Publications

Elham Kiyani, Mahdi Kooshkbaghi, Khemraj Shukla, Rahul Babu Koneru, Zhen Li, Luis Bravo, Anindya Ghoshal, George Em Karniadakis, Mikko Karttunen (2024). Characterization of partial wetting by CMAS droplets using multiphase many-body dissipative particle dynamics and data-driven discovery based on PINNs. Journal of Fluid Mechanics , Volume 985, A7.

Yuma Ishigami, Mandy S. Wong, Carlos Martí-Gómez, Andalus Ayaz, Mahdi Kooshkbaghi, Sonya M. Hanson, David M. McCandlish, Adrian R. Krainer, Justin B. Kinney (2024). Specificity, synergy, and mechanisms of splice-modifying drugs. Nature Communications 15, 1880 (2024).

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Elham Kiyani, Steven Silber, Mahdi Kooshkbaghi, Mikko Karttunen (2022). Machine-learning-based data-driven discovery of nonlinear phase-field dynamics. Physical Review E 106 (065303) (2022).

Nikolaos Evangelou, Noah J. Wichrowski, George A. Kevrekidis, Felix Dietrich, Mahdi Kooshkbaghi, Sarah McFann, Ioannis G. Kevrekidis (2022). On the parameter combinations that matter and on those that do not: data-driven studies of parameter (non)identifiability. PNAS Nexus (2022).

Chirangini Pukhrambam, Vadim Molodtsov, Mahdi Kooshkbaghi, Ammar Tareen, Hoa Vu, Kyle S. Skalenko, Min Su, Zhou Yin, Jared T. Winkelman, Justin B. Kinney, Richard H. Ebright, Bryce E. Nickels (2022). Structural and mechanistic basis of σ-dependent transcriptional pausing. Proceedings of the National Academy of Sciences 119 (23) (2022).

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Ammar Tareen, Mahdi Kooshkbaghi, Anna Posfai, William T. Ireland, David M. McCandlish, Justin B. Kinney (2022). MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect. Genome Biology 23, 98 (2022).

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Carola J. Maturana, Jessica L. Verpeut, Mahdi Kooshkbaghi, Esteban A. Engel (2021). Novel tool to quantify with single-cell resolution the number of incoming AAV genomes co-expressed in the mouse nervous system. Gene Therapy (2021): 1-6.

Liwei Zhuang, Peter Corkery, Dennis T. Lee, Seungjoon Lee, Mahdi Kooshkbaghi, Zhen‐liang Xu, Gance Dai, Ioannis G. Kevrekidis, Michael Tsapatsis (2021). Numerical simulation of atomic layer deposition for thin deposit formation in a mesoporous substrate. AIChE Journal (2021): e17305.

Caroline Moosmüller, Christopher J. Tralie, Mahdi Kooshkbaghi, Zehor Belkhatir, Maryam Pouryahya, José Reyes, Joseph O Deasy, Allen R. Tannenbaum, Ioannis G. Kevrekidis (2021). Periodicity Scoring of Time Series Encodes Dynamical Behavior of the Tumor Suppressor p53. IFAC-PapersOnLine 54, no. 9 (2021): 488-495.

Thomas N. Thiem, Mahdi Kooshkbaghi, Tom Bertalan, Carlo R. Liang, Ioannis G. Kevrekidis (2020). Emergent spaces for coupled oscillators. Frontiers in Computational Neuroscience 14 (2020): 36.

Felix Dietrich, Mahdi Kooshkbaghi, Erik M. Bolt, Ioannis G. Kevrekidis (2020). Manifold learning for organizing unstructured sets of process observations. Chaos: An Interdisciplinary Journal of Nonlinear Science 30, no. 4 (2020): 043108.

Seungjoon Lee, Mahdi Kooshkbaghi, Konstantinos Spiliotis, Constantinos I. Siettos, Ioannis G. Kevrekidis (2020). Coarse-scale PDEs from fine-scale observations via machine learning. Chaos: An Interdisciplinary Journal of Nonlinear Science 30, no. 1 (2020): 013141.

Alexander Holiday, Mahdi Kooshkbaghi, Juan M. Bello-Rivas, C. William Gear, Antonios Zagaris, Ioannis G. Kevrekidis (2019). Manifold learning for parameter reduction. Journal of computational physics 392 (2019): 419-431.

Luigi Acampora, Mahdi Kooshkbaghi, Christos E. Frouzakis, Francesco S. Marra (2019). Generalized entropy production analysis for mechanism reduction. Combustion Theory and Modelling 23, no. 2 (2019): 197-209.

Mahdi Kooshkbaghi, Christos E. Frouzakis, Konstantinos Boulouchos, Ilya V. Karlin (2016). Spectral quasi-equilibrium manifold for chemical kinetics. The Journal of Physical Chemistry A 120, no. 20 (2016): 3406-3413.

Mahdi Kooshkbaghi, Christos E. Frouzakis, Konstantinos Boulouchos, Ilya V. Karlin (2015). n-Heptane/air combustion in perfectly stirred reactors: Dynamics, bifurcations and dominant reactions at critical conditions. Combustion and Flame 162, no. 9 (2015): 3166-3179.

Mahdi Kooshkbaghi (2015). On the model reduction for chemical and physical kinetics. ETH Zurich.

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Mahdi Kooshkbaghi, Christos E. Frouzakis, Eliodoro Chiavazzo, Konstantinos Boulouchos, Ilya V. Karlin (2014). The global relaxation redistribution method for reduction of combustion kinetics. The Journal of chemical physics 141, no. 4 (2014): 044102.

Ilya V. Karlin, Shyam S. Chikatamarla, Mahdi Kooshkbaghi (2014). Non-perturbative hydrodynamic limits: A case study. Physica A: Statistical Mechanics and its Applications 403 (2014): 189-194.

Mahdi Kooshkbaghi, Christos E. Frouzakis, Konstantinos Boulouchos, Ilya V. Karlin (2014). Entropy production analysis for mechanism reduction. Combustion and flame 161, no. 6 (2014): 1507-1515.

Mahdi Kooshkbaghi, Bamdad Lessani (2013). A collocated grid, projection method for time‐accurate calculation of low‐Mach number variable density flows in general curvilinear coordinates. International Journal for Numerical Methods in Fluids 72, no. 3 (2013): 301-319.

Hossein Shokouhmand, Muhammad Fakoor Pakdaman, Mahdi Kooshkbaghi (2010). A similarity solution in order to solve the governing equations of laminar separated fluids with a flat plate. Communications in Nonlinear Science and Numerical Simulation 15, no. 12 (2010): 3965-3973.