Publications

Aesearch articles

• Ghorbani, Mahdi, et al. “GraphVAMPNet, using graph neural networks and variational approach to markov processes for dynamical modeling of biomolecules.” arXiv preprint arXiv:2201.04609 (2022).arXiv
• Ghorbani, Mahdi, et al. “Variational embedding of protein folding simulations using Gaussian mixture variational autoencoders.” The Journal of Chemical Physics 155.19 (2021): 194108.jcp
• Ghorbani, Mahdi, et al. “A replica exchange umbrella sampling (REUS) approach to predict host–guest binding free energies in SAMPL8 challenge.” Journal of computer-aided molecular design 35.5 (2021): 667-677. jcaid
• Ghorbani, Mahdi, Bernard R. Brooks, and Jeffery B. Klauda. “Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2.” Biophysical Journal (2021).BJ
• Ghorbani, Mahdi, Bernard R. Brooks, and Jeffery B. Klauda. “Critical sequence hotspots for binding of novel coronavirus to angiotensin converter enzyme as evaluated by molecular simulations.” The Journal of Physical Chemistry B 124.45 (2020): 10034-10047.JPCB
• Ghorbani, Mahdi, et al. “Molecular dynamics simulations of ethanol permeation through single and double-lipid bilayers.” The Journal of Chemical Physics 153.12 (2020): 125101.JCP