstract

Studying the dynamics of vesicles in simple shear flow is the first step to decipher the dynamics of cells in flows or the motion of vesicle-based nanoparticles in vessels for drug delivery. The deformation of vesicle in shear flow changes the permeability of its membrane and may lead to its rupture, both of which correlate with the transportation of vesicle cargos to their environment, especially important in drug delivery. The deformation of vesicles in shear flow not only depends on the physical properties of the whole system, such as temperature, but also on the mechanical properties of three media: vesicle membrane plus vesicle’s inner and outer fluid. The effect of the mechanical...

Effects of Graphene Nanopores and Temperature on DNA Sequencing Using Molecular Dynamics

, M.Sc. Thesis Sharif University of Technology Majdi, Amin (Author) ; Meghdari, Ali (Supervisor) ; Khoshnood, Atefeh (Co-Advisor)

Abstract

Distinguishing the structure of DNA is of outmost importance in the medicine and agriculture industry nowadays. Various methods have been suggested so far; however, high costs, incorrect results, and time-taking process are among main defects of them. Scientists try to find new ways for recognizing DNA structure and system in order to overcome such problems. One of these new methods is absorbing and passing DNA through Nano-pores in an electrolyte solution under the influence of an electrical field. The basis of this method is the ionized currents which occur due to the passing of DNA through Nano-pores. Because each DNA base pairs can form a barrier corresponding to a unique measured value,...

Role of Affective Commitment in the Relationship between Ostracism and Turnover Intention

, M.Sc. Thesis Sharif University of Technology Zeytonli, Asiyeh (Author) ; Banki, Sara (Supervisor)

Abstract

A lot of researchers have suggested that ostracism as a disruptive behavior, has been widespread among organizations and a lot of researches has been studied its consequences in recent years.This research studies ostracism’s consequences and proposes a theoretical model of organizational ostracism with affective commitment, intention to turnover and organizational dependability as one of affective commitment’s antecedents. This study has been done on 231 employees of three medium knowledge-based organizations to identify the effects of ostracism on employee’s turnover behavior. Results show that ostracism, due to its impact on the affective commitment of ostracized peoples, reduces this type...

Identifying Active Followership Behaviors in Interaction with Managers with Autocratic Leadership Style in an Iranian Organization

, M.Sc. Thesis Sharif University of Technology Ghahremani, Hamed (Author) ; Alavi, Babak (Supervisor) ; Banki, Sara (Supervisor)

Abstract

Purpose: The purpose of this thesis was to identify active followership behaviors of followers in interaction with autocratic leaders. An active follower thinks critically and takes initiatives.
Design: Given that Followership literature is still in its infancy, the research questions needed a qualitative approach, in this case grounded theory. In total, 19 top- & middle-level managers were interviewed as leaders and followers, accordingly, using semi-structured interviews.
Findings: 4 categories of active followership were found, each having 3-4 specific behaviors. These categories are: precautionary behaviors, facilitating behaviors, modificating behaviors, and consolidating...

An Investigation of the Mediating role of Organizational Cynicism on the Relations between the Politics Perception and Organizational Commitment

, M.Sc. Thesis Sharif University of Technology Taleghani, Mohammad (Author) ; Alavi, Babak (Supervisor) ; Banki, Sara (Supervisor)

Abstract

There is no consensus definition of cynicism in literature. In this research different definitions of cynicism have been investigated and two concept of organizational cynicism and trait cynicism have been taken into consideration. Organizational cynicism is a negative attitude that is prevalent in employees. In literature some antecedents and consequences of organizational cynicism have been suggested. It seems organizational cynicism can be investigated in a more complex relations. The focus of this research is on the mediating role of organizational cynicism on the likely relations between politics perception and organizational commitment. That is to say organizational cynicism can...

The Influence of Authentic Leadership on the Relationship between Transformational Leadership, and Feedback-seeking Behaviors

, M.Sc. Thesis Sharif University of Technology Fadaee, Mohsen (Author) ; Alavi, Babak (Supervisor) ; Banki, Sara (Supervisor)

Abstract

Feedback-seeking behavior is the effort of employees to get feedback from the environment and around people about their performance. One of the research questions in this field is about the factors that increase this behavior in the staff. Transformational leadership as a leadership style, stimulates, and motivates followers to achieving desirable operational results. In addition, an important consequence of this style could be increasing the followers' capabilities. Transformational leaders are trying to empower their followers to build and empower them, which can provide a strong incentive for employees to move and grow, which may encourage them to have a better performance. One of...

Applying Gamification in Corporate Entrepreneurship Culture, Specially Missionary Organizations; Through SafirFilm Case Study

, M.Sc. Thesis Sharif University of Technology Jafarian, Hamid Reza (Author) ; Yavari, Elham (Supervisor) ; Banki, Sara ($item.subfieldsMap.e)

Abstract

Although existing literature on organizational culture and its change process contains meaningful and rich theories but our studies show that there is no perfect and detailed framework on linking organizational culture change and corporate entrepreneurship culture. In addition to that, Gamification –defined as taking the game design elements into non-game contexts– is a fruitful and academically rich research area. Fortunately an idea proposed recently to explain a method for enhancements in organizational culture in general, and in corporate entrepreneurship culture in particularby Yavari and Jafarian based on using game mechanisms. In their paper "A Gamification-Based Method for Corporate...

Synthesis of Tin and Ti2n Nanostructured Coatings on Ti alloys Using Magnetron Sputtering System And Comparison of Their Biocompatibility Properties

, M.Sc. Thesis Sharif University of Technology Kalantari Saghafi, Mahsa (Author) ; Nemati, Ali (Supervisor) ; Khamse, Sara (Supervisor)

Abstract

Considering the importance of biocompatibility of implantable prothesis’, metallic alloys have weaker corrosion resistance than ceramics. In order to extend usage of nanomaterials to improve the bio-properties of materials, Nano-structured ceramic coatings are being suggested to improve corrosion resistance and biocompatibility of prosthesis. Meanwhile, very good properties of TiN, such as corrosion resistance and mechanical properties as a thin film coating are undeniable. In this study, TiN and Ti2N thin film were deposited on Ti-based substrate, using PVD and Magnetron sputtering at different argon to nitrogen ratio. The crystal structure of the films was examined using Grazing XRD...

The Instructional Effect of Dynamic-assessment, Non-dynamic Traditional Assesment, and Non-assessment Courses on Iranian EFL Learners' Interlanguage Pragmatic Production

, M.Sc. Thesis Sharif University of Technology Pakzadian, Sara Sadat (Author) ; Tajeddin, Zia (Supervisor) ; Alemi, Minoo (Supervisor)

Abstract

There are several methods proposed for the instruction and assessment of interlanguage pragmatic competence of foreign language learners. Dynamic assessment as one of the recent methods arising from Vygotsky’s sociocultural theory of mind incorporates assessment and instruction by engaging learners in a process of interaction with the mediator while the learners are trying to perform a challenging task. The present study aimed to explore the advantage of Dynamic Assessment as an instructional instrument over the Non-dynamic (traditional) Assessment and Non-assessment approaches and their effects on the Iranian intermediate level students. The target speech acts of apology, complaint, and...

Monitoring of Structure Characteristics, Humidity, Temperature and Torsion Using Optical Fiber Sensor

, Ph.D. Dissertation Sharif University of Technology Esmailzadeh Noghani, Fereshteh (Author) ; Bahrampour, Alireza (Supervisor) ; Tofighi, Sara (Supervisor)

Abstract

Fiber optic sensors have found industrial applications due to their unique characteristics and wide range of environmental parameters. Specifically, distributed optical fiber sensors which have applications in borders protection, intrusion detection, oil and gas leakage detection and smart irrigation of farms and gardens, have attracted significant attention from research groups around the world in recent years. According to the forecasts, among all kind of optical fiber sensors, the temperature and acoustic/vibration sensors will seize the market during the coming years. In this thesis, three kind of optical fiber sensors are proposed for environment health monitoring. First, distributed...

The Effect of Hydrophobic Mismatch and Rigidity of Protein on the Cluster Formation of Transmembrane Proteins in Biomembranes

, M.Sc. Thesis Sharif University of Technology Jafarinia, Hamid Reza (Author) ; Ahmadiyan, Mohammad Taghi (Supervisor) ; Jalali, Mir Abbas (Co-Advisor) ; Khoshnood, Atefeh (Co-Advisor)

Abstract

Membrane proteins aggregation is a very important biological phenomenon in a variety of cell functions. It has been suggested that aggregation behavior of membrane proteins is influenced by the shape of the hydrophobic domain of the proteins, proteins hydrophobic mismatch and bilayer curvature. However, in this study by means of coarse grained membrane simulations it has been found that in thermal equilibrium, protein-protein interactions also depend on protein rigidity and structural strength. Based on simulation results, we have observed stable large clusters even in the absence of hydrophobic mismatch between lipids and proteins. Interestingly, our results also indicate that proteins with...

A credible role of copper oxide on structure of nanocrystalline mesoporous titanium dioxide

, Article Journal of the Iranian Chemical Society ; Volume 5, Issue 3 , September , 2008 , pp. 367-374 ; 1735207X Rahimnejad, S. (Sara) ; Rahman Setayesh, S. (Shahrbanoo) ; Gholami, M. R. (Mohammad Reza) ; Sharif University of Technology

2008

Abstract

Copper oxide-titania catalysts with nanocrystalline mesoporous structure were prepared by sol-gel technique using tetra isopropyl ortho titanate (TiPT) as the inorganic precursor and amino-2 ethanol as the swelling agent. Characterization was performed using X-ray diffraction (XRD), fourier transformed infrared spectra (FTIR), scanning electron microscopy (SEM), diffuse reflectance UV-Vis spectroscopy (DRS), and N2 adsorption-desorption measurements. It was found that CuO (0.025-0.1 mol ratio) has some effect on the particle size, surface area, pore-volume, pore-diameter, crystallinity of the particles, and crystalline phase of TiO2 nanocrystalline. The results indicated that 0.1 CuO-TiO2...

Design and Fabrication of Microfluidic Biosensors based on Modified Electrospun Nanofibrous Membranes for Biomarkers Detection

, Ph.D. Dissertation Sharif University of Technology Mahmoudifard, Matin (Author) ; Vosoughi, Manuchehr (Supervisor) ; Soleimani, Masoud (Supervisor) ; Soudi, Sara (Supervisor)

Abstract

The accurate assessment of biomarkers likes proteins, hormones or other biomolecules that amount of them changes with state of disease or level of treatment and gives diagnostic information is a difficult duty. In these samples, pathogens exist in small quantity compared to other background molecules. Therefore, appropriate sampling process for concentrating and separating pathogens from the matrix should be developed in order to provide rapid and accurate pathogen detection test. In this thesis design and fabrication of microfluidic biosensors based on the modified nanofibrous membranes were investigated and explained. PES nanofibrous membrane with carboxyl functional groups for covalent...

Surfactant-assisted synthesis and characterization of hydroxyapatite nanorods under hydrothermal conditions

, Article Materials Science- Poland ; Volume 27, Issue 4 , 2009 , Pages 961-971 ; 01371339 (ISSN) Salarian, M ; Solati Hashjin, M ; Sara Shafiei, S ; Goudarzi, A ; Salarian, R ; Nemati, A ; Sharif University of Technology

2009

Abstract

Hydroxyapatite (HAp) nanorods with uniform morphology and controllable size were successfully synthesized by precipitating Ca(NO3) 24H2O and (NH4)2HPO4 in the presence of cetyltrimethylammonium bromide (CTAB) and polyethylene glycol 400 (PEG 400) as cationic surfactant and non-ionic cosurfactant, respectively, under hydrothermal conditions. The effect of hydrothermal temperature on the composition, morphology and size of HAp particles was studied using X-ray diffraction (XRD), Fourier transform infrared spectrometry (FTIR) and scanning electron microscopy (SEM). Results revealed that the morphology and size of HAp particles can be effectively controlled by the presence of CTAB and PEG...