Sharif Digital Repository

Background: Codon degeneracy and codon usage by organisms is an interesting and challenging problem. Researchers demonstrated the relation between codon usage and various functions or properties of genes and proteins, such as gene regulation, translation rate, translation efficiency, mRNA stability, splicing, and protein domains. Researchers usually represent segments of proteins responsible for specific functions or structures in a family of proteins as sequence patterns or motifs. We asked the question if organisms use the same codons in pattern segments as compared to the rest of the sequence. Methods. We used the likelihood ratio test, Pearson's chi-squared test, and mutual information... 

Synchronization behavior of electroencephalographic (EEG) signals is important for decoding information processing in the human brain. Modern multichannel EEG allows a transition from traditional measurements of synchronization in pairs of EEG signals to whole-brain synchronization maps. The latter can be based on bivariate measures (BM) via averaging over pair-wise values or, alternatively, on multivariate measures (MM), which directly ascribe a single value to the synchronization in a group. In order to compare BM versus MM, we applied nine different estimators to simulated multivariate time series with known parameters and to real EEGs. We found widespread correlations between BM and MM,... 

A method is developed to calculate the critical line of two dimensional (2D) anisotropic Ising model including nearest-neighbor interactions. The method is based on the real-space renormalization group (RG) theory with increasing block sizes. The reduced temperatures, Ks (where K=J/kBT and J, kB, and T are the spin coupling interaction, the Boltzmann constant, and the absolute temperature, respectively), are calculated for different block sizes. By increasing the block size, the critical line for three types of lattice, namely: triangular, square, and honeycomb, is obtained and found to compare well with corresponding results reported by Onsager in the thermodynamic limit. Our results also... 

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... 

Conventional models of cardiovascular system frequently lack required detail and focus primarily on the overall relationship between pressure, flow and volume. This study proposes a localized and regional model of the cardiovascular system. It utilizes noninvasive blood flow and pressure seed data and temporal cardiac muscle regional activity to predict the operation of the heart under normal and congestive heart failure conditions. The analysis considers specific regions of the heart, namely, base, mid and apex of left ventricle. The proposed method of parameter estimation for hydraulic electric analogy model is recursive least squares algorithm. Based on simulation results and comparison... 

Employing a biharmonic boundary integral method with linear elements, coarsening dynamics of nanodroplets on topographical step heterogeneity is investigated. It is shown that the step height and droplet configuration have an influential effect on the dynamics. Increasing the step height slows down the process while locating the droplets close to the step boosts the coarsening rate. Considering a slip boundary condition enhances the dynamics and reveals a transition in the droplet migration direction. Our results reveal that increasing the surface wettability weakens the dynamics. Various types of the disjoining pressure over the step are also considered and their effects on the coarsening... 

Considering high temperature and pressure during single bubble sonoluminescence collapse, a hot plasma core is generated at the center of the bubble. In this paper a statistical mechanics approach is used to calculate the core pressure and temperature. A hydrochemical model alongside a plasma core is used to study the bubble dynamics in two host liquids of water and sulfuric acid 85 wt % containing Ar atoms. Calculation shows that the extreme pressure and temperature in the plasma core are mainly due to the interaction of the ionized Ar atoms and electrons, which is one step forward to sonofusion. The thermal bremsstrahlung mechanism of radiation is used to analyze the emitted optical energy... 

This paper deals with the average consensus problem in a multi-agent system with switching interaction topology modeled as a weighted digraph. The convergence analysis is performed in both discrete-time and continuous-time dynamics based on the theory of infinite matrix products. Conditions for system convergence to average consensus are derived in the form of constraints on direct and reverse graphs and the structure of adjacency elements among the agents. Furthermore, a sufficient condition is provided for convergence to average consensus in systems in which the interaction topology is balanced over infinite contiguous non-overlapping time intervals instead of being balanced continuously.... 

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... 

Ground-state fidelity (GSF) and quantum renormalization group (QRG) theory have proven to be useful tools in the study of quantum critical systems. Here we lay out a general, unified formalism of GSF and QRG; specifically, we propose a method for calculating GSF through QRG, obviating the need for calculating or approximating ground states. This method thus enhances the characterization of quantum criticality as well as scaling analysis of relevant properties with system size. We illustrate the formalism in the one-dimensional Ising model in a transverse field (ITF) and the anisotropic spin-1/2 Heisenberg (XXZ) model. Explicitly, we find the scaling behavior of the GSF for the ITF model in... 

An HMM-based speech enhancement in Mel-frequency domain is introduced and improved. It is shown that hidden Markov modeling in the Mel-frequency domain is beneficial due to its effective representation of the speech spectrum; however, speech enhancement in this domain requires an inversion from the Mel-frequency to the spectral domain which introduces distortion artifacts for spectrum estimation. To reduce the distortion effects of the inversion and employ the advantages of robustness modeling in the Mel-frequency domain, a parallel cepstral and spectral (PCS) modeling is proposed. In PCS, a concurrent modeling in both cepstral and spectral domains is performed. The performances of the... 

Muscle force partitioning methods and musculoskeletal system simplifications are key modeling issues that can alter outcomes, and thus change conclusions and recommendations addressed to health and safety professionals. A critical modeling concern is the use of single-joint equilibrium to estimate muscle forces and joint loads in a multi-joint system, an unjustified simplification made by most lumbar spine biomechanical models. In the context of common occupational tasks, an EMG-assisted optimization method (EMGAO) is modified in this study to simultaneously account for the equilibrium at all lumbar joints (M-EMGAO). The results of this improved approach were compared to those of its... 

Purpose: Mass-spring-damper (MSD) models are often used for real-time surgery simulation due to their fast response and fairly realistic deformation replication. An improved real time simulation model of soft tissue deformation due to a laparoscopic surgical indenter was developed and tested. Method: The mechanical realization of conventional MSD models was improved using nonlinear springs and nodal dampers, while their high computational efficiency was maintained using an adapted implicit integration algorithm. New practical algorithms for model parameter tuning, collision detection, and simulation were incorporated. Results: The model was able to replicate complex biological soft tissue... 

In this paper the characteristic ratios and generalized time constant are defined for all-pole commensurate fractional order systems. The sufficient condition for stability of these systems in terms of their characteristic ratios is obtained. Also an analytical approach for characteristic ratio assignment (CRA) to have a non-overshooting fast closed loop step response is introduced. The proposed CRA method is then employed to design a fractional order controller. Computer simulation results are presented to illustrate the performance of the CRA based designed fractional order controllers  

The objective of this study was to propose a new analytical model for studying response of head impacts. Head is modeled by fluidfilled ellipsoidal shell of inconstant thickness impacted by a solid elastic sphere. Modeling the head as an ellipsoid is more realistic than modeling it as a sphere, the previous model existing in the literature [3]-[8]. In this model, the effect of Hertzian contact stiffness and local shell stiffness are combined to derive explicit equations for impact duration, the peak force transmitted to head, and the head injury criterion. One of the advantages of the model presented is sensitivity to the site of impact. A comparison between the present analytical results... 

A computational framework is presented, based on statistical shape modelling, for construction of race-specific organ models for internal radionuclide dosimetry and other nuclear-medicine applications. This approach was applied to the construction of a Japanese liver phantom, using the liver of the digital Zubal phantom as the template and 35 liver computed tomography (CT) scans of male Japanese individuals as a training set. The first step was the automated object-space registration (to align all the liver surfaces in one orientation), using a coherent-point-drift maximum-likelihood alignment algorithm, of each CT scan-derived manually contoured liver surface and the template Zubal liver... 

In this paper, issues related to the identifiability of a fractional order system having its input and output frequency contents are discussed. The effects of the commensurate order α in the identifiability of the model structure and model parameters are analytically studied. It is shown that both identifiabilities (model structure and model parameters) are reduced remarkably for smaller values of α. This phenomenon is observed even though the input signals are rich enough and system belongs to the model set. Our understanding is that the problem arises since differences among different members of the model set fall beyond the practically recognizable precision range. The issue is more... 

Chromatographic method development for preparative targets is a time-consuming and subjective process. This can be particularly problematic because of the use of valuable samples for isolation and the large consumption of solvents in preparative scale. These processes could be improved by using statistical computations to save time, solvent and experimental efforts. Thus, contributed by ESI-MS, after applying DryLab software to gain an overview of the most effective parameters in separation of synthesized celecoxib and its co-eluted compounds, design of experiment software that relies on multivariate modeling as a chemometric approach was used to predict the optimized touching-band... 

Statistical process control provides useful tools to improve the quality of multistage machining processes, specifically in continuous manufacturing lines, where product characteristics are measured at the final station. In order to reduce process errors, variation source identification has been widely applied in machining processes. Although statistical estimation and pattern matching-based methods have been utilized to monitor and diagnose machining processes, most of these methods focus on stage-by-stage inspection using complex models and patterns. However, because of the existence of high rate alarms and the complexity of the machining processes, a surrogate modelling is needed to solve... 

In this study, impact of initial ensembles on posterior distribution of ensemble-based assimilation methods is statistically analyzed. Along with, sampling performance as well as uncertainty quantification of these methods are compared in terms of their ability to accurately and consistently evaluate unknown reservoir model parameters and reservoir future performance. For this purpose, a synthetic test problem, which is a small but highly nonlinear reservoir model under two-phase flow, is utilized. Subsequently, different initial ensemble sets are considered and are updated through the assimilation process performed on the test problem using ensemble-based assimilation methods. Afterwards,...