Sharif Digital Repository

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... 

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... 

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... 

In this paper, we consider abnormality detection via diffusive molecular communications (MCs) for a network consisting of several sensors and a fusion center (FC). If a sensor detects an abnormality, it injects a number of molecules into the medium which is proportional to its sensing output. Two transmission schemes for releasing molecules into the medium are considered. In the first scheme, each sensor releases a different type of molecule (DTM), whereas in the second scheme, all sensors release the same type of molecule (STM). The molecules released by the sensors propagate through the MC channel and some may reach the FC where the final decision regarding whether or not an abnormality... 

Perovskite solar cells (PSCs) use perovskites with an APbX3 structure, where A is a monovalent cation and X is a halide such as Cl, Br, and/or I. Currently, the cations for high-efficiency PSCs are Rb, Cs, methylammonium (MA), and/or formamidinium (FA). Molecules larger than FA, such as ethylammonium (EA), guanidinium (GA), and imidazolium (IA), are usually incompatible with photoactive “black”-phase perovskites. Here, novel molecular descriptors for larger molecular cations are introduced using a “globularity factor”, i.e., the discrepancy of the molecular shape and an ideal sphere. These cationic radii differ significantly from previous reports, showing that especially ethylammonium (EA)... 

Diffusion weighted imaging is a non-invasive method for investigation of brain fiber bundles. In diffusion tensor imaging (DTI), the diffusion of water molecules is assumed Gaussian, therefore, it can just show a single fiber direction in a voxel. To overcome this limitation, a number of high angular resolution diffusion imaging methods have been proposed. One of these techniques is Q-ball imaging. Using this method, we can extract orientation distribution function (ODF) that shows the orientations of multiple fibers in a voxel. For extracting the fiber directions, the maxima of the ODFs are conventionally determined. However, the results of this approach are sensitive to noise. To improve... 

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... 

In the present work, an efficient method is theoretically investigated for extending high-order harmonics and ultrashort attosecond pulse generation in N2 and CO molecules by using the time-dependent density functional theory approach. Our results show that by utilizing chirped laser field in the presence of a low frequency field, not only is the harmonic cutoff extended remarkably but also the single short quantum trajectory is selected to contribute to the harmonic spectra. When a low frequency field is added to the two-color chirped laser field, the long quantum trajectories are suppressed and only the short quantum trajectories contribute to the higher harmonic emission mechanism. As a... 

Molecular dynamics simulation was applied in this study to scrutinize the interfacial properties of water nano-film confined between calcite mineral and hydrocarbon layer, as two intrinsically different media. Such system resembles the environment experienced by water molecules in the pore spaces of underground carbonate reservoirs. The interplay between water film and confining phases, oil and mineral, strongly influences hydrocarbon production process; however, there is a lack of detailed understanding of the involved interactions. MD simulations indicate development of several layers with different water densities in the confined brine. Water molecules form well-ordered structure in three... 

In this study, the effects of the remote intramolecular hydrogen bonding on the acidity of hydroxy-1,4-benzoquinone derivatives have been investigated ab initio by employing density functional theory (DFT) methods. The computational studies were performed for both gas and solution (H 2 O, DMSO, and MeCN solutions) phases. Our results indicated that remote hydrogen bonding could play an important role in increasing the acidity of hydroxy-1,4-benzoquinone. Noncovalent interaction reduced density gradient (NCI-RDG) methods were used to visualize the attractive and repulsive interactions in the studied acids and their conjugate bases. Natural bond orbital (NBO) analysis was performed to confirm... 

Natural nanochannels and those used for applied purposes are often several nanometers in diameter and have lengths up to micrometer scales. Since normally no pressure gradient, mechanical force or electrical field is exerted on fluids in these situations, the fluid flow within them is not single-file and can be bidirectional. For this reason, studying the behavior of bidirectional flows in the channels is of paramount importance. In this study, a comprehensive investigation on the straight and non-straight bidirectional water transfer through carbon nanotubes is conducted via extensive molecular dynamics simulations. The results indicate that by changing the length, the diameter and the... 

Single-molecule experiments have found near-perfect thermodynamic efficiency in the rotary motor F1-ATP synthase. To help elucidate the principles underlying nonequilibrium energetic efficiency in such stochastic machines, we investigate driving protocols that minimize dissipation near equilibrium in a simple model rotary mechanochemical motor, as determined by a generalized friction coefficient. Our simple model has a periodic friction coefficient that peaks near system energy barriers. This implies a minimum-dissipation protocol that proceeds rapidly when the system is overwhelmingly in a single macrostate but slows significantly near energy barriers, thereby harnessing thermal... 

Various mixtures of surfactants and nanosilica particles were investigated to assess their influence on rising bubble hydrodynamics. For this purpose, local velocities of rising bubbles were measured experimentally. Also, the effects of concentration of three types of surface-modified silica nanoparticles on density, viscosity, and surface tension of surfactant solutions were determined. Experimental results revealed that the simultaneous presence of nanoparticles and surfactant molecules led to the decrease of local velocities of rising bubbles. The presence of nanoparticles in surfactant solutions leads to a more reduction of bubble local velocity. This could be caused by the formation of... 

In the present study, a model was proposed to determine the elastic properties of the family of fullerenes at different temperatures (between 300 and 2000 K) using a combination of molecular dynamics simulation and continuum shell theory. The fullerenes molecules examined here are eight spherical fullerenes, including C60, C80, C180, C240, C260, C320, C500, and C720. First, the breathing mode frequency and the radius of gyration of the molecules were obtained at different temperatures by molecular dynamics simulations using AIREBO potential. Then, these data were used in a continuum model to obtain the elastic coefficients of these closed clusters of carbon in terms of temperature changes.... 

Molecular machines and surface rolling molecules show great potential to accomplish different tasks in several fields, such as bottom-up assembly and nanomanipulation. Many researchers have investigated molecular machines, most of which was on a flat single-crystal substrate. In this paper, we studied the influence of vacancies in different sizes on the motion of a nanocar, a nanotruck, and C60 on a gold substrate at different temperatures by employing classical all-atom molecular dynamics. At the temperature of 200 K, a hole or vacancy appears as a repellent obstacle in the path of C60, and at higher temperatures, C60 can enter this hole. Although C60 has enough energy to escape single-atom... 

The effects of liquid density variation at the bubble surface on the dynamics of a single acoustic cavitation bubble are numerically studied. The Gilmore model together with a comprehensive hydrochemical model is used. The evaporation and condensation of water vapor are included in the hydrochemical model. The simulation results are compared to those resulting from the widely known Keller-Miksis model, which assumes a constant liquid density at the bubble surface. The numerical results for a single argon bubble in water reveal that the pressure and the temperature inside the bubble in collapse phase significantly increase, when the non-constant liquid density is used. These differences... 

The unusual monosaccharaides such as deoxy-hexose sugars, including methyl-pentose and aldo-pentose, are promising and important sugars in life science. However, little research on H-bond interactions in these systems has been reported. The aldo-pentose has a proton instead of the CH2OH group on C5; conversely, methyl-pentose has a CH3 group on C5. The aim of the present study is to investigate the role and nature of intramolecular H-bonds on acidity of CH3-pentose sugars (L-fucose and L-rhamnose) and aldo-pentose sugars (D-xylose, L-lyxose, D-ribose, and L-arabinose) using B3LYP/6-311++G (d, p) level. The calculated acidity values (ΔHacid) of these Dexoy-hexose were found to be from 343 to... 

Easily assembled and biocompatible chitosan/hyaluronic acid nanoparticles with multiple stimuli-responsive ability are ideally suited for efficient delivery of therapeutic agents under specific endogenous triggers. We report a simple and versatile strategy to formulate oxidative stress and pH-responsive chitosan/hyaluronic acid nanocarriers with high encapsulation efficiencies of small drug molecules and nerve growth factor protein. This is achieved through invoking the dual role of a thioketal-based weak organic acid to disperse and functionalize low molecular weight chitosan in one-pot. Thioketal embedded chitosan/hyaluronic acid nanostructures respond to oxidative stress and show... 

Concentration procedures have always been implemented when trace analysis of compounds in real matrices is contemplated. A variety of concentration strategies have been reported aiming at decreasing the limits of detection (LODs). The optical concentration of the substance in solution is one of the novel concepts for the enhancement of the analytical sensitivity. In this study, the optical concentration has been measured by the trapping of gold nanoparticles ((Formula presented.) nm) dispersed in water at low-concentrations at the focal volume of the laser beam. The influence of factors such as the time of gold nanoparticle trapping, the size of the nanoparticles, the intensity of the laser...