Sharif Digital Repository

The urine formation and excretion system have long been of interest for mathematicians and physiologists to elucidate the obscurities within the process happens in renal tissue. In this study, a novel three-dimensional approach is utilized for modeling the urine concentrating mechanism in rat renal outer medulla which is essentially focused on demonstrating the significance of tubule's architecture revealed in anatomic studies and physiological literature. Since nephrons and vasculatures work interdependently through a highly structured arrangement in outer medulla which is dominated by vascular bundles, a detailed functional unit is proposed based on this specific configuration.... 

A multi-item multiperiod inventory control model is developed for known-deterministic variable demands under limited available budget. Assuming the order quantity is more than the shortage quantity in each period, the shortage in combination of backorder and lost sale is considered. The orders are placed in batch sizes and the decision variables are assumed integer. Moreover, all unit discounts for a number of products and incremental quantity discount for some other items are considered. While the objectives are to minimize both the total inventory cost and the required storage space, the model is formulated into a fuzzy multicriteria decision making (FMCDM) framework and is shown to be a... 

A computational model was developed to simulate drug distribution in the posterior segment of the eye after intravitreal injection and ocular implantation. The effects of important factors in intravitreal injection such as injection time, needle gauge and needle angle on the ocular drug distribution were studied. Also, the influences of the position and the type of implant on the concentration profile in the posterior segment were investigated. Computational Fluid Dynamics (CFD) calculations were conducted to describe the 3D convective-diffusive transport. The geometrical model was constructed based on the human eye dimensions. To simulate intravitreal injection, unlike previous studies... 

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... 

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  

Monitoring conformational changes in ion channels is essential to understand their gating mechanism. Here, we explore the structural dynamics of four outer membrane proteins with different structures and functions in the slowest nonzero modes of vibration. Normal mode analysis was performed on the modified elastic network model of channel in the membrane. According to our results, when membrane proteins were analyzed in the dominant mode, the composed pores, TolC and α-hemolysin showed large motions at the intramembrane β-barrel region while, in other porins, OmpA and OmpF, largest motions observed in the region of external flexible loops. A criterion based on equipartition theorem was used... 

Two artificial neural networks (ANNs) are constructed, trained, and tested to map inputs of a complex trunk finite element (FE) model to its outputs for spinal loads and muscle forces. Five input variables (thorax flexion angle, load magnitude, its anterior and lateral positions, load handling technique, i.e., one- or two-handed static lifting) and four model outputs (L4-L5 and L5-S1 disc compression and anterior-posterior shear forces) for spinal loads and 76 model outputs (forces in individual trunk muscles) are considered. Moreover, full quadratic regression equations mapping input-outputs of the model developed here for muscle forces and previously for spine loads are used to compare the... 

Multivariate curve resolution-particle swarm optimization (MCR-PSO) algorithm is proposed to exploit pure chromatographic and spectroscopic information from multi-component hyphenated chromatographic signals. This new MCR method is based on rotation of mathematically unique PCA solutions into the chemically meaningful MCR solutions. To obtain a proper rotation matrix, an objective function based on non-fulfillment of constraints is defined and is optimized using particle swarm optimization (PSO) algorithm. Initial values of rotation matrix are calculated using local rank analysis and heuristic evolving latent projection (HELP) method. The ability of MCR-PSO in resolving the chromatographic... 

In this paper, we investigated phase synchronization in delayed dynamical networks. Non-identical spiking Hindmarsh-Rose neurons were considered as individual dynamical systems and coupled through a number of network structures such as scale-free, Erdos-Rényi, and modular. The individual neurons were coupled through excitatory chemical synapses with uniform or distributed time delays. The profile of spike phase synchrony was different when the delay was uniform across the edges as compared to the case when it was distributed, i.e., different delays for the edges. When an identical transmission delay was considered, a quasi-periodic pattern was observed in the spike phase synchrony. There... 

Response surface methodology was used to investigate the effects of operating parameters such as impeller speed, binder mass and granulation time on the average size of granules produced in a lab scale conical high shear granulator. Two quadratic models were proposed to express granule mean size as a function of impeller speed and binder mass as well as impeller speed and granulation time. It was found out that in the studied domain, the influence of each parameter on granule size differs from one another. While increasing binder mass at constant quantity of powder increased the average size linearly, increasing impeller speed changed the mean size in accordance with quadratic trend. The... 

Steady blood flow through a circular artery with rigid walls is studied by COSSERAT Continuum Mechanical Approach. To obtain the additional viscosities coefficients, feed forward multi-layer perceptron (MLP) type of artificial neural networks (ANN) and the results obtained in previous empirical works is used. The governing filed equations are derived and solution to the Hagen-Poiseuilli flow of a COSSERAT fluid in the artery is obtained analytically by Homotopy Perturbation Method (HPM) and numerically using finite difference method. Comparison of analytical results with numerical ones showed excellent agreement. In addition microrotation and the velocity profile along the radius are... 

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... 

In this work, the 3D proton dose profile is calculated in a homogenous water phantom using a Monte Carlo application developed with the Geant4 toolkit. The effect of the ridge filter material (for SOBP widths of 6, 9 and 12 cm) on the homogeneity of the dose distribution, secondary neutron production and beam efficiency are investigated in a single ring wobbling irradiation system. The energy spectrum of secondary neutrons per primary proton at various locations around the phantom surface is calculated. The simulation revealed that most of the produced neutrons are released at slight angles which enable them to reach the patient and consequently to be hazardous. Also, the homogeneity of the... 

The effects of temperature, seed mass and agitation rate on agglomeration kinetics of aluminum hydroxide in Bayer process have been studied in a batch system. Collected raw data were analyzed and the kinetics data of agglomeration were derived through simulation of the process using a pre-developed software. The results showed that agglomeration kinetics constant (agglomeration kernel) increases with increase in temperature and agitation rate. Moreover a maximum value of agglomeration rate versus added seed mass was observed. Furthermore the magnitude of calculated activation energy of agglomeration was close to that of growth  

Simulating signal transduction in cellular signaling networks provides predictions of network dynamics by quantifying the changes in concentration and activity-level of the individual proteins. Since numerical values of kinetic parameters might be difficult to obtain, it is imperative to develop non-parametric approaches that combine the connectivity of a network with the response of individual proteins to signals which travel through the network. The activity levels of signaling proteins computed through existing non-parametric modeling tools do not show significant correlations with the observed values in experimental results. In this work we developed a non-parametric computational... 

Constrained clustering methods (that usually use must-link and/or cannot-link constraints) have been received much attention in the last decade. Recently, kernel adaptation or kernel learning has been considered as a powerful approach for constrained clustering. However, these methods usually either allow only special forms of kernels or learn non-parametric kernel matrices and scale very poorly. Therefore, they either learn a metric that has low flexibility or are applicable only on small data sets due to their high computational complexity. In this paper, we propose a more efficient non-linear metric learning method that learns a low-rank kernel matrix from must-link and cannot-link... 

The finite element method and molecular dynamics simulations are used for modeling the AFM microcantilever dynamics and the tip-sample interaction forces, respectively. Molecular dynamics simulations are conducted to calculate the tip-sample force data as a function of tip height at different lateral positions of the tip with respect to the sample. The results demonstrate that in the presence of nonlinear interaction forces, higher eigenmodes of the microcantilever are excited and play a significant role in the tip and sample elastic deformations. Using comparisons between the results of FEM and lumped models, how some aspects of the system behavior can be hidden when the point-mass model is... 

In this investigation, a systematic sequential intelligent system is proposed to provide the surgeon with an estimation of the state of the tool-tissue interaction force in laparoscopic surgery. To train the proposed intelligent system, a 3D model of an in vivo porcine liver was built for different probing tasks. To capture the required knowledge, three different geometric features, i.e. Y displacement of the nodes on the upper surface and slopes on the closest node to the deforming area of the upper edge in both X-. Y and Z-. Y planes, were extracted experimentally. The numerical simulations are conducted in three independent successive stages. At the first step, a well-known... 

This paper presents an investigation of the dynamics of two coupled non-identical FitzHugh-Nagumo neurons with delayed synaptic connection. We consider coupling strength and time delay as bifurcation parameters, and try to classify all possible dynamics which is fairly rich. The neural system exhibits a unique rest point or three ones for the different values of coupling strength by employing the pitchfork bifurcation of non-trivial rest point. The asymptotic stability and possible Hopf bifurcations of the trivial rest point are studied by analyzing the corresponding characteristic equation. Homoclinic, fold, and pitchfork bifurcations of limit cycles are found. The delay-dependent stability... 

This paper describes the development and implementation of MCRC software, chemometric software for Multivariate Curve Resolution of two-way Chromatographic data. MCRC software is developed for chemometric analysis of chromatographic data; however, it may also be used for other types of multivariate data. It consists of five groups of techniques for preprocessing, chemical rank determination, local rank analysis, multivariate resolution and peak integration. This software has the ability of the analysis of complex multi-component chromatographic signals of gas chromatography-mass spectrometry (GC-MS) and high performance liquid chromatography-diode array detection (HPLC-DAD). The software...