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#### Prediction of Protein Ligand Binding Affinity Using Deep Networks

, M.Sc. Thesis Sharif University of Technology ; Kalhor, Hamid Reza (Supervisor) ; Motahhari, Abolfazl (Co-Supervisor)
Abstract

Protein-ligand binding affinity is extremely important for finding new candidates in drug discovery and computational biochemistry. One of the physical characteristics for protein ligand interactions has been dissociation constant (KD) which can be obtain experimentally. However, there have been tremendous efforts to predict KD using modeling and computational approaches for protein-ligand interactions. In this project, we have exploited Convolutional Neural Network (CNN) model based on KDeep design, PDBBind version 2016 refined set training data, and examining it with KDeep core set test data. In order to modify KDeep,instead of 24 rotations (0, 90, 180 and 270 degrees in selection of two...

#### products of rotations by a given angle in the orthogonal group

, Article Bulletin of the Australian Mathematical Society ; Volume 97, Issue 2 , 2018 , Pages 308-312 ; 00049727 (ISSN) ; Sharif University of technology
Cambridge University Press
2018

Abstract

For every rotation of the Euclidean space ℝ(n≥3), we find an upper bound for the number such that is a product of rotations by an angle α( 0<≤π). We also find an upper bound for the number such that ρ can be written as a product of full rotations by an angle α. © 2017 Australian Mathematical Publishing Association Inc

#### On normal subgroups of the unit group of a quaternion algebra over a pythagorean field

, Article Bulletin of the Iranian Mathematical Society ; Volume 46, Issue 1 , June , 2020 , Pages 253-262 ; Sharif University of Technology
Springer
2020

Abstract

We investigate the structure of normal subgroups of the unit group of a quaternion algebra over a pythagorean field. © 2019, Iranian Mathematical Society

#### Design for Fabrication and Physical Parameter Optimization of Mems Parametric Exitation Gyrsocope

, M.Sc. Thesis Sharif University of Technology ; Salarie, Hassan (Supervisor)
Abstract

Recently, parametric excitation has been proposed and experimentally proven to provide micro gyroscopes with robustness to parameter variations and enhancement of sensitivity. harmonic excitation gyroscopes are very sensitive to response of a resonance at the resonant frequency; therefore it has to be created accurately. However, parametric excitation gyroscopes are not sensitive as a result of wide bound of frequency at drive mode, accordingly it is not necessary to be formed accurately in the same way as harmonic excitation gyroscope.

The produced stress at combs have a significance effect on robustness, sensitivity and calibration curves of parametric excitation gyroscope, as a...

The produced stress at combs have a significance effect on robustness, sensitivity and calibration curves of parametric excitation gyroscope, as a...

#### Customer Satisfaction in Airline Industry by Using SERVQUAL Model

, M.Sc. Thesis Sharif University of Technology ; Beirjandi, Heshmat (Supervisor)
Abstract

In today‘s world, the need for travel to different places for various reasons like politics, business and entertainment is unavoidable. This demonstrates the importance of the airline industry and the attention is achieved from the society. Different airlines try various strategies to satisfy more customers of this industry and of course more benefit would arise. These strategies would work more efficiently based on the outcome of a sound research on the exact needs of the customers, their perceived quality and expectations, and the gaps between the two and how they can be filled. This research follows the aim of understanding customer satisfaction for airline industry in Kish Island .In...

#### The prediction of hot flow behavior of Al-6%Mg alloy

, Article Mechanics Research Communications ; Volume 36, Issue 2 , 2009 , Pages 252-259 ; 00936413 (ISSN) ; Karimi Taheri, A ; Sharif University of Technology
2009

Abstract

In this research, the plastic flow behavior of Al-6%Mg alloy was studied by analyzing the results of hot compression tests in a range of temperature and strain rate. Then, an artificial neural network (ANN) model was trained at which the temperature, strain-rate, and strain parameters were used as the input layer and the flow stress as the output. The comparison of the predicted and experimental results of stress-strain curve proved the prediction capability of the ANN model. © 2008 Elsevier Ltd. All rights reserved

#### Efficient Resource Allocation in Next-Generation Networks

, M.Sc. Thesis Sharif University of Technology ; Movaghar, Ali (Supervisor)
Abstract

Network Function Virtualization (NFV) is a new paradigm for designing modern computer networks and data centers. NFV leverages the IT virtualization technologies to virtualize entire classes of network node functions into building blocks that may connect, or chain together to create communication services. In this research, we analysed and designed two offline and online algorithms for the problem of join optimization over placement and routing of network function chains in data centers. In the offline case, we showed that traditional randomized rouding works well and by help of chrnoff bound, we derive a new bound on performance gap. The online algorithm in both performance and resource...

#### On totally decomposable algebras with involution in characteristic two

, Article Journal of Algebra ; Volume 451 , 2016 , Pages 208-231 ; 00218693 (ISSN) ; Nokhodkar, A. H ; Sharif University of Technology
2016

Abstract

A necessary and sufficient condition for a central simple algebra with involution over a field of characteristic two to be decomposable as a tensor product of quaternion algebras with involution, in terms of its Frobenius subalgebras, is given. It is also proved that a bilinear Pfister form, recently introduced by A. Dolphin, can classify totally decomposable central simple algebras of orthogonal type

#### Design, simulation and fabrication of a MEMS accelerometer by using sequential and pulsed-mode DRIE processes

, Article Journal of Micromechanics and Microengineering ; Volume 27, Issue 1 , 2017 ; 09601317 (ISSN) ; Jafari, K ; Gharooni, M ; Sharif University of Technology
Institute of Physics Publishing
2017

Abstract

A sensitive half-bridge MEMS accelerometer fabricated by sequential and pulsed-mode processes is presented in this paper. The proposed accelerometer is analyzed by using conventional equations and the finite element method. The micromachining technology used in this work relies on two processes: sequential and pulsed-mode. In the sequential deep reactive ion etching process, a mixture of hydrogen and oxygen with a trace value of SF6 is used instead of polymeric material in the passivation step. The pulsed-mode process employs periodic hydrogen pulses in continuous fluorine plasma. Because of the continuous nature of this process, plus the in situ passivation caused by the hydrogen pulses,...

#### Sums of Squares in Local Rings

, M.Sc. Thesis Sharif University of Technology ; Gholamzadeh Mahmoudi, Mohammad (Supervisor)
Abstract

In this thesis, which is based on an article of Claus Scheiderer (Reference [21]), the relation between positive semi-definite elements of a semilocal ring, called psd, and elements of the ring which can be written as a sum of square elements of the ring and are called sos will be evaluated. In Chapter One, the concepts of prime cones, real spectrum of a ring and real ideals will be defined and then the relation between psd and sos elements in the total rings of quotients will be assessed. The Krull Valuation of an element which is a sum of squares will also be determined. In Chapter Two, the concept of totally positive elements in a ring will be defined and their properties will be...

####
Theoretical and Practical Study of Deformation Behavior of AlMg6 Alloy

,
Ph.D. Dissertation
Sharif University of Technology
;
Karimi Taheri, Ali
(Supervisor)
Abstract

Aluminum alloys are widely used in many applications in aerospace and automotive industries. Therefore, the study of the effects of different parameters such as chemical composition, temperature, strain, strain rate and recovery and recrystallization phenomena being more effective on controlling of microstructure and final properties of product, are more important. In this research, deformation behavior of AlMg6 alloy has been studied from two theoretical and experimental views as described below: In ambient temperature deformation, the mechanical properties in correlation on the microstructures developed at different temperatures have been assessed. The results of tensile test demonstrated...

#### Quadratic Forms and u-invariant

, M.Sc. Thesis Sharif University of Technology ; Gholamzadeh Mahmoudi, Mohammad (Supervisor)
Abstract

For a field of characteristic not two, the classical u-invariant is defined as the maximal dimension of anisotropic quadratic forms over F. Initially Kaplansky conjectured that u(F), when finite, is always a 2-power. Later Merkurjev constructed a field F such that u(F) = 6. This dissertation examines in detail the article: R. Elman, T. Y. Lam, Quadratic forms and the u-invariant. I. Math. Z. 131, 283-304 (1973). in which the notion of ”generalized u-invariant” (motivated by Pfister’s Local-Global Principle) was defined as the maximal dimension of anisotropic torsion quadratic forms over F. This is indeed a right generalization of the definition of the classical u-invariant since it not only...

#### Units in Witt Rings

, M.Sc. Thesis Sharif University of Technology ; Gholamzadeh Mahmoudi, Mohammad (Supervisor)
Abstract

This master’s thesis has three chapters. In the first and second chapters provided all the necessary preparations for the third chapter to describes the following article: Lewis, D. W, Units in Witt rings, Commun. Algebra 18, no. 10, 3295-3306 (1990).The first chapter includes an introduction of quadratic forms and Witt ring on fields with characteristic unequal 2, studing W b(F) in the category of commutative rings and introduction of formally real and nonreal fields. In this chapter there are important theorems such as Witt’s Decomposition and Cancellation Theorem, Cassels Representation, Springer and Pfister’s Local-Global Principle. The second chapter introduces the discretely valuated...

#### Micro-optoelectromechanical systems accelerometer based on intensity modulation using a one-dimensional photonic crystal

, Article Applied Optics ; Volume 55, Issue 32 , 2016 , Pages 8993-8999 ; 1559128X (ISSN) ; Abedi, K ; Jafari, K ; Gholamzadeh, R ; Sharif University of Technology
OSA - The Optical Society
2016

Abstract

In this paper, we propose what we believe is a novel sensitive micro-optoelectromechanical systems (MOEMS) accelerometer based on intensity modulation by using a one-dimensional photonic crystal. The optical sensing system of the proposed structure includes an air-dielectric multilayer photonic bandgap material, a laser diode (LD) light source, a typical photodiode (1550 nm) and a set of integrated optical waveguides. The proposed sensor provides several advantages, such as a relatively wide measurement range, good linearity in the whole measurement range, integration capability, negligible cross-axis sensitivity, high reliability, and low air-damping coefficient, which results in a wider...

#### On Hermitian Pfister forms

, Article Journal of Algebra and its Applications ; Volume 7, Issue 5 , 2008 , Pages 629-645 ; 02194988 (ISSN) ; Lequeu, E ; Gholamzadeh Mahmoudi, M ; Sharif University of Technology
2008

Abstract

Let K be a field of characteristic different from 2. It is known that a quadratic Pfister form over K is hyperbolic once it is isotropic. It is also known that the dimension of an anisotropic quadratic form over K belonging to a given power of the fundamental ideal of the Witt ring of K is lower bounded. In this paper, weak analogues of these two statements are proved for hermitian forms over a multiquaternion algebra with involution. Consequences for Pfister involutions are also drawn. An invariant uα of K with respect to a nonzero pure quaternion of a quaternion division algebra over K is defined. Upper bounds for this invariant are provided. In particular an analogue is obtained of a...

#### Design and fabrication of a micro-opto-mechanical-systems accelerometer based on intensity modulation of light fabricated by a modified deep-reactive-ion-etching process using silicon-on-insulator wafer

, Article Journal of Vacuum Science and Technology B ; Volume 40, Issue 4 , 2022 ; 21662746 (ISSN) ; Gharooni, M ; Salarieh, H ; Akbari, J ; Sharif University of Technology
AVS Science and Technology Society
2022

Abstract

Accelerometers that work based on intensity modulation of light are more sensitive, economically feasible, and have a simpler fabrication process compared to wavelength modulation. A micro-opto-electro-mechanical-system accelerometer based on intensity modulation of light is designed and fabricated. A movable shutter that is attached to the proof mass is designed to change the intensity of light. Moreover, the mechanical part is designed to improve the overall sensitivity and linear behavior in the measurement range. The designed accelerometer is fabricated by a deep-reactive-ion-etching (DRIE) process. The DRIE process used in this report is based on a Bosch-like process, which uses SF 6...

#### The photochromic switchable imidazoles: Their genesis, development, synthesis, and characterization

, Article Dyes and Pigments ; Volume 203 , 2022 ; 01437208 (ISSN) ; Mirzaee, M ; Hosseini, S ; Gholamzadeh, P ; Sharif University of Technology
Elsevier Ltd
2022

Abstract

Switchable photochromic dyes have benefited greatly from the use of heterocyclic chemicals. The imidazole group is particularly essential because it can be transformed into dimers, which can then be radicalized in the presence of light photons. Imidazole dimers have been optimized throughout thirty years of research, allowing derivatives with diverse colors, quick reversibility, and sensitivity to different wavelengths from UV to near IR ranges. These imidazole dimers are interesting to be used in the matrices of polymers, hydrogels, glasses, solar cells, and even pharmaceuticals. The goal of this review is to look at the history, development, and future of imidazole dimers. We will also...

#### P Fister’s Local-Global Principle

, M.Sc. Thesis Sharif University of Technology ; Gholamzadeh Mahmoudi, Mohammad (Supervisor)
Abstract

This master’s thesis has two major parts. The first part which includes chapters 1 to 8, describes the article A. Pfister, Quadratische Formen in beliebigen Körpern, Invent. Math. 1, (1966)pp. 116-132, and expresses important facts about the Witt ring W(K) of quadratic forms over an arbitrary field K of characteristic unequal to 2. Among those, it is shown that the order of each element in the additive group of W(K) is a power of 2, the Witt ring doesn’t have any zero divisor of odd dimension and a necessary and sufficient condition for W(K) to be an integral domain is given. The connections between the square class number of a field and the cardinality of its Witt ring and, providing some...

#### A high sensitive, low foot print, SU-8 material-based, light intensity modulated MOMS accelerometer

, Article Optical Engineering ; Volume 61, Issue 5 , 2022 ; 00913286 (ISSN) ; Salarieh, H ; Parsanasab, G. M ; Akbari, J ; Sharif University of Technology
SPIE
2022

Abstract

A high sensitive optical MEMS accelerometer is proposed, which works by changing the effective refractive index of a microring relied on intensity modulation of light wave. The proposed optical sensing system consists of a microring, waveguide, and a proof mass. Acceleration causes lateral displacement of the proof mass. The proof mass is in the optical coupling length of the microring, and the displacement of the proof mass changes effective refractive index of the microring. Changes of the effective refractive index of the microring result in wavelength shift. The mechanical and optical parts of the proposed accelerometer are designed, and the obtained functional characteristics are...