Sharif Digital Repository

A signaling pathway is a sequence of proteins and passenger molecules that transmits information from the cell surface to target molecules. Understanding signal transduction process requires detailed description of the involved pathways. Several methods and tools resolved this problem by incorporating genomic and proteomic data. However, the difficulty of obtaining prior knowledge of complex signaling networks limited the applicability of these tools. In this study, based on the simulation of signal flow in signaling network, we introduce a method for determining dominant pathways and signal response to stimulations. The model uses topology-weighted transit compartment approach and comprises... 

Dirac electrons in clean graphene can mediate the interactions between two localized magnetic moments. The functional form of the RKKY interaction in pristine graphene is specified by two main features: (i) an atomic-scale oscillatory part determined by a wavevector → connecting the two valleys; with doping another longer range oscillation appears which arises from the existence of an extended Fermi surface characterized by a momentum scale kF; (ii) an algebraic Rα decay in large distances where the exponent α=-3 is a distinct feature of undoped Dirac sea in two dimensions. In this work, we investigate the effect of a few per cent vacancies on the above properties. Depending on the doping... 

In this study, the nonlinear partial differential equations governing two phase flow through porous media are solved using two different methods, namely, finite difference and finite element. The capillary pressure term is considered in the mathematical model. The numerical results on a 2-D test case are then compared with the experimental drainage process and water flooding performed on a glass type micromodel. Based on the obtained results, finite difference technique needs less computational time for solving governing equations of two phase flow, but findings of this method show less agreement with the experimental data. The finite element scheme was found to be more adequate and its... 

In this work, we study the gas mixing behavior in a micro T-mixer using the direct simulation Monte Carlo (DSMC) method. The gas mixing process is monitored through a T-mixer, which is fed by two different CO and N2 gases; flowing into the T-mixer through the upper and lower inlets. We investigate the effects of axial and lateral wall temperature gradients on the mixing evolution at different rarefaction levels. The achieved results show that any temperature difference between the channel walls would result in an increase in mixing length for the chosen wall temperature gradient ranges and the studies pressure cases. Our observations show that a positive temperature gradient toward the... 

The theoretical need to recognize the link between the basic microstructure of nonlinear porous materials and their macroscopic mechanical behavior is continuously rising owing to the existing engineering applications. In this regard, a semi-analytical homogenization model is proposed to establish an overall, continuum-level constitutive law for nonlinear elastic materials containing prolate/oblate spheroidal voids undergoing finite axisymmetric deformations. The microgeometry of the porous materials is taken to be voided spheroid assemblage consisting of confocally voided spheroids of all sizes having the same orientation. Following a kinematically admissible deformation field for a... 

In this paper, the coupled thermo-mechanical simulation of hot isostatic pressing (HIPing) is presented for metal powders during densification process. The densification of powder is assumed to occur due to plastic hardening of metal particles. The constitutive model developed is used to describe the nonlinear behavior of metal powder. The numerical modeling of hot powder compaction simulation is performed based on the large deformation formulation, powder plasticity behavior, and frictional contact algorithm. A Lagrangian finite element formulation is employed for the large powder deformations. A modified cap plasticity model considering temperature effects is used in numerical simulation... 

A thermodynamic model considering flame propagation is presented to predict SI engine characteristics for hydrogen-methane blends. The partially charge stratification approach which involves micro direct injection of pure fuel or a fuel-air mixture, to create a rich zone near the spark plug, is proposed as a method to improve engine performance. Presented approach was validated with experimental data for the natural gas at lean condition. The model was generalized to predict the performance of engine for a variety of hydrogen contents in hydrogen-methane blends. Hydrogen molar concentrations of 0%, 15%, 30%, and 45% were used in the simulations. Results showed that partially charge... 

This paper presents a detailed frequency-domain system identification method applied to identify steering dynamics of a coastal patrol vessel using a data analysis software called CIFER. Advanced features such as the Chirp-Z transform and composite window optimization are used to extract high quality frequency responses. An accurate, robust and linear transfer function model is derived for yaw and roll dynamics of the vessel. To evaluate the accuracy of the identified model, time domain responses from a 45-45 zig-zag test are compared with the responses predicted by the identified model. The identified model shows excellent predictive capability and is well suited for simulation and... 

In this paper, two integral based methods are proposed to estimate the order and the parameters of simple fractional order models from the noisy step response data. Numerical simulation results show the efficiency of the proposed methods in the presence of the measurement noise  

In the current paper, we have investigated the generalized FitzHugh-Nagumo model. We have shown that symmetric bursting behaviors of different types could be observed in this model with an appropriate recovery term. A modified version of this system is used to construct bursting activities. Furthermore, we have shown some numerical examples of delayed Hopf bifurcation and canard phenomenon in the symmetric bursting of super-Hopf/homoclinic type near its super-Hopf and homoclinic bifurcations, respectively  

This work concerns with developing a non-equilibrium model of gravity drainage in a single block. The proposed model which considers both non-equilibrium effects of capillary pressure and relative permeabilities is used for prediction of oil recovery by gravity drainage from a single block. Close agreement observed between the model results and experimental data disclosed that the non-equilibrium assumption is completely reliable for modeling of gravity drainage. The results revealed that when the characteristic time of the saturation variation is comparable with the time required to establish capillary equilibrium, the non-equilibrium effects in gravity drainage must be considered. The... 

One concern of many investors is to own the assets which can be liquidated easily. Thus, in this paper, we incorporate portfolio liquidity in our proposed model. Liquidity is measured by an index called turnover rate. Since the return of an asset is uncertain, we present it as a trapezoidal fuzzy number and its turnover rate is measured by fuzzy credibility theory. The desired portfolio turnover rate is controlled through a fuzzy chance constraint. Furthermore, to manage the portfolios with asymmetric investment return, other than mean and variance, we also utilize the third central moment, the skewness of portfolio return. In fact, we propose a fuzzy portfolio mean-variance-skewness model... 

In a multi-agent system, the number and initial position of informed agents play a major role in the convergence of uninformed agents. In this paper, three different patterns of informed agents' initial positions are studied to see how the convergence percentage can be affected by the number of informed agents. The proposed initial locations are intuitive and inferred from the collective behavior in humans. To evaluate efficiency of the proposed methods and to compare them from different points of view, large number of computer simulations is performed and results are analyzed  

This paper presents analytical soltions for the nonlinear problem of electrostatically actuated torsional micromirrors considering the bending of the torsional beams. First the energy method is used for finding the equilibrium equations. Then the explicit function theorem is utilized for finding the equations governing the instability mode of the mirror. These equations are then solved using Homotopy Perturbation Method (HPM) for the especial case of α = 0 where α is a small nondimensional geometrical parameter defining the starting point of the underneath electrodes. Then straight forward perturbation method is applied for finding the pull-in angle and pull-in displacement of the... 

Network-on-Chips are now the popular communication medium to support inter-IP communications in complex on-chip systems with tens to hundreds IP cores. Higher scalability (compared to the traditional shared bus and point-to-point interconnects), throughput, and reliability are among the most important advantages of NoCs. Moreover, NoCs can well match current CAD methodologies mainly relying on modular and reusable structures with regularity of structural pattern. However, since NoCs are resource-limited, determining how to distribute application load over limited on-chip resources (e.g. switches, buffers, virtual channels, and wires) in order to improve the metrics of interest and satisfy... 

Finite element analysis is an effective tool to evaluate the material properties of living tissue. For an interactive optimization procedure, the finite element analysis usually needs many simulations to reach a reasonable solution. The metamodel analysis of finite element simulation can be used to reduce the computation of a structure with complex geometry or a material with composite constitutive equations. The intervertebral disc is a complex, heterogeneous, and hydrated porous structure. A poroelastic finite element model can be used to observe the fluid transferring, pressure deviation, and other properties within the disc. Defining reasonable poroelastic material properties of the... 

Fault detection (FD) in power electronic converters is necessary in embedded and safety critical applications to prevent further damage. Fast FD is a mandatory step in order to make a suitable response to a fault in one of the semiconductor devices. The aim of this study is to present a fast yet robust method for fault diagnosis in nonisolated dc-dc converters. FD is based on time and current criteria which observe the slope of the inductor current over the time. It is realized by using a hybrid structure via coordinated operation of two FD subsystems that work in parallel. No additional sensors, which increase system cost and reduce reliability, are required for this detection method. For... 

An analytical approach which is popular in micromechanical studies has been extended to the solution for the interference fit problem of the femoral stem in cementless total hip arthroplasty (THA). The multiple inhomogeneity problem of THA in transverse plane, including an elliptical stem, a cortical wall, and a cancellous layer interface, was formulated using the equivalent inclusion method (EIM) to obtain the induced interference elastic fields. Results indicated a maximum interference fit of about 210 μm before bone fracture, predicted based on the Drucker-Prager criterion for a partially reamed section. The cancellous layer had a significant effect on reducing the hoop stresses in the... 

Symmetric T junctions have been used widely in microfluidics to generate equal-sized microdroplets, which are applicable in drug delivery systems. A newly proposed method for generating unequal-sized microdroplets at a T junction is investigated theoretically and experimentally. Asymmetric T junctions with branches of identical lengths and different cross sections are utilized for this aim. An equation for the critical breakup of droplets at asymmetric T junctions and one for determining the breakup point of droplets are developed. A good agreement was observed between the theories (present and previous) and the experiments  

Five different approaches are presented to assign characteristic ratios for commensurate fractional order systems having order in (0,0.5]. Through the indirect methods, a closed-loop or plant transfer function is converted to a commensurate order one with an order greater than 0.5 so that the previously designed CRA method by the authors is applicable. The first method among the proposed direct ones is based on increasing the order of the desired closed-loop transfer function that allows the employment of positive characteristic ratios. In the second method the closed-loop response is sped up by augmenting an appropriate zero. The final method uses negative characteristic ratios to reach the...