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    Unbinding of kinesin from microtubule in the strongly bound states enhances under assisting forces

    , Article Molecular Informatics ; Volume 37, Issue 4 , April , 2018 ; 18681743 (ISSN) Khataee, H ; Naseri, S ; Zhong, Y ; Liew, A. W. C ; Sharif University of Technology
    Wiley-VCH Verlag  2018
    Abstract
    The ability to predict the cellular dynamics of intracellular transport has enormous potential to impact human health. A key transporter is kinesin-1, an ATP-driven molecular motor that shuttles cellular cargos along microtubules (MTs). The dynamics of kinesins depends critically on their unbinding rate from MT, which varies depending on the force direction applied on the motor, i.e. the force-unbinding rate relation is asymmetric. However, it remains unclear how changing the force direction from resisting (applied against the motion direction) to assisting (applied in the motion direction) alters the kinesin's unbinding and stepping. Here, we propose a theoretical model for the influence of... 

    Synthesis and Characterization of Hybrids 3D Graphene/gold Nanostructures for Supercapacitors and Electrochemical Biosensors

    , Ph.D. Dissertation Sharif University of Technology Saeidi, Mohsen (Author) ; Simchi, Abdolreza (Supervisor)
    Abstract
    Energy conversion and storage as well as life sciences are among the areas of our daily life. Interest in carbon nanomaterials for energy storage systems such as supercapacitors has enormously risen due to their attractive electrical conductivity, chemical inertness, and charge storage capacity. Producing these nanomaterials with a simple, scalable, and cost-effective method is the major problem for commercializing them. The reduction of graphitic oxide is a versatile procedure to prepare 3D graphene. Despite many green methods, the dynamics behind ultrafast thermal graphitization have remained elusive. Here, we demonstrate an effort to understand the graphitization mechanism of graphitic... 

    Synthesis and Characterization of Hybrids 3D Graphene/gold Nanostructures for Supercapacitors and Electrochemical Biosensors

    , Ph.D. Dissertation Sharif University of Technology Saeedi, Mohsen (Author) ; Simchi, Abdolreza (Supervisor)
    Abstract
    Energy conversion and storage as well as life sciences are among the areas of our daily life. Interest in carbon nanomaterials for energy storage systems such as supercapacitors has enormously risen due to their attractive electrical conductivity, chemical inertness, and charge storage capacity. Producing these nanomaterials with a simple, scalable, and cost-effective method is the major problem for commercializing them. The reduction of graphitic oxide is a versatile procedure to prepare 3D graphene. Despite many green methods, the dynamics behind ultrafast thermal graphitization have remained elusive. Here, we demonstrate an effort to understand the graphitization mechanism of graphitic... 

    Elastic properties of actin assemblies in different states of nucleotide binding

    , Article Cellular and Molecular Bioengineering ; Volume 5, Issue 1 , 2012 , Pages 1-13 ; 18655025 (ISSN) Ghodsi, H ; Kazemi, M. T ; Sharif University of Technology
    Abstract
    In this paper, the elastic properties of monomeric actin (G-actin) and the trimer nucleus (G-actin trimer) in different states of nucleotide binding are estimated using steered molecular dynamic (SMD) simulations. Three nucleotide binding states are considered: ADP- and ATP-bound actin and nucleotide-free actin assemblies. Our results show that nucleotide binding and the corresponding changes in structure have significant effects on the mechanical behaviors of actin assemblies. Simulations reveal that the deformation behavior of G-actin monomers is generally elastic up to engineering strains of 16 and 40% in the tension and shear tests, respectively. In addition, the G-actin trimers react... 

    Metabolic load comparison between the quarters of a game in elite male basketball players using sport metabolomics

    , Article European Journal of Sport Science ; Volume 21, Issue 7 , 2021 , Pages 1022-1034 ; 17461391 (ISSN) Khoramipour, K ; Gaeini, A. A ; Shirzad, E ; Gilany, K ; Chashniam, S ; Sandbakk, Ø ; Sharif University of Technology
    Taylor and Francis Ltd  2021
    Abstract
    Purpose: A basketball match is characterized by intermittent high-intensity activities, thereby relying extensively on both aerobic and anaerobic metabolic pathways. Here, we aimed to compare the metabolic fluctuations between the four 10-min quarters of high-level basketball games using metabolomics analyses. Methods: 70 male basketball players with at least 3 years of experience in the Iran national top-league participated. Before and after each quarter, saliva samples were taken for subsequent untargeted metabolomics analyses, where Principal component analysis (PCA) and Partial least squares-discriminant analysis (PLS-DA) were employed for statistical analysis. Results: Quarters 1 and 3... 

    کلیدواژه های تکراریCurcumin loading potentiates the neuroprotective efficacy of Fe3O4 magnetic nanoparticles in cerebellum cells of schizophrenic rats

    , Article Biomedicine and Pharmacotherapy ; Volume 108 , 2018 , Pages 1244-1252 ; 07533322 (ISSN) Naserzadeh, P ; Ashrafi Hafez, A ; Abdorahim, M ; Abdollahifar, M. A ; Shabani, R ; Peirovi, H ; Simchi, A ; Ashtari, K ; Sharif University of Technology
    Abstract
    Background: The aim of this study was to investigate the neurotoxic effects of Fe3O4 magnetic- CurNPs on isolated schizophrenia mitochondria of rats as an in vivo model. Methods: We designed CMN loaded superparamagnetic iron oxide nanoparticles (SPIONs) (Fe3O4 magnetic- CurNPs) to achieve an enhanced therapeutic effect. The physicochemical properties of Fe3O4 magnetic- CurNPs were characterized using X-ray diffraction (XRD), and dynamic laser light scattering (DLS) and zeta potential. Further, to prove Fe3O4 magnetic- CurNPs results in superior therapeutic effects, and also, the mitochondrial membrane potential collapse, mitochondrial complex II activity, reactive oxygen species generation,... 

    Mechanical differences between ATP and ADP actin states: A molecular dynamics study

    , Article Journal of Theoretical Biology ; Volume 448 , 2018 , Pages 94-103 ; 00225193 (ISSN) Mehrafrooz, B ; Shamloo, A ; Sharif University of Technology
    Academic Press  2018
    Abstract
    This paper aims to give a comprehensive atomistic modeling of the nanomechanical behavior of actin monomer. Actin is a ubiquitous and essential component of cytoskeleton which forms many different cellular structures. Despite for several years great effort has been devoted to the investigation of mechanical properties of the actin filament, studies on the nanomechanical behavior of actin monomer are still lacking. These scales are, however, important for a complete understanding of the role of actin as an important component in the cytoskeleton structure. Based on the accuracy of atomistic modeling methods such as molecular dynamics simulations, steered molecular dynamics method is performed... 

    Green porous benzamide-like nanomembranes for hazardous cations detection, separation, and concentration adjustment

    , Article Journal of Hazardous Materials ; Volume 423 , 2022 ; 03043894 (ISSN) Rabiee, N ; Fatahi, Y ; Asadnia, M ; Daneshgar, H ; Kiani, M ; Ghadiri, A. M ; Atarod, M ; Mashhadzadeh, A. H ; Akhavan, O ; Bagherzadeh, M ; Lima, E. C ; Saeb, M. R ; Sharif University of Technology
    Elsevier B.V  2022
    Abstract
    Green biomaterials play a crucial role in the diagnosis and treatment of diseases as well as health-related problem-solving. Typically, biocompatibility, biodegradability, and mechanical strength are requirements centered on biomaterial engineering. However, in-hospital therapeutics require an elaborated synthesis of hybrid and complex nanomaterials capable of mimicking cellular behavior. Accumulation of hazardous cations like K+ in the inner and middle ear may permanently damage the ear system. We synthesized nanoplatforms based on Allium noeanum to take the first steps in developing biological porous nanomembranes for hazardous cation detection in biological media. The...