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Modeling self-assembly of the surfactants into biological bilayer membranes with special chemical structures using dissipative particle dynamics method
, Article Scientia Iranica ; Volume 23, Issue 3 , 2016 , Pages 942-950 ; 10263098 (ISSN) ; Pishevar, A. R ; Saidi, M. S ; Shirani, E ; Sharif University of Technology
Sharif University of Technology
2016
Abstract
The aim of this study is to simulate the self-assembly of the surfactant molecules with special chemical structure and bending stiffiness into bilayer membranes using a mesoscopic Dissipative Particle Dynamics (DPD) method. The surfactants are modeled with special chemical structure and bending stiffiness. To confirm that the novel model is physical, we determine the interaction parameters based on matching the compressibility and solubility of the DPD system with real physics of the uid. To match the mutual solubility for binary uids, we use the relation between DPD parameters and x-parameters in Flory-Huggins-type models. Unsaturated bonds can change the stiffiness of a lipid membrane,...
Synthesis and cyto-genotoxicity evaluation of graphene on mice spermatogonial stem cells
, Article Colloids and Surfaces B: Biointerfaces ; Volume 146 , 2016 , Pages 770-776 ; 09277765 (ISSN) ; Akhavan, O ; Shamsara, M ; Daliri, M ; Dashtizad, M ; Farmany, A ; Sharif University of Technology
Elsevier
2016
Abstract
The present study analyzed the dose-dependent cyto- and genotoxicity of graphene oxide and reduced graphene oxide on spermatogonial stem cells (SSCs) for the first time. The results showed that graphene oxide significantly increased oxidative stress at concentrations of 100 and 400 μg/ml, while low concentrations did not have a significant effect. In addition, according to the MTT assay, the cell number decreased in high-concentration (100 and 400 μg/ml) graphene oxide-treated samples compared to untreated cells. However, a reduced graphene-treated sample demonstrated a significant increase in cell number. Moreover, microscopic analysis found high concentrations of graphene nanosheets in...
Unified model of brain tissue microstructure dynamically binds diffusion and osmosis with extracellular space geometry
, Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 94, Issue 3 , 2016 ; 15393755 (ISSN) ; Fotouhi, M ; Vejdani, K ; Kamali Zare, P ; Sharif University of Technology
American Physical Society
2016
Abstract
We present a universal model of brain tissue microstructure that dynamically links osmosis and diffusion with geometrical parameters of brain extracellular space (ECS). Our model robustly describes and predicts the nonlinear time dependency of tortuosity (λ=D/D∗) changes with very high precision in various media with uniform and nonuniform osmolarity distribution, as demonstrated by previously published experimental data (D = free diffusion coefficient, D∗ = effective diffusion coefficient). To construct this model, we first developed a multiscale technique for computationally effective modeling of osmolarity in the brain tissue. Osmolarity differences across cell membranes lead to changes...
Collaboration alignment in distributed interference management in uplink cellular systems
, Article 2016 IEEE International Symposium on Information Theory, 10 July 2016 through 15 July 2016 ; Volume 2016-August , 2016 , Pages 1456-1460 ; 21578095 (ISSN) ; 9781509018062 (ISBN) ; Maddah Ali, M. A ; Shariatpanahi, S. P ; Khalaj, B. H ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
Abstract
We consider a cellular wireless system including several interfering multi-user multi-antenna uplink channels, where the base station of each cell has to locally recover the messages of its corresponding users. We use a linear Wyner model, where each base station experiences interference only from the users in the two neighboring cells. Each base station is connected to the two nearby base stations through a backhaul link. The objective is to achieve the maximum degrees of freedom per cell, with minimum aggregated load in the backhaul. We propose a successive cooperative alignment scheme, in which each base station forms backhaul messages by combining the previous received backhaul messages...
Nanofibrous hydrogel with stable electrical conductivity for biological applications
, Article Polymer (United Kingdom) ; Volume 97 , 2016 , Pages 205-216 ; 00323861 (ISSN) ; Rezayat, S. M ; Vashegani Farahani, E ; Mahmoudifard, M ; Zamanlui, S ; Soleimani, M ; Sharif University of Technology
Elsevier Ltd
Abstract
3D hydrogel environment with both unique properties of nanofibrous structure and electrical character can provide a promising scaffold for skeletal muscle tissue engineering approaches. Herein, the poly acrylic acid (PAA)-based hydrogel was engineered to conductive one by aniline polymerization in the form of nanofibers. The poly aniline (PANi) nanofibers were made by the optimized chemical reactions between the surface carboxylate groups of based hydrogel and protonated aniline monomers. We found that the strong bonding which was created between PANi and camphor sulphonic acid (CSA) as a doping agent supporting the stable electrical property of composite hydrogel after incubation in cell...
Multi-objective dynamic cell formation problem: A stochastic programming approach
, Article Computers and Industrial Engineering ; Volume 98 , 2016 , Pages 323-332 ; 03608352 (ISSN) ; Rafiei, H ; Zohrevand, A. H ; Sharif University of Technology
Elsevier Ltd
Abstract
This paper addresses dynamic cell formation problem (DCFP) which has been explored vastly for several years. Although a considerable body of literature in this filed, two remarkable aspects have been significantly ignored so far, as uncertainty and human-related issues. In order to compensate such a shortage, this paper develops a bi-objective stochastic model. The first objective function of the developed model seeks to minimize total cost of machine procurement, machine relocation, inter-cell moves, overtime utilization, worker hiring/laying-off, and worker moves between cells; while the second objective function maximizes labor utilization of the cellular manufacturing system. In the...
Fabrication of porous gelatin-chitosan microcarriers and modeling of process parameters via the RSM method
, Article International Journal of Biological Macromolecules ; Volume 88 , 2016 , Pages 288-295 ; 01418130 (ISSN) ; Mashayekhan, S ; Baniasadi, H ; Sharif University of Technology
Elsevier B.V
Abstract
Porous gelatin-chitosan microcarriers (MCs) with the size of 350 ± 50 μm were fabricated with blends of different gelatin/chitosan (G/C) weight ratio using an electrospraying technique. Response surface methodology (RSM) was used to study the quantitative influence of process parameters, including blend ratio, voltage, and syringe pump flow rate, on MCs diameter and density. In the following, MCs of the same diameter and different G/C weight ratio (1, 2, and 3) were fabricated and their porosity and biocompatibility were investigated via SEM images and MTT assay, respectively. The results showed that mesenchymal stem cells (MSCs) could attach, proliferate, and spread on fabricated porous MCs...
Ion Channel Based Bio-Synthetic Modulator for Diffusive Molecular Communication
, Article IEEE Transactions on Nanobioscience ; Volume 15, Issue 5 , 2016 , Pages 418-432 ; 15361241 (ISSN) ; Ahmadzadeh, A ; Schober, R ; Nasiri Kenari, M ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2016
Abstract
In diffusion-based molecular communication (DMC), a transmitter nanomachine is responsible for signal modulation. Thereby, the transmitter has to be able to control the release of the signaling molecules employed for representing the transmitted information. In nature, an important class of control mechanisms for releasing molecules from cells utilizes ion channels which are pore-forming proteins across the cell membrane. The opening and closing of the ion channels is controlled by a gating parameter. In this paper, an ion channel based modulator for DMC is proposed which controls the rate of molecule release from the transmitter by modulating a gating parameter signal. Exploiting the...
The synergistic effect of surface topography and sustained release of TGF-β1 on myogenic differentiation of human mesenchymal stem cells
, Article Journal of Biomedical Materials Research - Part A ; Volume 104, Issue 7 , 2016 , Pages 1610-1621 ; 15493296 (ISSN) ; Mashayekhan, S ; Vakilian, S ; Ardeshirylajimi, A ; Soleimani, M ; Sharif University of Technology
John Wiley and Sons Inc
Abstract
A combination of topographical cues and controlled release of biochemical factors is a potential platform in controlling stem cells differentiation. In this study the synergistic effect of nanotopography and sustained release of biofunctional transforming growth factor beta 1 (TGF-β1) on differentiation of human Wharton's Jelly-derived mesenchymal stem cell (hWJ-derived UC-MSCs) toward myogenic lineage was investigated. In order to achieve a sustained release of TGF-β1, this factor was encapsulated within chitosan nanoparticles. Afterwards the aligned composite mats were fabricated using poly-E-caprolacton (PCL) containing TGF-β1-loaded chitosan nanoparticles and poly-L-lactic acid (PLLA)....
The nanofibrous PAN-PANi scaffold as an efficient substrate for skeletal muscle differentiation using satellite cells
, Article Bioprocess and Biosystems Engineering ; Volume 39, Issue 7 , 2016 , Pages 1163-1172 ; 16157591 (ISSN) ; Mahmoudifard, M ; Mohamadyar Toupkanlou, F ; Dodel, M ; Hajarizadeh, A ; Adabi, M ; Soleimani, M ; Sharif University of Technology
Springer Verlag
Abstract
Among polymers, polyaniline (PANi) has been introduced as a good candidate for muscle regeneration due to high conductivity and also biocompatibility. Herein, for the first time, we report the use of electrospun nanofibrous membrane of PAN-PANi as efficient scaffold for muscle regeneration. The prepared PAN-PANi electrospun nanofibrous membrane was characterized by scanning electron microscopy (SEM), Attenuated total reflectance fourier transform infrared spectroscopy (ATR-FTIR) and tensile examination. The softer scaffolds of non-composite electrospun nanofibrous PAN govern a higher rate of cell growth in spite of lower differentiation value. On the other hand, PAN-PANi electrospun...
BLESS: A simple and efficient scheme for prolonging PCM lifetime
, Article 53rd Annual ACM IEEE Design Automation Conference, DAC 2016, 5 June 2016 through 9 June 2016 ; Volume 05-09 , June-2016 , 2016 ; 0738100X (ISSN); 9781450342360 (ISBN) ; Jalili, M ; Sarbazi Azad, H ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2016
Abstract
Limited endurance problem and low cell reliability are main challenges of phase change memory (PCM) as an alternative to DRAM. To further prolong the lifetime of a PCM device, there exist a number of techniques that can be grouped in two categories: 1) reducing the write rate to PCM cells, and 2) handling cell failures when faults occur. Our experiments confirm that during write operations, an extensive non-uniformity in bit ips is exhibited. To reduce this non-uniformity, we present byte-level shifting scheme (BLESS) which reduces write pressure over hot cells of blocks. Additionally, this shifting mechanism can be used for error recovery purpose by using the MLC capability of PCM and...
Preparation of biodegradable gelatin/PVA porous scaffolds for skin regeneration
, Article Artificial Cells, Nanomedicine and Biotechnology ; 2016 , Pages 1-8 ; 21691401 (ISSN) ; Dadbin, S ; Frounchi, M ; Rajabi, S ; Sharif University of Technology
Taylor and Francis Ltd
2016
Abstract
Porous scaffolds composed of gelatin/poly (vinyl alcohol), (Gel/PVA), were prepared using combination of freeze gelation and freeze drying methods. The effect of polymer concentration, gelatin/PVA ratio, and glutaraldehyde/gelatin ratio (GA/Gel) was investigated on morphology of pores, swelling ratio, biodegradation, and skin cell culture. At optimum preparation conditions the scaffolds had uniform pore size distributions showing high swelling ratio of 23.6. The scaffolds were of biodegradable nature and almost degraded in 28 days. Human dermal fibroblast cells (HDF) were cultured on the scaffolds and MTS assay was conducted to evaluate the influence of PVA on growth and proliferation of the...
High antimicrobial activity and low human cell cytotoxicity of core-shell magnetic nanoparticles functionalized with an Antimicrobial Peptide
, Article ACS Applied Materials and Interfaces ; Volume 8, Issue 18 , 2016 , Pages 11366-11378 ; 19448244 (ISSN) ; Rai, A ; Pinto, S ; Evangelista, M ; Cardoso, R. M. S ; Paulo, C ; Carvalheiro, T ; Paiva, A ; Imani, M ; Simchi, A ; Durães, L ; Portugal, A ; Ferreira, L ; Sharif University of Technology
American Chemical Society
2016
Abstract
Superparamagnetic iron oxide nanoparticles (SPIONs) functionalized with antimicrobial agents are promising infection-targeted therapeutic platforms when coupled with external magnetic stimuli. These antimicrobial nanoparticles (NPs) may offer advantages in fighting intracellular pathogens as well as biomaterial-associated infections. This requires the development of NPs with high antimicrobial activity without interfering with the biology of mammalian cells. Here, we report the preparation of biocompatible antimicrobial SPION@gold core-shell NPs based on covalent immobilization of the antimicrobial peptide (AMP) cecropin melittin (CM) (the conjugate is named AMP-NP). The minimal inhibitory...
Paclitaxel molecularly imprinted polymer-PEG-folate nanoparticles for targeting anticancer delivery: Characterization and cellular cytotoxicity
, Article Materials Science and Engineering C ; Volume 62 , 2016 , Pages 626-633 ; 09284931 (ISSN) ; Darvishi, B ; Azizi Ishkuh, F ; Shahmoradi, E ; Mohammadi, A ; Javanbakht, M ; Dinarvand, R ; Atyabi, F ; Sharif University of Technology
Elsevier Ltd
2016
Abstract
The aim of this work was to synthesize molecularly imprinted polymer-poly ethylene glycol-folic acid (MIP-PEG-FA) nanoparticles for use as a controlled release carrier for targeting delivery of paclitaxel (PTX) to cancer cells. MIP nanoparticles were synthesized by a mini-emulsion polymerization technique and then PEG-FA was conjugated to the surface of nanoparticles. Nanoparticles showed high drug loading and encapsulation efficiency, 15.6 ± 0.8 and 100%, respectively. The imprinting efficiency of MIPs was evaluated by binding experiments in human serum. Good selective binding and recognition were found in MIP nanoparticles. In vitro drug release studies showed that MIP-PEG-FA have a...
Influence of Fe3O4 nanoparticles in hydroxyapatite scaffolds on proliferation of primary human fibroblast cells
, Article Journal of Materials Engineering and Performance ; 2016 , Pages 1-9 ; 10599495 (ISSN) ; Aghaie, E ; Nadernezhad, A ; Zargarzadeh, M ; Khakzad, A ; Shakeri, M. S ; Beygi Khosrowshahi, Y ; Siadati, M. H ; Sharif University of Technology
Springer New York LLC
2016
Abstract
Modern techniques for expanding stem cells play a substantial role in tissue engineering: the raw material that facilitates regeneration of damaged tissues and treats diseases. The environmental conditions and bioprocessing methods are the primary determinants of the rate of cultured stem cell proliferation. Bioceramic scaffolds made of calcium phosphate are effective substrates for optimal cell proliferation. The present study investigates the effects of two bioceramic scaffolds on proliferating cells in culture media. One scaffold was made of hydroxyapatite and the other was a mixture of hydroxyapatite and ferromagnetic material (Fe3O4 nanoparticles). Disk-shaped (10 mm × 2 mm) samples of...
The different fate of satellite cells on conductive composite electrospun nanofibers with graphene and graphene oxide nanosheets
, Article Biomedical Materials (Bristol) ; Volume 11, Issue 2 , 2016 ; 17486041 (ISSN) ; Soleimani, M ; Hatamie, S ; Zamanlui, S ; Ranjbarvan, P ; Vossoughi, M ; Hosseinzadeh, S ; Sharif University of Technology
Institute of Physics Publishing
2016
Abstract
Electrospinning of composite polymer solutions provides fantastic potential to prepare novel nanofibers for use in a variety of applications. The addition of graphene (G) and graphene oxide (GO) nanosheets to bioactive polymers was found to enhance their conductivity and biocompatibility. Composite conductive nanofibers of polyaniline (PANI) and polyacrylonitrile (PAN) with G and GO nanosheets were prepared by an electrospinning process. The fabricated membranes were investigated by physical and chemical examinations including scanning electron microscopy (SEM), Raman spectroscopy, x-ray diffraction (XRD) and tensile assay. The muscle satellite cells enriched by a pre-plating technique were...
Investigation of readout cell configuration and parameters on functionality and stability of bi-directional RSFQ TFF
, Article IEEE Transactions on Applied Superconductivity ; Volume 26, Issue 3 , 2016 ; 10518223 (ISSN) ; Zandi, H ; Foroughi, F ; Bozbey, A ; Fardmanesh, M ; Sharif University of Technology
Abstract
Considering the two main categories of rapid single flux quantum gates with destructive and nondestructive readout process, we have investigated the effects of readout cell topology and involved critical parameters on the proper functionality and stability of the states of the newly developed bidirectional T flip-flops (TFFs). It is observed that instabilities and fluctuations in the state of the gate (memory of TFF) after each transition determine the minimum time intervals between the clock pulses set by the ac bias current, further limiting the ultimate operation frequency of the circuits. The absolute values of the current levels of the junctions at each state, which play an important...
A comparative study of collagen matrix density effect on endothelial sprout formation using experimental and computational approaches
, Article Annals of Biomedical Engineering ; Volume 44, Issue 4 , 2016 , Pages 929-941 ; 00906964 (ISSN) ; Mohammadaliha, N ; Heilshorn, S. C ; Bauer, A. L ; Sharif University of Technology
Abstract
A thorough understanding of determining factors in angiogenesis is a necessary step to control the development of new blood vessels. Extracellular matrix density is known to have a significant influence on cellular behaviors and consequently can regulate vessel formation. The utilization of experimental platforms in combination with numerical models can be a powerful method to explore the mechanisms of new capillary sprout formation. In this study, using an integrative method, the interplay between the matrix density and angiogenesis was investigated. Owing the fact that the extracellular matrix density is a global parameter that can affect other parameters such as pore size, stiffness,...
Simulation of the effects of oxygen carriers and scaffold geometry on oxygen distribution and cell growth in a channeled scaffold for engineering myocardium
, Article Mathematical Biosciences ; Volume 294 , 2017 , Pages 160-171 ; 00255564 (ISSN) ; Mashayekhan, S ; Bastani, D ; Sharif University of Technology
Abstract
This study proposes a mathematical model to evaluate the impact of oxygen carriers and scaffold geometry on oxygen distribution and cell growth in a 3D cardiac construct using computational fluid dynamics (CFD). Flow equations, oxygen balance equation and cell balance equation were solved using special initial and boundary conditions. The modeling results revealed that 55% increase in cardiac cell density occurred by using 6.4% perfluorocarbon oxygen carrier (PFC) compared to pure culture medium without PFC supplementation. Moreover, the effects of the scaffold geometry on cell density were examined by changing the channel numbers and the construct length. A 30% increase in the average cells...
A multiscale approach for determining the morphology of endothelial cells at a coronary artery
, Article International Journal for Numerical Methods in Biomedical Engineering ; Volume 33, Issue 12 , 2017 ; 20407939 (ISSN) ; Saidi, M. S ; Firoozabadi, B ; Sharif University of Technology
Abstract
The morphology of endothelial cells (ECs) may be an indication for determining atheroprone sites. Until now, there has been no clinical imaging technique to visualize the morphology of ECs in the arteries. The present study introduces a computational technique for determining the morphology of ECs. This technique is a multiscale simulation consisting of the artery scale and the cell scale. The artery scale is a fluid-structure interaction simulation. The input for the artery scale is the geometry of the coronary artery, that is, the dynamic curvature of the artery due to the cardiac motion, blood flow, blood pressure, heart rate, and the mechanical properties of the blood and the arterial...