Farimani, Amir Barati - Carnegie Mellon University - Department of Biomedical Engineering

个人简介

Education B.S. Mechanical Engineering, Ferdowsi University of Mashhad, 2005 M.S., Mechanical Engineering, Tehran TMU University, 2008 Ph.D., Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, 2015 Bio Dr. Barati Farimani received his Ph.D. in 2015 in Mechanical Science and Engineering from University of Illinois at Urbana-Champaign. His PhD thesis was about "Detecting and Sensing Biological Molecules using Nanopores". He extensively used atomistic simulations to shed light on the DNA sensing and detection physics of biological and solid state nanopores. Right after that, he joined Professor Vijay Pande lab at Stanford. During his post-doc, he combined machine learning and molecular dynamics to elucidate the conformational changes of G-Protein Coupled Receptors (GPCRs). He specifically was focused on Mu-Opioid Receptors to elucidate their free energy landscape and their activation mechanism and pathway.

研究领域

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The main theme of our lab is doing research at the interface of bioengineering, machine learning and computation. We are combining molecular dynamic simulations, machine learning and statistical learning to understand and predict the properties and interactions of bio-molecules. To be more specific, we are focused on two types of problems: 1. Interactions and recognition of bio-molecules such as DNA with synthetic materials: We perform MD simulations to generate the trajectories. We use statistical learning techniques to learn the collective variables. This is an interesting area where statistical mechanic and machine learning coincides. 2. To understand small molecule and protein interaction. We are dealing with super high dimensional time-series data coming from MD simulations. Reducing the dimension of the data, and learning the reaction coordinates help us understand many fundamental biophysical and physiological mechanisms for protein conformation and dynamics.