Sharif Digital Repository

The ability to predict the cellular dynamics of intracellular transport has enormous potential to impact human health. A key transporter is kinesin-1, an ATP-driven molecular motor that shuttles cellular cargos along microtubules (MTs). The dynamics of kinesins depends critically on their unbinding rate from MT, which varies depending on the force direction applied on the motor, i.e. the force-unbinding rate relation is asymmetric. However, it remains unclear how changing the force direction from resisting (applied against the motion direction) to assisting (applied in the motion direction) alters the kinesin's unbinding and stepping. Here, we propose a theoretical model for the influence of... 

Due to the complexity of the human spinal motion segments, the intervertebral joints are often simulated in the musculoskeletal trunk models as pivots thus allowing no translational degrees of freedom (DOFs). This work aims to investigate, for the first time, the effect of such widely used assumption on trunk muscle forces, spinal loads, kinematics, and stability during a number of static activities. To address this, the shear deformable beam elements used in our nonlinear finite element (OFE) musculoskeletal model of the trunk were either substantially stiffened in translational directions (SFE model) or replaced by hinge joints interconnected through rotational springs (HFE model). Results... 

This research investigates the flexural behavior of a polymer concrete beam/pile encased with carbon fiber sleeve. The mechanical properties of carbon fiber sleeves in tension and cement and polymer concrete in compression were determined. Polymer concrete beams were tested in flexure to determine the bending moment capacity. Then, the test results were compared to the theoretical model results. Finally, a parametric study was conducted to determine the influence of beam/pile parameters on the capacity of the element. Based on the investigation, carbon fiber sleeve filled with polymer concrete exhibits outstanding structural performance including ductility and bending capacity  

In this research, the nonlinear elastic behavior of human extensor apparatus was investigated. To this goal, firstly the best material parameters of hyperelastic strain energy density functions consisting of the Mooney–Rivlin, Ogden, invariants, and general exponential models were derived for the simple tension experimental data. Due to the significance of stress response in other deformation modes of nonlinear models, the calculated parameters were used to study the pure shear and balance biaxial tension behavior of the extensor apparatus. The results indicated that the Mooney–Rivlin model predicts an unstable behavior in the balance biaxial deformation of the extensor apparatus, while the... 

We have developed an analytic approach to investigate the effect of group delay ripple of the dispersive devices on the performance of two major building blocks of microwave- photonic filters. Firstly, performance of PM-based block in the presence of an arbitrary group delay ripple (GDR) is analyzed and compared with the ripple-free case to reveal the destructive effects of added group delay ripple. In the next step, we repeat the proposed approach for the AM-based one; again, the performance is compared with the ripple-free case. Two distortion metrics are also introduced to quantify this distortion. Comparison of the performance of two building blocks in the presence of group delay ripple... 

The remediation of nonaqueous phase liquids (NAPLs) enhanced by surfactant and nanoparticles (NP) has been investigated in numerous studies. However, the role of NP-assisted surfactants in the dissolution process is still not well discussed. Besides, there is a lack of empirical dissolution models considering the effects of initial residual saturation Strap, NAPL distribution, and surfactant concentration in NAPL-aqueous phase systems. In this work, micromodel experiments are conducted to quantify mass transfer coefficients for different injected aqueous phases including deionized water, SDS surfactant solutions, and NP-assisted solutions with different levels of concentrations and flow... 

The present study employs Discrete Element Method (DEM) to establish a rheological model that relates the apparent viscosity of a granular material to shear rate, normal stress, and water saturation. In addition, a theoretical model was developed to determine water distribution and water-induced forces between particles for different saturations. The resulting forces were embedded in a 3D shear cell as a numerical rheometer, and a wet specimen was sheared between two walls. A power law rheological model was then obtained as a function of inertia number and saturation. It was found that up to a critical saturation, the apparent viscosity increased with saturation that was higher than that of... 

In this paper an analytical approach to study the effect of the substrate physical properties on the kinetics of adhesion and motility behavior of cells is presented. Cell adhesion is mediated by the binding of cell wall receptors and substrate's complementary ligands, and tight adhesion is accomplished by the recruitment of the cell wall binders to the adhesion zone. The binders' movement is modeled as their axisymmetric diffusion in the fluid-like cell membrane. In order to preserve the thermodynamic consistency, the energy balance for the cell-substrate interaction is imposed on the diffusion equation. Solving the axisymmetric diffusion-energy balance coupled equations, it turns out that... 

Control problem in a biological system is the problem of finding an interventional policy for changing the state of the biological system from an undesirable state, e.g. disease, into a desirable healthy state. Boolean networks are utilized as a mathematical model for gene regulatory networks. This paper provides an algorithm to solve the control problem in Boolean networks. The proposed algorithm is implemented and applied on two biological systems: T-cell receptor network and Drosophila melanogaster network. Results show that the proposed algorithm works faster in solving the control problem over these networks, while having similar accuracy, in comparison to previous exact methods. Source... 

Lander-Waterman's coverage bound establishes the total number of reads required to cover the whole genome of size G bases. In fact, their bound is a direct consequence of the well-known solution to the coupon collector's problem which proves that for such genome, the total number of bases to be sequenced should be O(G ln G). Although the result leads to a tight bound, it is based on a tacit assumption that the set of reads are first collected through a sequencing process and then are processed through a computation process, i.e., there are two different machines: one for sequencing and one for processing. In this paper, we present a significant improvement compared to Lander-Waterman's... 

In recent years, the management of health systems is a main concern of governments and decision-makers. Home health care is one of the newest methods of providing services to patients in developed societies that can respond to the individual lifestyle of the modern age and the increase of life expectancy. The home health care routing and scheduling problem is a generalized version of the vehicle routing problem, which is extended to a complex problem by adding special features and constraints of health care problems. In this problem, there are multiple stakeholders, such as nurses, for which an increase in their satisfaction level is very important. In this study, a mathematical model is... 

The electrical bending instability in charged liquid jets is the phenomenon determining the process of electrospinning. A model of this phenomenon is lacking however, mostly due to the complicated interplay between the viscosity and elasticity of the solution. To investigate the bending instability, we performed electrospinning experiments with a solution of polyethylene oxide in water/ethanol. Using a fast camera and sensitive multimeter, we deduced an experimental dispersion relation describing the helix pitch length as a function of surface charge. To understand this relation, we developed a theoretical model for the instability for a wide range of visco-elastic materials, from conducting... 

Aggregating fine-granular data measurements from smart meters presents an opportunity for utility companies to learn about consumers' power consumption patterns. Several research studies have shown that power consumption patterns can reveal a range of information about consumers, such as how many people are in the home, the types of appliances they use, their eating and sleeping routines, and even the TV programs they watch. As we move toward liberalized energy markets, many different parties are interested in gaining access to such data, which has enormous economical, societal, and environmental benefits. However, the main concern is that many such beneficial uses of smart meter big data... 

Techniques available in graph theory can be applied to signals recorded from human brain. In network analysis of EEG signals, the individual nodes are EEG sensor locations and the edges correspond to functional relations between them that are extracted from EEG time series. In this paper, we study EEG-based directed functional networks in Alzheimer's disease (AD). To this end, directed connectivity matrices of 25 AD patients and 26 healthy subjects are processed and a number of meaningful graph theory metrics are studied. Our data show that functional networks of AD brains have significantly reduced global connectivity in alpha and beta bands (P < 0.05). The AD brains have significantly... 

In this paper, a heuristic method for determining the optimal number of clusters is proposed. Four clustering algorithms, namely K-means, Growing Neural Gas, Simulated Annealing based technique, and Fuzzy C-means in conjunction with three well known cluster validity indices, namely Davies-Bouldin index, Calinski-Harabasz index, Maulik-Bandyopadhyay index, in addition to the proposed index are used. Our simulations evaluate capability of mentioned indices in some artificial and medical datasets. © 2008 IEEE  

Abnormalities in the topology of brain networks may be an important feature and etiological factor for psychogenic non-epileptic seizures (PNES). To explore this possibility, we applied a graph theoretical approach to functional networks based on resting state EEGs from 13 PNES patients and 13 age- and gender-matched controls. The networks were extracted from Laplacian-transformed time-series by a cross-correlation method. PNES patients showed close to normal local and global connectivity and small-world structure, estimated with clustering coefficient, modularity, global efficiency, and small-worldness metrics, respectively. Yet the number of PNES attacks per month correlated with a... 

Axon is an important part of the neuronal cells and axonal microtubules are bundles in axons. In axons, microtubules are coated with microtubule-associated protein tau, a natively unfolded filamentous protein in the central nervous system. These proteins are responsible for cross-linking axonal microtubule bundles. Through complimentary dimerization with other tau proteins, bridges are formed between nearby microtubules creating bundles. Formation of bundles of microtubules causes their transverse reinforcement and has been shown to enhance their ability to bear compressive loads. Though microtubules are conventionally regarded as bearing compressive loads, in certain circumstances during... 

Currently PM2.5 is a major air pollution concern in Tehran, Iran due to frequent high levels and possible adverse impacts. In this study, which is the first of its kind to take place in Tehran, composition and sources of PM2.5 and carbonaceous aerosol were determined, and their seasonal trends were studied. In this regard, fine PM samples were collected every six days at a residential station for one year and the chemical constituents including organic marker species, metals, and ions were analyzed by chemical analysis. The source apportionment was performed using organic molecular marker-based CMB receptor modeling. Carbonaceous compounds were the major contributors to fine particulate mass... 

The bioavailability of drugs can be improved by regulating the structural properties, particularly lipoid systems, such as niosomes, can increase cellular uptake. Herein, we optimized double emulsion and niosomal formulations for encapsulating anthocyanin-rich black carrot extract. Nanoparticles obtained by selected formulation were characterized in terms of morphology, particle size, drug encapsulation efficiency, in vitro release and cytotoxicity. The optimum conditions for niosomal formulation were elicited as 30 mg of cholesterol, 150 mg of Tween 20 and feeding time of 1 min at a stirring rate of 900 rpm yielding the lowest average particle size of 130 nm. In vitro release data showed...