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Synthesis, Characterization and Voltametric Study of Single Molecule Magnet Hybrid Salts [Mn3O(O2CMe)6(Pyr)3][Keggin-Polyoxometalates]Type
,
M.Sc. Thesis
Sharif University of Technology
;
Mohammadi Boghaei, Davar
(Supervisor)
Abstract
Molecular nanomagnets, also known as Single Molecule Magnets (SMMs) are a class of molecules that at low temperature exhibit magnetic hysteresis of pure molecular origin and not related to a cooperative effect. In the past fifteen years they have attracted great interest for their potentiality to act as magnetic memory units and for the many quantum effects in the dynamics of their magnetization. Organization of SMM on surfaces is the first step in order to address the magnetic state of a single molecule or to connect the molecule to a conducting substrate. The complex nature of SMMs and the peculiar origin of their magnetic bistability have been representing for half a decade an obstacle to...
Synthesis and Properties of Cationic Polynulcear Complexes of Manganese with the Anionic Keggin Type Polyoxometalates as Single Molecule Magnets Hx[Mn4O2(CH3COO)7(bipy)2]n[Kegiin-Polyoxometalates]m.yH2O
, M.Sc. Thesis Sharif University of Technology ; Mohammdi Boghaei, Davar (Supervisor)
Abstract
Single molecule magnets due to their magnetic tunneling effect and the interaction they have with an external magnetic field are used widely in quantum computing and also the storage of data with high capacities. Polyoxometalates that are used as counter ions for cationic single molecule magnets, are able to affect their spin-couple nature via a magnetic exchange and also have an influence on the crystal accumulation in order to change the magnetic property of the molecule. In this research the probability of sedimenting a cationic single molecule magnet, [Mn4O2(CH3COO)7(bipy)2]+, with the use of anionic polyoxometalates with Keggin structures has been investigated. Thus, the single...
Hydration strongly affects the molecular and electronic structure of membrane phospholipids
, Article Journal of Chemical Physics ; Volume 136, Issue 11 , 2012 ; 00219606 (ISSN) ; Partovi Azar, P ; Jadidi, T ; Nafari, N ; Maass, P ; Tabar, M. R. R ; Bonn, M ; Bakker, H. J ; Sharif University of Technology
Abstract
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
Membrane interactions control residue fluctuations of outer membrane porins
, Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 81, Issue 5 , May , 2010 ; 15393755 (ISSN) ; Mobasheri, H ; Ejtehadi, M. R ; Sharif University of Technology
2010
Abstract
Bacterial outer membrane porins (Omp) that have robust β -barrel structures, show potential applications for nanomedicine devices in synthetic membranes and single molecule detection biosensors. Here, we explore the conformational dynamics of a set of 22 outer membrane porins, classified into five major groups: general porins, specific porins, transport Omps, poreless Omps and composed pores. Normal mode analysis, based on mechanical vibration theory and elastic network model, is performed to study the fluctuations of residues of aforementioned porins around their equilibrium positions. We find that a simple modification in this model considering weak interaction between protein and...
Optimal control of rotary motors
, Article Physical Review E ; Volume 99, Issue 1 , 2019 ; 24700045 (ISSN) ; Mehdizadeh, A ; Sivak, D. A ; Sharif University of Technology
American Physical Society
2019
Abstract
Single-molecule experiments have found near-perfect thermodynamic efficiency in the rotary motor F1-ATP synthase. To help elucidate the principles underlying nonequilibrium energetic efficiency in such stochastic machines, we investigate driving protocols that minimize dissipation near equilibrium in a simple model rotary mechanochemical motor, as determined by a generalized friction coefficient. Our simple model has a periodic friction coefficient that peaks near system energy barriers. This implies a minimum-dissipation protocol that proceeds rapidly when the system is overwhelmingly in a single macrostate but slows significantly near energy barriers, thereby harnessing thermal...
Designing an intelligent controller for a molecular valve
, Article 2008 Proceedings of the ASME - 2nd International Conference on Integration and Commercialization of Micro and Nanosystems, MicroNano 2008, 3 June 2008 through 5 June 2008, Kowloon ; 2008 , Pages 195-201 ; 0791842940 (ISBN); 9780791842942 (ISBN) ; Alasty, A ; Sharif University of Technology
2008
Abstract
Too much effort has been done for manipulating individual atoms, using nano-manipulators and Scanning Tunneling Microscopes (STM). On the other hand, characterization and manipulation of nano-flows is of great concern. In the current work a molecular valve has been considered, which is made up of six atoms placed on the circumstance of a circle. A fuzzy controller has been designed for controlling the diameter of this molecular valve. The designed fuzzy controller used singleton fuzzifier, Mamdani inference engine, center average defuzzifier and exponential membership functions. A model based on the classical Molecular Dynamics (MD) is used for modeling the nano-system and passing the states...
Graphic: Graph-based hierarchical clustering for single-molecule localization microscopy
, Article 18th IEEE International Symposium on Biomedical Imaging, ISBI 2021, 13 April 2021 through 16 April 2021 ; Volume 2021-April , 2021 , Pages 1892-1896 ; 19457928 (ISSN); 9781665412469 (ISBN) ; Aziznejad, S ; Unser, M ; Sage, D ; Sharif University of Technology
IEEE Computer Society
2021
Abstract
We propose a novel method for the clustering of point-cloud data that originate from single-molecule localization microscopy (SMLM). Our scheme has the ability to infer a hierarchical structure from the data. It takes a particular relevance when quantitatively analyzing the biological particles of interest at different scales. It assumes a prior neither on the shape of particles nor on the background noise. Our multiscale clustering pipeline is built upon graph theory. At each scale, we first construct a weighted graph that represents the SMLM data. Next, we find clusters using spectral clustering. We then use the output of this clustering algorithm to build the graph in the next scale; in...
Conformation- and phosphorylation-dependent electron tunnelling across self-assembled monolayers of tau peptides
, Article Journal of Colloid and Interface Science ; Volume 606 , 2022 , Pages 2038-2050 ; 00219797 (ISSN) ; Hosseini, A ; Loloee, R ; Perry, G ; Lee, K. B ; Lund, M ; Ejtehadi, M. R ; Mahmoudi, M ; Sharif University of Technology
Academic Press Inc
2022
Abstract
We report on charge transport across self-assembled monolayers (SAMs) of short tau peptides by probing the electron tunneling rates and quantum mechanical simulation. We measured the electron tunneling rates across SAMs of carboxyl-terminated linker molecules (C6H12O2S) and short cis-tau (CT) and trans-tau (TT) peptides, supported on template-stripped gold (AuTS) bottom electrode, with Eutectic Gallium-Indium (EGaIn)(EGaIn) top electrode. Measurements of the current density across thousands of AuTS/linker/tau//Ga2O3/EGaIn single-molecule junctions show that the tunneling current across CT peptide is one order of magnitude lower than that of TT peptide. Quantum mechanical simulation...