Sharif Digital Repository

The nature of molecular transmitter imposes some limitations on the molecule production process and its storage. As these molecules act the role of the information carriers, their limitation affect the transmission process and the system performance considerably. In this paper, we focus on these limitations at the transmitter, the limited production rate and finite storage capacity. We consider a time-slotted communication where the transmitter opens its outlet and releases the stored molecules for a time duration to send bit '1' and remains silent to send bit '0'. By changing the duration molecules are released, we propose an adaptive pulse-width modulation. The objective is to find the... 

While ISI is a common issue in classical communications, it is more challenging and prominent in the context of molecular communication, because one cannot readily combat ISI with classical channel equalization techniques. This is due to the fact that transmitter can only release a positive amount of concentration of a specific molecule into the medium. Previous works have proposed use of chemical reactions to remove molecules from the environment, and to effectively simulate negative signals. However, the differential equation describing a diffusion-reaction process is non-linear. This precludes the possibility of using Fourier transform tools. In this paper, a solution for simulating... 

The nature of molecular transmitter imposes some limitations on the molecule production process and its storage. As the molecules act the role of the information carriers, the limitations affect the transmission process and the system performance considerably. In this paper, we focus on the transmitter's limitations, in particular, the limited molecule production rate and the finite storage capacity. We consider a time-slotted communication where the transmitter opens its outlets and releases the stored molecules for a specific time duration to send bit '1' and remains silent to send bit '0'. By changing the Release Duration (RD), we propose an adaptive RD modulation. The objective is to... 

Current techniques in sequencing a genome allow a service provider (e.g. a sequencing company) to have full access to the genome information, and thus the privacy of individuals regarding their lifetime secret is violated. In this paper, we introduce the problem of private DNA sequencing, where the goal is to keep the DNA sequence private to the sequencer. We propose an architecture, where the task of reading fragments of DNA and the task of DNA assembly are separated, the former is done at the sequencer(s), and the later is completed at a local trusted data collector. To satisfy the privacy constraint at the sequencer and reconstruction condition at the data collector, we create an... 

Chemical reactions are a prominent feature of molecular communication systems, with no direct parallels in wireless communications. While chemical reactions may be used inside the transmitter nodes, receiver nodes, or the communication medium, we focus on its utility in the medium in this paper. Such chemical reactions can be used to perform computation over the medium as molecules diffuse and react with each other (physical-layer computation). We propose the use of chemical reactions for the following purposes: 1) to reduce signal-dependent observation noise of receivers by reducing the signal density; 2) to realize molecular physical-layer network coding (PNC) by performing the natural XOR... 

In this paper, we study the zero error capacity of the molecular delay channel when multiple molecule types are available at the transmitter. In the molecular delay channel, each transmitted molecule (of any type) is received by a delay of at most k time slots. Depending on the number of molecules that the transmitter is allowed to release in each time slot, we consider the following three cases: (i) when the maximum number of the released molecules of each type in each time slot is restricted (ii) when the total number of the released molecules (regardless of their type) in each time slot is restricted, and (iii) when the transmitter can use only one molecule type (of its choice) in each... 

Flow velocity is an important characteristic of the fluidic mediums. In this article, we introduce a molecular based flow velocity meter consisting of a molecule releasing node and a receiver that counts these molecules. We consider both flow velocity detection and estimation problems, which are employed in different applications. For the flow velocity detection, we obtain the maximum a posteriori (MAP) decision rule. To analyze the performance of the proposed flow velocity detector, we obtain the error probability, its Gaussian approximation and Chernoff information (CI) upper bound, and investigate the optimum and sub-optimum sampling times accordingly. We show that, for binary hypothesis,... 

In this paper, we propose a theoretical framework for cooperative abnormality detection and localization systems by exploiting molecular communication setup. The system consists of mobile sensors in a fluidic medium, which are injected into the medium to search the environment for abnormality. Some fusion centers (FC) are placed at specific locations in the medium, which absorb all sensors arrived at their locations, and by observing its state, each FC decides on the abnormality existence and/or its location. To reduce the effects of sensor imperfection, we propose a scheme where the sensors release some molecules (i.e., markers) into the medium after they sense an abnormality. If the goal... 

Bacterial populations are promising candidates for the development of the receiver and transmitter nanomachines for molecular communication (MC). A bacterial receiver is required to uptake the information molecules and produce the detectable molecules following a regulation mechanism. We have constructed a novel bacterial MC receiver using an inducible bacterial L-rhamnose-regulating operon. The proposed bacterial receiver produces green fluorescent protein (GFP) in response to the L-rhamnose information molecules following a quite fast regulation mechanism. To fabricate the receiver, the bacterial population has been transformed using a plasmid harboring L-rhamnose operon genes and gene... 

In this paper we have studied the motion of a nanocar and nanotruck on gold substrate using the classical molecular dynamics method. Analyzing the motion regime of the nanocar at different temperatures is one of the main goals of this paper. In the past years, similar molecules such as Trimmer, Z-car and nanotruck have been simulated by Konyukhov and Akimov. To increase the modeling accuracy in this paper we have used classical molecular dynamics contrary to previous works which used a rigid body molecular dynamics method. The result of our simulations were compared qualitatively to the experimental tests performed by Zhang et al. [12]. There was a good agreement between the results achieved... 

In diffusive molecular communication (DMC), the transmitter has to be able to control the release of signaling molecules for modulation of the information bits. In natural cells, pumping ions is an important control mechanism for releasing molecules which is carried out by ion pumps embedded in the membrane. The activity of the ion pumps is controlled by a driving parameter. In particular, light driven pumps are controlled by light intensity and enable a high degree of spatial and temporal control for modulation functionality. In this paper, a modulator based on ion pumps is proposed for DMC which controls the release rate of the molecules from the transmitter by modulating a light intensity... 

Diffusion imaging with confinement tensor (DICT) is a new model that employs a tensorial representation of the geometry confining the movements of water molecules. The model differs substantially from the commonly employed diffusion tensor imaging (DTI) technique even at small diffusion weightings when the dependence of the signal on the timing parameters of the pulse sequence is concerned. In this work, we assess the accuracy of the two models on a data set acquired from an excised monkey brain. The publicly available data set features differing values for diffusion pulse duration and separation. Our results indicate that the normalized mean squared error is reduced in an overwhelming... 

We propose a novel method for the clustering of point-cloud data that originate from single-molecule localization microscopy (SMLM). Our scheme has the ability to infer a hierarchical structure from the data. It takes a particular relevance when quantitatively analyzing the biological particles of interest at different scales. It assumes a prior neither on the shape of particles nor on the background noise. Our multiscale clustering pipeline is built upon graph theory. At each scale, we first construct a weighted graph that represents the SMLM data. Next, we find clusters using spectral clustering. We then use the output of this clustering algorithm to build the graph in the next scale; in... 

In this study the extrudate swell of polymer solutions is estimated using the microstructure of polymer molecules. When a flexible polymer chain goes through a narrow die shear stress exerting on the chain will cause the polymer chain to be stretched along the flow direction. After emerging from die all external stresses vanish immediately and the chains tend to recover their previous state due to elastic recovery. This phenomenon will results in a gradual increase in extrudate diameter and this is used as the key idea for estimating swell ratio. A Giesekus based conformational model was used in order to predict polymer chains microstructure everywhere in the domain. The resulting PDE set... 

A systematic comparison of single and binary metal oxides TiO2, TiO2-Ga2O3 and TiO2-Er2O3 thin film gas sensors with nanocrystalline and mesoporous microstructure, prepared by a new particulate sol-gel route, was conducted. The gas sensitivity was increased by introduction of Ga2O3 and Er2O3 into TiO2 film via two mechanisms, firstly through the inhibition of anatase-to-rutile transformation, since the anatase phase accommodates larger amounts of adsorbed oxygen, and secondly through the retardation of grain growth, since the higher surface area provides more active sites for gas molecule adsorption. The binary metal oxide gas sensors exhibited a remarkable response towards low... 

Abstract New bi-anchoring donor-π-acceptor metal-free organic dyes based on diphenylamine as donor, and barbituric acid and thiobarbituric acid as the acceptor/anchor were synthesized, characterized and used in dye-sensitized solar cells applications. Among the fabricated dye sensitized solar cells, device based on the diphenylamine as donor, and barbituric acid as the acceptor exhibits a high power conversion efficiency of 1.53% with a short circuit current density of 3.71 mA cm-2, an open-circuit photo voltage of 0.55 V and a fill factor of 0.75% under AM 1.5 illumination (85 mW cm-2) compared to the other fabricated devices. The structure of synthesized dyes was optimized and their... 

Bacteriorhodopsin (bR) molecules were utilized as light-driven proton pumps for green as well as effective reduction of single-layer graphene oxide (GO) sheets. The bR molecules and graphene sheets were separated from each other in an aqueous environment by using a polytetrafluoroethylene membrane filter, in order to prevent their direct interactions (including attachment of the bR molecules onto the GO). Although reduction of GO using hydrazine or bR showed similar deoxygenation levels (based on X-ray photoelectron spectroscopy), the former resulted in formation of CAN bonds which can substantially decrease the electrical conductivity of the reduced sheets. The electrical characteristics of... 

Gels are composed of crosslinked polymer network and solvent molecules. When the main chain network is incorporated with functional groups that can undergo photo-chemical reaction upon light irradiation, the gel becomes light-responsive. Under irradiation, the photosensitive groups may undergo photo-ionization process and generate charges that are attached to the main chain or diffuse into the solvent. The newly generated ions disturb the osmotic balance of the gel medium. As a result, water molecules and mobile ions are driven into or out of the network to compensate the osmotic imbalance, which eventually leads to macroscopic swelling or shrinking of the gel. In this work, we develop a... 

This study reports the importance of physicochemical characteristics of the core-shell structured polymer-coated Fe3O4 cluster@SiO2 nanocomposite particles for designing the biocatalysts used for transesterification of soybean oil. To demonstrate this issue, two different types of polymer molecules such as polyethylenimine (PEI) and polyacrylic acid (PAA) each with two different molecular weights are employed. The highest fatty acid methyl esters (FAMEs) synthesis yield values are achieved by the lipases immobilized onto the low- and high-molecular-weight PEI-coated particles as compared to those of the low- and high-molecular-weight PAA-coated particles (i.e., ∼64.8% and ∼73.1% versus... 

Comprehensive structural/molecular simulations have been undertaken to study the poly(benzimidazoles) (PBI) membrane combined with four different nano-oxide materials (ZnO, Al2O3, SiO2 and TiO2) for purification and production of hydrogen from natural gases. Composite membranes were built with different amounts of nano-oxide materials to investigate the influence of nano-oxide content on the PBI membrane performance. Several structural characterizations such as FFV, WAXD and also a thermal one (glass transition temperature) were done to study the structural properties of all simulated membrane cells. Moreover, MSD and adsorption isotherms tasks were used to estimate the diffusivity and...