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A simple graphical approach to predict local residue conformation using NMR chemical shifts and density functional theory
, Article Journal of Computational Chemistry ; Volume 37, Issue 14 , 2016 , Pages 1296-1305 ; 01928651 (ISSN) ; Ebrahimi, H. P ; Fathi, F ; Bahrami Panah, N ; Jalali Heravi, M ; Tafazzoli, M ; Sharif University of Technology
John Wiley and Sons Inc
2016
Abstract
The dependency of amino acid chemical shifts on φ and ψ torsion angle is, independently, studied using a five-residue fragment of ubiquitin and ONIOM(DFT:HF) approach. The variation of absolute deviation of 13Cα chemical shifts relative to φ dihedral angle is specifically dependent on secondary structure of protein not on amino acid type and fragment sequence. This dependency is observed neither on any of 13Cβ, and 1Hα chemical shifts nor on the variation of absolute deviation of 13Cα chemical shifts relative to ψ dihedral angle. The 13Cα absolute deviation chemical shifts (ADCC) plots are found as a suitable and simple tool to predict secondary structure of protein with no requirement of...
Numerical and Experimental Study of Induced Drag Reduction Using a Wing Grid at Low Reynolds Numbers
, M.Sc. Thesis Sharif University of Technology ; Soltani, Mohamad Reza (Supervisor) ; Banazadeh, Afshin (Supervisor) ; Farahani, Mohammad (Co-Supervisor)
Abstract
Wing grids are among devices used for increasing wing performance. Wing grids decrease wing induced drag by breaking the wing main tip vortex to smaller vortices with lower turbulence intensity value. These devices are mostly used in low Reynolds regimes, and their effectiveness decreases as the Reynolds number increases. In most researches around the world, wing grids have simple design configurations, but in this research wing grids are designed in such a way that each grid has a minimum value of induced drag respectively. So, in addition to reducing baseline wing induced drag by breaking the main vortex to smaller vortices by means of wing grid, each grid has a minimum value of induced...
Design and Fabrication of a Quadrotor with Dihedral Angle Capability and its Dynamic Modeling and Motion Control
, M.Sc. Thesis Sharif University of Technology ; Alasti, Aria (Supervisor) ; Nejat Pishkenari, Hossein (Supervisor)
Abstract
As the leading kind of multi-rotors, quadrotors have become one of the most popular Unmanned Areal Vehicles (UAVs). These robots are very agile, but their speed is limited when performing decent maneuvers. In this project, a special quadrotor with dihedral-rotating arms is presented in order to increase the decent velocity of the vehicle. The conceptual and detailed designs of the vehicle are presented first, followed by the construction of the quadrotor. The fabricated quadrotor measures 25 cm in size, has a weight of about 1 kg, and can support up to 70 degrees of dihedral angle. Afterwards, the dynamic equations of the dihedral quadrotor are driven and simulated. The effects of dihedral...
Control of a Quadcopter for Rapid Descent
, Ph.D. Dissertation Sharif University of Technology ; Alasty, Aria (Supervisor) ; Nejat Pishkenari, Hossein (Supervisor)
Abstract
It is well-known that helicopters descending fast may enter a region in the velocity space called Vortex Ring State where the blade’s lift differs significantly from regular regions and includes high amplitude fluctuations. These fluctuations may lead to instability and therefore, this region is avoided, typically by increasing the horizontal speed. However, this region is not fully identified for multirotors, which their blades are rigid in contrary of helicopter’s blades which have two degrees of freedom. This project researches this phenomenon in the context of small-scale quadcopters. The region corresponding to the VRS is identified by combining first-principles modeling and wind-tunnel...
Elastic moduli tensors, ideal strength, and morphology of stanene based on an enhanced continuum model and first principles
, Article Mechanics of Materials ; Volume 110 , 2017 , Pages 1-15 ; 01676636 (ISSN) ; Ojaghnezhad, F ; Etehadieh, A ; Tabatabaei, M ; Sharif University of Technology
Elsevier B.V
2017
Abstract
The present work aims to provide an accurate description of the tensile behavior of the planar as well as low-buckled stanene and to capture their ideal strength in armchair (AC)- and zigzag (ZZ)-directions. For an accurate description of anisotropic response of such hyperelastic materials as stanene, consideration of a highly nonlinear constitutive model in which up to the fourth power of strains is incorporated is inevitable. By utilizing first principles calculations based on density functional theory (DFT), the second, third, fourth, and fifth order elastic moduli tensors corresponding to both planar and low-buckled states are obtained. Moreover, the morphology of the free-standing...
Efficient generation of self-avoiding, semiflexible rotational isomeric chain ensembles in bulk, in confined geometries, and on surfaces
, Article Computer Physics Communications ; Volume 270 , 2022 ; 00104655 (ISSN) ; Galata, A. A ; Sadeghi, M ; Kröger, A ; Kröger, M ; Sharif University of Technology
Elsevier B.V
2022
Abstract
We provide an efficient ready-to-run code gensaw that generates single or large ensembles of self-avoiding, flexible, semiflexible, rotationally isometric or helical chains in the bulk or subject to arbitrary confinement and tethering conditions, where we allow for arbitrary intramolecular bending and dihedral energy functions. The resulting configuration files are provided in various common formats and can be immediately used to do molecular simulations or statistical analysis. We work out analytic expressions for the mean squared end-to-end distance and gyration radius of the semiflexible, helical and rotational isomeric state models with a finite number of bonds and arbitrary interaction...