Sharif Digital Repository

Spatial confinement limits the conformational space accessible to biomolecules but the implications for bimolecular topology are not yet known. Folded linear biopolymers can be seen as molecular circuits formed by intramolecular contacts. The pairwise arrangement of intra-chain contacts can be categorized as parallel, series or cross, and has been identified as a topological property. Using molecular dynamics simulations, we determine the contact order distributions and topological circuits of short semi-flexible linear and ring polymer chains with a persistence length of lp under a spherical confinement of radius Rc. At low values of lp/Rc, the entropy of the linear chain leads to the... 

Linear chains with intra-chain contacts can adopt different topologies and allow transitions between them, but it remains unclear how this process can be controlled. This question is important to systems ranging from proteins to chromosomes, which can adopt different conformations that are key to their function and toxicity. Here, we investigate how the topological dynamics of a simple linear chain is affected by interactions with a binding partner, using Monte Carlo and Molecular Dynamics simulations. We show that two point contacts with a binding partner are sufficient to accelerate or decelerate the formation of particular topologies within linear chains. Computed "folding-time... 

The budding yeast Saccharomyces cerevisiae is the first eukaryote whose genome has been completely sequenced. It is also the first eukaryotic cell whose proteome (the set of all proteins) and interactome (the network of all mutual interactions between proteins) has been analyzed. In this paper we study the structure of the yeast protein complex network in which weighted edges between complexes represent the number of shared proteins. It is found that the network of protein complexes is a small world network with scale free behavior for many of its distributions. However we find that there are no strong correlations between the weights and degrees of neighboring complexes. To reveal... 

The characteristics of correlated networks, generated from uncorrelated networks, were studied. New correlated networks with a considerable clustering were obtained from the line graphs of uncorrelated network. The transformation by which random graphs were converted to their line (edge-dual) graphs was explained. The solution for site percolation on the transformed graphs was also studied  

Given an ensemble of random graphs with a specific degree distribution, we show that the transformation which converts these graphs to their line (edge-dual) graphs produces an ensemble of graphs with nearly the same degree distribution, but with degree correlations and a much higher clustering coefficient. We also study the percolation properties of these new graphs. © 2003 The American Physical Society  

Nowadays, the accelerated expansion of genetic data challenges speed of current DNA sequence alignment algorithms due to their electrical implementations. Essential needs of an efficient and accurate method for DNA variant discovery demand new approaches for parallel processing in real time. Fortunately, photonics, as an emerging technology in data computing, proposes optical correlation as a fast similarity measurement algorithm; while complexity of existing local alignment algorithms severely limits their applicability. Hence, in this paper, employing optical correlation for global alignment, we present an optical processing approach for local DNA sequence alignment to benefit both... 

Large-scale ab initio molecular-dynamics simulations have been carried out to compute, at human-body temperature, the vibrational modes and lifetimes of pure and hydrated dipalmitoylphosphatidylcholine (DPPC) lipids. The projected atomic vibrations calculated from the spectral energy density are used to compute the vibrational modes and the lifetimes. All the normal modes of the pure and hydrated DPPC and their frequencies are identified. The computed lifetimes incorporate the full anharmonicity of the atomic interactions. The vibrational modes of the water molecules close to the head group of DPPC are active (possess large projected spectrum amplitudes) in the frequency range 0.5-55 THz,... 

Optical tweezers are proven indispensable single-cell micro-manipulation and mechanical phenotyping tools. In this study, we have used optical tweezers for measuring the viscoelastic properties of human red blood cells (RBCs). Comparison of the viscoelastic features of the healthy fresh and atorvastatin treated cells revealed that the drug softens the cells. Using a simple modeling approach, we proposed a molecular model that explains the drug-induced softening of the RBC membrane. Our results suggest that direct interactions between the drug and cytoskeletal components underlie the drug-induced softening of the cells. © 2018 Optical Society of America  

Ischemic cerebral stroke is a major cause of death and morbidity. Currently, no neuroprotective agents have been shown to impact the clinical outcomes in cerebral stroke cases. Here, we report therapeutic effects of Se nanoparticles on ischemic stroke in a murine model. Anti-transferrin receptor monoclonal antibody (OX26)-PEGylated Se nanoparticles (OX26-PEG-Se NPs) were designed and synthesized and their neuroprotective effects were measured using in vitro and in vivo approaches. We demonstrate that administration of the biodegradable nanoparticles leads to resolution of brain edema, protection of axons in hippocampus region, and myelination of hippocampal area after cerebral ischemic... 

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... 

We investigate the structure and electronic properties of phosphatidylcholine (PC) under different degrees of hydration at the single-molecule and monolayer type level by linear scaling ab initio calculations. Upon hydration, the phospholipid undergoes drastic long-range conformational rearrangements which lead to a sickle-like ground-state shape. The structural unit of the tilted gel-phase PC appears to be a water-bridged PC dimer. We find that hydration dramatically alters the surface potential, dipole and quadrupole moments of the lipids and consequently guides the interactions of the lipids with other molecules and the communication between cells  

The structure and autoionization of water at the water-phospholipid interface are investigated by ab initio molecular dynamics and ab initio Monte Carlo simulations using local density approximation (LDA) and generalized gradient approximation (GGA) for the exchange-correlation energy functional. Depending on the lipid headgroup, strongly enhanced ionization is observed, leading to the dissociation of several water molecules into H+ and OH- per lipid. The results can shed light on the phenomena of the high proton conductivity along membranes that has been reported experimentally  

A novel intelligent semi-active control system for an eleven degrees of freedom passenger car's suspension system using magnetorheological (MR) damper with neuro-fuzzy (NF) control strategy to enhance desired suspension performance is proposed. In comparison with earlier studies, an improvement in problem modeling is made. The proposed method consists of two parts: a fuzzy control strategy to establish an efficient controller to improve ride comfort and road handling (RCH) and an inverse mapping model to estimate the force needed for a semi-active damper. The fuzzy logic rules are extracted based on Sugeno inference engine. The inverse mapping model is based on an artificial neural network... 

Using CNG as an additive for gasoline is a proper choice due to higher octane number of CNG enriched gasoline with respect to that of gasoline. As a result, it is possible to use gasoline with lower octane number in the engine. This would also mean the increase of compression ratio in SI engines resulting in higher performance and lower gasoline consumption. Over the years, the use of simulation codes to model the thermodynamic cycle of an internal combustion engine have developed tools for more efficient engine designs and fuel combustion. In this study, a thermodynamic cycle simulation of a conventional four-stroke spark-ignition engine has been developed. The model is used to study the... 

With the declining energy resources and increase of pollutant emissions, a great deal of efforts has been focused on the development of alternatives for fossil fuels. One of the promising alternative fuels to gasoline in the internal combustion engine is natural gas [1-5]. The application of natural gas in current internal combustion engines is realistic due to its many benefits. The higher thermal efficiency due to the higher octane value and lower exhaust emissions including CO2 as a result of the lower carbon to hydrogen ratio of the fuel are the two important feature of using CNG as an alternative fuel. It is well known that computer simulation codes are valuable economically as a cost... 

Gaining insight into possible vibratory responses of dynamical systems around their stable equilibria is an essential step, which must be taken before their design and application. The results of such a study can significantly help prevent instability in closed-loop stabilized systems by avoiding the excitation of the system in the neighborhood of its resonance. This paper investigates nonlinear oscillations of a rotary inverted pendulum (RIP) with a full-state feedback controller. Lagrange’s equations are employed to derive an accurate 2-DoF mathematical model, whose parameter values are extracted by both the measurement and 3D modeling of the real system components. Although the governing... 

A suction-controlled ring device has been developed to continuously measure the coefficient of lateral soil pressure in deformable unsaturated soil samples from the at-rest to the active condition under application of increasing vertical pressure and controlled matric suction. The device incorporates a thin aluminum specimen ring equipped with horizontal strain gages for recording the lateral soil strains. In addition, a sensor recording water volume changes is utilized to continuously monitor the degree of saturation of the soil sample during tests. The matric suction within the soil texture is controlled using the axis translation technique. In order to verify the performance of the ring... 

We introduce a new smooth, non-toxic, biocompatible method for cross-linking of gum tragacanth (GT), a polysaccharide of natural origin, in order to serve as a new supporting matrix for immobilization systems. The modified gum is used as a matrix for the catalysis of the conversion of benzyl penicillin to 6-aminopenicillanic acid (6-APA) by means of Escherichia coli ATCC11105 with penicillin G acylase (PGA) activity. The results show that GT beads can not only serve as a proper matrix for immobilization, but show enhanced hydrolysis rate and stability compared to other immobilization systems used for this reaction. This signifies the potential of GT as a biocompatible matrix for... 

The Class-E power amplifier has been widely studied and formulated in the literature. Although the majority of reported inductive coupling wireless power transfer (WPT) systems use a class-E power amplifier for driving the primary coil, still there is a lack of a comprehensive study on class-E circuit dedicated to WPT, providing a set of closed form design equations for proper class-E operation. This paper presents the required design equations needed to design a 'true' class-E circuit for WPT applications. Equations for the series-tuned secondary coil WPT system are presented, as well as two different design procedures for the parallel-tuned secondary coil. The derived equations have been...