Sharif Digital Repository

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... 

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... 

The emergence of textile-based wearable sensors as light-weight portable devices to monitor desired parameters, has recently gained much interest and has led to the development of flexible electronics on non-rigid substrates. The flexible biosensors may result in improved sports performance, to monitor the desired bodies for injuries, improved clinical diagnostics and monitor biological molecules and ions in biological fluids such as saliva, sweat. In addition, they could help users with different types of disorders such as blindness. In this context, new composite and nanomaterials have been found to be promising candidates to obtain improved performance of the textile based wearable... 

Molecular machines, such as nanocars, have shown promising potential for various tasks, including manipulation at the nanoscale. In this paper, we examined the influence of temperature gradients on nanocar and nanotruck motion as well as C60 - as their wheel - on a flat gold surface under various conditions. We also compared the accuracy and computational cost of two different approaches for generating the temperature gradient. The results show that severe vibrations and frequent impacts of gold atoms at high temperatures increase the average distance of C60 from the substrate, reducing its binding energy. Moreover, the temperature field drives C60 to move along the temperature variation;... 

Local velocities of bubbles rising in four different nanosilica solutions were investigated experimentally. Also, the density, viscosity, and surface tension of fumed nanosilica and modified nanosilica solutions were measured. Heat treatment and chemical functionalization were used to modify the properties of silica nanoparticles. It was found that the addition of nanosilica affected the hydrodynamics of the rising bubble by increasing the drag friction at the interface. However, environmentally responsive nanosilica particles behaved like surfactant molecules, due to the interfacial activity of hydrophilic and hydrophobic chains. Silica nanoparticles coated with both hydrophilic and... 

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... 

Symmetric lattice relaxation around a vacancy in diamond and its effect on many electron states of the defect have been investigated. A molecular approach is used to evaluate accurately electron-electron (e-e) interaction via a semiempirical formalism which is based on a generalized Hubbard Hamiltonian. Coupling of the defect molecule to surrounding bulk is also considered using an improved Stillinger-Weber potential for diamond. Strong dependence of the electronic energy levels to the relaxation size of the nearest neighbor (NN) atoms indicates that in order to obtain quantitative results the effect of lattice relaxation should be considered. Except for the high spin state of the defect 5A... 

In recent years, there has been increasing interest in damaged DNA and RNA nucleobases. These damaged nucleobases can cause DNA mutation, resulting in various diseases such as cancer. Alkylating agents are mutagenic and carcinogenic in a variety of prokaryotic and eukaryotic organisms. The present study employs density functional theory (DFT/B3LYP) with the 6-311++G(d,p) basis set to investigate the effect of chemical damage in O-alkyl pyrimidines such as O4-methylthymine, O2-methylcytosine and O 2-methylthymine. We compared the intrinsic properties, such as proton affinities, gas phase acidities, equilibrium tautomerization and nucleobase pair's hydrogen bonding properties, of these... 

The optimum convolution of dual short pulse for producing the maximum wakefield and the highest dissociation probability of CH4 has been investigated. By using three fundamental shapes of pulses though four different arrangements, the generated wake are considered in plasma. It is found that when the first and second pulses were rectangular-triangular and sinusoidal pulse shapes, respectively, the resultant wakefield amplitude is the highest. This effect opens up a new novel way by pulse shaping mechanism in the photo dissociation dynamics of molecules and controlling of chemical reactions in the desired channels by short pulse intense lasers for reducing the computation time of genetic... 

A general regularity was found based on an effective pair potential of Lennard-Jones LJ (12, 6), for both dense, nonmetallic and nonionic fluids and solids according to which (Z-1) v2 linearly varies with respect to ρ2 for each isotherm, and this equation of state (EoS I) is known as LIR. However, despite the fact that Ne is a simple spherical species, unexpectedly, its solid and liquid phases both show a significant deviation from EoS I. In this work, we have investigated the accuracy of the EoS I for other systems, including quantum light molecules, such as D 2, H 2 and He, in both fluid and solid states at different temperatures. Like Ne, we have noticed that these systems do not well... 

Binding of Mg 2+, Ca 2+, Zn 2+, and Cu + metal ions with 2′-deoxythymidine (dT) nucleoside was studied using a density functional theory method and a 6-311++G(d,p) basis set. This work demonstrated that the interaction of dT with these cations is tri-coordinated · (O2, O4′, O5′). Among the four types of cations, Zn 2+ cation exhibited the most tendency to interact with the dT. Cations via their interaction with dT can affect the N-glycosidic bond length, the values of pseudorotation of the sugar ring, the orientation of the base unit with respect to the sugar ring, and the acidity of the O5′H, O3′H, and N3H groups in the dT nucleoside. Natural bond orbital analysis was performed to calculate... 

Hexagonal array of Cu@CuO core-shell nanoparticles (NPs) on the a-C:H thin film was prepared by codeposition of RF-sputtering and RF-PECVD. The trace of hexagonal NPs supperlattice was recognized by AFM image and XRD result. On the basis of localized surface plasmon resonance (LSPR) of core-shell NPs, the prepared array detected a low flow rate of CO gas at room temperature. XPS results indicate that the surface of Cu@CuO core-shell NPs have no chemical reaction with CO molecule. The physical absorption of CO molecule on the surface of Cu@CuO core-shell NPs increases the LSPR absorbance and causes a red shift in LSPR wavelength. These experimental results are in agreement with Mie theory... 

(GraphPresented) The quantum optimal control theory in conjunction with time dependent density functional theory is used to optimize the laser pulse shape for dissociation of nitrogen molecule. For several initial peak intensities and frequency ranges, the optimum shapes are produced and compared to determine the most efficient pulse. Ehrenfest molecular dynamics model is also used to test the dissociation process. The corresponding snapshots of density and time dependent electron localization function are presented. It is noticed that when the frequency ranges of laser pulses are doubled, it leads to 60% faster dissociation of N2 molecule  

A quantum modeling of the CO adsorption on illuminated anatase TiO2 (0 0 1) is presented. The calculated adsorption energy and geometries of illuminated case are compared with the ground state case. The calculations were achieved by using DFT formalism and the BH and HLYP. Upon photoexcitation, an electron-hole pair is generated. Comparing of natural population in the ground state and the exited state, shows that an electron is trapped in a Ti4+ ion and a hole is localized in an oxygen ion. The photoelectron helps generation of a CO2 molecule on the TiO2 surface. As shown by optimization of these systems, the CO molecule adsorbed vertically on the TiO2 (0 0 1) surface in the ground state... 

The behaviour of solvatochromic absorbance probes (4-nitroaniline, 4-nitroanisole, and Reichardt's dye) within binary mixtures of polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether (Triton X-100 or TX-100)/organic solvents (2-propanol, hexanol, butyl acetate, THF, toluene, and p-xylene) was extensively explored by using solvatochromism and the quantum theory of atoms in molecules (QTAIM). To be more precise, the polarity parameters, ET N, and Kamlet-Taft parameters, such as the hydrogen bond donor ability (HBD) (α), hydrogen bond acceptor ability (HBA) (β), and dipolarity/polarizability (π∗), have been investigated in selected mixtures at 298 K. All binary mixtures exhibit complex... 

The aim of this study is to simulate the self-assembly of the surfactant molecules with special chemical structure and bending stiffiness into bilayer membranes using a mesoscopic Dissipative Particle Dynamics (DPD) method. The surfactants are modeled with special chemical structure and bending stiffiness. To confirm that the novel model is physical, we determine the interaction parameters based on matching the compressibility and solubility of the DPD system with real physics of the uid. To match the mutual solubility for binary uids, we use the relation between DPD parameters and x-parameters in Flory-Huggins-type models. Unsaturated bonds can change the stiffiness of a lipid membrane,... 

The interactions between four different gas molecules (methanol, o-xylene, p-xylene and m-xylene) and Ni-decorated monolayer MoS2 were investigated by means of density functional computations to exploit its potential application as a gas sensor. The electronic properties of the Ni-decorated monolayer MoS2 and gas molecule (adsorbent–adsorbate properties) strongly depend on the Ni-decorated monolayer MoS2 structure and the molecular configuration of the adsorbate. The adsorption properties of volatile organic compound (VOC) molecules on Ni-decorated MoS2 has been studied taking into account the parameters such as adsorption energy, energy bandgap, density of states, and Mulliken charge... 

The UiO-66 NH2 and ZIF-8 metal organic framework nanoparticles (NMOFs) were incorporated into the polyvinylidene fluoride (PVDF) nanofibrous membrane. Then, the chitosan nanofibers were coated on the PVDF nanofibers to produce the PVDF/chitosan nanofibers. The performance of synthesized PVDF/NMOFs single layer and PVDF/chitosan/NMOFs two layers nanofibrous membranes was investigated for BSA protein molecules and Cr(VI) ions separation via ultrafiltration membrane process. The potential of synthesized nanofibers was also examined for BSA and Cr(VI) adsorption in a batch system. The characteristics of synthesized nanofibrous membranes were determined using SEM, EDX, TGA, BET, porosity and... 

Equations of state based on the statistical associating fluid theory for potentials of variable range (SAFT-VR) and the perturbed chain statistical associating fluid theory (PC-SAFT) have been used to model the PVT behavior of ionic liquids and the solubility of H2S in six imidazolium-based ionic liquids. The studied systems included [bmim][PF6], [hmim][PF6], [bmim][BF4], [hmim][BF4], [bmim][NTF2] and [hmim][NTF2] at various temperatures and pressures.For pure components, parameters of the models have been obtained by fitting the models to experimental data on liquid densities; the average relative deviation between the calculated and experimental densities for ionic liquids is less than... 

Endothelial inflammation as a prominent precursor to atherosclerosis elicits a distinct pathological surface expression of particular vascular proteins. To exhibit a site-specific behaviour, micro- and nanoparticles, as carriers of therapeutics or imaging agents, can distinguish and use these proteins as targeted docking sites. Here, a computational patient-specific model capturing the exclusive luminal qualities has been developed to study the transport and adsorption of particles decorated with proper antibodies over an atherosclerotic plaque located in the LAD artery of the patient. Particles, in nano- and micron sizes, have been decorated with Sialyl Lewisx (sLex), P-selectin aptamer...