Sharif Digital Repository

The results of highthroughput practical single channel experiments should be formulated and validated by signal analysis approaches to increase the recognition precision of translocating molecules. For this purpose, the activities of the single nano-pore forming protein, OmpF, in the presence of nucleotides were recorded in real time by the voltage clamp technique and used as a means for nucleotide recognition. The results were analyzed based on the permutation entropy of current Time Series (TS), fractality, autocorrelation, structure function, spectral density, and peak fraction to recognize each nucleotide, based on its signature effect on the conductance, gating frequency and voltage... 

We study the translocation of stiff polymers through a nanopore, driven by the chemical-potential gradient exerted by binding proteins (chaperones) on the trans side of the pore. Bound chaperones prevent backsliding through the pore and, therefore, partially rectify the polymer passage. We show that the sequence of chain monomers with different binding affinity for the chaperones significantly affects the translocation dynamics. In particular, we investigate the effect of the nearest-neighbor adjacency probability of the two monomer types. Depending on the magnitude of the involved binding energies, the translocation speed may either increase or decrease with the adjacency probability. We... 

Combining the advection-diffusion equation approach with Monte Carlo simulations we study chaperone driven polymer translocation of a stiff polymer through a nanopore. We demonstrate that the probability density function of first passage times across the pore depends solely on the Péclet number, a dimensionless parameter comparing drift strength and diffusivity. Moreover it is shown that the characteristic exponent in the power-law dependence of the translocation time on the chain length, a function of the chaperone-polymer binding energy, the chaperone concentration, and the chain length, is also effectively determined by the Péclet number. We investigate the effect of the chaperone size on... 

We consider chaperone-assisted translocation of biopolymers with two distinct monomers or bases A and B, with the size of the chaperones being λα, where α is a monomer's size. The probability that A and B are neighbors in the biopolymer is PAB. A master equation is used, together with the detailed-balanced condition, in order to derive analytical results for the statistics of the first-passage times of the biopolymer as a function of PAB, λ, and the biopolymer's configuration. Monte Carlo simulations have also been carried out in order to compute the same quantities for biopolymers with 100-900 monomers and several λ. The results indicate nontrivial dependence of the variance of the... 

The distributed nature and complexity of computer networks and various services provided via them, makes the networks vulnerable to numerous attacks. The TCP/IP presumptions which are based on using this protocol to provide a simple, open communication infrastructure in an academic and collaborative environment, causes this protocol lack of built-in mechanisms for authentication, integrity and privacy. Even though in the last few years a more systematic approach to TCP/IP network security problem has been followed, a formal approach to this problem is lacking. In this paper, we propose using Description Logics as a formal model which could be used to analyze TCP/IP networks against attacks.... 

Controlled graphitization has become known as a practical method for improvement of wear resistance and machining properties in steels. In this paper, the effect of heat treatment on microstructure of CK45 steel has been investigated. Austenitising was carried out at 920 °C for 5 h. Besides, isothermal transformation was conducted at 750 °C in the time range of 1-20 h. In this work, full potential carbon resource was tried to be used around samples as a factor to prevent the burning of the limited carbon in steel and also to increase the percentage of sample surface carbon in order to improve wear capability and machining. The microstructure of the steel considerably changes by this heat... 

To synthesize a novel biopolymer-based superabsorbent hydrogel, 2-acrylamido-2-methylpropanesulfonic acid (AMPS) was grafted onto kappa-carrageenan (KC) backbones. The graft copolymerization reaction was carried out in a homogeneous medium and in the presence of ammonium persulfate (APS) as an initiator, N,N,N',N'-tetramethyl ethylenediamine (TMEDA) as an accelerator, and N,N'-methylene bisacrylamide (MBA) as a crosslinker. A proposed mechanism for KC-g-AMPS formation was suggested and the hydrogel structure was confirmed using FTIR spectroscopy. The affecting variables on swelling capacity, i.e., the initiator, the crosslinker, and the monomer concentration, as well as reaction temperature,... 

Synthesis of polyvinyl pyrrolidone (PVP) coated ultrasmall Gd2O3 nanoparticles (NPs) with enhanced T1-weighted signal intensity and r2/r1 ratio close to unity is performed by a microwave-assisted polyol process. PVP coated Gd2O3NPs with spherical shape and uniform size of 2.5 ± 0.5 nm have been synthesized below 5 min and structure and morphology confirmed by HRTEM, XRD and FTIR. The longitudinal (r1) and transversal relaxation (r2) of Gd2O3NPs is measured by a 3 T MRI scanner. The results showed considerable increasing of relaxivity for Gd2O3NPs in... 

This paper proposes a high performance voltage tracking and current sharing among parallel connected inverters by applying optimal control and minimizing the cost function. The control system forces the voltage of load to track the voltage reference, and the current of all inverters becomes equal. Therefore, both current sharing and voltage tracking are obtained. In addition, the smallest input energy and simplicity in control circuit are the other advantages of the suggested method. To show the performance of the proposed control scheme, the simulations with two-modular practical systems are performed and the results are provided. The results indicate that the control objectives are... 

An analytical model is proposed to study the effect of particle size on melting enthalpy and entropy of metallic nanoparticles (NPs). The Mott's and Regel's equations for melting entropy in the combination of core average coordination number (CAC) and surface average coordination number (SAC) of freestanding NPs are considered. Clusters of icosahedral (IC), body centered cubic (BCC), and body centered tetragonal (BCT) structure without any vacancies and defects are modeled. Using the variable coordination number made this model to be in good agreement with experimental and molecular dynamic (MD) results of different crystal structures. The model predicts melting entropy and enthalpy of... 

Adaptive Noise Cancellation (ANC) is a well-known technique for background noise reduction in automobile and vehicular environments. The noise fields in automobile and other vehicle interior obey the diffuse noise field model closely. On the other hand, the ANC does not provide sufficient noise reduction in the diffuse noise fields. In this paper, a new multistage post-filter is designed for ANC as a solution to diffuse noise conditions. The designed post-filter is a single channel Linear Prediction (LP) based speech enhancement system. The LP is performed by an adaptive lattice filter and attempts to extract speech components by using intermediate ANC signals. The post-filter has no... 

Modeling and analysis of information system vulnerabilities helps us to predict possible attacks to networks using the network configuration and vulnerabilities information. As a fact, exploiting most of vulnerabilities result in access rights alteration. In this paper, we propose a new vulnerability analysis method based on the Take-Grant protection model. We extend the initial Take-Grant model to address the notion of vulnerabilities and introduce the vulnerabilities rewriting rules to specify how the protection state of the system can be changed by exploiting vulnerabilities. Our analysis is based on a bounded polynomial algorithm, which generates the closure of the Take-Grant graph... 

In this paper, for the first time, we present a small signal circuit model of quantum dot laser considering two photon modes, i.e., ground and first excited states lasing. By using the presented model, effect of temperature variations on modulation response of quantum dot laser is investigated. Simulation results of modulation response are in agreement with the numerical and experimental results reported by other researchers  

Enzymatic decolorization of reactive blue 221 (RB221) using laccase was investigated in a dual-chamber microbial fuel cell (MFC). Suspended laccase was used in the cathode chamber in the absence of any mediators in order to decolorize RB221 and also improve oxygen reduction reaction in the cathode. Molasses was utilized as low cost and high strength energy source in the anode chamber. The capability of MFC for simultaneous molasses and dye removal was investigated. A decolorization efficiency of 87% was achieved in the cathode chamber and 84% COD removal for molasses was observed in the anode chamber. Laccase could catalyze the removal of RB221 and had positive effect on MFC performance as... 

InAlAs/InGaAs/InP high electron mobility transistors have higher mobility comparing to structures without indium. But existence of indium causes smaller Eg and as a result smaller breakdown voltage. However, increasing percentage of indium results in higher mobility and as a result higher current and transconductance. Therefore decreasing percentage of indium causes higher breakdown voltage at the sometime lower transconductance. One of the most important parameters that limit maximum output power of transistor is breakdown voltage. In this paper, InAIAs/InGaAs/InP HEMTs with different structures are simulated and a structure with a good transconductance and breakdown voltage is introduced  

A simple platform based on a hairpin oligonucleotide switch and multi-walled carbon nanotubes (MWCNTs) for the ultrasensitive detection of specific DNA sequences has been developed. In this approach, the π-stacking interaction of single-strand DNA-MWCNT was employed to construct an electrochemical DNA biosensor. Changes to the surface conductivity, based on the MWCNT replacement, were monitored by using the electrochemical species [Fe(CN)6]3-/4- as a redox probe. Morphological and voltammetric characterizations of the electrode surface were performed using atomic force microscopy (AFM), energy dispersive spectroscopy (EDS), cyclic voltammetry (CV), differential pulse voltammetry (DPV) and... 

With the growing rate of network attacks, intelligent methods for detecting new attacks have attracted increasing interest. The RT-UNNID system, introduced in this paper, is one such system, capable of intelligent real-time intrusion detection using unsupervised neural networks. Unsupervised neural nets can improve their analysis of new data over time without retraining. In previous work, we evaluated Adaptive Resonance Theory (ART) and Self-Organizing Map (SOM) neural networks using offline data. In this paper, we present a real-time solution using unsupervised neural nets to detect known and new attacks in network traffic. We evaluated our approach using 27 types of attack, and observed... 

Measurements and sensing implementations impose certain cost in sensor networks. The sensor selection cost optimisation is the problem of minimising the sensing cost of monitoring a physical (or cyber-physical) system. Consider a given set of sensors tracking states of a dynamical system for estimation purposes. For each sensor assume different costs to measure different (realisable) states. The idea is to assign sensors to measure states such that the global cost is minimised. The number and selection of sensor measurements need to ensure the observability to track the dynamic state of the system with bounded estimation error. The main question we address is how to select the state...