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154 results on '"Zarei, Zahra"'

2. A Machine Learning Approach to Robustly Determine Director Fields and Analyze Defects in Active Nematics

Author

Li, Yunrui, Zarei, Zahra, Tran, Phu N., Wang, Yifei, Baskaran, Aparna, Fraden, Seth, Hagan, Michael F., and Hong, Pengyu

Subjects
Condensed Matter - Soft Condensed Matter
Abstract

Active nematics are dense systems of rodlike particles that consume energy to drive motion at the level of the individual particles. They exist in natural systems like biological tissues and artificial materials such as suspensions of self-propelled colloidal particles or synthetic microswimmers. Active nematics have attracted significant attention in recent years due to their spectacular nonequilibrium collective spatiotemporal dynamics, which may enable applications in fields such as robotics, drug delivery, and materials science. The director field, which measures the direction and degree of alignment of the local nematic orientation, is a crucial characteristic of active nematic and is essential for studying topological defects. However, determining the director field is a significant challenge in many experimental systems. Although director fields can be derived from images of active nematics using traditional imaging processing methods, the accuracy of such methods are highly sensitive to the settings of the algorithms. These settings must be tuned from image-to-image due to experimental noise, intrinsic noise of the imaging technology, and perturbations caused by changes in experimental conditions. This sensitivity currently limits automatic analysis of active nematics. To address this, we developed a machine learning model for extracting reliable director fields from raw experimental images, which enables accurate analysis of topological defects. Application of the algorithm to experimental data demonstrates that the approach is robust and highly generalizable to experimental settings that are different from those in the training data. It could be a promising tool for investigating active nematics and may be generalized to other active matter systems.

Published
2023

4. From Disks to Channels: Dynamics of Active Nematics Confined to an Annulus

Author

Joshi, Chaitanya, Zarei, Zahra, Norton, Michael M., Fraden, Seth, Baskaran, Aparna, and Hagan, Michael F.

Subjects
Condensed Matter - Soft Condensed Matter
Abstract

Confinement can be used to systematically tame turbulent dynamics occurring in active fluids. Although periodic channels are the simplest geometries to study confinement numerically, the corresponding experimental realizations require closed racetracks. Here, we computationally study 2D active nematics confined to such a geometry -- an annulus. By systematically varying the annulus inner radius and channel width, we bridge the behaviors observed in the previously studied asymptotic limits of the annulus geometry: a disk and an infinite channel. We identify new steady-state behaviors, which reveal the influence of boundary curvature and its interplay with confinement. We also show that, below a threshold inner radius, the dynamics are insensitive to topological constraints imposed by boundary conditions. We explain this insensitivity through a simple scaling analysis. Our work sheds further light on design principles for using confinement to control the dynamics of active nematics.

Published
2023

5. Light-activated microtubule-based 2D active nematic

Author

Zarei, Zahra, Berezney, John, Hensley, Alexander, Lemma, Linnea, Senbil, Nesrin, Dogic, Zvonimir, and Fraden, Seth

Subjects
Condensed Matter - Soft Condensed Matter
Abstract

We characterize two-dimensional (2D) microtubule-based active nematics driven by light-responsive kinesin motor clusters. We assess two constructs of optogenetic kinesin: opto-K401, a processive motor, and opto-K365, a non-processive motor. Measurements reveal an order of magnitude improvement in the contrast of nematic flow speeds between maximally- and minimally-illuminated states for opto-K365 motors. Focusing on opto-K365 nematics, we characterize both the steady-state flow and defect density as a function of applied light and examine the transient behavior between steady-states. The steady-state nematic flow and defect densities are set by the applied light intensity across centimeter-sized samples, independent of initial conditions. Although nematic flow reaches steady-state within tens of seconds, the defect density exhibits transient behavior for 4 to 10 minutes, showing a separation between small-scale active reorganization and system-scale structural states. This work establishes an experimental platform to test theoretical frameworks which exploit spatiotemporally-heterogeneous patterns of activity to generate targeted dynamical states.

Published
2023

13. Contributors

Author

Abdalla, Amr, primary, Ahmad, Waqar, additional, Aryal, Prakash, additional, Asadi, Nooshin, additional, Bailera, Manuel, additional, Bakare, Idris, additional, Bakhtyari, Ali, additional, Bonyadi, Mohammad, additional, Camacho, Felipe Gomes, additional, Chen, Guoxing, additional, de Oliveira, Camilla Fernandes, additional, de Oliveira Junior, Silvio, additional, Delshah, Maryam, additional, Domingos, Meire Ellen Gorete Ribeiro, additional, dos Santos, Moisés Teles, additional, Dwivedi, Swarit, additional, Etezadi, Razieh, additional, Farooqui, Azharuddin, additional, Flórez-Orrego, Daniel, additional, Galeazzi, Andrea, additional, Gao, Xingyuan, additional, Harding, Jonathan, additional, Kanjilal, Baishali, additional, Kaur, Milanpreet, additional, Kawi, Sibudjing, additional, Khademi, Mohammad Hasan, additional, Kiani, Parvin, additional, Lak, Soheila Zandi, additional, Lisbona, Pilar, additional, Lotfi-Varnoosfaderani, Mohammad, additional, Mahinpey, Nader, additional, Makarem, Mohammad Amin, additional, Malaibari, Zuhair Omar, additional, Manenti, Flavio, additional, Masoumi, Arameh, additional, Meshksar, Maryam, additional, Mohandesi, Masoumeh, additional, Nasser, Galal, additional, Negri, Francesco, additional, Nogueira Nakashima, Rafael, additional, Noshadi, Iman, additional, Palizvan, Alireza, additional, Park, Song Won, additional, Pérez, Virginia, additional, Prifti, Kristiano, additional, Qiu, Shuxian, additional, Rahimpour, Hamid Reza, additional, Rahimpour, Mohammad Reza, additional, Salahi, Fatemeh, additional, Sanhoob, Mohammed, additional, Tanksale, Akshat, additional, Tsotsis, Theodore, additional, Tu, Xin, additional, Virla, Luis D., additional, Wang, Ni, additional, Wang, Yaolin, additional, Yousefi, Shabnam, additional, Zafarnak, Samira, additional, Zarei, Zahra, additional, Zarei-Jelyani, Fatemeh, additional, Zhao, Linghao, additional, and Zolghadri, Sara, additional

Published
2023
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16. Absolutely pure covers of sheaves.

Author

Hosseini, Esmaeil and Zarei, Zahra

Abstract

Let (X , X) be a scheme and X be the category of all sheaves of X -modules. Enochs' conjecture states that any covering class in X is closed under directed colimits. In this work, if Abs is the class of all absolutely pure objects in X , then we prove the validity of the conjecture for Abs . This gives a characterization of locally coherent schemes. In addition, we study some homological properties of absolutely pure sheaves of X -modules and answer a question raised in [P. Rothmaler, When are pure injective envelopes of flat modules flat? Comm. Algebra 30(6) (2002) 3077–3085]. [ABSTRACT FROM AUTHOR]

Published
2024
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22. Assessing global kidney cancer incidence and mortality rates according to population category by income levels in 2020: An ecological study

Author

Alivand, Soleyman, primary, Fattahi, Farinaz, additional, Zarei, Zahra, additional, Hosseinifard, Mehdi, additional, Nouralishahi, Atieh, additional, Karimi Aliabadi, Hakimeh, additional, Soltani Nejad, Simin, additional, Alivand, Noorbakhsh, additional, Molaee, Hanieh, additional, and Ghorbani Doshantapeh, Anna, additional

Published
2023
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33. Contributors

Author

Abreu, António, Ahmed, Arslan, Al-Tohamy, Rania, Ali, Sameh S., Anducho Reyes, Miguel Angel, Aslanbay Guler, Bahar, Ayranci, Inci, Aziz, Muhammad, Bastos, Reinaldo G., Baños Orozco, Maria de los Angeles, Beatriz, Fernanda Palmeira, Beaula, Winfred Sofi, Boichenko, Kateryna, Borah, Doljit, Borella, Lisa, Borowitzka, Michael A., Bose, Archishman, Brito-Bello, Alethia A., Buentello-Montoya, David A., Cadena Ramírez, Arturo, Caetano, Patrícia Acosta, Caltzontzin-Rabell, Valeria, Carlozzi, Pietro, Carrillo, Francisco, Cañizares–Villanueva, Rosa Olivia, Chen, Xiangxiang, Cherifi, Ouafa, Choo, Wu-Thong, Convey, Peter, Coronado-Apodaca, Karina G., Cruz, José Diogo, Dantas, Rui, da Silva, Mariana A., Deamici, Kricelle Mosquera, Deka, Dhanapati, Deprá, Mariany Costa, de Sá Caetano, Nídia, Dias, Rosangela Rodrigues, do Nascimento, Tatiele C., Díaz, Oliver, Dutra, Darissa Alves, EL Arroussi, Hicham, Eldiehy, Khalifa S.H., EL Mernissi, Najib, Elsamahy, Tamer, Estevam, Bianca Ramos, Fagundes, Mariane Bittencourt, Faraloni, Cecilia, Fattah, Islam Md Rizwanul, Ferreira, Gabriela Filipini, Figueiredo, Daniel, Flores-Tinoco, Valeria, Forero, Liliana Ardila, Galvão de Morais Júnior, Wilson, García-Gómez, Celestino, González, Enrique, Gorin, Kirill, Gotovtsev, Pavel, Gouveia, Luisa, Graciano, Dulce M., Guerra, Inês, Gutiérrez-Antonio, Claudia, Guzmán-Martínez, Carlos Eduardo, Haider, Muhammad Nabeel, Hellgardt, Klaus, Hernández, Salvador, Hong, Yu, Imamoglu, Esra, Incharoensakdi, Aran, Jacob-Lopes, Eduardo, Kalam, Md Abul, Kang, Hooi Siang, Kataki, Rupam, Khor, Wei Han, Kishi, Masatoshi, Kornaros, Michael, Krishnan, Vasumathi, Kuo, Po-Chih, Kusumo, Fitranto, Lafarga, Tomás, Le, Vy P., Leones-Cerpa, Jalelys Liceth, Leong, Hazel Jing-Yi, Letras, Pedro, Lopez-Arredondo, Damar, Machado, Marcio B., Machado, Richard Luan Silva, Mahlia, Teuku Meurah Indra, Malekshahi, Peyman, Manthos, Georgios, Maroneze, Mariana Manzoni, Martínez-Guido, Sergio Iván, Martins, José Moleiro, Martínez-Ruiz, Manuel, Martínez–Roldán, Alfredo de Jesús, Mata, Mário Nuno, Mathpati, Channamallikarjun Sidramayya, Maza-Madera, Freyle A., Melville, Lynsey, Moia, Isabela Calegari, Montenegro-Herrera, Carlos A., Morowvat, Mohammad Hossein, Moutinho, Mariana Miranda, Neviani, Matteo, O'Higgins, Linda, Ogunkunle, Oyetola, Ojeda-Delgado, Karina A., Onay, Melih, Onay, Aytun, Oncel, Suphi S., Paladino, Ombretta, Pereira, Hugo, Petrova, Maria, Pinheiro, Pricila Nass, Pispas, Konstantinos, Rahman, Khondokar M., Rahman, Mohammad Redwanur, Rahman, Md Mofijur, Raja, Rathinam, Rajabzadeh, Amin Reza, Ramírez Mérida, Luis G., Ranishree, Jayappriyan Kothilmozhian, Rincón, Bárbara, Rodríguez Padrón, Richard A., Rogov, Anton, Romanov, Alexander, Ríos Pinto, Luisa Fernanda, Samipour, Saeid, Sangregorio-Soto, Viyils, Santos Corrêa, Priscila, Schneider, Adriane Terezinha, Segredo-Morales, Elisabet, Sergeeva, Yana, Setoodeh, Payam, Sforza, Eleonora, Shanmugam, Kanmani, Shestakova, Alexandra, Sierra-Espinosa, Fernando Z., Silkina, Alla, Singaravelu, Pujithaa, Sivaramakrishnan, Ramachandran, Sánchez-Tuirán, Eduardo Luis, Sánchez-Zurano, Ana, Sukhinov, Daniil, Sun, Zhuang, Sun, Jianzhong, Sventzouri, Eirini, Takayama, Yoshiki, Tamhankar, Sarang, Teoh, Ming-Li, Touloupakis, Eleftherios, Trivellin, Nicola, Trzcinski, Antoine P., Vasilov, Raif, Vera Morales, Juan Manuel, Verma, Nikita, Villaró-Cos, Silvia, Vishnevskaya, Maria, Wang, Xiaoyan, Wen, Du, Yadav, Manishkumar Dinesh, Yarkent, Çağla, Zarei, Zahra, and Zepka, Leila Queiroz

Published
2025
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38. Optimization of dendrimer polyamidoamin eectrospun nanofibers: preparation and properties

Author

Zarei, Zahra, Mirjalili, Mohammad, Kermanshahi, Pouriya Norooz, and Universidade do Minho

Subjects
Engenharia e Tecnologia::Nanotecnologia, Dendrimer polyamide amine, Drug release, Tetracycline, Polyvinyl alcohol, Nanofibers wound dressing
Abstract

Background: The most common polymers in the treatment of wounds are natural (e.g., polysaccharides, proteins, and peptides) and synthetic polymers (e.g., poly-glycolic acid, polyacrylic acid, polylactic acid, and polyvinyl alcohol) due to their biodegradability, biocompatibility, and their structural resemblance to the macromolecules known to the human body. Objectives: The current study aimed to develop an electrospinning method using the nanofibers of polyvinyl alcohol (PVA)/carboxymethyl cellulose (CMC)/polyamide amine (PAMAM)/tetracycline (Tet) to cover the wound. The antibacterial effect of PAMAM was also tested against E. coli and S. aureus bacteria. Materials and Methods: The morphology of the composite nanofiber was studied by a field emission scanning electron microscope. Infrared spectroscopy (FTIR) was used to characterize the nano chemical structure. Results: Nanofibers were evaluated based on the release of different amounts of the antibiotic tetracycline (1%, 3%, 5%, and 7% by weight) while preventing wound infection. The findings indicated that the highest-profile release of all nanofibers occurred early within 12 hours. It was found that nanofiber membranes loaded with 1%, 3%, and 5% tetracycline released drugs for over 28 days, while those containing 7% tetracycline released drugs for more than 14 days. Conclusions: According to the findings related to the drug release of PVA/CMC/15% PAMAM/Tet and surface morphology of the nanofibers, the optimal amount of Tet was 5%. The results of FTIR spectroscopy indicated that the tetracycline and polyamidoamine were successfully placed in nanofibers.

Published
2022

42. Effect of hydrodynamic parameters on hydrogen production by Anabaenasp. in an internal-loop airlift photobioreactor

Author

Zarei, Zahra, Malekshahi, Peyman, Trzcinski, Antoine P., and Morowvat, Mohammad Hossein

Abstract

Global warming and air pollution caused by fossil fuel emissions have triggered the search for a clean, sustainable, and eco-friendly energy source such as H2, which can be produced by cyanobacteria and microalgae. In this study, Anabaenasp. was used in a photobioreactor to achieve biohydrogen production. To this end, hydrodynamic parameters such as gas holdup, liquid circulation velocity, oxygen mass transfer coefficient, and gas velocity were investigated. Results showed that the gas holdup, liquid circulation velocity, and oxygen mass transfer increased by increasing the inlet gas velocity without causing detrimental shear stress to cyanobacteria. A biomass concentration of 1.2 g L−1and a total H2production of 371 mL were recorded after 7 days using an inlet gas velocity of 0.524 cm s−1and a light intensity of 140 µmol photons m−2s−1. Using a superficial gas velocity of 0.524 cm s−1resulted in the optimum gas holdup, mass transfer, and light availability to Anabaenasp. The growth of cyanobacteria in an internal-loop airlift photobioreactor was found to be a cost-effective and environmentally friendly technology for hydrogen production.

Published
2023
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47. Investigation of Hydrodynamic Parameters in an Airlift Photobioreactor on CO 2 Biofixation by Spirulina sp.

Author

Zarei, Zahra, Malekshahi, Peyman, Trzcinski, Antoine P., and Morowvat, Mohammad Hossein

Abstract

The rise of CO2 concentration on Earth is a major environmental problem that causes global warming. To solve this issue, carbon capture and sequestration technologies are becoming more and more popular. Among them, cyanobacteria can efficiently sequestrate CO2, which is an eco-friendly and cost-effective way of reducing carbon dioxide, and algal biomass can be harvested as valuable products. In this study, the hydrodynamic parameters of an airlift photobioreactor such as gas holdup, mean bubble diameter and liquid circulation velocity were measured to investigate CO2 biofixation by Spirulina sp. The total gas holdup was found to increase linearly with the increase in the gas velocity from 0.185 to 1.936 cm/s. The mean bubble velocities in distilled water only and in the cyanobacterial culture on the first and sixth days of cultivation were 109.97, 87.98, and 65.89 cm/s, respectively. It was found that shear stress at gas velocities greater than 0.857 cm/s led to cyanobacterial death. After 7 days of batch culture, the maximum dry cell weight reached 1.62 g/L at the gas velocity of 0.524 cm/s, whereas the highest carbon dioxide removal efficiency by Spirulina sp. was 55.48% at a gas velocity of 0.185 cm/s, demonstrating that hydrodynamic parameters applied in this study were suitable to grow Spirulina sp. in the airlift photobioreactor and remove CO2. [ABSTRACT FROM AUTHOR]

Published
2022
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