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Probing the Relation Between Cell Function and Chromatin Interactions Using Community Detection Approaches
, M.Sc. Thesis Sharif University of Technology ; Rabiee, Hamid Reza (Supervisor) ; Jafari Siavoshani, Mahdi (Supervisor)
Abstract
Hi-C is a new technology invented to record the amount of interaction between all chromatin fragments. Chromatin interactions are manifestations of chromatin's 3D structure. It has been proved that different 3D structures of different cell types, despite having the same DNA, causes in different functionalities of cells. Therefore knowing chromatin structure, the factors affecting it and the way it affects cells' behaviors such as gene co-expression, sheds more light on the knowledge about cells and the methods that can change their fates. Finding the causes of diseases, designing more efficient drugs and progressing the conversion of different cell types into each other used for amending...
Numerical Analysis of Stresses and Steady State Creep Strain Rates Fields of a Short Fibre Composite
, M.Sc. Thesis Sharif University of Technology ; Abedian, Ali (Supervisor)
Abstract
A finite difference technique is developed to predict the second stage creep displacement rates and stress analysis of a short fiber metal matrix composite subjecting to a constant axial load. The exponential law is adopted to describe the matrix creep behavior. Also, a method for prediction of interfacial debonding at fiber/matrix interface is developed using a stress based method. The obtained results could greatly help to better understand the flow pattern of matrix material and the load transfer mechanism between fiber and matrix. The stress components and strain rates are also validated by the available FEM and experimental results
A new cross layer design of adaptive modulation and coding in finite buffer wireless links
, Article 2007 International Conference on Future Generation Communication and Networking, FGCN 2007, Jeju Island, 6 December 2007 through 8 December 2007 ; Volume 1 , 2007 , Pages 499-504 ; 0769530486 (ISBN); 9780769530482 (ISBN) ; Ashtiani, F ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2007
Abstract
In this paper, a cross-layer approach introducing new design parameters is developed for multi-rate wireless links. The novel design jointly exploits the finite-length queuing at the data link layer and the adaptation capability of the adaptive modulation and coding (AMC) scheme at the physical layer to optimize system performance for a wireless link. The analytical framework is based on discrete time Markov Chain. The performance metrics such as packet drop probability, channel packet error rate and packet loss rate are derived. Using these metrics, a constrained optimization problem is solved numerically to maximize the overall system throughput
Cross-layer optimization of adaptive modulation and coding preserving packet average delay time
, Article 2008 IEEE Global Telecommunications Conference, GLOBECOM 2008, New Orleans, LA, 30 November 2008 through 4 December 2008 ; December , 2008 , Pages 1278-1282 ; 9781424423248 (ISBN) ; Ashtiani, F ; Sharif University of Technology
2008
Abstract
In this paper we introduce a novel cross layer design between MAC and physical layers. Our novel design is based on controlling the adaptive modulation and coding (AMC) transmission mode at the physical layer according to the queue length of finite buffer at the data link layer and each transmission mode of AMC. The aim is optimizing system performance over a wireless link, preserving the important Quality of Service (QoS) parameter, packet average delay time. Analytical expressions such as packet drop probability, channel packet error rate, packet loss rate and packet average delay time are derived both analytically and through simulations according to the system and channel parameters....
Finite difference solution of steady state creep deformations in a short fiber composite in presence of fiber/matrix debonding
, Article Materials and Design ; Volume 31, Issue 5 , 2010 , Pages 2616-2624 ; 02641275 (ISSN) ; Abedian, A ; Mondali, M ; Sharif University of Technology
2010
Abstract
A finite difference technique is developed to predict the second stage creep displacement rates and stress analysis of a short fiber metal matrix composite subjecting to a constant axial load through a micromechanical approach. The technique is capable to take into account the presence of interfacial debonding as one of the main factors affecting the creep performance of short fiber composites. The exponential law is adopted to describe the matrix creep behavior. Also, a model for prediction of interfacial debonding at fiber/matrix interface is developed using a stress based method. The obtained results could greatly help to better understand the flow pattern of matrix material and the load...
A new analytical shear-lag based model for prediction of the steady state creep deformations of some short fiber composites
, Article Materials and Design ; Volume 30, Issue 4 , 2009 , Pages 1075-1084 ; 02641275 (ISSN) ; Abedian, A ; Ghavami, A ; Sharif University of Technology
2009
Abstract
A new analytical model based on the shear-lag theory is developed for stress analysis and prediction of the steady state creep deformation of short fiber composites subjected to an applied axial load. A perfect fiber/matrix interface is assumed and the steady state creep behavior of the matrix is described by an exponential law. The results obtained from the proposed analytical solution satisfy the equilibrium and constitutive creep equations. These analytical results are then validated by the FEM modeling. Interestingly, good agreements are found between the analytical and numerical predictions for all the stress and displacement rate components. © 2008 Elsevier Ltd. All rights reserved
An analytical model for prediction of the steady state creep deformations and stresses of short fiber composites
, Article 26th Congress of International Council of the Aeronautical Sciences 2008, ICAS 2008, Anchorage, AK, 14 September 2008 through 19 September 2008 ; Volume 2 , 2008 , Pages 2829-2840 ; 9781605607153 (ISBN) ; Abedian, A ; Ghavami, A ; Sharif University of Technology
2008
Abstract
A new analytical model based on the shear-lag theory is developed for stress analysis and steady state creep deformation of short fiber composites subjected to an applied axial load. A perfect fiber/matrix interface is assumed and an exponential law is considered for describing the steady state creep behavior of the matrix material. The matrix stress field components obtained from the proposed analytical solution satisfies the equilibrium and constitutive creep equations. Also, the obtained axial stress in the fiber in an average form satisfies the equilibrium requirements within the fiber and between the fiber and the matrix. Moreover, the above stress field components satisfy well the...
Unified structure of basic UWB waveforms
, Article IEEE Transactions on Circuits and Systems II: Express Briefs ; Volume 55, Issue 12 , 2008 , Pages 1304-1308 ; 15497747 (ISSN) ; Amini, A ; Marvasti, F ; Sharif University of Technology
2008
Abstract
In this brief, a generalized expression for the popular ultra wideband waveforms is derived. It is shown that all three waveforms used in ultra wideband (Gaussian, modified Hermite, and prolate spheroidal waveforms) fulfill the Sturm–Liouville differential equation. By using this unified structure, characteristics of the waveforms such as orthogonality, finite duration in time and frequency spectrum are explained. © 2008 IEEE
Salep-g-poly(sodium acrylate)/alumina as an environmental-sensitive biopolymer superabsorbent composite: Synthesis and investigation of its swelling behavior
, Article Advances in Polymer Technology ; Volume 31, Issue 1 , 2012 , Pages 41-51 ; 07306679 (ISSN) ; Pourjavadi, A ; Soleyman, R ; Ghavami, S ; Sharif University of Technology
2012
Abstract
A novel kind of a biopolymer-based superabsorbent composite, salep-g-poly(sodium acrylate)/alumina, was prepared from salep, sodium acrylate, and alumina by aqueous polymerization, using N,N'-methylenebisacrylamide (MBA) as a cross-linker and ammonium persulfate (APS) as an initiator. The reaction parameters [i.e., acrylic acid (AA), MBA, APS amounts, and neutralization percentage of AA as well as alumina/salep weight ratio] affecting the water absorbency of the hydrogel composite were optimized using systematic method to achieve a composite with high swelling capacity as possible. The swelling behavior of optimum superabsorbent composite was measured in various pH solutions. In addition,...
Novel superabsorbent hydrogel based on natural hybrid backbone: optimized synthesis and its swelling behavior
, Article Bulletin of the Korean Chemical Society ; Volume 30, Issue 11 , 2009 , Pages 2680-2686 ; 02532964 (ISSN) ; Soleyman, R ; Bardajee Rezanejade, G ; Ghavami, S ; Sharif University of Technology
2009
Abstract
The synthesis of a novel superabsorbent hydrogel with natural hybrid backbone via graft copolymerization of acrylamide (AAm) onto kappa-carrageenan (kC, as a polysaccharide) and gelatin (as a protein) under classic thermal conditions is described. The Taguchi method as a strong experimental design tool was used for synthesis optimization. A series of hydrogels were synthesized by proposed conditions of Qualitek-4 Software. Considering the results of 9 trials according to analysis of variance (ANOVA), optimum conditions were proposed. The swelling behavior of optimum hydrogel was measured in various solutions with pH values ranging from 1 to 13. In addition, swelling kinetics, swelling in...
UWB orthogonal pulse design using Sturm–Liouville boundary value problem
, Article Signal Processing ; Volume 159 , 2019 , Pages 147-158 ; 01651684 (ISSN) ; Mohajerin Esfahani, P ; Ghavami, M ; Marvasti, F ; Sharif University of Technology
Elsevier B.V
2019
Abstract
The problem of designing UWB pulses which meet specific spectrum requirements is usually treated by filtering common pulses such as Gaussian doublets, modified Hermite polynomials and wavelets. When there is the need to have a number of orthogonal pulses (e.g., in a multiuser scenario), a naive approach is to filter all the members of an orthogonal set, which is likely to destroy their orthogonality property. In this paper, we study the design of a set of pulses that simultaneously satisfy the orthogonality property and spectrum requirements. Our design is based on the eigenfunctions of Sturm–Liouville boundary value problems. Indeed, we introduce Sturm–Liouville differential equations for...
Analysis and fast estimation of energy consumption in template based QDI asynchronous circuits
, Article 2007 International Symposium on Integrated Circuits, ISIC, Singapore, 26 September 2007 through 28 September 2007 ; 2007 , Pages 445-448 ; 1424407974 (ISBN); 9781424407972 (ISBN) ; Mirza Aghatabar, M ; Pedram, H ; Hessabi, S ; Sharif University of Technology
2007
Abstract
In this paper we analyses the energy consumption of well known family of asynchronous circuits and present a new methodology for energy estimation of these circuits at intermediate-level of abstraction. Energy estimation is performed by simulating the intermediate format of the design. The number of Read and Write accesses on the ports of the concurrent processes are counted by analyzing the conditional and computational portion during the simulation which is the base of our estimation methodology. Our proposed power estimation scheme is faster than usual post-synthesis power estimation by an order of 9, while the estimated power resides in a boundary of 11% total imprecision. © 2007 IEEE
Nationwide prediction of drought conditions in Iran based on remote sensing data
, Article IEEE Transactions on Computers ; Vol. 63, issue. 1 , Jan , 2014 , p. 90-101 ; 0018-9340 ; Gharibshah, J ; Ghavami, S. M ; Beheshtifar, M ; Farshi, R ; Sharif University of Technology
2014
Abstract
Iran is a country in a dry part of the world and extensively suffers from drought. Drought is a natural, temporary, and iterative phenomenon that is caused by shortage in rainfall, which affects people's health and well-being adversely as well as impacting the society's economy and politics with far-reaching consequences. Information on intensity, duration, and spatial coverage of drought can help decision makers to reduce the vulnerability of the drought-affected areas, and therefore, lessen the risks associated with drought episodes. One of the major challenges of modeling drought (and short-term forecasting) in Iran is unavailability of long-term meteorological data for many parts of the...
UV-prepared salep-based nanoporous hydrogel for controlled release of tetracycline hydrochloride in colon
, Article Journal of Photochemistry and Photobiology B: Biology ; Volume 102, Issue 3 , March , 2011 , Pages 232-240 ; 10111344 (ISSN) ; Pourjavadi, A ; Ghavami, S ; Soleyman, R ; Jafarpour, F ; Sharif University of Technology
2011
Abstract
A highly swelling nanoporous hydrogel (NPH) was synthesized via UV-irradiation graft copolymerization of acrylic acid (AA) onto salep backbone and its application as a carrier matrix for colonic delivery of tetracycline hydrochloride (TH) was investigated. Optimized synthesis of the hydrogel was performed by the classic method. The swelling behavior of optimum hydrogel was measured in different media. The hydrogel formation was confirmed by Fourier transform infrared spectroscopy (FTIR) and thermo-gravimetric analysis (TGA/DTG/DTA). The study of the surface morphology of hydrogels using SEM showed a nanoporous (average pore size: about 350 nm) structure for the sample obtained under...
Graphene oxide strongly inhibits amyloid beta fibrillation
, Article Nanoscale ; Volume 4, Issue 23 , 2012 , Pages 7322-7325 ; 20403364 (ISSN) ; Akhavan, O ; Ghavami, M ; Rezaee, F ; Ghiasi, S. M. A ; Sharif University of Technology
2012
Abstract
Since amyloid beta fibrillation (AβF) plays an important role in the development of neurodegenerative diseases, we investigated the effect of graphene oxide (GO) and their protein-coated surfaces on the kinetics of Aβ fibrillation in the aqueous solution. We showed that GO and their protein-covered surfaces delay the AβF process via adsorption of amyloid monomers. Also, the large available surface of GO sheets can delay the AβF process by adsorption of amyloid monomers. The inhibitory effect of the GO sheet was increased when we increase the concentration from 10% (in vitro; stimulated media) to 100% (in vivo; stimulated media). Conclusion: our results revealed that GO and their surface...
Evaluation of crystalline changes and resistance to demineralization of the surface of human dental enamel treated with Er:YAG laser and fluoride using x-ray diffraction analysis and vickers microhardness
, Article Laser Physics ; Volume 28, Issue 6 , 2018 ; 1054660X (ISSN) ; Shahabi, S ; Ghavami lahiji, M ; Sadeghian, S ; Faal Nazari, N. S ; Sharif University of Technology
Institute of Physics Publishing
2018
Abstract
This study aimed to investigate the changes in crystalline structure and resistance to demineralization of human dental surface enamel treated with erbium-doped yttrium aluminium garnet laser (Er:YAG) laser and fluoride. The enamel surfaces were divided into four groups according to the treatment process including, (L): irradiated with Er:YAG; (F): treated with acidulated phosphate fluoride gel (LF): Pre-irradiated surfaces with Er:YAG subjected to acidulated phosphate fluoride gel and (FL): laser irradiation was performed on the fluoridated enamel surface. Before and after the treatment procedure, the samples were evaluated using X-ray diffraction, scanning electron microscope (SEM) and the...
Comparative assessment of the crystalline structures of powder and bulk human dental enamel by X-ray diffraction analysis
, Article Journal of Oral Biosciences ; Volume 61, Issue 3 , 2019 , Pages 173-178 ; 13490079 (ISSN) ; Hajizamani, H ; Shekofteh, K ; Otadi, M ; Ghavami Lahiji, M ; Faal Nazari, N. S ; Sharif University of Technology
Japanese Association for Oral Biology
2019
Abstract
Objectives: The aim of this study was to assess and compare the crystalline structures of both powder and bulk human dental enamel by X-ray diffraction analysis (XRD). Methods: The buccal surfaces of 60 selected noncarious third molars were divided into two groups of powdered and bulk enamel specimens. To prepare enamel powders, the enamel tissues were ground and powdered manually using a mortar and pestle. For bulk samples, the enamel slabs were sectioned using a low-speed diamond saw. The crystalline structures of samples were analyzed by XRD, and the obtained data were analyzed. The values of the lattice parameters were obtained using the equation of hexagonal crystalline structures. The...
Physiological temperature has a crucial role in amyloid beta in the absence and presence of hydrophobic and hydrophilic nanoparticles
, Article ACS Chemical Neuroscience ; Volume 4, Issue 3 , December , 2013 , Pages 375-378 ; 19487193 (ISSN) ; Rezaei, M ; Ejtehadi, R ; Lotfi, M ; Shokrgozar, M. A ; Abd Emamy, B ; Raush, J ; Mahmoudi, M ; Sharif University of Technology
2013
Abstract
Amyloid beta fibrillation can lead to major disorder of neurons processes and is associated with several neuronal diseases (e.g., Alzheimer's disease). We report here an importance of slight temperature changes, in the physiological range (35-42 °C), on the amyloid fibrillation process in the presence and absence of hydrophilic (silica) and hydrophobic (polystyrene) nanoparticles (NPs). The results highlight the fact that slight increases in temperature can induce inhibitory and acceleratory effects of hydrophobic and hydrophilic NPs on the fibrillation process, respectively. Using further in vivo considerations, the outcomes of this study can be used for considerable modifications on the...
Protein corona composition of gold nanoparticles/nanorods affects amyloid beta fibrillation process
, Article Nanoscale ; Volume 7, Issue 11 , Feb , 2015 , Pages 5004-5013 ; 20403364 (ISSN) ; Dinarvand, R ; Ghahremani, M. H ; Hormozi-Nezhad, M. R ; Mahmoudi, Z ; Hajipour, M. J ; Atyabi, F ; Ghavami, M ; Mahmoudi, M ; Sharif University of Technology
Royal Society of Chemistry
2015
Abstract
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...