Sharif Digital Repository

Active behavior in skeletal muscle soft tissue is affected by electrical, chemical and mechanical parameters. More realistic model of skeletal muscle demands detailed formulation which is able to involve other parameters in addition to mechanical ones. In this paper a new formulation for considering Ca2+ level (as the most important chemical factor) along with mechanical parameters in force producing process of skeletal muscle is introduced and validated comparing simulated results with some experimental data. Prepared skeletal muscle behavior is able to predict the maximum generated force in muscle according to the concentration of intracellular Ca2+ level and muscle contraction velocity... 

From scaling arguments and numerical simulations, we investigate the properties of the generalized elastic model (GEM) that is used to describe various physical systems such as polymers, membranes, single-file systems, or rough interfaces. We compare analytical and numerical results for the subdiffusion exponent β characterizing the growth of the mean squared displacement 〈 (δh)(2)〉 of the field h described by the GEM dynamic equation. We study the scaling properties of the qth order moments 〈 {divides}δh{divides}(q)〉 with time, finding that the interface fluctuations show no intermittent behavior. We also investigate the ergodic properties of the process h in terms of the ergodicity... 

The Possibility of the laser assisted sonofusion is studied via single bubble sonoluminescence (SBSL) in Deuterated acetone (C3D6O) using quasi-adiabatic and hydro-chemical simulations at the ambient temperatures of 0 and -28.5 °C. The interior temperature of the produced bubbles in Deuterated acetone is 1.6 × 106 K in hydro-chemical model and it is reached up to 1.9 × 106 K in the laser induced SBSL bubbles. Under these circumstances, temperature up to 107 K can be produced in the center of the bubble in which the thermonuclear D-D fusion reactions are promising under the controlled conditions. © 2016 Author(s)  

We present a perturbation theory to find the response of an anisotropic DNA to the external tension. It is shown that the anisotropy has a nonzero but small contribution to the force-extension curve of the DNA. Thus an anisotropic DNA behaves like an isotropic one with an effective bending constant equal to the harmonic average of its soft and hard bending constants. © 2008 American Institute of Physics  

Symmetric T junctions have been used widely in microfluidics to generate equal-sized microdroplets, which are applicable in drug delivery systems. A newly proposed method for generating unequal-sized microdroplets at a T junction is investigated theoretically and experimentally. Asymmetric T junctions with branches of identical lengths and different cross sections are utilized for this aim. An equation for the critical breakup of droplets at asymmetric T junctions and one for determining the breakup point of droplets are developed. A good agreement was observed between the theories (present and previous) and the experiments  

A multicomponent lattice Boltzmann scheme is used to investigate the surface coating of substrates with two topographical features by a gravity-driven thin liquid film. The considered topographies are U- and V-shaped grooves and mounds. For the case of substrates with two grooves, our results indicate that for each of the grooves there is a critical width such that if the groove width is larger than the critical width, the groove can be coated successfully. The critical width of each groove depends on the capillary number, the contact angle, the geometry, and the depth of that groove. The second groove critical width depends on, in addition, the geometry and the depth of the first groove;... 

Employing a biharmonic boundary integral method with linear elements, coarsening dynamics of nanodroplets on topographical step heterogeneity is investigated. It is shown that the step height and droplet configuration have an influential effect on the dynamics. Increasing the step height slows down the process while locating the droplets close to the step boosts the coarsening rate. Considering a slip boundary condition enhances the dynamics and reveals a transition in the droplet migration direction. Our results reveal that increasing the surface wettability weakens the dynamics. Various types of the disjoining pressure over the step are also considered and their effects on the coarsening... 

13C chemical shieldings and 14N and 2H electric field gradient (EFG) tensors of L-alanylglycine (L-alagly) dipeptide were calculated at RHF/6-31++G and B3LYP/6-31++G levels of theory respectively. For these calculations a crystal structure of this dipeptide obtained from X-ray crystallography was used. Atomic coordinates of different clusters containing several L-alagly molecules were used as input files for calculations. These clusters consist of central and surrounding L-alagly molecules, the latter forming short, strong, hydrogen bonds with the central molecule. Since the calculations did not converge for these clusters, the surrounding L-alagly molecules were replaced by glycine... 

We show that the hydrophobicity of sequences is the leading term in Miyazawa-Jernigan interactions. Being the source of additive (solvation) terms in pair-contact interactions, they were used to reduce the energy parameters while resulting in a clear vector manipulation of energy. The reduced (additive) potential performs considerably successful in predicting the statistical properties of arbitrary structures. The evaluated designabilities of the structures by both models are highly correlated. Suggesting geometrically nondegenerate vectors (structures) as proteinlike structures, the additive model is a powerful tool for protein design. Moreover, a crossing point in the log-linear diagram of... 

Nano-manipulation is one of the most important aspects of nano-robotics and nano-assembly. The positioning process is considered by many researches to be one of the most important parts of nano-assembly, but has been poorly investigated, particularly for biologic samples. This Letter is devoted to modelling the process of positioning a biomolecule with atomic force microscopy (AFM) in an aqueous media using molecular dynamics simulations. Carbon nanotube (CNT) and graphite sheet are selected as AFM tip and substrate, respectively. To consider the effects of the medium on the manipulation, several models for decreasing the calculations including implicit, coarse grained, and all-atom methods... 

Long-time interaction of dewetting nanodroplets is investigated using a long-wave approximation method. Although three-dimensional (3D) droplets evolution dynamics exhibits qualitative behavior analogous to two-dimensional (2D) dynamics, there is an extensive quantitative difference between them. 3D dynamics is substantially faster than 2D dynamics. This can be related to the larger curvature and, as a consequence, the larger Laplace pressure difference between the droplets in 3D systems. The influence of various chemical heterogeneities on the behavior of droplets has also been studied. In the case of gradient surfaces, it is shown how the gradient direction could change the dynamics. For a... 

Paenibacillus polymyxa ATCC 21830 was used for the production of curdlan gum for first time. A Box-Behnken experimental design was applied to optimize six variables of batch fermentation culture each at three levels. Statistical analyses were employed to investigate the direct and interactive effects of variables on curdlan production. Optimum cultural conditions were temperature (50. °C), pH (7), fermentation time (96. h), glucose (100. g/L), yeast extract (3. g/L) and agitation speed (150. rpm). The yield of curdlan production was 6.89. g/L at optimum condition medium. Response surface methodology (RSM) and artificial neural network (ANN) were used to model cultural conditions of curdlan... 

We study the phase diagram of the anisotropic spin-1 Heisenberg chain with single ion anisotropy (D) using a ground-state fidelity approach. The ground-state fidelity and its corresponding susceptibility are calculated within the quantum renormalization group scheme where we obtained the renormalization of fidelity preventing calculation of the ground state. Using this approach, the phase boundaries between the antiferromagnetic Néel, Haldane and large-D phases are obtained for the whole phase diagram, which justifies the application of quantum renormalization group to trace the symmetry-protected topological phases. In addition, we present numerical exact diagonalization (Lanczos) results... 

Dirac electrons in clean graphene can mediate the interactions between two localized magnetic moments. The functional form of the RKKY interaction in pristine graphene is specified by two main features: (i) an atomic-scale oscillatory part determined by a wavevector → connecting the two valleys; with doping another longer range oscillation appears which arises from the existence of an extended Fermi surface characterized by a momentum scale kF; (ii) an algebraic Rα decay in large distances where the exponent α=-3 is a distinct feature of undoped Dirac sea in two dimensions. In this work, we investigate the effect of a few per cent vacancies on the above properties. Depending on the doping... 

The main aim of this work was to assess the ability of Bayesian multivariate adaptive regression splines (BMARS) and Bayesian radial basis function (BRBF) techniques for modelling the gas chromatographic retention indices of volatile components of Artemisia species. A diverse set of molecular descriptors was calculated and used as descriptor pool for modelling the retention indices. The ability of BMARS and BRBF techniques was explored for the selection of the most relevant descriptors and proper basis functions for modelling. The results revealed that BRBF technique is more reproducible than BMARS for modelling the retention indices and can be used as a method for variable selection and... 

A multicomponent analysis method based on principal component analysis-artificial neural network model (PC-ANN) is proposed for the simultaneous determination of levodopa (LD) and benserazide hydrochloride (BH). The method is based on the reaction of levodopa and benserazide hydrochloride with silver nitrate as an oxidizing agent in the presence of PVP and formation of silver nanoparticles. The reaction monitored at analytical wavelength 440 nm related to surface plasmon resonance band of silver nanoparticles. Differences in the kinetic behavior of the levodopa and benserazide hydrochloride were exploited by using principal component analysis, an artificial neural network (PC-ANN) to resolve... 

A nonlocal harmonic elastic rod model is proposed to describe the elastic behavior of short DNA molecules. We show that the nonlocal interactions contribute to effective bending energy of the molecule and affect its apparent persistence length. It is also shown that the anomalous behavior which has been observed in all-atom molecular dynamic simulations [A. K. Mazur, Biophys. J. 134, 4507 (2006)] can be a consequence of both nonlocal interactions between DNA base pairs and the intrinsic curvature of DNA  

New studies regarding the sorption of fluids by solids are published every day. In performance testing, after the sorbent has reached saturation, it is usually removed from the sorbate bath and allowed to drain. The loss of liquid from the sorbents with time is of prime importance in the real-world application of sorbents, such as in oil spill response. However, there is currently no equation used for modeling the unsteady state loss of the liquid from the dripping sorbent. Here, an analytical model has been provided for modeling the dynamic loss of liquid from the sorbent in dripping experiments. Data from more than 60 sorbent-sorbate systems has been used to validate the model. The... 

We have studied the mechanical properties of a few-layer graphene cantilever (FLGC) using atomic force microscopy (AFM). The mechanical properties of the suspended FLGC over an open hole have been derived from the AFM data. Force displacement curves using the Derjaguin-Müller-Toporov (DMT) and the massless cantilever beam models yield a Young modulus of Ec ∼ 37, Ea ∼ 0.7TPa and a Hamakar constant of ∼ 3 × 10 -18J. The threshold force to shear the FLGC was determined from a breaking force and modeling. In addition, we studied a graphene nanoribbon (GNR), which is a system similar to the FLGC; using density functional theory (DFT). The in-plane Young's modulus for the GNRs were calculated from...