Omid Bavi
Assistant Professor of solid mechanics engineering
Academic Appointments
- Member of Iran Science Elites Federation
- Member of the Australian Society for Biophysics
Honors & Awards
- The Author of the Best educational book in 11th Festival of Books Educational Development of Ministry of Education (2014)
- The Author of the Selected educational book in 9th Festival of Books Educational Development of Ministry of Education (2012)
- The Author of the Selected educational book in 16th Festival of Books Educational Development of Ministry of Education (2019)
- Distinguished teaching professor of Mechanical engineering, Shiraz University of Technology (2021)
- Distinguished teaching professor of Mechanical engineering, Shiraz University of Technology (2022)
- Distinguished researcher of Mechanical engineering, Shiraz University of Technology (2022)
- Distinguished researcher of Mechanical engineering, Shiraz University of Technology (2023)
Contact
Email:
o.bavi@sutech.ac.ir
Professional Education
B.Sc.
o University: Isfahan University of Technology
Major: Mechanical Engineering-Solid Mechanics
M.Sc.
o University: Amirkabir University of Technology
Major: Mechanical Engineering-Applied Design
Ph.D.
o University: Sharif University of Technology
Major: Nanocompuatations (Nano-biomechanics)
Sabbatical.
o University: University of New South Wales (UNSW), Sydney, Australia
Research Experiences: Mechanosensitive Ion Channels, Transmembrane Proteins-lipid Interaction
Postdoctoral
o University: University of Tehran
Research Experiences: Transduction and Transportation in 2D Materials and Biomembranes
Courses
- Continuum Mechanics
- Advanced Engineering Mathematics
- Cold Plasma and Cell Interaction
- Nanocomputations
- Mechanics of Nanostructures
- Molecular Dynamics
Current Research
- Computational Nanomechanics
- Drug Delivery Systems
- Cell Mechanics
- Molecular Dynamics Simulation
- Composite Materials and Sandwich Structures
- Evolutionary Systems and Optimization Algorithms
- Finite element modeling
- Mechanosensitive ion channels
All Publications
Edited Book
- Electromagnetic Waves-Based Cancer Diagnosis and Therapy, Principles and Applications of Nanomaterials, Elsevier, Academic Press, 2023; Edited by Mona Khafaji and Omid Bavi; DOI: https://doi.org/10.1016/C2021-0-02047-2. Print ISBN: 978-0-323-99628-0
Book Chapters
- Principles of mechanosensing at the membrane interface, Springer Series in Biophysics, Navid Bavi, Yury A Nikolaev, Omid Bavi, Pietro Ridone, Adam D Martinac, Yoshitaka Nakayama, Charles D Cox and Boris Martinac, Series Ed.: Martinac, Boris, Springer Series in Biophysics, vol 19. Springer, Singapore, DOI: https://doi.org/10.1007/978-981-10-6244-5_4, Print ISBN:978-981-10-6243-8
- Mechanosensitivity of Ion Channels, Charles Cranfield; Anna Kloda; Evgeny Petrov; Andrew Battle; Takeshi Nomura; Paul Rohde; Charles Cox; Navid Bavi; Omid Bavi; Yoshitaka Nakayama; Yury Nikolaev; Pietro Ridone; Adam Martinac; Matthew baker; Kadla Rosholm and Boris Martinac; Encyclopedia of Biophysics, Springer, 2017. DOI: https://doi.org/10.1007/978-3-642-35943-9_376-1 . (PDF)
- Martinac, B., Nikolaev, Y.A., Silvani, G., Bavi, N., Romanov, V., Nakayama, Y., Martinac, A.D., Rohde, P., Bavi, O. and Cox, C.D., 2020. Cell membrane mechanics and mechanosensory transduction. In Current Topics in Membranes (Vol. 86, pp. 83-141). Academic Press. https://doi.org/10.1016/bs.ctm.2020.08.002
- Jokar, S., Khazaei, S., Gameshgoli, X. E., Khafaji, M., Yarani, B., Sharifzadeh, M., ... & Bavi, O. (2020). Amyloid β-Targeted Inhibitory Peptides for Alzheimer’s Disease: Current State and Future Perspectives. Exon Publications, 51-68. https://doi.org/10.36255/exonpublications.alzheimersdisease.2020.ch3
- Bavi, O., Bavi, N. and Shishesaz, M., 2013. Geometrical optimization of the overlap in mixed adhesive lap joints. The Journal of Adhesion, 89(12), pp.948-972.
- Bavi, O., Vossoughi, M., Naghdabadi, R. and Jamali, Y., 2014. The effect of local bending on gating of MscL using a representative volume element and finite element simulation. Channels, 8(4), pp.344-349.
- Bavi, Omid, Manouchehr Vossoughi, Reza Naghdabadi, and Yousef Jamali. "The Combined Effect of Hydrophobic Mismatch and Bilayer Local Bending on the Regulation of Mechanosensitive Ion Channels." PloS one 11, no. 3 (2016): e0150578.
- Bavi, N., Nakayama, Y., Bavi, O., Cox, C.D., Qin, Q.H. and Martinac, B., 2014. Biophysical implications of lipid bilayer rheometry for mechanosensitive channels. Proceedings of the National Academy of Sciences, 111(38), pp.13864-13869.
- Bavi, Omid, Charles D. Cox, Manouchehr Vossoughi, Reza Naghdabadi, Yousef Jamali, and Boris Martinac. "Influence of Global and Local Membrane Curvature on Mechanosensitive Ion Channels: A Finite Element Approach.", Membranes 6, no. 1 (2016): 14.
- Bavi, N., D. M. Cortes, C. D. Cox, P. R. Rohde, W. Liu, J. W. Deitmer, O. Bavi, P. Strop, A. P. Hill, D. Rees, B. Corry, E. Perozo and B. Martinac (2016). "The role of MscL amphipathic N terminus indicates a blueprint for bilayer-mediated gating of mechanosensitive channels." Nat Commun 7. doi: 10.1038 /ncomms11984
- N. Bavi, O. Bavi, M. Vossoughi, R. Naghdabadi, A.P. Hill, B. Martinac and Y. Jamali. Nanomechanical properties of MscL α helices: A steered molecular dynamics study. Channels, 2017. 11(3): p. 209-223
- Martinac, A. D., Bavi, N., Bavi, O., & Martinac, B. (2017). Pulling MscL open via N-terminal and TM1 helices: A computational study towards engineering an MscL nanovalve. PloS one, 12(8), e0183822. doi:10.1371/journal.pone.0183822
- Bavi, N., Martinac, A.D., Cortes, D.M., Bavi, O., Ridone, P., Nomura, T., Hill, A.P., Martinac, B. and Perozo, E., 2017. Structural Dynamics of the MscL C-terminal Domain. Scientific reports, 7(1), p.17229.
- Martinac, Adam D., Navid Bavi, Omid Bavi, and Boris Martinac. "A Computational Study Towards Engineering an MscL Nanovalve." Biophysical Journal 114, no. 3 (2018): 112a.
- Martinac, Boris, Navid Bavi, Pietro Ridone, Yury A. Nikolaev, Adam D. Martinac, Yoshitaka Nakayama, Paul R. Rohde, and Omid Bavi. "Tuning ion channel mechanosensitivity by asymmetry of the transbilayer pressure profile." Biophysical reviews (2018): 1-8. https://rdcu.be/bbZh8
- Khafaji M, Zamani M, Golizadeh M, Bavi O. Inorganic nanomaterials for chemo/photothermal therapy: a promising horizon on effective cancer treatment. Biophysical reviews 2019:1-18.
- Cranfield CG, Kloda A, Nikolaev YA, Martinac AD, Ridone P, Bavi N, et al. Mechanosensitivity of Ion Channels. Encyclopedia of Biophysics. https://link.springer.com/referenceworkentry/10.1007/978-3-642-35943-9_376-2; 2019, p. 1-11.
- http://en.sutech.ac.ir/mae/wp-content/uploads/my_user_uploaded_files/26ef2cfdd269ef0537340a73449f178254170b5a/Mechanosensitivity-of-Ion-Channels-.pdf
- Roohi R, Heydari M, Bavi O, Emdad H. Chebyshev polynomials for generalized Couette flow of fractional Jeffrey nanofluid subjected to several thermochemical effects. Engineering with Computers 2019:1-17
- Jokar S, Khazaei S, Behnammanesh H, Shamloo A, Erfani M, Beiki D, Bavi O. Recent advances in the design and applications of amyloid-β peptide aggregation inhibitors for Alzheimer’s disease therapy. Biophysical Reviews. 2019 Nov 12:1-25.
- Hajishamsaei, M., Pishevar, A., Bavi, O., & Soltani, M. (2020). A novel in silico platform for a fully automatic personalized brain tumor growth. Magnetic Resonance Imaging, 68, 121-126. doi:https://doi.org/10.1016/j.mri.2019.12.012
- Jokar S, Erfani M, Bavi O, Khazaei S, Sharifzadeh M, Hajiramezanali M, et al. Design of Peptide-based Inhibitor Agent against Amyloid-β Aggregation: Molecular Docking, Synthesis and in vitro Evaluation. Bioorganic Chemistry. 2020:104050. https://doi.org/10.1016/j.bioorg.2020.104050
- Shadloo-Jahromi A, Kharati-Koopaee M, Bavi O. Friction factor calculation in nanochannels comprising different wall hydrophobicities and superhydrophobic structures: Molecular dynamic simulations. International Communications in Heat and Mass Transfer. 2020 Oct 1;117:104763. https://doi.org/10.1016/j.icheatmasstransfer.2020.104763
- S. Bahari, R. Davarnejad, O. Bavi, S.V. Mohammadi, "Osmotic water permeability of aquaporin-1 under radial tensile and compressive stimuli", Desalination, 492, 1 2020, 114524 https://doi.org/10.1016/j.desal.2020.114524
- Nikfarjam, Z., Bavi, O. and Amini, S. Potential effective inhibitory compounds against Prostate Specific Membrane Antigen (PSMA): A Molecular Docking and Molecular Dynamics Study, Archives of Biochemistry and Biophysics, 699, 108747, 2021 https://doi.org/10.1016/j.abb.2020.108747
- Badjian, H., A. Setoodeh, M. Salehi and O. Bavi MICRO/MACROMECHANICAL ANALYSIS AND OPTIMIZATION OF THE FLEXURAL STRENGTH OF LaRC-SI/PmPV/CNT NANOCOMPOSITE SQUARE PLATE USING GENETIC ALGORITHM. vol. 12(1), pp. 41-55, 2021.
- Bavi, O. and F. Ghadak Possibility of making aerophobic surfaces by nanoprotrusions: an investigation of atomic-scale friction of the air–solid interfaces. Physical Chemistry Chemical Physics, vol. 23(8), pp. 4711-4717, 2021.
- Rasouli, A., Y. Jamali, E. Tajkhorshid, O. Bavi and H. N. Pishkenari Mechanical properties of ester- and ether-DPhPC bilayers: A molecular dynamics study. Journal of the Mechanical Behavior of Biomedical Materials, vol. 117, pp. 104386, 2021.
- Shadloo-Jahromi, A., M. Kharati-Koopaee, and O. Bavi, Molecular dynamics simulation of fluid flow through nanochannels consisting of different superhydrophobic patterns. International Communications in Heat and Mass Transfer, 2021. 124: p. 105278.
- Heydari, M.H. and Bavi, O., 2021. An optimal variational iteration method for investigating the physical behavior of quasi-steady squeezing flow confined between parallel rigid walls. Physica Scripta, 96(11), p.114012.
- Mohammadi, M.M. and Bavi, O., 2021. DNA sequencing: an overview of solid-state and biological nanopore-based methods. Biophysical Reviews, pp.1-12.
- Badjian, H., Setoodeh, A.R., Bavi, O. and Rabczuk, T., 2021. Enhanced mechanical properties of epoxy-based nanocomposites reinforced with functionalized carbon nanobuds. Applied Physics A, 127(12), pp.1-16.
- Nikfarjam, Z., Zargari, F., Nowroozi, A. and Bavi, O., 2022. Metamorphosis of prostate specific membrane antigen (PSMA) inhibitors. Biophysical Reviews, pp.1-13.
- Khafaji, M., Bavi, O. and Zamani, M., 2022. Gold-based hybrid nanostructures: more than just a pretty face for combinational cancer therapy. Biophysical Reviews, pp.1-10.
- Bavi, O., Hosseininia, M., Heydari, M.H. and Bavi, N., 2022. SARS-CoV-2 rate of spread in and across tissue, groundwater and soil: A meshless algorithm for the fractional diffusion equation. Engineering analysis with boundary elements.
- Heydari, M.H., Bavi, O. An efficient wavelet method for nonlinear problems arising in heat transfer. Engineering with Computers 38, 2867–2878 (2022). https://doi.org/10.1007/s00366-021-01437-0
- Heydari, M.H., Bavi, O. An optimization method based on the Legendre wavelets for 3D rotating, squeezing and stretching magnetohydrodymanic flow in a channel with porous wall. Engineering with Computers 38 (Suppl 3), 2583–2592 (2022). https://doi.org/10.1007/s00366-021-01421-8
- Mohammadi, Mohammad M., Omid Bavi, and Yousef Jamali. "DNA sequencing via molecular dynamics simulation with functionalized graphene nanopore." Journal of Molecular Graphics and Modelling (2023): 108467.
- Maymand, Vahid Mahmoudi, Omid Bavi, and Abbas Karami. "Probing the mechanical properties of ORF3a protein, a transmembrane channel of SARS-CoV-2 virus: Molecular dynamics study." Chemical Physics 569 (2023): 111859.
- Bavi O, Hosseininia M, Hajishamsaei M, Heydari MH. Glioblastoma multiforme growth prediction using a Proliferation-Invasion model based on nonlinear time-fractional 2D diffusion equation. Chaos, Solitons & Fractals. 2023 May 1;170:113393.
- Ghadirian F, Abbasi H, Bavi O, Naeimabadi A. How living cells are affected during the cold atmospheric pressure plasma treatment. Free Radical Biology and Medicine. 2023 Aug 20;205:141-50.
- Bavi, O., M. Hosseininia, and M. H. Heydari. "A mathematical model for precise predicting microbial propagation based on solving variable‐order fractional diffusion equation." Mathematical Methods in the Applied Sciences 46, no. 16 (2023): 17313-17327.
Conference Papers
- Bavi, O., Seddighi, M., Bavi, N., “Investigation of effective parameters on dynamic behavior of a sandwich plate with composite Skins” 2ndInternational Conference on composite characterization, Fabrication and application (CCFA-2), 2010. Kish Island, Iran.
- O. Bavi, M. Vossoughi, R. Naghdabadi, and Y.Jamali “Investigation of gating mechanisms of mechanosensitive ion channels using continuum mechanics”; 5th International Conference on Nanostructures (ICNS5); 6-9 March 2014, Kish Island, Iran
- N. Bavi, Y. Nakayama, Q. H. Qin, O. Bavi and B. Martinac ; “Finite Element Simulation and Patch Fluorometry of Azolectin Lipid Vesicles”; 5th International Conference on Nanostructures (ICNS5); 6-9 March 2014, Kish Island, Iran
- Mousaei, M., Bavi, O., Jamali, Y., Ejtehadi, M. R., “The effect of a gain of function mutant (G22N) on the mechanical properties of TM1 helix in MscL: A Steered Molecular Dynamic study” In: Proceedings of the 6th International Conference in Nanostructures (ICNS6), 2016, Kish Island, Iran.
- O. Bavi, N., Vosoughi, M., Naghdabadi, R. and Jamaly, Y. “Mechanical properties of the pore-lining alpha helix of a mechanosensitive ion channel MscL using steered molecular dynamics simulation”. In: Proceedings of the 39th Annual Conference of the Australian Society for Biophysics (ASB2015), University of New England, NSW, Australia.
- Bavi, Navid, Charles D. Cox, Omid Bavi, and Boris Martinac. "Perturbation of Bilayer Surface Tension Differentially Modulates Mechanosensitive Ion Channels." Biophysical Journal 112, no. 3 (2017): 416a.
- Bavi, Omid, Bavi, Navid, and Vaez Allaei, S. Mehdi. “Biophysical Interactions of 5-Fluorouracil with lipid bilayers: a molecular dynamics study” (PDF) In: Proceedings of the 7th International Conference in Nanostructures (ICNS7), 2018, Tehran, Iran
- A. Rasouli, Y. Jamali, O. Bavi, H. Zohoor and H. Nejat Pishkenari "Steered Molecular Dynamics study of the Nanomechanical Properties of the Archaeal MscL" (PDF) ۷th International Conference on Nanostructures (ICNS7) April 2018, Tehran, Iran
- S. Jokar, O. Bavi, A. Shamloo and D. Beiki. “Hexapeptide Amide; An appropriate probe for inhibition of the ß-sheet conformation formation of amyloid β-protein” First Conference on Computation of Nanostructures (CCNS2018)- Sharif University of Technology, Tehran- Iran
- Martinac, A. D., Bavi, N., Cortes, M. D., Bavi, O., Nomura, T., Martinac, B., & Perozo, E. (2017). Structural Dynamics of the MSCL C-Terminal Domain. Biophysical Journal, 112(3), 413a.
- Bavi, N., C. D. Cox, O. Bavi, and B. Martinac. "The role of surface tension in ion channel mechanosensitivity." In European Biophysics Journal with Biophysics Letters, Vol. 46, Pp. S243-S243. 233 Spring St, New York, NY 10013 USA: Springer, 2017.
- Omid Bavi, Manouchehr Vossoughi, Reza Naghdabadi and Yousef Jamali, Bio-Nano Channels: Cell Growth Control, Mechanotherapy and Safe Drug Delivery, Nanotechnology Magazine, Issue 10 no. 15, 2017. Pages 34-41 (PDF)
- Shomali, A.; Bavi, O.; Chini, F and Allaei, SMV. “Self-assembly of amphipathic molecules in Stearyl alcohol monolayer around a carbon nano tube: An all atom molecular dynamic study” 24th Annual IASBS Meeting on Condensed Matter Physics & School on Complex Systems, June 19 ‐ 20, 2018, Zanjan, Iran
- Shomali, A.; Bavi, O.; Chini, F and Allaei, SMV. “A molecular dynamic study on hole formation in Stearyl alcohol monolayers utilized for reducing the rate of water evaporation” 24th Annual IASBS Meeting on Condensed Matter Physics & School on Complex Systems, June 19 ‐ 20, 2018, Zanjan, Iran
- Jokar, S.; Bavi, O.; Shamloo, A. and Beiki, D. “Computational studies on mechanism of amyloid β-protein inhibition by Hexapeptide amide” Asian Biophysics Association Symposium in conjunction with the Australian Society for Biophysics. Dec 2 ‐ 6, 2018. RMIT University, Melbourne, Australia
- Khafaji, M.: Bavi, O. and Vossoughi, M. “Superparamagnetic Nanoparticles as Stimuli-Responsive Co-Delivery System for Chemo-Photothermal Therapy” Asian Biophysics Association Symposium in conjunction with the Australian Society for Biophysics. Dec 2 ‐ 6, 2018. RMIT University, Melbourne, Australia
- Khafaji, M.: Bavi, O.; Vossoughi, M. and Irajizad, A. “A thermo-responsive plasmo-magnetic hybrid nanostructure as an active platform for photothermal therapy and targeted drug delivery” Asian Biophysics Association Symposium in conjunction with the Australian Society for Biophysics. Dec 2 ‐ 6, 2018. RMIT University, Melbourne, Australia
- Bavi, O.; Bavi, N.; Beydaghi, P.; Naghdabadi, R. and Allaei, SMV. “Measurement of the Elastic Properties of Proteins Using a Fast and Robust Molecular Mechanics Approach” Asian Biophysics Association Symposium in conjunction with the Australian Society for Biophysics. Dec 2 ‐ 6, 2018. RMIT University, Melbourne, Australia (PDF)
- Shadloo-Jahromi A, Kharati-Koopaee M, Bavi O."Atomistic Study of the Effects of Superhydrophobic Surfaces on Friction Factor of Water Flow in Nanochannels" 8th International Conference on Nanostructures (ICNS8) April 2020, Tehran, Iran
- Shadloo-Jahromi A, Kharati-Koopaee M, Bavi O." Molecular dynamic study of friction factor of water flowing through nanochannels with different wall hydrophobicity" 8th International Conference on Nanostructures (ICNS8) April 2020, Tehran, Iran
- Nikfarjam Z, Amini Komeijani S, Bavi O." Importance of Studying the Presence of Zinc Metal in the Structure of Glutamate Carboxypeptidase II (PSMA) : A Molecular Dynamics Study " 8th International Conference on Nanostructures (ICNS8) April 2020, Tehran, Iran
- Bahari S, Mohammadi S.V., Davarnejad R, Bavi O." A Closer Atomistic Look to Evolution of Active Nanopores of The Human Tetrameric Aquaporin-1" 8th International Conference on Nanostructures (ICNS8) April 2020, Tehran, Iran
- Nikfarjam Z., Bavi O. and Amini Komeijani S., A Molecular Docking and Molecular Dynamics Study on Prostate- Specific Membrane Antigen (PSMA) to design effective small molecules as inhibitors, 44th Meeting of Australian Society for Biophysics, Sydney- Australia, December 2020,
- Zargari, F., Nikfarjam, Z., Bavi, O. and Ghorbanipour, M., Theoretical studies on the selectivity of inhibitors on FGFRs by molecular dynamic simulations and free energy calculations, 44th Meeting of Australian Society for Biophysics, Sydney- Australia, December 2020,
- Jokar, S., Erfani, M., Bavi, O. and Beiki, D., Evaluation of the Intermolecular Interactions between the Peptide-based Inhibitors and Amyloid-β Monomer/Fibril Structures, 44th Meeting of Australian Society for Biophysics, Sydney- Australia, December 2020,
- Borazjani, H., Rouzegar, S.J. and Bavi, O, The potential role of the physical and chemical arrangement of erythrocytes membrane molecules on its mechanical behavior: A molecular dynamics simulation, 44th Meeting of Australian Society for Biophysics, Sydney- Australia, December 2020,
- Mohammadi, M.M., Bavi, O. and Jamali, Y. DNA Sequencing Using Functionalized Graphene Nanopore, 45 th Annual Meeting of the Australian Society for Biophysics, Melbourne, Australia, 2021
- Mahmoudi, V., Bavi, O. Investigation of Mechanical Properties of ORF3a, a Transmembrane Ion Channel of SARS-CoV-2 Virus: A Molecular Dynamic Simulation, 30th Annual International Conference of the Iranian Society of Mechanical Engineers, Tehran, Iran, 2022.
- Borazjani, H., Rouzegar, S.J., and Bavi, O. Investigation of mechanical properties of erythrocyte membrane: A molecular dynamics simulation, 30th Annual International Conference of the Iranian Society of Mechanical Engineers, Tehran, Iran, 2022
- Mohammad-aghaie, D., Dashti, M.A., and Bavi, O. Effect Assessment of HBD-2 and HD-5 on SARS-CoV-2 Membrane model, A Molecular Dynamics Simulation Study Content. The 23rd European Conference on the Dynamics of Molecular Systems (MOLEC 2022) Hamburg, Germany, August 2022.