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Predicting the cardiac troponin I (cTnI) aptamer/methylene blue configuration using computational modeling studies: a screening search method for constructing aptasensors
, Article ChemistrySelect ; Volume 5, Issue 35 , September , 2020 , Pages 10958-10969 ; Khajehsharifi, H ; Hashemnia, S ; Shahrokhian, S ; Sharif University of Technology
Wiley-Blackwell
2020
Abstract
Acute Myocardial Infarction (AMI) is the most common cause of mortality, and cardiac troponin I (cTnI) is the gold standard for AMI diagnosis. Some aptamers have been reported to detect cTnI, but there is rarely any structural information on their binding with cTnI. There are many studies involving electrochemical aptasensors with methylene blue (MB) as a redox indicator that does not provide any significant new information. Our study, however, involves the computational modeling of the complexes of a documented 40-mer ssDNA-cTnI aptamer with its target and MB. Here, MB was used as a model system to investigate the rather complex interaction modes between small redox molecules and a...
Modeling of damage in soft biological tissues
, Article Biomechanics of Living Organs: Hyperelastic Constitutive Laws for Finite Element Modeling ; 2017 , Pages 101-123 ; 9780128040607 (ISBN); 9780128040096 (ISBN) ; Fereidoonnezhad, B ; Sharif University of Technology
Elsevier Inc
2017
Abstract
The mechanical responses of biological tissues are well characterized by hyperelastic or viscoelastic models within the physiological loading range. However, during supra-physiological mechanical loading, as occurs during interventional procedures such as balloon angioplasty and arterial clamping, damage may occur in the tissue. The continuum and computational treatments of damage in soft biological tissues have attracted considerable attention over the recent years. In this chapter, we review the state of the art of this challenging area. We summarize and critically discuss various damage models, which are based on continuum damage mechanics, the theory of pseudo-elasticity, and the...
Modeling and evaluation of service composition in commercial multiclouds using timed colored petri nets
, Article IEEE Transactions on Systems, Man, and Cybernetics: Systems ; 2017 ; 21682216 (ISSN) ; Etesami, S. E ; Ghorbani, N ; Akhavan Niaki, A ; Sousa, L ; Movaghar, A ; Sharif University of Technology
Abstract
The increasing demand for Web services encourages commercial cloud service providers to publish their own services with various functional and nonfunctional capabilities in different cloud platforms. The aggregation of atomic services from multiple service repositories is the main idea of the service composition concept in multiclouds. The cloud Web service composition is a suitable way for satisfying users' complex requests by integrating services from different clouds in order to create a new value-added composite service. The time required to serve a composite service by a multicloud environment is an important parameter, which depends on different factors, ranging from the service...
Modeling and evaluation of service composition in commercial multiclouds using timed colored petri nets
, Article IEEE Transactions on Systems, Man, and Cybernetics: Systems ; Volume 50, Issue 3 , 2020 , Pages 947-961 ; Etesami, S. E ; Ghorbani, N ; Akhavan Niaki, A ; Sousa, L ; Movaghar, A ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2020
Abstract
The increasing demand for Web services encourages commercial cloud service providers to publish their own services with various functional and nonfunctional capabilities in different cloud platforms. The aggregation of atomic services from multiple service repositories is the main idea of the service composition concept in multiclouds. The cloud Web service composition is a suitable way for satisfying users' complex requests by integrating services from different clouds in order to create a new value-added composite service. The time required to serve a composite service by a multicloud environment is an important parameter, which depends on different factors, ranging from the service...
A front-end tool for automated abstraction and modular verification of actor-based models
, Article Proceedings - Fourth International Conference on Application of Concurrency to System Design, ACSD 2004, Hamilton, Ont., 16 June 2004 through 18 June 2004 ; 2004 , Pages 145-148 ; 0769520774 (ISBN); 9780769520773 (ISBN) ; Shali, A ; Jaghoori, M. M ; Iravanchi, H ; Movaghar, A ; Sharif University of Technology
2004
Abstract
Actor-based modeling is known to be an appropriate approach for representing concurrent and distributed systems. Rebeca is an actor-based language with a formal foundation, based on an operational interpretation of the actor model. We develop a front-end tool for translating a subset of Rebeca to SMV in order to model check Rebeca models. Automated modular verification and abstraction techniques are supported by the tool
Modeling behavior in compositions of software architectural primitives
, Article Proceedings - 19th International Conference on Automated Software Engineering, ASE 2004, Linz, 20 September 2004 through 24 September 2004 ; 2004 , Pages 371-374 ; 0769521312 (ISBN); 9780769521312 (ISBN) ; Medvidovic, N ; Sirjani, M ; Arbab, F ; Sharif University of Technology
2004
Abstract
Software architectures and architectural styles are increasingly used for designing large-scale software systems. Alfa is a framework for the composition of style-based software architectures from a small set of primitives. It models the behavior of architectural components and connectors as orderings among events at their inputs and outputs. Formalizing such behavior is useful for checking conformance of architectures to their styles. We therefore propose a formal approach that uses data-abstract constraint automata to model the behavior of Alfa's compositions, and to verify their behavioral style conformance. We have also developed an automated conformance analyzer for Alfa. © 2004 IEEE
Friendship modeling for cooperative co-evolutionary fuzzy systems: A hybrid GA-GP algorithm
, Article 22nd International Conference of the North American Fuzzy Information Processing Society, NAFIPS 2003, 24 July 2003 through 26 July 2003 ; Volume 2003-January , 2003 , Pages 61-66 ; 0780379187 (ISBN); 9780780379183 (ISBN) ; Mosavat, I ; Abbasi, S ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2003
Abstract
A novel approach is proposed to combine the strengths of GA and GP to optimize rule sets and membership functions of fuzzy systems in a co-evolutionary strategy in order to avoid the problem of dual representation in fuzzy systems. The novelty of proposed algorithm is twofold. One is that GP is used for the structural part (Rule sets) and GA for the string part (Membership functions). The goal is to reduce/eliminate the problem of competing conventions by co-evolving pieces of the problem separately and then in combination. Second is exploiting the synergism between rules sets and membership functions by imitating the effect of "matching" and friendship in cooperating teams of humans,...
Prediction of critical micelle concentration of some anionic surfactants using multiple regression techniques: A quantitative structure-activity relationship study
, Article Journal of Surfactants and Detergents ; Volume 3, Issue 1 , 2000 , Pages 47-52 ; 10973958 (ISSN) ; Konouz, E ; Sharif University of Technology
2000
Abstract
Computer-assisted methods were employed to develop a statistical relationship between molecular-based structural parameters and log critical micelle concentration (CMC) of some anionic surfactants. The CMC of 31 alkyl sulfates and alkanesulfonates were used for model generation. Among different models, two equations were selected as the best, and their specifications are given. The statistics of these models together with cross-validation results indicate the capability of both models to predict the CMC of anionic surfactants. Three descriptors of Wiener number, reciprocal of the dipole moment, and reciprocal of the Randic index appear in the models. Results indicate that topological...
Analysis and Modeling of Base Plates Under the Effect of Different Loads
, M.Sc. Thesis Sharif University of Technology ; Mofid, Masoud (Supervisor)
Abstract
In steel structured buildings the connection of columns to foundations is of practical significance. This connection customarily is performed by a base plate, which is connected to the foundation with bolts. The columns and base plates are usually prepared separately, and later are welded together by contractors. Due to the errors in the process of fabrication, these plates are proposed with larger dimensions than those suggested by the designers. However, it is believed that the utilization of stiffeners, which are welded to the columns in a perpendicular state, reduces the stress field inside the base plates significantly. Therefore, by use of stiffeners the thickness of base plates can be...
Modeling of asphaltene deposition during miscible CO2 Flooding
, Article Petroleum Science and Technology ; Vol. 32, Issue. 18 , 2014 , Pages 2183-2194 ; ISSN: 10916466 ; Dabir, B ; Asghari, K ; Shahvaranfard, A ; Sharif University of Technology
Abstract
The authors present the results of numerical tests and simulations to investigate and analyze the likelihood of asphaltene precipitation and deposition during CO2 flooding in a reservoir. The effects of asphaltene precipitation on oil properties such as oil viscosity and density during miscible CO2 flooding process were elaborated by using Winprop software of Computer Modeling Group. Also oil properties change during CO 2 miscible flooding by numerical slim tube were investigated by a compositional simulator (GEM). A fluid sample of Saskatchewan Reservoir that had been flooded miscibly with CO2 was chosen for performing the sensitivity analyses. The results showed that asphaltene...
Porosity variation below a fluid-porous interface
, Article Chemical Engineering Science ; Vol. 107 , April , 2014 , pp. 311-316 ; ISSN: 00092509 ; Morad, M. R ; Matyka, M ; Liu, B ; Malekmohammadi, R ; Weise, J ; Kuypers, M. M. M ; Sharif University of Technology
Abstract
The correct quantification of porosity is essential in all studies pertaining to porous media. A host of existing works employs a constant, bulk value for porosity, even when the porous sample is attached to a free fluid. Since the volume fraction of the solid matrix near the interface region differs from that in the core, the porosity undergoes a spatial variation. Here we present a novel relation for the porosity as a function of depth below the interface, using the concept of surface roughness applied on the classical definition of open porosity. This relation has been verified by computational modeling as well as non-invasive laser experiments. It has been shown that this depth-dependent...
Analytical modeling of oil production from a matrix block by free fall gravity drainage mechanism
, Article Energy Exploration and Exploitation ; Volume 31, Issue 6 , October , 2013 , Pages 821-832 ; 01445987 (ISSN) ; Ardakany, M ; Ghazanfari, M ; Sharif University of Technology
2013
Abstract
Free fall gravity drainage is the most effective mechanism in gas invaded zone of fractured reservoirs. Although several analytical models have been proposed to characterize this mechanism, most of them suffer from inadequate reality, such as neglecting capillary pressure. In this study, a new analytical model was proposed to predict the oil recovery versus time for a homogeneous matrix block under a free fall gravity drainage mechanism. Considering the effect of viscous, gravity as well as capillary forces, the model was developed. This model is applicable to different conditions of gravity and capillary force, as well as when both forces are active. Along with core scale experimental data...
Risk assessment of vapor cloud explosions in a hydrogen production facility with consequence modeling
, Article Journal of Research in Health Sciences ; Volume 13, Issue 2 , 2013 , Pages 181-187 ; 16822765 (ISSN) ; Jafari, M. J ; Badri, N ; Sharif University of Technology
2013
Abstract
Background: New technologies using hazardous materials usually have certain risks. It is more serious when the technology is supposed to be applied in a large scale and become widely used by many people. The objective of this paper was to evaluate the risk of vapor cloud explosion in a hydrogen production process. Methods: Potential hazards were identified using the conventional hazard identification method (HAZID). The frequency of the proposed scenarios was estimated from statistical data and existing records. The PHAST professional software was applied for consequence modeling. Both individual and societal risks were evaluated. This cross-sectional study was conducted from June 2010 to...
Uncertainty in probabilistic trust models
, Article Proceedings - International Conference on Advanced Information Networking and Applications, AINA ; 2012 , Pages 511-517 ; 1550445X (ISSN) ; 9780769546513 (ISBN) ; Jalili, R ; IEEE Comput. Soc. Tech. Comm. Distrib. Process ; Sharif University of Technology
2012
Abstract
Computational models of trust try to transfer the concept of trust from the real to the virtual world. While such models have been widely investigated in the past decade, the uncertainty involved in trust computation has been overlooked in the literature. In this paper, uncertainty of probabilistic trust models is quantified using confidence intervals and its factors are determined through simulation. The results confirm the importance and highlight the amount of uncertainty in the Beta and HMM (Hidden Markov Model) trust models. In addition, an uncertainty-driven method is proposed which reduces the risk involved in the trust-based utility maximization according to uncertainty
Personalized design of ankle-foot prosthesis based on computer modeling of amputee locomotion
, Article Assistive Technology ; September , 2018 ; 10400435 (ISSN) ; Mohammadi Moghaddam, M ; Farahmand, F ; Sharif University of Technology
Taylor and Francis Inc
2018
Abstract
This study proposes a computer modeling approach to find the optimal damping coefficients of the viscoelastic ankle-foot prostheses for each specific amputee. A two-dimensional locomotion model was developed for a transtibial amputee and personalized using his body measures and the reference gait pattern of an equivalent able-bodied subject. By employing the forward dynamic simulation, the amputee’s locomotion was synthesized for different prosthetic settings to find the optimal damping coefficients, based on a kinematics and a total work cost function. Results indicated a good agreement between the model predictions and the experimental observations. © 2018, © 2018 RESNA
Controlling best response dynamics for network games
, Article IEEE Transactions on Network Science and Engineering ; March , 2018 ; 23274697 (ISSN) ; Maazallahi, A ; Habibi, J ; Habibi, M ; Sharif University of Technology
IEEE Computer Society
2018
Abstract
Controlling networked dynamical systems is a complex endeavor, specifically keeping in mind the fact that in many scenarios the actors that are engaged in the dynamism behave selfishly and therefore only take into account their own individual utility, a setting that has been widely studied in the field of game theory. One way that we can control the system dynamics is through the use of control parameters that are at our disposal, but finding optimal values for these parameters is a complex and time consuming task. In this paper we use the relation between network structural properties and control parameters to create a mathematical model that uses learning methods to find optimal values...
Enhanced Waddington landscape model with cell-cell communication can explain molecular mechanisms of self-organization
, Article Bioinformatics ; Volume 35, Issue 20 , 2019 , Pages 4081-4088 ; 13674803 (ISSN) ; Moradi, P ; Sharifi Zarchi, A ; Hosein Khalaj, B ; Berger, B ; Sharif University of Technology
Oxford University Press
2019
Abstract
The molecular mechanisms of self-organization that orchestrate embryonic cells to create astonishing patterns have been among major questions of developmental biology. It is recently shown that embryonic stem cells (ESCs), when cultured in particular micropatterns, can self-organize and mimic the early steps of pre-implantation embryogenesis. A systems-biology model to address this observation from a dynamical systems perspective is essential and can enhance understanding of the phenomenon. Results: Here, we propose a multicellular mathematical model for pattern formation during in vitro gastrulation of human ESCs. This model enhances the basic principles of Waddington epigenetic landscape...
Personalized design of ankle-foot prosthesis based on computer modeling of amputee locomotion
, Article Assistive Technology ; Volume 32, Issue 2 , 2020 , Pages 100-108 ; Mohammadi Moghaddam, M ; Farahmand, F ; Sharif University of Technology
Taylor and Francis Inc
2020
Abstract
This study proposes a computer modeling approach to find the optimal damping coefficients of the viscoelastic ankle-foot prostheses for each specific amputee. A two-dimensional locomotion model was developed for a transtibial amputee and personalized using his body measures and the reference gait pattern of an equivalent able-bodied subject. By employing the forward dynamic simulation, the amputee’s locomotion was synthesized for different prosthetic settings to find the optimal damping coefficients, based on a kinematics and a total work cost function. Results indicated a good agreement between the model predictions and the experimental observations. © 2018, © 2018 RESNA
System-level assertion-based performance verification for embedded systems
, Article 13th International Computer Society of Iran Computer Conference on Advances in Computer Science and Engineering, CSICC 2008, Kish Island, 9 March 2008 through 11 March 2008 ; Volume 6 CCIS , 2008 , Pages 243-250 ; 18650929 (ISSN); 3540899847 (ISBN); 9783540899846 (ISBN) ; Gharehbaghi, A. M ; Hessabi, S ; Sharif University of Technology
2008
Abstract
As contemporary digital systems specifically embedded systems become more and more complex, taking advantage of system-level design is being more widespread. Many embedded systems must operate under strict timing constraints. One of the best methods for examining timing constraints in an embedded system can be done via the performance verification. In this paper an assertion-based verification methodology has been proposed for verifying system-level timing constraints in an embedded system. Performance assertions are specified by an assertion language at the transaction-level of abstraction. A Turing machine and a structure named performance evaluator have been coupled to provide a...
Numerical simulation of three-dimensional flow and analysis of filling process in compression resin transfer moulding
, Article Composites Part A: Applied Science and Manufacturing ; Volume 37, Issue 9 , 2006 , Pages 1434-1450 ; 1359835X (ISSN) ; Sharif University of Technology
2006
Abstract
In compression resin transfer moulding (CRTM), resin flows inside a mould filled with fibrous reinforcement as a result of resin injection and mould compression. This process facilitates the resin flow through the fibrous reinforcement particularly for high fiber content parts. This paper presents the numerical simulation of filling process of CRTM in full three-dimensional domain. A mathematical model of three-dimensional resin flow inside the CRTM mould is presented. An effective elastic modulus is introduced for multi-layer preforms connecting the mould closing speed to deformation rate of individual layers. Control volume/finite element method (CV/FEM) is used and the numerical algorithm...