Sharif Digital Repository

A large amount of the discovered oil reserves are reserved in carbonate formations, which are mostly naturally fractured oil-wet. Wettability alteration towards more water-wet state reduces the capillary barrier, hence improving the oil recovery efficiency in such reservoirs. In this study, wettability alteration towards favorable wetting state was investigated by combining modified low salinity brine with surfactant during water flooding. The diluted brine was modified by increasing the concentration of Mg2+ and SO4 2−, individually as well as both ions in combination. Different brine formulations were tested experimentally through the observations of contact angle measurements and... 

In this paper, we have proposed, designed, implemented, and characterized a low-cost camera-based microarray scanner which is capable of imaging fluorescently-labeled DNA or Protein microarrays. The proposed system is designed to simultaneously measure two different fluorescent dyes using two parallel channels which increase the overall scan speed. We have shown that the wide dynamic range of system makes it able to detect fluorophore densities from 100-106 molecule/μm2. In each capture, a 5.6 mm × 3.7 mm field is imaged on a 22.3 mm × 14.9 mm (18 megapixels) CMOS sensor. Therefore, the microarray can be scanned with ∼ 1μm2 spatial resolution which is high enough to distinguish borders of... 

The modification of the surface wetting characteristics in fractured oil-wet carbonate reservoirs, by reversing wettability from oil-wet to water-wet, leads to improved oil recovery. However, in order to obtain a successful oil recovery process, it is crucial to understand the active mechanisms of wettability alteration. This study looks at the effect of sulfate ions as one of the most promising wettability influencing ions on the wetting properties of oil-wet calcite; the effect is studied both with and without the presence of cationic surfactant and possible mechanisms of wettability alteration are explored. A number of analytical techniques were utilized to analyze the mineral surface... 

In dye-sensitized solar cells recombination reactions at the TiO2 photoanode with the electrolyte interface plays a critical role in cell efficiency. Recombination of injected electrons in the TiO2 with acceptors in the electrolyte usually occurs on uncovered areas of TiO2 surfaces. In this work, we report electropolymerization of polymer films on nanoporous TiO2 electrode surfaces using an ionic liquid as the growth medium. The choice of ionic liquid as the growth medium for this study is based on the insolubility of dye N719 in this electrolyte, thus avoiding dye molecule detachment from the TiO2 photoanode surface over the entire potential range investigated during the... 

High Density Lipoprotein (HDL) is a lipid-protein complex responsible for transporting cholesterol and triglyceride molecules, as these compounds are unable to dissolve in aqueous environments such as a bloodstream. Among the most well-known possible structures, the belt-like structure is the most common shape proposed for this vital bimolecular complex. In this structure, the protein scaffold encompasses the lipid bilayer and a planar circular structure is formed. Several HDL simulations with embedded components in the lipid section were performed. Here, we applied a series of molecular dynamic simulations using the MARTINI coarse grain force field to investigate an HDL model, with pores of... 

In this paper, a simple memory limited transmitter for molecular communication is proposed, in which information is encoded in the emission rate of the molecules. Taking advantage of memory, the proposed transmitter reduces the ISI problem by properly adjusting its emission rate, which can be interpreted as water-filling on the expected interference. The error probability of the proposed scheme is derived and the result is compared with the error probability of the optimal transmitter obtained by dynamic programming methods. Furthermore, for the special case of channel with one symbol memory, a tight lower bound on error probability is derived. Numerical results show that the performance of... 

A mixture of the platinum(0) complex [Pt(PtBu3)2] and tetrakis(acetonitrile)copper(i) hexafluorophosphate in acetone activated a water molecule and gave the hydride platinum(ii) complex [PtH(CH3CN)(PtBu3)2]PF6, 1, and the hydroxide Cu(i) species. The crystal structure of complex 1 was determined by X-ray crystallography, indicating a distorted square planar geometry around the platinum center. Although three possible mechanisms are proposed for this transformation, monitoring of the reaction using NMR spectroscopy at low temperature reveals that a cooperative pathway involving formation of a Pt0-CuI dative bond complex is the most probable pathway. The hydride platinum complex 1 is stable in... 

This paper studies the problem of receiver modeling in molecular communication systems. We consider the diffusive molecular communication channel between a transmitter nanomachine and a receiver nano-machine in a fluid environment. The information molecules released by the transmitter nano-machine into the environment can degrade in the channel via a first-order degradation reaction and those that reach the receiver nanomachine can participate in a reversible bimolecular reaction with receiver receptor proteins. Thereby, we distinguish between two scenarios. In the first scenario, we assume that the entire surface of the receiver is covered by receptor molecules. We derive a closed-form... 

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,... 

Photosynthesis includes capturing sunlight by an assembly of molecules, called chlorophylls, and directing the harvested energy in the form of electronic excitations to the reaction center. Here we report, using real-space density functional theory and time-dependent density functional theory together with GW calculations, the optical and electronic properties of the two main chlorophylls in green plants, namely, chlorophylls a and b. Furthermore, we estimate the dipole and primitive quadrupole electric moments of these molecules. We employ Casida's assignment ansatz to study the absorption spectra of the chlorophylls in the two main red and blue regions at various environments with... 

In diffusion-based molecular communication (DMC), a transmitter nanomachine is responsible for signal modulation. Thereby, the transmitter has to be able to control the release of the signaling molecules employed for representing the transmitted information. In nature, an important class of control mechanisms for releasing molecules from cells utilizes ion channels which are pore-forming proteins across the cell membrane. The opening and closing of the ion channels is controlled by a gating parameter. In this paper, an ion channel based modulator for DMC is proposed which controls the rate of molecule release from the transmitter by modulating a gating parameter signal. Exploiting the... 

CO2 injection has proved to be the most common and efficient enhanced oil recovery techniques which leads to more residual oil recovery. Unfavorable sweep efficiency which results in fingering propagation and causes early gas breakthrough is the most challenging issue of gas flooding process. The aim of this work is to study foam stability and analyze the mobility of CO2 foam stabilized by mixture of raw silica nanoparticles and ethyl hexadecyl dimethyl ammonium bromide (cationic surfactant). The result is obtained through both dynamic and static techniques using a new adsorption index.NPS-stabilized foams are generated using Ross-Miles method. A novel index for the adsorption of surfactant... 

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... 

Electrospray ionization of 2,6-naphthalenedicarboxylic acid readily affords its doubly deprotonated dicarboxylate dianion (1 2-). This species clusters with background water and added alcohols in an ion trap at ∼10-3 Torr. Sequential solvation is observed to afford mono and dicoordinated ions. Surprisingly, the latter cluster (1 2- • 2TFE) is protonated by 2,2,2-trifluoroethanol (TFE) whereas 1 2-and 1 2- • TFE are not even though δHacid(TFE)=361.7±2.5kcalmol-1 (as given in the NIST website at http://webbook.nist.gov) and the B3LYP/6-31+G(d,p) proton affinities are 384.7 (1 2-), 377.6 (1 2- • TFE), and 362.7 (1 2- • 2TFE) kcal mol-1. That is, only the weakest base in this series, and the... 

Although the capability of using sulfate anion as a wettability modiffier is well established, no systematic investigation on the effect of sulfate ions and natural surfactants in the crude oil including asphaltene and resin on the interfacial tension (IFT) of acidic crude oil (ACO)/sulfate were performed. In this regards, the fluid/fluid interactions are tested through the IFT measurements for ACO, asphaltene and resin extracted from ACO in the presence of sulfate salts including Na2SO4, MgSO4 and CaSO4 while the concentration of each salt ranges between 0 and 45000 ppm. The obtained results demonstrate that the capability of asphaltene molecules is higher for IFT reduction compared with... 

A kinetic model based on a mechanistic approach was developed for thermal hydrocracking of a paraffinic feedstock. The hydrocarbon feed was described as a mixture of representative molecules based on structural group analysis (SGA) where information from elemental analysis, H1, and C13-NMR of the feed were used to obtain the average concentration of various structural groups from which representative molecules were constructed. The behavior of the feedstock under reaction conditions was described in terms of the reaction of the individual molecules. The reaction of each of the representative molecules and the corresponding product distribution was based on free radical mechanisms. The... 

Classical molecular dynamics simulations are used to compute the solvation free energy of two pharmaceutical solids, namely ibuprofen and acetaminophen in carbon dioxide (CO2), over the density range of interest in supercritical processes. In order to examine the influence of the solvent model on the resulting free energies, three popular CO2 models (Zhang, EPM2, and TraPPE) are studied. Relatively large discrepancies for the solvation free energy exist between these CO2 models, suggesting that the former is sensitive to the different balances between dispersive and electrostatic forces used in these models. In particular, for the solvation of the highly polar (dipole moment of ∼5.2 Debye)... 

Effect of nanosecond lasers on the methane dissociation is experimentally studied by using three different laser wavelengths at 248 nm, 355 nm and 532 nm. C2H2 generation is measured as a major reaction product in experiments and the energy consumptions in production of this component are measured as 5.8 MJ/mol, 3.1 MJ/mol and 69.0 MJ/mol, for 355 nm, 532 nm and 248 nm wavelengths, respectively. The mechanism of conversion and production of new stable hydrocarbons is also theoretically investigated. It is found that in theoretical calculations, the ion-molecule reactions should be included and this leads to a unique approach in proper explanation of the experimental measurements  

The fragmentation dynamics of CH4 and H2CO molecules have been studied with ultra-short pulses at laser intensityof up to 1015Wcm-2. Three dimensional molecular dynamics calculations for finding the optimized laser pulses are presented based on time-dependent density functional theory and quantum optimal control theory. A comparison of the results for orientation dependence in the ionization process shows that the electron distribution for CH4 is more isotropic than H2CO molecule. Total conversion yields of up to 70% at an orientation angle of 30o for CH4 and 65% at 900 for H2CO are achieved which lead to enhancement of dissociation probability  

Experimental data of the DNA cyclization (J-factor) at short length scales exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length scales and it also facilitates DNA loop formation at these lengths. To account for the bending asymmetry, we consider the asymmetric elastic rod (AER) model which has been introduced and parametrized in an earlier study [B. Eslami-Mossallam and M. R. Ejtehadi, Phys. Rev. E 80, 011919 (2009)]. Exploiting a coarse grained representation of the DNA molecule...