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... 

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... 

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,... 

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... 

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  

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  

As computer simulation increasingly supports engineering design, the requirement for a computer software environment providing an integration platform for computational engineering software increases. A key component of an integrated environment is the use of computational engineering to assist and support solutions for complex design. In the present paper, an integrated software environment is demonstrated for multi-disciplinary computational modeling of structural and geotechnical problems. The SUT-DAM is designed in both popularity and functionality with the development of user-friendly pre- and post-processing software. Pre-processing software is used to create the model, generate an... 

In this paper, the influence of powder-tool friction on the mechanical properties of the final product is investigated in pressing metal powders. A computational algorithm is presented for simulation of frictional contact in the compaction process of powder. The large deformation finite element (FE) formulation is characterized by the use of penalty approach in which a plasticity theory of friction is incorporated to simulate sliding resistance at the powder-tool interface. The constitutive relations for friction are derived from a Coulomb friction law. A double-surface cap plasticity model is employed together with the nonlinear contact friction behavior in numerical simulation of powder... 

In this paper, an atomistic–continuum homogenization multiscale method is developed to study the nonlinear behavior of heterogeneous nanomaterials. The atomistic representative volume element (RVE) with vacancy and/or void defects are analyzed by employing the fully atomistic method, in which the nucleation, migration, and elimination of dislocation, as well as the dislocation-vacancy interaction, are captured. The coarse-scale material domain is modeled within the framework of the nonlinear finite element method, and the impression of nanoscale material defects is investigated by upscaling the stress tensor and tangent modulus from the atomistic RVE based on the Hill-Mandel principle. The... 

In this paper, a new criterion for passivity of haptic devices is obtained. This criterion creates a relationship between Coulomb friction coefficient, viscous friction coefficient, sampling rate, and the maximum simulated stiffness. The process of derivation of the passivity criterion is described in detail. This criterion is improved compared with other existing criteria and predicts passivity in haptic rendering more accurately. In particular, for speeds of less than 5 cm/s, the new passivity criterion should replace the previous criteria to avoid unwanted vibrations of stiff virtual walls. Analytical and numerical investigations are presented to validate the new criterion. A specific... 

The field emission properties of MoO2 nanostars grown on a silicon substrate and their emission performance in various vacuum gaps are reported in this article. A new structure of molybdenum oxides, named a nanostar, is grown by thermal vapor deposition with a length of ̃1 μm, a thickness of ̃50 nm, and its width in the range of 500-700 nm. The morphology, structure, composition, and chemical states of the prepared nanostars were characterized by scanning electron microscopy, high-resolution transmission electron microscopy, X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS). According to XRD analysis, the grown nanostructures are composed of both crystalline Mo4O11 and... 

Several exoskeletons with various configurations and degrees-of-freedoms (DOFs) have been introduced in the literature, but not many have addressed the optimal selection of the mechanism's DOFs. In the proposed system a semi-passive toe joint is introduced to achieve several advantages. The performance of the proposed novel passive toe joint is evaluated experimentally. In addition, the semi-passive abduction/adduction DOFs in the hip joint and eversion/inversion DOFs in ankle joint is proposed to facilitate turning while providing more comfort during normal walking. The effect of passive DoFs existence on the user comfortability is studied with the aid of three kinematic indices. In the... 

This paper models the dielectric corona pre-ionization, capacitor transfer type of flat-plane transmission line traveling wave transverse excited atmospheric pressure nitrogen laser by a non-linear lumped RLC electric circuit. The flat-plane transmission line and the pre-ionizer dielectric are modeled by a lumped linear RLC and time-dependent non-linear RC circuit, respectively. The main discharge region is considered as a time-dependent non-linear RLC circuit where its resistance value is also depends on the radiated pre-ionization ultra violet (UV) intensity. The UV radiation is radiated by the resistance due to the surface plasma on the pre-ionizer dielectric. The theoretical predictions...